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Kitzmiller v. Dover Area School District

Trial transcript: Day 21 (November 4), AM Session, Part 2


THE COURT: All right. You may resume, Mr. Harvey.



Q. Dr. Minnich, through the peer review process, I learned that I misspoke in my examination, and that the Snoke-Behe article was, in fact, in the peer reviewed publication?

A. Okay.

Q. That was your understanding, that it was in a peer reviewed publication?

A. It was.

Q. But it doesn't actually mention either intelligent design or irreducible complexity, correct?

A. Right.

Q. And have you read it?

A. I read the abstract.

Q. So you didn't read the actual paper itself?

A. I haven't.

Q. And this morning, I was talking with you about whether there was an objective quantifiable measure for design, and I'd just like to restate the question. Are you aware of any objective quantifiable measure for the design of biological systems?

A. There are a lot of numbers that have been proffered, but they're all based on assumptions in terms of mutation rates and functions. So --

Q. No, I mean, for design. Are there -- there's no objective quantifiable measure for the design of biological systems, in other words, how much design there, is there, correct?

A. Well, that's a good question. You know, not that I'm -- I can't put my hand on a number, but --

Q. I couldn't either.

A. But again, I think -- let's look at it. It's an intuitive --

Q. Let's actually look at slide 13. This is a quote that you used in your direct testimony, and this comes from the paper by Lenski, Pennock and others, correct?

A. Correct.

Q. You focused on last, the highlighted quotation there?

A. I did.

Q. You bolded it as a matter of fact?

A. I did.

Q. Now to be fair, you did read the entire quote, including the sentence before it, but I want to just emphasize it. It does say, quotes, There now exists substantial evidence concerning the evolution of complex features that supports Darwin's general model, close quote. That's in there, correct?

A. These are, again, inferences. I don't know of the step-by-step, you know, mutation, selective scenario for any biochemical pathway.

Q. Right, but that statement is in there?

A. Right.

Q. And now I'd like, Matt, if you could bring up slide 14. And from that article and the quotation that I just read and the entire quotation, you draw the conclusion that we lack intermediate structures, we lack fossils, and we don't have adequate knowledge of how natural selection can introduce novel genetic information, correct?

A. Correct.

Q. Now with respect to fossils, you're not a paleontologist, right? We already talked about that.

A. I am not a paleontologist. But you read the literature, and that's one of the problems, that the intermediates are not present.

Q. But if a qualified paleontologist came into the courtroom and said, that's not true, you wouldn't be in any position to rebut that, would you?

A. I could look at some of the papers that I quoted, in Morris in particular. I mean, there are some molecular biologists that have hypothesized the lack of intermediate fossils was due to homeotic gene mutations in the production of hopeful monsters in that they never existed to explain why we can't find that. That hasn't panned out. But it's a recognized problem in terms of the fossil record.

Q. Now you said in your direct testimony with respect to intermediate structures, you said yesterday that we don't have the phylogenic history of any biochemical pathway or subcellular organelle?

A. Correct.

Q. The mitochondrion is a subset of your organelle, right?

A. That's correct.

Q. Please turn to Exhibit P-841 in your notebook. That's an article that was published in Science magazine in March of 1999?

A. Correct.

Q. And that's, of course, one of the leading peer review journals in the world, correct?

A. Correct.

Q. I'm going to ask Matt to highlight some of the -- the third sentence in the abstract, Matt, that begins, gene sequence. You're not aware of this paper, are you, Dr. Minnich?

A. I'm trying to remember if this was one that was mentioned in my deposition.

Q. I think it may have been. But in any event, this says, quotes, Gene sequence data strongly support a monophyletic origin of the mitochondrion from a eubacterial ancestor shared with a subgroup of the alpha-proteo bacteria, closed quotes?

A. Correct.

Q. Then if you would please look at figure 2 in this publication. Matt, could you go to figure 2? And actually, if you could highlight the first sentence. That says that, that neat little chart that we're looking at there is a tree of the phylogenetic relationships among mitochondria and alpha-proteo bacteria, correct?

A. Correct.

Q. So we do have the phylogenetic history of the mitochondrion?

A. No, we don't. This is inferred from sequence comparisons, and there's all kinds of problems inherent with this type of approach that some of the papers I use address this. If you look at ribosome--

COURT REPORTER: Could you slow down, please, and repeat that?

THE WITNESS: Sorry. If you look at -- you can get one phylogenetic tree. If you use some other parameter sequence or protein analysis, you can get another phylogenetic tree. So to say that this is the true phylogenetic history of mitochondria is incorrect.


Q. You've never published that in any peer reviewed scientific literature, have you?

A. No, I haven't.

Q. So you reject what this scientific, these scientists have published in Science magazine in favor of your subjective conclusions that have been published nowhere and shared with none of your scientific colleagues, true or false?

MR. MUISE: Objection, Your Honor. First of all, the question is extremely argumentative. I understand it's cross examination. But -- and it's assuming evidence that was not introduced into this testimony -- into his testimony. All -- he said, he gave his specific example of why this did not, does not purport to reach what it reached. And then he asked him a question, and we have to go back and review all the additional components he added to it, but it was certainly assuming facts not in evidence.

THE COURT: He asked whether he rejected what the scientists published.

MR. MUISE: That's correct, Your Honor. Then there was the follow-up question is my objection.

THE COURT: No, within the question that you objected to, he asked him whether he disagreed with what the scientists had published.

MR. MUISE: That's a fine question, Your Honor. I have no problem with that.

THE COURT: Then he went on to, in the balance of his question, he then went on to describe his methodology, and it is argumentative, but as you characterize, it is appropriate cross examination, and on that basis, I'll overrule the objection. Do you recall the question?

THE WITNESS: Could you --

THE COURT: We can have it read back.

THE COURT: Wendy, if you would.

MR. HARVEY: Let's see how argumentative it was. I forget.

THE COURT: Don't prompt me. I can reconsider.

(Whereupon, the court reporter read back the referred-to question.)

THE WITNESS: I want to qualify that, Steve. I mean, I can respect this type of work, but remember, when we're studying evolution, we're trying to figure out, you know, from a historic perspective, looking way back in time, and this is one tool that can be used in terms of sequence comparison.

But as I mentioned, and I'm not denigrating the work that these scientists have done. I mean, I respect what they've done. But we have to recognize that these types of studies have been done for the last 30 and 40 years. And as we get more information, it's revised.

My point is, the phylogenetic history, the true phylogenetic history is not revealed in this sequence comparison. It's an inference that may or may not be correct. Okay. And even in this point in terms of whether a prokaryotic organism can evolve into a mitochondria, I don't have any problem with that, you know, in terms of an evolutionary scenario.

I'm just saying, to use this and say, this is, you know, hard fact, this is how it happened, I don't even think these scientists would come to that conclusion solely on this.


Q. Well, they've published this article saying that these are the phylogenetic relationships?

A. Under the criteria that they're using to measure it. Then there are assumptions and inferences built into that, that I'm sure they would, they probably have qualified in this paper someplace. I haven't read it.

Q. So you're not agreeing with these scientists, are you?

A. I'm not disagreeing with them. I'm just saying that this -- when I say, a phylogenetic history, I mean, a true history, a historical account that we actually know. And we may never know it. And this may be the best guess. But that's the point.

Q. So are you looking for detailed explanation and evidence of every step along the way? Is that what you would need before you would accept that?

A. Not to that degree. But, I mean, a consistent history. There's a lot of inference in these types of things, and we've got to recognize that.

Q. These systems evolved, Dr. Minnich, over many years. Agree?

A. Oh, I agree. That's part of the problem.

Q. Over a billion years, correct?

A. Correct.

Q. And that's part of the problem, your testimony exactly, because it's hard to put together through science precisely what happened over a billion years ago? We don't have a video camera running?

A. This is the problem that we have in terms of studying evolution. As Ernst Mayer says, and I quoted him in my expert report, the normal laws in the natural sciences, experimental sciences don't apply to evolution when we're trying to figure out what happened at a deep distance in time, just built-in assumptions and inferences, and that's what we have.

Q. So the scientific community actually has done a lot of work in these questions of intermediate structures, but it's your testimony, it's just not enough because we haven't gotten far enough, is that correct, in the scientific world, I mean?

A. To a degree. I mean, I would qualify it.

Q. Okay.

A. I mean, again, if you're -- and I'm the first one to say that we look for a natural cause first, but --

Q. We'll come back to that. But you also testified about biochemical pathways, and you said we don't understand the evolutionary history of any biochemical pathway?


A complete pathway. There are adaptational responses that have been reported, and it's good science. You can take a recalcitrant molecule chlorinated by phenol that normally isn't broken down by organisms and expose organisms under selective condition and you can get a modified enzyme that will now cleave off that chlorine or introduce a new -- I mean, there are some slop in enzymes that can broaden in terms of sub straight recognition.

Q. So scientists have been looking at and do know a certain amount about the evolution of biochemical pathways, and that's reported in the peer reviewed scientific literature?

A. Adaptive responses for sure and looking at sequence comparisons of highly conserved pathways like glycolysis or the Krebs cycle. But in terms of the origin of those, we don't have a good history of it.

Q. Well, take a moment to look at what has been marked as P-842.

A. Got it.

Q. You've seen this paper before, haven't you?

A. I have. I think this was in my deposition.

Q. And these are some research from the Air Force Research Laboratory who did some work on the biochemical pathway by which certain bacteria breakdown a substance called DNT?

A. Correct. It's very important.

Q. That's like TNT, except this is dinitroluene, correct?

A. Uh-huh.

Q. These researchers, this was published in a peer reviewed scientific journal?

A. Yes.

Q. And if you look on -- at figure 1, which is on page 113. And Matt, perhaps if you can bring that up for us. These researchers, based on their own original data, have published the organization and evolution of the bacteria that breaks down DNT?

A. Right. This is an adaptational response.

Q. And that's a DNT -- this process by which these bacteria breakdown DNT, that's a biochemical pathway?

A. Correct.

Q. So we do have published information in this scientific literature about the evolution of biochemical pathways?

A. Steve, you're extrapolating from the data here. I mean, not all these enzymes evolved specifically to break down this compound. I mean, you're mixing and matching enzymes, I'm sure, from pathways that had some other property.

Q. You're not disagreeing with these scientists from the Air Force Research Academy, are you, Dr. Minnich?

A. This is an adaptational response, okay. This is microevolution. I have no problem with that. That's not what we're discussing. These enzymes were present. You probably modified one or brought some in by lateral gene transfer from another system that can attack these problems. I mean, this is critical.

The Air Force is working on this because TNT reservoirs in their munitions dumps are a problem for environment. And, yes, we can take organisms that -- and adapt them by selective pressure to modify enzymes that they have and attack these compounds. I have no problem with that.

Q. Well, you're the one who said, we lack intermediate structures, and now -- and you specifically mentioned subcellular organelles and biochemical pathways, and now we've seen literature that's in the scientific literature that addresses these points exactly. And if I understand your testimony, it's just not -- we just don't know enough to satisfy you that natural selection can drive the evolutionary process?

A. I don't think you understand my position, okay. I mean, this is an adaptational response. This entire pathway didn't evolve to specifically attack this substraight, all right. There was probably a modification of two or three enzymes, perhaps cloned in from a different system that ultimately allowed this to be broken down.

I mean, I've got good colleagues in my own department that are working on the same problem. And I don't think they pretend to know that the evolution of the pathway from start to finish in their system.

Q. There's a lot of work in this area of intermediate structures, isn't that true?

A. Right.

Q. Now if you go to -- well, actually let's just think back for a minute. One of the claims you made in addition to no fossil record and lack of intermediate structures, you also said that we don't have adequate knowledge of how natural selection can introduce novel genetic information, right?

A. The problem -- information is recognized in biological sciences as one of the major areas that we don't fully comprehend.

Q. I'm not talking about the origin of the gene or the origin of the genetic code. We may talk about that, if we have time later. But you said that we don't have any information -- we don't have adequate knowledge of how natural selection can introduce novel genetic information. That was your testimony, according to that slide, right?

A. That was the purpose of the Lenski paper addressing that specific paper with virtual organisms.

Q. That was your testimony, you say we don't have that, right?

A. It's a qualified statement. You know, I'm not going to make an absolute. Yes, you can get gene duplication. You have the immune system that can generate by cassette shuffling and differential in electron splicing. An incredible amount of diversity.

Q. Please look at has been marked as P-245.

A. Is it up front or --

Q. It's to the front. And we can bring it up in the system.

A. Got it.

Q. Do you have that in front of you?

A. Yes.

Q. You've seen this article before, haven't you?

A. Yeah. I think this was at my deposition as well.

Q. This is an article that was published in Nature Reviews, which is affiliated with Nature, the journal, and it's by a scientist by the name of Manyuan Long and others, right?

A. Correct.

Q. Manyuan Long is at the University of Chicago, isn't he?

A. I'll take your word for it.

Q. Well, he's a very eminent scientist as well?

A. Right.

Q. He's done a lot of work on the origin of how natural selection can introduce novel genetic information, isn't that true?

A. That's not my specific area, but, right.

Q. And I'd like to just read you a quote from Dr. Long's paper here, the paper with others. The first, not the abstract, Matt, but the first paragraph of this paper.

These scientists say, quotes, Although interest in evolutionary novelties can be traced back to the time of Darwin, studies of the origin and evolution of genes with new functions have only recently become possible and attracted increasing attention.

The available molecular techniques and rapidly expanded genome data from many organisms means that searching for and characterizing new genes is no longer a formidable technical challenge.

Also, molecular evolution and molecular population genetics have provided useful analytical tools for the detection of the processes and mechanisms that underlie the origin of new genes. Do you see that?

A. I see it.

Q. And wouldn't you agree with me that, there is a great deal of scientific information that's published in the literature by Dr. Long in particular, but others as well, on the subject of how natural selection can introduce novel genetic information?

A. Correct.

Q. In fact, this paper cites 122 references. Do you see that?

A. Well, I'll take your word for it.

Q. Now turning to the subject of design engineering, which you covered in your direct testimony. I'm afraid we won't have time to discuss the subject of your testimony in as much detail as I'd like. I'd probably take more than a day, but --

THE COURT: We can only hope not. We'll keep within our time frame.

MR. HARVEY: No, Your Honor, actually we've spoken together, and I'm going to try to stop by 11:30, if not sooner.

THE COURT: All right.

MR. HARVEY: Matt, can you bring up that slide, please?


Q. This is the slide you used in your direct testimony, isn't it?

A. Correct.

Q. And so it's your testimony, as set forth on this slide, the last bullet, that Dr. Alberts advocates incorporating design engineering into our biology curricula as a means to dissect the interactions of the macromolecular machines now identified in even the simplest cell, right?

A. Correct.

Q. Yesterday, you told me that you put your report together in a hurry, didn't you?

A. I did, yeah. I had a time constraint.

Q. Did you have a chance to examine Dr. Alberts -- did you read Dr. Alberts --

A. I read Dr. Alberts' paper and, in fact, if you want to -- I'm inferring this from one section, if you want me --

Q. Yeah. Please, Matt, pull up P-725.

A. Okay.

Q. Now this is Dr. Alberts' paper that you were referring to, correct?

A. Correct.

Q. And if you go to the end of this, the very last page of the paper, Matt, please, of the text. Now you say this paper stands for that Dr. Alberts advocates the incorporation of design and engineering into our biology curriculum.

What Dr. Alberts says actually is, quotes, Most important for the future of our field, the departmental structures at most universities seem to have thus far prevented any major rethinking of what preparation in mathematics, what preparation in physics, and what preparation in chemistry is most appropriate for either the research biologist or the medical doctors who will be working 10 or 20 years from now.

The result is a major mismatch between what today's students who are interested in biology should be learning and the actual course offerings that are available to them. It is largely for this reason I believe that so many talented young biologists feel that mathematics, chemistry, and physics are of minor importance to their career.

It is my hope that some of the young scientists who read this issue of Cell will come to the realization that much of the great future in biology lies in gaining a detailed understanding of the inner workings of the cells, many marvelous protein machines.

With this perspective, students may well be motivated to gain the background in quantitative sciences that they will need to explore this subject successfully. Do you see that?

A. I do.

Q. He's not talking about design engineering, is he, introducing design engineering into the biology curricula?

A. If you look at the acknowledgments, I am indebted to Jonathan Alberts for his explanations of how engineers analyze machines. On the other part, if I can find the right quote, at the heart of such methods is a simplification and the idealization of a real world machine as a composition of discreet elements.

Engineers recognize certain fundamental behaviors in nature and then create an idealized element to represent each of those behaviors. Most simply, they classify elements as those that store kinetic energy, and those that store potential energy, and those that dissipate energy.

Any particular part of a machine might be modeled as consisting of one or more of these basic constituent elements. It seems reasonable to expect that different, but analogous approaches, could probably be applied to the protein machines that underlie the workings of all living cells.

This is an engineering approach to looking at the intricate coordinated interaction of molecular machines. And I agree with him. The reason that we need chemistry and physics and mathematics is because these are required rigorously in an engineering curriculum.

Q. But my point was a little different. My point is that, you have rather fundamentally misread Dr. Alberts and fundamentally not stated correctly what he's saying in this paper. He nowhere advocates the incorporation of design engineering into our biology curriculum. He's clearly discussing physics, mathematics, and chemistry. Isn't that true?

A. No, it's not. If you read this paper carefully, he's saying that we have to approach the intricacies of the cellular machines much like an engineer systems analyst approaches the workings in a factory or some other assembly.

Q. We don't have time to read the paper together, but -- so we'll perhaps, later today we can do that. But --

MR. MUISE: Your Honor. The witness has answered the question, and he interrupted him. I'd like to have the witness completely answer the question before he interrupts him.

THE COURT: Did you finish your answer?

THE WITNESS: I did. I want to say that, I read this paper carefully. I think it's profound, and I agree with Dr. Alberts, you know, as he's saying in here, the age of cloning and DN A sequencing is over. We're going into (inaudible) and the hard core analysis of these machines, and we're going to have to take a different approach. So --

THE COURT: I'm sorry. You can finish.

THE WITNESS: I'm done.

THE COURT: All right. Next question.


Q. Just one final point before we move off this article. On the first page of this -- and, Matt, if you could go to the first page. In the lower left-hand column at the bottom, where it says, ordered movements. And he says, quotes, Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like the machine invented by humans to deal, etc. So just to rehit a point that we hit this morning. This is talking about being -- these protein assemblies being like machines invented by humans, correct?

A. That's correct.

Q. Now you claim that intelligent design can be tested, correct?

A. Correct.

Q. Matt, please bring up slide 40. And that's your claim right there that you put up during your direct testimony to state that intelligent design can be tested, right?

A. Right. I think it's falsifiable.

Q. And neither you nor Dr. Behe have run that test, have you?

A. We talked about that yesterday. And I even, I think, gave a -- an experiment that would be doable. And in thinking about it last night, I might try it to see if I can get a type III system to change into a flagellum.

Q. You haven't run that test, right?

A. I've done parts of it. I know that the type III secretory system will secrete flagellum.

Q. True or false, you haven't done that test?

A. No.

Q. Correct? You haven't done that test?

A. What's the point? I mean --

Q. I'm asking you whether you have done the test that you propose for intelligent design? That's a yes or no question.

A. No, I have not.

Q. Okay. Now Dr. Behe hasn't either, has he?

A. I'm not aware of it, no.

Q. And yesterday, Mr. Muise read a statement to you that was read to the Dover High School biology students that said that a scientific theory is a well-tested explanation, correct?

A. That's part of the definition, yes.

Q. And you agreed that, that was the definition of scientific theory, it includes the concept of being well-tested, correct?

A. Again, I would qualify that by saying, we're in a different arena when we're talking about evolution. The experimental sciences aren't necessarily -- can be directive of this. It's a historical science.

Q. I'm just asking you if you agree, just asking you, reminding you and asking you to confirm that yesterday, you said that a scientific theory has to be well-tested, correct?

A. Well-tested or consistent with the information that we have. This, again, I think, in this situation, a lot of evolutionary science wouldn't fit your definition of science as well.

Q. And I take it, you see where I'm going with this. Intelligent design, according to you, is not tested at all, because neither you nor Dr. Behe have run the test that you, yourself, advocate for testing intelligent design, right?

A. Well, turn it around in terms of these major attributes of evolution. Have they been tested? You know, have they been tested in terms of identifying macroevolution? You see what I'm saying, Steve? I mean, it's a problem on both sides.

Q. Actually, we're going to talk about that in just a minute. But right now, I'm just asking you to agree with me that intelligent design doesn't qualify as a scientific theory, because it's not well-tested, it's not tested at all?

A. I wouldn't say that it isn't tested at all. There's some papers that have been published that deal with some of the questions of evolution and from a design perspective.

Q. You told us, this was the test, didn't you?

A. This specific test, no, has not been done.

Q. Now this test actually is not a test of intelligent design, it's a test of evolution, isn't it?

A. Yes.

Q. And what you're suggesting here is that, scientists should try in their laboratories to grow a bacterial flagellum, to watch it evolve and develop in their laboratories, right?

A. The point of this point is that, if the flagellum is not irreducibly complex, you should be able to develop one.

Q. In a laboratory?

A. In a laboratory.

Q. Now some scientists live to ripe old ages, right?

A. Yeah, they do. Some don't.

Q. How long have bacteria been on the Earth?

A. Since -- I think 3.8 billion years is the estimate.

Q. So you're suggesting that, to prove evolution, someone should in a laboratory do what it took the entire universe or could have taken the entire universe and billions of years to accomplish, isn't that what you're suggesting?

A. No, not really. This is -- I mean, let's be realistic here. Getting an organism versus an organelle is quite different. And like I said, I would say, take a type III system with a missing flagellar components and see if they can assemble into a functional flagellum. That's a more doable experiment than Mike has proffered here.

Q. Yesterday, you said that evolution cannot explain the origin of life, the origin of the genetic code, or the structure and development of life. Did I hear you correctly?

A. Correct.

Q. And would you agree with me that those are some fundamental scientific issues?

A. They are.

Q. And they're fundamental scientific issues that have not been answered by science, right?

A. People are working on it.

Q. That's right. Scientists are working on these and many other fundamental questions of science, right?

A. Correct.

Q. Intelligent design can't answer these questions, can it?

A. They can be inferred. I mean, look at it this way. We know that the smallest free living organism, the microplasma, have on the order -- (inaudible) is doing these experiments right now on the order of 350,000 nucleotides in their genome. So to be an independent, free-living organism, you've got to have that much information.

He's doing mutagenesis to find how many genes can actually be knocked out in this smallest free-living organism to determine that irreducibly set of genes required. That's a problem. To be a replicating organism, you've got to have all this information at a minimum.

Q. You're not aware of any scientists that are trying to use the theory of intelligent design to solve these fundamental scientific issues, are you?

A. I think that -- from a theoretical standpoint, looking at these in terms of developing the questions and the systems to look at. I mean, give us a chance, all right.

Q. None of that research is going on right now, is it?

A. Some of the work. The theoretical work is. I mean, Mike Behe published this paper. Axe published his paper in terms of evolution and proteins. That addresses these issues.

Q. Would you agree with me that a fundamental proposition of intelligent design is that it wants to suggest that an unspecified intelligent agent is responsible for -- let me withdraw that and restate it --

A. Okay.

Q. -- so that you can agree with it. Would you agree with me that a fundamental proposition of intelligent design is that it wants to insert an unspecified intelligent designer as the answer when it finds questions which science has not yet answered?

A. I would qualify that again, Steve. I guess I can see where that seems to be a leading question. In other words, you're saying, it's an argument out of ignorance. And I don't think it is. Again, it's an argument out of our common cause and effect experience where we find these machines or information storage systems. From our experience, we know there's an intelligence behind it.

Q. So, for example, with the -- with respect to the origin of life -- actually, let's make sure we understand. When we say, the origin of life, we mean the beginning of life on this planet, correct?

A. Right, if it's 3.8 billion years, there was prokaryotes that appeared, and they were independent self-replicating organisms.

Q. Some people refer to this loosely as the prebiotic soup?

A. Prior to that, yes.

Q. Are you saying that intelligent design posits that the source of the origin of life is the intelligent designer?

A. Yes, yes. It doesn't specify who it is. I mean, you can have panspermia, according to Crick, Spores being blown in by solar winds. But I think --

Q. But the scientific answer to the question of the origin of life or the origin of the genetic code or the development in structure of life is not that the intelligent designer did it, it's that science is still looking at these fundamental scientific questions, working on them, and thinking that, some day, we might have the answers to these questions. Isn't that a scientific approach to that question?

A. Steve, I said yesterday, as a scientist, you always look for a natural answer first. But I have in my hotel room a textbook that I am reviewing on genomes. In there, there is a chapter on the origin of genomes. I wish I had it to read to you. It's all conjecture and assumption and given this, then this. There's not a lot of fact there. Okay.

So this has been a very recalcitrant problem. And we're dealing with again the origin of information. And we know again, from our experience, information-rich systems are associated with intelligence. So we look for a natural explanation, but we're drawing blanks.

Q. So if I understand this, we have fundamental scientific questions, science looks for natural explanations, has many, many scientists working on this, publishing in peer reviewed journals, and doesn't have any definitive answers. Intelligent design says, the intelligent designer did it. That's really what we're talking about here, isn't it, Dr. Minnich?

A. It goes back to the basic question. The design that we see in nature, is it real or apparent? Okay. Is there a natural explanation for what you're asking? To this point in time, there isn't. Now I don't think that's a negative statement, but I again would emphasize, from our experience of cause and effect, when you have a code, you've got a coder behind it. And this is the most sophisticated code that we're talking about.

Q. Does intelligent design make any scientific predictions?

A. It does.

Q. Like what?

A. Well, I wish I had my computer with me. I've got a whole list of them in terms of predictions that people in this area are working on. My prediction in working on type III secretory systems before was that flagellum could be used as a machine to secrete other than flagellar proteins. Before we even knew what type III secretion systems were, we were predicting that the TTSS was either the flagellum basal body or something that looked exactly like it. That turned out to be true.

Yersinia passasist is non-modal. We made a prediction that it would (inaudible) the organism to express flagellum inside a host cell, and I think we have good evidence for it. E-coli 0157, very virulent strengths coming out of Czechoslovakia and Germany are non-modal.

I had a bet over a beer with a microbiologist, director of microbiology at the FDA, that the mutation would be in --

COURT REPORTER: Hold on, please.

THE COURT: While she's doing that, we'll think about what the things are that people bet over.

THE WITNESS: I got a beer out of it. So in terms of, you know, junk DNA, I mean, there's some predictions in that area as well. In terms of mutational rates, there's some predictions.


Q. You're referring to work that you do in your laboratory, right?

A. The work, the stuff that I just referred to, yes.

Q. Now you made three claims here in your testimony. You claim that some -- you may have made others, but these are three you've made. You've claimed that some biological systems are irreducibly complex, right?

A. Correct.

Q. And you claim that irreducibly complex systems cannot evolve, right?

A. I didn't say that. I didn't say that.

Q. Well, you're claiming that irreducibly complex systems were intelligently designed, right?

A. It's a hallmark of intelligence. When we find them, by experience, there's an intelligence associate with them. You can have an aboriginal structure, and it can evolve or adapt as required of the organism. And I am not against the fact that the type III secretory system could have been co-opted from the flagellum.

Q. But in your work as a scientist, your day job, if you will, you only -- the only principles you use are the principles of what you call irreducible complexity, right?

A. I think that's -- as I mentioned, that's -- it uses a molecular in terms defining genes involved in a specific system.

Q. And some people in the, who do what you do, would refer to these as knockout techniques, right?

A. Pardon me? I didn't hear.

Q. Some people who do what you do would refer to these as knockout techniques?

A. Correct.

Q. And they're -- the specific techniques are mutagenesis and genetic screen and selections?

A. Correct.

Q. And these are standard techniques used in biology and microbiology?

A. They go all the way back to Beatle and Tatum.

Q. Would you agree with me, if you ask most scientists who work in the field and use these techniques, if they use intelligent design principles, they would not know what you are talking about?

A. I don't think they would interpret them in that reference. But it's consistent with the idea of irreducible complexity. If these systems weren't irreducibly complex, you know, mutagenesis wouldn't work.

Q. Does intelligent design recognize the age of the Earth?

A. Does intelligent design recognize the --

Q. Yeah, does the intelligent design theory recognize the age of the Earth?

A. I'm not sure what you mean by that question.

Q. The Earth is 4.5 million years old, give or take a year or two, right?

A. Right, I don't have a problem with that.

Q. Does intelligent design theory accept the age of the Earth?

A. Yes.

Q. Are you familiar with Of Pandas and People?

A. I am.

Q. We already looked at that. Please take a look at page 92. It's your understanding that Pandas is a representative of intelligent design, right?

A. Yes, although, as we mentioned before, it's dated.

Q. Matt, if you -- actually, we can pull it up on the screen. Matt, at the lower right-hand corner. The sentence that begins, while design proponents. It says that, While design proponents are in agreement on these significant observations about the fossil record, they are divided on the issue of the Earth's age.

Some take the view that the Earth's history can be compressed into a framework of thousands of years, while others adhere to the standard old-earth chronology. Do you see that?

A. I see it.

Q. So that says that design proponents are split on that topic?

A. There are some young-earth creationists in the intelligent design community.

Q. Does intelligent design tell us how things were designed or created?

A. No, they're inferred.

Q. Does intelligent design tell us how the bacterial flagellum was designed or created?

A. No.

Q. Intelligent design doesn't ask who the designer is, does it?

A. No.

Q. That's a religious question?

A. Correct.

Q. There are no studies or experiments that can be done to find out the nature of the intelligent designer, correct?

A. Correct.

Q. Does intelligent design ask any questions about the abilities of the intelligent designer?

A. Not that I'm aware of.

Q. Is that a religious question?

A. Yeah, I would assume so, right.

Q. And the same with the limitations of the designer. The intelligent design doesn't ask any questions about the limitations of the designer, does it?

A. I'm not sure what you mean by limitations.

Q. Ability to do things or limits on abilities to do things. Does the intelligent design tell us anything about the limits on the abilities of this intelligent designer to design and create?

A. Not that I'm aware of, no.

Q. Does intelligent design tell us when the intelligent designer designed and created life and living things?

A. No.

Q. Do you believe that the intelligent designer intervened at various points in the history of the Earth?

A. Are you asking me personally or from a -- from the intelligent design community? I mean, there's --

Q. From the intelligent design community?

A. I mean, there's positions all over the spectrum.

Q. Is it -- does intelligent design tell us how many designers there are? Is it just one or could it be more?

A. It could be more.

Q. So it could be a whole family of designers, right?

A. I suppose so.

Q. It could be competing designers? We could have one designer who's designing good things and another designer who's designing bad things, right?

A. I don't -- yeah, what's your point?

Q. Well, does intelligent design tell us whether there could be --

A. No, no.

Q. -- both multiple designers? Are they all working for the same purpose? Does intelligent design tell us anything about that?

A. No, it doesn't.

Q. So it's possible that there is an evil designer, isn't that true?

A. The problem of the Odyssey is a theological question. I don't know where you're going with this, Steve. You know, I suppose so. I mean, from our common experience, yeah, technology is double-edged.

Q. Is there any scientific intelligent design research program going on to determine when the designer acted or she acted or they acted; how he, she, or they acted; why he, she, or they acted; or who he, she, or they are?

A. No. No.

Q. Would it be fair to say that intelligent design does not exclude the possibility of a supernatural cause as the designer?

A. It does not exclude.

Q. And, in fact, a designer could be a deity, correct?

A. It could be.

Q. And that would clearly be supernatural, right?

A. Right, but that's -- that would be a philosophical addition to that science isn't going to take, isn't going to tell us. I think I made that clear.

Q. But intelligent design holds open the possibility that the designer might be supernatural?

A. Flip it around. If you're a true naturalist, then you can use your data to argue for atheism or materialism. So regardless of which side you fall on this question, there are metaphysical implications.

Q. Intelligent design theory specifically holds open the possibility that the designer is supernatural, true or false?

A. True.

Q. Do you agree that the current rule of science is methodological naturalism?

A. Do I agree that that's the --

Q. That's the current rule of science, isn't it?

A. That's a definition of science that has not always been in place. It's the standard technique that we use again looking for a natural cause.

Q. That's the current definition of science and has been for sometime, correct, not definition, the current rule of science?

A. I think the current rule is coming from the Aguillard decision in Arkansas from my understanding.

Q. Well, actually in the scientific world, methodological naturalism has ruled for quite a long time before the Supreme Court made that decision, isn't that true?

A. Right, but I think it's a definition that would perhaps surprise Newton and Keplar and other scientists that have --

Q. And in order for intelligent design to be considered science, the definition of science has to be broadened to consider supernatural causes, true?

A. I want to qualify it. Can I qualify it? Again, if you go back to the basic question, we see design in nature. Is it real or apparent? If you are only going to accept natural causes, then you've just removed half the equation, so you're not going to see it, even if it's staring you in the face. So in that aspect, that's a definitional fiat.

Q. Well, the answer to my question, and I understand you had a qualification, was true. For intelligent design to be considered science, the definition of science or the rules of science have to be broadened so that supernatural causes can be considered, correct?

A. Correct, if intelligent causes can be considered. I won't necessarily -- you know, you're extrapolating to the supernatural. And that is one possibility.

Q. I only have 45 seconds left, Dr. Minnich.

A. Okay.

Q. Would you agree that the theory of intelligent design takes us only as far as needed to prove or to infer the existence of an intelligent designer and then it stops there and that's where theology takes over? Would you agree with that?

A. Philosophy or theology.

MR. HARVEY: No further questions.

THE COURT: All right. Thank you, Mr. Harvey. And we'll have redirect from Mr. Muise.



Q. Good afternoon, Dr. Minnich. I know you've been up there for a long time, and I'll try to get through this as rapidly as I can, consistent with the court reporter being able to take down my rapid speech.

Dr. Minnich, yesterday you were asked about an article, and I believe it was a -- it was marked as Plaintiffs' Exhibit 853. If you could look on the exhibit binder that you have there. And if I'm referring to the correct one, it's the one that had some explanation of the bacterial flagellum?

A. I remember the paper.

MR. HARVEY: We'd be happy to put them up there, if that would be helpful.

THE WITNESS: I got it.


Q. Do you have that article, sir?

A. 853? Got it.

Q. Is that the one that had the diagram of the bacterial flagellum?

A. Yes.

Q. Now during the questioning by Mr. Harvey, he was comparing the explanation, more likely the description of the bacterial flagellum in that particular article, which, I believe, was described as a creationist article, with your diagram, as he was referring to it. And I have it up here on the slide, and the diagram also is Defendants' Exhibit 203-B.

And I believe you drew some comparisons of how this diagram resembled the diagram in the article as well as the way it's labeled on Exhibit 203-B and the way it's labeled in that article that was described as a creationist article. Do you recall that, sir?

A. I do.

Q. There are similarities in the labeling between the two?

A. Yes.

Q. Now the diagram that he described as your diagram, where is this diagram from, Exhibit 203-B?

A. It's from a standard biochemistry textbook, because you see down in the right-hand corner, Voet and Voet.

Q. Is Voet and Voet a creationist textbook?

A. No, no. That's the most popular biochemistry textbook.

Q. And the labels that appear on this diagram, are those labels that you put on or are those labels that Voet and Voet regarded or used to describe the aspects of the flagellum?

A. Those are in the textbook.

Q. And those labels that are in the textbook, are those the same labels that the scientific community uses to identify those parts of the flagellum?

A. Yes.

MR. HARVEY: Objection, Your Honor. Leading. I don't mind him leading to develop the testimony, but that's a -- that's beyond developing the testimony, and that's the conclusion.

THE COURT: We'll note that. But he answered the question. I'll overrule the objection, and we'll move on.


Q. Sir, in your direct testimony, we referred to an article by, I believe it's David DeRosier, is that correct? Is that his name?

A. Correct.

Q. It's marked as Defendants' Exhibit 274. And the title of the article was Turn of the Screw, The Bacterial Flagellar Motor. And in your testimony, you referred to a quote, More so than other motors, the flagellum resembles a machine designed by a human, end quote. Was that a direct quote from out of the article?

A. It was.

Q. It David DeRosier a creationist?

A. Not to my knowledge.

Q. And where did this article appear?

A. In Cell.

Q. Cell journal?

A. Right.

Q. Is that a creationist journal?

A. No.

Q. You were asked some questions about peer reviewed articles and whether there's peer review articles that mention intelligent design specifically, and you indicated in your response to Mr. Harvey that there was some risk. What are the risks?

A. I think --

MR. HARVEY: Your Honor, I'm going to object on the grounds of relevance and hearsay, if that's where he's going.

MR. MUISE: Your Honor, I mean, it's only fair. If he's going to challenge him about articles being in there, and he's claiming there's risks, he has every right to explain what those risks are, to complete the testimony as to why there aren't the intelligent design or calling intelligent design. And I think he's somebody that's in that community that has to publish, and he obviously feels there's risks.

THE COURT: I'll give you some latitude. I'll overrule the objection. You can answer the question.

THE WITNESS: There is risks. I mean, there's career risks involved. Even as -- this paper that I submitted for this conference in Rhodes Greece, we included a section on the philosophical implications of the flagellum. I thought long and hard about submitting that, because of the implications being identified publicly as a design adherence.

In fact, I wrote that when I was in Baghdad, and I was ready to send it and debating whether I would do it. I think I mentioned in my deposition, we came under a mortar attack, and I hit the send button saying, I might not be here tomorrow anyway, so be it. You know, it is risky business. I think it's risky for me to be at this trial in terms of the fallout that I've had in my own institution.


Q. Sir, you were asked a question of who you thought the designer was, and you said your personal opinion was that it was God, is that correct?

A. Correct.

Q. Was that a scientific conclusion or a scientific opinion?

A. No.

Q. Now we've heard testimony in this case that Dr. Ken Miller, one of the Plaintiffs' experts, he testified that God is the architect of the natural law, which he believes is what drives evolution. Is Dr. Miller's non-scientific personal opinion regarding God as being the architect of the laws that drive evolution, is that any different than the opinion that you're offering here?

A. I would -- I'd have to -- I mean, I think Ken and I are in pretty close agreement, except on the degree of intervention from our own personal concept of a God.

Q. But in terms of the nature of the opinion, being a non-scientific claim, is it similar to --

A. Right, right.

MR. MUISE: May I approach the witness, Your Honor?

THE COURT: You may.


Q. I'll hand you what has been marked as Defendants' Exhibit 223. Do I have the right number on the front cover there, sir?

A. Yeah.

MR. HARVEY: Your Honor, may he just wait one second while I get the actual exhibit here?


Q. Open to page 292, please. And this exhibit is a book, Finding Darwin's God, written by Kenneth R. Miller, correct?

A. Correct.

Q. Would you read the last three sentences on page 292?

A. Starting with, there is grander?

Q. No, what kind?

A. Oh. What kind of God do I believe in? The answer is in those words. I believe in Darwin's God.

Q. So Dr. Ken Miller believes in Darwin's God?

A. That's what he says. I haven't read this book, so I don't know what that means.

Q. Does that claim make evolution a religious belief?

A. I don't know how to respond to that. I don't think so.

Q. Now Mr. Harvey was asking you questions about the fact that -- he was using terms of construction, creation, building, and in terms of intelligent design, and how life may have first arose. In terms of evolution, at some point, life had to have been constructed, built, or created, is that true?

A. True.

Q. So should we describe evolution as creation-evolution?

A. No, no.

Q. So those sorts of labels are misrepresentative, are they not?

A. Right.

Q. Now you asked some questions about Paley's, Paley's arguments, correct?

A. Yeah, Paley was brought up.

Q. Was he making an argument based on logic or an argument that was theology?

A. It was based on logic, inference to our common experience.

Q. And I believe you said that went back to the Greeks, is that correct?

A. Right.

Q. Now you were given a hypothetical scenario about walking through the woods and tripping over a cell phone, I guess, to modernize the example, according to Mr. Harvey. Do you remember that little discussion you had with Mr. Harvey?

A. Right.

Q. You said, based on, I believe, the nature of that cell phone, you could infer some design, correct?

A. Right.

Q. Now from an evolution perspective then, if you tripped over this cell phone, you would have to conclude that at some point, there was Paley's watch, however many years ago, is that correct?

MR. HARVEY: Objection, Your Honor, continue leading of the witness. This is on issues of the nature of their theory, and I don't think it's appropriate for Mr. Muise to testify in the form of cross examination.

THE COURT: Why don't you rephrase? I think it was somewhat leading. I'm going to give you some latitude because of the time constraints we have placed, but I think that's unduly leading. I'll sustain the objection.


Q. From an evolution perspective, if you came across the cell phone in the woods --

A. I think I understand. In terms of what would the pre-cursor? I mean, there would be -- you know, I don't know if I want to go there.

Q. Would Paley's watch, if it came before in time, necessarily have to be some sort of a pre-cursor under an evolutionary perspective?

A. Yeah, I don't know. I mean, to a degree, when we look at these machines and where they came from, you have to assume that it evolved from some pre-cursor. So it could be in a general sense equivalent to a watch evolving into another machine.

Q. Using that example, has the theory of evolution demonstrated a step-by-step process by which you could have a Paley's watch become a cell phone?

A. No, it hasn't. In fact, I think that's one of the interesting things in the Morris paper. When he looks at something intricate, developmental pathways, he likens it, in terms of one interpretation, as there's a tool box with a given set of tools that can be plugged into the requirements for the specific organism.

It's almost -- it's kind of an analogy to an engineering type of thing. And I think Jim Shapiro refers to that in some of his more recent papers.

Q. Taking that scenario to a living. I think you used a mouse. You would have to, for example, have a pathway that would develop a bacterial flagellum into a mouse, is that correct?

A. Well, I mean, that's -- the first organisms were prokaryotic, so in terms of the evolutionary history, yeah, you've got to have intermediates that lead to an organism that can contemplate its own existence, I guess.

Q. Do we presently have those pathways?

A. No.

Q. Now are you the only scientist who makes a claim that we don't have an adequate phylogenetic history of a subcellular organelle?

A. No.

Q. Are there others that you had mentioned in your direct testimony?

A. Right. I think we referenced several of them.

Q. Do you recall some of the names of those scientists?

A. Harold, Shapiro. And I think it's even eluded to in the paper by Lenski.

Q. Are any of those scientists intelligent design advocates?

A. No.

Q. Dr. Minnich, you were asked about this summary slide that I put up here, particularly that third bullet point. We do not have adequate knowledge of how natural selection can introduce novel genetic information. Are you the only scientist that has that particular view?

A. No. I mean, it's an active area of research.

Q. Was that a point that you derived from the Lenski paper that appeared in Nature?

A. Correct.

Q. I believe this article actually appeared in 2003, correct?

A. Correct.

Q. Sir, you were asked the question about methodological naturalism and the definition of science and whether or not the definition of science would have to be expanded to include supernatural causes in order for intelligent design to be considered. Do you recall that testimony?

A. Right.

Q. In what sense were you using supernatural causes in your answer?

A. I think anything above our normal experience.

Q. Using that understanding of supernatural causes, would that include, for example, Francis Crick's hypothesis of direct panspermia?

A. Correct.

Q. And would that also include the program of NASA, the SETI program, Searching For Intelligence?

A. Correct.

Q. Isn't it true, from a scientific perspective, those two that I just mentioned in which you consider as part of the supernatural are actually considered natural explanation?

A. Right, in actuality, it would be.

Q. So in essence, the definition of science need not be changed to actually include intelligent design, is that correct?

A. No.

Q. Is that correct?

A. Yeah, that's --

Q. Is that correct, sir?

A. Correct.

Q. Now when you were talking about extrapolating or making logical inferences based on our common experience to reach a conclusion, a scientific conclusion, you were saying, that's sort of the logical inference that intelligent design makes, is that correct?

A. Correct.

Q. Though I'm hesitant to raise this, I want to revisit the Big Bang. We might as well finish with a bang, Your Honor, since it's the last day.

THE COURT: We've had the flagellum, son of flagellum return, we might as well have the Big Bang.

MR. HARVEY: Let me object on the grounds that any questions about the Big Bang are outside the scope of the cross examination and, I believe, also outside the scope of the original direct.

THE COURT: I'll allow you to try to tie it in.

MR. MUISE: It's regarding the inference, Your Honor.

THE COURT: Why don't you get a question on. Then you can object to the question. The mere mention, although I understand why it has triggered an objection, is not good enough. Let's let Mr. Muise get a question on the floor.


Q. Are you aware of the logical inference or the scientific inference that was employed in the Big Bang theory?

A. Right, in terms of extrapolating back from an expanding universe to a point of singularity, but it appears to be like an explosion, from our experience.

Q. Do we have any common experience of universes exploding?

A. No, no. You know, if I could expand just a little bit in terms of, methodological naturalism can put a stricture on a number of scientific endeavors in terms, as you elude to, the Big Bang. Super strings employs multiple dimensions that are outside of our experience, but it doesn't stop physicists from working on these ideas.

So, you know, there is some latitude in terms of scientific inquiries that are beyond the aspects of methodological naturalism.

MR. MUISE: I have no further questions, Your Honor.

THE COURT: All right. Thank you, Mr. Muise. Final round.

MR. HARVEY: No, Your Honor.

THE COURT: Giving it up?

MR. HARVEY: I'm not giving it up. I think we've made our points.

THE COURT: Giving up your round?


MR. MUISE: I think they ought to give up.

THE COURT: I didn't read it that way. Thank you, sir. You may step down. That concludes your testimony. All right, counsel. Let's take the exhibits first, and then we'll decide what we're going to do from here. We have, with respect to Dr. Minnich, we have D-201- A. Are you ready for the exhibits?

MR. MUISE: Yes, Your Honor. You said, D, correct, Your Honor?

THE COURT: That's correct, D-201 A, which is the CV. D-251, which is the Woese article. D-252 is the Lenski article. D-255 is the Conway article. D-203 is the cover of the magazine or the Cell cover, excuse me. D-253 is the Alberts article. D-254 is the witness's article. D-257 is the Losick and Shapiro article. I don't have other Defendants' exhibits, but I'll take them if you have them, Mr. Muise.

MR. MUISE: I was following in order, and then we kind of went out of order. Did you have 252, Your Honor?

THE COURT: Say it again.

MR. MUISE: Did you have 252?

MR. HARVEY: Yes, he did.

THE COURT: I did take 252. That's the Lenski article.

MR. MUISE: Yes, Your Honor. And 255.

THE COURT: I have that. That's the Conway article.

MR. MUISE: And 274.

THE COURT: 274, I did not have.

MR. MUISE: The DeRosier article, the Turn of the Screw.

THE COURT: All right.

MR. MUISE: I believe that should be all of them.

THE COURT: All right. Are you moving for the admission of all of those, including 274?

MR. MUISE: Yes, Your Honor.

THE COURT: Objection?


THE COURT: All right. Then all of those exhibits are admitted. On cross, we have P-853, which is the Not So Blind Watchmaker article. All of these are Plaintiffs' exhibits. 845 is the Morris review. 837 is the Nguyen article. 614 is the Minnich -- is the actual expert report of the witness.

284 is the note, bacteria type III secretion system. P-74 is the Sayer article. 852 is the Alberts article. 848 is the Alberts and Labov article. 847 is the Ratliff article. 841 is the Gray article. 842 is the Johnson and Spain article. And 725 is the additional Alberts article.

What's your pleasure with respect to those -- well, first of all, do you have any others, Mr. Harvey?

MR. HARVEY: No, that's it, Your Honor.

THE COURT: Are you moving for the admission of all those?

MR. HARVEY: Yes, Your Honor,

MR. MUISE: We would object specifically to 852. That was apparently some article in the New York Times by Bruce Alberts that we had had --

THE COURT: Was that a letter?

MR. HARVEY: Yes, Your Honor.

MR. MUISE: It was a news article that he had written. We made the hearsay objection. You had him adjust his question, and we're objecting obviously to the article coming in.

MR. HARVEY: Your Honor, withdraw that exhibit.

THE COURT: All right. Then with the withdrawal of that, any objection to the other exhibits, Mr. Muise?

MR. MUISE: No, Your Honor.

THE COURT: All right. Then the remainder of the exhibits as named will be admitted. Save Plaintiffs' 852. On redirect, Mr. Muise, you referred to Defendants' Exhibit 223, which may be in already. I'm not sure.

MR. MUISE: It should be, Your Honor. That's actually one of the books I had spoken with --

THE COURT: That's in, so we're not going to worry about it. Did I miss any exhibits?

MR. HARVEY: Your Honor, just one thing. We're not moving in P-614. That is the expert report.

THE COURT: I wondered about that actually as I looked at it. You don't want to put that in, I didn't assume. Okay. We'll withdraw 614. All right. Now it's just about the noon hour.

And what we must do yet, in addition to hearing your closing arguments, which will be the last thing we do today is, we've got to handle the exhibits, and then have a final word with counsel on your submissions. It's my understanding that you're going to work through the lunch hour on some things that you may not yet have had an opportunity to agree upon, or have you agreed on those things?

MR. MUISE: I think we had the demonstrative exhibits, that issue. I think we pretty much have it worked out. Mr. Walczyk and I have to discuss a few things. We're hoping to get that done and marked properly during the lunch hour.

THE COURT: All right.

MR. MUISE: I think it will be stipulated to. It will be something easy to get into the record.

THE COURT: Then it would be time, it seems to me, to take that after lunch, and then we'll do that and have a word about some areas that I may want you to highlight in your submissions, and then we'll have the closing arguments at that point.

MR. MUISE: My understanding, too, is, there is going to be some additional argument. Is that what you're talking about the submissions?

THE COURT: The way I see it is this. I want to hear you on, obviously, the demonstrative exhibits. You think you've got that wrapped up or you will have that wrapped up. It appeared to me that, from what I've heard from you and also heard from Liz, is that you seem to have some mechanism on the deposition designations that I can work with, and that seems to be agreed.

If you want to put that on the record, we can put it on the record. We need to hear some argument, final argument. There has been fairly extensive argument as it relates to the newspaper articles in the two York newspapers and their admissibility.

I will tell you that, so that you don't waste the time that you can otherwise use for the exhibits that, as it relates to the editorials and the letters, and to some degree, to some parts of the articles, and I'll clarify this when we get into the argument, I'm inclined to allow you to, in particular, to allow the Defendants to further brief that as a part of your submission.

I'm not sure that I'm going to rule on the admissibility of the -- I will rule on the admissibility of the articles on the disputed points, that is the statements of, in particular, various board members as reported therein and for that purpose.

As the articles and the editorials and the letters go to the effect prong, I may defer a ruling on that. I'll hear additional argument, if you want to make it, this afternoon. I'm not sure that I'm prepared to rule on that, and you may want to make a submission. Certainly the Plaintiffs have made a submission.

I have that. You may want to incorporate that in your argument that you're going to make. I'm not certain that I want to rule on that this afternoon. But we'll take that and --

MR. MUISE: I think Mr. Walczyk is going to be arguing that part, and I thought my understanding was, the question of the admissibility, and not so much as getting into the effect argument, but that was going to be something --

THE COURT: And that's correct, and that's precisely why, because I think they're intertwined, and I'll make that clear this afternoon. I'm not so sure that I want to render a ruling on that. I want to allow you every opportunity, and the Plaintiffs, if they choose, to elaborate on that as it goes to the effect of prong. Do you want to say something, Mr. Rothschild?

MR. ROTHSCHILD: Just another issue on the designation that I just wanted to make clear on the record. We are going to submit a list of designations, counter designations, including where there are objections. And we're prepared to submit that. And the Defendants may want to respond that. Another thing, and this is not something quite --

THE COURT: Let me just stop you. But you're going to key that in a way, as I understand it, that I can -- that I can work with it and deal with it outside --


THE COURT: -- the ambit of the trial.

MR. ROTHSCHILD: We're going to have page and line numbers and also highlighted transcripts, so it will be fairly reasonably easy to follow. The other thing, and this is something frankly, I think, counsel and I have not discussed.

At least in what Plaintiffs have designated, there are exhibits, many of which have been introduced in this trial, but some which have not. In particular, we took the depositions of Mr. Buell and Dr. Thaxton. There were exhibits, we think, that have been properly authenticated, and we'll include that in our chart as well.

To be fair to the Defendants, they may not have considered those yet and may want a chance to object to those, and we would hope that that does just happen in the following week.

THE COURT: You're going to include them in what?

MR. ROTHSCHILD: In addition to the highlighted --

THE COURT: In your designations?

MR. ROTHSCHILD: Correct. We will indicate in the chart the exhibits that come in, that were part of the page and line testimony. We'll indicate what the exhibits are, and we probably should look at them, and there may be some that we withdraw. And Defendants, I'm sure, would want an opportunity to respond to those.

THE COURT: Let me ask you this on that point. Do you need more time? I don't have to have that today. Do you need more time than today to get together on that? That's perfectly fine for me.

MR. MUISE: I think perhaps in doing that, part of next week and, I imagine, we had some discussion that perhaps, if we could leave the record open so we can clean this all up, this being a bench trial, through the next week.

THE COURT: That's fine. That's fine.

MR. MUISE: We're going through the findings and testimony and see if there was any exhibits that might have been lost. We've been able to work out a lot of things throughout this trial, so I don't see this being any different.

THE COURT: Inasmuch as my guess is that none of us were planning on laboring through this through the weekend.

MR. MUISE: I don't know, Your Honor. Speak for yourself.

THE COURT: Then I think, to get it right, you should do that. I'm particularly concerned about those exhibits, and you may have exhibits. That way, I get a very accurate recitation of what each of you want me to do, and I can rule that way. So that's not problematic.

In fact, I -- in all seriousness, I can't begin to consider this, won't begin until I get your submissions until I get the findings, and that's about 21 days out, I guess, until I get everybody's findings. I think we're on a 14/7 time frame, something like that. Is that right?

MR. ROTHSCHILD: So you don't want everybody here to be camping out outside the courthouse?


MR. ROTHSCHILD: That's right. We have 14 days for initial pleadings, and then 7 days following for responses which, I think, we all agreed was not meant to be a paragraph-by-paragraph response, but simply an opportunity to respond to things selectively.

THE COURT: Right. And so not until that period ends, or at least not until the 14-day period ends, would I need that, and if you get it in within that period of time, that's certainly fine for me.

MR. ROTHSCHILD: One other loose end that I think was largely resolved yesterday. I think Defendants agreed that the Barbara Forrest reports and not-testified-about exhibits would come in for the narrow purposes of her admissibility for the -- for any appellate record, and we would -- we will plan on giving you a list of those exhibits. We'll give Liz a list and, of course, Defendants as well, so you're aware.

THE COURT: Dr. Forrest's report is what exhibit number? Do you have that?

MR. ROTHSCHILD: This would also include the many exhibits, numbered exhibits.

THE COURT: I understand. You mean, the exhibits as referenced in her report?

MR. ROTHSCHILD: Correct. 347 was the first report, and 349 was the supplemental.

THE COURT: So 347 and 349 would come in based on that stipulation, Mr. Muise, is that correct?

MR. MUISE: That's correct, Your Honor.

THE COURT: So we don't have to cover that then this afternoon together with the exhibits. I will consider them for the purposes as stated, is that correct, as part of the record?

MR. ROTHSCHILD: That's correct.

THE COURT: I think that's the appropriate way to handle that. Anything else before we break for lunch?

MR. THOMPSON: Your Honor, may I make a statement? I'm going to be leaving before the afternoon closing arguments, but, as the head of the Thomas More Law Center, I wanted to thank Your Honor on the record for the fair hearing we've had and for all of the indulgences that you've given us, recognizing that we're a firm in Ann Arbor, and we've been coming here.

I wanted to acknowledge your patience and the fair trial, and at the same time, acknowledge the professionalism and the cooperation that the law firm of Pepper Hamilton has given us, and not only the lawyers, but the support staff. As Your Honor knows, the Thomas More Law Center and the ACLU and the Americans United for Separation of Church and State have widely different views of the establishment clause, but I must say that, both the attorneys for the ACLU and the Americans United for Separation of Church and State have given us the same professional courtesies.

And for that, I wanted to thank you before I disappeared in the afternoon. I've got a long standing commitment to be in the State of Oklahoma. So again, thank you very much, Your Honor.

THE COURT: I understand, Mr. Thompson. It was my intention to recognize counsel, and I will recognize counsel this afternoon. But I certainly appreciate those comments as they relate to the Court, but I also acknowledge and will again acknowledge the very professional and the cordial relations, not only between counsel, but between counsel and the Court.

And your professional demeanor throughout this trial is appreciated. I understand that Mr. Gillen is not feeling well this morning. I hope that he joins us this afternoon.

MR. MUISE: He'll be here, Your Honor. I'll make sure he's here.

THE COURT: I trust that you'll get our friend, Mr. Gillen, rallied in time to make the afternoon session. It would be most unfortunate, having sat through this, if he missed it. But I thank you for that.

MR. THOMPSON: Thank you, Your Honor.

THE COURT: All right. Anything further before we break for lunch? All right. Let's break until, I'll give you an ample opportunity to go through everything and get started this afternoon. We'll comfortably finish this afternoon, and we will reconvene at 1:30 to take up the additional unresolved evidentiary matters and to then conclude the trial with the closing arguments by counsel. We'll be in recess until 1:30.

(Whereupon, a lunch recess was taken at 12:05 p.m.)


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