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BarryA Responds to His Critics at Panda’s Thumb

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As I write this there have been 80 comments to my posts about the evidence issues implicated by the plaintiffs’ literature bluff at the Dover trial.  Our friends at Panda’s Thumb have also opened a thread to discuss my posts see (here) and also (here).  For those interested in my response to PT, read on.

1.  The Literature Bluff and Jones reliance on it.

To set the stage once again, here is the passage from the transcript where plaintiffs make their literature bluff followed by the passage from Judge Jones’ opinion where he swallowed it hook, line and sinker:

Q (from plaintiffs lawyer). We’ll return to that in a little while. Let’s turn back to Darwin’s Black Box and continue discussing the immune system. If you could turn to page 138?  Matt, if you could highlight the second full paragraph on page 138?  What you say is, “We can look high or we can look low in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system.”  That’s what you wrote, correct?

A (from Behe). And in the context that means that the scientific literature has no detailed testable answers to the question of how the immune system could have arisen by random mutation and natural selection.
 

[Behe’s answer here is critical to the analysis.  His assertion is obviously NOT that there are no books or articles that generally discuss the evolution of the immune system.  Of course there are.  His assertion is that none of the books and articles provide detailed testable answers about how the immune system could have arisen through Neo-Darwinian mechanisms.  If he were to be impeached by the 58 books and records, the material impeaching him must go to what he said, not something he did not say.]

Q. Now, you were here when Professor Miller testified?
A. Yes.
Q. And he discussed a number of articles on the immune system, correct?
 

A. Yes, he did. . . .
 

Q. And these are not the only articles on the evolution of vertebrate immune system?

A. There are many articles.

[Behe concedes there are “many” articles that generally discuss the evolution of the immune system.  If that were the issue to which the 58 books and articles went, plaintiffs were impeaching him on a point he had conceded, which was strange indeed.]
 

Q. May I approach?

THE COURT: You may.

Q. Professor Behe, what I have given you has been marked Plaintiff’s Exhibit 743.  

Q. And there are fifty-eight articles in here on the evolution of the immune system?
 

A. Yes. That’s what it seems to say . . .
 

Q. I’m going to read some titles here. We have Evolution of Immune Reactions by Sima and Vetvicka, are you familiar with that?

A. No, I’m not . . .
 

Q. You haven’t read those chapters?
 

A. No, I haven’t.
 

Q. You haven’t read the books that I gave you?
 

A. No, I haven’t.  I have read those papers that I presented though yesterday on the immune system.

Q. And the fifty-eight articles, some yes, some no?

A. Well, the nice thing about science is that often times when you read the latest articles, or a sampling of the latest articles, they certainly include earlier results.  So you get up to speed pretty quickly.  You don’t have to go back and read every article on a particular topic for the last fifty years or so.

Q. And all of these materials I gave you and, you know, those, including those you’ve read, none of them in your view meet the standard you set for literature on the evolution of the immune system?  No scientific literature has no answers to the question of the origin of the immune system?

A. Again in the context of that chapter, I meant no answers, no detailed rigorous answers to the question of how the immune system could arise by random mutation and natural selection, and yes, in my, in the reading I have done I have not found any such studies.
 

[This question and this answer are the nub of the issue.  Plaintiffs are trying to impeach Behe on a matter about which he does not disagree with them.  It is a matter of apples and oranges.  Behe says there are no books and articles giving a detailed account of the evolution of the immune system through Neo-Darwinian mechanisms, and plaintiffs attempt to impeach him by showing him a stack of books and articles that discuss the evolution of the immune system generally – do those books and articles actually impeach Behe’s assertion?  There is no way to tell on this record.]

Here is the excerpt from Jones’ opinion where he relies on the literature bluff.

“The immune system is the third system to which Professor Behe has applied the definition of irreducible complexity. Although in Darwin’s Black Box, Professor Behe wrote that not only were there no natural explanations for the immune system at the time, but that natural explanations were impossible regarding its origin. (P-647 at 139; [128]2:26-27 (Miller)). However, Dr. Miller presented peer-reviewed studies refuting Professor Behe’s claim that the immune system was irreducibly complex. Between 1996 and 2002, various studies confirmed each element of the evolutionary hypothesis explaining the origin of the immune system. ([129]2:31 (Miller)). In fact, on cross-examination, Professor Behe was questioned concerning his 1996 claim that science would never find an evolutionary explanation for the immune system. He was presented with fifty- eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution, and that it was not “good enough.” ([130]23:19 (Behe)).”

Note that Jones ignored the distinction Behe made.  Behe said there were no DETAILED ACCOUNTS of the evolution of the immune system through Neo-Darwinian mechanism.  By the time it got to Jones’ opinion Behe was being quoted as saying there are no accounts of any kind of the evolution of the immune system.  As is clear from the transcript above, Behe said exactly the opposite.  Behe’s position is that yes, there are general accounts, just no detailed accounts.

2.  The books and articles were important for the information contained in them, or they were important for nothing at all.
 

Before I get into the specific criticisms, one thing should be made clear.  Over and over again, both in response to my posts and in their own posts, my critics keep saying that the only thing the plaintiffs were trying to prove with the 58 books and articles was the mere existence of the books and articles.  By this I take it they mean that the mere existence of 58 books and articles about the evolution of the immune system refuted Behe’s assertion that there are no detailed accounts of the evolution of the immune system by random mutation and natural selection.  This is one of the silliest arguments I have ever heard, and it is difficult for me to credit that grown people would make it. 

The title of a book or article is evidence of nothing.  Only the information contained in a book or article is relevant.  Can I prove the existence of time travel by introducing as an exhibit a book entitled “A Connecticut Yankee in King Arthur’s Court?”  Of course not.  Because when one opens the book it is clearly a work of fiction.  Can I prove that scientists have developed a detailed account of the evolution of the immune system by introducing a book entitled “A Detailed Account of the Evolution of the Immune System?”  No, no, no.  The important thing about a book is not the promise of the title, but whether it delivers on the promise.  

That is why introducing 58 books and articles for no other purpose than to prove the existence of 58 books and articles with “evolution” and “immune system” in their title proves nothing.  Did any of these books actually deliver on the promise of their title?  On this record there is no way to tell.  Therefore, the point of my posts is that the evidence is meaningless and should have been excluded both as irrelevant (Rule 402) and as Hearsay (Rule 802) UNLESS the procedures of Rule 803(18) were followed.  Since the procedures of that rule were not followed, the defendants’ lawyers should have objected to it, and Jones should have (1) excluded it and (2) not relied on it in his opinion.

3.  The Second Post Was Based On A Review of the Transcript.
 

One critic quotes my second post where I said that after it became apparent that there was no testimony that the 58 books and articles were authoritative, they should have been objected to and excluded.  Then he chides me for being inconsistent by quoting from the first post where I said that based on the quotes in Gil’s thread it appeared that an authoritative foundation had been laid.

The answer to this is simple.  In my first post I included the following disclaimer:

“I was going to post this in Gil’s “Literature Bluffing” thread, but it got too long, so I am putting it in this post.  Let me preface this comment by stating that I have not reviewed the transcript of the Dover trial in detail, and I am basing what I am about to say on the information in the thread to Gil’s post.”

I wrote my second post after reading Behe’s testimony.  From that review it was clear that he had not stipulated that the 58 books and articles were authoritative.  Indeed, how could he since he was not even asked the question?

4.  PT Does Not Get the Basic Point.
 

One critic says:  “What Eric Rothschild (plaintiffs’ lawyer) was going after in the cross-examination was Behe’s claim that the scientific literature didn’t discuss the evolution of the immune system.”

Nonsense.  Pure drivel.  Behe admitted there were “many” articles discussing the evolution of the immune system:

Q. And these are not the only articles on the evolution of vertebrate immune system?

A. There are many articles.

Again, Behe’s point was not that there were no articles discussion the evolution of the immune system generally, but no articles providing a detailed account of its evolution through Neo-Darwinian mechanisms.

5.  There is more than one way to establish an article is authoritative.
 

My critics say that under my interpretation of Rule 803(18), a learned treatise can never be used to impeach an expert unless the expert that is being impeached admits that it is authoritative and that he agrees with it.  They say that under my view of the rule the following exchange could take place:  [Expert:]  ‘I’m sorry, I have no knowledge of this textbook that is basic to this field.’ [Lawyer:]‘Your honor, move to exclude this on the grounds that my expert doesn’t know a thing about it.’ [Court:] ‘Granted.’”

I never said this; indeed, I said just the opposite (see comment 39 to my second post).

In order to comply with Rule 803(18), the plaintiffs should have asked Behe one by one if each of the 58 books and articles was authoritative.  I am sure that after reviewing them one by one Behe would have said that all or most of them were.  For those that Behe refused to admit were authoritative, plaintiffs could have had another expert testify they were.

The first step of Rule 803(18) is usually not hard to meet.  My point is simply this.  There has to be some evidence from a person qualified to comment on the issue that a book or article is authoritative.  The judge is not entitled to simply assume that books and articles with fancy titles are authoritative. 

In the PT example, if expert A truly is unaware of a definitive work in the field, then the opposition could call expert B to testify that the work is definitive, and then impeach A with the work even if he had never read it.

6.  The books and articles were offered to prove the truth of the matters they asserted.
 

Another critic writes:  “Actually, BarryA is wrong on another count. The books and articles weren’t inadmissible because they were not hearsay. All of his discussion about learned treatises and the parameters of Federal Rule of Evidence 803(18) is meaningless. The books and articles weren’t offered to prove the truth of any statement contained in them. They were offered instead to contradict Behe’s claim that there were no peer-reviewed articles discussing the evolution of the immune system. That being the case, they’re not hearsay and there’s no reason to exclude them from evidence. Fed. R. Evid. 801(c).”

Wrong.  Please see comment 2 above.

 

 

 

Comments
Lampreys have a partial system and it functions. Therefore Behe was wrong to say that the system had to arise all at once. It's very simple.Nickm
August 14, 2006
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NickM: Would someone explain to me how this squares with Behe’s claim that IC systems have to arise all at once, “because any precursor missing a part would be by definition nonfunctional”? Geez NickM, do you even understand the debate? In order for NS to act on some structure/ feature that structure/ feature has to be fully present and functioning. In the lamprey scenario you would have to demonstrate how that immune system arose via some blind watchmaker-type process BEFORE using that as a stool to climb to higher verts. Then to get to the higher verts you have to demontrate that blind watchmaker-type processes allowed those to "evolve" again BEFORE getting to their immune system. Is the lamprey immune system IC? Can we take the lamprey immune system, replace a human's immune system with it and have the human survive infections? If not then any point using that system is moot. IOW a lamprey immune system although containing less components than a human immune system does nothing to help your argument. You see NickM YOU don't get it. Without the detail Behe talks about- the SAME detail that anti-IDists require of ID- NO ONE should be able to censor ID from science classroom discussions- that is IF science is about discovering the reality to our existence. Seeing that NickM appears to be fond of transposons- Dr. Spetner discussing transposons:
The motion of these genetic elements to produce the above mutations has been found to a complex process and we probably haven’t yet discovered all the complexity. But because no one knows why they occur, many geneticists have assumed they occur only by chance. I find it hard to believe that a process as precise and well controlled as the transposition of genetic elements happens only by chance. Some scientists tend to call a mechanism random before we learn what it really does. If the source of the variation for evolution were point mutations, we could say the variation is random. But if the source of the variation is the complex process of transposition, then there is no justification for saying that evolution is based on random events.
Joseph
August 14, 2006
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Tada! “presumably”, “inferred rapid appearance”, “suggested sudden”, bada bigga banga bing, just love that astronomy comparison. Voila - Immunity Big Bang! This is just one of the speculative points in the paper. This is foolish. The transposon model is exactly the model that explains the sudden emergence of the recombination system of adaptive immunity. As for the PNAS paper mentioned by MichaelJ, the key figure in the paper shows that lampreys have only 12 of the 16 components found in vertebrate immune systems -- and yet lampreys have functioning immune systems anyone. Would someone explain to me how this squares with Behe's claim that IC systems have to arise all at once, "because any precursor missing a part would be by definition nonfunctional"? PS: My chronology post still needs to be freed from the spam buffer, for whoever has the power to do that.Nickm
August 13, 2006
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Hmm...
So Behe was not overwhelmed with the titles of 58 titles because he’s seen the bluffs before. A little as well on data-base searches:
Was not supposed to be in quotes above.Charlie
August 13, 2006
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Behe is no stranger to literature bluffs and web searches: http://www.arn.org/docs/behe/mb_evolutionaryliterature.htm
Michael J. Behe Discovery Institute July 31, 2000 I. Summary Although several persons have cited numerous references from the scientific literature purporting to show that the problem of irreducible complexity I pointed out in Darwin's Black Box is being seriously addressed, the references show no such thing. Invariably the cited papers or books either deal with non-irreducibly complex biochemical systems, or do not deal with them in enough detail for critical evaluation. I strongly emphasize, however, that I do not prefer it that way. I would sincerely welcome much more serious, sustained research in the area of irreducible complexity. I fully expect such research would heighten awareness of the difficulties of Darwinian evolution.... A prominent claim I made in Darwin's Black Box is that, not only are irreducibly complex biochemical systems unexplained, there have been very few published attempts even to try to explain them. This contention has been vigorously disputed not so much by scientists in the relevant fields as by Darwinian enthusiasts on the Internet. Several web-savvy fans of natural selection have set up extensive, sophisticated sites that appear to receive a significant amount of notice. They influence college students, reporters, and, sometimes, academic reviewers of my book ... The Empty Box site is, I think, actually a valuable resource, containing links to many reviews, comments and other material, both critical and favorable, related to my book. One subsection of the site is entitled "Alive and Published," and contains citations to a large number of papers and books which Catalano believes belie my claim that "There has never been a meeting, or a book, or a paper on details of the evolution of complex biochemical systems." (Behe 1996) (p. 179) The citations were solicited on the web from anyone who had a suggestion, and then compiled by Catalano. Something, however, seems to be amiss. The assertion here that very many papers have been published clashes with statements of the reviews I quoted earlier which say, for example, that "The problems have indeed been sorely neglected." (Cavalier-Smith 1997) Would reviewers such as Jerry Coyne and Tom Cavalier-Smith--both antagonistic to my proposal of intelligent design--be unaware of the "hundreds, possibly thousands, of scientific papers that deal with this very subject"? Both claims--that the problems have been neglected and that the problems are being actively investigated--cannot be correct. Either one set of reviewers is wrong, or there is some confusion about which publications to count. Which is it? In the context of my book it is easy to realize that I meant there has been little work on the details of the evolution of irreducibly complex biochemical systems by Darwinian means. I had clearly noted that of course a large amount of work in many books and journals was done under the general topic of "molecular evolution," but that, overwhelmingly, it was either limited to comparing sequences (which, again, does not concern the mechanism of evolution) or did not propose sufficiently detailed routes to justify a Darwinian conclusion.... Such books simply don't address the problems I raise. (For instance,) Molecular Evolution by Wen-Hsiung Li (Li 1997) is a fine textbook .... (but) Since those investigators who do work in that area have not yet published a detailed Darwinian pathway in the primary literature (1), we can conclude that the answer will not be found in a more general text. ... Catalano's site lists other books that I specifically discussed in Darwin's Black Box, where I noted that, while they present mathematical models or brief general descriptions, they do not present detailed biochemical studies of specific irreducibly complex systems. (Gillespie 1991; Selander et al. 1991) There is no explanation on Catalano's web site of why he thinks they address the questions I raised. The site also points to papers with intriguing titles, but which are studies in sequence analysis, such as "Molecular evolution of the vertebrate immune system" (Hughes and Yeager 1997) and "Evolution of chordate actin genes: evidence from genomic organization and amino acid sequences." (Kusakabe et al. 1997) As I explained in Darwin's Black Box, sequence studies by themselves can't answer the question of what the mechanism of evolution is. ...
So Behe was not overwhelmed with the titles of 58 titles because he's seen the bluffs before. A little as well on data-base searches:
Another website that has drawn attention (as evidenced from the inquiries I receive soliciting my reaction to it) is authored by David Ussery (Ussery 1999), ... For example, in a section on intracellular vesicular transport he notes that I stated in Darwin's Black Box that a search of a computer database "to see what titles have both evolution and vesicle in them comes up completely empty." (Behe 1996) (p. 114) My search criterion, of having both words in the title, was meant to be a rough way to show that nothing much has been published on the subject. Ussery, however, writes that, on the contrary, a search of the PubMed database using the words evolution and vesicle identifies well over a hundred papers. Confident of his position, he urges his audience, "But, please, don't just take my word for it--have a look for yourself!" (Ussery 1999) The problem is that, as I stated in the book, I had restricted my search to the titles of papers, where occurrence of both words would probably mean they concerned the same subject. Ussery's search used the default PubMed setting, which also looks in abstracts. ... Since the word evolution has many meanings, and since the word vesicle can mean just a container (like the word "box"), Ussery picked up equivocal meanings. The paper cited above shows Ussery's misstep in an obvious way. However, there are other papers resulting from an Ussery-style search where, although they do not address the question I raised, the unrelatedness is not so obvious to someone outside the field...
But I bet I'm not showing the critics here anything new with reference to these websites claiming to have refuted Behe.Charlie
August 13, 2006
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To all commenters: Thank you for a great discussion. BarryABarryA
August 13, 2006
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Tribune 7 - funny how many questions are cleared up when one actually reads what was said at Dover. As I mentioned a few days ago, the Thumbsmen are building a legend around this supposed failure on Behe's part in the trial, and those of us who read the transcripts see it as an unjust fabrication. Andrea -
As for Behe’s keyword searching, well, I wish it was that easy to learn about the content of science papers.
Is it a sound strategy when Darwinists do it to show how often "evolution" shows up in the literature as opposed to "ID" or "design theory"? Especially when IDers can't even publish without removing such terms, and then can't even tell the judge why they can't. Andrea-
To the later posts that mention that Behe was aware of the latest literature regarding the transposition hypothesis, of course we knew he did, since that was the object of my initial PT essay, to which Behe directly responded months before.
So when the developments arise in the literature Behe is made aware of them, and responds. Your essay was in the New York Times, was it?Charlie
August 13, 2006
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I sent a post with a bunch of links in it summarizing the chronology. Probably those links made it get stuck in the spam buffer.Nickm
August 13, 2006
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The chronology is getting people confused here. Basically, we have: 1996 -- Darwin's Black Box, Behe's "no answers" claim 1996-2004 -- various research findings support the transposon hypothesis (reviewed in the Nature Immunology essay). The transposon hypothesis finds its way into immunology textbooks, popular science articles, and the review literature, as well as the peer-reviewed research 2002 -- Matt Inlay's TalkDesign.org essay "Evolving Immunity" makes the ID critic community generally aware of just how bad Behe's immune system chapter is, compared to the peer-reviewed literature. http://www.talkdesign.org/faqs/Evolving_Immunity.html May 17, 2005 -- Behe deposition, Behe admits not being familiar with 3 important papers on evolutionary immunology, makes his statements about expecting to be informed about papers by email, Scientific American, New York Times, etc. http://www2.ncseweb.org/kvd/index.php?path=depo/ May 30, 2005 -- Andrea Bottaro posts on PT "The Revenge of Calvin and Hobbes", which cites the Kapitonov and Jurka article (just published in the June 2005 PLoS Biology) http://www.pandasthumb.org/archives/2005/05/the_revenge_of.html May 31, 2005 -- Behe responds on ID the Future, emphasizes his requirement for near-infinite detail http://www.idthefuture.com/2005/05/calvin_and_hobbes_are_alive_and_well_in_.html June 2, 2005 -- Bottaro replies in "Behe's meaningless complexity" http://www.pandasthumb.org/archives/2005/06/behes_meaningle.html September 26, 2005 -- Kenneth Miller cites 8 immune system evo articles against Behe in his direct testimony http://www.talkorigins.org/faqs/dover/day1pm.html#day1pm93 October 18, 2005 -- Behe's direct testimony. Behe rebuts Ken Miller by arguing that: (1) Behe ran a computer search on the articles for the terms "random mutation" and "natural selection" and didn't find them, and (2) the articles weren't detailed enough http://www.talkorigins.org/faqs/dover/day11am.html#day11am221 October 19, 2005 -- On cross-examination Rothschild (1) gets Behe to admit that transposition is a form of mutation, and is mentioned throughout the papers, and that the selective advantage of the immune system is pretty obvious, and (2) performs the long-prepared stack-up-the-literature cross, getting Behe make the absurd claim that it wasn't enough detail http://www.talkorigins.org/faqs/dover/day12pm.html November 7, 2005 -- Behe claims his testimony went swimmingly (reply to a reporter who thought the opposite). Brushes off the immune system episode. Testifying in Dover Trial Was No "Ordeal" http://www.idthefuture.com/2005/11/testifying_in_dover_trial_was.html December 20, 2005 -- Judge Jones issues opinion, cites Behe immune system example http://www.talkorigins.org/faqs/dover/day12pm.html January 2006 -- Behe replies to the decision and says again the immune system stuff wasn't detailed enough, again showing he doesn't get it http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=697 May 2006 -- Bottaro et al. Nature Immunology article and Supplemental Material. http://www.nature.com/ni/journal/v7/n5/abs/ni0506-433.html I have seen no reply to the NI article from anyone yet, despite it being all over the evolution blogs.Nickm
August 13, 2006
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Hurrah for Tribune7. As you are probably already aware, I decided his information fit better as a separate post instead of as comment 92 to this post.BarryA
August 13, 2006
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To the later posts that mention that Behe was aware of the latest literature regarding the transposition hypothesis, of course we knew he did, since that was the object of my initial PT essay, to which Behe directly responded months before. It would have been truly bizarre if he later said he was not aware of those papers. He was not aware however of most of the literature in the field (and of a few later papers specifcally on trnasposition, if I am not mistaken), which was the point that was made above. As for Behe's keyword searching, well, I wish it was that easy to learn about the content of science papers. (At cross, Behe IIRC agreed that transposition is in fact a form of mutation, and that the fact that increased antigen receptor diversity is selectively beneficial is pretty much uncontroversial.)Andrea
August 13, 2006
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Did anyone read my rebuttal to Andrea's claim of evidence in the recent paper on Rag1 and Rag2 re: immunology? Here's the paper Andrea claimed for evolution of immunology... http://www.pnas.org/cgi/content/full/103/10/3728. I highlighted portions of it in the comments section here: https://uncommondescent.com/index.php/archives/1421#comments It is very telling what Andrea considers as evidence agaisnt Behe and pro-evo. It also explains why Behe, nor ID need not worry and in fact can march forward. If this is what Andrea calls evidence for evolutionary pathways, then it is not science, but historic speculation. It is scifi history. And if this paper is representative of the other 58 papers and books, then the evidence is slim at best. A bunch of guessing, highly paid, highly educated - guessing. Call it a hypothesis - but it aint testable yet - again. This is why Reverse Engineering wins and thus Design will win out. Because, by the time we figure out(that's reverse engineer for the PhDs in da house) all those "infinite details" we'll be designing with them. Maybe Andrea should reread the suggested paper posted here as evidence. Since the scientist themselves state about immunology the following mix mash of assumptive logic: The evolutionary shift that presumably accompanied this event correlates with the phylogenetically inferred rapid appearance of the entire complex of Ig/TCR/MHC-mediated adaptive immunity (3, 8, 9). The suggested sudden emergence of this system has been referred to as an immunological “big bang” (10). Tada! "presumably", "inferred rapid appearance", "suggested sudden", bada bigga banga bing, just love that astronomy comparison. Voila - Immunity Big Bang! This is just one of the speculative points in the paper. Please see the above link for the rest of my highlighting or read the PNAS paper for more speculative "scenario" posing. You can shred "as evidence" the paper's attempt of 'evolutionary hypothesis' without being an immunologist or biologist. The fortunate thing about all this is I can read english. It is speculation thru out. Please point to us Andrea in this one paper alone the detailed pathways that are known which conclusively provide evidence of unguided RM/NS. Then point to the lab test which makes it undeniable that RM/NS did it. Then we might have something at which to look upon and thus the NYT would indeed have it listed as frontpage news. Some real observable data. But until then, its great fiction. Seriously, if this is McEvo's best evidence, no wonder Behe does not need to dabble in such non-sensical diatribes. And again, he is correct - with such a breakthru, you would think the news would be as Big as... well, as Big as the BIG BANG. Barry made a good point about the law, the Judge was wrong. And the 58 papers if measured by this one that Andrea thinks is evidence highlights the false dogma pushed upon our educational systems and on the public. It also shows why one must be vigilent in what they accept as "evidence". Reading thru that paper for "evidence of historical evolution" which leads to testable hypothesis shows to the contrary, there is no such evidence and that Andrea's claims are overstated. This would lead one to believe that the ACLU lawyers were overstating their case as well - whats new. On the other hand, the more important aspect of learning how the immunological system performs, comparative analysis is useful, worth funding, and can increase our knowledge base for future medical breakthrus and better living. But just because scientist push 'evolution' into speculative "scenarios" in a paper - does not make it so.Michaels7
August 13, 2006
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Yes, we know of that response by Behe, So when you said "he learns of breakthroughs in the field from the pages of the New York Times and such” you were, um, what?tribune7
August 13, 2006
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Oh, good, looks like we are getting back to the evidence and its interpretation, finally. Thanks. Now, let's get to it: Nick: I find Behe’s response to your above claim to be of interest: [snip] Yes, we know of that response by Behe, and I linked and responded to it myself in the second link I provided above: http://www.pandasthumb.org/archives/2005/06/behes_meaningle.html As I have discussed above, Behe's is a particularly weak objection to the findings supporting the evolution of the VDJ recombination system, first because the standards he raises are obviously empirically unattainable, and second because by setting them he completely deflates the importance of his own brain-child, IC. But rather than quoting Behe, I'd like to know what you guys think of the issue yourselves.Andrea
August 13, 2006
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Nick and Andrea, You two took some real cheap shots:
Q. May I approach, Your Honor? THE COURT: You may. Q. I'm just going to quickly identify what these articles are. Exhibit P-256, "Transposition of HAT elements, links transposable elements, and VDJ recombination," that's an article in Nature by Zau, et al. P-279, an article in Science, "Similarities between initiation of VDJ recombination and retroviral integration," Gent, et al. "VDJ recombination and RAG mediated transposition in yeast," P-280, that's in Molecular Cell by Platworthy, et al. P-281 in the EMBO Journal, "En vivo transposition mediated VDJ recombinates in human T lymphocytes," Messier, et al, spelled like the hockey player. P-283, it says PLOS Biology, do you recognize that journal title? A. Yes. It stands for Public Library of Science. Q. And that's an article by Kapitnov and Gerka, RAG 1-4 and VDJ recombination, signal sequences were derived from transposons." P-747, an article in Nature, "Implications of transposition mediated by VDJ recombination proteins, RAG 1 and RAG 2, for origins of antigen specific immunities," Eglewall, et al. P-748 in The Proceedings of the National Academy of Science, "Molecular evolution of vertebrate immune system," Bartle, et al., and now finally Exhibit P-755 in Blood , "VDJ recombinates mediated transposition with the BCL 2 gene to the IGH locus and follicular lymphoma." Those were the articles in peer reviewed scientific journals that were discussed by Mr. Miller which you listened in on, correct? A. I recognize most of them. Some of them I don't recall, but that's fine. Q. They discuss the transposing hypothesis? A. Yes, they do.
tribune7
August 13, 2006
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Nick and Andrea have been implying Behe was ignorant of the challenges that arose to IC, specifically regarding the development of adaptive immune system. I went back and checked the transcripts and lo and behold Behe was specifically addressed on that issue. Note the papers he cites and the conferences he attends. A bit more than Scientific American and the New York Times. Here is how it goes:
Q. I just want to make a point clear. You said there were two examples where those who claim that irreducible complexity does not work or is not a valid explanation, they use experimental evidence, and that was the blood clotting system and the lac operon. How does the immunity system, is that experimental evidence or is that a theoretical claim? A. No, this is mostly a theoretical claim. There is no experimental evidence to show that natural selection could have produced the immune system. And I think that's a good example of the different views that people with different theoretical frameworks bring to the table. If we could show the next slide. Professor Miller shows this slide from a reference that he cited by Kapitonov and Jurka, and he has titled Summary, Between 1996 and 2005, each element of the transposon hypothesis has been confirmed. He has this over this diagram. But again, as I mentioned previously, whenever you see diagrams like this, we're talking about sequence data, comparison of protein, sequences, or gene sequences between organisms. And such data simply can't speak to the question of whether random mutation and natural selection produced the complex systems that we're talking about. So Professor Miller -- so, in my view, this data does not even touch on the question. And yet Professor Miller offers as compelling evidence. And one more time, I view this as the difference between two people with two different expectations, two different theoretical frameworks, how they view the same data. And I'd like to take a little bit of time to explain why such studies do not impress me. And I'll do so by looking at one of the papers that Professor Doolittle -- I'm sorry, Professor Miller, that's his name, cited in his presentation, Kapitonov and Jurka, that was published this year. I just want to go through, and just kind of as a quick way to show why I am not persuaded by these types of studies. I want to excerpt some sentences from this study to show what I consider to be the speculative nature of such studies. For example, in this excerpt, the authors say, something indicates that they may be important. This may indicate. It may be encoded. It might have been added. If so, it might have been derived. Alternatively, it might have been derived from a separate unknown transposon. It was probably lost. And we have a lot more of those, one more slide at least. It says, we cannot exclude the possibility. In any case, the origin appears to be a culmination of earlier evolutionary processes. If so, this might have been altered. Again, without going into the detail of the article, I just wanted to emphasize those phrases to point out what I consider to be the very speculative nature of such papers. Here's what I view to be the problem. The sequence of the proteins are there. The sequence of the genes are experimentally determined. And the question is, what do we make of that information? People like Professor Miller and the authors of this paper working from a Darwinian framework simply fit that data into their framework. But to me, that data does not support their framework. It does not offer experimental evidence for that framework. They're simply assuming a background of Darwinian random mutation and natural selection and explaining it -- or fitting it into that framework, but they're not offering support for it. Q. Dr. Behe, is there another paper that scientists point to for the support that the immune system can be explained by this Darwinian process? A. Yes, there is. There is one more that I have to discuss. Here is a recent paper, again the year 2005, by Klein and Nikolaidis entitled The Descent of the Antibody-Based Immune System by Gradual Evolution. And on the next slide is an excerpt from the initial part of their discussion where they say, quote, According to a currently popular view, the Big Bang hypothesis, the adaptive immune system arose suddenly, within a relatively short time interval, in association with the postulated two rounds of genome-wide duplications. So these people, Klein and Nikolaidis, are going to argue against what is the currently popular view among immunologists and people who study the immune system on how that system arose. Q. And what is the Big Bang hypothesis that's referred to here? A. Well, that's kind of a label that they put on to kind of indicate the fact that the immune system appears in one branch of animals, the vertebrates, and any obvious pre-cursors or functional parts of such a system do not appear to be obvious in other branches of animals. So it seems like the immune system arose almost complete in conjunction with the branching of vertebrates from invertebrate. Q. Do scientists acknowledge that or treat that as a problem for Darwin's theory? A. Well, in my experience, no, nobody treats such a thing as a problem for Darwin's theory. Q. Do you consider it a problem? A. I certainly consider it a problem. But other scientists who think that Darwinian evolution simply is true don't consider much of anything to be a problem for their theory. Q. Why do you consider it a problem? A. Because the -- as Darwin insisted, he insisted that adaptations had to arise by numerous successive slight modifications in a very gradual fashion. And this seems to go against the very gradual nature of his view. Q. Now has this paper been held up by scientists as refuting claims against intelligent design? A. Yes, it has. As a matter of fact, Professor Miller cited it in his expert report, although he didn't refer to it in his testimony. Additionally, I attended a meeting on evolution at Penn State in the summer of 2004 where one of the authors, Juan Kline, spoke on his work, and he interpreted it in those terms. Q. Now we have some quotes, I believe, from this paper that you want to highlight? A. Yes. Again, I want to pull out some excerpts from that paper just to show you why I regard this as speculative and unpersuasive. For example, they start with, by saying, quote, Here, we sketch out some of the changes and speculate how they may have come about. We argue that the origin only appears to be sudden. They talk about something as probably genuine. It probably evolved. Probably would require a few substitutions. It might have the potential of signaling. It seems to possess. The motifs presumably needed. One can imagine that a limited number. It might have been relatively minor. Quote, The kind of experimental molecular evolution should nevertheless shed light on events that would otherwise remain hopelessly in the realm of mere speculation. They're talking about experiments that have yet to be done. Next slide, I have even more such quotations. These factors are probably genuine. Nonetheless. They might have postdated. Nevertheless. Albeit. It seems. This might have been. These might represent. They might have been needed. This might have functioned. This might have. And this might have contributed. So again, this is just a shorthand way of trying to convey that, when I read papers like this, I do not see any support for Darwin's theory. I read them as speculative and -- but nonetheless, people who already do believe in Darwin's theory fit them into their own framework. Q. Now Dr. Miller cited numerous papers in his testimony to support his claims on irreducible complexity, the type III secretory system, and so forth. Have you done a review of those papers and have some comments on them that you prepared slides for? A. Yes, I did. I went through many of the papers that Professor Miller cited, as many as I could, and simply, as a shorthand way of trying to indicate or trying to convey why I don't regard any of them as persuasive, I simply did a search for the phrases, random mutation, which is abbreviated here in this column, RM, and the phrase, natural selection. Random mutation, of course, and natural selection are the two elements of the Darwinian mechanism. That is what is at issue here. And so this is, you know, this is, of course, a crude and perhaps shorthand way, but nonetheless, I think this illustrates why I do not find any of these papers persuasive. When I go through the papers that Professor Miller cited on the blood clotting cascade, Semba, et al, Robinson, et al, Jiang and Doolittle, there are no references to those phrases, random mutation and natural selection. Q. Some of your indications on this slide, you have 0 with asterisks and some without. Is there a reason for that? A. Yes. The papers that have asterisks, I scanned by eye. I read through them visually. Ones that do not have an asterisk, I was able to do a computer search for those phrases because they are on the web or in computer readable form. I have a number of other such tables. On the next one are references that Professor Miller cited on the immune system. And again, none of these references contain either those phrases, random mutation and natural selection. There were a couple more references on the immune system that Professor Miller cited, and they didn't contain those phrases either. In references for the bacterial flagellum and the type III secretory system, there was one paper by Hauch, a review in 1998 that did use the phrase natural selection. However, that phrase did not occur in the body of the paper. It was in the title of one of the references that Hauck listed. And on the next slide, I think there are papers cited by Professor Miller on common descent of hemoglobin. And again, those phrases are not there. I think there's another slide or two, if I'm not mistaken. This is the one on what he described as molecular trees, Fitch and Margoliash, from 1967. And I didn't find the phrase there either. So again, this is a shorthand way of showing why I actually considered these off-the-point and unpersuasive. Q. So all these papers that are being used to provide evidence for Darwin's theory of evolution, in particular, the mechanism evolution of natural selection, yet they don't mention random mutation or natural selection in the body of the works? A. That's correct. Q. Could you summarize the point then, Dr. Behe, that you are making with, referring to these studies and the comments you made about the speculative nature of some of these studies? A. Yes. Again, much of these studies, in my view, are speculative. They assume a Darwinian framework. They do not demonstrate it. And certainly, you know, certainly scientists should be free to speculate whatever they want. You know, science usually starts with speculation, but it can't end with speculation. And a person or, and especially a student, should be able to recognize and differentiate between speculation and actual data that actually supports a theory.
And here's some more. Guess MB does keep up with things -- at least according the Dover transcript. LOL
Q. Is this -- so you've done work in this area with the histone H4 and the molecular clock? A. Yes, uh-huh. I've written this commentary in 1990 in a journal called Trends in Biochemical Sciences, commenting on the work of somebody else who experimentally took an organism called yeast into the lab and altered its histone H4 and actually chopped off a couple amino acids at the beginning portion of that protein. And when he looked, it seems that it didn't make any difference to the organism. The organism grew just as well without those mutations, which is surprising, which is not what you would expect if all of those residues were critical for the function of that protein, histone H4. Later on, in the year 1996, I and a student of mine, Sema Agarwal, we were interested in this problem of histone H4 and molecular clock, and so we experimentally altered some amino acid residues into protein and changed them into different amino acids, with the expectation that these might destroy the function of the protein. But it turned out not to. These positions, these amino acids could be substituted just fine, which is unexpected, and which kind of complicates our interpretation of the molecular clock hypothesis. So there are two complications; complications upon complications. One, we would expect the number of mutations to accumulate with generation time, but it seems to accumulate, for some unknown reason, with absolute time. And the second is that, proteins accumulate mutations at different rates. We would expect that it would have to do with how vulnerable they are to mutations, and mutations might destroy the function of one protein that evolved slowly, but that is not experimentally supported. Q. Now has this problem been discussed in the scientific literature? A. Yes, this has been continuously discussed ever since the idea of the molecular clock hypothesis was first proposed in the early 1960's by two men named Emile Zuckerkandl and Linus Pauling. And here are a couple of papers which deal with the difficulties of the molecular clock hypothesis. Here's a recent one, Gillooly, et al, published in the Proceedings in the National Academy of Sciences, entitled The Rate of DNA Evolution, Effects of Body Size and Temperature on the Molecular Clock. In this publication, they say that, in fact, the size of an organism and temperature can affect how fast or how slow this clock might tick. Francisco Ayala has written on this frequently. Here's one from 1997. And I should say, Francisco Ayala is a very prominent evolutionary biologist. He wrote an article in 1997 entitled Vagaries of the Molecular Clock. And I think the title gets across the idea that there are questions with this hypothesis. And in 1993, a researcher named Tomoka Ohta published an article in the Proceedings of the National Academy of Sciences entitled An Examination of the Generation-time Effect on Molecular Evolution in which she considers exactly that complication that the textbook Voet and Voet pointed out, this generation-time effect. You know, why shouldn't organisms that reproduce more quickly accumulate more mutations. I have another slide just from one more recent paper. This paper by Drummond, et al, is entitled Why Highly Expressed Proteins Evolve Slowly. And it's referring to the sequence evolution that I've been discussing. It was published in the Proceedings of the National Academy of Sciences, and this was from an online version. This is so recent that I don't think it has yet appeared in print. The point I want to make with this is that, these people treat this question as a currently live question. They start off by saying, a central problem in molecular evolution is why proteins evolve at different rates. So that question I was trying to illustrate with histone H4, why does one protein tick faster and another one tick more slowly, that's still -- that is still unknown. And I think I will skip the rest of this slide and go to the next slide and just point out a couple words here. Drummond, et al, say, Surprisingly, the best indicator of a protein's relative evolutionary rate is the expression level of the encoding gene. The only point I want to make with this is that, they are reporting what is a surprise, what was not expected, which was not known, you know, 40 years ago, which has only been seen relatively recently. And they say, quote, We introduce a previously unexplored hypothesis, close quote. And the point I want to emphasize is that, here in this paper published, you know, weeks ago, that they are exploring new hypotheses to try to understand why proteins have the sequences that they do.
tribune7
August 13, 2006
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BarryA: "Nick, I clicked on your first link and got only the list of authors and the first paragraph. Is this the right link?" On the right side, click on "Download pdf" to get the file.ofro
August 13, 2006
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Nick: I find Behe's response to your above claim to be of interest:
Professor Bottaro, perhaps sensing that the paper he cites won’t be persuasive to people who are skeptical of Darwinian claims, laments that “Behe and other ID advocates will retreat further and further into impossible demands, such as asking for mutation-by-mutation accounts of specific evolutionary pathways...” Well, yes, of course that’s exactly what I ask of Darwinian claims — a mutation-by-mutation account of critical steps (which will likely be very, very many), at the amino acid level. But that’s neither a “retreat” (In Darwin's Black Box (page 176)I implied that many small details would be necessary for a real Darwinian explanation)nor is it unreasonable — that’s simply what’s necessary to actually explain the appearance of a complex, functional system in a Darwinian fashion, to show that it could indeed happen as Darwinists claim. Proteins change single mutation by single mutation, amino acid by amino acid, so that’s the level of explanation that is needed. What part of “numerous, successive, slight” is so hard to understand? And not only a list of mutations, but also a detailed account of the selective pressures that would be operating, the difficulties such changes would cause for the organism, the expected time scale over which the changes would be expected to occur, the likely population sizes available in the relevant ancestral species at each step, other potential ways to solve the problem which might interfere, and much more. Alternatively, Darwinists could present a series of experiments showing that RM/NS is capable of building a system of the complexity of the adaptive immune system. Professors Orr and Bottaro seem to think that because Darwinists’ fantastic claims are very difficult to support in a convincing fashion, then they should just be given a pass, and that everyone should agree with them without the required evidence. Fuggedaboudit. As Russell Doolittle helpfully showed, Darwinists find it easy to imagine that evolution could proceed along pathways which nature would never allow. Like Calvin and Hobbes, in their imaginations they hop into a box and fly over treacherous evolutionary terrain that nature would have to try to cross on foot. There is no reason for skeptics to trust Darwinists’ imaginations.
Scott
August 13, 2006
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Nick, I clicked on your first link and got only the list of authors and the first paragraph. Is this the right link?BarryA
August 13, 2006
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Say, does anyone want to bother to read what Andrea and I wrote about this back in May? We said what we had to say back then, and despite Andrea's repeated linking, the questions etc. here indicate that no one has read it (or at least no one has bothered to mention it, which is very very odd, given the topic): Bottaro, Andrea, Inlay, Matt A., and Matzke, Nicholas J. (2006). "Immunology in the spotlight at the Dover 'Intelligent Design' trial." Nature Immunology. 7(5), 433-435. May 2005. The article is freely online here: http://www.nature.com/ni/journal/v7/n5/abs/ni0506-433.html Supplementary Material: http://www2.ncseweb.org/kvd/exhibits/immune/index.htmlNickm
August 13, 2006
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That the “evolution” of a system occured is not the issue. It is the mechanism which drives the change which is the issue: was it purely undirected external natural forces in conjunction with fortuitous mutations, or preprogrammed information [which may or may not be taking cues from the environment]? The molecular mechanism of transposition is well studied. Transposons are excising and inserting themselves all the time in various genomes. It is a standard natural process. Experiments show that the immune system RAG genes act basically like standard transposons. This is one of several confirmations of the model. This constitutes an answer to how adaptive immunity evolved, therefore Behe's statement that there are "no answers" was wrong. Behe tries to escape this embarrassing conclusion by moving the goalposts to where evolutionists have to provide every single mutation over a half-billion years, and also they evidently have to prove that every single mutation was not due to sneaky intervention by God. This new standard is ludicrous and would destroy science if consistently applied. The judge was perfectly well aware that the articles didn't meet Behe's new standard of near-infinite detail. He noted it explicitly in his decision: We find that such evidence demonstrates that the ID argument is dependent upon setting a scientifically unreasonable burden of proof for the theory of evolution. Showing the ludicrous nature of Behe's demand for near-infinite detail was the actual main point of the immune system episode at the trial. The fact that you guys don't get it is actually pretty funny, because it just means you will keep making the same mistakes that led to Behe's cross-examination collapse in the first place.Nickm
August 13, 2006
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NickM --So, you think scientists have to ignore massive amounts of evidence for the evolution of a system, . . . I'd think you'd at least should have "the ultimate logic" of it before making such an assumption. Why assume? Why not get those all those small details and observe it occurring in a controlled setting?tribune7
August 13, 2006
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Jason, “I guess maybe we can blame extreme biases Barry?” Precisely. And the remedy is to call it “utter nonsense,” as you did. There is usually no need to attack the person’s integrity. Just a guess here, but I suspect you are a young guy. I know exactly how you feel. Many years ago in my first run for the legislature I was the classic angry young man, and my campaign speeches reflected it. I will never forget the day one of my campaign staffers (an ex-marine) said to me, “Barry, you’ve got to stop [vulgar term for urinating] napalm.” He was right. I lost that election. Two years later in the next campaign I moderated my language and demeanor, and I won that race. If you review my posts and comments you will see that I hit hard, especially with the use of sarcasm. But I hope that I am attacking only stupid arguments, not the people who make them. This is what charity requires.BarryA
August 13, 2006
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What did Behe say at deposition? That he had not read the papers shown to him, because he “would be waiting for larger news stories to point to these things”. THAT’S NOT WHAT BEHE SAID! Bizarre. --- Q: So in your efforts to keep abreast of the literature on the evolution of the immune system, neither of these articles is something that you have stumbled upon? A: I have not read these, and I would be waiting for larger news stories to point to these things — to point to significant developments in understanding these systems. ---- i.e., Behe had not read the papers shown to him, but he would have if they had been in "larger news stories". "Their conclusion is- Behe gets all his scientific info. from the NY Times “and such.” That is utter nonsense. From Behe’s quote alone, it’s obvious that’s not at all what he was saying." (emphasis added) Of course it's nonsense, but it's not what I said either. I said, instead, that "he has not read all of the literature, and learns of breakthroughs in the field from the pages of the New York Times and such." See the difference? Who's putting words in other people's mouth? And again, everyone seems to be getting very excited about this, but has anyone bothered reading the links I provided here at UD days ago, and would like to discuss them?Andrea
August 13, 2006
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Nick. This is NOT difficult to understand. Behe made it clear that the INFORMATION IN THE PAPERS is available in other areas. The information itself, the breaktrhoughs, the work, the pathways discussed are within other papers, reviews, etc. He made that quite clear when he said the stuff about information being shared among many papers. I have a feeling you'll do anything, distort any quote to claim that Behe is some fool sitting on the sidelines, refusing to do any scientific work. That's surely how you're coming off in this thread.JasonTheGreek
August 13, 2006
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That's also not what he said Nick. He said that he hasn't seen any detailed step by step pathways in any of the literature. He says that he has to put in less effort, not in that he's sitting on his butt, but that others started sending him all the info. so he didn't have to do as much leg work to search for all the information. You and Andrea both are misconstruing what Behe has said on the subject. You didn't show above that he missed the information in the 2 articles- you merely showed that he doesn't think the work meets the challenge put with in DBB! You've no idea if he has or hasn't read the information and work from those papers. He made it perfectly clear that most papers cite others and info. within others, thus you need not read EVERY paper on earth, but that most of what you do read has the info. from the other papers and work in them.JasonTheGreek
August 13, 2006
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His point was that he HAS read the literature but he doesn’t see the evidence that the system has come about via NS and RM, or that there’s a truly detailed step by step pathway found. If Behe "HAS" read the literature, why then did Behe admit he had never read the three key peer-reviewed articles we showed him at the deposition?Nickm
August 13, 2006
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Matzke said:
So, you think scientists have to ignore massive amounts of evidence for the evolution of a system, until such time as they completely understand every last detail about it?
That the "evolution" of a system occured is not the issue. It is the mechanism which drives the change which is the issue: was it purely undirected external natural forces in conjunction with fortuitous mutations, or preprogrammed information [which may or may not be taking cues from the environment]? And 3 or 4 papers which speculate about the relationship to preceeding sub-systems does not constitute massive amounts of evidence that it was indeed the unguided process of NS + RM which was responsible for the change.Scott
August 13, 2006
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Regarding "sitting on his butt", let's look at the Behe deposition, p. 231: Q. Since the publication of Darwin's Black Box, have you continued to survey the scientific literature in the way you did to write Darwin's Black Box for answers to the questions of the evolution of the immune system? A. Well, since the book has been published, I have certainly kept my eye out, but I have had to make a lot less effort because people send me candidate articles, e-mail me about them. So I do try to keep abreast of that, yes. And then after that, we showed Behe several key articles that Behe had not seen, and then Behe explained his lack of knowledge by saying that he would have expected to see discussion in Annual Reviews journals, Scientific American, the New York Times, or other secondary literature. (And I showed above that he missed already-published artices in Annual Review of Immunology, Scientific American, and Science News. This is part of how we knew Behe would flop on cross-examination: Rather than actually familiarizing himself with the scientific literature, Behe comes up with excuses for not dealing with the scientific literature. This may be good for his mental health and for keeping his fans content, but it is totally unimpressive to the neutral observer who can compare the hard work of hundreds of scientists, vs. Behe's hand-waving dismissals.Nickm
August 13, 2006
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I guess maybe we can blame extreme biases Barry? I just really don't see how one could conclude something like 'Behe gets all his scientific information from the Times' from Behe's quote. I'd wager if I showed this quote to 100 people, maybe 2 would come to this conclusion, and I have no idea what we could blame their mistaken conclusion on. I'd expect more from scientists in general.JasonTheGreek
August 13, 2006
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