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BarryA Responds to His Critics at Panda’s Thumb

Barry Arrington
August 12, 2006
Intelligent Design
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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
Charlie, I forgot about this thread completely, as I was participating in a very similar conversation in a different thread: https://uncommondescent.com/index.php/archives/1447 If you're still interested in continuing this converstation, please make a post in either thread stating so. I'll check in later and see what's up. One note, you wrote: "Aside - how is a scientific model testable if it does not include the necessary parameters, variables, calculations, etc.?" If a model makes a prediction, it doesn't need to include all the parameters, variables, and calculations to be testable and therefore scientific. It's important to note that to qualify as a prediction, the prediction must be made BEFORE the evidence is discovered. For example, in the transposon model, the prediction was made that the RAG genes once contained transposase activity. This prediction was made several years before transposase activity was discovered in the existing RAG genes. So here we have a model that made a prediction (that the RAG genes once had transposase activity), and the verification of that prediction (by discovering transposase activity in the existing RAG genes). I keep forgetting one important part of the scientific method, observation. Usually, most hypotheses are generated by first making an observation of the natural world. The hypothesis is an attempt to explain that observation (or a series of observations). A scientific hypothesis will make testable predictions, and by validating those predictions, the hypothesis is supported. So in the transposon model, first it was observed that the recombination signal sequences (RSSs) had similarity to sequences of transposons. Based on a few other observations about the mechanism of recombination, the hypothesis that the recombination system evolved from a transposon was made. This led to multiple predictions, one of which was that the RAG genes were once transposases. Compare this to ID. IDists observed that many biological systems are extremely complex. They also observe that intelligent agents are capable of producing systems of great complexity. So they form the hypothesis that biological systems are a result of intelligent agents. So how do they test this hypothesis? What predictions flow logically from this hypothesis?minlay
August 28, 2006
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Minlay: That if it wasn’t POSSIBLE for IC systems to evolve, then they must have originated by ID. That is still false. IC is NOT anti-evolution- IC is anti- blind watchmaker. Until you grasp that simple concept you will never grasp the debate. Minlay: How can ID be a better alternative is there’s no empirical evidence for the creation of the immune system by ID? And again if EVERY time we observe functioning systems which exhibit..."the ordering of separate components to achieve an identifiable function that depends sharply on the components" (DBB) and we know the cause it is ALWAYS via intelligent agency. Always. 100%. Therefore to claim any system which exhibit "...the ordering of separate components to achieve an identifiable function that depends sharply on the components", arose via some blind watchmaker-type process is indeed an extra-ordinary claim.Joseph
August 18, 2006
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Not that I make any pretense that anyone would be waiting with bated breath for my grand pronouncements but I will be out of town for a week starting late this morning. Just so you know I am not hiding from any forthcoming challenges.Charlie
August 16, 2006
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I believe that Darwinism is a congenital conditon closely linked to if not identical with political liberalism. There is no question that the vast majority of university professors are left-leaning ethical and moral relativists. Good point, John. There are a lot of things that the academy accepts or embrances with little or no evidence, yet it persecutes those who express skepticism -- even mild skeptism -- of evolution.tribune7
August 16, 2006
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Matt, I'm told I am duplicating my comment, so it must be caught by the spam-filter. I'll try again tomorrow if it doesn't show up.Charlie
August 16, 2006
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Matt, I was not in any chatrooms/boards/blogs before Uncommon Descent. I don't know what people discussed then but from reading Behe I know he has been badly misunderstood and misrepresented. We have seen it continuing in these threads, ten years after the publication of Black Box. Was Behe in any of these rooms focusing on the logical impasse to the exclusion of the empirical argument? You said:
However, all of this is besides the point
It's central to my point. Perhaps my only real point - Rothschild pulled a literature bluff, as these threads have contended, and did so knowing that it was a bluff that did not address Behe's project, either today, last year, or ten years ago.
Unfortunately, Charlie, I still disagree. In DBB, he still talks about “detailed” and “testable”, but doesn’t specify what he means. By the standards which you boldfaced in his early work, I interpretted that to mean that all that would be required was a detailed and testable model for the origin of the V(D)J recombination system, which the transposon model is.
I think if you look again you will find all of the criteria covered the first time out, even in the few quotes I mustered scanning my copy of DBB. Here's the DBB info again (I think I've put the bolds where I had them before)::
But that work, valuable though it is, does not address in molecular detail the question of how immune systems originated. page 136 (edit - I think I meant 176) No one has ever explained in detailed, scientific fashion how mutation and natural selection could build the complex, intricate structures discussed in this book. In fact, none of the papers published in JME over the entire course of its life as a journal has ever proposed a detailed model by which a complex biochemical system might have been produced in a gradual. step-by-step Darwinian fashion…. No papers were published in PNAS that proposed detailed routes by which complex biochemical structures might have developed. There is no publication in the scientific literature - in prestigious journals, specialty journals, or books - that describes how molecular evolution of any real, complex, biochemical system either did occur or even might have occured. There are assertions that such evolution occured, but absolutely none are supported by pertinent experiments or calculations. page 185
Here are the parts I bolded, extracted:
#1address in molecular detail the question of how immune systems originated #2detailed, scientific fashion how mutation and natural selection could build the complex, intricate structures discussed in this book #3 - detailed model by which a complex biochemical system might have been produced in a gradual. step-by-step Darwinian fashion #4detailed routes by which complex biochemical structures might have developed #5There are assertions that such evolution occured, but absolutely none are supported by pertinent experiments or calculations
Matt said:
By the standards which you boldfaced in his early work, I interpretted that to mean that all that would be required was a detailed and testable model for the origin of the V(D)J recombination system
Behe's intial requirements included both #1 - the origin of immune system, as well as the #2 - building of the system. Explained in # 2 - scientific fashion: implying the scientific method - discovery, demonstration, observation, testing, hypothesizing, calculating, etc. Aside - how is a scientific model testable if it does not include the necessary parameters, variables, calculations, etc.? Matt said:
In DBB, Behe did not request a “mutation-by-mutation” account.
But he did. He asked for the production in a #3 - gradual, step-by-step (mutation-by-mutation) #3 - Darwinian fashion (RM and NS). Behe responded to Andrea:
What part of “numerous, successive, slight” is so hard to understand?
He asked as well for #4 - detailed routes (Not a beginning, an end, and a stop-over here or there, but the route). #5 - supported by pertinent experiments and calculations. We are talking a Darwinian process here. Everyone knows what that entails: gradual, step-by-step change by natural, heritable variation (mutations) acted upon by natural selection. How does a Darwinian model (Behe's continued criterion) not include descriptions of these? If Darwinian processes rely upon natural selection a model must show how the stops are selectable. If a Darwinian process requires that a change become fixed in a population a model must show how that could happen. He asked for the calculations from the start. What would be calculable but tinescales and population sizes? Nope. Behe never moved his goal posts and the literature presented to him did not address his question. (Here's hoping my formatting is accurate .... submit comment...)Charlie
August 16, 2006
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Unfortunately, Charlie, I still disagree. In DBB, he still talks about "detailed" and "testable", but doesn't specify what he means. By the standards which you boldfaced in his early work, I interpretted that to mean that all that would be required was a detailed and testable model for the origin of the V(D)J recombination system, which the transposon model is. However, when that information was presented to Behe in Andrea's Panda's Thumb post last year, Behe's response was: "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." In DBB, Behe did not request a "mutation-by-mutation" account. This is not what is implied when you hear the words "detailed" and "testable". I'm not sure if you were in chatrooms in the late 90's or early 2000's, but the discussions were all focused on the logical argument of IC. Whether or not it was even possible for IC systems to evolve. The empirical argument came along later. However, all of this is besides the point. What significance is it that Behe demands a mutation-by-mutation account? What does it mean that biologists cannot meet that demand? Would you agree that the research has progressed significantly in the past few years? In DBB, Behe tried to use the logical argument of IC to support his claim that ID was a better option. That if it wasn't POSSIBLE for IC systems to evolve, then they must have originated by ID. However, you can't make that leap logically if your argument against the evolvability of IC systems is not that it's impossible, but just that it hasn't been proven yet. How can ID be a better alternative is there's no empirical evidence for the creation of the immune system by ID?minlay
August 15, 2006
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I believe that Darwinism is a congenital conditon closely linked to if not identical with political liberalism. There is no question that the vast majority of university professors are left-leaning ethical and moral relativists. They do not believe in absolute truths of any sort. They are incapable of taking a firm stand and prefer to remain noncommital at any cost. They are also great joiners and tend to spontaneously aggregate in enclaves or "groupthinks." Thomas Henry Huxley and his grandson Julian Huxley are perfect examples of this condition. They, like all of us, are victims of their fate and, as near as I am able to ascertain, there is absolutely nothing that can be done for them. By way of contrast it is difficult to imagine more scholars more independent than Leo Berg or Richard B. Goldschmnidt or Robert Broom or Pierre Grasse or Otto Schindewolf or the greatest skeptic of them all, William Bateson. They stood firm and paved the way for the inevitable demise of the Darwinian myth. I am delighted to identify with them. "A dwarf standing on the shoulders of a giant may see farther than a giant himself." Robert Burton I am that dwarf. "No sadder proof can be given by a man of his own littleness than disbelief in great men." Thomas Carlyle "A past evolution is undeniable, a present evolution undemonstrable." John A. DavisonJohn A. Davison
August 15, 2006
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NickM: Lampreys have a partial system and it functions. Lampreys have a complete system. True if compared with a human immune system the lamprey system would appear to be partial. If you are using the lamprey system to get a human system you have quite a bit of explaining to do- first start with lampreys and demonstrate how they arose via some blind watchmaker-type process. NickM: Therefore Behe was wrong to say that the system had to arise all at once. How did the lamprey immune system arise? And also in the ID scenario IC systems do NOT have to arise all at once. The selection process is different. NickM: It’s very simple. And you are simply wrong. MInlay: I don’t believe that’s correct. Behe claims that for an IC system to evolve, all the core parts must come together in one step. THat is "to evolve via some blind watchmaker-type process"- please keep that in mind. Minlay: The entire point of IC is that each system is [b]irreducible[/b]. If each system can be broken down into smaller subsystems, then they’re reducible and evolvable. It all depends on the function(s) of the subsystems: Irreducible Complexity is an Obstacle to Darwinism Even if Parts of a System have other Functions:Joseph
August 15, 2006
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Excellent points, Charlie. What we have learned in this discussion children is that Behe does depend on Scientific American and the New York Times to keep up with things and has been consistent in his thinking since DBB in 1996.tribune7
August 14, 2006
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*knew* By the way, I don't know how I drew that guy with the glasses up there, I was trying to cite chapter 8 of Darwin's Black Box. I need some typing skills.Charlie
August 14, 2006
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So, once again, the papers offered in Dover did not address Behe's project. Reject his standards as you will, but note they have been the same for 10 years now, and Rothschild new what they were when he offered his irrelevant literature.Charlie
August 14, 2006
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Matt Inlay, At this point I can only say I think we fundamentally disagree. Nevertheless, I thank you for taking the time to read what we've written and to visit and offer your expertise and comments for the benefit and enlightenment of our readers. regards, Salvadorscordova
August 14, 2006
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Matt, I said Behe didn't move the goalposts, and you repeat that he did. Well, an element of conflict in any discussion's a very good thing. It means everybody is taking part and nobody's left out. http://en.wikiquote.org/wiki/Harvey The goalposts in 1996 (as referenced above):
But that work, valuable though it is, does not address in molecular detail the question of how immune systems originated. page 136 No one has ever explained in detailed, scientific fashion how mutation and natural selection could build the complex, intricate structures discussed in this book. In fact, none of the papers published in JME over the entire course of its life as a journal has ever proposed a detailed model by which a complex biochemical system might have been produced in a gradual. step-by-step Darwinian fashion…. No papers were published in PNAS that proposed detailed routes by which complex biochemical structures might have developed. There is no publication in the scientific literature - in prestigious journals, specialty journals, or books - that describes how molecular evolution of any real, complex, biochemical system either did occur or even might have occured. There are assertions that such evolution occured, but absolutely none are supported by pertinent experiments or calculations. page 185
The goalposts in 1999: Science And Evidence For Design In The Universe: The Proceedings Of The Wethersfield Institute 2000 Essay: Design At The Foundation Of LIfe 1999
For our purposes, however, the important point to keep in mind is that comparing sequences does not allow one to conclude how complex molecular machines, such as the cilium or flagellum, could have arisen step by Darwinian step. (My emphasis. Dadrwinian steps = random mutation and natural selection, numerous, successive, slight) In order to do that you have to build models, do experiments and so forth. It turns out that virtually none of the papers in the Journal of Molecular Evolution over the past decade has done such experimental work or model building.(ref. DBB, chapter 8)... Again, I hasten to say that sequence analysis is interesting and can tell us many things, but sequnce analysis alone cannot say how complex molecular machines could have been produced in a Darwinian fashion. ... page 125 The few that do consider the problems of Darwinian evolution are invariably too broad to test rigorously. page 126 The goalposts in 2000:
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. Molecular Evolution by Wen-Hsiung Li (Li 1997) is a fine textbook which does an admirable job of explicating current knowledge of how genes change with time. That knowledge, however, does not include how specific, irreducibly-complex biochemical systems were built. As I explained in Darwin's Black Box , comparing sequences is interesting but cannot explain how molecular machines arose. Li's book also contains chapters on the mechanisms (such as gene duplication, domain shuffling, and concerted evolution of multigene families) that are thought to be involved in evolution at the molecular level. Again, however, no specific system is justified in Darwinian terms.
http://www.arn.org/docs/behe/mb_evolutionaryliterature.htm In 2005:
In order to show that Darwin’s mechanism of RM/NS is responsible for either a new structure or a new function for an old structure, one has to show, as Darwin insisted, that there is a pathway leading to the structure by “numerous, successive, slight modifications”, each of which is an improvement for the organism. That is a much, much more difficult task than simply showing similarities between features. ... 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?
http://www.idthefuture.com/2005/05/calvin_and_hobbes_are_alive_and_well_in_.html The goalposts in Dover:
Well, those books do seem to have the titles that you said, and I’m sure they have then chapters in them that you mention as well, but again I am quite skeptical, although I haven’t read them, that in fact they present detailed rigorous models for the evolution of the immune system by random mutation and natural selection
(Darwinian, well, neo-Darwinaina, terms).Charlie
August 14, 2006
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By Salvador, "A very good example of this is in the evolutionary pathways of Eukaryotes and Prokaryotes. What seemed an immutable hypothesis before, upon further careful scrutiny begins to fall appart. Behe’s standards have scientific value because, what if, upon further scrutiny the transposon hypothesis collapses. It does no service to the cause of science to be leaving stones unturned which may legitimately sink a hypothesis." Unfortnately, Behe's standards are meaningless because they can never be fulfilled for any biological system. Behe hasn't presented evidence against the transposon model per se, if he could do that it would be valuable. All Behe has done is say the evidence for the transposon model isn't good enough. That isn't very useful to the scientific community.minlay
August 14, 2006
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Hi Charlie, The problem is that Behe's statements were more vague in DBB than they have been recently. In DBB, the implication was that "detailed" and "testable" meant what other scientists thought they meant, that is, providing details and can be tested. After all, DBB was written for a general audience, and so there was a lot of interpretation required in his writing. That requirement has been met in spades. However, once this data was presented to Behe, he then changed his requirements, adding in the stricter requirements. Maybe you disagree with the interpretation, but since Behe has still never written a formal definition of IC, this entire debate has had to rely on intepretations. Try to remember, irreducible complexity was presented as a logical argument in DBB. Now it has shifted entirely to an empirical one. "You admit that the articles and books heaped upon him did not answer what he asked, so you admit it was a literature bluff." Absolutely not. The literature provides what the scientific community considers to be the best answer to the origin of the immune system. It was not intended to convince Behe that the immune system evolved, because he moved the goalposts so far away that NO data could ever solve the issue to his satisfaction. The presentation of the 58 articles was meant to demonstrate to the judge and the audience just how far out of touch with reality Behe's statements are. And as evidenced by the judge's decision, it succeeded. Judge Jones, like the rest of the scientific community, sees that Behe has placed an unreasonable burden of proof on evolution. If you don't think it's unreasonable, then try applying those same standards to ID.minlay
August 14, 2006
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Matt, Thanks for your patient and polite responses (and admissions). But in your last comment you said that Behe has moved the goalposts. When did he do this? In Darwin's Black Box I find the goalposts right where he showed them to be in Dover.
A search of the immunological literature shows ongoing work in comparative immunology (the study of immune systems from various species). But that work, valuable though it is, does not address in molecular detail the question of how immune systems originated. page 136 No one has ever explained in detailed, scientific fashion how mutation and natural selection could build the complex, intricate structures discussed in this book. In fact, none of the papers published in JME over the entire course of its life as a journal has ever proposed a detailed model by which a complex biochemical system might have been produced in a gradual. step-by-step Darwinian fashion.... To take up the questions raised in this book, one would need to find papers with titles such as "Twelve Intermediate Steps Leading to the Bacterial Photosynthetic Reaction Center", "A Proto-Cilium Could Generate a Power Stroke Sufficient to Turn a Cell by Ten Degrees", "Intermediates in Adenosine Biosynthesis Effectively Mimic Adenosine Itself in RNA Function", and "A Primitive Clot Made of Randomly Aligned Fibers Would Block Circulation in Veins Smaller tha. 0.3 Millimeters". But the papers are missing. Nothing remotely like this has been published. page 176 No scientific journal will publish patently incoherent papers, so no studies asking detailed questions of molecular evolution are to be found. page 177 No papers were published in PNAS that proposed detailed routes by which complex biochemical structures might have developed. Surveys of other biochemical journals shows the same result: sequences upon sequences, but no explanations. page 178 There is no publication in the scientific literature - in prestigious journals, specialty journals, or books - that describes how molecular evolution of any real, complex, biochemical system either did occur or even might have occured. There are assertions that such evolution occured, but absolutely none are supported by pertinent experiments or calculations. page 185
So, you might want to say that Behe is asking the impossible, but he has always asked the same thing. The goalposts in Dover are where they have always been, and Behe's opponents should have known where they were. You admit that the articles and books heaped upon him did not answer what he asked, so you admit it was a literature bluff.Charlie
August 14, 2006
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Matt Inlay: I agree with the first part, but not the second.
I appreciate your very direct response, Matt. Futhermore thank you for visiting. However, I must protest, that if one is pretending Behe's claim was refuted, one must fairly represent what his claim was. Whether the standards of proof are disagreeable with you and the rest of Behe's critics is a separate matter. However, in the debates of this variety, I would expect that a person's ideas are represented accurately, and I'm afraid, you, Andrea, and Nick have not been doing that. Regarding detailed models, granted we may not have or ever have historical facts, but I don't think it's too much to ask to give parameters for the amounts of population resources needed and the kinds of selection pressures which must exist, the mutation rates involved, and the limits to collateral damage to other parts of the organism given those parameters. The question again was not just phylogeny or availability of parts but the pathway to their integration. One very substantial problem is the viability of the organism in transition from innate immunity to combinatorial immunity. The problem that the enitire population is dead before this transition occurs is substantial. We know what happens to immunity deficient individuals. These details have been glossed over, and it is in the study of these details that a hypothesis that once seemed immutable is overturned. A very good example of this is in the evolutionary pathways of Eukaryotes and Prokaryotes. What seemed an immutable hypothesis before, upon further careful scrutiny begins to fall appart. Behe's standards have scientific value because, what if, upon further scrutiny the transposon hypothesis collapses. It does no service to the cause of science to be leaving stones unturned which may legitimately sink a hypothesis. Granted, I'm very biased, but I can tell you of one immuno-pharmacologist who jumped ship because all that was offered were speculations such as those offered in those papers. She was recently featured here: Caroline Crocker. She was very friendly to the Darwinian story all of her life, but at somepoint, the explanations become horribly wanting, and, as she has suggest, isn't "we don't know" a better representation of the state of affairs than bold proclamations misleading the public that these miniscule predictions come even close really solving the most glaring issues? Any way, thank you for visiting. Salvadorscordova
August 14, 2006
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By Charlie: "So the question is, is the lamprey immune system a subset of, say, man’s, or is it a different system. Nobody ever said there couldn’t be simpler versions of a given IC system. It is certainly true that you can whack a mouse with a hammer, but that does not make the mouse trap any less IC, nor indicate that a hammer evolved into the mousetrap." This type of reducibility I'm not discussing here. The kind of reducibility I'm discussing would be a mousetrap missing a part that performs a function other than trapping mice. I'm talking about a subset of an IC system that is functional. Since an IC system, by definition, cannot be simplified and retain it's existing function, the functions change as the number of parts are reduced. As for the lamprey immune system, the adaptive part is very different from the jawed vertebrate adaptive immune system. They don't possess any of the components of the V(D)J recombination system, at least to my knowledge. It's not a good example of the ABCD vs. ABC systems I was thinking of.minlay
August 14, 2006
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By Salvador: "I’ll pose the same question to you that I did to, Nick. Do you recognize that Behe’s conception of “detatailed and testable” is not the same as your conception of “detailed and testable”, hence your suggestions of Behe being refuted are Equivocations not refutations." I agree with the first part, but not the second. Behe has arbitrarily created definitions of detailed and testable that no other scientist would use. The 58 articles provide an immense number of details on the how the system evolved, and each article tests the transposon model. So for Behe to claim that the articles are not detailed and testable, when they are certainly detailed and testable by mainstream science's standards, is IMO ridiculous. I think that it's Behe that's equivocating by using commonly used terms and redefining them.minlay
August 14, 2006
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Hi Charlie, You wrote: "It is a logically possible route, empirical evidence of its plausibility is required." I'm not sure I understand your use of the word "required". Required for what? I would suggest that the 58 articles do address the plausibility of the transposon model, but not to the degree demanded by Behe. "He that failing an empirical demonstration of the indirect route at least a step by step accounting of the plausible(not necessarily the historically accurate) mutations, effects and selectability would do to answer his challenge." We don't yet have a step-by-step model for the entire V(D)J recombination system (it's much, much more complex than what Behe originally presented). However, we have a lot of evidence that support what we think are the first few steps, namely, the integration of a transposon into an antigen receptor gene through a transposition reaction. There is a ton of empirical evidence that supports the mechanism of mutation (transposition), and that the RAG genes were transposases (after all, they still possess the transposase activity), and that an ancestral antigen receptor gene existed to serve as the target of the transposition reaction. In terms of the selectability of such a system, I would argue that it's fairly non-controversial to propose that any mechanism that introduces diversity into an antigen receptor gene would be immediately beneficial to that organism. However, I realize that that may not satisfy the skeptics here, but there are strains of bacteria that have evolved a similar trick quite recently. "Even though you are satisified with the robustness of evolutionary theory are you admitting that the 58 titles did not do this?" It depends on how much detail you "require". Behe moved the goalposts so far back that no evidence will ever be able to satisfy those demands. Of course, that's what Behe had in mind when he moved them. The point we're all trying to make is that Behe's demands are entirely unreasonable. It is not how science proceeds. If you go by Behe's made-up standards, then I'd have to say no, the articles don't meet them. However, would you be willing to agree that the 58 articles increase the plausibility of the transposon model?minlay
August 14, 2006
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Sorry for the bad edits: comment 111 should say "in response to Charlie:" comment 112, after second blockquote should be: "Behe has cut off the logical route of direct Darwinian evolution of IC. He says that failing an empirical demonstration of the indirect route at least a step by step accounting of the plausible (not necessarily the historically accurate) mutations, effects and selectability would do to answer his challenge.Charlie
August 14, 2006
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Matt Inlay, I'll pose the same question to you that I did to, Nick. Do you recognize that Behe's conception of "detatailed and testable" is not the same as your conception of "detailed and testable", hence your suggestions of Behe being refuted are Equivocations not refutations. Salvadorscordova
August 14, 2006
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Matt,
Hi Charlie, the problem here is that Behe cannot logically claim that an IC system is irreducible if he concedes that co-option is a plausible route to evolution.
You've expanded this. It is a logically possible route, empirical evidence of its plausibility is required.
Furthermore, an empirical demonstration of the evolution of an IC system isn’t necessary to demonstrate the robustness of evolution as a theory of origins.
Behe has cut of the logical route of direct Darwinian evolution of IC. He that failing an empirical demonstration of the indirect route at least a step by step accounting of the plausible(not necessarily the historically accurate) mutations, effects and selectability would do to answer his challenge. Even though you are satisified with the robustness of evolutionary theory are you admitting that the 58 titles did not do this?Charlie
August 14, 2006
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Matt,
Furthermore, if functional subsets of IC systems are discovered, then we have clear, empirical evidence that those IC systems are reducible.
in response Charlie:
So the question is, is the lamprey immune system a subset of, say, man’s, or is it a different system. Nobody ever said there couldn’t be simpler versions of a given IC system. It is certainly true that you can whack a mouse with a hammer, but that does not make the mouse trap any less IC, nor indicate that a hammer evolved into the mousetrap.
Charlie
August 14, 2006
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By Charlie, "Yes, Behe presents IC as a logical problem for such an evolution. However, he never, not from Black Box on, has denied the possibility of co-option, or indirect pathways. What he does say is that there is no empirical demonstration of such an evolution at the molecular level. Thus, it is not logically impossible, only more and more unlikely as the complexity increases, and something that is not demonstrated." Hi Charlie, the problem here is that Behe cannot logically claim that an IC system is irreducible if he concedes that co-option is a plausible route to evolution. Furthermore, if functional subsets of IC systems are discovered, then we have clear, empirical evidence that those IC systems are reducible. Furthermore, an empirical demonstration of the evolution of an IC system isn't necessary to demonstrate the robustness of evolution as a theory of origins. As I described in comment 34 of another thread: https://uncommondescent.com/index.php/archives/1447 science progresses by forming models and testing them. Immunologists have been testing the transposon model for over 25 years now and have found a ton of evidence supporting it. Their consensus is that the transposon model is the current, best explanation for the origin of the V(D)J recombination system. If you think there's a better model out there, like ID, please present it.minlay
August 14, 2006
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I am at the mercy of the moderator regarding this post, but I think dialog between adherents of not only diametrically opposed faiths but world views won't change anyone's opinion, but even worst, I don't think the Darwinians would ever consider evidence, no matter its integrity. I agree with John, and would go further: this is a waste of time. On another thread I posted on plasma cosmology. Perhaps the electrical universe point of view is considered too "out there", perhaps the more conventional plasma cosmology is more "credible" but in truth it is equally opposed. Yet despite the evidence, despite the fact of observations of what is clearly explained as the behavior of plasma, main stream scientists cling to unobservable concepts such as "dark matter", "dark energy" and twist and contort language. Sound familiar? That is all relevant to ID because despite the issue that Casey Luskin raised of testability, it won't mean a damn to your "opponents". But the leaders have an agenda. The followers obey the leaders. They will interpret black as white and white as black. And they will ostracize anyone who proposes an alternative to their cherished "Humanistic religion", as James P. Hogan calls it. They find comfort in believing there is nothing greater than the human mind, and that nothing exists outside of matter and energy, although I'm sure they have no clue what matter and energy are. Superstrings and multiverses and the observer (man) creates the universe. Does anyone else find those concepts humorous. Of course, the proponents are laughing all the way to the bank. And as Eric Lerner wrote, and he has made great progress in nuclear fusion on a shoe string budget, science has suffered and stagnated. Look at this essay about the "lawn sprinkler"; NASA personnel got indignant and defend the lawn sprinkler, despite all the contrary evidence. http://www.thunderbolts.info/tpod/2006/arch06/060210hhtornado.htm Excerpt: The explanation begins with these words: “Stellar jets are analogous to giant lawn sprinklers. Whether a sprinkler whirls, pulses or oscillates, it offers insights into how its tiny mechanism works. Likewise stellar jets, billions or trillions of miles long offer some clues to what's happening close into the star at scales of only millions of miles, which are below even Hubble's ability to resolve detail”. Those who know what a plasma discharge is might say, “if you think a lawn sprinkler offers a good analogy for the picture above, put a sprinkler in space and try it”. Any attempt to understand stellar jets across light years of space in terms of a nozzle on one end should be a career-ending embarrassment. ################################## To the contrary, anything that opposes the High Priesthood is career ending. And I think the Darwinians don't embarass easily! And so with the Darwinians. No matter how embarassing their concepts, they won't give them up, even if experiments do verify ID or anything contradicting their "faith". Here's Casey's link: http://www.evolutionnews.org/2006/01/intelligent_design_is_empirica.html So, I suggest the molecular biologists who support I.D. still do the work, keep their heads down until tenure, but have no delusions that whatever they discover and verify will ever be acceptable to the "opposition". Let judge Jones rule an end to "Global Warming" -- for his next trick.P. Phillips
August 14, 2006
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Michael Behe is a fine biochemist and a decent man. To see him treated like this makes me sick to my stomach. Got that! Write that down. He once explained to me that he does not choose to engage in the ephemeral world of cyberspace. He has got better sense than I have! I do it mostly for recreation myself and for Darwinian "steer" goring. Darwinians are intellectual geldings don't you know. It is hard to believe isn't it? I love it so! "A past evolution is undeniable, a present evolution undemonstrable." John A. DavisonJohn A. Davison
August 14, 2006
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Nick Matzke, Does the lamprey have a partial version of the immune system present in 'higher' vertebrates. ie: jawed ones? Or does it have its own, simpler, yet functioning immune system? Do you think that that the system the lamprey uses evolved into the more complex one, say that of man, or do you think that the two are examples of convergent evolution? In insisting that this conversation go off-topic have you conceded the points of the OP and the related posts? Minlay, You are representing a slightly twisted version of IC. Behe does not claim that all the parts must come together at once in order for it to evolve. You are talking only about a direct Darwinian pathway. Yes, Behe presents IC as a logical problem for such an evolution. However, he never, not from Black Box on, has denied the possibility of co-option, or indirect pathways. What he does say is that there is no empirical demonstration of such an evolution at the molecular level. Thus, it is not logically impossible, only more and more unlikely as the complexity increases, and something that is not demonstrated. Is the immune system present in the lamprey ABC of the system ABCD in higher vertebrates? Or is it, perhaps, AGM, arrived at independantly of ABCD? So the question is, is the lamprey immune system a subset of, say, man's, or is it a different system. Nobody ever said there couldn't be simpler versions of a given IC system. It is certainly true that you can whack a mouse with a hammer, but that does not make the mouse trap any less IC, nor indicate that a hammer evolved into the mousetrap.Charlie
August 14, 2006
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[quote]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.[/quote] I don't believe that's correct. Behe claims that for an IC system to evolve, all the core parts must come together in one step. If an IC system has a core of 4 parts (parts A, B, C, and D), all four parts would have to assemble at once, and we should not expect to find a system containing 3 of those parts. However, if we find a subsystem with parts A, B, and C, and we also find in this organism part D (either alone or as a component of another subsystem), then the evolution of the 4 part IC system is entirely feasible. It's irrelevant whether or not the subsystem composed of parts A, B, and C is IC because it still demonstrates how a 4-part IC system can evolve from a 3-part IC system. From there it's not a giant leap to envision how the 3-part could have evolved from a 2-part, and so on and so on. The entire point of IC is that each system is [b]irreducible[/b]. If each system can be broken down into smaller subsystems, then they're reducible and evolvable.minlay
August 14, 2006
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