Kitzmiller v. Dover Area School District

THE COURT: All right. Good morning to all in what, I believe, will prove to be the final day of this case. And we remain in the cross examination of the expert witness, and I'll turn it back over to you, Mr. Harvey. You may proceed.

CROSS EXAMINATION ( CONTINUED)

BY MR. HARVEY:

Q. Good morning, Dr. Minnich.

A. Good morning.

Q. I'm willing to pretend that we're doing this in front of an empty courtroom, if you are. That will make it a little bit easier for me; perhaps for you, too.

A. Okay.

Q. When we left off yesterday, we were talking about the argument of irreducible complexity and where it finds its origins. And I'd like you to turn to what's been marked as P-845. And, Matt, if you could bring that up on the screen. Please let me know when you have that in front of you.

A. Okay. I've got it.

Q. Or you can look on the monitor, if that's easier for you. This is a publication from the Institute for Creation Research in 2005, and it's authored by a man named Dr. Henry Morris. Have you ever heard of Dr. Henry Morris?

A. I have.

Q. He's actually the founder and president of the Institute for Creation Research, isn't he?

A. That's my understanding, yes.

Q. And he's really the founder of the creation-science movement, is that your understanding?

A. I haven't followed that movement that closely, but I'll take your word for it.

Q. And what he's got here is, he's reviewed a book called The Design Revolution by William Dembski. And I'd like to just ask you some questions about some of the things that are said in here, but first, have you read this review before today?

A. I haven't. I haven't seen it.

Q. Well, if you turn to the first page -- and, Matt, if you could bring it up -- there's a statement on the right-hand side where he says, We do appreciate the abilities and motives of Bill Dembski, Phil Johnson, and the other key writers in the intelligent design movement. They think that if they can just get a wedge into the naturalistic mind set of the Darwinists, then later, the Biblical God can be suggested as the designer implicit in the concept. Do you see that?

A. I do.

Q. And I would like to know if you agree with me that, that's what the design proponents are trying to do?

A. No, I don't think so at all. I mean, that's a pretty subjective statement.

Q. Well, if you just turn to the second page of that, there's a statement there -- and I'm going to ask Matt to highlight this, too. It begins with the word second. It is not really a new approach. Matt, can you bring that up? Referring to the intelligent design approach, it says, quotes, Second, it is not really a new approach, using basically the same evidence and arguments used for years by scientific creationists but made to appear more sophisticated with complex nomenclature and argumentation, end quotes. Do you see that?

A. Yeah, I see it.

Q. Do you agree that's a true statement?

A. Well, I would -- in terms of the context, I'd rather read the whole article. I don't agree that's necessarily true at all. Part of it is true. I think some of the arguments that the creationists proffered back in the '80's are legitimate and they can be used, just looking from the scientific approach.

Q. Well, I'd like to ask you about another statement in this article by Henry Morris, and it's in the right-hand side, and I'll ask Matt to flag that as well. Highlight it, please. And I want to know whether this -- you know this to be true.

Quotes, These well-meaning folks did not really invent the idea of intelligent design, of course. Dembski often refers, for example, to the bacterial flagellum as a strong evidence for design, and indeed it is, but one of our ICR scientists, the late Dr. Dick Bliss, was using this example in his talks on creation a generation ago, close quotes.

Did you know that a man named Dr. Dick Bliss, who's affiliated with the Institute for Creation Research, was using --

MR. MUISE: Objection, Your Honor. He's asserting this as a statement of truth. And this is a hearsay statement. If he wants to ask him if he agrees with that statement, that's something totally different, but he's asserting this to be a truthful statement.

THE COURT: Let's let him finish the question, and I'll take the objection. Finish you shall your question, please.

BY MR. HARVEY:

Q. Dr. Minnich, I'd like to know whether you know that a man named Dr. Dick Bliss, who was affiliated with the Institute for Creation Research, was using the bacterial flagellum as part of his argument for creationism years before the intelligent design movement picked up on it?

THE COURT: All right. The objection is overruled for the record. You can answer the question.

THE WITNESS: No, I wasn't aware of it, but I'm not surprised. Again, like I asserted yesterday that, the bacterial flagellum is one of the organelles that we know the most about of any. And so it's natural to look at this structure as a model for either evolution or irreducible complexity. So I'm not surprised. I didn't know it, but I'm not surprised.

BY MR. HARVEY:

Q. Now you and Dr. Behe claim that the bacterial flagellum is irreducibly complex and thus could not evolve. Is that a fair statement of your position?

A. Correct. There is some -- right. It's irreducibly complex in terms of the genetic analysis of the structure.

Q. Please tell me whether you agree with this statement. Neither you nor Dr. Behe has set out to do any original research to show that the bacterial flagellum could not have evolved, as you contend?

A. I think the work that I've published on for the last 12 years bears on this question of irreducible complexity, but I'm not aware of specific experiments addressing, you know, I mean, real lab experiments addressing the evolution of this structure.

There have been plenty of publications comparing the flagellum with the type III secretory system and whether it's an intermediate. So, in that sense, I think some of my work bears on that as well.

Q. So in other words, you agree with the statement I said?

A. Repeat the statement.

Q. Neither you nor Dr. Behe has set out to do any research to show that the bacterial flagellum could not have evolved?

A. I want to qualify that. You know, the thing that's interesting to me was, back in 1994, my laboratory, my students and I were the first to propose that the bacterial flagellum could be used for other than secretion of flagella proteins. We were the first to actually predict that the type III secretory system, which we didn't know existed at that time period, would either be the basal body of the flagellum or a structure that looked very much like it. Okay.

So I think that I have had some impact in this area directly. And the ironic thing is that, presenting this at scientific meetings and in grant proposals, it was considered a whimsical idea because there was no apriority evidence that the secretion of virulence factors or the flagellum had anything to do with each other.

Q. Well, would it be fair to say that, neither you nor Dr. Behe has published any papers in scientific journals on whether -- on the evolution or not of either the type III secretory system or the bacterial flagellum?

A. I'm not funded to look at the evolution of the flagellum. I'm funded to look at its effect in terms of regulation and virulence and type III secretion.

Q. In other words, the statement I just said was true?

A. That's not the emphasis of my work.

Q. Now you did publish a paper, you told us about in your direct testimony, with Steven Meyer, correct?

A. Correct.

Q. That was published in some conference proceedings with respect to a conference that took place in Greece?

A. That's correct.

Q. And Steven Meyer is not a biologist, correct?

A. He's not. He's a philosopher of science.

Q. So he's not a scientist?

A. Well, he's a philosopher of science. He's trained as a physicist, my understanding, and work in that area for a while.

Q. Now this was a conference for engineers who used natural mechanisms to devise new technologies, do I understand that correctly?

A. Correct.

Q. It wasn't a conference for biologists or it wasn't a conference on evolutionary biology, was it?

A. It was a conference that included biologists and engineers and architects, as I discussed yesterday, looking at design in nature.

Q. And the paper that you published was only minimally peer reviewed, isn't that true?

A. For any conference proceeding, yeah. You don't go through the same rigor. I mentioned that yesterday. But it was reviewed by people in the Wessex Institute, and I don't know who they were.

Q. I'd like you to take a look at what's been marked as P-837. Matt, if you could bring that up.

A. May I just look off the screen?

Q. Yes. And in that paper, you cite several peer reviewed papers, including a paper in the Journal of Molecular Biology that suggests that the bacterial flagellum was the evolutionary pre-cursor to the type III secretory system, isn't that correct?

A. Correct.

Q. And this actually is the paper you cite?

A. Correct.

Q. And from this paper, and this is in your report at -- you stated this in your report at page 9. We'll bring that up. It's P-614. Matt, could you highlight the sentence that says, neither standard neo-Darwinism, in the bottom paragraph. It begins with -- it's the third sentence. It begins, Given that neither. And from this paper, P-837, you draw the conclusion, as stated in your report, and this, I believe, is a quotation from the article, the conference proceeding paper, that, quotes, Neither standard neo-Darwinism nor co-option, has adequately accounted for the origin of these machines, or the appearance of design that they manifest. One might now consider the design hypothesis as the best explanation for the origin of irreducibly complex systems in living organisms. Isn't that true?

A. Yes, that's correct.

Q. Now the paper that we just looked at, the one that you were relying on, that's a paper in a peer review journal, isn't that right?

A. That's correct.

Q. And actually, you're aware that there are a number of papers in peer review journals on this same subject?

A. I am.

Q. For example, please take a look at what's been marked as P-284.

A. Got it.

Q. And if you look in the abstract, there's a sentence that I just want to bring you to, that I think it summarizes what we need to discuss. It's the fourth sentence in the abstract, Matt. The one that begins, Our analysis.

This says that, Our analysis indicates that the type III secretory system and the flagellar export mechanism share a common ancestor, but they have evolved independently from one another. Do you see that?

A. I see it.

Q. Unlike your paper, that is a peer reviewed scientific paper, correct?

A. In that -- in that sense, yeah. Again, mine is a conference paper, so --

Q. This is a true peer reviewed paper, correct?

A. Correct.

Q. Now I'd like you to look at another, if you turn to Exhibit P-740. This is another paper in a peer reviewed scientific journal called Trends in Microbiology, is that correct?

A. Correct.

Q. I think I'd like to go to the second page of this, the paragraph on the right-hand side that begins on the right-hand side, Matt, about halfway down that paragraph, the sentence beginning with the words, regarding the bacterial flagellum, and the rest of that paragraph.

Now this says that, quotes, Regarding the bacterial flagellum and the TTSS's, we must consider three, and only three, possibilities. First, the TTSS came first. Second, the flagellar system came first. Or third, both systems evolved from a common pre-cursor. At present, too little information is available to distinguish between these possibilities with certainty. Do you see that?

A. I see it.

Q. Now I could show you, and I have in my notebook, a number of other peer reviewed scientific journals that discuss this subject. But would you agree with me that the -- that how the bacterial flagellum and the type III secretory system evolved is an unsettled scientific question?

A. Well, that's part of why we're here. It's a good scientific debate. And that's how science works. I think if you read -- if you read the conclusion of this paper, Bill Sayer is favoring the fact that the flagellum came first.

And I think that the arguments and the evidence, not only the ones that we proffered in our conference paper, but the new evidence that's comes out, favors that, that scenario. I mean, this is -- the type III secretory system is limited, to our knowledge now, to a narrow group of gram negative organisms, that the type III secretory system, from what we know now, only is designed to effect eukaryotic organisms either in a symbiotic relationship or a parasitic relationship.

So eukaryotic organisms evolved after prokaryotic organisms. The structure is directly to eukaryotic organisms. And you have to postulate that all the other bacteria, as they evolved, lost this TTS system, and that was only retained by this select group, you know.

So I think the evidence is getting to the point that we're going to side with the fact that the flagellum came first, more complex structure came first before the TTSS.

Q. There's actually a number of scientific papers that go the other way, isn't that correct?

A. Well, I think so. I think it's part of the nature of this debate. I mean, there's some subjectivity to it. If you look at Bill Sayers' first paper, just based on the sequence analysis, there's much tighter similarity between the type III secretory system proteins than there are in flagellum, which is an indication in evolutionary terms that these came later. They haven't evolved as much as the flagellar system.

Q. The point is not that the chicken or the egg came first, Dr. Minnich, it's that a lot of highly qualified scientists are looking at this question and trying to determine the evolution of the type III secretory system --

A. You bet.

Q. -- and the bacterial flagellum. That's a true statement, isn't it?

A. That's a true statement.

Q. There's a number of papers that have been published in peer reviewed scientific journals on both sides of this question, and the papers are inconclusive, correct?

A. They're inconclusive, but I think if you look at the more recent ones, you know, the gavel is falling on the side of the flagellum first.

Q. Well, the real point of this is that, none of those highly qualified scientists who are doing research and publishing in peer reviewed scientific data are suggesting in any way that these systems did not evolve, but were instead created abruptly by an intelligent design agent?

A. I never said that the flagellum was created abruptly. I have no idea in terms of how it came about. I just look at the structure. And it has the signature of irreducible complexity and design. It's a true rotary engine. I just come back to that. It doesn't say anything about where it came from, when it was made, or who was involved in it, or what was involved in it.

Q. Let me reask the question again, leaving out the word abruptly. None of the many highly qualified scientists who are doing research in this area right now and publishing in peer reviewed scientific journals are in any way suggesting that these systems, the type III secretory system and the bacterial flagellum, did not evolve, but instead were created by an intelligent designer, right?

A. No, we're looking at the function of these systems and how they could have been derived one from the other. And it's a legitimate scientific inquiry. And it's good. I mean, I have no problem with that.

Q. In your direct testimony, you showed us pictures and made reference to macromolecular machines, right?

A. I did.

Q. You call them nanomachines, as we discussed yesterday?

A. These refer to either way in the literature.

Q. You are not suggesting, are you, Dr. Minnich, that these are actually machines, are you? You're saying that they're like machines, aren't you?

A. If you read Bruce Alberts' review article, he specifically states -- and we can look it up, if you want. Why do we call them machines? Because they are machines.

Q. You think that Dr. Alberts says, these are machines?

A. Well, let's look at the paper.

Q. Well, actually, I just want to know what your understanding is. I was under the impression that machines were created by human beings, that a machine was, by definition, something created by a human being. Do you agree with that?

A. Yeah, I mean, that's our -- that's our reference.

Q. And you're not aware of any machines that were created by any being other than a human being, are you?

A. Well, isn't that what we're talking about? Isn't that the surprise that, when we open up the cell and we find these macromolecular machines, that all of my colleagues refer to them as, or nanomachines, that these were unanticipated. So we've got to -- and they function as machines, invented like humans, as David DeRosier says, or these other people.

Q. Well, my question to you is, are you aware of any machines that were invented, created, or designed by anyone other than a human being?

A. I think it would boil down to a definition of a machine, you know. Some animals can put together some, you know, crude devices to, you know.

Q. With the exception of possibly animals and human beings, are you aware of any other beings that have ever created, invented, or designed a machine?

A. No.

Q. Now you relied in your testimony and the argument that you presented in your direct evidence, in your direct testimony, excuse me, on quotations from a number of eminent scientists, isn't that true?

A. I did. And I think I qualified as well that these are all individuals that are evolutionists. So I'm not trying to, you know, put words in their mouths or say they agree with me. I'm just looking at what their statements say.

Q. The three scientists you mentioned were Dr. Woese, Dr. Alberts, and Dr. Simon Conway Morris?

A. Correct.

Q. Those are three of the most eminent scientists in the world, would you agree?

A. I agree.

Q. And let's talk about Dr. Woese for just a second. In your testimony, you rely on an article by Woese and two quotes in particular. Matt, please put up slide number 10. This was a quotation from Dr. Woese that you cited in your direct testimony, correct?

A. In my direct or my deposition, I think I had included past this last phrase here.

Q. And you also rely on another quotation from Dr. Woese, which is slide 28, Matt, please. Do you remember talking about this in your direct testimony?

A. Yes.

Q. Now, Matt, please put up D 251 at page 176. In the upper left-hand corner, Matt, the first two-thirds of the paragraph. Dr. Minnich, would you agree with me that Dr. Woese, this eminent scientist, completely rejects the machine analogy. Would you agree with that?

A. I think, in this article, he is really objecting to the point from molecular biology, looking totally at the cell as a reductionist point of view, because from a reductionist point of view, you do end up looking at organisms as machines. In that sense, I think he's referring to it, that in his view, the organism is more than the sum of its parts, and this has in part been ignored by molecular biology, and he wants to bring things back to the higher level in terms of organismal biology and evolutionary studies in terms of the origin of these.

Q. Please tell me. I'm going to read a passage to you, and tell me if I've correctly quoted Dr. Woese in a peer reviewed scientific journal.

Quotes, Let's stop looking at the organism purely as a molecular machine. The machine metaphor certainly provides insights, but these come at the price of overlooking much of what biology is. Machines are not made of parts that continually turn over, renew. The organism is. Machines are stable and accurate because they are designed and built to be so. The stability of an organism lies in resilience, the homeostatic capacity to reestablish itself. Did I read that correctly?

A. Right.

Q. Dr. Woese rejects the machine analogy, correct?

A. He rejects the machine analogy because, you know, this is based on our -- and I brought up this point yesterday in terms of the bacterial flagellum. When it's referred to as a machine that looks like it was invented by a human more than any other machine is an under statement because of these very parameters as well. It is resilient. It can self-assemble. We can't make anything like it. So our analogy, I think, is limited more than anything else.

Q. Matt, pull up slide 16, please. This is a slide that you used in your direct testimony?

A. Right.

Q. And this is referring to an article in the journal Cell by Dr. Alberts?

A. Correct.

Q. And Matt, please pull up slide 17. And you rely actually on the table of contents from that journal in support of your argument that these are like a machine, right?

A. I have that quote in there, right, directly from the table of contents.

Q. Right. And if you look at the article itself, as opposed to the table of contents, although I think it's clear from the table of contents, he's quite clear in saying that, these protein assemblies that he's discussing in his article are like machines invented by humans, correct?

A. Correct.

Q. And are you aware that, moving from the machine analogy just to the overall substance of intelligent design, that Dr. Alberts completely rejects the conclusions that you purport to draw from his work?

A. Oh, I'm aware that he is a strong advocate of evolution. He's even co-authored a manual for teaching evolution at the secondary level in high school.

Q. Matt, please pull up P-852. You can either look on the screen or you can look in your book, whatever is more convenient for you.

A. What was the number again?

Q. 852.

A. Right.

Q. This is a letter to the editor that Dr. Alberts, who, by the way, was the president of the National Academy of Sciences for 12 years, right?

A. I am aware of that.

Q. This is a letter to the editor that Dr. Alberts published in the New York Times. And I'm going to read it to you. An please tell me if I've quoted it correctly. In Design for Living, on February 7, Michael J. Behe quoted me recalling how I discovered that the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered some 40 years ago.

Dr. Behe then paraphrases my 1998 remarks that the entire cell can be viewed as a factory with an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. That I was unaware of the complexity of living things as a student should not be surprising.

In fact, the majestic chemistry of life should be astounding to everyone. But these facts should not be misrepresented as support for the idea that life's molecular complexity is a result of intelligent design. To the contrary, modern scientific views of the molecular organization of life are entirely consistent with spontaneous variation and natural selection driving a powerful evolutionary process.

In evolution, as in all areas of science, our knowledge is incomplete. But the entire success of the scientific enterprise has depended on an insistence that these gaps be filled by natural explanations, logically derived from confirmable evidence. Because intelligent design theories are based on supernatural explanations, they can have nothing to do with science.

Were you aware that, that's Dr. Alberts' position on the subjects that you've discussed in your direct testimony?

A. I am aware. I haven't read this letter until now, but I'm not surprised. I would disagree with the bottom though. Because intelligent design theories are based on supernatural explanations, they can have nothing to do with science. You know, we're not -- I'm the first person to say, we look for a natural explanation, but this is -- the entire success -- the scientific enterprise has depended on an insistence that these gaps be filled by natural explanations.

We don't have a natural explanation yet for these macromolecular machines. That's the whole point. And again, going back, I think Dr. Alberts perhaps was caught in his own language. All right. And I find this amazing that, you know, we use this language, this description of machines, and elegant chemistry, and then go back and say, but this is entirely derived from natural process of evolution and change over time.

Q. Matt, will you please pull up Exhibit P-848. And Dr. Minnich, you can take a look at that either on the screen or in your book.

A. Okay.

Q. This P-848 is an article that Dr. Alberts published with a man named Jay Labov in a journal called Cell Biology in the summer of 2004, isn't it?

A. Right.

Q. And in this article, Dr. Alberts summarizes the efforts of the National Academies of Science to address challenges to the teaching of evolution in the nation's public schools. Isn't that true?

A. I haven't read this article.

Q. So you weren't aware of that?

A. Oh, I'm aware of it, right, that he's -- his position.

Q. Dr. Alberts has made it very clear in the scientific community that he does not believe that intelligent design qualifies as science, correct?

A. Again, I haven't read the specifics of this. I don't know what he's basing his conclusion on.

Q. Well, I'm asking you if you knew that Dr. Alberts has made it very --

A. I'm aware that the National Academy of Science has come out against the teaching of evolution, as well as the AAAS and a number of other societies. In fact, I was even informed Saturday before I came out here that the American Society for Soil Science had come out making a statement against intelligent design, which I find incredible.

Q. We discussed Dr. Woese just a couple minutes ago. And you, in your reports, cite and quote from a 2004 article by Dr. Woese to suggest that the modern day supports of evolutionary theory are ripe with problems. That's true, right? You said that in your expert report?

A. Correct. And I also quoted, I think, more of a light on Morris's papers as well illuminating that the problems that we have in evolution.

Q. We'll talk about Dr. Simon Conway Morris in just a minute. But you're aware that Dr. Woese completely rejects the idea that intelligent design is science, right? You're aware of that?

A. I haven't talked to Dr. Woese, so I'm not sure of his personal opinion. I know he's an evolutionist, so it doesn't surprise me. But you're asking if I know specifically, and I don't.

Q. I haven't spoken to him either, although I'm sure it would be a fascinating conversation.

A. I would like to.

Q. If you could turn to what's been marked as P-847. And this is an article from an online publication called Wired Magazine?

A. Right.

Q. Have you ever heard of this publication?

A. I have.

Q. And if you go to page 6 of this, there's a quote from Dr. Woese in there, and I just want to know if you were aware that he had said this?

MR. MUISE: Objection, Your Honor. Again, it's an assertion that he is asking whether he's aware that he said that. He's asserting he actually did say this. We don't have any foundation for this. It's obviously trying to be offered for the truth that he actually asserted this statement. He said he doesn't have any personal knowledge of this statement.

MR. HARVEY: I am trying to determine whether he knows that Dr. Woese actually made a statement in here that completely rejects and rebuts the position that this witness offered in direct testimony. He can either say he's aware of it or aware of the position or he's not.

THE COURT: Why doesn't it go to the truth?

MR. HARVEY: Actually, I am not offering this for the truth. I am asking this witness if he's aware of that. And that tends to impeach his direct testimony.

THE COURT: Well, I think the proper way to do it is to ask him if he's aware of a statement without reference to the exhibit. I think that will cure the objection for the moment.

MR. MUISE: Well, the way he asserted it, are you aware that he made this statement. He is asserting that Dr. Woese actually made that statement.

THE COURT: I think the proper phraseology for the question is a statement that, and I'll allow that, without reference to the article. And I'll sustain the objection to that extent.

BY MR. HARVEY:

Q. Well, Dr. Minnich, are you aware that Dr. Woese has stated that, To say that my criticism of Darwinists says that evolutionists have no clothes is like saying that Einstein is criticizing Newton, therefore Newtonian physics is wrong. Intelligent design --

MR. MUISE: Again, Your Honor.

THE COURT: Hold on. Hold it. That's not consistent with the ruling on the objection. I don't want you to read the statement into the record. I'll allow you to paraphrase this statement without reference to the article. That's the only way we're going to be able to do this. If his answer is in the negative, then we move on.

MR. HARVEY: I misunderstood your ruling.

BY MR. HARVEY:

Q. Dr. Minnich, you're not surprised -- you wouldn't be surprised at all to learn that Dr. Woese has stated publicly that intelligent design is not science, would you?

A. Again, I haven't talked to Dr. Woese specifically on this area, so I'm not aware of the statements.

Q. So you're not aware at all that Dr. Woese has come out publicly and said that intelligent design is not science?

A. I haven't.

MR. MUISE: Objection, Your Honor. He's making an assertion. Does he know? Do you know if? I mean, I'll --

THE COURT: I'll allow that question without reference to the article. No, the objection is overruled. And the answer stands.

BY MR. HARVEY:

Q. You mentioned Simon Conway Morris. Simon Conway Morris is a leading paleontologist, correct?

A. He is.

Q. He is perhaps the foremost expert on the Cambrian explosion?

A. Right, based on his work on the Burgess Shale.

Q. And he's a renowned evolutionary biologist?

A. He's written extensively on the subject, yes.

Q. Are you aware that Dr. Simon Conway Morris has taken the position that intelligent design is not science?

A. I am not aware of that. But again I would like to, you know, for the record, state, in his paper, the problem of convergence in evolution, the channeling, in his mind, brings up the question of teleology, directly quoted from his paper, and he cites two authors that have been involved in intelligent design. So I think he's looking at the possibility, you know, as a scientist and looking at the claims.

Q. You're aware that in the paper you're referring to, Dr. Conway Morris said that, if, with the underline on it, if evolution is in some sense channeled, then this reopens the controversial prospect of teleology?

A. Correct.

Q. Now I'd like to ask you about some other questions. In your direct testimony, you said that you infer the existence of intelligence by standard scientific reasoning. Did I hear you correctly?

A. Correct.

Q. And is the explanation of intelligent design that you provided to this Court similar to the presentation that you would make if we were a group of scientists and you were trying to persuade us that ID, intelligent design, is scientifically valid?

A. Yes.

Q. And you testified that it's a legitimate scientific practice to draw conclusions from published studies or data that are different than those drawn by the scientists who actually compiled the data, correct?

A. It happens all the time.

Q. And you cited Drs. Crick and Watson as an example, correct?

A. Right.

Q. They relied on data published by another scientist, and they drew their own conclusions about that data?

A. There's always the cross fertilization of data and ideas, and somebody will synthesize a new model, and it can be tested.

Q. Drs. Crick and Watson won a Nobel Prize for the conclusions they drew from that other scientist data, correct?

A. Correct.

Q. Now the way they did that is, they published their thinking in peer reviewed scientific journals for the scrutiny of their colleagues, true?

A. In a one-page article in 1953 in Nature, right, the first publication on the structure of DN A.

Q. Nature, that's a peer reviewed scientific journal?

A. It is.

Q. Is that the probably the number one most respected peer reviewed scientific journal in the world?

A. I think Nature, Science, PNAS, Cell, would all fit in that.

Q. Now Dr. Crick and Watson didn't win a Nobel Prize by trying to convince school boards, average citizens, lawyers, the press?

A. I made that clear yesterday, that I wasn't equating what we were doing with the work of Watson and Crick. I'm not so presumptuous or arrogant to make such a comparison.

Q. Well, it's important to publish your scientific conclusions in peer reviewed journals so that other scientists, people who are qualified to evaluate those conclusions and the evidence from which those conclusions are drawn, so that those people, your colleagues, so that they can look at your conclusions and determine whether they make sense or not?

A. I agree.

Q. Hence the expression, publish or perish, right?

A. Right. And publish and perish as well.

Q. That's your second very good joke in this -- leading all expert witnesses.

A. I'm concerned, you know. There's a risk involved. That paper that I published for the conference proceedings ran a lot of risk in terms of the implications and how people would review my work based on the conclusions that I was making. And that's part of the problem, is that, to endorse intelligent design comes with risks, because it is a position against the consensus. And science is not a democratic process. But peer review works both ways. And it is, like I said, it's dangerous. I'm taking a risk in putting these ideas out, as well as everybody else in this area that's trying to get published.

Q. And that's because the, really the entire scientific community rejects the idea that intelligent design is science, isn't that correct?

A. That is correct, at this point. And that is the history of science as well.

Q. And this explains why you have not published any articles on intelligent design in any peer reviewed scientific journals, correct?

A. By your definition, no. But I have one in a conference proceedings, so I'm willing to put my ideas out there. And, but again, my focus in my laboratory is on pathogenesis. That's my primary concern. And that's what I publish on. And that's -- you know, I have to keep my lab funded.

The implications, I think, contribute to our idea of intelligent design. And I certainly don't hide my feelings or arguments as well. I mean, I've talked about this. I've been open about it with my colleagues. I think the more we discuss it, the merits of some of these things are understood, and they're not dismissed outright before being weighed, which is the tendency.

Q. Dr. Minnich, you're not aware of any research articles advocating intelligent design in any peer reviewed scientific journals, are you?

A. I think yesterday there was, as I mentioned, there were around, between, I don't know, seven and ten. I don't have the specific ones. But Dr. Axe published one or two papers in the journal Biological Chemistry that were specifically addressing concepts within intelligent design. Mike Behe had one. Steve Meyer has had one.

So, you know, I think the argument that you're not publishing in peer reviewed literature was valid. Now there are a couple out there. How many do we have to publish before it is in the literature and being evaluated? I mean, do we have to have 25? 50? I mean, give me a number.

Q. Let's just talk about Dr. Axe. Those papers don't advocate intelligent design, do they?

A. That's the intent in terms of looking at protein sequence and domains and sequence space.

Q. He doesn't mention the words intelligent design anywhere in those articles, isn't that correct?

A. There's a reason for that.

Q. And you mentioned something by Dr. Behe, is that right?

A. Correct.

Q. That's the article with Snoke?

A. Yes.

Q. That wasn't in a scientific journal, was it?

A. Well, refresh my memory. I haven't read the papers.

Q. So you don't know -- if Dr. Behe testified that that wasn't in a scientific journal, you wouldn't question it?

A. I wouldn't dispute it, no.

Q. Intelligent design posits the existence of an intelligent agent who devised a plan, a pattern, a blueprint for living things, isn't that correct?

A. I don't agree with that definition. I think intelligent design is looking at nature and asking, are the complex structures that we find possibly developed by natural cause alone or not? Is a design real or apparent?

Q. You testified about the book Of Pandas and People in your direct?

A. Right.

MR. HARVEY: Your Honor, may I approach?

THE COURT: You may.

BY MR. HARVEY:

Q. I've handed you a copy of Of Pandas and People, opened to page 14. In the lower right-hand side, there's a statement there?

A. Okay.

Q. It's actually the last sentence on that page. Intelligent design, by contrast, locates the origin of new organisms in an immaterial cause, in a blueprint, a plan, a pattern devised by an intelligent agent. Isn't that what the book says?

A. Right. I mean, in that sense, yes, there's an intelligent cause behind the specified complexity that we find in nature.

Q. And intelligent design also, another way of saying the same concept is that, intelligent design posits the concept of a master intellect, isn't that right?

A. To a degree, yes, but it doesn't indicate or identify master intellect, who it is.

Q. Now you think that the intelligent agent is the God of Christianity, isn't that true?

A. Are you asking me personally?

Q. Yes.

A. Okay. Yes, my personal opinion, but that's not based on a scientific conclusion.

Q. You're affiliated with the Discovery Institute, right?

A. I'm a fellow.

Q. And you're proud of your association with the Discovery Institute?

A. Yeah, it's a good network for --

Q. And you're familiar with Philip Johnson?

A. I am familiar with Philip Johnson.

Q. He also thinks that the intelligent designer is the God of Christianity, isn't that true?

A. That's my understanding, yes.

Q. And Michael Behe is a fellow of the Discovery Institute?

A. He is.

Q. And he also thinks that the intelligent designer is the God of Christianity, correct?

A. I haven't asked Mike directly, but he's a Catholic, I know, so I assume so.

Q. William Dembski, you know that he thinks the intelligent designer is the God of Christianity, right?

A. Correct. But again, these are personal opinions that aren't based on looking at the science.

Q. I understand. Dean Kenyon is a fellow with the Discovery Institute?

A. I'm not sure, but I'll take your word for it.

Q. Do you know Charles Thaxton?

A. I know Charles Thaxton.

Q. He's a fellow with the Discovery Institute, right?

A. I believe so.

Q. Do you know he thinks the intelligent agent is the God of Christian?

A. I'm aware of that.

Q. Nancy Pearcy. She's a fellow with the Discovery Institute?

A. Correct.

Q. And she thinks that the intelligent agent is the God of Christianity, isn't that right?

A. Correct.

Q. Now I want to ask you about -- we talked just about the term intelligent design. As I understand it, intelligent design, as an argument, is saying that this intelligent designer not only designed living things, but also built living things. Do you agree?

A. Repeat the question.

Q. Sure. Intelligent design, as a concept or an argument, is saying that the intelligent designer not only designed living things, but the intelligent designer built living things?

A. I haven't heard that inference before. I mean, there are parts of that I would agree with, but in terms of aboriginal forms or whatever, there is nothing in terms of the mechanism implicit in intelligent design that I'm aware of.

Q. Well, the statement that I said, that's -- that flows logically from the concept?

A. Right.

Q. You're not saying that the intelligent designer drew up this blueprint and then set it aside, are you?

A. No, no, no.

Q. The intelligent designer designed and built these things?

A. Correct.

Q. Designed and created these things, correct?

A. Well, your use of the word created, invented, whatever. I mean, it was a creative process at some point, whoever the designer was.

Q. But you would agree with me, whether we want to say built or created, made, constructed, put together, it's all the same thing? The intelligent designer designed and created these living things. That's the logical implication of intelligent design?

A. Again, I go back to what Ii said yesterday. As biologists, all of us look at nature and we see design. It's overwhelming by our own admission. The question is, is it real design or only apparent design? Or is it a combination of both? You know, and I think those are legitimate scientific questions to be asked.

Q. I'm anxious to explore that with you, but first I have to get this cleared up. You agree that it's intelligent design and construction, building, creation, it's both concepts, correct?

A. Correct, given some of the structures we find in the simplest cells that supersede anything that our engineers can build at present, yeah, I would say it's a source of intelligence.

Q. Wouldn't it be more correct to call the argument or the theory, intelligent design and creation?

A. No. You know, I think I resent the consistent misrepresentation of intelligent design with creationism.

Q. Well, intelligent design and construction, would that be better?

A. Okay.

Q. You can accept --

A. At some point. All we can say is that, there's design -- I think it's real. There's a designer. I don't know who it is or what it is, you know, from the science that I'm deriving that assertion from. Science isn't going to tell me.

Q. Have you ever worked with an architect, for example, on your house or --

A. You bet.

Q. They refer to themselves -- sometimes you can go to an architect that design, and then you can go to a contractor, or you can go to one that does it all together, and that's called design build. Are you familiar with that?

A. Correct.

Q. And that's really what you're saying here, is that the intelligent designer designed and built, correct?

A. Right.

Q. Now you have stated that intelligent design has a positive case and a negative case?

A. Correct.

Q. And the positive case is based on the appearance of design in nature. Is that true?

A. Correct.

Q. And according to you, we infer design when we see a purposeful arrangement of parts?

A. Correct.

Q. Like a hand or an eye?

A. We're really restricted to the molecular level at this point. We don't know, you know, all of the variables involved in the eye or the hand. We look at molecular machines. Those are well-defined. All the parts are known. I'll leave it at that. At the molecular level.

Q. The focus of your thinking has been on molecular machines, I recognize that. But more broadly speaking, the intelligent design position asserts, as an illustrative proposition, that, for example, the hand is a purposeful arrangement of parts and, therefore, we can infer that the hand was designed?

A. I haven't made that assertion.

Q. Are you familiar with the Reverend William Paley?

A. I am.

Q. And Reverend William Paley posited the argument for the existence of God based on design in nature, correct?

A. Correct.

Q. And that's often times referred to, and if you look it up in the dictionary, you'll find it referred to as the teleological argument, right?

A. Correct, purpose.

Q. And you would agree, that's not a scientific argument?

A. Again, I think it is. It's addressing the question, is the design real or apparent? There are two answers to the question, both of them very interesting, and both of them are packed metaphysically. So, right. I think we can look now and start dissecting what are the properties of real design.

Q. So you understood -- you understand today, Dr. Paley's argument, as it's expressed in academic circles, as a scientific argument?

A. It's a philosophical argument looking at nature in that sense. It was the argument, I think, that was really important for Darwin to address. I don't think we can really understand Darwin's contribution until we understand the argument of design, that he was really supplanting with natural selection and variation.

Q. And intelligent design is making essentially the same argument that Dr. Paley made, except that it leaves God out, correct?

A. It doesn't identify who the designer is, okay. But I think the arguments are a little bit more sophisticated based on what we know now compared to what Paley knew.

Q. I'm anxious to discuss that with you, but it is essentially the same argument with God left out, correct?

A. To a degree in terms of addressing nature and asking -- seeing design and asking, is it real or just apparent.

Q. And just let me see if I understand the argument.

A. And it goes back to the Greeks. I mean, this argument didn't initiate with Paley.

Q. I just want to make sure I understand the argument. I'm walking through a field, and I find a cell phone. I pick up the cell phone. I say, that cell phone was obviously designed and, therefore, there must be a designer. That's the inference that I draw. And that's the basic argument of intelligent design, right?

A. That's the argument from Paley using a watch instead of a cell phone, but, yeah.

Q. I thought I'd modernize it.

A. Yeah, okay. Were there any minutes on it?

Q. That's essentially the same argument -- and just in its essence, the core, the reasoning, I'm asking, that's essentially the same argument intelligent design is making, right?

A. I'll agree with that.

Q. And in that argument, we see something created by -- the cell phone is, of course, created by a human, right?

A. Correct.

Q. So the design theorist sees an item that's designed by a human and the theorist knows about the creative and designing capacities of humans, right?

A. Right.

Q. And so it's a very logical inference to say, I know that that was designed by humans. I also know something about the creative or designing capacities of humans. And it's a very logical conclusion to say, that was designed by a human -- designed by intelligence and, therefore, there must be intelligence, right?

A. Correct.

Q. Now when we move into the natural world, things get a little different, because when we -- we don't know when we pick up a natural object whether it was designed by an intelligent agent, right? I mean, I recognize --

A. That's the question. That's the question.

Q. That's the question.

A. That's the question at bay here, right. I mean, we know what it takes to write software for an algorithm for your program to call up a specific routine. I'm saying, when I work with cells and look at the instructions, the algorithm to make a flagellum, it's pretty darn sophisticated.

In fact, it's more sophisticated than anything Microsoft has come up with yet. I know what it takes for software engineers, to a degree, although I'm not one, to write code. And here's a code that's much more sophisticated. Is this a product of the natural random events of chemistry and physics or is there a design behind it?

When we find information storage systems, in our own experience of cause and effect, day-to-day, by scientific reasoning, standard scientific reasonings, we can say, if we find code, that there's an intelligence associated with it. Again, where there's an alphabet, musical scale, numerals or symbols involved with mathematics, and here we have a true digital scale or code that's more sophisticated again than -- so that's -- yes, that's the argument.

Q. Let's return to that field for just a minute. And this time, let's -- we don't find a cell phone, but instead, we find a mouse. And we pick up the mouse. And we can feel the mouse's heart beating in our hands. And we want to know something about this mouse.

Well, would you agree with me that we don't know -- at the beginning of the argument for design, we don't know who created that mouse, who designed that mouse?

A. Correct.

Q. And we don't know anything about the capacities, desires, intents, or other characteristics of any designing intelligence, correct?

A. Not from looking at the mouse.

Q. And so, therefore, wouldn't you agree with me that the analogy between the cell phone and inferring the existence of human intelligence is not at all similar to looking at something in nature and inferring the existence of some intelligent agency? Wouldn't you agree with me? That's just not logical?

A. I disagree with you. I mean, you're dealing with a life organism versus an inanimate construct or contrivance by a human. In one sense, yes, they're different. But in terms of teasing them apart and looking at the inner workings of individual cells, I think we can infer, if we see the arrangements of parts for a purpose, that, in our own experience, we can infer design. It's perfectly legitimate. Tell me why it isn't.

Q. Luckily, or unluckily, for you, you're the one answering the questions today.

A. Correct.

Q. Now a few minutes ago, I suggested to you that intelligent design is just a strip down version of Dr. Paley's argument without the reference to God, right?

A. I wouldn't call it strip down. I think it's a little more sophisticated than Paley's original arguments. In fact, I find it interesting that Anthony Flew, who is the leading apologist for atheism in the UK, looking at the arguments from intelligent design, has decided that atheism is no longer a valid position for him, having, as a philosopher, worked in this area for 60, 70 years. He's in his 80's. It didn't require any religious conversion.

Q. Well, what I'm trying to explore with you, Dr. Minnich, is that -- and we'll talk about molecular biology some more at length in just a few minutes -- but that intelligent design, in its essence, is making, as you agreed with me previously, is making the same essential fundamental argument that Dr. Paley made, except it's not inferring the existence of God, it's just inferring the existence of design, correct?

A. Correct.

Q. And now you said -- and Matt, I'd like you to pull up that slide I just handed you. Second bullet point. You said in your direct testimony that the strength of the inference is quantitative. The more parts that are arranged and the more intricately they interact, the stronger is our confidence in design. Correct?

A. Correct.

Q. Now if I understand your argument, what you're saying is that, and this is what distinguishes your argument from Dr. Paley and the point you were just trying to make a minute ago, is that, you claim that science has discovered a lot more design than was around in Dr. Paley's time and, therefore, it's fair and logical to revisit this argument, although albeit without the reference to God, correct?

A. Correct.

Q. And, in fact, you say that the inference is quantitative, right? That's the word you used?

A. Right.

Q. That quantitative means, obviously, a quantity?

A. Right. I think it's -- the argument goes from our own experience with machines to the more complex a machine, the more difficult it is to modify.

Q. Well, I'm trying to get Dr. Paley's argument without God up in the modern times to understand it. And at the time that Dr. Paley wrote, there was very complex natural systems known then, correct?

A. Well, qualify that statement for me. What do you mean, in terms of --

Q. I'll give you an example from one of my -- I'd like to think he's an eminent forebear, but I'm not sure. Dr. William Harvey. Do you remember that name?

A. Correct, studied blood circulation.

Q. Right. He discovered the circulatory system for the blood, right?

A. Correct. And actually, he used the design inference to do it, because he saw the way that the blood system was constructed and looked at it as a plumbing problem really.

Q. And Dr. Harvey died in 1657, didn't he?

A. Correct.

Q. And so at the time that Dr. Paley was thinking about these issues, there were, in fact, some very complicated systems in nature that were known to him?

A. I would qualify that. I mean, they were complicated systems, especially based on the knowledge they had, whether you're talking about the eye, which we still view is very complicated, or circulatory systems. But I don't think -- I don't know what you're inferring.

Q. Well, you said in your direct testimony that there have been developments in the last 30 or 40 years, I forget what you said, in molecular biology that indicate a design that is much more than was previously known, and from that, it's fair to revisit this argument?

A. Well, I think just looking at Dr. Alberts' statement in his article, that his view of the cell as a graduate student, and his statement that we've always underestimated the cell. And that's -- I think that's a true statement.

Q. So there's been something that's happened over the last 30 or 40 years that, in the scientific world, that causes you and others to revisit the essence of the argument advanced by Dr. Paley?

A. Correct. That's fair to say.

Q. In fact, you claim that's developments in molecular biology?

A. Correct.

Q. And I think you said in your report that we've -- the last 30 or 40 years have been the golden age of molecular biology?

A. Correct.

Q. Now I'd like to know whether there was some event or some -- strike that -- some quantitative measure at which point it became appropriate to revisit the design argument?

A. That's a good question. No, I think it's a culmination of information from a number of different fields and the fact that you're seeing kind of a convergence in physics as well to come to some of these conclusions.

Q. So when we say quantitative as scientists --

A. I'm talking about specific molecular machines in reference to this. I'm not saying that there's a quantifiable number of papers that are going to trip the scale to intelligent design revisited versus our adherence to evolutionary biology as a sole explanatory source for what we see in nature.

Q. Well, you're also, or you'll admit, there's no quantifiable amount of design. We don't get to a certain amount of design after Dr. Paley and say, there's an objective measure of design, and we passed it, correct?

A. I think you can look and do it comparatively, maybe qualitatively compared to what we know that human engineers design compared to what we find in subcellular systems.

Q. There's no objective measure for design, true or false?

A. I think there is an objective measure for design. I mean, we use it. I think design engineers use it all the time.

Q. There's no objective quantifiable measure for design, true or false?

A. False.

Q. You agree with me -- let's move to a different subject now, Dr. Minnich. You agree with me that evolution is generally accepted in the scientific community?

A. I do, and I think it's a critical subject in my discipline, and I am -- I want to state for the record that I am fully behind the teaching of evolution, and I think that part of the problem is, we haven't taught it enough and critically enough.

Q. Would you agree with me that, in a public high school, it's appropriate to teach evolution?

A. Absolutely.

Q. Would you agree with me that, at a public high school, it's appropriate to teach all aspects of evolution, including the common ancestry between humans and other species?

A. Absolutely.

Q. Now a few minutes ago, we talked about the positive case for intelligent design, and I'd like to now talk with you about the negative case for intelligent design, right?

A. Okay.

Q. There is a negative case for intelligent design, right?

A. Well, let's discuss it. Tell me what you have in mind.

Q. Well, the negative case for intelligent design, according to you, is based on the inability of evolution to explain the overwhelming appearance of design in nature?

A. Correct, I made that statement.

Q. And have you ever heard of the two-model approach?

A. Yes, I have.

Q. And wouldn't you agree with me that, that negative argument for intelligent design is based on the two-model approach?

A. Not necessarily. I'd qualify it.

Q. Well, you're essentially saying, are you not, that we purport to be able to disprove or challenge evolution, and if evolution is wrong, therefore, it must be intelligent design?

A. No. I'm saying, I think that there are aspects of evolution that are very important in our understanding of nature, and I think intelligent design really addresses the mechanism of natural selection and variation as the generative force behind going from the simple to the complex.

It doesn't address common descent or even macroevolution. I think a lot of us are satisfied with that as well. But we lack the mechanism in the intermediates at this point.

Q. So intelligent design accepts some degree of change over time?

A. Oh, nobody is even debating that.

Q. But intelligent design is also suggesting that other aspects of the theory of evolution are either wrong or subject to challenge, correct?

A. In the aspect of natural selection and variationism mechanism to drive evolution from the simple to the complex.

Q. And the contention of intelligent design is, if that's true, what you just said, that evolution can't explain that, then that's proof for intelligent design?

A. I think it's consistent with an intelligence behind the complexity that we find in nature. It's a valid argument or derivative from that, yes.

Q. Wouldn't you agree with me that, it logically doesn't follow to say, if one proposition is untrue, that is the propositions about evolution that you purport to challenge, that from that it flows that it must be intelligent design? That's not logical?

A. No, it's perfectly logical. I'm saying that there is -- as I said yesterday, I think natural selection and variation is very important in terms of preservation of phenotypic characteristics. I'm not convinced it can generate the deep complexity of life that we find.

Let me put it this way. If you're a materialist or a naturalist, essentially, you believe in spontaneous generation. You believe that the Earth in its primordial condition produced all of the pre-cursors that allowed for the assembly of the first replicating organism that was dependent upon those pre-cursor compounds in this soup for its survival, and then turned around and taught itself how to do biochemistry and organic chemistry at a level that's more sophisticated than any chemist on this planet in terms of the specifities of the reactions, the yields, and the overall intricacy of those things.

So that's what -- that's at the level in terms of the logic that we're dealing with here. Okay. Do you believe that?

Q. Well, let's just say, suppose for just a second that the theory of evolution was proved to be wrong today. Then you would agree with me that that is no support whatsoever for the theory of intelligent design, right?

A. No, I would disagree. I would qualify that. If evolution is disproven -- I don't know what you mean by disproven. Common descent, macroevolution, adaptation. No one is questioning adaptational responses of organisms. Spontaneous generation or the first appearance of life, the origin of life.

If that's disproven, then you can infer an intelligence. But that doesn't rule out a natural cause. All you can say is, there may be an intelligence behind it at some level from the science.

Q. So you would draw from that negative argument about evolution a positive argument about intelligent design? Do I understand you correctly?

A. The positive argument is that we know when we find irreducible -- irreducibly complex systems or information storage and processing systems, from our own experience of cause and effect, that there is an intelligence associated with it.

And so, it is logical to assume, when we find these systems in a cell, if we can -- if the flagellum is irreducibly complex, then, yes, there's an intelligence behind it. That's a uniformitarianism deduction from cause and effect that we know from our everyday today experience.

Q. I'd like to discuss that with you, but it's a long subject, and I think it might be appropriate to take a break right now.

THE COURT: All right. Let's do that. We'll take our mid-morning break at this time. We'll return in about 20 minutes, and we'll pick up Mr. Harvey's examination. Are we on track, Mr. Harvey, to get this witness finished this morning?

MR. HARVEY: Yes, Your Honor. I have every intention.

THE COURT: With an appropriate time for Mr. Muise to engage in redirect and recross.

MR. HARVEY: Yes, Your Honor.

THE COURT: Do you want to say something?

MR. MUISE: No, I'm just waiting for the, all rise, Your Honor. I'm anticipating the break.

THE COURT: All right. See ya in a bit.

(Whereupon, a recess was taken at 10:15 a.m. and proceedings reconvened at 10:40 a.m.)