RationalWiki:Kitzmiller v. Dover annotated transcript/P043

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Trial transcript: Day 12 (October 19), PM Session, Part 1

THE COURT: Be seated, please. All right, good afternoon to all. We continue with Mr. Rothschild's cross examination.

CONTINUED CROSS EXAMINATION

BY MR ROTHSCHILD:

Q. Good afternoon, Professor Behe.

A. Good afternoon, Mr. Rothschild.

Q. Let's go on to immune system. That's another biochemical system that you argued in Darwin's Black Box and you argue in your testimony is irreducibly complex, is that correct?

A. Yes.

Q. And I'm correct in understanding that you have not written any peer reviewed articles in scientific journals arguing that the immune system is in fact irreducibly complex?

A. No. My argument is in my book, that's right.

Q. And nobody else has written any articles in peer reviewed scientific journals arguing that the immune system is irreducibly complex?

A. Nobody has used those terms, but there are articles which speak of the requirement for multiple parts.

Q. They discuss what the immune system is comprised of?

A. Yes, in terms of it needing different several different parts.

Q. But those are not articles that argue for the irreducible complexity of or do not argue that the immune system can't evolve because it is irreducibly complex?

A. No, they don't argue that.

Q. Similarly you have not written any articles in peer reviewed scientific journals arguing that the immune system is intelligently designed?

A. Yes. Similarly that argument is in my book, so no, I didn't do it in peer reviewed articles.

Q. And nobody else has either?

A. That's correct.

Q. Is it the case that the AIDS virus is irreducibly complex?

A. I think that's something that would have to be argued on the basis of the evidence.

Q. You don't have a position on that?

A. No, I don't.

Q. What about anthrax?

A. I don't on that either.

Q. What about the Type 3 secretory system? Is that an irreducibly complex system?

A. I would have to, I do not right now have a position on that. So, no, I do not argue that.

Q. Okay. I mean, are there some pathogens that are irreducibly complex?

A. Well, I can't think of any right now, but there certainly may be. I don't rule it out.

Q. Isn't it the case, Professor Behe, that we only have about four irreducibly complex systems and the rest are not? I mean, you've got the cilium, the bacterial flagellum, the immune system, the blood clotting cascade, is that it?

A. No, I disagree. I think probably many other systems are, but I always want to be careful in my claims and so I stick to examples that I think are the best examples.

Q. But you don't know about any others besides the four written in your book?

A. I don't -- well, I certainly have my thoughts on the matter.

Q. Okay.

A. And I certainly that that irreducible complexity is a much, much better problem than, and it's not just confined to the examples in Darwin's Black Box. But in order to be as careful as I can I just talk about the best examples that I know of.

Q. And so the examples that I asked you about, which are harmful systems like the AIDS virus or harm up to us anyway, AIDS virus, Type 3 secretory system, anthrax, those are the kinds of systems that may very well be irreducibly complex?

A. They may well be, yes.

Q. And if they are and the immune system is also irreducibly complex, they're in sort of mortal opposition to each other?

A. Well, the phrase mortal opposition is not a scientific term. One can have a philosophical position on that I suppose, but I do not think that, I certainly wouldn't use that phraseology in describing it.

Q. But they are in opposition to each other, one's purpose is to destroy the other?

A. Now you're using the word purpose in a non-scientific sense. I think you're using it more in terms of what, more a philosophical sense. Certainly the AIDS virus -- pardon?

Q. I'm not. I'm asking purpose in the sense of its function. The immune system's function is to combat these pathogens' function, correct?

A. The purpose of the immune system, yes, is to defend an organism against pathogens. I would not say that the purpose of the AIDS virus is to destroy the immune system. I think its purpose, if anything one could say that its purpose is to replicate. But even that I would be a little uncomfortable with.

Q. So acquired immune deficiency disease is not combatting the immune system?

A. You're asking if I thought that was the purpose of the AIDS virus.

Q. Its function.

A. I do not think that is its function, no.

Q. But in any event you do agree that the immune system, its function is to combat these kind of viruses?

A. Yes. Among other things, yes.

Q. Can you explain why would the intelligent designer design one irreducibly complex system and then another one to combat it or fight it?

A. The question of the intentions of the designer is a question that is separate from and beyond the question of whether there is design. We can know something that is designed without knowing what the designer intended for it. If I might just give an example from our everyday world, we can look at something like a gun or some such thing, realize immediately that it was designed, and not know what the purpose of it is for.

Q. But we do know a lot about the intentions, desires, motives, needs of the intelligent actors who designed those guns, correct?

A. I'm going to say I don't think so. Certainly we know that if a gun were made by a human being and we know, we have other information from other sources about that, so from that other information we can certainly deduce, make good arguments about what those might be, but the case remains that that is separate information, separate from the structure of the gun, and we decide that the gun is designed by looking at the structure of it, or get away from guns, just any mechanical complex object.

Q. 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. 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.

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. 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.

Q. And the kind of mutation being discussed in here is a transposition in most of these?

A. You have to -- it depends on how you look at it. In many of them they're not actually discussing mutation. They're discussing similarities and sequences between parts of the immune system in vertebrates and some elements of transposons.

Q. But it does discuss the transpositions, correct?

A. It does, yes.

Q. In many of the articles, maybe all of them?

A. That's correct.

Q. You indicated earlier when we were discussing your paper with Dr. Snoke that transpositions are a kind of mutation, correct?

A. Yes, they are.

Q. Now, you on Monday showed the court, or maybe it was Tuesday you showed the court that you had done a literature search of articles on the immune system looking for the words "random mutation," correct?

A. Yes.

Q. But you didn't search for transpositions, is that correct?

A. That's correct.

Q. And that word appears in a number of the titles here?

A. It does, but the critical difference is the word random. There's lots of mutations, and it's entirely possible that intelligent design or some process of the development of life can occur by changes in DNA, but the critical factor is are such changes random, are they not random, so just there are also many occurrences of the word mutation, but it was not just mutation that is the critical element of Darwinian theory. It is random mutation.

Q. But in modern Darwinian theory transposition is one of the kind of mutations that natural selection acts upon, correct?

A. It is a mutation, and natural selection can act upon it.

Q. So the word mutation didn't show up, or random mutation, but a form of mutation that natural selection can act upon appears throughout these articles, correct?

A. Yes, that is right.

Q. And you also noted that natural selection does not appear in these articles?

A. That's correct.

Q. The selectability of the immune function, that's not really a controversial proposition, is it?

A. I'm sorry? What do you mean?

Q. The selectability of the immune system that that is a selectable function, I mean that's not very controversial, is it? It's a good thing, right?

A. If you mean is it beneficial for an organism to have one, I'm going to have to say that it's general, it's good for systems that, for organisms that depend on it to have one. But when you're thinking about evolution, one of the things you have to think about to have a rigorous understanding of it is what it is changing from and what is it changing to. The question is is a particular mutation that happens going to have a net beneficial effect or a net detrimental effect is an open question, and in any step one can look at, that question arises very pointedly, is this going to help or is it going to hurt.

Q. But these articles do discuss immune systems that are different from the vertebrate immune system, correct?

A. Which one is that, sir?

Q. The articles about the transposon hypothesis.

A. I think most of them are trying to look at connections between vertebrate immune systems and precursor elements.

Q. And those precursors have some form of immune system, though not as robust as the vertebrate immune systems?

A. I'm not sure what you're referring to, sir.

Q. You said they're referring to precursors, those precursors are precursors that have immune systems, correct? Just not the kind we have?

A. Well, I don't think so. Transposons are thought to have arisen from I think bacterial-like elements which do not have immune systems, and so I'm not quite sure how to take your question.

Q. We'll get back to that. Now, these articles rebut your assertion that scientific literature has no answers on the origin of the vertebrate immune system?

A. No, they certainly do not. My answer, or my argument is that the literature has no detailed rigorous explanations for how complex biochemical systems could arise by a random mutation and natural selection and these articles do not address that.

Q. So these are not good enough?

A. They're wonderful articles. They're very interesting. They simply just don't address the question that I pose.

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

A. There are many articles.

Q. May I approach?

THE COURT: You may.

Q. Professor Behe, what I have given you has been marked Plaintiff's Exhibit 743. It actually has a title, "Behe immune system articles," but I think we can agree you didn't write these?

Other Links: "Immunology in the spotlight at the Dover 'Intelligent Design' trial" The cross-examination of Behe's claims about the immune system was written up in a May 2005 article in the journal Nature Immunology. List of publications presented to Behe This is a simple list, without commentary, of the article, books, and book chapters presented to Dr. Behe during his cross-examination. Annotated Bibliography on the Evolutionary Origin of the Vertebrate Immune SystemTitle of web site This page by Nick Matzke contains annotations and quotes for each publication in the Behe cross-examination list, as well as a description of how the list was assembled, an introduction to the science, and a summary of significant discoveries in evolutionary immunology. Longer, Unannotated Bibliography on the Evolutionary Origin of the Immune System This longer bibliography shows that the literature in the Annotated Bibliography is just a small sample of the available literature. Contains a quantitative analysis by Matzke. Press accounts of the event Several journalists have recounted this episode as a key moment in the trial. A. I'll have to look through. No, I did not.

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. So in addition to the, some of these I believe overlap with the eight that I previously identified that Dr. Miller had talked about, so at a minimum fifty new articles?

A. Not all of them look to be new. This one here is from 1991 that I opened to, I think it's under tab number 3, it's entitled "Evidence suggesting an evolutionary relationship between transposable elements and immune system recombination sequences." I haven't seen this article, but I assume that it's similar to the ones I presented and discussed in my testimony yesterday.

Q. And when I say new, I just meant different from the eight that I identified with Dr. Miller.

A. Yes, that's right.

Q. A minimum of fifty, and you're right they're not all new. Some go back as early as 1971, and they go right through 2005, and in fact there's a few that are dated 2006, which I guess would indicate a forthcoming publication.

A. I assume so.

Q. Okay. So there's at least fifty more articles discussing the evolution of the immune system?

A. And midpoint I am, I certainly haven't had time to look through these fifty articles, but I still am unaware of any that address my point that the immune system could arise or that present in a detailed rigorous fashion a scenario for the evolution by random mutation and natural selection of the immune system.

Q. I think you said in your deposition you would need a step-by-step description?

A. Where in my deposition did I say that?

Q. Do you remember saying that?

A. I probably said something like that, but I would like to see it.

Q. Is that your position today that these articles aren't good enough, you need to see a step-by-step description?

A. These articles are excellent articles I assume. However, they do not address the question that I am posing. So it's not that they aren't good enough. It's simply that they are addressed to a different subject.

Q. And I'm correct when I asked you, you would need to see a step-by-step description of how the immune system, vertebrate immune system developed?

A. Not only would I need a step-by-step, mutation by mutation analysis, I would also want to see relevant information such as what is the population size of the organism in which these mutations are occurring, what is the selective value for the mutation, are there any detrimental effects of the mutation, and many other such questions.

Q. And you haven't undertaken to try and figure out those?

A. I am not confident that the immune system arose through Darwinian processes, and so I do not think that such a study would be fruitful.

Q. It would be a waste of time?

A. It would not be fruitful.

Q. And in addition to articles there's also books written on the immune system?

A. lot of books, yes.

Q. And not just the immune system generally, but actually the evolution of the immune system, right?

A. And there are books on that topic as well, yes.

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. Origin and Evolution of the Vertebrate Immune System, by Pasquier. Evolution and Vertebrate Immunity, by Kelso. The Primordial Vrm System and the Evolution of Vertebrate Immunity, by Stewart. The Phylogenesis of Immune Functions, by Warr. The Evolutionary Mechanisms of Defense Reactions, by Vetvicka. Immunity and Evolution, Marchalonias. Immunology of Animals, by Vetvicka. You need some room here. Can you confirm these are books about the evolution of the immune system?

A. Most of them have evolution or related words in the title, so I can confirm that, but what I strongly doubt is that any of these address the question in a rigorous detailed fashion of how the immune system or irreducibly complex components of it could have arisen by random mutation and natural selection.

Q. Or transposition and natural selection?

A. Or transposition is a form of mutation, so when I say random mutation, that includes that, yes.

Q. Okay. Even though we have all these articles we have seen discussing the transpositions and the transposon hypothesis?

A. Well, again as I have tried to make clear in my testimony yesterday, often times people when they're working under the aegis of a theory simply assume some component of it, and my example of that was the ether theory of the propagation of light. All of the physicists of the relevant era, the late 19th century, including the most eminent ones, thought that that happened and they thought that ether was absolutely required by their theory, but it had turned out later not to exist. And so as somebody who's not working within a Darwinian framework, I do not see any evidence for the occurrence of random mutation and natural selection.

Q. Let me give you some space there.

A. Thank you.

(Brief pause.)

Q. There's also books on the immune system that have chapters on the evolution of the immune system?

A. Yes, and my same comment would apply to those.

Q. I'm just going to read these titles, it sounds like you don't even need to look at them?

A. Please do go ahead and read them.

Q. You've got Immune System Accessory Cells, Fornusek and Vetvicka, and that's got a chapter called "Evolution of Immune Sensory Functions." You've got a book called The Natural History of the Major Histocompatability Complex, that's part of the immune system, correct?

A. Yes.

Q. And here we've got chapter called "Evolution." Then we've got Fundamental Immunology, a chapter on the evolution of the immune system.

A. lot of writing, huh?

A. Well, these books do seem to have the titles that you said, and I'm sure they have the chapters in them that you mentioned 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.

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.

Q. Let me see if I can summarize the intelligent design project. You've studied peer reviewed articles about the structure and function of the cell, correct?

A. Yes.

Q. And you conclude from them that certain structures are irreducibly complex that could not have evolved through natural selection, and therefore are intelligently designed?

A. I conclude from them that we see very detailed molecular machinery in the cell, that it strongly looks like a purposeful arrangement of parts, that in fact a purposeful arrangement of parts is a hallmark of intelligent design. I surveyed the literature and I see no Darwinian explanations for such things. And when one applies one's own reasoning to see how such things would be addressed within a Darwinian framework it's very difficult to see how they would, and so one concludes that one explanation, Darwinian processes, doesn't seem to have a good answer, but that another explanation, intelligent design, does seem to fit better.

Q. And that conclusion tells you design is not one that's being asserted by the people who wrote the articles about the structure and function of the cell?

A. That's correct.

Q. And as we discussed before, one, a conclusion that many have actively disagreed with?

A. That's correct, too.

Q. And you stated that if the natural mechanism is to be accepted, its proponents must publish or perish?

A. I'm sorry.

Q. And then you stated in the Darwin's Black Box that, "If the natural mechanism is to be accepted, its proponents must publish or perish."

A. I'm sorry, can I see that phrase?

Q. Yes, could you go to page 185 and 186 in the chapter "Publish or Perish"?

A. Yes. Okay, and what are you referring to here, sir?

Q. You stated in this book that on the subject of molecular evolution the advocates of the natural mechanism, the Darwinian mechanism, must publish or perish, correct?

A. I'm hanging up on the word natural mechanism. Where does that occur? I don't see that.

Q. The Darwinian mechanism?

A. Okay, Darwinian mechanism. Okay, yes, that's correct.

Q. You conclude the chapter called "Publish or Perish" by saying, "In effect, the theory of Darwinian molecular evolution has not published, and so it should perish," right?

A. That's correct, yes.

Q. And then all these hard working scientists publish article after article over years and years, chapters and books, full books, addressing the question of how the vertebrate immune system evolved, but none of them are satisfactory to you for an answer to that question?

A. Well, see, that again is an example of confusing the different meanings of evolution. As we have seen before, evolution means a number of things, such as change over time, common descent, gradualism and so on. And when I say Darwinian evolution, that is focusing exactly on the mechanism of natural selection. And none of these articles address that.

Q. Again at the same time you don't publish any peer reviewed articles advocating for the alternative, intelligent design?

A. I have published a book, or -- I have published a book discussing my ideas.

Q. That's Darwin's Black Box, correct?

A. That's the one, yes.

Q. And you also propose tests such as the one we saw in "Reply to My Critics" about how those Darwinians can test your proposition?

A. Yes.

Q. But you don't do those tests?

A. Well, I think someone who thought an idea was incorrect such as intelligent design would be motivated to try to falsify that, and certainly there have been several people who have tried to do exactly that, and I myself would prefer to spend time in what I would consider to be more fruitful endeavors.

Q. Professor Behe, isn't it the case that scientists often propose hypotheses, and then set out to test them themselves rather than trusting the people who don't agree with their hypothesis?

A. That's true, but hypothesis of design is tested in a way that is different from a Darwinian hypotheses. The test has to be specific to the hypothesis itself, and as I have argued, an inductive hypothesis is argued or is supported by induction, by example after example of things we see that fit this induction.

Q. We'll return to the induction in a few minutes.

A. Yes, sir. Mr. Rothschild, would you like your books back? They're heavy.

Q. Help me get to sleep tonight.

A. Thank you.

(Brief pause.)

Q. Now, you raised a couple of other areas where the theory of evolution or science generally doesn't have complete answers, correct? I'll give one example, that's the evolution of the phenomenon of sexual reproduction.

A. Yes.

Q. And you don't claim to be an expert on the issue of sexual reproduction, or the evolution of sexual reproduction, and we're trying to afford all puns here.

A. No, I do not.

Q. And you have no explanation for how or why the phenomenon of sexual reproduction was intelligently designed?

A. No, I don't have an explanation for that either, no.

Q. Then you also brought up the subject of origins of life, and I think we can agree that there are many, many, many unanswered questions on that subject, correct?

A. Yes, I certainly can agree to that, and it makes a person who is not presuming an unintelligent framework to look at that with great suspicion.

Q. Intelligent design has not explained how the first biological life arose on earth, has it?

A. In the sense that it has not proposed a step-by-step pathway whereby that happens, but I think an excellent case can be made, although I did not do so myself in my book, that in fact the origin of the first life, since from what we know is a cell is the smallest free living organism that we know of and is a very complex object and has purposeful arrangement of parts, I think has, a strong argument could be made that in fact intelligence was needed in the origin of life.

Q. But you haven't argued that?

A. I have not.

Q. You have not written any peer reviewed articles on it?

A. No.

Q. And nobody has written any peer reviewed articles on the, in the scientific journals on the intelligent design of the origin of life, correct?

A. Well, actually that's not quite right. There's that article "Directed Panspermia" that was discussed earlier by Francis Crick and Leslie Orgel. They in fact explicitly argue that one hypothesis one might advance is that the origin of life on earth is the result of intelligent activity, in their case they envisioned space aliens sending a rocket ship to earth. So I don't think your statement is quite true.

Q. So we'll just have to go back to the question of origin of life in the universe, which that wouldn't answer?

A. Well, as they explained in their article, nonetheless the question of the origin of life on earth is a historical question of great interest, and they speculated that conditions wherever life arose first might have been quite different from conditions on the earth, so that perhaps life could have arisen more easily there. And so they did not, though I certainly share your concern, they, Francis Crick and Leslie Orgel did not think that that particular question was particularly, that it ultimately couldn't be answered.

Q. And those arenas where life, where the origination of life might be easier to accomplish, they were still talking about natural product, is that correct?

A. They were, yes, they had in mind a natural process, and I could take this opportunity to remind, to reiterate that intelligent design does not rule out natural processes.

Q. So per your article considers that highly implausible.

A. I certainly do consider it implausible.

Q. Professor Behe, you discussed a while yesterday the concept of the molecular clock.

A. Yes.

Q. That was in response to a point Ken Miller had made in his testimony?

A. That's correct.

Q. May I approach?

THE COURT: You may.

Q. Can you pull up the biochemical similarity slide? Now, these are, you can flip through them, these are slides that Dr. Miller used when discussing the issue that you then responded to with the molecular clock?

A. Yes.

Q. And let's look at the first page of that slide, Dr. Miller's, and he's discussing a problem he has with Pandas, correct?

A. Yes, that's right.

Q. And looking at the first page, what he wrote on the slide, or actually quoted from Pandas is, "When measurements of the similarities between proteins were put side by side, the pattern that emerges contradicts the expectations based on Darwinism," and he goes on, in Pandas on page 37, "Notice that the cytochrome C of this insect exhibits the same degree of difference from organisms as diverse as humans, penguin, snapping turtle, tuna, and lamprey, and the reason this finding is so surprising is that it contradicts the Darwinian expectation."

And then on the next page it states, next page of his slide, I'm still quoting from page 37, it states that, "Darwinism would predict a greater molecular distance from the insect to the amphibian and to the living fish, greater distance still as to reptiles, and greater than that to the mammal. Yet this pattern is not found." And then go on to the next slide, still quoting from Pandas on page 36, it says, "To use the classic Darwinian scenario, amphibians are intermediate between fish and other land dwelling vertebras."

And turning to the next slide, quoting from page 140, it talks about corresponding to the expected transitions from fish to amphibian to reptile to mammal. And if you go to the last page of the slide, Dr. Miller's illustrations in an illustration of his own what the problem is, right? "Pandas misleads students as to the actual prediction of evolutionary theory by pretending that evolution predicts a linear sequence, tuna, frog, turtle, chicken, horse. Amphibians are intermediate between fish and birds and mammal," right?

A. Yes.

Q. And that's not what the Darwinian theory suggests, correct? It does not project that the sequence is in that order, linear, tuna, frog, turtle, chicken, horse, correct? That's not what Darwinian evolution states, correct?

A. You'll have to help me and tell me what Darwinian evolution does state.

Q. You understand Darwinian evolution to propose a tree in which animals of this kind are on a tree with a common ancestor, not linear in this sequence, and if you could go to the page two prior, Matt? And just focusing on that tree, that's what evolutionary biologists who are working from the evolutionary theory, that's what they believe is the correct way to describe the phylogeny, correct?

A. I'm afraid this is using an extremely simplified diagram to make points which do not follow from it.

Q. Dr. Behe, I'm not asking about the timing. I just want to talk about the sequence, okay? And you would agree that what evolutionary theory predicts, forgetting about the timing and how the molecular clock works, is that the phylogeny is in that tree form and not tunas becoming frogs becoming chickens becoming horses, right? Instead it's common ancestry, right?

A. Certainly Darwinian theory predicts common, or posits common ancestry. The question that Pandas existing, is addressing however, is not that. It's why these proteins have the particular sequences they do.

Q. But when Pandas says to use the classic Darwinian scenario amphibians are intermediate between fish and the other land dwelling vertebrates, that's not a correct characterization of the theory of evolution, is it?

A. No, that isn't, no.

Q. It isn't. And whatever the right answer is about the molecular clock, it has nothing to do with that statement, correct? It doesn't make that statement correct?

A. The molecular clock does not say that. That statement is not accurate.

Q. Matt, could you pull up pages 99 to 100 and highlight our favorite passage? That was the passage we spent some time on yesterday, " 5intelligent design means that various forms of life began abruptly through an intelligent agency, with their distinctive features already intact, fish with fins and scales, birds with feathers, beaks, and wings, etc." You said a few things about this passage. One is you don't like it so much.

A. I certainly would have written it differently.

Q. You don't think it's an accurate representation of intelligent design?

A. I think intelligent design is described better elsewhere in the book.

Q. Okay, and you also testified that intelligent design has advanced beyond where it was with Pandas?

A. That's correct.

Q. And you also said -- Matt, if you could pull down highlighted text and highlight page 99, or you can just look in your book Professor Behe, there we go, that you didn't read the graphic up here, Figure 4.4, to have anything to do with the issue of common descent, correct?

A. Yes, that's right. The way I read it, it was trying to describe what they perceived as the fossil record.

Q. Now, yesterday I asked you about the book Design of Life.

A. I had forgotten.

Q. The book the new version of Pandas to use a very colloquial term that Dr. Dembski is working on?

A. Yes.

Q. And that was the one where he said you were an author, but at least right now you're not, right?

A. That's right.

Q. Professor Behe, what I have given you is what we have marked as P-775, which is a chapter from the draft manuscript of Design of Life. This was produced to plaintiffs in this litigation, and you see it's got, this chapter is headed "The Fossil Record."

A. Yes.

Q. And if you flip to page 22 of that chapter?

A. I'm sorry, page 52 did you say?

Q. 22.

A. 22?

Q. The subchapter is headed "Sudden Emergence."

A. Yes, I see that.

Q. Is that a term that you have heard used in the intelligent design community?

A. Is it in Pandas?

Q. I'm asking you just based on your own experience.

A. It's not that familiar, no.

Q. Some familiarity?

A. I may have heard of it, but I can't, you know, say for sure.

Q. Okay. And what it says here, if we go to, it says right under that heading, " 5there's a fourth option for explaining the gaps in the fossil record besides imperfection of the record, insufficient search, and punctuated equilibrium. There is also sudden emergence." And do you recall from our discussion yesterday there was a similar breakdown in Pandas on pages and 97?

A. Yes, I think they also gave four possibilities.

Q. Okay, and it says, "Explain the gaps in the fossil record by means of sudden emergence is to say that the gaps are real, that the discontinuities in the fossil record represent discontinuities in the history of life. Sudden emergence isn't just saying the transitional links containing major groups of organisms are absent from the fossil record. It's saying that the transitional links are absent, period. They never existed." That's what it says?

A. That's correct, that's what it says.

Q. And we had some back and forth yesterday about abrupt appearance of fossils as opposed to abrupt beginning of life or appearance of life, and this is pretty clear to take pains to distinguish the two, isn't it?

A. Yes, it seems that that's exactly what they're trying to say.

Q. Okay. If you could turn to page 28 of the manuscript?

MR. MUISE: Your Honor, I'm going to object insofar as this document is being offered for the truth of the matter asserted. As his testimony already previously identified, he's not an author, he has no part in it. If he's going to be asking him to I guess to try to impeach something that may have been said, I'm not sure what the purpose is. It appears right now he's trying to offer it for the truth of the matter asserted inside, in this document, which is a draft that Dr. Behe has no part in taking.

MR ROTHSCHILD: Dr. Padian would kill me if I introduced this for the truth of the matter asserted. I'm not suggesting that at all, Your Honor. It's for impeachment. He has made statements about the contents of Pandas and what it means and the development of intelligent design, and its for purposes of impeachment and that only.

MR. MUISE: Again, Your Honor, you've got a draft document that has, he's had no part in it. How does that impeach what's the development of intelligent design? He's certainly had no part to contribute in this, to fix errors and corrections that may have been made, it's not used to establish anything other than he's trying to offer it to assert the truth that's in the document.

THE COURT: Well, I don't think he is offering it for the truth. I don't see that. So I can discard that as a reason. Certainly --

MR ROTHSCHILD: May I offer one more?

THE COURT: Certainly -- go ahead.

MR ROTHSCHILD: Dr. Behe, has made some pretty stark claims about what intelligent design is and isn't about. He made it about Pandas. He's just made it about intelligence design generally. It makes certain claims, it doesn't make other claims, and this document goes to that issue.

THE COURT: Well, you don't doubt the authenticity of the document, do you?

MR. MUISE: My understanding is it's a draft document. That's --

THE COURT: Well, it's more than a draft document. It's a draft document of a -- well, it's a draft document to be sure, but it is a draft document of a succeeding volume, is it not, Of Pandas and People? We know that, don't we?

MR. MUISE: You know what, Your Honor? I'm not exactly sure if that's the case. I believe there was some discussion this may not even be for a high school level. I'm not sure, I mean, it's not Volume 3 of Pandas and people. I believe it has a different name. It's certainly a book that in develop Dr. Behe's had no part in the development of this particular book.

THE COURT: However, he said he might in the future.

MR. MUISE: He might in the future, but not right now. So what's in it right now has not relevant to what's right now.

THE COURT: Oh, I think it's highly relevant. No, I think that unless you can come up with something that calls into question the authenticity of it, and I don't think you can, I think what your argument there goes to exactly what it is, whether it in fact is a Volume 3 or not, the court is familiar enough with what it is, having had meanderings on this in the course of the litigation that we're certainly familiar. I don't think there's any issue about what it is. There may be an issue as to its intended audience. I think to the extent that it is hearsay, it has a high degree of reliability.

I think it meets the test under Rule 807. I think it's proper for questioning. I don't take it for the truth. I'm not accepting it for the truth. Again this is a bench trial. I don't, I think it's not inappropriate for him to question. I will guard the record insofar as I will not allow Mr. Rothschild to simply read passages that are not related to questions, and I'll take your timely objections as I did with the other material in that regard. Do you want to say something else?

MR. MUISE: No.

MR ROTHSCHILD: Your Honor, just for the record, this was produced through defendant's counsel while Dr. Dembski was still their expert.

THE COURT: Well, I'm well aware with how it emerged, so we don't need to discourse about that.

MR ROTHSCHILD: Matt, could you highlight the bottom paragraph through the Figure 6.8?

BY MR ROTHSCHILD:

Q. This passage of the draft manuscript reads, "Sudden emergence holds that various forms of life began with their distinctive feature already intact, fish with fins and scales, birds with feathers and wings, animals with fur and mammary glands. Sudden emergence is the face value interpretation of the fossil record. It interprets the structural differences separating the major types of organisms in the fossil record as a generally true reflection of biological diversity and natural history." First of all, the use of the word "true" in science is somewhat problematic I think you have told us?

A. I don't think I have ever mentioned anything on that topic.

Q. And if we could look to the top part of this, sudden emergence through up to the mammary glands, I'm going to ask Matt to pull up a comparison we made between Pandas and this document, and what we see is intelligent design means has been removed and we've got, "sudden emergence holds," taken out the words intelligent agency, and it's not just fish and birds that came out already intact but also mammals. But it's a pretty similar statement, isn't it, Professor Behe?

A. The writing is similar. I think this is an improvement to tell you the truth, because now it doesn't say intelligent design means that. Intelligent design does not mean that.

Q. Sudden emergence means that?

A. Yes. That's a separate idea. It is not intelligent design.

Q. I thought you weren't familiar with that idea.

A. I'm sorry?

Q. I thought you weren't familiar with that idea that relates to the intelligent design movement.

A. Well, I'm reading the text there, so that's how I became familiar.

Q. In your own mind it's a different concept?

A. It most certainly is. Like in saying intelligent design, the core claim is that intelligence was involved in the process of producing something. But if you want to make other claims about it, like how it was done, when it was done and so on, then you need further evidence, and it seems here, it looks like from my brief reading of the text that they are making a further claim beyond the claim of intelligent design, and properly they're calling it something else here. It was incorrect in the first edition to call it intelligent design, but here they call it by some other name. And so I see no difficulty in saying that sudden emergence means this. I just point out that it does not say that intelligent design means that.

Q. Hopefully we won't be back in a couple of years for the sudden emergence trial. But this clearly does as the passage we read --

THE COURT: Not on my docket, let me tell you.

Q. Related cases, Your Honor? Going back to the full text that we were looking at before we did the comparison, this surely is a direct challenge to the proposition of common descent, isn't it?

A. Yes. It's a direct challenge, yes, that's correct.

Q. And it says, "In making that challenge accordingly, the history of life is properly to be represented as shown in Figure 6-8." Do you see that?

A. Yes, I do.

Q. Matt, if you could turn to the next page and highlight that first indication there? It says here Figure 6-8, insert Figure 4-4 on page 99 of Pandas and that's the figure that we looked at before in Pandas on which, with the bars?

A. Okay.

Q. Right? Okay, that's the figure, the same figure 4.4 which they're saying is 6.8?

A. Yes, it looks to be the same.

Q. They're relying on that figure in support of their challenge to common descent, correct?

A. It seems that they're using a similar figure, perhaps even identical now, to support this claim.

MR ROTHSCHILD: Your Honor, I have one last set of questions. I can proceed or --

THE COURT: We've been out about an hour. How long is the line of questioning?

MR ROTHSCHILD: I think it's in the half an hour --

THE COURT: All right, why don't we take a break at this point, I think that's probably appropriate, and we'll break for about twenty minutes, and then we'll pick it up with your last line of questioning at that point. All right? We'll be in recess.

(Recess taken at 2:36 p.m. Proceedings resumed at 3:03 p.m.)