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| Date: 2002/05/06 19:19:54, Link 128.111.106.148 | ||
| Author: niiicholas | ||
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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 smilies:    Trying a URL: Talkorigins webpage link test ...hey, that worked pretty well.. A graphic: ...hmm, it stuck the code at the end of the post, I'll move it up.  I won't even trying the Flash movie posting option... nic |
| Date: 2002/05/17 02:35:38, Link 128.111.106.148 | ||
| Author: niiicholas | ||
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Howdy, Wes has kindly made me a moderator on this forum. I'd like to briefly mention a few things for background's sake. As other things come up they will be added to this thread (or the thread can be bumped if someone needs an introduction). First, the title of the forum. Here is the reference (from Wes):
Guidelines: 1) This is a public-viewing, but restricted posting forum. Posting access is granted by (I think) either Wes or me, basically if we feel like the poster will contribute to the purpose of this particular forum, detailed below. 2) The purpose of this forum is to give ID skeptics a place to gather references, citations, bits of arguments, etc., in one place, either just for reference, or for a possible future article or FAQ. The idea is to do things on a thread-specific basis. A random example thread title might be "Examples of co-option in evolution", and the person who starts the thread says something like: "I would like this thread to focus on well-documented examples of cooption in evolution. The reason, of course, is that antievolutions frequently assert, without documentation, that change-of-function is a very low probability event, and use this pseudo-argument to brush off the "what about cooption?" objection to the arguments of Behe and Dembski regarding the nonevolution of functional complexity. The best way to rebut the IDists' assertion is simply to list the numerous examples of cooption in evolution, with references. So, if you come across a good example, mention it and if possible cite what references you have; others may be able follow up suggestions of places to look, e.g. "I think I read an essay by Gould on this once". Additional things worth posting in a thread like this: - links to other threads discussing cooption - links to high-quality webpages - links to the Pubmed abstracts of specific papers - references on the topic generally, e.g. papers on the topic of the fate of gene duplications, for example. - images and highly relevant quotes can be posted also Both molecular and macro cases are welcome, part of the point of this thread is to show that the same process occurs commonly in both realms." See how this would work? The potential topics are endless, but hopefully when you run across something, e.g. "Hey, a new article on the evolution of blood-clotting!", you can check the forum to see if there is already a thread on blood-clotting, and add the reference there. 3) Discussions of the above are welcome in this forum, however if very long-winded debates develop they are better put in the general ID discussion. Also, active debates with internet IDists should be conducted in the general ID discussion (where they have a chance to fight back); I think a good policy would be to stick a link to a debate thread in the relevant thread here. The main focus here is on "collaborative informational resource gathering/displaying" -- hopefully it will develop into a high-quality resource for ID skeptics across the net. Have fun, nic niiicholas@yahoo.com |
| Date: 2002/05/17 21:43:08, Link 128.111.106.148 | ||
| Author: niiicholas | ||
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Here is a fantastic recent example from your friend and mine, Jonathan Wells. There You Go Again: A Response to Kenneth R. Miller Jonathan Wells Discovery Institute April 9, 2002
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 128.111.106.148 |
| Author: niiicholas |
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Hi, Following my own suggestion, here is a thread devoted to collection material/links/references relevant to blood-clotting and the claims IDists make about it. As there is not yet a single webpage anywhere that has gathered all of the relevant material in a single place, this might as well be it. Perhaps at some point it could be edited into a FAQ, or could inspired someone to write a FAQ (since much of the hard work of finding the references, IDist quotes, etc., would be done). Specifically relevant would be things like: 1) blood-coagulation/clotting (or hemolyph coagulation for you invertebrates out there), especially e.g. webpages/literature that describe the basics in an easily understandable manner such that a FAQ reader could be referred there 2) references to articles/lit. on the evolution of blood clotting 3) Links to/quotes of antievolutionist assertions regarding blood-clotting, with commentary on problems if you are inspired 4) Links to the various webpages already out there rebutting IDist claims. Awhile ago I did a search and dug up a pretty good starting reference list, I'll post that in a moment. nic |
| Date: 2002/05/17 22:09:17, Link 128.111.106.148 | ||
| Author: niiicholas | ||
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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. Thanks, nic |
| Date: 2002/05/17 23:18:58, Link 128.111.106.148 | ||||
| Author: niiicholas | ||||
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! g'night, nic |
| Date: 2002/05/24 19:42:53, Link 128.111.106.148 |
| Author: niiicholas |
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Some good discussion and links on a bio.com article discussing the homology between a blood-clotting protein and a cone-snail venom protein (!!!) was posted on this II thread. nic |
| Date: 2002/05/24 20:25:51, Link 128.111.106.148 | ||||||||||||||||||||
| Author: niiicholas | ||||||||||||||||||||
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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. nic 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. Further support:
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? nic *** Added in edit, Dec. 2002: Actually, Behe did not. It looks like it is on pp. 82 and 84, but on p. 86 Behe limits the system to only four components. This was pointed out to me by DNAunion here: http://iidb.org/ubb....759&p=2 On p. 86, Behe writes,
(copying from DNAunion) Ken Miller, here, http://www.millerandlevine.com/km/evol/design2/article.html ...writes:
...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 128.111.106.148 |
| Author: niiicholas |
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A recent post on talk.origins by Dunk discussing some recent (2002) literature, with quotes: Here is the google link nic |
| Date: 2002/05/24 22:27:00, Link 128.111.106.148 | ||
| Author: niiicholas | ||
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. Thanks, nic |
| Date: 2002/05/24 23:23:13, Link 128.111.106.148 | ||
| Author: niiicholas | ||
Ken Miller's take, and further debates online about some of the points, are linked from here: http://www.millerandlevine.com/km/evol/wells-april-2002.html nic |
| Date: 2002/05/24 23:28:42, Link 128.111.106.148 |
| Author: niiicholas |
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Here is a muddled page in support of Behe's IC blood-clotting argument, I list it as it draws heavily from Behe's chapter & gives a sense of Behe's specific arguments there (including Behe's inclusion of Hageman factor in the IC system): Irreducible Complexity? Blood Clotting! at www.doesgodexist.org, by Robert Harsh nic |
| Date: 2002/05/24 23:51:37, Link 128.111.106.148 | ||||
| Author: niiicholas | ||||
A somewhat interesting but mildly confused article in Geology News, "Geoscience at the BA: Clots have been with us for 400 million years", reporting on a talk by Colin Davidson (Imperial College School of Medicine) on the evolution of blood-clotting, especially regarding the role of large (genome or chromosome) duplications. I say the article is confused as punctuated equilibrium is invoked as having something to do with the situation, which AFAICT it doesn't, and as none of the connections of blood-clotting to more ancient protease cascade systems are discussed. The interesting quotes concern gene duplication:
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. nic |
| Date: 2002/05/25 00:35:53, Link 128.111.106.148 | ||||
| Author: niiicholas | ||||
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An interesting paragraph from a recent article that continues the debate between Behe and Shanks & Joplin, regarding the (chemical) specificity necessary for ICness vs. "simple interactive" systems or what-have-you. Niall Shanks and Karl Joplin, "Behe, Biochemistry, and the Invisible Hand," Philo, Volume 4, Number 1. Link: http://www.philoonline.org/library/shanks_4_1.htm Regarding blood-clotting & specificity, they write:
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. nic |
| Date: 2002/05/26 00:55:42, Link 198.81.17.59 | ||||||||
| Author: niiicholas | ||||||||
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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. Thanks, nic |
| Date: 2002/05/28 15:10:09, Link 128.111.106.148 | ||
| Author: niiicholas | ||
I came across a new article on the evolution of photosynthesis; there are a number of articles on this topic, I will post them as I rediscover them, others may have come across interesting stuff also.
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| Date: 2002/05/29 23:30:40, Link 128.111.106.148 | ||
| Author: niiicholas | ||
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Hi, This would seem to be as good a place as any to collect links/references to things like Johnson's - works - reviews of his works - interviews - online talks ...etc. I think there is already at least one fairly comprehensive PJ links page on the web so maybe we could just 'high-grade' particularly interesting things here. E.g., I started this thread because I just heard about this link: Berkeley’s Radical An Interview with Phillip E. Johnson Johnson bares his soul & gives quite a detailed history of his own 'evolution'.
Not a man with small goals, PJ. Note also the "scientific key" to the whole ID argument (according to Johnson): "No natural processes create genetic information." Hmm. I think I'll start a thread. nic |
| Date: 2002/05/30 00:02:55, Link 128.111.106.148 | ||||||||||
| Author: niiicholas | ||||||||||
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Hi, While reading this interview with Phil Johnson, leader of the ID movement: Berkeley’s Radical An Interview with Phillip E. Johnson ...I was struck by this section:
Note that the "scientific key" to the whole ID argument (according to Johnson) is this: "No natural processes create genetic information." This strikes me as easily and trivially refutable by numerous examples. Anything that starts with genetic information amount X, and ends up with genetic information amount X+Y, should qualify. The classic case would be X=information in a genome before a gene duplicates & diverges under selection, and X+Y being the information in the genome after this has occurred. Another less-often considered example should be (IMO) when a mutation (let's say "beneficial to at least part of the population" to avoid the obvious objection) arises in a *population*. Here, X=information in the genomes of a population Y=information in the beneficial mutation I realize that "information" has no single definition in biology, one could also argue that "new information" would arise through novel combinations of alleles, etc. For the purposes of this thread, I suggest the following working definition: Genetic information=functional DNA that encodes useful/beneficial proteins or regulatory sequences ...as this is what the IDers mean by "genetic information" (except of course when they are challenged on the topic, wherein they promptly begin the obfuscation and goal-post moving, rather like eternally elusive creationist definition of "kind"). So, let's use this thread to accumulate examples of natural processes increasing "genetic information" in the above-described sense. Other things that might be relevant, e.g. studies of the increase of Shannon information in selective algorithms, could also be posted, just note the form of information as relevant. nic PS: I'll start off with one of my favorite examples: Sdic, sperm dynein intermediate chain, a new gene which evolved over the past few million years by the duplication, fusion, and modification of two genes that are now on each side of Sdic on the chromosome. Here is a brief introduction from Ian Musgrave:
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:
Have fun, nic |
| Date: 2002/05/30 00:51:24, Link 128.111.106.148 | ||
| Author: niiicholas | ||
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Here is a whole double issue of JME with a large group of articles devoted to evolution-of-genetic-code issues: Volume 53 - Number 4/5, 2001 http://link.springer.de/link/service/journals/00239/tocs/t1053004.html
Funny that Paul Nelson's views were not included, eh? I just received a good private message on this topic from a new poster & I encouraged him to post it in the general discussion, I'll then post a link to it from this thread. nic |
| Date: 2002/05/30 01:14:38, Link 128.111.106.148 | ||||||
| Author: niiicholas | ||||||
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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:
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| Date: 2002/05/30 01:49:29, Link 128.111.106.148 | ||||||||
| Author: niiicholas | ||||||||
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. Thanks, nic |
| Date: 2002/05/30 20:33:50, Link 128.111.106.148 | ||
| Author: niiicholas | ||
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Howdy, Just a little background in case we've got any lurkers who haven't taken biochemistry lately... In the canonical genetic code that everyone learns in textbooks there are 20 amino acids -- however, chemically many more amino acids are possible. As I understand it there are many cases where organisms will produce an amino acid chain using the canonical code, and then post-translationally modify some of the amino acids, effectively resulting in the usage of more than 20 amino acids by the organism, although technically the normal genetic code is still used. However, there are some cases where the canonical code has been modified to include a noncanonical amino acid *during* translation. A few weeks ago a new example of this was published, and in the AE general discussion a new poster Ed has alerted us to how this example fits in with the 'stop codon alteration' pattern that is so common in genetic code changes. Here is the link to Ed's post "Stop codon thievery" I'll quote Ed's post for the sake of thoroughness: ============= A very recent example of a "stop" codon being sometimes coopted for another use is the subject of two papers and a "perspective" (1-3) in the 24 May 2002 issue of Science. These all are reporting on the "new" amino acid "pyrrolysine", which is coded for by the (usually) stop codon UAG in a certain methanogenic archaeon's mRNA. To quote from (1):
Reference (1) goes into some depth, with references, as to how the stop signal is subverted in the case of selenocysteine, the only other non-canonical amino acid known to be specified by the code and not built by modification after translation. In the selenocysteine case, only a minority of the UGA codons are used to code the amino acid: most are still stop codons. Signals elsewhere in the mRNA determine which. It is still unknown just how the UAG coding pyrrolysine works, however. (1) Atkins JF, Gesteland R. Science 2002 May 24;296(5572):1409-10 (2) G. Srinivasan et al., Science 296, 1459 (2002). (3) B. Hao et al., Science 296, 1462 (2002). ============= Thanks Ed, keep it up! Nic |
| Date: 2002/05/31 01:31:35, Link 128.111.106.148 | ||||
| Author: niiicholas | ||||
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Another classic case is the evolution of antifreeze genes from proteases in arctic & subarctic fish, which has happened independently at least a couple of times: I believe this article is freely available online from PNAS: Proc. Natl. Acad. Sci. USA Vol. 94, pp. 3485-3487, April 1997 Origin of antifreeze protein genes: A cool tale in molecular evolution John M. Logsdon Jr. and W. Ford Doolittle http://www.pnas.org/cgi/content/full/94/8/3485
Here is Figure 1: 
(source) Thanks, nic |
| Date: 2002/05/31 01:44:19, Link 128.111.106.148 | ||
| Author: niiicholas | ||
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Interesting...scrolling down to the bottom of the PNAS article, there is a link to a Science article that cited it. Guess what? Plants have evolved antifreeze proteins as well: A Carrot Leucine-Rich-Repeat Protein That Inhibits Ice Recrystallization Dawn Worrall, Luisa Elias, David Ashford, Maggie Smallwood, * Chris Sidebottom, Peter Lillford, Julia Telford, Chris Holt, Dianna Bowles http://www.sciencemag.org/cgi/content/full/282/5386/115
Thanks, nic |
| Date: 2002/06/11 00:44:21, Link 128.111.106.148 |
| Author: niiicholas |
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This thread is for accumulating examples of cooption/change of function from the literature, and citations of the importance of this process in the literature. The purpose of examining this is that Behe and Dembski both fail to give cooption the attention it absolutely deserves. In particular the occurence of cooption disproves Behe's IC argument. Thanks, nic |
| Date: 2002/06/11 01:03:11, Link 128.111.106.148 | ||
| Author: niiicholas | ||
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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):
(bold added) This long-standing hypothesis regarding the origin of feathers has been strengthened by recent discoveries of fossil dinosaurs with non-flight feathers. E.g. the fantastic pictures here: http://research.amnh.org/vertpaleo/dinobird.html E.g.:  |
| Date: 2002/06/11 01:24:42, Link 128.111.106.148 | ||
| Author: niiicholas | ||
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Found this key Darwin quote on the ISCID forum: Chapter 6 of Origin of Species Here is the link: http://www.talkorigins.org/faqs/origin/chapter6.html Note especially how closely Darwin ties the change-of-function argument to his "organs of extreme perfection" line which is so often quoted by antievolutionists. Why don't they ever acknowledge that Darwin himself listed numerous cases of homologous structures being adapted for wildly different functions?
(bold added) Thanks, nic |
| Date: 2002/06/11 05:07:37, Link 128.111.106.148 | ||||
| Author: niiicholas | ||||
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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:
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| Date: 2002/06/11 05:41:00, Link 128.111.106.148 | ||||
| Author: niiicholas | ||||
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... nic |
| Date: 2002/09/21 13:06:12, Link 198.81.16.151 |
| Author: niiicholas |
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This thread is for accumulating (1) Assertions (2) Links to articles (3) Facts ...regarding the question "where do peppered moths rest during the day". The importance of this topic lies in that many have argued that peppered moths don't rest where Kettlewell thought they did, and that therefore his experiments were invalid, and that therefore the entire peppered moth bird-predation-theory is without support. Or something. Another avenue taken by Jonathan Wells in particular is the "this means that textbook photos of moths are fake and a fraud has been committed on students" avenue. I suggest that we collect pictures that we can find on the web, with comments on the source (if we can find 'em), whether or not they are staged (if known), with a goal of getting a sense of whether or not textbook pictures are misleading. nic |
| Date: 2002/09/21 13:15:43, Link 198.81.16.151 | ||||||||||||||
| Author: niiicholas | ||||||||||||||
An initial list of Wells utterances on moths and tree trunks:
(courtsey KC) |
| Date: 2002/09/21 13:26:13, Link 198.81.16.151 | ||
| Author: niiicholas | ||
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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 198.81.16.152 | ||||
| Author: niiicholas | ||||
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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: http://www.talkorigins.org/faqs/wells/#mothmaj ) 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. nic |
| Date: 2002/09/22 23:37:02, Link 198.81.17.171 | ||
| Author: niiicholas | ||
Here is the only review of Hooper that has come out thus far by a Real Live Peppered Moth Researcher: Bruce Grant. His take is notably different than the press commentary on Hooper.
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| Date: 2002/09/24 03:36:07, Link 198.81.16.51 |
| Author: niiicholas |
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Another review (or rebuttal of positive Hooper reviews, actually) on Intelligent Design Update yahoogroup: http://groups.yahoo.com/group/IntelligentDesignUpdate/message/112 ...quite good IMO, several points that haven't been made by anyone else yet... nic |
| Date: 2002/09/24 03:44:53, Link 198.81.16.51 | ||
| Author: niiicholas | ||
Online letters on the Salon.com review of Hooper: http://www.salon.com/books/letters/2002/09/20/moths/index1.html The Wells FAQ is referenced :-) |
| Date: 2002/09/24 04:48:34, Link 198.81.16.24 |
| Author: niiicholas |
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This thread is for accumulating links and posts on the topic of predictions made by the modern theory of evolution, i.e. the theory that processes we observe or directly infer today (especially random mutation (broadly construed to include everything from point mutations to genome duplications) and natural selection, but also the well-known sidekicks such as genetic drift, neutral evolution, etc.), were also acting in the long-distant past and produced the biodiversity of today. This was prompted by Jesse's excellent post at ARN on this topic, which we should quote somewhere: ARN post nic |
| Date: 2002/09/26 00:13:06, Link 172.191.200.144 | ||||
| Author: niiicholas | ||||
Here is another Wells gaffe:
Michael Majerus took the trouble to respond to this himself:
yersinia |
| Date: 2002/10/01 13:47:50, Link 198.81.26.142 | ||||
| Author: niiicholas | ||||
This thread is for references to lit. on, or relevant to, the origins of F1F0 ATPase. I just came across some and I know of some others, I will post them whenever I dig 'em up.
Some have argued that the ATPase may be descended from a pyrophophatase, so this is relevant:
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| Date: 2002/10/01 14:02:37, Link 198.81.26.142 | ||
| Author: niiicholas | ||
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Here's a different one: http://www.pnas.org/cgi/content/abstract/152445399v1
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| Date: 2002/11/28 23:11:25, Link 12.225.105.174 |
| Author: niiicholas |
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Similar to the prokaryotic flagella thread. Introductory material: http://www.wikipedia.org/wiki/Flagellum (don't confuse eukaryotic cilia/flagella with prokaryotic flagella) http://www.wikipedia.org/wiki/Evolution_of_flagella Here we have the interesting sideshow of Margulis' and fans' hypothesis that the cilium is derived from a spirochete. For many critical comments on this see: Cavalier-Smith T. Int J Syst Evol Microbiol 2002 Mar;52(Pt 2):297-354 The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. |
| Date: 2002/12/01 20:38:22, Link 198.81.26.142 | ||
| Author: niiicholas | ||
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Might as well add these as I'm discussing them over at EvC: http://www.evcforum.net/ubb/Forum10/HTML/000029.html On the evolution of PCP degradation:
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| Date: 2002/12/02 18:55:21, Link 172.191.11.209 | ||
| Author: niiicholas | ||
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This is a "data accumulation" thread for me (and anyone else interested in Croizat) to learn the basics. To start off: http://zoo.bio.ufpr.br/diptera/bz023/leon.htm
So, perhaps both a loon and brilliant in his way. Lotsa info here, including some vituperative anti-Darwin, and anti-Mayr stuff from late Croizat: http://www.ento.psu.edu/home....ate.htm |
| Date: 2002/12/02 19:12:32, Link 172.191.11.209 | ||
| Author: niiicholas | ||
http://gsa.confex.com/gsa/2002AM/finalprogram/abstract_37210.htm
A good short summary of biogeography that puts Croizat in context: http://www.msu.edu/course/zol/370/lindell/10-10-02,%20method.html |
| Date: 2002/12/03 23:13:15, Link 172.172.193.79 |
| Author: niiicholas |
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Another Miller article, presents his argument on cilia missing parts: "Answering the Biochemical Argument from Design" The ID movement pretends that its biochemical arguments against evolution are new, novel, and scientific. In fact, they are nothing of the sort. http://www.millerandlevine.com/km/evol/design1/article.html |
| Date: 2002/12/07 15:23:08, Link 152.163.188.164 |
| Author: niiicholas |
| bump |
| Date: 2002/12/08 00:10:21, Link 152.163.188.164 | ||
| Author: niiicholas | ||
Looks like this bit got nuked in the server crash. The 1969 paper on Hagemann factor loss in whales has been cited, but there is an interesting 1998 paper:
...obvious implications concerning the origin of whales... |
| Date: 2002/12/08 00:57:42, Link 152.163.188.164 |
| Author: niiicholas |
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Here's a good example of a debate that rapidly focused on the ambiguities in the defn of IC: http://iidb.org/ubb....1759&p= ...other examples welcome. Also, cites of IDists using/defining IC, SC, etc. in conflicting ways. |
| Date: 2002/12/08 14:34:57, Link 152.163.188.164 | ||
| Author: niiicholas | ||
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 128.111.106.15 | ||
| Author: niiicholas | ||
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 128.111.106.15 | ||
| Author: niiicholas | ||
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: http://vms.cc.wmich.edu/~rudged/index.html One of Rudge's articles is online: (another version of this was published in something like the Journal of Biological Education "Does being wrong make Kettlewell wrong for science teaching?" from here: http://www.ed.psu.edu/CI/journals/2001aets/01file1.asp Rudge's current and upcoming articles are listed here: http://homepages.wmich.edu/~rudged/vita.html#refereed_journal_articles |
| Date: 2002/12/12 21:44:25, Link 128.111.106.15 |
| Author: niiicholas |
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Other Biston researcher webpages: Bruce Grant http://faculty.wm.edu/bsgran/ Michael Majerus http://www.gen.cam.ac.uk/dept/majerus.html Books by Majerus: amazon.com link |
| Date: 2002/12/13 01:13:29, Link 128.111.106.15 | ||
| Author: niiicholas | ||
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And in the "duplicated genes aren't necessarily selectively neutral, dammit" category: (bold added)
What would be interesting to know would be the relative roles of regulation mutations vs. gene duplications in effecting adaptation (via amount of proteins produced) to changing conditions as discussed above. One would think that regulatory changes would be the more "elegant" or "efficient" way to adapt, but apparently evolution doesn't know or care, at least sometimes... (it may be that regulatory changes have a "limit" that could only be exceeded by duplicating the gene...but now I'm at the limits of my knowledge...) nic (PS: The assumption that duplicating a gene doubles the level of a particular protein may not be a good one, particularly if the expression of the gene is regulated by some kind of feedback mechanism...just something to keep in mind) |
| Date: 2002/12/13 01:25:37, Link 128.111.106.15 |
| Author: niiicholas |
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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 128.111.106.15 | ||||||
| Author: niiicholas | ||||||
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Post your favorite Internet resources for searching for accurate (peer-reviewed lit., high-quality science journalism, educational websites not directly evo/creo related, sequence or fossil data, etc.) scientific information on evolution. Related hints and tips should also be added as appropriate, perhaps this would have potential as a FAQ at some point. When posting links to journals, please make a note regarding access. E.g.: PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi This is the National Library of Medicine's free search engine for "biomedical" literature, but in practice it includes all major general science journals, anything related to molecular biology, many more general biology journals (weaker on ecology etc.), and in general gobbs of evolution stuff on your topic of interest. GUIDE: For an author search, do "lastname firstinitials" without commas or periods. Separate multiple authors with commas. For example, Thornhill and Ussery wrote an article outlining the various ways that "irreducibly complexity" can evolve. Search PubMed on "ussery d, thornhill" and you get: A classification of possible routes of Darwinian evolution HINT: Searching on keywords or authors will never get you everything interesting on the first shot. A key feature is the "Related Articles" link to the upper-right of each reference. For example, here is an article on changes-of-function in evolutionary history:
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:
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| Date: 2002/12/13 02:14:51, Link 128.111.106.15 |
| Author: niiicholas |
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PubMed Central: http://www.pubmedcentral.nih.gov/ ...is a central archive of scientific literature that is freely available to the public without subscription. Sometimes the whole journal is free, sometimes the material is made freely available after 6 months. Oftentimes you will have to complete a free registration to access free content. I believe this is the current list of journals with free online content: http://www.pubmedcentral.nih.gov/ Top journals from this list for evolution-related stuff: Genome Biology Proceedings of the National Academy of Sciences of the United States of America (also at http://www.pnas.org ) Journal of Biology A free article from the last one, advocating open access to scientific lit -- a logical position, considering how most of this research is taxpayer-funded: Open access to the scientific journal literature Peter Suber J Biol. 2002; 1(1): 3 http://jbiol.com/content/1/1/3 A list of journals with full-text access for subscribers (the subscribers are usually university libraries, generally they are available to anyone within the University's edu domain) tied into the PubMed search engine is here: http://www.ncbi.nlm.nih.gov/entrez/journals/loftext_noprov.html nic PS: Another important journal: Evolution Archives back to 1996: http://lsvl.la.asu.edu/evolution/contents.html From 2000 on: http://evol.allenpress.com/ Current issue: http://evol.allenpress.com/evolonline/?request=get-current-issue Several critques of ID have been published in Evolution: link to search results |
| Date: 2002/12/13 03:35:04, Link 128.111.106.15 | ||
| Author: niiicholas | ||
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History of mousetraps: http://www.uh.edu/engines/epi1163.htm
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| Date: 2002/12/13 03:41:18, Link 128.111.106.15 |
| Author: niiicholas |
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The History of the Mousetrap http://inventors.about.com/library/inventors/blmousetrap.htm http://inventors.about.com/library/inventors/blmousetrap2.htm Some patented mousetraps:       |
| Date: 2002/12/17 15:28:17, Link 128.111.106.15 | ||
| Author: niiicholas | ||
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 128.111.106.15 |
| Author: niiicholas |
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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 128.111.106.15 | ||
| Author: niiicholas | ||
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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 128.111.106.15 | ||
| Author: niiicholas | ||
In the "nonmotile appendages can have a dispersal-related function despite being nonmotile" category:
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| Date: 2002/12/18 12:20:34, Link 198.81.26.142 | ||
| Author: niiicholas | ||
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Here is a masterful bit of propaganda from the DI's John West (he is a political scientist, literally). Particularly annoying is the "truth is established by endless repetition" tactic used by demagogues in the media, and by IDists regarding Icons of Evolution. http://www.nationalreview.com/comment/comment-west121702.asp This guy oughta read the Icons FAQs: http://www.talkorigins.org/faqs/wells/ http://www.ncseweb.org/icons/ http://www.nmsr.org/iconanti.htm If there was ever a bit of propaganda that deserved a refutation, it is below, so if you can't resist spending some time debunking this, CC your replies here.
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| Date: 2002/12/18 13:00:29, Link 198.81.26.142 |
| Author: niiicholas |
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Here it is, I hadn't seen it before The Wedge: A Christian Plan to Overthrow Modern Science? Doubting Thomas, Feature Story, No. 6, April/May 1999. By Keith Lankford http://www.stephenjaygould.org/ctrl/archive/thomas_wedge.html Some minor inaccuracies and now a little out of date, but it features: - a cogent comparison of ID to the 1950's Velikovskian movement - a fair amount of material about Ed Larson, author of Summer of the Gods, and his conflict with the DI over his book being cited as part of the "Wedge" strategy. |
| Date: 2002/12/18 15:40:56, Link 198.81.26.142 | ||
| Author: niiicholas | ||
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Atrazine degradation pathways appear to have arisen recently: This lab studies 'em: http://www.cbs.umn.edu/bpti/mice/faculty/wacket1.htm ...Some of their papers are free online: DeSouza, M. L., J. Seffernick, B. Martinez, and M. J. Sadowsky, L. P. Wackett (1998) Atrazine catabolism genes atzABC are widespread and highly conserved J. Bacteriol. 180(1):1951-1954. http://jb.asm.org/cgi/content/full/180/7/1951 De Souza, M. L., L. P. Wackett, and M. J. Sadowsky (1998) The atzABC genes encoding atrazine catabolism are located on a self-transmissible plasmid in Pseudomonas sp. strain ADP. Appl. Envir. Microbiol. 64(6): 2323-2326. http://aem.asm.org/cgi/content/full/64/6/2323 M.L. deSouza, D. Newcombe, S. Alvey, Crowley, D.E., A. Hay, M.J. Sadowsky, and L.P. Wackett (1998) Molecular basis of a bacterial consortium: Interspecies catabolism of atrazine. Appl. Environ. Microbiol. 64(1):178-184. http://aem.asm.org/cgi/content/full/64/1/178 In the latter paper, it looks as if three different enzymes found in different bacteria were first combine in multispecies consortia that could metabolize atrazine, and that eventually the 3 genes were combined on a plasmid which then spread around the world in an evolutionary eyeblink. If this is basically what happened it is yet another method of producing IC (as well as new information).
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| Date: 2002/12/18 18:24:58, Link 172.172.59.216 | ||
| Author: niiicholas | ||
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Over at ARN, Mike Gene is again claiming that the question "What should make one suspect ID?" has not/cannot be sufficiently answered by ID skeptics. The implication is basically that ID skeptics are close-minded and unable to consider the matter in a neutral, open, explorative way. http://www.arn.org/ubb/ultimatebb.php?ubb=get_topic;f=13;t=000536 But there are lots of things that would make me suspect ID. Note that these things are not the same things that would prove it beyond a reasonable doubt, although a lot of these "evidences for suspicion" put together might fit that bill. MG specifically put forward the flagellum as an example, conveniently a particularly ancient system for which the kinds of evidence available for e.g. the immune system are much more difficult to come by.
As JP has noted in the thread, many answers to the "suspect" question have already been provided, it's just that Mike Gene doesn't like them because design does not entail that these things exist. That's pretty much the problem with Mike-Gene-design, it doesn't appear to entail anything in particular at all. Even IC systems are apparently accessible to evolution under MG-ID, so if the tremendously complicated immune system is shown to have plenty of evidence of gradual natural origins, he can just shrug it off and say that ID designed something more remote, like the flagellum. Still, an observation does not have to be *entailed* by design in order to be an observation that would legitimately raise suspicion. Evolution does not predict that any particular transitional fossil will be found, just that some will be found somehwere, and these legitimately raise suspicion. Presumably even a rarified design hypothesis predicts that some kind of positive evidence will be found somewhere. I would suspect (not conclude) design for the flagellum if there were evidence for any of the following: 1) A purpose other than maximizing the reproduction of the genes of the bacterium in question, that fits with some hypothesized designer. E.g., mousetraps are designed for trapping mice that are annoying humans. Note that in contrast, evolutionary theory predicts this for all complex "designed" systems. Find a counterexample and you've disproved evolution. Find a counterexample with a purpose that fits some specific designer hypothesis and you've got reason to suspect that designer hypothesis. 2) True IC, i.e. if the parts of the flagellum really did not have any function apart from contributing to flagellar function, i.e. that any subset of flagellar parts really was "by definition nonfunctional". This was Behe's original attempted argument, and if it had held up under the weight of evidence then he would have had something. 3) Biologically impossible transplants of the complex "design" across phylogenetic lines. This is seen *in spades* in human design systems. However, in biological systems, such transplants appear to be limited in numerous ways: a) Basically limited to single-celled critters without protected germ-line cells b) Most commonly there to prokaryotes that are *known* to do all kinds of conjugation, DNA uptake, etc. b.5) In eukaryotes, the most impressive cases lateral transfer are the cases of symbiosis, in which the genomes of the host and symbiont are in close association for millions of years and transfers can occur bit-by-bit while maintaining function c) Suspicions of transplants are often confirmed by finding plasmids, insertion remnants, and evidence of other known lateral transfer mechanisms d) Transplants are most common between prokaryotes (a) closely related or (b) living in close proximity e) Apparently limited to relatively simple systems (single operon?), and the more complex the system, the more closely related must be the donor/acceptor. The most complex system transferred that I can think of is Type III virulence systems, and (IIRC) these are all restricted to a relatively narrow group. As an example of the contrast seen in human designs, the following highly complex systems originated locally and were rapidly transplanted into any manner of larger devices (cars, planes, boats, etc.) without any regard for the kinds of biological, ecological, and phlyogenetic patterns described above: - computers - GPSs - satellite phones - emergency transponders 4) It occurs to me suddenly that the pattern that all of these designed transplants follow is that they are useful *to the designer*, i.e. safety, navigation, etc. So, even in a case where the lateral transfers were biologically possible, if the pattern of transfer fit the purposes of a hypothesized designer(s), I would suspect design. 5) Evidence of "front-loading", e.g. if many bacteria had buried instructions for flagella, protected somehow from degradative mutations (not a tough burden for your average superadvanced designer), that were waiting to be "turned on" at some point in the future for some purpose of a hypothesized designer (this is a modified version of Behe's supercell idea) 6) A communication-to-intelligent-beings signal encoded in the flagellar genes. E.g., a prime number sequence apparently cleverly encoded in the essential nucleotides or amino acids of the flagellum. I say "apparently" because just the bare fact of a prime number sequence would not constitute proof, only suspicion (which is all MG wants anyway), unlike in astronomy it is just possible that there are ways for biological mechanisms to generate primes (although it is quite a stretch from 17-year cicadas to genome sequences). I'm sure there's more...I won't, however, say the one that I think MG prefers, namely "it looks designed", because it's pretty clear that natural selection can produce complex "designed" adaptation when the adaptation benefits the genes of the organism. Even Mike Gene concedes this, so IMO it appears that he is being inconsistent when he places the thus-far-unverified-in-biology ID hypothesis on the same footing as the well-verified-in-biology NS hypothesis. Why not also include Lamarkian evolution and complexity theory on the same footing also? I would say that each of these has at least a wee bit of positive evidence raising a little bit of suspicion, unlike ID. Links to other threads and CCed posts on this topic would be worthwhile. |
| Date: 2002/12/19 00:04:03, Link 128.111.106.15 | ||||||
| Author: niiicholas | ||||||
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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 128.111.106.15 |
| Author: niiicholas |
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I rediscovered the Breakpoint article, it has a list of links at the bottom: The Moth Myth BreakPoint with Charles Colson July 25, 2002 Nothing Natural about This Selection http://www.breakpoint.org/Breakpo....yth.htm |
| Date: 2002/12/20 01:10:56, Link 128.111.106.15 |
| Author: niiicholas |
|
Intelligent Design jargon explained! By Casey Luskin http://www.ideacenter.org/idjargon.htm Lesse, by my count there were 3-4 terms discussed and none were significantly clarified...basically "trust me, ID is for real". |
| Date: 2002/12/20 02:11:24, Link 128.111.106.15 | ||
| Author: niiicholas | ||
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: http://www.talkorigins.org/faqs/wells/default.htm#mothgrant Too bad Wells didn't take the opportunity to attempt to rebut a review that actually had the space to debunk his arguments in the detail they deserve. ICONS OF EVOLUTION? Why much of what Jonathan Wells writes about evolution is wrong by Alan D. Gishlick http://www.ncseweb.org/icons/ |
| Date: 2002/12/20 20:53:02, Link 198.81.26.142 |
| Author: niiicholas |
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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 198.81.26.142 | ||
| Author: niiicholas | ||
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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 198.81.26.142 |
| Author: niiicholas |
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This was just pointed out on an II thread: The Online Biology Textbook Lots of good graphics. Although, they need a new horsey graphic:  More like this: http://www.talkorigins.org/faqs/horses/horse_evol.html#part2 ...fortunately, Wells apparently prefers the older view of things, despite what you might think from the title of Icons of Evolution. On page 199 he wrote, "The mere existence of extinct side-branches doesn't rule out the possibility that the evolution of modern horses was directed. A cattle drive has a planned destination, even though some steers might stray along the way." Discussed here: http://www.talkorigins.org/faqs/wells/#horses Another resource: Also the UC Museum of Paleontology Online: http://www.ucmp.berkeley.edu/ Teachers e-volution forum: http://www.ucmp.berkeley.edu/education/evoforum/ |
| Date: 2002/12/21 16:50:30, Link 198.81.26.142 |
| Author: niiicholas |
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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 198.81.26.142 |
| Author: niiicholas |
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Over on this ARN thread, http://www.arn.org/ubb/ultimatebb.php?ubb=get_topic;f=13;t=000536;p=2 ...Joy & Mike Gene are missing JP's point. As explanatory hypotheses in science, an unconstrained supernatural designer and an unconstrained natural designer (or an unconstrained designer of unspecified supernaturalness or naturalness) have the same problem: they have no empirical implications. (I am speaking of "constraint" in terms of "explanatory constraint" here -- an omnipotent designer or super-technological designer would be all-powerful but would still be a "constrained" explanation if his actions followed a pattern motivated by a specific goals. But an unconstrained ID hypothesis is essentially what is often called "rarified design") Note that the point is not that we have to know these things about the IDer ahead of time, the point is that we have to hypothesize something with some empirical implications so that we have some idea of what kinds of evidence would strengthen or weaken our confidence in the hypothesis. Otherwise nothing is getting explained at all, even hypothetically. The two major explanatory constraints that can begin to elevate design hypotheses to something above the "IDdidit" level are, I think: 1) Designer methods/capabilities 2) Designer goals ...although there may be others. Notably, for human-design hypotheses we have a lot of evidence informing both #1 and #2, even for prehistoric cases. For SETI, the scientists involved are quite clearly hypothesizing that alien designers will be like us in certain minimal but ways, namely: 1) Designer methods/capabilities: radio 2) Designer goals: interstellar communication (with us or others) If either of these hypotheses is wrong, then even if the universe is teeming with intelligent life, we will not discover it through SETI no matter how much money and time are put in. This is not a weakness but a strength: the status of the hypothesis can be fairly rigorously evaluated at any point. Currently it is: 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 12.225.105.174 | ||||
| Author: niiicholas | ||||
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I think that several considerations have to be added to Hunter's post before serious discussion can be had. 1) "Congruence" and "noncongruence" are not either/or entities, they a matter of degree. Given N species being analyzed, there are something like (2n-3)!/(2n-2(n-2)! hypothetically possible ways of arranging them into a tree (Theobald 2002), and the (dis)similarity between two trees can be rigourously quanitified.This equation will differ slightly depending on whether the trees are rooted vs. unrooted, binary splits only, etc. Regardless, the number of possible trees gets very big very fast: 4 species = 15 possible trees, 8 species = 135,135 possible trees. You can randomly generate tree diagrams at this cool page (Phylogeny and Reconstructing Phylogenetic Trees) and get the idea very quickly what the odds are of getting the same tree twice by random chance. So the question is not whether two phylogenies from different data sources/research labs are congruent or incongruent, full stop, the question is how congruent or incongruent are they? Most of the examples touted as showing "incongruence" are actually quite minor phylogenetic disagreements. E.g., the interrelationships of different groups of bats is a pretty trivial issue in the context of vertebrates or animalia. If the microbats grouped most closely with anthropoid apes, and the macrobats with giraffes, then we'd have a significant disagreement. This kind of thing does not happen in multicellular organisms with protected germ line cells, rather different datasets keep returning highly congruent phylogenies. So, just like any scientific measurement, there will be noise in input data. The analogy here is to radiometric dating: if two measurement dates of a moon rock return ages of 4.6 and 4.5 billion years, this is very minor disagreement relative to the result (100 million years sounds like alot but is only a 2% disagreement). If someone were to go around saying "geological measurements disagree by 100 million years and this is evidence against an old earth" they would be wrong. Similar minor disagreements, such as Teeling et al.'s 2002 bat study, should not be cited as evidence for Hunter's proposition "there are also plenty of character/species sets that do not produce congruent phylogenies". A real disagreement would occur if all of these different bat species did not group together and instead were randomly associated with the outgroup taxa, but as we can see this did not occur: [img]http://www.pnas.org/content/vol99/issue3/images/medium/pq0224771001.gif[/[img] The odds of all these bat species grouping together by chance are astronomical. 2. Scale of the study and range of dataset As the age-of-the-moon example points out, what is important in considering disagreement in results is not the absolute measurement, but the size of the disagreement relative to the scale of the study. 100 million years sounds like alot but is peanuts in terms of the age of the earth. Such a disagreement would be major, however, in a radiometric dating of dinosaur bones, and a data source with a smaller error would have to be used. Radiometric datasets have ranges and scales over which they are useful, due essentially to their rate of decay. You use uranium-lead to date the age of the moon, because it has a half-life of hundreds of millions of years, but it would be ridiculous to use it for dating an archeological artifact because the answer you would get (assuming the artifact was, say, something that had been forged by remelting the ore) would be "0 +/- millions of years". Similarly, the half-life of C-14 is only ~5,000 years, so it is excellent for archeology but for anything older than 50,000 years it is useless (a result of "50,000 years old" for a carbon date essentially means "this sample is between 50,000 and infinite years old"). In the first case, the noise is much larger than the signal, and in the second case the signal is much smaller than the noise (these are slightly different, think about it for a sec.). With molecular sequences the same factors must be taken into account. I don't currently have access to Hunter's cited Balter (1997), " Morphologists learn to live with molecular upstarts", but I would note that there is apparently a contrasting commentary (Mindell 1997) on that very article from the next month of Science, entitled ""Misleading" molecules?". Probably the basic point is that the particular mtDNA sequences being used evolve too quickly (certain mtDNA sequences are, after all, used for tracing migration patterns within the human species), such that sequence similarity is low and therefore "noise" in the form of mutational biases is larger than the signal. Certainly comparing chickens, amphibians, and fish is a long ways from what one normally sees mtDNA used for, e.g. species within a genus. (Note in passing: not all mtDNA within a mitochondrion is the same. It's possible that the above study used a very slowly evolving mtDNA sequence and similarity between e.g. birds and fish was high, e.g. >75%. But I doubt it. Let's get the Balter and Mindell articles and see what they say, shall we?) In summary, anytime one sees a cited "incongruence" they must consider the dataset is appropriate for the scale of the analysis. If sequence similarity is approaching randomness then mutational biases are increasingly important to consider. 3. Actual violation of lineal descent. This is commonly the case for single-celled prokaryotes without protected germline DNA. If you like, the tree hypothesis has been falsified, because it is known and has been observed in the lab that they can trade DNA laterally. But this leaves the evidence for the common descent of e.g. all animals unquestioned. Much more can be said here because LGT is itself a nonrandom process and certainly some things are harder to LGT than others, but this is another topic. If we saw the kinds of disagreements in animals that we have in prokaryotes, as we have no mechanism for significant LGT in animals (viral transfers is about it I think), this would be a significant problem for the common descent theory. But we don't. "Disagreements" that I have seen cited for multicellular critters basically fall into the above categories. In summary, in answer to Hunter's question,
...basically, these explanatory mechanisms are allowed when they themselves are well-supported by available data. We can measure mtDNA rates of change and mutational biases. We can observe and explain why LGT occurs in prokaryotes but not in mammals. We can measure the degree of disagreement between trees and determine if the error is equivalent to 100 million years/4.6 billion years or not. There is a massive literature on all of this, which is why I'm surprised that Hunter thinks that biologists haven't thought about it. The best introduction to it all is Theobald's FAQ at that talkorigins archive, referenced below. It references a lot of articles with titles like "Testing Common Descent" about the probabilities of hitting on congruent trees by chance. Refs: Theobald, Doug. 2002. 29 Evidences for Macroevolution Teeling, Emma C. et al. 2002 Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats Proc. Natl. Acad. Sci. USA, Vol. 99, Issue 3, 1431-1436. (bold added below)
Originally posted here: ICSID thread |
| Date: 2002/12/24 02:32:17, Link 12.225.105.174 |
| Author: niiicholas |
| Wow. This just goes to show that everything is relative. |
| Date: 2002/12/24 02:39:32, Link 12.225.105.174 | ||
| Author: niiicholas | ||
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 12.225.105.174 | ||
| Author: niiicholas | ||
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 12.225.105.174 | ||||||
| Author: niiicholas | ||||||
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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. yersinia PS: There is also the interesting question of: If the hypothesized IDer decided that there needed to be some carnivorous canine-type critters in Australia, why bother with all the genetic engineering that would be required, when a simple aboriginal boat sufficed to bring dingos to Australia only ~15,000 years ago? Such ID puzzles are absolutely ubiquitous in biogeography. To me they indicate strongly that whatever creativity made these wonderful adaptations was, for some odd reason, highly constrained so that "design information" could not be transmitted across deep water barriers and instead had to be re-invented from scratch each time the adaptation was "needed" in particular locations. Strangely, such geographical constraints did not apply to flying birds, sea mammals, and other easily-dispersed organisms. If you can find an ID theory that can explain this (and "the designer's actions are mysterious" is not an explanation), I'll eat my hat. If on the other hand you give natural selection the credit for these instances of creativity, then I guess natural selection can "design" things after all, and quite skillfully too... |
| Date: 2002/12/26 14:19:39, Link 12.225.105.174 | ||||||||||||
| Author: niiicholas | ||||||||||||
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: 
In short: You and Cre8tionist have proposed that convergences like the placental/marsupial wolf are better explained by intelligent design for the same function. I pointed out that rather than the "same" design being transplanted, it looks more like it was independently invented by modification of different starting points, and that the convergence is superficial in that the true relationships of the organisms remain clear based on homologies. But, if you are going to maintain the hypothesis that ID accounts for the complex carnivory specializations of wolves and thylacines, you have to explain why it appears that the design wasn't transplanted, but rather re-invented. If a designer wanted carnivores in Australia, it would have been much easier just to put some dogs on a boat, as the stone-age Aborigines did, rather than do all of that complex creative genetic engineering twice in two different ways. Ditto for carnivorous marsupial "cats" in isolated south America, cacti vs. south African succulents, lemurs in Madagascar, Hawaiian honeycreepers, and of course Darwin's finches. Why should independent design correlate so well with geographical isolation? Did the IDer not know of boats? |
| Date: 2002/12/26 16:57:06, Link 12.225.105.174 | ||
| Author: niiicholas | ||
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I think I started a thread on this back in before The Great Server crash; there was a PNAS paper on yucca moth mouthparts, or something. Here is another case: Source: http://www.sciencedaily.com/releases/2002/12/021226071202.htm T.o. discussion: here
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| Date: 2002/12/26 19:34:24, Link 12.225.105.174 | ||||
| Author: niiicholas | ||||
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Another post: Well, I am glad that Cornelius concedes that ID-design is different from regular design inferences, in that while we always have (even if approximate) models for the designer in the cases of forensics, archaeology, and even SETI, no such model shall be forthcoming for ID. Therefore we can expect nothing in particular if ID is true, and thus have no way to strengthen or weaken our confidence in the hypothesis. I say this somewhat in jest, because Hunter in fact only uses the "there ain't no hypothetical model for the designer" argument as a defense, in fact he makes a few characterizations at times. Things have to "make sense" with regard to some unspecified criteria:
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 12.225.105.174 |
| Author: niiicholas |
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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 12.225.105.174 | ||
| Author: niiicholas | ||
In the "cytoskeletal protein homologs found in prokaryotes" category:
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| Date: 2002/12/31 17:16:02, Link 12.225.105.174 |
| Author: niiicholas |
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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 12.225.105.174 | ||
| Author: niiicholas | ||
Regarding Google, Dunk has a very good post here.
E.g., Dunk's post is: http://groups.google.com/groups?....ink.net nic PS: If you surf with Internet Explorer, don't forget about the Google Search Toolbar (*very* cool): http://toolbar.google.com/ |
| Date: 2002/12/31 17:37:05, Link 12.225.105.174 | ||
| Author: niiicholas | ||
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 198.81.26.142 | ||
| Author: niiicholas | ||
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. nic |
| Date: 2003/01/07 21:20:14, Link 128.111.106.15 | ||||
| Author: niiicholas | ||||
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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. ARN thread 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:
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| Date: 2003/01/11 18:16:37, Link 68.6.113.238 |
| Author: niiicholas |
| 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 128.111.106.15 | ||||
| Author: niiicholas | ||||
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 128.111.106.15 | ||||
| Author: niiicholas | ||||
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Hey, 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: http://www.arn.org/ubb/ultimatebb.php?ubb=get_topic;f=13;t=000568 ...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):
 ,  , and  . 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 68.6.113.238 | ||||
| Author: niiicholas | ||||
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Bump as this thread is being cited on ISCID: http://www.iscid.org/ubbcgi....279&p=2 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? Nick |
| Date: 2003/01/18 23:54:17, Link 128.111.106.15 | ||
| Author: niiicholas | ||
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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:
nic |
| Date: 2003/01/19 00:48:17, Link 128.111.106.15 | ||
| Author: niiicholas | ||
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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, nic [edit: cross-posted to II evo board: Vagueness and Explanatory Constraints http://www.iidb.org/vbb/showthread.php?s=&postid=791441#post791441 ] |
| Date: 2003/01/19 04:19:00, Link 128.111.106.15 | ||
| Author: niiicholas | ||
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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 68.6.113.238 | ||||||
| Author: niiicholas | ||||||
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Some good stuff I found and posted in response to Nelson Alonzo here: http://www.arn.org/ubb/ultimatebb.php?ubb=get_topic;f=13;t=000576;p=3
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