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Kitzmiller v. Dover Area School District

Trial transcript: Day 20 (November 3), PM Session, Part 1


THE COURT: Be seated, please. All right, good afternoon to everyone. We have the first witness then of the afternoon.

MR. MUISE: Your Honor, I know there was a discussion during the lunch break over the exhibits, and if we perhaps maybe could move for those admissions, I believe there's no objections on any of the exhibits.

THE COURT: Do you want to do them now? All right, sure.

MR. MUISE: So it might be worthwhile to get that housekeeping measure taken care of.

THE COURT: All right, I'll just read the numbers and not describe them if you think there's no objection, and you can for the sake of speed, D-4, D-5, D-7, D-9, D-10, D-19, actually these are all defendant's, 20, 21, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 54, 164, 284, 286, 287, 85, 86, 100, 116. What did I miss on the defendant's exhibits?

MR. MUISE: I believe that's the complete list. I don't think Mr. Gillen reviewed --

THE COURT: Say again? I'm sorry.

MR. MUISE: Yes, I believe that was the complete list, Your Honor. That's all the exhibits.

MR. ROTHSCHILD: Your Honor, you said 285, and I didn't have that on my list. So --

THE COURT: No, if I said it I misspoke. and 286. If I said that I misspoke.

MR. ROTHSCHILD: And then I thought there was an Exhibit 50, and I don't remember what it is, but I have that on my list.

THE COURT: What is D-50? Why don't we check?

MR. ROTHSCHILD: D-50 is --

COURTROOM DEPUTY: It's already in. It's already in.

MR. ROTHSCHILD: My mistake. Thank you.

THE COURT: You got to get up pretty early to keep up with Liz, Mr. Rothschild.

MR. ROTHSCHILD: 5:20 this morning, Your Honor.

THE COURT: Anything else? Any objections?

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

MR. ROTHSCHILD: No objection.

THE COURT: All right, they're all admitted the. Cross, P-817, P-91, and P-179. Any additional exhibits that I've missed? And are you moving for those, or are you moving those in I should say.

MR. ROTHSCHILD: Those we are moving in, and if you could just give me just one moment, I believe that's everything.

(Brief pause.)

MR. ROTHSCHILD: That's it, Your Honor.

THE COURT: All right. No objection? All right, then they're admitted as well. All right. Having covered that, we're ready.

MR. MUISE: Thank you, Your Honor. Defendants call Dr. Scott Minnich.

(Dr. Scott Minnich was called to testify and was sworn by the courtroom deputy.)

COURTROOM DEPUTY: State your name, and spell it for the record, please.

THE WITNESS: My name is Scott A. Minnich. S-C-O-T-T, middle initial A, M-I-N-N-I-C-H.


Q. Good afternoon, Dr. Minnich.

A. Good afternoon.

Q. Your Honor, may I approach?

THE COURT: You may.

(Brief pause.)

Q. Dr. Minnich, I've just provided you with two binders. One of them is a black binder marked as exhibits, which have some of the exhibits that we'll be using for the course of your testimony to assist you in your reference. In the blue binder is a copy of the demonstrative exhibits that we'll be using through the course of your testimony again to assist you from the witness stand. Sir, where do you reside?

A. In Moscow, Idaho.

Q. And, sir, I'd ask you if you could please open up that exhibit binder, the black binder if you could, to Exhibit 201-A, as in Alpha. It should be under Tab 1?

A. Got it.

Q. Is that a copy of your curriculum vitae, sir?

A. It is. It's an abbreviated form for a grant that was submitted.

Q. I want to, I want you to refer to it as we go through some of your background and qualifications to give expert opinions in this case. Sir, what is your profession?

A. I'm an associate professor at the University of Idaho in microbiology.

Q. Are you a tenured professor?

A. I am.

Q. And you said you teach at the University of Idaho?

A. Correct.

Q. How long have you taught there?

A. Since 1989.

Q. Where else have you taught?

A. I was at Tulane for a year previous to that.

Q. And what subjects have you taught at the University of Idaho?

A. General microbiology for undergraduate majors. Food microbiology, molecular genetic techniques. I currently teach a 600 level course, six credit course in infectious disease for first year medical students.

Q. And what other subjects do you presently teach?

A. Infectious disease and general microbiology.

Q. You've been teaching science at the college and graduate level for approximately eighteen years, is that correct?

A. Correct.

Q. You said you're a microbiologist. Could you explain for us what it is that you do as a microbiologist?

A. Well, the primary focus is microorganisms, in my particular case pathogenic organisms or infectious disease agents. All the biological sciences, you know, the disciplines have kind of bled together. So we do molecular biology, biochemistry, and are even doing a little bit of cell biology, but primarily molecular genetics is my bread and butter.

Q. And how would that different at all with say a biochemist?

A. Again, you know, those are somewhat artificial distinctions. I mean, we're more focused at genetic programming of organisms and how they respond to their environment, biochemists may be looking at specific, you know, organelles or suborganelles and how they're assembled, and we do a little bit of that as well.

Q. How would a microbiologist then differ from a cell biologist?


A cell biologist is looking at more global effects, you know, cell responses, involves generally a lot of microscopy, and we don't do a lot of that.

Q. And I know during the course of your testimony we're going to be using some difficult scientific terms and so forth, so I would ask if you could, we need to speak slowly and loud and clearly so our court reporter here can do his best job taking all this down, okay?

A. I'll do my best.

Q. What is the name of the department that you teach in at the University of Idaho?

A. My department is microbiology, molecular biology, and biochemistry.

Q. Does that department then include all three of those disciplines that we discussed, cell biologists, biochemists, and microbiologists?

A. Correct.

Q. Now, sir, in your work and in your profession do you conduct experiments?

A. I do.

Q. What is the focus of your experimental work?

A. Right now we're focused on I'd say the discipline of host parasite interactions. So we work on bacterial infectious agents and how they adapt during the infectious process.

Q. Does that focus on the bacterial flagellum and the type three secretory systems?

A. It is. We've worked on that for the last ten years in terms of these are two systems that in our organism the genus Yersinia have opposing regulations. So outside the host the cells build a flagellum. Once they inspect a mammalian host, flagellum biosynthesis is turned off and you turn on the weapons systems that these organisms have. So we've used those two aspects kind of as opposing markers to follow regulatory events.

Q. So the focus of your experimental work, I assume also the focus of your research, and that would include the bacterial flagellum and the type three secretory systems?

A. Correct.

Q. Sir, do you incorporate intelligent design into your experimental and research work?

A. I think the principles of intelligent design are what we would call reverse engineering would be, you know, a very prominent part of what we do.

Q. And we're going to get into a little bit more detail about that later in your testimony. Sir, I want to talk about your education. What degrees do you hold and where did you get them from?

A. I have an undergraduate degree, a BS in bacteriology and public health from Washington State University.

Q. What year was that, sir?

A. Good question. 1975.

Q. If you want to look at your CV to help refresh --

A. Okay.

Q. Okay, go ahead.

A. I obtained a masters degree in microbiology from the University of Idaho, and a Ph.D. from Iowa State University in 1981 in microbiology.

Q. Now, when you got your Ph.D. in microbiology, what was the dissertation that you wrote?

A. My research dissertation was on the development of a rapid immunoassay for the detection of salmonella. So it was really the first application of enzyme immunoassays, which are kind of a standard diagnostic procedure now, to detecting salmonella.

Q. Would you give us a thumbnail sketch of what this was about?

A. Yeah, it's an antibody based assay, and our goal was to make something that was very rapid. So the problem that we had, you know, particularly in the food industry that it could take up to a week using conventional microbiological techniques to verify, detect and verify that salmonella was present. This was a rapid screening procedure that reduced that time period to about 24 to 36 hours. So for the food industry there was, you know, incredible savings in terms of warehousing costs before food is released. The FD A has zero tolerance with respect to salmonella in foods. So the test was developed as a prototype as a graduate student, and then through the next four years it was commercialized and applied to the food industry. Variants of that procedure are still used today.

Q. You got to see your work go from the inception of an idea through the experimental all the way to the commercialization of the idea?

A. Correct.

Q. Did this work also include work on the bacterial flagellum?

A. It did, because the antibodies we were using were directed against the flagellar filament, which is distinctive for the salmonella. We had to have an assay that incorporated the detection of over 2,400 different what we call serotypes, or variants, of salmonella.

Q. Sir, do you belong to any professional memberships?

A. I do. I'm a member of the American Association for the Advancement of Science and the American Society for Microbiology.

Q. I want to talk about some of you, we have listed here positions and honors. That's how you have it listed in your CV. You were on a sabbatical from October of 2003 to May of 2004, is that correct?

A. That's correct.

Q. And for what purpose?

A. I was a subject matter expert for the Defense Intelligence Agency in Iraq. So I served with the Iraq Survey Group looking for weapons of mass destruction.

Q. What was the purpose of the need for a microbiologist to be part of this survey group?

A. Well, that was the focus of the Iraq Survey Group based on the intelligence that Iraq had reestablished both their chemical and biological weapons, or their nuclear, but we weren't part of that aspect, but their programs. So our job was to travel around the country and look for these materials.

Q. How were you selected for that position?

A. I had a phone call in September of 2003, actually August of 2003, asking if I had any students in my laboratory that had military experience. In part because we're registered with the Center of Disease Control to work with select agents, and that requires now with the new regulations after 9/11 that everybody in my laboratory has FBI clearance, and so I think we were on a checklist of people that worked with organisms that were of concern and, you know, my remark was no, I didn't have any students that fit that category, but in subsequent conversations, you know, I was intrigued by the idea, and volunteered.

Q. And why did you volunteer?

A. I volunteered because I grew up in a military family. Both my father and father-in-law are West Pointers, and it's an area that I'm very interested in. Obviously, I mean, it's work that we do, and it was an opportunity to do field work and serve my country at the same time.

Q. Sir, you said you've been teaching at the University of Idaho since 1989 in microbiology, correct?

A. Right.

Q. Is that correct?

A. That's correct.

Q. You also were a post-doctoral fellow at Princeton University from 1984 to 1987, is that correct?

A. That's correct.

Q. Could you tell us what that was?

A. This was after my doctorate, working in a laboratory, the primary focus was developmental regulation of flagellum biosynthesis, and one of the model organisms for this system, caulobacter crescentus.

Q. So during this period of research you worked on flagellar biosynthesis, is that correct?

A. That's correct.

Q. And you also were a post-doctoral fellow at Purdue University from 1981 to 1983, is that correct?

A. That's correct.

Q. And what did you do there?

A. There I was working in a molecular genetics laboratory. The project focused on cloning and studying the regulation of a toxin made by bacillus thuringiensis. So that sounds kind of esoteric, but this is the BT toxin that was put into plants by Monsanto. So really the first application of genetic engineering in agricultural crops. So we cloned the gene, studied its regulation, we handed it over to Monsanto, it was modified, put into maize, soybeans, you name it, cotton.

Q. Now, when you were at Purdue University doing this work did you also engage in any collaborative efforts with other faculty at Purdue University?

A. Yes. There was an individual in the food science department, Dr. Swaminathan, that had worked on for years on salmonella detection. We knew each other's work, so we started collaborating. And I actually took my graduate work ideas that he had as well and took our assay to the next level. So it was a very profitable interaction. Dr. Swaminathan I think is just retiring this year as branch chief for enteric disease at the Center for Disease Control.

Q. During that collaborative effort did you work on the bacterial flagellum?

A. We did. Again this was the focus of what we called the antigen that we were trying to detect.

Q. Now, you've published articles in peer reviewed science journals, is that correct?

A. I have.

Q. Approximately how many?

A. 25 to 30. I'm missing a few on here, but --

Q. And what are some of the journals that you've published in?

A. Proceedings of the National Academy of Science, Journal of Molecular Biology, and Molecular and Microbiology, and Journal of Bacteriology, which are really the primary journals for what I work on. Applied Environmental, there are a few others.

Q. Has there been a focus of your peer reviewed science journal articles?

A. Over the last ten years we've focused on flagellum biosynthesis and type three secretory system regulation and pathogenic organisms.

Q. And again this is the focus of your experimental work?

A. Correct.

Q. Through your experiments, your research, and your writings have you become familiar with the scientific evidence as it relates to Darwin's theory of evolution?

A. I have.

Q. Would it be fair to say that your focus is principally on the molecular level?

A. Correct.

Q. So you're a fellow with The Discovery Institute, is that correct?

A. I am.

Q. And what does that mean?

A. My name is on one of their web pages listed as a fellow. So it's more of a networking opportunity, you know, for people that are interested in this area of intelligent design.

Q. Are you an employee of The Discovery Institute?

A. No. No, I'm not.

Q. Do they have any control over the work that you do?

A. None whatsoever.

Q. Do they direct your work?

A. No.

Q. So is it fair to say that you're not on The Discover Institute payroll?

A. I'm not.

Q. Has anyone ever accused you of that?

A. Yeah, there was an incident in 2003 in May when Robert Pennock was invited to give a seminar --

MR. HARVEY: Objection. Relevance, hearsay.

MR. MUISE: Your Honor, we'll all say we've been hearing a lot of testimony today, or throughout the course of this trial, vilifying Discovery Institute, you know, talking about this grand agenda. Some of it's been expressed by their experts. I'm going through his qualifications and I'm just demonstrating that a lot these accusations aren't true, that these are independent scientists who are working on this for scientific reasons.

THE COURT: But he's not being offered to defend The Discovery Institute.

MR. MUISE: That's correct, Your Honor, but the fact is in terms of his, in terms of his background and qualifications, I mean this is how they've been really vilifying these individuals --

THE COURT: I say again, I understand that, and in another time and in another place he might be competent to talk about how as a fellow The Discovery Institute ran into some difficulties, but for today I think it's stipulated, his credentials are stipulated to, and now we're going to get sidetracked on why his bona fides as a fellow at The Discovery Institute were called into question, and I just don't think that's relevant. I understand, it is not central or necessarily important to me that we engage in an independent debate on The Discovery Institute. It's just not helpful to me, and I'll tell you that. So why don't we proceed. I'll sustain the objection.


Q. Sir, you're an advocate for intelligent design?

A. I am.

Q. Is Darwin's theory of evolution inconsistent with your private religious beliefs?

A. No.

Q. Do you have a religious equipment to intelligent design?

A. I don't.

Q. Why did you get involved with intelligent design?

A. I read Mike Behe's book soon after it was published, and of course he uses the bacterial flagellum as a paradigm for, you know, his term irreducible complexity, and I had arrived at some of these same conclusions. So it intrigued me, there was a friend I had in the physics department that was interested in these questions as well. So I think together we started looking into these questions and what intelligent design was and what it claimed, and so it kind of blossomed from there.

Q. So how long have you been involved with or associated with intelligent design?

A. Probably since about 1997, `98, or so.

Q. Have you ever been involved with creationism or creation science?

A. No.

Q. Why not?

A. You know, I'm old enough that I was around during those debates, and I never participated because I don't agree with the approach. I don't think you mix religion with your science. I don't think you use Genesis as a filter of how you interpret your scientific data, you know, empirical evidence.

Q. So what is your commitment then to intelligent design?

A. I think it fits. I think it's a good paradigm. We can discuss that as we go through some of the slides, but it's consistent with the empirical evidence and standard scientific reasoning that we employ.

Q. Do you perceive efforts on the part of opponents of intelligent design to equate intelligent design with creationism?

A. I think there is. You know, often times when it's mentioned in the press it's referred to as intelligent design creationism, anti-evolutionism, you know, these types of terms are often equated, and I think that's a misrepresentation.

Q. Sir, is there unanimity amongst biologists regarding all aspects of Darwin's theory of evolution?

A. No, there isn't.

Q. Is intelligent design different in that respect?

A. No. There's a broad spectrum of people in terms of, you know, how they interpret the data.

Q. Does intelligent design continue to develop?

A. Yes. I mean, it's I think developed quite a bit since my involvement, and maybe if you trace it back to the early 90's.

Q. Now, sir, you testified that you authored numerous peer reviewed articles, many in scientific journals, and I believe you testified the one area in which you published the most was on the topics of molecular biology and in the past ten years specifically the bacterial flagellum and the type three secretory system. Is that fair?

A. Correct.

Q. Have you authored any articles appearing in peer reviewed science journals that make intelligent design arguments?

A. Not directly.

Q. You say not directly. Are there articles that provide support for intelligent design arguments that you've published?

A. I think so. I think all of them do. I think they're, you know, dissecting intricate components of subcellular organelles that support the general contention of irreducible complexity and design.

Q. I want to ask you if you agree with this testimony that was provided by Dr. Miller. He testified that, "It is a standard scientific practice for scientists to point to the scientific literature, to point to observations and experiments that have been done by other people in other laboratories, have been peer reviewed, have been published, and to cite to that evidence, cite to those data, and to cite to those experiments in their arguments." Do you agree with that?

A. I agree with that. That's standard practice in scientific, you know, endeavors.

Q. And is that what intelligent design is doing?

A. Yes.

Q. This is something that scientists do routinely?

A. Oh, yes. It's critical.

Q. I want to ask you if you also agree with Dr. Miller that the question is not whether you or any other scientists have done experiments in your own laboratories that have produced evidence for a particular claim, the question is whether or not the inference that you or other scientists drawing your analysis from that data are supported. Do you agree with that?

A. I do. I think, you know, that's part of the scientific endeavor. I mean, either you're doing your own experiments and the data that you generate you try to fit into the general knowledge that's available, whether it's consistent or inconsistent, and you can look at other people's data through this published and view it perhaps from a different perspective and come up with a new interpretation. And that's standard. I think Watson and Crick are examples of that in terms of doing minimal experiments, but at the same time taking information from various sources and melding it into an explanatory model, and so that can be profitable.

Q. Explain for us what you -- you mentioned Crick and Watson. What are you referring to?

A. Well, the fact that, you know, they really didn't do any wet lab experiments. They took Shordhop's work from Columbia University, Rosalyn Franklin's x-ray crystallography data coordinate in terms of the structure of nucleotides and built models and came up with a double helical structure, so --

Q. And those are the two that received the Nobel prize for --

A. Right.

Q. -- developing the architecture I guess of the double helix, DNA?

A. Right, solving instruction.

Q. Now, is this method, this process, is this what intelligent design advocates are engaged in?

A. Well, I don't want to equate it with, you know, in terms of something that is critical as a double helix, but at the same time we're looking at across the landscape of empirical data and asking the question does it fit with the Darwinian mechanism of mutation and natural selection to generate, you know, the deep diversity of life.

Q. Now, you testified previously that you though do experiments that you believe supports intelligent design?

A. I do. I do.

Q. Are there peer reviewed articles that make arguments for aspects of intelligent design that you're aware of?

A. I think there are around ten of them now that are in the literature that address this, I'm not sure of an exact number, but within the last couple of years.

Q. Do you perceive a bias against publishing intelligent design articles in science journals?

A. I think there's --

MR. HARVEY: Objection, Your Honor. Speculation.

MR. MUISE: I'm asking for his perception, Your Honor.

THE COURT: I think it's a fair question. I'll overrule the objection. You can answer.

THE WITNESS: I think that's on public record, there's a paper published by a journal from the Smithsonian Institute last summer by Stephen Meyer. Brixter and Berg was the editor, and I think it was a --

MR. HARVEY: Your Honor, objection. Hearsay. He has no firsthand knowledge of it.

THE COURT: Well, the question was a yes or no question. The answer was yes. That was accepted. The objection was overruled on that basis. If he gets into the particulars he may be getting into hearsay.

MR. MUISE: But he testified as to perception. If he has an understanding, he said it's a public record. I mean, you're saying that --

THE COURT: A newspaper article is not a public record, and you've certainly argued vigorously in this case that it's not, and we've spent a lot of time on that. Mr. Muise. You want to tell me now it's a public record? We can spare a lot of argument tomorrow if it is.

MR. MUISE: Your Honor, I mean, a public record not in the sense of I think the term that you're using with the hearsay.

THE COURT: No, it's not in the way that I'm using it. It's the way that we've argued it. Don't insult my intelligence. It's not. The objection is sustained.

MR. MUISE: I understand, Your Honor. And I certainly did not intend to convey any message that I was --

THE COURT: I understand that. Let's keep going. Proceed.


Q. Sir, you authored an article entitled Genetic Analysis of Coordinate Flagella in Type Three Regulatory Circuits and pathogenic Bacteria, correct?

A. I did.

Q. And was this article published?

A. It was published in the proceedings of a meeting in 2004.

Q. And who was it published by?

A. The Wessex Institute. It's an institute of higher education in the U.K.

Q. It's not a religious organization?

A. No.

Q. This article was part of a conference, is that correct?

A. That's right. It was a conference titled "Design In Nature II" that was held in Rhodes, Greece in July of that year.

Q. And what was this conference about?

A. The conference I think would fit under the broad category of a new area in science called biomimetics where engineers, architects are brought together with biologists to, as a mechanism of cross fertilization. Engineers are recognizing that biological systems have solved some pretty difficult problems, and so there's a lot in terms of nanotechnology structural analysis that can be gleaned from biological systems.

Q. Do you consider this article to be an intelligent design article?

A. Primarily it's a review of our work looking at coordinate regulation in type three systems, but there's a section where I address intelligence aspects of it.

Q. Who attended this conference? I believe you said there were engineers and scientists?

A. Biologists, engineers, design engineers, aircraft engineers, architects.

Q. Was this a creationists conference?

A. No.

Q. Now, this article that was published by the Wessex Institute, was it peer reviewed?

A. There was, you had to submit the paper before it would be accepted or before you could provide or present it at the conference. So I actually wrote that when I was in Baghdad, communicated it by e-mail, and it was peer reviewed, I'm not sure what the peer review is, it's not as rigorous as, you know, a primary journal article, but there is that process.

Q. Could you just briefly explain for us what this article is about? We're going to be talking about it in more detail later in your testimony, but if you could just give us sort of a thumbnail sketch?

A. Well, it looks at the work that we've been involved with why bacteria repress motility in a mammalian host environment and how they activate type three secretion systems and why these systems are segregated. It also addressed the question that had come up in these debates on intelligent design that the type three secretory system represented a structural intermediate for the flagellum, and Ken Miller has published on this. And so there were arguments against that position in particular.

Q. Did this conference demonstrate the utility of intelligence design as a scientific theory?

A. I think so, in terms of our approach and what we found out.

Q. How so?

A. Well, again the types of the questions we asked looking for reasons why these two systems would be regulated in an opposing manner, the reverse engineering techniques that proved profitable. We also, although I don't want to bore everybody with the details, but in part to me the most interesting aspect is that one of the organism we work with, yersinia pestis, which causes the bubonic plague, so this is an organism that's estimated to have killed two hundred million people in recorded history, activates its virulence genes by temperature.

So we were interested in terms of what's the thermostat, how does the cell sense temperature and how does it shut genes off and turn others on, and it turned out through a genetic approach mutational analysis that the trigger, from one sense you can look at this almost as kind of dissecting the trigger of a nuclear weapon in terms of its potential effect, turned out to be DN A itself, which was a surprise to us.

It told us that the DN A molecule is just not a reservoir for digital information, but the three-dimensional structure that it can conform to under different environments imparts information as well, and that was a surprising observation and I think we did that by reverse engineering and looking at temperature parameters of DN A molecules.

Q. Sir, are you familiar with the book Of Pandas and People?

A. I am.

Q. Did you contribute to any portions of this book?

A. I did not.

Q. Are you aware of any prior drafts of this book?

A. No.

Q. I take it then you didn't contribute to any prior drafts of the Pandas book?

A. I didn't.

Q. Sir, is it your understanding that this book Pandas is part of the controversy in this lawsuit?

A. I'm aware of that.

Q. What is your understanding of how this book will be used at the Dover High School?

A. It's mentioned in a short statement read to students before the, to biology students, 9th grade biology students, and it's also on deposit or reserve or in the library as, you know, a reference in the library.

Q. Now, this book was published in 1993, correct?

A. That's correct.

Q. Would you recommend that it be used as the primary text for a biology class?

A. No, I would not.

Q. Why not?

A. Well, it's not a primary biology text, and I think that's stated in the introduction.

Q. And the other reason?

A. Well, it's outdated as well. It's an old book. I mean, in the course of biology ten years is light years now in terms of our progression.

Q. Would you recommend that it be used in the manner that Dover High School is using it?

A. I do.

Q. Do you have experience with this book being used in a biology course at the high school level?

A. I do. I had children that attended private school in Moscow, Idaho. Being a scientist they asked me to review their biology curriculum. They had, you know, a curriculum that I thought was inadequate. I recommended that they use Miller and Levine, which I think is the same book that's being used in Dover, and supplement it with Pandas and People.

Q. What year was this?

A. I'm not sure exactly. I'd say `95 or `96.

Q. Are they still using the Pandas book?

A. They still have it. In fact, I got a copy from them.

Q. Why did you recommend Pandas as a supplement?

A. It addresses some of the aspects of Darwinian evolution from a different perspective in terms of the fossil record, in term of other interpretations of homology, molecular aspects. There was I think in this book a brief introduction to, although not stated, but irreducible complexity, the blood clotting system, that Mike Behe contributed.

Q. Did you think it was beneficial for the students to have exposure to this book?

A. Yes. I think any time you expose students to, you know, different interpretations it's good. It promotes critical thinking.

Q. Have you subsequently had any experience with these students from this school since recommending this curriculum change?

A. Two of the students came through our department and have since graduated, and they were excellent students. Both of them I think had published peer reviewed papers by the time they had finished their undergraduate degrees, which is an outstanding achievement for undergraduates.

Q. Do you have any way of assessing their critical thinking skills compared with other students?

MR. HARVEY: Objection, Your Honor. Beyond the scope of the expert report. I have not objected for a few questions here, figuring a little latitude is appropriate, but it's clearly not the area with which he's been proffered and the content of his expert report.

THE COURT: Mr. Muise?

MR. MUISE: I'm going to move on, Your Honor. I think what it's establishing is obviously with regard to his expertise from the perspective of science education. I haven't proffered him obviously yet as an expert.

THE COURT: Well, just the critical skills of the students who would have, along with his own child --

MR. MUISE: I'm sorry, Your Honor?

THE COURT: Whose critical skills are we talk about?

MR. MUISE: The students'.

THE COURT: The students in his own child's class?

MR. MUISE: No, these are students who have gone through this biology course where the curriculum included Pandas as part of the supplemental books, and --

THE COURT: That would appear to be beyond the scope of this report. I think you can probably concede that point.

MR. MUISE: Well, in the report he specifically talks about Pandas being a good book and it promotes good science education.

THE COURT: If I recall the testimony correctly, correct me if I'm wrong, sir, this is a school that your child attends and they use Pandas as an ancillary resource?

THE WITNESS: Right. I mean, my children have since graduated, but --

THE COURT: But when they were there they used it?

THE WITNESS: They did, right.

THE COURT: I don't know what basis he could judge -- well, I do know the basis he could judge, but it does appear to go outside the report, Mr. Muise. Unless you can, if you can point me to something in the report, and it's a long report, if there's something in there that you want to hang your hat on, I'll listen.

MR. MUISE: Well, it's not just the report. He was asked about these same questions during his previous deposition, and on his report he said, "I read and am familiar with the text of Pandas, it's a good text, it critically analyzes various aspects of Darwin's theory, it asks critical questions in terms of the evidence and mechanism required to drive evolution. Such questions are essential for the advancement of science, makings students aware of the controversy in the science community, it's good to students and it's good to science."

COURT REPORTER: Mr. Muise? Mr. Muise?

THE COURT: Yes, we have lots of time. Slow your cadence down if you could.

MR. MUISE: Your Honor, I mean I can, I think I've got through the testimony of the part that I wanted to and I can move on to the next --

THE COURT: Well, that may be a fair question once we get out of the -- we're still on qualifications, are we not?

MR. MUISE: We are.

THE COURT: All right. Why don't you -- I'll reserve judgment. If you want to come back around and lay a foundation for that question on your examination, I'll hear any objection Mr. Harvey has at that time. So why don't we move on. I'll sustain it, but with needs to reassert it, I think there's maybe a foundational problem with the question, too, but that wouldn't stop you necessarily from asking it under different circumstances.


Q. Dr. Minnich, do you think that schools should teach students the theory of evolution?

A. Absolutely.

Q. Why?

A. It's critical. I mean, it's critical to biology to have a firm foundation in evolution.

Q. By advocating intelligent design is it your goal to not have the theory of evolution taught in a biology class?

A. Not at all.

Q. Has that ever been your goal?

A. No.

Q. At this point do you believe that intelligent design should be fully integrated into a science curriculum?

A. I don't.

Q. Why not?

A. Well, you've got an old textbook and you lack the standards for teachers and assessment for students.

Q. You think it's appropriate to supplement the science curriculum by making the students aware of intelligent design as Dover has done in this case?

A. Yes, I think it's advantageous.

Q. There's one last area on your CV I want to address, and that's the research support.

A. Correct.

Q. What is significant about research support for a scientist?

A. Well, to be successful and to do experiments you've got to have extramural support and, you know, it's to be likened to running a small business within a research community. You know, I have to pay my graduate students, technicians, pay for supplies, animal care, and there's overhead associated with it as well. So funding is very important.

Q. Have you been awarded any significant grants?

A. Well, right now we have an NIH grant for five years for, with myself and two collaborators, for 1.8 million dollars.

Q. And what is significant about NIH grants?

A. Well, I mean for infectious disease that's the primary source for funding. It's competitive.

Q. Now, the research that you're being funded by NIH, does that include research on the flagellum and the type three secretory system?

A. It does.

MR. MUISE: Your Honor, may it please the court, I tender Dr. Scott Minnich as an expert in microbiology, evolution, intelligent design, and science education.

MR. HARVEY: Your Honor, I don't believe this expert was proffered previously in science education, and I'm not aware of that. His reference in the expert report to Pandas and People being good science, and his general statement about it being good to make students aware of the controversy, but there's no reference to an expert in science education.

MR. MUISE: Your Honor, I mean we stipulated to the qualifications of the matters that were covered in the expert report. He testified that using Pandas, making students aware of intelligent design, was good for science education. He's been teaching science for eighteen years at the college level.

THE COURT: Did you have a, and I may have known this and forgotten it, but was there a written stipulation as to the expert or just simply an understanding?

MR. MUISE: There's a written stipulation I believe, I don't have a copy in front me, but I believe it says effective of the matters that were covered in the expert reports, that their experts would testify as to the matters addressed in the expert reports.

MR. HARVEY: Your Honor, addressing the defendant's pretrial memorandum, it says will testify, it says questions, in other words critical questions in terms of the evidence and mechanism required to drive evolution are essential to the advancement of science and that making students aware of the controversy in the science community is good for students and is good for science.

THE COURT: Well, we're having a bench trial, and your objection is that he's being offered on science education. But it seems to me that the real objection gets to potential testimony that would be outside of his report, isn't it?

MR. HARVEY: That's correct, Your Honor. And I don't believe he has been qualified in the area of teaching at the high school level for example.

THE COURT: Well, I understand that, and that may go to a specific objection, but so we don't waste time on this, which becomes at some point a semantical argument, I'll take a precise objection as it goes to his testimony on that point, but I'm going to overrule your objection at this point and allow him to testify on that basis. I think that's the better course rather than to try to split hairs at this point as to what he's qualified to testify, what area he's qualify to testify. And you have his report. If you have an objection as to an individual question or an area that Mr. Muise gets into, I'll hear your objection on that, all right? So we accept him for the purposes and qualifications as set forth by Mr. Muise, and Mr. Muise, you may proceed with your examination.


Q. Thank you, Your Honor. Dr. Minnich, I want to first review with you the opinions you intend to offer in this case before we get to the basis for these opinions. Sir, do you have an opinion as to whether intelligent design is science?

A. I do.

Q. What is that opinion?

A. It is.

Q. Do you have an opinion as to whether intelligent design makes testable scientific claims?

A. I do.

Q. And what is that opinion?

A. It does.

Q. Do you have an opinion as to whether intelligent design causes a causative argument for design?

A. I do.

Q. What is that opinion?

A. It does.

Q. Do you have an opinion as to whether intelligent design requires the action of a supernatural creator?

A. I do.

Q. What is that opinion?

A. It does not.

Q. Do you have an opinion as to whether intelligent design is creationism?

A. I do.

Q. What is that opinion?

A. It is not.

Q. Do you have an opinion as to whether intelligent design is a religious belief?

A. I do.

Q. And what is that opinion?

A. It is not.

Q. Do you have an opinion as to whether Darwin's theory of evolution is a fact?

A. I do.

Q. And what is that opinion?

A. It is not.

Q. Do you have an opinion as to whether there are gaps and problems with Darwin's theory of evolution?

A. I do.

Q. Sir, what is that opinion?

A. There are such gaps.

Q. Do you have an opinion as to whether making students aware that Darwin's theory is not a fact promotes good science education?

A. I do.

Q. And what is that opinion?

A. I think it does. It does.

Q. Do you have an opinion as to whether making students aware of the existence of gaps and problems with Darwin's theory of evolution promotes good science education?

A. I do.

Q. And what is that opinion?

A. It does, definitely.

Q. Do you have an opinion as to whether making students aware of intelligent design promotes good science education?

A. I do.

Q. And what is that opinion?

A. It does.

Q. Sir, do you have an opinion as to whether providing students with the opportunity to review the book Of Pandas and People promotes good science education?

A. It does.

Q. Do you have an opinion on that?

A. I do, and it does.

Q. Thank you. Sir, I want to talk now about the, turn now to the nature of the intelligent design argument, and I believe you have provide some demonstratives to assist in your testimony here, is that correct?

A. That's correct.

Q. Sir, what is intelligent design?

A. We have summarized here in the first slide. I'll just read it, "Intelligent design is a scientific theory, and it holds that the deep complexity and clearly evident design in organisms is the result of an intelligent agent or cause. Given that even the simplest cells are comprised of nanomachines that currently defy our own intelligent capability to produce, yet have the general features of many machines we have made on a larger scale, intelligent design theory is simply an inference to the best explanation as to the origin of the design." If I could just summarize this perhaps in a more simpler form?

Q. Yes.

A. All biologists recognize design in nature. So I think the question boils down to whether or not it's real design or apparent design, as some people hold. Thirty years ago we didn't know about molecular machines and this concept of irreducible complexity, which we'll talk more about. We didn't know the sophistication of the information storage system in nucleic acids of RN A and DN A that have been likened to digital code that surpasses anything that a software engineer at Microsoft at this point can produce. Certainly Darwin didn't know about this.

So we don't have a Darwinian mechanism to explain these things in terms of natural selection and mutation or variation. On the positive side, because these are similar to machines that we have made in a macro scale, we know what it takes to make them. We know digital information storage systems that we can infer design, looking at the empirical evidence, and maybe a uniformitarian aspect of cause and effect in the world that we live in, when we find these things they're the product of intelligence.

So we're looking at the empirical evidence. We find irreducible complex systems. When we find these in any other context they're the product of intelligence, we infer by standard scientific inference or reasoning that these systems are also the product of intelligence, and we leave it at that.

Q. Is intelligent design based on any religious beliefs or convictions?

A. No. Again, it's looking at the public evidence or the empirical evidence.

Q. And if you could just summarize the intelligent design argument, I know you have an exhibit to assist you.

A. Yes, we'll just go this, we infer design when we see parts that appear to be arranged for a purpose. The strength of the inference is quantitative. The more parts that are arranged, the more intricately they interact, the stronger our confidence is for design. The appearance of design in aspects of biology is overwhelming by the community's own admission. Since nothing other than intelligence cause has been demonstrated to be able to yield such a strong appearance of design, Darwinian claims notwithstanding, the conclusion that design seen in life is real design is rationally justified.

Q. Does intelligent design make a causative argument for design?

A. Again it does. I mean, there's a negative aspect in the sense that for any of these systems that we'll talk about we don't have a Darwinian mechanism to explain them. The positive side is we do know where such systems originate from our own experience of cause and effect.

Q. The purposeful arrangement of parts?

A. The purposeful arrangement of parts in molecular machines that have the appearance of machines that we make that are the product of intelligent design engineers.

Q. Now, does the book Pandas make this point?

A. It talks about, and there's a quote here, the ordering of independent pieces into a coherent whole to accomplish a purpose which is beyond any single component of the system is characteristic of intelligence. So this is kind of a prestatement I think before the coining of the term irreducible complexity.

Q. And the quote you read was from page 144, is that correct?

A. Correct.

Q. And that's Defendant's Exhibit 220. Sir, is intelligent design science?

A. It is. Again just to restate, it's looking at the empirical evidence, the public evidence.

Q. And from this empirical evidence it makes inferences, is that correct?

A. Right, using standard scientific reasoning of cause and effect we see machines that in every aspect look like machines that engineers produce. We don't have a Darwinian mechanism to explain these things in terms of the intermediates. So we can infer that these are the product of intelligence.

Q. Sir, can you give us an example of design at the molecular level?

A. Yeah, I've got a couple of slides, you know, this is I'm sure has been hammered to some degree already, but this is a bacterial flagellum. This is a system that I work on.

THE COURT: We've seen that.

A. I know.

Q. You're going to see a little bit more of it, Your Honor.

A. I kind of feel like Zsa Zsa's fifth husband, you know? As the old adage goes, you know, I know what to do but I just can't make it exciting. I'll try.

THE COURT: Any further questions, Mr. Muise?

MR. MUISE: He's doing fine right now, Your Honor.

THE COURT: For our last witness we get stand-up. You may proceed.

A. All right, this is out of a standard biochemistry textbook that's used for the advanced graduate, or undergraduate and graduate students, Voet and Voet, but it's a cartoon of bacterial flagellum from a grand negative organism, and this is what we refer to as the parts. I mean, we've got a drive shift here, this is the hook protein, or the U joint, it spins. This is the propeller, or the filament. We've got bushings, we've got a stator and a rotor. This thing self assembles from the inside out in a programmed manner. Most of my research has focused on the genetic programming of when to make these things, and also on the assembly of the filaments. But it's a true rotary engine. The size of is about 45 nanometers. So forty-five billionths of a meter in size.

Q. You specialize your focus and research on the flagellum, is that correct?

A. That's correct.

Q. And you've done experiments on flagellum?

A. I have.

Q. And have written peer reviewed articles about it?

A. Yes.

Q. Now, as your prior testimony intimated there's been a good deal of focus on the bacterial flagellum. I guess we could probably call this the bacterial flagellum trial. Why the focus on this particular organelle?

A. Well, I think it's, I mean it's just a logical thing, because of all the molecular machines that we know about in biological systems, we know more about the bacterial flagellum than any. I mean, this was first discovered in E. coli and salmonella, which are really the gold standard for doing molecular genetics, and teasing apart these types of machines.

This in terms of organelle development synthesis, we know an incredible amount about it. It's also been a primary model system starting in the early days for signal transduction, a field of biology in terms of how an organism reads its environment and makes appropriate decisions in terms of, you know, in this case directional flow. So it has served us very well in terms of working out simple signal transduction systems which have paid off an astonishing coin as we've applied the same principles of their study to higher organisms. So in essence this is a system that will maker or break, you know, intelligent design, because it's the one we know the most about.

Q. So it's a system that we have a lot of data available, correct?

A. Correct.

Q. And it's a well defined system?

A. It's well defined. I mean, we know all the genes involved, we know a lot about its assembly, but there's still questions about how the motor actually works, some of the biophysics, but other than that I think of any molecular machine this one is the most well understood and most defined.

Q. Sir, would it be fair to say that this is not just an organelle that intelligent design proponents have randomly selected to use for their arguments?

A. No, no, not at all.

Q. Is it fair to say that if you were going to find support for your arguments or support against your arguments, this would probably be the organelle that you would have to address in the literature?

A. Sure.

Q. Now, Dr. Behe and you just covered some of the components of the bacterial flagellum, and they appeared to be identified or named in using names that we sort of recognize as part of engines and as part of machines. Are those labels that scientists actually apply to these components?

A. Right. I mean, again this is out of a textbook, and you know, some may say that well, if you draw something to look like a machine it becomes a machine, but this is a true rotary engine, and by definition it's got to have a rotor and stator and drive shaft and U joint for propulsion. It's an amazing engine I don't think just to me, but, you know, the people, those of us that work on it are fascinated by it.

In E. coli these things will rotate at about 17,000 RPM's on average, although there's some marine vibrios where these engines have been blocked at 100,000 RPM's. It's essentially a massless engine, so it can reverse direction in less than a quarter turn of the rotor. So, you know, it's got two gears, forward and reverse, water cooled, battery powered. It's a fascinating system.

Q. Now, the conclusion that something was designed, does that require knowledge of the designer?

A. No. Absolutely not.

Q. Why not?

A. Well, I mean, we can infer design, but the science isn't going to tell us anything about the designer unless it's, you know, signed on one of these components, and we haven't found that yet.

Q. So is it accurate for people to claim or to represent that intelligent design holds that the designer is God?

A. No, absolutely not.

Q. Has science answered this question, the source of design --

A. No.

Q. -- in your view?

A. No.

Q. Now, we're going to, we'll be returning to the bacterial flagellum a little bit later. I put up here a quote that I believe we heard already once in this trial from Theodosius Dobzhansky, did I pronounce that right?

A. Correct, Russian evolutionist.

Q. It says, "Nothing in biology makes sense outside the light of Evolution." Do you agree with this quote?

A. I don't. Not to belittle the importance of evolution, but this hasn't been my experience.

Q. Why?

A. Well, let's go to the next slide, and I've got a couple of quotes that I picked from my expert report. This is from a review by Carl Woese, it was published last year. He talks about this aspect, if could read it, "Molecular biology's success over the last century has come solely from looking at certain ones of the problems biology poses (the gene and the nature of the cell) and looking at them from a purely reductionist point of view," and this is part of Carl's point, you know, he disagrees with reductionism.

"It's produced an astounding harvest." So a reductionist approach to biology has been astounding. "The other problems, evolution and the nature of biological form, molecular biology chose to ignore, either failing outright to recognize them or dismissing them as inconsequential as historical accidents, fundamentally inexplicable, and irrelevant to our understanding of biology. Now, this should be cause for pause."

So here you have, you know, Carl Woese really saying that there's this period in the last fifty years when molecular biology has kind of reigned that we've ignored the question of evolution, and this is a period I think where we've had the greatest increase in our understanding of biological systems I'd say probably over the whole millennium beforehand.

Q. And who is Carl Woese?

A. He's a professor at the University of Illinois, a prominent evolutionary biologist. I have utmost respect for him.

Q. He's not an intelligent design advocate?

A. No, no.

Q. And if you'd just note, this is, it's listed here as Defendant's Exhibit 251, if you can just confirm that that's the exhibit that you're referring to, and it should be in your exhibit binder under Tab 5.

A. Yes, that's correct.

Q. And that's the article A New Biology For

A New Century?

A. Correct.

Q. I believe you have some additional demonstratives to make this point?

A. Yes. The next slide, this is a paper published in Cell in 2000. So Cell I think is most prestigious journal for biologists to publish in. Primary research articles of some length. It won't go into the nature of science. Simon Conway Morris is a paleontologist at Cambridge University. This is the introduction to his paper which is a review titled Evolution: Bringing Molecules Into the Fold. "When discussing organic evolution the only point of agreement seems to be: `It happened.' Given, therefore, this history and the most recent and spectacular advances in microbiology, it may seem curmudgeonly, if not perverse, to even hint that our understanding of evolutionary processes and mechanisms is incomplete. Yet, this review has exactly that intention."

So again this is one of the most prominent paleontologists, worked on the Burgess shale, Cambrian explosion, remarking that molecular biology had spectacular advances and, you know, I think with this knowledge, and going back and addressing fundamental questions in terms of evolution is justified. When you consider that statement, you know, the only consensus seems to be that it happened. Beyond that, you know, mechanisms, our understanding of mechanisms, processes, are incomplete.

Q. In this article, I believe it's marked as Defendant's Exhibit 255, and it's Tab 9 in your exhibit binder, can you verify that for us, sir?

A. That's correct.

Q. I'll move to the next exhibit, which is a paper by Lenski, et al., and I believe it's marked as Defendant's Exhibit 252, which will be under Tab 6 in the exhibit binder that you have. Are you familiar with this paper and its findings?

A. I am.

Q. What does this paper purport to conclude?

A. Well, if you go to -- well, this is a paper addressing evolutionary origin of complex features, really looking at the infusion of new genetic information in organisms and trying to look at, you know, the mechanism of that.

Q. Now, Professor Pennock is one of the co-authors of this paper, is that correct?

A. That's correct.

Q. And he's an expert who testified for plaintiffs, and he appeared rather giddy about the results that they achieved in this paper. Do you share his enthusiasm?

A. I like the paper, and I like the quotes. The thing that I hesitate when I bring this up first you all is, and I'll show you in the next slide, but this is out of Richard Lenski's lab, and they've been doing experiments over the last twenty years, long-term evolutionary of E. coli and hemostats or fermenters, looking at changes over, up to 40,000 generations, and --

Q. These are on living --

A. Living, on escherichia coli, again our standard model for these type of studies, and this in less than 20,000 generations they see the infusion of new information, but this is a mathematical model. These are virtual organisms. So I think there's a limitation, which I mentioned in my expert report.

Q. How do the results of these digital organisms compare with Lenski's results with living organisms?

A. Well, again you see change at a faster pace than the real experiment, so I think it's somewhat backward, I'm not a computer scientist, I don't understand the software, so there's limitation there as well and I'm the first to admit it, but as I read this paper it seems like there's a targeted logical program that these organisms can adapt to by mutation, much like viruses in your computer systems. So that's what they're measuring this change to.

Q. You picked a particular quote from this paper I guess to emphasize your points regarding that quote from Dobzhansky, is that correct, on this next line?

A. Right. That, and also the fact that students are often confronted with the absolute statement that Darwinism is fact, or if not evolution is fact and, you know, this is from the introduction of this paper that was, you know, in Nature. From the outset Darwin realized that organs of extreme perfection and complication, such as the eye, posed a difficulty to his theory." I mean, this is the argument of design.

"Such features are much too complex to appear de novo, and he reasoned that they must evolve by incremental transitions through many intermediate states, sometimes undergoing changes in function." This is variation in natural selection. "Now, there exists substantial evidence concerning the evolution of complex features that supports Darwin's general model. Nonetheless, it's difficult to provide a complete account of the origin of any complex feature, owing to the extinction of intermediate forms, imperfection of the fossil record, and incomplete knowledge of the genetic and developmental mechanisms that produced such features."

So in summary, if you go to the next slide, there's this admission in this paper, in Simon Conway Morris's paper, Woese addresses these facts as well, that we lack intermediate structures, we lack fossils, we don't have an adequate knowledge of how natural selection can introduce novel genetic information. That's the point of this paper with virtual organisms and mathematical and computer simulation, and then from my own experience going back to Dobzhansky's quote, "Nothing in biology makes sense outside the light of information," I have my own experience as well that I would like to --

Q. Please tell us your experience with regard to that quote that nothing makes sense in biology in light of evolution.

A. In my entire academic training as an undergraduate or graduate student or as a post-doc at Purdue and Princeton University, I never once took a formal course in evolution. In fact, when I requested it as a graduate student, you know, to include it on my graduate student study plan, it was refused by my committee with a, you know, you don't have time to do it, it's not necessary.

So that has been my experience as a biologist and a practicing, you know, experimental biologist, I've never been required to take a single course in evolution. My exposure formally was in my undergraduate 100 and 200 level introductory biology classes were we got basic evolution, you know, Haeckel's embryos, peppered moths, founder effect. So the basis tenets were there, but in terms of really looking at this in detail, I haven't.

Now, this isn't unique to me. When I, in my department of molecular biology, microbiology, and biochemistry there's only one other faculty member, although we've had three or four that have joined the department in the last year, so I can't say that absolutely, but since my tenure there in 1989 one person has took an actual course in evolution as a graduate student. So I find this amazing that, you know, we're doing hard-core molecular biology, and this was never part of our training.

I'm the only person and one other faculty member that have read Darwin, which again, you know, I think is a problem. I would like to correct that. I think it should be required that all students in biology read Darwin's Origin of the Species and be required to take a rigorous course at some level, preferably early on in their undergraduate degree careers, in evolution, because, you know, I find this ironic situation that although I've never been required to take this material, you know, in my training, the point now where I'm questioning its importance in my discipline, you know, has been quite an amazing experience.

Q. How so has it been quite an amazing experience?

A. Well, it's difficult to say. I mean, it's almost like you're a heretic in the camp. I mean, I'll put it like that.

Q. So to sort of summarize through some of these quotes from prominent evolutionary biologists and from your own experience, we had the greatest advances in biology perhaps in this last half century, and it's been primarily at the molecular level, is that fair to say?

A. Correct. I mean, molecular biology is focusing primarily on E. coli first and then extrapolating what we learn there to more difficult systems, eukaryotic systems, yeah, it's been an incredible period.

Q. Yet evolution has been practically inconsequential in the development of this information that we've gathered?

A. Carl Woese states that in his paper. I mean, some people considered it inconsequential. It was ignored, a historical accident.

MR. MUISE: Your Honor, I'm going to start moving into another area. I don't know if this may be a time to break.

THE COURT: Yeah, why don't we, I think that makes good sense. Why don't we break here for about twenty minutes, and we'll resume with the witness's testimony after that intermission, and we will return after the break. Thank you.

(Recess taken at 2:14 p.m. Proceedings resumed at 2:36 p.m.)


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