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Date: 2002/05/06 02:19:43, Link
Author: Wesley R. Elsberry
DeLay was asked where kids should go to college. The questioner apparently asked this in the context of teaching creationism.

Houston Chronicle article

William Dembski is mentioned in the above article.

Note the mode of discussion DeLay's spokesman, Jonathan Grella, uses in talking about Barry Lynn. "Guilt by association" tactics seem to come in both rightist and leftist flavors.

As a student at A&M, I have to say that I saw no evidence of a lack of conservatism on campus.  I didn't live in the dorms, so I can't speak to the reports of rampant hanky-panky.

Dallas Morning News article

Date: 2002/05/06 02:25:59, Link
Author: Wesley R. Elsberry
I would like to announce the availability of the "Finite Improbability Calculator".

The Finite Improbability Calculator is a tool for exploring the very small probabilities encountered in applying some of the formulas in William Dembski's "No Free Lunch" to biological phenomena. Some basic functions are implemented, such as factorial, change of base, permutation, and combination. Further, several of the formulas found in section 5.10 of "No Free Lunch" are implemented.

I did this as an aid to my own analysis of Dembski's work, and realized that others could benefit from it as well. The routines are specifically made so that they handle very large and very small numbers without causing floating-point overflow or underflow errors.

Comments are welcome.

Date: 2002/05/06 02:31:29, Link
Author: Wesley R. Elsberry
I was able to attend the event due to good timing on other travel.  

Eugenie Scott moderated.  William Dembski and Michael Behe presented on "intelligent design" and were questioned by Robert Pennock and Kenneth Miller.

Dembski used a lot of negative argumentation in his presentation.   One of the parts which wasn't so negative included his capsule example of specified complexity as needing a long message and an independent pattern to match it.  Dembski invoked the bacterial flagellum as an example of specified complexity in biology.  He floated the claim that the only known examples of successful co-option come from human engineering.  He touted section 5.10 of his book, "No Free Lunch", as giving the probability calculations needed to find "horrendous" probabilities of getting a flagellum.  While Dembski had a section of his talk devoted to talking about "arguing from ignorance", it did not seem to me that he actually disposed of the issue.  Dembski reiterated the claim that design is a notion belonging to statistics and complexity theory.  And to top things off, Dembski even repeated his claim that there is a room at the Smithsonian devoted to artifacts known to be designed but for which no purpose is known.

Of course, there is no such room, which can be confirmed by contacting the Smithsonian, as Jeff Shallit has done.  There was once an exhibit (1980-81) with one display case in which some artifacts were displayed.

I have to wonder why it is that if design is properly a statistical and complexity theoretic notion, why hasn't Dembski published his "design inference" in that literature.  It would seem to be a neutral ground in which to gain some credibility for the concept.  I don't think that the statisticians really care about the evolution/creation issue, so the whole thing about the "Darwinist conspiracy" should be a non-issue in that context.

Rob Pennock tried to get Dembski to commit to saying what sorts of things can be taught if one accepts "intelligent design" by contrasting that to what science already has resolved.  Issues like the age of the earth and whether a global flood could be taught were brought up.  But Dembski dodged making any stand on these issues, saying that his stance is that "design" is detectable.  I think this showed that Dembski is simply evasive on these points which might lose the ID movement the support of YEC fellow-travelers.  Others have opined that this showed Dembski's fortitude in refusing to grant Pennock any points.

Miller tried to get Dembski to state when the intelligent designer had to infuse the "specified complexity" seen in various events mentioned by Dembski and other ID advocates.  Did the origin of life 3 billion years ago indicate an intervention by the intelligent designer?  Maybe, maybe not was about the extent of Dembski's reply.  For the bacterial flagellum, the Cambrian explosion, the emergence of various animal groups, "maybe, maybe not" was the sum total of Dembski's stance.  The specified complexity might have been input at the origin of the universe, and subsequent examples would have to be examined in detail.  ID could thus be compatible with some form of Deism, or an interventionist theology, but doesn't seem to have any way within it to decide between the two.

Michael Behe gave his usual talk on "irreducible complexity", including some discussion of mousetraps.

Ken Miller presented a four-step logical argument based upon things that Behe has said in the past.  Behe stated flatly that the second point was something he had never said, but Miller was able to pop up the full quote and citation showing that Behe had, indeed, said just that.  Miller then proceeded to show that for each of three biological systems that Behe has used in the past (the blood clotting cascade, the bacterial flagellum, and the eukaryotic cilium) that functional systems with fewer parts do exist.  Behe was caught flat-footed by Miller's citation of work from 1969 documenting that dolphins and whales lack Hagemann factor from their blood clotting cascade.  "I feel sorry for the dolphins," said Behe.  "There's no need to feel sorry for the dolphins," said Miller, "they are doing just fine."  Take away 40 proteins from the bacterial flagella, or 80% of the system, said Miller, and you still have a fully functional Type III secretory system.  Behe objected that these were not exactly the same proteins, but Miller countered that in each case they were quite similar with high sequence similarity in conserved regions.  For the eukaryotic cilium, Miller presented the case of cilia from eel sperm, that are missing several parts found in other cilia, but which are still fully functional.

One criticism of Miller's presentation would be that Behe kept saying that Miller was not taking into account Behe's full argument.  I think that Behe would have a point here if he could just cite the places where he had retracted the claims that Miller did critique.

Pennock made an incredibly telling point, in that neither Behe nor Dembski would reduce "irreducible complexity" to an independent and objective criterion that would not require Behe to pass judgment on whether a system was actually IC or not.  Pennock proposed that the use of knockout experiments could establish what is or is not IC.  Behe said that this would be a good place to start, but that he would reserve judgment.

Each of the participants was asked to give a URL.

Kenneth Miller

Rob Pennock

Michael Behe

William Dembski

Eugenie Scott

Date: 2002/05/06 11:04:52, Link
Author: mark isaak
It occurred to me that ID and sympathetic magic probably share a common psychological basis.  In sympathetic magic, it is believed that there is a link between A and B because A shares properties with B.  For example, a voodoo doll shares appearance with a person, so a link is supposed to exist between them, and harming the doll is supposed to harm the person.  (There is more to it than that, but that is enough for illustration.)

With ID, life and machines share some properties in common, such as moving parts and a certain amount of complexity.  That is enough to suggest a link between them, which leads to the idea of designers for both.

I think I'm overanalyzing the situation.  Probably the psychology behind ID is much more basic, and I don't need to draw in sympathetic magic.  But you wanted the bullitin board tested, so I had to write something.

Date: 2002/05/06 11:21:46, Link
Author: Dr.GH
Howdy,

The (briefly) available recordings of the presentations were interesting.  I would very much like to contrast the oral presentations to the published positions.  Do you (or anyone else) know how to get transcripts?  The ARN folks (PLA etc...) seem to have them, but seem disinclined to sharee them with evilutionists.

Date: 2002/05/06 12:26:38, Link
Author: Wesley R. Elsberry
Transcripts would be good.  I'm trying to work out the issues on making transcripts available.  There was a complaint from one of the participants about making the audio recordings available.  Hopefully, there won't be such issues over the transcript.

Date: 2002/05/06 12:31:50, Link
Author: Wesley R. Elsberry
I don't think it is an overanalysis of the situation.  Take a look, for instance, at William Dembski's book, No Free Lunch, and section 1.8 therein.  Within that, you'll find him discussing an argument by analogy eerily similar to your description.

Date: 2002/05/06 18:55:34, Link
Author: scarletohairy
Well, analogies may work.  Who's to say?  Actually, science.  When science finds no reason to connect elements in the world, it needs to refrain from assuming connections.  Sympathetic magic has not been found to work, so science need not assume the claimed connections.  Likewise, the analogy between machines and biological structures, although it may sometimes help thinking about either (e.g., about energy flows, work, and so on), requires no assumption about commonality in design.

Date: 2002/05/06 19:19:54, Link
Author: niiicholas
testing, testing, 1 2 3...

Wow, this looks like a spiffy software package, all the code tags are right above there...

Quote
Curious green ideas sleep furiously


...well, it's sticking all of the tags at the *end* of the line, regardless of the cursor position.

Trying smilies:
:0  ???  :D

Trying a URL:
Talkorigins webpage link test

...hey, that worked pretty well..


A graphic:

...hmm, it stuck the code at the end of the post, I'll move it up.



I won't even trying the Flash movie posting option...

nic

Date: 2002/05/07 00:47:12, Link
Author: Wesley R. Elsberry
There are a number of critical reviews of Dembski's "The Design Inference".

Review by Ellery Eells

Review by Wesley R. Elsberry

Review by Fitelson et alia

Review by Richard Wein

Date: 2002/05/07 00:58:23, Link
Author: Wesley R. Elsberry
I have an extended critique of this book at this page.

Date: 2002/05/07 02:24:06, Link
Author: Wesley R. Elsberry
My page on William A. Dembski.  This links to his own pages and essays, and also to critical views of his ideas.

Please use this thread for pointing out new essays, books, criticism, and news concerning William Dembski.

Date: 2002/05/07 10:07:10, Link
Author: Wesley R. Elsberry
Intelligent Design advocates often deploy very negative analogies concerning their critics.  Such analogies have included things like the former Soviet regime, McCarthyites, and Nazis.

This thread is for documenting specific instances where ID advocates engage in political speech at the expense of their critics.

I'll start things off with a recent example.

Mark Hartwig: Compares Darwinists to Nazis

Mark Hartwig has taken over the "Weekly Wedge Update".  In his column for May 5, 2002, Hartwig makes an analogy between "Darwinists" and the Nazi oppressors of Czechoslovakia.

Quote
The intimidation tactics, however, signal something important about Darwinists. That "something" was explained in an insightful little piece by one A.J. Obrdlik. Published in 1942, it was a study of "gallows humor" in Czechoslovakia during the Nazi occupation. In that article, Obrdlik made a very keen observation:

Gallows humor is a reliable index of the morale of the oppressed whereas the reaction to it on the part of the oppressors tells a long story about the actual strength of the dictators: If they can afford to ignore it, they are strong; if they react wildly with anger, striking their victims with severe reprisals and punishment, they are not sure of themselves, no matter how much they display their might on the surface.

With the growing success of the Wedge, I'm sure we're going to see a lot more of this stuff. But Darwinist tactics will become a lot less intimidating as people realize that they signify not strength but panic.




Date: 2002/05/16 16:52:01, Link
Author: Wesley R. Elsberry
On the ARN forum, "Ex-YEC-er" made this comment:

Quote
As far as the Brainstorm forum is concerned, my experiences differ significantly from yours, perhaps because I tend to be critical of Dembski's arguments. When mentioning references to Wesley Elsberry my posting was removed by the moderator. "No interest in the gospel of Elsberry...". When I forwarded my response to the administrator to Dembski (I was responding to his posting), Dembski had me banned and warned me that any attempt to complain about this would likely lead to my permanent banishment from the forum.


ARN forum thread on flagellar evolution

This, of course, intrigues me.

If anyone knows who "Ex-YEC-er" is, please ask him or her to get in touch with me about this.

Also, if you have direct experience with ISCID moderation removing or editing posts based upon references to particular critics, I would like to hear from you.

Date: 2002/05/17 02:35:38, Link
Author: niiicholas
Howdy,

Wes has kindly made me a moderator on this forum.  I'd like to briefly mention a few things for background's sake.  As other things come up they will be added to this thread (or the thread can be bumped if someone needs an introduction).

First, the title of the forum.  Here is the reference (from Wes):

Quote

"The time has come," the Walrus said, "to speak of many things.  Of shoes and ships and sealing wax, of cabbages and kings."

-- Lewis Carroll



Guidelines:

1) This is a public-viewing, but restricted posting forum.  Posting access is granted by (I think) either Wes or me, basically if we feel like the poster will contribute to the purpose of this particular forum, detailed below.

2) The purpose of this forum is to give ID skeptics a place to gather references, citations, bits of arguments, etc., in one place, either just for reference, or for a possible future article or FAQ.  

The idea is to do things on a thread-specific basis.  A random example thread title might be "Examples of co-option in evolution", and the person who starts the thread says something like:

"I would like this thread to focus on well-documented examples of cooption in evolution.  The reason, of course, is that antievolutions frequently assert, without documentation, that change-of-function is a very low probability event, and use this pseudo-argument to brush off the "what about cooption?" objection to the arguments of Behe and Dembski regarding the nonevolution of functional complexity.

The best way to rebut the IDists' assertion is simply to list the numerous examples of cooption in evolution, with references.  So, if you come across a good example, mention it and if possible cite what references you have; others may be able follow up suggestions of places to look, e.g. "I think I read an essay by Gould on this once".

Additional things worth posting in a thread like this:

- links to other threads discussing cooption
- links to high-quality webpages
- links to the Pubmed abstracts of specific papers
- references on the topic generally, e.g. papers on the topic of the fate of gene duplications, for example.
- images and highly relevant quotes can be posted also

Both molecular and macro cases are welcome, part of the point of this thread is to show that the same process occurs commonly in both realms.
"

See how this would work?  The potential topics are endless, but hopefully when you run across something, e.g. "Hey, a new article on the evolution of blood-clotting!", you can check the forum to see if there is already a thread on blood-clotting, and add the reference there.


3) Discussions of the above are welcome in this forum, however if very long-winded debates develop they are better put in the general ID discussion.  Also, active debates with internet IDists should be conducted in the general ID discussion (where they have a chance to fight back); I think a good policy would be to stick a link to a debate thread in the relevant thread here.  The main focus here is on "collaborative informational resource gathering/displaying" -- hopefully it will develop into a high-quality resource for ID skeptics across the net.

Have fun,

nic
niiicholas@yahoo.com

Date: 2002/05/17 10:02:05, Link
Author: Wesley R. Elsberry
This forum is for brief posts relating upcoming or past events having to do with "intelligent design".  Discussion should be taken to the "All About Antievolution -> Intelligent Design" forum or one of the fora under "Specifically About Intelligent Design".

Please provide a link to online articles or announcements.  A short summary would be appropriate to describe what is linked.

Wesley

Date: 2002/05/17 11:12:21, Link
Author: Wesley R. Elsberry
2002/05/10

Jonathan Wells's "Icons of Evolution" has been produced as a film suitable for television broadcast by "Coldwater Media".  It premiered in Seattle at Seattle Pacific University.

Origins of life film to premiere at SPU

Not the Whole Truth, a review by Roger Downey.

Documentation of the history of the DeHart case.  DeHart was featured in the "Icons" video.

Please add "Icons" video related links to this thread.

Date: 2002/05/17 19:19:04, Link
Author: Wesley R. Elsberry
In this ARN forum topic, the issue of arguing concerning optimality was raised.  The person bringing this up cited Dembski, but several of his ideas seem to stem from Paul Nelson's presentation back at the 1997 NTSE conference.

Basically, ID advocates object to optimality arguments by biologists when these venture into the realm of contrasting natural mechanisms with supposed supernatural mechanisms.  Paul Nelson made the observation that such argumentation presupposes certain "theological themata".  Nelson also asserted that in order to argue that some state observed in nature was sub-optimal, one would have to reliably know what the absolute optimal state was, and calculate an optimality deficit figure.

I responded to Nelson's assertion that knowledge of absolute optimality was a necessary part of a sub-optimality argument some time ago on the talk.origins newsgroup.  The response can be seen here, but the essential message is that a valid sub-optimality argument can be warranted on a strictly relative basis, with no need for absolute optimality to be known.

I also responded to William Dembski's essay on optimality argumentation, pointing out several problems in his argumentation.  Dembski's essay is here, and my response is here.



Date: 2002/05/17 19:40:34, Link
Author: Wesley R. Elsberry
The "Coldwater Media" video of Jonathan Wells's "Icons of Evolution" premiered on 2002/05/10, and since has been reported to have aired on several television stations in Ohio.  This deployment seems to be obviously political in nature, with an aim to influence voters, who in turn would influence the Board of Education to include "intelligent design" in school science standards, or at the least officially single out evolutionary biology as "controversial" and require the teaching of "evidence against" evolution.  These two ways of stating things are pretty much synonymous for "intelligent design" advocates.

Anyone with information on specific times, locales, and dates when the "Icons" video has been aired is requested to add to
this thread in the "Intelligent Design News" forum.

Date: 2002/05/17 21:43:08, Link
Author: niiicholas
Here is a fantastic recent example from your friend and mine, Jonathan Wells.


There You Go Again:
A Response to Kenneth R. Miller
Jonathan Wells
Discovery Institute
April 9, 2002


Quote

The believers in Darwinian evolution who currently dominate our educational establishment think that all students--even those headed for careers in auto mechanics or real estate--should believe, as they do, that all of us are descended from ape-like creatures through genetic accidents and survival of the fittest.

Promoters of this doctrine have recently been urging the Ohio State School Board to adopt science standards that would require all high school graduates to memorize Darwinian theory without questioning it, and without being exposed to any of the mounting evidence against it. To help in this campaign, the promoters enlisted the support of Brown University biology professor Kenneth R. Miller, who represented them before the Board on March 11.

Miller is not a disinterested scientific expert. As the co-author of an introductory biology textbook that has been purchased for use in the Ohio public school system, he has a substantial personal stake in the controversy. In 2000, I published a book, Icons of Evolution, criticizing the way biology textbooks--including Miller’s--systematically distort the scientific evidence to provide support for Darwin’s theory. In his appearance before the Ohio State School Board, Miller attempted to respond to some of my criticisms.

In his eagerness to defend Darwinian orthodoxy, however, Miller bungled the attempt.


It takes a rather amazing amount of gall for Wells to accuse Ken Miller of not being a "disinterested scientific expert" because of Miller's interest in his textbook, when Wells obviously has (at the very least) a similar level of interest in his own book Icons.

Also interesting in the above quote is how Wells appears to (now) be denying the common descent of humans and apes, whereas if you read Icons of Evolution carefully one finds quotes like (paraphrase) "it is clear that the human species has a history".  AFAICT Wells actually does believe in some kind of guided evolution (i.e. he disagrees only with the "genetic accidents and survival of the fittest" bit), that's probably what he would say about the first sentence if pressed, but it is interesting how he managed not to distinguish his view from the special creationist view.

Returning to the fold under pressure, perhaps...

Date: 2002/05/17 22:00:37, Link
Author: niiicholas
Hi,

Following my own suggestion, here is a thread devoted to collection material/links/references relevant to blood-clotting and the claims IDists make about it.  As there is not yet a single webpage anywhere that has gathered all of the relevant material in a single place, this might as well be it.  Perhaps at some point it could be edited into a FAQ, or could inspired someone to write a FAQ (since much of the hard work of finding the references, IDist quotes, etc., would be done).

Specifically relevant would be things like:

1) blood-coagulation/clotting (or hemolyph coagulation for you invertebrates out there), especially e.g. webpages/literature that describe the basics in an easily understandable manner such that a FAQ reader could be referred there

2) references to articles/lit. on the evolution of blood clotting

3) Links to/quotes of antievolutionist assertions regarding blood-clotting, with commentary on problems if you are inspired

4) Links to the various webpages already out there rebutting IDist claims.

Awhile ago I did a search and dug up a pretty good starting reference list, I'll post that in a moment.

nic



Date: 2002/05/17 22:09:17, Link
Author: niiicholas
These are the results of a computer search last year on terms like "evolution blood coagulation."  I was pretty careful checking abstracts etc. to avoid including "false hits" -- (e.g., "evolution" has a chemical meaning unrelated to biological evolution).

For fun, I added asterisks (*) to refer to papers that Behe referenced in Darwin's Black Box.  The others are the ones he missed, or that were published 1996 or later.

I'll quote the whole URL in code brackets, hopefully they'll fit.


Code Sample

Banyai, L., Varadi, A. and Patthy, L. (1983). “Common evolutionary origin of the fibrin-binding structures of fibronectin and tissue-type plasminogen activator.” FEBS Letters, 163(1): 37-41. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=6685059&dopt=Abstract

Bazan, J. F. (1990). “Structural design and molecular evolution of a cytokine receptor superfamily.” Proceedings of the National Academy of Sciences of the United States of America, 87(18): 6934-6938. Link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=2169613

Blake, C. C. F., Harlos, K. and Holland, S. K. (1987). “Exon and Domain Evolution in the Proenzymes of Blood Coagulation and Fibrinolysis.” Cold Spring Harbor Symposia on Quantitative Biology: The Evolution of Catalytic Function, LII: 925-932. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=3454300&dopt=Abstract

Crabtree, G. R. (1986). “The Molecular Genetics of Fibrinogen.” Journal of Cellular Biochemistry Supplement(10 PART A): 229.  

Crabtree, G. R., Comeau, C. M., Fowlkes, D. M., Fornace, A. J., Jr., Malley, J. D. and Kant, J. A. (1985). “Evolution and structure of the fibrinogen genes: Random insertion on introns or selective loss?” Journal of Molecular Biology, 185(1): 1-20.  

Di Cera, E., Dang, Q. D. and Ayala, Y. M. (1997). “Molecular mechanisms of thrombin function.” Cell Mol Life Sci, 53(9): 701-730.  

Doolittle, R. F. (1985). “More homologies among the vertebrate plasma proteins.” Biosci Rep, 5(10-11): 877-884. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=3938299&dopt=Abstract

Doolittle, R. F. (1990). “The Structure and Evolution of Vertebrate Fibrinogen A Comparison of the Lamprey and Mammalian Proteins,” in ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY: FIBRINOGEN, THROMBOSIS, COAGULATION, AND FIBRINOLYSIS. C. Y. Liu and Chien, S. New York, Plenum Press. 281. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=2102616&dopt=Abstract

Doolittle, R. F. (1992). “A detailed consideration of a principal domain of vertebrate fibrinogen and its relatives.” Protein Science, 1(12): 1563-1577. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=1304888&dopt=Abstract

Doolittle, R. F. (1992). “Early Evolution of the Vertebrate Fibrinogen Molecule.” Biophysical Journal, 61(2 PART 2): A410.  

Doolittle, R. F. (1992). “Early Evolution of the Vertebrate Fibrinogen Molecule.” FASEB Journal, 6(1): A410.  

Doolittle, R. F. (1992). “Stein and Moore Award address. Reconstructing history with amino acid sequences.” Protein Science, 1(2): 191-200. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=1339026&dopt=Abstract

*Doolittle, R. F. (1993). “The Evolution of Vertebrate Blood Coagulation - a Case of Yin and Yang.” Thrombosis and Haemostasis, V70(N1): 24-28. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8236110&dopt=Abstract

Doolittle, R. F. and Feng, D. F. (1987). “Reconstructing the Evolution of Vertebrate Blood Coagulation from a Consideration of the Amino Acid Sequences of Clotting Proteins.” Cold Spring Harbor Symposia on Quantitative Biology: The Evolution of Catalytic Function, LII: 869-874. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=3483343&dopt=Abstract

Doolittle, R. F., G., Spraggon and J., Everse S. (1997). “Evolution of vertebrate fibrin formation and the process of its dissolution.” Ciba Found Symp, 212: 4-17; discussion 17-23. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9524761&dopt=Abstract

Doolittle, R. F. and Riley, M. (1990). “The amino-terminal sequence of lobster fibrinogen reveals common ancestry with vitellogenins.” Biochemical and Biophysical Research Communications, 167(1): 16-19. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=2310387&dopt=Abstract

Edgington, T. S., Curtiss, L. K. and Plow, E. F. (1985). “A linkage between the hemostatic and immune systems embodied in the fibrinolytic release of lymphocyte suppressive peptides.” Journal of Immunology, 134(1): 471-477.  

Ghidalia, W., Vendrely, R., Montmory, C., Coirault, Y., Samama, M., Lucet, B., Bellay, A. M. and Vergoz, D. (1989). “Overall study of the in vitro plasma clotting system in an invertebrate, Liocarcinus puber (Crustacea Decapoda): Considerations on the structure of the Crustacea plasma fibrinogen in relation to evolution.” Journal of Invertebrate Pathology, 53(2): 197-205.  

Hervio, L. S., Coombs, G. S., Bergstrom, R. C., Trivedi, K., Corey, D. R. and Madison, E. L. (2000). “Negative selectivity and the evolution of protease cascades: the specificity of plasmin for peptide and protein substrates.” Chemistry & Biology, V7(N6): 443-452.  

Hewett-Emmett, D., Czelusniak, J. and Goodman, M. (1981). “The evolutionary relationship of the enzymes involved in blood coagulation and hemostasis.” Annals of the New York Academy of Sciences, 370(20): 511-527.  

Holland, S. K., Harlos, K. and Blake, C. C. F. (1987). “Deriving the generic structure of the fibronectin type II domain from the prothrombin Kringle 1 crystal structure.” EMBO (European Molecular Biology Organization) Journal, 6(7): 1875-1880.  

Jordan, R. E. (1983). “Antithrombin in vertebrate species: conservation of the heparin-dependent anticoagulant mechanism.” Archives of Biochemistry and Biophysics, 227(2): 587-595.  

Kant, J. A., Fornace, A. J., Jr., Saxe, D., Simon, M. J., McBride, O. W. and Crabtree, G. R. (1985). “Evolution and organization of the fibrinogen locus on chromosome 4: Gene duplication accompanied by transposition and inversion.” Proceedings of the National Academy of Sciences of the United States of America, 82(8): 2344-2348.  

Kornblihtt, A. R., Pesce, C. G., Alonso, C. R., Cramer, P., Srebrow, A., Werbajh, S. and Muro, A. F. (1996). “The fibronectin gene as a model for splicing and transcription studies.” FASEB Journal, 10(2): 248-257.  

Laki, K. (1972). “Our ancient heritage in blood clotting and some of its consequences.” Annals of the New York Academy of Sciences, 202(4): 297-307.  

Neurath, H. (1984). “Evolution of proteolytic enzymes.” Science, 224(4647): 350-357. Link: http://www.jstor.org/journals/00368075.html

Neurath, H. (1986). “The Versatility of Proteolytic Enzymes.” Journal of Cellular Biochemistry, 32(1): 35-50.  

Neurath, H. (1986). “The Versatility of Proteolytic Enzymes.” Journal of Cellular Biochemistry Supplement(10 PART A): 229.  

Oldberg, A. and Ruoslahti, E. (1986). “Evolution of the fibronectin gene: Exon structure of cell attachment domain.” Journal of Biological Chemistry, 261(5): 2113-2116.  

Opal, S. M. (2000). “Phylogenetic and functional relationships between coagulation and the innate immune response.” Critical Care Medicine, V28(N9 SUPPS): S77-S80.  

Pan, Y. and Doolittle, R. F. (1991). “Distribution of Introns in Lamprey Fibrinogen Genes.” Journal of Cellular Biochemistry Supplement(15 PART D): 75.  

Pan, Y. and Doolittle, R. F. (1992). “cDNA sequence of a second fibrinogen alpha chain in lamprey: an archetypal version alignable with full-length beta and gamma chains.” Proceedings of the National Academy of Sciences of the United States of America, 89(6): 2066-2070. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=1549566&dopt=Abstract

Patthy, L. (1985). “Evolution of the Proteases of Blood Coagulation and Fibrinolysis by Assembly from Modules.” Cell, 41(3): 657-664. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=3891096&dopt=Abstract

Patthy, L. (1990). “Evolution of blood coagulation and fibrinolysis.” Blood Coagulation and Fibrinolysis, 1(2): 153-166. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=2130927&dopt=Abstract

Patthy, L. (1990). “Evolutionary Assembly of Blood Coagulation Proteins.” Seminars in Thrombosis and Hemostasis, 16(3): 245-259. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=2237446&dopt=Abstract

Patthy, L. (1999). “Genome evolution and the evolution of exon-shuffling—a review.” Gene, 238(1): 103-114. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10570989&dopt=Abstract

Roberts, Lewis R., Nichols, Lanita A. and Holland, Lene J. (1995). “CDNA and amino-acid sequences and organization of the gene encoding the B-beta subunit of fibrinogen from Xenopus laevis.” Gene (Amsterdam), 160(2): 223-228.  

Sosnoski, D. M., Emanuel, B. S., Hawkins, A. L., Van Tuinen, P., Ledbetter, D. H., Nussbaum, R. L., Kaos, F. T., Schwartz, E., Phillips, D. and et al. (1988). “Chromosomal localization of the genes for the vitronectin and fibronectin receptors .alpha. subunits and for platelet glycoproteins IIb and IIIa.” Journal of Clinical Investigation, 81(6): 1993-1998.  

Wang, Y. Z., Patterson, J., Gray, J. E., Yu, C., Cottrell, B. A., Shimizu, A., Graham, D., Riley, M. and Doolittle, R. F. (1989). “Complete sequence of the lamprey fibrinogen .alpha. chain.” Biochemistry, 28(25): 9801-9806.  

Xu, X. and Doolittle, R. F. (1990). “Presence of a vertebrate fibrinogen-like sequence in an echinoderm.” Proceedings of the National Academy of Sciences of the United States of America, 87(6): 2097-2101. Link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=2315305

Zhang, Y. L., Hervio, L., Strandberg, L. and Madison, E. L. (1999). “Distinct contributions of residue 192 to the specificity of coagulation and fibrinolytic serine proteases.” Journal of Biological Chemistry, V274(N11): 7153-7156. Link: http://www.jbc.org/cgi/content/full/274/11/7153

Zimmermann, E. (1983). “[The evolution of the coagulation system from primitive defense mechanisms].” Behring Institute Mitteilungen, 82(73): 1-12.  



Many of these articles are however tough to get (unless you're at UCSD, unsurprisingly), so I've only read a few.

Others are welcome to add stuff as they see fit.

Thanks, nic



Date: 2002/05/17 23:18:58, Link
Author: niiicholas
Quote (Wesley R. Elsberry @ May 17 2002,19:19)
In this ARN forum topic, the issue of arguing concerning optimality was raised.  The person bringing this up cited Dembski, but several of his ideas seem to stem from Paul Nelson's presentation back at the 1997 NTSE conference.

Basically, ID advocates object to optimality arguments by biologists when these venture into the realm of contrasting natural mechanisms with supposed supernatural mechanisms.  Paul Nelson made the observation that such argumentation presupposes certain "theological themata".  Nelson also asserted that in order to argue that some state observed in nature was sub-optimal, one would have to reliably know what the absolute optimal state was, and calculate an optimality deficit figure.

I responded to Nelson's assertion that knowledge of absolute optimality was a necessary part of a sub-optimality argument some time ago on <a href="news:talk.origins" target="_blank">the talk.origins newsgroup</a>.  The response can be seen here, but the essential message is that a valid sub-optimality argument can be warranted on a strictly relative basis, with no need for absolute optimality to be known.

I also responded to William Dembski's essay on optimality argumentation, pointing out several problems in his argumentation.  Dembski's essay is here, and my response is here.

I agree that there are plenty of cases when the assertion "this biological design is suboptimal relative to what someone with foresight would have designed for this purpose" is a perfectly legimate inference, although of course sometimes things will be ambiguous.

I was interested in this little bit here:

Quote

Basically, ID advocates object to optimality arguments by biologists when these venture into the realm of contrasting natural mechanisms with supposed supernatural mechanisms.  Paul Nelson made the observation that such argumentation presupposes certain "theological themata".  


I take this to be a reference to the IDist counterargument, "'God wouldn't have done it that way' is a theological argument".

It seems to me that this criticism is only correct insofar as the attributes of God are really up-for-grabs; for most antievolutionists it is in fact rather clear what kind of God is being hypothesized, and once that hypothesis has been suggested then it seems to me perfectly fair for a skeptic to point out where facts disagree with the hypothesis.

However, the IDists have really argued themselves into a pickle on this one.  Recall that ID "officially" says that nothing is known about the designer, i.e. whether it is supernatural or natural ID.  Therefore, if a skeptic points out that a suboptimal design is well explained by the foresight-lacking mechanism of natural selection, whereas an intelligent designer using foresight would easily have avoided the suboptimality, then the IDists have no recourse to the "that's a theological argument" line.  The only way they can use this argument (which would still have the problems mentioned above) is if they admit that they are bringing God into it as the designer!

g'night, nic

Date: 2002/05/18 03:24:15, Link
Author: Wesley R. Elsberry
Here's a reference that Ken Miller cited in the AMNH debate on 2002/04/23:

Quote
Robinson, A. Jean, Kropatkin, Mona, and Aggeler, Paul M.  1969.   Hageman Factor (Factor XII) Deficiency in Marine Mammals. Science 166:1420-1422.


Marine mammals lack one of the "parts" of the blood-clotting system whose absence supposedly renders the system non-functional.

Mark Todd pointed this one out to Miller, having heard about it from some of the veterinarians who I work with, too.  I don't think that they mentioned this bit around me.

Date: 2002/05/18 16:46:53, Link
Author: ExYECer
I have contacted you and will be more than willing to describe what happened to me on the ISCID brainstorm boards, even though this may mean permanent banishment per Dembski's orders.

Date: 2002/05/19 09:52:51, Link
Author: Lizard
In KC, the local ID people rented a movie theater and "premiered" another video, "Unlocking the Mystery of Life" on 5/16. This one is offered on the ARN website also. Nobody I know went to see it. Apparently, it has some neato special effects taking you inside the amazing complexities of a cell, showing the amazingly complex mechanisms of the bacterial flagellum, etc. Are these the only two examples of "IC" they can think of?  ???

Date: 2002/05/19 14:25:05, Link
Author: Wesley R. Elsberry
One of the staples of the antievolution movement is the deployment of "quotations".  When one examines the antievolutionary literature, one will note a relative superabundance of quoted material within it.  Closer examination will reveal that many of these supposed quotations are quoted out of context, have been edited to adjust their meaning to something in line with the argument the antievolutionist wants to make, are from "experts" of dubious reputation or from long ago, are patched together from widely separated sentences in the source, or otherwise fail to accurately reflect the intent and meaning of the author.

In this thread, I would like people to contribute examples of misquotations deployed by antievolutionists.  This should include the citation of the misquotation (who deployed the quote and where), the misquotation itself, and the original quote with sufficient context to show that the antievolutionist did indeed engage in misquotation.

I'll also encourage people to contribute such examples to my quotation database at this URL.

Additonally, people are directed to Michael Hopkins's Quotation and Misquotations FAQ at the TalkOrigins Archive.

Date: 2002/05/20 12:03:29, Link
Author: Wesley R. Elsberry
There are some issues that exploration of Dembski's formulae reveal.

p_dco = p_orig * p_local * p_config

Dembski provides two basic equations for probabilities.  The one for p_local is defined on NFL p.293.  Both p_orig and p_config are calculated on the basis of what Dembski calls a perturbation probability.  Dembski provides a variety of forms or approximations to a perturbation probability (NFL pp.297,299,300,301).

p_local calculations (NFL p.293)

p_local = (units in system * substitutions / total different units)^(units in system * copies)

What is interesting here is that numbers for "substitutions" and "copies" are simply invented by Dembski, not referenced as the result of empirical study on the system in question.  Yet the equation is highly sensitive to changes in these numbers.  For the numbers provided by Dembski (50 units in the system, 4289 total different units, 5 copies, 10 substitutions), the resulting probability is 4.502871e-234 (all calculations done via the Finite Improbability Calculator).  If we change "substitutions" to 11 instead of 10, the resulting probability is 1.003831e-223, or about 11 orders of magnitude.  If we change "copies" to 4 instead of 5, the resulting probability is 2.102769e-187, or about 47 orders of magnitude different.  This extreme sensitivity is something which Dembski does not even note in his discussion.

The other numbers in the calculation would at first glance appear to be more stable.  But the total number of units, 4289, is simply taken as the number of proteins which the E. coli genome is known to code for.  There is no justification given for using this number in the context of flagellar construction.  It is well known in developmental biology that not all proteins coded for are present or expressed within a cell at all times, yet this is exactly the sort of counterfactual assumption Dembski makes in deploying this number.  If we assume a mere 10% of possible proteins are not present at the time of flagellar construction, the calculated probability changes to 1.246450e-222, or 12 orders of magnitude more likely.  Even the number 50, for proteins used within the flagellum, is not beyond critical examination.  There is no indication that this is the minimum number of proteins necessary for flagellar construction, just that this is the characteristic number seen in E. coli flagella.  Change this to 49, and the probability rises to 1.481864e-231, or about 3 orders of magnitude more likely.

Dembski has failed to establish the biological relevance of his p_local calculation.  He has overlooked the developmental aspect of the E. coli cell entirely.  His invented parameters are not grounded in empirical research.  The extreme sensitivity of his provided equation to changes in values of all parameters lends little confidence to the results.  In no sense does he justify this calculation as providing an upper bound on the probability of even "random localization", as he must if this calculation is supposed to be relevant in any sense to the issue at hand.  And, of course, there is no justification for the assumption that "random localization" is the sole relevant chance hypothesis to be considered.

Date: 2002/05/21 20:32:31, Link
Author: Lizard
Now IDers are putting on a full-court press to have ID taught in Nebraska K-12 schools. They are testifying before the Nebraska BOE, and the local Rationalists are scrambling to get pro-science people to testify in favor of science.

What the ID promoters learned in Kansas, they are applying in Ohio. What they are learning in Ohio, they're applying in Nebraska. And so on and on ID strategy evolves. It's scary how relentless they are.

It would be extremely useful to have a comprehensive anti-ID resource for activists in Ohio, Nebraska, Washington and elsewhere to go to for information, ideas, tactics, etc. Could that be part of our website?

My organization, KCFS, sponsored a meeting of pro-science activists from 9 or 10 states about a year ago. One great project that came out of it was an "Activists' Handbook" that is in the process of being readied for the Web. I recommend that we link to it and think of other helpful content for anti-creationist activists to include.

My $.02.

Liz

Date: 2002/05/21 21:09:49, Link
Author: Wesley R. Elsberry
The antievolution group in Nebraska appears to be Concerned Citizens for Objective Science Education.

Right on the home page, this group quotes Charles Darwin.

Quote
A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question.


It is an interesting quote, now seen in the presentations of several "intelligent design" advocates.  Their deployment of it is flawed, however.  ID advocates don't "balance" facts and arguments for "intelligent design" against facts and arguments for evolutionary biology.  The ID advocacy strategy is one of negative argumentation.  This is apparently a cover for their inconvenient situation, which is that they seem to have no "facts and arguments" for their position.

But even that is not the whole story.  The quote from Darwin is lifted from an interesting context.  I will provide the complete paragraph here.

Quote
This Abstract, which I now publish, must necessarily be imperfect. I cannot here give references and authorities for my several statements; and I must trust to the reader reposing some confidence in my accuracy. No doubt errors will have crept in, though I hope I have always been cautious in trusting to good authorities alone. I can here give only the general conclusions at which I have arrived, with a few facts in illustration, but which, I hope, in most cases will suffice. No one can feel more sensible than I do of the necessity of hereafter publishing in detail all the facts, with references, on which my conclusions have been grounded; and I hope in a future work to do this. For I am well aware that scarcely a single point is discussed in this volume on which facts cannot be adduced, often apparently leading to conclusions directly opposite to those at which I have arrived. A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question; and this cannot possibly be here done.


-- Origin of Species

Darwin's statement does not support the notion, common among ID advocates, that in any educational circumstance when one mentions evolutionary biology one must then launch into discussion of the top ten reasons ID advocates are antievolutionists.  Darwin recognizes that the context matters, even if ID advocates fail to take the point.

A Nebraska group opposed to "intelligent design" being inserted into the science curriculum is the Nebraska Religious Coalition for Science Education.

Date: 2002/05/22 12:07:18, Link
Author: Wesley R. Elsberry
Creative Loafing Atlanta has an excellent front-page article on "intelligent design" and the textbook disclaimers mandated by the Cobb County school board.

Sidebar articles cover scientists responding to "intelligent design" and the Cobb County disclaimer, where Ken Miller is featured in both of those pieces.

Date: 2002/05/22 13:23:17, Link
Author: Glenn Branch
A review of the Icons video appeared in Seattle Weekly here.

Date: 2002/05/22 13:30:08, Link
Author: Glenn Branch
Here's AIG's take.

Date: 2002/05/23 08:35:09, Link
Author: Wesley R. Elsberry
A popular antievolution argument often deployed by "intelligent design" advocates concerns the non-universality of the genetic code:Jonathan Wells, Paul Nelson, Stephen Meyer, Michael Behe, and Cornelius G. Hunter.

I'm opening this thread for discussion of the canonical genetic code and its variants, and also for examination of the claims of ID advocates concerning the canonical code.

Kenneth Miller of Brown University has a couple of essays on this topic: here and here.

Date: 2002/05/23 08:55:32, Link
Author: Wesley R. Elsberry
The canonical genetic code

It is tough to represent tabular information in a proportional font.  So I will present a list representing the canonical genetic code.  There are three items separated by commas in each line.  The first is a representation of a codon, a nucleotide triplet.  Each base is represented by a letter: "a" for adenine, "g" for guanine, "c" for cytosine, and "u" for uracil.  The second item is either an amino acid or a "stop", where each amino acid is represented by a three-letter abbreviation.  The third item is a single-letter code for an amino acid.

uuu,phe,f
ucu,ser,s
uau,tyr,y
ugu,cys,c
uuc,phe,f
ucc,ser,s
uac,tyr,y
ugc,cys,c
uua,leu,l
uca,ser,s
uaa,stop,x
uga,stop,x
uug,leu,l
ucg,ser,s
uag,stop,x
ugg,trp,w
cuu,leu,l
ccu,pro,p
cau,his,h
cgu,arg,r
cuc,leu,l
ccc,pro,p
cac,his,h
cgc,arg,r
cua,leu,l
cca,pro,p
caa,gln,q
cga,arg,r
cug,leu,l
ccg,pro,p
cag,gln,q
cgg,arg,r
auu,ile,i
acu,thr,t
aau,asn,n
agu,ser,s
auc,ile,i
acc,thr,t
aac,asn,n
agc,ser,s
aua,ile,i
aca,thr,t
aaa,lys,k
aga,arg,r
aug,met,m
acg,thr,t
aag,lys,k
agg,arg,r
guu,val,v
gcu,ala,a
gau,asp,d
ggu,gly,g
guc,val,v
gcc,ala,a
gac,asp,d
ggc,gly,g
gua,val,v
gca,ala,a
gaa,glu,e
gga,gly,g
gug,val,v
gcg,ala,a
gag,glu,e
ggg,gly,g

Here's a page with a table showing the canonical code and the full expansion of the abbreviations.

Date: 2002/05/23 09:44:21, Link
Author: Thomas Foley
Hi folks.

For anyone that couldn't be bothered digging around on ccose.org, here are the three "bullet points" that "Maureen" is petitioning for inclusion in the Nebraska standards:

Quote
Investigate and distinguish the data and testable theories of science from religious or philosophical claims that are made in the name of science.
(Suggested inclusion in Section 12.8.1, which is "12th Grade Standard - History and Nature of Science - Science as a Human Endeavor" or 12.8.2, which is "12th Grade Standard - History and Nature of Science - Nature of Science".)

Investigate and understand the full range of scientific views on biological evolution that exist.
(Suggested inclusion in Section 12.4.3, which is "12th Grade Standard - Life Science - Theory of Biological Evolution".)

Investigate and understand why some topics, such as biological evolution, may generate controversy.
(Suggested inclusion in Sections 12.4.3, 12.8.1, 12.8.2 or 12.8.3, which is "12th Grade Standard - History and Nature of Science - History of Science".)


Right out of the Discovery Institute's 'foot-in-the-door' playbook, by the looks of it, although "Maureen" says she has no connection whatsoever with the DI.

I e-mailed "Maureen" a couple of days ago and received quite a lengthy and very friendly reply, to which I'm in the midst of responding.

Date: 2002/05/23 09:48:03, Link
Author: Wesley R. Elsberry
How many codes could there be?

The simple answer is "lots".  The canonical genetic code has 64 entries coding for 21 different things (20 amino acids plus a "stop" signal).  It is called "degenerate", which is a fancy way of saying that there are more codes than there are things coded for, which results in some redundancy in the canonical code.  If you look closely at how codons are matched with amino acids, you will likely notice that in many cases a change in the third base of the codon results in no change in the coded-for amino acid.  This results in a typical clustering of codons, so that a change of one base has about a one-in-five chance of causing no change at all in what amino acid is coded for.  In other words, the canonical genetic code is not as "brittle" as it could be.  I hope to explore that more thoroughly later.

But back to the question of interest.  How many "genetic codes" could there be?  Let me be clear here.  The phrase "genetic code" is sometimes sloppily used to refer to the specific sequence of bases observed in the genome of an organism.  That's not the way I am using it here.  The "genetic code" is used here as the way in which triplets of three nucleotide bases are mapped to corresponding amino acids for the purpose of protein synthesis.  Figuring out how many different ways such a code can be instantiated can be approached through combinatorial "counting rules".

The first "counting rule" of interest is the factorial function.  Given some positive integer number n of items, the factorial is defined as the product of every positive integer greater than or equal to one and less than or equal to n.  The number of different ways 64 symbols can be represented as a sequence is factorial(64) (or 64!), or about 1.268869e89.  Since a degenerate genetic code doesn't have 64 different symbols, but rather 64 positions for symbols, this represents an upper bound on the number of possible genetic codes using triplet codons.

So what counting rule gives us what we want?  The answer is the "partition rule".  This tells us that the number of ways that k different symbols can be arranged to fill n spaces when we know how many of each of the k symbols there are.  The rule is

n! / (m_1! * m_2! * ... * m_k!)

The sum of m_1 through m_k = n

For 21 symbols, the worst case situation would be if most of the code specified a single amino acid.  This occurs if one symbol is repeated 44 times and the remaining symbols have 1 instance each.  In this case, application of the partition rule tells us that there are 4.8e34 possible codes of that sort.

The best case situation is where all the codes are as nearly evenly represented as possible.  This is the case when one symbol has 4 instances and the remaining 20 symbols each have 3 instances.  In this case, there are about 1.4e72 possible different codes of that sort.

If we take the distribution of symbols in the canonical code, we have 64! / (4!6!2!2!2!2!2!4!2!3!6!2!1!2!4!3!6!4!1!2!4!), or about 2.3e69 possible different codes of that sort.

It is interesting that the actual canonical genetic code has a distribution that would permit almost as many variants as the very best case situation.

Next up will be considering what the numbers mean for evolutionary biology.

Date: 2002/05/23 16:32:16, Link
Author: theyeti
Awhile back I had a discussion about the DI's wacko response to the PBS evolution series here.  Scroll down a few messages.  There are some links to some good recent papers in that thread.  The references are:

Trends in Biochemical Sciences 2001, 26:591-596

Proc Natl Acad Sci U S A 1995 Mar 92:2441-5

J. Biol. Chem., Vol. 276, Issue 10, 6881-6884, March 9, 2001

Proc. Natl. Acad. Sci. USA, Vol. 97, Issue 15, 8392-8396,       July 18, 2000

Annu. Rev. Biochem. 2000. 69:617-650.

theyeti

Date: 2002/05/23 20:58:45, Link
Author: Wesley R. Elsberry
2002/05/23

Skip Evans, Network Project Director at the National Center for Science Education, has a response to the DI CRSC "Icons" video: Discovery Institute Pioneers the Mis-infomercial.

Date: 2002/05/23 22:08:15, Link
Author: Wesley R. Elsberry
Jonathan Wells has a very interesting report on the debate before the Ohio Board of Education.  Wells and Stephen Meyer of the Discovery Institute's Center for Renewal of Science and Culture were matched up against Kenneth Miller and Lawrence Krauss.

Other resources of interest in the Ohio situation:

Ohio Citizens for Science, a group for the acceptance of the new science standards as written by the advisory team.

Science Excellence for All Ohioans, a group advocating the inclusion of "intelligent design" in the K12 science curriculum, or at least something singling out evolutionary biology as a subject requiring "teaching the controversy".

Substandard Education for All Ohioans, a parody site poking fun at the antievolution stance of the page just above.

Events from Ohio, a collection of resources at the National Center for Science Education.

Date: 2002/05/23 22:43:25, Link
Author: Wesley R. Elsberry
Dembski now has his own collection of links to his writing, at DesignInference.com.

Date: 2002/05/24 01:06:23, Link
Author: Wesley R. Elsberry
This forum should be used for multi-user contributions to topics common in discussion of antievolution.

Posts should make specific additions to the stated topic, such as contributing URLs, bibliographic citations, and essays.

Date: 2002/05/24 01:28:43, Link
Author: Glenn Branch
In addition, the Cleveland Plain Dealer has conveniently collected its stories on the continuing controversy here.

Date: 2002/05/24 12:59:02, Link
Author: Wesley R. Elsberry
Stephen Jay Gould died of cancer at age 60 on 2002/05/20.

A number of obituaries have run.


Mercury News/Philadelphia Inquirer

Salon

BBC News/SCITECH

Harvard Gazette

Nature

Boston Globe

Yahoo!

CNN

Washington Post

Newsday

Boston Herald

Washington Post: Scientist who wrote rings around the earth

Chronicle of Higher Education

Nando Times

MSNBC

Date: 2002/05/24 13:11:11, Link
Author: Wesley R. Elsberry
Problem with Mercury News/Philadelphia Inquirer obituary

An obituary for Stephen Jay Gould by the Mercury News/Philadelphia Inquirer quoted many people about Gould.  Here's what they reported from Henry Morris and Richard Dawkins:

Quote
``We would honor him as a worthy opponent and will miss his great writing,'' said Henry Morris, founder and president emeritus of the Institute for Creation Research in El Cajon. ``Many of us creationist scientists thoroughly enjoyed reading -- and quoting from -- his books.''

Evolutionary biologist Richard Dawkins, a longtime critic of Gould, once wrote: ``He massively over-hyped his own work, and has a grossly exaggerated opinion of the worth of his ideas.''


-- Mercury News/Philadelphia Inquirer obituary

While the reporters went to the trouble of talking to Henry Morris, they apparently failed to give Dawkins the same courtesy, citing instead something written in another context an unspecified length of time ago.  Unfortunately, the text does not emphasize the point that Dawkins's comments were not made in the context established by the Morris quote just previous, which has misled some readers already.

I wrote Richard Dawkins about the Mercury News/Philadelphia Inquirer obituary, and he gave me permission to publicly release the following quote:

Quote
For good or ill, Steve Gould had a huge influence on American scientific culture, and on balance the good came out on top. Although we disagreed about much, we shared much too, including a spellbound delight in the wonders of the natural world, and a shared conviction that such wonders deserve nothing less than a purely natural explanation. His powerful voice will echo on for a long time.

Date: 2002/05/24 14:04:09, Link
Author: Wesley R. Elsberry
The Fourth World Skeptics Conference sponsored by CSICOP, June 20-23, 2002, in Burbank, California, will feature a panel on "Evolution and Intelligent Design".

The moderator will be Massimo Pigliucci.  Panelists will include William Dembski and Paul Nelson of the Discovery Institute's Center for Renewal of Science and Culture, Kenneth Miller of Brown University, and myself (Texas A&M, if you don't know already).

Date: 2002/05/24 19:42:53, Link
Author: niiicholas
Some good discussion and links on a bio.com article discussing the homology between a blood-clotting protein and a cone-snail venom protein (!!!) was posted on this II thread.

nic



Date: 2002/05/24 19:53:47, Link
Author: Wesley R. Elsberry
Stephen Meyer compares Ken Miller to Himmler

This one is reported by no less an authority than Jonathan Wells.

Quote
Another interesting aspect of the press conference was a statement by Ken Miller, featured on the evening news, to the effect that ID advocates are trying to present their views to the public "without the approval of science." Afterwards, in private, Steve Meyer kept repeating Miller's pompous declaration with a heavy German accent, sounding for all the world like Heinrich Himmler, Hitler's propaganda chief.


-- Jonathan Wells on 2002/03/11 session with the Ohio BOE

Date: 2002/05/24 20:25:51, Link
Author: niiicholas
Some more stuff I've gathered on the mysterious missing Hagemann factor case:

1) I went and re-checked Darwin's Black Box and Behe does indeed include the component as part of the IC blood-clotting system.***

2) Here is the abstract of the Robinson et al. paper that Wes cited:

Quote

Robinson, A. Jean, Kropatkin, Mona, and Aggeler, Paul M.  1969.   Hageman Factor (Factor XII) Deficiency in Marine Mammals. Science 166:1420-1422.

Hematologic and coagulation studies were conducted on Atlantic bottlenose dolphins and killer whales. Hematologic values were similar to those in man. These animals differed from other mammals in that the Hageman factor (factor XII) was absent and this absence caused marked prolongation of coagulation. Levels of VIII and V were high and those of VII and X were low compared with levels in man.


The paper mentions at the end a longish list of birds, reptiles, etc. that don't have Hagemann factor either, surprise suprise, although it mentions that at least some of these have other factors that may compensate...

Also of interest are the names of the orcas: "Orky" "Snorky" "Corky". Don't see those names as headers in scientific tables every day...

3) The conclusions of the Robinson et al. (1969) paper are backed up by this recent paper:

Quote

Pubmend citation

Thromb Res 1998 Apr 1;90(1):31-7

Whale Hageman factor (factor XII): prevented production due to pseudogene conversion.

Semba U, Shibuya Y, Okabe H, Yamamoto T.


In Southern blot analysis of the Hind III-digested whale genomic DNA obtained from the livers of two individual whales, we detected a single band with a size of five kilobase pairs which hybridized to full length guinea pig Hageman factor cDNA. We amplified two successive segments of the whale Hageman factor gene by polymerase chain reaction (PCR), and sequenced the PCR products with a combined total of 1367 base pairs. Although all of the exon-intron assemblies predicted were identical to those of the human Hageman factor gene, there were two nonsense mutations making stop codons and a single nucleotide insertion causing a reading frame shift. We could not detect any message of the Hageman factor gene expression by northern blot analysis or by reverse transcription-polymerase chain reaction (RT-PCR) analysis. These results suggest that in the whale, production of the Hageman factor protein is prevented due to conversion of its gene to a pseudogene. The deduced amino acid sequence of whale Hageman factor showed the highest homology with the bovine molecule among the land mammals analyzed so far.


In other words, this is a classic textbook-style case of pseudogene production, as well as being yet another bit of evidence supporting the whale-artiodactyl connection that has been suggested by various molecular studies and supported by recently discovered transitional fossils, see J. G. M. Thewissen's whale evolution page here.

4) It should be pointed out that while Behe includes Hageman factor (= Factor XII) as part of the IC blood-clotting system in DBB, the likely ID defense will be to take the "eternally receding IC system" approach wherein they declare this part non-essential and therefore not "part" of the IC "system" (if it's not part of the system, what it is a part of?).  

According to this t.o. POTM, it is indeed questionable how necessary Factor XII is for blood-clotting:

Quote

In this view, 3 factors included in the older scheme
(Factor XII = Hageman, prekallikrein and HMK) are now excluded, since deficiencies do not cause clinical disease, although they are associated with long clotting times in vitro. The role of XI isn't clear, since deficieny isn't invariably associated with disease.


...although one wonders if "deficiencies" means "complete absense", as it is apparent that Factor XII does play some important roles, e.g. the introduction to Semba et al. (1998) states:

Quote

Hageman factor (factor XII) is an initiation factor of plasma protease cascades, such as the intrinsic blood coagulation pathway and the plasma kinin system [1 and 2]. Important roles of the plasma kinin system in inflammatory responses in infection have been demonstrated. Microbial proteases such as Pseudomonas aeruginosa elastase, and negatively charged bacterial components such as endotoxin are capable of activating Hageman factor and prekallikrein [3, 4, 5 and 6].


...sounds like a handy thing to have around for sure.  Certainly on the above quote we can say that Hageman factor is necessary for "Hageman factor-dependent cascade activation", which just goes to show that just about anything can be considered "essential for function" depending on where one draws the lines of the "system".  

An even better feature of Semba et al. (1998) is that they propose a hypothesis for why Hagemann factor has been lost in marine mammals:

Quote

Saito et al. reported that all marine mammals examined by them did not possess coagulation activities equivalent to Hageman factor and prekallikrein [8]. Their explanation of this observation is as follows: the lack of these initiation factors of the intrinsic blood coagulation pathway must be advantageous to the marine mammals in prevention of disseminated intravascular coagulation syndrome which might occur in the semi-static state of blood circulation in the skin and the lungs under high hydrostatic pressure.

[...]

3. Discussion
The present study demonstrates that the Hageman factor gene converted to a pseudogene by the point mutations in exons coding for the protease domain in the whale. This conversion explains the absence of Hageman factor in whale plasma [8]. Messenger RNA of whale Hageman factor was not also detected in the liver mRNA fraction even by Southern blot analysis of the RT-PCR products. This result suggests very high instability of whale Hageman factor mRNA. Since only the 3' half of the whale Hageman factor gene has been analyzed so far, final conclusions about the mechanism of the blocked expression of the whale Hageman factor gene message cannot yet be drawn.

Participation of the intrinsic blood coagulation pathway in the disseminated intravascular coagulation syndrome has been suspected. The whale may dive to depths of 1000 m, where a semi-static state of blood circulation in the skin and the lungs might occur due to the high hydrostatic pressure. The fact that the initiation factor of the intrinsic blood coagulation system is not produced in the whale would support the clinical suspicion about the participation of this system in the disseminated intravascular coagulation syndrome.

We have been postulating that Hageman factor and the plasma kinin system play important roles in the host defense of land mammals. However, our hypothesis does not explain why Hageman factor-deficient individuals are not suffering from infectious deseases. Therefore, there may be an opposite hypothesis: the plasma kinin system does not play an essential role in host defense. From a superficial point of view, the present study might support this opposite hypothesis. However, Saito et al. reported that a significant amount of high-molecular weight kininogen was present in whale plasma [8]. This concentration corresponds to 30% of that in human plasma. We presently confirmed this using dolphin plasma (data not shown). If we take into account that the significant amount of high-molecular weight kininogen is present even in whale plasma, we could speculate that the important roles of the plasma kinin system are compensated by an unknown system(s) in Hageman factor-deficient individuals as well as in the marine mammals.

The deduced amino acid sequence of whale Hageman factor closely resembles that of the bovine molecule including the Pro-rich region where almost no homology is observed among the human, guinea pig, and bovine molecules [16]. Recently, Shimamura et al. [19] described their opinion that whales (including dolphins and porpoises), ruminants (cows, chevrotains, deer, sheep), and hippopotamuses form a monophyletic group. This is based on their analyses of two retroposons in the genomes of 15 mammalian species. Our present data support their opinion.


So, we appear to have parts being lost, perhaps "parts" being replaced or compensated for, and generally a lot of evolution going on.  One wonders how any of this would be explained on a "IDdidit" just-so story.

nic

PS: Looking up 'related articles' in Pubmed reveals that decreased Factor XII activity is associated with increased miscarriage in humans:

Quote

PubMed link

Fertil Steril 2002 Feb;77(2):353-6

Coagulation factor XII activity, but not an associated common genetic polymorphism (46C/T),is linked to recurrent miscarriage.

Iinuma Y, Sugiura-Ogasawara M, Makino A, Ozaki Y, Suzumori N, Suzumori K.

Department of Obstetrics and Gynecology, Nagoya City University Medical School, Mizuho-ku, Nagoya 467-8601, Japan. iinuma@med.nagoya-cu.ac.jp

OBJECTIVE: To investigate whether a factor XII genetic polymorphism is associated with first-trimester embryonal loss. DESIGN: Prospective case-control study. SETTING; Nagoya City University Hospital. PATIENT(S): Eighty-three patients with a history of two or more unexplained first-trimester recurrent miscarriages and 67 controls with no obstetric complications or history of miscarriage. MAIN OUTCOME MEASURE(S): Plasma factor XII activity, a genetic polymorphism (46 C-->T) of factor XII, lupus anticoagulant, and beta(2)glycoprotein I dependent anticardiolipin antibodies. RESULT(S): Ten of the 83 patients and 1 of the 67 controls had decreased factor XII activity; the difference in frequency was statistically significant. Wild-type (CC), heterozygote (CT), and homozygote (TT) allele patterns were observed in 8, 36, and 39 patients, respectively, compared with 11, 20, and 36 of the patients and controls, respectively. The mean (+/- SD) corresponding factor XII activity was 154.8 +/- 44.8%, 112.7 +/- 30.2%, and 66.2 +/- 29.2% in patients and 164.6 +/- 26.7%, 114.3 +/- 28.1%, and 70.4 +/- 18.1% in controls. The two groups did not differ in the frequency of the T allele or categories of factor XII activity. CONCLUSION(S): Factor XII activity overall, but not the 46C/T common genetic polymorphism, is associated with recurrent miscarriage.
(bold added)

...which sure seems to imply that it is important for something.


Further support:

Quote

Pubmed link

Fertil Steril 2001 May;75(5):916-9

Factor XII but not protein C, protein S, antithrombin III, or factor XIII is a predictor of recurrent miscarriage.

Ogasawara MS, Aoki K, Katano K, Ozaki Y, Suzumori K.

Department of Obstetrics and Gynecology, Nagoya City University Medical School, Nagoya, Japan.

OBJECTIVE: To investigate whether a decrease in the values of protein C (PC), protein S (PS), antithrombin III (ATIII), factor XII (FXII), or factor XIII (FXIII) has predictive value for subsequent miscarriages. DESIGN: Prospective study. SETTING: Nagoya City University Medical School. PATIENT(S): A total of 536 patients with a history of two or more first-trimester miscarriages. INTERVENTION(S): One hundred and twelve patients treated with low-dose aspirin were excluded from the analysis. MAIN OUTCOME MEASURE(S): The subsequent pregnancy outcome of 424 patients was compared for abnormal and normal levels of each parameter. RESULT(S): There were no differences in the subsequent miscarriage rates between abnormal and normal values of PC, PS, ATIII, and FXIII. However, the rate with abnormal FXII is significantly higher than that with normal FXII. CONCLUSION(S): A decrease in FXII (but not in PC, PS, ATIII, or FXIII) predicts subsequent miscarriage in patients with a history of first-trimester recurrent miscarriages.



Here is another example of why missing Factor XII is not a good thing:

Quote

Ann Thorac Surg 2002 Jan;73(1):286-8

Huge left atrial thrombus with mitral stenosis in congenital factor XII deficiency.

Hasegawa T, Uematsu M, Tsukube T, Takemura Y, Okita Y.

Department of Surgery, Division II, Kobe University School of Medicine, Japan.

Factor XII deficiency has been reported to be a risk factor for thromboembolism as a result of inactivation of fibrinolysis. We describe a case of a huge left atrial thrombus with mitral stenosis, which was successfully removed surgically in a Factor XII deficient patient.

pubmed link


...and yet the ancestors of whales clearly had Hageman Factor, but lost it.  How is this possible unless Behe's argument about IC is fundamentally flawed?

nic


*** Added in edit, Dec. 2002:

Actually, Behe did not.  It looks like it is on pp. 82 and 84, but on p. 86 Behe limits the system to only four components.  This was pointed out to me by DNAunion here:

http://iidb.org/ubb....759&p=2

On p. 86, Behe writes,

Quote

”Leaving aside the system before the fork in the pathway, where some details are less well known, the blood-clotting system first the definition of irreducible complexity. … The components of the system (beyond the fork in the road) are fibrinogen, prothrombin, Stuart factor, and proaccelerin. Just as none of the parts of the Foghorn [Leghorn] system is used for anything except controlling the fall of the telephone pole, so none of the cascade proteins are used for anything except controlling the formation of a blood clot. Yet in the absence of any one of the components, blood does not clot, and the system fails.” (Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p86)


(copying from DNAunion)

Ken Miller, here,

http://www.millerandlevine.com/km/evol/design2/article.html

...writes:

Quote

Consider, for example, the intricate cascade of proteins involved in the clotting of vertebrate blood. This has been cited as one of the principal examples of the kind of complexity that evolution cannot generate, despite the elegant work of Russell Doolittle (Doolittle and Feng 1987; Doolittle 1993) to the contrary. A number of proteins are involved in this complex pathway, as described by Behe:

When an animal is cut, a protein called Hagemann factor (XII) sticks to the surface of cells near the wound. Bound Hagemann factor is then cleaved by a protein called HMK to yield activated Hagemann factor. Immediately the activated Hagemann factor converts another protein, called prekallikrein, to its active form, kallikrein. (Behe 1996a, 84)

How important are each of these proteins? In line with the dogma of irreducible complexity, Behe argues that each and every component must be in place before the system will work, and he is perfectly clear on this point:

. . . none of the cascade proteins are used for anything except controlling the formation of a clot. Yet in the absence of any of the components, blood does not clot, and the system fails. (Behe 1996a, 86)

As we have seen, the claim that every one of the components must be present for clotting to work is central to the "evidence" for design. One of those components, as these quotations indicate, is Factor XII, which initiates the cascade. Once again, however, a nasty little fact gets in the way of intelligent design theory. Dolphins lack Factor XII (Robinson, Kasting, and Aggeler 1969), and yet their blood clots perfectly well. How can this be if the clotting cascade is indeed irreducibly complex? It cannot, of course, and therefore the claim of irreducible complexity is wrong for this system as well. I would suggest, therefore, that the real reason for the rejection of "design" by the scientific community is remarkably simple – the claims of the intelligent design movement are contradicted time and time again by the scientific evidence.


...the second quote is pretty clearly out-of-context and Miller should have noted that Behe left himself some wiggle room in DBB concerning everything "before the fork" -- most of the cascade.  Behe only explicitly includes four parts in the IC system.



Date: 2002/05/24 21:25:14, Link
Author: niiicholas
A recent post on talk.origins by Dunk discussing some recent (2002) literature, with quotes:

Here is the google link

nic

Date: 2002/05/24 22:27:00, Link
Author: niiicholas
An attempt to list the major relevant articles/books in the ID blood-clotting discussion:

Code Sample

Darwin's Black Box : The Biochemical Challenge to Evolution
by Michael J. Behe
http://www.amazon.com/exec/obidos/ASIN/0684834936/

Behe and the Blood Clotting Cascade (1997)
T.O. POTM on blood-clotting pointing out the sequence patterns
http://www.talkorigins.org/origins/postmonth/feb97.html

A Delicate Balance
by Russell F. Doolittle
http://bostonreview.mit.edu/br22.1/doolittle.html
Originally published in the February/ March 1997 issue of Boston Review

Behe Responds to the Boston Review
Letter to the Boston Review
by Michael J. Behe
(listed as copyright 1999, Behe originally posted the material to the Boston Review discussion bord in Spring 1997)
http://www.arn.org/docs/behe/mb_brrespbr.htm

Finding Darwin's God, Miller (1999)
Amazon.com link
http://www.amazon.com/exec/obidos/ASIN/0060930497/

In Defense of the Irreducibility of the Blood Clotting Cascade (July 31, 2000)
Response to Russell Doolittle, Ken Miller and Keith Robison
by Michael J. Behe
http://www.discovery.org/viewDB/index.php3?program=CRSC%20Responses&command=view&id=442

Design on the Defensive, (Fall (?) 2000)
Ken Miller's page responding to Behe's review of Miller's book
http://biocrs.biomed.brown.edu/Darwin/DI/Design.html

(Ken Miller evolution page: http://www.millerandlevine.com/km/evol/index.html)

Miller's response to Behe's (2000) "In defense of the IC of the Blood Clotting Cascade."
Introduction to Miller's argument on blood-clotting: http://www.millerandlevine.com/km/evol/DI/Clotting.html
...linked from Miller's 'Design on the Defensive' (http://www.millerandlevine.com/km/evol/DI/Design.html)

The Evolution of Vertebrate Blood Clotting
Miller's "original draft" (longer description than in the book) on the evolution of blood-clotting. Linked from the above reference: http://www.millerandlevine.com/km/evol/DI/clot/Clotting.html

Comments on Ken Miller's Reply to My Essays (Behe, January 2001)
A response to Ken Miller, but blood-clotting isn't mentioned.
http://www.discovery.org/viewDB/index.php3?program=CRSC%20Responses&command=view&id=579


There may be additional relevant online articles, I will add them if anyone suggests them.

Thanks, nic



Date: 2002/05/24 23:23:13, Link
Author: niiicholas
Quote
Jonathan Wells has a very interesting report on the debate before the Ohio Board of Education.  


Ken Miller's take, and further debates online about some of the points, are linked from here:

http://www.millerandlevine.com/km/evol/wells-april-2002.html

nic



Date: 2002/05/24 23:28:42, Link
Author: niiicholas
Here is a muddled page in support of Behe's IC blood-clotting argument, I list it as it draws heavily from Behe's chapter & gives a sense of Behe's specific arguments there (including Behe's inclusion of Hageman factor in the IC system):

Irreducible Complexity? Blood Clotting! at www.doesgodexist.org, by Robert Harsh

nic

Date: 2002/05/24 23:51:37, Link
Author: niiicholas
A somewhat interesting but mildly confused article in Geology News, "Geoscience at the BA: Clots have been with us for 400 million years", reporting on a talk by Colin Davidson (Imperial College School of Medicine) on the evolution of blood-clotting, especially regarding the role of large (genome or chromosome) duplications.  I say the article is confused as punctuated equilibrium is invoked as having something to do with the situation, which AFAICT it doesn't, and as none of the connections of blood-clotting to more ancient protease cascade systems are discussed.  The interesting quotes concern gene duplication:

Quote

Evolution at molecular level

The basic tenets of molecular biology make understanding evolution at the molecular level possible. Genes are encoded by DNA, also known as nucleic acid, and composed of long strings of four biochemical units termed bases (shortened to A, G, C, and T). The linear order or sequence of these bases encodes special signals for starting and stopping as well code-script read in triplets for amino acids.

These chains of amino acids - of which there are 20 - form proteins and are the products of most (but not all) genes. We can, therefore, determine the determine the protein amino acid sequence of genes by decoding the triplet DNA sequences and compare it to any other gene. The more evolutionarily similar two organisms, the greater the similarity of amino acid sequences when comparing homologous genes. This is because there has been less time for the natural mutation process - such as inborn errors in DNA replication - to act on a gene's DNA sequence. When comparing most human and chimpanzee proteins one finds 98 to 100% identity, but the same proteins shared with bacteria the identity drops between 30 to 60% or less.

Proteins also exist in the genomes of most organisms that share a high degree of identity, and who share a common ancestor. The best understood mechanism of gene duplication occurs during the production of gametes in sexual organisms. This process is called meiosis in which the two sets of chromosomes - one from each parent - line up and the threads of DNA cross, break and rejoin so that DNA is exchanged between parental chromosomes - so generating diversity.

Usually this is an equal and reciprocal exchange, but occasionally the result is unequal and one of the chromosomes acquires a little more DNA containing an extra gene,or part of one. If the gamete with extra DNA acquires an entire gene it is referred to as "gene duplication by unequal crossover".

In blood clotting, two of the similar proteases, Factor VII (FVII) and X (FX), are within close proximity on chromosome 13 in humans indicating that unequal crossover played a role in the evolution of blood clotting.

Complete genome duplication

Another mechanism of gene duplication is through complete genome duplication. The entire genome of brewer's yeast Saccharomyces cerevisiae has been sequenced, and provides evidence of complete genome duplication by the genetic redundancy and conserved arrangement of the remaining duplicated genes. One way that genome duplication can occur is through polyploidy and subsequent degeneration back to a lower ploidy state. (Polyploidy is where the cell nucleus contains multiple sets of chromosomes.  Humans are diploid meaning we have two copies of each chromosome but the toad Xenopus laevis has four copies of each chromosome and therefore an additional two copies of each gene.)

Such duplicated genes can take one of two career paths. The majority of gene duplicates enter "early retirement" as the constant mutational pressure results in amino acid substitutions that render the protein non-functional. In the rare event that the amino acid substitution is beneficial, the duplicated gene can participate in natural selection and acquire a new function or interaction within an existing pathway - such as blood clotting.

" It appears that the physiologically important 'extrinsic' pathway as we know it mammals evolved by two rounds of genome or chromosomal duplication and one tandem duplication prior to a last common ancestor with fish ~400 MYA and after the origin of the vertebrates ~520 MYA. This brief window of evolutionary time indicates that a flurry of duplication events occurred to generate the clotting pathway and supports the theories of punctuated evolution.

"The evolutionary time frame of blood clotting evolution is supported by investigations into other gene families such as Hox genes and the genes of the MHC. Investigations in other systems support the two large-scale duplication of the ancestral vertebrate genome as well. The debatable issue is when both duplications occurred." says Davidson.


However, in the conclusion Davidson is also quoted as saying:

Quote

Fundamental evolutionary event

"Vertebrates are one of the planet's most diverse and successful group of animals colonizing both the water and land. Vertebrates share common developmental physiology, and anatomy and are distinguished from invertebrates by complex systems such as immune, nervous, endocrine and blood clotting systems.

"Since blood transports and mediates many of the above vertebrate innovations it seems certain that the protective function of blood clotting was a fundamental evolutionary event. A more primitive state of blood clotting than that found in jawless vertebrates is likely not present in any living creature and died with the primitive vertebrates in the Cambrian.

"The origin of vertebrate blood clotting, like the origin of life must have been a rare event, yet without protection from bleeding it would not have been possible for the radiation of vertebrates from fish to dinosaurs and ultimately humans."


I think it is a mistake to compare the origin of blood-clotting to the origin of life, or even to imply that it is rare: it is apparent that a similar system has arisen in arthropods at least (see Miller's (1999) discussion of the evolution of decapod blood-clotting), and it seems quite likely various clotting systems will be discovered in other complex metazoans (perhaps descended from a primitive ancestral system, but still with considerable independent evolution in each lineage, as e.g. with eyes).  One can even argue that the pitch of trees is a clotting system. Perhaps Davidson is a wee bit vertebrate-biased.

nic

Date: 2002/05/25 00:35:53, Link
Author: niiicholas
An interesting paragraph from a recent article that continues the debate between Behe and Shanks & Joplin, regarding the (chemical) specificity necessary for ICness vs. "simple interactive" systems or what-have-you.

Niall Shanks and Karl Joplin, "Behe, Biochemistry, and the Invisible Hand," Philo, Volume 4, Number 1.

Link: http://www.philoonline.org/library/shanks_4_1.htm

Regarding blood-clotting & specificity, they write:

Quote

Behe bolsters his attack on the BZ reaction with a truly bizarre argument derived from the fact that the reagents in the BZ reaction have a wide variety of uses—in Behe’s terminology, they have low specificity. For example, one ingredient, sodium bromate, is a general purpose oxidizing agent, and ingredients other than the ones we mentioned can be substituted. In our reaction, we mentioned the use of cerium ions, but iron or manganese ions will work just as well. He points out that the reaction is easy to set up and runs over a wide range of concentrations.21

If this is the case, then mousetraps are not irreducibly complex either. The steel used in their construction has a wide range of uses, as does the wood used for the base. You can substitute plastic for wood, and any number of metals for the spring and hammer. Mousetraps are easy to make (which is why they are cheap) and will work with metals manifesting a wide range of tensile strengths. But the fact that they are easy to make does not mean they assemble just by chance. Mousetraps need a maker just as much as the BZ system needs chemical mechanisms governed by the laws of chemistry. Either the BZ system is an irreducibly complex system, or the complexity of mousetraps is not a model for irreducible complexity. Take your pick, for you cannot have it both ways.

This matter is made all the more acute because crucial components of Behe’s own examples of irreducible complexity have multiple uses and lack substrate specificity (interact with a wide variety of substrates). For example, plasminogen (a component of the irreducibly complex blood-clotting cascade) has been documented to play a role in a wide variety of physiological processes, ranging from tissue remodeling, cell migration, embryonic development, and angiogenesis, as well as wound healing.22 And though Behe tells us that plasmin (the activated form of plasminogen), “. . . acts as scissors specifically to cut up fibrin clots,”23 we learn in one of the very papers he cites that, “Plasmin has a relatively low substrate specificity and is known to degrade several common extracellular-matrix glycoproteins in vitro.”24

[...]

22. See Thomas H. Bugge, Keith W. Kombrinck, Matthew J. Flick, Cynthia C. Daugherty, Mary J. Danton, Jay L. Degan, “Loss of Fibrinogen Rescues Mice for the Pleiotropic Effects of Plasminogen Deficiency,” Cell 87 (1996): 709–19.

23. See Behe, Darwin’s Black Box, 88.

24. See Bugge, et al., “Loss of Fibrinogen Rescues Mice,” 709.



Blood-clotting comes up again here:

Quote

In our original article we pointed to the gene coding for the protein p53. Lab mice have been created in which this gene has been knocked out. In support of our claims about the existence of redundancy in biochemical systems, we pointed out that, though this protein was involved in a number of important biochemical and biological processes, its removal did not result in a catastrophic disruption of the developmental process. There was redundancy, and other proteins could conspire to do the work of the missing protein.

Behe acknowledges this case, but draws his reader’s attention to the blood-clotting cascade originally discussed in his book:

Yet contrast this case [p53] with that of mice in which the gene for either fibrinogen, tissue factor, or prothrombin has been knocked out. . . . The loss of any one of those proteins prevents clot formation—the clotting cascade is broken. Thus Shanks and Joplin’s concept of redundant complexity does not apply to all biochemical systems.41

Again, suppose this point is right. What is its relevance when the role of redundant complexity lies in its ability to account, in natural, evolutionary terms, for the origins of irreducible complexity? And origins, as Behe points out, is the central issue. Loss of functional genes reduces redundancy to yield an irreducibly complex system. All Behe’s example shows is that further losses at this point can catastrophically disrupt the system.

We also think, however, that Behe has oversold the irreducible complexity of the blood-clotting cascade. The cascade itself has features that manifest redundant complexity. The real situation is thus more complex than Behe’s carefully massaged description would lead you to believe. Plasminogen deficient (Plg-/-)—hence plasmin deficient—mice have been studied. As noted earlier, plasmin is needed for clot degradation (it cuts up the fibrin), yet:

Plasmin is probably one member of a team of carefully regulated and specialized matrix-degrading enzymes, including serine-, metallo-, and other classes of proteases, which together serve in matrix remodeling and cellular reorganization of wound fields. . . . However, despite slow progress in wound repair, wounds in Plg-/- mice eventually resolve with an outcome that is generally comparable to that of control mice. Thus an interesting and unresolved question is what protease(s) contributes to fibrin clearance in the absence of Plg?42

Behe cited this very paper, so we must assume that he, too, knows that parts of his clotting-cascade are redundantly complex. In this case, healing delayed is not healing denied!

[...]

41. See Behe, “Self-Organization and Irreducible Complexity,” 161.

42. See Bugge, et al. “Loss of Fibrogen Rescues Mice,” 717.


...Bugge et al. rides again!  (This was a paper which Doolittle misread, or at least oversimplified, in his Boston review article, which gave Behe an opportunity to dodge the real issue, namely how Doolittle has been able to predict the presence of blood-clotting proteins in various species (with simpler systems, no less) unless Doolittle's model for the evolution of blood-clotting has significant validity.)

Brief commentary on Shanks & Joplin: while they have introduced the useful notion of "redundant complexity", and in the above 2001 Philo paper have tied the concept to the "scaffolding" model for the origin of IC (i.e., reduce redundancy and you end up with IC), I don't think that they have a general solution to the origin of IC unless they incorporate cooption/change of function into their analysis.  I can only think of a few examples where "loss of scaffolding" explains the origin of an IC system, but many where cooption of a part/system to a new function explains it.  Perhaps more importantly, the processes are not mutually exclusive and so in some cases both processes might operate in succession.

nic

Date: 2002/05/25 01:56:40, Link
Author: Wesley R. Elsberry
Jonathan Wells: Darwinism analogous to former Soviet regime

Quote
These critics include embryologists, paleontologists, biochemists, molecular biologists, medical doctors, philosophers, and even lawyers. Unfortunately, the North American science-and-religion establishment has largely turned a deaf ear to these critics, preferring instead to abandon classical theology and embrace metaphysical materialism and moral relativism. But I see the situation as analogous to the last years of Soviet communism. A small, powerful elite controls all the official information outlets while the evidence against the official position swells quietly, like a wave building offshore. Someday soon, to the surprise of many people in academia and the media, the wave will break. I predict that the Darwinist establishment will come apart at the seams, just as the Soviet Empire did in 1990.


-- "Darwinism: Why I Went for a Second Ph.D." by Jonathan Wells

Date: 2002/05/25 02:03:31, Link
Author: Wesley R. Elsberry
Phillip Johnson: Compares Gould to Gorbachev

It seems timely to revisit this offering by "wedge" strategist, DI CRSC advisor, and author of the rejected Santorum amendment, Phillip E. Johnson.

Quote
Gould’s uncomfortable situation reminds me of the self-created predicament of Mikhail Gorbachev in the last years of the Soviet Empire. Gorbachev recognized that something had gone wrong with the Communist system, but thought that the system itself could be preserved if it was reformed. His democratic friends warned him that the Marxist fundamentalists would inevitably turn against him, but he was unwilling to endanger his position in the ruling elite by following his own logic to its necessary conclusion. Gould, like Gorbachev, deserves immense credit for bringing glasnost to a closed society of dogmatists. And, like Gorbachev, he lives on as a sad reminder of what happens to those who lack the nerve to make a clean break with a dying theory.


-- Phillip E. Johnson's "The Gorbachev of Darwinism" (1998)

Date: 2002/05/25 02:22:21, Link
Author: Wesley R. Elsberry
William Dembski: Compares Darwinism to former Soviet regime

Quote
Dembski, whose recent book, "The Design Inference," presents in great detail how the Intelligent Design argument satisfies logic and probability, likes to compare the movement's influence on science to the freedom and democracy movements and their effect on Eastern Europe. Criticism of Darwinism now threatens the hegemony of Darwinism, he says, just as the move toward freedom upset the Soviet empire.


Stephen Goode's "Scientists Find Evidence of God" (1999/04/19)

Date: 2002/05/25 02:32:00, Link
Author: Wesley R. Elsberry
Phillip Johnson: Compares Methodological Naturalism to former Soviet regime

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Behind this student movement is a more general intellectual movement that will bear fruit in the coming century. It is a bit thin on the ground for now, but so was the Christian faith in the first century. Materialism as a philosophy is superficially powerful but moribund, as we saw when the Soviet Union collapsed without a struggle a decade ago. Methodological naturalism is a branch on the materialist tree that will lose its power to intimidate when the tree is known to be hanging in midair.


-- Phillip Johnson, Foreword to "Unapologetic Apologetics" (2001)

Date: 2002/05/25 03:58:59, Link
Author: Wesley R. Elsberry
Phillip Johnson: Compares Darwinism to the Soviet Union

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Darwinian evolution with its blind watchmaker thesis makes me think of a great battleship on the ocean of reality.  Its sides are heavily armored with philosophical barriers to criticism, and its decks are stacked with big rhetorical guns ready to intimidate any would-be attackers.  In appearance, it is as impregnable as the Soviet Union seemed to be only a few years ago.


-- Phillip E. Johnson, "Darwin On Trial" (2nd ed.), p.169.

Date: 2002/05/25 04:51:48, Link
Author: Jesse
John Calvert: compares KCFS to Nazis

from a series of letters in the Pratt Tribune (Calvert's letter can also be found here):

Quote
One thing that Jack Krebs and I agree with is that Pratt can be likened to an outpost under siege in a cultural war.

...

My wife and I just returned from a trip to Belgium. We visited Bastogne where a few brave Americans of the 101st Airborne Division were surrounded by the German Army during the battle of the bulge. The German attack was led by a crack SS unit that took no prisoners.

What were we fighting against in Bastogne? We were fighting against a Nazi regime that used the philosophy of Naturalism to justify a eugenics program of terrifying proportions. Naturalism is the belief that all phenomena result only from the laws of chemistry and physics and that teleological or design explanations are not valid. Naturalism is not science. It is a belief system.

In the same manner, the defenders in Pratt are fighting against Naturalism, although they may not realize it. Rather than fighting against science, they are actually fighting for science. They are fighting for science that is driven by logic and critical thinking rather than by a philosophy that teaches to the exclusion of all other teachings that we are the products of only chance and necessity. They are fighting for science that is driven by the scientific method rather than science that is driven by a philosophy of Naturalism.

...

Rather than using logic and good science to support its assault on the brave contingent in Pratt, the KCFS is using tactics one would expect from those that besieged Bastogne: scare tactics, misinformation and no substantive discussion of the real issues.

...

So, we are back looking at Pratt as the bombs fall. The question is whether the Board and the Community will be supported by the rest of us as they have had the guts that General McAullife and the other brave Americans had that cold winter day in Bastogne 54 years ago. McAullife's reply was very simple when asked to surrender: "Nuts!" McAullife and the 101st were subsequently relieved by elements of Patton's Third Army. In the same way we all need to rise up and put our hands together for the Pratt Board and Pratt Citizens that have just characterized the outrageous censorship by the science establishment as "Nuts!"


Jack Krebs' reply to this letter, along with a longer response to the charges made by Calvert, can be found here:

http://www.sunflower.com/~jkrebs....art%201



Date: 2002/05/25 10:32:18, Link
Author: Wesley R. Elsberry
William Dembski: Compares opponents at Baylor University to Napoleon

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Dembski, as the director of the center, also commented on the report in a one-paragraph e-mail message following its release. "The report marks the triumph of intelligent design as a legitimate form of academic inquiry. This is a great day for academic freedom," Dembski began. He concluded by observing that "Dogmatic opponents of design who demanded the Center be shut down have met their Waterloo. Baylor University is to be commended for remaining strong in the face of intolerant assaults on freedom of thought and expression."


-- Christianity Today: "Baylor's dismissal of Polyani Center director Dembski was not a smart move." (2000/10/23)

Date: 2002/05/25 10:45:31, Link
Author: Wesley R. Elsberry
William Dembski: Approves of comparing opponents at Baylor University to McCarthyites

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Baylor University President Robert Sloan has removed me as director of the Michael Polanyi Center despite his having personally solicited me to come to Baylor and establish the Center as a means of furthering work on intelligent design. Some Baylor faculty have exerted enormous pressure on Baylor to disassociate the university from me and my research. Earlier President Sloan had properly characterized these efforts as "intellectual McCarthyism."


-- William Dembski: Press release (2000/10/19)

Date: 2002/05/25 12:35:26, Link
Author: ExYECer
Quote (theyeti @ May 23 2002,16:32)
Awhile back I had a discussion about the DI's wacko response to the PBS evolution series here.  Scroll down a few messages.  There are some links to some good recent papers in that thread.  The references are:

Trends in Biochemical Sciences 2001, 26:591-596

Proc Natl Acad Sci U S A 1995 Mar 92:2441-5

J. Biol. Chem., Vol. 276, Issue 10, 6881-6884, March 9, 2001



Annu. Rev. Biochem. 2000. 69:617-650.

theyeti

Let me add some links to the references

Proc. Natl. Acad. Sci. USA, Vol. 97, Issue 15, 8392-8396, July 18, 2000 Interpreting the universal phylogenetic tree, Carl R. Woese

This article was referenced by others, a few quotes

Quote

Archaeal Phylogeny Based on Ribosomal Proteins
Oriane Matte-Tailliez , Céline Brochier , Patrick Forterre and Hervé Philippe


Until recently, phylogenetic analyses of Archaea have mainly been based on ribosomal RNA (rRNA) sequence comparisons, leading to the distinction of the two major archaeal phyla: the Euryarchaeota and the Crenarchaeota. Here, thanks to the recent sequencing of several archaeal genomes, we have constructed a phylogeny based on the fusion of the sequences of the 53 ribosomal proteins present in most of the archaeal species. This phylogeny was remarkably congruent with the rRNA phylogeny, suggesting that both reflected the actual phylogeny of the domain Archaea even if some nodes remained unresolved. In both cases, the branches leading to hyperthermophilic species were short, suggesting that the evolutionary rate of their genes has been slowed down by structural constraints related to environmental adaptation. In addition, to estimate the impact of lateral gene transfer (LGT) on our tree reconstruction, we used a new method that revealed that 8 genes out of the 53 ribosomal proteins used in our study were likely affected by LGT. This strongly suggested that a core of 45 nontransferred ribosomal protein genes existed in Archaea that can be tentatively used to infer the phylogeny of this domain. Interestingly, the tree obtained using only the eight ribosomal proteins likely affected by LGT was not very different from the consensus tree, indicating that LGT mainly brought random phylogenetic noise. The major difference involves organisms living in similar environments, suggesting that LGTs are mainly directed by the physical proximity of the organisms rather than by their phylogenetic proximity



Proc. Natl. Acad. Sci. USA, Vol. 98, Issue 3, 805-808, January 30, 2001 The universal nature of biochemistry  Norman R. Pace


Next reference

Lluís Ribas de Pouplana, Paul Schimmel, Aminoacyl-tRNA synthetases: potential markers of genetic code development, Trends in Biochemical Sciences 26 (10) (2001) pp. 591-596.


Operational RNA code for amino acids in relation to genetic code in evolution.  Ribas de Pouplana, L ... Schimmel P
J Biol Chem 2001 Mar 9;276(10):6881-4.

Some links to research


AMINOACYL-TRNA SYNTHESIS  Annu. Rev. Biochem. 2000 , Vol. 69: 617-650.

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Aminoacyl-tRNAs are substrates for translation and are pivotal in determining how the genetic code is interpreted as amino acids. The function of aminoacyl-tRNA synthesis is to precisely match amino acids with tRNAs containing the corresponding anticodon. This is primarily achieved by the direct attachment of an amino acid to the corresponding tRNA by an aminoacyl-tRNA synthetase, although intrinsic proofreading and extrinsic editing are also essential in several cases. Recent studies of aminoacyl-tRNA synthesis, mainly prompted by the advent of whole genome sequencing and the availability of a vast body of structural data, have led to an expanded and more detailed picture of how aminoacyl-tRNAs are synthesized. This article reviews current knowledge of the biochemical, structural, and evolutionary facets of aminoacyl-tRNA synthesis.

Date: 2002/05/25 15:52:03, Link
Author: Dr.GH
Saddly, the ARN crash denied the opportunity to quote Dembski calling his critics "leftists."  It was in the thread called something like "Removing hypotheticals" or some such.

Date: 2002/05/25 17:54:10, Link
Author: Wesley R. Elsberry
William Dembski: Forrest and the "leftist" remark

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Barbara Forrest's letter is the worst sort of leftist guilt-by-association diatribe.


-- William Dembski, post to ARN discussion forum, 2002/04/17 03:38 PM

Date: 2002/05/26 00:55:42, Link
Author: niiicholas
Ooh, another great opportunity for collaboration.  This is a huge topic with a lot of literature, so unless one happens to be a biochemist who did their PhD. on the topic it is hard for one person to scrape together the diverse information & references that are necessary to explain the problems with Paul Nelson's pseudoargument to the public.  I think Ken Miller's replies had some difficulty in this regard (and I don't even recall the statement "universal genetic code" being in the actual Evolution series -- is this just me missing it or is it actually there?)

The most complete presentation of Nelson v. common descent that I can recall was a longish talk that I recall listening to online -- but I can't find it at the moment.  Is there a good online essay where Paul Nelson actually lays out the argument from "the genetic code isn't quite universal" to the conclusion "common descent is false [to some unspecified degree]"?

Anyhow, Nelson's argument went like this:

- the code was thought to be universal, and this was crowning evidence for common descent because the code couldn't change because intermediate stages are fatal so it must have come from a common ancestor

[actually, it was just one of many pieces of evidence, but whatever]


- but it's not quite universal, therefore either:

(a) the code can change after all
(b) common descent is false

- Nelson doesn't like (a), citing a (single) paper that criticizes another (single) scientist's proposal about how a codon assignment could change.

- therefore evolutionists are dogmatically clinging to an auxilliary hypothesis that is shielding their main theory from rigorous testing.

I'm sure I'm oversimplifying, I heard the talk last year, but that's basically it.


However, I recall doing some digging on these arguments for an ARN post or two, I will see if I can find them...

Hmm, as usual the ARN UBB search engine is proving useless.  Well, here's some general points regarding "deviant/noncanonical genetic codes":

(1) Deviant genetic codes are most common in critters/organelles with small or otherwise weird genomes, e.g. ciliates (which Nelson specifically mentions IIRC):

Quote

Pubmed link

The molecular basis of nuclear genetic code change in ciliates

Quote: "Most changes in the genetic code involve termination: this may be because stop codons are rare, occurring only once per gene, and so changes in termination are likely to be less deleterious than change in sense codons. This would be particularly true for those species of ciliates whose genes reside on gene-sized chromosomes and/or have short 3' untranslated regions. In addition, termination is a competition for stop-codon-containing ribosomal A sites between release factors and tRNAs. Consequently, relatively small changes either in the tRNAs or in eRF1 may shift this balance toward partial or complete readthrough in some cases. For instance, Bacillus subtilis uses in-frame UGA codons extensively to encode tryptophan; however, this readthrough is inefficient, and UGA is also used as a stop codon [33, 34] . The abundance of stop codon reassignments relative to amino acid codon reassignment, however, could also be an observer bias. In-frame stop codons are much easier to detect in protein coding sequences than amino acid replacements, especially if the latter have similar properties."



(2) Some organisms, extant today, have ambiguous codon assignments (i.e. one codon codes for both an amino acid and 'stop' at the same time, proving that this is not necessarily a fatal situation, contra Paul Nelson.

[I've seen this stated in an article somewheres, if anyone else finds examples they might post them.  They pretty clearly refute the "transitional stages impossible" contention.]


(3) Deciding whether or not the code is optimal, how optimal, and how much a potential "frozen accident" is by no means a simple question as Nelson seems to assume.

The below paper argues for optimality in at least one sense, but note the back-and-forth, and how what constitutes "optimal" may be different for different organisms at different times (& which may thus result in the evolution of code deviants).

Quote

Pubmed link -- free online BTW

Mol Biol Evol 2000 Apr;17(4):511-8

Early fixation of an optimal genetic code.

Freeland SJ, Knight RD, Landweber LF, Hurst LD.

Department of Ecology, Princeton University, University of Bath, Bath, England.

The evolutionary forces that produced the canonical genetic code before the last universal ancestor remain obscure. One hypothesis is that the arrangement of amino acid/codon assignments results from selection to minimize the effects of errors (e.g., mistranslation and mutation) on resulting proteins. If amino acid similarity is measured as polarity, the canonical code does indeed outperform most theoretical alternatives. However, this finding does not hold for other amino acid properties, ignores plausible restrictions on possible code structure, and does not address the naturally occurring nonstandard genetic codes. Finally, other analyses have shown that significantly better code structures are possible. Here, we show that if theoretically possible code structures are limited to reflect plausible biological constraints, and amino acid similarity is quantified using empirical data of substitution frequencies, the canonical code is at or very close to a global optimum for error minimization across plausible parameter space. This result is robust to variation in the methods and assumptions of the analysis. Although significantly better codes do exist under some assumptions, they are extremely rare and thus consistent with reports of an adaptive code: previous analyses which suggest otherwise derive from a misleading metric. However, all extant, naturally occurring, secondarily derived, nonstandard genetic codes do appear less adaptive. The arrangement of amino acid assignments to the codons of the standard genetic code appears to be a direct product of natural selection for a system that minimizes the phenotypic impact of genetic error. Potential criticisms of previous analyses appear to be without substance. That known variants of the standard genetic code appear less adaptive suggests that different evolutionary factors predominated before and after fixation of the canonical code. While the evidence for an adaptive code is clear, the process by which the code achieved this optimization requires further attention.


...and also note the rather unambiguous first sentence of the introduction of this article:

Quote

All known nonstandard genetic codes appear to be secondarily derived minor modifications of the canonical code (Osawa 1995).


Here is their conclusion FYI:

Quote

The Mechanism of Adaptive Code Evolution

This leads to the question of the evolutionary mechanisms responsible for an adaptive canonical code. The many models of precanonical code evolution, reviewed extensively elsewhere (Knight, Freeland, and Landweber 1999 ), permit two major possibilities: that an adaptive code was selected from a large pool of variants, or that an adaptive code arose de novo by code expansion (or simplification) within adaptive, error-minimizing constraints. Individual codon reassignments, necessary for adaptive code shuffling, are certainly possible, but the question remains unresolved, and two lines of evidence increasingly favor the latter explanation.

First, the notion of code expansion from a simpler primordial form, although still lacking in detail, is now associated with a diverse body of empirical and phylogenetic evidence (Knight, Freeland, and Landweber 1999 ). It seems unlikely that clear patterns of biosynthetic relatedness would be found in a code which had undergone extensive codon assignment shuffling. Additionally, while adaptive code structure is unlikely to be an artifact of a stereochemically determined code, empirical evidence suggests that stereochemistry is not without a role. For example, RNA molecules artificially selected to bind Arginine contain disproportionately many CGN/AGR codons (Knight and Landweber 1998 ). If all or most amino acids show stereochemical affinities for their corresponding codons, this would suggest that natural selection worked in concert with stereochemical interactions and biosynthetic expansion to produce the canonical code de novo, "choosing" the current 20 amino acids as those that satisfied criteria for both stereochemical affinity and error minimization. This interpretation would thus offer a novel insight into the selection of the proteinaceous amino acids from the near-infinite possibilities of both prebiotic syntheses and biosynthetic modification.

Conclusions

We have presented comprehensive evidence that the standard genetic code is a product of natural selection to minimize the phenotypic impact of genetic error; the arrangement of codon assignments meets, to an extraordinary degree, the predictions of the adaptive hypothesis and cannot be explained as an artifact of stereochemistry, biosynthetically mediated code expansion, or analytical methodology. However, the process by which an adaptive code evolved at present remains unclear, and yet its resolution may be of key importance to our understanding of the amino acid components universal to life.


This is the Osawa reference which looks to be key:

Osawa, S. 1995. The evolution of the genetic code. Oxford University Press, Oxford, England.


Anyhow, as usual when one begins to investigate the actual biology of an ID argument, one finds that the IDists are taking a thoroughly myopic view instead of looking at the broad range of evidence that is necessary.

Thanks, nic

Date: 2002/05/27 08:50:39, Link
Author: Wesley R. Elsberry
This thread is for documenting the various young-earth arguments and responses to those arguments.

I'll start off with one that is based upon ecology.

The Population Argument

The following quotes are selected from an online essay of mine.

Quote
Certain proponents of "scientific creationism" (SciCre) have put forward an argument that humans could not have evolved, simply because human population size shows that humans have only been around a few thousand years.  Those putting forward the argument tie the original population size to either two (sometimes Adam and Eve, sometimes Noah and his wife) or eight (Noah's immediate family), note a current population figure, and derive a rate of increase by use of some Biblical chronology to either creation, Noah's birth, or The Flood.  It should be noted that biblically, what should be argued is either descent from two (Adam and Eve) or from six (Noah's sons and their wives).  While some admit up front that the calculation of rate of increase yields an average value and that the actual rate of increase varies, many do not. The crux of the argument comes when they use the derived rate of increase for comparison to the deep time that evolutionary timetables give.  The numbers of humans that would be present, they say, were evolution true, would be far greater than what we observe today, and thus evolution of humans must be false. Some are precise enough to restrict their conclusion to only humans, others leave how much is disproved unspecified.  Some utilize the numbers to infer intermediate population sizes.
 
I am going to point out some problems with the SciCre population argument.  First, the argument assumes what it is supposed to prove. Second, all such arguments yield absurd values for population sizes at historical times.  Third, the argument ignores what is known about population dynamics from other species.  Fourth, final population size is an unreliable indicator of initial population time.  I am only interested in the anti-evolutionary components of the SciCre population argument; use of the population argument in apologetics is not something I care about.  I don't think that anyone can demonstrate that real population dynamics disbar Global Flood scenarios, so if use in apologetics is all that is intended from some source, I have no real beef with it.


Quote
Third, the argument ignores what is known about population dynamics from other species.  Various other species can be observed to sometimes reproduce exponentially, but we observe that such populations fluctuate, stabilize, or crash.  In no case do exponentially reproducing populations "take over the world" as SciCre'ists assure us would be the case if evolution were true.  In recent times, human population growth has been exponential, but this does not mean that the human population has been growing exponentially for all its residence time.  Just as the number of E. coli present in your gut will not tell us your birthday or the time of your last use of an antibiotic, so human population size is decoupled from when Homo sapiens arose, or even when a bottleneck may have occurred.


Quote
In short, the SciCre population argument fails on many different criteria.  Honest creationists should eschew its use.


-- Population Size and Time of Creation or Flood

Interestingly, the population argument is not listed among those that "Answers in Genesis" recommends that YECs should not use.

Date: 2002/05/28 09:54:22, Link
Author: theyeti
Niiicolas:
Quote

The most complete presentation of Nelson v. common descent that I can recall was a longish talk that I recall listening to online -- but I can't find it at the moment.  Is there a good online essay where Paul Nelson actually lays out the argument from "the genetic code isn't quite universal" to the conclusion "common descent is false [to some unspecified degree]"?


Here are a few links from various places.

PBS Charged with "False Claim" on "Universal Genetic Code"  From ARN.  The title says it all...

A "Dying Theory" Fails Again  Miller's response.

Reply To Kenneth Miller On The Genetic Code.  The DI's wacky response to Miller.

DI Fails Again to "Crack" the Code.  Miller's second response.

That's it for the DI vs. Miller spat AFAIK.  A couple of others:

Is Common Descent an Axiom of Biology?  This one's by Nelson.  Scroll down a bit and you'll see his genetic code arguments.

Should We Stop Criticizing the Doctrine of Universal Common Ancestry?  By our dear friend Jonathan Wells.  He uses the genetic code argument, along with a number of other really bad ones.  I don't think that Wells does much more than assert his position, but this is a good article to keep handy next time someone says that Wells accepts common ancestry, though he's ambiguous as usual.

Date: 2002/05/28 15:10:09, Link
Author: niiicholas
I came across a new article on the evolution of photosynthesis; there are a number of articles on this topic, I will post them as I rediscover them, others may have come across interesting stuff also.

Quote

Reaction centres: the structure and evolution of biological solar power
Peter Heathcote b, Paul K. Fyfe a and Michael R. Jones a
Trends in Biochemical Sciences 2002, 27:79-87

Abstract  



Reaction centres are complexes of pigment and protein that convert the electromagnetic energy of sunlight into chemical potential energy. They are found in plants, algae and a variety of bacterial species, and vary greatly in their composition and complexity. New structural information has highlighted features that are common to the different types of reaction centre and has provided insights into some of the key differences between reaction centres from different sources. New ideas have also emerged on how contemporary reaction centres might have evolved and on the possible origin of the first chlorophyll–protein complexes to harness the power of sunlight.

[...I'll quote the last part of the review to give a sense of where things are at...]

Common structural blueprint

The crystallographic information summarized in Fig. 4 highlights structural features that are common to all types of reaction centre [3,10,25] . At the heart of each complex is a core domain consisting of an arrangement of two sets of five transmembrane  helices. This protein scaffold encases six (bacterio)chlorin and two quinone cofactors that are arranged in two pseudosymmetric membrane-spanning branches. These cofactors catalyse the photochemical transmembrane electron transfer reaction that is the key to the photosynthetic process. Added to this basic structural blueprint are a variety of protein–cofactor structures, such as antenna complexes, the oxygen-evolving complex or Fe–S centres, which represent further adaptations. In particular, in the PSII reaction centre and all known Type I reaction centres, the core electron transfer domain is flanked by two homologous antenna domains, each consisting of a bundle of six membrane-spanning  helices binding antenna pigments [24], and antenna chlorophylls are also bound to the ten-helix core ( Fig. 4). These antenna domains are not present in purple bacteria such as Rhodobacter sphaeroides or green filamentous bacteria such as Chloroflexus.

Which is the oldest reaction centre?

The realization that all reaction centres are based on a common design has provoked much discussion over the evolutionary links between the different complexes and the nature of the ancestral reaction centre. This is a challenging topic because it is clear that chlorophyll-based photosynthesis is a very old process that appeared during the first few hundred million years of evolution [38]. One approach to this problem has been to examine which of the five distinct groups of photosynthetic bacteria represents the oldest photosynthetic lineage, through phylogenetic studies of both photosynthetic and non-photosynthetic proteins. However, such studies have produced conflicting results, with green filamentous bacteria, heliobacteria and purple bacteria all being identified as the oldest lineage in different studies [39–42] . The problem of tracing the evolutionary development of modern day photosystems is not helped by some of the variety and complexity exhibited by photosynthetic organisms, which indicates some interchange of photosynthetic components by lateral gene transfer between groups during the course of evolution [41,43] . At present, it is probably prudent to conclude that the use of this approach requires additional data and a more extensive analysis.

Primordial reaction centre: Type I, Type II or both?

Setting aside the question of which is the oldest photosynthetic organism, several models have been proposed to account for the development of modern day reaction centres from simpler ancestors [41]. Most recently, a new evolutionary scheme for contemporary reaction centres has been proposed that envisages the ancestral reaction centre as homodimeric, with the three-domain antenna–core–antenna organization seen in extant Type I complexes [37]. It is proposed that this ancestral reaction centre had two membrane-spanning electron transfer chains, each terminating in a loosely bound quinone that could dissociate when reduced and move into the membrane pool, and that it occupied a membrane that had already developed a fully functional anaerobic respiratory chain, in accordance with the 'respiration early' hypothesis [44]. Therefore, the ancestral reaction centre proposed had a mixed character, with the three-domain organization and (possibly) symmetric electron transfer characteristic of contemporary Type I reaction centres but a capacity to reduce the intramembrane quinone pool, as seen in contemporary Type II reaction centres [37].


The future ... and the dim, distant past

The increasingly detailed crystallographic information now available for the cyanobacterial Type I and Type II reaction centres is provoking renewed interest in the detailed mechanism of these elegant transducers of energy. In particular, the first crystallographic glimpses of the machinery for oxygen evolution are both intriguing and exciting, and will trigger much re-evaluation of our current understanding of a reaction that is of obvious importance to aerobes such as ourselves. It is also becoming apparent that a detailed understanding of quinone chemistry of the homodimeric reaction centres from heliobacteria and green sulfur bacteria might help to focus ideas about the nature of the ancestral reaction centre and the evolutionary route that has led to contemporary complexes.

Finally, peering even further back in evolutionary time, an intriguing question that remains relatively unexplored concerns the origins of the ancestral reaction centre. What was the function of this (bacterio)chlorophyll-containing membrane protein before it evolved into a system capable of harnessing light energy? One suggestion is that early organisms used pigment–protein complexes to protect themselves against the ultraviolet (UV) radiation that bathed the surface of the planet before the development of the atmospheric ozone layer [45]. Such proteins might originally have operated by absorbing high-energy UV photons and dissipating the energy through internal conversion between the (bacterio)chlorophyll Soret absorbance transition and the visible-region absorbance bands, before emitting the energy as a much more benign visible or near-infrared photon [45]. Light-activated electron transfer might originally have developed as an extension to this photoprotective function, excited state energy being converted first into the energy of a charge separated state (similar to the P870+HA- state formed in the purple bacterial reaction centre) and subsequently lost as heat as the charge-separated state recombines (as occurs in purple bacterial reaction centres when forward electron transfer from HA- is blocked). Another suggestion is that photosynthetic function evolved from bacteriochlorophyll-containing proteins involved in infrared thermotaxis [46]. Whatever the truth, addressing these questions requires a journey back to an early stage in the evolution of life, and presents a fascinating challenge.


[37] Baymann F. et al. (2001) Daddy, where did PS(I) come from?
Biochim. Biophys. Acta, 1507:291-310. MEDLINE Cited by

[38] Nisbet E.G. and Sleep N.H. (2001) The habitat and nature of early life.
Nature, 409:1083-1091. Cited by

[39] Olsen G.J. et al. (1994) The winds of (evolutionary) change: breathing new life into microbiology.
J. Bacteriol., 176:1-6. MEDLINE Cited by

[40] Gupta R.S. et al. (1999) Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis.
Mol. Microbiol., 32:893-906. MEDLINE Cited by

[41] Xiong J. et al. (1998) Tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from Heliobacillus mobilis.
Proc. Natl. Acad. Sci. U. S. A., 95:14851-14856. Full text MEDLINE Cited by

[42] Xiong J. et al. (2000) Molecular evidence for the early evolution of photosynthesis.
Science, 289:1724-1730. Full text MEDLINE Cited by

[43] Blankenship R.E. (2001) Molecular evidence for the evolution of photosynthesis.
Trends Plant Sci., 6:4-6. Full text Cited by

[44] Castresana J. et al. (1994) Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen.
EMBO J., 13:2516-2525. MEDLINE Cited by

[45] Mulkidjanian A.Y. and Junge W. (1997) On the origin of photosynthesis as inferred from sequence analysis.
Photosynth. Res., 51:27-42.

[46] Nisbet E.G. et al. (1995) Origins of photosynthesis.
Nature, 373:479-480.

Date: 2002/05/28 19:50:34, Link
Author: rafe gutman
am i to understand that dembski thinks that all proteins interact with the same binding affinity?  that's a pretty ridiculously wrong assumption.

also, does dembski think that all proteins are expressed at equal concentrations in the bacterium at any given time?  that is also fabulously wrong.

i also noticed that dembski does not factor in the volume of the cell in his calculation.  his formula would give the same value for the flagellar components expressed in the bacterium at physiological concentrations as it would for 4900 individual proteins floating around a pool.

i noticed a distinct similarity between dembski's formula and a common situation used in probability questions in introductory statistics.  a box is filled with pieces of paper with numbers written on them.  the student is asked to calculate the probability of a certain outcome when one or more pieces of paper are removed from the box, with replacement.  by "replacement", i mean that each time a piece is drawn, it is put back into the box before the next piece is drawn.  does dembski really believe that a cell behaves in this manner?  that the bacterium will "draw" 250 proteins from a pool at random (with replacement), test the entire combination for flagellar formation, then if it fails put them all back and start over again?

how can anyone take this seriously?

Date: 2002/05/29 13:18:37, Link
Author: Thomas Foley
William Dembski: In academia, "creationist" = "holocaust denier"

Quote
[I]t seems to me that [Robert] Pennock and MIT Press have deliberately tried to undermine my standing in the academic community. Pennock chose popular and outdated work of mine, positioned various critiques of my work with it, gave me no opportunity to reply to my critics, and packaged it all in a volume titled "Intelligent Design Creationists and Their Critics," thus casting me as a creationist, which in contemporary academic culture is equivalent to being cast as a flat earther, astrologer, or holocaust denier.


How Not to Debate Intelligent Design - (2001/01/08)

Date: 2002/05/29 14:03:24, Link
Author: Wesley R. Elsberry
Michael Shermer, a critic of "intelligent design", has made such a comparison before.

Quote
In Why People Believe Weird Things I compared these evolution deniers to Holocaust deniers, pointing out how they use the same style of argumentation and commit the same fallacies of logic in their parallel attempts to distort the historical record for political, ideological, or religious purposes.


-- Michael Shermer's "ID Works In Mysterious Ways"

I don't want anyone to get the idea that invidious comparisons are exclusively employed by ID advocates.  I do want to document that ID advocates do deploy invidious comparisons, and show something of the poor level of justification usually given for the deployment of such comparisions by the ID advocates.

Date: 2002/05/29 17:18:59, Link
Author: Dr.GH
These are some of the articles I have in my abiogensis bibliography.  I have mentioned to
Ian the notion of a collaboration.  While I am waiting for his reply, I am working on an
annotated bibliography.  Articles marke with an * are referenced in Wells’ Icons ...

*Castresana, Jose, Matti Saraste
1995 “Evolution of energetic metabolism: the respiration-early hypothesis” Trends in
Biochemical Science 20:443-448

Dismukes, G. C., V. V. Klimov, S. V. Baranov, Yu. N. Kozlov, J. DasGupta, A.
Tyryshkin.
2001 “The Origin of Atmospheric Oxygen on Earth: The Innovation of Oxygenic
Photosynthesis”  PNAS-USA vl 98 no. 5: 2170-2175

Kasting, J.F.
1993 “Algae and oxygen in Earth's ancient atmosphere” (Tech. Comment) and B.
Runnegar “Responce to Kasting.” Science 259: 835.

Kolber, Z. S., C. L. Van Dover, R. A. Niederman, P. G. Kalkowski
2000 Bacterial photosynthesis in surface waters of the open ocean” letters Nature
v.407:177-179

Olendzenski, Lorraine, Olga Zhaxybayeva, J. Peter Gogarten
2000 “How Much Did Horizontal Gene Transfer Contribute to Early Evolution?:
Quantifying Archaeal Genes in Two Bacterial Lineages ” (Abstract) General Meeting of
the NASA Astrobiology Institute.

*Schwartz, Robert M., Margret O. Dayhoff
1978  “Origins of Prokaryotes, Eukaryotes, Mitochondria, and Chloroplasts” Science Vol
199 395-403

Date: 2002/05/29 23:30:40, Link
Author: niiicholas
Hi,

This would seem to be as good a place as any to collect links/references to things like Johnson's

- works
- reviews of his works
- interviews
- online talks

...etc.  I think there is already at least one fairly comprehensive PJ links page on the web so maybe we could just 'high-grade' particularly interesting things here.

E.g., I started this thread because I just heard about this link:

Berkeley’s Radical
An Interview with Phillip E. Johnson


Johnson bares his soul & gives quite a detailed history of his own 'evolution'.

Quote

You have said there is no natural explanation for the rise of genetic information. How important is that question in the debate?

PJ: The Wedge of Truth is all about those issues. The scientific key is, "No natural processes create genetic information." As soon as we get that out, there’s only one way the debate can go because Darwinists aren’t going to come up with a mechanism. They’ll start out talking about the peppered moth, and when that self-destructs, then they’ll say, "Oh, self-organizing systems, or the fourth law of thermodynamics," and other nonsense, which is just covering up ignorance.

Genetic information is the issue, but it isn’t the final issue. After you make that breakthrough, then you see other ways in which the theory is questionable. Darwinists will say, "Oh, well, maybe the mechanism has some problems, but the "fact of evolution"—common ancestry—is not in question. We distinguish the fact of evolution from the mechanism of evolution."

But that’s a bogus distinction because the "fact"—common ancestry—incorporates the mechanism. It’s just a matter of "now you see it, now you don’t." They are saying the mechanism by which a father and mother give birth to children is the same mechanism by which our "bacterial ancestors" gave birth to human beings. They say it’s all a process of natural reproduction and naturally occurring variation in the offspring.

Biologists affiliated with the Intelligent Design movement nail down the distinction by showing that DNA mutations do not create evolution in any significant sense. Instead, they make birth defects, so the whole thing is false from the get-go. There is no way you can establish that a bacterium is the parent of a complex animal. There is no mechanism to make the change, no historical or fossil evidence that such a change ever occurred, and there’s no way to duplicate the process in a lab.

Once you get that in the debate, then we will be poised for a metaphysical and intellectual reversal that is every bit as profound as the one with Copernicus. People will say, "My gosh, we’ve been completely misled by this fundamental truth of the creation story of our culture. We can no longer understand the world that way."

How do you change the way people regard the authority of science? Get them to think of it as a much more limited thing. Science is very reliable when scientists stick to the kinds of things that can be tested by refutable experiments, but much of what they tell us is outside that. When they have to fake the mechanisms, it becomes a very dubious philosophy. That raises the question of why so many very brilliant people were misled for so long and did such a good job of rationalizing these things.

When the mechanism of Darwinism becomes discredited, it’s like a train that’s been turned around. You can say, "Well, that’s interesting, but the train is still in the same place. The world, Yale, Berkeley, are still there. The New York Times is still telling us what to think. So why isn’t everything different?" Well, it is different, but you can’t see it yet. The train is turned in the opposite direction. It’s going to start out very slowly, but it’s moving on the logical tracks towards something very different, and when we get there, our great-great-grand-children will see how different things are.


Not a man with small goals, PJ.

Note also the "scientific key" to the whole ID argument (according to Johnson): "No natural processes create genetic information."  Hmm.  I think I'll start a thread.

nic

Date: 2002/05/30 00:02:55, Link
Author: niiicholas
Hi,

While reading this interview with Phil Johnson, leader of the ID movement:

Berkeley’s Radical
An Interview with Phillip E. Johnson


...I was struck by this section:

Quote

You have said there is no natural explanation for the rise of genetic information. How important is that question in the debate?

PJ: The Wedge of Truth is all about those issues. The scientific key is, "No natural processes create genetic information." As soon as we get that out, there’s only one way the debate can go because Darwinists aren’t going to come up with a mechanism. They’ll start out talking about the peppered moth, and when that self-destructs, then they’ll say, "Oh, self-organizing systems, or the fourth law of thermodynamics," and other nonsense, which is just covering up ignorance.

Genetic information is the issue, but it isn’t the final issue. After you make that breakthrough, then you see other ways in which the theory is questionable. Darwinists will say, "Oh, well, maybe the mechanism has some problems, but the "fact of evolution"—common ancestry—is not in question. We distinguish the fact of evolution from the mechanism of evolution."

But that’s a bogus distinction because the "fact"—common ancestry—incorporates the mechanism. It’s just a matter of "now you see it, now you don’t." They are saying the mechanism by which a father and mother give birth to children is the same mechanism by which our "bacterial ancestors" gave birth to human beings. They say it’s all a process of natural reproduction and naturally occurring variation in the offspring.

Biologists affiliated with the Intelligent Design movement nail down the distinction by showing that DNA mutations do not create evolution in any significant sense. Instead, they make birth defects, so the whole thing is false from the get-go. There is no way you can establish that a bacterium is the parent of a complex animal. There is no mechanism to make the change, no historical or fossil evidence that such a change ever occurred, and there’s no way to duplicate the process in a lab.

Once you get that in the debate, then we will be poised for a metaphysical and intellectual reversal that is every bit as profound as the one with Copernicus. People will say, "My gosh, we’ve been completely misled by this fundamental truth of the creation story of our culture. We can no longer understand the world that way."

How do you change the way people regard the authority of science? Get them to think of it as a much more limited thing. Science is very reliable when scientists stick to the kinds of things that can be tested by refutable experiments, but much of what they tell us is outside that. When they have to fake the mechanisms, it becomes a very dubious philosophy. That raises the question of why so many very brilliant people were misled for so long and did such a good job of rationalizing these things.

When the mechanism of Darwinism becomes discredited, it’s like a train that’s been turned around. You can say, "Well, that’s interesting, but the train is still in the same place. The world, Yale, Berkeley, are still there. The New York Times is still telling us what to think. So why isn’t everything different?" Well, it is different, but you can’t see it yet. The train is turned in the opposite direction. It’s going to start out very slowly, but it’s moving on the logical tracks towards something very different, and when we get there, our great-great-grand-children will see how different things are.


Note that the "scientific key" to the whole ID argument (according to Johnson) is this: "No natural processes create genetic information."  

This strikes me as easily and trivially refutable by numerous examples.  Anything that starts with genetic information amount X, and ends up with genetic information amount X+Y, should qualify.  The classic case would be X=information in a genome before a gene duplicates & diverges under selection, and X+Y being the information in the genome after this has occurred.

Another less-often considered example should be (IMO) when a mutation (let's say "beneficial to at least part of the population" to avoid the obvious objection) arises in a *population*.  Here,

X=information in the genomes of a population
Y=information in the beneficial mutation

I realize that "information" has no single definition in biology, one could also argue that "new information" would arise through novel combinations of alleles, etc.  For the purposes of this thread, I suggest the following working definition:

Genetic information=functional DNA that encodes useful/beneficial proteins or regulatory sequences

...as this is what the IDers mean by "genetic information" (except of course when they are challenged on the topic, wherein they promptly begin the obfuscation and goal-post moving, rather like eternally elusive creationist definition of "kind").

So, let's use this thread to accumulate examples of natural processes increasing "genetic information" in the above-described sense.  Other things that might be relevant, e.g. studies of the increase of Shannon information in selective algorithms, could also be posted, just note the form of information as relevant.

nic

PS: I'll start off with one of my favorite examples:

Sdic, sperm dynein intermediate chain, a new gene which evolved over the past few million years by the duplication, fusion, and modification of two genes that are now on each side of Sdic on the chromosome.

Here is a brief introduction from Ian Musgrave:

Quote

My second favorite example is the Sdic gene, where the annexin and dynenin intermediate chain genes were duplicated in tandem, then the intervening sequences deleted to form a single new gene, (the Sperm specific dynenin intermediate chain gene Sdic). The good thing about this example is that a previously non-coding part of the sequence became the protein coding sequence, and the protein coding sequence has a non-coding role.


Capy P. (1998 Dec 10). Evolutionary biology. A plastic genome [news; comment] Nature, 396, 522-3.

Nurminsky DI, Nurminskaya MV, De Aguiar D, and Hartl DL. (1998 Dec 10). Selective sweep of a newly evolved sperm-specific gene in Drosophila [see comments] Nature, 396, 572-5.



Here is the Nurminsky et al. 1998 article:

Quote

pubmed link

Nature 1998 Dec 10;396(6711):572-5

Selective sweep of a newly evolved sperm-specific gene in Drosophila.

Nurminsky DI, Nurminskaya MV, De Aguiar D, Hartl DL.

Harvard University, Department of Organismic & Evolutionary Biology, Cambridge, Massachusetts 02138, USA.

The pattern of genetic variation across the genome of Drosophila melanogaster is consistent with the occurrence of frequent 'selective sweeps', in which new favourable mutations become incorporated into the species so quickly that linked alleles can 'hitchhike' and also become fixed. Because of the hitchhiking of linked genes, it is generally difficult to identify the target of any putative selective sweep. Here, however, we identify a new gene in D. melanogaster that codes for a sperm-specific axonemal dynein subunit. The gene has a new testes-specific promoter derived from a protein-coding region in a gene encoding the cell-adhesion protein annexin X (AnnX), and it contains a new protein-coding exon derived from an intron in a gene encoding a cytoplasmic dynein intermediate chain (Cdic). The new transcription unit, designated Sdic (for sperm-specific dynein intermediate chain), has been duplicated about tenfold in a tandem array. Consistent with the selective sweep of this gene, the level of genetic polymorphism near Sdic is unusually low. The discovery of this gene supports other results that point to the rapid molecular evolution of male reproductive functions.



Since then, this article has been published:

Quote

Pubmed link

Nurminsky D, Aguiar DD, Bustamante CD, Hartl DL.
Chromosomal effects of rapid gene evolution in Drosophila melanogaster.
Science. 2001 Jan 5;291(5501):128-30.

Rapid adaptive fixation of a new favorable mutation is expected to affect neighboring genes along the chromosome. Evolutionary theory predicts that the chromosomal region would show a reduced level of genetic variation and an excess of rare alleles. We have confirmed these predictions in a region of the X chromosome of Drosophila melanogaster that contains a newly evolved gene for a component of the sperm axoneme. In D. simulans, where the novel gene does not exist, the pattern of genetic variation is consistent with selection against recurrent deleterious mutations. These findings imply that the pattern of genetic variation along a chromosome may be useful for inferring its evolutionary history and for revealing regions in which recent adaptive fixations have taken place.



This article is a good review of the general topic of the evolution of new genes:

Quote

pubmed link

Curr Opin Genet Dev 2001 Dec;11(6):673-80

Evolution of novel genes.

Long M.

Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago Illinois 60637, USA. mlong@midway.uchicago.edu

Much progress in understanding the evolution of new genes has been accomplished in the past few years. Molecular mechanisms such as illegitimate recombination and LINE element mediated 3' transduction underlying exon shuffling, a major process for generating new genes, are better understood. The identification of young genes in invertebrates and vertebrates has revealed a significant role of adaptive evolution acting on initially rudimentary gene structures created as if by evolutionary tinkers. New genes in humans and our primate relatives add a new component to the understanding of genetic divergence between humans and non-humans.


Have fun,
nic

Date: 2002/05/30 00:51:24, Link
Author: niiicholas
Here is a whole double issue of JME with a large group of articles devoted to evolution-of-genetic-code issues:

Volume 53 - Number 4/5, 2001
http://link.springer.de/link/service/journals/00239/tocs/t1053004.html

Quote

Articles
261-268
Lluís Ribas de Pouplana, James R. Brown, Paul Schimmel
Structure-Based Phylogeny of Class IIa tRNA Synthetases in Relation to an Unusual Biochemistry
Article in: PDF | HTML-Frames

269-281
David H. Ardell, Guy Sella
On the Evolution of Redundancy in Genetic Codes
Article in: PDF | HTML-Frames

282-289
Yoshikazu Nakamura
Molecular Mimicry Between Protein and tRNA
Article in: PDF | HTML-Frames

290-298
Shigehiko Kanaya, Yuko Yamada, Makoto Kinouchi, Yoshihiro Kudo, Toshimichi Ikemura
Codon Usage and tRNA Genes in Eukaryotes: Correlation of Codon Usage Diversity with Translation Efficiency and with CG-Dinucleotide Usage as Assessed by Multivariate Analysis
Article in: PDF | HTML-Frames

299-313
Robin D. Knight, Laura F. Landweber, Michael Yarus
How Mitochondria Redefine the Code
Article in: PDF | HTML-Frames

314-326
Shin-ichi Yokobori, Tsutomu Suzuki, Kimitsuna Watanabe
Genetic Code Variations in Mitochondria: tRNA as a Major Determinant of Genetic Code Plasticity
Article in: PDF | HTML-Frames


Funny that Paul Nelson's views were not included, eh?

I just received a good private message on this topic from a new poster & I encouraged him to post it in the general discussion, I'll then post a link to it from this thread.

nic

Date: 2002/05/30 01:14:38, Link
Author: niiicholas
One more article.

Here's the short version of the case as I now understand it.

- In the beginning, scientists thought the genetic code was universal (maybe; this is the standard line, whether all relevant experts also assumed this initially seems to me to be uncertain, at least I've not seen any analysis of the topic).

- in the 1980's it was documented that this was not the case

- In the late 1980's Osawa proposed the "codon disappearence" theory for the evolution of code changes, described in the Schultz & Yarus (1996) article referenced below thusly:

Quote

Codon reassignment to new amino acids within large, complex, relatively modern genomes (Osawa et al. 1992) poses interesting mechanistic problems. Osawa and Jukes have proposed (1989), and reaffirm in recent publications (1992; Osawa and Jukes 1995), that during codon reassignment every example of a codon in an entire genome must mutate or otherwise disappear as a result of mutational change in genomic GC content. Subsequent to its total disappearance, a codon can be captured by, e.g., an anticodon mutation in a dispensable tRNA, thereby reappearing with a new identity. We will call this the ``codon disappearance'' theory, after its characteristic intermediate state.


- In the mid-1990's another theory was proposed, apparently right in Schultz & Yarus' 1996 article:

Quote

We find the absolute disappearance of hundreds, thousands, or tens of thousands of examples of a codon by mutation pressure alone, in diverse independent cases, an improbable evolutionary scenario. Total disappearance should be an extremely slow occurrence, because mutation pressure and genetic drift in large populations are among the weakest evolutionary forces, producing only very slow changes in genomic composition. Furthermore, back mutation increases in effectiveness as the goal is approached because of the accumulation of codons related to the disappearing codon by single mutation. Finally, complete disappearance of codons in eukaryotes would be hindered by coherent areas of varied GC content along chromosomes (Sharp and Lloyd 1993; Ikemura and Wada 1991). Because codon choice follows GC content, such areas can provide sheltered enclaves for particular codons (Santos and Tuite 1995).

Though total disappearance is difficult to prove, mutation pressure certainly causes codon frequencies to change. Evolution to very low frequencies and inefficient translational function is well supported (e.g., Kano et al. 1993). But we argue that mutation and drift in codon frequency over entire genomes are vulnerable to being overtaken by faster evolutionary processes such as selection. Thus the question: Are there plausible faster processes, perhaps selection-driven processes, for codon reassignment?

Schultz and Yarus characterized a nonanticodon tRNA site (1994a,b) where particular nucleotide sequences allow a tRNA to read an unusual near-cognate codon. More generally, several sites are known where single mutations in nonanticodon nucleotides (reviewed in Yarus and Smith 1995) enhance tRNA ability to read (at least) two codons, (at least) one of which is forbidden by normal base-pairing and wobble rules. Schultz and Yarus suggested (1994c) that such equivocal adapters could catalyze codon reassignment for one of the codons being ambiguously read. (For clarity in what follows, a codon read in more than one way is said to be ``ambiguous''; a tRNA which reads normal codons as well as codons not normally assigned is said to be ``equivocal.'';) In the particular case in which reassignment is initiated by a mutation that impairs normal translation of a codon, reassignment via an equivocal adapter tRNA might evolve quickly by selection for improved translation of the newly ambiguous codon. Transitional coding ambiguity could finally be resolved by, for example, loss or mutation of the original tRNA, and anticodon mutation to equivocal complementarity in the new (equivocal) tRNA, so that the amino acid of the previously equivocal tRNA is reassigned. We will call this the ``ambiguous intermediate'' theory.



Here is the reference, and some of Schultz & Yarus' (1996) lines of evidence for the ambiguous intermediate theory:

Quote

JME link
J Mol Evol 1996 May;42(5):597-601

On malleability in the genetic code.

Schultz DW, Yarus M.

To explain now-numerous cases of codon reassignment (departure from the "universal" code), we suggest a pathway in which the transformed codon is temporarily ambiguous. All the unusual tRNA activities required have been demonstrated. In addition, the repetitive use of certain reassignments, the phylogenetic distribution of reassignments, and the properties of present-day reassinged tRNAs are each consistent with evolution of the code via an ambiguous translational intermediate.

[...]

Firstly: at the heart of our proposal lies the supposition that codons are read ambiguously by two tRNAs (or a tRNA and an RF, in the case of terminators), specifying insertion of more than one amino acid (or an amino acid as well as stop). In contrast, the assumption that codons vanish before reassignment, which is characteristic of codon disappearance theory, is mandated by the assertion that codons cannot have two meanings.

In strict form, this axiom of nonambiguity contradicts chemical principle. An infinite free energy difference between reaction pathways is required to select one reactant and reject another absolutely. The strict absence of ambiguity is also contradicted by experiment. Cumulative missense translation in normal E. coli has been estimated at 4 × 10-4 per codon (Ellis and Gallant 1982). Total miscoding per peptide chain is the much larger sum over the hundreds of codons in the protein. Therefore an appreciable basal ambiguity (yielding ~ 10% of the average 250-amino-acid protein with a variant sequence) is evident, and tolerated, in wild-type cells.

Further, cells are unharmed even when this substantial basal ambiguity is increased dramatically. We have constructed strains containing equivocal E. coli tRNAs that demonstrate suppressor efficiencies of 50 to nearly 100%, making a stop codon ambiguous (Schultz and Yarus 1994a,b). Ribosomal ambiguity mutations (RAM) increase misreading of stop codons up to 100-fold in cells that remain viable (Strigini and Brickman 1973; Andersson et al. 1982). Most specifically, the general error frequency can be increased 13-fold (using 5 µg/ml streptomycin) and cells continue to grow exponentially at a rate close to controls. After more than 400 generations in streptomycin, there is no detectable decrease in cellular viability (Gallant and Palmer 1979). Thus ambiguity at a variety of codons (to >=1 error in the average 250-amino-acid protein) is well tolerated, or has no apparent phenotype. The limited ambiguity we posit as the initiating event in codon reassignment, occurring at one (or a few) codon(s) and perhaps initially quantitatively small, seems quite plausible in this context.

Nor is coding ambiguity limited to prokaryotes. Eukaryotes have basal levels of coding ambiguity which are probably similar to prokaryotes (Gallant and Palmer 1979). Normal yeast glutamine tRNAs are known to read equivocally at the first codon position (Weiss and Friedberg 1986; Edelman and Culbertson 1991). Similar ambiguities can be exploited for an organism's own purposes, as when animal and plant viruses purposefully use ambiguous stop condons to adjust the level of stop readthrough to an essential gene product. This misreading by a wild-type tRNA is known to approach 5% at stop codons within a special mRNA context (Skuzeski et al. 1991; Feng et al. 1990). Thus, during codon reassignment there seems to be no reason that all codons must invariably be read without ambiguity.

[note here that ambiguity is not exactly vanishingly rare and therefore the assumption that intermediates would be nonviable is false]

Secondly: There is no definite direction to reassignment in codon disappearance theory; dispensable RNA genes may capture unassigned codon by, e.g., random single base changes in their anticodons (Osawa and Jukes, 1989). However, we first argue that known reassignments (Table 1) are very nonrandom. We then argue the nonrandomness supports ambiguous intermediate theory because it is explicable by types of equivocal reading already demonstrated in tRNAs.

[...]

However, 14 of 14 single-nucleotide reassignments in Table 1 parallel the activities of known equivocal tRNAs. That is, all 14 changes might be mediated by tRNAs reading a single base equivocally, using G-U (anticodon-codon) wobble at the first position, or C-A or G-A mispairing at the third codon position. Equivocal C-A third-position mispairing has long been known from study of tRNA opal (UGA) suppressors (Hirsh 1971). We recently constructed two new tRNAs that demonstrate in vivo the required equivocal G-U and C-A readings (Schultz and Yarus 1994b), thereby potentially accounting for ten assignments (Table 1). This congruence, in fact, first drew our attention to the possibility that tRNAs might mediate codon reassignment. The remaining exceptional wobble, transitional G-A pairing at the third position, has also been detected in the equivocal tRNA repertoire in vitro, using cytoplasmic and chloroplast tRNA Cys (Nicotiana) as UGA suppressors (Urban & Beier, 1995). The remaining 15th case requires a more unusual first/second-position double miscoding. However, the Candida albicans tRNA translating the reassigned CUG codon has been independently shown to be capable of a similar doubly equivocal coding (Santos et al. 1993; see below). Thus 15 of 15 known reassignments can be matched with known tRNA capabilities.

Thirdly: Phylogenetic distribution of reassignment is consistent with ambiguous intermediates. Tourancheau et al. (1995) have made the initially surprising observation that UAA/UAG in ciliates have been reassigned to glutamine at least three times independently (on the basis of the rRNA tree), instead of depending on a common ancestral reassignment. This striking phylogenetic cluster of identical but independent reassignments has no apparent explanation in the codon disappearance scheme. However, such a cluster is easily explained within the ambiguous intermediate mechanism by a tendency to equivocal reading of these codons inherited from an ancestor. Such an ambiguity might be conserved within a group of species if used for an important regulatory event like stop codon readthrough. These authors also found no correlation between GC content of the ciliates and reassignment, which might have been expected if evolutionary change in GC content drives the process.

Fourthly: Molecular fossil and functional evidence of translational ambiguity accompanies known cases of reassignment. We have previously pointed out that sequenced tRNAs that have captured new codons, such as the UAA and UAG reading tRNAs from the ciliate Tetrahymena thermophila (Hanyu et al. 1986), contain unusual nucleotide sequences that we have identified as enhancers of equivocal coding in E. coli (Schultz and Yarus 1994c). Thus the structure of these three related isoaccepting tRNAGln sequences suggests the existence of an ancestor that coded equivocally.

[...]

In summary: We acknowledge the significance of codon reassignment, and do not argue against change in GC content as a significant evolutionary event (e.g., Sueoka, 1993). But we do argue that codon reassignment is unlikely to be carried out entirely by the slow processes of mutation pressure and drift. Additionally, the axiom of nonambiguity fundamental to codon disappearance theory is not justified. The evident nonrandomness of known reassignments, the clustering of similar changes in phylogeny, and the properties of reassigned tRNAs, where known, are strikingly consistent with ambiguously translating intermediates. These phenomena are unexpected or contradictory to codon disappearance theory, acting in isolation.

In this connection, there is no logical incompatibility between mutational change in GC content and ambiguous intermediates. Schultz and Yarus (1994c) have noted that these may occur together. In fact, a codon which has become rare might also be expected to evolve a rare cognate tRNA. Such a rare tRNA would be more vulnerable than usual to competition during translation, including competition from an equivocal adaptor translating its codon. Thus not only might mutation pressure be overtaken by faster selection, but the initial effects of mutation pressure might facilitate the overtaking mechanism. Quantitative modeling of this process might prove rewarding.

Finally: if ambiguous intermediate theory gives a good account of modern coding changes, it thereby becomes a preferred route by which a limited ancestral code could have been transformed to the present ``universal'' genetic code. In fact, coding transitions via ambiguous intermediates would likely be easier during the formation of the code than today.

Other aspects of ambiguous intermediate and codon disappearance schemes can be compared in the previous note by Osawa and Jukes (1995), and in Schultz and Yarus (1994c), to which the interested reader is directed for references and details which do not appear here.




Date: 2002/05/30 01:49:29, Link
Author: niiicholas
Reviewing this 1993 article by Paul Nelson and Jonathan Wells:

Quote

Is Common Descent an Axiom of Biology?

http://www.arn.org/docs/nelson/pn_darwinianparadigm061593.htm

[Editorial note:  The following discussion paper was written for the conference, “The Darwinian Paradigm: Problems and Prospects,” held June 22-25, 1993, at the Pajaro Dunes beach community on Monterey Bay, near Watsonville, California.  The conference was organized by Phillip Johnson.  Attendees included Michael Behe, Walter Bradley, John Angus Campbell, William Dembski, Dean Kenyon, Stephen Meyer, Paul Nelson, David Raup, Siegfried Scherer, Jonathan Wells, and Kurt Wise.]

-------------------------------------------------------------------

To:                  Pajaro Dunes Conference Participants
From:              Paul Nelson and Jonathan Wells
Date:               15 June 1993
Re:                  Discussion paper for Topic Area I (homology, etc.)


...and skipping to the genetic code section, we find that Nelson & Wells are indeed assuming that the "functional invariance" thesis was dropped, without evidence, to protect common descent:

Quote

The Universal Genetic Code Argument for Common Descent

Lest it be thought that this pattern of reasoning – namely, sacrificing the auxiliary theory to save common descent – is an isolated example, we offer another, perhaps more striking case.

Most of us are familiar with the universal genetic code argument for common descent.  The argument first appeared in the mid to late 1960s, after the structure of the code was elucidated.  It is now widespread.[33]

[they quote several quotes to this effect]


...and then, they argue that "functional invariance" is highly probable and therefore scientists are unjustifiably dropping the "functional invariance theory" to protect common descent:

Quote

Postulating that such fundamental variations occurred is, however, very far from knowing how they occurred. "Direct replacements of one amino acid by another throughout proteins," argue Osawa et al., "would be disruptive in intact organisms and even in mitochondria."[45]  That is, we should not think that the body of molecular knowledge motivating functional invariance can be jettisoned at will. (Yes, if common descent is true, and variant codes exist, functional invariance has to go to the wall. Yet functional invariance still seems to be true, or at least highly probable.)  Rather, taking common descent as given, we are now faced with another novel research problem: "How could non-disruptive code changes occur?"[46]



I find this article fascinating because it exemplifies one particularly devious tactic of the ID movement: rather than taking the obvious, but difficult, route of simply arguing that common descent is true or false to some specific degree, based on this and that specific evidence, they try to make the convert the entire argument into one about the intellectual credibility of the biologists, and therefore the thesis the IDists are really trying to advance is something like "mainstream biologists are biased and would believe in evolution no matter what the evidence."  As in Nelson & Wells' conclusion:

Quote

Suppose Darwin had it right, namely, that "all the organic beings which have ever lived on this earth have descended from some one primordial form."[52]  The existence of this "one primordial form," the common ancestor, establishes a theoretical domain that logically subsumes all biological and paleontological phenomena.  That is, even if life had multiple origins, we will be unable, having assumed the truth of common descent, to provide any evidence for that possibility: all observed organisms, whether recent or extinct, will necessarily lie within what might be called the "common ancestor horizon."

If this seems counter-intuitive, try the following thought experiment. Assume the truth of common descent, and then attempt to construct an empirical argument against it. No imaginable evidence one might bring to bear, however striking – e.g., organisms for which no transitional stages seem possible, multiple genetic codes – will be able to overturn the theory. If there really was a common ancestor, then all discontinuities between organisms are only apparent, the artifacts of an incomplete history. An ideally fine-grained history would reveal the begetting relations by which all organisms have descended from the common ancestor.

If the axiom thesis is correct, then the theory of common descent will indeed be refractory to the evidential challenges thrown up by biological experience. One can see the point in Mayr's recent claim that common descent

has been gloriously confirmed by all researches since 1859. Everything we have learned about the physiology and chemistry of organisms supports Darwin's daring speculation that "all the organic beings which have ever lived on this earth have descended from some one primordial form..."[53]

One wonders what we could have learned about organisms, since 1859, that would not have confirmed common descent.

We offer the axiom thesis, not because we are persuaded of its truth, but to provide a starting point or focus for discussion. How, really, do the patterns of living things count for, or against, the notions of primary continuity (common ancestry) or primary discontinuity (polyphyly)? If common descent cannot be dislodged by the "evidence," then how should we go about evaluating it?


I propose a (new??) term for this style of argument: Argumentum ad Innuendo.

Thanks, nic



Date: 2002/05/30 08:41:26, Link
Author: efvinson
A very recent example of a "stop" codon being
sometimes coopted for another use is the subject of two papers and a "perspective" (1-3) in the 24 May 2002 issue of Science. These all are reporting on the "new" amino acid "pyrrolysine", which is coded for by the (usually) stop codon UAG in a certain methanogenic archaeon's mRNA. To quote from (1):
Quote

The way in which pyrrolysine is encoded bears striking parallels to the encoding of the 21st amino acid, selenocysteine. Selenocysteine is found in Archaea, eubacteria and animals, including mammals . Both nonstandard amino acids are encoded by the RNA nucleotide triplets (codons) that signify a command to stop translation of mRNA into protein (UGA is the "stop codon" encoding selenocysteine). The notion that at least 22 amino acids are directly encoded by the nucleotide sequence of mRNA reflects the greater richness of the genetic code than is apparent from the standard textbook account.

Originally, the coding problem was defined in terms of how the 20 common amino acids could be specified by four RNA nucleotides. As the triplet nature of the genetic code began to unfold in the early 1960s, it might have been tempting to speculate that some of the 64 possible codons encoded the many rare amino acids found in proteins. However, it became clear that 20 is the correct number of amino acids, and that the great majority of nonstandard amino acids are created by chemical modifications of standard amino acids after translation. In 1986 came the surprise discovery that the nonstandard amino acid selenocysteine is directly specified by the genetic code and is not created by posttranslational modification. Selenocysteine is now joined by pyrrolysine, and together these two amino acids demonstrate that the genetic code can be expanded by redefining the meaning of a stop codon.   {references omitted}




Reference (1) goes into some depth, with references, as to how the stop signal is subverted in the case of selenocysteine, the only other non-canonical amino acid known to be specified by the code and not built by modification after translation. In the selenocysteine case, only a minority of the UGA codons are used to code the amino acid: most are still stop codons. Signals elsewhere in the mRNA determine which. It is still unknown just hoe the UAG coding pyrrolysine works, however.

(1) Atkins JF, Gesteland R. Science 2002 May 24;296(5572):1409-10
(2) G. Srinivasan et al., Science 296, 1459 (2002).
(3) B. Hao et al., Science 296, 1462 (2002).

Date: 2002/05/30 08:52:12, Link
Author: Lizard
I met Maureen Fritts last June at the IDnet's DDDII conference in Kansas City. I attended her concurrent session on how to build an organization using the Internet. Her co-presenter was one of the "Managing Directors" of IDnet (www.intelligentdesignnetwork). She seems to be very smart and good at what she's doing. I believe she's from Nebraska. She discovered my name on the Internet somewhere and sent me a rather strange e-mail. I don't remember the content.

I don't know whether Maureen is affiliated with the DI or IDnet formally, but she's working for the cause.

Date: 2002/05/30 12:59:58, Link
Author: theyeti
Quote
If this seems counter-intuitive, try the following thought experiment. Assume the truth of common descent, and then attempt to construct an empirical argument against it. No imaginable evidence one might bring to bear, however striking – e.g., organisms for which no transitional stages seem possible, multiple genetic codes – will be able to overturn the theory.


That's got to be the stupidest argument I've ever seen.  If common descent is true, then there will be no empirical evidence against it.  What they're basically saying is "true theories can't be shown to be false empirically".  Why don't they just say that differing genetic codes are empirical evidence against common descent and be done with it?  How does it make sense to construct a thought experiment where we try to hold two contradictory notions at once, i.e., common descent is both true and shown to be false by the evidence?

Anyway, Nelson & Wells' contention that biologists dropped the "no viable intermediates" claim in order to protect common descent is demonstrably false.  It was dropped because it was shown to be wrong, empirically.  Not only does the example of ambiguous codes demonstrate this, but also the ability of researchers to alter the codes of living organisms.  Ironically, the DI aticle that responds to Miller alludes to this:

Quote
Experiments to change the identity of transfer RNA (tRNA)--another possible mechanism by which genetic codes might reassign codon “meanings”--have shown that the intermediate steps must be bridged by intelligent (directed) manipulation. In one such experiment, for instance, Margaret Saks, John Abelson, and colleagues at Caltech changed an E. coli arginine tRNA to specify a different amino acid, threonine. They accomplished this, however, only by supplying the bacterial cells (via a plasmid) with another copy of the wild-type threonine tRNA gene. This intelligently-directed intervention bridged the critical transition stage during which the arginine tRNA was being modified by mutations to specify threonine. [6]


Notice that they're trying to do with this experiment what they do with animal and plant breeding.  When mutation and selction are shown to be sufficient to cause substantial morphological change, they dismiss it outright because it was really just "intelligent design" even though it has nothing to do with ID as they conceive it.  And here, the ability of the code to change is dismissed because it was caused by "intelligent design", as if plasmid transfers never happen in the wild.    

Anyway, here are the refs for the papers cited:

6. Margaret E. Saks, Jeffrey R. Sampson, and John Abelson, “Evolution of a Transfer RNA Gene Through a Point Mutation in the Anticodon,” Science 279 (13 March 1998):1665-1670.

7. Jennifer Normanly, Richard C. Ogden, Suzanna J. Horvath & John Abelson, “Changing the identity of a transfer RNA,” Nature 321 (15 May 986):213-219.

I haven't read them as I don't have online access to either journal (though I might just get off my butt and walk the 100 yards to the library.)  I am interested in seeing how these papers compare to the DI quote-mining spin.

theyeti

P.S.  Just noticed that the DI has a typo in their reference for the Normanly et al paper.  It looks like it's from 1986, in which case they're using a reference that's much too old given that they're lots of recent ones.

Date: 2002/05/30 16:43:39, Link
Author: theyeti
Here's another well studied one:

The jingwei gene in Drosophila.

(quick side note:  you find most of these suckers in well studied organisms like Drosophila whose genome has been sequenced.  The particular significance of this is that we can trace the ancestry of the gene in question by looking at closely related species Drosophila, whose common ancestry is not even doubted by YECs.  Their only recourse here would be to claim that the gene had always existed and that every other species of Drosophila had lost the gene independently.  This would a) be extremely unparsimonious, given that it requires multiple parallelisms with no known non-random mechanism and b) force us to ignore all of the other evidence of recent origin.)  

Onto jingwei:

In a 1993 issue of Science, Manyuan Long, and CH Langley published their findings of a novel Drosophila gene, located on chromosome 3, that is found in sister species D. teissieri and D. yakuba and thus presumably first appeared in the common ancestor of both.  They dubbed this new gene jingwei (jwg).  The evidence that they uncovered, especially the lack of introns, suggested that the gene was derived from a retrotransposed mRNA from an alcohol dehydrogenase (adh) gene on chromosome 2.  Further results suggested that jwg is not a pseudogene as was first thought, but is rather a functional novel gene, though its exact function is still not clear.  The gene not only has specific RNA expression patterns, but has also undergone extensive evolution without suffering from any frameshift or nonsense mutations that are the hallmark of pseudogenes; the evidence strongly suggests that jwg has been under positve Darwinian selection.  Not only that, but Long and Langely’s results suggest that selection is playing a role throughout the origin of new genes, rather than being initially relaxed as was previously thought.
 
Perhaps the most interesting aspect of jwg is that its gene product is a chimera, meaning that it has function portions that are derived from different ancestral genes (aka gene fusion).  The C-terminal portion of jwg was almost certainly derived from the ancestral adh gene via retrotransposition, but that left the origin of the N-terminal exons still unexplained.  Did they come from non-coding upstream regions of DNA, or were they derived from parts of non-related functional genes?  Further study by Long et al. (1999) demonstrated that the N-terminal regions were the result of duplications of exons from a gene named yellow-emperor (ymp).  A follow-up study by Wang et al. (2000) showed that ymp is also a functional gene whose first three exons are the donor for the recruited portion of jwg.









Quote
Fig. 2.—Origin of the three novel proteins, YMP-1, YMP-2, and JGW, as a consequence of exon recombination. E1–E12 represent exons 1–12 of ymp (for the origin of YMP-1 and YMP-2); E1–E3, making up JGW, are the first three exons of ynd (Long and Langley 1993 ), a duplicate copy of ymp. The hatched boxes are the regions encoding protein sequences, with different patterns showing different peptide sequences. The open boxes represent untranslated regions (UTRs) of mRNAs (the open boxes on the left represent 5' UTRs; those on the right represent 3' UTRs)
{from Wang et al, 2000}

That's not the world's best image, but it gets across the general idea of how these new genes evolve.  Notice also that this graphically demonstrates the evolution of the yellow emperor genes as well.  As for jingwei, the basic idea is as follows, and I'd like to get it (and all other such examples) into a fancy colored graphic when possible (if anyone knows of a good program for this, let me know.)

Ald ---> retrotransposition ---> Jingwei Ct portion

YMP --> duplication of first three exons ---> exon shuffling ---> fusion of Jingwei Nt and Ct portions.


Refs:

Long M, Langley CH, Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila.  Science 1993 Apr 2;260(5104):91-5
PubMed

Long M, Wang W, Zhang J., Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila.  Gene 1999 Sep 30;238(1):135-41
full text pdf

Luque T, Marfany G, Gonzalez-Duarte R., Characterization and molecular analysis of Adh retrosequences in species of the Drosophila obscura group.  Mol Biol Evol 1997 Dec;14(12):1316-25
PubMed

Wang W, Zhang J, Alvarez C, Llopart A, Long M., The origin of the Jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melanogaster.  Mol Biol Evol 2000 Sep;17(9):1294-301
full text



Date: 2002/05/30 20:33:50, Link
Author: niiicholas
Howdy,

Just a little background in case we've got any lurkers who haven't taken biochemistry lately...

In the canonical genetic code that everyone learns in textbooks there are 20 amino acids -- however, chemically many more amino acids are possible.  As I understand it there are many cases where organisms will produce an amino acid chain using the canonical code, and then post-translationally modify some of the amino acids, effectively resulting in the usage of more than 20 amino acids by the organism, although technically the normal genetic code is still used.

However, there are some cases where the canonical code has been modified to include a noncanonical amino acid *during* translation.  A few weeks ago a new example of this was published, and in the AE general discussion a new poster Ed has alerted us to how this example fits in with the 'stop codon alteration' pattern that is so common in genetic code changes.

Here is the link to Ed's post "Stop codon thievery"

I'll quote Ed's post for the sake of thoroughness:

=============
A very recent example of a "stop" codon being
sometimes coopted for another use is the subject of two papers and a "perspective" (1-3) in the 24 May 2002 issue of Science. These all are reporting on the "new" amino acid "pyrrolysine", which is coded for by the (usually) stop codon UAG in a certain methanogenic archaeon's mRNA. To quote from (1):

Quote

The way in which pyrrolysine is encoded bears striking parallels to the encoding of the 21st amino acid, selenocysteine. Selenocysteine is found in Archaea, eubacteria and animals, including mammals . Both nonstandard amino acids are encoded by the RNA nucleotide triplets (codons) that signify a command to stop translation of mRNA into protein (UGA is the "stop codon" encoding selenocysteine). The notion that at least 22 amino acids are directly encoded by the nucleotide sequence of mRNA reflects the greater richness of the genetic code than is apparent from the standard textbook account.

Originally, the coding problem was defined in terms of how the 20 common amino acids could be specified by four RNA nucleotides. As the triplet nature of the genetic code began to unfold in the early 1960s, it might have been tempting to speculate that some of the 64 possible codons encoded the many rare amino acids found in proteins. However, it became clear that 20 is the correct number of amino acids, and that the great majority of nonstandard amino acids are created by chemical modifications of standard amino acids after translation. In 1986 came the surprise discovery that the nonstandard amino acid selenocysteine is directly specified by the genetic code and is not created by posttranslational modification. Selenocysteine is now joined by pyrrolysine, and together these two amino acids demonstrate that the genetic code can be expanded by redefining the meaning of a stop codon.   {references omitted}


Reference (1) goes into some depth, with references, as to how the stop signal is subverted in the case of selenocysteine, the only other non-canonical amino acid known to be specified by the code and not built by modification after translation. In the selenocysteine case, only a minority of the UGA codons are used to code the amino acid: most are still stop codons. Signals elsewhere in the mRNA determine which. It is still unknown just how the UAG coding pyrrolysine works, however.

(1) Atkins JF, Gesteland R. Science 2002 May 24;296(5572):1409-10
(2) G. Srinivasan et al., Science 296, 1459 (2002).
(3) B. Hao et al., Science 296, 1462 (2002).
=============

Thanks Ed, keep it up!

Nic



Date: 2002/05/31 00:21:26, Link
Author: theyeti
Here's the most recent one that I know of off hand:

PNAS, Vol. 99, Issue 7, 4448-4453, April 2, 2002

Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster

Quote
Non-protein-coding RNA genes play an important role in various biological processes. How new RNA genes originated and whether this process is controlled by similar evolutionary mechanisms for the origin of protein-coding genes remains unclear. A young chimeric RNA gene that we term sphinx (spx) provides the first insight into the early stage of evolution of RNA genes. spx originated as an insertion of a retroposed sequence of the ATP synthase chain F gene at the cytological region 60DB since the divergence of Drosophila melanogaster from its sibling species 2-3 million years ago. This retrosequence, which is located at 102F on the fourth chromosome, recruited a nearby exon and intron, thereby evolving a chimeric gene structure. This molecular process suggests that the mechanism of exon shuffling, which can generate protein-coding genes, also plays a role in the origin of RNA genes. The subsequent evolutionary process of spx has been associated with a high nucleotide substitution rate, possibly driven by a continuous positive Darwinian selection for a novel function, as is shown in its sex- and development-specific alternative splicing. To test whether spx has adapted to different environments, we investigated its population genetic structure in the unique "Evolution Canyon" in Israel, revealing a similar haplotype structure in spx, and thus similar evolutionary forces operating on spx between environments.


This is an RNA gene, and the role that RNAs play in terms of regulation is only now starting to be fully realized.  RNA genes can probably evolve by retrotransposition easier than protein coding genes can, since the characteristic 5' truncation is less likely to have a major effect, and there is no worry about frameshifts.  In the case of small RNAs, there should be no 5' truncation.  (Retrogenes and processed pseudogenes are caused when a reverse transcriptase creates a cDNA from a mature mRNA (or other RNA).  The reverse transcrpitase starts at the poly A tail and works its way 3'.  However, if the mRNA is of decent size, it usually falls off before finishing, resulting in a cDNA that is truncated at the 5' end.  This truncation, along with a degenerate poly A tail and flanking repeats, are smoking gun evidence of a retrogene or processed pseudogene.  There's just no denying it, Johnson.)  Furthermore, many small RNAs can act as anti-sense oligos, binding complemetary mRNA or DNA for regulation.  These are easy to evolve, because they can be derived straight from the complemetary strand of the gene they regulate.

There is a furhter significance to this example in the fact that sphinx was derived from retrotransposition of an ATP synthase gene.  But sphinx is not a protein coding gene as ATP synthase is, so the functionality of the sequence is not derived from the already adapted sequence of ATP synthase.  Rather, this is more like a random sequence becoming functional, and is thus similar to the example of URF13 that Dembski sweats over in NFL (idea: let's apply Dembski's uniform probability to sphinx like he did with URF13 and see if it beats his universal probability bound.  Better yet, let's multiply the probabilities of both).

On top of all of this, we have a (potential) transposition event too.  So the origin of the gene goes something like this:

Quote
Although the role of retroposition is well defined in the origin of this gene, it should be pointed out that this is an unusual retroposition process. An independent DNA transposon, S element, moved together in the process with the ATP synthase chain F gene. A consequence of this process leaves a partial S fragment attached to the ATP synthase element-derived region in spx. There are several hypothetical scenarios for the origin of this complex structure. The first hypothesis is that the retroposed sequence of ATP synthase gene might have been inserted first into the S element located in the current position of the chromosome. Then the chimeric gene structure evolved by using the sequence of degenerated S element as the recipient site for splicing of the newly created intron between the recruited exon and ATP synthase chain F derived exon. The second hypothesis is that the retrosequence might have landed first in the S element, located in another portion of the genome, before the S element carrying the retrosequence jumped into the current position and degenerated in the S element structure. The third hypothesis is that the portion of the S element, which was located upstream of spx, might have been cotranscribed with the ATP synthase chain F gene and retroposed. The observation that the short repeats flank both S element fragment and the ATP synthase derived portion of spx is consistent with the third hypothesis.


theyeti



Date: 2002/05/31 01:31:35, Link
Author: niiicholas
Another classic case is the evolution of antifreeze genes from proteases in arctic & subarctic fish, which has happened independently at least a couple of times:

I believe this article is freely available online from PNAS:

Proc. Natl. Acad. Sci. USA
Vol. 94, pp. 3485-3487, April 1997

Origin of antifreeze protein genes: A cool tale in molecular evolution
John M. Logsdon Jr. and W. Ford Doolittle

http://www.pnas.org/cgi/content/full/94/8/3485

Quote

Where do new genes come from? Duplication, divergence, and exon shuffling are the expected answers, so it is especially exciting when new genes are cobbled together from DNA of no related function (or no function at all). In this issue, Chen et al. (1) describe an antifreeze glycoprotein (AFGP) gene in an Antarctic fish that has arisen (in part) from noncoding DNA. Further, they show that a very similar AFGP from an Arctic fish is the product of some completely unrelated molecular processes (2). Together, these papers shed light on a number of key issues in molecular evolution.

In the late 1960s Arthur DeVries showed that freezing resistance in Antarctic fish was due to blood serum glycoproteins that lowered their freezing temperature below that of the subzero sea surrounding them (3, 4). The ensuing years have witnessed a great deal of work on AFPs (antifreeze proteins; not all are glycoproteins) in a number of phylogenetically diverse fish species, much of it by DeVries and his colleagues (5-7), revealing a number of types differing in their structure and amino-acid composition. These proteins, despite their diversity, function in similar ways to deter ice crystal growth (7, 8). But where did they come from, and how did they arise?

Birth of a Gene

In the first of the two papers, Chen et al. (1) demonstrate that an AFGP gene from the Antarctic notothenioid Dissostichus mawsoni derives from a gene encoding a pancreatic trypsinogen. The relationship of these two genes is not simply one of duplication and divergence (9), co-option/recruitment (10), or exon shuffling (11), processes that have been appreciated by molecular evolutionists for some time now. Instead, the novel portion of the AFGP gene (encoding the ice-binding function) derives from the recruitment and iteration of a small region spanning the boundary between the first intron and second exon of the trypsinogen gene (Fig. 1). This newborn segment was expanded and then iteratively duplicated (perhaps by replication slippage or unequal crossing-over) to produce 41 tandemly repeated segments. Nonetheless, the contemporary AFGP gene retains, as its birthmark, sequences at both ends which are nearly identical to trypsinogen. Retention of the 5 end of the trypsinogen gene may be significant, since this region encodes a signal peptide used for secretion from the pancreas into the digestive tract. Chen et al. (1) hypothesize that an early version of the notothenioid AFGP gene may have had its first function preventing freezing in the intestinal fluid, with this function later expanded into the circulatory system by way of its expression in the liver.


Here is Figure 1:



Quote

Figure 1. Comparison of gene structures and their sequence similarities. The regions shown represent genomic regions encompassed by sequenced cDNAs, and are not to scale. Exons are shown as large boxes; introns are shown as thinner boxes; inferred initiation and termination codons are indicated. Untranslated regions are hatched, and regions encoding putative signal peptides are stippled. Regions in different genes that are the same color share sequence similarity, but only regions of the same color shade are homologous; dotted lines delineate regions of clear homology between Dissostichus trypsinogen and AFGP genes. The open region of the trypsinogen gene is absent in AFGP. The segment below the double-headed arrow represents expansion of a sequence element present in the Dissostichus trypsinogen gene that appears to have given rise to the canonical AFGP repeat; its subsequent tandem iteration is shown by thin dashed lines. AFGP repeats are numbered and discontinuities are indicated for presentation. Regions between the AFGP repeats (spacers; indicated as either yellow or black) are the presumed sites of posttranslational cleavage. A discontinuity in the intron Dissostichus AFGP gene is shown to represent an internal segment not present in the homologous trypsinogen gene intron.


(source)

Thanks, nic



Date: 2002/05/31 01:44:19, Link
Author: niiicholas
Interesting...scrolling down to the bottom of the PNAS article, there is a link to a Science article that cited it.  Guess what?  Plants have evolved antifreeze proteins as well:

A Carrot Leucine-Rich-Repeat Protein That Inhibits Ice Recrystallization

Dawn Worrall, Luisa Elias, David Ashford, Maggie Smallwood, * Chris Sidebottom, Peter Lillford, Julia Telford, Chris Holt, Dianna Bowles

http://www.sciencemag.org/cgi/content/full/282/5386/115

Quote

It appears that proteins have been coopted to antifreeze activity from other functions quite recently in evolution (20). In plants, pathogenesis-related proteins such as the (1-3)endoglucanase and chitinase of winter rye (5) and the PGIP-related carrot protein have been recruited. The cell wall is modified in response to both low temperature and pathogen attack (21). Because ice crystallizes in the apoplast, proteins involved in such cell wall modification are well suited for cooption into antifreeze activity if their protein structures permit.

PGIPs belong to a large family of proteins known as the leucine-rich-repeat (LRR) proteins (22). LRR proteins contain 10 to 30 repeated units of a ~24-amino acid peptide containing regularly spaced leucine residues. The carrot AFP consensus sequence is similar to the motif found in other LRR proteins (Fig. 3B). One LRR protein exhibits an unusual nonglobular protein structure with a solvent-exposed parallel  sheet (23), and this structure has been compared with the related parallel  sheet found in pectin-degrading enzymes such as pectate lyase (22). In this context, it may be relevant that fish AFPIII contains a  sheet on its presumptive ice-binding face (24) and that the AFPII ice-binding face may also contain a  sheet structure (25).

The co-option of an LRR protein into antifreeze function in carrot suggests an additional common structural feature of AFPs. Of the seven AFPs known (1, 2), four contain repeated sequences. Thus, a repetitive structure may correlate with antifreeze activity.

The carrot AFP can be stably produced in tobacco plants grown under normal greenhouse conditions. The RI properties of this protein may be useful for improving food storage and protecting crop plants against cold temperatures.


Thanks, nic

Date: 2002/05/31 21:33:37, Link
Author: Wesley R. Elsberry
I'll be on a panel to discuss "intelligent design" at CSICOP's Fourth World Skeptics Conference, June 21, 2002, in Burbank, California.

The panel will be moderated by Massimo Pigliucci.  Other panelists are Kenneth Miller of Brown University, William Dembski of the Discovery Institute's Center for Renewal of Science and Culture, and Paul Nelson, also of the DI CRSC.

My abstract for my set 15-minute presentation was printed in the conference program, so it's public knowledge now.

Quote
Title of talk: "Beyond the 'wedge': Intelligent design, science, and culture

Abstract: The "intelligent design" movement is primarily coordinated by the Discovery Institute's Center for Renewal of Science and Culture (DI CRSC). While the highest-profile activity of the DI CRSC so far has been its anti-evolutionary activism, its long-term goals are far more ambitious. As promulgated in the "wedge" document, early versions of the DI CRSC web site, and seen in the actions of the Fellows of the CRSC, no less than the re-definition of science itself is intended. Despite statements that ID is primarily a scientific research program, the fact is that  most of the effort of the CRSC Fellows is directed into political action. While scientific justification was one of the primary goals outlined in the "wedge" document, this area remains little-developed and apparently has been abandoned.  The current and projected activities of the DI CRSC indicate that the next 25 years will be filled with more confrontation with mainstream science.


Links:

CSICOP

CSICOP Fourth World Skeptics Conference

The DI CRSC "Wedge" document

I would appreciate comments on things to bring up during the panel session.

Date: 2002/06/01 21:07:55, Link
Author: Michael
Quote (Wesley R. Elsberry @ May 27 2002,08:50)
Interestingly, the population argument is not listed among those that "Answers in Genesis" recommends that YECs should not use.
Interestingly, the population argument is not listed among those that "Answers in Genesis" recommends that YECs should not use.


That is because AiG uses the argument.

Where are all the people?
Quote

What if people had been around for one million years?

Evolutionists claim that mankind evolved from apes about a million years ago. If the population had grown at just 0.01% per year since then (doubling only every 7,000 years), there could be 10^43 people today—that’s a number with 43 zeros after it. This number is so big that not even the Texans have a word for it! To try to put this number of people in context, say each individual is given ‘standing room only’ of about one square metre per person. However, the land surface area of the whole Earth is ‘only’ 1.5 x 10^14 square metres. If every one of those square metres were made into a world just like this one, all these worlds put together would still ‘only’ have a surface area able to fit 10^28 people in this way. This is only a tiny fraction of 10^43 (10^29 is 10 times as much as 10^28, 10^30 is 100 times, and so on). Those who adhere to the evolutionary story argue that disease, famine and war kept the numbers almost constant for most of this period, which means that mankind was on the brink of extinction for most of this supposed history.10 This stretches credulity to the limits.


Consider http://evolutionlie.faithweb.com/ which Sarfati apparently served as an advisor for:

Quote

30. World Population Growth Rate -- In recent times is about 2% per year. Practicable application of growth rate throughout human history would be about half that number. Wars, disease, famine, etc. have wiped out approximately one third of the population on average every 82 years. Starting with eight people, and applying these growth rates since the Flood of Noah's day (about 4500 years ago) would give a total human population at just under six billion people. However, application on an evolutionary time scale runs into major difficulties. Starting with one "couple" just 41,000 years ago would give us a total population of 2 x 10 to the89th. The universe does not have space to hold so many bodies.


One thing that you might mention is that these sort of calculations which very quickly generate impossibly high populations are an important foundation of Darwin's concept of natural selection.

Date: 2002/06/01 22:24:40, Link
Author: Michael
Sometime what a first might seem a simple question in the end can start lengthy philosophical debates and turn out not to be so simple after all.

Consider Michael Behe.  His views are often classified as a variety of evolution denial.  

There can be no doubt that he rejects the modern understanding of the process of evolution.  I believe that a convincing case has been made that he has done so due to religious motivations.  Many biologists have also taken him to task for a lack of understanding of evolutionary biology as well.  If the above is to be considered correct than Behe has a lot in common with the YEC Henry Morris whose views are clearly motivated by religious beliefs.

But Behe differs from Morris in an important way.  Behe accepts that he shares a common ancestor with a chimp.  Thus he can be said to accept some form of evolution beyond the "microevolution" only proposed by most special creationists.  So can he be said to "accept evolution"?  Should the term "evolutionist" be restricted to those who accept most mainstream scientific ideas about evolution?

Behe clearly thinks that God outright created "irreducibly complex" structures and thus arguably can be classified as a type of creationist.  (And "creationist" here is not merely being used for those who believe in some sort of creator like Theodosius Dobzhansky.)

People in the context of the evolution/creation debate have not been using terms like "evolutionist" or "creationist" in the same way.  This can often result in misunderstandings or talking past each other.  It would be a good thing if some some sort of understanding of where to draw the lines in the sand.

So who is an evolutionist?
Who is a creationist?
Who is an anti-evolutionist?

One might note that this sort of arguments can considered analogous to the splitter-lumper debates in systematics.  Sometimes sensu lato or sensu stricto are added to a name of a taxon to make it clear if that taxon is being defined as a splitter would define it or as a lumper would define it.  So maybe if agreement is not readed we can say that Behe is an evolutionist s.l. but not an evolutionist s.s.  That would be a fairly ugly "solution."

Date: 2002/06/03 21:54:07, Link
Author: rafe gutman
IDists like to complain that they are being treated unfairly, that their ideas are being dismissed without being considered or discussed.  that may be a fair complaint, but when these very same IDists abuse any display of open-mindedness made by members of the scientific community, they absolve their right to complain.  i'd like this thread to be a place where ID critics can post examples of IDists confusing open-mindedness with support.

one example of this is when IDists use book sales as an indicator of the success of ID.  considering that an individual has to first buy the book in order to read it, it doesn't necessarily mean that they will then agree with the arguments presented within.  on that note, it is interesting what IDists consider to be an endorsement of their work.  consider this one, which is printed on the dust jacket of no free lunch:
Quote
I disagree strongly with the position taken by William Dembski. But I do think that he argues strongly and that those of us who do not accept his conclusions should read his book and form our own opinions and counter-arguments. He should not be ignored.

Michael Ruse, Lucyle T. Werkmeister Professor of Philosophy, Florida State University; editor of Biology and Philosophy; author of Monad to Man and many other books on Darwinism


IDists have even tried to spin disagreement in their favor:
Quote
"If we're generating such strong, visceral responses, we must be doing something right." william dembski


so even if a scientist disagrees with ID, they interpret that to mean that ID is taken seriously.

i'd like to keep this thread open to more quotes and examples of how IDists have preyed upon the open-mindedness of scientists and perverted their comments to support ID.

Date: 2002/06/04 16:32:54, Link
Author: Glenn Branch
Note that in the March 14, 2002, Washington Times, Behe is quoted as now rejecting theistic evolution: "ID differs not only from creationism but a third option, theistic evolution, which says God employed the Darwinian process. Behe says that concept is 'no threat to Christian beliefs' and he once agreed with it, but it isn't supported by the biological evidence." The article in question is reproduced at the ARN site here; look in the sixth paragraph from the bottom.

Date: 2002/06/04 16:45:54, Link
Author: Lizard
I'd be interested to hear what "evidence" Behe thinks rules out theistic evolution. If he's talking about "irreducible complexity," I don't see how that -- or anything, for that matter -- could rule out God's involvement in the diversification of life on earth.

Date: 2002/06/07 17:01:12, Link
Author: Glenn Branch
Behe is presumably rejecting the evolution (or the Darwinian) component of theistic evolution, not the theistic component, on what he takes to be empirical grounds.

Date: 2002/06/11 00:44:21, Link
Author: niiicholas
This thread is for accumulating examples of cooption/change of function from the literature, and citations of the importance of this process in the literature.

The purpose of examining this is that Behe and Dembski both fail to give cooption the attention it absolutely deserves.  In particular the occurence of cooption disproves Behe's IC argument.

Thanks, nic

Date: 2002/06/11 01:03:11, Link
Author: niiicholas
I was struck by this passage from Maynard Smith's The Theory of Evolution.  It almost sounds like it was written to respond to Behe, except that it was written in 1958 (I think; I have the 1993 Canto edition which is the fourth edition):

Discussing the origin of feathers, Maynard Smith writes  (pp. 303-304):

Quote

This example will help to explain one of the difficulties often encountered in explaining evolution in terms of natural selection.  It often seems that a perfected organ, although efficient at performing its function, is far too complex to have arisen by one or a few mutations, and yet is such that any intermediate stage between the absence of the organ and its full development would be incapable of performing this function. Thus it is inconceivable that the flight feathers of a bird could have arisen by a single mutation, but the intermediate stages between a scale and a feather would be useless for flight.  In this case the difficulty disappears once it is realized that during the early stages of the evolution of feathers, the latter were probably of selective advantage because they conserved heat, and only later did they become functional in flight.

This is a very common feature of evolution; a new structure evolves at first because it confers advantage by performing one function, but in time it reaches a threshold beyond which it can effectively perform a different function. We saw earlier that something of this kind occurred during the evolution of the elephant's trunk.  The flying membranes of bats and of pterodactyls were probably used in gliding before they were of any use in flapping flight, and, as Spurway has pointed out, small membranes along the sides of the body are found in some arboreal mammals which do not even glide, and these folds of skin render such animals more difficult to see by eliminating the shadows they would otherwise case.  Similarly, lungs were a selective advantage to fish living in stagnant waters, enabling them to breathe air, long before the descendants of these fish walked on land; in modern teleost fishes the lung has lost its function as a breathing organ, and has been transformed into a hydrostatic organ, the swim bladder.  These examples show that there is no reason to suppose that even the most complex structures underwent a long period of evolution and elaboration before they could function, and so confer selective advantage; rather their function may have changed once or even several times in the course of evolution.


(bold added)

This long-standing hypothesis regarding the origin of feathers has been strengthened by recent discoveries of fossil dinosaurs with non-flight feathers.  E.g. the fantastic pictures here:

http://research.amnh.org/vertpaleo/dinobird.html

E.g.:





Date: 2002/06/11 01:24:42, Link
Author: niiicholas
Found this key Darwin quote on the ISCID forum:

Chapter 6 of Origin of Species

Here is the link:
http://www.talkorigins.org/faqs/origin/chapter6.html

Note especially how closely Darwin ties the change-of-function argument to his "organs of extreme perfection" line which is so often quoted by antievolutionists.  Why don't they ever acknowledge that Darwin himself listed numerous cases of homologous structures being adapted for wildly different functions?

Quote

If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case. No doubt many organs exist of which we do not know the transitional grades, more especially if we look to much-isolated species, round which, according to my theory, there has been much extinction. Or again, if we look to an organ common to all the members of a large class, for in this latter case the organ must have been first formed at an extremely remote period, since which all the many members of the class have been developed; and in order to discover the early transitional grades through which the organ has passed, we should have to look to very ancient ancestral forms, long since become extinct.

We should be extremely cautious in concluding that an organ could not have been formed by transitional gradations of some kind. Numerous cases could be given amongst the lower animals of the same organ performing at the same time wholly distinct functions; thus the alimentary canal respires, digests, and excretes in the larva of the dragon-fly and in the fish Cobites. In the Hydra, the animal may be turned inside out, and the exterior surface will then digest and the stomach respire. In such cases natural selection might easily specialise, if any advantage were thus gained, a part or organ, which had performed two functions, for one function alone, and thus wholly change its nature by insensible steps. Two distinct organs sometimes perform simultaneously the same function in the same individual; to give one instance, there are fish with gills or branchiae that breathe the air dissolved in the water, at the same time that they breathe free air in their swimbladders, this latter organ having a ductus pneumaticus for its supply, and being divided by highly vascular partitions. In these cases, one of the two organs might with ease be modified and perfected so as to perform all the work by itself, being aided during the process of modification by the other organ; and then this other organ might be modified for some other and quite distinct purpose, or be quite obliterated.

The illustration of the swimbladder in fishes is a good one, because it shows us clearly the highly important fact that an organ originally constructed for one purpose, namely flotation, may be converted into one for a wholly different purpose, namely respiration.

[note: Darwin gets this one backwards, Maynard-Smith's version is the currently accepted one]

[...]

In considering transitions of organs, it is so important to bear in mind the probability of conversion from one function to another, that I will give one more instance. Pedunculated cirripedes have two minute folds of skin, called by me the ovigerous frena, which serve, through the means of a sticky secretion, to retain the eggs until they are hatched within the sack. These cirripedes have no branchiae, the whole surface of the body and sack, including the small frena, serving for respiration. The Balanidae or sessile cirripedes, on the other hand, have no ovigerous frena, the eggs lying loose at the bottom of the sack, in the well-enclosed shell; but they have large folded branchiae. Now I think no one will dispute that the ovigerous frena in the one family are strictly homologous with the branchiae of the other family; indeed, they graduate into each other. Therefore I do not doubt that little folds of skin, which originally served as ovigerous frena, but which, likewise, very slightly aided the act of respiration, have been gradually converted by natural selection into branchiae, simply through an increase in their size and the obliteration of their adhesive glands. If all pedunculated cirripedes had become extinct, and they have already suffered far more extinction than have sessile cirripedes, who would ever have imagined that the branchiae in this latter family had originally existed as organs for preventing the ova from being washed out of the sack?


(bold added)
Thanks, nic



Date: 2002/06/11 05:07:37, Link
Author: niiicholas
Now, to show that cooption is not only well-known to the old and grey (or dead), but is very much a concept in modern use:

Consider this article:

Quote

link

Trends Genet 2001 Mar;17(3):120-3
Were protein internal repeats formed by "bricolage"?

Lavorgna G, Patthy L, Boncinelli E.

DIBIT, Istituto Scientifico H. S. Raffaele, Via Olgettina 60, 20132 Milan, Italy. giovanni.lavorgna@hsr.it

Is evolution an engineer, or is it a tinkerer--a "bricoleur"--building up complex molecules in organisms by increasing and adapting the materials at hand? An analysis of completely sequenced genomes suggests the latter, showing that increasing repetition of modules within the proteins encoded by these genomes is correlated with increasing complexity of the organism.



The introduction reveals just how far the IDists are from the biologists on understanding the origins of new genetic information and new functions:

Quote

Evolution has brought about the formation of organisms of increasing complexity. This process involved mechanisms, such as exon-shuffling [1] and gene duplication, [2] that increased intermolecular duplications of the more sophisticated proteomes. For example, gene duplication contributed to the origin and evolution of vertebrates, which appear to possess several copies of an ancestral set of genes. [3] A single gene in flies usually has three or four paralogous genes in mammals, and this spare genetic capacity has permitted new possibilities, allowing the acquisition of new biochemical functions and expression capabilities. [4]

More than two decades ago, when only a handful of eukaryotic genes were cloned, Francois Jacob had already envisioned some of these basic evolutionary mechanisms. [5] In fact, he argued that evolution could work as a tinkerer, rather than an engineer, implying that evolutionary processes construct things with the materials at hand and the outcome bears the constraints imposed by those materials. [6] Translated into molecular terms, the raw materials are the existing set of genes, which can be, in part or entirely, elaborated again and redeployed to a new function during evolution. Extending to Jacob's view of `recyclement' of biological material, we investigated systematically the possibility that, besides the increase of inter-molecular duplications, an increase of intra-molecular duplications accompanied the evolution of proteins.

We decided to look for repeated protein modules, as opposed to short, low-complexity sequence repeats (i.e. runs of Qs, STSTSTSTS, etc) because, in several instances, modules of proteins are used to build the function of many multidomain proteins. As a result, we found, with a few exceptions, that:

1. There is a correlation between the complexity of functions controlled by the proteome of a given organism and its degree of internal repetitiveness.

2. The above correlation is often observed both for interdomain comparisons (e.g. archaeal proteins have, on average, more internal repeats than bacterial ones) and intradomain comparisons (e.g. human proteins have more internal repeats than those belonging to Drosophila melanogaster).

3. We also detected a decrease in the number of internal repeats following `reductive' evolution, in which the biological complexity of an organism is lower than that of its ancestor (occurring in, for example, endosymbiotic organisms).

A previous paper by Marcotte et al [7]., reported an analysis of 16 completely sequenced genomes (11 bacterial, four archaeal and one eukaryal), in which eukaryotic proteins displayed significantly more repeats than procaryotic ones. This study, which considered repeats containing both low-complexity and high-complexity sequences, was somewhat hindered by the availability of completely sequenced genomes ¯ then relatively scarce. In fact, some of the conclusions we reached are fairly subtle. For example, the increase of the protein repetitiveness from Bacteria to Archaea involves only small percentage changes, possibly because the trend was coupled with the massive gene exchange that occurred later in the microbial world. [8] A sufficiently high number of sequences needed to be analyzed to make our observations significant.

[& towards the end]

5. Mechanisms involved in intramolecular duplication
What mechanisms could have caused or favored the phenomenon of the increase of intramolecular duplications during evolution? There is a strong evidence for the involvement of intronic recombination and exon shuffling in the occurrence of gene insertions. [19] Intriguingly, we found the highest level of intramolecular duplications within high eukaryotic genomes, like C. elegans, D. melanogaster and Homo sapiens, whose genes are characterized by the presence of large numbers of exons and introns. [19] The invention of modular proteins could have been the mysterious force driving the acceleration of evolution and leading to a spectacular burst of evolutionary creativity ¯ the `Big Bang' of metazoan evolution ¯ that caused the sudden appearance of several phyla of animals with different body plans during the Cambrian period. [19]

Archaeal proteins, although belonging to intronless organisms, were found to possess, on average, a higher repetitiveness than the relatively less-evolved bacterial ones. Studies on the evolution of multidomain prokaryotic proteins have given insights on how they may be constructed without the assistance of introns. For example, a modular protein of Peptostreptococcus magnus is the product of a recent intergenic recombination of two different types of streptococcal surface protein. [20] Also, gene rearrangements can be facilitated by the presence of special recombinogenic DNA sequences in intermodule linker regions. [21] It has been proposed that an evolutionary bottleneck, such as the increased selective pressure given by the presence of antibiotics, could favor the creation of these advantageous chimeras. [21] A similar or identical environmental challenge could have been the stimulus directing the rapid evolution of new bacterial proteins and leading to the formation of the archaeal domain.

6. Conclusion
The data reported here, although suggestive, need to be extended. This will be possible when some more of the several genome sequencing projects currently underway are completed. However our results provide another indication that biological evolution works like a tinkerer, "who does not know exactly what he is going to produce, but uses whatever he finds around him whether it be pieces of string, fragments of wood, or old cardboards; in short, it works like a `bricoleur' who uses everything at his disposal to produce some kind of workable object". [5]

[...]

5. F. Jacob, Evolution and tinkering. Science 196 (1977), pp. 1161¯1166.

6. F. Jacob, Molecular tinkering in evolution. In: D. Bendall, Editor, Evolution from Molecules to Man, Cambridge University Press (1983), pp. 131¯144.

Date: 2002/06/11 05:41:00, Link
Author: niiicholas
Following the tangent of the evolution of repeats *within* protein sequences:

Quote

Protein Repeats: Structures, Functions, and Evolution  

pp. 117-131 (doi:10.1006/jsbi.2001.4392)  

Miguel A. Andrade*, ,  Carolina Perez-Iratxeta*, ,  Chris P. Ponting  

Internal repetition within proteins has been a successful strategem on multiple separate occasions throughout evolution. Such protein repeats possess regular secondary structures and form multirepeat assemblies in three dimensions of diverse sizes and functions. In general, however, internal repetition affords a protein enhanced evolutionary prospects due to an enlargement of its available binding surface area. Constraints on sequence conservation appear to be relatively lax, due to binding functions ensuing from multiple, rather than, single repeats. Considerable sequence divergence as well as the short lengths of sequence repeats mean that repeat detection can be a particularly arduous task. We also consider the conundrum of how multiple repeats, which show strong structural and functional interdependencies, ever evolved from a single repeat ancestor. In this review, we illustrate each of these points by referring to six prolific repeat types (repeats in -propellers and -trefoils and tetratricopeptide, ankyrin, armadillo/HEAT, and leucine-rich repeats) and in other less-prolific but nonetheless interesting repeats.

http://www.idealibrary.com/servlet/citation/1047-8477/134/117

pubmed

[...see especially the ribbon models in this paper]

CONCLUSIONS
Our survey of protein repeats has highlighted the multifunctionality of repeat types, their structural
differences, and their proliferations in different evo-lutionary
lineages. One likely reason for their evo-lutionary success is that repeat-containing proteins are relatively “cheap” to evolve. By this we mean that large and thermodynamically stable proteins may arise by the simple expedient of intragenic du-plications, rather than the more complex processes of de novo a-helix and b-sheet creation. This is sup-ported by the larger sizes of most repeat-containing
structures relative to compact domains (Fig. 4).

This does not, of course, present a complete an-swer
to their success since it addresses the question of how repeat-containing proteins arose, rather than why they have been selected for and fixed in evolu-tionary lineages on so many separate occasions. As suggested throughout this review, the reasons for the functional successes of repeat classes may be a proclivity of repeat assemblies to acquire different molecular functions, namely, the association with
different protein ligands. This, in turn, might be associated with the large solvent-accessible surface areas, presented by extended “open” assemblies, that are available for interactions with ligands. This is because burial of nonpolar residues at protein–protein interfaces is thought to be an important contributor to heterodimer stability (Tsai et al.,
1997).

In understanding the evolution of repeats, one major problem remains. Repeats are defined as oc-curring multiply, and all repeats in a family are homologous. This means that these repeats all evolved from a common ancestor, which necessarily must have contained only a single repeat. This is
apparently contradictory, since it is not expected that a single repeat could exist in isolation, as a single folded functional unit. Rescue is at hand if one suggests that the family’s common ancestor indeed represented a single repeat, but one that formed homooligomers. The homooligomeric structure of the ancestor might mirror that of the intrachain repet-itive structure of its modern homologue, except in its multichain character. This scenario has recently been suggested for the evolution of the b-trefoil fold (Ponting and Russell, 2000).

A problem with this proposal is that there are few, if any, known examples where homologous multire-peat assemblies are formed both from oligomers of single repeats and from a single chain of multiple repeats. However, this might not be too surprising since the highly cooperative process of folding a mul-tirepeat protein must be significantly more favor-able
than folding a homooligomeric protein from its constituent monomers. This is because the kinetic folding pathways of multirepeat protein structures may be nucleated at many positions. In this way ancient oligomeric single repeat proteins might have been driven to extinction by their monomeric multi-ple repeat-containing homologues.


There is an interesting analogy here to the "serial homology" concept in traditional organismal evolution -- e.g. the duplication and specialization of segments.  The same idea -- duplication and divergeence -- appears to occur on several different molecular levels, to wit:

- duplication of segments of a protein, followed by rapid divergence (the above paper)

- taking a homodimer, homotrimer, etc., duplicating the gene, and then specializing each gene in the e.g. heterodimer.  This is yet another way to produce IC by the way

- traditional gene duplication

- duplication of whole chromosomes/genomes -- many chunks will decay but some may get new functions.

All this could be treated in much more detail.  However, antievolutionists consistently fail to realize the importance of duplication, and write as if it didn't exist.  E.g., John Bracht's recent post to metanexus:

Quote

Knotty Pine and Corroding Coins: John Bracht

link

For concreteness, consider an example. Think of a man-made outboard motor. This system contains many of the same structures found in the bacterial flagellum: a motor (including stator, rotor, and acid-powered drive), drive shaft, u-joint, and propeller. Now, imagine starting with a basic rowboat and trying to evolve an outboard motor via the co-optation model. Perhaps, somehow, the metal outer skin of the boat peels up in the back and this forms a useful rack for a fishing pole, and is available to provide the internal support and external protective casing for the motor. Perhaps a support rod works loose from the hull and is available to be made into a drive shaft. But how do we move on from here to build up the motor, in functional steps, from existing parts? The problem is this: the various parts are already adapted to their old functions. To build an outboard motor, the old functions must be replaced by new functions. New functions require modifications of the old parts, and since the motor system doesn't work until all the parts are assembled, we inevitably need a large amount of coordinated change in various components before we can build the new system. For instance, the peeled-away metal on the back (previously adapted to form a watertight hull) will have to undergo extensive modification, including careful bending or shaping, and drilling holes in appropriate places to support motor components (all without letting the hull become leaky). The support rod from the hull, destined to become the drive shaft, will also need modification for attaching gears and the universal joint (and the removal of the support rod must not weaken the structural integrity of the boat). And so on.


IMO there is a clear assumption here that we are dealing with *one* copy of everything, that the old function is lost as the new function is gained.  But just ain't so...

nic

Date: 2002/09/05 10:03:05, Link
Author: Wesley R. Elsberry
Check out the Pensacola News Journal "For The Record" page.

Search for "hovind".  The mention is in the "felony arrests" section.

Wesley

Date: 2002/09/05 20:37:59, Link
Author: pzmyers
Should we rejoice that one of the enemies of rational thought is continuing his process of self-destruction, or feel regret that we might lose a clown who makes creationism look even more ridiculous than it already is?

Date: 2002/09/05 22:11:31, Link
Author: Lizard
You sure this is our Dr. Dino? Assault, battery and burglary doesn't sound like his style. Where did you find out he assaulted one of his tenants? Where are the details?

Date: 2002/09/05 22:32:53, Link
Author: pzmyers
Quote (Lizard @ Sep. 05 2002,22:11)
You sure this is our Dr. Dino? Assault, battery and burglary doesn't sound like his style. Where did you find out he assaulted one of his tenants? Where are the details?

There are some details here.

Date: 2002/09/06 09:34:28, Link
Author: anapsid
You may access the whole Hovind "rap sheet" at
<http://205.152.130.8/cv_web_1.asp?ulname=Hovind&ufname=Kent&ucasetype2=&ucase=&ucit=&ufromdate=&utodate=&ucasetype=>

Watch the "wrap"

Also, in reading the messages from Internet Infidels - I note that Paul Jewell, the "witness" that said Hovind was just standing there - is married to "Marlissa", Hovind's scheduling secretary.  Marlissa is also Hovind's daughter, making Jewell a son-in-law.

Date: 2002/09/06 10:18:56, Link
Author: Wesley R. Elsberry
To avoid the cut-and-paste job, here is a link to the Escambia County Clerk of the Court record for Kent E. Hovind.

You can follow the links from that document to see progress in the case, or any additional legal interactions that may arise between Hovind and Escambia County.

Date: 2002/09/06 10:26:19, Link
Author: Wesley R. Elsberry
The Escambia County Property Appraiser has online searchable records.  When one searches for "Hovind Kent", one finds these results.  It is interesting that the property where Hovind was arrested does not appear in this list.

Date: 2002/09/06 10:59:59, Link
Author: pzmyers
Quote (anapsid @ Sep. 06 2002,09:34)
You may access the whole Hovind "rap sheet" at
<...>

Just http://205.152.130.8/cv_web_1.asp?ulname=Hovind&ufname=Kent is adequate.

Date: 2002/09/06 16:08:22, Link
Author: Dr.GH
The arrest was reported at Cummings St.  The arrest report indicated 100 Cummings, but this may be an error.  100 Cummings Rd is owned by WEAVER, BARRY D JR, apparently unrelated.   FAITH FELLOWSHIP BAPTIST CHURCH,  HOVIND KENT TRUSTEE, owns 2 lots on Cummings Rd 21, and 23.

Dr. Dino also owns quite a bit of N PALAFOX HWY, where JEWELL, PAUL DAVID (Witness, employee, and Son in law?) just happens to live; listed as 5270 N PALAFOX ST PENSACOLA in the arrest report.

Date: 2002/09/07 07:33:29, Link
Author: Wesley R. Elsberry
An Indianapolis Star editorial by Andrea Neal shows that the Discovery Institute's "Center for (the Renewal of) Science and Culture"'s propaganda machine continues to bamboozle the credulous public.

Neal buys into several falsehoods told by the DI C®SC.  First and foremost, Neal seems to think that there is some scientific content to "intelligent design" claims.  Second, Neal asserts ID represents cutting-edge science rather than warmed-over nineteenth century apologetics.  Third, Neal buys the tale that there is no religious component to the ID movement.

The question to pose to those who think that "intelligent design" is science is to ask where the science is.  The only things cited by Neal add up to critiques of the sufficiency of current natural explanations.  There is nothing beyond assertion that ID has any role whatever in accounting for biological complexity.  I've asked some of the "scientists at top institutions" that Neal refers to for a progress report on the ID community making a positive case for ID conjectures, and in each instance have received answers that translate into an admission of "no progress" since 1997.

The assertion that there is any "cutting edge" to the ID wedge fails the most cursory examination of the evidence.  Phillip Johnson's original ID tome, "Darwin On Trial", simply goes to show that there is hardly an antievolution chestnut that he doesn't like.  Many of the favorites of the young-earth creationist movement are happily recycled by Johnson.  The whole "irreducible complexity" edifice erected by Michael Behe is simply a more technical gloss on the ancient "what good is half a wing" canard common in YEC circles.  Behe's innovation resides in locating systems in which there is both a paucity of evidence and no expectation that further evidence bearing on the origin of the structures will be forthcoming.  That's a prerequisite for any argument from ignorance that is expected to hold up over time.  But the central part of ID argumentation can be traced to the Reverend William Paley's arguments made in 1802.  The scientific community actually did take up such arguments and examine them seriously -- and decided that they did not fit the evidence.  ID is not "cutting edge".  At best, it's "reheated leftovers".

Neal asserts that skeptics cannot show any religious underpinnings of ID in court because ID is "a scientific possibility".  Neal is obviously ignorant of the massive paper trail left by the "scientists at top institutions" of the DI C®SC concerning the goals and motivations of the ID movement, most succinctly expressed in the famous "Wedge" document.  This will be one of the easiest tasks for skeptics to accomplish in court, not one of the hardest.

Neal's innovation in the editorial is to characterize opposition to the ID movement as "anti-religious".  This, of course, is bunk.  Plenty of religious people are part of the community of skeptics of ID.  The panelists at the recent CSICOP Fourth World Skeptics Conference session on evolution and intelligent design included two ID advocates and two ID skeptics, all Christian believers.

Neal ends with this:

Quote
Teaching intelligent design to our children is gaining strength too, as it should. Students need to know the latest research about how it all began, even if it points to an all-knowing creator.

It would be a sad irony to let Darwin write the final chapter because we fear where science might lead us.


Why should a set of religiously-motivated conjectures based solely upon negative argumentation and wishful thinking be taught to students as if it were "research"?  Why should students be given the mistaken impression that such conjectures represent the "latest" in scientific thinking, when in fact various components of these arguments can be traced back decades or centuries?

But the capping irony is the construction of Neal's final sentence.  Science should lead, all right, and it is precisely because the politics of the ID movement lead it rather than the science that we should reject these premature moves to force ID into school science curricula.  Let ID prove itself in the marketplace of scientific ideas, and then it will be ready for inclusion in science education.  It is not there yet, and even ID advocates say that they are just beginning now to see glimmers of the formation of an ID research program.  The unseemly haste with which the ID advocates push for inclusion of their untested and unresearched claims into school curricula bespeaks an unscientific attitude, one more similar to a salesman trying to offload stock that is past its sell-by date.  Something smells fishy in that.

Date: 2002/09/08 19:46:24, Link
Author: Lizard
Once again, a misinformed journalist equates evolutionary science with "origins science," a term invented by creationists to give the impression that evo is all about how life originated. Every single time this canard comes up, it needs to be debunked.

Wesley, your post here is eloquent. I hope you sent it to Ms. Neal.

Date: 2002/09/16 07:46:44, Link
Author: Wesley R. Elsberry
William Dembski comments upon the paper John Wilkins and I wrote last year:

Quote
(1) Then why not withhold judgment in the Contact example and simply attribute a long sequence of prime numbers from outer space to unknown causes? The problem is that Wilkins and Elsberry's revised filter scotches all design inferences and not just the ones they don't like in biology. For the ID critic, the answer is not to revise the filter but to try to substitute a different picture of scientific rationality (e.g., Sober's likelihood approach). But that is deeply problematic itself.

(2) With regard to false positives, to say that the design filter does not commit false positives if there is specified complexity remains true. And to say that an attribution of specified complexity may be mistaken is also true -- and not inconsistent with the latter claim. There's a difference between specified complexity as it subsists in nature and our knowledge of it. You might want to reread my post about what sort of property is specified complexity.  


Thread on ISCID Brainstorms board

Dembski is incorrect in his assertion in (1).  Our revised filter does not eliminate all design inferences.  We went to some trouble to distinguish two classes of design inferences, ordinary and rarefied.  Ordinary design inferences are still just as valid as they ever were under our revised filter.  But the revised filter makes it clear that the epistemic warrant for rarefied design inferences is an illusion based upon invalid analogy to ordinary design inferences.

I find the point of (2) to be exactly what I've forwarded as a critique in the past, notably in my presentation at the "Interpreting Evolution" conference in 2001.  I have not been shy in saying before that Dembski's explanatory filter/design inference (EF/DI) is only reliable in the sense Dembski gives when one has complete knowledge, i.e., the true causal history is already known.  In that case, one has no need for Dembski's EF/DI -- it's entirely superfluous.  It is only in the case of limited knowledge that false positives become an issue, but these cases are also the only ones where Dembski's EF/DI could possibly have any utility.

It's nice to have Dembski confirm that I was right in making that critique.

Date: 2002/09/18 03:38:03, Link
Author: Wesley R. Elsberry
William Dembski has offered a very interesting piece concerning what he believes needs to be demonstrated to show that natural selection is a sufficient causal explanation for some system.  See it on the ISCID Brainstorms board.

The basic gist is relatively straightforward, though the notation looks a bit overblown.

Dembski starts with an analogy to demonstrating common ancestry of two lineages X and Y, whose initial states X_0 and Y_0 are actually the single common ancestor of all derived X_n and Y_n.   Dembski asserts:

Quote
In the best circumstance, each such X(i) and Y(j) must be explicitly exhibited and any arrows of causation connecting two organisms must produce small incremental changes that are highly probable on the basis of the Darwinian selection mechanism. The more intermediates that are missing from this picture and the more handwaving and just-so story-telling to describe the arrows of causation, the more problematic the evolutionary explanation.


It should be noted that common ancestry is not dependent upon the mechanism of natural selection being operative at every step, or indeed at any step.  Dembski's scenario completely ignores the evidence of molecular biology in applying sequence comparisons, which is largely based upon the evidence of the X_n and Y_n extant organisms, rather than X_0, Y_0, or any intermediates, since the molecular data from long extinct organisms is generally not available for anlaysis.  Nor does natural selection eschew incorporation of "large" changes, should such change have an adaptive advantage for the bearer.  It is well-developed in the evolutionary literature that "small" changes are more likely to have an adaptive advantage than "large" changes, and thus we should expect more "small" changes to be observed in lineages undergoing selection.  But that doesn't limit natural selection to *only* using "small" changes, as Dembski seems to imply above.  These departures Dembski takes from the biological reality of inferring common ancestry of lineages suggest that Dembski's approach is problematic.

As G.G. Simpson pointed out, intermediates are always missing, except where they are found.  Let me point out  what should count as a non-problematic example of common ancestry of two lineages, Globigerinoides trilobus and Orbulina universa.  A very good plate appears in the paper by Pearson et alia.

Quote
Pearson, P.N.; Shackleton, N.J.; and Hall, M.A., 1997.  Stable isotopic evidence for the sympatric divergence of _Globigerinoides_trilobus_ and _Orbulina_universa_ (planktonic foraminifera).  Journal of the Geological Society, London, v.154, p.295-302.


Figures from this paper are reproduced on the web in this page by Don Lindsay.

Pearson et alia adduce other evidence than what Dembski has offered in his argument.  They examine stable isotopic evidence to show that the divergence of G. trilobus into O. universa occurred sympatrically.  This also has a bearing on the sufficiency of the evolutionary account of common ancestry of these two species.  Notably, though, Pearson et alia do not invoke natural selection as the sole mechanism of change in this divergence.  The fact of the divergence is an issue separate from the underlying mechanism.

Dembski's underlying analogy for the remainder of his argument concerning the sufficiency of evolutionary explanations for IC systems excludes relevant classes of evidence, unnecessarily invokes a particular process as needed to be demonstrated, and ignores actual biological practice in showing common ancestry of lineages.  This, to say the least, is an inauspicious beginning for the remainder of his argument.

Date: 2002/09/21 13:06:12, Link
Author: niiicholas
This thread is for accumulating

(1) Assertions
(2) Links to articles
(3) Facts

...regarding the question "where do peppered moths rest during the day".  The importance of this topic lies in that many have argued that peppered moths don't rest where Kettlewell thought they did, and that therefore his experiments were invalid, and that therefore the entire peppered moth bird-predation-theory is without support.  Or something.

Another avenue taken by Jonathan Wells in particular is the "this means that textbook photos of moths are fake and a fraud has been committed on students" avenue.  I suggest that we collect pictures that we can find on the web, with comments on the source (if we can find 'em), whether or not they are staged (if known), with a goal of getting a sense of whether or not textbook pictures are misleading.

nic



Date: 2002/09/21 13:15:43, Link
Author: niiicholas
An initial list of Wells utterances on moths and tree trunks:

Quote
...peppered moths don't even rest on tree trunks
[Jonathan Wells,  Icons of Evoluton, p.140]


Quote
Peppered moths don't rest on tree trunks
[Icons of Evoluton, p. 148 (section heading)]


Quote
...peppered moths do not normally rest on tree trunks
[Icons of Evoluton, p. 149]


Quote
the fact that peppered moths do not rest on tree trunks...
[Icons of Evoluton, p. 153]


Quote
Peppered moths do not rest on tree trunks in the wild.
[Icons of Evoluton, p 260 (suggested textbook warning label)]
   

Quote
4) In the 1980's, several researchers showed independently that peppered moths do not rest on tree trunks in the wild.
[Jonathan Wells, http://www.calvin.edu/archive/evolution/199903/0348.html ]


Quote
BUT EVERYONE, INCLUDING MAJERUS, HAS KNOWN SINCE THE 1980'S THAT PEPPERED MOTHS DO NOT REST ON TREE TRUNKS IN THE WILD
[Calvin debate, http://www.calvin.edu/archive/evolution/199903/0348.html ]


(courtsey KC)

Date: 2002/09/21 13:26:13, Link
Author: niiicholas
This thread is for accumulating links on Judith Hooper's recent book Of Moths and Men.

We might as well start with the link to the book:

Of Moths and Men at amazon.com

Most reviews of the book are positive, but my is not.  Mine, posted at amazon.com:

Quote
Hooper gets the science wrong, August 27, 2002

Reviewer: ntamzek (see more about me) from Santa Barbara, CA United States


The fundamental rule of science journalism should be "first, get the science right". Unfortunately, Hooper's book is marred by One Big Mistake: namely, Hooper misrepresents the state of the scientific question on Kettlewell's explanation for industrial melanism in the peppered moth, namely differential predation by birds against moth morphs more or less cryptic in polluted woodlands. Reading Hooper's book, one would think that this thesis, what I call the "Bird Predation Theory" (BPT), was on the rocks. But this just ain't so -- if we read peppered moth researcher Michael Majerus' (2002) book Moths, we find him writing on page 252,

========
[E]very scientist I know who has worked on melanism in the Peppered moth in the field still regards differential predation of the morphs in different habitats as of prime importance in the case. The critics of work on this case and those who cast doubt on its validity are, without exception, persons who have, as far as I know, never bred the moth and never conducted an experiment on it. In most cases they have probably never seen a live Peppered moth in the wild. Perhaps those who have the most intimate knowledge of this moth are the scientists who have bred it, watched it and studied it, in both the laboratory and the wild. These include, among others, the late Sir Cyril Clarke, Professors Paul Brakefield, Laurence Cook, Bruce Grant, K. Mikkola, Drs Rory Howlett, Carys Jones, David Lees, John Muggleton and myself. I believe that, without exception, it is our view that the case of melanism in the Peppered moth still stands as one of the best examples of evolution, by natural selection, in action.
========

Hooper, however, presents the peppered moth case as if it were falling apart, a story which of course the press reviews have uncritically repeated.

Hooper's hero in the book is the one critic of the bird predation thesis who is actually a moth expert, Ted Sargent, although even here Sargent is actually an expert on an entirely different family of moths (the Underwings, e.g. Catocala) and has done almost no work on peppered moths. Hooper, however, gives Sargent a huge platform and gives his numerous critics, and their published rebuttals to Sargent, very short shrift. Hooper portrays Sargent as a lone rebellious American taking on the dogmatic British establishment, but of course American peppered moth researcher Bruce Grant, who supports the BPT and has done numerous studies on peppered moths specifically, is not given the same chance to make his case.

As for Sargent's actual arguments against the bird predation thesis, both Bruce Grant and Laurence Cook wrote articles rebutting Sargent's critique, but Hooper gives Cook's article merely a brief brush-off in a paragraph, completely ignoring, for example, Cook's statistical analysis of all the previous peppered moth experiments, proving a correlation between moth fitness and morph frequency with a >99% confidence. This was a direct rebuttal to Sargent's most important argument, that the statistical support for the bird predation thesis was weak, but Hooper doesn't deal with it directly like she should if she is going to advocate an alternative view.

Hooper does come up with a few arguments that not even the creationists have proposed -- most importantly, that Kettlewell faked his results, or almost as bad, unconsciously mislead himself. This is despite the fact that the predation and mark-release-recapture experiments have been repeated by other researchers and have in the main confirmed his results (see the articles by Cook, Grant, and the books by Majerus 1998 and 2002 for detailed reviews). The most astounding passage in Of Moths and Men occurs when Hooper spends a paragraph "squinting" at the tables in Kettlewell's paper, and she notes that Kettlewell's moth recapture numbers increase suddenly on July 1, 1953. The implication is that Kettlewell fudged things somewhere.

But a modicum of investigation shreds Hooper's fraud hypothesis. What Hooper fails to look at seriously was that when Kettlewell released more moths, he recaptured more. Kettlewell started releasing far more moths on June 30th, and started catching far more moths on the morning of July 1st. In fact, when one does a linear regression, one discovers that "number of moths released" explains 80% of the variance in "number of moths recaptured". This is a nice strong linear relationship. Fraud is not a necessary explanation. Why didn't Hooper realize the obvious answer? Later in the book, Sargent keys off the same change in numbers, and he too mysteriously ignores the obvious explanation -- as in most of the book, Sargent's word is taken as gospel and is substituted for rigorous scientific evaluation.

In addition to the major issues discussed above, Hooper's book is peppered with small but disturbing mistakes of logic and science; there is a particularly nasty one about genetics that shows up Hooper's amateurishness (and frankly, that of her editors and glowing reviewers) rather blatantly. I will, however, leave these as exercises for future reviewers to acknowledge or not, so that readers of the reviews may distinguish the critical thinkers from the whatever-a-science-journalist-says-must-be-true types.

The peppered moth story is an awfully good story; but just as this doesn't make it true, it doesn't make it too good to be true either. Hooper's story, the story of a rebel (Sargent) overturning an oppressive orthodoxy is a "good story" also. As Hooper should know, the only way to tell if a "good story" is a true one is by a careful, balanced and weighted review of the evidence. The peppered moth researchers have and are doing this repeatedly, as every bit of new evidence comes in; this is their job as scientists; and their scientific conclusion is that Kettlewell's central finding, that bird predation is the agent of selection, remains firm. Hooper, however, chooses sensationalism, psychoanalysis, and a very selective review of authorities and evidence to reach her conclusion that the bird predation thesis is unsupported; this is the central flaw of her book.

Reader beware.


(9 of 19 people found this review helpful!;)



Date: 2002/09/21 18:43:23, Link
Author: Wesley R. Elsberry
More instances of Wells holding forth on where peppered moths do or do not "normally" rest:

Quote
4. "students should know that the pictures were faked": This goes without saying.  Since biologists have known since the 1980s that peppered moths do not normally rest on tree trunks, not to tell students that the pictures were staged (in many cases by gluing or pinning dead moths to desired backgrounds) constitutes as clear a case of scientific fraud as any on record.  Yet I'm aware of no sincere efforts by Darwinists to inform students of this -- despite their pious declarations of good intentions. Almost all recent (1998-2000) biology textbooks use such photos without any indication that they were staged.  As a scientist, I find this absolutely inexcusable.  If dogmatic Darwinists were as smart as they pretend to be, they would be actively campaigning -- for their own good! -- to rid textbooks of this fraud.  Acquiescence in scientific misconduct will not look good on their resumes.

(Source)


Quote
Then there's the story of peppered moths. Most current biology textbooks carry photos of these moths on tree trunks, claiming that experiments performed in the 1950s showed that natural selection (stemming from camouflage differences and predatory birds) made dark- colored moths more common during the Industrial Revolution. But Martin omits the fact that this textbook story is now very much in doubt, because biologists discovered in the 1980s that peppered moths don't normally rest on tree trunks. All the textbook photos have been staged- -some by gluing or pinning dead moths in place.

(Source)


Quote
1. Since 1988, it has been well known to everyone who studies peppered moths that tree trunks are not their normal resting places. Michael Majerus lists six moths on exposed tree trunks over a forty year period, but this is an insignificant proportion of the tens of thousands that were observed during the same period. There simply is no question about it: peppered moths do not normally rest on tree trunks in the wild.

(Source)


Quote
Regarding the peppered moths: Kettlewell's experiments supposedly demonstrated that cryptic coloration and selective bird predation are the principle causes of industrial melanism were discredited by (a) findings in the 1960's and 1970's that other factors (such as migration and non-visual selection) had to be invoked to account for observed geographical distributions, (b) reports that the rise and fall of melanism were not correlated with lichen cover on tree trunks in the U.S. or many parts of the U.K., © research in the 1980's showing that peppered moths in the wild do not normally rest on tree trunks (where Kettlewell conducted his experiments), and (d) revelations that all photographs of peppered moths on tree trunks have been staged, either by manually positioning live moths or by pinning or gluing dead ones.

(Source)


Ah, this is the one that I wanted to track down specifically:

Quote
BUT EVERYONE, INCLUDING MAJERUS, HAS KNOWN SINCE THE 1980'S THAT PEPPERED MOTHS DO NOT REST ON TREE TRUNKS IN THE WILD. This means that every time those staged photographs have been knowingly re-published since the 1980's constitutes a case of deliberate scientific fraud. Michael Majerus is being dishonest, and textbook-writers are lying to biology students. The behavior of these people is downright scandalous.

Fraud is fraud. It's time to tell it like it is.

(Source)


Wesley

Date: 2002/09/22 10:01:39, Link
Author: ExYECer
I am not sure if these have been mentioned but an interesting 'discussion' between Wells and Musgraeve can be found at Peppered moths

Quote

…Using caged moths, Mikkola (1984) observed that `the normal resting place of the Peppered Moth is beneath small , more or less horizontal branches … probably high up in the canopies, and the species probably only exceptionally rests on tree trunks…'
…In twenty-five years of field work, Clarke (1985) and his colleagues found only one peppered moth on a tree trunk…

…in the 1980s…biologists found that in the wild peppered moths do not rest on tree trunks…

Source

Quote
   (2) Even if the correct number were 168 rather than 6, this would still represent only a tiny percentage of the tens of thousands of peppered moths studied by field researchers between the 1950s and 1990s.


Source


Exposed tree trunks versus tree trunks

Quote
   (3) I do not claim that peppered moths NEVER rest on tree trunks, but only that they do not NORMALLY rest on tree trunks in the wild. This is the conclusion of everyone who has studied the natural resting-places of peppered moths, including Majerus. In addition to the conclusions you already cite from my work, I could add the following from Majerus's book: "Peppered moths do not naturally rest in exposed positions on tree trunks.... Data on the natural resting sites of the peppered moth are pitifully scarce, and this in itself suggests that peppered moths do not habitually rest in exposed positions on tree trunks.


Source

And this incredible ignorant comment

Quote
  Finally, Thomas claims - without mentioning specifics - that I misrepresent a 1985 paper by Clarke, Mani & Wynne.  Clarke et al. (1985) wrote that "all we have observed is where the moths do NOT spend the day.  In 25 years we have found only two" - one on a tree trunk, and another on a wall near a mercury vapor trap.  To appreciate the significance of this - and the numbers cited in the other papers - it is helpful to note that Steward (1977) listed 52 studies conducted between 1952 and 1974, involving a total of 8,426 peppered moths.  Clearly, the one moth reported by Clarke et al. (1985), and the six moths reported by Majerus (1998) as resting on exposed tree trunks, represent only a vanishingly small percentage of all peppered moths studied.
Source

Date: 2002/09/22 14:40:18, Link
Author: niiicholas
Wells has an unusual talent for mixing several obfuscations together into a story that looks convincing to anyone who hasn't done some reading of the actual moth experts.

Some things to watch out for:

Obfuscation between "moths don't rest on exposed positions on tree trunks" and "moths don't rest on tree trunks".  Wells' quotes usually say the former, but Wells will argue the latter.

Obfuscation about what "'normal' resting position" means to the experts Wells cites.

Audience-dependent obfuscation about whether or not to mention Majerus' data on the natural resting positions of moths.  Wells has been bashed about the head so many times with this that in his most recent writing (reviewing Hooper's book for Christianity Today, here) he has finally brought the data forth rather than having a skeptic do it.  However, reports indicate that his normal strategy in front of friendly audiences is to not mention this inconvient data at all and instead talk about "fraudulent photos" in textbooks (but if peppered moths do rest on tree trunks at least sometimes, then any objection to the photos has become moot).

In every Wells debate on peppered moths that I've read, his ultimate last-ditch position on peppered moths is to talk about how small those observed numbers are in proportion to the thousands of moths observed over the years.  E.g., here:

Quote

Nevertheless, many defenders of Darwinian evolution rush to protect the peppered moth icon as though their religion depended on it. In 2000, I wrote a book pointing out that the peppered moth story—though of limited significance in itself—is part of a larger pattern of systematic misrepresentation serving to prop up Darwin's theory. Kevin Padian, a Berkeley professor and president of the National Center for Science Education, a militantly pro-Darwin advocacy group, responded by likening me to the sociopathic antihero of the film The Talented Mr. Ripley. According to Padian, "a particularly egregious example of Mr. Wells's talents is his treatment of the peppered moth." Padian then went on to defend the classic story by claiming that peppered moths "rest on tree trunks 26% of the time" (The Quarterly Review of Biology, March 2002).

Padian bases his astonishing claim (which contradicts the published scientific literature) on the fact that 47 moths were found resting in the wild between 1964 and 1996, and that one quarter of these were on tree trunks. During the same period, however, many thousands of moths were caught in nighttime traps, so the 47 found in natural resting positions were less than 1 percent of the moths studied, and much less than 1 percent of all peppered moths living in the wild. Padian might as well claim that a quarter of all ocean fish are visible to predatory birds because he did statistics on the few that can be spotted from a boat.

Character assassination supported by transparently bogus statistics—how does a highly placed scientist end up indulging in such tactics? Obviously, the peppered moth story involves more than objective science.


'Course, Wells doesn't mention that the "many thousands of moths" caught in traps were caught in traps that attract moths with light or pheromones and which are therefore utterly irrelevant to determining natural resting positions.  All this was pointed out to Wells in the very first moth debate on the Calvin listserv:

(URLs reviewed here:
http://www.talkorigins.org/faqs/wells/#mothmaj )

Fracks response to the traps claim:

Quote

[Frack, "RE: My last word":
http://www.calvin.edu/archive/evolution/199904/0207.html ]

I have only one comment on Wells's "last word". He wrote:

> 1. Since 1988, it has been well known to everyone who studies peppered
> moths that tree trunks are not their normal resting places. Michael
> Majerus lists six moths on exposed tree trunks over a forty year period,
> but this is an insignificant proportion of the tens of thousands that were
> observed during the same period. There simply is no question about it:
> peppered moths do not normally rest on tree trunks in the wild.


I have already been contacted by a list member asking me about the "tens of thousands" of moths. Attentive readers will probably have noticed that we were talking about Majerus's sample of field collected moths from resting positions as 47, and Wells's incessant "one moth". Wells has found me out. You can now be told the truth that the normal resting position of peppered moths is in the bottom tray of light traps, for that is where these specimens were "observed."


...and yet, you will find Wells ending every debate on peppered moths (with Frack, Miller, Dave Thomas, and probably others) with this false Ace.

And, of course, tactically leaving out important pieces of information like this is exactly what the Matt Daemon character in "The Talented Mr. Ripley" did at the beginning of the movie (the part cited in the Padian review), and is indeed the major fault of all of Wells' antievolution polemics.

nic



Date: 2002/09/22 23:37:02, Link
Author: niiicholas
Here is the only review of Hooper that has come out thus far by a Real Live Peppered Moth Researcher: Bruce Grant.  His take is notably different than the press commentary on Hooper.

Quote

http://www.sciencemag.org/content/vol297/issue5583/#books  
Science 297, 940-941 (2002)

EVOLUTION:
Sour Grapes of Wrath

A review by Bruce S. Grant

------------------------------------------------------------

Of Moths and Men: Intrigue, Tragedy and the Peppered Moth
Judith Hooper
Fourth Estate, London, 2002. 397 pp. £15.99. ISBN 1-84115-392-3.

Of Moths and Men The Untold Story of Science and the Peppered Moth
Norton, New York, 2002. 397 pp. $26.95, C$38.99. ISBN 0-393-05121-8.
------------------------------------------------------------

Mark Twain once quipped that reports of his death had been exaggerated. Recent reports exaggerate the death of industrial melanism as an exemplar of natural selection. The latest is Judith Hooper's Of Moths and Men, which promises "the untold story of science and the peppered  moth." What it delivers is a quasi-scientific assessment of the evidence for natural selection in the peppered moth (Biston betularia), much of which is cast in doubt by the author's relentless suspicion of fraud. This is unfortunate. Hooper is a gifted writer. In places, her prose is quite enjoyable, even brilliant. But, sadly, the book is marred by numerous factual errors and by misrepresentations of concepts and controversies.

The fundamental problem is Hooper's failure to clearly distinguish the evidence for natural selection and the mechanism of selection. A dead body with a knife in its back is evidence that a murder has been committed. An inability to establish beyond reasonable doubt the guilt of the leading suspect does not mean that the murder did not occur.

Population geneticists define evolution as a change in allele (gene) frequency. Adult peppered moths come in a range of shades from mottled gray (pale) to jet black (melanic). We know from extensive genetic analysis that these phenotypes result from combinations of multiple alleles at a single locus. Changes in the percentages of the phenotypes in wild populations are well documented. The changes continue and are observable even now. The steady trajectory and speed of changes in allele frequencies indicate that this evolution results primarily from natural selection. J. B. S. Haldane's original calculation of a selection coefficient was estimated  from the number of generations it took for the melanic phenotype to effectively replace the pale phenotype during the 19th century. More detailed records document recent changes. For example, near Liverpool, England, the melanic phenotype declined from 93 to 18% in 37 generations (one generation per year); this change is consistent with a 15% selective disadvantage to genotypes with the dominant (melanic) allele.

We have amassed enormous records of changes in allele frequency in peppered moth populations that cannot be explained in the absence of natural selection. But what is the mechanism of selection? Even the answer "we have no clue" would not invalidate the conclusion that selection has occurred. Fortunately, the circumstances have left clues.

Geographic and temporal variations in the incidence of  melanism correlate with atmospheric levels of SO2 and suspended particles. (The correlations are not perfect; gene flow by migration spreads alleles, even into populations where they are deleterious.) Light reflectance from tree bark declines as suspended particles increase. Across a range of  backgrounds, the pale and melanic phenotypes are differently conspicuous to the human eye. As early as 1896, J. W. Tutt suspected that birds were selectively eating conspicuous phenotypes in habitats variously modified by industrial fallout; H. B. D. Kettlewell first tested Tutt's idea in the 1950s.

It is on Kettlewell and his experiments that Hooper focuses her attention. In a biography more akin to character assassination than to objective disclosure, she portrays Kettlewell as an insecure misfit so driven to please his "boss," E. B. Ford, that he is suspected (by Hooper) of fudging his data. She bases her case on experimental design changes that Kettlewell himself described in his papers and on a sudden increase in the recapture rate of marked moths released in polluted woodlands. Several obvious things that Hooper left unexamined affect the size of moth catches, and her case is unconvincing. In addition, she presents it as if the very evidence for natural selection in peppered moths depends on the validity of Kettlewell's experiments. But even the evidence for bird predation does not depend on them.

Fortunately, science assesses the correctness of work by testing its repeatability. Kettlewell's conclusions have been considered in eight separate field studies, of various designs, performed between 1966 and 1987. Some of the design changes--such as reducing the density of moths, randomly
assigning moths to trees, altering locations on trees where moths were positioned, and positioning killed moths to control for differences in viability and dispersal--were made to correct deficiencies identified in his original experiments. L. M. Cook's regression analysis of fitness estimates from these experiments plotted against phenotype frequencies at their various locations shows the studies to be remarkably consistent (1).

Other mechanisms of selection have been proposed. An inherent physiological advantage of melanic over pale phenotypes is consistent with the rise and spread of melanism, but the widespread decline in melanism that  followed the Clean Air Acts obviates that interpretation. Although the possibility remains that physiological differences might be facultative (changing with conditions), so far no experimental work supports this idea. To date, only selective predation by birds is backed by experiment.

Hooper's book turns bizarre when she showcases American biologist T. D. Sargent as a wounded iconoclast whose career was stultified because Kettlewell dismissed his work. She argues that Sargent is now under attack because he questions the "classical explanation" for industrial melanism. Hooper garbles the controversy regarding background  selection by moths, and she entertains Sargent's protracted speculation about phenotypic induction. (He has offered no evidence that melanism is an induced character in adult peppered moths.) But most egregious is Sargent's assertion that studies in North America falsify the classical explanation. The history of melanism in American peppered moths--which are conspecific with Kettlewell's moths, not a separate species as Hooper indicates--closely parallels what has  occurred in Britain, and melanism is correlated in like manner with levels of atmospheric pollution (2). The American studies corroborate rather than contradict the classical explanation.

The case for natural selection in the evolution of melanism in peppered moths is actually much stronger today than it was during Kettlewell's time. Textbook accounts should be expanded to reflect this newer information, and they should not cite Of Moths and Men as a credible resource.

References

1.    L. M. Cook, Biol. J. Linn. Soc. 69, 431 (2000).
2.    B. S. Grant, L. L. Wiseman, J. Hered. 93, 86 (2002).
------------------------------------------------------------
The author is in the Department of Biology, College of William and Mary, Williamsburg, VA 23187-8795, USA. E-mail: Geometrid@aol.com




Date: 2002/09/24 03:36:07, Link
Author: niiicholas
Another review (or rebuttal of positive Hooper reviews, actually) on Intelligent Design Update yahoogroup:

http://groups.yahoo.com/group/IntelligentDesignUpdate/message/112

...quite good IMO, several points that haven't been made by anyone else yet...

nic

Date: 2002/09/24 03:44:53, Link
Author: niiicholas
Quote (niiicholas @ Sep. 24 2002,03:36)

Online letters on the Salon.com review of Hooper:

http://www.salon.com/books/letters/2002/09/20/moths/index1.html

The Wells FAQ is referenced :-)

Date: 2002/09/24 04:48:34, Link
Author: niiicholas
This thread is for accumulating links and posts on the topic of predictions made by the modern theory of evolution, i.e. the theory that processes we observe or directly infer today (especially random mutation (broadly construed to include everything from point mutations to genome duplications) and natural selection, but also the well-known sidekicks such as genetic drift, neutral evolution, etc.), were also acting in the long-distant past and produced the biodiversity of today.

This was prompted by Jesse's excellent post at ARN on this topic, which we should quote somewhere:

ARN post

nic

Date: 2002/09/24 13:45:26, Link
Author: rafe gutman
have you ever heard behe (or more recently dembski) imply that subsets of IC systems have no function?  i certainly have.  however, in a recent internet discussion over on ISCID, dembski clearly stated that that was false, and that ID critics were misrepresenting their opinion.  in his own words,
Quote
You've charged me with moving the goalposts and adjusting the definition of irreducible complexity because I require of evolutionary biologists to "connect the dots" in a causally convincing way. The dots here are functional precursors that could conceivably have evolved into the final system of interest. You state that previously I claimed that the dots couldn't exist because they wouldn't be functional. Please show me in Michael Behe's writings or my own where we deny that IC systems can be made up of subsystems that can be functional in their own right. The point is not whether subsystems can be functional on their own but whether they can exhibit the same function in the same manner as the system in question. You misrepresent our position.

then later, when presented with quotes implying such (which will be given later):
Quote
I wrote, "Please show me in Michael Behe's writings or my own where we deny that IC systems can be made up of subsystems that can be functional in their own right." Both Behe and I have always defined IC with reference to the basic function of the system in question (if we've not said it explicitly -- and I have in NFL -- then a charitable reading would have granted that -- neither Behe nor I are that stupid). We therefore left open the possibility of subsystems having function in their own right. You and Yersinia charge us with a denial.

one of the key arguments of irreducible complexity being a roadblock to evolution is the lack of "functional intermediates" for selection to act upon.  if a purportedly IC system has 20 components, and homologues to all 20 are observed in 20 separate systems, then an IDist might propose that all 20 components had to come together in one step in order for the IC system to evolve.  of course, to say this is to deny that 3, or 5, or 10 components could have a function all to their own (whether it be the IC function or something else).  i'd like this thread to serve as a place where ID critics could post quotes of behe or dembski, or any other IDist where they propagate this myth.  please indicate the source of the quote in your post.  i'll post my initial contributions below.

Date: 2002/09/24 14:05:49, Link
Author: rafe gutman
michael behe's original definition of irreducible complexity:
Quote
"a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease function.  an irreducibly complex biological system, if there is such a thing, would be a powerful challenge to darwinian evolution.  since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on." (DBB page 39)


dembski's definition of IC, NFL:
Quote
"A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, non-arbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system." (page 285)


Quote
"a flagellum without its full complement of protein parts does not function at all. Behe therefore concludes that if the Darwinian mechanism is going to produce the flagellum, it will have to do so in one generation." (page 251)


Quote
"To achieve an irreducibly complex system, the Darwinian mechanism has but two options. First, it can try to achieve the system in one fell swoop. But if an irreducibly complex system's core consists of numerous and diverse parts, that option is decisively precluded. The only other option for the Darwinian mechanism then is to try to achieve the system gradually by exploiting functional intermediates. But this option can only work so long as the system admits substantial simplifications. The second condition [that the irreducible core of the system is at the minimal level of complexity needed to perform its function] blocks this other option. Let me stress that there is no false dilemma here-it is not as though there are other options that I have conveniently ignored but that the Darwinian mechanism has at its disposal." (page 287)


by john bracht in a metanexus article entitled: Knotty Pine and Corroding Coins
Quote
"In order for the fitness function to have smoothly sloped sides rather than sharp cliffs, there must be a way to gradually build a flagellum with fitness increases at each step as parts of the system are added. It is common for biologists to do mutation experiments in which they destroy some component of a molecular system and see whether it still works; with the flagellum they have found that all the components are required for function. In other words, the intermediates are non-functional and thus convey no selective advantage."

and also:
Quote
"In contrast to the coin-flipping machines in which a sequence has progressively greater selective value the more heads it contains, there is no advantage in having a nearly complete flagellum."

from washington times article entitled: Challenging Darwin by jen waters:
Quote
"Mr. Behe argues that cells are full of "molecular machines." All the parts must be there at once for the "molecular machines" to work correctly. (In the same way, all the pieces of a mousetrap must be present for it to operate properly.) Taking away parts from the molecular machines of a cell would make them stop working, which is why Mr. Behe believes life appears to be designed."


does anyone have any more examples?  also, if you have examples where behe or dembski acknowledge that subsets of IC systems can be functional, let me know.  so far, i've found no such acknowledgement in any of their popular writings.

Date: 2002/09/25 09:07:10, Link
Author: ExYECer
I am not sure how strong the case is. In NFL it seems to me that Dembski has redefined Behe's original statement by focusing on _original function_  or _basic function_. The problem is that once intermediates of a different function are allowed that IC systems seem to lose their relevance. Only if it can be argued that an IC system has to maintain its original function in its intermediates can one argue ala Dembski/Behe.

Allowing different intermediate functions opens the door even wider for evolutionary mechanisms.

Dembski's NFL arguments surely suggest a new variant though I would disagree with Dembski about Behe's original IC claim.

Quote

The concept of an "invariant" was introduced, something which falsifies a hypothesis, or posit. Irreducible complexity, Dembski said, is Darwin's invariant, but only when defined in the right way. Dembski then "tightenened Behe's invariant" and talked about many of the standard criticisms of irreducible complexity (scaffolding can support IC structures, co-optation, remove 2 parts and function is restored, etc), and presented a new revised version of irreducible complexity:

• 1. Removal of one part destroys original function.
• 2. Removal of multiple parts kills system's original function
• 3. System has numerous complex interacting parts
• 4. System is minimally complex in relation to its minimal function for selective advantage.


Source

Seems that Dembski admits that a redefinition of Behe's original function was needed.


Yet Dembski also argues

Quote

Dembski discussed Michael Behe and his "irreducible complexity" approach to ID, and mentioned that Behe is coming to Albuquerque next March. Amazingly, Dembski described several effective critiques of Behe's ideas, including scaffolding, co-aptation, redundant complexity, ignorance of the scientific literature, appeals to ignorance, incremental indispensability, and reducible complexity. But Dembski blew off all the criticisms, as if simply mentioning their existence effectively counters them. Here's an example: Dembski mentioned scaffolding and the Roman arch example, which Massimo Pigliucci happened to have presented to NMSR at his talk on August 11th. Here, a mound is built, then stones are place on top to make the arch; once the last stone is in place, the mound is removed, leaving the arch in apparent "irreducible complexity" (take away any stone and the whole thing falls down). Dembski's counter to this example was to claim you can't have "delayed gratification," i.e. that in living systems, you would need the arch to work right away, and wouldn't possibly have a "mound" stage.

Dembski described his addition to Behe's "irreducible complexity" required to tighten it up: it's a system where removal of a single part destroys the original function, removal of multiple parts destroys the original function, the system comprises numerous and diverse parts, and (Dembski's innovation) the system is minimally complex for the required functionality. He calls this "Irreducible Complexity 2.0 (read two-point-oh), and claims this is the "Darwin-stopping invariant." In five to ten years, Dembski said, "Darwinism" will stand alongside failed theories like alchemy and perpetual motion. He said Darwin's unpaid debt is an unpayable debt, and that leaves only Design.


Source

Date: 2002/09/26 00:13:06, Link
Author: niiicholas
Here is another Wells gaffe:

Quote

(4) In the 1980's, several researchers showed independently that peppered moths do not rest on tree trunks in the wild. The moths normally fly only at night, and before dawn they apparently take up positions high in the canopy, underneath horizontal branches. In 40 years of field work, only one peppered moth was found resting on a tree trunk in the wild. Although some uncertainty remains about where the moths actually do rest during the day, it is absolutely clear that they do not rest on vertical tree trunks.

[ http://www.calvin.edu/archive/evolution/199903/0348.html ]


Michael Majerus took the trouble to respond to this himself:

Quote

4) This is just wrong. Dr Wells' who gives the impression in his response that he has read my book, obviously has not. If he had, he would have seen that in Tables 6.1 and 6.2 I myself have recorded 168 peppered moths on tree trunks or at trunk/branch joins. If Dr Wells' wishes his views to be taken seriously, he should ensure that his research is thorough.

[ http://www.calvin.edu/archive/evolution/199904/0103.html ]


yersinia

Date: 2002/09/26 10:25:36, Link
Author: Wesley R. Elsberry
Quote
Clearing up confusion requires a careful and consistent use of terms.  In this book, "creation science" refers to young-earth, six-day special creation.  "Creationism" means belief in creation in a more general sense.  Persons who believe that the earth is billions of years old, and the simple forms of life evolved gradually to become more complex forms including humans, are "creationists" if they believe that a supernatural Creator not only initiated this process but in some meaningful sense controls it in furtherance of a purpose.  As we shall see, "evolution" (in contemporary usage) excludes not just creation-science but creationism in the broad sense.  By "Darwinism" I mean fully naturalistic evolution, involving chance mechanisms guided by natural selection.

(Source: Phillip E. Johnson, Darwin on Trial (2nd ed.), Intervarsity Press, p.4 (footnote).)


[Fixed typo.]



Date: 2002/09/26 18:25:37, Link
Author: pzmyers
Quote (Wesley R. Elsberry @ Sep. 26 2002,10:25)
Quote
Clearing up confusion requires a careful and consistent use of terms.  In this book, "creation science" refers to young-earth, six-day special creation.  "Creationism" means belief in creation in a more general sense.  Persons who believe that the earth is billions of years old, and the simple forms of life evolved gradually to become more complex forms including humans, are "creationists" if they believe that a supernatural Creator not only initiated this process but in some meaningful sense controls it in furtherance of a purpose.  As we shall see, "evolution" (in contemporary usage) excludes not just creation-science but creationism in the broad sense.  By "Darwinism" I mean fully naturalistic evolution, involving chance mechanisms guided by natural selection.

(Source: Phillip E. Johnson, Darwin on Trial (2nd ed.), Intervarsity Press, p.4 (footnote).)


[Fixed typo.]

It's nice to have an authoritative, canonical source to justify our use of the term "creationist" from now on.

It is rather interesting that by Johnson's definition, only Young Earth Creationists are practicing "creation science", which leaves one wondering what Old Earth Creationists and IDists are doing.

Date: 2002/09/30 11:08:38, Link
Author: Wesley R. Elsberry
On September 26th, 2002, the Cobb County school board voted unanimously for a provision that singles out evolutionary biology as controversial and requires teachers to engage in "discussion of disputed views of academic subjects".

Cobb County policy

There will be "implementing regulations" related to this policy.  I see a high potential for mischief at the administrative level.  The policy does not stipulate that the level of "dispute" must be scientific in nature, which opens the door to any sort of "dispute", no matter how lacking in scientific merit it might be.

Here's an article on how teachers are reacting to the change:

Cobb teachers ponder new evolution rule

Wesley

Date: 2002/09/30 16:12:55, Link
Author: Wesley R. Elsberry
Henry Schaefer, UGa professor and Fellow of the Discovery Institute's Center for (the Renewal of) Science and Culture, has an op-ed piece in the Atlanta Journal-Constitution.

Standard evolutionary theory has shortcomings

It looks to me like the usual admixture of arrogance and ignorance on the part of a religiously-motivated antievolutionist.  But your mileage may vary...

Notice that while Henry feels free to hand out grades to natural selection, gravity, and quantum mechanics, he doesn't proceed to use the same evaluation framework for "intelligent design".  That's OK, the evaluation process is trivial, and I can apply it quite easily here.  Henry uses two criteria given by Stephen Hawking for good theories:

Quote
A theory is a good theory if it satisfies two requirements. It must accurately describe a large class of observations on the basis of a model that contains only a few arbitrary elements. And it must make definite predictions about the results of future observations.


Does ID describe a large class of observations?  No.  Does ID have a model with only a few arbitrary elements? No.  In fact, there is no ID model.  ID is just "nature didn't do it" repeated ad nauseum.

Does ID provide a basis to make definite predictions about the results of future observations?  Definitely not.  William Dembski specifically excludes this in his essay on "Testability".  Dembski also excludes ID predictions on the basis that designers are "innovators" (see NFL).

So, going by the standards that Henry has validated, I see no way to award ID more than an "F" for goodness of theory.

Yet Henry does, I believe, wish to see ID taught in Cobb County science classrooms as one of those "disputed views" that the recent policy change now countenances.  It certainly isn't because of the scientific content, which leaves one wondering why...

Wesley

Date: 2002/09/30 22:44:52, Link
Author: anapsid
Though it will probably never get printed, I felt compelled to rebut Schafer's op-ed piece, and sent this to the Atlanta Journal Constitution.  Yes, I know it's snotty!

Henry Schafer's Little Strawmen

In the 9-28-02 Guest Column, chemist Henry Schaefer becomes another in the line of Discovery Institute Fellows who first veil their affiliation and true agenda - intelligent design/neocreationism - and second, concoct arguments against evolution that are outdated, spurious, or totally irrelevant.

We start with Schaefer's definition of evolution:  "...the claim that random mutations and natural selection can fully account for the complexity of life, and particularly macroscopic living things."  Newsflash, Henry:  Evolution is not defined in this way by anyone except the Discovery Institute and other creationist organizations.  It is obvious that Schaefer has done no reading of the evolutionary literature, and is unaware of the other factors that are involved in the evolution of species.  For a layman's introduction, Carl Zimmer's At the Water's Edge would be a great place to start.

Next we hear about Piltdown Man and the fossil hoax (singular) from China.  But does Schafer tell you that the Piltdown hoax was debunked in the 1950's by evolutionists, or that most scientists were skeptical of it from the start, or that the Chinese hoax was also rapidly exposed by evolutionists, or that there exist extensive transitional fossil records for whales, horses, and humans, to name just a few?  Heck no.

Lastly, Schaefer spouts three "reservations concerning the standard evolutionary model" (the Discovery Institute's model, I presume), which do not rise above Arguments from Personal Incredulity.

He points to the Miller-Urey model as not being THE complete explanation for the origin of life,  not mentioning that this was a 1953 experiment and that there are now 50 years of additional data.  Is there a consensus about THE mechanism of the origin of life?  No.  It's pretty hard to run that clock backwards.  However, Schaefer does not mention ANY current research in complexity theory or work on self-replicating systems, concepts about which he is surely aware.  It is ignorant if not dishonest to dismiss origin-of-life research on the basis of one 50-year-old experiment.  However, that's what the Discovery Institute does.

Second, he doesn't like the amount of stasis in the fossil record, and what appears to him to be the relatively rapid formation of species (though we could still be talking millions of years here).  To grab and modify an old campaign slogan, "It's the environment, stupid."  Survival depends upon the ability of a species to adapt to a particular environment.  If the environment is static, there is no impetus for species to change significantly.  If the environment changes, new adaptations are likely and necessary.  Biology 101.

For Schaefer's third "area of reservation" (large scale changes) I can only add that Zimmer's book sheds a lot of light in this area.  Perhaps Schaefer should enlarge his reading material beyond that given to him by the Discovery Institute, and read some real evolutionary biology before he deigns to have expertise in the area.



:angry:

Date: 2002/10/01 13:47:50, Link
Author: niiicholas
This thread is for references to lit. on, or relevant to, the origins of F1F0 ATPase.  I just came across some and I know of some others, I will post them whenever I dig 'em up.

Quote

http://www.pnas.org/cgi/content/abstract/202149599v1

Subunit rotation of ATP synthase embedded in membranes: a or ß subunit rotation relative to the c subunit ring

Kazuaki Nishio *, Atsuko Iwamoto-Kihara *, Akitsugu Yamamoto , Yoh Wada *, and Masamitsu Futai *
*Division of Biological Sciences, Institute of Scientific and Industrial Research, Osaka University, Core Research for Evolutional Science and Technology (CREST) of the Japan Science and Technology Corporation, Osaka 567-0047, Japan; and Department of Physiology, Kansai Medical University, Moriguchi, Osaka 570-8506, Japan



Edited by Paul D. Boyer, University of California, Los Angeles, CA, and approved August 15, 2002 (received for review March 13, 2002)

ATP synthase FoF1 (3ß3ab2c10-14) couples an electrochemical proton gradient and a chemical reaction through the rotation of its subunit assembly. In this study, we engineered FoF1 to examine the rotation of the catalytic F1 ß or membrane sector Fo a subunit when the Fo c subunit ring was immobilized; a biotin-tag was introduced onto the ß or a subunit, and a His-tag onto the c subunit ring. Membrane fragments were obtained from Escherichia coli cells carrying the recombinant plasmid for the engineered FoF1 and were immobilized on a glass surface. An actin filament connected to the ß or a subunit rotated counterclockwise on the addition of ATP, and generated essentially the same torque as one connected to the c ring of FoF1 immobilized through a His-tag linked to the  or ß subunit. These results established that the c10-14 and 3ß3ab2 complexes are mechanical units of the membrane-embedded enzyme involved in rotational catalysis.


Some have argued that the ATPase may be descended from a pyrophophatase, so this is relevant:

Quote

Proc. Natl. Acad. Sci. USA, 10.1073/pnas.212410399

Pyrophosphate-producing protein dephosphorylation by HPr kinase/phosphorylase: A relic of early life?

In most Gram-positive bacteria, serine-46-phosphorylated HPr (P-Ser-HPr) controls the expression of numerous catabolic genes (10% of their genome) by acting as catabolite corepressor. HPr kinase/phosphorylase (HprK/P), the bifunctional sensor enzyme for catabolite repression, phosphorylates HPr, a phosphocarrier protein of the sugar-transporting phosphoenolpyruvate/glycose phosphotransferase system, in the presence of ATP and fructose-1,6-bisphosphate but dephosphorylates P-Ser-HPr when phosphate prevails over ATP and fructose-1,6-bisphosphate. We demonstrate here that P-Ser-HPr dephosphorylation leads to the formation of HPr and pyrophosphate. HprK/P, which binds phosphate at the same site as the ß phosphate of ATP, probably uses the inorganic phosphate to carry out a nucleophilic attack on the phosphoryl bond in P-Ser-HPr. HprK/P is the first enzyme known to catalyze P-protein dephosphorylation via this phospho-phosphorolysis mechanism. This reaction is reversible, and at elevated pyrophosphate concentrations, HprK/P can use pyrophosphate to phosphorylate HPr. Growth of Bacillus subtilis on glucose increased intracellular pyrophosphate to concentrations (6 mM), which in in vitro tests allowed efficient pyrophosphate-dependent HPr phosphorylation. To effectively dephosphorylate P-Ser-HPr when glucose is exhausted, the pyrophosphate concentration in the cells is lowered to 1 mM. In B. subtilis, this might be achieved by YvoE. This protein exhibits pyrophosphatase activity, and its gene is organized in an operon with hprK.

Date: 2002/10/01 14:02:37, Link
Author: niiicholas
Here's a different one:

http://www.pnas.org/cgi/content/abstract/152445399v1

Quote

Published online before print September 17, 2002
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.152445399
Evolution of moth sex pheromones via ancestral genes

Wendell L. Roelofs *, Weitian Liu *, Guixia Hao *, Hongmei Jiao *, Alejandro P. Rooney , and Charles E. Linn Jr. *
*Department of Entomology, Cornell University, Geneva, NY 14456; and Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762

Contributed by Wendell L. Roelofs, July 28, 2002

Mate finding in most moth species involves long-distance signaling via female-emitted sex pheromones. There is a great diversity of pheromone structures used throughout the Lepidoptera, even among closely related species. The conundrum is how signal divergence has occurred. With strong normalizing selection pressure on blend composition and response preferences, it is improbable that shifts to pheromones of diverse structures occur through adaptive changes in small steps. Here, we present data supporting the hypothesis that a major shift in the pheromone of an Ostrinia species occurred by activation of a nonfunctional desaturase gene transcript present in the pheromone gland. We also demonstrate the existence of rare males that respond to the new pheromone blend. Their presence would allow for asymmetric tracking of male response to the new blend and, thus, evolution of an Ostrinia species with structurally different sex pheromone components.




Date: 2002/10/01 16:56:30, Link
Author: johndcal
SUN VALLEY, CA - October 1, 2002 - A long-standing offer to prove evolution has been accepted by John D. Callahan, a theistic evolutionist and president of Faith & Reason Ministries: Reconciling Christianity with Accepted Science, http://www.faithreason.org/. The offer is being made by Dr. Kent Hovind, a young-Earth creationist and leader of Creation Science Evangelism, http://www.drdino.com/.

Callahan writes Dr. Hovind, in a widely distributed open letter: "I accept your offer to prove evolution and win $250,000. I will prove secular, scientific evolution as it is appropriately taught in our schools. As you stipulate, this includes both the large-scale evolution of the universe, from the Big Bang, and Darwinian biological evolution. I could appeal to the mountain of empirical evidence (observation and experimentation) from many areas of science, which puts evolution beyond doubt to almost all scientists. However, this would be overkill, and since evolution is so simple to prove, I will do it in this letter. You insist evolution is an unsubstantiated, immoral religion; this is incorrect."

"First consider biological evolution. Besides innumerable transitional fossils -- dating billions of years to very primitive forms -- there are many living species (of the millions on Earth) and breeds that are obvious cousins and direct descendants of one another. An illustration is the domestic dog, which can produce a generation 30 times faster than man. From gray wolf populations the domestic dog has evolved (naturally and via human intervention) into dozens of species and hundreds of breeds (enormous gene pool) over the last 10,000 years. These are more than minor variations and indicative of macroevolution. Further, since a gray wolf has evolved into a pug dog, an ape has surely evolved into a Homo erectus and then a man."

"As far as large-scale evolution, the cosmic background radiation confirms the Big Bang and structure of the universe. Also light travels at 186,000 miles per second. Thus when astronomers look at distance objects, they are looking back in time. This 'time travel' clearly shows the evolution of the universe, from quasars and primitive galaxies (billions of years ago) to the modern appearance of our local universe. In addition we see stars in various stages of evolution, nucleosynthesis in supernova 1987A, molecules in space, and solar systems forming from dust and gas. Not every detail is understood, such as dark matter and energy, but this in no way negates the basic age and evolution of the universe."

"However, evolution makes no statement as to the existence of God. (For proof of His being, please see http://www.faithreason.org/.) Therefore I address your point, '1. Time, space, and matter came into existence by themselves,' by stating that God created the universe with physical and spiritual laws facilitating evolution. Moreover, God is present and working in our lives and the universe, but not as envisioned by modern creation mythology: young-Earth creationism (your conviction), old-Earth creationism, and intelligent design theory."

"Please send my $250,000 to the address above. Thanks. If you wish more detail, from the ever-increasing mountain of empirical evidence, I would be happy to present before your review committee (or debate) provided you sponsor a public event and pay my traveling expenses (outside the Los Angeles, CA area)."

Dr. Hovind's challenge has been a rallying cry for creationists, and he asserts few, if any, legitimate inquires have been made -- and certainly no proof. However, evolutionists contend Dr. Hovind is not open to empirical evidence and scientific method. How will Dr. Hovind respond to the Callahan letter, which claims to concisely prove evolution consistent with belief in God?

Date: 2002/10/06 13:08:15, Link
Author: Michael
Answers in Genesis in Kingdom of the plants there there is no evidence progymnosperms ever existed.  Nevermind we have fossils!  This was initially pointed out in this thread.

The Institute of Creation research made a really nasty misrepresentation by falsely citing a paper as saying the closure temperature for helium in zircons is 196 degrees below zero.  Reverse the sign and it would be much closer to what the cited paper really said.  See this thread for details.

Date: 2002/10/07 08:31:20, Link
Author: Wesley R. Elsberry
Dembski on publishing:

Quote
Baylor's Mr. Dembski also has little interest in publicizing his research through traditional means. "I've just gotten kind of blasé about submitting things to journals where you often wait two years to get things into print," he says. "And I find I can actually get the turnaround faster by writing a book and getting the ideas expressed there. My books sell well. I get a royalty. And the material gets read more."

(Source: Darwinism Under Attack, The Chronicle of Higher Education, 2001/12/21)

Date: 2002/10/10 19:52:48, Link
Author: Wesley R. Elsberry
This thread is for items relating to the Ohio Board of Education's consideration of new science standards.

An interesting press statement came out today.

Quote
October 10, 2002
Press Conference Statement of
Professor Joseph F Koonce
Chair, Dept of Biology
Case Western Reserve University
jfk7@po.cwru.edu
216-368-3561

Many claims have been made in recent months as to what Ohio scientists think about intelligent design "theory." However, until now, no data existed on this issue. My colleagues and I set about to collect the data so that the public may gain an accurate impression of what Ohio's scientists think. The results are gratifying and unequivocal.

Nine out of ten Ohio scientists from Ohio public, private (including both secular and religious) universities say that intelligent design is primarily a religious view and is simply not part of science.

We designed and conducted this survey with the Internet Public Opinion Laboratory at the University of Cincinnati.  We sent out email messages around the state to faculty in departments of astronomy, biology, chemistry, geology, physics and other natural sciences, inviting them to answer a set of questions and to give their thoughts about the evolution-intelligent design debate.  The survey ran between September 26 and October 9.

Prior to polling the scientists, the Institute for Policy Research at the University of Cincinnati included questions on the September Ohio Poll (conducted September 4 through 15, 2002) asking the general public to respond to two questions about intelligent design. Like the scientists, a clear majority of Ohio residents found intelligent design to be religious, and not a scientific view.

Next Monday and Tuesday the Ohio Board of Education will vote on whether to include intelligent design or other forms of anti-evolutionism in the new K-12 science standards.  Intelligent design advocates claim life is too complex to have developed without the intervention of a supernatural being or force, and they claim their view is scientific. Clearly Ohio's citizens are not convinced that this argument should be taught as science.

I want to make clear that I am a religious person myself. As a Roman Catholic, I do believe in God and in concurrence with teachings of the Catholic Church, I have never found these beliefs in conflict with Evolutionary Theory.  Science addresses the nature of the physical universe, not the supernatural or the eternal. Like me, 84% of my colleagues also report that they find evolutionary theory compatible with belief in God.

I wish this would lay to rest the destructive notion that science and religion are at war in America. There is no such inherent conflict. Science and religion can promote and enhance each other without having to pretend we know less than we actually do about how the world is constructed and how it functions.

Most all of Ohio's science professors (92%) thought "Ohio high school students should be tested on their understanding of the basic principles of the theory of evolution in order to graduate." When asked if such students should also be tested on their knowledge of the concept of "Intelligent Design" in order to graduate, 90% said "no." Only 2% said that intelligent design was strongly supported by scientific evidence.

The survey also explored scientists' views on antievolutionism beyond the intelligent design movement. Some critics of evolution claim evidence against the theory of evolution has caused it to fall out of favor among scientists. This is clearly not the case in Ohio where the vast majority (93%) of science professors said they were not aware of "any scientifically valid evidence or an alternate scientific theory that challenges the fundamental principles of the theory of evolution."

We are extremely pleased with the response. Nearly 500 scientists responded, a rate of 31%.  The survey had an error of plus or minus 4.5 percent. Equally pleasing was the outpouring of gratitude for providing the opportunity to express their concern with the erosion of scientific literacy in the developing K-12 standards for Ohio.

Date: 2002/10/10 23:05:23, Link
Author: Wesley R. Elsberry
The CWRU poll made the news.

Professors say intelligent design is not scientific theory - Akron Beacon Journal, OH

Date: 2002/10/11 05:08:01, Link
Author: Wesley R. Elsberry
Ohio draft standards

And a newspaper article about the BOE's consideration of "intelligent design": Committee members propose final changes to science standards, AP story

Date: 2002/10/11 11:05:56, Link
Author: Wesley R. Elsberry
Another news item on Ohio...

Schools panel to decide evolution angle Monday (Plain Dealer, 2002/10/11)

And the Ohio Citizens for Science web page.

Date: 2002/10/11 12:55:11, Link
Author: Wesley R. Elsberry
Answers In Genesis has a response to Kent Hovind concerning their list of arguments that creationists should not use.

Date: 2002/10/11 15:07:50, Link
Author: Wesley R. Elsberry
Another news report on the Ohio poll...

Ohio poll: 'Design' theory is religious (Cincinnatti Post, 2002/10/11)

Date: 2002/10/11 15:18:41, Link
Author: Wesley R. Elsberry
The creationism issue came up in a debate between candidates for Georgia state school superintendent.

State school chief hopefuls have free-wheeling debate (Atlanta Journal-Constitution 2002/10/10)

Quote
The issue that generated the most spirited debate was whether schools should teach creationism.

Christmas said she would stay out of such local issues, but added, "Schools are about teaching scientific theories, not religious principles." Cox said she would not shy away from debates like the one Cobb County officials had this month because they teach "students to live in a free society with free ideas and to talk about them civilly."

Date: 2002/10/11 15:27:57, Link
Author: Wesley R. Elsberry
Kansas got the national spotlight in 1999 when creationists rewrote the science standards and excised evolution from them.  Since then, some creationist board members were voted out, and evolution was restored to the science standards.  The voters of Kansas will be making choices between candidates again this year.  Will we see a cyclical pattern of change in the science standards?

Here's a news item concerning two of the candidates in Kansas and some mention of their views on evolution.

Board of ed hopefuls have similar stances (Newton Kansan, 2002/10/09)

Quote
Neither candidate distinguished himself. Even on the divisive issue of teaching evolution vs. creationism, candidates basically agreed on what policy should be. Both said they would not support the teaching of creationism as an alternative to evolution.

"I support academic freedom," Willard said. "That means giving the scientific evidence on all sides of the issue and encourage them to make up their minds. I think that is what education is about, teaching kids to inquire and come to a decision."

"I would not teach creationism as an alternative to evolution," Anstine said. "In my mind creationism is a function of my home, my wife and eight kids. It is a function of our church. We've been there for more than 40 years. I think the creation story and other parts of religion are taught by the home."

Date: 2002/10/11 17:19:16, Link
Author: Dr.GH
Thanks for the update.

Date: 2002/10/12 01:59:54, Link
Author: Wesley R. Elsberry
The genome of the mosquito Anopheles gambiae and the malaria parasite Plasmodium falciparum have been mapped and were published in issues of Science and Nature early in October.

See the Science News Online article for more information.

Date: 2002/10/12 02:30:11, Link
Author: Wesley R. Elsberry
A Boston Globe article highlights research aimed at finding recently evolved genes in the human genome with implications for health care and future research.

MIT scientists develop way to catch evolution in the act (Boston Globe, 2002/10/10)

Date: 2002/10/12 11:15:58, Link
Author: Wesley R. Elsberry
More on the Polls in Ohio

From the AIBS lists...

Quote
Please forward this far and wide!


Dear Colleagues,

       Before the Ohio Board of Education gives any more consideration to including
intelligent design, alternatives to evolution or the "teach the controversy"
approach, they need to listen to what Ohio's best educated scientists said in a
new poll.  The Biology Department at Case Western Reserve University and the
Internet Public Opinion Laboratory at the University of Cincinnati conducted an
e-mail poll of all the 4 year college and university science faculty they could
get e-mail addresses for, and also placed two questions about intelligent
design on the Ohio Poll to gather opinions of the general public.  A quick
summary of the results are given below, followed by the complete press releases
from the University of Cincinnati, Case Western Reserve University and
Professor Joseph F Koonce, Chair, Department of Biology at Case Western Reserve
University.

       As far as support for intelligent design goes, only 4% of the scientists
polled thought there was a valid scientific challenge to evolution, only 7%
thought there was scientific evidence supporting intelligent design (2% strong
evidence, 5% percent some evidence), and only 5% said intelligent design was
not primarily a religious view.  The bottom line for supporters of intelligent
design is it is at BEST only a fringe view, but more accurately recognized as
the newest species of creationism to evolve.

Best wishes and please pass this on!

Steve Edinger, M.S.
President, Ohio Citizens for Science

       Among the survey's findings were:

-       Nine out of 10 scientists (91%) felt the concept of intelligent design was
unscientific and the same number responded that it was a religious view

-       A vast majority (93%) of the scientists were not aware of "any scientifically
valid evidence or an alternate scientific theory that challenges the
fundamental principles of the theory of evolution"

-       Almost all scientists (97%) said they did not use the intelligent design
concept in their research

-       Ninety percent of the responding scientists stated that they felt no
scientific evidence supports intelligent design, while 2% were unsure

-       Approximately 7% felt that intelligent design had some support from
scientific evidence

-       Some 84% felt acceptance of the evolution theory was "consistent with
believing in God"

        A total of 460 professors responded or a rate of 31%.  The survey had an
error of plus or minus 4.5%.  "We are extremely pleased with the response,"
says Koonce





********************************************************************************


Internet Public Opinion Laboratory

Department of Political Science
University of Cincinnati


By: George Bishop, PhD
Professor of Political Science          For Release: October 10, 2002
Director
Internet Public Opinion Laboratory
Department of Political Science
University of Cincinnati


Majority of Ohio Science Professors and Public Agree: "Intelligent Design"
Mostly about Religion

"Intelligent Design": Is it science or religion? The idea that an intelligent
designer or a supernatural force created the universe and guided the
development of human life has become the center of a heated controversy among
Ohio educators. As the State Board of Education in Ohio wrestles with the
policy issue of whether to teach "intelligent design" in public school science
classes the latest statewide surveys of Ohio citizens and science professors in
Ohio indicate that the concept of "intelligent design" is viewed by the vast
majority of scientists and a clear majority of the public as basically a
religious explanation of human origins.

These findings are based on: (1) an Internet survey of 460 science professors
teaching at both public and private four-year colleges and universities in
Ohio, sponsored by the Biology Department at Case Western Reserve University in
Cleveland and conducted by the Internet Public Opinion Laboratory at the
University of Cincinnati between September 26 and October 9, 2002; and (2) an
Ohio Poll of 900 adults conducted by the Institute for Policy Research at the
University of Cincinnati between September 4 and September 15, 2002.

Public Ignorance and Public Opinion

Despite significant coverage and editorials on the ID issue in Ohio's news
media in recent months, most Ohioans still know little or nothing about
"intelligent design". In the most recent Ohio Poll, conducted between September
4 and September 15, 2002, respondents were first asked: " Do you happen to know
anything about the concept of 'intelligent design'?" The vast majority (84%)
said "no"; 14% said "yes"; and the rest (2%) were "not sure". Not surprisingly,
college graduates were significantly more likely to say they knew something
about it (28% of them) than were high school graduates (7%) or those with less
than a high school education (6%).

Whether they knew anything about it or not, respondents were then given a brief
description of the concept of intelligent design identical to the one used in a
statewide Cleveland Plain Dealer Poll conducted this past spring:

"The concept of 'intelligent design' is that life is too complex to have
developed by chance and that a purposeful being or force is guiding the
development of life."

"What is your opinion-do you think the concept of 'intelligent design' is a
valid scientific account of how human life developed, or is it basically a
religious explanation of the development of human life?"

Given this description, the majority of Ohioans (54%) viewed it as basically a
religious explanation of human origins; less than 1 out of 4 (23%) thought it
was a valid scientific account; 7% believed it was a mix of religious and
scientific accounts; and 17% said they were "not sure."

Views of Ohio Science Professors

Not unexpectedly, those who have the academic training and expertise (PhDs) to
teach the basic natural and physical sciences in Ohio's public and private
universities regarded the concept of "intelligent design" as an unscientific
notion. More than 9 out of 10 (91%) thought it was primarily a religious view.
The vast majority (93%) of science professors said they were not aware of "any
scientifically valid evidence or an alternate scientific theory that challenges
the fundamental principles of the theory of evolution." Only a tiny percentage
of them (7%) thought that "intelligent design" was either "strongly" or
"partly" supported by scientific evidence. Most (90%) believed there was no
scientific evidence at all for the idea of "intelligent design". And 3% were
"not sure". Furthermore, when asked if they ever used the ID concept in their
research, virtually all of them (97%) said "no."

Ohio's science professors felt just as strongly about what should or should not
be taught about the controversy in Ohio schools. Most all of them (92%) thought
" Ohio high school students should be tested on their understanding of the
basic principles of the theory of evolution in order to graduate." When asked,
however, if such students should also be tested on their knowledge of the
concept of "Intelligent Design" in order to graduate, most of them (90%) said
"no."

Perhaps the most surprising finding in the survey is that the great majority of
Ohio science professors (84%) thought that accepting the theory of evolution
was "consistent with believing in God." Only 9% thought it was not; and the
rest (7%) just weren't sure. Most critics of teaching evolution in Ohio's
schools commonly assume it's basically inconsistent with believing in God.
Evidently, most of Ohio's science professors-those who understand the theory of
evolution best-do not share that widespread view.

Further statistical analysis of the data from the survey of Ohio science
professors showed only minor differences in responses across scientific fields
such as astronomy, biology, chemistry, geology, physics, and other natural
sciences.

Survey Methodology


Ohio Poll

The sampling error for the Ohio Poll of 900 adults is +/-3.3%. A description of
the methodology for the Ohio Poll conducted from September 4 through 15 can be
found at the following website:

http://www.ipr.uc.edu/PDF/OhioPoll/op092502.pdf



Internet Public Opinion Laboratory (IPOL): Methodology

An e-mail invitation to participate in this web-based survey was sent to all
professors (approximately 1500) currently on the faculty in four-year, public
and private colleges and universities in Ohio for the following fields:
Astronomy, biology, chemistry, geology, physics, and other natural sciences.
Their e-mail addresses were identified through a combination of listings on the
various college and departmental websites, supplemented by further examination
of other university information sources. Four hundred and sixty (460)
professors responded to the e-mail invitation, a response rate of 31%.

The sampling error for a sample size of 460 cases is approximately plus or
minus 4.5%. As in any other survey, in addition to sampling error, other
sources of error such as non-response and the wording and context of the
questions asked can affect the results and conclusions of the study.


The results reported here for the Internet survey of Ohio science professors
were based on the following questions (Note: Percentages Rounded)

1.      Are you aware of any scientifically valid evidence or an alternate
scientific theory that challenges the fundamental principles of the theory of
evolution?

a.      Yes              4%
b.      No              93
c.      Not Sure         2

2.      The concept of "Intelligent Design" is that life and the universe are too
complex to have developed without the intervention of a purposeful being or
force to guide the development of life. Which of the following do you think
best describes "Intelligent Design"?

a.      It is strongly supported by scientific evidence  2%
b.      It is partly supported by scientific evidence            5
c.      It is not supported at all by scientific evidence       90
d.      Not Sure                                                             3

3.      Do you think the concept of "Intelligent Design" is primarily a religious
view?"

a.      Yes             91%
b.      No               5
c.      Not Sure         4

4.      Do you think Ohio high school students should be tested on their
understanding of the basic principles of the theory of evolution in order to
graduate?

a.      Yes             92%
b.      No                4
c.      Not Sure          3

5.      Do you think Ohio high school students should be tested on their knowledge
of the concept of "Intelligent Design" in order to graduate?

a.      Yes               6%
b.      No               90
c.      Not Sure          4

6.      Do you use the concept of Intelligent Design in your research?

a.      Yes               2%
b.      No               97
c.      Not Sure          1


7.      Do you think accepting the theory of evolution is consistent with believing
in God?

a.      Yes             84%
b.      No                9
c.      Not Sure          7

********************************************************************************
University of Cincinati

October 10, 2002
Contact: Carey Hoffman


NEW POLL DATA SHOWS OHIOANS SEE 'INTELLIGENT DESIGN'
AS A RELIGION-BASED CONCEPT

       Cincinnati   The controversial concept of "intelligent design" theory, now
under consideration by the Ohio Board of Education, is seen by Ohio scientists
and the general public as basically a religious explanation of human origins.
That's according to a new study released today that was conducted jointly by
researchers at the University of Cincinnati and Case Western Reserve University.

       Two surveys were analyzed to produce the findings - an Internet survey of 460
science professors from across Ohio and an Ohio Poll of 900 adults conducted in
September. A summary analysis of the data by UC's George Bishop accompanies
this release.

       Bishop is a professor of political science and director of UC's Internet
Public Opinion Laboratory. A widely-known expert on public opinion surveying,
he has done extensive work on the topics of Americans' religious world views
and beliefs about human origins. Bishop can be reached in his office this
afternoon after 3 p.m.

       Case Western's work was led by Joseph Koonce, chair of the biology department.
Case Western will host a press conference in Cleveland this afternoon at 2:45
p.m. in Room 405 of Clapp Hall to discuss the study.

Media contacts: George Bishop, University of Cincinnati.
Joseph Koonce, Case Western Reserve University.
Susan Griffiths, Case Western Reserve University Communications Office.

110-02  -30-


*******************************************************************************


Case Western Reserve University

October 10, 2002                                Contact:        Susan Griffith
                                                               Senior Media Relations Representative


CWRU FACULTY REPORT FINDINGS
ON EVOLUTION, INTELLIGENT DESIGN POLL OF OHIO'S SCIENTISTS

       CLEVELAND--Nine out 10 Ohio scientists from secular and religious colleges and
universities responding to a survey say that intelligent design is primarily a
religious view and not part of science.  Case Western Reserve University
faculty reported on the findings of the Internet poll during a news conference
Thursday, October 10.

       "This is the first time we have hard data on what Ohio's scientists think
about the issue of intelligent design versus evolution," says Joseph Koonce,
CWRU chair and professor of biology.

       Koonce designed the Internet survey with the Internet Public Opinion
Laboratory at the University of Cincinnati.  He sent out e-mail messages around
the state to faculty in departments of astronomy, biology, chemistry, geology,
physics and other natural sciences, urging them to answer a set of questions
and to give their thoughts about the evolution-intelligent design debate.  The
survey was conducted between September 26 and October 9.

       Prior to polling the scientists, the Institute for Policy Research at the
University of Cincinnati included questions on the September Ohio Poll
(conducted September 4-15) about intelligent design, asking the general public
to respond to a similar Internet poll on their views of intelligent design and
evolution.  Like the scientists, a clear majority of Ohio residents found
intelligent design to be religious, and not a scientific view.

       Findings from the polls, come days before the State Board of Education faces
the issue at its meeting on next Monday on whether to include intelligent
design or other forms of anti-evolutionism in the new K-12 science standards.
Intelligent design advocates claim life is too complex to have developed
without the intervention of a supernatural being or force, and they claim their
view is scientific.

       Most all of Ohio's science professors (92%) thought "Ohio high school students
should be tested on their understanding of the basic principles of the theory
of evolution in order to graduate."  Scientist responded negatively (90%) to
the testing about the knowledge of "intelligent design" as a requirement to
graduate.

       The survey also explored scientists' views on antievolutionism beyond the
intelligent design movement.  Some critics of evolution claim evidence against
the theory of evolution has caused it to fall out of favor among scientists.
This is clearly not the case in Ohio where the vast majority (93%) of science
professors said they were not award of "any scientifically valid evidence or an
alternative scientific theory that challenges the fundamental principles of the
theory of evolution."

       Finally, the survey investigated the popular theme of a war between science
and religion in America and found no such conflict.  The great majority of Ohio
science professors (84%) thought that accepting the theory of evolution was
"consistent with believing in God."  Only nine percent thought it was not; and
the rest (7%)  were not sure.  Most critics of teaching evolution in Ohio's
schools commonly assume it is inconsistent with believing in God.  Evidently,
most of Ohio's science professors-those who understand the theory of evolution
best-do not share that view.

       Among the survey's findings were:

-       Nine out of 10 scientists (91%) felt the concept of intelligent design was
unscientific and the same number responded that it was a religious view

-       A vast majority (93%) of the scientists were not aware of "any scientifically
valid evidence or an alternate scientific theory that challenges the
fundamental principles of the theory of evolution"

-       Almost all scientists (97%) said they did not use the intelligent design
concept in their research

-       Ninety percent of the responding scientists stated that they felt no
scientific evidence supports intelligent design, while 2% were unsure

-       Approximately 7% felt that intelligent design had some support from
scientific evidence

-       Some 84% felt acceptance of the evolution theory was "consistent with
believing in God"

        A total of 460 professors responded or a rate of 31%.  The survey had an
error of plus or minus 4.5%.  "We are extremely pleased with the response,"
says Koonce

       For further information, contact Koonce.



*******************************************************************************


October 10, 2002
Press Conference Statement of
Professor Joseph F Koonce
Chair, Dept of Biology
Case Western Reserve University



Many claims have been made in recent months as to what Ohio scientists think
about intelligent design "theory." However, until now, no data existed on
this issue. My colleagues and I set about to collect the data so that the
public may gain an accurate impression of what Ohio's scientists think. The
results are gratifying and unequivocal.

Nine out of ten Ohio scientists from Ohio public, private (including both
secular and religious) universities say that intelligent design is primarily
a religious view and is simply not part of science.

We designed and conducted this survey with the Internet Public Opinion
Laboratory at the University of Cincinnati.  We sent out email messages
around the state to faculty in departments of astronomy, biology, chemistry,
geology, physics and other natural sciences, inviting them to answer a set
of questions and to give their thoughts about the evolution-intelligent
design debate.  The survey ran between September 26 and October 9.

        Prior to polling the scientists, the Institute for Policy Research
at the University of Cincinnati included questions on the September Ohio
Poll (conducted September 4 through 15, 2002) asking the general public to
respond to two questions about intelligent design. Like the scientists, a
clear majority of Ohio residents found intelligent design to be religious,
and not a scientific view.

       Next Monday and Tuesday the Ohio Board of Education will vote on
whether to include intelligent design or other forms of anti-evolutionism in
the new K-12 science standards.  Intelligent design advocates claim life is
too complex to have developed without the intervention of a supernatural
being or force, and they claim their view is scientific. Clearly Ohio's
citizens are not convinced that this argument should be taught as science.

I want to make clear that I am a religious person myself. As a Roman
Catholic, I do believe in God and in concurrence with teachings of the
Catholic Church, I have never found these beliefs in conflict with
Evolutionary Theory.  Science addresses the nature of the physical universe,
not the supernatural or the eternal. Like me, 84% of my colleagues also
report that they find evolutionary theory compatible with belief in God.

I wish this would lay to rest the destructive notion that science and
religion are at war in America. There is no such inherent conflict. Science
and religion can promote and enhance each other without having to pretend we
know less than we actually do about how the world is constructed and how it
functions.

Most all of Ohio's science professors (92%) thought "Ohio high school
students should be tested on their understanding of the basic principles of
the theory of evolution in order to graduate." When asked if such students
should also be tested on their knowledge of the concept of "Intelligent
Design" in order to graduate, 90% said "no." Only 2% said that intelligent
design was strongly supported by scientific evidence.

The survey also explored scientists' views on antievolutionism beyond the
intelligent design movement. Some critics of evolution claim evidence
against the theory of evolution has caused it to fall out of favor among
scientists. This is clearly not the case in Ohio where the vast majority
(93%) of science professors said they were not aware of "any scientifically
valid evidence or an alternate scientific theory that challenges the
fundamental principles of the theory of evolution."

We are extremely pleased with the response. Nearly 500 scientists responded,
a rate of 31%.  The survey had an error of plus or minus 4.5 percent.
Equally pleasing was the outpouring of gratitude for providing the
opportunity to express their concern with the erosion of scientific literacy
in the developing K-12 standards for Ohio.




*******************************************************************************




Please see the Ohio Citizens for Science's web page at:

http://ecology.cwru.edu/ohioscience/


---------------------------------------------------------------------------
Steven A. Edinger, Physiology Lab Instructor

064 Irvine Hall
Department of Biological Sciences               steven.edinger.1@ohio.edu
Ohio University                                 Office:  (740) 593-9484
Athens, Ohio  45701-2979                        Fax:  (740) 593-0300
---------------------------------------------------------------------------

******************************************************
"Nothing in biology makes sense except in the light of
evolution."  Theodosius Dobzhansky, 1973
******************************************************

Date: 2002/10/12 16:54:41, Link
Author: Wesley R. Elsberry
More news from Ohio...

Evolution may be hot topic, but barely makes ripple in races (Akron Beacon Journal, 2002/10/12)

The contentious debate over evolution and "teaching the controversy" doesn't seem to be having an effect on most of the political races for positions on the board of education.

Date: 2002/10/13 05:41:59, Link
Author: Wesley R. Elsberry
State refuses to advance intelligent design theory (Canton Repository, 2002/10/13)

Quote
Pat Barron, facilitator for the writing team, said the panel held “considerable discussion about what to put in, what to leave out” and examined virtually every piece of public input.

“To have intelligent design in the standards as something that is documented in science, (they) just didn’t believe that there’d been sufficient research evidence,” she said.


That's a considerable understatement.

Date: 2002/10/13 05:50:39, Link
Author: Wesley R. Elsberry
Darwin's theory 'may explain ill health' (BBC News, 2002/10/12)

Quote
Professor Randolph Nesse believes that conditions like heart disease, obesity and drug abuse can all be explained by the fact that the human body was not designed for the 21st Century.

He suggests many serious illnesses occur because the human body has failed to evolve and is still designed for a much simpler existence.

Date: 2002/10/13 06:03:22, Link
Author: Wesley R. Elsberry
Chinese Hominid Challenges Out-of-Africa Origin of Modernman (People's Daily, 2002/10/12)

Quote
A recent finding in the dating of Chinese hominid fossils has challenged the prevailing "out-of-Africa" theory regarding the origin of modern man.

With a new dating method, scientists determined that Liujiang Hominid roamed south China approximately 70,000 to 130,000 years ago, rather than 30,000 years ago or less as it was previously believed. This new finding supports the theory that modern Chineseman originated in what is present-day Chinese territory rather than the mainstream "out of Africa" hypothesis which held that modern humans evolved from African ancestors alone.


The article claims that the "out-of-Africa" theory dates to 1987.  The writer is only about a century and a bit off.

-------------

Man or ape? African fossil sparks verbal war (Independent Online, South Africa, 2002/10/11)

Quote
Their claim is that Toumai will overturn the conventional view of mankind, because the evolutionary split between apes and humans clearly occurred far earlier than molecular studies suggest.

Nonsense, say a team led by Milford Wolpoff of the University of Michigan, who suggest the ape-like features found on Toumai mean he was no more than that - an ape.

Date: 2002/10/13 06:08:58, Link
Author: Wesley R. Elsberry
Radioactive sand causes mutations in human DNA (Genome News Network, 2002/10/11)

Quote
Radiation has been known to cause cancer and damage to human cells, but it has been less clear to what extent it affects human DNA. Now, researchers have observed that high levels of naturally occurring radiation significantly increase the number of mutations in human DNA.




Date: 2002/10/14 09:36:00, Link
Author: Wesley R. Elsberry
DNA analysis cracks HIV case (Health News, 2002/10/14)

Quote
The case is the first time that "phylogenetic analysis" - a study of the mutation rate of an organism - has been used in a court of law, according to Dr David Hillis of the University of Texas in Austin and colleagues.

This case demonstrates that it is now possible to trace the pathway of infections of viruses among individuals within a population, Hillis said.

Date: 2002/10/14 10:23:14, Link
Author: Wesley R. Elsberry
Another press item on Ohio.

School Board Panel Puts Final Touches On Science Standards (WCMH, 2002/10/14)

Quote
A final draft of the standards takes an evolution-only approach, despite efforts by some board members to add a concept called "intelligent design," the idea that a higher power must have designed life because it is so complex.

Critics say the concept is a version of divine creation, which the U.S. Supreme Court has barred from being taught in public schools.

Date: 2002/10/14 10:42:06, Link
Author: Wesley R. Elsberry
Battle of the bugs (Independent, UK, 2002/10/14)

Quote
Earlier this year, scientists took the decision to deliberately introduce a ladybird from Australia to the Galapagos in order to curb the continuing expansion of the cottony cushion scale insect. This pest, whose presence on the islands was first reported in 1982, has over the past 20 years become enemy number one for 19 Galapagos plants, including six endangered species, of which two are on the verge of extinction.


This is the first use of biocontrol in the Galapagos Islands.  The article touches upon the testing and evaluation process.

Date: 2002/10/14 19:34:39, Link
Author: Wesley R. Elsberry
Another news item:

Ohio Panel Gives Evolution Nod (Dayton Daily News (AP), 2002/10/14)

Quote
A state school board panel Monday recommended that Ohio science classes emphasize both evolution and the debate over its validity.

The committee left it up to individual school districts to decide whether to include in the debate the concept of ``intelligent design,'' which holds that the universe is guided by a higher intelligence.

Date: 2002/10/14 20:09:31, Link
Author: Wesley R. Elsberry
Darwin to receive Scots honour (BBC News, 2002/10/14)

Quote
Scotland's capital city is finalising plans to honour biologist Charles Darwin.

A plaque will be unveiled in memory of the scientist who developed the revolutionary theory of natural selection.

Date: 2002/10/15 08:09:49, Link
Author: Wesley R. Elsberry
More news.  Same data, different interpretation.

Intelligent design absent from science standards (Zanesville Times Recorder, 2002/10/15)

Quote
The evolution section of the standards does include instructions to teach "how scientists continue to investigate and critically analyze aspects of evolutionary theory."

The language was adopted over the objections of board member Marlene Jennings of Kirtland, who called it an attempt to insert intelligent design into the standards surreptitiously.

But board member Michael Cochran of Blacklick, who introduced the language, said Jennings was twisting the words.

"This just reflects that there is some debate in the scientific community currently," he said. "There are none of the buzz words that point to other theories."


Note that Cochran is on record as saying that this particular phrasing is not about opening the door to "intelligent design" discussion.  My bet is that Cochran is either being disingenuous or just plain lying.  So watch what "intelligent design" advocates say about this part of the proposed standards; if they tout it as a victory for their viewpoint, that makes a stronger case for deliberate deception on Cochran's part.

Date: 2002/10/15 18:16:13, Link
Author: Wesley R. Elsberry
The Ohio Board of Education Vote

What the news outlets say...

Ohio OKs Creation in Science Class (Newsday (AP), 2002/10/15)

Quote
The state school board said Tuesday it will adopt a science curriculum that leaves it up to school districts whether to teach the concept of "intelligent design," which holds that the universe is guided by a higher intelligence.


Same AP story, different headline.  This link gives more of the AP story.

School board panel: Ohio students should be taught evolution (Wilmington News Journal (AP), 2002/10/15)

Another story on the local impact:

State decision not likely to have great impact on local processes, educator says (Wilmington News Journal, 2002/10/15)

Quote
I think it could excite some people to think that things are going to happen that probably won’t," said Melissa Snyder, Blanchester Schools’ director of instruction. "I know that our science teachers are going to go ahead and teach science.

"They want to meet the state’s standards, but I don’t think they’re going to open up a bunch of controversial topics just because there’s some language at the state. They pretty well respond to the community and to their students’ interests and needs, as far as what they need to know in science."

Date: 2002/10/15 18:23:14, Link
Author: Wesley R. Elsberry
And a response from "intelligent design" advocates:

Intelligent Design Debate 'A Small First Step' States Ohio Roundtable (PR Newswire, 2002/10/15)

Quote
"The debate over intelligent design as a viable addition to state science standards proves just how inflexible the education establishment has become. According to recent polls, over 80% of Ohioans would prefer to have an open classroom environment for the discussion of scientific theories of origins. Yet changing a handful of words in the standards has created near hysteria among many in the education establishment.
   Today's vote by the board is a small first step in the direction of open dialogue and freedom of thought. It falls far short of acknowledging the tremendous outpouring of public support for change in the state standards."

Date: 2002/10/15 18:55:36, Link
Author: Wesley R. Elsberry
Op-ed piece on the coming elections...

Showdown is likely over SBOE election (Doug Anstaett, The Kansan Online, 2002/10/15)

Quote
And our view is that faith issues must continue to be separated from the teaching of scientific fact in our public schools.

Science is science. Faith is faith.

Churches can teach what they want. That freedom is protected by the U.S. Constitution.

But our public schools must stick to the facts, even if some of those facts are still in dispute.

Date: 2002/10/15 20:32:26, Link
Author: Wesley R. Elsberry
Discovery Institute Claims Victory in Ohio

Ohio Board Backs Academic Freedom and Encourages Critical Analysis of Evolution (DI CRSC, 2002/10/15)

Quote
The Board's approach was anticipated by a proposal made earlier in the year by Dr. Meyer. Testifying before the Board of Education in March 2002, Meyer proposed requiring students to understand the scientific arguments for and against Darwinian evolution and allowing (but not requiring) local districts to include "intelligent design" as part of teaching the scientific controversy over evolution.


Like I noted earlier, Cochran's statement that the language wasn't about admitting "intelligent design" looks like it was either disingenuous or deliberate deception.

Date: 2002/10/16 09:03:08, Link
Author: Wesley R. Elsberry
Op-ed gives BOE kudos for decision...

School board did right thing on evolution (Lancaster Eagle-Gazette, 2002/10/16)

Quote
Board members stressed that they do not believe that the standards encourage students to learn intelligent design or other concepts not rooted in science. We agree. A science curriculum should stick to proven scientific facts.

The 19-member board voted unanimously to adopt the standards, and we are pleased that even those who pushed for intelligent design are receptive to the compromise.

In the end, decisions over teaching intelligent design ended up where they should with the local districts.


News item on the BOE vote...

State approves new science guidelines (Lancaster Eagle-Gazette, 2002/10/16)

Quote
The new science standards, used as a baseline for the state's proficiency exams, do include teaching evolution in biology classes in high school and middle school. But they also include the caveat that teachers discuss "how scientists continue to investigate and critically analyze aspects of evolutionary theory."

That language, added Monday during a committee meeting, was deemed innocuous but important by board members sympathetic to intelligent design, the belief that a higher power played a role in the creation of all life.

"This is not ID," said board member Deborah Owens Fink of Akron, who introduced the analysis language. "This is not introducing religious perspectives. This is only introducing scientific perspectives."


That's not what the Discovery Institute thinks.  I think Owens-Fink is, like her colleague Michael Cochran, being either disingenuous or deliberately deceptive on this.  The test will be whether "intelligent design" is permitted or encouraged as an alternative "scientific" view to be discussed when evolution is mentioned in science classes.

Date: 2002/10/17 04:01:00, Link
Author: Wesley R. Elsberry
Op-ed on the BOE decision...

A waste of time: School board mentality is unevolved (Cliff Radel, Cinncinnatti Enquirer, 2002/10/17)

Quote
The board's decision was by design. But, it wasn't intelligent.

Made in the spirit of compromise with certain board members, being open-minded, bowing to thousands of e-mails pushing intelligent design - take your pick - this decision sets a vile precedent. It opens the floodgates to every half-baked, crackpot notion about any subject taught in school.

Above all, it amounts to a waste of precious time.

Date: 2002/10/17 04:12:00, Link
Author: Wesley R. Elsberry
The Moonie take on the Ohio decision...

Ohio schools to teach evolution 'controversy' (Larry Elder, Washington Times, 2002/10/17)

Quote
    In the first of the two changes, the definition of science has been broadened to "a systematic method of continuing investigation" of nature. It replaced the previous contention that science is limited to "natural explanations," which, according to some, rules out any concept of a Creator.
    Ms. Princehouse said the change is "innocuous." But Mr. Lattimer said it allows students to consider that a higher force can be part of how science interprets the world.
    The second statement requires that teachers "describe how scientists continue to investigate and critically analyze aspects of evolutionary theory."
    The decision by a five-member standards committee followed a year of hearings and public opinion polls indicating that Ohioans liked the idea of "teaching the controversy."

Date: 2002/10/18 08:24:32, Link
Author: Wesley R. Elsberry
Commentary by Pamela Winnick

Inherited Debate: Ohio classrooms get a second opinion on evolution (National Review Online, Pamela Winnick, 2002/10/18)

Quote
In what could turn out to be a stunning victory for opponents of evolution, the Ohio Department of Education voted 17-0 on Tuesday to pass a "resolution of intent" to adopt science standards that would allow students to "investigate and critically analyze" Darwin's theory of evolution. With additional hearings scheduled for November and a final vote to be held in December, Ohio is likely to become the latest battleground in the never-ending debate over how life began.


Quote
Pamela R. Winnick, a lawyer admitted to practice in New York, has been a reporter for the Pittsburgh Post-Gazette and the Toledo Blade. A 2001 Phillips Foundation fellow, she is writing a book about the politics of evolution.


When one looks into the fellowship Winnick received, it appears that she is being paid as a partisan anti-evolutionist, not just as an investigative reporter.  I've never seen the partisan nature of Winnick's fellowship noted in relation to her "news" stories.



Date: 2002/10/20 12:35:55, Link
Author: Wesley R. Elsberry
SEAO plans to capitalize on BOE wording

RESOLUTION OF INTENT TO ADOPT SCIENCE STANDARDS (accessed 2002/10/20)

Quote
Overall, we commend the State Board for making these changes. This recognizes, in part, the results of public input which show that a large majority of Ohioans favors the teach-the-controversy approach. This also acknowledges a growing number of credentialed scientists, including over fifty from Ohio, who endorse a teach-the-controversy approach to biological evolution. We feel that the changes that have been made will align the new standards with the Santorum language in the federal education bill, the 'No Child Left Behind Act' of 2001. In addition, these changes will contribute substantially to better objectivity in biological origins instruction.

Date: 2002/10/20 12:41:56, Link
Author: Wesley R. Elsberry
Most schools steering clear of evolution (Atlanta Journal-Constitution, 2002/10/20)

Quote
The mercury rose a notch or two in Cobb County this year as the community debated how evolution should be taught.

The reality is that, in Georgia, evolution rarely is.

Teachers veer away from discussing the topic and the state requires little learning in that area, educators say.

Date: 2002/10/20 12:53:20, Link
Author: Wesley R. Elsberry
Selman v. Cobb County: court battle over creationism (JTA News, 2002/10/16)

Quote
Selman dismisses charges by Cobb backers of creationism that he is anti-religion and said 95 percent of the phone calls he has gotten have been positive.

“I’m not against anybody’s religion,” Selman said. “I want everybody to practice what they believe. I practice [Judaism] the way I want to.”

Date: 2002/10/21 01:09:40, Link
Author: Wesley R. Elsberry
Amateurs find fossil of `world's oldest spider' (icWales. 2002/10/21)

Quote
A TEAM of amateur palaeontologists has stumbled upon the fossil of what they say could be the world's oldest spider.

The remains of a spider-like creature discovered in a sandstone quarry in Mid Wales are expected to send a wave of excitement through arachnologists.

Date: 2002/10/21 11:26:19, Link
Author: Wesley R. Elsberry
Hovind's side of the story

Quote
It is obvious that the reporting officer saw none of the events described in the report and is taking the word of two people with a history of violence and mental illness. It is my sincere belief that the report is deliberately worded to make me look guilty and make officer Burk’s unnecessary arrest look justified. No one in the house was ever touched or threatened in any way except me.


It's an interesting read.

Date: 2002/10/23 11:53:04, Link
Author: Wesley R. Elsberry
Intelligent Design advocate lauds state plan on teaching evolution (Cleveland Plain Dealer, 2002/10/23)

Quote
"Our slogan to the press is, Teach the controversy,' " said Johnson, widely regarded as the father of the modern intelligent-design movement.

Ohio's decision to allow that controversy in science classrooms has drawn fire from the science community, which has accused the intelligent design advocates of attempting to slip religion into the classroom by the back door.

That doesn't bother Johnson, who said the scientific establishment keeps the Darwin "myth" afloat by controlling funding and keeping research it doesn't like out of scholarly journals. Ohio, Johnson said, has "liberated" teachers to teach all sides of origins.


The article dances around the political aspect of Johnson's talk.  We have the indication of press manipulation, and elsewhere there is mention of planning in Kansas being less well done than it was in Ohio.  Hello?  The press just doesn't seem to get it.

Date: 2002/10/24 08:58:29, Link
Author: Wesley R. Elsberry
Darwinism in Crisis

Quote
For well over a century now the reigning scientific view has been that the existence of life in the universe could be explained on the basis of natural processes alone. In the light of new research in science and philosophy by a group of first-rank Christian scholars, this view is no longer tenable and is being challenged around the world.

YOU ARE INVITED TO THIS RARE OPPORTUNITY TO COME AND LEARN ABOUT “INTELLIGENT DESIGN” THEORY FROM THE VERY SCHOLARS WHO HAVE STARTED THIS REVOLUTION IN THE HISTORY OF IDEAS!

Witness the news media and academic community from around southern California ask the tough questions about the “Intelligent Design” Revolution.

WHEN: Thursday evening, October 24, 2002 from 7:00 to 9:30PM

WHERE: Chase Gymnasium on the Biola University campus in La Mirada

COST: $10 per person. Tickets are available at the door only. Best seats available for early arrivals.


I plan on going, but I can't say that I was specifically requested as part of the academic community in SoCal.  I can well imagine that they may have requested press coverage, but I haven't heard anybody say that they've encouraged the skeptics to attend.

This is held just prior to the Research & Progress in Intelligent Design (RAPID) Conference at Biola.  I tried to register for this conference, but was told it is a closed event.

Notice that Biola's Christian Apologetics program, which is organizing the "Darwinism in Crisis" panel, identifies the group as "Christian scholars".  It is a refreshing break from the false claim of "top scientists" deployed in the past by the Discovery Institute.



Date: 2002/10/25 13:53:28, Link
Author: Wesley R. Elsberry
Astrobiology Update: Oxygen-making Microbes Came Last, Not first (SpaceRef.Com, 2002/10/25)

Quote
"What paleontologists and geologists have had to do is reconstruct evolutionary events because biologists haven't had a very good evolutionary tree of bacteria," says Blank. To get a better family tree, Blank took advantage of growing genome archives and studied 38 genes in the whole gene sequences of 53 species of extant bacteria, including Cyanobacteria. By mapping out the rates of change in the slowest-changing genes, Blank was able to generate a bacterial evolutionary history that shows cyanobacteria branching off last.




Date: 2002/10/29 23:53:59, Link
Author: Wesley R. Elsberry
Publishers alter texts to try to make grade (Houston Chronicle, 2002/10/29)

Quote
Bowing to political pressure, publishers of social studies textbooks have changed passages dealing with events ranging from the Alamo to last year's terrorist attacks.

The publishers are hoping the changes will help their 200 textbooks gain approval next month from the State Board of Education. That approval is key to getting a piece of the $345 million market.

[...]

For example, a reference in a sixth-grade social studies book to glaciers forming the Great Lakes "millions of years ago" was changed to "in the distant past."

Robert Raborn, a member of the conservative Citizens for a Sound Economy, had complained that "millions of years ago" supported the theory of evolution and excluded theories such as intelligent design.


How can ID be excluded by a reference to millions of years, when ID advocates won't take a stand on how old the earth is?

Date: 2002/10/30 00:03:26, Link
Author: Wesley R. Elsberry
Despite failing, Taft is better choice for Ohio (News-Messenger, 2002/10/28)

Quote
At a recent joint appearance before a group of Ohio newspaper editors, Hagan challenged Taft on his stance on the intelligent design vs. evolution debate before the state school board. Hagan said that if he were the governor, he would speak forcefully on the issue, telling Ohioans that intelligent design can be taught in comparative religion classes or philosophy classes but that it does not belong in science classes.

He then asked Taft for his opinion. Taft evaded the question by saying that a committee was working on the issue. An editor followed up: OK, so a committee is looking into it, but what is your position, Gov. Taft? The governor refused to answer.

The reason: Taft can't win votes by telling us his position. But he can lose votes, so he keeps quiet.

That's not leadership, governor. Tell us what you think. Tell us what needs to be done. Make the hard decisions and then force the Legislature to deal with it. If you get another four years, you need to show that you deserved it.


In a lukewarm endorsement of Taft for re-election as governor of Ohio, the editorial gives us this vignette of an encounter on the campaign trail.  The editorial writer nails it on the head, and reminds me of Acton's aphorism that all that is necessary for evil to succeed is for good men to do nothing.

Date: 2002/11/04 21:02:45, Link
Author: Wesley R. Elsberry
Birds of a Feather (USC Research, 2002/10/30)

Quote
Scientists from the Keck School of Medicine of USC for the first time have shown experimentally the steps in the origin and development of feathers, using the techniques of molecular biology.

Their findings will have implications for the study of the morphogenesis of various epithelial organs – from hairs to lung tissue to mammary glands – and is already shedding light on the controversy over the evolution of dinosaur scales into avian feathers.

Date: 2002/11/10 15:28:27, Link
Author: Jacor
I just want to make the observation that if the level of scientific "thought " as presented by the person with the title of "Information Representative" of AiG is true of the actual science used by them.  I predict that within 2 generations of Creationists being able to teach their "science" as a valid alternative theory, society will be well on its way back to pre-scientific levels of health and knowledge.  This is due to the superficial level of thinking that is encouraged.

John Verderame, in a fairly detailed non-answer to my statement on why I did not accept his generalizations as answers to my specific questions. gave this Bio.  "I have a B.S. in Biology and a Master of Theology degree from a highly respected Seminary and almost 30 years of work experience both in ministry and in the fields of biology and astronomy, so have done some studying too."

In response to my observation that the problem with relying on the Bible to answer anything that is not currently in the "known" column in science is that it discourages the original research needed to find the answers.  His response was "prove that".  He also referred me to a list of "research" done by creationists.
Here is what I found.

Dr Steve Austin PhD, describes self as Creationist Geology Professor, B.S. (Geology), University of Washington, Seattle, WA, M.S. (Geology), San Jose State University, San Jose, CA, Ph.D. (Geology), Pennsylvania State University, University Park, PA.
Only acknowledged publications are in Creationist publications, and are not on field of specialty of Geology.  No original research.

Dr Don Batten  He is doing work that any self-respecting agriculturist does.  He might have a new hybrid, but no original research.  Does have publications in Creationist publications on mutation as evidence of divine intervention, other than "the Bible tells me so", no supporting evidence.  He makes unsupported statements about the number of nucleotides that can be changed before becoming fatal (3).  I will point out that 3 nucleotides do not make up a single gene.  His degree is in Horticulture.

Dr John Baumgardner  (B.S, M.S., PhD (UCLA)) is a geophysicist employed at the Los Alamos National Laboratory in New Mexico. His work involves detailed computer modeling of the structure and processes of the earth's interior, as well as a variety of other fluid dynamics phenomena.  
Only published works supporting Creationism is at 3 Creation Conferences, and are not related to his field of study.  
Is this supposed to impress me?  Especially since his bio states that he changed majors to prove creationism is correct.  Since he has not run any tests to prove or disprove his hypothesis he can not claim that his belief is anything other than an opinion.

Jerry Bergman  PhD Psychology  Published in Creationist publications on topic of why there is no scientific support for evolution.
I know a master level psychologist that believes that watermelons are cucumbers left on the vine too long.  So?

I do not see any original research here.  How does this disprove my statement?

Dr. Verderame's response:  "(What are YOUR credentials, that you are in such a position to pass judgment?)"

Like an idiot I actually sent them.  AAS Nursing, BS double major Chemistry and Biology

His response: "Please don't expect any further responses.  We are not getting anywhere.

Have a good weekend.

John"

Since the following are verbatim quotes from him in two earlier communications I must state that I do not have his permission to quote this, however I am quoting just to show his level of response when he can't think of anything better.
He cited Pasteur as being the perfect "Creationist Scientist" because he developed the germ theory despite opposition by scientific thought.  In response I sent an abbreviated history of contributors to the germ theory going back to 50 AD.  He now changes his argument to:
JV:  "What is your point?  Of course, no theory arises in isolation.  We point out that evolution has its basis in ancient Greek philosophy.  But Darwin helped to systematize and quantify the concept so that those who followed him recognize his work as a watershed.  Same with Pasteur.  
I could not resist, so my response and his reply follows.
He inserted responses in my answer and they are designated as "JV".

Technically since Pasteur did not publish, and Koch provided the proof, Koch should be credited with the formulation of the theory.
JV:  Nice try.  So 'publishing' is what distinguishes the men from the boys, eh?

Otherwise credit would have to go to Henle in 1840. As pointed out in the section on Koch, just like evolution, the Germ Theory continues to "evolve."

JV:  Which you have yet to demonstrate ;-)  Throw the word around all you want.  But back it up with facts.  You know those microorganisms Pasteur and Koch played with?  Make one.  Starting with nothing.  And then, if you can do it, prove to me it took no intelligence to do it.

I could not reply to his comments as he cut communication with me.  The range of topics had grown to the proportion that there was no cohesive way to respond to all of them in each communication.  The list kept growing as Dr. Verderame added to the list each time.  I think he was planning on overwhelming me with the sheer volume of topics.

Paul C



???

Date: 2002/11/25 20:18:13, Link
Author: Mr. Davies
Hello all,


Thank you for this board for discussion.

I have a question about ID.  In particular, does ID make any assumption in the identity of the designer?  If so who, if not, why not?

Date: 2002/11/26 16:08:25, Link
Author: theyeti
Quote (Mr. Davies @ Nov. 25 2002,20:18)
Hello all,


Thank you for this board for discussion.

I have a question about ID.  In particular, does ID make any assumption in the identity of the designer?  If so who, if not, why not?

Basically no.  The whole premise of the modern ID argument (and that of Paley I suppose) is that one can detect design in the absence of any knowledge of the designer.  

Why not?  I'll try to expand on that later.

theyeti

Date: 2002/11/26 17:20:32, Link
Author: theyeti
Hello all.  What follows is a brief essay (or rant if you prefer) about the claim that ID is an appeal to the best explanation, specifically within the framework of ID's supposed explanatory power.  This is posed as an answer to the question, "what's the logical fallacy here?"  


It's not so much a logical fallacy.  It's just that they're plain wrong as far as explanatory power is concerned.  To actually explain something, you not only need to give an account of why something happened, but why it should have happened and why it didn't happen differently.  In other words, your theory should predict the observed outcome, or at least predict a set of possible outcomes (the smaller the better) that overlap what's observed.  It's pretty safe to say that evolutionary biology predicts a much smaller set of possible outcomes than does ID, which itself predicts an infinite set of outcomes (which is to say that it predicts nothing at all).  So the plain fact of the matter is that ID is not only fails to be the best explanation, but it fails to be any kind of explanation at all.  Evolutionary biology on the other hand, while not only giving us a general explanation for the diversity and unity of living things, also gives us a research paradigm for explaining the exact genesis of specific structures and functions within living things.  Note that this is something that ID doesn't even aspire to.

The hypocritical IDist retort to this is to claim that evolutionary biology predicts an infinite set of outcomes, and is thus not testable itself.  Of course if this were really true, then the IC and SC arguments against evolution would not be logically tenable.  These arguments fail because they don't match up to the facts (and in the case of SC, because it's an excercise in question begging).  But they really can't have it both ways.  They can't claim that IC or SC falsify evolution while simultaneously claiming that evolution isn't falsifiable.

The mere fact that they try to make these arguments shows that evolutionary biology is constrained by what it can predict, and therefore can explain not just why things are as we see them, but why they're not somehow wildy different.  Consider for example if every species on Earth were morphologically and biochemically distinct.  Darwinian evolution could certainly not explain that.  Or what if there were only one species and there had always been only one species?  Again, Darwinian evolution would be untenable.  I often think that people are so used to the facts of nature as they are that they don't stop to think about situations that might make non-evolutionary accounts far superior.  (I also think this is why biologists, who are more aware of the facts of nature than your average joe, have a particularly hard time not accepting evolution.)  But in all of these cases, whether whether nature is like it is now or whether it's completely different, ID accounts for it either way by invoking the same uninformative explanation: The Designer wished it such.

Now it's not impossible to get explanatory power out of this.  But in order to do so you have to ask why the designer wished it such.  This is not an unreasonable demand, as IDists often claim it is.  When we see some sort of putative designed human artifact, the first thing we want to know is what it's for.  And implicit in this demand is knowing how and why a human would have built such a thing, because of course we don't expect humans to be able or willing to build just anything.  In other words, the set of possible outcomes is limited when we assume human construction.  If we can say what object X is for and why humans living in location Y would have built such a thing, then we've gone a long way towards explaining the genesis of object X.  But what's really senseless is that the IDists not only don't want to engage in this sort of discourse, they even claim that it's unscientific!

Naturally, they have their reasons.  Trying to bring the designer and its attributes into the discussion would force a few things.  1) They'd have to admit that it's all speculation.  There's nothing wrong with that per se, because every scientific hypothesis starts out as being speculative, but it would raise the issue of the acutal testing of ID hypotheses, and the lack of data on the Designer would make this difficult.  Furthermore, real world data can eliminate several popular Designer hypotheses if we insist on taking the scientific approach to ID.  2) The Big Tent philosophy, who's purpose is to allow any and every ID hypothesis (except maybe the Raelins) equal access, thus swelling the ranks.  This is just a political strategy.  3) They'd have to start comparing ID to Darwinian evolution.  As it is now, it's advantageous to be completely devoid of any theoretical basis, because it lets them sit back and take pot shots at Darwinian evolution without having to account for the so-called mysteries that they invoke with a model of their own.  And surely there are other reasons, but it's not necessary to figure them all out.  The important point is that they've chosen to uncouple the ID argument from the only thing that would actually give it some explanatory power, which is some actual considerations about what it is that's doing the design, how it's being done, why it's being done, when it was being done, etc., etc., etc...

The uncoupling of the ID argument with any considerations of the desiger is exactly what makes ID devoid of any exaplanatory power.  In the absence of a real design hypothesis, ID cannot ever be a scientific theory.  Instead it's just an argument, and the only point to the argument is to prove a designer, not actually to explain anything.  And it's not even a very good argument.  AFAICT, the ID argument has in remained essentially unchanged since Paley.  It was logically unsound to begin with, as shown by Hume, and then Darwin came along and demonstrated why it's unreliable.  Can anyone tell me what new and interesting explanations for the properties of living things that Paley or his followers were able to come up with?

theyeti



Date: 2002/11/26 17:52:15, Link
Author: theyeti
Okay, now for why ID doesn't identify the designer.  Here is what I posted in a thread in the "collaborations" section

Quote
Naturally, they have their reasons.  Trying to bring the designer and its attributes into the discussion would force a few things.  1) They'd have to admit that it's all speculation.  There's nothing wrong with that per se, because every scientific hypothesis starts out as being speculative, but it would raise the issue of the acutal testing of ID hypotheses, and the lack of data on the Designer would make this difficult.  Furthermore, real world data can eliminate several popular Designer hypotheses if we insist on taking the scientific approach to ID.  2) The Big Tent philosophy, who's purpose is to allow any and every ID hypothesis (except maybe the Raelins) equal access, thus swelling the ranks.  This is just a political strategy.  3) They'd have to start comparing ID to Darwinian evolution.  As it is now, it's advantageous to be completely devoid of any theoretical basis, because it lets them sit back and take pot shots at Darwinian evolution without having to account for the so-called mysteries that they invoke with a model of their own.


I suppose you could divide this into the empirical, the political, and the theoretical respectively.  Keep in mind though that this is at least partially a matter of my opinion, since trying to figure out why they do what they do is a matter of speculation itself.  I think that these reasons are certainly in opperation at least some of the time, but they are not the only ones.  I will try to cull some remarks from IDists from other boards later if I have a chance, and let you see their view.  

One thing that persists among "leading" IDists in their writing is that figuring out the attributes or identity of the designer is a question for philosophy or religion.  But this is clearly wrong, because once we've make detecting design something which can be answered via science, we've also made detecting the designer part of science also.  For example, it would be foolish to say that we've concluded that Stonehenge was designed, but that the scientific method couldn't deduce who designed it or for what reason.  In fact, that's the whole point of sciences that study design, like archeaology or forensics, which the IDists often cite as evidence that their methodology is actually being used.  (This is the crucial difference which shows that their methodology is actually not being used.)  Exactly what the IDists' motivations are for this claim are a matter of speculation, but certainly they'd rather give specific religious interpretations preeminence, which the Wedge Strategy shows is the primary goal of the movement.

theyeti

P.S.  The OP here is kind of in the wrong forum, since it deals with AiG, which is a YEC outfit, and this forum is for ID.  However, we're just now getting this board up and running full steam, so it's not like there are a bunch of threads competing for attention.  Try to be patient; we'll try to generate some steady activity here soon.

Date: 2002/11/26 21:59:55, Link
Author: Jacor
I am having a hard time understanding the difference between creationism and ID.  As far as I can tell the only obvious difference is that ID has replaced the term "God" or "creator" with the word "designer."
This is a difference with no real difference.  Just like back in the hyperinflationary times of the 70's: a title change was supposed to make you not notice that your income only increased by 2.5% per year while inflation ran at 18%-24% per year.  The assumption was that by making you think that you had gotten a promotion you also would not notice that you were doing the same job.

I do know that a lot of people, in the area I live ( less than 4 blocks from UNC-G), cannot identify evolution as a biological theory.  Instead they apply it to theories relating to the genesis of the universe, complex systems in chemistry and physics, as well as the development of speciation of plants and animals, and anything else in the sciences that they perceive as a threat to their religious values.
It appears that the education system is already providing a group of people, susceptible to ID arguments, that are poorly grounded in critical thinking skills, never mind science.
Paul C

Date: 2002/11/26 23:01:09, Link
Author: Mr. Davies
Interesting.

By not identifying the designer, they leave open everyone's ideal of the designer as a possibility.  That is definitely the big tent approach but tents generally have a hard time holding up under adverse conditions.

Would it not be a prudent strategy for the anti-ID, or in my estimation, the pro-science (anti anything to me makes it sound so negative) help them out by postuating the drunk designer, the "I don't care how I made you 'cause you'll die soon enough" designer, and on.  It would even be fascinating to have them say that their could be more than one designer.

Of course, my statement would most likely work on people with critical thinking skills.  Now I have noticed that IDists are more likely to be gifted than say your typical YEC with critical thinking, but their compartmentalization still makes their arguements, again in my estimation, rather entertaining as they switch standards to allow themselves to hold onto ID.  What I've seen is if they go too far one way, then on something they may care and know alot about, watchin their own arguements get beaten over the head by applying their logic on ID to their particular "thing" is great for a few minutes at least.

My particular reason was that while I was flirting with my daughter's single and rather cute science teacher, I asked if her were going to touch on evolution as they are in middle school.  She seemed to want to see where I stood on the subject and said that there were "issues" and mentioned "Dr. Behe" was working on those issues.  When I mentioned that Behe's concerns were addressed and that ID was not much more than the God of the Gaps repackage, she grew suddenly withdrawn and our conversation did not go much further.  That was a shame as she's quite nice looking and has nice legs.

For the UNC-G, I live in Johnson County, one of the many "Yankees" who have started to occupy the rest of Dixie.

Date: 2002/11/28 23:02:57, Link
Author: RBH
Mr. Davies suggested that
Quote
It would even be fascinating to have them say that their could be more than one designer.

I tried that on ISCID.  It stimulated some responses, and I may yet do some more on it when I have time.

RBH

Date: 2002/11/28 23:11:25, Link
Author: niiicholas
Similar to the prokaryotic flagella thread.

Introductory material:

http://www.wikipedia.org/wiki/Flagellum
(don't confuse eukaryotic cilia/flagella with prokaryotic flagella)


http://www.wikipedia.org/wiki/Evolution_of_flagella


Here we have the interesting sideshow of Margulis' and fans' hypothesis that the cilium is derived from a spirochete.  For many critical comments on this see:

Cavalier-Smith T. Int J Syst Evol Microbiol 2002 Mar;52(Pt 2):297-354
 
The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.

Date: 2002/12/01 20:38:22, Link
Author: niiicholas
Might as well add these as I'm discussing them over at EvC:
http://www.evcforum.net/ubb/Forum10/HTML/000029.html


On the evolution of PCP degradation:

Quote

Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach.

Trends Biochem Sci 2000 Jun;25(6):261-5

Copley SD.

Dept of Chemistry and Biochemistry and Cooperative Institute for Research in Environmental Studies, University of Colorado at Boulder, Boulder, CO 80309, USA. copley@cires.colorado.edu

The pathway for degradation of the xenobiotic pesticide pentachlorophenol in Sphingomonas chlorophenolica probably evolved in the past few decades by the recruitment of enzymes from two other catabolic pathways. The first and third enzymes in the pathway, pentachlorophenol hydroxylase and 2,6-dichlorohydroquinone dioxygenase, may have originated from enzymes in a pathway for degradation of a naturally occurring chlorinated phenol. The second enzyme, a reductive dehalogenase, may have evolved from a maleylacetoacetate isomerase normally involved in degradation of tyrosine. This apparently recently assembled pathway does not function very well: pentachlorophenol hydroxylase is quite slow, and tetrachlorohydroquinone dehalogenase is subject to severe substrate inhibition.


[On the key step of the origin of PcpC, the central step in the origin of PCP degradation]

Recruitment of a double bond isomerase to serve as a reductive dehalogenase during biodegradation of pentachlorophenol.

Biochemistry 2000 May 9;39(18):5303-11

Anandarajah K, Kiefer PM Jr, Donohoe BS, Copley SD.

Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Campus Box 216, Boulder, Colorado 80309-0216, USA.

Tetrachlorohydroquinone dehalogenase catalyzes the replacement of chlorine atoms on tetrachlorohydroquinone and trichlorohydroquinone with hydrogen atoms during the biodegradation of pentachlorophenol by Sphingomonas chlorophenolica. The sequence of the active site region of tetrachlorohydroquinone dehalogenase is very similar to those of the corresponding regions of maleylacetoacetate isomerases, enzymes that catalyze the glutathione-dependent isomerization of a cis double bond in maleylacetoacetate to the trans configuration during the catabolism of phenylalanine and tyrosine. Furthermore, tetrachlorohydroquinone dehalogenase catalyzes the isomerization of maleylacetone (an analogue of maleylacetoacetate) at a rate nearly comparable to that of a bona fide bacterial maleylacetoacetate isomerase. Since maleylacetoacetate isomerase is involved in a common and presumably ancient pathway for catabolism of tyrosine, while tetrachlorohydroquinone dehalogenase catalyzes a more specialized reaction, it is likely that tetrachlorohydroquinone dehalogenase arose from a maleylacetoacetate isomerase. The substrates and overall transformations involved in the dehalogenation and isomerization reactions are strikingly different. This enzyme provides a remarkable example of Nature's ability to recruit an enzyme with a useful structural scaffold and elaborate upon its basic catalytic capabilities to generate a catalyst for a newly needed reaction.

[atrazine degradation, a similar case]
Melamine deaminase and atrazine chlorohydrolase: 98 percent identical but functionally different.

J Bacteriol 2001 Apr;183(8):2405-10

Seffernick JL, de Souza ML, Sadowsky MJ, Wackett LP.

Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, USA.

The gene encoding melamine deaminase (TriA) from Pseudomonas sp. strain NRRL B-12227 was identified, cloned into Escherichia coli, sequenced, and expressed for in vitro study of enzyme activity. Melamine deaminase displaced two of the three amino groups from melamine, producing ammeline and ammelide as sequential products. The first deamination reaction occurred more than 10 times faster than the second. Ammelide did not inhibit the first or second deamination reaction, suggesting that the lower rate of ammeline hydrolysis was due to differential substrate turnover rather than product inhibition. Remarkably, melamine deaminase is 98% identical to the enzyme atrazine chlorohydrolase (AtzA) from Pseudomonas sp. strain ADP. Each enzyme consists of 475 amino acids and differs by only 9 amino acids. AtzA was shown to exclusively catalyze dehalogenation of halo-substituted triazine ring compounds and had no activity with melamine and ammeline. Similarly, melamine deaminase had no detectable activity with the halo-triazine substrates. Melamine deaminase was active in deamination of a substrate that was structurally identical to atrazine, except for the substitution of an amino group for the chlorine atom. Moreover, melamine deaminase and AtzA are found in bacteria that grow on melamine and atrazine compounds, respectively. These data strongly suggest that the 9 amino acid differences between melamine deaminase and AtzA represent a short evolutionary pathway connecting enzymes catalyzing physiologically relevant deamination and dehalogenation reactions, respectively.




Date: 2002/12/02 18:55:21, Link
Author: niiicholas
This is a "data accumulation" thread for me (and anyone else interested in Croizat) to learn the basics.

To start off:

http://zoo.bio.ufpr.br/diptera/bz023/leon.htm

Quote

León Croizat and the panbiogeography, never a serious scientist

Morrone JJ. 2000. Between the taunt and the eulogy: Leon Croizat and the panbiogeography. INTERCIENCIA 25: (1) 41-47.
Abstract:
The Italian botanist Leon Croizat (1894-1982) is a controversial figure in the most recent history of biogeography. Based on the metaphor that "life and earth evolve together" -which means that geographic barriers and biotas coevolve- Croizat developed a new biogeographic methodology, which he named 'panbiogeography '. This method was basically to plot distributions of organisms on maps and connect the disjunct distribution areas or collection localities together with lines called tracks. Croizat found that individual tracks for unrelated groups of organisms were repetitive, and considered the resulting summary lines as generalized tracks which indicated the preexistence of ancestral biotas, subsequently fragmented by tectonic and/or climatic changes. Some authors, mainly those belonging to the dispersalist establishment, have dismissed Croizat's contributions, considering him as idiosyncratic, or a member of a lunatic fringe. Others have considered Croizat as one of the most original thinkers of modern comparative biology, whose contributions advanced the foundations of a new synthesis between earth and life sciences. Following its synthesis with phylogenetic systematics, Croizat's panbiogeography has emerged as being central to vicariance or cladistic biogeography. In spite of this synthesis, some authors currently agree in the distinction between Croizat's panbiogeography and cladistic biogeography.


So, perhaps both a loon and brilliant in his way.


Lotsa info here, including some vituperative anti-Darwin, and anti-Mayr stuff from late Croizat:

http://www.ento.psu.edu/home....ate.htm

Date: 2002/12/02 19:12:32, Link
Author: niiicholas
http://gsa.confex.com/gsa/2002AM/finalprogram/abstract_37210.htm

Quote

THE EMERGENCE OF VICARIANCE BIOGEOGRAPHY: FROM WEGENER TO CROIZAT AND THE CLADISTS
HALLAM, Anthony, School of Earth Sciences, Univ of Birmingham, Edgbaston, Birmingham B15 2TT United Kingdom, A.Hallam@bham.ac.uk.

One of the strongest arguments that Wegener put forward to support his continental drift hypothesis derived from biogeography. The conventional interpretation of the close taxonomic relationships of Mesozoic terrestrial organisms between the southern continents was of land bridges that had subsequently foundered beneath the South Atlantic and Indian Oceans. Wegener cited this biogeographic evidence in support of his hypothesis, pointing out that neither the geological evidence (absence of granitic rocks) nor the geophysical evidence (high density of ocean floor) supported the idea of foundered continents, and that the only plausible alternative was that the Atlantic and Indian Oceans had opened in the fairly recent geological past. Later last century this notion led directly to the concept of vicariance biogeography, following the work of Croizat, which focussed on the spatiotemporal analysis of distribution patterns of organisms and is different from phenetic biogeography, which investigates similarities between biotas in terms of numbers of taxa in common. Croizat's so called generalised tracks indicated the distribution pattern of an ancient biota before it vicariated. The tracks for terrestrial organisms may cross oceans and hence could not be explained by present-day biogeography. With the general acceptance of plate tectonics by the early 1970s, Croizat's work was used to create a new school of vicariance biogeography. The early work was characterised by a polemical approach that virtually denied any validity to the alternative dispersalist school. Many have subsequently reacted against this excessive polarisation, and dismissive attitudes towards dispersalist mechanisms, but without question a new scientific rigour has been introduced, with more emphasis being placed on testing models and with ad hoc hypothesising being discouraged. An important difference quickly emerged, however, between Croizat and the other vicariance biogeographers, who supported cladistic methods of taxonomic analysis, whereas Croizat favoured conventional phenetic methods.

2002 Denver Annual Meeting (October 27-30, 2002)

Session No. 141
Paleobiogeography: Integrating Plate Tectonics and Evolution
Colorado Convention Center: A102/104/106
8:00 AM-12:00 PM, Tuesday, October 29, 2002




A good short summary of biogeography that puts Croizat in context:

http://www.msu.edu/course/zol/370/lindell/10-10-02,%20method.html

Date: 2002/12/02 21:29:28, Link
Author: RBH
Last month I gave a colloquium on ID for high school biology teachers, and as a followup, I've been sending them resources.  In aid of that, I put together a short essay, something like theyeti's.  I plan to distribute it to them in the not-to-far distant future.  Comments/critiques welcome.

***************
In his post on ISCID John Wilkins wrote
Quote
Let us begin by asking how science tells us anything at all. In my view, science is the recognition of patterns in data, and the generation of models that are adequate to delivering those patterns as explanation. The information in science, the "signal" from the physical world, is the information of measurement - Fisher Information, AKA the Cramer-Rao Bound (which is, roughly, where the second derivative of the estimate of the accuracy of a measurement is zero). In my view, science is induction from data, and the models retain the information content of the measurements just to the extent they are accurate. (Note: induction may not be a justification of models, but it sure as #### is the way we gather our data together so we can make reliable inferences; still, let's not open that can of undergraduate Humean worms.) The information content of a scientific explanation is just the preserved accuracy of the data in the model.

Anything that we know through science we know from empirical data. So a design inference has to be not only consonant with data, but licensed by the patterns that exist in the data. To be achievable, we need to understand (that is, have a model of) design and designers.  (emphasis added)


And consider this from my OP in the Multiple Designers Theory thread on ISCID
Quote
D. There is a finite and limited number of multiple designers.  This premise is more difficult to support by empirical evidence than the others, but it is logically necessary to prevent the MDT enterprise from degenerating into a mere list of designed phenomena, a cosmic oddity shop of designs. Scientific theories condense (superficially) disparate phenomena into similarity classes and explain the behavior of instances of the classes by invoking general principles and laws that refer to those classes rather than to individual instances. If the number of designers is unlimited then in the limit each class would have just one member, and (since in that case no multi-member classes exist) no general laws are possible and therefore there is no science. It is logically possible that there is an infinite number of designers, but in that case no scientific study of design is possible. It is therefore a scientifically sterile speculation. (emphasis added)


As I read them, IDists argue that the Explanatory Filter (nowadays pretty much reduced to the assertion that IC structures or processes cannot be produced by evolution) detects a property (improbability) of some objects or processes in the world, and therefore (since that property is asserted to be shared by a set of objects and/or processes), there is a class of natural-world phenomena, a class defined solely by improbability, that evolutionary theory can't explain because it is not a similarity class in the terms of models based in evolutionary theory.  Their only common property, improbability, does not define a class that enters the theoretical laws and models of evolutionary biology.  Therefore the class is asserted to require some other kind of explanation, an intelligent design explanation.

There have been two general kinds of counter-arguments offered in the various critiques of current approaches to ID.  One focuses on the probability estimates.  An important component of this critique is the argument that "improbability" is not a property of an object or process but rather is a characterization of an object or process with reference to some probability density function (PDF), and the alleged improbability of some biological structures and processes is in large part due to an inappropriate choice of PDF for the estimates.  Thus the 'class' formed by highly improbable objects like bacterial flagella and blood clotting biochemical cascades is an artifact of the (idiosyncratic, unjustified) choice of PDF rather than being some intrinsic property of the phenomena.  "Probability" is not an inherent property of an instance; it is a description of a relation between an instance and a PDF.

The second general sort of counter-argument is to the effect that allegedly unevolvable structures and processes (whether the probabilities are correctly estimated or not) can in fact be accommodated in classes appropriate to causal models from evolutionary biology, and are therefore explained by those models.  Thus it is argued that while "direct" incremental evolution of some biological structure may not be possible, indirect routes (cooption, scaffolding, etc.) can account for the naturalistic evolution of the objects and processes.  In addition, "direct" incremental evolution may be actually be possible given that different evolutionary operators induce fitness landscapes with very different topographies, so what appears to require saltational cliff-climbing on one fitness landscape might be simple one-step-at-a-time incremental evolution on a gentle slope of another landscape.  On those arguments the probability estimates do not define a class of phenomena that must be explained in some way that evolutionary theory doesn't provide.

In addition, ID has serious explanatory problems.  By explicitly disavowing conjectures about the number and nature of purported intelligent designing agents and by avoiding hypotheses about the means by which abstract designs are transmitted to or implemented in matter and energy, IDists deliberately eviscerate their ability to provide a scientific explanatory model.  With no hypotheses about designers or mechanisms of design implementation, nothing holds the class of improbable structures and processes together except the (inappropriate) probability estimates.  The examples that have been offered have no properties in common but the probability estimates.  They constitute a mere oddity shop of disparate phenomena bound together by nothing but purported improbability.

The class of allegedly improbable structures and processes offered in the ID literature floats alone in empty conceptual space, unconnected to any causal or correlational explanatory model.  The class of improbable phenomena is not part of a relational structure of classes to which natural (or non-natural) laws and generalities apply.  No laws or generalities have been offered by IDists that go beyond a mere claim of the existence of a class of improbable instances.  IDists offer no testable hypotheses about relationships between the class of purportedly improbable instances and anything else in or out of the world of physical matter and energy, and so there is no scientific explanatory power in ID.

****************
btw, I note with fascination that this board censored John's use of H***!

RBH



Date: 2002/12/03 23:13:15, Link
Author: niiicholas
Another Miller article, presents his argument on cilia missing parts:

"Answering the Biochemical Argument from Design"

The ID movement pretends that its biochemical arguments against evolution are new, novel, and scientific. In fact, they are nothing of the sort.

http://www.millerandlevine.com/km/evol/design1/article.html

Date: 2002/12/05 13:40:26, Link
Author: Wesley R. Elsberry
Phillip Johnson on Ohio

The Dick Staub Interview: Phillip Johnson

Quote
What does Ohio's decision on science requirements mean for the Intelligent Design Movement?

The recent decision of the Ohio Science Standards Committee of the State School Board has been a big breakthrough. [Critics] are calling it a compromise, but it isn't. It's our position. It allows teachers to present evidence against the theory of evolution. This evidence includes the facts that the drawings of embryos in the textbooks are fraudulent and that the peppered moth experiment was botched if not an outright hoax.


It looks like the statements from board members that their proposed language did not represent an opening for "intelligent design" arguments are considered by Johnson to be pure flapdoodle.

Date: 2002/12/05 14:24:43, Link
Author: Wesley R. Elsberry
Phillip Johnson compares "Darwinists" to Napoleon's army in Moscow

Quote
They have lost a big one. They're like Napoleon's army in Moscow. They have occupied a lot of territory, and they think they've won the war. And yet they are very exposed in a hostile climate with a population that's very much unfriendly.

That's the case with the Darwinists in the United States. The majority of the people are skeptical of the theory. And if the theory starts to waver a bit, it could all collapse, as Napoleon's army did in a rout.

(Source: The Dick Staub Interview: Phillip Johnson
)

Date: 2002/12/05 17:13:26, Link
Author: rafe gutman
allen orr recently wrote a review of dembski's "no free lunch" in the boston review.  dembski wrote a response to it, and orr responded to that:

http://bostonreview.mit.edu/BR27.5/exchange.html

this article is currently being discussed on several intelligent design fora (such as ARN and ISCID), but considering the intense moderation/censorship of those sites, i thought i would bring the topic here for discussion.  those critics of ID who are concerned that their comments will be censored can post them here.

here is the intro:
Quote
Allen Orr wrote an extended critical review (over 6000 words) of my book No Free Lunch for the Boston Review this summer (http://bostonreview.mit.edu/BR27.3/orr.html). The Boston Review subsequently contacted me and asked for a 1000 word response. I wrote a response of that length focusing on what I took to be the fundamental flaw in Orr's review (and indeed in Darwinian thinking generally, namely, conflating the realistically possible with the merely conceivable). What I didn't know (though I should have expected it) is that Orr would have the last word and that the Boston Review would give him 1000 words to reply to my response (see the exchange in the current issue at http://bostonreview.mit.edu/BR27.5/exchange.html).



In his reply Orr takes me to task for not responding to the many particular objections he raised against my work in his original review, suggesting that this was the result of bewilderment on my part and intelligent design running out of steam and not, as was the case, for lack of space. This sort of rule-rigging by Orr and the Boston Review -- give the respondent a little space, and then let the original author crow about winning -- is to be expected. I actually find it encouraging, taking it as an indication of intelligent design's progress. Orr's review and follow-up hardly spell the death-knell for intelligent design or for my work in this area. Sooner or later (and probably sooner) Orr will find himself in a forum on intelligent design where the rules of engagement are not rigged in his favor. I look forward to his performance then.




Date: 2002/12/05 21:47:17, Link
Author: charlie d
Somebody should explain to PJ the difference between evidence disproving a theory, and evidence disproving evidence for a theory (assuming that it does, which in the case of the peppered moth is clearly not the case).  Must be a lawyer thing, that he can't see the difference.

None of the "Icons" (even if they were largely correct, rather than essentially an overinflated hodgepodge of willful misrepresentations) comes even close to being  "evidence against the theory of evolution".  For that, I guess, we'll have to wait for the results of that famous ID research that's going on somewhere.

Date: 2002/12/06 00:40:46, Link
Author: ExYECer
Leo

 
Quote
ID does not have a problem with the idea that living things may have been designed through a long series of mutations (and whether this is true makes another interesting investigation). But it's the 'random' part that ID claims is demonstrably false.
Nor is Darwinism random either so I guess ID has nothing much against Darwinism? But the problem for ID is that it has to eliminate natural mechanisms in order to infer design. But if specifications can be generated for almost any hypothesis, not much would be left to chance or regularity (can we say false positives? The eye looks design just like a camera lense for instance?). ID is not helping us resolve much in understanding how these supposedly designs happened. In fact its failure to be able to distinguish between intervention and 'front loading' makes its approach not much different from methodological naturalism, other than that ID does not seem to be interested or able to propose its own hypotheses and thus seems to be limited to disproving hypotheses, just like good old science but more restricted. Mutations are still random 'with respect to function/benefit'. Its that simple. That mutations are not random in time, location or environment is hardly a surprise but so far mutations seem to remain random wrt their benefit of the organism in a given environment.
ID'ers make vague claims that science cannot explain 'X' and if history is a predictor of the future will continue to be shown wrong.

So far ID has failed to show how it can reliably identify rarefied design. In fact it has major problems with issues such as specification (almost anything can be specified and thus not much chance remain: can we say false positives?). CSI and the law of conservation of CSI seem to be failing to deliver. The law of conservation of CSI _in a closed system_ or more correctly since it is not really a conservation law despite the confusing use of terms by Dembski, CSI in a closed system can only decrease. Sound familiar? Entropy in a closed system can only increase... Of course in an open system CSI can increase just like entropy can decrease. Its that simple.

Perhaps Dembski and the ID movement could benefit from a more rigorous derivation of their claims (See Wolpert's comments for instance). But I foresee that any such effort will be the downfall of ID since the law of conservation of CSI will wither away as just a variant of the 2nd law. Specification will be shown to be either too subjective and all inclusive or impossible to specify in a mathematically sound format. The ID filter will be seen to not deal well with false positives, 'we don't know'.

As Miller stated so well, most scientists are not interested in the intelligent design claims for the simple reason that ID cannot really be helpful in scientific inquiry. Dembski himself has condemned ID to such a status of irrelevance with his latest posting.

Date: 2002/12/06 00:43:50, Link
Author: ExYECer
Arn Moderator 4 wrote:

I've deleted a couple of non-substantial posts already. I'm going to pay special attention to this thread. No short quip posts. Substance and respect, please, if you will.

Thus my to the point and substantial posting in response to Dembski. If such approaches are considered spamming and worthy of envoking rule 6 then perhaps I should break up the posting on lets say 6 smaller pieces? But that seems contradictory to the 3 postings per day rule. In effect ARN moderator 4's suggestion would enforce a large posting instead of multiple smaller ones.

Dr Dembski

I find it fascinating how you are hopping from 'No Free Lunch' theorems as a foundation of your argument to 'No free lunch principle'.

     
Quote

The Design Inference laid the groundwork. This book demonstrates the inadequacy of the Darwinian mechanism to generate specified complexity. Darwinists themselves have made possible such a refutation. By assimilating the Darwinian mechanism to evolutionary algorithms, they have invited a mathematical assessment of the power of the Darwinian mechanism to generate life's diversity. Such an assessment, begun with the No Free Lunch theorems of David Wolpert and William Macready (see section 4.6), will in this book be taken to its logical conclusion. The conclusion is that Darwinian mechanisms of any kind, whether in nature or in silico, are in principle incapable of generating specified complexity. Coupled with the growing evidence in cosmology and biology that nature is chock-full of specified complexity (cf. the fine-tuning of cosmological constants and the irreducible complexity of biochemical systems), this conclusion implies that naturalistic explanations are incomplete and that design constitutes a legitimate and fundamental mode of scientific explanation.
Source

and several other references to the importance of the NFL theorems.

It is interesting to find out that one of the fundamental principles of your book has now been side tracked when it became clear that the NFL theorems are likely not relevant for evolutionary mechanisms.It still saddens me that you accuse people of 'smuggling in' CSI, especially Tom Schneider who has succesfully disproven most of your claims about Ev.
So now the question is reduced to, smuggling in of complex specified information. How it such information 'smuggled in'? Your limited applicable "Conservation of information" theorem, also known as the second law of thermodynamics shows that in a closed system indeed information can only decrease. But what about an open system, information is imparted on the system by making choices, whether it be intelligent design or some vetting algorithm like natural selection which transforms information about the environment into the genome. The reason why this works so well for DNA is because it has some very useful properties, it can store historical information, it can copy/duplicate such information. Your argument that 'No free lunch' theorems/principles show that information/entropy can only increase/decrease through intelligent design is begging the question indeed. What is the difference between intelligent design and natural design I ask you? In both cases, choices are made that lead to increased correlation between the genome and the environment, hence information is transfered from the environment into the genome. Furthermore your argument about front loading becomes meaningless, where is this front loading supposed to have taken place? It must have happened before the laws of physics came into existence and in any event your approaches do not even allow us to distinguish between front loaded and intervention design. As Murray has so very aptly argued, this makes intelligent design nothing different from methodological naturalism.

So what do we have so far

1. NFL theorems are not really that important anymore
2. NFL principles are now the 'hot topic' of course they lack even more in mathematical foundation despite Dembski's assertion The No Free Lunch Principle states that if you have some naturalistic process whose output exhibits specified complexity, then that process was front-loaded with specified complexity. as argued by Wolpert, one of the authors of the NFL theorems
       
Quote

I say Dembski "attempts to" turn this trick because despite his invoking the NFL theorems, his arguments are fatally informal and imprecise. Like monographs on any philosophical topic in the first category, Dembski's is written in jello. There simply is not enough that is firm in his text, not sufficient precision of formulation, to allow one to declare unambiguously `right' or `wrong' when reading through the argument. All one can do is squint, furrow one's brows, and then shrug.
and

       
Quote

Indeed, throughout there is a marked elision of the formal details of the biological processes under consideration. Perhaps the most glaring example of this is that neo-Darwinian evolution of ecosystems does not involve a set of genomes all searching the same, fixed fitness function, the situation considered by the NFL theorems. Rather it is a co-evolutionary process. Roughly speaking, as each genome changes from one generation to the next, it modifies the surfaces that the other genomes are searching. And recent results indicate that NFL results do not hold in co-evolution.
3. Conservation of information laws seem to be nothing different from the SLOT
4. Intelligent design cannot distinguish itself from methodological naturalism when it is unable to distinguish between front loading and intervention.
5. Specified complexity seems to be a subjective and meaningless concept in that one could easily specify any chance/regularity hypothesis, leading to countless false positives. May I point in this context to the very to the point analysis by Sobel

       
Quote

From this second illustration can be gathered that Dembski.s theory enables a moderately imaginative person,
with a list of possible delimitations of an event, easily eliminate relevant chance-hypotheses for the event; if they all
make more probable that not its non-occurrence, and avoiding .false negatives. concerning relevant chance-
hypotheses for this event is somewhat (it need not be very) important to him.  From the two illustrations, one may
gather that by the lights of Dembski.s book, we are entitled, and will always be entitled  to conclude, that not much
happens by chance.
As far as the flagellum is concerned Ken Miller has posted a prepublication  of an article that will appear in volume entitled "Debating Design: from Darwin to DNA," edited by Michael Ruse and William Dembski, which will be published by Cambridge University Press volume early in 2003. In another pre publication Miller addresses "Answering the Biochemical Argument from Design".

But what I find most telling is that the design inference has now retreated from trying to provide scientific contributions to a mere 'Intelligent design, in contrast to Darwinism, is not a theory about process but about creative innovation." It should not come as a surprise that intelligent design researchers have been less than succesful in finding funding for research into something that seems to be unable to contribute much to the scientific discussion.

Not surprisingly, Darwinism, which does propose real scientific pathways allowing us to extend our understanding of how life evolved, has a burden that indeed ID need not deal with, providing for hypotheses which can be disproven. Intelligent design, unable to even address if innovation occurs as an intervention or as some form of front loading has to deal with the fact that its foundations on NFL theorems, conservation of specified complexity and specification are falling apart fast. Dembski argues "The formal theory for specifications that I develop maps onto the biology unproblematically" but I have yet to see anything resembling such a theory. In fact the 'theory' seems to show that specification depends inherently on subjective interpretation and can in principle be extended to any hypothesis. (See also Sobel) The specification of the flagellum shows how meaningless 'specification' really is. It looks like an outboard engine. Well, the inner ear looks like a drum, can we now infer design for the ear? Snowflakes look like little sculptures once magnified enough. The sunset looks like an expressionistic painting. Need I say more?

To state that biology has remained empty handed in explaining biological complexity seems to show a tendency to ignore the known literature on these topics. But I doubt that Dembski is interested in discussing how ID fares compared to scientific inquiry into these topics, after all ID has no burden at all. Of course if Dembski applied his argument consistently he would have to argue that ID bears the burden of providing convincing evidence of design and its designers but ID is not interested in process and seems to be stuck detecting rarefied intelligent design using a faulty filter. See for instance the excellent article by Welsberry and Wilkins The advantages of theft over toil: the design inference and arguing from ignorance where they show how Dembski's filter fails to incorporate 'we don't know' and provides a priveleged and unwarranted position to the design inference.

That Dembski has abandoned much hope for a scientific breakthrough for ID seems obvious when he argues for political approaches instead. It seems that the 'Wedge strategy' is alive and well.. Of course Bruce Gordon seems to have realized how

       
Quote

"... the theory has been prematurely drawn into discussions of public science education where it has no business of appearning without broad recognition from the scientific community ... inclusion of design theory as part of the standard discourse of the scientific community, if it ever happens, will be the result of a long and difficult process of quallity research and publication. It also will be the result of overcoming the stigma that has become attached to design research because of the anti-evolutionary diatribes of some of its proponents on the one hand and its appropriation for the purpose of Christian apologetics on the other. ...If design theory is to make a contribution to science, it must be worth pursuing on the basis of its own merits, not as an exercise in Christian 'cultural renewal,' the weight of which it cannot bear.... In conclusion, it is crucial to note that design theory is at best a supplementary consideration introduced alongside (or perhaps onto by way of modification) neo-Darwinian biology and self-organizational complexity theory. It does not mandate the replacement of these highly fruitful research paradigms, and to suggest that it does is just so much overblown, unwarranted, and ideologically driven rhetoric." Bruce Gordon, ex-CRSC Fellow, Science and Theology 2:1 (2001), p. 9
See also Here

Perhaps Dembski may help us understand where he believes ID should be going, other than following the inevitable political route now that the bridges to a scientific route seems to have been  burned effectively by Dembski's latest admissions of what ID is and isn't. I had some hopes that ID would provide for a positive research program that would expand our understandings but that does not seem to be a burden ID is willing or able to carry.

I am also interested in why, if Dembski believes that the rules of engagement are fixed in favor of evolutionists, he did not invite Wesley Elsberry for instance or Richard Wein to present their case at the last RAPID meeting? Seems that ID has only itself to blame here.

[PS: I will be addressing some historical revisionism of Behe's IC "This becomes immediately evident from reading Behe since in his definition of irreducible complexity, the function of the system in question always stays put." and many other interesting issues raised by Dembski. ]

And some reference about evolution and biological complexity

ev: Evolution of Biological Information

Evolution of Biological Complexity

Genomic Complexity in Micro Organisms and Digital Organisms

Some Techniques for the Measurement of Complexity in Tierra

The Evolution of Complexity and the Value of Variability

   
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The hypothesis that environmental variability promotes the evolution of organism complexity is explored and illustrated, in two contexts. A coevolutionary `Iterated Prisoner's Dilemma' (IPD)
ecology, populated by strategies determined by variable length genotypes, provides a quantitative demonstration, and an example from evolutionary robotics (ER) provides a more qualitative and naturalistic exploration.
In the ER example, the above hypothesis
is illustrated in real environments, and the organism complexity is seen in robots exhibiting relatively complex behaviours and neural dynamics.
Implications are drawn for the emergence of complexity in general, and also for artificial evolution as a design methodology.
Complexity and Self-Organization

What is complexity

 
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The physical complexity of a sequence refers to the amount of information that is stored in that sequence about a particular environment. For a genome, this environment is the one in which it replicates and in which its host lives, a concept roughly equivalent to what we call a niche.
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Information is a statistical form of correlation, and thus requires, mathematically and intuitively, a reference to the system that the information is about.
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As we saw above, information is revealed, in an ensemble of adapted sequences, as those symbols that are conserved (fixed) under mutational pressure. Imagine then that a beneficial mutation occurs at a variable position. If the selective advantage that it bestows on the organism is sufficient to fix the mutation within the population,(24) the amount of information (and hence the complexity) has increased. A beneficial mutation that is lost before fixation does not decrease the amount of information, nor does this happen if a neutral mutation drifts to fixation.
In this paper Adami clarifies many of the concepts relevant to complexity such as information, entropy etc.

Date: 2002/12/06 19:28:27, Link
Author: Tom Ames
Most of my scientist colleagues are highly skeptical of the value of addressing anti-evolutionist tactics head-on. Generally, the thinking is that the stuff is so self-evidently wrong that there is no need to waste time on it. They're right in some senses, of course. But the antievolution movements might better be seen as part of a wider attempt to reduce the influence science has on public policy and public education. It seems clear that the DI/CRSC for example are engaged in this general anti-science campaign, wherein they hope to replace science's authority with a more religiously conservative one.

What I wonder is this: is the focus on evolution and its teaching in public schools necessarily the best place to take a stand against anti-science/anti-rationality movements? In a sense, I believe that the teaching of evolution in public high schools might be a distraction. We're talking about a high school biology unit that takes up maybe a week, but probably more like a single day of classes. Given the complexity of the material, it is doubtful that it can be covered adequately in the time alotted.

And (despite our fondest wishes) it really does seem to be controversial among most people. In a sense we might be taking a stand at the most politically difficult-to-defend point (analogous maybe to defending late-term abortions in order to ensure pro-choice policies).

Might there be a compromise that allows the scientifically minded to better convey the importance of rational empiricism, while eliminating the heat caused by "forcing" a controversial topic upon unwilling local school boards? Can we better maintain the separation between church and state by focusing on issues that are more salient to the largest group of people? Or is this truly a case of a "slippery slope" whereby giving in on any point will be surrendering a bulwark against further attacks?

Date: 2002/12/06 23:01:40, Link
Author: Michael
The time for Kent Hovind's trials is approaching.

It appears that the county changes IP numbers periodically possibly to try to force people to see the disclaimer.  Currently Hovind's court records can be found at:

Kent Hovind Charges

If the above stops working then try Escambia County Clerk's Records Page push accept, click "County Criminal / Misdemeanor"and punch in Kent Hovind's name.

The now infamous felony charge will have jury selection on Monday, December 9 if the records are up-to-date.
The judge trial for the alleged (and about as obviously true as one can get) building code violation will be on December 13 at 8:30 A.M.

Date: 2002/12/07 13:22:54, Link
Author: ExYECer
Originally posted by mturner:
Originally posted by Ex_YEC_er:
If that is the case then intelligence and volition cannot be intelligent design since ID is infered through the elimination of chance and regularity.

So what is it ?



Quote
Wrong as always. When are you going to accept that ID is about no such thing.


As I said before you seem to be unfamiliar with the major proponents' arguments in the ID world. Dembski's design inference argues, incorrectly I might add, that rarefied design can be infered through the elimination of chance/regularity hypotheses. In fact if such a hypothesis cannot be rejected then ID has to be rejected.

 
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For ID, volition and intelligence are regularity, and evolution is the product of this regularity, not the product of chance, as you Darwinists would have us believe.



Why is it that opponents of Darwinism so often seem to fail to understand that chance is but ONE aspect of the mechanism. In fact it it Dembski who seems to be arguing that Intelligent Design cannot be captured in regularity or if it can then it is not design anymore. If Mturner wants to argue against Dembski that's fine with me, join the fast growing club of those who object on scientific reasons to the Dembski design inference.

 
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ID does not deny the existance of random causation, the way you deny the existence of intelligent causation.

Shameless misrpresentation of my arguments I would argue. I in fact accept intelligent causation in nature. If you want to argue, please at least present my arguments correctly or run the risk of being called on spinning strawmen.

 
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Randomness and regularity  both exist, there is no effort to "eliminate" them, but regularity (intelligence/volition) acting in direct response to chaotic, random  environmental change (chance) is what brings about organismic adaptation and evolution; not Darwinism's random, accidental mutation supposedly being "regulated" by chaotic, random, accidental, environmental pressures. Absurd.

Welcome aboard opposing the ID inference ala Dembski/Behe then. Of course you seem to be somewhat unfamiliar with the supporting evidence and lacking in supporting evidence for your thesis but I will ignore that for the moment since I am thrilled to have you oppose Dembski's design inference.

 
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And so that is what ID is really about, and what Darwinism is really about, whether you like it or not, and whether or not you can ever bring yourself to face that, for you, painful truth.

So far it seems that mturner is having some problems facing the truths. I will be kind and gentle when introducing him/her to the facts of life.

Welcome aboard the anti-Dembski-ID train though. It is comforting to see that even pro-Intelligent design people are realizing that Dembski's arguments are just not useful in infering rarefied intelligent design. Of course without Dembski's attempt to bring ID into science, one may wonder what will happen to ID as a scientific movement? That presumes of course that such a movement ever existed in any serious manner.  :D



Date: 2002/12/07 13:42:54, Link
Author: ExYECer
In response to my posting of my reply to Dembski ARN moderator 4 now has found another objection :-)

Quote
I still don't like your tone. It "saddens" you, that Dembski "accuses"? That sucks, and is disrespectful.


He therefor has banned me from further participation in the thread. I would like to extend my appreciations to ARN moderator 4 for all his good work ;)



Date: 2002/12/07 14:00:23, Link
Author: theyeti
Hi Tom, Welcome to AE.

I disagree that we should just "give in" to the creationists/IDists when it comes to teaching evolution in public schools.  Right now my ideas are kind of scatter-shot and I haven't organized them completely.  But what follows is the basic outline.

1.  First of all, I think there is real value to teaching kids evolutionary theory.  Just like introducing them to any science, it helps them understand why scientists think like they think and do what they do.  I consider it no less valuable than introducing them to basic physics or chemistry.  As for myself, highschool biology was a major turning point, and learning about evolution was one of the more fascinating parts of it.  This is largely why I chose to persue a career in biology.  If we remove or water down evolution, or obscure it by introducing pseudoscience along side, then we may be doing kids and our society a serious disservice.  Furhtermore, any highschool student who goes to college and majors in biology, or even just takes an intro class, is going to have to understand evolutionary theory, and it's best if they get a good taste of it when they're in highschool.  Professors already complain that they have to spend too much class time just catching the students up to where they should have been before taking the class.  We live in a country where most of our scientists have to be imported.  Let's not make things worse.

2.  The fact that evolution is controversial in our culture is not a legitimate reason to quit teaching it or water it down in science class.  It is not controversial for scientists, though of course many subtheories within evolutionary theory are.  The reason evolutionary biology is controversial in our culture is because creationists/IDists spend millions of dollars on an everpresent and highly dishonest propaganda campaign.  By allowing this to affect what we do and don't teach in schools, we're effectively allowing anyone who can stir up a controversy to dictate our science cirricula.  Our science cirricula should be dictated by scientific consensus, not by noisy ideologues.  The cure to their propaganda is better information and teaching.  By removing or watering-down evolution, we will only make the problem worse.  

3.  The goal of the cre/ID crowd is to use to science class for religious and/or ideological indoctrination.  The various "compromises" they suggest are just stepping-stones to their ultimate goal, put forth in lieu of other strategies that have been struck-down by the courts.  If we allow them to teach creationism/ID along side evolution, then we have an equally serious problem on our hands (from a church/state separation viewpoint), which is to prevent them from pushing religious doctrine.  I see alowing pseudoscience into classrooms as making our job tougher, rather than diffusing the situation.  

Anyway, that's my thoughts as disorganized as they are.  The NCSE has a few articles about why we should teach evolution, and maybe I'll post them later time permitting.

theyeti

Date: 2002/12/07 15:23:08, Link
Author: niiicholas
bump

Date: 2002/12/07 21:27:59, Link
Author: rlbennett
Quote (ExYECer @ Dec. 07 2002,13:42)
In response to my posting of my reply to Dembski ARN moderator 4 now has found another objection :-)

Quote
I still don't like your tone. It "saddens" you, that Dembski "accuses"? That sucks, and is disrespectful.


He therefor has banned me from further participation in the thread. I would like to extend my appreciations to ARN moderator 4 for all his good work ;)

Well, at least it saddened you.  Why does that suck?  Sucks for you.  I don't think it is possible to read Dembski writings any other way but as accusing evolutionists.

Date: 2002/12/08 00:05:34, Link
Author: Wesley R. Elsberry
The ISCID moderator (John Bracht, if my sources know what they are talking about) recently posted concerning how ID critics came in 4 categories.

Quote
1. Open-minded skeptic: I'm interested, but not convinced.
2. Closed-minded skeptic: Not convinced and no longer interested in being convinced. Call me only if something new develops somewhere to cause quite a commotion.
3. Debunker: Not convinced; no longer interested in being convinced; interested only in convincing others they are wrong.
4. Debunking Crusader: Debunking to save humanity.

(Source: On Criticism - Four Types of Critics )


I've asked for what category I might be classed in.  Stay tuned for the results...

Wesley

Date: 2002/12/08 00:10:21, Link
Author: niiicholas
Looks like this bit got nuked in the server crash.  The 1969 paper on Hagemann factor loss in whales has been cited, but there is an interesting 1998 paper:

Quote

http://www.ncbi.nlm.nih.gov/entrez....9678675

Thromb Res 1998 Apr 1;90(1):31-7
 
Whale Hageman factor (factor XII): prevented production due to pseudogene conversion.

Semba U, Shibuya Y, Okabe H, Yamamoto T.

Department of Clinical Laboratory Medicine, School of Medicine, Kumamoto University, Honjo, Japan.

In Southern blot analysis of the Hind III-digested whale genomic DNA obtained from the livers of two individual whales, we detected a single band with a size of five kilobase pairs which hybridized to full length guinea pig Hageman factor cDNA. We amplified two successive segments of the whale Hageman factor gene by polymerase chain reaction (PCR), and sequenced the PCR products with a combined total of 1367 base pairs. Although all of the exon-intron assemblies predicted were identical to those of the human Hageman factor gene, there were two nonsense mutations making stop codons and a single nucleotide insertion causing a reading frame shift. We could not detect any message of the Hageman factor gene expression by northern blot analysis or by reverse transcription-polymerase chain reaction (RT-PCR) analysis. These results suggest that in the whale, production of the Hageman factor protein is prevented due to conversion of its gene to a pseudogene. The deduced amino acid sequence of whale Hageman factor showed the highest homology with the bovine molecule among the land mammals analyzed so far.


...obvious implications concerning the origin of whales...

Date: 2002/12/08 00:57:42, Link
Author: niiicholas
Here's a good example of a debate that rapidly focused on the ambiguities in the defn of IC:

http://iidb.org/ubb....1759&p=

...other examples welcome.

Also, cites of IDists using/defining IC, SC, etc. in conflicting ways.

Date: 2002/12/08 07:33:53, Link
Author: Wesley R. Elsberry
Newspaper: at least six no votes expected on science standards

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Some members of the state Board of Education say they feel pressured by Gov. Bob Taft’s office and his eight appointees on the panel to vote unanimously for the curriculum guidelines. Only a majority is required for approval.

“It’s all coming through the governor’s office — a call here, a comment there,” board member Martha Wise of Avon told the newspaper. “It’s a very heavy-handed way of dealing with the situation. This is our vote. It’s not the governor’s vote.”

Date: 2002/12/08 08:46:22, Link
Author: Bebbo
While on the subject of ISCID, does anyone else find it strange that discussion of purpose of design is shyed away from even though the ISCID home page says something like "retraining the scientific mind to see purpose in nature"?

--
Dene

Date: 2002/12/08 08:51:05, Link
Author: Bebbo
Quote (ExYECer @ Dec. 07 2002,13:42)
In response to my posting of my reply to Dembski ARN moderator 4 now has found another objection :-)

Quote
I still don't like your tone. It "saddens" you, that Dembski "accuses"? That sucks, and is disrespectful.


He therefor has banned me from further participation in the thread. I would like to extend my appreciations to ARN moderator 4 for all his good work ;)

Moderation at ARN is a mess. The choice of moderator is strange considering posts of his I've seen in the past. It's obvious that one moderator is not enough for that forum, and he's too partisan anyway.

Btw, does anyone else think that Chris Langan is an unpleasant character? Besides his overbearing arrogance, his metaphors are sometimes weird.

--
Dene

Date: 2002/12/08 10:24:40, Link
Author: Bebbo
Quote (Wesley R. Elsberry @ Dec. 08 2002,00:05)
The ISCID moderator (John Bracht, if my sources know what they are talking about) recently posted concerning how ID critics came in 4 categories.

Quote
1. Open-minded skeptic: I'm interested, but not convinced.
2. Closed-minded skeptic: Not convinced and no longer interested in being convinced. Call me only if something new develops somewhere to cause quite a commotion.
3. Debunker: Not convinced; no longer interested in being convinced; interested only in convincing others they are wrong.
4. Debunking Crusader: Debunking to save humanity.

(Source: On Criticism - Four Types of Critics )


I've asked for what category I might be classed in.  Stay tuned for the results...

Wesley

Hmmm, I always thought the ISCID moderator is Micah Sparicio (sp?).

--
Dene

Date: 2002/12/08 13:27:05, Link
Author: pzmyers
Quote (Bebbo @ Dec. 08 2002,08:51)
Btw, does anyone else think that Chris Langan is an unpleasant character? Besides his overbearing arrogance, his metaphors are sometimes weird.

Yes.

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'By the way, I know what you're thinking. "Did he fire six shots or only five?" Well, to tell you the truth, in all this excitement, I've kinda lost track myself. But being as this is a .44 Magnum, the most powerful handgun in the world, and would blow your head clean off, you've gotta ask yourself one question: "Do I feel lucky?"'


I really think that talking about blowing a critic's head off is creepy and inappropriate...and for the moderator to then chime in with a joke about him needing a new suit is rather appalling.

Date: 2002/12/08 14:29:58, Link
Author: Bebbo
Quote

Quote (pzmyers @ Dec. 08 2002,13:27)
[quote=Bebbo,Dec. 08 2002,08:51]Btw, does anyone else think that Chris Langan is an unpleasant character? Besides his overbearing arrogance, his metaphors are sometimes weird.

Yes.

Quote
'By the way, I know what you're thinking. "Did he fire six shots or only five?" Well, to tell you the truth, in all this excitement, I've kinda lost track myself. But being as this is a .44 Magnum, the most powerful handgun in the world, and would blow your head clean off, you've gotta ask yourself one question: "Do I feel lucky?"'


I really think that talking about blowing a critic's head off is creepy and inappropriate...and for the moderator to then chime in with a joke about him needing a new suit is rather appalling.

I'm not sure if the Dirty Harry quote was just for fun or aimed at Mellott. What I found creepy was this one:

Quote

You know, I really get a kick out of certain “Scientists” – the kind of “Scientist” who’s always knocking philosophy. When you tree one of these Scientists and ask him to vocalize about why he hates philosophy, he vulcanizes about the evils of nebulosity, nihilism and deconstructionism. But then when you bag him, mount his skin on your trophy wall and turn off the lights, there it is on his hide in glow-in-the-dark green paint: “I was a nihilist who tried to deconstruct nature despite my nebulous grasp of reality.”


It reminded me of someone I've debated with on Usenet who uses phrases like "beaten up" to describe someone she self-proclaimededly beat in a debate.

So far Chris Langan is the one with the biggest chip on his shoulder that I've encountered on the net for a while.

--
Dene

Date: 2002/12/08 14:34:57, Link
Author: niiicholas
Quote (Bebbo @ Dec. 08 2002,08:46)
While on the subject of ISCID, does anyone else find it strange that discussion of purpose of design is shyed away from even though the ISCID home page says something like "retraining the scientific mind to see purpose in nature"?

--
Dene

That is funny, isn't it.

"Look, there's purpose in biology!"

"But what's the purpose?"

"Sorry, can't talk about that!"

Date: 2002/12/08 21:44:52, Link
Author: JxD
Quote
In his reply Orr takes me to task for not responding to the many particular objections he raised against my work in his original review, suggesting that this was the result of bewilderment on my part and intelligent design running out of steam and not, as was the case, for lack of space. This sort of rule-rigging by Orr and the Boston Review -- give the respondent a little space, and then let the original author crow about winning -- is to be expected. I actually find it encouraging, taking it as an indication of intelligent design's progress. Orr's review and follow-up hardly spell the death-knell for intelligent design or for my work in this area. Sooner or later (and probably sooner) Orr will find himself in a forum on intelligent design where the rules of engagement are not rigged in his favor. I look forward to his performance then.
 It is almost like they revamped the moderation on purpose, doesn't it?  Here fishy fishy fishy. . .  I can't believe Dembski has resorted to these childish taunts.

Date: 2002/12/08 22:26:49, Link
Author: theyeti
A new study finds dozens of retrogenes in Drosophila.

Retroposed New Genes Out of the X in Drosophila

Esther Betrán, Kevin Thornton, and Manyuan Long

Genome Res 2002 Dec;12(12):1854-9

PubMed

Full text  (may need subscription)

Abstract:
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New genes that originated by various molecular mechanisms are an essential component in understanding the evolution of genetic systems. We investigated the pattern of origin of the genes created by retroposition in Drosophila. We surveyed the whole Drosophila melanogaster genome for such new retrogenes and experimentally analyzed their functionality and evolutionary process. These retrogenes, functional as revealed by the analysis of expression, substitution, and population genetics, show a surprisingly asymmetric pattern in their origin. There is a significant excess of retrogenes that originate from the X chromosome and retropose to autosomes; new genes retroposed from autosomes are scarce. Further, we found that most of these X-derived autosomal retrogenes had evolved a testis expression pattern. These observations may be explained by natural selection favoring those new retrogenes that moved to autosomes and avoided the spermatogenesis X inactivation, and suggest the important role of genome position for the origin of new genes.


I'm going to include this little quote from the opening paragraph because it's useful IMO as a summary of sources of new gene evolution, and with references to the earliest papers about them:

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New genes that originated by various molecular mechanisms are an essential component in understanding the evolution of genetic systems (Long 2001). These mechanisms include the classic mechanism of duplication (Ohno 1970), exon shuffling (Gilbert 1978), retroposition (Brosius 1991), and gene fusion through deletions or recruitment of new regions (Nurminsky et al. 1998), or a combination of these mechanisms (Long and Langley 1993; Begun 1997; Nurminsky et al. 1998).


Here are a few other important passages:

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There is increasing evidence, fortunately, that retroposition, which generates new genes in new genomic positions via reverse transcription of mRNA from a parental gene, is important for the origin of new gene functions (Brosius 1999). In mammalian systems, a classic example is the human retrogene Pgk-2 with male specific function (McCarrey and Thomas 1987). Pgk-2 is autosomal (chromosome 19) whereas the parental copy Pgk-1 is X-linked. Pgk-2 evolved late spermatogenesis-specific expression. [theyeti:  I think I posted Pgk-2 before the crash.  I will do it again shortly] This new expression pattern is related to the fact that late spermatogenesis cells are the only ones that do not express Pgk-1 because of male germline X inactivation (McCarrey 1994). Subsequent analyses of retroposed genes in mammalian genomes suggested that retroposition had efficiently sown the seeds of evolution in genomes (Brosius 1991).
...
We have identified, from the annotated genes in the D. melanogaster genome, all pairs of homologs (70% amino acid identity or more) that are located on different chromosomes with hallmarks of retroposition (Table 1). Twenty-four young paralogous pairs fulfilled these criteria: 23 pairs in which the new copy lost the introns (CG12628, one of the 23, is additionally flanked by short repeats), and one pair with no introns in either copy but with the new copy retaining a degenerated poly-A tract (CG 12324/Rp515A). Interestingly, CG12628, which seems to be the youngest of the described retrogenes, is the only one that retains the direct repeats, a hallmark of the recent insertion event. Some other retrogenes also retained a degenerated poly-A tract: CG12628, CG10174, and CG13732. The parental genes have diverse functions, consistent with results from the human genome (Gonçalves et al. 2000).
...
Four possible explanations could account for the observed pattern: (1) nonrandom generation of retrogenes by a disproportionate number of X-linked genes that express in the germline cells; (2) negative selection against insertions in the X chromosome; (3) different recombination rates (or possibly deletion rates) between the autosomes and the X chromosome; and (4) positive Darwinian selection favoring retrogenes generated from the X chromosome to the autosomes.
...
The fourth hypothesis, positive selection, seems more parsimonious to interpret the excess of retroposition from X to autosomes. X inactivation during early spermatogenesis could produce a selective advantage for the retroposed genes with novel functions that escape X linkage and become expressed in testis, as previously suggested (Lifschytz and Lindsley 1972; McCarrey 1994). X inactivation early in spermatogenesis is well documented in Drosophila, mouse, and human (Lifschytz and Lindsley 1972; Richler et al. 1992). Thus, a mutant with a newly retroposed gene on autosomes will have some advantage over an X-linked form, because the mutant can carry out a new function putatively required in male germline cells after the X chromosome becomes inactivated. This hypothesis assumes that retroposition occurs from genes on all chromosomes with the same probability but natural selection favors the ones that avoid X-linkage by moving to an autosome and developing expression in testis.


theyeti

Date: 2002/12/09 07:07:07, Link
Author: Wesley R. Elsberry
Of mice and men

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Despite the vast areas of commonality between the two species, the research identifies genetic territories that have undergone huge divergence. Mouse genes involved in sex, courtship, smell and immunity are fundamentally different from anything seen in the human genome. The nocturnal mouse uses olfactory cues for marking territory and identifying possible mates; the genes of the mouse immune system are immensely evolved compared to ours, indicating the faster genetic "arms race" between mice and their parasites – a product of the large litter size and short generation time of the fast-breeding rodent.

So although the mouse genome opens the prospect of strides in the understanding of human disease, it also provides biologists with the raw data on which to build insights into our common evolutionary history.

Date: 2002/12/09 18:12:01, Link
Author: Wesley R. Elsberry
Hartwig's "Darwinian Resolution"

Mark Hartwig responds to the AAAS anti-ID resolution with the following:

Quote
Placed side-by-side with other public statements, the resolution and op-eds show how widespread Darwinist anxiety has become. [1] More importantly, however, they also reveal why Darwinists are losing ground: namely, because they are misleading their supporters.


How are supporters being misled?

Quote
In his op-ed for the Beacon Journal, Leshner attributed the ID movement’s success to “a sophisticated marketing campaign based on a three-pronged penetration of the scientific community, educators, and the general public.” This echoes a key theme of ID foes, which says the ID movement is succeeding by duping the public with shrewd tactics and a big-bucks marketing campaign.

Such claims are a great way to rally the troops: “Don’t worry boys, they’re just shooting blanks.” But they’re also a great way to get those troops mowed down, due to cockiness and lack of preparation.

Imagine someone repeating Leshner’s claim in a public forum. It would be a small matter to show that the balance of marketing power lies with the Darwinists. Indeed, the byline for Leshner’s piece in the Beacon-Journal notes that his organization “has 134,000 members serving 10 million scientists worldwide and publishes the weekly journal Science.”

[details of the marketing plan for the Evolution TV series skipped - WRE]

With the financial and talent resources that the Darwinist establishment has at its disposal, anyone repeating Leshner’s claim in a public forum is likely to end up looking foolish or disingenuous.


Note carefully what Hartwig does not do: he does not show that the claim in question is false, but rather engages the tu quoque fallacy.  AAAS has a lot of members and sends them information, sure, but what has that got to do with the issue of whether ID's success is due to marketing or to content?  Where is it that Leshner misleads?  It appears to me that the person looking foolish or disingenuous is likely to be the one who had to use tu quoque in order to have the semblance of a response.

Next up, Hartwig tries again on another issue:

Quote
The same is true for anyone who tries to defend the notion that there is no evidence against evolution and that ID success is a matter of deception and style rather than substance. Darwinist leaders have repeated these claims for years, arguing that dissent is unreasonable and should be banished from science classrooms. Such tactics are an easy mark for ID proponents, who have responded by publicizing scientific evidence against naturalistic evolution, by documenting the pervasiveness of egregious errors in biology textbooks’ treatment of evolution, and by doggedly insisting that debate be based on facts and reason rather than alleged motives.


And again Hartwig fails to touch the issue, which is whether ID advocacy has any content of its own.  Even Hartwig can't name any, for his list is composed entirely of negative arguments concerning evolutionary biology and meta-arguments about debating style.

Again, where is it that Leshner misled anyone?  Hartwig certainly develops no argument that such was the case.

Wesley

Date: 2002/12/09 18:37:52, Link
Author: Glenn Branch
David Berlinski published "Has Darwin Met His Match?" in the December 2002 issue of Commentary (vol. 114, no. 5, pp. 31-41). Here Berlinski, a Senior Fellow of the Discovery Institute's Center for Science and Culture, chastizes not only "Darwinians" but "design theorists" for accepting theories that are empirically vacuous:
Quote
...Darwinian theorists may be observed standing in silence. They are looking upward, apparently much occupied in assessing cracks in the ceiling. Beyond saying that that is just the way things are, what could they say? ... Design theorists may now be observed standing in companionable silence alongside Darwinian biologists. They, too, seem to be gazing upward, studying the same queer little cracks in the ceiling.

(From p. 33.) A fascinating, if florid, article. I rushed out and bought a copy of his Black Mischief: Language, Life, Logic, Luck (second edition, Boston: Harcourt Brace Jovanovich, 1988) for purposes of comparison. If anyone wants to talk about Berlinski, here's a thread.

Date: 2002/12/10 15:37:01, Link
Author: katerina
Quote
originally posted by Chris LanganYou know, I really get a kick out of certain “Scientists” – the kind of “Scientist” who’s always knocking philosophy. When you tree one of these Scientists and ask him to vocalize about why he hates philosophy, he vulcanizes about the evils of nebulosity, nihilism and deconstructionism. But then when you bag him, mount his skin on your trophy wall and turn off the lights, there it is on his hide in glow-in-the-dark green paint: “I was a nihilist who tried to deconstruct nature despite my nebulous grasp of reality.”


Didn't y'all recognize the cultural origin of this 'treeing'?

People in the South used to talk about treeing African-Americans.

Now, on the subject of Chris' mixed metaphors.

1.  He is just a bad writer and lacking in intellectual training.  (it's not deconstructionism but deconstruction)

2.  He has something going on mentally-wise.  There's a lot of projection and dream-like shifting in his mixed metaphors.  I would say he is something of a looney.

3.  I have considered starting a collection of his speech against the Academy that he protests too much.  Read him long enough and it does sound like the focus of his envy is on the fact that he doesn't get to slave away teaching dolts for little remuneration with colleagues who are themselves a over-complicated egotists, as we professors must do daily.

Date: 2002/12/10 17:11:20, Link
Author: Wesley R. Elsberry
On the rarity of calculations using Dembski's EF/DI

From t.o. ...

In article <3df60bc3-robomod@ediacara.org>,
Mike Goodrich  <goodrich_ms@yahoo.com> wrote:
>Mark VandeWettering wrote:
>> In article <3df3c928-robomod@ediacara.org>, Mike Goodrich wrote:

MG> I sure hope that even though you don't know all my intentions, and even
MG> though a certain amount of contrivance regarding matter, energy, and the
MG> laws of physics are involved you are still making the judgment that my
MG> posts are designed, thus confirming the utility of Demski 'sThree Part
MG> Filter.

MV> Your posts have actually very few signs of design.   But I am fascinated:
MV> can you describe how Dembski's three part filter can be used to determine
MV> that your postings are the result of intelligent design?

MG>Actually I think it would be far more instructive for you to describe
MG>how Dembski's filter would not be useful in determing that
MG>intelligent design was not the best mode of explanation for my
MG>postings, asuuming that is what you think..  It would be a good
MG>excercise in thinking out of the box for you.  (But I won't hold my
MG>breath)

I don't know that it is more "instructive", since those making the positive claim have the burden of proof.  Mike's claim that Dembski's EF/DI has "utility" is a positive claim, and thus it is Mike who has the burden of proof here.

Does Mike take up his burden?  Rather predictably, Mike attempts to shift the burden to others.  This is simple abandonment of the claim.  Mike apparently has no clue how to actually use Dembski's EF/DI, and rather than forthrightly admit this, Mike tries to distract others from recognizing this.

But Mike is not the only person for whom Dembski's EF/DI is simply too cumbersome to apply to real-world problems.  Dembksi himself has attempted only four applications of varying degrees of completeness in the period from 1996 to the present.  Which reminds me of the following:

[Quote]

Thus far Gell-Mann's theory has resisted detailed applications to real-world problems.

[End Quote - WA Dembski, "No Free Lunch", 2002, p.133]

Dembski's criticism of Gell-Mann's "effective complexity" is far more apposite when applied to his own concept of "specified complexity".  No one but Dembski has, to my knowledge, even attempted a calculation of the sort required by Dembski's description of his EF/DI.  Hmm... Actually, I may be the only other person than Dembski to attempt a calculation following his EF/DI as it was described in "The Design Inference".  I seem to recall a post here in t.o. some years back showing that solutions of the "travelling salesman problem" were examples of specified complexity.

So what would have to happen for Mike to become the very first person other than William Dembski and Dembski's critics to actually apply Dembski's EF/DI, and not simply assert that it is applicable?

Dembski lays out his "argument schema" for his somewhat revised EF/DI in "No Free Lunch" on pages 72-73.  Mike should refer to it for the full specification of what has to happen for an analysis to match the technical requirements of the EF/DI.  Failure to fully apply this framework is rampant, as analysis of Dembski's four examples shows.

First, observe an event.  It is interesting that while Dembski says that "subject S learns that an event E has occurred", Dembski is fond of using hypotheticals instead of real-world events.

Second, generate a set {H} of chance hypotheses relevant to the production of event E.  This seems to be a stumbling block, for one can note that failure is common in this regard.  Fully 25% of Dembski's proffered calculations (one of them) is notable for *not* including natural selection among relevant chance hypotheses (see section 5.10 of "No Free Lunch").

Third, identify a "rejection function f" and "rejection region R" such that E is in R and R "is an extremal set of f".  Even Dembski skipped this part in section 5.10 of "No Free Lunch".  Don't forget the gammas and deltas discussed on p.72!  This requires math, not handwaving.

Fourth, identify the "background knowledge K" that "explicitly and univocally identifies the rejection function f" from step (3).  Again, this step is notable by how seldom it is actually deployed, as can be seen by its absence from the discussion in section 5.10 of "No Free Lunch".

Fifth, identify the "probabilistic resources" for E "to occur and be specified relative to S's context of inquiry".  BTW, Mike, S is you in this discussion.  And again, even Dembski omits this step from section 5.10 of "No Free Lunch".

Sixth, fix a significance level alpha so that events less probable than alpha remains improbable conditioned on each of the chance hypotheses in {H} even when the probabilistic resources of (5) are applied.  This one requires some knowledge of probability and statistics, and thus may prove more difficult for Mike than it was for Dembski.

Seventh, confirm that the probability of the rejection region R is less than alpha for all of the chance hypotheses in {H}.  Again, this requires actual math, not vague handwaving, and may prove somewhat difficult for Mike.

Step 8 is just a conclusion that E exhibits specified complexity.  Mike has shown no problem in jumping to conclusions regardless of the lack of warrant for them, so assuming he makes it through the preceding steps, this one should pose no difficulty.  In fact, this step is so easy that most of the "examples" cited by Dembski are composed entirely of the assertion that some phenomenon E exhibits specified complexity with no accompanying justification of any sort whatsoever.  In the overwhelming majority of cases, no "calculation" of any kind is offered.

If Dembski's EF/DI did have "utility" for some applications, it seems to me that someone somewhere in the six years that it has been available publicly should have picked it up and applied it to accomplish something non-trivial.  Even if Mike successfully deployed the full EF/DI apparatus (an event that itself discourages breathholding), the end result (a conclusion that Mike's posts show "design" sensu Dembski) is trivial and would not support Mike's claim that Dembski's EF/DI has "utility" in any non-trivial sense.

There are other approaches to analysis of events based on algorithmic information theory that can do the useful,
utilitarian tasks that Dembski talks about in making ordinary design inferences without the many drawbacks that critics have noted in Dembski's EF/DI apparatus.  Wherever someone wishes to apply the EF/DI, they very likely would be better off using an alternative analytical tool.  However, the alternatives do not lead to a conclusion, either deductively or inductively, of intelligent agent causation.  So far, the only "utility" that has been demonstrated for Dembski's EF/DI is based not upon its "application to real-world problems", but rather in its very existence as a tool for Christian apologetics.  The various failures to completely deploy the EF/DI seem to have no effect on its effectiveness in apologetics.

Date: 2002/12/10 18:20:47, Link
Author: pzmyers
Quote (katerina @ Dec. 10 2002,15:37)

I presume that your description of students as "dolts" and our colleagues as "over-complicated egotists" is an attempt to project Langan's opinion, rather than yours? I hope?

Date: 2002/12/10 18:53:30, Link
Author: katerina
Irony, darling.

Chris envies the university position that he doesn't have.

On the other hand, he seems to think that we just sit around in smoking rooms making fun of the non-university folk, when, in fact, we deal with a lot of nasty stuff.

Date: 2002/12/10 21:00:03, Link
Author: theyeti
This one appears to be somewhat speculative (and I don't have the full text) but it's highly relevant nonetheless.

Mol Neurobiol 2002 Oct-Dec;26(2-3):235-50

Structure of the sodium channel gene SCN11A: evidence for intron-to-exon conversion model and implications for gene evolution.

Dib-Hajj SD, Tyrrell L, Waxman SG.

Quote
Exon/intron boundaries in the regions encoding the trans-membrane segments of voltage-gated Na channel genes are conserved, supporting their proposed evolution from a single domain channel, while the exons encoding the cytoplasmic loops are less conserved with their evolutionary heritage being less defined. SCN11A encodes the tetrodotoxin-resistant (TTX-R) sodium channel Nav1.9a/NaN, which is preferentially expressed in nociceptive primary sensory neurons of dorsal root ganglia (DRG) and trigeminal ganglia. SCN11A is localized to human chromosome 3 (3p21-24) close to the other TTX-R sodium channel genes SCN5A and SCN10A. An alternative transcript, Nav1.9b, has been detected in rat DRG and trigeminal ganglion. Nav1.9b is predicted to produce a truncated protein due to a frame-shift, which is introduced by the new sequence of exon 23c (E23c). In human and mouse SCN11A, divergent splicing signals prevent utilization of E23c. Unlike exons 5A/N in genes encoding TTX-sensitive sodium channels, which appear to have resulted from exon duplication, E23c might have evolved from the conversion of an intronic sequence. Although a functional role for Nav1.9b has yet to be established, intron-to-exon conversion may represent a mechanism for ion channels to acquire novel features.


Given that intronic sequences, with the exception of some 5' and 3' conserved bases, are sequence non-specific, this would be the equivalent of a more or less random sequence being converted into a biological function.

theyeti

edited to add this diddy:

Evolution of voltage-gated Na(+) channels.



Date: 2002/12/10 21:00:15, Link
Author: pzmyers
Quote (katerina @ Dec. 10 2002,18:53)
Irony, darling.

Chris envies the university position that he doesn't have.

On the other hand, he seems to think that we just sit around in smoking rooms making fun of the non-university folk, when, in fact, we deal with a lot of nasty stuff.

Just making sure.

What a silly stereotype, though. We don't have smoking rooms. As everyone knows, we are so pc that we don't allow smoking, unless it is Sacred Weed.

Date: 2002/12/10 23:26:33, Link
Author: theyeti
Birth of two chimeric genes in the Hominidae lineage.


Courseaux A, Nahon JL.

Science 2001 Feb 16;291(5507):1293-7

PubMed, Full text (May require subscription)

Quote
How genes with newly characterized functions originate remains a fundamental question. PMCHL1 and PMCHL2, two chimeric genes derived from the melanin-concentrating hormone (MCH) gene, offer an opportunity to examine such an issue in the human lineage. Detailed structural, expression, and phylogenetic analysis showed that the PMCHL1 gene was created near 25 million years ago (Ma) by a complex mechanism of exon shuffling through retrotransposition of an antisense MCH messenger RNA coupled to de novo creation of splice sites. PMCHL2 arose 5 to 10 Ma by an event of duplication involving a large chromosomal region encompassing the PMCHL1 locus. The RNA expression patterns of those chimeric genes suggest that they have been submitted to strong regulatory constraints during primate evolution.


Here is the proposed model for the evolution of these genes (B):

(Larger Image)
Quote
(B) Proposed model for the emergence of MCH-derived sequence onto chromosome 5p. (a) An AROM mRNA initiating in the CS3-5 region and ending at poly A (b) polyadenylation site was retrotransposed onto the equivalent of chromosome 5p at the time of Catarrhini divergence 25 to 30 Ma. (b) After this first event or concurrent to it, an Alu sequence was inserted in intron A and a fragment corresponding to the 3' end of the retrotransposed mRNA (part of exon II-intron A-Alu) was broken and transposed to the downstream insertion site. This led to the PMCHL gene versions observed in Cercopithecoidea and Hominoidea.


theyeti



Date: 2002/12/10 23:46:58, Link
Author: ExYECer
Moderator 4 (aka Jack F) has decided to ban me for two weeks for posting the following message on an off topic board at ARN

Quote

I'll lose interest in ARN soon, but have followed some posts that I was interested in before I decided to quit. But I happened to see this post by Mike B.

I was threatened with removal after two postings, one which asked why YXCs post was spam and one that simple said I agreed with Douglas, XYCs post should stay because it brought up interesting points for discussion on Dembski's overly repetitive arguments. I then suggested a new direction for the thread to focus of Dembski's limiting the definintion of Direct evolution and IC.

Tell Mike B, I formally left ARN (had my membership removed) because I could ignore a lot from Jazz, but not this hair trigger threat to ban me simply because I was in agreement with another poster. In none of my posts did I call call Jazz out as a horrible moderator, then everything I post there after gets deleted.

Mike B, know what you are talking about before you criticize another poster for being disgruntled. I did not highjack a single thread (ala DNAunion and his obsession with Julie/Wolf), nor did I make joking threats (ala CML). Or post little sidetracking quips (ala Jazz himself on
several posts).

RB


Jack responded that

Quote

I just deleted a post from XYC. He posts a note from RB slamming the site.


Funny how Moderator 4 seems to consider RB's response to be 'slamming the site'.

Date: 2002/12/11 07:23:30, Link
Author: katerina
Wull yeah.  It's a silly stereotype.

I just recently clued into this facet of Monsieur Langan's character.  The word that keeps coming to mind is 'penis envy', but I don't know why or if that is valid.

But come on.  If you have never been in a science lab, what do you know about what is going on there?  And if you have never been involved with or been a research scientist, you don't really have a good idea of the financial tension, the long hours, the bizarro lab politics (on occasion), etc.

And if you have never been involved with or been a tenure-track professor, then you have no idea of what the isolation, the carrot-stick tension, the publish or perish pressure, the student loan repayment pressure, is like.

Chris gives professors the kind of prestige that the rest of the American culture does not.

So it's a little sicko.  He envies us.  But he is precisely not the sort of person we care to envy us.

Date: 2002/12/11 07:30:30, Link
Author: katerina
I have some of that thread saved somewhere--the back and forth between Rb and Jesse.

Date: 2002/12/11 13:33:28, Link
Author: Wesley R. Elsberry
New standards play down `intelligent design'

Quote
The debate on whether intelligent design should be taught in Ohio schools has raged for months as the state board of education considered the new science standards. The standards are guidelines for teaching science to the state's 1.8 million public school students.

The new science standards emphasize evolution but allow critical analysis of the theory. However, the board added an amendment saying the standards do not mandate the teaching or testing of intelligent design.

Date: 2002/12/11 13:45:12, Link
Author: Wesley R. Elsberry
Evolution disclaimer supported

Quote
High school biology textbooks would include a disclaimer that evolution is only a theory under a change approved Tuesday by a committee of the state's top school board.

If the disclaimer wins final approval, it would apparently make Louisiana just the second state in the nation with such a provision. The other is Alabama, which is the model for the disclaimer backers want in Louisiana.


The article quotes Darrell White, who was one of the agitators for last year's legislation aimed at declaring Charles Darwin, noted abolitionist, to have been a racist.

Date: 2002/12/11 14:23:50, Link
Author: Bebbo
If you work on the basis that the Wedge Update is an exercise in intellectual buffoonery then it all make sense!

--
Dene

Date: 2002/12/11 17:24:31, Link
Author: Wesley R. Elsberry
Why antibiotics in meat should give you pause

Quote
In other words, evolutionary biology should matter to just about everybody in America - and would, if they paid heed to several new studies confirming what some scientists have argued for years: that antibiotics are dangerously overused, especially to enhance the growth of farm animals.

The result has been the swift evolution of bacteria that are resistant to commonly used antibiotics, such as Ampicillin, Erythromycin and Ciprofloxacin - which you may remember as Cipro, the drug of choice in last year's anthrax attacks.

You don't have to live on a farm to care about this. According to two of the studies, these drug-resistant strains are probably as close as your nearest supermarket, or even in the package of raw chicken you bought to make tonight's dinner.

In a study conducted by Consumers Union, researchers found Campylobacter in 42 percent of nearly 500 broiler chickens purchased in 25 different cities, and Salmonella in 12 percent.

Date: 2002/12/12 16:52:18, Link
Author: Michael
The felony charges against Hovind have been dropped.



Date: 2002/12/12 17:23:25, Link
Author: theyeti
Annu Rev Plant Biol 2002;53:503-21

Complex evolution of photosynthesis.

Xiong J, Bauer CE.

Quote
The origin of photosynthesis is a fundamental biological question that has eluded researchers for decades. The complexity of the origin and evolution of photosynthesis is a result of multiple photosynthetic components having independent evolutionary pathways. Indeed, evolutionary scenarios have been established for only a few photosynthetic components. Phylogenetic analysis of Mg-tetrapyrrole biosynthesis genes indicates that most anoxygenic photosynthetic organisms are ancestral to oxygen-evolving cyanobacteria and that the purple bacterial lineage may contain the most ancestral form of this pigment biosynthesis pathway. The evolutionary path of type I and type II reaction center apoproteins is still unresolved owing to the fact that a unified evolutionary tree cannot be generated for these divergent reaction center subunits. However, evidence for a cytochrome b origin for the type II reaction center apoproteins is emerging. Based on the combined information for both photopigments and reaction centers, a unified theory for the evolution of reaction center holoproteins is provided. Further insight into the evolution of photosynthesis will have to rely on additional broader sampling of photosynthesis genes from divergent photosynthetic bacteria.


theyeti

Date: 2002/12/12 20:58:50, Link
Author: niiicholas
Interesting.  Here's another one by the same folks:

Quote

A cytochrome b origin of photosynthetic reaction centers: an evolutionary link between respiration and photosynthesis

J Mol Biol 2002 Oct 4;322(5):1025-37
Xiong J, Bauer CE.

Department of Biology, Texas A&M University, College Station, TX 77843, USA.

The evolutionary origin of photosynthetic reaction centers has long remained elusive. Here, we use sequence and structural analysis to demonstrate an evolutionary link between the cytochrome b subunit of the cytochrome bc(1) complex and the core polypeptides of the photosynthetic bacterial reaction center. In particular, we have identified an area of significant sequence similarity between a three contiguous membrane-spanning domain of cytochrome b, which contains binding sites for two hemes, and a three contiguous membrane-spanning domain in the photosynthetic reaction center core subunits, which contains binding sites for cofactors such as (bacterio)chlorophylls, (bacterio)pheophytin and a non-heme iron. Three of the four heme ligands in cytochrome b are found to be conserved with the cofactor ligands in the reaction center polypeptides. Since cytochrome b and reaction center polypeptides both bind tetrapyrroles and quinones for electron transfer, the observed sequence, functional and structural similarities can best be explained with the assumption of a common evolutionary origin. Statistical analysis further supports a distant but significant homologous relationship. On the basis of previous evolutionary analyses that established a scenario that respiration evolved prior to photosynthesis, we consider it likely that cytochrome b is the evolutionary precursor for type II reaction center apoproteins. With a structural analysis confirming a common evolutionary origin of both type I and type II reaction centers, we further propose a novel "reaction center apoprotein early" hypothesis to account for the development of photosynthetic reaction center holoproteins.


Did I mention that I really like accumulating the refs and links on topics like this in topic-specific UBB threads?  Quite a useful thing to have around IMO...

Date: 2002/12/12 21:02:38, Link
Author: niiicholas
Philosopher/Historian of science, who has authored a PhD and several articles on Kettlewell's work, has weighed in against Jonathan Wells:

Quote

Cryptic designs on the peppered moth.

Rev Biol Trop 2002 Mar;50(1):1-7
Rudge DW.

Department of Biological Sciences, Institute for Science Education, Western Michigan University, 3134 Wood Hall, Kalamazoo, MI 49008-5410, USA. david.rudge@wmich.edu

In a provocative recent book, Jonathan Wells (2000) decries what he discerns as a systematic pattern in how introductory biology textbooks "blatantly misrepresent" ten routinely cited examples offered as evidence for evolution. Each of these examples, according to Wells, is fraught with interpretive problems and, as such, textbooks that continue to use them should at the very least be accompanied by warning labels. The following essay critiques his reasoning with reference to one of these examples, the phenomenon of industrial melanism. After criticizing Wells's specific argument, the essay draws several conclusions about the nature of science lost in his account.


Rudge's webpage is here:
http://vms.cc.wmich.edu/~rudged/index.html

One of Rudge's articles is online:
(another version of this was published in something like the Journal of Biological Education

"Does being wrong make Kettlewell wrong for science teaching?"

from here:
http://www.ed.psu.edu/CI/journals/2001aets/01file1.asp

Rudge's current and upcoming articles are listed here:
http://homepages.wmich.edu/~rudged/vita.html#refereed_journal_articles



Date: 2002/12/12 21:44:25, Link
Author: niiicholas
Other Biston researcher webpages:

Bruce Grant
http://faculty.wm.edu/bsgran/

Michael Majerus
http://www.gen.cam.ac.uk/dept/majerus.html

Books by Majerus:
amazon.com link

Date: 2002/12/12 22:52:24, Link
Author: theyeti
Here is a good example of novel gene evolution due to duplication.

Nat Genet 2002 Apr;30(4):411-5

Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey.

Zhang J, Zhang YP, Rosenberg HF.

Quote

Abstract:

One of the two ribonuclease genes in a leaf-eating monkey has adapted to a role in the digestion of bacterial RNA. Following duplication of the ancestral ribonuclease gene, adaptation occurred through a series of changes in the amino acid sequence of the protein it encodes. This example is a good illustration of how specialization of protein function after gene duplication can be as source of novel protein functions.


Quote

A subfamily of Old World monkeys, colobines are unique primates that use leaves rather than fruits and insects as their primary food source; these leaves are then fermented by symbiotic bacteria in the foregut13. Similar to ruminants, colobines recover nutrients by breaking and digesting the bacteria with various enzymes, including pancreatic ribonuclease (RNASE1), which is secreted from the pancreas and transported into the small intestine to degrade RNA.
[...]
...we detected one RNASE1 gene in each of the 15 non-colobine primates examined, including 5 hominoids, 5 Old World monkeys, 4 New World monkeys and 1 prosimian. We determined the DNA sequences of these RNASE1 genes; the deduced protein sequences are shown in Fig. 1a. The phylogenetic tree of the RNASE1 sequences (Fig. 2a) is consistent with the known species relationships16 at all nodes, with greater than 55% bootstrap support, suggesting that the RNASE1 genes are orthologous. By contrast, two RNASE1 genes were found in the Asian colobine, douc langur (Pygathrix nemaeus). Phylogenetic analysis (Fig. 2a) suggests that these two genes were generated by recent duplication postdating the separation of colobines from other Old World monkeys (cercopithecines). The branch lengths of the gene tree indicate that the nucleotide sequence of one daughter gene (RNASE1) has not changed since duplication, whereas that of the other gene (RNASE1B) has accumulated many substitutions.
[...]
Taken together, these analyses suggest that the synonymous and noncoding sites at the RNASE1B locus are not subject to selective constraints and that the accelerated evolution of the coding sequence of RNASE1B is due to positive Darwinian selection.
[...]
Earlier studies showed that, for most mammalian genes, the rate of radical substitution is lower than that of conservative substitution, owing to stronger purifying selection on radical substitution22. In RNASE1B, however, the opposite is found. The number of radical substitutions per site since duplication (0.067) is significantly greater than that (0.012) of conservative substitutions per site (P<0.02; Fisher's exact test). There are nine amino-acid substitutions in the mature peptide of RNASE1B, and seven of them involve charge changes. Unexpectedly, all seven charge-altering substitutions increase the negative charge of the protein.
[...]
The charge-altering substitutions reduced the net charge of RNASE1B from 8.8 to 0.8 (at pH 7) and the isoelectric point from 9.1 to 7.3 (Fig. 1a). Because RNA is negatively charged, the net charge of RNase influences its interaction with the substrate and its catalytic performance23. We therefore hypothesized that the charge-altering substitutions may have changed the optimal pH of RNASE1B in catalyzing the digestion of RNA.
[...]
We determined that the optimal pH for human RNASE1 is 7.4, a value that is within the pH range (7.4–8.0) measured in the small intestine of humans24, 25. The same optimal pH was observed for RNASE1 of rhesus monkey and douc langur (Fig. 4a). Probably because of foregut fermentation and related changes in digestive physiology, the pH in the small intestine of colobine monkeys shifts to 6–7 (ref. 13). Notably, the optimal pH for douc langur RNASE1B was found to be 6.3 (Fig. 4a). At pH 6.3, RNASE1B is about six times as active as RNASE1 in digesting RNA, and the difference in their activities is statistically significant (P<0.001, t-test). These results suggest that the rapid amino acid substitutions in RNASE1B were driven by selection for enhanced RNase activity at the relatively low pH environment of the colobine small intestine.


Long story short:  Monkey shifts diet from fruits and insects to leaves.  This causes foregut fermentation which lowers pH in the digestive tract.  A ribonuclease gene duplicates, and one of the duplicates evolves through positive selection for optimal activity at the lower pH.    

Another paper concerning this (shorter for those who don't want to plow through the one above) is here:

Hughes AL.  Adaptive evolution after gene duplication., Trends Genet 2002 Sep;18(9):433-4.

theyeti

Date: 2002/12/12 23:28:37, Link
Author: theyeti
Ah, another example of ribonuclease duplication.

Proc Natl Acad Sci U S A 1998 Mar 31;95(7):3708-13

Positive Darwinian selection after gene duplication in primate ribonuclease genes.

Zhang J, Rosenberg HF, Nei M.

Full Text

Quote

Abstract:

Evolutionary mechanisms of origins of new gene function have been a subject of long-standing debate. Here we report a convincing case in which positive Darwinian selection operated at the molecular level during the evolution of novel function by gene duplication. The genes for eosinophil cationic protein (ECP) and eosinophil-derived neurotoxin (EDN) in primates belong to the ribonuclease gene family, and the ECP gene, whose product has an anti-pathogen function not displayed by EDN, was generated by duplication of the EDN gene about 31 million years ago. Using inferred nucleotide sequences of ancestral organisms, we showed that the rate of nonsynonymous nucleotide substitution was significantly higher than that of synonymous substitution for the ECP gene. This strongly suggests that positive Darwinian selection operated in the early stage of evolution of the ECP gene. It was also found that the number of arginine residues increased substantially in a short period of evolutionary time after gene duplication, and these amino acid changes probably produced the novel anti-pathogen function of ECP.




theyeti

Date: 2002/12/13 01:13:29, Link
Author: niiicholas
And in the "duplicated genes aren't necessarily selectively neutral, dammit" category:

(bold added)
Quote

Genome Biol 2002;3(2):RESEARCH0008
 
Selection in the evolution of gene duplications.

free online at pubmed central


Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV.

National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA. fkondras@ncbi.nlm.nih.gov

BACKGROUND: Gene duplications have a major role in the evolution of new biological functions. Theoretical studies often assume that a duplication per se is selectively neutral and that, following a duplication, one of the gene copies is freed from purifying (stabilizing) selection, which creates the potential for evolution of a new function. RESULTS: In search of systematic evidence of accelerated evolution after duplication, we used data from 26 bacterial, six archaeal, and seven eukaryotic genomes to compare the mode and strength of selection acting on recently duplicated genes (paralogs) and on similarly diverged, unduplicated orthologous genes in different species. We find that the ratio of nonsynonymous to synonymous substitutions (Kn/Ks) in most paralogous pairs is <<1 and that paralogs typically evolve at similar rates, without significant asymmetry, indicating that both paralogs produced by a duplication are subject to purifying selection. This selection is, however, substantially weaker than the purifying selection affecting unduplicated orthologs that have diverged to the same extent as the analyzed paralogs. Most of the recently duplicated genes appear to be involved in various forms of environmental response; in particular, many of them encode membrane and secreted proteins. CONCLUSIONS: The results of this analysis indicate that recently duplicated paralogs evolve faster than orthologs with the same level of divergence and similar functions, but apparently do not experience a phase of neutral evolution. We hypothesize that gene duplications that persist in an evolving lineage are beneficial from the time of their origin, due primarily to a protein dosage effect in response to variable environmental conditions; duplications are likely to give rise to new functions at a later phase of their evolution once a higher level of divergence is reached.


[...]

Discussion:

[...]
Thus, the observation that purifying selection appears to act on all recent duplicates and examination of the functions of recently duplicated genes do not support the notion that gene duplication results in true functional redundancy and duplications may achieve fixation despite being redundant [26]. The alternative hypothesis - that gene duplications are fixed in a population by positive selection in all organisms - is supported by a combination of evidence of adaptive duplications from many types of living organisms: prokaryotes [31,33,45,46,48,50,55,56], protists [35,58,59], plants [39,44], fungi [43,49], invertebrates [40,41,51,52,53], non-mammalian vertebrates [54], as well as mammalian somatic tissues [34,36,37,38]. Combining these observations with the suggestion that gene duplication may be a general mechanism of adaptation to various conditions of environmental stress [32,33,46,48,49,50,52,53,55,60], we suggest that, in both prokaryotes and eukaryotes, most paralogs that are fixed in a population have a direct effect on fitness from the moment of duplication, and aid in the adaptation to various environmental conditions, primarily through a protein dosage effect.

That the short-term benefit of a gene duplication is a direct effect on protein dosage also stems from a variety of experimental observations in a number of organisms, prokaryotic and eukaryotic. Gene duplication may be a temporary mechanism to increase protein or RNA dosage, as in the case of rRNA genes in amphibian oocytes and ciliate macronuclei, the chorion genes in some dipterans, actin genes in chicken as well as drug transporters in somatic tissues (see [34,37] for reviews). Protein dosage effects have also been demonstrated in a number of other studies of inheritable adaptive gene duplications [32,34,35,43,44,46,49,51,53,61]. Furthermore, there is evidence from the analysis of the yeast genome that duplicated genes tend to be from those sets of functions that are more highly expressed [62], supporting a general role for selection on protein dosage in duplicated genes.
[...]
[...]
The present observation that duplicated genes experience a substantial relaxation of selection compared to unduplicated genes is compatible with the traditional view that gene duplications make a major contribution to the evolution of new gene functions. Additionally, the repertoire of protein functions among recent duplicates suggests that many gene duplications contribute to adaptation of the organism to various forms of environmental stress. The results of the present analysis of recent duplications suggest a two-stage evolutionary model of gene duplication: in the first stage, immediately after duplication and during the early phase of their evolution, paralogs are retained and are subject to purifying selection because of the short-term advantage of protein dosage regulation; at a later stage in their evolution, gene duplications are likely to provide a long-term advantage by enabling the creation of new functions.


What would be interesting to know would be the relative roles of regulation mutations vs. gene duplications in effecting adaptation (via amount of proteins produced) to changing conditions as discussed above.  One would think that regulatory changes would be the more "elegant" or "efficient" way to adapt, but apparently evolution doesn't know or care, at least sometimes...

(it may be that regulatory changes have a "limit" that could only be exceeded by duplicating the gene...but now I'm at the limits of my knowledge...)

nic

(PS: The assumption that duplicating a gene doubles the level of a particular protein may not be a good one, particularly if the expression of the gene is regulated by some kind of feedback mechanism...just something to keep in mind)

Date: 2002/12/13 01:25:37, Link
Author: niiicholas
This thread is for links, refs, etc. on transitional fossils.

The big momma of 'net resources is:

Kathleen Hunt's Transitional Vertebrate Fossils MegaFAQ

...however, it was mostly written in 1995 or so, and an awful lot has been discovered since then.  But with Hunt's FAQ can as a starting point, I suggest we use this thread to "enhance" the material there with:

1) Online pictures we discover

2) Refs and pics of new discoveries (let's see, since 1995 there've been more transitionals discovered for whales, manatees, birds, ...and of course humans).

3) Online discussions of the topic

4) Review articles etc.

...all with the primary focus of rebutting the "there ain't no transitional fossils" claim.


Here is my favorite:

AMNH page on a feathered dromeosaur

Date: 2002/12/13 01:53:48, Link
Author: niiicholas
Post your favorite Internet resources for searching for accurate (peer-reviewed lit., high-quality science journalism, educational websites not directly evo/creo related, sequence or fossil data, etc.) scientific information on evolution.

Related hints and tips should also be added as appropriate, perhaps this would have potential as a FAQ at some point.

When posting links to journals, please make a note regarding access.

E.g.:

PubMed
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi

This is the National Library of Medicine's free search engine for "biomedical" literature, but in practice it includes all major general science journals, anything related to molecular biology, many more general biology journals (weaker on ecology etc.), and in general gobbs of evolution stuff on your topic of interest.

GUIDE:
For an author search, do "lastname firstinitials" without commas or periods.  Separate multiple authors with commas.

For example, Thornhill and Ussery wrote an article outlining the various ways that "irreducibly complexity" can evolve.  Search PubMed on "ussery d, thornhill" and you get:

A classification of possible routes of Darwinian evolution


HINT:
Searching on keywords or authors will never get you everything interesting on the first shot.  A key feature is the "Related Articles" link to the upper-right of each reference.

For example, here is an article on changes-of-function in evolutionary history:

Quote

Bioessays 1999 May;21(5):432-9
 
Generation of evolutionary novelty by functional shift.

Ganfornina MD, Sanchez D.

Biology Department, University of Utah, Salt Lake City 84112, USA. lazarillo@bioscience.utah.edu

That biological features may change their function during evolution has long been recognized. Particularly, the acquisition of new functions by molecules involved in developmental pathways is suspected to cause important morphologic novelties. However, the current terminology describing functional changes during evolution (co-option or recruitment) fails to recognize important biologic distinctions between diverse evolutionary routes involving functional shifts. The main goal of our work is to stress the importance of an apparently trivial distinction: Whether or not the element that adopts a new function (anything from a morphologic structure to a protein domain) is a single or a duplicated element. We propose that natural selection must act in a radically different way, depending on the historic succession of co-option and duplication events; that is, co-option may provide the selective pressure for a subsequent gene duplication or could be a stabilizing factor that helps maintain redundancy after gene duplication. We review the evidence available on functional changes, focusing whenever possible on developmental molecules, and we propose a conceptual framework for the study of functional shifts during evolution with a level of resolution appropriate to the power of our current methodologies.


But what else exists out there on this topic?  Trying different keywords is a possibility, e.g. "cooption", "co-option", "co-optation", "change in function", "functional shift", etc., but this is tedious.  Instead, once you've found one good article, click on "Related articles":

Articles related to Ganfornina and Sanchez 1999

...and you get a pile:

Quote

1:  Ganfornina MD, Sanchez D. Related Articles, Links  

Generation of evolutionary novelty by functional shift.
Bioessays. 1999 May;21(5):432-9. Review.
PMID: 10376014 [PubMed - indexed for MEDLINE]

2:  True JR, Carroll SB. Related Articles, Links  

Gene co-option in physiological and morphological evolution.
Annu Rev Cell Dev Biol. 2002;18:53-80.
PMID: 12142278 [PubMed - in process]

3:  Van de Peer Y, Taylor JS, Braasch I, Meyer A. Related Articles, Links  

The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes.
J Mol Evol. 2001 Oct-Nov;53(4-5):436-46.
PMID: 11675603 [PubMed - indexed for MEDLINE]

4:  Eizinger A, Jungblut B, Sommer RJ. Related Articles, Links  

Evolutionary change in the functional specificity of genes.
Trends Genet. 1999 May;15(5):197-202. Review.
PMID: 10322487 [PubMed - indexed for MEDLINE]

5:  Taylor JS, Van de Peer Y, Meyer A. Related Articles, Links  

Genome duplication, divergent resolution and speciation.
Trends Genet. 2001 Jun;17(6):299-301. Review.
PMID: 11377777 [PubMed - indexed for MEDLINE]

6:  Thornton JW, DeSalle R. Related Articles, Links  

Gene family evolution and homology: genomics meets phylogenetics.
Annu Rev Genomics Hum Genet. 2000;1:41-73. Review.
PMID: 11701624 [PubMed - indexed for MEDLINE]

7:  Otto SP, Yong P. Related Articles, Links  

The evolution of gene duplicates.
Adv Genet. 2002;46:451-83. Review.
PMID: 11931235 [PubMed - indexed for MEDLINE]

8:  Krakauer DC, Nowak MA. Related Articles, Links  

Evolutionary preservation of redundant duplicated genes.
Semin Cell Dev Biol. 1999 Oct;10(5):555-9. Review.
PMID: 10597640 [PubMed - indexed for MEDLINE]

9:  Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV. Related Articles, Links  

Selection in the evolution of gene duplications.
Genome Biol. 2002;3(2):RESEARCH0008.
PMID: 11864370 [PubMed - indexed for MEDLINE]

[etc.]


Also, be sure to try the "Sort by" window and selected "Pub Date" to bring up the most recent articles.  Doing this on the above article brought up:

Quote

1:  Woolhouse ME, Webster JP, Domingo E, Charlesworth B, Levin BR. Related Articles, Links  

Biological and biomedical implications of the co-evolution of pathogens and their hosts.
Nat Genet. 2002 Dec;32(4):569-77.
PMID: 12457190 [PubMed - in process]

2:  Manley GA. Related Articles, Links  

Evolution of structure and function of the hearing organ of lizards.
J Neurobiol. 2002 Nov 5;53(2):202-11. Review.
PMID: 12382276 [PubMed - in process]

3:  Prince VE, Pickett FB. Related Articles, Links  

Splitting pairs: the diverging fates of duplicated genes.
Nat Rev Genet. 2002 Nov;3(11):827-37.
PMID: 12415313 [PubMed - in process]

4:  Karev GP, Wolf YI, Rzhetsky AY, Berezovskaya FS, Koonin EV. Related Articles, Links  

Birth and death of protein domains: A simple model of evolution explains power law behavior.
BMC Evol Biol. 2002 Oct 14 [epub ahead of print]
PMID: 12379152 [PubMed - as supplied by publisher]

[etc.]

Date: 2002/12/13 02:14:51, Link
Author: niiicholas
PubMed Central:

http://www.pubmedcentral.nih.gov/

...is a central archive of scientific literature that is freely available to the public without subscription.  Sometimes the whole journal is free, sometimes the material is made freely available after 6 months.

Oftentimes you will have to complete a free registration to access free content.

I believe this is the current list of journals with free online content:
http://www.pubmedcentral.nih.gov/

Top journals from this list for evolution-related stuff:

Genome Biology

Proceedings of the National Academy of Sciences of the United States of America
(also at http://www.pnas.org )

Journal of Biology

A free article from the last one, advocating open access to scientific lit -- a logical position, considering how most of this research is taxpayer-funded:
Open access to the scientific journal literature
Peter Suber
J Biol. 2002; 1(1): 3
http://jbiol.com/content/1/1/3






A list of journals with full-text access for subscribers (the subscribers are usually university libraries, generally they are available to anyone within the University's edu domain) tied into the PubMed search engine is here:

http://www.ncbi.nlm.nih.gov/entrez/journals/loftext_noprov.html


nic

PS: Another important journal:

Evolution
Archives back to 1996:
http://lsvl.la.asu.edu/evolution/contents.html

From 2000 on:
http://evol.allenpress.com/

Current issue:
http://evol.allenpress.com/evolonline/?request=get-current-issue

Several critques of ID have been published in Evolution:  link to search results

Date: 2002/12/13 03:35:04, Link
Author: niiicholas
History of mousetraps:

http://www.uh.edu/engines/epi1163.htm

Quote

"Build a better mousetrap, and the world will beat a path to your door," Emerson supposedly wrote. But writer Jack Hope finds what Emerson really wrote: "If a man has good corn, or wood, or boards, or pigs, to sell ... you will find a broad hard-beaten road to his house." [1] Nothing there about mousetraps. In 1889, seven years after Emerson died, someone quoted him as having said, "If a man can write a better book, preach a better sermon, or make a better mousetrap than his neighbor ..." and so on.

Emerson meant that quality prevails in the marketplace, and that comes to light in an odd way with the history of mousetraps. We've made a vast investment of ingenuity in them. By now the Patent Office has issued over 4400 mousetrap patents. Yet only twenty or so of those patents have ever made any money.

Today some 400 people still apply for mousetrap patents each year. That leaves me to wonder whether mousetraps really promise a fast track to inventive success, or if they're simply born of some morbid fascination with killing mice.

Actually, the mousetrap problem was solved in 1899 by one John Mast of Lititz, Pennsylvania. Mast filed for a patent on his now-familiar snap-trap. A heavy spring-steel wire swings down and breaks the mouse's neck when he nibbles cheese on the trigger mechanism. That was only ten years after the mousetrap quotation became common currency. The inventive muse (or maybe the inventive mouse!;) keeps generating mousetrap patents, but none has yet beaten the snap-trap in the marketplace. No one has really built a better mousetrap.

Before (and after) Mast, inventors cooked up an unending series of gadgets for mashing, cutting, and maiming mice -- for drowning them -- for catching them alive. Early in the 20th century, people tried electrocution. The problem is, an electrocuted mouse continues to fry until someone smells the mess.

In the end, esthetics and mercy are twin factors that've strongly determined what the public will and will not use. In the 1980s, a superglue trap came out. It worked, but homeowners found themselves faced with a screaming mouse, still living, glued to a piece of sticky cardboard, dying of exhaustion. If mice have to be killed, most people can deal with a quickly broken neck. The more gruesome stuff won't sell in the long run.

And when snap-trap makers found most people throwing the trap out with the mouse, not even trying to disengage it, they followed the public's lead and began advertising snap-traps as "disposable."

So while the mousetrap has become an icon for inventive creativity, the public eventually stipulates what's acceptable and what is not -- in the grisly business of holding a competing species at bay.

I'm John Lienhard, at the University of Houston, where we're interested in the way inventive minds work.

(Theme music)

--------------------------------------------------------------------
1. Hope, J., A Better Mousetrap. American Heritage, October 1996, pp. 90-97.
Here's a mousetrap for you! See the following website: http://www.lightlink.com/bbm/wmouse.html.



Clipart

The Conventional Snap Trap

Date: 2002/12/13 03:41:18, Link
Author: niiicholas
The History of the Mousetrap
http://inventors.about.com/library/inventors/blmousetrap.htm

http://inventors.about.com/library/inventors/blmousetrap2.htm

Some patented mousetraps:










Date: 2002/12/13 10:07:02, Link
Author: Wesley R. Elsberry
Paul,

I'm not sure that John is disagreeing with Kitcher.  Kitcher is talking about postulates, things that are assumed to be true for some line of inquiry.  Rarefied design as an inference, though, is something that some people assert can be concluded from particular premises.

The problem with a postulate of the sort that Kitcher discusses, though, is that someone like Paul Nelson will come along and claim that what is being argued is theology and not science (as your 1997 NTSE talk set forth).

If "postulating an unobserved Creator" were as generally productive as "postulating unobserved particles" has been in physics, I don't think that we would be having this sort of discussion now.  Postulating unobserved particles has led to specific hypotheses and experiments aimed at producing empirical data which would bear on whether outcomes based on the existence of those heretofore unobserved particles are actually there.  So far in ID, though, there is no similar push to test the postulate: once the unobserved Creator is postulated, no evidence concerning whether that Creator exists is sought after or solicited.

But I wonder if this is going far afield from the topic of the first post.

Have readers of Dembski really been "thrown" by the "reliability issue"?  Is it the critics who have the "lust for certainty"?  I don't think so.

Let's revisit some history.  Back in 1998, Dembski published his book, "The Design Inference".  Before TDI came out, though, Dembski had a short piece published in "First Things" which discussed what TDI would be about.  Here's a snippet of that article:

Quote
Biologists worry about attributing something to design (here identified with creation) only to have it overturned later; this widespread and legitimate concern has prevented them from using intelligent design as a valid scientific explanation.

Though perhaps justified in the past, this worry is no longer tenable. There now exists a rigorous criterion—complexity-specification—for distinguishing intelligently caused objects from unintelligently caused ones.

(Source: http://www.firstthings.com/ftissues/ft9810/dembski.html)


This claim has not been explicitly retracted.  It is echoed in the pages of "No Free Lunch" (p.6, IIRC).  It sure looks like a claim concerning certainty to me.

In that initial post, Dembski writes:

Quote
I argue that we are justified asserting specified complexity (and therefore design) once we have eliminated all known material mechanisms. It means that some unknown mechanism might eventually pop up and overturn a given design inference.


This seems to me to be inconsistent with, if not contradictory to, the earlier claim.  Perhaps, though, you have a different perspective that can accommodate both the "untenable worry" claim and the later admission that Dembski's "design inferences" can be overturned with additional knowledge.

Until such time as we get a statement from Dembski that the "untenable worry" claim is retracted, though, I think the critics are completely correct to hammer on this point.  Else we have the apparently inconsistent stance that the critics responding to the "untenable worry" claim are mistaken because application of the EF/DI is fallible, coupled with the continued use of the "untenable worry" claim whose basis is that application of the EF/DI is infallible for distinguishing intelligently caused objects.

Quote
This is known as having your cake and eating it. Polite society frowns on such obvious bad taste.


Wesley

Date: 2002/12/13 11:13:00, Link
Author: theyeti
I normally avoid the ARN peanut gallery threads, but I came across this and just had to post it.

Someone claims, ARN also seems to be getting into censorship mode recently.

And then Jazzraptor replies:

Quote

I really resent this comment. You have political opponents of ID frequenting IDist discussion boards trying to shout down or spam any hint of discussion, and the ID boards are guilty of censorship? Critics typically outnumber IDist here 2 to 1 onthe threads. They often avoid engaging in discussion, but merely link to anti-ID sites! Why aren't you criticizing this bizarre phenomenon?

Here's an example. Some poor guy asks for data supporting ID. If someone doesn't have data supporting ID . . . they should have stayed off of the thread. Right? Is that what happened? No. Look at post 1:

quote:
------------------------------------------------------------------------
You may be out of luck here. There is no valid scientific data because ID does not do that kind of scientific research . . .
------------------------------------------------------------------------

Look at post 2:

quote:
------------------------------------------------------------------------
See www.talkdesign.org and www.talkreason.org for sites which contain a lot of material about the lack of substance to ID.
------------------------------------------------------------------------

Go down and look at XYC's posts on the thread for the very worst examples of this mindless, thoughtless form of anti-ID propaganda. I can't call it anything else. This thread marked a turning point for me, because I recognised that THIS indeed is a form of censorship.  NOT anything that I've done. Give me one example where I've engaged in censorship here at ARN. Pretty much anything goes idea-wise. Please do not confuse me disallowing a form of censorship with censorship itself.


So let's get this straight.  Expressing one's opinion about a controversial subject and providing links to further information is a form of censorship, but deleting people's posts simply because you don't like them isn't?!  And what is this "shut-down or spam any hint of discussion" nonsense?  Since when did the ID critics have a means to "shut down" anything?  Is he calling Ex-YECer's cross-posting of very lengthy posts spam?  (He quickly deletes or bitches about everything Ex-YECer posts, regardless of any potential infraction of the supposed rules.)  This is just too much.  Black is white.  Freedom is slavery.  Blech!

theyeti

Date: 2002/12/13 11:27:00, Link
Author: theyeti
Curr Opin Genet Dev 2002 Dec;12(6):711-8

Conflict begets complexity: the evolution of centromeres.

Malik HS, Henikoff S.

Quote

Abstract:

Centromeres mediate the faithful segregation of eukaryotic chromosomes. Yet they display a remarkable range in size and complexity across eukaryotes, from approximately 125 bp in budding yeast to megabases of repetitive satellites in human chromosomes. Mapping the fine-scale structure of complex centromeres has proven to be daunting, but recent studies have provided a first glimpse into this unexplored bastion of our genomes and the evolutionary pressures that shape it. Evolutionary studies of proteins that bind centromeric DNA suggest genetic conflict as the underlying basis of centromere complexity, drawing interesting parallels with the myriad selfish elements that employ centromeric activity for their own survival.


Quote
...
Despite these difficulties, recent studies have begun to provide `evolutionary snapshots' of the centromere. They suggest that different sequence variants jockey for evolutionary dominance, even as homogeneous arrays of satellite repeats are destroyed by the insertion of a variety of mobile elements. Parallel studies of centromere-binding proteins also suggest that competition may drive the sequence complexity at centromeres, and may be responsible for rapidly changing karyotypes throughout evolution.
...

Female meiotic success as a major evolutionary force

Another means to turn the tables on `centromere-drive' would be to alter the meiotic tetrad at female meiosis, in effect switching the preferred position in the tetrad to an unpreferred position. One case where centromeres exploit female meiosis is evident in the relative ability of Robertsonian fusions –– when acrocentrics (chromosomes in which the centromere is towards one end) fuse at their centromeres to form a metacentric (chromosomes in which the centromere is in the middle) –– to survive female meiosis relative to its two acrocentric ancestors. In humans and chicken, Robertsonian fusions do better than acrocentrics in female meiosis, whereas the reverse is true in mice [37 and 38]; there is no difference in male meiotic transmission. A survey of karyotype evolution in mammals reveals that genomes have a high proportion of all acrocentric (e.g. mouse) or all metacentric (e.g. human) karyotypes with a distinct paucity of `mixed' karyotypes. This suggests that the switch in female meiotic `preference' has occurred frequently in mammalian evolution and can quickly reshape karyotypes once it happens ( Fig. 4). No other selective force would be expected to make such a rapid impact on karyotype evolution [38].
...

Conclusions

In yeast that have symmetric meioses, centromere competition is not expected to occur at all; removal of this genetic conflict may have allowed the optimal co-evolution of centromeric histones and centromeres, along with the gradual simplification of the centromeric sequences themselves. Under this model, S. cerevisiae centromeres, which are believed to consist of one nucleosome each, represent the ultimate stage of centromere optimization, whereas other genomes, including our own, constantly struggle with the consequences of unfair advantages in female meiosis.

Update

In humans, the bias in favor of transmitting Robertsonian fusions in female meiosis has been documented [37 and 38], but Daniel et al. [48 and 49] also reiterate another dramatic effect of Robertsonians –– reduced male fertility. Among families with Robertsonian arrangements coming to prenatal diagnosis, there are 2.4 fold fewer male parent carriers compared to female parents. This is despite the fact that in their progeny there is an ~1:1 ratio of male:female transmission of Robertsonian rearrangements. This points to a significant decline in fertility in male carriers of Robertsonian fusions, compared to female carriers. This duality (i.e. increased chromosomal transmission in female meiosis offset by lowered male fertility) provides strong support for the centromere-drive model.



theyeti

Date: 2002/12/13 12:12:26, Link
Author: theyeti
Curr Issues Mol Biol 2002 Jul;4(3):65-76

Transposable elements and the evolution of eukaryotic complexity.

Bowen NJ, Jordan IK.

Quote
Eukaryotic transposable elements are ubiquitous and widespread mobile genetic entities. These elements often make up a substantial fraction of the host genomes in which they reside. For example, approximately 1/2 of the human genome was recently shown to consist of transposable element sequences. There is a growing body of evidence that demonstrates that transposable elements have been major players in genome evolution. A sample of this evidence is reviewed here with an emphasis on the role that transposable elements may have played in driving the evolution of eukaryotic complexity. A number of specific scenarios are presented that implicate transposable elements in the evolution of the complex molecular and cellular machinery that are characteristic of the eukaryotic domain of life.


Will want to get the full text and see some of these "specifc scenarios" for the evolution of "complex molecular and cellular machinery"...  

Let me know if you can get your hands on it Nic (or anyone).

theyeti

Date: 2002/12/13 17:32:40, Link
Author: Glenn Branch
On December 12, 2002, the Louisiana Board of Elementary and Secondary Education (BESE) voted 7–3 not to require new biology textbooks to include a disclaimer about evolution, overruling a measure approved by the Student and School Standards/Instruction Committee on December 10. The committee approved the measure, which would have required a version of the Alabama disclaimer (see NCSE Reports 1995; 15 [4]: 10–1) to be placed in 9th through 12th grade biology textbooks, during a session described as “sometimes contentious” by the Baton Rouge Advocate (2002 Dec 11). Speaking on behalf of the measure, board member Jim Stafford explained, “I don’t believe I evolved from some primate”; board president Paul Pastorek, however, said, “I am not prepared to go back to the Dark Ages.” John W Oller Jr, a young-earth creationist appearing on behalf of the Louisiana Family Forum, argued that a disclaimer was necessary to counter the inaccuracies of the biology textbooks. Among the opponents of the disclaimer at the December 12 meeting of the BESE was J Michael Malec of the American Civil Liberties Union of Louisiana, who reminded the board of the Tangipahoa, Louisiana, Parish Board of Education’s failed attempt to require a spoken evolution disclaimer (see RNCSE 2000; 20 [1–2]: 4–5): “This board should not travel down the road that Louisiana officials have traveled with serious consequences. It should learn from these errors of judgment and reject this disclaimer” (Advocate 2002 Dec 13).

Date: 2002/12/13 22:09:48, Link
Author: m1isaak
A premise of intelligent design is that we know nothing about the Designer.  Therefore we cannot predict qualities of design (such as optimization) based upon supposed qualities of the desiger (such as omniscience).  This is true; we cannot infer conclusions based on the unknown.  However, the IDists assert that the design of life is now established.  And we know a lot about life.  If we provisionally accept design, we can base inferences on life and begin to say things about the Designer.

IDists seem reluctant to take this step.  Yet it is a logical -- I would say inevitable -- extension of their research.  And it is perfectly in line with their stated goal (e.g., "to see purpose in nature", from the subtitle on ISCID Forums home page).  If IDists will not undertake this line of investigation, it is up to us to do so.

So, what are some aspects of life that could indicate qualities of the Designer?  Here are a few that come to mind:

- Pain and suffering.  The "problem of evil" has been around for millennia.  Intelligent Design theory requires we address it.

- Suboptimal processes.  Some designs appear jury-rigged or otherwise inefficient.

- Profligate variety.  There is much more variety in the world than is apparently necessary.

Since the question of suffering is the most interesting of these, my focus will be on it.

What does suffering tell us about the Designer?  To begin, we can say that it must either be deliberate or incidental.  If incidental, it may arise either because the Designer doesn't care or can't do anything about it.  The case where an aspect of life is incidental is perhaps less interesting, since it says basically that the aspect isn't designed after all.  That could explain suboptimal processes, but for the other aspects, it seems to contradict the premise that life is designed.  The suffering and the variety that we see in life are fundamental.  They are part of the complexity that IDists claim as evidence for design in the first place.  In fact, many of the design examples that IDists use, from bomardier beetles to flagella to the immune system, either contribute to the suffering or are defenses that would be meaningless without it.

There are still apologists who claim that suffering is not part of design.  A common claim is that suffering is the result (via the Fall of Adam) of having free will.  This claim, however, is vacuous rationalization.  Adam did not choose to redesign cobras to put poison into their fangs.  Free will does not make infants die of malaria.  No, suffering is an integral part of life, and is as much designed as life is.

So Design Theory implies that the Designer deliberately planned for people to suffer.  What sort of Designer does that imply?

One possibility is that the Designer is simply evil.  This hypothesis, however, is contradicted by the observation that there is a great deal of pleasure to be found in the world, too.  Thus Design Theory must reject the hypothesis of a purely evil God.  For the same reasons, however, Design Theory must reject the hypothesis of a purely good God.

Another possibility is that there is more than one designer, and that different designers are responsible for different lifeforms and/or different aspects of life.  Multiple Designers Theory was introduced by RBH on ISCID on 28 September 2002.  (http://www.iscid.org/ubb/ultimatebb.php?ubb=get_topic;f=6;t=000172)  It explains such things as predador/prey and host/parasite arms races, intermittent interventions, and different solutions to a common problem.  It also has a venerable tradition in religions.  The designers may be dualistic, as in Zoroastrianism, or polytheistic, as in Celtic and Scandinavian tradition.

A somewhat related hypothesis is that the Designer's character is inconstant.  This hypothesis is expressed in the article, "God Diagnosed With Bipolar Disorder" in The Onion (http://www.theonion.com/onion3716/god_diagnosed_bipolar.html).  This article is satire, but Design Theory forces us to take the idea seriously.

It might still be argued that suffering is an unavoidable consequence of a greater good.  To some extent, this is certainly the case.  Pain, for example, often gives warning that allows us to avoid serious injury.  Still, much suffering would seem to be avoidable. Smallpox and polio have caused a great deal of suffering in the past, and yet the planet has been virtually free of them for the last few decades.  Could the designer simply not have created them in the first place?  Other more complex banes of humanity, including salmonella, onchocerciasis, and malaria, appear just as unnecessary.

It is possible that design is as inscrutible as the designer.  As expressed by Pope:

Quote
All nature is but art, unknown to thee;
All chance, direction, which thou canst not see;
All discord, harmony not understood;
All partial evil, universal good;
And spite of pride, in erring reason’s spite,
One truth is clear, Whatever is, is right.
[Alexander Pope, Essay on Man, i, 289-294]


This philosophy, that suffering is good for reasons we can't understand, contradicts the premise that purpose can be found in nature.  It claims that not only is the designer unknown, but so is the design.  If we accept Design Theory, we must reject this position and assume that design has implications.

Pope's view of an inscrutible purpose to design is the only way I can see to allow anything close to a traditional designer into Design Theory.  However, in the process, it makes Design Theory useless.  It is worth noting that Pope's view is compatible with evolution, but Dembski's The Design Inference contradicts its first two lines.  Design theory is more compatible with multiple designers or an unconstant designer.

Date: 2002/12/14 21:30:27, Link
Author: SLP
Quote (katerina @ Dec. 11 2002,07:23)
I just recently clued into this facet of Monsieur Langan's character.  The word that keeps coming to mind is 'penis envy', but I don't know why or if that is valid.

But come on.  If you have never been in a science lab, what do you know about what is going on there?  And if you have never been involved with or been a research scientist, you don't really have a good idea of the financial tension, the long hours, the bizarro lab politics (on occasion), etc.

And if you have never been involved with or been a tenure-track professor, then you have no idea of what the isolation, the carrot-stick tension, the publish or perish pressure, the student loan repayment pressure, is like.

Chris gives professors the kind of prestige that the rest of the American culture does not.

So it's a little sicko.  He envies us.  But he is precisely not the sort of person we care to envy us.

Indeed.

Hello, Kat.

Sorry I did not respond to that email a while back - I hit the delete button instead of the respond button..

Anyway, being banned at ARN and all, I only occasionally stop by to read the sycophants pile on the critics (and get trounced), but this Langan thing is amazing.

I recall reading an old Guiness book of world records years ago, and the record for the highest measured IQ.

The guy worked as a janitor because he claimed that he did not want to be taken advantage of and that the CIA had been pestering him, or something odd like that.

Perhaps it is that folks with super-high IQs also get a dose of instability/paranoia/various other complexes to go along with it.
I think Kat's assessment makes a lot of sense - angry at not being 'recognized' as the super-genius he thinks he is has probably fostered a great deal of resentment and he is lashing out.
Problem is, I don't see what a "self-creating universe" has to do with evolution, but then, I am just a lowly scientist with no philosophy training.

If I may be so bold as to make a prediction - 10 years from now, Langan will have a solid following - primarily ID-types and various hangers-on, none with any real smarts themselves.

His CTMU will still be unpublished - at least via traditional means, and will, regardless, be little mnore than a punchline.

But then, again, I am just a scientist... :(

Date: 2002/12/14 22:54:30, Link
Author: Alan
Quote (SLP @ Dec. 14 2002,21:30)
If I may be so bold as to make a prediction - 10 years from now, Langan will have a solid following - primarily ID-types and various hangers-on, none with any real smarts themselves.

Yes.  Even though no one will be sure how Langan's theory supports ID, his say so, along with his high IQ, will be enough.  Being able to say the smartest guy in America is on our side is enough for the ID-types.

Date: 2002/12/15 07:44:24, Link
Author: Wesley R. Elsberry
From the ISCID thread.:

Mark,

Quote
Does Wesley's dissatisfaction just boil down to two things.


I get the feeling that rather than inquire whether this is the case, that this post is trying to assert this.

Quote
1) In the last decade, the ID God hypothesis hasn't produced any or enough as useful predictions as the micro-billiard ball hypothesis, supposedly over the same time span with adjustments for the number of people working on each.

Since both seem so equally simple, he ain't asking for much! Maybe another weeks extension will help.


This has the character of a strawman argument.  If Mark would re-read what I wrote, he would find no reference to "the last decade".  What I did discuss, and what Mark does not touch upon, is the privileged position of a postulated Creator in ID conjectures.  Once postulated, no attempt is made to determine whether the postulate is valid, and even broaching the topic is anathema to many ID advocates.  This contrasts strongly with how certain other "unobservable" postulates are treated in science.  Kitcher's insight is still quite useful.

Quote
2) Dembski was initially much to over-enthusiastic about his claims, unlike those poor, humble and tentative neo-Darwinists.

It seems that recently Dr. Dembski has become more tentative as well, I wonder if that will really be the case with the opposition?

Is that it!


IMO, humble or not, Dembski continues to be "much too over-enthusiastic about his claims".  Page 6 of "No Free Lunch" only dates back to January of 2002, after all.  I'm sure Bill does not need anyone to attempt to defend his arguments with another instance of the tu quoque fallacy, though.

Wesley



Date: 2002/12/16 01:51:08, Link
Author: Wesley R. Elsberry
Mark,

Quote
Wesley, you say this about the God idea behind ID,

quote:
--------------------------------------------------------------------------------
Once postulated, no attempt is made to determine whether the postulate is valid, and even broaching the topic is anathema to many ID advocates.
--------------------------------------------------------------------------------

Really! How do you know they haven't been thinking of ways to do this all along and they're only in alpha stage before they're ready to release their beta's on the road to release candidate for version one. Hopefully, they wouldn't charge too much extra for later service packs like Microsoft.

If that's the case then my first comment stands. I'm being charitable and don't feel that they're trying to be deceptive. However, you seem to think that they are. Now that's juicy, do you have evidence for that charge or is that just how you feel about the situation?


This is getting bizarre.  A false dilemma is provided here by Mark to go with the strawman of the first post.  I haven't said anything here about "deception", and I don't feel like being treated to a smorgasbord of fallacies.  Mark's mindreading skills seem to be, ahem, not very well developed.

Since I don't claim to be a mindreader, I'm not
particularly interested in the "bare possibility" that the situation in ID advocacy will change drastically next week.  I am interested in what has been observed thus far, and nothing Mark provides here would indicate that my reportage has been anything but dead-on accurate.  Many ID advocates have dismissed suggestions that the existence or nature of a postulated "designer" be explored rather than being treated as a "brute given".  If Mark insists, I'll be happy to start a thread on collecting instances to document this claim.  But I think that this should be stipulated.  It is not an extraordinary claim.

Quote

quote:
--------------------------------------------------------------------------------
IMO, humble or not, Dembski continues to be "much too over-enthusiastic about his claims". Page 6 of "No Free Lunch" only dates back to January of 2002, after all.
--------------------------------------------------------------------------------

It's almost 2003 after all, so nothing he's written since counts?  


Dembski provided both tentative and non-tentative claims concerning his EF/DI in NFL.  See page 6 for a non-tentative claim, and page 14 for a tentative-style claim.  Nothing he has written since has been a retraction of the non-tentative statements used in NFL.  At least, nothing that I've seen does that.  I'd appreciate a reference if the "untenable worry" claim has been explicitly retracted.

Wesley

Date: 2002/12/16 03:09:49, Link
Author: Wesley R. Elsberry
Frances,

Quote
Wesley raised some very good points. Lets stick to his arguments and try to refrain from distracting from them through the use of strawmen.


I was actually trying to steer discussion back around to Dembski's arguments given in the initial post.  Perhaps I should have left Paul's interchange with John alone, but I thought I could clarify things there pretty quickly and move on.  I may have been wrong about how quickly...

I appreciate the moderator letting the discussion continue in this thread at all, since it doesn't really seem to have a "brainstorming" style topic.  It is a pretty straightforward response to criticism, and in this case the critics have chosen to get somewhat involved.  (My involvement needs to be limited, as I'm getting acquainted with LaTeX for preparation of my dissertation and also have the usual daytime job.  Well, perhaps not that usual.)

Anyway, I think that what should be followed are Dembski's arguments.

Here's one:

Quote
(William A. Dembski:) Briefly, the claim that specified complexity is a reliable marker of design means that if an item genuinely instantiates specified complexity, then it was designed. As I argue and continue to maintain, no counterexamples to this claim are known.


I was there when Ken Miller presented the Krebs cycle as a counterexample to Dembski on June 21st of this year.  I think that Dembski should note that counterexamples have been proposed by Miller and also Rob Pennock.  Now, it is a given that these have not been demonstrated to Dembski's personal satisfaction, but I think Dembski's phrasing of his claim is somewhat misleading to the reader.

Further, I think the claim doesn't mean much, anyway.  Since 1996, Dembski has provided EF/DI calculations, in various degrees of completeness, for a total of four events.  


  • The Caputo case
  • The Contact primes sequence
  • Dawkins's METHINKS IT IS LIKE A WEASEL string
  • The E. coli flagellum


(If I've missed an application of the EF/DI that comes with actual numbers and complies with more than two or three of the seven steps outlined on pages 72-73 of NFL, please let me know so I can expand the list.)

That's not much of an empirical base upon which to build such sweeping claims as the "no counterexamples" claim above.

Back in 2001 at Haverford College, I made the point to Dembski that collecting "confirming" cases does nothing to test his EF/DI.  I suggested that he apply his EF/DI and perform calculations for a number of events that could be agreed have sufficient evidence of natural causation to provide real tests of his EF/DI.  These included the Krebs cycle, since shown by Miller to be a real counterexample (well, he convinced me).  I also suggested the mammalian middle ear impedance-matching system and "fairy rings" as good candidates for testing the EF/DI.

I think I brought up the point that the EF/DI should be applied to a broad range of biological phenomena at the June 21st get-together at the Fourth World Skeptics conference.  Create a workbook style presentation of a series of EF/DI calculations starting with small-scale events that everyone can agree should not trigger a "design inference" and work up to larger-scale events that biologists have evidence for saying that natural causes are sufficient.  Is the EF/DI a good guide to classifying biological phemomena?  Until we see a series of real examples of complete application of it, I think that the issue is still wide open.

Well, I'll come clean.  I expect that if such a workbook were attempted, that the EF/DI would find "design" at ludicrously small-scale events, ones that not even Bill Dembski would want to go on record as saying that they must be considered to be "due to design".  I think that Dembski's statement at the end of TDI that a "design" conclusion is not easily reached via the EF/DI is simply false.  A simple way to show me wrong is to actually produce such a compendium of example EF/DI calculations, where the EF/DI performs in a stable manner and produces expected (by ID advocates, natch) results.

The production of such a workbook would also do much to vitiate another criticism of mine, which is that the EF/DI framework is too unwieldy to be applied.  Dembski says of Gell-Mann's "effective complexity" that it "resists detailed application to real-world problems" (I think that's verbatim, but I don't have NFL in front of me.  Check around page 133.).  I think Dembski's EF/DI very much "resists detailed application to real-world problems", and the fact that Dembski has offered so few EF/DI calculations (even including the only partially complete E. coli flagellum example) supports my view.  Of the four examples, the Contact primes examples is plainly fictitious, neither the Caputo case nor the METHINKS string yield an improbability smaller than Dembski's "universal small probability", and the E. coli flagellum example suffers from a large number of defects.  Does it really take a year-and-a-half, on average, to apply the EF/DI to any sort of problem, no matter how trivial or how many steps are skipped?

I'd be interested in hearing if any third party has attempted to apply or applied the seven-step process outlined on pages 72-73 of NFL.  I no of no such examples yet.

Wesley

Date: 2002/12/16 11:25:41, Link
Author: katerina
I opened a board with the following url

http://pub46.ezboard.com/fouttakesfrm10

called "outtakes"  as a means to capture some of the arbitrary deletions by Jack Foster.

Notably, the entire thread about the 'walkout' is here.

A few of us scan the threads fairly routinely and start copying them over as soon as they seem to speed up.

Not entirely uncoincidental is the association of deleted threads with certain individuals associated with the discovery institute.

Date: 2002/12/17 05:46:31, Link
Author: Bebbo
Quote (katerina @ Dec. 16 2002,11:25)
I opened a board with the following url

http://pub46.ezboard.com/fouttakesfrm10

called "outtakes"  as a means to capture some of the arbitrary deletions by Jack Foster.

Notably, the entire thread about the 'walkout' is here.

A few of us scan the threads fairly routinely and start copying them over as soon as they seem to speed up.

Not entirely uncoincidental is the association of deleted threads with certain individuals associated with the discovery institute.

What members of the DI post at ARN? The only ones I know of are William Dembski and Phillip Johnson. Dembski rarely posts, and Johnson hasn't been seen for a while under his last known nom de net.

--
Dene

Date: 2002/12/17 10:53:57, Link
Author: PEPCIS
Quote (theyeti @ Nov. 26 2002,17:52)
One thing that persists among "leading" IDists in their writing is that figuring out the attributes or identity of the designer is a question for philosophy or religion.  But this is clearly wrong, because once we've make detecting design something which can be answered via science, we've also made detecting the designer part of science also.  For example, it would be foolish to say that we've concluded that Stonehenge was designed, but that the scientific method couldn't deduce who designed it or for what reason.  In fact, that's the whole point of sciences that study design, like archeaology or forensics, which the IDists often cite as evidence that their methodology is actually being used.  (This is the crucial difference which shows that their methodology is actually not being used.)  Exactly what the IDists' motivations are for this claim are a matter of speculation, but certainly they'd rather give specific religious interpretations preeminence, which the Wedge Strategy shows is the primary goal of the movement

theyeti posted: "One thing that persists among "leading" IDists in their writing is that figuring out the attributes or identity of the designer is a question for philosophy or religion.  But this is clearly wrong, because once we've make detecting design something which can be answered via science, we've also made detecting the designer part of science also.  For example, it would be foolish to say that we've concluded that Stonehenge was designed, but that the scientific method couldn't deduce who designed it or for what reason.  In fact, that's the whole point of sciences that study design, like archeaology or forensics, which the IDists often cite as evidence that their methodology is actually being used.  (This is the crucial difference which shows that their methodology is actually not being used.)  Exactly what the IDists' motivations are for this claim are a matter of speculation, but certainly they'd rather give specific religious interpretations preeminence, which the Wedge Strategy shows is the primary goal of the movement."

I'd like to say that it's refreshing to hear an evolutionist saying the opposite of what the majority on their side claim.  I personally perceive that the main reason you see ID'ers staying away from identifying the Designer is a reaction to evolutionists who insist that any inquiry which gives even a semblance of similarity to creation ideas needs to be quashed pronto.

Most of the reactions that I see on the internet by evolutionists involve them stating that religion has absolutely no place in any scientific investigation.  Naturally, if an ID'er should mention a Deity, he/she would immediately be branded as a scientific heretic for allowing religion in the investigation.

Date: 2002/12/17 15:28:17, Link
Author: niiicholas
Quote

I'd like to say that it's refreshing to hear an evolutionist saying the opposite of what the majority on their side claim.  I personally perceive that the main reason you see ID'ers staying away from identifying the Designer is a reaction to evolutionists who insist that any inquiry which gives even a semblance of similarity to creation ideas needs to be quashed pronto.

Most of the reactions that I see on the internet by evolutionists involve them stating that religion has absolutely no place in any scientific investigation.  Naturally, if an ID'er should mention a Deity, he/she would immediately be branded as a scientific heretic for allowing religion in the investigation.


The problem, of course, with supernatural explanations is that are usually unconstrained -- anything can be explained, so nothing is explained.  Such explanations -- and here I think that "superadvanced aliens" and "unspecified designer" are also in the same epistemic category -- deserve to be excluded.

However, if the designer hypothesis is constrained enough, so that certain things are expected and other things are not, then it is at least potentially testable and hence potentially scientific.  E.g. "stone age humans did that" is a perfectly testable hypothesis for Stonehenge, even if the reasons aren't completely known.

Date: 2002/12/17 18:45:01, Link
Author: rafe gutman
i'd like to use this thread to collect references to articles and research relevant to the evolution of the immune system.  i imagine that i'll be the only one contributing to this, but others are certainly welcome.  i included several references in my posts in an ISCID thread on the topic, and i'll probably copy my posts from there to here.

there are also some good references here.

Date: 2002/12/17 18:58:06, Link
Author: rafe gutman
from the ISCID thread:

Quote
martin poenie:  Again Inlay refers to ITAMs in a tunicate gene. This is a reference to a protein called A74 that has no similarity to any other known protein. So what are ITAMs? ITAMs are an arrangement of two tyrosines in a peptide with a certain spacing between them. Tyrosines are widely used in cell signaling. When phosphorylated, they can become ligands for proteins with SH2 domains. What makes ITAMs special is that there are proteins such as ZAP70 that contain dual SH2 domains and bind to the ITAM phosphorylated tyrosines as a unit. At present, no such protein has been identified in tunicates. The ITAM motif is based on four residues. It is possible that these are ordinary SH2 binding sites and that no dual SH2 domain-containing will be found. Until and unless one does find such a protein this is not a compelling argument. If proteins with these dual SH2 domains are found in tunicates, then it becomes a good argument.

rafe:  i'm not an expert on signal transduction, but it seems pretty clear that A74 is involved in immune-related signal transduction, and that tyrosine phosphorylation of the ITAM is part of it. as for the SH2-containing proteins, i should point out that homologues for syk and ZAP70 have been discovered in organisms as distant as hydra [1], and as similar (to tunicates) as sea urchin [2]. additionally, a CD45 homologue, which can augment signaling through ITAMs, was found in hagfish [3]. so while we don't have a tunicate syk-family homologue, many of the other pieces are already in place. it's not unreasonable to think that the downstream targets of A74 will be identified soon, i guess we can reserve judgement til then. do you think it will be homologous to syk/ZAP70?

references
[1] Steele RE, Stover NA, Sakaguchi M.
Appearance and disappearance of Syk family protein-tyrosine kinase genes during
metazoan evolution.
Gene. 1999 Oct 18;239(1):91-7.

[2] Sakuma M, Onodera H, Suyemitsu T, Yamasu K.
The protein tyrosine kinases of the sea urchin Anthocidaris crassispina.
Zoolog Sci. 1997 Dec;14(6):941-6.

[3]Nagata T, Suzuki T, Ohta Y, Flajnik MF, Kasahara M.
The leukocyte common antigen (CD45) of the Pacific hagfish, Eptatretus stoutii:
implications for the primordial function of CD45.
Immunogenetics. 2002 Jul;54(4):286-91.


i should also note, in reference to dr. poenie's argument, that the genome of a tunicate has been sequenced and dozens of zap-70/syk homologues have been found.  i'm not sure what the best way to search through it is, but i entered "syk" into the search engine for the tunicate genome and found a bunch of hits.  here's one

Date: 2002/12/17 20:27:28, Link
Author: niiicholas
I would just like to say that I think the name Ciona intestinalis sounds like a disease rather than a tunicate.

(or, maybe, the scientist who named it thought it resembled a bit of intestine)

Ciona genome homepage

Date: 2002/12/17 20:39:37, Link
Author: niiicholas
Some articles on virulence functions for:

(1) Type III secretion systems
Cornelis GR, and Frédérique Van Gijsegem. Assembly and function of Type III secretory systems. Annual Reviews Microbiology. 2000. 54:735-774.

In the "T3SS are not good for you" theme:

Quote

For a rather long period, it was assumed that gram-negative bacteria do not "secrete" proteins into their environment but only export proteins in their strategic periplasm. However, research in the last two decades has revealed that gram-negative bacteria do indeed transfer proteins across their sophisticated outer membrane, and they do this by a variety of systems that are now classified into four major types and several minor ones. Type I, exemplified by the hemolysin secretion system of Escherichia coli, is a rather simple exporter that is based on only three proteins, one of which belongs to the ABC transporters. Type II is a very complex apparatus that extends the general secretory pathway and transfers fully folded enzymes or toxins from the periplasm to the extracellular medium, across the outer membrane. Type IV, another complex system that transfers pertussis toxin among others, is related to the apparatus of Agrobacterium spp. that transfers DNA to plant cells. Finally, type III, the subject of this review, is a sophisticated apparatus that couples secretion with pathogenesis.

In bacteria that are pathogenic for animals, type III secretion systems allow extracellular bacteria adhering to the surface of a host cell to inject specialized proteins across the plasma membrane. This system probably also allows bacteria residing in vacuoles to inject proteins across the vacuolar membrane. The injected proteins subvert the functioning of the aggressed cell or destroy its communications, favoring the entry or survival of the invading bacteria. Type III is thus not a secretion apparatus in the strict sense of the term but rather a complex weapon for close combat. It contributes to a number of totally different animal diseases with a variety of symptoms and severities, from fatal septicemia to mild diarrhea and from fulgurant diarrhea to chronic infection of the lung. Type III secretion has been extensively studied in Yersinia spp. (reviewed in 25), in Salmonella spp. (reviewed in 47), in Shigella spp. (reviewed in 138), and in enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli (EHEC) (40, 50, 72). It has also been described in Pseudomonas aeruginosa (TL Yahr & DW Frank, Genbank PAU56077), Chlamydia trachomatis and Chlamydia pneumoniae (73A), Bordetella bronchiseptica (MH Yuk, ET Harvill, JF Miller, Genbank AFO49488), Bordetella pertussis (78A) and in Burkholderia pseudomallei (The Sanger Center, Cambridge, UK). It is surprising that Salmonella typhimurium and Yersinia spp. have not only one type III system but two (61, 104; S Carlson & DE Pierson, Genbank AFO055744; The Sanger Center, Cambridge, UK), presumably playing their role at different stages of the infection (Figure 1).


Type III systems in animal pathogens. Illustrated are the various bacterial pathogens endowed with type III secretion, injecting effectors into the cytosol of a eukaryotic target cell. See Table 3 for references.

(bold added)



(2) In the "Flagella aren't necessarily good for you either" category:

Giron JA, Torres AG, Freer E, Kaper JB. The flagella of enteropathogenic Escherichia coli mediate adherence to epithelial cells. Molecular Microbiology 2002 Apr;44(2):361-79

Date: 2002/12/17 21:06:24, Link
Author: niiicholas
In the "nonmotile appendages can have a dispersal-related function despite being nonmotile" category:

Quote

Knutton S, Shaw RK, Anantha RP, Donnenberg MS, Zorgani AA. The type IV bundle-forming pilus of enteropathogenic Escherichia coli undergoes dramatic alterations in structure associated with bacterial adherence, aggregation and dispersal.  Mol Microbiol 1999 Aug;33(3):499-509
 
BFP, a plasmid-encoded type IV bundle-forming pilus produced by enteropathogenic Escherichia coli (EPEC), has recently been shown to be associated with the aggregation of bacteria and dispersal of bacteria from bacterial microcolonies. In standard 3 h HEp-2 cell assays, EPEC adhere in localized microcolonies; after 6 h, bacterial microcolonies are no longer present, indicating that bacterial aggregation and dispersal occurs in vitro during EPEC adhesion to cultured epithelial cells. To examine the role of BFP in EPEC aggregation and dispersal, we examined HEp-2 cell adhesion of strain E2348/69 and defined E2348/69 mutants by immunofluorescence and immunoelectron microscopy. BFP was expressed initially as approximately 40 nm diameter pilus bundles that promoted bacteria-bacteria interaction and microcolony formation. BFP subsequently underwent a striking alteration in structural organization with the formation of much longer and thicker ( approximately 100 nm diameter) pilus bundles, which frequently aggregated laterally to form even thicker bundles often arranged in a loose three-dimensional network; EPEC dispersal from bacterial microcolonies was associated with this transformation of BFP from thin to thick bundles. Bacterial dispersal and transformation of BFP from thin to thick bundles did not occur with a bfpF mutant of strain E2348/69. It is concluded that BFP promotes both the formation and the dispersal of EPEC microcolonies, that the dispersal phase requires BfpF and that dispersal is associated with dramatic alterations in the structure of BFP bundles.

[...]

As dispersal of bacteria from microcolonies occurred between 3 h and 6 h, we examined cells at intermediate times in order to follow the dispersal process and any associated change in BFP morphology. At 4 h, by both immunofluorescence (Fig. 6A, arrow) and scanning electron microscopy (Fig. 7A, arrows), one could start to see the formation of thick BFP bundles within some bacterial microcolonies and, by scanning electron microscopy, bacteria appeared to have been lost from regions of the microcolony in which thick BFP bundles had formed (Fig. 7A). At 5 h, significant dispersal of bacteria from many microcolonies had occurred, although this varied from colony to colony.


Fig. 7. Scanning electron micrographs of HEp-2 cells infected with EPEC strain CVD206 for 4 h (A), 5 h (B) and 6 h © showing stages in bacterial dispersal. After 4 h, thick BFP bundles are forming within this bacterial microcolony, and bacteria look as though they may have been lost from these regions of the microcolony (A, arrows). After 5 h, dispersal of bacteria from some microcolonies is almost complete, and only a few small bacterial aggregates remain attached to thick BFP bundles (B, arrows); in contrast, there is no evidence of BFP transformation or bacterial dispersal in the microcolony seen on the right (B, asterisk). After 6 h, bacterial dispersal is virtually complete; one of the few remaining bacteria from this microcolony is anchored to the thick BFP bundles by thin bundles (C, arrows). Scale bars: A, 1 m; B, 2 m; C, 0.5 m.

[...]

BfpF and bacterial dispersal

BfpF has been shown to be required for the dispersal of EPEC from bacterial microcolonies (Bieber et al., 1998). We therefore examined a bfpF mutant of E2348/69 in order to determine whether the observed morphological transformation of BFP was affected by this component of the BFP operon. In 3 h assays, we confirmed previous observations that a mutation in bfpF resulted in increased localized adhesion and that bfpF mutants are hyperpiliated compared with the wild-type strain. Furthermore, the mutation did not affect the ability of this strain to produce A/E lesions. Other than the size of microcolonies, this phenotype showed no alteration after 6 h (Fig. 8); bacteria remained hyperpiliated (Fig. 8A), adherent bacteria produced A/E lesions (Fig. 8C and D), but there was no transformation of thin BFP bundles to thick bundles (Fig. 8A and B) and no dispersal of bacteria from microcolonies (Fig. 8A, B and D).


The original description of BFP defined a role in bacteria-bacteria interaction and microcolony formation (Girón et al., 1991); recently, it has been shown that BFP also promotes dispersal of bacteria from aggregates (Bieber et al., 1998). Bieber et al. (1998) ended their paper by suggesting that 'to dissociate from the aggregate, bacteria would need to shed or distangle their pilus filaments from each other, a process that may require BfpF-mediated, energy dependent pilus retraction or a conformational change in the pilus quaternary structure'. This study, which has now demonstrated that EPEC aggregation and dispersal occurs in vitro during infection of cultured epithelial cells, suggests that the latter may be the case and that BFP undergoes a dramatic BfpF-dependent change in quaternary structure, the consequences of which are (i) a change from a thin to a thicker BFP bundle structure; (ii) disruption of bacteria-bacteria interactions; and (iii) dispersal of EPEC from bacterial microcolonies. The advantage to the organism of such a mechanism is that dispersal of bacteria primed to produce A/E lesions would be expected to lead to infection of new epithelial sites within the small bowel and, therefore, to a more efficient colonization of the gut. It has been known for some time that EAF plasmids are important in EPEC pathogenicity; BFP, by promoting more efficient colonization, is one likely reason why typical EPEC, which possess EAF plasmids, are more virulent than atypical EPEC, which lack EAF plasmids (Levine et al., 1985), and also more virulent than EPEC BfpF mutants, which lack the ability to disperse from microcolonies (Bieber et al., 1998).

Although we suggest a causal relationship between BfpF function, transformation of BFP morphology and bacterial dispersal, the data do not, in fact, demonstrate such a relationship, and so we cannot rule out the possibility that the converse is true, namely that BfpF is involved in other events that promote dispersal of bacteria from microcolonies, which leads, in turn, to the formation of the thick BFP bundles. BFP are very hydrophobic pili and, as bacteria disperse from an aggregate, it could be that the thin BFP filaments become more accessible to each other and are able to associate to form the thick BFP bundles.

In addition to playing a role in bacterial dispersal, an adhesive role for BFP has also been suggested (Girón et al., 1991). While the aim of this study was to examine the role of BFP in bacterial aggregation and dispersal, some of the observations have relevance to the possible role of BFP in cell adhesion. For example, the data suggest that BFP may be involved in initial EPEC adhesion, but that intimin-mediated intimate attachment is required for subsequent adhesive events. Also, the presence of cell-associated BFP after dispersal of all CVD206 bacteria after 6 h demonstrates that this form of BFP can adhere to the surface of HEp-2 cells. However, the role of BFP in EPEC adhesion to cultured and intestinal epithelial cells is the subject of a separate study to be published elsewhere (S. Knutton et al., manuscript in preparation).

[well, "nonmotility" is debatable, but this doesn't appear to be directional movement, i.e. swimming or crawling]

This study confirmed a role for BfpF in microcolony dispersal (Bieber et al., 1998) and showed that this protein, while not required for thin BFP bundle assembly, is involved either directly or indirectly in transformation from thin to thick BFP bundles. Based on the similarity between BfpF and PilT, the putative nucleotide-binding protein of P. aeruginosa, it has been proposed that BFP may play an analogous role to that proposed for PilT in type IV pilus function, namely as an energy source for the retraction of BFP (Anantha et al., 1998). The proposed function of PilT is based on electron microscopic studies of the distribution of antibody and bacteriophage binding to pili from wild-type and mutant P. aeruginosa strains (Bradley, 1974). The mutant used for these studies was subsequently found to have a mutation in pilT, which is also required for twitching motility (Whitchurch et al., 1991). As proteins in the PilT family are proposed to reside in the cytoplasm, our finding that BfpF appears to have a profound effect on the quaternary structure of BFP outside of the bacteria is surprising. However, as BFP has a marked propensity to intertwine in rope-like bundles, it is possible that retraction of individual pili within a bundle mediated by BfpF leads to thickening of the bundle in much the same way as pulling on an individual fibre leads to thickening of a twine. Thus, our study provides additional evidence that type IV pili such as BFP are not fixed structures, but are capable of dynamic alterations that influence bacterial adherence and pathogenesis.

Date: 2002/12/17 22:17:31, Link
Author: rafe gutman
although it doesn't reference anything, i came across a post of mine where i present a model for the origin of the adaptive immune system.  since it's original material (the wording, that is, the model itself has been around for awhile), i thought i'd post it here as well:

Quote
here's a run down of the general details of this model

1. the RAG genes and RSSs were originally a transposon, and the RAG proteins had transposase activity.
2. a gene existed in the ancestor to the jawed vertebrates that encoded a receptor with at least one immunoglobulin domain
3. this gene was only expressed in a somatic lineage, like hemocytes
4. the receptor could activate a pathway somehow involved in immune-related function
5. the RAG transposon integrated into the receptor near the binding site-coding region.
6. once inserted, the transposase
would be under the receptor's transcriptional control.
7. the RAG's ability to reassemble the receptor gene once activated was sloppy, and made slight sequence changes upon reassembly.
8. those changes were beneficial to the host

and the evidence supporting it:

1. there seems to be ample evidence suggesting that the RAG genes were once transposases, do you dispute this? the fact that they have transposase activity (in vitro) basically says it all.

2. the immunoglobulin domain is well-represented in nearly all organisms (even prokaryotes, i think). because its structure is so stable, a large portion of cell-surface molecules possess it, even some related to immunity (outside of the jawed vertebrates). however, no direct homologue to the antibody proteins have been found. so here is a prediction of the model: a non-rearranging receptor with an immunoglobulin domain existed in the ancestor to the jawed vertebrates. of course, this ancestral gene may no longer exist, but if it is ever discovered, that would fill in a major hole.

3. a lot of genes have tissue specific expression. as for the extant antibody genes, they are heavily regulated by enhancers (because of the need to prevent premature recombination, or recombination on both alleles). there's no reason to think that the enhancer wasn't there in the ancestral receptor (such as, if it was located between the V and J segments).

4. see 2.

5. this is the only step that appeals to chance. as yersinia said, there could have been many integrations by transposons (our genome is littered with remnants of retrotransposons). all it takes is one to be beneficial, and it will become fixed into the population.

6. a common molecular technique is transgenics, where whole genes are inserted into the chromosome randomly. one of the main problems with this approach is the lack of consistency in transgene expression. this is because the transgene becomes subject to the local transcription control. unless the transgene has a really powerful promoter, it's uncertain whether or not it will be expressed correctly.

7. the current mechanism of RAG-mediated recombination is sloppy. one of the reason is through the generation of hairpin loops at the two exposed ends. this is intrinsic to the activity of the RAG and is common to transposases (in fact, this is one of the observations that led scientists into thinking the RAGs were originally transposons).

8. here the evidence may never be to your satisfaction, but it's very reasonable to suppose that a high rate of mutation would benefit immune receptors. why do you think new flu vaccines come out every season? because the influenza's receptors can mutate very rapidly to avoid host recognition. furthermore, they don't need to mutate drastically and change the total structure of their receptors, only just enough to hamper the host's receptor's binding ability. if during tthe lifetime of the first RAG-integrated organism, one of the thousands to millions of hemocytes alive at the time form a receptor beneficial to the host, this will increase the host's chances for survival and the nature will have something to select upon.

maybe this requires more evidence to convince you, but is it really that unreasonable?

Date: 2002/12/17 22:24:04, Link
Author: rafe gutman
here's a link to a recent article on the discovery of lymphocytes in lamprey:

http://sciencenow.sciencemag.org/cgi/content/full/2002/1003/3

another post i found on ISCID:

Quote
a couple of interesting papers on the immune system have popped up recently:

1.  Mayer WE, Uinuk-Ool T, Tichy H, Gartland LA, Klein J, Cooper MD.
Isolation and characterization of lymphocyte-like cells from a lamprey.
Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14350-5.

this paper presents evidence for the existence of lymphocytes (cells intimately involved in the adaptive immune response) in lampreys, which don't have an adaptive immune system.  previously, one could have argued that rearranging antigen receptors and lymphocytes were irreducible.  now it doesn't look like that is the case.

2.  Uinuk-Ool T, Mayer WE, Sato A, Dongak R, Cooper MD, Klein J.
Lamprey lymphocyte-like cells express homologs of genes involved in
immunologically relevant activities of mammalian lymphocytes.

Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14356-61.

this article, the complement to the previous article, shows that the lamprey lymphocytes express genes similar to ones expressed in mammalian lymphocytes.  these genes are also involved in the adaptive immune response in mammals, so it's strange that they are present in lamprey.  incidently, both these articles are freely accessible online.

3.  Dodds AW.
Which came first, the lectin/classical pathway or the alternative pathway of
complement?
Immunobiology. 2002 Sep;205(4-5):340-54.

this article provides a model for the evolution of the complement system.  if paul wants to call the author's model "storytelling", he's free to do so, but now it's not just some random internet poster's idea.

i won't quote his model (it spans 2 pages), but he does say this about the model:

"the scheme outlined in figures 5 and 6 involves a stepwise increase in effectiveness of the system, each step giving benefit to the species involved."

since the time this thread began, probably a dozen articles have been published that support the notion that the immune system evolved.  has ID advanced in any way since then?




Date: 2002/12/17 22:32:20, Link
Author: rafe gutman
here's an extremely important article from nature immunology:

Nat Immunol 2002 Dec;3(12):1200-7
 
Identification of diversified genes that contain immunoglobulin-like variable regions in a protochordate.

Cannon JP, Haire RN, Litman GW.

[1] Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Avenue, Tampa, FL 33612, USA. [2] All Children's Hospital, 801 Sixth Street South, St. Petersburg, FL 33701, USA.

The evolutionary origin of adaptive immune receptors is not understood below the phylogenetic level of the jawed vertebrates. We describe here a strategy for the selective cloning of cDNAs encoding secreted or transmembrane proteins that uses a bacterial plasmid (Amptrap) with a defective beta-lactamase gene. This method requires knowledge of only a single target motif that corresponds to as few as three amino acids; it was validated with major histocompatibility complex genes from a cartilaginous fish. Using this approach, we identified families of genes encoding secreted proteins with two diversified immunoglobulin-like variable (V) domains and a chitin-binding domain in amphioxus, a protochordate. Thus, multigenic families encoding diversified V regions exist in a species lacking an adaptive immune response.

pubmed link

link to article

incidently, i did a blast search of one of these genes on the recently-sequenced ciona intestinalis (tunicate) genome, and got a hit.

Date: 2002/12/17 22:38:08, Link
Author: rafe gutman
last one for now:

pubmed link

Immunobiology 2002 Sep;205(4-5):467-75

The biological functions of MBL-associated serine proteases (MASPs).

Hajela K, Kojima M, Ambrus G, Wong KH, Moffatt BE, Ferluga J, Hajela S, Gal P, Sim RB.

Department of Biochemistry, University of Oxford, UK.

The Mannose-binding lectin-associated serine proteases (MASPs) have been the subject of intensive research particularly over the past 10 years. First one, then two, and currently 3 MASPs have been characterized. Initially it was thought likely that the MBL + MASPs system would resemble very closely the C1 complex of the complement classical pathway, and that MASP1 and MASP2 would have similar activities to their classical pathway homologues C1r and C1s. MASP2 does certainly have similar activities to C1s, but MASP1 does not have the activities of either C1r or C1s. MASP1 has been thought to act on the complement system by cleaving C3 directly, but work with recombinant and purified native MASP1 shows that direct C3 cleavage by this protease is very slow, and may not be biologically significant. MASP1 and MASP2 appear not to have such a narrow specificity as C1r and C1s, and may have significant substrates other than complement proteins. As an example, MASP1 does cleave fibrinogen, releasing fibrinopeptide B (a chemotactic factor) and also cleaves and activates plasma transglutaminase (Factor XIII). These reactions are also relevant to defence against microorganisms, and may represent a biologically significant action of MASP1.


this is a review article that mentions an interesting finding, that a serine protease exists that has substrates in two functionally different pathways, the blood-clotting system and the complement system.  i looked up the reference, but the article it mentions hasn't been published yet.  i guess we'll have to wait til then to see the details.

Date: 2002/12/18 00:26:24, Link
Author: Wesley R. Elsberry
Paul,

Quote
3. Wesley, I recall that I brought up the Kreb's cycle at the CSICOP discussion, not Ken Miller. If you have the video or audio tape, could you check for me please? Thanks.


My VCR has taken up the habit of eating tapes, so I won't be putting in my copy until I get a new VCR.

I couldn't say from recall that you didn't mention the Krebs cycle first, since you preceded Ken, but I do recall that Ken specifically discussed the Krebs cycle as a counterexample to Dembski's EF/DI.  That's because Ken used my "origination probability calculator" to "do the calculation", putting his finding on a par with the discussion by Dembski of the E. coli flagellum.  The same equations were used in both cases.  (Ken's presentation even included a slide with a screenshot of my web page.  More of Dembski's equations are implemented on my Finite Improbability Calculator.)

I recall that you disputed Ken's use of the Krebs cycle on the grounds that the evolutionary scenario Ken cited was not complete enough to satisfy you.  That was during the panel discussion.  If I find my audio tapes, I'll give them a listen.

Wesley

Date: 2002/12/18 12:20:34, Link
Author: niiicholas
Here is a masterful bit of propaganda from the DI's John West (he is a political scientist, literally). Particularly annoying is the "truth is established by endless repetition" tactic used by demagogues in the media, and by IDists regarding Icons of Evolution.

http://www.nationalreview.com/comment/comment-west121702.asp

This guy oughta read the Icons FAQs:
http://www.talkorigins.org/faqs/wells/
http://www.ncseweb.org/icons/
http://www.nmsr.org/iconanti.htm

If there was ever a bit of propaganda that deserved a refutation, it is below, so if you can't resist spending some time debunking this, CC your replies here.

Quote

December 17, 2002, 9:20 a.m.
Darwin in the Classroom
Ohio allows alternatives.

By John G. West Jr.

After months of debate, the Ohio State Board of Education unanimously adopted science standards on Dec. 10 that require Ohio students to know "how scientists continue to investigate and critically analyze aspects of evolutionary theory."

Ohio thus becomes the first state to mandate that students learn not only scientific evidence that supports Darwin's theory but also scientific evidence critical of it. While the new science standards do not compel Ohio's school districts to offer a specific curriculum, Ohio students will need to know about scientific criticisms of Darwin's theory in order to pass graduation tests required for a high-school diploma.

Ohio is not the only place where public officials are broadening the curriculum to include scientific criticisms of evolution. In September the Cobb County School District in Georgia, one of the largest suburban school districts in the nation, adopted a policy encouraging teachers to discuss "disputed views" about evolution as part of a "balanced education." And last year, Congress in the conference report to the landmark No Child Left Behind Act urged schools to inform students of "the full range of scientific views" when covering controversial scientific topics "such as biological evolution."

After years of being marginalized, critics of Darwin's theory seem to be gaining ground. What is going on? And why now?

Two developments have been paramount.

First, there has been growing public recognition of the shoddy way evolution is actually taught in many schools. Thanks to the book Icons of Evolution by biologist Jonathan Wells, more people know about how biology textbooks perpetuate discredited "icons" of evolution that many biologists no longer accept as good science. Embryo drawings purporting to prove Darwin's theory of common ancestry continue to appear in many textbooks despite the embarrassing fact that they have been exposed as fakes originally concocted by 19th-century German Darwinist Ernst Haeckel. Textbooks likewise continue to showcase microevolution in peppered moths as evidence for Darwin's mechanism of natural selection even though the underlying research is now questioned by many biologists.

When not offering students bogus science, the textbooks ignore real and often heated scientific disagreements over evolutionary theory. Few students ever learn, for example, about vigorous debates generated by the Cambrian Explosion, a huge burst in the complexity of living things more than 500 million years ago that seems to outstrip the known capacity of natural selection to produce biological change.

Teachers who do inform students about some of Darwinism's unresolved problems often face persecution by what can only be termed the Darwinian thought police. In Washington state, a well-respected biology teacher who wanted to tell students about scientific debates over things like Haeckel's embryos and the peppered moth was ultimately driven from his school district by local Darwinists.

Science is supposed to prize open minds and critical thinking. Yet the theory of evolution is typically presented today completely uncritically, as a dogma to be accepted rather than as a theory to be explored and questioned. Is it any wonder that policymakers and the public are growing skeptical of such a one-sided approach?

A second development fueling recent gains by Darwin's critics has been the demise of an old stereotype.

For years, Darwinists successfully shut down any public discussion of Darwinian evolution by stigmatizing every critic of Darwin as a Biblical literalist intent on injecting Genesis into biology class. While Darwinists still try that tactic, their charge is becoming increasingly implausible, even ludicrous. Far from being uneducated Bible-thumpers, the new critics of evolution hold doctorates in biology, biochemistry, mathematics and related disciplines from secular universities, and many of them teach or do research at American universities. They are scientists like Lehigh University biochemist Michael Behe, University of Idaho microbiologist Scott Minnich, and Baylor University philosopher and mathematician William Dembski.

The ranks of these academic critics of Darwin are growing. During the past year, more than 150 scientists — including faculty and researchers at such institutions as Yale, Princeton, MIT, and the Smithsonian — adopted a statement expressing skepticism of neo-Darwinism's central claim that "random mutation and natural selection account for the complexity of life."

Deprived of the stock response that all critics of Darwin must be stupid fundamentalists, some of Darwin's public defenders have taken a page from the playbook of power politics: If you can't dismiss your opponents, demonize them.

In Ohio critics of Darwinism were compared to the Taliban, and Ohioans were warned that the effort to allow students to learn about scientific criticisms of Darwin was part of a vast conspiracy to impose nothing less than a theocracy. Happily for good science education (and free inquiry), the Ohio Board of Education saw through such overheated rhetoric. So did 52 Ohio scientists (many on the faculties of Ohio universities) who publicly urged the Ohio Board to require students to learn about scientific criticisms of Darwin's theory.

The renewed debate over how to teach evolution is not likely to stop with Ohio.

Under the No Child Left Behind Act, every state must enact statewide science assessments within five years. As other states prepare to fulfill this new federal mandate, one of the looming questions will be what students should learn about evolution. Will they learn only the scientific evidence that favors the theory, or will they be exposed to its scientific criticisms as well?

Ohio has set a standard other states would do well to follow.

— John West is a senior fellow of the Seattle-based Discovery Institute and chair of the department of political science at Seattle Pacific University.

Date: 2002/12/18 13:00:29, Link
Author: niiicholas
Here it is, I hadn't seen it before

The Wedge: A Christian Plan to Overthrow Modern Science?
Doubting Thomas, Feature Story, No. 6, April/May 1999. By Keith Lankford

http://www.stephenjaygould.org/ctrl/archive/thomas_wedge.html

Some minor inaccuracies and now a little out of date, but it features:

- a cogent comparison of ID to the 1950's Velikovskian movement

- a fair amount of material about Ed Larson, author of Summer of the Gods, and his conflict with the DI over his book being cited as part of the "Wedge" strategy.

Date: 2002/12/18 15:40:56, Link
Author: niiicholas
Atrazine degradation pathways appear to have arisen recently:

This lab studies 'em:
http://www.cbs.umn.edu/bpti/mice/faculty/wacket1.htm


...Some of their papers are free online:

DeSouza, M. L., J. Seffernick, B. Martinez, and M. J. Sadowsky, L. P. Wackett (1998) Atrazine catabolism genes atzABC are widespread and highly conserved J. Bacteriol. 180(1):1951-1954.
http://jb.asm.org/cgi/content/full/180/7/1951

De Souza, M. L., L. P. Wackett, and M. J. Sadowsky (1998) The atzABC genes encoding atrazine catabolism are located on a self-transmissible plasmid in Pseudomonas sp. strain ADP. Appl. Envir. Microbiol. 64(6): 2323-2326.
http://aem.asm.org/cgi/content/full/64/6/2323


M.L. deSouza, D. Newcombe, S. Alvey, Crowley, D.E., A. Hay, M.J. Sadowsky, and L.P. Wackett (1998) Molecular basis of a bacterial consortium: Interspecies catabolism of atrazine. Appl. Environ. Microbiol. 64(1):178-184.
http://aem.asm.org/cgi/content/full/64/1/178

In the latter paper, it looks as if three different enzymes found in different bacteria were first combine in multispecies consortia that could metabolize atrazine, and that eventually the 3 genes were combined on a plasmid which then spread around the world in an evolutionary eyeblink.  If this is basically what happened it is yet another method of producing IC (as well as new information).

Quote

Atrazine is the most widely used s-triazine herbicide; it is utilized globally to control broadleaf weeds. Atrazine has been deployed only over the last 40 years and was previously considered to be nonmetabolizable by the majority of soil bacteria. During the first 35 years of its use, bacterial atrazine catabolism was proposed to occur largely via N-dealkylation reactions, resulting in the accumulation of aminotriazine compounds in both soils and laboratory media (3-5, 11, 20, 21). More recently, pure cultures of bacteria that catabolize atrazine to CO2 have been described (8, 26, 27, 30, 37).

The nearly simultaneous reports of atrazine-mineralizing pure cultures by five research groups (8, 26, 27, 30, 37) after years of unsuccessful efforts suggested a recent evolutionary origin and distribution of atrazine degradation genes. Consistent with this, all of the recently identified atrazine-degrading bacteria, isolated from around the world, have been shown to contain similar genes that encode enzymes which catabolize atrazine to cyanuric acid (16) (see Fig. 1). Cyanuric acid can be used by many soil bacteria as the sole nitrogen source (10-12, 19, 23). The enzymes for atrazine catabolism to cyanuric acid are encoded by the atzABC genes, which are found on a self-transmissible plasmid in Pseudomonas sp. strain ADP, the best characterized atrazine-metabolizing bacterium studied at the molecular level (7, 16, 17, 26, 32). Moreover, multiple insertion sequence-like elements have been identified in DNA flanking the atz genes. These studies are beginning to yield insights into atrazine gene evolution and dispersion.

These data also provide the tools for investigating bacterial atrazine genes in situ or in microbial consortia cultured in the laboratory on atrazine. For example, an atrazine-catabolizing consortium was reported in 1994 (3), but that predated the identification of catabolic genes and pure cultures which metabolize atrazine to carbon dioxide. More recently, a stable aerobic consortium was obtained from an agricultural soil and characterized with respect to its ability to catabolize atrazine (1, 2).

The present study was conducted to determine whether the genes and metabolism of the consortium (1, 2) resembled those found in recently described atrazine-metabolizing pure cultures. Our results show that different consortium members separately contained the atzA, -B, and -C genes. Coupled with biochemical studies, this revealed the interspecies metabolic interactions relevant to atrazine catabolism by the consortium. Our findings begin to provide a framework for understanding how catabolic pathways may evolve and the different conditions under which pure-culture or consortial metabolism may be selected for during the global recycling of organic matter.

[...]

The present study extends previous work by demonstrating the individual metabolic and genetic contributions of consortium members that use a proposed recently evolved catabolic pathway (16). Atrazine and related s-triazine herbicides have been in commercial use for approximately 40 years. The wide use of s-triazine herbicides has led to their detection as contaminants in groundwater (6, 28, 29) and to point source soil contamination problems where these herbicides have been spilled. Previously, many isolates and mixed cultures that partially degrade atrazine have been found (3, 10); more recently, several bacterial pure cultures which can completely mineralize atrazine and other s-triazines have been isolated (8, 26, 27, 30, 37). In 1995, Mandelbaum et al. (26) isolated a single atrazine-mineralizing bacterium from a mixture of bacteria originally reported to be a consortium (24, 25), which suggested that the isolate arose from gene transfer which occurred in the mixed culture. The possibility of this has been heightened by our observation that the atzABC genes are located on a 96-kb plasmid, with at least two genes having flanking regions with high homologies to known insertion sequence elements (16). Thus, the present study may offer a window to the evolution of a catabolic pathway by beginning to reveal how genes move from a consortium to individual strains and how mixed cultures containing metabolically cooperating genes may be stably maintained.

Date: 2002/12/18 17:03:28, Link
Author: theyeti
Quote
Ohio thus becomes the first state to mandate that students learn not only scientific evidence that supports Darwin's theory but also scientific evidence critical of it. While the new science standards do not compel Ohio's school districts to offer a specific curriculum, Ohio students will need to know about scientific criticisms of Darwin's theory in order to pass graduation tests required for a high-school diploma.


I believe the technical term for this is "lie".  The vaugely worded sentence does not compel students to learn anything, especially no unspecified "evidence against evolution".  For them to try to spin this as requiring or even encouraging the teaching of ID is exceptionally mendacious.

The major tactic that West uses here is to speak in generalities while avoiding specifics whenever possible.  So we have statements like, "the underlying research is now questioned by many biologists."  How many is many?  Five?  There's precious little to debunk science-wise because West avoids making any positive statements that can be debunked.  This mysterious "evidence against evolution" is never brought out at all, except for a reference to the Cambrian Explosion, but even here he offers no details, and instead simply claims that it was "seemingly" too fast while omitting the actual time frame (several million years).  Peppered Moths and Haeckel's embryos cannot under any stretch of the imagination be construed as "evidence against evolution".  At most they should simply be omitted as evidence for evolution.  So we're not left with any indication as to what this "evidence against evolution" is at all.  (When this question was put to ARNies, there were no answers that could withstand simple criticism IIRC; given that IDists agree on precious little, including common descent, one is left wondering just what this vauge reference means.  Added in edit: here is the thread.)  What we are left with is spin, spin, spin.  For example this:

Quote
After years of being marginalized, critics of Darwin's theory seem to be gaining ground. What is going on? And why now?


This guy must not get out much.  The efforts in Ohio and Georgia are simply two examples of anti-evolutionist activity that's been going on for decades now.  They are not "gaining ground", they're doing what they've always done.  Having been shot down by the courts simply means that they're changing tactics.

Quote
Teachers who do inform students about some of Darwinism's unresolved problems often face persecution by what can only be termed the Darwinian thought police. In Washington state, a well-respected biology teacher who wanted to tell students about scientific debates over things like Haeckel's embryos and the peppered moth was ultimately driven from his school district by local Darwinists.


DeHart was teaching creationism, plain and simple.  It wasn't until much later, with the goading of the Discovery Institute, that he brought in materials about the peppered moth etc.  The whole affair dragged on for several years, and eventually local parents had enough.  But the DI sent in Jonathan Wells and its other minions to support DeHart, who steadfastly refused to cater to any of the school board's wishes.  So locals get upset and the DI sends in its troops from out of town, and they bandy about accusations of "thought police".  What nerve.

Quote
A second development fueling recent gains by Darwin's critics has been the demise of an old stereotype.

For years, Darwinists successfully shut down any public discussion of Darwinian evolution by stigmatizing every critic of Darwin as a Biblical literalist intent on injecting Genesis into biology class. While Darwinists still try that tactic, their charge is becoming increasingly implausible, even ludicrous.


Ludicrous?  The stated goal of the C®SC is religious apologetics, and they actively court biblical literalists.  Talk about doublethink!  

Quote
The ranks of these academic critics of Darwin are growing. During the past year, more than 150 scientists — including faculty and researchers at such institutions as Yale, Princeton, MIT, and the Smithsonian — adopted a statement expressing skepticism of neo-Darwinism's central claim that "random mutation and natural selection account for the complexity of life."


The statement that these people signed onto was carefully worded such that it's not controversial at all.  Nevertheless, most of the signatories were not biologists, and 150 is an insignificant number anyway.  There are tens of thousands of scientists who accept Darwinian evolution.  Nor is there any indication that their number is growing in any major way; all of these people were most likely evolution-doubters prior to the DI's propaganda efforts.  Same is true with the Ohio list.

There's really nothing new here.  Same old canards, same old arguments from authority, same old carefull avoidance of any straitforward scientific claims, same old demonization and hypocritical cries of persecution.

theyeti



Date: 2002/12/18 18:13:47, Link
Author: rafe gutman
from nature science update:

Back two bases

Stripped down genetic code provides candidates for first molecules of life.

Chemists in the United States have constructed the simplest possible genetic language. Like Morse or binary code, it has only two letters - but it can orchestrate some of the basic molecular reactions needed for life to evolve.

This stripped-down genetic scheme might provide clues about how life began in the chemical soup of the early Earth, say its developers John Reader and Gerald Joyce of the Scripps Research Institute in La Jolla, California1.

Today, the recipes for life - RNA and DNA - are normally written in a four-letter molecular alphabet: the bases adenine (A), guanine (G) and cytosine ©, together with thymine (T) in DNA or uracil (U) in RNA. Each gene in DNA is a sequence of A's, G's, C's and T's.

But these bases aren't easy to make from the chemical constituents of the early Earth, point out Reader and Joyce. So they may not have been available to build molecules capable of carrying out the basic chemical processes of life, such as replication and catalysis.

A simpler two-base molecule might have stood a better chance, argue the duo. They have made a two-letter ribozyme - a molecule that helps another to stick to it. These catalysed link-ups are necessary to construct the molecular chains of the genetic molecules DNA and RNA.

Most biological catalysts, or enzymes, are proteins. But ribozymes are made from RNA. Because they can both catalyse reactions and hold and transmit genetic information, RNAs could have provided the molecular basis of life before proteins and DNA evolved.

Pair bonding

Using just two bases, Reader and Joyce mimicked the R3 ligase ribozyme, a stretch of RNA that latches onto another RNA molecule.

Part of the R3 ribozyme has a base sequence that matches that on its RNA target molecule. The researchers constructed this binding sequence and target from A and U bases alone.

Then, for technical reasons, they replaced the A's with a non-natural base called diaminopurine (D). The resultant ribozyme can be copied without the need for G or C bases. Copying is a necessary part of the process of finding a two-letter mimic.

The researchers then eliminated all of the G's that they could from the R3 molecule while still retaining some of its catalytic behaviour (it can manage without C's). All but three could go; if the researchers took any of those out, the molecule was no longer catalytic.

To get further, the researchers abandoned rational design and turned to in vitro evolution. They replaced the remaining G's at random with U or D, while shuffling a few of the other U's and D's in the molecule.

None of the products made this way is a particularly stunning catalyst. But they work. The best, containing just U and D, links to the RNA target 36,000 times faster than in the absence of any catalyst at all. In other words, a two-letter ribozyme is a lot better than nothing.

D isn't too difficult to create from the kind of ingredients that were probably available on the early Earth, say Reader and Joyce. They also point out the advantage of an RNA-like molecule that contains no C: cytosine decomposes quite quickly if it gets warm.

Date: 2002/12/18 18:24:29, Link
Author: rafe gutman
here's a good recent discussion of the implications of the finding of a proto-immunoglobulin in amphioxus, branchiostoma floridae:

(in nature immunology)

The origins of the adaptive immune system: whatever next?

Quote
The discovery of a V-like Ig multigene family in the protochordate amphioxus provides new insights into the evolution of the adaptive immune response.


Diversity is at the same time the essential product of evolution and the essential substrate on which it must act. Although diversity can be the result of many different pressures and mechanisms, it is particularly evident and rapidly evolving in the responses of hosts to pathogens and parasites. Of the many defense systems described from the simplest single-celled bacteria to the most complicated plants and animals, none has been more intensively studied than the mammalian adaptive immune system. It has only recently become apparent that the adaptive immune system arose in the jawed vertebrates, but little is known about the deeper origins of this system or the relationship with other defense systems in nonvertebrate organisms. In this issue of Nature Immunology, Litman and colleagues describe a set of newly identified sequences from the protochordate amphioxus (Fig. 1), which make up a diversified multigene family and could hold some clues to the emergence of the adaptive immune system.


for the rest of the article, follow the link at the top.

Date: 2002/12/18 18:24:58, Link
Author: niiicholas
Over at ARN, Mike Gene is again claiming that the question "What should make one suspect ID?" has not/cannot be sufficiently answered by ID skeptics.  The implication is basically that ID skeptics are close-minded and unable to consider the matter in a neutral, open, explorative way.

http://www.arn.org/ubb/ultimatebb.php?ubb=get_topic;f=13;t=000536

But there are lots of things that would make me suspect ID.  Note that these things are not the same things that would prove it beyond a reasonable doubt, although a lot of these "evidences for suspicion" put together might fit that bill.

MG specifically put forward the flagellum as an example, conveniently a particularly ancient system for which the kinds of evidence available for e.g. the immune system are much more difficult to come by.

Quote

Tell me what would cause you to suspect the flagellum as designed. Thus far, not one ID critic has shared a useful criterion.


As JP has noted in the thread, many answers to the "suspect" question have already been provided, it's just that Mike Gene doesn't like them because design does not entail that these things exist.  That's pretty much the problem with Mike-Gene-design, it doesn't appear to entail anything in particular at all.  Even IC systems are apparently accessible to evolution under MG-ID, so if the tremendously complicated immune system is shown to have plenty of evidence of gradual natural origins, he can just shrug it off and say that ID designed something more remote, like the flagellum.

Still, an observation does not have to be *entailed* by design in order to be an observation that would legitimately raise suspicion.  Evolution does not predict that any particular transitional fossil will be found, just that some will be found somehwere, and these legitimately raise suspicion.  Presumably even a rarified design hypothesis predicts that some kind of positive evidence will be found somewhere.

I would suspect (not conclude) design for the flagellum if there were evidence for any of the following:

1) A purpose other than maximizing the reproduction of the genes of the bacterium in question, that fits with some hypothesized designer.  E.g., mousetraps are designed for trapping mice that are annoying humans.  Note that in contrast, evolutionary theory predicts this for all complex "designed" systems.  Find a counterexample and you've disproved evolution.  Find a counterexample with a purpose that fits some specific designer hypothesis and you've got reason to suspect that designer hypothesis.

2) True IC, i.e. if the parts of the flagellum really did not have any function apart from contributing to flagellar function, i.e. that any subset of flagellar parts really was "by definition nonfunctional".  This was Behe's original attempted argument, and if it had held up under the weight of evidence then he would have had something.

3) Biologically impossible transplants of the complex "design" across phylogenetic lines.  This is seen *in spades* in human design systems.  However, in biological systems, such transplants appear to be limited in numerous ways:

a) Basically limited to single-celled critters without protected germ-line cells
b) Most commonly there to prokaryotes that are *known* to do all kinds of conjugation, DNA uptake, etc.
b.5) In eukaryotes, the most impressive cases lateral transfer are the cases of symbiosis, in which the genomes of the host and symbiont are in close association for millions of years and transfers can occur bit-by-bit while maintaining function
c) Suspicions of transplants are often confirmed by finding plasmids, insertion remnants, and evidence of other known lateral transfer mechanisms
d) Transplants are most common between prokaryotes (a) closely related or (b) living in close proximity
e) Apparently limited to relatively simple systems (single operon?), and the more complex the system, the more closely related must be the donor/acceptor.  The most complex system transferred that I can think of is Type III virulence systems, and (IIRC) these are all restricted to a relatively narrow group.

As an example of the contrast seen in human designs, the following highly complex systems originated locally and were rapidly transplanted into any manner of larger devices (cars, planes, boats, etc.) without any regard for the kinds of biological, ecological, and phlyogenetic patterns described above:

- computers
- GPSs
- satellite phones
- emergency transponders

4) It occurs to me suddenly that the pattern that all of these designed transplants follow is that they are useful *to the designer*, i.e. safety, navigation, etc.  So, even in a case where the lateral transfers were biologically possible, if the pattern of transfer fit the purposes of a hypothesized designer(s), I would suspect design.

5) Evidence of "front-loading", e.g. if many bacteria had buried instructions for flagella, protected somehow from degradative mutations (not a tough burden for your average superadvanced designer), that were waiting to be "turned on" at some point in the future for some purpose of a hypothesized designer (this is a modified version of Behe's supercell idea)

6) A communication-to-intelligent-beings signal encoded in the flagellar genes.  E.g., a prime number sequence apparently cleverly encoded in the essential nucleotides or amino acids of the flagellum.  I say "apparently" because just the bare fact of a prime number sequence would not constitute proof, only suspicion (which is all MG wants anyway), unlike in astronomy it is just possible that there are ways for biological mechanisms to generate primes (although it is quite a stretch from 17-year cicadas to genome sequences).

I'm sure there's more...I won't, however, say the one that I think MG prefers, namely "it looks designed", because it's pretty clear that natural selection can produce complex "designed" adaptation when the adaptation benefits the genes of the organism.  Even Mike Gene concedes this, so IMO it appears that he is being inconsistent when he places the thus-far-unverified-in-biology ID hypothesis on the same footing as the well-verified-in-biology NS hypothesis.  Why not also include Lamarkian evolution and complexity theory on the same footing also?  I would say that each of these has at least a wee bit of positive evidence raising a little bit of suspicion, unlike ID.

Links to other threads and CCed posts on this topic would be worthwhile.

Date: 2002/12/18 19:36:32, Link
Author: theyeti
Quote (niiicholas @ Dec. 18 2002,18:24)
Over at ARN, Mike Gene is again claiming that the question "What should make one suspect ID?" has not/cannot be sufficiently answered by ID skeptics.  The implication is basically that ID skeptics are close-minded and unable to consider the matter in a neutral, open, explorative way.

After having gone 'round and 'round with Mike about this issue several times, he finally let loose the notion that he's using "suspect" in a completely different way than I was.  As he was using it, he seemed to mean "suspect as a possibility" whereas I figured he meant, "suspect as being reasonably likely".  Given the first meaning, it's a somewhat trivial question.  I would simply say that I would suspect design as a possibility for the same reason that Paley did.  Living things and their parts are complex, and do serve functions (i.e. have teleos) like our designs.  So I accept ID as a possiblity, if a remote one.  Yet it's another story entirely whether or not ID is testable, and whether or not the available evidence supports it. What I do soundly reject is Paley's logic in concluding that this is a sufficient hallmark of design.  And then there's this guy named Darwin who showed that the Palian argument generates false positives.  

Suspecting that ID is true, on the other hand, carries with it a much higher burden of evidence, and it depends entirely on what theory of ID you're talking about, which itself will depend on some assumptions about the designer.  But mainstream IDists reject this entirely, instead claiming that "design" can be detected in the absence of any theory about who, how, when, where, etc., that would actually lead to specific predictions.  They claim that design can be detected because of the supposed impossibility of natural mechanisms.  But when someone answers Mike by saying that this would need to be demonstrated, he complains about it being an unfair demand!  Having been shown this point, Mike still advances the notion that no one's interested or capable of answering his question, even though he knows it's not true.  He simply maintains it as a rhetorical device.

theyeti (aka Grape Ape)

Date: 2002/12/18 20:41:39, Link
Author: theyeti
Here is a good timeline of the whole DeHart affair:

http://www.scienceormyth.org/discoveryinstitute.html

It's amazingly long and complex.  DeHart apparently taught creationism for many years before being asked to stop, and before being used as a pawn of the DI.

theyeti

Date: 2002/12/18 20:59:41, Link
Author: pzmyers
The whole question is more than a little silly. It's the job of the proponents to come up with the evidence to persuade the critics.

Can you imagine ol' Charlie Darwin popping around to Richard Owen's house and asking him, "What can I do to convince you of my theory"? If he had so little confidence in his own knowledge of what constituted strong evidence, it would no good to beg for help from his foes.

Mike Gene's question is basically an admission that he's floundering and clueless.

Date: 2002/12/19 00:04:03, Link
Author: niiicholas
This is a big enough topic to deserve a thread separate from the origin of information or the origin of particular systems.

Short version: there is lots of evidence that multiple-parts-required metabolic pathways have originated via known evolutionary processes, in human and even lab lifetimes.

Here is a synthesis article I just came across:

Quote

Curr Opin Struct Biol 2002 Jun;12(3):374-82
 
Pathway evolution, structurally speaking.

Rison SC, Thornton JM.

Department of Biochemistry and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.

Small-molecule metabolism forms the core of the metabolic processes of all living organisms. As early as 1945, possible mechanisms for the evolution of such a complex metabolic system were considered. The problem is to explain the appearance and development of a highly regulated complex network of interacting proteins and substrates from a limited structural and functional repertoire. By permitting the co-analysis of phylogeny and metabolism, the combined exploitation of pathway and structural databases, as well as the use of multiple-sequence alignment search algorithms, sheds light on this problem. Much of the current research suggests a chemistry-driven 'patchwork' model of pathway evolution, but other mechanisms may play a role. In the future, as metabolic structure and sequence space are further explored, it should become easier to trace the finer details of pathway development and understand how complexity has evolved.



Then of course we have:

Quote

Trends in Biochemical Sciences
Volume 25, Issue 6, 1 June 2000, Pages 261-265
Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach

Shelley D. Copley


The pathway for degradation of the xenobiotic pesticide pentachlorophenol in Sphingomonas chlorophenolica probably evolved in the past few decades by the recruitment of enzymes from two other catabolic pathways. The first and third enzymes in the pathway, pentachlorophenol hydroxylase and 2,6-dichlorohydroquinone dioxygenase, may have originated from enzymes in a pathway for degradation of a naturally occurring chlorinated phenol. The second enzyme, a reductive dehalogenase, may have evolved from a maleylacetoacetate isomerase normally involved in degradation of tyrosine. This apparently recently assembled pathway does not function very well: pentachlorophenol hydroxylase is quite slow, and tetrachlorohydroquinone dehalogenase is subject to severe substrate inhibition.


An important update:

Quote

J Bacteriol 2003 Jan;185(1):302-10
 
A Previously Unrecognized Step in Pentachlorophenol Degradation in Sphingobium chlorophenolicum Is Catalyzed by Tetrachlorobenzoquinone Reductase (PcpD).

Dai M, Rogers JB, Warner JR, Copley SD.

The first step in the pentachlorophenol (PCP) degradation pathway in Sphingobium chlorophenolicum has been believed for more than a decade to be conversion of PCP to tetrachlorohydroquinone. We show here that PCP is actually converted to tetrachlorobenzoquinone, which is subsequently reduced to tetrachlorohydroquinone by PcpD, a protein that had previously been suggested to be a PCP hydroxylase reductase. pcpD is immediately downstream of pcpB, the gene encoding PCP hydroxylase (PCP monooxygenase). Expression of PcpD is induced in the presence of PCP. A mutant strain lacking functional PcpD has an impaired ability to remove PCP from the medium. In contrast, the mutant strain removes tetrachlorophenol from the medium at the same rate as does the wild-type strain. These data suggest that PcpD catalyzes a step necessary for degradation of PCP, but not for degradation of tetrachlorophenol. Based upon the known mechanisms of flavin monooxygenases such as PCP hydroxylase, hydroxylation of PCP should produce tetrachlorobenzoquinone, while hydroxylation of tetrachlorophenol should produce tetrachlorohydroquinone. Thus, we proposed and verified experimentally that PcpD is a tetrachlorobenzoquinone reductase that catalyzes the NADPH-dependent reduction of tetrachlorobenzoquinone to tetrachlorohydroquinone.

Introduction

Pentachlorophenol (PCP) is a widely used and highly toxic wood preservative. It was first introduced as a pesticide in 1936 (7) and is not known to be a natural product. Despite its recent introduction into the environment and its high toxicity, several strains of Sphingobium chlorophenolicum (previously Sphingomonas chlorophenolica) (24) that can mineralize PCP have been identified. The best studied of these are strains ATCC 39723 (19), RA-2 (23), and UG30 (6). It appears that S. chlorophenolicum has assembled a new metabolic pathway capable of converting this anthropogenic compound into a recognizable metabolite. Our previous studies suggest that this pathway has been assembled by patching together enzymes from at least two different metabolic pathways (8). PCP hydroxylase (PCP monooxygenase; EC 1.14.13.50) and 2,6-dichlorohydroquinone dioxygenase may have originated from enzymes that hydroxylated a naturally occurring chlorinated phenol and then cleaved the resulting hydroquinone. Tetrachlorohydroquinone (TCHQ) dehalogenase appears to have originated from a glutathione-dependent double bond isomerase such as maleylacetoacetate isomerase or maleylpyruvate isomerase (which are involved in degradation of tyrosine and benzoate, respectively) (2). If this pathway has evolved recently in response to the introduction of PCP into the environment, then it would not be expected to perform at the high level characteristic of pathways that have evolved over periods of millions or billions of years. Indeed, the PCP degradation pathway shows signs of immaturity in several respects. First, PCP hydroxylase, the first enzyme in the pathway, is very inefficient in vitro (P. M. Kiefer and S. D. Copley, unpublished data), and appears to severely limit the flux of PCP through the pathway in vivo (17). Second, TCHQ dehalogenase is profoundly inhibited by its aromatic substrate (K. Anandarajah, P. M. Kiefer, and S. D. Copley, unpublished data). Third, TCHQ dehalogenase expression is not regulated in tandem with the other known enzymes in the pathway but is apparently constitutive (21). All of these findings are consistent with the idea that the PCP degradation pathway has been patched together rather recently and has not been fine-tuned to perform as effectively as do most bacterial metabolic pathways.

The gene encoding PCP hydroxylase (pcpB) is immediately upstream of two additional genes. pcpR encodes a regulatory protein that responds to PCP (5). pcpD, which is immediately downstream of pcpB, resembles genes for the reductase components of two-component oxygenases, some of which hydroxylate aromatic compounds. Based upon this resemblance, it has been proposed that PcpD is a reductase that facilitates the hydroxylation of PCP by PCP hydroxylase (19), and the annotation of PcpD in GenBank states that it is PCP 4-monooxygenase reductase. We suspected that this assignment was incorrect because PCP hydroxylase is a flavin monooxygenase, and such enzymes do not generally require reductases. Consequently, we undertook studies to determine whether PcpD is required for degradation of PCP. We find that transcription of pcpD is induced by PCP, as previously reported for pcpA (29) and pcpB (20). A mutant strain in which PcpD has been knocked out is able to remove PCP from the medium when it is present at low concentrations, but not when it is present at high concentrations. In contrast, the knockout strain can remove tetrachlorophenol (TCP) from the medium as well as the wild-type strain, even at high concentrations. These results suggest that PcpD may catalyze a step that is critical for degradation of PCP but not TCP and therefore must involve the chlorine at the 4 position of PCP. Based upon the expected mechanism of the hydroxylase reaction, the sequence of PcpD, and our experimental results, we propose that PcpD is a tetrachlorobenzoquinone (TCBQ) reductase required for degradation of PCP but not TCP.

Date: 2002/12/19 10:55:55, Link
Author: katerina
Sorry, I probably got the name of the thing wrong.  iscid. I thought about that later.

I don't really know much nor care much about ID.

I only follow the board because I have some friends on it and because the antics and whining is really quite a diversion.

Date: 2002/12/19 16:45:38, Link
Author: m1isaak
An additional consequence I would expect from ID (in addition to what others have already said) is that design would not be limited to life.  If the qualities of a bacterial flagellum indicate design, then I would expect such flagella, or things of comparable complexity and functionality, to occur on rocks, hail stones, stream banks, etc.  If non-life doesn't "look designed," that is strong evidence against design, period.

Suppose though, design was limited to life.  In that case, I would expect one of three patterns, depending on how nearly omnipotent the designer is.  If the designer were omnipotent, I would expect all life forms to appear suddenly, with no history of vastly different extinct forms.  If the designer were somewhat less powerful, I would expect an evolutionary history of life on earth, but with novel forms appearing much more frequently later in history as the designer gets more practice and more working parts.  If the designer didn't have much more technical prowess than we do now, then I would expect the designer to use evolution.  Evolution gives a designer the ability to make life that doesn't need constant tinkering as environments change, and it allows a single design to diversify.

The first two of those possibilities are contradicted by observations of the fossil record.  That leaves only a designer who uses evolution.  Since IDists reject evolution, they themselves reject what I see as the only possibility of design.

Date: 2002/12/19 18:10:14, Link
Author: charlie d
To me, at the molecular level, an ID hypothesis would be probably warranted (though not proven) by evidence for bona fide teleology, such as real directed mutation mechanisms, or clearcut - not a posteriori - front-loading.  

At the organismal/ecological level, I would be swayed by mechanisms of homeostasis going counter reproductive advantage, for instance if preys ceased to escape from predators when predator numbers decline.  Something like mass lemming suicide, if it were real, would be suggestive evidence too.

Of course, in all these cases the hard part would still be to test the actual ID hypothesis vs alternative naturalistic explanations, but at least the secret ID scientists would have something real to work on.

But I agree, these standards are already too high compared to what Mike seems to be looking for, i.e. some sort of admission for "soft" ID.

Date: 2002/12/19 20:01:20, Link
Author: Wesley R. Elsberry
I agree with John's clarification.

So, what are the central issues?  I'm thinking those are the issues from Dembski's topic-opening post.

The title of the thread talks about a "lust for certainty".  I think I've established that the claims of certainty can be found in Dembski's work.  That critics chose to respond to those claims should have been expected.  The more tentative claims came later and did not displace the non-tentative claims, leading to a state of inconsistency in Dembski's claims.

The claim by Dembski that there exist no counterexamples to his claim that his EF/DI is "reliable" is either abysmally weak (based on less than a handful of worked examples) or actually false (since various critics have put forward candidate counterexamples).

I've had a look at Demsbki's essay on "logical underpinnings" but I don't yet wish to comment.  I'm getting acquainted with BibTeX at the moment.

Wesley

Date: 2002/12/20 01:06:29, Link
Author: niiicholas
I rediscovered the Breakpoint article, it has a list of links at the bottom:

The Moth Myth
BreakPoint with Charles Colson
July 25, 2002
Nothing Natural about This Selection

http://www.breakpoint.org/Breakpo....yth.htm

Date: 2002/12/20 01:10:56, Link
Author: niiicholas
Intelligent Design jargon explained!
By Casey Luskin
http://www.ideacenter.org/idjargon.htm

Lesse, by my count there were 3-4 terms discussed and none were significantly clarified...basically "trust me, ID is for real".

Date: 2002/12/20 01:15:32, Link
Author: theyeti
I decided to start this thread to collect references about protein evolution specifically as it relates to folding.  First I'll repost an essay that I posted to the ISCID forum, skipping the irrelevant parts:

[...]

Now for some more general stuff about protein folding and evolution.  Josh gives us a very educational post about some of the complexities of protein folding and what it means to biology.  I'm going to skip most of the stuff about the dynamics of protein folding, because I think, at least as it relates to the suboptimality argument, I've addressed that above, and also because I don't have the necessary background in physics to know that much about it.  I think Josh can appreciate that, because he notes that there's tons of stuff that we don't know.  The literature on the dynamics of protein folding is very large, but it's also difficult to read (for me anyway).  But I have reviewed some of the literature at it pertains to the evolution of protein folds, and I'll present some of that.

First of all, it’s a misconception even among many biochemists that all proteins need to fold to be functional.  In fact, the importance of disordered proteins and those with long disordered regions is now becoming more clear.  Try searching the lit for “intrinsically disordered proteins” and you’ll come up with a number of hits.  These proteins (or certain domains) are unfolded and yet are perfectly functional, and in many cases are just as highly conserved as folded protein domains, though often of lower sequence complexity [1] (and hence, easier to evolve via random generation).  In fact, there is evidence that disordered proteins outnumber ordered proteins, but that the ordered ones represent more resolved structures in the PDB simply because (big shock) they’re easier to crystallize.  So one possible way for folded proteins to come about is by evolving from functional yet disordered proteins, and in this case there would never be a period of time when there was not a selectable function.  And of course it’s not like there are only two kinds of proteins, folded and unfolded.  There is also the intermediate molten globule state.  

However, most protein folds are thought to evolve from other folds.  This can be seen with the arrangement of protein folds into scale free networks.  Two recent papers on this are relevant.  The first one is Proc Natl Acad Sci U S A 2002 Oct 29;99(22):14132-6, Expanding protein universe and its origin from the biological Big Bang.  I posted a number of excerpts from this paper here, so I won’t bother reproducing them.  The point however is that the scale-free network in which protein folds fit is highly indicative of a duplication / divergence process from one or a few initial folds.  The second paper, which came out about the same time, is Nature 2002 Nov 14;420(6912):218-23, The structure of the protein universe and genome evolution.  Here’s the abstract:

Quote
Despite the practically unlimited number of possible protein sequences, the number of basic shapes in which proteins fold seems not only to be finite, but also to be relatively small, with probably no more than 10,000 folds in existence. Moreover, the distribution of proteins among these folds is highly non-homogeneous -- some folds and superfamilies are extremely abundant, but most are rare. Protein folds and families encoded in diverse genomes show similar size distributions with notable mathematical properties, which also extend to the number of connections between domains in multidomain proteins. All these distributions follow asymptotic power laws, such as have been identified in a wide variety of biological and physical systems, and which are typically associated with scale-free networks. These findings suggest that genome evolution is driven by extremely general mechanisms based on the preferential attachment principle.


So both of these papers support the idea that an evolutionary process not only can account for the emergence of protein folds, but that the distribution of folds is a predicted consequence of evolution.

Now finally, if you want a “beginning to end” account for protein evolution, there is this recent review article (and there are others out there):

FEBS Lett 2002 Sep 11;527(1-3):1-4, Molecular evolution from abiotic scratch.

I’ll see if I can reproduce what they’ve got listed as the five stages of protein evolution, though I’ll have to skip the discussion:

1. Homopeptides of Ala and Gly encoded by (GCC)-(GGC) duplexes.
2. Mixed peptides of two alphabet types.
3. Chains of optimal length close the ends by interactions between two amino acid residues.
4. The loops are joined in linear arrays and form folds (domains)
5. Modern, multidomain proteins are formed.

I don’t know if this model will last, or even if it can stand up to serious scrutiny right now, but it’s the kind of thing that needs to be explored in detail before we can really say anything about the likelihood of protein evolution de novo.  Keep in mind that this particular model is trying to account for the evolution of proteins from the origin of life, which is necessarily tricky because it’s difficult to learn about this just from looking at modern life.  However, once you have a functioning cell, I don’t see any problem with the ability of current theory to account for protein evolution.  

[This last reference is at the end here for no real good reason]

1. Proteins 2001 Jan 1;42(1):38-48, Sequence complexity of disordered protein.
Quote
Intrinsic disorder refers to segments or to whole proteins that fail to self-fold into fixed 3D structure, with such disorder sometimes existing in the native state. Here we report data on the relationships among intrinsic disorder, sequence complexity as measured by Shannon's entropy, and amino acid composition. Intrinsic disorder identified in protein crystal structures, and by nuclear magnetic resonance, circular dichroism, and prediction from amino acid sequence, all exhibit similar complexity distributions that are shifted to lower values compared to, but significantly overlapping with, the distribution for ordered proteins.

Date: 2002/12/20 02:11:24, Link
Author: niiicholas
This was posted on the DI website.  

Quote

Alan Gishlick and the NCSE: Full of Sound and Fury, Signifying Nothing New on the Icons of Evolution

Jonathan Wells
Discovery Institute
December 13, 2002

On November 22, 2002, the National Center for Science Education posted Alan D. Gishlick’s “Icons of Evolution?: Why much of what Jonathan Wells writes about evolution is wrong” on their website.

Gishlick’s piece is a long-winded version of a review of my book, Icons of Evolution: Why much of what we teach about evolution is wrong (Regnery, 2000), that he and NCSE President Kevin Padian published in March, 2002, in The Quarterly Review of Biology. Like their review, Gishlick’s new essay is primarily an attempt to defend the icons; and like the review, Gishlick’s essay is heavily seasoned with ad hominem attacks on me. But it adds nothing substantially new to the debate.

One point that Gishlick’s essay establishes beyond a shadow of a doubt, however, is that the icons of evolution are NOT simply textbook mistakes. In their March book review, Padian and Gishlick likened me to “kids who used to write to the letters page of Superman comics years ago” to complain about trivial typos. “Okay, kid,” they wrote, “mistakes happen, but did it really affect the story?” Apparently, Gishlick has decided that the icons of evolution are not simply mistakes that can be corrected or ignored; instead, they must be defended at all costs. Gishlick’s essay thereby reaffirms what I wrote in my response to published book reviews (including the one by him and Padian) a few months ago:

“If Darwinists could show that my criticisms of the icons of evolution were unwarranted, or if they would stop trying lamely to defend the icons and simply replace them with better evidence, I would drop my case. But Darwinists cannot defend the icons, and they cannot afford to abandon them, so they resort to insults and smears.”

Unfortunately for Gishlick, the cats are already out of the bag. When I lectured to biology students on a state university campus recently, their professors were incredulous when I told them that some people still defend the Miller-Urey experiment, Haeckel’s embryo drawings and the peppered myth. The NCSE’s desperate attempts to defend the indefensible are not fooling biologists in the field.

For more information, and for my previous responses to the sorts of things Gishlick rehashes in his essay, see my postings on the Discovery Institute website, especially the following:

“Critics Rave Over Icons of Evolution: A Response to Published Reviews” (June 12, 2002)

“Inherit the Spin: Darwinists Answer ‘Ten Questions’ with Evasions and Falsehoods” (January 15, 2002)

“Desperately Defending the Peppered Myth: A Response to Bruce Grant” (October 2, 2002)

“Moth-eaten Statistics: A Reply to Kenneth R. Miller” (April 16, 2002)

“There You Go Again: A Response to Kenneth R. Miller” (April 9, 2002)


Funny, Bruce Grant (lots of articles linked) was originally supposed to be one of the experts who had overturned the icon, but now the foremost American expert on the peppered moth has been relegated to being a non-authority by Wells.

Grant's most pointed comments are here:
http://www.talkorigins.org/faqs/wells/default.htm#mothgrant

Too bad Wells didn't take the opportunity to attempt to rebut a review that actually had the space to debunk his arguments in the detail they deserve.

ICONS OF EVOLUTION?
Why much of what Jonathan Wells writes about evolution is wrong
by Alan D. Gishlick
http://www.ncseweb.org/icons/



Date: 2002/12/20 11:51:39, Link
Author: ExYECer
I find it fascinating how Wells, convinced of his own arguments, refuses to consider anything that shows that his portrayals of the 'Icons' left much to be considered.

I am glad that Wells is on the side of the ID movement.

Date: 2002/12/20 12:51:11, Link
Author: charlie d
Yes, nice strategy.  
According to Wells, if people ignore his arguments on the Icons, it's because they are not able to answer the arguments.
If they answer the arguments, by showing that Wells is wrong, it's because they have to defend the Icons "at all costs".
And if they change whatever there is to be changed about the Icons, it's because Wells' arguments were right in the first place.

LOL, what a smoke seller!

Date: 2002/12/20 14:27:40, Link
Author: zygotecowboy
I'd have to agree with Charlie. It seems MG is on a fishing expedition to get ID critics to admit to some low standard for recognizing ID. It's just low-ball rhetorical tactic to make your opponents look foolish. Let's say someone admits to some sort of low standard that would allow them to "suspect ID" (whatever that means.) MG will scour the literature for something that fits that standard. Then the critic is left with two options: 1) accepting an ID suspicion, or 2) rescinding on the low standard the critic originally accepted. MG can then cry foul and claim the critic is moving the goal posts.

zc

Date: 2002/12/20 16:49:51, Link
Author: Bebbo
As an aside about Mike Gene. He's made some comments about people not using their real name, but he's posting under a pseudonym too. Does anyone know who he is? I've reason to believe that he's a particular member of the Discovery Institute or someone associated with him.

--
Dene

Date: 2002/12/20 17:07:05, Link
Author: charlie d
Hi Bebbo:

I doubt Mike Gene would make such a silly comment; what he was complaining about was the number of anonymous ID critics at ARN who say they are ("pose" as) scientists.  Of course, one could actually spot a poseur rather quickly, so I am afraid that Mike has to accept the fact that those are real scientists, and that no scientists, anonymously or not, appear interested in defending ID on ARN.  The only people really making noise about actual identities are Chris and Genie.  

Anyway, whether Mike is or not who you think he is, I think you should probably delete the name from the previous post, to respect his privacy, or to avoid associating the wrong person with Mike's work.  

Thanks!

Date: 2002/12/20 18:10:56, Link
Author: zygotecowboy
There isn't too much too this article, but one thing struck me:

Quote
William Dembski argues that the way we detect design is by looking for an unlikely (high information) state of affairs which matches a pre-existing pattern. The pattern which must be matched is called a "specification." Thus, the notion of specified complexity or complex specified information is simply lots of information which conforms to a specific pattern.

In biology, some systems have many interacting parts and are thus complex (high information).


First, CL is equating unlikelihood with "high information". He then does the same thing with complexity and "high information" again. Now, I'm fully aware that WAD has defined complexity as the inverse of probability, but is it fair to equate any of these to "high information"
(whatever that means)?

zc

Date: 2002/12/20 18:39:43, Link
Author: Bebbo
charlie d wrote:

>I doubt Mike Gene would make such a silly comment;
>what he was complaining about was the number of
>anonymous ID critics at ARN who say they are ("pose"
>as) scientists.

Whether or not they're "posing" as scientists I don't think Mike should be commenting negatively that others use a pseudonym when he does too.

>Of course, one could actually spot a poseur rather
>quickly, so I am afraid that Mike has to accept the fact
>that those are real scientists, and that no scientists,
>anonymously or not, appear interested in defending ID
>on ARN.  The only people really making noise about
>actual identities are Chris and Genie.  

Gawd, that pair! Btw, I saw a post, which has since been deleted, by Genie (posted by the user askfifi) saying that her and Chris's ARN accounts had been deleted. I wonder what's going on.

--
Dene

Date: 2002/12/20 19:01:23, Link
Author: Bebbo
Quote (zygotecowboy @ Dec. 20 2002,18:10)
There isn't too much too this article, but one thing struck me:

Quote
William Dembski argues that the way we detect design is by looking for an unlikely (high information) state of affairs which matches a pre-existing pattern. The pattern which must be matched is called a "specification." Thus, the notion of specified complexity or complex specified information is simply lots of information which conforms to a specific pattern.

In biology, some systems have many interacting parts and are thus complex (high information).


First, CL is equating unlikelihood with "high information". He then does the same thing with complexity and "high information" again. Now, I'm fully aware that WAD has defined complexity as the inverse of probability, but is it fair to equate any of these to "high information"
(whatever that means)?

zc

They seem to be conflating the vernacular sense of complex with Dembski's specific usage which means low probability - "high information" in their words.

All Dembski has offered is a formalisation of what Creationists have been banging on about for years, which is most notoriously framed in the "tornado in a junkyard" analogy. The advantage for the IDers is that the word "information" lends an unwarranted aura of sophistication to their argument because they get the chance to refer to information theory.

--
Dene

Date: 2002/12/20 20:53:02, Link
Author: niiicholas
I probably made a mistake in mentioning a specific personality. Recommend we keep the focus on the topic rather than on personalities.

And having had my pseudonym "exposed" myself awhile ago, I strongly recommend against trying to figure out who pseudonyms are, people have a right to privacy whether or not they have a good reason. 'Net pseudonyms are the norm in discussion forums.  

Another thing that would make me suspect ID: if the various IC systems usually proposed to be the result of "interventions" (even this low level of detail is rarely reached) all showed some kind of common signature apart from adaptive complexity, this might be suspicious (depending on the signature).

Date: 2002/12/20 21:02:53, Link
Author: niiicholas
Over at the ID network's response to the AAAS resolution:

[url=http://www.intelligentdesignnetwork.org/ResponseToAAAS.htm#Reason 6 text]Here if the internal spaces don't muck it up[/url]

...it is written:

Quote

6. The AAAS claim that a design inference is not testable is simply disingenuous. An inference of design is testable. Many scientific disciplines test for design every day, including routine testing of radio and light waves for alien intelligence by the SETI program.

   If ID is not testable and thus "non-scientific," then neither are several other disciplines currently held to be scientific. For example, in the SETI program, researchers are testing patterns in light and radio waves from outer space for non-human alien intelligence. ID and SETI both use the same design detection methodology. How could the SETI enterprise be considered scientific if its design detection methods are not scientifically valid? If design cannot be falsified, how can the AAAS consider it to be false? The AAAS claim that a design inference is not testable is refuted every day by countless design detection experts whose livelihood depends on design detection (e.g., forensic scientists, arson and crime investigators, cryptologists, archaeologists and SETI researchers).

   How does one "test" a design inference? A pattern or system that yields an inference of design must satisfy all of three criteria. If it cannot, then a design inference is not warranted (i.e., design is rejected as an explanation).

  • First, the pattern must exhibit apparent design - something that appears to be "specified." A specification is a pattern that has been configured for a purpose or that conveys some meaning or message that is independent of the significance of the individual events that make up the pattern. For example, the pattern "DESIGN" appears designed because it reflects meaning that is independent of the significance of each of the six letters that comprise it. DNA has the same characteristic.

  • Second, there must be no adequate natural explanation for the pattern. It cannot be a pattern that is required to appear by the operation of natural law. For example, a salt crystal and a river channel are regular patterns that can be explained by natural law (electromagnetism, gravity, erosion, moving water, the natural terrain). However, the precise sequence of the genetic symbols in "message bearing" DNA are not dictated by any known law.

  • Third, the pattern must be sufficiently complex that its arrangement by chance and law alone is statistically improbable. As mentioned above, the chance formation of the necessary DNA sequence for the first cell would appear to be statistically impossible.

       These general criteria are used in the analysis of patterns in all design detection sciences - archaeology, forensic sciences, cryptanalysis and the search for extraterrestrial intelligence. They are deemed adequate to test for design in those sciences. Why not in evolutionary biology? No scientific rational has been provided for accepting design detection methodologies in these other historical sciences and rejecting them in evolutionary biology.

    [italics original]


  • Point #2 looks like GOTG to me...

    There are lots of other problems here but this was particularly clear IMO.

    Date: 2002/12/20 21:49:41, Link
    Author: niiicholas
    This was just pointed out on an II thread:

    The Online Biology Textbook

    Lots of good graphics.  Although, they need a new horsey graphic:



    More like this:
    http://www.talkorigins.org/faqs/horses/horse_evol.html#part2

    ...fortunately, Wells apparently prefers the older view of things, despite what you might think from the title of Icons of Evolution.  On page 199 he wrote,

    "The mere existence of extinct side-branches doesn't rule out the possibility that the evolution of modern horses was directed. A cattle drive has a planned destination, even though some steers might stray along the way."

    Discussed here:
    http://www.talkorigins.org/faqs/wells/#horses


    Another resource:

    Also the UC Museum of Paleontology Online:
    http://www.ucmp.berkeley.edu/

    Teachers e-volution forum:
    http://www.ucmp.berkeley.edu/education/evoforum/

    Date: 2002/12/21 00:03:28, Link
    Author: Dr.GH
    SLP, "Perhaps it is that folks with super-high IQs also get a dose of instability/paranoia/various other complexes to go along with it."

    My sense is that people that used to be called "severely intelligent” (say the 4+ standard deviations above average group) have only the typical range and incidence  of mental illness.  They tend, in my experience, to view symbols as real a bit easier than most.  My brother for example views money as the way to keep score in what he sees as a game.  And so he has amassed a very high score.  But this is common enough, and well accepted as normal.  

    Many severely intelligent children become very frustrated with teachers and can become disciplinary problems.  They also can become angry when other children change “rules” in play activities directly to prevent the brighter child from always winning.  This may account for something that I have often seen; the severely intelligent generally find that whatever they are currently interested in is totally compelling to them.  The interests and concerns of others are only grudgingly attended, if at all.

    Mentally ill people with very high intelligence can be much more visible than those who are less bright, as they are less likely to become jailed or hospitalized.



    Date: 2002/12/21 07:25:48, Link
    Author: Bebbo
    Seems that ISCID feels money is necessary to get improved constributions to the Brainstorms forum:

    http://www.iscid.org/ubb/ultimatebb.php?ubb=get_topic;f=6;t=000262

    Overthrowing materialism doesn't come cheap I guess!

    --
    Dene

    Date: 2002/12/21 09:50:18, Link
    Author: Bebbo
    Quote (dayton @ Dec. 21 2002,08:54)
    So what happened to get mturner, Genie, and Chris banned at ARN?  Did some thread that I missed go down in flames?  Does anyone know?

    I've also been wondering about Chris and Genie, but I didn't know mturner had also been banned. It looks like they've got rid of Mod 4 (aka jazzraptor). Curiouser and curiouser.

    --
    Dene

    Date: 2002/12/21 10:08:24, Link
    Author: pzmyers
    Quote (Bebbo @ Dec. 21 2002,09:50)
    I've also been wondering about Chris and Genie, but I didn't know mturner had also been banned. It looks like they've got rid of Mod 4 (aka jazzraptor). Curiouser and curiouser.

    --
    Dene

    Errm, who is "they"?

    Date: 2002/12/21 16:50:30, Link
    Author: niiicholas
    You're kidding.  I thought Chris Langan was the new ARN luminary, and a moderator himself to boot.

    I never could figure out what CTMU had to do with ID (or what it was at all), but then I didn't try very hard.

    Date: 2002/12/21 18:45:33, Link
    Author: niiicholas
    Over on this ARN thread,

    http://www.arn.org/ubb/ultimatebb.php?ubb=get_topic;f=13;t=000536;p=2

    ...Joy & Mike Gene are missing JP's point.  As explanatory hypotheses in science, an unconstrained supernatural designer and an unconstrained natural designer (or an unconstrained designer of unspecified supernaturalness or naturalness) have the same problem: they have no empirical implications.  

    (I am speaking of "constraint" in terms of "explanatory constraint" here -- an omnipotent designer or super-technological designer would be all-powerful but would still be a "constrained" explanation if his actions followed a pattern motivated by a specific goals.  But an unconstrained ID hypothesis is essentially what is often called "rarified design")

    Note that the point is not that we have to know these things about the IDer ahead of time, the point is that we have to hypothesize something with some empirical implications so that we have some idea of what kinds of evidence would strengthen or weaken our confidence in the hypothesis.

    Otherwise nothing is getting explained at all, even hypothetically.

    The two major explanatory constraints that can begin to elevate design hypotheses to something above the "IDdidit" level are, I think:

    1) Designer methods/capabilities
    2) Designer goals

    ...although there may be others.  Notably, for human-design hypotheses we have a lot of evidence informing both #1 and #2, even for prehistoric cases.

    For SETI, the scientists involved are quite clearly hypothesizing that alien designers will be like us in certain minimal but ways, namely:

    1) Designer methods/capabilities: radio
    2) Designer goals: interstellar communication (with us or others)

    If either of these hypotheses is wrong, then even if the universe is teeming with intelligent life, we will not discover it through SETI no matter how much money and time are put in.  This is not a weakness but a strength: the status of the hypothesis can be fairly rigorously evaluated at any point.  Currently it is:

  • Positive evidence: none
  • Negative evidence: a little bit (nothing found with current restricted detection limits)

    As for the general likelihood of intelligent life in the universe, this can begin to be assessed if we constrain our "existence of intelligent life" hypothesis to something like "basically like human life and formed by the same processes we think created us".

    If, on the other hand, our "existence of intelligent life" hypothesis is "intelligent life of unknown characteristics formed by unknown processes" then we have no basis on which to procede and the hypothesis is relegated to the shrugworthy category of "undetectable invisible pixies exist".

    As for ID, I think that IDists do specify constraints #1 and/or #2 fairly regularly, it's just that they usually do it in passing (or even in a semi-hidden fashion) rather than explicitly, they tend to deny such specifications in public, and when an ID skeptic thinks they detect a specific hypothesis and raises counterevidence that weakens it, the IDist tends to deny that such a specific hypothesis was ever proposed.  Such vagueness may be helpful in debates, but it stands no chance of moving the ID ball towards the goal line of science.
  • Date: 2002/12/21 20:24:42, Link
    Author: theyeti
    My suspicion is that a few IDists complained to the ARN management, however one does that, and they finally decided to take charge.  There had been at least a few IDists who objected to Langan's insulting behavior only to have his venom turned on them.  How ironic is it for an ISCID fellow to get banned from an ID board?  I guess the only question now is if ARN will return to a semi-interesting board.  Although I'd get a real kick out of hearing some details about the banning if anyone hears about them. ;)

    theyeti

    Date: 2002/12/22 01:01:15, Link
    Author: Dr.GH
    For the last few months the only reason to look in on ARN at all was to watch the meltdown.

    Honestly, is there a single interesting scientific position that any IDiot has ever offered on the ARN board?  

    A bit over a year ago, I was taken in by an argument about Wells' Icons Chapter 2 about the oxidation state of the Hadean/Archaen and the origin of life.  1400 journal pages, 8 books and a year later, I have learned that neither DNAUnion or Mike Gene knew what they were talking about. (Nor does Wells)  

    I learned nothing at all from DNAUnion, Mike Gene or Wells, other than they are too incompetent to even  read the freely available literature.  (OK, so it wasn't free.  But I would say that I spent less than $500 on books, copying and journal fees.  Well, less than $600)

    Date: 2002/12/22 07:59:24, Link
    Author: Bebbo
    Quote (pzmyers @ Dec. 21 2002,10:08)
    Quote (Bebbo @ Dec. 21 2002,09:50)
    I've also been wondering about Chris and Genie, but I didn't know mturner had also been banned. It looks like they've got rid of Mod 4 (aka jazzraptor). Curiouser and curiouser.

    --
    Dene

    Errm, who is "they"?

    "They" is whoever runs ARN.

    --
    Dene

    Date: 2002/12/23 18:43:37, Link
    Author: Glenn Branch
    Heir spends family fortune to discredit evolution theory

    Date: 2002/12/23 23:25:12, Link
    Author: Michael
    The procedings Hovind's building code violation charge appear to have been delayed for quite some time.  He appeared on December 13 as scheduled but the whole thing has been reset and arraigments are now scheduled for May 27.

    Court Record for this charge

    Date: 2002/12/23 23:39:22, Link
    Author: niiicholas
    I think that several considerations have to be added to Hunter's post before serious discussion can be had.  

    1) "Congruence" and "noncongruence" are not either/or entities, they a matter of degree.  Given N species being analyzed, there are something like (2n-3)!/(2n-2(n-2)!;) hypothetically possible ways of arranging them into a tree (Theobald 2002), and the (dis)similarity between two trees can be rigourously quanitified.

    This equation will differ slightly depending on whether the trees are rooted vs. unrooted, binary splits only, etc.  Regardless, the number of possible trees gets very big very fast: 4 species = 15 possible trees, 8 species = 135,135 possible trees.

    You can randomly generate tree diagrams at this cool page (Phylogeny and Reconstructing Phylogenetic Trees) and get the idea very quickly what the odds are of getting the same tree twice by random chance.

    So the question is not whether two phylogenies from different data sources/research labs are congruent or incongruent, full stop, the question is how congruent or incongruent are they?  Most of the examples touted as showing "incongruence" are actually quite minor phylogenetic disagreements.  E.g., the interrelationships of different groups of bats is a pretty trivial issue in the context of vertebrates or animalia.  If the microbats grouped most closely with anthropoid apes, and the macrobats with giraffes, then we'd have a significant disagreement.  This kind of thing does not happen in multicellular organisms with protected germ line cells, rather different datasets keep returning highly congruent phylogenies.

    So, just like any scientific measurement, there will be noise in input data.  The analogy here is to radiometric dating: if two measurement dates of a moon rock return ages of 4.6 and 4.5 billion years, this is very minor disagreement relative to the result (100 million years sounds like alot but is only a 2% disagreement).  If someone were to go around saying "geological measurements disagree by 100 million years and this is evidence against an old earth" they would be wrong. Similar minor disagreements, such as Teeling et al.'s 2002 bat study,  should not be cited as evidence for Hunter's proposition "there are also plenty of character/species sets that do not produce congruent phylogenies".  A real disagreement would occur if all of these different bat species did not group together and instead were randomly associated with the outgroup taxa, but as we can see this did not occur:

    [img]http://www.pnas.org/content/vol99/issue3/images/medium/pq0224771001.gif[/[img]

    The odds of all these bat species grouping together by chance are astronomical.


    2. Scale of the study and range of dataset

    As the age-of-the-moon example points out, what is important in considering disagreement in results is not the absolute measurement, but the size of the disagreement relative to the scale of the study.  100 million years sounds like alot but is peanuts in terms of the age of the earth.  Such a disagreement would be major, however, in a radiometric dating of dinosaur bones, and a data source with a smaller error would have to be used.  

    Radiometric datasets have ranges and scales over which they are useful, due essentially to their rate of decay.  You use uranium-lead to date the age of the moon, because it has a half-life of hundreds of millions of years, but it would be ridiculous to use it for dating an archeological artifact because the answer you would get (assuming the artifact was, say, something that had been forged by remelting the ore) would be "0 +/- millions of years".  Similarly, the half-life of C-14 is only ~5,000 years, so it is excellent for archeology but for anything older than 50,000 years it is useless (a result of "50,000 years old" for a carbon date essentially means "this sample is between 50,000 and infinite years old").  In the first case, the noise is much larger than the signal, and in the second case the signal is much smaller than the noise (these are slightly different, think about it for a sec.).

    With molecular sequences the same factors must be taken into account.  I don't currently have access to Hunter's cited Balter (1997), " Morphologists learn to live with molecular upstarts", but I would note that there is apparently a contrasting commentary (Mindell 1997) on that very article from the next month of Science, entitled ""Misleading" molecules?".  Probably the basic point is that the particular mtDNA sequences being used evolve too quickly (certain mtDNA sequences are, after all, used for tracing migration patterns within the human species), such that sequence similarity is low and therefore "noise" in the form of mutational biases is larger than the signal.  Certainly comparing chickens, amphibians, and fish is a long ways from what one normally sees mtDNA used for, e.g. species within a genus.  

    (Note in passing: not all mtDNA within a mitochondrion is the same.  It's possible that the above study used a very slowly evolving mtDNA sequence and similarity between e.g. birds and fish was high, e.g. >75%.  But I doubt it.  Let's get the Balter and Mindell articles and see what they say, shall we?)

    In summary, anytime one sees a cited "incongruence" they must consider the dataset is appropriate for the scale of the analysis.  If sequence similarity is approaching randomness then mutational biases are increasingly important to consider.


    3. Actual violation of lineal descent.  This is commonly the case for single-celled prokaryotes without protected germline DNA.  If you like, the tree hypothesis has been falsified, because it is known and has been observed in the lab that they can trade DNA laterally.  But this leaves the evidence for the common descent of e.g. all animals unquestioned.  Much more can be said here because LGT is itself a nonrandom process and certainly some things are harder to LGT than others, but this is another topic.  If we saw the kinds of disagreements in animals that we have in prokaryotes, as we have no mechanism for significant LGT in animals (viral transfers is about it I think), this would be a significant problem for the common descent theory.  But we don't.  "Disagreements" that I have seen cited for multicellular critters basically fall into the above categories.

    In summary, in answer to Hunter's question,

    Quote

    My point is not to say explanatory mechanisms are out of bounds or that complicating factors should not be expected, but merely to raise the question: At what point does the use of these explanatory mechanisms become ad hoc and do we consider the Step 1 in the syllogism falsified?


    ...basically, these explanatory mechanisms are allowed when they themselves are well-supported by available data.  We can measure mtDNA rates of change and mutational biases.  We can observe and explain why LGT occurs in prokaryotes but not in mammals.  We can measure the degree of disagreement between trees and determine if the error is equivalent to 100 million years/4.6 billion years or not.

    There is a massive literature on all of this, which is why I'm surprised that Hunter thinks that biologists haven't thought about it.  The best introduction to it all is Theobald's FAQ at that talkorigins archive, referenced below. It references a lot of articles with titles like "Testing Common Descent" about the probabilities of hitting on congruent trees by chance.

    Refs:

    Theobald, Doug. 2002.  29 Evidences for Macroevolution

    Teeling, Emma C. et al. 2002 Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats Proc. Natl. Acad. Sci. USA, Vol. 99, Issue 3, 1431-1436.

    (bold added below)

    Quote

    Molecular phylogenies challenge the view that bats belong to the superordinal group Archonta, which also includes primates, tree shrews, and flying lemurs. Some molecular studies also challenge microbat monophyly and instead support an alliance between megabats and representative rhinolophoid microbats from the families Rhinolophidae (horseshoe bats, Old World leaf-nosed bats) and Megadermatidae (false vampire bats). Another molecular study ostensibly contradicts these results and supports traditional microbat monophyly, inclusive of representative rhinolophoids from the family Nycteridae (slit-faced bats). Resolution of the microbat paraphyly/monophyly issue is essential for reconstructing the temporal sequence and deployment of morphological character state changes associated with flight and echolocation in bats. If microbats are paraphyletic, then laryngeal echolocation either evolved more than once in different microbats or was lost in megabats after evolving in the ancestor of all living bats. To examine these issues, we used a 7.1-kb nuclear data set for nine outgroups and twenty bats, including representatives of all rhinolophoid families. Phylogenetic analyses and statistical tests rejected both Archonta and microbat monophyly. Instead, bats are in the superorder Laurasiatheria and microbats are paraphyletic. Further, the superfamily Rhinolophoidea is polyphyletic. The rhinolophoid families Rhinolophidae and Megadermatidae belong to the suborder Yinpterochiroptera along with rhinopomatids and megabats. The rhinolophoid family Nycteridae belongs to the suborder Yangochiroptera along with vespertilionoids, noctilionoids, and emballonuroids. These results resolve the apparent conflict between previous molecular studies that sampled different rhinolophoid families. An important implication of rhinolophoid polyphyly is independent evolution of key anatomical innovations associated with the nasal-emission of echolocation pulses.


    Originally posted here:

    ICSID thread



    Date: 2002/12/24 01:13:01, Link
    Author: JxD
    From the MegaBoards:
    Quote
    Topic: CTMU: Reality Principle (33 of 33), Read 6 times
    Conf: Reality Theory
    From: Chris Langan
    Date: Friday, December 20, 2002 07:51 PM
    [snip]
    >Would someone tell me, please, how to
    >find the ARN debate? Is it open to the
    >public?
    >
    >Thanks in advance,
    >
    >Paul

    Hi, Paul. My advice would be "don't bother". Genie and I are pretty much through with the place (ARN) unless we receive a full apology for the abuse we've suffered there over the last 6 weeks, not only from an army of vicious, pea-brained, officially-shielded trolls euphemistically called "ID critics", but also from the "management" (if one can call it that, given the jungle-like atmosphere). Whatever they're doing over there at ARN, it seems to have very little to do with substantively discussing the issues.

    Genie and I were two of the only ARN posters who had the guts to use our real names - so did a few of those who joined us there from this board - and we only started posting there in self-defense because I was being viciously slurred behind my back. Unfortunately, we rapidly learned that the place is a superconducting troll magnet that deceptively calls itself an "ID-friendly forum" while appointing anonymous, ID-hating trolls as "moderators" for the sake of "fairness" and a "balanced view". To capture the feeling, envision a half-dozen pro-ID posters fighting for their lives on one side of a scale, dozens of closed-minded, dimwitted anti-ID atheists and materialists piled up in layers on the other side of the scale, and the "management" holding both thumbs on the anti-ID side of the scale just to make sure that the trolls feel comfortable and appreciated even when hurling offal like petulant monkeys (a frequent occurrence). Calling such a situation "balanced" is a bit like saying that Osama bin Laden deserves the Nobel Peace Prize...and make no mistake, there are a few participants over there at ARN who would probably say exactly that!

    Anyway, insofar as the price for submitting one constructive pro-ID (or for that matter pro-CTMU) post at ARN is up to ten or twenty snide retorts and a shrug of the shoulders from the "ID-friendly management", you'd have to be a masochist to bother. Don't get me wrong - there are a few nice people at ARN, including a single ID-friendly moderator who now happens to be gone for the holidays (and whose wrists often seem to be bound even when he's there). But they often can't get a word in edgewise, and the vast majority of other participants can be more or less aptly described as atheist-materialist pond scum. Unfortunately, this seems to include a few so-called "theists" who turn on other theists with an eagerness to rival that of the atheists themselves.

    Genie and I are very glad to be out.

    Chris

    Quote
    mbjturner
    Regular Customer
    Posts: 138
    (12/20/02 3:40:30 pm)

    Hi all;

    I got confirmation from Eddie in administration that CML and genie were also suspended, so I accept that as fair. MG was involved, but his posts weren't as down and dirty as ours were, so I don't mind that much that he was 'spared'. My real relief is to discover that it was not some behind the scenes political armtwisting on Langan's part. Maybe the realm of ineffable anonymity is starting to get its s--t back together.

    Date: 2002/12/24 02:32:17, Link
    Author: niiicholas
    Wow.  This just goes to show that everything is relative.

    Date: 2002/12/24 02:39:32, Link
    Author: niiicholas
    Quote (charlie d @ Dec. 20 2002,12:51)
    Yes, nice strategy.  
    According to Wells, if people ignore his arguments on the Icons, it's because they are not able to answer the arguments.
    If they answer the arguments, by showing that Wells is wrong, it's because they have to defend the Icons "at all costs".
    And if they change whatever there is to be changed about the Icons, it's because Wells' arguments were right in the first place.

    LOL, what a smoke seller!

    I noticed recently that the QRB has ended it's free-online-access startup policy (or whatever it was called) and that therefore the Padian and Gishlick review is no longer available to non-subscriber public types...making the various asundry links from Wells FAQs rather useless.

    Could this be remedied, or perhaps QRB will release their papers for free after a year or some such?

    Date: 2002/12/24 03:34:11, Link
    Author: niiicholas
    In the "yes, IDists have in fact argued that IC precludes the existence of precursors with other functions" category:

    Quote

    NO FOREBEARS
    There seem to be no obvious evolutionary forebears in nature, and certainly no fossil record, to explain how such a machine might have been selected for through a series of random mutations in some simpler flagellum-like structures.

    "If you don't have intermediate structures, it could mean one of two things, " Behe said. "Either we just haven't found them, or they are not there. It's a good bet, with these biochemical machines, that they aren't there."


    Nature's diversity beyond evolution
    Debate over 'intelligent design'

    Carl T. Hall, San Francisco Chronicle
    Sunday, March 17, 2002

    Date: 2002/12/24 09:26:59, Link
    Author: pzmyers
    How curious. Did you see this comment from bertvan?
    Quote

    I just received an email from Genie.

    Genie:
    Please remove mine and Chris's name from your post immediately. We have not been "banned"! I will be sending a complaint to the administrator. Please, bertvan, you are not a moderator and it is not your position to report on the moderation of ARN members.

    Bertvan: I thought I saw a post from Askfifi, claiming they were banned. However I feel sufficiently chastised for mentioning it, something that apparently is not “my position to do”. I must have been mistaken. I’ll let Genie’s denial speak for itself - “immediately!“ [Big Grin]

    Genie:
    I have very little time over this holiday season and I do not want to spend any of it in negative interactions. I'm sure you can understand that. I know you are a friend of mturner's but I would appreciate it if you could not mention us in a negative way in the future, particularly not falsely.

    Bertvan: I also here-by give notice that I don’t wish anyone to “mention me in a negative way in the future, particularly not falsely.” How anyone manages to disagree with something I might post, and obey that admonition, I’ll leave each individual to try to figure out for himself.

    Date: 2002/12/24 18:27:43, Link
    Author: Glenn Branch
    Quote
    I noticed recently that the QRB has ended it's free-online-access startup policy (or whatever it was called) and that therefore the Padian and Gishlick review is no longer available to non-subscriber public types...making the various asundry links from Wells FAQs rather useless.

    Could this be remedied, or perhaps QRB will release their papers for free after a year or some such?


    I'll check with QRB after I return from vacation.

    Date: 2002/12/25 05:43:37, Link
    Author: Wesley R. Elsberry
    Evolution's Sweet Tooth

    Quote
    Like icing on a cake, the surfaces of most animal cells are covered with sugars. These molecular sugar chains are capped off by a kind of sugar called sialic acid. While one particular sialic acid - called N-glycolylneuraminic acid (abbreviated as "Gc" in this article) - is found on most animal cells, it is not easily detectable on human cells.

    This is due to a genetic mutation that occurred many years ago, sometime after our last common ancestor with the great apes. All mammals except for humans tend to have about equal proportions of Gc and another sialic acid called N-acetylneuraminic acid ("Ac") in the body. Humans, meanwhile, only have trace amounts of Gc, but double the amount of Ac.

    Date: 2002/12/25 05:54:39, Link
    Author: Wesley R. Elsberry
    Phoenixville School District Addresses Evolution Alternatives

    Quote
    New wording in the Phoenixville Area School District's mission statement is already accomplishing its purpose: provoking discussion of hot-button issues such as evolution alternatives.

    [...]

    The mission statement was altered at the urging of school board vice president, David M. Langdon.

    Langdon had sought a more detailed statement, urging the teaching of "intelligent design" as an alternative to evolution.

    [...]

    Langdon, a software quality-control manager who earned a bachelor's degree in biochemistry at Lehigh University, is a devout Christian and said he believes the Biblical account of creation is literally true. He criticized the way evolution is taught.

    "My opinion is that evolution has some problems with it that the scientific community doesn't want to talk about," Langdon said.


    As John Stear points out, "Creationism is not the alternative to evolution; ignorance is."

    Date: 2002/12/25 13:00:17, Link
    Author: charlie d
    Biochemistry major at Lehigh, uh?  I wonder who Mr. Langdon's advisor was...
    ;)

    Anyway, the statement in question is:
    "critical thinking, along with objective and thorough investigation of data and theories in all areas of study is necessary to ensure the success of the educational program."  

    I am surprised they didn't teach that already in Phoenixville: it sure would have helped Mr. Langdon's get a better critical understanding of creationism!



    Date: 2002/12/26 02:19:56, Link
    Author: niiicholas
    A post from ICSID here:

    Perhaps the reason that Hunter finds the evidence for common descent weak is that he misunderstands crucial points.

    E.g., he has repeatedly alleged, without evidence, that designed objects will produce nested hierarchies.  But it just ain't so:

    Quote

    source

    Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent nested hierarchy. The difference drawn here between "subjective" and "objective" is crucial and requires some elaboration, and it is best illustrated by example. Different models of cars certainly could be classified hierarchically - perhaps one could classify cars first by color, then within each color by number of wheels, then within each wheel number by manufacturer, etc. However, another individual may classify the same cars first by manufacturer, then by size, then by year, then by color, etc. The particular classification scheme chosen for the cars is subjective. In contrast, human languages, which have common ancestors and are derived by descent with modification, generally can be classified in objective nested hierarchies (Pei 1949; Ringe 1999). Nobody would reasonably argue that Spanish should be categorized with German instead of with Portugese. The difference between classifying cars and classifying languages lies in the fact that, with cars, certain characters (for example, color or manufacturer) must be considered more important than other characters in order for the classification to work. Which types of car characters are more important depends upon the personal preference of the individual who is performing the classification. In other words, certain types of characters must be weighted subjectively in order to classify cars in nested hierarchies; cars do not fall into natural, unique, objective nested hierarchies.

    Because of these facts, a cladistic analysis of cars will not produce a unique, consistent, well-supported tree that displays nested hierarchies. A cladistic analysis of cars (or, alternatively, a cladistic analysis of imaginary organisms with randomly assigned characters) will of course result in a phylogeny, but there will be a very large number of other phylogenies, many of them with very different topologies, that are as well-supported by the same data. In contrast, a cladistic analysis of organisms or languages will generally result in a well-supported nested hierarchy, without arbitrarily weighting certain characters (Ringe 1999). Cladistic analysis of a true genealogical process produces one or relatively few phylogenetic trees that are much more well-supported by the data than the other possible trees.

    The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of "cladistic hierarchical structure" (also known as the "phylogenetic signal") in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al. 2001; Klassen et al. 1991).


    He also severely misunderstands convergence.  Convergence can only produce functionally-relevant similarities, because that is all that selection can "see".  Homologies, i.e. similarities between systems that are not necessary for functional similarity between systems, are what allows paleontologists to easily distinguish between these placental wolf and marsupial "wolf" skulls that cre8tionist posted in another thread:



    I invite readers to go to The Thylacine Museum and look at the side-by-side comparison of 'wolf' skulls (with cool magnifier lense).

    The caption reads:

    Quote

    Portrayed here are side-by-side images demonstrating the anatomical differences between the skulls of the Grey wolf (Canis lupus) and the thylacine (Thylacinus cynocephalus).  In the dorsal view, note that the thylacine has a much broader forehead than the wolf, and there are differences in the design of the zygomatic arches and brain case.  Also, the rostrum (snout) of the thylacine is far narrower than that of the wolf, and the thylacine has proportionately larger eye sockets which are rather more square in shape.  In the ventral view, one can easily see the great differences in dentition that  readily distinguish the two species as being members of distinct mammal groups.  The dentition of both species will be represented in greater detail on the following page.  Also visible in the ventral view is the thylacine's maxillary palatal vacuity (the two parallel openings in the roof of the mouth).  This is a feature that the wolf and other placental mammals do not have.


    ...on the next page...

    Quote

    Here I show some diagrams which I have prepared to illustrate the extreme difference in dental anatomy which exists between the thylacine and its placental counterpart, the wolf.  The images are portrayed at life size.  Although there are also a number of notable differences in post cranial skeletal structure between the thylacine and wolf, I felt that the dentition represented one of the most striking dissimilarities.  As you can easily see in the image of the maxilla, the thylacine has 8 top incisors, whereas the wolf has only 6.  In the mandible however, the thylacine and wolf have an equal number of incisors.  Another major difference is the presence of a specialized shearing tooth, the carnassial, in the wolf.  This tooth design is a trademark of the wolf and other members of the placental mammal family Carnivora.  Also make note that unlike the wolf, the thylacine lacks large grinding surfaces on its molars.  Altogether, the wolf has a complement of 42 teeth, and the thylacine 46.


    I can't post the images here because they are copyright protected, but the differences in the tooth-numbering are dramatic.

    All commonly-sighted cases of "uncanny convergence" in biology turn out, on investigation, to be externally impressive but superficial when you get down to details.  This is notably different from the kinds of things that have happened in aircraft design, e.g. the addition of (the same) transponders, GPS units, computers, TV screens, etc., to planes of widely different models.

    This has been pointed out many times over the years, so I'm not sure why these cases still get seriously cited.

    yersinia

    PS: There is also the interesting question of:

    If the hypothesized IDer decided that there needed to be some carnivorous canine-type critters in Australia, why bother with all the genetic engineering that would be required, when a simple aboriginal boat sufficed to bring dingos to Australia only ~15,000 years ago?

    Such ID puzzles are absolutely ubiquitous in biogeography.  To me they indicate strongly that whatever creativity made these wonderful adaptations was, for some odd reason, highly constrained so that "design information" could not be transmitted across deep water barriers and instead had to be re-invented from scratch each time the adaptation was "needed" in particular locations.  Strangely, such geographical constraints did not apply to flying birds, sea mammals, and other easily-dispersed organisms.

    If you can find an ID theory that can explain this (and "the designer's actions are  mysterious" is not an explanation), I'll eat my hat.  If on the other hand you give natural selection the credit for these instances of creativity, then I guess natural selection can "design" things after all, and quite skillfully too...

    Date: 2002/12/26 14:19:39, Link
    Author: niiicholas
    Quote

    You argue that designed objects will not produce nested hierarchies. I already gave the aircraft example, let's consider the example a bit further. Consider all machines that use gasoline as a fuel. Within that set you have various subsets, such as those that move and do not move. Of those that move, some fly, others move along the surface of the earth. In the latter, you have various numbers of wheels, such as 2, 4, 6, 8, …, and a few outliers with odd number of wheels. Of those with 4 wheels, you have different ratios of interior volume to overall size (eg, vans have a higher ratio). Of those with lower ratios you have different carburetors (fuel injection for sports cars), and so forth. I am contriving this example off the top of my head, but perhaps you can explain why this cannot be a case of a nested hierarchy. In support of your claim you pasted a few paragraphs from a web document which does not support your claim. The web document is discussing the relationships, across designed objects, of characters which have no influence on performance or are constant over the entire set. What we have called in this thread "arbitrary design decisions."


    Did you even read the quote?  The very first sentence pointed out that anything can be subjectively classified into a nested hierarchy if you arbitrarily pick characters.  This is exactly what you do above.  The point is that your "tree" would not be produced by an analysis of other subsystems of gasoline-driven machines, e.g. tires, liscense plates, GPS units, radios, onboard computers, whatever.  On the other hand, in biology there are a large number of systems (genes, limbs, skulls, etc.) that produce highly-congruent nested trees.  Other fairly similar examples are things like languages and scribe-copied documents, both of which are produced by a process of copying and gradual modification (although in these cases the possibility of lateral transfer is somewhat higher than it is in eukaryote biology).

    As for web references, if they cite the primary literature then you either have to show they are mis-using the literature, or that the literature itself is wrong.  Theobald cites a large number of papers discussing the difference between arbitrary and natural hierarchies -- designed objects like cars and planes produce the former, copied & gradually modified objects (like languages, scribe-copied documents, and...organisms) produce the latter.

    I'll include some of Theobald's refs so that interested parties can look them up:

    Archie, J. W. (1989) "A randomization test for phylogenetic information in systematic data." Systematic Zoology 38: 219-252.

    Faith, D. P., and Cranston, P. S. (1991) "Could a cladogram this short have arisen by chance alone?: on permutation tests for cladistic structure." Cladistics 7: 1-28.

    Farris, J. S. (1989) "The retention index and the rescaled consistency index." Cladistics 5:417-419.

    Felsenstein, J. (1985) "Confidence limits on phylogenies: an approach using the bootstrap." Evolution 39: 783-791.

    Hillis, D. M. (1991) "Discriminating between phylogenetic signal and random noise in DNA sequences." In Phylogenetic analysis of DNA sequences. pp. 278-294 M. M. Miyamoto and J. Cracraft, eds. New York: Oxford University Press.

    Hillis, D. M., and Huelsenbeck, J. P. (1992) "Signal, noise, and reliability in molecular phylogenetic analyses." Journal of Heredity 83: 189-195. PubMed

    Ringe, D. (1999) "Language classification: scientific and unscientific methods." in The Human Inheritance, ed. B. Sykes. Oxford: Oxford University Press, pp. 45-74.

    Quote

    You seem to be extrapolating from the discussion given there on arbitrary design decisions to conclude that designed objects cannot produce nested hierarchies. Perhaps I am misunderstanding you.


    Of course designed objects can produce just about anything, because a hypothetical designer can always be invented who wants to produce X for goodness-knows-what reason.  This is a major problem for ID "theory", no predictions are made unless some specifications are put on the hypothetical IDer, and no one wants to even hypothesize any such specifications (you don't have to have foreknowledge of the designer, just a hypothesis...this is how science proceeds).

    But you said that ID predicts congruent phylogenies.  I am arguing that this is not established or even likely based on what we know about designed objects.  

    Quote

    Is there more than one cost function?


    This section seems like you are trying to say something about how the designer would design things so that congruent phylogenies resulted due to functional constraints, or something.  But what you have to explain, in order to explain things as well as current theory, is how all of those arbitrary characters (many of them, such as DNA degeneracy, absolutely known to be functionless differences) produce statistically the same nested hierarchical trees!  If you can't do that then there's no reason to switch from the current explanation.

    Quote

    Can homologies arise from different genes?

    You next go on to discuss homologies, but I'm not sure what the point is. You state that paleontologists can easily distinguish between the placental wolf and marsupial wolf skulls, as though I had stated otherwise. Of course they can, they can also easily distinguish between the bat's wing and human hand, but this does not prevent the pentadactyl pattern from being claimed as evidence for evolution. You pasted a figure of the two skulls which appear highly similar yet are supposed to have evolved independently. You say the similarities are "superficial." I have heard this said many times before, but how is it that these similarities are superficial whereas homologies such as the pentadactyl pattern, which exhibit a large degree of variance (compare the porpoise, bat and horse) are significant?


    Because the homologies all correlate with each other to a high degree of statistical confidence, producing a Linnean-type classification, whereas those features that you would expect would be the important features (as revealed by you example of classification of gas-driven machines based on function, or John Bracht's imaginings that amino acid sequence won't turn out to be largely degenerate with respect to structure and function after all) in fact don't correlate with the Linnean-type classification.

    If the genes and proteins of penguins, sharks, dolphins, seals, etc. grouped together, and bats and birds grouped together, etc., then you'd have an argument, but they don't.  This is a massive mystery from an ID perspective but easily explained by evolution.

    Quote

    We should also note that homologies can develop from different genes, or otherwise follow different development patterns.


    This is an argument of Wellsian origin and depends largely on obfuscatory use of quotes and words like "different" (and Wells' unique views about the unimportance of DNA, which are rebutted in detail this ISCID thread).  Similar genes perform similar developmental functions a very long ways back, e.g. Hox genes and front-to-back patterning:




    Quote

    An interesting challenge?

    Finally, you issued a challenge which sounded interesting but, forgive me if I am slow this morning, I had trouble following. You wrote:

    quote:
    --------------------------------------------------------------------------------
    If the hypothesized IDer decided that there needed to be some carnivorous canine-type critters in Australia, why bother with all the genetic engineering that would be required, when a simple aboriginal boat sufficed to bring dingos to Australia only ~15,000 years ago? -- Yersinia
    --------------------------------------------------------------------------------

    Can you elaborate a bit?


    In short:

    You and Cre8tionist have proposed that convergences like the placental/marsupial wolf are better explained by intelligent design for the same function.

    I pointed out that rather than the "same" design being transplanted, it looks more like it was independently invented by modification of different starting points, and that the convergence is superficial in that the true relationships of the organisms remain clear based on homologies.

    But, if you are going to maintain the hypothesis that ID accounts for the complex carnivory specializations of wolves and thylacines, you have to explain why it appears that the design wasn't transplanted, but rather re-invented.  If a designer wanted carnivores in Australia, it would have been much easier just to put some dogs on a boat, as the stone-age Aborigines did, rather than do all of that complex creative genetic engineering twice in two different ways.

    Ditto for carnivorous marsupial "cats" in isolated south America, cacti vs. south African succulents, lemurs in Madagascar, Hawaiian honeycreepers, and of course Darwin's finches.  Why should independent design correlate so well with geographical isolation?  Did the IDer not know of boats?

    Date: 2002/12/26 16:57:06, Link
    Author: niiicholas
    I think I started a thread on this back in before The Great Server crash; there was a PNAS paper on yucca moth mouthparts, or something.

    Here is another case:

    Source: http://www.sciencedaily.com/releases/2002/12/021226071202.htm


    T.o. discussion: here

    Quote

    UC Riverside Study Suggests Placentas Can Evolve In 750,000 Years Or Less; Guppy-Like Fish Help Fill In The Gaps In The Evolution Of Complex Organs

    RIVERSIDE, Calif. -- Dec. 20, 2002 -- Evolutionary biologists have long been intrigued by how natural selection -- the process in nature by which the organisms best suited to their environment are the ones most likely to survive and leave descendants -- gradually creates a complex organ such as the eye, heart, or kidney.
    Now UC Riverside biologists, David Reznick and Mark Springer, along with Mariana Mateos, research associate at the University of Arizona, present in the journal Science a model system for studying the evolution of complex organs. They focus on the placenta (the organ that provides nutrients for the fetus and eliminates its waste products) in the fish genus, arguing that placentas serve as a good stand-in for complex organs whose histories have eluded evolutionary biologists.

    The dilemma posed by complex adaptation, which are organs of extreme complexity that have evolved through the action of natural selection, is that these organs demand contributions from a large number of adaptations at individual genetic loci to function properly. Darwin addressed the difficulty of complex adaptations with his treatment of the evolution of the eye. "He had to use organisms from different classes," explained Reznick, "because there isn't a living group of related organisms that have all the steps for making an eye." The organisms in Darwin's model are, however, distantly related to one another.

    Darwin proposed that complex eyes could have been formed with a succession of photosensitive organs, each a bit more complex than its predecessor and each favored by natural selection because of the advantages that the possessor received. Visualizing such a process would be easiest if steps in this sequence were preserved in closely related living organisms; but no such sequence exists for eyes because the intermediate stages have been lost through extinction.

    Reznick and his colleagues studied guppy-like fish in the genus Poeciliopsis. They report that placentas have evolved independently three times in closely related Poeciliopsis species. Other species in the genus lack placentas, and some have partial maternal provisioning via tissues that may be precursors of placentas. "Thus the fish present the full trajectory of steps involved in the evolution of this organ," said Reznick. "It allows researchers to examine what's been added, or what has changed, and eventually identify the genes associated with the evolution of each trait."

    The study by Reznick and colleagues first argues that the placenta is a complex organ, in the sense that it represents a composite of many adaptations and is controlled by many genes. "The origin of complex, novel organs plays a key role in evolution since they often define new categories of animals, such as the placenta for placental mammals," said Reznick. "They are also a source of controversy both within evolutionary biology and between evolutionary biology and the religious public. This is because their origin unfolds on a time scale considerably longer than human existence, so the process must be inferred indirectly."

    In the Science paper, the researchers show that: 1) Fish in the genus Poeciliopsis have placentas in various stages of evolution, and 2) There are clusters of closely related species that either have highly evolved placentas, placentas in intermediate stages of evolution, or no placentas at all. These provide ideal material for studying how such complexity evolves.

    The researchers then use the combination of molecular and geological data to yield estimates for how long it took the placenta to evolve in some lineages. Based on collected data, they find that the shortest time interval between a poeciliid species with a placenta and its last common ancestor without one was 750,000 years, suggesting that placentas can evolve in 750,000 years or less.

    "This result demonstrates that complex organs can evolve rapidly, on the same scale as predicted by a theoretical estimate of 400,000 years for the evolution of the eye," said Springer.

    Reznick has been collecting comparative life history data for around 15 years. For the study, he traveled around Latin America collecting the fish, going to museums to work with their collections, and then doing the appropriate dissections at UC Riverside. Several UC Riverside undergraduate students contributed to the dissections. Reznick also worked on live fish in his laboratory on campus.

    The molecular work for the study was done by Mateos over the past two years. Springer did the phylogenetic work for the study. His statistical methods helped the researchers make inferences about how traits have evolved from the combination of DNA sequence data (collected by Mateos) and the descriptions of modes of reproduction (generated by Reznick).

    The UC Riverside Department of Biology serves three main functions: undergraduate instruction, graduate education, and research in basic biology. The department conducts research and teaching in many areas of life science including cell biology, conservation biology, developmental biology, ecology, evolution, molecular biology, physiology, and population biology. The department is part of the College of Natural and Agricultural Sciences, a multi-departmental unit dedicated to instruction and basic research in the physical and life sciences, and also to 'mission-oriented' applied research in the agricultural sciences. The Biology major is a popular undergraduate major on the UC Riverside campus, with approximately 1000 students currently enrolled. Biology also provides much of the undergraduate instruction for majors in other life science departments and other science majors.




    Date: 2002/12/26 18:14:50, Link
    Author: Dr.GH
    I am having a weird case of deja vu.  The embryonic surfperch ( Embiotocidae ) have huge fins which are bright red with blood.  These have long been recognised to function in the exchange of nutrients and gases with the mother.

    Date: 2002/12/26 19:34:24, Link
    Author: niiicholas
    Another post:

    Well, I am glad that Cornelius concedes that ID-design is different from regular design inferences, in that while we always have (even if approximate) models for the designer in the cases of forensics, archaeology, and even SETI, no such model shall be forthcoming for ID.  Therefore we can expect nothing in particular if ID is true, and thus have no way to strengthen or weaken our confidence in the hypothesis.

    I say this somewhat in jest, because Hunter in fact only uses the "there ain't no hypothetical model for the designer" argument as a defense, in fact he makes a few characterizations at times.  Things have to "make sense" with regard to some unspecified criteria:

    Quote

    With regard to the complex carnivory specializations you mention, ID is more interested in understanding the function and reason (or perhaps lack thereof) behind the different designs, not trying to justify the actions of the designer. So your challenge, as it stands, is fairly weak. To beef it up you need to show that those different specializations are unnecessary or absurd. As I said to RBH, the way to falsify design is:

    1) Show that the designer's actions make little sense,
    2) Show that naturalistic mechanisms are sufficient to explain the origin of species,
    3) Show that the preponderance of scientific evidence/analysis strongly points to evolution.

    Any of these is sufficient to falsify ID, or at least effectively falsify it by rendering ID redundant.


    The "origin of species" is a somewhat different topic and can be address elsewhere; I expect that if the usual examples of observed speciation or inferred very-recent-speciation were cited, he would back up the goalposts to the level of genus, family, order, phylum, etc.  But that's another thread.

    I think, though, that #1 and #3 are pretty easily satisfied by the Thylacine example:

    Quote

    Sarcastic and rhetorical barbs about how the designer didn't create according to your personal sensibilities will only backfire, but a serious and plausible challenge on #1 will work for you. For example, in this example you bring up, show that one of the specializations is unquestionably superior to the other, even if transplanted into those other species in that other environment and niche.


    Well, how's this: the introduction of the dingo appears to have quite rapidly caused the extinction of the thylacine, which was extinct from mainland Australia before Europeans arrived.  Thylacine species persisted for tens of millions of years in the Australian fossil record, into the period of human habitation, and yet some stone-age boat people (unintentionally) killed them off by transplanting an apparently superior design, the dingo.

    The only place that thylacines hung on until the 1900's was in the isolated island of Tasmania, where dingos and bounty hunters reduced their population to fatally low numbers by the 1930's.

    (one of several web sources on this)

    As if this wasn't enough, this appears to be a general pattern with only a few exceptions: placentals have proven to be superior competitors for the same ecological niches, which is why there are precious few marsupials in South America (formerly an Australia-like place before the Panamanian isthmus connected it to North America), and why so many marsupials are endangered in Australia, while things like feral rats, cats, rabbits, and dogs (dingo) are thriving wildly.

    By any standard of "good design", it appears that the hypothetical IDer's actions "make little sense": to carefully craft all of these marsupial species for parallel ecological niches on separate landmasses, let them be fruitful and multiply for millions of years, followed by prompt extermination once tectonic accidents or stone-age boats allow apparently superior designs to invade.

    Date: 2002/12/27 00:08:00, Link
    Author: Wesley R. Elsberry
    From an ISCID thread:

    Cornelius G. Hunter wrote:

    Quote
    I don't think we have scientific reason or evidence to believe complex systems such as echolocation or the DNA code could have evolved.


    Hmm.  I don't think that we have scientific reason or evidence to indicate that echolocation is due to anything other than evolutionary processes.

    There are several different approaches to biosonar.  The examples of bats and odontocetes are pretty sophisticated, but those of oilbirds and honey badgers are relatively simple.  Even humans can use hearing for directional cues, as several aids for the blind demonstrate.

    So I'd like to know what, specifically, puts the dolphin biosonar system (the one I'm most familiar with) outside the scope of evolutionary process.

    Wesley



    Date: 2002/12/27 00:54:53, Link
    Author: niiicholas
    It appears that the thread has devolved into several subtopics that are not strictly related to phylogenetic tree (non)congruence.  Hunter's non-congruence reasons for why we should doubt the common descent of (say) Animalia appear to have been rebutted, as he is now raising numerous different issues that would take their own threads to address:

    - Arguments about genes/development/homology
    - Can speciation occur by natural processes?
    - Can mutation+selection produce creative evolution?

    I think that these questions are perhaps the real reasons that Hunter doubts common descent of animal species, not because the phylogenetic evidence is against it.

    I think that the thylacine example is worth cogitating on further regarding ID vs. evolution, as it is not an isolated event but rather an instance of a very common phenomenon in biology: in geographically isolated regions, relatively unrelated organisms adapt to fill quite specific niches, but do it by "reinvention" that always differs in the details.  Information transplants are not seen.  

    I would humbly note that this is what Darwin realized about the Galapagos species of turtles (and later, finches) once the taxonomists got to work on them back in Britain.  He and many other world travellers have made remarks like "it is as if different creators acted in different places" or words to that effect.

    When convergent organisms are transplanted by humans or natural events, a very common occurence is extinction of the native species.  It's almost like whatever the creative force is draws its power from the size and time of isolation of the land mass in question...

    Date: 2002/12/27 08:22:29, Link
    Author: Wesley R. Elsberry
    Cornelius G. Hunter wrote:

    Quote
    I am not familiar with the dolphin's biosonar, but I am somewhat familiar with human-made radar and sonar systems. For those who may not be familiar with the bat's echolocation system, we should briefly explain that it maps out objects around it as small as a mosquito by sensing the echoes of its own squeaks. Its squeaks are well beyond the range of human hearing and are emitted at up to 2,000 times per second. Next it determines both range and direction to the mosquito by sensing the echo while filtering out echoes from the squeaks of nearby bats. Anyone familiar with today’s sonar or radar systems knows the immense complexity involved with such systems: the problems of sensing the echo in the presence of the transmitted signal which can be billions of times stronger, of filtering out spurious signals such as echoes of older transmissions, of combining the echo information with knowledge of your own motion, and so forth. Yet the bat’s detection abilities are superior to those of the best electronic sonar equipment.

    Evolution, on the other hand, has been shown to be able to make rather limited modifications to multi cellular organisms. These might include resistance to pesticides, minor morphological changes (eg, beak size and shape), more major morphological changes in the case of breeding (eg, dogs), coloration, etc. My list here (off the top of my head) is not close to being complete and I do not want to short-change evolution, but I trust I'm not missing anything too significant. My point is merely that, relative to the sorts of changes required to create a biosonar system, the observed evolutionary changes are rather minor. It is also worth noting that the observed evolutionary changes are made possible by a complex cellular machine that evolution cannot explain, aside from speculation.

    I think it is fair to say that there does not exist empirical evidence supporting the claim that biosonar systems could have evolved. I would say it is, as you put it, "outside the scope of evolutionary process," at least the known process. The idea that it evolved likely arises from a prior commitment to the truth of evolution rather than biosonar systems appearing to have evolved.

    It is probably worth exploring the question of whether it is at least a reasonable conjecture that such systems could have evolved? Personally, I would require any such attempt to include a fairly detailed explanation of the steps involved, where each step

    (i) consists of changes of the type and magnitude that are empirically observed, and
    (ii) confers increased fitness, or is reasonable for us to imagine given what we know about population genetics and neutral mutations.

    Also, I would require that the mutations required, in total, pass a likelihood test. That is, given

    (i) the number of bat populations and the number of years available, and
    (ii) the immense design space involved,

    is the evolutionary pathway anything more than astronomically unlikely. I feel these requirements are reasonable, and I have not seen any explanation that comes close. And I do not think it is because they are trivial and therefore taken for granted. In fact, correct me if I am wrong, I suspect we do not even have all the details of the bat's system so as to know what the required mutations are in the first place, let alone their individual effects at each step in the process.


    This appears to be a classic argument from incredulity.  It echoes early reactions against Donald Griffin's discovery of echolocation via ultrasound in bats, where is was considered inconceivable that such lowly creatures could have technology which was then new to human technology.

    I'm going to discuss dolphin biosonar for two reasons.  The first is that dolphin biosonar is the sort I am most familiar with.  The second is that Hunter's claim was about biosonar generally, not limited to bats in particular.

    The first issue to note is that the receiving system in dolphins need not be considered to be out of reach of evolutionary process.  I'm going to use human auditory performance as a becnhmark, since humans are a well-studied non-echolocating mammal with fairly generic capabilities.  One piece of evidence concerns the performance of humans given a biosonar task.  A study by Fish et alia (1976) demonstrated that human divers could perfrom about as well on a target discrimination task as did the dolphins, when the humans were given the dolphin biosonar signal shifted into the range of human hearing.  This indicates that even a rather general mammalian auditory system (as seen in humans) is sufficient to the task of deciphering biosonar information.  It also indicates that the general mammalian auditory system is an adequate starting point for an evolutionary process ending in biosonar capability.

    What changes to the general mammalian auditory condition must occur to derive a dolphin-like system?  Either of two parameters in cochlear construction will extend frequency response on the high end: increase the stiffness of the basilar membrane or reduce the width of the basilar membrane.  This falls into the category of "minor morphological change".  Dolphin cochleas have slightly fewer turns than in humans, but a bit over double the variation in width along the basilar membrane.  The minimum width of the dolphin basilar membrane is a bit less than a third of that of the human basilar membrane.

    Neurologically, dolphin basilar membranes have about the same numbers of inner and outer hair cells as seen in humans.  There are some differences in the brain, though.  The auditory cortex in dolphins is enlarged relative to that seen in humans.  Dolphins and bats each have lost the lateral superior olive, a structure implicated in coordinating eye movement with auditory cues in humans.  Dolphins are known to process clicks differently than tonal stimuli; this is something that is not seen in humans.  Dolphin evoked potentials show a faster response to click stimuli than to tonal stimuli.

    Psychoacoustics also demonstrate differences in quantity rather than quality between dolphin and human hearing.  Johnson's 1968 study on temporal auditory summation in dolphins showed that dolphin and human time constants were close in the range of 0.5 to 10 kHz.  Critical ratios are similar for dolphins and humans, although critical bandwidths are larger in the dolphin than in humans by a little more than double.  For frequency discrimination, dolphins perform similarly to humans, but at a higher frequency range.  Dolphin sound localization capabilities are also similar to those in humans.

    I still don't see any show-stoppers in what we know about the dolphin receiving system's characteristics.

    That leaves the transmitting system for possible show-stopping adaptations.  I think I'll write a post on that separately.

    Wesley

    Date: 2002/12/27 08:34:19, Link
    Author: Wesley R. Elsberry
    Archived post from the ISCID thread:

    I'll keep my comments here brief since the issue of biosonar is pretty tangential to the thread topic.

    Hunter's reply lacks the specificity that I requested.  The objection seems to be raised in a general, rather hand-wavy way.  I'd also caution against trying to take cues from human technology for whether particular tasks are difficult for biological systems.  As we know from computer science, many tasks that are easy for animals are difficult for computers, and vice versa.  The application of accurate mathematics is a snap for computers, but hard for humans.  Machine translation of human languages is a classic case of something that is easy for humans (who have both of the relevant languages), but has turned out to be very tough for the computers.

    I've taken my continued discussion of biosonar in dolphins to  another thread so that I won't be cluttering up this thread with it.

    Wesley

    Date: 2002/12/27 10:36:51, Link
    Author: Wesley R. Elsberry
    Cornelius G. Hunter wrote:

    Quote
    I'm not sure how I could have been more specific. I discussed the fact that the evolution of biosonar systems is significantly beyond the observed and known evolutionary process, I discussed the complexity of the process in general, and I laid out the requirements for establishing the reasonableness of the hypothesis. I gave 3 specific requirements: (i) lay out steps which are of observed type and magnitude, (ii) steps must not degrade fitness, and (iii) mutations required must pass a likelihood test. What more could I provide, especially given the lack of specificity in the available evolutionary conjectures on this hypothesis? Am I supposed to derive hypothetical evolutionary scenarios for you and then find point out their weaknesses when no such scenarios exist in the first place? If you find my response "hand-wavy" then you must find evolution to be far more so.


    One way to be more specific, overlooked by Hunter, would be to name an adapatation necessary to dolphin biosonar and present an argument as to why it could not arise via evolutionary process.  This specific form of argument is notable by its absence from Hunter's discussion.  While I disagree with Bill Dembski's mode of argument and conclusions concerning the E. coli flagellum, at least he made an attempt at a specific argument in that case.

    It is nowhere near a "fact" that "the evolution of biosonar systems is significantly beyond the observed and known evolutionary process".  Begging the question is not a valid argument.  I've already pointed out simple examples of biosonar, which even if we agree to disagree concerning the examples of dolphins and bats remain as an impediment to the scope of Hunter's claim.

    I'm not the one making universal claims about what is not possible.  That would be Hunter.  So far, though, I haven't seen anything that would cause me to think that the biosonar of dolphins poses a difficulty for evolutionary process.  Nothing in Hunter's discussion so far changes that.

    Quote
    Obviously, conjectures about the future can work both ways, and what we are left with is our current list of evidences and analyses. These do not bode well for evolution.


    I think that we will have to agree to disagree on that conclusion as well.  It looks like a non sequitur to me.

    Charles Darwin wrote:

    Quote
    Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject my theory.


    Wesley



    Date: 2002/12/27 11:39:22, Link
    Author: ExYECer
    Cornelius states that

     
    Quote

    Unfortunately, evolution has always relied on #1 to establish itself as a scientific fact.
    It seems that Cornelius may be unfamiliar with the scientific evidence supporting evolution if he believes that evolution has ALWAYS relied on #1 to establish itself as a scientific fact.

    Reality will show that it is #3 and #2 which are the methods through which science has established evolution as a viable theory. I am somewhat surprised to see Cornelius make the statement and others such as    
    Quote
    To me it is clearly flawed, and it is little wonder that evolutionists dwell so much on #1. It clearly is the motivation for the theory.
    Which suggests to me that he has not really looked at the scientific evidence supporting evolution. It may be helpful if Cornelius could help us understand how he reaches conclusions like the ones above or    
    Quote
    I'm merely claiming that the scientific evidence points away from this.
    What scientific evidence points away from naturalistic pathways?

    If Cornelius really believes that God and thus ID fails if we can show that naturalistic pathways are sufficient or that natural pathways explain the preponderance of evidence then for all practical purposes we can consider ID to be refuted. ID by itself according to Cornelius' definition seems to be providing us with nothing more to understand the world around us, it merely makes claims based on a religious motivation without attempting to provide for a better explanation than that provided by scientific inquiry. And for good reasons since I do not believe that ID in this format can do much to compete with science.
    ID seems to require that we ignore the vaste amounts of data that support #2 and #3 while focusing on the strawman of #1. If Cornelius were serious about the statement that    
    Quote
    ID is using all our knowledge to identify evolution as flawed.
    then he would not have focused on making claims that evolution focuses on #1. Hundreds, thousands of papers on evolutionary mechanisms and theory would put significant doubt on the validity or even supportability of Cornelius' claims.

    Cornelius also states that
     
    Quote

    We had a good and fruitful discussion. My hunch that evolution is quite flexible vis-à-vis these phylogenetic results, if anything, were corroborated
    seems to ignore the strengths of the phylogenetic results vis-a-vis common descent and seems to focus on the fact that scientific theory can adapt to our increasing knowledge. So far the arguments seem to not really focus on scientific arguments but rather on hand waving, strawmen arguments while ignoring the vaste amounts of evidences supporting the fact of evolution.

    In a previous posting Cornelius confused my comments about nested hierarchies with correlated characteristics. Nested hierarchies are als correlated but correlated characteristics need not be hierarchical.

    Finally Cornelius wondered why I made the following statement

    [quote]
    We should be careful not to mix our faith and science, since both will suffer. -- Francis
    [quote]

    Cornelius states that:

    "This obviously does not derive from science nor the Scriptures, so I'm not sure why you say this."

    If science has to give way to our theological thinking then both science and theology will suffer. Of course science and theology can live together in their own realm but when it gets misapplied like for instance found in many YEC approaches, it becomes a destructive force to science and religion. As an ex-YEC-er I have seen much of this.

    In Christ
    F

    Date: 2002/12/28 09:38:18, Link
    Author: Wesley R. Elsberry
    From an ISCID thread:

    Cornelius G. Hunter wrote:

    Quote
    Wesley:

    Respectfully, I think it is important to be clear and consistent on who is making what claim. Let me clarify that my position on the evolution of biosonar systems and macro evolution in general is that such evolution is unlikely and does not constitute a good scientific theory. I am not making a universal statement as you suggest. In fact, my comment which you originally responded to, and which you quoted in your first post was that:


    quote:
    --------------------------------------------------------------------------------
    I don't think we have scientific reason or evidence to believe complex systems such as echolocation or the DNA code could have evolved.
    --------------------------------------------------------------------------------

    It is not clear to me how you concluded that my claim is that such evolution is impossible. It is worth pointing out, however, that this amounts to a shifting of the burden of proof, and is a common mode of argument. In fact, it seems that in every extended discussion of this sort I am, at one point or another, asked to provide evidence that evolution is false (as though the theory is true until proven false), or more commonly, as here, am told that this is my claim and that I've failed to support it. This is so common, it is not surprising that Darwin used it:


    quote:
    --------------------------------------------------------------------------------
    If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case. – Darwin, Origin
    --------------------------------------------------------------------------------

    Darwin allowed that if the skeptic could find a complex organ that evolution could not produce then the theory would be disproven. But it would be impossible for a skeptic to prove that evolution could never create complexity, for that would be tantamount to proving a universal negative.

    You write:


    quote:
    --------------------------------------------------------------------------------
    One way to be more specific, overlooked by Hunter, would be to name an adapatation necessary to dolphin biosonar and present an argument as to why it could not arise via evolutionary process. -- Wesley
    --------------------------------------------------------------------------------

    It is ironic that, on the one hand, while I am not making a universal claim you criticize me for doing so, but then on the other hand you suggest this is what is required for me to criticize evolution effectively. What you suggest is, of course, precisely the requirement that Darwin laid out, and it places the critic in an impossible position. And importantly, it makes science vulnerable to any idea that cannot be falsified.

    You write:


    quote:
    --------------------------------------------------------------------------------
    It is nowhere near a "fact" that "the evolution of biosonar systems is significantly beyond the observed and known evolutionary process". Begging the question is not a valid argument. -- Wesley
    --------------------------------------------------------------------------------

    It would help me if you could point out how I was begging the question, as I certainly try to avoid fallacious arguments. I thought I was merely pointing out the facts of the situation when I said that :


    quote:
    --------------------------------------------------------------------------------
    My point is merely that, relative to the sorts of changes required to create a biosonar system, the observed evolutionary changes are rather minor. … I would say it is, as you put it, "outside the scope of evolutionary process," at least the known process.
    --------------------------------------------------------------------------------

    How is this begging the question?

    You write:


    quote:
    --------------------------------------------------------------------------------
    I've already pointed out simple examples of biosonar, which even if we agree to disagree concerning the examples of dolphins and bats remain as an impediment to the scope of Hunter's claim. -- Wesley
    --------------------------------------------------------------------------------

    I'm not following here. Can you clarify what you see the implications are of the simple examples of biosonar?

    I like your quote from Darwin:


    quote:
    --------------------------------------------------------------------------------
    Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject my theory. – Darwin
    --------------------------------------------------------------------------------

    In other words, we need to consider all the factors, such as the explanatory power, supporting evidence in addition to the problems. I could not agree more. In fact, it is the many problems with the positive evidences, as set forth by evolutionists, which caught my interest originally. The problem of complexity is less interesting as it is fairly obvious.

    --Cornelius


    Pointing out a sentence that does not contain a universal claim doesn't exculpate one from defending a universal claim made elsewhere.  Here's one from Hunter:

    Quote
    I think it is fair to say that there does not exist empirical evidence supporting the claim that biosonar systems could have evolved.


    That's a universal claim.  It's also a negative claim, which means that if any evidence exists which supports evolvability of biosonar, the claim is false.

    So Hunter's universal claim is false, because there does exist empirical evidence that biosonar systems could have evolved.  I've already mentioned the simple systems of oilbirds and honey badgers, which Hunter has thus far avoided taking up.  I've also gone into some detail concerning comparing the dolphin receiving system with that of a general non-echolocating mammal, Homo sapiens.  These represent empirical evidence that biosonar is not "beyond the scope of evolutionary process".

    I can understand Hunter's haste in trying to frame up a critic in an attempt to avoid the consequences of making such an egregiously false claim.  However, I'm not the type to take those sorts of shenanigans lightly.  Hunter's claim that no evidence exists to support the evolvability of biosonar is one that he bears the burden of proof for.  It may have been unwise of Hunter to put himself in the position of proving a universal negative, but he has no one else to blame for it.

    Perhaps the reason that sooner or later Hunter gets called upon to prove evolution false is simply that he makes such claims, and critics naturally call upon Hunter to either support or retract them.

    The "sorts of changes required to produce a biosonar system" are "relatively minor" and fully within the scope of evolutionary process, as far as I can tell.  Hunter's statement is begging the question because he is taking as a fact something that has not been established.  I suppose Hunter could respond that that is merely the use of a false premise instead, but in either case his argument is hosed.

    Simple examples of biosonar imply that Hunter's claim that "no evidence exists" to support the evolvability of biosonar is simply wrong.  If evolutionary process can explain simple biosonar, Hunter's universal is false.  Further, the facts of dolphin biology do support the possibility of dolphin biosonar being derivable from a generalized mammalian condition.

    Hunter's response to the Darwin quote I provided seems not to touch the issue identified by Darwin.

    Wesley



    Date: 2002/12/28 12:09:54, Link
    Author: Bebbo
    Quote (dayton @ Dec. 24 2002,07:30)
    Thank you, JXD.  Im' glad we now we know how Chris Langan really feels about ARN.  :)

    The curious thing is that Langan's partner was using a nom de net of Genie, not her real name, contrary to what he says.

    I think ARN is well rid of Langan and his sidekick.

    --
    Dene

    Date: 2002/12/30 08:49:00, Link
    Author: niiicholas
    In the "cytoskeletal protein homologs found in prokaryotes" category:

    Quote

    II thread

    Science News Article

    Week of March 31, 2001; Vol. 159, No. 13

    Bacterial cells reveal skeletal structures
    Jessa Netting

    Bacteria are different from you and me. Always the minimalists, they lack features that plant and animal cells usually can't do without: a nucleus, special organelles, and an internal skeleton made of protein, to name a few. But research reported in the March 23 Cell knocks out one plank of this standard profile—bacteria, too, have a protein skeleton, or cytoskeleton.


    A fluorescent tag for a specific bacterial protein reveals a helical skeleton.
    Carballido-López


    "This is akin to finding the platypus, a mammal that lays eggs," says Laura J.F. Jones, who revealed the skeleton in Bacillus subtilis with her colleagues Rut Carballido-López and Jeffery Errington, all of Oxford University in England.

    The researchers say their finding helps illuminate the origins of our own cell structure and eliminates a fundamental difference between two of the most basic groups of organisms, prokaryotes (bacteria and blue-green algae) and eukaryotes (plants, animals, and protozoans).

    "Spectacular" is the how cell-mechanics researcher Piet De Boer of Case Western Reserve University in Cleveland rates the Oxford team's unmasking of a bacterial cytoskeleton. "Bacteria have really been thought of as bags of enzymes without much of an internal structure at all," says De Boer.

    Bacteria were believed to have only a tough cell wall for support. Even powerful electron microscopes have failed to turn up any distinct internal structure. In contrast, eukaryotic cells, which evolved after bacteria, have a network of filaments for support and movement. A protein known as actin forms much of this cytoskeleton, which can look like a bushy spray of fibers.

    In the past decade, bacteriologists have searched for complex structures in bacteria by using techniques for tagging proteins with fluorescent markers. These studies, which can illuminate otherwise hidden structures, have yielded evidence of a higher level of organization than previously believed, says De Boer.

    Using fluorescent tags made with antibodies that can bind to specific proteins, the Oxford investigators looked for a bacterial cytoskeleton in the rod-shaped B. subtilis. "It seemed likely to me that something as important as the cytoskeleton must have evolved quite early, so I almost expected to find actin in bacteria even though the textbooks say it is absent," says Errington.

    He and his colleagues focused on two bacterial proteins, MreB and Mbl, because of evidence that the genes coding for them have roles in determining cellular shape. Disabling the gene for MreB resulted in rounded cells, while disabling the gene for Mbl yielded elongated, twisted bacteria. Using a different fluorescent antibody to light up the intact protein in each altered cell, the researchers revealed complex internal structures made of either MreB or Mbl.

    "We were ecstatic when we saw the first MreB and Mbl images, because they immediately told us that the proteins probably made filaments like actin," says Errington. Coiling within the cell as they did, the filaments clearly could determine cell shape in normal bacteria, he says.

    Errington likens the filamentous structure to a scaffold: It doesn't have great strength itself, but instead provides the internal framework for a sturdier exterior shell, in this case the bacterium's tough cell wall.

    The finding suggests that the cytoskeleton evolved before bacteria and our own cellular ancestors split into two groups, says Errington. Having a cytoskeleton isn't a defining feature of eukaryotic cells after all, he asserts.

    References:

    Jones, L.J.F., R. Carballido-Lopez, and J. Errington. 2001. Control of cell shape in bacteria: Helical, actin-like filaments in Bacillus subtilis. Cell 104(March 23):913.

    Date: 2002/12/30 14:51:11, Link
    Author: theyeti
    I thought we had a thread for the evolution of the genetic code, and some of the IDists claims about it.  I guess it got lost in the server crash.  Anyway, I thought I'd start this one up anew, and post a recent paper that's relevant to the origins of the genetic code.

    Philos Trans R Soc Lond B Biol Sci 2002 Nov 29;357(1427):1625-42

    No accident: genetic codes freeze in error-correcting patterns of the standard genetic code.

    Ardell DH, Sella G.


    Quote
    The standard genetic code poses a challenge in understanding the evolution of information processing at a fundamental level of biological organization. Genetic codes are generally coadapted with, or 'frozen' by, the protein-coding genes that they translate, and so cannot easily change by natural selection. Yet the sta