RationalWiki:Kitzmiller v. Dover annotated transcript/P042

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Trial transcript: Day 12 (October 19), AM Session, Part 2

THE COURT: All right. We resume with Mr. Rothschild.

MR ROTHSCHILD: Thank you.

CROSS EXAMINATION ( CONTINUED)

BY MR ROTHSCHILD:

Q. Professor Behe, I'd like to turn our attention now to Darwin's Black Box. What you explain in Darwin's Black Box is that, modern science has been able to explore life at the molecular level in a way that was not possible with Darwin, is that right?

A. That's right.

Q. Or actually for sometime after?

A. That's correct.

Q. And it's that life at the molecular level that you are referring to when you call it Darwin's Black Box, something he couldn't look into?

A. That's correct.

Q. In fact, in the book, you call it the last black box?

A. Is that right? Could you show me where I do that?

Q. Sure.

A. I'm sorry.

Q. If you could turn to page 13.

A. Yes.

Q. Okay. And if you look at the paragraph, you quote from a ditty from Jonathan Swift?

A. Yes.

Q. And then you say, in the late 20th century, we are in the flood tide of research on life, and the end is in sight. The last remaining black box was the cell, which was opened to reveal molecules, the bedrock of nature, the last black box, correct?

A. I'm sorry. Yes. Okay, the last remaining black box was the cell, yes.

Q. Okay. And then you conclude at the end of that paragraph, that black box now stands open?

A. Yes.

Q. And I think you've testified, and I think it's apparent in your book that, science has discovered a level of complexity that prior generations of scientists never predicted?

A. That's correct.

Q. And your conclusion is that, that complexity provides an insurmountable obstacle to Darwinian evolution?

A. Well, you always try to avoid words like insurmountable, but it certainly points to severe problems for it, yes.

Q. And you reached the conclusion that certain biochemical systems could not be produced by natural selection because they are irreducibly complex?

A. Again, you've got to be careful about using absolutes like could not, but it certainly seems like they could not.

Q. And these systems also have what you describe as a purposeful arrangement of parts?

A. Yes.

Q. And, therefore, you concluded they were intelligently designed?

A. Yes.

Q. And in terms of the structure of the systems, you base your conclusions on work on the structure and function of those molecular systems done by other scientists?

A. That's correct.

Q. Many other scientists?

A. That's correct.

Q. And you read a lot of papers that published in peer review journals describing the structure and function of the systems that you discuss in the book?

A. That's correct.

Q. And those scientists in those papers don't argue that their work supports irreducible complexity as you define it?

A. That's correct.

Q. Or intelligent design?

A. That's correct.

Q. And, in fact, a good number of them would have actively opposed that?

A. And still do.

Q. And the -- Matt, if you could pull up page 39, please, and highlight the bottom paragraph there at the bottom. This is the place in Darwin's Black Box where you explain what you mean by irreducibly complex?

A. Yes.

Q. And as you testified, I believe, on Monday, a scientist named Alan Orr noted an ambiguity in your definition?

A. Yes.

Q. And you responded to that?

A. Yes.

Q. And you tweaked that definition?

A. Right.

Q. Matt, could you pull up the tweaked definition that he created? And I have inserted the words which is necessarily composed to make this paragraph consistent with the tweaking you described you did in response to Alan Orr. And I'm going to read that. And I've called it here the modified definition of irreducible complexity from Darwin's Black Box.

What it says is, By irreducibly complex, I mean a single system which is necessarily composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.

An irreducibly complex system cannot be produced directly, that is by continuously improving the initial function which continues to work the same mechanisms by slight successive modifications of a pre-cursor system, because any pre-cursor to an irreducibly complex system that is missing a part is, by definition, non-functional.

An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually, it would have to arise as an integrated unit in one fell swoop for natural selection to have anything to act on.

So that's the last paragraph on page 39 adding the words that you did in response to Dr. Orr?

A. Yes.

Q. And when you say, it would have to arise as an integrated unit in one fell swoop for natural selection to have anything to act on, what you're saying is, whatever the proposed pre-cursor was, would die because it doesn't have all of its parts?

A. No, that's not correct. Die is not -- the function of a system is not to live, it's to do something particular. You say that the system did not work, it did not do its function. For example, the bacterial flagellum would not work without the necessary parts.

Q. And, therefore, there would be no successive generation because that flagellum would not move on to the next generation?

A. No, that's not right. A bacterium that is missing a flagellum would certainly go on and continue to grow. It can reproduce and so on. But the flagellum doesn't work. And this is from my article, I believe, in Biology and Philosophy, where I responded to Professor Orr.

And in that article, I specifically said that he had a misconception that irreducible complexity meant that an organism could not live without this, without the system that we were talking about. And that's not what I meant by it.

Q. So the organism with half a flagellum or parts of a flagellum could continue to live in that circumstance, it just wouldn't have an operating flagellum?

A. Sure, yes.

Q. Now could you turn again to Exhibit 718, which is that article, Reply to my Critics, that you just discussed?

A. Yes.

Q. Okay. On -- could you turn to page 695?

A. Yes.

Q. And in the first full paragraph, you repeat some of the text that we just saw from Darwin's Black Box about why irreducible complex systems are obstacles for Darwinian explanations?

A. Yes.

Q. And then you write, However, commentary by Robert Pennock and others has made me realize that there is a weakness in that view of irreducible complexity. The current definition puts the focus on removing a part from an already functioning system.

And then continuing on after footnote 5, you say, The difficult task facing Darwinian evolution, however, would not be to remove parts from sophisticated pre-existing systems, it would be to bring together components to make a new system in the first place.

Thus, there is an asymmetry between my current definition of irreducible complexity and the task facing natural selection. I hope to repair this defect in future work. That's what you wrote, correct?

A. Yes.

Q. You haven't repaired that defect, have you, Professor Behe?

A. No, I did not judge it serious enough to do so yet.

Q. So the defect you identified was, you were starting with the function and working backwards, removing parts, correct?

A. That's correct, yes.

Q. And natural selection is actually operating in the opposite direction, you start with the pre-cursors and then develop until you get to the system you're studying?

A. Yes, that would be a more difficult task.

Q. That's the asymmetry?

A. Yes.

Q. And that asymmetry has not been repaired?

A. That asymmetry is not really relevant to biological circumstances. In the sentence that you skipped over in that paragraph, I talk about what Professor Pennock discussed in his book in making this point.

If I could just quote from that. He says, Thus, seeking a counterexample to irreducible complexity entower a battle. Pennock writes about a part in a sophisticated chronometer whose origin is simply assumed which breaks to give a system that he posits can nonetheless work in a simpler watch in a less demanding environment.

So I viewed Professor Pennock's objection -- of course, Professor Pennock is a philosopher, and that was an interesting philosophical turn on my discussion, I thought, but that is not -- that is not -- I did not consider that to be relevant to biology.

Q. Okay. The task facing natural selection, that's not relevant to biology?

A. No, the particular pathway that Professor Pennock had in mind where one assumes that one has a very sophisticated pre-existing system whose origin has been left unexplained and has just postulated, which then goes on to breakdown and give less sophisticated parts, that is the part that I don't think is really relevant to biology.

Q. If you start with the system and then break it down removing parts, that's not relevant to biology?

A. Well, that's not the difficult task facing evolution.

Q. Right. And you're not testing the natural -- the difficult task facing evolution, which starts from the pre-cursors and moves forward to the system you're studying. You're going backwards. Isn't that what irreducible complexity proposes?

A. It does not propose that anything goes backwards. It asks, how do we identify this problem for Darwinian evolution? And if you can remove a part, and a system no longer works, then the system needs those parts to work.

And so the problem, how you put that together by numerous successive slight modifications, as Charles Darwin thought one had to do, is, I think, illustrated by that.

Q. In any event, you have not repaired this asymmetry?

A. That's correct.

Q. And that article was written four years ago, correct?

A. Yes.

Q. Now you've used the expression, produced directly. I think that's in the definition. Matt, if you could pull that back up. And if I understand what you mean by directly, it means, for example, in the case of the flagellum, that it has to be steps in which there's a rotary motor that continues to become the rotary motor, that is the flagellum?

A. Yes. By direct, I mean that it essentially worked, as the definition says, it works by the same mechanism, has the same number of parts; essentially, it's the same thing.

Q. Same thing. And then if you could turn to page 40 of Darwin's Black Box. Matt, if you could highlight the first paragraph. You acknowledge another possibility?

A. That's correct.

Q. You say, Even if a system is irreducibly complex and thus could not have been produced directly, however, one cannot definitively rule out the possibility of an indirect, circuitous route, right?

A. Yes.

Q. And by indirect, you mean evolution from a pre-cursor with a different function than the system being studied?

A. Yes, different function, perhaps different number of parts, and so on.

Q. And one example of that is what's discussed in, among evolutionary biologists, as the concept of exaptation, correct?

A. Yeah -- well, before I say, yes, I'd just like to say, the word exaptation is oftentimes used in loose sense, but, yes, that's generally correct.

Q. And that is a concept that people in the field of evolutionary biology consider to be a valid concept, a valid description of the way more and more complex systems get developed?

A. Let me say --

Q. I'm not asking you to agree with it. I'm asking you, is that what an evolutionary biologist proposes?

A. Again, let me make clear what we're talking about here. Some evolutionary biologists certainly think that exaptation is real and that it's important and so on. But simply saying that this part over here was exapted from that part over here does not give an explanation of how random mutation and natural selection could have gotten it from one state to the other.

Q. But it is certainly, exaptation -- for example, a bird wing developing from some kind of feathered structure on a dinosaur that didn't necessarily allow flight, that's what evolutionary biologists propose, and they call it exaptation?

A. That's entirely possible, and that's consistent with intelligent design, because intelligent design only focuses on the mechanism of how such a thing would happen. So the critical point for my argument is, how such things could develop by random mutation and natural selection.

Q. And again, intelligent design doesn't describe how it happened?

A. That's correct, only to say that intelligence was involved somewhere in the process.

Q. Okay. Now you go on in this passage and say, As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously, and as the number of unexplained irreducibly complex biological systems increases, our confidence that Darwinian's criterion of failure has been met and skyrockets toward the maximum that science allows?

What you're saying there is, you know, it could happen, I'm not ruling it out, but it's really improbable?

A. Yes, it's improbable.

Q. Okay. And you haven't -- and based on that, you conclude that intelligent design is a much more probable explanation?

A. Not just based on that, based on the purposeful arrangement of parts.

Q. Fair enough. And you haven't actually quantified this, have you?

A. Not explicitly, but as a biochemist who understands what it takes to, for example, for a protein to function, for two proteins to bind specifically to each other, and so on, I rely on my experience of that in arriving at this conclusion.

Q. And you've seen how long it takes for the prokaryotes to bind?

A. 10 to the 16th in one ton of soil, yes, uh-huh.

Q. Now just to be clear -- in this passage, you say, irreducibly complex biological systems, right?

A. I'm sorry?

Q. In this passage, you say, As the number of unexplained irreducibly complex biological systems increases, right, that's what it says there?

A. Yes. Yes, I do, uh-huh.

Q. But you took pains on Monday to communicate to the Court that when you're talking about irreducible complexity, you're just talking about it at the molecular level?

A. Yes, that should be biochemical instead of biological.

Q. Fair enough. You don't make claims about irreducible complexity at the organ level?

A. That's correct.

Q. Or at the organism level?

A. That's correct.

Q. In fact, you don't have any expertise or training in the organ or organism level?

A. That's correct, yes.

Q. You also have no expertise in paleontology?

A. That's correct.

Q. Or physics?

A. That's correct, too.

Q. Sorry. Couldn't resist. We've gone a long time. But you agree that intelligent design, as opposed to just Michael Behe, is making an argument for intelligent design far beyond the cellular level, correct?

A. I'm sorry?

Q. Intelligent design, as a scientific proposition and the individuals who advocate for it, are arguing for intelligent design beyond the cellular level?

A. Some people certainly do, based not on my argument but other arguments.

Q. So it's not based on your argument?

A. Yes.

Q. And, for example, in Pandas, that's certainly in play intelligent design of not just biochemical structures but higher level forms?

A. Well, let me just correct myself. They're not basing it on my argument in regard to irreducible complexity, but they are basing it on the purposeful arrangement of parts, which is certainly what I discuss in Darwin's Black Box.

Q. In Darwin's Black Box, you talk about a purposeful arrangement of parts, and you actually say, you know, using that standard, almost anything looks design, right?

A. I don't think I said that.

Q. We'll return to that. In any event, in Pandas, there are arguments for intelligent design of higher level biological life?

A. Yes, there are.

Q. And we're clear, that's not based on your work?

A. It's not based on any concept of irreducible complexity. It is based on a concept that I discuss in Darwin's Black Box, the purposeful arrangements of parts.

Q. That purposeful arrangement of parts, that's not -- you didn't originate that?

A. No, I didn't.

Q. At least, it goes back to Reverend Paley?

A. Yes, it does. Further back than that.

Q. Now let's start with the bacterial flagellum. You've made a point about how complicated and intricate it is?

A. Yes.

Q. And it really is. I mean, it looks remarkable. But a lot of biological life is pretty remarkable?

A. That makes me very suspicious.

Q. You're suspicious about how remarkable biological life is?

A. No, it makes me suspicious, you know -- that was a joking way to say that I think much of biological life may bespeak design.

Q. Plants and photosynthesis, that's very complicated, right?

A. Sure is, yes.

Q. Just the physical beauty of a flower is amazing?

A. Amazing in a different sense. Of course, when you're talking about physical beauty, now you're thinking more of an aesthetic and philosophical concept, yes.

Q. The features seem to be arranged in a way that gives it great attractiveness?

A. Well, okay, but you're now speaking of something that I was not speaking of. When I talked about the purposeful arrangement of parts, it was for some function of the system, not necessarily to be perceived as pretty.

Q. Fair enough. The entire human body, that's an amazing biological structure?

A. I'm thinking of examples.

Q. Hopefully, not mine.

A. Rest assured. Sure. Yes.

Q. We're stipulated here. Because we can make an agreement about that. The human body, in its entirety, is an amazing biological system?

A. Yes, it's amazing, yes, uh-huh.

Q. And just my hand?

A. Yes.

Q. Muscles and joints and bones and nerves. I can grab things with it. I can point.

A. Yes, that is certainly a very impressive biological system.

Q. Is that a purposeful arrangement of parts?

A. Is it a purposeful arrangement of parts? Yes, I think it is.

Q. And the physical world, too, the stars and planets and gravity, also amazing?

A. They are certainly amazing, yes.

Q. And they function in conjunction with each other to do things, create gravity, light, things like that, that are pretty remarkable?

A. Gravity is remarkable. Light is remarkable. But you're going to have to be very careful about the sorts of conclusions you draw from these things, because -- and simply because you don't want to just become overenthused about the beauty of nature and try to turn that into an argument.

Q. But it actually -- I mean, it functions. Light, I mean, it functions. And gravity, it functions?

A. Yes.

Q. And interaction of different elements on the periodic table combine to make substances in the chemical world, things we rely upon for our life and all of biological life actually relies on, right?

A. Yes, that's certainly true.

Q. And we don't rule out natural explanation for all of these amazing phenomena, do we?

A. Well, you're going -- I don't rule out natural explanations for anything, including intelligent design. Intelligent design does not rule out natural explanations. However, you're going to have to make some distinctions between how phenomena work and what phenomena strike many people as somehow ordered to, or is necessary for specific purposes such as the existence of life.

Q. It's really a definitional issue?

A. I'm sorry. What is a definitional issue?

Q. You just described it. I mean, you got to be careful about how we're talking about how everything has different functions when we're making assessments about whether the natural explanations are valid?

A. I couldn't --

Q. I'll withdraw that, Professor Behe. You made the claim that scientists who discuss cellular systems are calling them machines, correct?

A. Yes.

Q. And you said, they're not comparing them to machines, they're calling them machines?

A. Right.

Q. One of the scientists you referred to was Dr. DeRosier?

A. Yes.

Q. And what you said, what you quoted from his article was, More so than other motors, the flagellum resembles a machine designed by a human?

A. Yes.

Q. So he's not saying, the flagellum is a machine, he's saying, it resembles a machine?

A. No, he's saying, it resembles a machine designed by a human. There are other machines in the cell that may not resemble machines designed by humans, but I think, as many people can see when looking at an illustration of the bacterial flagellum, this is a machine that looks like something that a human might have designed.

Q. It looks like it?

A. That's what science has to go on; what we can see, what we can measure, and so on.

Q. It resembles it?

A. Exactly.

Q. Okay. And when you quoted to -- and he's also saying, you know, other cellular systems don't resemble machines so much, right? More so than other motors, the flagellum resembles a machine designed by a human?

A. He's saying that more other machines in the cell don't so much resemble machines designed by humans, but he is certainly not saying that they are not machines, at least in my reading.

And in that issue -- not -- in a previous issue of Cell, the one that I pointed to earlier, a number of scientists were discussing molecular machines that do not resemble things that do not visually resemble machines that we have in our world.

Q. But here he is saying, resembles a machine designed by a human. That's your point, right?

A. That's what' he said.

Q. It looks like a machine a human would design?

A. It resembles a machine designed by a human, yes.

Q. Now the intelligent designer, when he was forming a bacterial flagellum millions or billions of years ago, you're not suggesting he was actually modeling his design after a manmade rotary motor which didn't exist until the last century?

A. I'm sorry. Could you say that again?

Q. Yeah. You're talking about things that resemble machines designed by humans. You're not suggesting that the intelligent designer, when the -- when he or she or they designed the first bacterial flagellum millions or billions of years ago, was modeling its design after manmade rotary motors which didn't exist until the last century?

A. I'm not quite sure how exactly to address this question. When you're inferring design, you do not ask yourself whether a designer had some particular, you know, look in mind. You're asking whether, in the structure of this system, you see a purposeful arrangement of parts.

And I think, in the case of the bacteria flagellum, the fact that it does resemble something from our everyday world is due to the fact that its function is similar to some things that we find in our everyday world such as propulsive motors, like outboard motors on boats, and, therefore, the functional engineering requirements would be similar for such a machine in the cell as well as in our everyday world.

Q. Another example you gave was, and just to be clear, Dr. DeRosier is in no way suggesting that his article has anything to do with intelligent design?

A. Not that I know of.

Q. Or irreducible complexity?

A. Not that I know of.

Q. And then you also cited to Bruce Alberts?

A. Yes.

Q. And I think he is or was the head of AAAS?

A. No, he was the head of the National Academy of Sciences.

Q. Better yet. And what you quoted from him was, Why do we call the large protein assembles that underlie cell function protein machines? Precisely because, like machines invented by humans, these protein assemblies contain highly coordinated living parts. He used the expression, like a machine?

A. Yes, he did.

Q. And I think what we all learned in grade schools, when you make a comparison, use like, that's called a simile?

A. It may be, but I think the point that he was trying to convey is that these things work like the machines that we have in our everyday world. And so, in fact, they are.

Q. Do you watch football, Professor Behe?

A. I do on occasion, yes.

Q. I watched the Notre Dame/USC game last weekend. It was quite a game?

MR. MUISE: I might have to interpose an objection here, Your Honor.

MR ROTHSCHILD: I told Mr. Muise his alma mater did themselves proud, despite the final result.

BY MR ROTHSCHILD:

Q. And one of the things the announcer said was about one of the USC offensive linemen is, he's like a mountain?

A. Yes.

Q. Now you don't understand it to say, he was made like a mountain was, not by wind or erosion or physical processes on land mass?

A. No, of course not. People use words like that in loose senses all the time. But in this particular case, Dr. Alberts was making a specific comparison to the physical functioning of these things and liking it to the physical functioning of machines in our everyday world.

They require a precise arrangement of parts. They act by transducing energy in order to accomplish some function and so on.

Q. So when the same announcer said, the running back is like a bulldozer, that was closer?

A. No, I think that's silly.

Q. I think it is, too, Professor Behe. And you have never talked to Bruce Alberts about what exactly he meant when he used the expression, like a machine?

A. No, I didn't.

Q. That's your interpretation?

A. Yes, it is.

Q. And that's true for the other articles you cited about whether biochemical systems are machines as opposed to being like machines?

A. Well, again, I think we're getting into a semantical distinction -- or just into semantics. If something acts like a machine, and something has a function, and so on, then it is a machine.

Q. Now you talked at some length on Monday about the issue of whether the type III secretory system might be a pre-cursor to the bacterial flagellum, or the reverse, that it is a descendent of the bacterial flagellum, or they might have been a common ancestor, right? You looked at some articles on that subject?

A. Yes.

Q. The papers that were discussing that, they were all discussing this complicated issue within the framework of evolution, correct?

A. Sure. Evolution understood as common descent, yes.

Q. None were suggesting intelligent design?

A. No, they did not.

Q. They were just scientists trying to figure out whether it was A that evolved into B, or B that evolved into A, or A and B evolving from C?

A. That's right. They were taking the mechanism of natural selection and random mutation for granted. They were not demonstrating it. They were not making arguments for it. They were taking it as an assumption.

Q. And in terms of what the order is, they have -- they haven't nailed it down yet, right?

A. Not only haven't they nailed it down, but they have proposed completely opposite scenarios whereby one can't tell which arose first or second or even if they arose from each other at all.

Q. And you don't expect the dialogue to stop there, do you?

A. I don't expect it to, but it may.

Q. Okay. But scientists, as they do with many subjects on which there's disagreement, may continue to be making arguments and writing papers and submitting them to peer review journals and doing experiments to see if they can come up with a consensus answer on the subject?

A. Sure. And they may write books to try to come up with an answer, too, as well.

Q. That's how you get the royalties, right?

A. (No response.)

Q. You recently visited the University of Minnesota, didn't you?

A. Yes.

Q. You spoke with a University Professor named James Kurzinger?

A. Yes, I did.

Q. He actually asked you whether the type III secretory system is a subset of the bacterial flagellum, is that right?

A. I don't think he said exactly that, but I'm not -- we did talk about the flagellum and the type III secretory system, but I'm not prepared to say exactly how the conversation went.

MR ROTHSCHILD: May I approach the witness, Your Honor?

THE COURT: You may.

BY MR ROTHSCHILD:

Q. And James Kurzinger is a scientist?

A. He identified himself as such.

Q. And this is -- this Exhibit 724 is an article in the Minnesota Daily. It's an opinion piece. And it says, Intelligent Design 101, Short on Science, Long on Snake Oil. And it goes on to describe --

MR. MUISE: I'm objecting that his use of this document again is hearsay. He doesn't have recollection of this, of this conversation. I'm not sure if he's going to be using this to try to refresh his recollection.

MR ROTHSCHILD: It recounts a conversation, and I am going to ask Professor Behe whether that conversation occurred.

MR. MUISE: He's going to ask him the conversation, Your Honor, he can't just read --

THE COURT: Well, to the extent that you're going to try to characterize the -- I think you've appropriately characterized what the exhibit is, Mr. Rothschild. So why don't you move on to your question.

MR ROTHSCHILD: Okay. He has expressed a vague recollection of what happened, so I'm going to read him the passages in here.

THE COURT: I understand.

MR ROTHSCHILD: Okay.

THE COURT: I understand. I think the objection went to the fact that you were beginning to read or extensively characterize --

MR ROTHSCHILD: Fair enough.

THE COURT: -- the exhibit.

BY MR ROTHSCHILD:

Q. Just for some more foundation. In the first paragraph, it says, Intelligent design's leading scientist, Dr. Behe, a professor of biochemistry, visited the U, which I understand to be the University of Minnesota, last week as a guest of the McLauren Institute, and that, in fact, did occur?

A. Yes, I visited Minnesota as a guest of the McLauren Institute.

Q. And if you could turn to the third page of the document. And there's some discussion on that third page about the bacterial flagellum and the type III secretory system?

A. Yes.

Q. And Mr. Kurzinger makes his own observation about the type III secretory system being a subset of the bacterial flagellum?

A. I'm sorry. Could you say that again?

Q. In the paragraph that begins, much to Dr. Behe's distress --

MR. MUISE: Objection, Your Honor, that's hearsay. He's pointing to a paragraph for the truth of what's in the statement.

THE COURT: Well, it's sustained to the extent that you're going to read it. He can read it and put it into context.

BY MR ROTHSCHILD:

Q. Could you read the paragraph that says, much to Dr. Behe's distress?

A. Out loud, or --

Q. Please.

A. Okay. This paragraph says, Much to Dr. Behe's distress, the TTSS is a subset of the bacterial flagellum. That's right, a part of the supposedly irreducible bacterial outboard motor has a biological function.

Q. And I'm not going to ask you about whether you were distressed or not. But the next paragraph then says that he asked you about this at lunch, correct?

A. That's what it says, yes.

Q. And you did have lunch that day?

A. We had lunch, and I recall a conversation about this, but again, I don't recall many details.

Q. Okay. And according to Dr. Kurzinger, you acknowledged that the claim that --

MR. MUISE: Objection, Your Honor. He's referring to an editorial, and he's trying to recount this as an exact conversation. Dr. Behe doesn't have recollection of what occurred. This article has no relevance.

THE COURT: The next paragraph starting with, when I asked Dr. Behe, I think, is where you're going.

MR ROTHSCHILD: Yes.

THE COURT: Why don't you go right to that, as it's expressed there, instead of trying to paraphrase it.

BY MR ROTHSCHILD:

Q. It says, When I asked Dr. Behe about this at lunch, he got a bit testy, but acknowledged that the claim is correct. Paren, I have witnesses. He added that the bacterial flagellum is still irreducibly complex in the sense that the subset does not function as a flagellum.

My question here is, is Mr. -- Dr. Kurzinger's account that you agreed that the claim that the TTSS is a subset of the bacterial flagellum, did you agree to that?

A. I don't recall, but I would, if I was going to answer it very carefully, I would make a lot of distinctions before saying so.

Q. Okay. But you don't recall whether you said that or not?

A. No, I don't.

Q. Okay. And then you go on to say that you still think -- well, I'll leave that. Your argument is that, even if the type III secretory system is a pre-cursor to the bacterial flagellum, is a subset, the bacterial flagellum is still irreducibly complex because that subset does not function as a flagellum?

A. That's correct, yes.

Q. And, therefore, the bacterial flagellum must have been intelligently designed?

A. Well, again, the argument is that, there is -- that when you see a purposeful arrangement of parts, that bespeaks design, so, yes.

Q. And yesterday, you testified that, that doesn't mean the bacterial flagellum was necessarily designed, appeared abruptly in one fell swoop, correct?

A. That's correct.

Q. Could have been designed slowly?

A. That's correct.

Q. So under this scenario, at some period of time, the bacterial flagellum wouldn't have had all of its parts until the design was completed?

A. Could you say that one more time?

Q. Yeah. Under this scenario of slow design -- which was what I experienced with my kitchen -- at some period of time, the bacterial flagellum wouldn't have had all its parts until the design was completed?

A. That's right.

Q. And so without all its parts, it wouldn't be functional?

A. That's right. Not as a flagellum, yes.

Q. So that is a phenomenon in both intelligent design and natural selection?

A. I'm not quite sure what you mean.

Q. In slow design, the bacterial flagellum has some prior existence, it doesn't have all its parts, right?

A. Well, if -- until it has all its parts and it starts functioning, I guess it's problematic to call it a flagellum.

Q. It has some subset?

A. I guess things that will eventually be part of the flagellum would begin to appear, yes.

Q. Just not function like a flagellum?

A. Yes, the system would not yet function as a flagellum.

Q. Just like has been suggested for natural selection?

A. I'm sorry.

Q. Just like has been suggested for natural selection?

A. I'm not quite sure what you mean.

Q. Natural selection also suggests that there was a subset of parts that would eventually comprise the bacterial flagellum, but didn't work as the bacterial flagellum?

A. No. Natural selection, if I remember your question correctly, natural selection does not suggest that. People see that there is a subset of proteins in the flagellum which share a lot of sequencology with proteins that act as a type III secretory system.

Nobody, nobody has said how natural selection could get you the type III secretory system, the flagellum could get you from the -- even if you had the type III secretory system, nobody has said how you could get from that to the flagellum. Nobody has said how you could get from the flagellum to the type III secretory system.

So this is an example again of conflating different levels of evolution. We see evidence for common descent, evidence for relationship, but we see nothing, nothing that bears on the question of random mutation and natural selection.

Q. Let me see if I've got this right. In natural selection, the argument is that, there was a subset of parts, right, like the type III secretory system, that eventually evolved to become the bacterial flagellum, right? That's the argument?

A. I would want more detail. Are you saying that in --

Q. I'm not asking you to agree with the argument, Professor Behe. I'm just trying to walk us through this. The argument for the evolution of something like the bacterial flagellum, just to use that as an example, is that, at sometime it had a subset of proteins, maybe looking something like the type III secretory system, and eventually it evolved to become the bacterial flagellum? That's the argument, right?

A. I would have to see the argument written down. As you characterize it, I'm not quite sure what it is.

Q. Okay. But you're not disputing that the theory of evolution says, at some point we had a subset of proteins, then we had eventually all the proteins that make up whatever system we're discussing?

A. That sounds okay.

Q. Good. In slow design, same thing. At some point, we had a subset of the proteins, and eventually, we got to the whole thing?

A. That's right. The crucial question -- the only question is the mechanism.

Q. Okay. So in the case of evolution, there is a mechanism that's been proposed, natural selection?

A. Yes.

Q. And you've agreed that natural selection certainly is a phenomena that operates in the natural world?

A. That is correct.

Q. Including at the biochemical level?

A. That's right.

Q. Then we've got slow design, and there we have no mechanism at all, no description of a mechanism?

A. We have no description of a mechanism. We do infer design though from the purposeful arrangement of parts.

Q. Now yesterday, I asked you some questions about the designer's abilities. And you said, all we know about its abilities is that it was capable of making whatever we have determined is design. That's the only statement we can make about the designer's abilities?

A. Yes.

Q. And in terms of the designer's -- as a scientific statement?

A. That's correct.

Q. And the only thing we know scientifically about the designer's motives or desires or needs is that, according to your argument, the only thing we would know scientifically about that is that it must have wanted to make what we have concluded as design?

A. Yes, that's right.

Q. In fact, the only way we can make the statement scientifically that a designer exists is that it made whatever we conclude was design?

A. Yes, that's right.

Q. I want to ask you exactly, and this question is particularly about how -- about the flagellum design. Was the design limited to the original blueprint for the first bacterial flagellum?

A. I'm not sure what you mean by the blueprint for the flagellum.

Q. The plan?

A. The plan? Did the plan cause the flagellum to occur?

Q. Is that all of intelligent design? The designer planned the bacterial flagellum?

A. Well, no. The designer would also have to somehow cause the plan to, you know, go into effect.

Q. It would have to make the thing?

A. No, it had to -- well, it would have to have processes by which it would be made.

Q. I mean, it's got to actually be constructed. We're not talking about a bacterial flagellum in the mind's eye of the designer. It's actually something we now know physically exists?

A. That's right.

Q. Had to be created?

A. Well, you're using -- in what sense are you using the word created? Created can mean -- can have several different senses.

Q. You're uncomfortable about that word?

A. Yes, because it's a loaded word in these circumstances.

Q. Okay. Created can mean the same thing as made, right?

A. We use the word create when we refer to things that are made by artists and engineers and so on, yes.

Q. Okay. In that sense, the designer created the bacterial flagellum?

A. I might say that, it might be a very indirect process by which such a thing was made. So when you say that the designer made the flagellum, it is not necessary to think that somehow the protein parts of this were somehow immediately brought together. It might have been a long process.

Q. Did the intelligent designer design each and every protein of the flagellum?

A. That is a difficult question to address, and there's lots and lots of distinctions to make. When you ask whether the parts of the flagellum themselves require design, you have to then focus in on those parts.

As I tried to emphasize earlier in my testimony when we talk about parts, some people have a simple view, picture in their minds something simple, but each of the parts is itself a very complicated molecular entity. And as my work with David Snoke shows, that even getting small changes in pre-existing proteins, that is parts, is no easy task. So the question --

Q. Unless you have a whole ton of soil?

A. I'm sorry?

Q. Unless you have a whole ton of soil?

A. So that's actually an excellent question. Did those parts themselves also have to be designed? And I think right now, the question is open.

Q. Did the intelligent designer identify -- design every individual flagellum in every bacteria or just the first lucky one?

A. Well, since organisms, biological organisms can reproduce, of course, then if one has the genes and the proteins and information for a flagellum, then by the normal processes of biological reproduction, more copies of the -- of that structure can occur.

Q. So the answer is, just the first one?

A. That's all that would be needed. That's all we can infer, yes.

Q. Now you have this first flagellum, first bacteria that has a flagellum. And that has -- those -- that bacteria with flagellums have had mutations in their flagellums?

A. Sure. Genes undergo mutations, yes.

Q. And did the designer also design every mutation of the flagellum since its inception?

A. No, you can't -- you certainly can't say that. There is certainly random processes that go on in our world, or for processes, that for all we can tell, certainly appear to be random. So there's no -- nothing that requires us to think that any mutation, any change that subsequently occurs to this structure either was intended or -- was intended.

Q. Is that a no or an I don't know?

A. Can you restate the question?

Q. I asked you the question, did the designer design every mutation of the flagellum since the first one? And I'm asking you whether the answer is no or, better phrase, we don't know?

A. Well, that's -- that's a very tricky question. But the proper answer is that, we don't know.

Q. Is the information necessary to answer that question observable?

A. The question of whether the designer designed every single mutation?

Q. Since that first lucky flagellum?

A. Is it observable? Hum. We can certainly observe mutations, but unless the mutations and changes and so on further go on to form a purposeful arrangement of parts, then we cannot deduce simply from their occurrence that they were designed.

Q. There could be multiple designers, correct?

A. Yes, I wrote that in Darwin's Black Box.

Q. Could even be competing designers?

A. That's correct.

Q. Are you aware of any irreducibly complex systems that have just come into existence in the last five years?

A. Biological systems or mechanical systems or in our everyday world or other ones?

Q. No, Professor Behe, biological systems?

A. The last five years? You mean, brand new irreducibly complex systems?

Q. Yes.

A. I'm sorry. Brand new ones, not ones that are just --

Q. That are still around, that's right?

A. -- reproduced? Not that I'm aware of, no.

Q. Last 10 years?

A. No.

Q. 50 years?

A. Not that I know of, no.

Q. A hundred years?

A. All of the structures that I wrote about in Darwin's Black Box and have considered are much older than that.

Q. So scientifically, we can't even make -- we can't even state right now that an intelligent designer still exists, correct?

A. That's correct, yes.

Q. Is that what you want taught to high school students?

A. What are you referring to by that?

Q. That scientific -- after teaching them about intelligent design, sign -- and telling them that, that is a scientific proposition, that right now, scientifically, we can't even tell you that an intelligent designer exists? Is that what you want taught to high school students?

A. Well, let's make a couple distinctions. First of all, when I say, when you use the word taught, again, a lot of people have in mind instructing students that this is correct.

Q. That's not what I mean, Professor Behe.

A. Well, I'm sorry. I was unable to figure out exactly what you meant. If you're asking --

Q. Tell them about it, Professor Behe. Make them aware. Give them information.

A. Make them aware that some people say that, from the purposeful arrangement of parts, we can conclude that something was designed, but many other questions we can't determine, including whether there were multiple designers, whether the designer is natural or not, whether the designer still exist? Yes, I think that would be a terrific thing to point out to students.

It shows the limitations of theories. It shows that some evidence bears on one topic, but does not bear on others. I think that would be terrific pedagogy.

Q. Right. Okay. You've taken the position in this courtroom that intelligent design is open to direct experimental rebuttal, correct?

A. Yes.

Q. And you stated that very clearly in your article Reply to my Critics?

A. Yes.

Q. And the way you said this could be done, and why don't we turn to that document, which is Exhibit 718. If you could turn to page 697. Matt, if you could highlight in the second paragraph the passage that starts, To falsify such a claim, and go to the bottom of the paragraph.

And you're asking the question here, or stating, intelligent design is open to direct experimental rebuttal, correct?

A. Yes.

Q. And you said, To falsify such a claim, a scientist could go into the laboratory, place a bacterial species lacking a flagellum under some selective pressure, for mobility, say, grow it for 10,000 generations, and see if a flagellum, or any equally complex system, was produced.

If that happened, my claims would be neatly disproven. Now the test you've described, that would falsify the claim, your claim that the bacterial flagellum is irreducibly complex in the way you've described it, and could, in fact, evolve from pre-cursors, right, if that was successful?

A. That would show that my claim that it required design -- required intelligent design was incorrect.

Q. Let's break that down. You have this concept of irreducible complexity, right?

A. Yes.

Q. And you stated that the bacterial flagellum is irreducibly complex, right?

A. That's correct.

Q. And this test would, if it was successful, demonstrate that the bacterial flagellum is not irreducibly complex. We can, in fact, put a bacterial species lacking a flagellum under some selective pressure, and eventually it's going to get that flagellum, right?

A. Well, just a distinction. It wouldn't demonstrate that it wasn't irreducibly complex. It would demonstrate though that random mutation and natural selection could produce irreducibly complex systems.

Q. Fair enough. It could evolve, and that would falsify your claim that an irreducibly complex system, like a bacterial flagellum, could not evolve through random mutation and natural selection?

A. That's right, yes.

Q. But that claim that an irreducibly complex system cannot evolve through random mutation and natural selection, that's not your whole case for intelligent design, correct?

A. That's right, it's the purposeful arrangement of parts.

Q. And we saw that bacterial flagellum, right? It's -- I say, it looks like a machine. You say, it is a machine. Right?

A. Yes.

Q. And it sure works like one?

A. Yes.

Q. So it's got a purposeful arrangement of parts whether it's irreducibly complex or not?

A. It is irreducibly complex. The question is whether an irreducibly complex system can be put together by random mutation and natural selection.

Q. Okay. So my question is, how would you falsify the claim that a biological system, like the bacterial flagellum, which is clearly a purposeful arrangement of parts, is not intelligently designed?

A. Well, since it's an inductive argument, since the purposeful arrangement of parts is an inductive argument, then in order to falsify an induction, you have to find an exception to the inductive argument.

So if somebody said that, when you see this purposeful arrangement of parts -- and again, the -- as I stress, the argument is quantitative, when there is a certain degree of complexity and so on. If it was shown that that did not always, did not always bespeak design, then the induction would not be reliable, and we would -- so -- and the argument would be, would be defeated.

Q. Now you, in fact, have stated that intelligent design can never be ruled out, correct?

A. Yes, that's right.

Q. Now let's turn to your test here of whether bacterial flagellum could evolve through random mutation and natural selection. 10,000 generations, that's your proposal, correct?

A. Right.

Q. And it sounds like a lot, but you actually testified that, that would just take a couple of years, right?

A. Right.

Q. And, you know, based on your understanding of normal laboratory procedures, even the best laboratories, how much bacteria would be made a part of that test?

A. Oh, probably at the best, 10 to the 10th, 10 to the 12th, at the outside.

Q. Now you haven't tested intelligent design yourself this way, have you?

A. No, I have not.

Q. And nobody in the intelligent design movement has?

A. That's correct.

Q. And nobody else has?

A. I'm sorry?

Q. And nobody else has, outside the intelligent design movement?

A. Well, I'm not sure -- I don't think I would agree with that. I think the experiments described by Barry Hall were actually in an attempt to do exactly that. He wanted to see if he could, in his laboratory, re-evolve a lac operon. His first step in that process in the mid 1970's were the experiments that I discussed here yesterday, knocking out the beta galactosidase gene.

His intention was, from things he has written later, was to see how that would evolve and then knock out two steps at a time, and eventually see how he could get really the whole functioning system. But he had such trouble with just getting that one step to go, and since he could not knock out anything else, and get it to re-evolve, he gave up.

And so I would count his efforts as a test of that, and say that the test, you know, that it was, it did not falsify intelligent design thinking.

Q. And I had actually made a blood pact with my co-counsel not to ask you about the lac operon, but now I had to violate it.

A. Too late.

Q. How many years has he done this experiment?

A. I think he was working on it for 20 years or so.

Q. In any event, that's the lac operon. But for bacterial flagellum, you're not aware of that test being done?

A. No.

Q. Certainly not by anybody in the intelligent design movement?

A. No.

Q. Okay. So you can't claim that the proposition that the bacterial flagellum was intelligently designed is a well-tested proposition?

A. Yes, you can, I'm afraid. It's well-tested from the inductive argument. We can, from our inductive understanding of whenever we see something that has a large number of parts, which interacts to fulfill some function, when we see a purposeful arrangement of parts, we have always found that to be design.

And so, an inductive argument relies on the validity of the previous instances of what you're inducing. So I would say that, that is tested.

Q. Professor Behe, you say right here, here is the test, here is the test that science should do, grow the bacterial flagellum in the laboratory. And that hasn't been done, correct?

A. That has not been done. I was advising people who are skeptical of the induction that, if they want to essentially come up with persuasive evidence that, in fact, an alternative process to an intelligent one could produce the flagellum, then that's what they should do.

Q. So all those other scientists should do that, but you're not going to?

A. Well, I think I'm persuaded by the evidence that I cite in my book, that this is a good explanation and that spending a lot of effort in trying to show how random mutation and natural selection could produce complex systems, like Barry Hall tried to do, is likely to result -- is not real likely to be fruitful, as his results were not fruitful. So, no, I don't do that in order to spend my time on other things.

Q. Waste of time for Barry Hall?

A. I'm sorry?

Q. Waste of time for Barrie Hall?

A. No, certainly not a waste of time. It was very interesting. He thought that he would learn things. And he did learn things. But they weren't the things that he started out to learn. He thought that he would be able to see the evolution of a complex system. And he learned how difficult that was.

Q. In any event, you have not undertaken the kind of test you describe here for any of the irreducibly complex systems you have identified?

A. I have not.

Q. And neither has anybody else in the intelligent design movement?

A. That's -- well, actually, I think some people are testing, not the bacterial flagellum, but are testing other things on protein structure, which I would probably count under that.

Q. Count as irreducibly complex systems?

A. Well, I wouldn't really call them irreducibly complex in that sense, but I think bear on the question.

Q. Okay. So in terms of irreducibly complex structures, you haven't done any tests, right?

A. That's right.

Q. You're not planning on any tests --

A. That's right.

Q. -- of the type you described here?

A. Well, I'm doing my theoretical work with David Snoke and hope to continue that, so I think that bears on this question.

Q. Bears on it, but it's not testing an irreducibly complex system in the way you described in this article?

A. That's right.

Q. And nobody else, you're not aware of anybody else in the intelligent design movement doing a test of the type you described here of an irreducibly complex system?

A. No, not yet.

Q. Now you talked about how, you know, your proposal here would take approximately two years, right?

A. Yes, yes.

Q. I'm sorry. I'm pointing to down here, and that's -- you're not that good a mind reader. Now bacteria had been on the Earth for billions of years, correct?

A. That's right.

Q. And the bacterial population that exists in the world and has ever existed in the world is orders and orders of magnitude greater than ever could be in one laboratory experiment?

A. That's right. It should be about 10 to the 40th or so, I would estimate.

Q. And I think you said, 10 to the -- what was your proposal for the laboratory, 10 to the -- you had said that you had a suggestion for how much we would study in one laboratory?

A. 10 to the 10th and 10 to the 12th, that's correct.

Q. And you talked about selective pressures that the bacterial flagellum could be exposed to, but a laboratory could never recreate all the selective pressures that have existed in the environment for the last three and a half billion years?

A. Well, that's certainly true. But a scientist -- scientists nonetheless try to understand parts of nature, even though nature is very much bigger than a laboratory. And in many other instances, such as people investigating origin of life and so on, they nonetheless try to understand what the proper environment would be to study, and so they can kind of focus their efforts on what would be the most promising type of environment, and so make it more likely to discover something that was there than just focusing on the whole world.

Q. But it's entirely possible that something that couldn't be produced in the laboratory in two years, or a hundred years, or even in the laboratory that was in operation through all of human existence, could be produced over three and a half billion years? You have to agree with that, Professor Behe?

A. It's entirely possible, but we can only know if that is the case if we have, if we have experiments to back it up or calculations to back it up.

Q. Experiments and inferences, right?

A. That's right.

Q. And so you agree, something we couldn't -- that couldn't happen in two years, much better chance over three and a half billion years?

A. Absolutely.

Q. Okay. And that's why the age of the earth is so important to a scientific theory about biological life, isn't it, Professor Behe?

A. It's very important.

Q. But intelligent design, that's a who cares, right? It could be -- the universe could be -- or the Earth could be billions of years old or 10,000 years old, and it doesn't matter to intelligent design?

A. Intelligent design is not a person, so it doesn't have feelings like you are describing.

Q. It's a movement, right?

A. Intelligent design is a scientific theory that focuses on a particular question. There are many scientific theories that focus on particular questions that do not have anything to do with other interesting questions. The scientific theory of intelligent design focuses on discerning design, and that's it.

Q. Okay. So it doesn't take a position on the age of the Earth?

A. Theories don't take positions.

Q. Okay. The intelligent design -- you described intelligent design as not making any claims about the age of the Earth, correct?

A. That's correct.

Q. And, of course, the prospects for evolution of a function or a system are also greater if the subject population is greater?

A. That's correct.

Q. And no human laboratory can duplicate the entire population of any kind of organism, correct?

A. That's correct.

Q. Okay. And no human laboratory can duplicate all of the selective pressures that have existed in the billions of years that bacteria have been around?

A. That's correct. So we can't rule out all explanations. We have to investigate to see what are likely.

Q. Professor Behe, the tests you proposed here regarding the bacterial flagellum is like asking Dr. Padian to grow a bird wing in a laboratory, isn't it?

A. The test that is sufficient for a theory is proportional to what the theory claims. I'm no physicist, but in physics, there have been claims, many claims that required enormous amounts of effort by the entire physical community to build large structures, took many years to do so.

And nonetheless, they thought that this effort was worth it, because they wanted to be sure of the answer. In biology, the claim that random mutation and natural selection can produce systems like the flagellum or other molecular machines is a very large claim. And one can't simply say that because it would be hard to test it, we will just assume it's true.

So if somebody wants to be sure or somebody wants to -- wants to -- wants to respond to a skeptic with evidence that would convince somebody that was not already convinced of the theory, then there is no escaping the fact that you have to show that your theory can do what you claim for it.

Q. And so to do that, what scientists advocating for the theory of evolution, including natural selection, have to do is create a laboratory that repeats human life -- that contains all of human life in deep time?

A. I'm sorry. One more time.

Q. In order to validate this big claim that the theory of evolution makes, what you're really saying is, they've got to create a laboratory that includes all of biological life and operates over deep time?

A. No, I didn't say that at all. I said, if it can be demonstrated that random mutation and natural selection can produce complex systems, then intelligent design would be falsified. One doesn't have to, you know, re -- show that something of the complexity of a flagellum would be made.

But if one saw that something somewhat less complex might be made in a reasonable time, then one might be able to extrapolate. You'd have to pay attention to the details of the system. So it's not, you know -- you don't need a worldwide laboratory and a billion years to test this. You can do things like Barry Hall tried to do.

Q. That can't recreate the opportunities that were there for biological organisms throughout time?

A. There are always opportunities for biological organisms. Biological organisms compete with each other. If one manages to compete more successfully, it will -- it will out grow others. And so there is no reason we can't expect something, like in Barry Hall's experiments, to show us some new interesting structure.

And if that occurred, that would be a real feather in the cap of people who think Darwinian theory is correct.

Q. Let's move onto the blood clotting cascade. Now you showed us some slides yesterday, or the day before, that show that certain organisms maintain a blood clotting function with less than all the parts that mammals have, correct?

A. That's correct.

Q. Okay. But that's not what you said in the blood clotting section in Pandas. You said, all the parts have to be, correct?

A. No, I didn't.

Q. Let's turn to pages 145 -- page 145 in Pandas, P-11. And this is the section on blood clotting?

A. Page 145?

Q. Right.

A. This is part of it.

Q. Right. And if you could turn to page 146.

A. Yes.

Q. And, Matt, if you could highlight that top paragraph, that one that continues over. You say, All of the proteins had to be present simultaneously for the blood clotting system to function, right?

A. That's right, all the proteins I was talking about.

Q. Okay. And then I understand, on Monday, you were distinguishing that there are different parts of the pathway, there are different parts of the pathway?

A. Yes.

Q. And what you said in -- on Monday is that, some of those parts, we have a harder time understanding than other parts?

A. Right.

Q. Okay. And, therefore, you just focus on a subset of the parts, right?

A. Right.

Q. Now you've got this whole cascade. You've got a diagram in Pandas. You got a diagram in your book, Darwin's Black Box. And you show it as a multi-protein system that includes that -- I think you said, intrinsic part of the pathway?

A. Yes, uh-huh.

Q. So that's the whole blood clotting cascade, correct?

A. That's as it's presented in textbooks, yes.

Q. And you presented it that way in Darwin's Black Box?

A. Yes, I did. I used that figure, yes.

Q. Okay. And you used it that way in Pandas, correct?

A. I used it -- a very similar figure, yes.

Q. And one whole system, one whole blood clotting cascade?

A. These are all the proteins that have been determined to affect blood clotting, yes.

Q. Okay. So -- but your claim in court is that, eh, let's ignore parts of it, some of those parts don't matter, we're just looking at a subset, right?

A. I made proper distinctions about what is required and about what we don't have sufficient information to make claims about that, yes.

Q. But those other parts never suggested are not part of the blood clotting cascade, right, the intrinsic pathway?

A. Well, I'm afraid I did. I -- well, I quoted a section of my book showing that I was confining my argument to the proteins at the end of the pathway.

Q. Matt, could you go to page 143 in Pandas so that we can have the picture of the system. I understand what you're saying, Professor Behe. You did indeed, in Darwin's Black Box, define the blood clotting system in a particular way, right, meaning --

A. Yes.

Q. And what you called irreducible complex didn't include, I guess, what's sort of in that top left-hand corner of the cascade?

A. That's correct.

Q. But that's not the entire cascade?

A. Well, there are many more proteins that affect blood clotting. But when I was talking about the concept of irreducible complexity, I wanted to make sure that we were talking about ones whose function was as clear as possible, so I limited it to that.

Q. You defined the system down more narrowly?

A. I'm sorry?

Q. You defined the system more narrowly?

A. That's right, yes.

Q. And so I guess what you're saying is, part of the system -- part of the blood clotting system that works in all of our bodies is irreducibly complex, but as it gets more complicated, it's not irreducibly complex?

A. No, I didn't say that. I said that the portion of the blood clotting system that I was focusing on was irreducibly complex. There might be components which affect blood clotting which can or can't be removed and help or not help but not break the system. But I was focusing my argument on irreducible complexity on the proteins I cited in my testimony.

Q. You define the system in whatever way is convenient to the argument?

A. I define the system very carefully to make sure that people understand what I'm talking about. I use the standard figure of the blood clotting cascade from a biochemistry textbook, because that's what is understood as the protein system that affects blood clotting.

Q. Now let me just make sure I understand the argument. What I think you said was, when I looked at -- the subset of the blood clotting cascade included fibrinogen, prothrombin, proaccelerin, and activated Stuart factor. Those are the things you say in Darwin's Black Box constitute the irreducibly complex system?

A. Okay.

Q. Is that correct?

A. Yes.

Q. And could you look on page 145 of Pandas?

A. Yes.

Q. Okay. And, Matt, could you highlight in the middle of the first column where it starts, We may try many smaller sets. You say here, We may try many smaller sets of components to get started; fibrinogen, prothrombin, activate the Stuart factor, and proaccelerin. And then you give some other alternatives. But then you say, death is nearly always the certain result, right?

A. Yes, I did.

Q. Okay. So that's actually saying, those four parts of the system, if that's all you got, not good enough?

A. Excuse me a second. Let me read this, please. Yeah, with those four, the system would not work.

Q. With those four, the system would not work?

A. Yes.

Q. Those are the four you just agreed were enough to make your irreducibly complex system?

A. Well, those are the four that I said that, if you knock them out of the current system, the system would not function.

Q. So here you're saying, just having those four -- you're saying, that's the irreducibly complex system, and the rest of it we can forget, and now we look at that irreducibly complex system, and death would be the certain result?

A. I'm -- I'm not -- I'm not -- I'm not understanding the distinction you're making, sir.

Q. Well, we looked at the puffer fish, right?

A. Yes.

Q. And it was missing some parts of the blood clotting cascade. But you said, from my argument, that doesn't matter, because that's not what I'm talking about, right?

A. Yes.

Q. You said, what I am talking about is these four factors here, right? I won't say them again because I'll just butcher them. Stuart factor and its friends. You said in your testimony on Monday, those four, those you need?

A. Yes.

Q. That's enough. That's irreducibly complex.

A. I didn't say, that's enough. I said that we certainly need those.

Q. And now you're saying here, those four, not enough, they're just -- they're just dead?

A. Well, again, I said that they were necessary. I don't think I said they were sufficient.

Q. You didn't identify any other systems?

A. Again, I was trying to identify parts which were certainly necessary, but I don't think I said that I was describing a minimal system.

Q. Could you turn to page 86 in Darwin's Black Box, and the first continuing paragraph?

A. Yes.

Q. Okay. And this is the chapter where you're talking about how the blood clotting cascade is irreducibly complex?

A. Right.

Q. And you say, The function of the blood clotting system is to form a solid barrier at the right time and place that is able to stop blood flow out of an injured vessel. The components of the system beyond the fork in the pathway -- that's the part we don't know so much about?

A. Yes.

Q. -- are fibrinogen, prothrombin, Stuart factor, and proaccelerin, factors that, by themselves, you die from, right?

A. I'm sorry? The factors --

Q. The factors that -- it says, The components of the system beyond the fork in the pathway are fibrinogen, prothrombin, Stuart factor, and proaccelerin. And those are the factors that, in Pandas, you say, if that's all you got, you're dead?

A. I -- I -- these are the factors which, if you break them, will cause the clotting system to stop working.

Q. That's the system, right? That's what it says in Darwin's Black Box? Those four components, that's the system?

A. The total system? Does it say that?

Q. It says, the system.

A. I'm sorry. Where are you reading from now?

Q. Page 86, Professor Behe. We know it's not the total system. There's a whole lot that we don't know about, right, and that the puffer fish can do without. But the system you're talking about, the single system that's irreducibly complex, that's those four components, correct?

A. No. Again, I said that we should focus our attention on those, because a lot more is known about them, and if you remove them, the system will certainly be broken.

Q. Right above what we just read, it says, The blood clotting system fits the definition of irreducible complexity?

A. I'm sorry. Can you tell me exactly where you are?

Q. Yes, the first full sentence on this page.

A. That begins, Leaving aside the system before the fork in the pathway?

Q. Yes. Leaving aside the system before the fork in the pathway, where some details are less well-known, the blood clotting system fits the definition of irreducible complexity. So we're leaving aside that stuff before the fork?

A. Okay.

Q. We're leaving the stuff aside that we know the puffer fish can do without. And you're saying, The blood clotting system fits the definition of irreducible complexity. That is, it is a single system composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causing the system effectively to cease functioning.

It talks more about the function. It says, The components of the system beyond the fork in the pathway are fibrinogen, prothrombin, Stuart factor, and proaccelerin. That's your irreducibly complex system, isn't it, Professor Behe?

A. No, it's not. Again, I was confining my discussion to the point after the fork in the pathway because, as I said in the book, much more is known about that. But the fork in the pathway is essentially two different ways to activate the pathway.

And while you can do without one way to activate the pathway, you can't do without both ways to activate the pathway. Something has to activate it.

Q. So you have to have those four, right?

A. Yes, those four are needed for the system to work. But -- and I confined my discussion to them. But they're not sufficient for a functioning system.

Q. You need the stuff before the pathway, too?

A. You need some of the stuff, yes.

Q. Except for the puffer fish?

A. Well, again, like I said, some of the stuff. The puffer fish itself has the extrinsic pathway, which is one way to trigger the remaining steps. It's missing the intrinsic pathway. But nonetheless, it still has one way to turn the pathway on.

Q. It has those four things?

A. It does, yes.

Q. Which we know, by themselves, cause death?

A. By themselves, they would cause the system to start stop functioning.

Q. Sounds like a bigger mistake than Dr. Doolittle made, Professor Behe?

A. I'm not sure what you are referring to.

Q. Well, you spent a lot of time trashing Dr. Doolittle and his work, his article in the Boston Review. Your mistake here is quite a bit more substantial than misinterpreting a mice study, isn't it?

A. I'm not even quite sure what you are referring to as my mistake.

Q. I'll withdraw that question, Professor Behe. It's surely not your contention that the mistake you understand Dr. Doolittle to have made basically invalidates the possibility that the blood clotting system could have evolved?

A. No, of course not. The only point I was making with that discussion was that he did not know how Darwinian processes produced it. It was not an argument saying that -- or it was not -- did not go to the point of whether or not that could happen.

Q. Okay. And that was an article, whether right or wrong, that was not in a peer reviewed scientific journal?

A. That's correct.

Q. Dr. Doolittle, as you showed us, has actually written quite a bit on the subject of the blood clotting cascade in peer reviewed scientific journals?

A. He certainly has.

Q. Including what we saw about the puffer fish?

A. That's correct.

Q. And by contrast, how many peer reviewed articles are there explaining the blood clotting -- why the blood clotting cascade cannot evolve because it is irreducibly complex in the way you describe?

A. Well, I'm going to say that the articles which elucidate the structure of the blood clotting pathway are the ones which demonstrate that. I will agree that there certainly are no arguments or directly to that point. But as I tried to show in my book, Darwin's Black Box, that's an implication that can easily be drawn from those studies.

Q. So these are all those other articles based on the research of other scientists that you interpret differently than those scientists do?

A. That's right. I was proposing a newer idea.

Q. Okay. And how many peer reviewed articles are there in scientific journals discussing the intelligent design of the blood clotting cascade?

A. Well, again, since we infer design by the purposeful arrangement of parts, then the peer reviewed articles in science journals that demonstrate that the blood clotting system is indeed a purposeful arrangement of parts of great complexity and sophistication, there are probably a large number of those.

Q. Again, those are those articles by other scientists based on experimental research, right?

A. They are certainly by other scientists, not by myself, and they are certainly based on experiments.

Q. And none of those articles are arguing that the blood clotting cascade are intelligently designed -- is intelligently designed?

A. That's correct.

Q. And there are no peer reviewed articles arguing that the blood clotting cascade is intelligently designed, right, in scientific journals?

A. I wrote my argument in a book, so, yes, that's correct.

Q. And before we leave the blood clotting system, can you just remind the Court the mechanism by which intelligent design creates the blood clotting system?

A. Well, as I mentioned before, intelligent design does not say, a mechanism, but what it does say is, one important factor in the production of systems, and that is that, at some point in the pathway, intelligence was involved.

MR ROTHSCHILD: This would be a good time for a break, Your Honor.

THE COURT: All right. Why don't we take our lunch break at this point, and we will be in recess until 1:35 this afternoon. We'll resume cross examination at that time. Thank you.

(Whereupon, a lunch recess was taken at 12:10 p.m.)