Monday, August 07, 2006

Dover- Behe's response to the Immunology document stack.

Added insert(....10-8-06)
I just read BarryA's description here of Rule 803(18) which he says applies directly to this situation and demonstrates Judge Jones incompetence in his reliance upon this stunt.


Appenix A of the booklet is Behe’s response to the judgement which contains this little rather funny snippet:
(11) 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.” (23:19 (Behe)).
Several points:
1) Although the opinion’s phrasing makes it seem to come from my mouth, the remark about the studies being “not good enough” was the cross-examining attorney’s, not mine.
2) I was given no chance to read them, and at the time considered the dumping of a stack of papers and books on the witness stand to be just a stunt, simply bad courtroom theater. Yet the Court treats it seriously.
3) The Court here speaks of “evidence for evolution”. Throughout the trial I carefully distinguished between the various meanings of the word “evolution”, and I made it abundantly clear that I was challenging Darwin’s proposed mechanism of random mutation coupled to natural selection. Unfortunately, the Court here, as in many other places in its opinion, ignores the distinction between evolution and Darwinism. I said in my testimony that the studies may have been fine as far as they went, but that they certainly did not present detailed, rigorous explanations for the evolution of the immune system by random mutation and natural selection — if they had, that knowledge would be reflected in more recent studies that I had had a chance to read (see below).
4) This is the most blatant example of the Court’s simply accepting the Plaintiffs’ say-so on the state of the science and disregarding the opinions of the defendants’ experts. I strongly suspect the Court did not itself read the “fifty eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system” and determine from its own expertise that they demonstrated Darwinian claims. How can the Court declare that a stack of publications shows anything at all if the defense expert disputes it and the Court has not itself read and understood them?
In my own direct testimony I went through the papers referenced by Professor Miller in his testimony and showed they didn’t even contain the phrase “random mutation”; that is, they assumed Darwinian evolution by random mutation and natural selection was true — they did not even try to demonstrate it. I further showed in particular that several very recent immunology papers cited by Miller were highly speculative, in other words, that there is no current rigorous Darwinian explanation for the immune system. The Court does not mention this testimony.

22 Comments:

Blogger allygally said...

Behe admitted that he had not read up to 50 articles on HIS SPECIALITY, the evolution of the immune system, plus books and chapters on the evolution of the immune system by respectable scientists. Not exactly the actions of a dedicated scientist nor a point in his favour.

From trial transcripts day12 pm.

“A minimum of fifty, and you're right
2 they're not all new. Some go back as early as
3 1971, and they go right through 2005, and in
4 fact there's a few that are dated 2006, which
5 I guess would indicate a forthcoming
6 publication.
7 A. I assume so.
58 8 Q. Okay. So there's at least fifty more
9 articles discussing the evolution of the immune
10 system?
11 A. And midpoint I am, I certainly haven't had
12 time to look through these fifty articles, but I
13 still am unaware of any that address my point
14 that the immune system could arise or that
15 present in a detailed rigorous fashion a
16 scenario for the evolution by random mutation
17 and natural selection of the immune system.”

When the lawyer led him with the question “Are these not good enough?”, Behe deliberately misread the meaning and responded “They are excellent articles”, when it was clear that the question was: “Here are 50 articles which generally find evidence in opposition to your views. Is that not good enough to persuade you? Should not at least have read them?”.

Given that the implication of Behe’s answers was that he had not read the articles, then persuasion by their content was out of the question. Of course if you never listen to different points of view and information you cannot be persuaded that you are wrong!

There’s lots more, none of it to Behe’s credit. Read the whole transcript here.

http://www2.ncseweb.org/kvd/trans/2005_1019_day12_pm.pdf

4:44 pm  
Blogger allygally said...

Behe says "2) I was given no chance to read them, and at the time considered the dumping of a stack of papers and books on the witness stand to be just a stunt, simply bad courtroom theater. Yet the Court treats it seriously."

This bleating. As I said above. If there are 50 articles and a number of books on his speciality, he should have read them out of professional objectivity. How can he continue practice at the sharp end of his science if he does not read the literature?

4:50 pm  
Anonymous Anonymous said...

"If there are 50 articles and a number of books on his speciality, he should have read them out of professional objectivity. How can he continue practice at the sharp end of his science if he does not read the literature?"

The problem is that Behe's ID work is largely seperate from his professional work as a Biochemist, making the literature in question (and much of his testimony) outside his speciality.

However that's the defense's problem, not the plaintiffs'. If they put up an 'expert witness,' it is their reponsibility to ensure that this witness is sufficiently knowledgable to withstand cross-examination on the areas in which they are testifying. Behe could reasonably have expected to have been cross-examined on any of his examples of Irreducible Complexity, so should have made sure that he was well-prepared to discuss research efforts on the evolution on any of them.

This sort of intellectual laziness seems to be fairly typical of Behe. He has done little since Darwin's Black Box came out, and seems content to do the minimum to keep himself on the creationist lecture circuit.

1:23 am  
Anonymous Anonymous said...

If you even want to begin a serious defense of Behe/IC/ID on the immune system point, you have to defend Behe's 1996 statement:

"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." (Darwin's Black Box, p. 138)

And you have to read this:

Supplementary Material for: 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.
http://www2.ncseweb.org/kvd/exhibits/immune/index.html

4:43 am  
Blogger Andrew Rowell said...

Allygally & Anon,

Miller says that the stack of papers proves his view of the state of research regarding the origin of the immune system.

Behe says that that stack of papers proves his view of the state of research regarding the origin of the immune system.

Did Judge Jones read the pile before coming to the conclusion that Miller was right and Behe was wrong? How exactly did Judge Jones come to the conclusion that Miller was correct?

4:39 pm  
Blogger allygally said...

Andrew Rowell said...

Allygally & Anon,

"Miller says that the stack of papers proves his view of the state of research regarding the origin of the immune system."

The books and articles show that there is a body of research into immune systems. If you are going to decide what "view" it "proves", you have to read it. Behe admitted that he hadn't read it.

"Behe says that that stack of papers proves his view of the state of research regarding the origin of the immune system."

Behe did not read the research, even although his flagship hypothesis is that the immune system could not have evolved through RMNS. Which shows that he is lazy, incompetent and probbaly afraid to see the research in case it shows how wrong he is. And if he had not read it, how could he have an opinion on its contents?

"Did Judge Jones read the pile before coming to the conclusion that Miller was right and Behe was wrong?"

The judge is an expert in the law, not evolutionary biology. The point is that Behe, the so-called scientfic expert, DID NOT read the articles.


"How exactly did Judge Jones come to the conclusion that Miller was correct?"

The judge did not say that Miller "was correct". He said, based on the evidence presented to his court, including the fact that the defendents' "expert" witness had not even read the relevant literature, that ID is not science. Which is an entirely different conclusion.

6:26 pm  
Blogger Andrew Rowell said...

Allygally,

Dumping a huge pile of papers, chapters and books in a courtroom is just silly behaviour and for Miller to do it and for Judge Jones to take it seriously does neither of them credit.

As Behe pointed out no-one can read everything so we rely on good review articles to keep us up to date with a wider spectrum of science. Behe claims that he was up to date with the most recent reviews on the evolution of the immune system and that if anything had changed dramatically since DBB then he would have been alerted to it by this mechanism.

6:38 pm  
Blogger allygally said...

Andrew said "As Behe pointed out no-one can read everything"

So why would you expect a judge to read it? And Behe claims (see below) that he doesn't need to read anything.

"Behe claims that he was up to date with the most recent reviews on the evolution of the immune system and that if anything had changed dramatically since DBB then he would have been alerted to it by this mechanism."

That's what he claimed during the trial. In fact we know he thinks reading the literature is a worthless exercise. As Anon pointed out earlier..

"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." (Darwin's Black Box, p. 138)

And the fact remains, he admitted that he did not read the relevant literature. If anyne is sloppy, it's Behe.

8:55 pm  
Anonymous Hrafn said...

"Behe says that that stack of papers proves his view of the state of research regarding the origin of the immune system."

No he did not! He said that he hadn't read the stack. Therefore he cannot know what the stack proves.

1:19 pm  
Blogger Andrew Rowell said...

Hrafn,

OK if you prefer....Behe is saying that the little stack in court is just a part of a larger stack which proves his view of the state of research about the origin of the immune system.

What was he supposed to do? Read them in the courtroom and provide a running commentary?

1:48 pm  
Anonymous Hrafn said...

"Dumping a huge pile of papers, chapters and books in a courtroom is just silly behaviour and for Miller to do it and for Judge Jones to take it seriously does neither of them credit."

Firstly, it wasn't Miller who did this, it was Rothschild.

Secondly, how else was Rothschild to confront Behe with the existence of literature on the evolution of the immune system, whose existence Behe denied?

Confronting Behe with this pile of literature was directly relevant to impeaching Behe's testimony of its non-existence!

If Behe didn't want to be made to look an idiot on the stand, he should have done his homework more thoroughly before making such sweeping statements.

1:52 pm  
Anonymous Hrafn said...

"Behe is saying that the little stack in court is just a part of a larger stack which proves his view of the state of research about the origin of the immune system."

Your claim is false as a matter of pure logic.

Behe claimed that there was no literature on the evolution of the immune system. Rothschild presented him with counter-examples, refuting his claims. No "larger stack" can as a matter of pure logic refute these counter-examples. The counter-examples exist, therefore Behe's claim is false.

"What was he supposed to do? Read them in the courtroom and provide a running commentary?"

1) In presenting himself as an expert witness on the subject, he obliged himself to be aware of the literature on the subject, so should have had at least a general idea as to the contents of the pile.

2) If he wanted to familiarise himself with it further, he should have requested a recess in order to skim them to see exactly what issues they were covering, and then presented arguments why they didn't provide adequate explanations of the evolution of the immune system.

Throughout his cross-examination, Behe proved himself to be an ill-prepared and incompetent expert witness.It was Rothschild's job to highlight this as much as possible, and you can hardly blame him for doing his job well.

2:05 pm  
Blogger Andrew Rowell said...

Hrafn,
"Behe claimed that there was no literature on the evolution of the immune system."

Where exactly did Behe make such a ridiculous statement?

2:16 pm  
Anonymous Hrafn said...

"Where exactly did Behe make such a ridiculous statement?"

He made it in Darwin's Black Box:
"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."

The lack of an evolutionary explanation of the immune system, and other such examples, lies at the heart of Behe's claims of Irreducible Complexity. Therefore, if he wished to give credible testimony on IC, he had to make sure that he was fully aware of evolutionary research into them.

2:37 pm  
Blogger Paul (probably - maybe Liz) said...

Allygally: This may have been responded to lower down - but if a pile of stuff is dumped on a table, how can you tell even whether you have read any of it? He wasn't given time to review them THERE. And had the court read them? Did the court know that they were evidence in support of the plaintiff's claim?

10:45 am  
Blogger allygally said...

Paul said "... if a pile of stuff is dumped on a table, how can you tell even whether you have read any of it? He wasn't given time to review them THERE."

Paul. If he wanted to read them he could have done so before the court case (makes sense if he is the "expert witness") or he could have asked for time to read them or at least scan them for content. The defence lawyers could have made some objection or intervention. They did not.

In fact Behe stated that reading the articles would be worthless

from day 12 pm of the trial;

"64 24 Q. It would be a waste of time?
25 A. It would not be fruitful."

Behe is quite open. He says that he did not and does not want or need to read the literature. He is lazy and incompetent. His actions are non/un/ even anti-scientific.

The relevant part of testimony is on day 12pm transcripts of the trial. Avaailable from the NCSE website.here
http://www2.ncseweb.org/wp/?page_id=11

some of it is pasted below (I think some sort of limit has cut what I pasted...) but you can get the whole thing at the website above.

49 6 Q. We'll get back to that. Now, these
7 articles rebut your assertion that scientific
8 literature has no answers on the origin of the
9 vertebrate immune system?
10 A. No, they certainly do not. My answer,
11 or my argument is that the literature has no
12 detailed rigorous explanations for how complex
13 biochemical systems could arise by a random
14 mutation and natural selection and these
15 articles do not address that.
50 16 Q. So these are not good enough?
17 A. They're wonderful articles. They're very
18 interesting. They simply just don't address
19 the question that I pose.
51 20 Q. And these are not the only articles on
21 the evolution of vertebrate immune system?
22 A. There are many articles.
52 23 Q. May I approach?
24 THE COURT: You may.
53 25 Q. Professor Behe, what I have given you has
17
1 been marked Plaintiff's Exhibit 743. It
2 actually has a title, "Behe immune system
3 articles," but I think we can agree you didn't
4 write these?
5 A. I'll have to look through. No, I did not.
54 6 Q. And there are fifty-eight articles in here
7 on the evolution of the immune system?
8 A. Yes. That's what it seems to say.
55 9 Q. So in addition to the, some of these I
10 believe overlap with the eight that I previously
11 identified that Dr. Miller had talked about, so
12 at a minimum fifty new articles?
13 A. Not all of them look to be new. This one
14 here is from 1991 that I opened to, I think it's
15 under tab number 3, it's entitled "Evidence
16 suggesting an evolutionary relationship between
17 transposable elements and immune system
18 recombination sequences." I haven't seen this
19 article, but I assume that it's similar to the
20 ones I presented and discussed in my testimony
21 yesterday.
56 22 Q. And when I say new, I just meant different
23 from the eight that I identified with
24 Dr. Miller.
25 A. Yes, that's right.
18
57 1 Q. A minimum of fifty, and you're right
2 they're not all new. Some go back as early as
3 1971, and they go right through 2005, and in
4 fact there's a few that are dated 2006, which
5 I guess would indicate a forthcoming
6 publication.
7 A. I assume so.
58 8 Q. Okay. So there's at least fifty more
9 articles discussing the evolution of the immune
10 system?
11 A. And midpoint I am, I certainly haven't had
12 time to look through these fifty articles, but I
13 still am unaware of any that address my point
14 that the immune system could arise or that
15 present in a detailed rigorous fashion a
16 scenario for the evolution by random mutation
17 and natural selection of the immune system.
59 18 Q. I think you said in your deposition you
19 would need a step-by-step description?
20 A. Where in my deposition did I say that?
60 21 Q. Do you remember saying that?
22 A. I probably said something like that, but
23 I would like to see it.
61 24 Q. Is that your position today that these
25 articles aren't good enough, you need to see
19
1 a step-by-step description?
2 A. These articles are excellent articles I
3 assume. However, they do not address the
4 question that I am posing. So it's not that
5 they aren't good enough. It's simply that they
6 are addressed to a different subject.
62 7 Q. And I'm correct when I asked you, you would
8 need to see a step-by-step description of how
9 the immune system, vertebrate immune system
10 developed?
11 A. Not only would I need a step-by-step,
12 mutation by mutation analysis, I would also
13 want to see relevant information such as what
14 is the population size of the organism in which
15 these mutations are occurring, what is the
16 selective value for the mutation, are there any
17 detrimental effects of the mutation, and many
18 other such questions.
63 19 Q. And you haven't undertaken to try and
20 figure out those?
21 A. I am not confident that the immune system
22 arose through Darwinian processes, and so I do
23 not think that such a study would be fruitful.
64 24 Q. It would be a waste of time?
25 A. It would not be fruitful.
20
65 1 Q. And in addition to articles there's also
2 books written on the immune system?
3 A. A lot of books, yes.
66 4 Q. And not just the immune system generally,
5 but actually the evolution of the immune system,
6 right?
7 A. And there are books on that topic as well,
8 yes.
67 9 Q. I'm going to read some titles here. We
10 have Evolution of Immune Reactions by Sima and
11 Vetvicka, are you familiar with that?
12 A. No, I'm not.
68 13 Q. Origin and Evolution of the Vertebrate

11:17 am  
Blogger allygally said...

Paul said "And had the court read them? Did the court know that they were evidence in support of the plaintiff's claim?"

If the defence's expert witnesses cannot be bothered (indeed says it would not be fruitful)to read the documents, why should you demand that the judge read them? And how do you know he did not?

In any case the very existence of the articles shows that the field of immune biology is developing and that it provides at least prime facie evidence which Behe, if he was a serious person, would have read and been familiar with... don't you agree?

Paul, I am honestly puzzled at the inability of Andrew and yourself to see what is front of your face. The ID people had a golden opportunity, which they had long said they wanted, to put the evidence from both sides to a disinterested forum, to put their "facts" to the forum, and their people up to argue their POV. They did so and lost comprehensively. What good does it do to search every nook and crannie of the reports of the case looking for some minute or imagined bias or fault in process? The case is lost. Dembski in particular has all but admitted it in public, and gone all religious. What keeps you going, if not blind faith?. Which is not, of course, science.

11:32 am  
Blogger Andrew Rowell said...

Paul & Allygally,

I was interested to see that this issue is also being discussed over at Uncommon Descent and I put the added note in at the top to this effect.

I think that some useful points have come out of this over there....maybe I should start a new thread...

11:00 pm  
Anonymous Hrafn said...

The Uncommon Descent posting seems to be a piece of 'Monday Morning Quarterbacking' of highly doubtful legitimacy. We have no way of knowing whether BarryA's objections would have been upheld by a judge, let alone whether they would have had any real impact (or merely slowed down proceedings while the plaintiffs' attorney dotted his 'i's and crossed his 't's).

Regardless, the defense did not make these objections, Behe's testimony was entered into evidence, and Jones was perfectly reasonable in including this evidence in the basis of his ruling. This is how an adverserial court system works.

Judge Jones is not to blame for any shortcomings in Behe's knowledge, or for shortcomings in the defense generally.

3:51 am  
Blogger Ian Musgrave said...

As a working scientist, I have to concur with other commenters that Behe's lack of knowledge of the literature in the field is very problematic. While I would not expect him to be intimately acquainted with all those papers, but when he is making a blanket statement that there is no publication which describes the evolution of any complex system (a claim he has consistently made, and is in the afterword of the latest reprint of DBB), he should have some minimal familiarity with the field. 50 papers is not much, it’s about the standard size of a reference list for most journals. I am junior co-author of a massive review on neuropeptides, and I had to keep track of a large number of papers on neuropeptides and their role in the immune system (many more than got into the actual review). I certainly can't cite chapter and verse from these papers now, but I know the key papers, the most recent papers and the key arguments used in these papers.

Behe, claiming there is no evidence, should have a keen understanding of the literature; these papers should not have surprised him. Especially as the RAG transposase hypothesis is the major theory for the evolution of the adaptive immune system. Especially since it has made several testable predictions, which have indeed been tested and confirmed (and has even been published in Scientific American, something that Behe said was required o take a theory seriously).

Behe's claim that there were "zero" references to random mutation is wrong, and disingenuous at the best, as in the trial he admitted the papers talked about specific types of random mutation (transposition). As well, the random mutation aspect is so well known that it often doesn't need to be explicitly addressed, you can read through many papers on mutations and antibiotic resistance, where they don't discuss the "random" nature at all, because it has been so well established previously. As for natural selection, it is extensively discussed (although using technical language Behe's simple word search won't pick up, see for example Gould, S. J., Hildreth, J. E. and Booth, A. M. (2004). "The evolution of alloimmunity and the genesis of adaptive immunity." Quarterly Review of Biology 79(4): 359-382 which deals with natural selection extensively).

Behe's claim that he pointed out that later articles were speculative is also disingenuous. Apart from the fact that there were many established papers with solid experiential evidence that he ignored, these "speculative" articles were making specific testable hypotheses, not hand waving. See the massive bibliography of the evolution of the immune system and its introduction. And follow the link to the annotated bibliography to see exactly how much information we have on the immune system, and how badly Behe misunderstands it.

4:36 am  
Anonymous Hrafn said...

I have since noticed that BarryA has posted multiple threads on this issue. The one I was responding to above was his 'After Further Review, It Was Not Judge Jones Only.'

The one Andrew was referring to was his 'In Defense of the Defendants’ Lawyers in the Dover Case.' However I do not think that BarryA's interpretation of Rule 803(18) is necessarily either correct or even relevant (in that it wasn't specific statements within the publications that was of issue, so much as their very existence).

7:58 am  
Anonymous Hrafn said...

In this post Wesley Elsberry rather thoroughly shreads BarryA's abuse of Rule 803(18).

I should note that I seldom find Uncommon Descent to be well informed, and the opinions and antics of its denizens tend to be clownish in the extreme.

12:43 am  

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