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|Date: 2002/05/06 19:19:54, Link|
testing, testing, 1 2 3...
Wow, this looks like a spiffy software package, all the code tags are right above there...
...well, it's sticking all of the tags at the *end* of the line, regardless of the cursor position.
Trying a URL:
Talkorigins webpage link test
...hey, that worked pretty well..
...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...
|Date: 2002/05/17 02:35:38, Link|
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):
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.
|Date: 2002/05/17 21:43:08, Link|
Here is a fantastic recent example from your friend and mine, Jonathan Wells.
There You Go Again:
A Response to Kenneth R. Miller
April 9, 2002
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|
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.
|Date: 2002/05/17 22:09:17, Link|
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.
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.
|Date: 2002/05/17 23:18:58, Link|
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:
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!
|Date: 2002/05/24 19:42:53, Link|
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.
|Date: 2002/05/24 20:25:51, Link|
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:
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:
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:
...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:
...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:
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.
PS: Looking up 'related articles' in Pubmed reveals that decreased Factor XII activity is associated with increased miscarriage in humans:
...which sure seems to imply that it is important for something.
Here is another example of why missing Factor XII is not a good thing:
...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?
*** 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:
On p. 86, Behe writes,
(copying from DNAunion)
Ken Miller, here,
...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|
A recent post on talk.origins by Dunk discussing some recent (2002) literature, with quotes:
Here is the google link
|Date: 2002/05/24 22:27:00, Link|
An attempt to list the major relevant articles/books in the ID blood-clotting discussion:
There may be additional relevant online articles, I will add them if anyone suggests them.
|Date: 2002/05/24 23:23:13, Link|
Ken Miller's take, and further debates online about some of the points, are linked from here:
|Date: 2002/05/24 23:28:42, Link|
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
|Date: 2002/05/24 23:51:37, Link|
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:
However, in the conclusion Davidson is also quoted as saying:
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.
|Date: 2002/05/25 00:35:53, Link|
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.
Regarding blood-clotting & specificity, they write:
Blood-clotting comes up again here:
...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.
|Date: 2002/05/26 00:55:42, Link|
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):
(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).
...and also note the rather unambiguous first sentence of the introduction of this article:
Here is their conclusion FYI:
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.
|Date: 2002/05/28 15:10:09, Link|
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.
|Date: 2002/05/29 23:30:40, Link|
This would seem to be as good a place as any to collect links/references to things like Johnson's
- reviews of his works
- 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:
An Interview with Phillip E. Johnson
Johnson bares his soul & gives quite a detailed history of his own 'evolution'.
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.
|Date: 2002/05/30 00:02:55, Link|
While reading this interview with Phil Johnson, leader of the ID movement:
An Interview with Phillip E. Johnson
...I was struck by this section:
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.
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:
Here is the Nurminsky et al. 1998 article:
Since then, this article has been published:
This article is a good review of the general topic of the evolution of new genes:
|Date: 2002/05/30 00:51:24, Link|
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
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.
|Date: 2002/05/30 01:14:38, Link|
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:
- In the mid-1990's another theory was proposed, apparently right in Schultz & Yarus' 1996 article:
Here is the reference, and some of Schultz & Yarus' (1996) lines of evidence for the ambiguous intermediate theory:
|Date: 2002/05/30 01:49:29, Link|
Reviewing this 1993 article by Paul Nelson and Jonathan Wells:
...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:
...and then, they argue that "functional invariance" is highly probable and therefore scientists are unjustifiably dropping the "functional invariance theory" to protect common descent:
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:
I propose a (new??) term for this style of argument: Argumentum ad Innuendo.
|Date: 2002/05/30 20:33:50, Link|
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):
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!
|Date: 2002/05/31 01:31:35, Link|
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
Here is Figure 1:
|Date: 2002/05/31 01:44:19, Link|
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
|Date: 2002/06/11 00:44:21, Link|
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.
|Date: 2002/06/11 01:03:11, Link|
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):
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:
|Date: 2002/06/11 01:24:42, Link|
Found this key Darwin quote on the ISCID forum:
Chapter 6 of Origin of Species
Here is the link:
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?
|Date: 2002/06/11 05:07:37, Link|
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:
The introduction reveals just how far the IDists are from the biologists on understanding the origins of new genetic information and new functions:
|Date: 2002/06/11 05:41:00, Link|
Following the tangent of the evolution of repeats *within* protein sequences:
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:
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...
|Date: 2002/09/21 13:06:12, Link|
This thread is for accumulating
(2) Links to articles
...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.
|Date: 2002/09/21 13:15:43, Link|
An initial list of Wells utterances on moths and tree trunks:
|Date: 2002/09/21 13:26:13, Link|
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:
(9 of 19 people found this review helpful!
|Date: 2002/09/22 14:40:18, Link|
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:
'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:
Fracks response to the traps claim:
...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.
|Date: 2002/09/22 23:37:02, Link|
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.
|Date: 2002/09/24 03:36:07, Link|
Another review (or rebuttal of positive Hooper reviews, actually) on Intelligent Design Update yahoogroup:
...quite good IMO, several points that haven't been made by anyone else yet...
|Date: 2002/09/24 03:44:53, Link|
Online letters on the Salon.com review of Hooper:
The Wells FAQ is referenced :-)
|Date: 2002/09/24 04:48:34, Link|
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:
|Date: 2002/09/26 00:13:06, Link|
Here is another Wells gaffe:
Michael Majerus took the trouble to respond to this himself:
|Date: 2002/10/01 13:47:50, Link|
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.
Some have argued that the ATPase may be descended from a pyrophophatase, so this is relevant:
|Date: 2002/10/01 14:02:37, Link|
Here's a different one:
|Date: 2002/11/28 23:11:25, Link|
Similar to the prokaryotic flagella thread.
(don't confuse eukaryotic cilia/flagella with prokaryotic 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|
Might as well add these as I'm discussing them over at EvC:
On the evolution of PCP degradation:
|Date: 2002/12/02 18:55:21, Link|
This is a "data accumulation" thread for me (and anyone else interested in Croizat) to learn the basics.
To start off:
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:
|Date: 2002/12/02 19:12:32, Link|
A good short summary of biogeography that puts Croizat in context:
|Date: 2002/12/03 23:13:15, Link|
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.
|Date: 2002/12/07 15:23:08, Link|
|Date: 2002/12/08 00:10:21, Link|
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:
...obvious implications concerning the origin of whales...
|Date: 2002/12/08 00:57:42, Link|
Here's a good example of a debate that rapidly focused on the ambiguities in the defn of IC:
...other examples welcome.
Also, cites of IDists using/defining IC, SC, etc. in conflicting ways.
|Date: 2002/12/08 14:34:57, Link|
That is funny, isn't it.
"Look, there's purpose in biology!"
"But what's the purpose?"
"Sorry, can't talk about that!"
|Date: 2002/12/12 20:58:50, Link|
Interesting. Here's another one by the same folks:
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|
Philosopher/Historian of science, who has authored a PhD and several articles on Kettlewell's work, has weighed in against Jonathan Wells:
Rudge's webpage is here:
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?"
Rudge's current and upcoming articles are listed here:
|Date: 2002/12/12 21:44:25, Link|
Other Biston researcher webpages:
Books by Majerus:
|Date: 2002/12/13 01:13:29, Link|
And in the "duplicated genes aren't necessarily selectively neutral, dammit" category:
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...)
(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|
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|
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.
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.
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
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:
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:
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:
|Date: 2002/12/13 02:14:51, Link|
...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:
Top journals from this list for evolution-related stuff:
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
J Biol. 2002; 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:
PS: Another important journal:
Archives back to 1996:
From 2000 on:
Several critques of ID have been published in Evolution: link to search results
|Date: 2002/12/13 03:35:04, Link|
History of mousetraps:
|Date: 2002/12/13 03:41:18, Link|
The History of the Mousetrap
Some patented mousetraps:
|Date: 2002/12/17 15:28:17, Link|
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 20:27:28, Link|
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|
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:
(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|
In the "nonmotile appendages can have a dispersal-related function despite being nonmotile" category:
|Date: 2002/12/18 12:20:34, Link|
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.
This guy oughta read the Icons FAQs:
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.
|Date: 2002/12/18 13:00:29, Link|
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
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|
Atrazine degradation pathways appear to have arisen recently:
This lab studies 'em:
...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.
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.
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.
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).
|Date: 2002/12/18 18:24:58, Link|
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.
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.
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:
- 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: 2002/12/19 00:04:03, Link|
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:
Then of course we have:
An important update:
|Date: 2002/12/20 01:06:29, Link|
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
|Date: 2002/12/20 01:10:56, Link|
Intelligent Design jargon explained!
By Casey Luskin
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 02:11:24, Link|
This was posted on the DI website.
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:
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
|Date: 2002/12/20 20:53:02, Link|
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|
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:
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|
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:
...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."
Also the UC Museum of Paleontology Online:
Teachers e-volution forum:
|Date: 2002/12/21 16:50:30, Link|
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|
Over on this ARN thread,
...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:
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: 2002/12/23 23:39:22, Link|
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:
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,
...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.
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)
Originally posted here:
|Date: 2002/12/24 02:32:17, Link|
|Wow. This just goes to show that everything is relative.|
|Date: 2002/12/24 02:39:32, Link|
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|
In the "yes, IDists have in fact argued that IC precludes the existence of precursors with other functions" category:
Nature's diversity beyond evolution
Debate over 'intelligent design'
Carl T. Hall, San Francisco Chronicle
Sunday, March 17, 2002
|Date: 2002/12/26 02:19:56, Link|
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:
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:
...on the next page...
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.
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|
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.
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.
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.
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.
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:
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|
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:
T.o. discussion: here
|Date: 2002/12/26 19:34:24, Link|
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:
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:
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 00:54:53, Link|
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: 2002/12/30 08:49:00, Link|
In the "cytoskeletal protein homologs found in prokaryotes" category:
|Date: 2002/12/31 17:16:02, Link|
If I had a month or two, I would review the literature on the question of "optimality" of the genetic code. It seems to me that there are many different ways that the code could be optimal, and other variations which might not make any difference.
E.g., if every amino acid kept the same number of codons, etc., but the standard table was simply "flipped" right-to-left, would this make any difference?
I have no idea myself, but such things are important to think about. Wes had some pretty good stuff on this posted somewhere at one point...
|Date: 2002/12/31 17:21:59, Link|
Regarding Google, Dunk has a very good post here.
E.g., Dunk's post is:
PS: If you surf with Internet Explorer, don't forget about the Google Search Toolbar (*very* cool):
|Date: 2002/12/31 17:37:05, Link|
Please give us your informed opinion when you get a chance to read it. A freely online 2001 PNAS article (from related articles) provides something of a preview:
Doolittle and Patthy are referenced, unfortunately little of Doolittle's and none of Patthy's blood-clotting stuff is in widely available online journals...they all seem to be down at UCSD however.
|Date: 2003/01/03 20:59:18, Link|
Ah, that's it. Lots of good material there.
Briefly, here is an important argument rarely made:
1) Number of combinatorially possible codes:
Lots and lots and lots
2) Number of "optimal" codes:
A lot less, but probably still lots
If #2 is true, then the argument for the monophyly of extant life based simply on the canonical code (leaving aside all of the other evidence for the monophyly of life) remains strong, because there would be no reason for independent origination events to land on one or the other of the equally optimal codes.
E.g., if n = # of equally optimal codes = 10, then the random probability of (say) the three domains of life landing on the same code is p = 1*1/10*1/10, or 1/100. This is already quite a coincidence on the independent origins hypothesis. The probability of (say) 20-odd animal phyla landing choosing the same code out of a range of 10 equally optimal codes would be 1/10^20, already quite astronomical.
And of course if there were more like 1000 or 1 million equally optimal codes, then the random probability of independent origins hitting on the same code goes up exponentially factor.
Note that these results hold even if the canonical code is literally "one in a million", since there are many more combinatorially possible codes than a mere million.
The only way for the independent design hypothesis to produce nonrelated organisms with the same code is to postulate some motive for the IDer to design things this way on purpose -- but postulating motives is something that IDists refuse to do, at least officially.
|Date: 2003/01/07 21:20:14, Link|
Hey Nelson, welcome to AE.
Unfortunately I don't have a week to really wrap my head around the cytosine deamination issue. However I guess I was the "provoker" of the Mike Gene article you cite in that I posted the article "Confounded cytosine" which he is reacting to.
So if debate of this topic begins (by people other than me), let's start by accumulating the relevant links etc. on this thread and then go from there.
Here is an ARN post with some discussion, including some quotations from the article, with the hopes of laying out what Poole et al. were arguing. Unfortunately this argument is embedded in a more complex discussion of various topics related to RNAworld and the origin of the genetic code which makes simple quoting difficult and I think confused subsequent discussion as it is not at all clear that the IDists involved accept or reject either RNAworld or a gradual origin of the genetic code and DNA.
Begin re-post of summary of Poole et al.:
I do believe I provoked this particular MG essay when I posted this reference on ISCID:
There argument is complex but here is the gist:
|Date: 2003/01/11 18:16:37, Link|
|If you get an IDist to give you a non-question-begging definition of information, let us know...|
|Date: 2003/01/13 22:17:00, Link|
Originally posted here.
Strange that this ARN missive doesn't recognize the Raelian's oh-so-crucial "starting point":
I do agree with the ARN wedge update about one thing: your starting point is important. For instance, if you start out by ignoring evidence contrary to your position, there is no end to the silly conclusions you will come to.
|Date: 2003/01/13 23:05:54, Link|
Ever see a thread/post and said "Hey! That thread/post is so good it should be recorded for posterity"? I have.
Here is an example. Art wrote a great post, with pics, over on this ARN thread:
...on how the widely divergent Silversword alliance clearly demonstrates how Jonathan Wells is wrong about RM-NS and morphological "macroevolution".
Art's post repeated below
About your question as to possible known correlations between mutations in developmentally-important genes and macroevolutionary events, I submit the following for your consideration.
First, another accursed pubmed abstract (that need not be read in detail - instead, just note that some of the genes mentioned are the same as those you have agreed represent developmentally-important ones in which non-lethal mutations are known):
It doesn’t take much of an eye to see stupendous morphological differences, easily dramatic enough to qualify as possibly macroevolutionary in nature. Of course, this could only be if it could be shown that these plants share a common ancestry.
And indeed it can be so shown. By a standard that even the staunchest YECer accepts, it can be strongly concluded that each of these (as well as other members of the Silversword alliance) share a common ancestry. This is because, the vast morphological differences aside, they are interfertile. As interestingly, for a number of other reasons (biological, geographic, historical, and molecular), it can be safely concluded that these vastly-different plants diverged from a common ancestor that looked something like
Reflect, now, on the abstract. In this study, evidence for positive selection of alleles (that must have arisen via mutation - this follows from the natural history of the different genera) of developmentally-important genes - genes involved in flower structure and evolution - was described. While it’s not a videotape, it stands as evidence of the sort that Wells claims does not exist - namely, that changes in developmentally-important genes are important in macroevolutionary progressions.
(Keep in mind that among the dramatic morphological differences that are seen in these examples are ones that involve floral structures. Also, while others might argue with me, I would claim here that the range of morphologies shown in this post exceeds the range seen in placental mammals - just to give readers an idea of the scope of the differences.)
(These images, and many others, can be found at the Silverswords link given above.)
(Hint: Hit "reply with quote" in UBBs to get access to the formatting)
|Date: 2003/01/15 02:53:25, Link|
Bump as this thread is being cited on ISCID:
In the "origin of new information in the evolution of humans" category:
Another one for good measure:
[added in edit: oh wait, this was discussed in detail by theyeti back on p. 1
Some points that I think IDists in particular tend to neglect:
1) These are not rare cases, rather discoveries like those referenced here happen every day. The origin of novel genes with divergent functions via natural processes is a ubiquitous and continuing occurrence.
2) I think it is useful to point out how the reconstructed origins of these various genes are *not* due to some single-step process -- rather, we have alternating rounds of duplication, mutation (and *way more* than just point mutation, e.g. exon shuffling) and selection. IDists will often say something like "gene duplication does not create new information because you just have a copy of the gene". But no biologist invokes gene duplication alone. Why don't IDists ever address the case of a gene duplication where one of the copies is mutated and selected, resulting in (1) the original gene and (2) a modified copy with different function. How can the progression of one gene-->two genes with distinct useful functions *not* be an increase in genetic "information" in any biologically relevant sense?
3) If the process described in step 2 is accepted, repeat in a few billion organisms for a few billion years. Does this not go at least a fair distance in explaining the information content of genomes?
4) If the leader of the ID movement, Phil Johnson, is horribly, blatantly wrong about simple biological facts, why has he not been criticized by other IDists? Are they perhaps similarly mislead?
|Date: 2003/01/18 23:54:17, Link|
I noticed Charlesbois's article also, comments are here:
Re-evolution of complex characters
IMO this quote is the key one for putting some balance into discussions where Woese, Doolittle, etc. are cited:
|Date: 2003/01/19 00:48:17, Link|
I was thinking about posting this on this ISCID thread, and then I thought, "why bother?" Besides I am too busy to start a big debate.
Here is the thread, started by Mike Gene:
Topic: Brainstorming Lessons
link to thread
I quote the end of RBH's post:
I agree that it is ID that is squelching hypotheses, namely the details in origins scenarios that make them testable (strengthenable or weakenable, not always strict true/false).
There is nothing wrong with going out on a limb and proposing hypotheses with specifity that goes beyond the data; this is how science proceeds into the unknown. This is why OOL researchers propose specific hypotheses, test them, and then revise -- e.g. RNAworld has become pretty well supported as a stage preceeding the origin of modern life, but difficulties in prebiotic syntheses of RNA are provoking studies of RNA precursors, e.g NA or PNA "worlds".
The way science does *not* proceed is by maximizing vagueness, e.g. "a designer did something somewhere sometime for unhypothesized reasons by unhypothesized means". With ID, not even the laws of physics are considered legitimate constraints on the hypothesized IDer(s). I would argue that every successful (e.g. archaeology/forensics) or viable (e.g. SETI) "ID-detecting" discipline has hypothesized far more details regarding the IDer(s) than any hypothesis put forward by Mike Gene or anyone else in the ID movement.
The problem with ultravague hypotheses is that they are explanatorily unconstrained; the problem with an unconstrained hypothesis is that there is no objective way to strengthen it or weaken it by consideration of further data.
E.g., with Mike Gene's front-loading via mutational bias idea (leaving aside questions of what the actual biases are, which Art and others will have to work out), it seems to me that front-loading via evolution is approximately the most difficult and clumsy possible way to design something that I can think of. It would be like trying to type with your elbows even though you had fingers. Trying to get to, say, multicellularity through a nonspecific mutational bias would be rather like trying to convert from the Articles of Confederation to the Constitution via a bias in the replacement frequencies of various letters.
Such a conversion could be accomplished either by intelligent or algorithmic selection of specific letters (in the case of biology we should convert this analogy to natural selection's *documented* ability to sweep specific beneficial nucleotide substitutions to fixation in the population, to avoid the usual Dawkins-METHINKS debates) -- but if these capabilities are in play, what's the point of the mutational bias? The mutations will happen slightly slower without the bias (well, assuming that the necessary mutations are those included in the bias, which seems completely unsubstantiated to me), but they will happen sooner or later and then can get selected. (In the case of an IDer, they would presumably not even bother with waiting for the mutations and just design straight-up whatever they wanted to design).
Do these considerations have any weight in weakening Mike Gene's hypothesis? Only if you hypothesize some things about the designer, which Mike Gene does not, because his hypothesis is basically "someone frontloaded something for no specified reason" and thus considerations of efficiency, effectiveness, etc. (even though these are often invoked by Mike Gene and others in support of ID in other situations) will just be brushed aside as "we don't know anything about the IDer".
IMO, this "unconstrainedness" of ID-movement "hypotheses" is their central weakness. This is a problem that supernatural hypotheses have, but is common to "superpowerful but unspecified aliens" "completely unspecified designer(s)", etc., as well. ("Unspecified natural processes" falls in the same boat, BTW) None of them predict or explain anything without further details. Full exhaustive detail is not necessary, but a least enough detail to make us expect some pattern in the data that we wouldn't otherwise expect, and which could be weakened by other patterns, is what it takes to get started.
Vagueness will insulate an idea from refutation but will also doom it to the land of non-explanation.
End of Saturday Night Sermon,
[edit: cross-posted to II evo board:
Vagueness and Explanatory Constraints
|Date: 2003/01/19 04:19:00, Link|
Michael Denton has said a lot of things over the years. However on the whole he appears to have moved in a wholly evolutionary direction after he kicked off "the modern ID movement" with his 1986 book Evolution: Theory in Crisis.
E.g., here is a quote that I'd read but never had handy:
originally posted here
From Darwinism Defeated?, 1999:
(some typos may remain, I fixed one)
There is no point in quote mining, so whatever anti-evolution statements one comes across from Denton are fine also.
|Date: 2003/01/23 04:54:45, Link|
Some good stuff I found and posted in response to Nelson Alonzo here:
So even for systems that are remote from us by 3 billion years there has been some recent progress.
What I'd really be interested in, Nelson, is your opinion on the vertebrate immune system. IC or not? Evolved or not? Behe says IC, and intelligently designed.
|Date: 2003/01/24 04:34:13, Link|
For the fossil record's first feat, I submit:
Nature 421, 335 - 340 (2003); Four-winged dinosaurs from China
XING XU*, ZHONGHE ZHOU*, XIAOLIN WANG*, XUEWEN KUANG†, FUCHENG ZHANG* & XIANGKE DU‡
lots of discussion at II evo board
Since the paper is up for free I will put the pics in here:
And check out 2g for the definitely non-trivial (although the exact function may be up for grabs) hind leg feathers:
At the end they say:
...in case this wasn't clear, ref 45 is to the Archaeoraptor forgery, meaning that one of the pieces of the Archaeoraptor was a chunk of M. gui.
Truth was stranger than fiction in this case...
|Date: 2003/01/25 18:00:34, Link|
Charlie D gives a great brief intro on why adaptive mutation ain't:
Topic: Directed mutation
Originally posted by charlie d:
I have no idea when that paper was written, but it lists no references later than 1995. Thus, its enthusiasm for the "targeted mutation" phenomenon, its belief that it represents a fundamental challenge to the prevailing genetic paradigm, and its conclusion that "there is no explanation for it", is not surprising, considering that the hypothesis itself began to crumble in earnest in 1996 with the publication of this article by Prival and Cebula:
Prival MJ, Cebula TA Adaptive mutation and slow-growing revertants of an Escherichia coli lacZ amber mutant. Genetics 1996 Dec;144(4):1337-41,
and eroded further after this article by Patricia Foster (who was one of the original discoverers of the adaptive mutations phenomenon):
Foster PL. Nonadaptive mutations occur on the F' episome during adaptive mutation conditions in Escherichia coli. J Bacteriol. 1997 Mar;179(5):1550-4.
These and other findings prompted Foster herself to write the now classic review (available for free here): Foster PL. Adaptive mutation: has the unicorn landed? Genetics. 1998 Apr;148(4):1453-9,
a virtual obituary for the "lamarckian" interpretation of the phenomenon.
A more detailed review is this one (but subscription is required to access the actual paper): Foster PL. Mechanisms of stationary phase mutation: a decade of adaptive mutation. Annu Rev Genet. 1999;33:57-88.
At the current state of affairs, it is very clear that mutations during "adaptive mutagenesis" are not specifically directed towards the gene(s) under selection, i.e. they are entirely darwinian (random wrt to fitness), and are often the result of generalized hypermutation mechanisms (the last important piece of the puzzle being the publication of this paper last year): Hendrickson H, Slechta ES, Bergthorsson U, Andersson DI, Roth JR. Amplification-mutagenesis: evidence that "directed" adaptive mutation and general hypermutability result from growth with a selected gene amplification. Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):2164-9.
For those interested in the most recent and actual history of the "targeted mutation" saga, I recommend this recent excellent review of the issue, available for free here: Rosenberg SM Evolving responsively: adaptive mutation. Nat Rev Genet 2001 Jul;2(7):504-15
|Date: 2003/01/25 19:17:43, Link|
Re-posting my reply:
It is quite interesting how hostile and demanding "open-minded skeptic" Mike Gene is towards MDT given his continual begging for leniency regarding the almost unbelievably vague and subtle form of ID that he advocates. It is clearly a result of his uniteleological bias, and once this is exposed we can see the reason of his persecution of us.
But MDT follows quite naturally from several premises followed regularly by Mike Gene:
1) Loosen up on science's preference for parsimony
2) Take "it looks as if it were designed for..." intuitions seriously
3) Always keep in the front of one's mind the perceived biases of your opponents
The central insight of MDT is that an awful lot of things "look like they were designed for" subverting other designs. If this intuition is to be taken seriously, then MDT is the obvious outcome -- and a revolutionary one given the SDT-focus of the ID movement to date. There are, to be sure, some cases in things like development where "conflicting" designs may appear to result in a larger goal, but in all these cases both designs are explained by co-replicating genomes that have the same interest in survival, so this is easily identifiable.
In that ARN thread, MG also points to some of the widespread commonalities amongst life. Does this point to SDT or MDT? Neither; it points to common descent. As Dembski and others have pointed out, SDT is fully compatible with common descent; so is MDT.
Of course MDT advocates believe, in common with all other ID theories, that the first life was designed; however, the great thing about MDT is that it gives us much more insight into *how* it was designed compared to MG ID or SDT in general, which all advocate the "poof" model.
If I might for a moment advocate my own subspecies of MDT, namely ITWA theory (Invisible Tinkering Warring Army theory), this point will soon become clear. The basic biochemistry of life has been shown by nonteleological scientists to have several peculiar features:
1) A strange dependence on RNA for core processes, which just happens to have both self-replication and enzymatic capabilities, unlike DNA and proteins
2) A considerable degree of optimization, but optimization that appears to have simpler precursors -- e.g. the genetic code is thought to have started with just a few amino acids, which happen to be the most common ones in various core protein processes
3) A limited number of "basic" protein folds, DNA motifs, etc.
This list could be greatly expanded.
The point of all this is that it appears that the last common ancestor (not necessarily a single cell, perhaps a "gene pool" of laterally-transferring bacteria) was not itself a "design from scratch", but instead the product of a tinkering of earlier, simpler designs. ITWA theory assimilates all of the work of nonteleologist scientists on RNAworld etc. and incorporates it into its own theory. Some version RNAworld existed at some stage, but in order to gain an advantage over other ITWAs, one ITWA added DNA to store genetic information. This allowed for much longer genomes and greater complexity. Further tinkers expanded the genetic code, etc.
One of these variants was so superior that all competitors, except perhaps things like parasitic viruses and RNA viroids, were exterminated. And this is the LCA of life. (this may be a somewhat oversimplified picture, extermination was not necessarily a sudden process and we could have had multiple "tinker sweeps to fixation" as various innovations took over; but I am just exploring here).
So one of the ITWAs "won" the battle. So why, a skeptic would ask, did the process not stop here? Victory had been had!
Well, as anyone who studies the history of combat knows, once one army triumphs, a common result is for the army to split up and fight over the spoils. Repetition of this process results in the modern world of innumerable battling (and sometimes self-serving cooperating) ITWAs.
This is a far more detailed and testable explanation than "somebody designed some things for no detailed reason a few billion years ago", which appears to be what the more subtle forms of ID amount to.
|Date: 2003/01/27 19:39:19, Link|
Topic: List of IC systems
An awful lot of entries in the NCBI protein database listing MotA, ExbB, and TolQ as being a "family", in opposition to what Mike Gene has been suggesting
Hmm, well a standard protein BLAST on E coli ExbB gives me this taxonomy report:
An E. coli "biopolymer transport exbB protein"
Here is the link
Here are some of the results *outside* the proteobacteria:
The distribution taxonomy report for ExbB is, in fact, rather like the taxonomy report for standard protein blast of E. coli's MotA protein: lots and lots of enterobacteria and proteobacteria, and a few hits out in spirochetes and other various deeply divergent bacteria.
Here is said taxonomy report
Are we to conclude that MotA is just as likely to be of late origin and derived as ExbB?
...methinks the database may be a wee bit biased towards certain intensively-studied gram-negative bacteria groups and that therefore seeing many hits in those groups and few outside means very little in terms of relative significance. As I showed, you have to put MotA and ExbB in the same distribution bucket regardless.
Regarding low e-values:
Based on your blanket skepticism of marginal e-values, you may want to argue that some MotA proteins are of independent origins and convergent on standard MotA's. Many of these scores are non too impressive, yet some are MotAs (or PomA, a related motor) despite this:
These kinds of things ought to at least be mentioned and discussed before reckless statements are made about absolutely no evidence for precursors to flagellar proteins, that's my only point. For some reason you guys prefer to sweep it under the rug by unsupported arguments about ExbB's narrow distribution. Just acknowledge that this little bit of the biological world is a bit disharmonious with the flagellum-was-specially-created thesis. All I've been saying, and now documenting, is that ExbB homologs are at least as widely distributed as MotA, and possibly more widely distributed.
|Date: 2003/01/28 04:00:49, Link|
[deleted] reposting formatting didn't work.
The thing to do would be to plot the daily normalized recapture rates (and capture rates of wild moths) for all the different experiments one could find (or at least Kettlewell) vs. days past full moon or some such. Based on the Dorset 1955 data and on the daily (rather than aggregated into phase bins) Birmingham 1953 data it would appear that recapture rates increase as the full moon is decreasing. Birmingham 1955 shows the opposite pattern however.
Better yet would be to plot nightly lunar radiance or some such vs. capture & recapture rates, and delineating different traps (pheromone vs. light) -- although, both kinds of traps could show a response as the moths could be influenced by moon phase regardless of trap type.
We should archive Tom Curtis' posts or maybe get him to synthesize them into a Wells FAQ subFAQ however, they are quite the debunking of Wells and Wells defender Steve Jones who does some really atrocious statistics...
PS: I find it hard to believe that there is no published literature on moon phase (and related factors, e.g. cloud cover) vs. capture/recapture rates for moths. Those moth guys spend a lot of time hanging around at night...
|Date: 2003/01/28 21:38:27, Link|
FWIW this page on a survey protocol for an endangered moth species (Silphium Borer Moth) says:
link to google archive page
And Shapiro says in his essay:
"Moth collectors agree broadly that light traps attract very little when the moon is full."
BTW, this page has some older moth lit (well, short news bits from New Scientist), e.g. Cherfas 1986 and 1987:
Hang on, I just came up with some lit.
|Date: 2003/01/28 22:05:09, Link|
Unfortunately most fields don't have the nice PubMed-style search engine. But with the annoying-but-relevant BIOSIS I was able to turn up quite a bit.
Quoted below are the results of a search on "moon moth", removing only the totally irrelevant:
Quick summary based on a non-thorough read-through of the abstracts:
Authors peak captures during:
New moon: 4 articles
(1 pheromone; 1 light trap; 1 artificial lights (noctural insects in general but Leptioptera in particular; one couldn't tell)
Full moon: 1 article
(2 species in the same genera though)
Significant effect, direction not specified in abstract:: 4 articles
(all light traps IIRC)
Lack of effect reported: 1 article
Other, discusses moon & moths but not capture rates: 3 articles
Peak "activity" at *both* new and full moon: 1 article
So it would appear that in general Shapiro's contention is supported. Note that peppered moths are not included in any of the studies, and that it is apparent that different moth species do different things.
It would be nice to know the direction of effect for the 4 studies where this is not clear...
If anyone knows Tom Curtis they might let him know about this thread, he might be interested.
|Date: 2003/02/01 17:14:48, Link|
Link to the other peppered moth thread:
...contains my review of Hooper...
|Date: 2003/02/01 18:22:00, Link|
Link to thread discussing the moon phases and moth capture rates:
|Date: 2003/02/01 18:29:43, Link|
In the "another whole kind of motility" category:
If all Mycoplasma are derived parasites of eukaryotes (?) then presumably this motility system is of relatively late origin.
|Date: 2003/02/02 05:53:36, Link|
Put your favorite examples here!
Discussed on Evolving Inventions:
Other relevant articles:
A detailed review of the origin of feathers:
In fact, right now we are living through the merging of developmental biology with the modern synthesis, e.g.:
|Date: 2003/02/02 06:43:20, Link|
Originally posted over at ARN, perhaps this could serve as starting material for an overall "progressive case for the origins of complexity" FAQ, i.e. that starts with the small processes and then builds them up.
Feel free to add relevant links, posts, etc., especially to threads that better document specific points, e.g. adaptive radiation, transitional fossils, IC, etc.
Original thread: http://www.arn.org/cgi-bin....#000004
Berthajane, Vivid, et al.,
I've often thought that there should be a FAQ somewhere specifically on the evolution of complexity, since that is what is the sticking point for a lot of people.
I don't really have the time to write a FAQ or even do more than hit-and-run post, but perhaps I can communicate how I think it might go. Perhaps you can comment if you think all of this is old hat and would be pointless and unconvincing to you in a FAQ or if you think it would be worth reading.
OK, here goes.
The case for RM & NS producing complexity is cumulative. You start from small-scale processes and then work up.
1) "Microevolution" -- local adaptation: drug resistance, peppered moths, pesticide resistance, guppy size change, etc. Presumably everyone accepts this.level of evolution.
It is worth considering, for a moment, some of the implications of even this minor level of evolution:
a) Microevolutionary forces can, in short order, take a single mutation in a single individual and spread it to fixation, so that it exists in every member of a population of millions. All of the millions of bad mutations don't matter a bit, they rarely made it further than a generation or two. That one-in-a-million lucky mutation is the one that natural selection picks (even if it is lost by chance the first few times, sooner or later it or an equivalent mutation will spread far enough that its success becomes guarenteed).
Also, note that even at this minor level we have a fair bit of design-mimicking occurring. Peppered moths, for example, don't change color in any random direction, they change color to match the color of tree bark (please refer to the Wells FAQ before critiquing the peppered moth example). Modern militaries only got around to producing decent camoflague in the mid-1900's.
Now think about all the other amazing instances of camoflague in the animal (and plant! world.
A few examples:
A frog in Madagascar:
Those were fairly modest examples.
Look for the plants in this picture, they're in plain view:
The well-named Lithops:
And here, which one is the ant and which one is the ant-mimicking spider?
(hint: count legs)
Here is a fairly decent webpage on mimicry (Kimballs pages are about the best online pseudo-bio text I've seen, decent pictures etc)
Camoflague and prey-mimicry combined in this one:
(Click here for an II thread discussing anglerfish evolution BTW)
Anyhow, I went on a tangent with camoflague and mimicry. My point: I submit that all of these cases are rather easily explained by "microevolution" of the peppered moth type (and there are many other studies of natural selection for camoflague BTW) -- indeed, many of these impressive designs are specific to species in genera or families with completely different coloration...e.g. anglerfish that live so deep that no light reaches them don't bother with camoflague.
If this kind of thing is conceeded, then we've already allowed that microevolution has a rather substantial ability for "creativity" and acheiving very specific "designs".
(b) Returning to the population-genetics-level processes described at the top of (a)...Now think about them happening continually (many different mutations will be under the influence of selection in any given species at any given point in time) for millions of years. Here we add in speciation, both due to geographical separation (allopatric) and niche partitioning (sympatric). Many species going in many different directions. Many recent adaptive radiations of species, where very-closely related species are morphologically very different and "designed" for very different niches, could be cited. Here are a few:
Kimball's speciation page
Darwin's Finches (Darwin did not even realize they were all finches for years after he collected them; they fill the niches fufilled by various birds on continents -- seed eaters, insect eaters, woodpecker, warbler, etc.):
(this, BTW, is the most important point about Darwin's Finches, although Peter & Rosemary Grant's studies of recent natural selection are also interesting)
The Hawaiian honeycreepers are even better examples. These are all closely related (well, were, some were driven extinct when Europeans and their pets invaded):
And be sure to check out Art's post on the Hawaiian Silversword Alliance (sounds like an army in an online wargame, I know...):
Some of these Silverswords are trees, some are little herbs, and yet they are all closely related and many are even interfertile
© If it is conceeded that RM & NS can account for the rather astounding diversity of the above groups, then we've agreed that natural evolutionary processes can account for family-level diversity. Now, if the same processes produced orders (e.g. the various mammal groups) and classes (e.g., reptiles, amphibians, etc.), we should see some fossil evidence of this, and we do. In the case of vertebrates, rather a lot, and a bunch of new ones in the last 10 years. Just to review what we've got intermediates or close-offshoots for:
walking sirienians (manatees etc., forget what they're descended from)
...and of course, humans.
Why any of these should exist, except on the hypothesis that all modern organisms originated by modification of previous organisms by a process limited to fairly gradual changes (like RM&NS) is a useful question to consider.
2) Turning from morphology to molecules: while the lower levels of evolution and adaptation might be explained basically by selection of point mutations, at some point new genetic information has to be created. There is a mechanism for this, namely the combination of gene duplication (and variations on this, e.g. deletions, rearrangments, etc.) with the mutation-and-selection processes discussed back in 1a.
Even unmodified gene duplications are often selected; e.g., some DDT resistant mosquitos have 100+ copies of a DDT-resistance gene (see Weiner, Beak of the Finch). Plus we have genome duplications, duplication of whole segments of chromosomes, etc. These kinds of processes give evolution a lot of material to play with, and there are numerous documented and published cases of observed or recent origins of novel genes by various combinations of the above processes.
Lots of them are described in this origin of information thread
And of course the same kinds of adaptive radiation patterns found in morphology can be found in molecules, and here we even have hard-and-fast evidence that directional natural selection was operating millions of years back in the unobservable past, in the form of substitution biases, e.g.:
As for the origin of new morphology, the combination of the origins-of-genes processes described above, with recent knowledge of the genes patterning development, has made this much clearer. E.g.:
3) OK, so at this point we perhaps have reached the amount of evolution that Mike Behe accepts or at least doesn't argue about, that is: a heck of a lot. I tend to be of the opinion that if natural evolutionary processes can produce new genes, novel morphological traits, and even body plans, we ought to expect that it's powerful enough to do just about anything that that we see in biology today. But, some will raise IC at this point, arguing that, sure, evolution could have produced mammals, humans, wings, whales, innumerable new genes and adaptations, but that a designer still intervened to produce a certain class of system (*really* complex or rather simple-but-irreducible, depending on who you talk to...) that Behe calls IC.
This has been discussed to death in numerous places, but suffice it to say that for the most complicated of Behe's IC systems, namely the vertebrate immune system, Behe's claims about lack of evidence for an evolutionary origin, and lack of scientific publications on the topic of the origin of the immune system, he has been decisively refuted.
Read this: Evolving Immunity by Matt Inlay
Then read: This ISCID thread where IDists were hapless in their attempt to defend Behe
If natural processes can produce even ridiculously complex IC like this, then there is no particular reason to invoke ID to explain IC.
4) Finally, once all of the above is accepted or considered probable, we are in a position to consider the origin of eukaryotes and prokaryotes. In my opinion, if RM&NS processes can create something like the metazoan phyla and the immune system, there's no reason to suspect that anything else was responsible for earlier events.
We are however getting into events that occurred on a microscopic scale 1+ billion years ago, so details are necessarily much more speculative. All I can recommend is some of the better reading I've found on these topics:
Maynard Smith and Szathmary, Major Transitions in Evolution, 1995. Here is a brief review by someone.
The short version of the above is their 1998 Origins of Life but it is pretty much pointless compared to the bigger book.
The other good source is pretty much anything written by Cavalier-Smith (type his name in here), e.g. this series of articles:
Hope that helps,
Reposting this to AE...
|Date: 2003/02/06 03:00:49, Link|
I think it all depends on what your (group) goals really are. If one of the goals is to promote ID/provide a forum for IDists to publish, or to critique modern evolutionary theory, then just say it up front and go ahead and do it, it's your journal.
If on the other hand you want something with broader appeal, you will have to find some method of editing/review that excludes things like "Yet Another Article Based on a Misunderstanding of the 2nd Law of Thermodynamics" or "Re-publication of Article by IDist X" or "Miscellaneous Antievolutionary Ramblings". Perhaps some requirement that contributions represent something *novel*, that "move the ball foward" (or backward, even), whatever the ball may be, would be a position-neutral way of doing this.
E.g., "A Hypothetical Explicit Model for the Main Periods of Intervention in the Evolution of Life by an Intelligent Designer". IMO the most important thing is not going around trying to prove evolution wrong, it is for ID to come up with its own explicit hypotheses and proposing/conducting tests of them. Explicit hypotheses "advance the ball" of the discussion even if they are wrong.
|Date: 2003/02/07 01:12:06, Link|
Although the basics of how the eubacterial flagellum works are reasonably well-known
(see Howard Berg's article in Physics Today, Motile Behavior of Bacteria for a good introduction)
...one remaining mystery surrounds the exact mechanism by which the flow of H+ powers rotary motion.
Here is Berg's figure of the flagellum:
H+, aka protons, hydrogen ions, or "acid", flow from the inter-membrane space (where ATPases, photosynthesis, and other processes store them at high concentration) into the cell (down, in Berg's figure) where they are at lower concentration.
Somehow this energy is converted into motion of the cell. A number of diverse models have been proposed for how exactly this might occur. Mike Gene briefly reviews a couple of them in his argument for the nonevolution of the flagellum here.
He includes a figure derived from a paper on the question of motor mechanism:
The grey round thing represents the FliG protein (the part of the C-ring that interacts with the motor proteins, MotA and MotB) and the pinkish things with the H+ or Na+ flowing through them represent the MotAB complex.
[WARNING: beginning marginally informed speculation section. Treat as one would treat a mathematical "conjecture" -- or rather just a conjecture, I'm sure math is more formal about such things]
Perhaps we can imagine two main classes of models:
1) Those in which the H+ flow plays a *direct* role in rotating the flagellum (e.g., the "proton turbine model" in the left of the figure). This is, BTW, an appealingly simple model for motor operation: the protons just flow on through and the charges interact with the diagonally-positioned charges on the C-ring, sort of like wind blowing on a windmill. Presumably a conformation change in FliC could reverse the diagonal direction and presto, rotation in the opposite direction.
2) Those in which the H+ flow causes some conformation (shape) change in the MotAB complex, which then interacts to "push" (speaking very basically; could be a Brownian ratchet for instance) on the C-ring. How a conformation change in FliC would produce reverse rotation on this model is obscure to me, although I'm sure there's a way.
Based on the idea that MotAB had flagellum-independent origins in the form of proteins homolgous to ExbB (and ExbD IIRC), can we make any guess as to which of these might be more likely?
The difficulty with #1 would appear to be that both the proto-FliC and proto-ExbB would have to be at least crudely adapted to accepting proton flow.
It seems to me that #2 might be more likely if MotAB evolved from ExbB-like ion channels and if those channels functioned by conducting H+ through them and using the resulting conformation changes to perform work elsewhere at a distance. The proto-MotB (already adapted for performing H+-powered work on some other protein) might be the only thing that would have to mutate in order to get some crude purchase on the proto-FliC (the base of a transport system, but that's another part of the story).
Anyway, the basic idea is that it would be cool, for instance, if one could predict which functional model to prefer based on an evolutionary based on homology with ExbB...
All of this depends upon further understanding of how the Exb complex works however. Something to work on...
(PS: THis is one of the Mot-homolog articles, it appears that they go for the conformation-change model also):
|Date: 2003/02/07 01:31:24, Link|
This would appear to be in support of the "the proton passes through the MotAB complex, and the resulting change of shape moves the FliG & C-ring"
Let's see if this graphic works:
Eric Cascales Roland Lloubès James N Sturgis Molecular Microbiology Volume 42 Issue 3 Page 795 - November 2001
The TolQ-TolR proteins energize TolA and share homologies with the flagellar motor proteins MotA-MotB
|Date: 2003/02/07 01:48:37, Link|
Bracht on the flagellum:
The Bacterial Flagellum: A Response to Goodenough
|Date: 2003/02/07 02:27:38, Link|
In the "A Different Way to Control a Bacterial Flagellum" category:
1) Yet another non-bidirectional flagellum
2) This flagellum has required parts that other flagella don't require (MotC and MotD)
3) Other flagella have required parts (e.g. CheZ) that this flagellum doesn't require
4) I always thought it made more sense to regulate the motor rather than the C-ring (or at least it was easier to imagine); it appears that Sinorhizobium meliloti agrees.
5) Does "rigid flagella" indicate that these guys get away without even hook proteins (the more-flexible proteins at the base of the external rod structure)?
6) Chemotaxis systems in general are a huge mess in terms of IC-interpretation. In some cases similar systems are coupled to wildly different motility systems (and probably even to nonmotility systems; cells have to react in multiple ways including motion), and some motile cells appear to get by without the chemotaxis system at all; see:
|Date: 2003/02/08 01:11:48, Link|
Link to extended discussion on the relative basal-ness of MotA vs. ExbB:
|Date: 2003/02/08 02:39:54, Link|
Fun article, a latter day version of Purcell's "Life at Low Reynolds Number":
The efficiency of propulsion by a rotating flagellum
Note: the mathematical tractability of calculating diffusion and velocity for bacteria & their flagella should not be neglected. E.g. it seems that the propulsion or dispersal potential of various "crude" flagella could be calculated.
|Date: 2003/02/15 00:57:38, Link|
Stop the presses! Tubulin (not just the tubulin homolog FtsZ) found in prokaryotes.
Obviously, research is just beginning on this bacterium and proteins. However, it is interesting in light of one of Mike Gene's essays on his webpage:
But here we have tubulin evidently doing something prokaryotic.
Never heard of these Prosthecobacter guys before?
|Date: 2003/02/17 15:41:23, Link|
This thread is devoted to the Argument from Ignorance and what happens to various sciences if it were allowed the same free reign that IDists give the Argument from Ignorance in biology.
Similarly, because the origin of the rings of Saturn is still unknown except for some general models and scraps of data, we should have "serious doubt" that current physical theory can account for it.
Any schmoe in any field can go dig up something unexplained (or only generally explained, as in the cases of both the flagellum and the rings of Saturn) in any field, that is old enough or otherwise "distant" enough to make evidence hard to come by. None of this justifies "serious doubt" in a well-established theory, especially for problems that are routinely brought up and solved within the field ("complex adaptive structure #1241" in biology, evolutionary theory has already explained a number of complex adaptive structures so what difference does one more make?).
On Mike Gene's logic these mysterious, highly symmetrical structures should put mainstream geology into "serious doubt":
...and these should put mainstream anthropology/archeology into doubt:
The "Bahgdad Battery" -- apparently a 2200 year old battery.
And yes, both of these puzzles have been invoked in support of radical theories like, oh I don't know, alien intervention in the history of life.
I guess we should be teaching this "serious doubt" about mainstream science in school earth sciences and history classes also, just to be fair.
Post your favorite mysteries here!!
|Date: 2003/02/17 17:16:08, Link|
More from Dembski on the flagellum:
Dembski's latest article:
Still Spinning Just Fine: A Response to Ken Miller
There are severe problems with basically every paragraph of Bill Dembski's latest, I will focus on just one:
Dembski writes in Still Spinning Just Fine that:
However, with confronted with rather a lot of literature on the origin and evolution of the immune system (one of Behe's originally identified IC systems from Darwin's Black Box, plus lots of evidence of precursors in organisms without the full system, not a single IDist was able to defend the previous statements of Behe and Dembski along the lines of "the entire biological community ha[s]n't figured out how those systems arose." A few of the more sophisticated ID-friendlies even appeared to agree that the gradual evolution of the "IC" immune system was a perfectly reasonable idea supported by a fair number of observations and peer-reviewed articles.
This was all done right here on ISCID not few months ago:
Organisms using GAs vs. Organisms being built by GAs
And yes, this will keep getting brought up as long as Dembski keeps repeating the same false line that biologists are clueless about how complex multipart systems can originate.
As for what things like the Type III secretion system do and do not prove (as well as for citations of important bits of evidence that Dembski failed to deal with, things like the Exb homologs of the flagellum motor proteins, and the archaeal flagellum--Type IV secretion system homologies), there's not much point in repeating them yet again, so I've been accumulating a list of the relevant links here:
Antievolution.org resource thread on the prokaryote flagella (there's more than one kind of flagellum, durnit!!! )
|Date: 2003/02/17 18:07:21, Link|
I got some replies to this quote I posted in response to Nelson Alonso:
So even for systems that are remote from us by 3 billion years there has been some recent progress.
...from this ARN thread:
...and then Nelson replied and I replied:
And he also wrote:
(I don't see any good reason for MG's breaking what is otherwise convention and splitting off FlG's C-terminal end as a "separate" part, seems to me this is a special maneuvure not utilized elsewhere)
....And when Nelson still wasn't impressed, I wrote:
Um, Nelson, you didn't even read the quote I provided:
Of course, given the uncertainty surrounding phylogenetic events 3.5 billion years ago, not to mention lateral transfer events etc., the most reasonable thing to do would be to say that we have no particularly good information about what came before what. But then there goes any confidence in the assertion that bacteria have always had flagella or have no precursor homologous proteins, which has been a big chunk
of your argument.
Regarding the probability of this ion channel hooking up to the base of a primitive Type III pili, the exact mechanism of coupling proton flow to motion is still up in the air. However, you wouldn't have to get a fully functioning flagellum out of it, even undirected wiggling would enhance dispersal. This provides the starting point for natural selection to refine the procedure.
As you and Mike Gene point out, such a getting-the-process-started mutation is an unlikely "completely chance event" -- but just like any mutation, this is not a one-try event!!! Give a few gaztrillion bacteria a few million years! And we are clearly no longer dealing with the fortuitous de novo synthesis of a whole bunch of proteins, as Dembski suggests, or even the fortuitous cooption of dozens of individual proteins all at once, as Mike Gene sometimes mischaracterizes cooption. We are just hypothesizing a mutation crudely coupling two pre-existing systems.
As for similarity in function, Kojima and Blair note that this basic ion-channel system has been successfully coupled to diverse systems:
And then in reply to a few objections from Mike Gene:
An awful lot of entries in the NCBI protein database listing MotA, ExbB, and TolQ as being a "family", in opposition to what Mike Gene has been suggesting
An E. coli "biopolymer transport exbB protein"
Here is the link
Here are some of the results *outside* the proteobacteria:
The distribution taxonomy report for ExbB is, in fact, rather like the taxonomy report for standard protein blast of E. coli's MotA protein: lots and lots of enterobacteria and proteobacteria, and a few hits out in spirochetes and other various deeply divergent bacteria.
Here is said taxonomy report
Are we to conclude that MotA is just as likely to be of late origin and derived as ExbB?
...methinks the database may be a wee bit biased towards certain intensively-studied gram-negative bacteria groups and that therefore seeing many hits in those groups and few outside means very little in terms of relative significance. As I showed, you have to put MotA and ExbB in the same distribution bucket regardless.
Regarding low e-values:
Based on your blanket skepticism of marginal e-values, you may want to argue that some MotA proteins are of independent origins and convergent on standard MotA's. Many of these scores are non too impressive, yet some are MotAs (or PomA, a related motor) despite this:
These kinds of things ought to at least be mentioned and discussed before reckless statements are made about absolutely no evidence for precursors to flagellar proteins, that's my only point. For some reason you guys prefer to sweep it under the rug by unsupported arguments about ExbB's narrow distribution. Just acknowledge that this little bit of the biological world is a bit disharmonious with the flagellum-was-specially-created thesis. All I've been saying, and now documenting, is that ExbB homologs are at least as widely distributed as MotA, and possibly more widely distributed.
|Date: 2003/02/17 19:06:37, Link|
I'd forgotten that I'd accumulated these, they were posted originally in the ISCID immune system thread:
Dr. Dembski writes:
A few of the examples are described here.
Here is a list, just off the top of my head. References can be found easily by searching PubMed so I trust you will not mind if for the purposes of space I just list some of the cases I know about without giving refs for all of them.
The recent-origin Drosophila genes jingwei and sdic
Nylon degradation genes (multiple independent origins)
Recent origin of antifreeze genes in fish (and plants)
Antibiotic and antipesticide genes
Here is a case of the origin of an autotransporter (AT) gene, lav by domain shuffling; I quote just a bit, the whole rather long article with all of their documenting evidence is freely online at pubmed:
Mortlock, R. P., editor (1992). The Evolution of Metabolic Function Boca Raton Fla., CRC Press, pp. 1-339.
Table of contents:
On atrazine resistance (lots of articles here)
The degradation of pentachlorophenol by the recent assembly of a multiple-parts-required pathway, e.g.:
Copley SD. Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach. Trends Biochem Sci. 2000 Jun;25(6):261-5.
Anandarajah K, Kiefer PM Jr, Donohoe BS, Copley SD. Recruitment of a double bond isomerase to serve as a reductive dehalogenase during biodegradation of pentachlorophenol. Biochemistry. 2000 May 9;39(18):5303-11.
An even more sophisticated example is Johnson et al.'s (2002) article, "Origins of the 2,4-Dinitrotoluene Pathway". 2,4-dinitrotoluene (DNT) is another recently human-introduced compound, and yet bacteria have assembled a quite complex pathway for its degradation. The summary of the reconstructed evolution of the pathway is also quite complex (and detailed):
Otto SP, Yong P. The evolution of gene duplicates. Adv Genet 2002;46:451-83 Related Articles, Links
Betran E, Long M. Expansion of genome coding regions by acquisition of new genes. Genetica. 2002 May;115(1):65-80.
Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV. Selection in the evolution of gene duplications. Genome Biol 2002;3(2):RESEARCH0008 (free online)
Eizinger A, Jungblut B, Sommer RJ. Evolutionary change in the functional specificity of genes. Trends Genet 1999 May;15(5):197-202
Hughes A. Adaptive evolution after gene duplication. Trends Genet 2002 Sep;18(9):433
Ganfornina MD, Sanchez D. Generation of evolutionary novelty by functional shift. Bioessays. 1999 May;21(5):432-9.
Long M. Evolution of novel genes. Curr Opin Genet Dev 2001 Dec;11(6):673-80
True JR, Carroll SB. Gene Co-Option in Physiological and Morphological Evolution. Annu Rev Cell Dev Biol. 2002
Here's a case of cooption in a slightly different sense, but returning to one of my original points: microbes "designed" to subvert the immune system:
|Date: 2003/02/17 20:12:31, Link|
Old posts on the topic:
Mot homologies in context of Musgrave's Flagellum FAQ
The bacterial flagellum evolved (scroll down to get the best post)
Beating a dead horse, or, flagellating the flagellum
Evolving the Bacterial Flagellum by Mike Gene (and unfortunately, MG's essay still hasn't been finished as far as I can tell)
|Date: 2003/02/17 22:06:54, Link|
|Date: 2003/02/18 18:45:12, Link|
Heh. Check this out. I never spent much time on the nonstructural components of the bacterial flagellum, since pretty much everyone focuses on the structural parts, but Dembski in his recent essay apparently was getting nervous that too many structural parts had been given alternative functions, and so he made reference to all of the nonstructural genes involved.
So I did a search on chemotaxis genes. Look what I found:
My brief summary: some good hints about the ultimate origin of histidine kinases, some faint hints about the ultimate origin of response regulators, but: clear evidence that key flagellar chemotaxis proteins served a multitude of other roles prior to being flagellar.
|Date: 2003/02/19 03:09:08, Link|
In the "just how precise would the organization of flagellum operons really have to be to get a minimal functioning flagellum?" category:
|Date: 2003/02/20 01:34:35, Link|
There is a certain sad irony here, and I'm not talking about meningitis being a disease of the brain...
|Date: 2003/02/20 02:10:10, Link|
[cross-posted to t.o. and AE]
The release of this *can't* be accidental. I don't think the DI has ever published a random "let's restate our same old arguments for no explicit reason" article like this. But "Media Advisory on Evolution Controversies" is a particularly oblique term methinks.
And any mention of the Stevolutionists is conspicuous by it's absence.
Perhaps they've been getting a few skeptical calls from press people?
Media Advisory on Evolution Controversies
February 19, 2003
Contact: Mark Edwards, 206-292-0401 x 107 firstname.lastname@example.org
As you report on controversies over evolution and intelligent design, here are some facts you might find useful:
1. There is a growing scientific controversy over Darwinian evolution.
a) Today there are critics of Darwinian evolution within the scientific community, including biologists at mainstream American universities. In 2001, more than 100 scientists including scholars at such institutions as Yale, Princeton, MIT, and the Smithsonian signed a public statement announcing that they were "skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged." [A complete list of these scientists can be found in A Scientific Dissent from Darwinism.]
b) Because of the scientific critics of Darwin's theory, it is misleading to present the modern controversy over Darwinian evolution as a simplistic battle between "science" and "religious fundamentalists." Accurate reporting on this issue should do justice to the complexities of the real situation, not resurrect stereotypes from the fictional movie Inherit the Wind.
2. It is constitutional and legal for teachers to teach about the scientific controversies surrounding Darwinian evolution.
a) The courts have frowned upon raising religious objections to evolution in science classrooms, but these legal restrictions are irrelevant to discussions of scientific controversies over evolution.
b) According to law professor David DeWolf, co-author of the leading law review article about how to teach the evolution controversy legally, there is absolutely no constitutional problem with acquainting students with scientific criticisms of Darwin's theory currently being made by scientists. [See David DeWolf et. al., Teaching the Origins Controversy: Science, Or Religion, Or Speech? Utah Law Review (2000)].
"Teaching a variety of scientific theories about the origins of humankind to schoolchildren might be validly done with the clear secular intent of enhancing the effectiveness of science instruction."
- U.S. Supreme Court, Edwards vs. Aguillard Ruling (1987)
3. The failure of biology curricula to discuss the weaknesses as well as the strengths of Darwin's theory is attracting increased criticism from educators, scientists, and the general public.
a) According to biology professor Scott Minnich of the University of Idaho, Darwinian evolution has become "the exceptional area that you can't criticize" in science education, something he considers "a bad precedent." In his view, we need to "teach it more, and teach it critically."
b) According to a 2001 Zogby Poll, an overwhelming majority of Americans (71%) believe that "biology teachers should teach Darwin's theory of evolution, but also the scientific evidence against it."
c) Recent scientific reports have shown that some of the most common scientific proofs for Darwin's theory that are cited in high school and college textbooks are now widely known to be flawed, notably Haeckel's embryos and the Peppered Moth experiments [see linked NY Times' articles].
4. Federal education policy as articulated by Congress now calls for an balanced approach when teaching about controversial scientific topics such as evolution.
a) In the Conference Report to the landmark No Child Left Behind Act of 2001, Congress clearly advised states to provide for the balanced treatment of controversial scientific issues like evolution. According to Congress, "where topics are taught that may generate controversy (such as biological evolution), the curriculum should help students to understand the full range of scientific views that exist, why such topics may generate controversy, and how scientific discoveries can profoundly affect society." (This language originally came from Sen. Rick Santorum , R-PA, and is sometimes called The Santorum Amendment.)
b) U.S. Senator Robert Byrd (Dem-WV) expressed the sentiments of many lawmakers when he declared that "it is important that students be exposed not only to the theory of evolution, but also to the context in which it is viewed by many in our society. If students cannot learn to debate different viewpoints and to explore a range of theories in the classroom, what hope have we for civil discourse beyond the schoolhouse doors?" [Congressional Record, June 13, 2001]
5. Darwin himself would have likely agreed to a 'teach the controversy' approach.
In The Origin of Species Darwin wrote: "A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question."
Can teachers discuss the scientific controversy over Darwinian theory? Yes, in fact, good education demands it.
About Discovery Institute
Discovery Institute is non-profit, non-partisan policy and research organization on issues from transportation to technology to tax policy. In science education, it supports a "teach the controversy" approach to Darwinian evolution. Its Center for Science and Culture has more than 40 affiliated biologists, biochemists, physicists, philosophers and historians of science, and public policy and legal experts, most of whom also have positions with colleges and universities.
-------------------------------------------------------------------------------Discovery Institute is a non-profit, non-partisan, public policy think tank headquartered in Seattle dealing with national and international affairs. The Institute is dedicated to exploring and promoting public policies that advance representative democracy, free enterprise and individual liberty. For more information visit Discovery's website at http://www.discovery.org.
Please report any errors to email@example.com
|Date: 2003/02/20 22:54:56, Link|
|Date: 2003/02/21 02:47:25, Link|
Martino Rizzotti published a book, Early Evolution, in 2000, which presents a reasonably detailed scenario deriving the flagellum from an F1F0 ATPase. Compared to other options it is not particularly convincing, although he does rather better at it than one might otherwise expect.
But, it is published, here are some online links:
Cavalier-Smith was fairly critical of the book in his review, but does cite the flagellum scenario in passing in one of his articles.
|Date: 2003/02/24 20:18:43, Link|
Evolution and Ant Agriculture: a response to Ilíon.
Some of his other posts:
Successful predictions of evolutionary theory
Here's da whole thing:
In the "Still Spinning Just Fine" thread, Ilíon brought to our attention the purportedly co-evolved ant-fungus-mold-bacterium system as a case that presents difficulties for the traditional Darwinian paradigm. As an ant evolution researcher, I am of the opinion that the ant/fungus/mold/bacterium relationship is fascinating regardless of one's perspective, and think that the topic merits its own thread. I also happen to think that much of what we know about the workings (and even the existence) of this complex relationship is a direct consequence of the use of Darwinian theory by biologists, and I echo Marc's sentiments that the system is a fine example of evolutionary biology in practice.
This is a long post, and it has the following structure:
1. Quick background.
In a nutshell, there are some 200+ species of ants in the new world tropics that are obligate fungivores. These are mostly small, inconspicuous ants, but the group also includes the famous and economically important leaf-cutter ants. These ants are involved in a largely mutualistic relationship with a fungus. The fungus is eaten by the ants, but the fungus also depends on the ants for its propogation: a true agricultural system. In the past 4 years, a twist has been discovered: an Escovopsis mold that is a specialized parasite of the ant fungus, and a Streptomyces bacterium that produces an antibiotic that the ants use to combat the parasitic Escovopsis.
The attine ants
The discovery of the Streptomyces
Ulrich Mueller's publications
photo gallery of Atta leaf-cutters and gardens
photo gallery of Acromyrmex leaf-cutters
photo gallery of Mycocepurus, a more "primitive" attine.
(note, the final three links are shameless self-promotion of my brand-new web site)
2. The role of evolutionary theory in ant/fungus research.
To say that most of what we know about fungus-growing ants and their fungi stems directly or indirectly from evolutionary research would not be an exaggeration. To say that everything we know about the Escovopsis parasite is due to evolutionary research is a simple, observational truth.
I bring this up because Ilíon wrote:
But this discovery is just the tip of the iceberg. Biologists have flocked to the attine/fungus system because the system raises so many interesting evolutionary issues, some of which may be easily resolved and others of which are real head-scratchers. Besides the discovery of the fungal parasite, here are a few other bits of knowledge that owe their existence to evolutionary theory. It is by no means an exhaustive list. (Note: by ‘evolutionary theory', I don't mean as Ilíon insinuates that observations are merely reported in ‘Darwinspeak'. I mean that these discoveries were motivated by Darwinian research questions, or that their discovery would not have happened without knowledge of common descent or natural selection.)
1. Ant fungi have been transmitted horizontally between ant nests, in addition to vertical transmission from parent to daughter colony. This result emerged from phylogenetic analysis (See Mueller, U.G. 2002. American Naturalist 160(supplement): s67-s98.).
2. Attine ant species with more complex caste systems are polyandrous (See Murakami, T. et al 2000. Behav. Ecol. SocioBiol.48:276-284.)
3. Escovopsis fungi likely had a single origin (See Currie et al 2003. Science 299:386-388.)
4. The fungal cultivars do sometimes depart from the ant mutualism and become free-living (See Mueller, U.G. 2002. American Naturalist 160(supplement): s67-s98.).
I don't bring up these examples as a demonstration that Darwinian evolutionary theory is ultimately the best explanation of the ant/fungus/mold/bacteria relation. Rather, I bring them up to show that Darwinian theories have been extremely fruitful in both bringing this system to light and in stimulating further research. The ability to generate questions is *extremely* important in scientific theories, and the ‘head scratching' produced by Darwinian theories is a natural consequence of their usefulness. Head-scratching means questions, and questions mean research. A theory that doesn't raise questions does not provide a useful substrate for science.
It is worth noting that so far answers have been forthcoming to these questions, which I take as an indication that we are on the right track.
It is also worth noting that little, if anything, in this system can be traced to creationist or Intelligent Design thought. Simply put, advocates of those schools will need to provide quite a bit more detail about how, where, and when design was affected in this system before a design research program will be possible. If you would like to see design adopted by scientists working in this system, you've got to provide an alternative that is more useful in the lab and in the field than Darwinism. This will entail doing better than making non-committal statements about the "unknowability" of the design process of the sort that permeates I.D.ist writings. Meanwhile, Darwinian reseach keeps suggesting and finding new players in the symbiosis.
3. Some quibbles over technical issues.
Some of my issues are with Ilíon, but most are with the NYTimes article that Ilíon cites.
1. A literal single origin, where one colony picks up one fungus and the rest is history. I think this is the interpretation that you object to. Not without reason, IMHO.
2. Multiple origins, but all the fungal cultivars involved are closely related and share a common ancestor. If that ancestor left no descendants that are not cultivated by ants in the present day, then the fungi will still trace back to a single node on the phylogeny as an artifact of extinction, even though there may actually have been multiple domestication events.
3. Multiple origins, but when the ants lose their fungi they re-acquire not from the wild but from another ant nest. There is some evidence that this is what modern attine ants do when they lose their fungus. This way the fungus spreads laterally among colonies, and given a stochastic process of fungal lineage loss throughout the population all colonies will eventually come to cultivate a single lineage. The other original fungal lineages, having gone extinct, will not appear in the phylogenetic analysis and the phylogeny will trace back to a single node.
The take-home message is that "single origin" claims can be a bit misleading. Currently there is no way to test between these different possibilities, so for the time being we are stuck with a "single origin" only in the broad sense.
4. The evidence for common descent and natural selection in the ant/fungus/mold/bacteria system.
One compelling reason to look for evolutionary processes as explanations for the ant/fungus/mold/bacteria relationship is that there is a great deal of evidence for common descent and for Darwinian evolution in these organisms. Here it is, in no particular order:
Social Evolution in Ants
In the past, I've also written threads on ARN about sex ratios and evolution, here:
Successful predictions of evolutionary theory
There. Now I'm done.
|Date: 2003/02/24 20:27:35, Link|
The creos have taken up Behe's banner on this one.
Mostly good for the pics, and a JBS Haldane quote that I would like to follow up:
Design in Living Organisms: Motors
by Jonathan Sarfati
Creation Ex Nihilo Technical Journal 12(1):3–5, 1998
|Date: 2003/02/27 19:45:43, Link|
IDEA club (/center) responds to Project Steve in their page:
Scientists and other Intellectuals that Doubt Darwinism and other Naturalistic Theories of Origins
An incomplete and continually updated list
I hadn't seen this page before, but Casey Luskin (and perhaps others...) compiled all the various lists of creationist scientists, DI list-signers, etc. This is actually a useful service as we can see how many Steves there are in all the lists put together (note that the net is quite wide, being very much international and non-biology specific).
At the end Luskin says there's 9 Steves in the list. For your enjoyment, here they are (the list is in subsections but the numbers are cumulative as different lists are appended):
In case you weren't counting:
Number of (probable) YECs: 5
Number of biologists = 0. Organometallic chemistry is as close as they get...
|Date: 2003/03/02 21:03:25, Link|
On the subject of how a proto-flagellum would be positioned on the cell surface, it occurred to me awhile ago that it wouldn't matter if the cell was spherical shaped (coccus).
E.g. like this bacterium:
This is aside from the question of whether flagellum positioning is needed even in your average cell, e.g. it seems that E. coli does just fine by having several randomly-placed (or perhaps random but spaced-apart) peritrichous flagella.
A page describing the various ways flagella are distributed on bacteria.
|Date: 2003/03/02 21:49:25, Link|
Links/material on this topic that refute various common antievolutionist distortions of the topic:
II Evo forum thread
|Date: 2003/03/09 20:01:34, Link|
Jarrell and others have written a detailed review of prok. motility. Very useful article.
Microbiology 2003 Feb;149(Pt 2):295-304
Prokaryotic motility structures.
Bardy SL, Ng SY, Jarrell KF.
Department of Microbiology and Immunology, Queen's University, Kingston, ON, Canada K7L 3N6.
Prokaryotes use a wide variety of structures to facilitate motility. The majority of research to date has focused on swimming motility and the molecular architecture of the bacterial flagellum. While intriguing questions remain, especially concerning the specialized export system involved in flagellum assembly, for the most part the structural components and their location within the flagellum and function are now known. The same cannot be said of the other apparati including archaeal flagella, type IV pili, the junctional pore, ratchet structure and the contractile cytoskeleton used by a variety of organisms for motility. In these cases, many of the structural components have yet to be identified and the mechanism of action that results in motility is often still poorly understood. Research on the bacterial flagellum has greatly aided our understanding of not only motility but also protein secretion and genetic regulation systems. Continued study and understanding of all prokaryotic motility structures will provide a wealth of knowledge that is sure to extend beyond the bounds of prokaryotic movement.
PMID: 12624192 [PubMed - in process]
- They say the archaeal flagellum is powered by a proton gradient. This contradicts my earlier thought which was that it was ATP-powered. However, they cite no demonstration of the power source. I would keep the question in mind, but here is what they say:
"The other major subdivision of prokaryotes is the domain Archaea. Members are motile via a structure that appears to be fundamentally distinct from the bacterial counterpart in composition and, likely, assembly (Thomas et al., 2001). The archaeal flagellum is a rotary structure, driven by a proton gradient, and it is thinner than typical bacterial flagella."
- A more detailed review of spirochete flagella which are weird.
- A nice review of current knowledge on the archaeal flagellum proteins, several identified similarities/homologies to type IV pilins...
- The archaeal flagellum probably/usually has hook and filament proteins, and they find at least a bit of evidence that the difference between the two is not so great:
"In archaea, there are always multiple (2–6) flagellin genes present (Sulfolobus solfataricus appears to be an exception). Thus far the only components of the archaeal flagellum identified are the flagellins themselves, where it appears that the multiple flagellins are all present as structural components of the assembled flagellum. Recent work indicated that the hook protein might in fact be a minor flagellin, FlaB3 in the case of Methanococcus voltae (Bardy et al., 2002) (Fig. 4)."
- Type IV pili movies (twitching motility etc.):
Type IV pili movies
- Ratchet structure review; it would be nice to know the genes involved, particularly if there is any rotary motion involved...
- Here's a whole new kind of motility, the contractile cytoskeleton (in a prokaryote)
Spiroplasma melliferum is one of the smallest free-living organisms on earth with a genome size about half that of E. coli. Surprisingly, this bacterium is motile, though nonflagellated, and it lacks any genes analogous to ones involved in flagellation as well as known gliding genes. This organism lacks a cell wall but has a membrane-bound internal cytoskeleton, composed primarily of a unique 59 kDa protein, which is thought to act as a linear motor, in contrast to the rotary motor of the flagellum (Trachtenberg, 1998) (Fig. 9). The cytoskeleton is attached to the cytoplasmic membrane, possibly through one or more of the approximately seven proteins that co-purify with it. The cytoskeleton is involved in motility due to its linear contraction and its close interaction with the cytoplasmic membrane (Trachtenberg & Gilad, 2001). The cytoskeleton exists as a seven fibril ribbon that extends the length of the cell. A conformational switch in the monomer leads to length changes: because of the strong interconnectiveness of the cytoskeleton subunits, changes in any part of the fibril are transmitted to neighbours and ultimately to the attached membrane. Though poorly studied at present, this motility structure represents a truly novel approach to motility using what appears to be a much smaller complement of genes than that required for flagellation. Identification of the roles of the cytoskeleton co-purifying proteins will be a major advance in the elucidation of this motility structure."
Conclusion: not much on evolution but good overview review.
While motility is commonplace among the prokaryotes, it is important to note the variety of structures responsible for motility. These structures vary depending not only on the organism in question, but also on the particular environment. Study of the bacterial flagellum has provided insights into many aspects of prokaryotic cellular activities including genetics and regulation, physiology, environmental sensing, protein secretion and assembly of complex structures. Continued study of all prokaryotic motility structures will provide knowledge that is likely to reach far beyond the topic of motility.
|Date: 2003/03/13 14:54:32, Link|
Charlie D. has expressed the problems with Mike Gene's frontloading in about the most succinct way, ever, I think:
Originally posted by Mike Gene:
The key is always to remember how ID critics view ID proponents - ID proponents are either stupid, ignorant, deluded, or evil. The ID critics argue with me not to understand my views, or even objectively compare views, but because they are looking for ways to rationalize my existence. Someway, somehow, I must be fitted into the precast stereotypes. That's their only interest in these debates (that is, when they are not politicking).
Talk about projecting and sterotyping, Mike! LOL.
Personally, I think your theories have muddled considerably in the past few months. As such, they may seem to you they "explain" more things, but in fact to me they are far less interesting.
Right now, your hypothesized designers seem to me completely schizophrenic. On one side, they seem like totally anal micromanagers: they gave their colonizing bacteria supersophisticated micromachines made up of (altogether) probably hundreds of complex proteins, to do things like syntesizing more proteins, degrading proteins through the ubiquitin system, replicating DNA and correcting replication errors, generating energy, etc etc, even allowing them to swim.
On the other side, the same alien bioengineers were supposedly complete laissez-faire evolutionists, providing bacteria with a minimalist compendium of protein domains (to the point of purposefully avoiding hydrophobic aminoacids!, and a front-loaded genetic system that would introduce mutations at high frequency in these very simple protein domains to allow them to later develop more complex domains, so that those bacteria could evolve freely in a fully darwinain fashion.
So bacteria were both very simple, and programmed to evolve, and very complex, with all sorts of unevolvable, rigid micromachines. They had very simple protein domains and a system to mutate them at high frequency, and very complex proteins, with fully formed domains, in which changes in domain structure almost invariably kill the original function. Extreme mutability and error correction. On the one side the bioengineers spent countless alien-hours designing a system for bacteria to swim, and on the other their evolvable bacteria evolved probably a half dozen equally efficient motility systems on their own, thanks to their evolvability.
Whenever the evolution of something seems hard to figure out, it's because that something was designed; whenever it seems pretty straightfoward, it's because it was designed to evolve. Basically, your model right now it's not just indistinguishable from evolutionary theory, it's indistinguishable from pretty much anything. Pardon our lack of enthusiasm, if you know what I mean.
The non-teleologist also wants the teleologist to prove the impossible, namely, demonstrate that non-teleological processes couldn't produce some aspect of biotic reality.
Wrong, at least as far as I am concerned. I just want evidence that teleology can generate any aspect of current biotic reality. We have plenty of positive evidence of the existence and power of non-teleologic processes - none of teleology. It's up to the teleologicians to show there's something there, other than smoke and mirrors.
|Date: 2003/03/15 01:37:14, Link|
Rather like what the remarkably simple, 1-component (dimer) PPase does with phosphates:
Hmm, might not be working, look here:
...and both are coupled to H+ gradients, and use the same basic fold, what a coincidence! It just looks like all of that rotating complexity may be useful and efficiency-increasing add-on rather than an absolutely necessary part of primitive cellular energetics.
1) TTSS with nonvirulence, nonflagellar functions, and
2) Basal homologs of the TTSS.
These are predictions that only further data can resolve, however. In general, you'll forgive me for sticking with Baltscheffsky until some IDist (1) acknowledges his existence and (2) explains how they don't greatly weaken the ID argument based on the F1F0 ATPase.
|Date: 2003/03/15 02:05:37, Link|
Some ISCID threads on this:
Topic: Is the DNA code universality strong evidence for evolution?
Topic: Common descent
|Date: 2003/03/15 04:56:51, Link|
Free online article comparing PPases and F1F0-ATPases:
|Date: 2003/03/21 00:31:33, Link|
Well, as predicted, the people who actually know something about peppered moths are much more critical of Judith Hooper's book Of Moths and Men. All I'm waiting for now is a review from M.E.N. Majerus.
David Rudge, Untitled book review of Judith Hooper's Of Moths and Men, Journal of the History of Biology, Spring 2003, pp. 207-209
Judith Hooper, Of Moths and Men: An Evolutionary Tale: Intrigue, Tragedy and the Peppered Moth (New York: W.W. Norton; London: Fourth Estate, 2002), xx + 377 pp., illus., $26.95.
[note weird inversion of "Of Moths and Men" in first sentence. Guess the journal editor is a bit overworked...]
Of Men and Moths is a popularized account of Bernard Kettlewell’s investigations of the phenomenon of industrial melanism, the rapid rise in frequency of dark forms of many moth species downwind of manufacturing centers that occurred as an apparent consequence of large-scale air pollution associated with the industrial revolution. Kettlewell’s experiments are widely cited as demonstrating that this change is due to natural selection, and, in particular, the selective advantage of dark coloration against birds in sootdarkened environments. Hooper accuses Kettlewell of committing fraud and members of E.B. Ford’s Oxford School of Ecological Genetics of conspiring to hide details of outstanding problems surrounding the phenomenon to advance their own pan-selectionist agenda. The book concludes by reviewing how the career of a lone dissenter, Ted Sargent, was derailed as a result of his heresy. The subtitle is apt, but not for reasons the author intends. The intrigue surrounding this book rests in making sense of why someone with Hooper’s gift for science writing would stoop to the trumped-up fiction of scientific fraud to sell a book; the tragedy is the pernicious effects this book will have on biology education and the history of science community.
While Kettlewell was highly regarded as a naturalist, his colleagues had less respect for him as a scientist. It is also fair to say that the phenomenon is more complicated than textbooks would have us believe and that several of the techniques and assumptions Kettlewell used have been called into question. Hooper’s evidence that Kettlewell committed fraud, a claim neither historians nor any of the numerous researchers on industrial melanism who have attempted to extend Kettlewell’s work have *ever* made, is an apparent discrepancy in his 1953 recapture results. Calling attention to the fact that the figures went up the day Ford wrote a letter sympathizing with Kettlewell’s results thus far, Hooper alleges that as a result of exhaustion, sickness, alcohol, tobacco, and his own insecurities, Kettlewell resorted to falsifying his data to placate Ford. Using historical meteorological records, she considers and triumphantly rejects one alternative explanation. There are many other reasons for why the recapture figures might have risen (for example, on this day Kettlewell began using three times as many moths). Significantly, not even Ted Sargent, one of Kettlewell’s most vocal critics who Hooper interviews, agrees with Hooper’s claim that Kettlewell committed fraud (p. 255).
The portrayals of Kettlewell’s and Ford’s scientific work are distorted by Hooper’s obvious agenda and littered with interpretive errors (see B. Grant, “Sour Grapes of Wrath,” Science 297 : 940–941). Much of the book is devoted to spreading gossip. While some use of anecdotes is warranted to humanize the story, the emphasis on details of their private lives results in caricatures that make the respect and affection their colleagues had for Kettlewell and Ford (both privately and publicly) a complete mystery. The relevance of these anecdotes to Hooper’s accusations is also unclear. Repeated references to Ford’s reputation as a misogynist, his homosexuality, his mysterious young ward, and the sordid circumstances surrounding the suicide of Kettlewell’s daughter suggest that, in lieu of evidence, Hooper has resorted to dredging up every bit of dirt she could find on Kettlewell and Ford to coax the reader into believing they were capable of committing fraud.
Hooper’s second thesis is more problematic. She alleges that researchers on industrial melanism have conspired to hide outstanding problems and ostracize those who dare to question the standard story. This elite group centered in Britain supposedly have the power to jeopardize Ted Sargent’s candidacy for tenure at Amherst in the U.S., yet curiously cannot prevent the publication of articles that raise questions about the standard account. Surely the primary source of Sargent’s tenure problems has to do with the excessive stress science departments place on external funding, a concern his British colleagues no doubt share.
Sadly this book will undoubtedly be used by creationists and intelligent design theorists in their ongoing assault on the teaching of evolution. The several outstanding interpretive problems surrounding the phenomenon of industrial melanism and Kettlewell’s work do not imply it should be removed from textbooks and indeed may augment its value for the teaching of science (see D.W. Rudge, “Does Being Wrong Make Kettlewell Wrong for Science Teaching?” Journal of Biological Education 35 : 5–11). The most pernicious effect of this book however, will be upon the history of science community. It is a warning to scientists of what can happen to the memories of you and your loved ones if your papers fall into the wrong hands.
David Wÿss Rudge
David Rudge links for those interested in his other work:
Dave Rudge's Home Page
Rev Biol Trop 2002 Mar;50(1):1-7
Cryptic designs on the peppered moth.
Department of Biological Sciences, Institute for Science Education, Western Michigan University, 3134 Wood Hall, Kalamazoo, MI 49008-5410, USA. firstname.lastname@example.org
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.
|Date: 2003/03/21 01:32:44, Link|
A coupla recent flag-related articles, my summaries of evo-interesting bits in .
|Date: 2003/03/21 03:03:24, Link|
If anyone has text access and could send me the pdf of the previous article I'd be grateful. I did a google search but no one has put it on the web yet.
I did turn this up, though, dunno how I missed it before:
A Scenario for the Evolution of Hemostasis
by Kevin O'Brien
I've often thought that such an article could be written, I just didn't know who would do it. But someone has.
I recommend we attempt to get some version of this on talkdesign.org if theyeti et al. consider it reasonable and if we can get permission (its a t.o. poster, I don't think that would be a problem).
It would need a fair bit more editing though...
|Date: 2003/03/25 20:49:43, Link|
EMBO Reports 4, 3, 235 (2003)
A rather uncritical review:
Gabby Dover is at the University of Leicester, UK, and is author of Dear Mr Darwin: Letters on the Evolution of Life and Human Nature (2000).
Of Moths And Men: An Evolutionary Tale
by Judith Hooper
W. W. Norton & Co., New York, USA
ISBN 0 393 05121 8
|Date: 2003/03/29 16:15:44, Link|
Here is a thread with some striking pics on human tails and natural variation in the tailbone:
Baby with tail 'reincarnation of Hindu god'
|Date: 2003/03/29 17:43:32, Link|
A recent post of mine that I rather like:
(follows some discussion of eye evolution)
Topic: Distinguishing Mechanisms of Co-option, started by John Bracht
This is the problem with the "vague designer" hypothesis -- an uncharacterized designer could, for all we know, do things however the heck he wants. The "vague designer" hypothesis can "explain" not only observations supporting standard evolutionary biology but also any other set of observations.
Darwin had a similar problem: once he had convinced someone that the special creation "poof" model was untenable, a common response was to retreat to a vaguer position such as "the plan of Creation" or whatnot. There are some great Darwin quotes somewhere on just how scientifically useless such statements are, unfortunately I can only find one at the moment:
To get a little more specific, consider one major difference between human intelligent design and "design" as seen in biology. Human designs -- such as transistors, computers, radios, plastics, GPS systems, etc., etc., -- get invented in one place and then transplanted wholesale into a multiude of other "lineages" -- cars, boats, planes, rockets, etc. In biology, on the other hand, the transmittance of designs through lineages appears to be strictly limited to that allowed by known processes of heredity, namely:
1) Lineal descent (parents to children, species to descendent species). This is the major one.
2) or, sometimes, lateral gene transfer (although this seems to be limited to fairly simple systems that can fit on plasmids and subject to a number of other constraints, e.g. rare in things like metazoans with protected germline cells).
In other words, in human design you see an invention originate and then get basically simultaneously integrated across a wide range of "lineages". In biological design the invention sits in whatever lineage it originated in (small groups of genes on mobile genetic elements being the exception, with a known and observed natural mechanism).
The fact that putative instances of cooption (the "same" structure being used for different functions) appear to follow the above pattern to a tee seems to me to be a perfect example of John's request regarding:
There is no reason for us to expect a designer to constrain design-transmittance to the processes of heredity; and yet we see such constraints, as we would expect based on common descent (= the continous operation of everday heredity).
However, a typical response that I've seen is to invoke front-loading, or "maybe the designer constrained himself to work within lineages for some reason", or "the designer might work in mysterious ways", or some other backup defense in order to save design from the falsification given in the above argument. And this gets us back to Darwin's point about how vague designer-talk is scientifically vacuous and actually does no explaining at all.
In summary, you need at least a somewhat specific model of the designer (this does *not* require foreknowledge, just like any proposed hypothesis does not require foreknowledge) in order to have something with scientific tractability. If ID stays in the "vague" category -- then it will never rise above the level of other such vague ideas ("an immaterial innate force causes design").
PS: Another similar test is that:
1) Evolved cooptions will always have the "purpose" of increasing the reproduction of the genes of the organism carrying the new adaptation, but
2) There is no reason to expect such from IDed cooptions, indeed in human designs the designs are always meant to serve the purposes of the designer.
This is also, IMO, a good test, but again the IDist can escape by post-hoc appeals to a designer that mimics evolution for some reason. In doing so they escape the frying pan of falsification but fall into the fire of scientific vacuousness.
|Date: 2003/03/31 22:14:27, Link|
New TCS article gives us the short version of current euk. phylogeny & who may and may not be primitively non-ciliated:
|Date: 2003/03/31 22:22:48, Link|
Note that while flagella do not apparently make use of a secretin as the outer membrane pore, type III virulence systems do. And furthermore, the outer membrane ring of the flagellum *is* secreted by a type II rather than Type III virulence system, an interesting similarity.
Other points here:
- 6+ secretion systems in one critter
- both type II and type III SS have virulent and non-virulent uses
|Date: 2003/03/31 22:46:04, Link|
Since this came up again with the discussion with Nelson Alonso on the ISCID thread, I just came across a review of a recent workshop on evolutionary immunology. I quote the bit about the origin of recombining receptors:
(the bit about the regulation of lamprey receptors is key...)
In the conclusion the old theme of change-of-function is emphasized:
...this last bit seems to be saying that understanding the evolution of a complex system is much easy when you have a good phylogenetic understanding of the system (as with the immune system) than when you don't (e.g. most of Behe's IC systems, which originated in single-celled organisms).
|Date: 2003/03/31 22:49:44, Link|
In the "here is part of what non-rearranging receptors do" category:
|Date: 2003/03/31 23:29:49, Link|
Wow, thanks for the info Erik.
I think that the variability of the coccyx is interesting as it is just the kind of thing that CD mentions a bunch of times in OoS -- that structures that have lost utility become more variable...
|Date: 2003/04/04 21:26:21, Link|
Good little one that Ian Musgrave posted at t.o. in rebuttal to a creo reiterating Behe's argument regarding Ken Miller's citation of Barry Hall's work on lactose metabolism:
|Date: 2003/04/04 23:21:16, Link|
|Date: 2003/04/04 23:50:11, Link|
As Commentary has once again indulged Berlinski's meanderings around evolutionary theory (they never appear to run out of purple ink for his prose), I am starting a thread to discuss him, accumulate links, etc., perhaps eventually have a FAQ.
Eye-evolution specific, or general picking of nits, as there are many to pick with Berlinski and he sure loves doing it to the Darwinists...
First, background links on Berlinski and his writings:
Recent articles under discussion:
(Berlinski on ID and evolution; full-text must be purchased, but his section on the eye is hosted by the DI under The Vexing Eye)
(Commentary. April 1, 2003: On the 1994 paper by Nilsson and Pelger on eye evolution, and the usage thereof. Online at the DI with a few typos and weirdly-formatted equations)
(Berlinski reviews Dawkins Climbing Mount Improbable and comments on eye evolution at length) (also hosted by the DI)
And the famous:
|Date: 2003/04/05 00:33:05, Link|
There are some great t.o. posts on Berlinski that never got turned into FAQs:
Here is the link to the google search, see the part-by-part critique "Response to Berlinski" by Paul J. Gans replying to "A Deniable Darwin".
If you scroll down a bit you even find some Berlinski posts from 1996 where various t.o. regulars hand him his head on topics like molecular evolution.
|Date: 2003/04/05 00:55:52, Link|
Here is the Berlinski-relevant bit of my recent t.o. post:
A mistaken popularization, even fairly widely repeated, does not amount to "scientific fraud" as Berlinski alledges. Further, it should be noted that some sites follow the paper closely, e.g. good ol' Don Lindsay's site from 1998 is fine and worth recommending to people.
Nilsson ('s lab?) describes this 1994 paper as "theoretical modelling", with full computer simulations in the "something we will do" category:
...however, I strongly doubt that the calculations that they performed to determine eye acuity (their measure of eye "goodness") were done by hand. The paper repeatedly speaks of functions, curves, etc. which, in order to plot them, would always be done with a computer. Therefore it was a computer model of a sort, although not what I would call "a stochastic computer simulation" which is what Dawkins was implying had occurred (he did not use those exact words, mind you).
I think that people have a kind of mystical notion about computer models, that if the model is "more complex than I can understand" then it is equivalent to "they modelled the world in all necessary detail inside the computer!!". This is particularly true if someone presents a nice animation as the output. This is not the case. All computer models are gross simplifications, and IMO there is no particular hard-and-fast distinction between a theoretical model where calculations are done with a computer and a computer simulation where there is some attempt to perform a simulation with random inputs and explicit time-steps. It is, to plagiarize from Darwin, a difference of degree, not of kind.
"Mere calculations" computer models, e.g. the kind that can be done in a spreadsheet, have a very valid place. E.g. for a class I once simulated atmospheric temperature profiles in various latitudinal zones (a 2-D climate model) in Excel. You can reproduce some important features of the atmosphere using this kind of simple model (and in fact modern Global Climate Models are in part just a repetition of this kind of model in 3D).
So, to sum up my assessment of Berlinski:
The DI reports that Nilsson says this, here:
"Evolution" Series Claim on Eye Evolution More Fiction than Fact
...but there is no indication that the complexities of defining "computer model" were discussed.
...well, Nilsson says that he is doing just that now.
Here I strongly disagree. This is exactly one of the things that they documented IMO: that at least at the morphological level, just such a continuum exists, given the starting point. Only small quantitative variations in "cell" position, thickness, density, etc. are required.
This is true as far as I can tell; however we *know* that variation + selection results in the kinds of gradual "microevolutionary" changes that Nilsson & Pelger were modelling in their paper. The only changes they invoked in their model were of the finch-beak-size variation type: small and quantitative. This is pretty much the point of their paper.
True, but this gets us back to what a naive view of a "computer model" Berlinski's depiction is. Still, Dawkins shouldn't have implied that such existed.
(But: Didn't the "Evolution" special have a section wherein Nilsson or somebody constructed a *physical* model of their eye evolution scenario, where various stages could be enacted, variations tried, and the resulting "vision" actually seen? I remember someone gradually inflating a lens or something at any rate, and the picture moving from blurry to being focused.)
Tis true, there was no "homing" in the form of a search algorithm --however, they did demonstrate progressive advantage for eye shapes approaching Mattieseen's ratio. The relative advantage can be calculated, which is what they did.
Mistakes happen. I can think of more than a few that Berlinski has made, and yet he is the one declaring the central theory of modern biology to be no better than ID (which he now considers similarly unsupported).
BTW, it appears that someone has kindly put an HTML version of the Nilsson article online here (there is no pdf that I am aware of anywhere):
A pessimistic estimate...
(unfortunately there are no graphics included, and a few typos/format issues)
They probably did, somewhere. It is not the duty of authors to chase down every representation of their work, particularly *in other countries*. It might surprise Berlinski but not every country has the United States' hangup with evolution.
What, are they obligated to dig through every popular science book, look up the original literature on every single topic and determine the degree of accuracy of representation? This can be done but it is not a small matter. I suspect that Berlinski's evolution-related works would not fare well. For instance:
I don't have answers to all of these questions, but just as an amateur I can provide some. Unfortunately Berlinski never saw fit to look any of these up, and none of his DI fellows have bothered to correct him since the article came out in 1996. Roughly in order:
1) Male-eating is a subset of the widespread practice (in arthropods) of males offering up nutrient "gifts" to females for the purposes of (1) obtaining copulation and (2) prolonging copulation and preventing other males from copulating. And it is not true that the males always get eaten -- some of them will run for their lives at the first hint of hostility. This is only my hazy summary, but there is a massive literature on the topic. See e.g.:
Choe, Jae C., Crespi, Bernard J. The Evolution of Mating Systems in Insects and Arachnids. Cambridge, 1997.
...I would like to see a theory other than evolution devote the kind of attention and scientific sophistication that evolutionary theory has brought to the issue. What evolution predicts is that there will be a selective benefit for whatever apparently crazy behavior one sees (assuming it is a species-wide trait that easily could/should be something else). And apparently entomologists have confirmed that this is the case in the spider that Berlinski cites, even though he seems not to appreciate the significance of the fact.
2) "Why is the pitcher plant carnivorous, but not the thorn bush?"
If Berlinski had bothered to get up off his tush and go to the library to consult the literature -- which after all is what libraries are for -- he wouldn't have been so mystified. In a 1989 article by Thomas Givnish (of the Dept. of Botany, University of Wisconsin) entitled "Ecology and Evolution of Carnivorous Plants," Berlinski's question is anticipated and answered. I have included translation of the scientific jargon [in square brackets like this] for non-nerds in the audience.
In other words, the main answer to Berlinski's question is that nitrogen fixation doesn't work in the oxygen-poor muck of stagnant bogs, which gives the advantage to plants with an alternative means of acquiring nitrogen, namely carnivory. The secondary answer to Berlinski's question is that nitrogen fixing plants still need to get their trace nutrients (such as phosphorous) from the soil, and have the special requirement of molybdenum, so that in places where these nutrients are absent carnivorous plants have a further advantage.
Givnesh, T. J. (1989). Ecology and Evolution of Carnivorous Plants. Plant-Animal Interactions. W. G. Abrahamon. New York, McGraw-Hill Book Company: 243-290.
3) "[w]hy does the Pacific salmon require fresh water to spawn, but not the Chilean sea bass?"
I have no idea. Salmon are however related to a number of freshwater fish like trout. Are seabass? Is there an icthyologist in the audience? Did Berlinski ever consult one?
4) "Why has the British thrush learned to hammer snails upon rocks, but not the British blackbird, which often starves to death in the midst of plenty?"
I doubt that this even occurs as a regular matter. Why did Berlinski never provide a citation? I expect that the specialization of bird species on different foods would however be an important thing to consider.
5) "Why did the firefly discover bioluminescence, but not the wasp or the warrior ant."
Last I checked, wasps and ants were colonial social species where the queen is fertilized by one or a few males, IIRC just once before a long period of hive-making. Fireflies are, I expect, totally different. There are however chapters on both groups in Choe & Crespi (1996).
6) "why do the bees do their dance, but not the spider or the flies"
Well, gee, maybe because bees are colonial honey gatherers that live or die as a hive, and need to communicate the good nectar sources, while flies and spiders do nothing of the sort.
7) "why are women, but not cats, born without the sleek tails that would make them even more alluring than they already are?"
Berlinski is speaking for himself regarding attaction to tails, but the topic was recently discussed on t.o.:
...and I can add:
...and note that humans are descended from large, brachiating -- and not coincidentally, tailless -- apes.
Berlinski's comparison of geology to evolution is more apt than he knows. He can see how geology gives good overall explanations of mountains, if not every detail -- but for some reason he can't see that evolution does the same with organisms. Evolution predicts correlation of traits with the environment. Berlinski never looks at the environment (physical and ecological) in which his particular traits of interest occur, so he doesn't understand why they occur.[/quote]
Returning to Berlinski's original article in this thread:
If Dawkins' mistake is fraud, then Berlinski's multiple and repeated mistakes amount to a far ranging conspiracy (perhaps, a conspiracy to keep himself from understanding biology). I suggest that pronouncing on biology, without first knowing any, is the greater sin.
This anti-Berlinski rant has been developing in my head for some time. Thanks to Sunday morning for allowing its expression...
|Date: 2003/04/05 01:05:24, Link|
Hmm. Perhaps we should have a FAQ, "20 questions with David Berlinski" where all of his various questions are answered, and then we ask him some questions of our own.
Add such things to this thread if they occur to you.
|Date: 2003/04/05 01:55:45, Link|
Here is a bit of startling naivete from Berlinski's latest ("A Scientific Scandal"). I may send this bit as a letter to commentary or somthing.
While Berlinski should be congradulated for pointing out Dawkins' inaccurate popularization of Nilsson and Pelger's article on eye evolution as a stochastic computer simulation (it was actually a mathematical model), Berlinski should remove the plank from his own (discussion of the) eye. In "A Scientific Scandal" he asserts that one of the problems for eye evolution that Nilsson and Pelger did not consider was how the skull would be "reconstructed" to include eye sockets.
But as any decent student who has taken high school biology would know (at least as long as evolution was not expunged due to creationist political armtwisting), eyes evolved before bones! Cephalochordates, the closest invertebrate relatives of vertebrates, have primitive eyes but no bones. In fact, based on genetic evidence many biologists now think that vertebrate eyes share a common ancestral eyespot with insect eyes, the common ancestor being a perhaps millimeter-long, nearly transparent but eyespot-equipped worm.
Unfortunately, it is a typical creationist strawman to envision eye evolution as occurring on some kind of mythical eyeless fish with a fully-formed skull, brain, etc. On the contrary, biologists (who actually know some biology) know that all manner of gradations of eye complexity exist in extant organisms, from creatures with an "eye" consisting of a single photoreceptor cell, through all of the various stages that Nilsson and Pelger depict, to the "advanced" camera eyes of mammals and cephalpods. Sometimes the whole sequence from eyespot to advanced eye with lens can be seen in a single group (e.g. snails), yet another thing which Berlinski would have known if he'd followed the reference that Nilsson and Pelger gave to the actual classic work on eye evolution, a monster 56 page article by Salvini-Plawen and Mayr in the journal Evolutionary Biology (volume 10, 1977) that reviewed hundreds of papers on eyes across the animal kingdom, entitled "On the evolution of photoreceptors and eyes". Complex eyes with lenses have even evolved in single-celled dinoflagellates, which have no brains, blood vessels, or numerous other features Berlinski is concerned about.
Berlinski on the other hand has a brain as well as eyes, but apparently does not see when it comes to biology. He is not a creationist but he certainly seems to hang out with them and uncritically repeats many of their arguments, unaware of the biological facts which contradict them. If Berlinski is going to declare as bunk the central organizing theory of biology, he should be taking the matter up with biologists in the professional literature, rather than in forums like Commentary, wherein elementary questions like "which came first, skulls or eyes?" can be botched and yet still get published.
|Date: 2003/04/05 02:47:35, Link|
BTW, Nilsson is interviewed in the PBS "Evolution" series, and the segment is online here:
Evolution of the Eye
Zoologist Dan-Erik Nilsson demonstrates how the complex human eye could have evolved through natural selection acting on small variations. Starting with a simple patch of light sensitive cells, Nilsson's model "evolves" until a clear image is produced. Examples of organisms that still use the intermediary forms of vision are also shown. From Evolution: "Darwin's Dangerous Idea."
(1) "Computer model" or "computer simulation" is never mentioned, all anyone talks about is Nilsson's "calculations". So the whole DI stink about this starting in 2001 was really about Dawkins, because the video represents Nilsson's work accurately.
(2) Nilsson does show a physical model he has constructed which allows one to "see" what the eye would "see" at various stages in the eye sequence.
|Date: 2003/04/05 02:56:54, Link|
Section of Futuyma's textbook on the evolution of complex features.
Features the snail eye continuum from Salvini-Plaw and Mayr:
|Date: 2003/04/05 11:07:10, Link|
Other Nilsson papers (Web of Science search):
FROM CORNEA TO RETINAL IMAGE IN INVERTEBRATE EYES
TRENDS NEUROSCI 13 (2): 55-64 FEB 1990
VISION OPTICS AND EVOLUTION - NATURES ENGINEERING HAS PRODUCED ASTONISHING DIVERSITY IN EYE DESIGN
BIOSCIENCE 39 (5): 298-307 MAY 1989
ODSELIUS R, NILSSON DE
REGIONALLY DIFFERENT OMMATIDIAL STRUCTURE IN THE COMPOUND EYE OF THE WATER-FLEA POLYPHEMUS (CLADOCERA, CRUSTACEA)
P ROY SOC LOND B BIO 217 (1207): 177-& 1983
Also see the PubMed search.
Regarding Nilsson and Pelger 1994, Web of Science reveals that it has been cited 32 times in their database. It would be instructive I think to see how many papers actually characterize the paper as a stochastic simulation. For instance, Thornhill and Ussery 2000 ("A classification of possible routes of Darwinian evolution," J THEOR BIOL 203 (2): 111-116 ISI PubMed) write:
...which seems pretty reasonable to me.
|Date: 2003/04/05 11:18:43, Link|
Here's another gem from Berlinski 2003. Berlinski lists a larger number of problems that he has with the paper. One of them is that Nilsson and Pelger don't give any details about how they calculated optical acuity:
The graphics he is referring to are Figure 1a, 1b, and 1c (attached).
|Date: 2003/04/05 11:41:53, Link|
But did he actually read the paper? Nilsson and Pelger in fact spend a paragraph explaining the calculation of each graph.
For Figure 1a, they say:
Looks like Nilsson 1990 (see reference above) might be the place to see how this was calculated. Is Nilsson required to repeat all his previous work in every new article, for the benefit of people like Berlinski?
For Figure 1b, Nilsson and Pelger write,
Look at that, an equation, with these references to the theory cited:
Did Berlinski really look up these references and not find the relevant theory?
For Figure 1c, Nilsson and Pelger write,
Hmm, they say the optical theory is in:
...which would, I expect, have some equations in it. Did Berlinski really look this up? If not, how can he say,
(leaving aside the equation that they do include, which sure seems like details to me)
|Date: 2003/04/05 23:21:11, Link|
Yet another kind of bacterial motility:
Omigod! Yes another nonflagellar swimming system!! That designer sure was a busybody!
My cursory thoughts:
1) This page on spiroplasma:
...says that sprioplasmas are related to gram-positive bacteria, and have no cell wall, have a cytoskeleton and membranes with cholesterol. This all seems to go along fairly well with Cavalier-Smith's proposed scheme for the evolution of eukaryotes as something like:
gram-negative --> gram-positive --> early divergence from archaeabacteria --> eukaryotes
...even if this doesn't pan out it is an interesting bit of (vague) convergence.
2) I don't really even understand how the spiroplasma swimming works so speculating on evolution is pointless, however it sounds rather more like what Lynn Margulis thought spirochetes worked like when she proposed the spirochete-->eukaryotic cilium hypothesis. I doubt that spiroplasma-->cilium has any prospects either but it is interesting.
3) Even so, the more ways there are to swim, the more it seems that Dembski has drawn the target around the arrow with the flagellum.
It was suggested that this is vaguely like spirochetes, but not really IMO.
|Date: 2003/04/06 00:06:05, Link|
|Date: 2003/04/06 13:13:29, Link|
Here is a good one:
...coudla written it myself, although I didn't.
|Date: 2003/04/08 23:41:28, Link|
[note, the thread title is wrong as Glenn points out, it should be "Wiker". I am officially dumb.]
Just came across this:
Does Science Point to God?
The Intelligent Design Revolution
By Benjamin D. Wiker
|Date: 2003/04/08 23:54:59, Link|
Here's a great little tidbit:
A classic example of:
The fact that the laws of the universe are perfect for life is evidence for a Designer. The fact that the laws of the universe can't produce life is evidence for a Designer.
(from The Quixotic Message
|Date: 2003/04/09 00:01:56, Link|
The poem is online here:
...it is not the kind of thing however one can absorb in a speed-read so I refrain judgement.
Anyone know of any informed commentary on Lucretius' poem? Ah here's one. So far this seems to support Whitaker's contention:
|Date: 2003/04/09 00:09:00, Link|
More is on the way in the future:
|Date: 2003/04/09 01:23:39, Link|
This comes up often in Ev/Cre debates, basically "where the press got it wrong". I just discovered that there is whole journal devoted to the topic of science & the public:
E.g. here's an interesting article:
|Date: 2003/04/10 23:56:26, Link|
A few key papers on the origin of the innate immune system:
|Date: 2003/04/12 18:33:05, Link|
A highly entertaining new ISCID thread on the
Intelligent Design of Immunity
|Date: 2003/04/13 17:51:01, Link|
I'm going to post some posts here for safekeeping on this thread:
Nelson, what is this babble about an immune system producing "not enough specific antibodies to make a difference"?
Way back on the other thread, charlie pointed out to you:
1) Many innate receptors have similar specificity to "naive" (first-generation lymphocyte) recombinant antibodies. Most of the antibodies in your and my blood, right now, are therefore "not specific enough to make a difference". According to you.
2) Specificity is not produced just by having cells that mysteriously produce lots of specific antibodies, it is produced by the selective replication of those very few lymphocytes that happen to match whatever the antigen is. Further somatic mutation and selection is what produces many copies of the very few antibody phenotypes that are "specific enough to make a difference".
3) Therefore at no point are huge numbers of diverse, "single specificity" antibodies produced.
So speaking crudely, phylogenetically, we have this sequence of organisms:
(a) invertebrates, with many non-rearranging receptors of moderate specificity (similar to the specificity of "naive" antibodies)
(b) cartilagenous fish, which add diverse rearranging receptors of moderate specificity, genes in VDJ VDJ VDJ arrangement
© "lower" vertebrates, which have diverse rearranging receptors of moderate specificity in a VVVV DDDD JJJJ-type arrangement
(d) mammals, like lower vertebrates except that a few of the rearranging receptors, which happen to match the antigen, get replicated and gradually improve from moderate specificity to high specificity via somatic mutation & selection.
(charlie can refine the above if I garbled things)
And yet, Nelson, you've been proclaiming for endless pages that there is some sort of requirement somewhere to produce large numbers high-specificity antibodies with different specificities.
Please, Nelson, can you help us out here?
Thanks, that's what I was trying to explain when I wrote,
Yet another supposed reason for the unevolvability of VDJ recombination hits the dust!! It's like shooting skeet.
All Nelson has left is that:
(1) the exact non-rearranging ancestor receptor has not yet been identified, and (2) that he thinks a transposon insertion, a well-known natural event that is happening all the time (it causes some cancers for instance) is "non-Darwinian" and for some mysterious reason therefore an intelligent intervention.
Regarding (1), even though (a) Ig domains are common, (b) we know that non-rearranging receptors would work because we have a bunch of them, and © due to selection for immune system diversity sequence homology will decay very fast.
To emphasize the Ig domain point:
...all those circles are Ig(-like) domains.
Regarding (2), there are a multitude of transposon types and events; there is no need to postulate intelligent intervention in order to explain a transposon inserting into a non-rearranging receptor. Plus, there is the published literature and experiments which the immunologists view as having tested and strengthened the hypothesis.
|Date: 2003/04/14 01:38:47, Link|
Well, famed antievolutionist demagogue Phil Johnson took the opportunity to try to spread his message to the Boy Scouts. Speaking as an Eagle Scout I find the whole thing intensly annoying, but that's another story.
There are a number of dumb things in this article, but it would have behooved PJ to actually do some reading on the history of the Boy Scouts before spouting off. But this is PJ we're talking about, he's still repeating Wells' errors on the peppered moth etc...
The Boy Scouts were founded by Robert Baden-Powell. See here for an extensive webpage on him and the history of scouting:
Now, Robert's father was:
The Rev. Baden Powell, F.R.S.,
Savilian Professor of Geometry,
...and he lived from 1796-1860. "F.R.S." means "Fellow of the Royal Society", and yes, this means he was well aware of Darwin and his Origin of Species. Baden-Powell senior even contributed a positive review:
Further down on the page we have:
& here is quote of what Baden Powell senior had to say about Darwin:
And Darwin wrote in a letter:
Anyway, this is Baden Powell's father, not the founder of scouts himself. Baden Powell jr. was a military man, not a scientist, and never said much about Darwin one way or the other, although:
Heh. Here's the Darwin quote from B-P jr:
Hmm, I guess other people have made my connections before:
A discussion at a scouting forum:
|Date: 2003/04/30 18:28:04, Link|
The topic of so-called "junk" DNA (or, apparently disposable noncoding DNA, more neutrally) has come up endless times in various online debates. Often, someone will find a new article indicating a function for some bit of DNA, and declare that the "junk" hypothesis is dead and that those evil materialists were blinded by their evil materialism for ever believing it.
The situation is of course much more complex, so link/post articles, posts (both sides), etc. in this thread.
|Date: 2003/04/30 18:43:15, Link|
Here is a post I wrote in response to Nelson Alonso:
On Paul Nesselroade's current column
Folks, *these* are the observations that led, and still lead, to the "junk DNA" suggestion. Unless a junk DNA critic comes up with an explanation for why species A will have 100 times as much DNA as very similar species B, they haven't explained "junk DNA". The question is (1) why are eukaryotic genomes primarily made up of repetitive sequences and (2) why can the amounts of these sequences vary so much within closely-related groups?
IDists who talk about junk DNA with out bringing up the above observations front-and-center are not even talking about the actual issue.
Nature Reviews Genetics article
Here is the bit I'm talking about. As you can see, there are a variety of "live" hypothesis among evolutionary biologists, both pro- and anti- "junk", even though they are supposedly all nasty materialists:
|Date: 2003/04/30 18:50:00, Link|
A good complement to a junk DNA FAQ would be a "mechanisms of mutation" FAQ, which I don't think exists anywhere. People seem to treat mutation as some kind of magically process and therefore get mislead into all kinds of directed mutation, etc. stuff.
Most stuff on the web appears to be either lecture outlines or very technical "my research is"-type pages.
But there is some good stuff. For example:
Mutation, Mutagens, and DNA Repair
|Date: 2003/05/05 17:50:36, Link|
Another Nelson debate:|
"Mini-IC systems?" But I thought that IC meant that the *whole thing* was IC?
ExbB and ExbD act on TonB, IIRC there's another ExbBD pair homolog that acts on something else. And motAB act on fliG in a similar fashion. Which is why Kojima & Blair wrote in Biochemistry (2001, vol. 40, pp. 13041-50),
None of this is disputed, but all it is saying is that "beneficial mutations are unlikely" which is no surprise to evolutionary biology. All that is needed is one rare beneficial mutation amongst millions of ones that "don't work" and selection will pick it out. And, FWIW, mutation experiments seem to indicate that there is a fair bit of flexibility where motor function is retained despite mutation in the MotB--rotor interface.
This depends upon a particular model of the mechanism of flagellar rotation, which is an unsolved question (Hey! A place for the IDer to act in modern times! Unless you're a nasty methodological naturalist...). Based on the ExbBD homology, I would expect that the ion channel is essentially internal to the ExbBD system and that the energy resulting from H+ flow is transferred through the protein structure via conformational change to act on the flagellum base (or on TolB etc.) to do work at a distance. Call it a prediction if you like. The electrostatic model certainly is elegant, but based on ExbBD homologs being independent units doing "work at a distance" in several different systems, it seems unlikely. Time will tell.
IIRC the 3 alpha and 3 beta subunits of the F1 ATPase are thought to be homologs of each other, with only the beta subunits retaining ATPase activity:
The similarity of the beta subunit to FliI is something like 33% which is highly statistically significant, well above the ambiguous level:
...the assumption of homology seems to be confirmed by the fact that the resulting protein complex fits well into their model of T3SS structure.
It seems highly unlikely that the different rod proteins have radically different functions. Probably their retention has to do with starting and stopping the rod construction process, wherein it would be helpful to have a tightly-controlled starting and stopping points, but where simpler mechanisms could suffice at first, e.g. just generating a certain amount of one rod protein.
All that is required to get from one rod protein to several is the sub-functionalization of gene copies, which you, Nelson, have enthusiastically endorsed in other threads.
So, are they part of the IC system or not, and how many orders of magnitude difference in probability does this decision result in?
An example (one of many) was cited in the original immune system thread.
Huh? There are many kinds of pili, the term basically means "sticky-outy bit" as far as I can tell. And it seems that basically every transport system that has been identified has versions that support extracellular extensions. They all have to secrete proteins, in order to get the pilus proteins to the outside. You are focusing on the abilities of the P pilus, built on a Type I transporter IIRC, but we are talking about type III secretion systems. It appears that flagell