RationalWiki:Kitzmiller v. Dover annotated transcript/P004
- 1 Day 1 (26 Sept 2005): Morning Session - Direct of Dr. Kenneth Miller
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- 2 Day 1 (26 Sept 2005): Afternoon Session - Direct (continued) of Dr. Kenneth Miller
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- 2.71 End of Direct examination
- 3 Footnotes
Day 1 (26 Sept 2005): Morning Session - Direct of Dr. Kenneth Miller
THE COURT: All right. Thank you, Mr. Gillen. Before we get to our first witness on behalf of the plaintiffs, let me welcome our spectators to this and the parties, of course, and the media to this important case.
We're going to be in -- although this is a relatively large courtroom, we're going to be in fairly close quarters for a while. Those of you who are going to stick around will be here for the next week and for, it looks like, all of October, as well. I have been struck in the pretrial proceedings with the sense of decorum on the part of the parties and the spectators. I believe that that will continue, so it's not necessary for me to say much besides I want you to do that and respect the witnesses on both sides as they testify and avoid any expressions that would disrupt the Court in any way. I certainly haven't seen that, and I don't expect to see that in this case.
You would do me a favor and you would do counsel a favor and the parties a favor if you would restrict your movement in and out of the courtroom during testimony to a minimum. That's not to say that you can't leave, but don't leave lightly just because you're bored and you want to go out into the hallway and then filter back in again. If you must leave, that's certainly acceptable, but we want to keep the traffic to a minimum because I think that that keeps us better focused.
We will take breaks at reasonable intervals, and I assure you we'll have lunch, as well, a lunch break, and we will take this in a way that is deliberate and yet recognizes that we're going to be here awhile and we have plenty of time to try this case.
So with that -- now, Mr. Rothschild, you're not going to move for the admission, I don't think, at this point, of any exhibits, or are you with respect to your opening? Do you want to do that?
MR. ROTHSCHILD: No, I'm not, Your Honor.
THE COURT: I assume not. With that, then we can start with your first witness.
With the opening statements over, the real trial begins. First, the plaintiffs bring their witnesses. Before this happens, however, the judge reminds the public spectators of the behaviour expected of them—respect the witnesses, don't just leave and re-enter the room at a whim etc.
Section 1 
MR. WALCZAK: Plaintiffs call Kenneth Miller.
KENNETH R. MILLER, PH.D., called as a witness, having been duly sworn or affirmed, testified as follows:
THE CLERK: Please be seated and state your name. Please spell your name for the record.
THE WITNESS: Sure. Good morning, Your Honor.
THE COURT: Good morning.
THE WITNESS: My name is Kenneth R. Miller, K-e-n-n-e-t-h, initial is R., M-i-l-l-e-r.
THE COURT: You may proceed.
DIRECT EXAMINATION BY MR. WALCZAK:
Q. Good morning, Dr. Miller.
A. Good morning.
Q. Where do you live?
A. (Home address in Massachusetts stated, redacted by RationalWiki)
Section 1 notes
The first witness is Ken Miller, a professor of biology. He is here directly examined by one of the plaintiff's lawyers, Witold J. Walczak of the ACLU.
NB: some personal details mentioned in the transcript which are irrelevant to the matter at hand have been redacted by RationalWiki in an effort to preserve the privacy of witnesses, and in some cases, their children. The home address of Dr Miller is the first such example.
Section 2 
Q. What do you do?
A. I'm a professor of biology at Brown University.
Q. I'd like to direct your attention to what's been marked as Plaintiffs' Exhibit 214. Do you recognize this document?
A. Yes, I do. It's the first page of my resume or, as we academic guys call it, my curriculum vitae.
Q. Is this a fair and accurate representation of your background?
A. Yes, it is. The individual document is a few months out of date, but, yes, that is.
Q. I'd like to use this to go over your background. Focusing first on your education, you graduated from Brown University in 1970?
A. That's correct.
Q. And then you got a Ph.D.?
A. At the University of Colorado in 1974.
Q. And did you do a Ph.D. dissertation?
A. Yes, I did.
Q. And what was that on?
A. The Ph.D. dissertation was on the structure and location of the coupling factor on the thylakoid membrane or, as I once explained to my mother, I'm trying to figure out and tried to figure out in the thesis how plants capture the energy of sunlight and convert it into chemical energy and food.
Section 2 notes
Dr. Miller is being set up to be formally recognized by the Court as an "expert" witness. An "expert" witness is permitted to give an opinion as evidence, whereas a regular witness generally isn't.
The rules about expert witnesses are governed by Article 7 of the United States Federal Rules of Evidence.
The early questions are formalities designed to give the witness' background and establish their expertise in one or more subject areas. When all of this is complete, the plaintiff lawyers will then ask the judge for Dr. Miller to be accepted as an "expert" witness for a specific subject. Unless the defense have some strong grounds to object, this is usually approved by the judge. This process will be repeated for all of the expert witnesses.
Here Miller is asked how and where he got his Ph.D.
Section 3 
Q. Dr. Miller, I'm likely going to have to ask you to explain things the way you would to your mother a number of times during this testimony. Please bear with me.
A. Thank you, sir. I will keep that in mind.
Q. I'd like to focus now on your professional experience concerning your academic appointments. After you got your Ph.D., what did you do next?
A. I went to Harvard University to join the faculty as a junior faculty member, and I spent two years there in the position of lecturer in biology and then four years as assistant professor of biology.
Q. And then in 1980 you went to Brown University?
A. That's correct. I got a job offer from my undergraduate alma mater and jumped at the chance and returned to Brown in 1980. Two years later I was given tenure and promoted to associate professor, and four years after that, I was promoted to full professor, which is a rank I still hold.
Q. And you continue to teach at Brown today?
A. Yes, sir, I do.
Q. And you've been there consistently since 1980?
A. I have left town once or twice, but, yes, sir, I have been there consistently.
Q. And what do you teach at Brown?
A. I teach courses in molecular and cellular biology, and I also teach what is, in many years, the largest course that a university gives freshmen, an introductory to general biology course.
Section 3 notes
Section 4 
Q. Does that freshman-level course include a section on evolution?
A. Yes, it does. No course in biology would be complete without it.
Q. Dr. Miller, are you still involved in scientific research?
A. Yes, sir, I am. Not as much as I used to be, but I have a small lab and I have a couple of undergraduate students who work with me and I continue to do research.
Q. And remembering that I'm on your mother's level, could you just briefly describe the area of your scientific research?
A. Well, I continue to be interested in the structure and function of biological membranes. My main research tool is the electron microscope. And the main area in which I work right now is the process by which proteins go through, pass through biological membranes. And that's very important to cell biologists because it concerns basically how things get where they're supposed to be. Cells depend upon proteins getting to the proper destinations, and I'm trying to work on part of the mechanism of how they get there.
Section 4 notes
The first zinger in Miller's testimony: "No course in biology would be complete without" talking about evolution.
Miller's research involves cell membranes and related proteins.
Section 5 
Q. Now, directing your attention, again, on the first page still, to professional service and associations, it appears that you are a member of a number of professional associations, for instance, the American Association for the Advancement of Science. What is that?
A. The American Association for the Advancement of Science is, I believe, the largest scientific organization in the United States. It has tens of thousands of members. It includes scientists of all disciplines. And it probably, if any single organization can fairly be said to speak for the scientific community of the United States, it is that association. It's often called simply AAAS.
Q. And I note you're also a member of the American Society for Cell Biology. What is that?
A. The American Society for Cell Biology is one of the largest organizations of experimental biologists in the United States. It has seven or 8,000 members. As many as 12,000 people attend its annual meetings. And it is one of the, as I said, major organizations promoting experimental biology in the country.
Section 5 notes
Now we start to go through Dr. Miller's extensive list of professional association memberships.
Section 6 
Q. Now, I note you have held a number of positions as -- for instance, the chair of the American Society for Cell Biology program committee. It looks like you've had two stints as the chair of the education committee. What do those committees do?
A. Well, the program committee is the committee that organizes the scientific program of the annual meeting with more than 3,000 contributed talks and papers. And when I chaired the program committee, I was, in effect, the director of the scientific meeting picking the major talks, the symposia, organizing the poster sessions and so forth.
The education committee is a committee that promotes and supports scientific education at all levels. Almost all of our members teach at one university level or another, whether it's at the graduate level, perhaps in medical school or undergraduate colleges, and we organize programs to help our members stay abreast of new developments in teaching technology and to promote science teaching and education.
The committee also has, as does the society, a very strong interest in promoting K through 12 science education throughout the country, and we often weigh in on important issues that we believe affect the future of science education in the country.
Section 6 notes
"What do those committees do?"—we're slowly getting to the point of Miller's testimony: the difference between real science and ID.
Section 7 
Q. How do you become a chair of these committees?
A. I'm often -- when one is named a chair, one receives both congratulations and condolences at the same time. I believe that I was named the chair of the program committee because the newly-elected president of the society in that year, Susan Gerbi, was a colleague of mine and she wanted to leave her imprint on the scientific meeting, and therefore she was very comfortable with me heading the program committee. You might say that I got that job through the old girl network.
The education committee, however, is a different matter. I have been interested in education for quite a long time. I spend a lot of my time and energy teaching at the university level, and I've also been involved in writing textbooks at both the college and the high school level.
My colleagues on the committee and colleagues in the society are aware of that and several elected councils of the society thought that I would be basically the best person to chair that committee.
Section 7 notes
Section 8 
Q. I note you're also the past editor of a number of journals, for instance, the Journal of Cell Biology, the Journal of Cell Sciences, Advances in Cell Biology. First of all, what are these publications?
A. Well, the two journals that you mentioned are two of the leading journals in the field of cell biology. And I served a term as one of a panel of editors on each of these journals, and my function in that respect was to take manuscript submissions, scientific papers that were forwarded to me by the editor-in-chief of the journal, papers that had been submitted for publication, pick out referees or reviewers, often two or three or four scientists to critique those, look for scientific flaws, decide if they should be revised and decide if they have publishable quality. They would then report back to the editor.
I would then make an initial decision, all editors do, on whether or not they were suitable for publication, whether or not they needed to be revised, whether or not they should be rejected, and forward that decision to the editor-in-chief, who would then make the final decision.
In the case of the series Advances in Cell Biology, this was a series of monographs, which are papers, review papers written by individual scientists. And in that case, my authority was somewhat greater and somewhat different in that I solicited manuscripts from various scientists who were doing cutting-edge work. I asked them to summarize their work and the work in the field, and I then bundled these 10 or 15 papers a year into this proceeding, which was designed to keep scientists abreast of cutting-edge developments in the field.
Section 8 notes
Section 9 
Q. I'd like to direct your attention to Page 2 of your curriculum vitae. There's a topic there, it says, Scientific Papers. There are a lot of listings on Pages 2 through 5. Do you know how many are listed there?
A. Actually, I haven't counted them. I think it's in the neighborhood of 45 to 55, somewhere in that vicinity.
Q. Now, the heading there says, Scientific Papers. Is there some particular meaning to that?
A. Yeah, most scientists would understand it right away. What this means, in more specific terms, is that these are scientific research papers that have been published in peer-reviewed scientific journals.
Q. And this concept of peer review, for us non-scientists, what does that mean?
A. Peer review is the essence of the scientific process. It means, basically, that when you've done research that you think is sufficiently important and rigorous to merit attention and publication, you send it off to a journal. The journal will then have several of your colleagues in the field, people who can be disinterested, objective, and critical evaluators, tear your paper apart, if they possibly can, try to find flaws, try to find problems with it. The editor will then mediate whether your paper is going to be rejected or perhaps revised a little bit.
But it is the essence -- peer review is the essence of the give and take that goes forward in the scientific community to try to ensure, especially in leading journals, that the papers that are published are scientifically accurate, that they meet the standards of the scientific method, and that they are relevant and interesting to other scientists working in the field.
Section 9 notes
Miller doesn't obsess over or even bother counting the number of papers he has counted, but they're about as numerous as the Discovery Institute's own list of ID-supporting "peer-reviewed" papers (which are quite terrible and often only tangentially related) even seven years later.
Miller also here explains the peer-review process for the layman.
Section 10 
Q. If you could turn to Page 6. I note there's a heading there that says, Secondary Textbooks and Teaching Materials. And if you could flip over to Page 7 first. At the top there it says, College Textbooks. Are you the author of some college textbooks?
A. Yes, yes, I am. Together with a colleague named Joseph Levine, I have coauthored two college textbooks in general biology that were published by the D.C. Heath Company. That company has now gone out of business, and those two textbooks which were published in 1990 and 1993 are out of print. At the peak of their usage, they were used by more than 200 colleges and universities around the country.
We are currently at work on a new college-level manuscript, and we hope to have that published in the years ahead. I notice -- I mentioned the CV was a little bit out of date -- it says, Expected publication, 2005, W. H. Freeman Company. We and our publishers, Freeman, have had a parting of the ways because we had a fundamental disagreement on what this book should be like, so we are currently considering other offers of publication. So this book will not be published this year.
Q. You mentioned that this book is not still in use at the college and university level. Why is that?
A. It's not still in use because it was last copyrighted in 1994, and by science standards, that's an ancient text. Science moves so quickly that material in a textbook that's ten years old is certainly going to be seriously out of date. And I think that's one of the reasons why even those instructors who liked and really enjoyed working from our book would certainly not use it today, simply because there's too much science that has passed under the bridge.
Section 10 notes
"Science moves so quickly that material in a textbook that's ten years old is certainly going to be seriously out of date."—the most recent edition at that time of Of Pandas and People was similarly old, having been published in 1993.
Section 11 
Q. Now, if you would flip back to Page 6 of your curriculum vitae, I note that you have also been the author of a number of high school textbooks. When did you first start writing those textbooks?
A. To be perfectly honest, I first started writing when I was persuaded by Joseph Levine, my coauthor, that this would be a good thing to do, and we first started writing our first manuscript in 1982.
Q. And the first publication was in 1990?
A. The first publication was in 1990, so it took us eight years to go from conceiving and beginning the manuscript to our first publication.
Q. Now, I note there appear to be -- I don't know if it's a number of different editions or these are different books. Could you explain that?
A. Yeah. All of these books have been published by the Prentice Hall Company, which is now a division of Pearson Publishing. And I tried on this to list a number of different editions. The first book -- they all have catchy titles like Biology. The first book, you'll notice, is simply called Biology, and it came out in five different editions, first through fifth. The second book is called, Biology, the Living Science. It came out in two editions. The third book, we liked that original title, I guess, and just went back to plain old Biology, but that is an entirely different book from the earlier Biology.
High school teachers, I have to say, have a way to distinguish these books. They name them by the animals on their cover. So high school teachers will know the first book is the elephant book, the second book is the lioness book, and the current book, the one near the bottom, as the dragonfly book. So altogether, these books have -- there have been three different books, and they have appeared in the neighborhood of 11 or 12 different editions.
Section 11 notes
Section 12 
Q. I show you what's been marked as Plaintiffs' Exhibit 31. Is this the cover of the dragonfly book that you mentioned?
A. Yes, sir, it is.
Q. And this is the 2004 edition?
A. This, I believe, is the cover of the 2004 copyright, correct.
Q. And are you working on yet another edition of this book?
A. Yes, sir. This weekend Joe and I were working on final revisions for what will be a 2007 copyright of this book, and we are about six months away from starting on a complete rewrite of the entire textbook.
Q. Is this a textbook that's used in the Dover Area School District, to your knowledge?
A. My understanding, sir, is that it is.
Q. And is it used anywhere else besides Dover?
A. It is used in each and every one of the 50 states of the United States and several foreign countries.
Section 12 notes
Miller's own highschool textbook was much more up-to-date.
Section 13 
Q. Do you know how many high schools use your biology book?
A. I can't give you a number in terms of the number of schools, but I have been told by my publisher that about 35 percent of the high school students in the United States use one or another of the various textbooks we've been discussing.
Q. And what topics are covered in this biology textbook?
A. Soup to nuts. We start out with the nature of science, the nature of biology. We talk about the structure of the cell, cell biology. We talk about molecular biology and genetics, ecology, evolution. We do a phylogenetic survey, which is a biologist's term for looking at all the various categories of living things, and we conclude the book by looking at the various systems of the human body.
So we try to provide in the book not a curriculum, but a resource bank from which teachers can draw as they put their curriculum together for the types of courses that students need to take in Pennsylvania and other states to meet state requirements.
Section 13 notes
Section 14 
Q. And as part of your process in writing and developing these books, are you familiar with, say, the competition, competing high school biology textbooks?
A. Certainly. It is a free market and a competitive market, and it always pays to keep an eye on the competition, so I keep an eye on the other books, as well. And they do the same for us, of course.
Q. And do you send your manuscripts, if that's the right term, to high school teachers for feedback about whether the subject is presented right or for any reason?
A. Yes, we do.
Q. And why do you do that?
A. We do that for a couple of reasons. Joe and I are presumed to know the scientific field, but every time we write a chapter and we edit our chapters for each other, we, first of all, send it to a scientific expert to make sure that we've got the science right. Even if it's my own field of cell biology, I'm eager to see a critical opinion from another researcher to see if I got it right.
But we also send these chapters to individual experts in secondary school education, individual high school teachers, and focus groups or panels of high school educators to critique whether or not we have explained things in a way that they think their 14- and 15-year-old students will understand, whether the text is interesting, and whether the text is going to be helpful to them in the classroom in the goal of getting students turned on to science.
Section 14 notes
Section 15 
Q. So do you make changes in each subsequent edition in response to the feedback you've gotten from high school teachers?
A. Yes, we do, quite a few changes.
Q. Now, isn't it unusual for a research scientist to also be a high school textbook author?
A. I suppose it is.
Q. Why do you do it?
A. Originally, when I was approached by Dr. Levine, I told him to take a hike. I said I wasn't interested in this. At the time I was a few months short of a tenure decision, and the only thing that matters at a research university is getting my scientific papers out, getting my grants funded, and getting the respect of my colleagues in the field. But he managed to show me a few existing books that were used in high schools, and he pointed out at the time I had two young daughters and most scientists would like nothing more than to see their children go into science.
And as I leafed through the books, they were all perfectly okay, but I found two problems with them. One is they were dreadfully boring. I couldn't look at these books and imagine why anyone would want to go into science. And then the second thing is, they sort of gave the impression that everything had been discovered. And any person in experimental science knows that's just not true.
So I called Joe back, and I said, Joe, let's do this, because I'd like to write a book with you that would turn kids on to science, that would tell them about the great unexplored territory that lies out there and would tell them that the most interesting thing one can possibly do, short of a career in law, of course, is to have a career in science.
Section 15 notes
Section 16 
Q. Have you ever testified in court before as an expert witness?
A. No, sir, I have never testified in court as an expert witness.
Q. Have you testified in court on the subject of biology and evolution as you will be doing today?
A. Well, earlier, actually last year, I did testify in federal court as a fact witness in a trial that related to the teaching of evolution.
Q. And what was that case?
A. I believe you'll correct me if I have this slightly wrong, but the case is known as Selman versus Cobb County. And it concerned a case in which the Cobb County Board of Education had attached a warning sticker to all textbooks that contained material about evolution. And this warning sticker or this label had a three-sentence admonition to students.
A number of parents, as I understand the case, a number of parents in the district objected to this sticker being placed on textbooks. They filed a lawsuit in federal court. I was contacted by attorneys for the plaintiffs. They pointed out that my book was one of the ones that had had the sticker placed on it, and they asked me if I could come as a witness of fact to tell the Court how textbooks are put together, what the decisions were that I made into my textbook, and perhaps also to comment on whether or not I thought the sticker was an appropriate tool to advance education.
Q. And you did, in fact, testify, I believe it was in November of 2004, in the Selman case?
A. Yes, sir, that's correct, I did.
Section 16 notes
Getting closer to the meat now: Miller says that he has never before testified as an expert witness, but he had been a witness in the earlier Selman v. Cobb County textbook warning sticker case testifying about how textbooks are created.
Section 17 
Q. I'll ask you about your experience with creationism and creationists. Have you been involved with the creationist movement?
A. I suppose you could say I have been involved with the movement, yes.
Q. And could you tell us how you got into this?
A. The very first year that I taught at Brown University, in the fall I taught part of a very large freshman-level introductory biology course. So a lot of students saw me as a new professor at Brown, and I guess they rather liked my energy, enthusiasm, and teaching style.
And in the spring, when I was not teaching, I was setting up my research laboratory, a group of students came to me and they said, we really like your lectures in Bio 11, which was the course. I said, gee, thanks a lot.
And they said, there's a fellow whom the Christian students association is bringing to campus. His name is Henry Morris. He is the founder and the president of the Institute for Creation Research in California, and he has dared any scientist on campus to debate him. You're pretty good at giving lectures, why don't you debate this guy? And at first I told the students, no, I'm not interested. And they said, why? And I said, because I'm a cell biologist, I'm not an evolutionary biologist. I want to set up my research lab, so please go away.
But they were very persistent, and they started to pester me and say, well, does that mean this guy is right? I said, no, it doesn't mean this guy is right. And they said, well, if he's not right, why don't you debate him?
So finally I agreed to go ahead and do this. I had a couple of conditions I attached to doing that. I'm glad I did. One of those conditions was that the students would get me audiotapes, books, and pamphlets of the so-called creationism or creation science movement so that I could see what the arguments were that I was likely to face.
And my recollection is I spent almost four solid weeks listening to the arguments presented, looking up the arguments, because many of them were in geology and physics and astronomy and way outside of my scientific field, making sure that I understood them and preparing for that debate.
And we finally debated in April of 1981. We had the debate, as it turns out, at the largest building on our campus, which is the hockey rink, and it drew nearly 3,000 people. It was very interesting. And I believe, on the basis of reports of a wager made by the science writer and the religion writer for the Providence Journal, I believe that I prevailed in the debate, though one can never say for sure. And over the next several years, I engaged, I think, in three more debates with scientific creationists.
Section 17 notes
Section 18 
Q. And have you also written articles critiquing creationism? And I guess I would direct your attention to Page 5 of your curriculum vitae, and there's a section, Articles in Defense of Scientific Integrity.
A. Yes, I have. And this section lists three of them. And these date from the period when I was debating scientific creationists in the early 1980s. I wrote an article for teachers in the American Biology Teacher. I took some of the arguments I had faced in the debate and I put answers out in a small journal called Creation Evolution so that other people who might engage in debate could have the benefit of my research and experience on this.
And I also wrote an article for -- an edited volume edited by the very distinguished anthropologist, Ashley Montagu, on scientific creationism in 1984. So, yes, I have written on the subject.
Section 18 notes
Section 19 
Q. I'm going to ask you about your experience now with intelligent design. Have you been involved in debates, public debates, over the notion of intelligent design?
A. Yes, sir, I have.
Q. And when was the first one?
A. Well, the first one I didn't actually know was going to be about intelligent design. I was approached by an organization of -- I believe of largely Evangelical Christians known as the American Scientific Affiliation, and they asked me if I would come to their summer meeting, I think it was in Asheville, North Carolina, it was in North Carolina, and debate a biochemist from Lehigh University on the subject of a textbook for public schools called Of Pandas and People.
And I had never heard of the book at the time. They mailed me a copy. I read through the book. And I was unfamiliar with the person who opposed me in debate at that time, but his name was Michael Behe, and as I mentioned, he's a biochemistry professor from Lehigh University. And that was the first place where I heard the term "intelligent design" used in place of the more familiar creation science, which I had debated with various people in the early 1980s.
Q. Was this the only debate you had on intelligent design?
A. No, sir, it isn't. And I'm sorry that I cannot give you an exact number, but if you count point counterpoint debates in print, radio debates, and debates in person, I would expect that probably I have debated on the issue of intelligent design 12 or times, quite a few more times than I debated scientific creationism.
Section 19 notes
Miller's first contact with ID came from a debate with Michael Behe, which was effectively a case of "intelligent design" being substituted for "creation science." Miller has by this point debated more against design proponents than with overt creation scientists.
Section 20 
Q. And you have also written articles about intelligent design. I direct your attention to Page 6 under Essays and Reviews. Now, are some of these articles about the concept of intelligent design?
A. Yes, sir, they are. The 1994 article called Life's Grand Design in Technology Review actually foreshadowed many of the arguments of intelligent design, so it clearly was on that issue. And then the last three articles that are listed, the one in Natural History magazine, the one in 2003 in the volume edited by Neil Manson, and the one in 2004, which is listed there in press but now, in fact, has been published -- I said this was just a tad out of date -- all of these deal with intelligent design.
Section 20 notes
Section 21 
Q. I want to talk about one more listing on your curriculum vitae, and that's on Page 7 under General Audience Books. There is one book there that I think has a provocative title, Finding Darwin's God. What's that about?
A. I meant the title to be provocative. This is a general audience book or a trade book, as publishers call it. And one of the experiences that I had over the years appearing in public and talking about evolution is that many people would tell me that no matter how compelling the scientific arguments were that I made in favor of evolution, they were bothered by the fact that it was perfectly obvious that evolution was an inherently atheistic or God-denying theory.
And I'd just sort of shake my head and shrug and say, I don't think so, and point out the fact that I'm a person of faith and a regular churchgoer, and I certainly don't see any conflict. And they would ask me to explain, and I would explain. Another day I would explain, another day I would explain again. And finally I decided, you know, I should probably write a book about this because a lot of people are interested.
So I wrote a book called Finding Darwin's God, and the subtitle of that book I think is more revealing of content, and that is, A Scientist's Search for Common Ground Between God and Evolution. And what I tried to do in the book was twofold, first to explain why science, sciences and the scientific community, find evolution to be so useful, so valuable, and so compelling as a scientific explanation, and then, secondly, to explain how a person of faith -- although I'm a Roman Catholic, I tried to construe this in a vary broad way so that I would say how a person following any of the great Abrahamic religions could appreciate evolution in the context of their faith. And I hope very much I was successful in doing that.
Q. Now, that's not a scientific publication, you said that's a trade publication?
A. It certainly is not a scientific publication. Everything that a scientist writes or says is not necessarily a scientific statement or a scientific publication.
Section 21 notes
Miller wrote a pop-sci book arguing against the idea that evolution is inherently atheistic.
Section 22 
MR. WALCZAK: Your Honor, at this time we would proffer Dr. Miller as an expert in biology, evolution, instructional biology materials for high school students, creationism, and intelligent design.
THE COURT: All right. Thank you. Cross-examination?
MR. MUISE: Your Honor, pursuant to the stipulation of the parties, we would agree that the experts are qualified to testify within their area of expertise, the only exception being plaintiffs' expert Barbara Forrest, which we will then, at that time, take the opportunity to voir dire. But we don't have any objections based on that stipulation.
THE COURT: I understand. Thank you, Mr. Muise. You may proceed. And he is admitted for that purpose for the record.
MR. WALCZAK: Thank you.
THE WITNESS: Thank you, Your Honor.
Section 22 notes
Based on the examination above, at this point Mr Walczak asserts that Dr Miller is "an expert in biology, evolution, instructional biology materials for high school students, creationism, and intelligent design." The judge asks defence lawyer Robert Muise his opinion; he agrees that all of the plaintiff's experts are "qualified to testify within their area of expertise," with the sole exception of Barbara Forrest which he says that he will bring up at the appropriate time.
Section 23 
DIRECT EXAMINATION (continued) BY MR. WALCZAK:
Q. Dr. Miller, I want to ask you five questions to elicit your opinions about the big issues in this case. Do you have an opinion about whether evolution is a testable theory that is accepted by the scientific community?
A. Yes, sir, I do.
Q. And what is your opinion?
A. My opinion is that evolution is an eminently testable theory and that it is broadly and generally accepted by the scientific community.
Section 23 notes
Walczak continues his direct examination of Miller. He asks if evolution is an accepted and testable theory; Miller replies that it is "eminently" so.
Section 24 
Q. Do you have an opinion about whether intelligent design is a testable theory that is accepted by the scientific community?
A. Yes, I do.
Q. And what is that opinion?
A. My opinion is that intelligent design is not a testable theory in any sense, and that as such, it is not generally accepted by the scientific community.
Q. Do you have an opinion about whether intelligent design is or even can be properly considered a scientific theory?
A. Yes, I do.
Q. And what is that opinion?
A. My opinion is that intelligent design is not science, and therefore it cannot be construed as a scientific theory in any sense whatsoever.
Section 24 notes
In contrast, Miller says that ID is neither testable, accepted, nor science.
Section 25 
Q. Do you have an opinion about whether intelligent design is a particular religious view, namely a form of creationism?
A. Yes, sir, I do.
Q. And what is that opinion?
A. I believe that intelligent design is inherently religious and it is a form of creationism. It is a classic form of creationism known as special creationism.
Section 25 notes
Miller calls ID inherently religious, and a form of creationism: this is the conclusion that will be drawn by the judge at the end of the trial.
Section 26 
Q. Do you have an opinion about whether the four-paragraph statement read by the Dover School District promotes students' understanding of evolution in particular and science generally?
A. Yes, I do.
Q. And what is your opinion?
A. I think the statement by the Dover Board of Education falsely undermines the scientific status of the theory of evolution, and therefore it certainly does not promote student understanding or even critical thinking, and I think it does a great disservice to science education in Dover and to the students of Dover.
Section 26 notes
In his opening statement defence lawyer Patrick Gillen contended that the statement read to students "would, in fact, enhance the biology curriculum." Miller here claims the opposite.
Section 27 
Q. Let's now explore the basis for your opinions. What is science?
A. You ask a good question. It's useful, I think, to parse it to where the word comes from. The word "science" comes from the Latin word scientias, which means knowledge. And in the most general sense, the word "science" is sometimes used to just say learning systematic knowledge, for example, library science or political science.
But I think that in the context in which the word "science" is going to be used in this case, what we mean by "science" is what we would call natural science, sciences such as chemistry, physics, and astronomy. And natural sciences I think are best described as the systematic attempt to provide natural explanations for natural phenomena.
Section 27 notes
Section 28 
Q. Are there rules for scientific inquiry?
A. Yes, there are.
Q. And what are these rules?
A. Well, you just heard one of the rules in the definition of science, which is that science tries to provide natural explanations for natural phenomena. So one of the most basic rules of science is that we tend -- what we require, the practitioners of science seek their explanations in the world around us, in things we can test, we can observe, and we can verify. Now, there are certain rules of procedure, as well. And among those are that scientific inquiry must be open, that it must be subject to duplication, replication, test and examination by other scientists. For example, I could never publish a result saying I had made an observation on a particular protein without also telling people what my methods were and how I made that observation. And the point is to make my work and my observation testable.
And then the final and sort of open rule basically is that science is always an activity in which everything in science is open to critical examination, replication, peer review, and discussion by other scientists.
Q. Is this just a view held by Professor Miller?
A. No, I don't think so. I think the way I have described science and the process of science would be generally held by most members in the scientific community.
Section 28 notes
Section 29 
Q. I'd like to direct your attention to what's been marked as Plaintiffs' Exhibit 649. Do you recognize this publication?
A. Yes, sir, I do.
Q. I note at the bottom it says, National Academy of Sciences. Now, this is an organization that we're going to be hearing about repeatedly. What is the National Academy of Sciences?
A. Well, if my recollection serves me well, the National Academy of Sciences is an organization that was established by act of Congress, I believe when Abraham Lincoln was president, and it consists of the elite and most accomplished scientists in every scientific field.
One of the greatest honors that an American scientist or, actually, even a foreign scientist, because we have foreign associate members in our national academy, one of the greatest honors that a scientist can receive is to be tapped for membership in the National Academy of Sciences.
I believe the National Academy of Sciences is also charged with advising the president and the Congress on matters of scientific interest and importance.
Q. Are the publications of the National Academy of Sciences something that are reasonably relied on by scientists in the field?
A. Absolutely, yes.
Section 29 notes
Section 30 
Q. I'd like to direct your attention to Page 27 of Exhibit 649. I've asked you before to highlight a passage on this page. Is that correct, Dr. Miller?
A. Yes, you have.
Q. Could you please read for the record the highlighted passage?
A. Be glad to. This is the opening of the third section of this book, and it opens basically by defining science. And it says, and I quote, Science is a particular way of knowing about the world. In science, explanations are restricted to those that can be inferred from confirmable data, the results obtained through observations and experiments that can be substantiated by other scientists. Anything that can be observed or measured is amenable to scientific investigation. Explanations that cannot be based on empirical evidence are not part of science.
Q. Do you agree with that statement?
A. I certainly do.
Section 30 notes
Section 31 
Q. How long have these rules of science been in effect?
A. I'm tempted to say forever, but I think certainly for the last 200 years of contemporary science, the notion that science -- in other words, all of the 19th Century and all of the 20th Century and now into the 21st -- the notion that science can only deal with empirical data, what we can see, what we can observe, and what we can measure, has been part of the common understanding of science in all people in all cultures.
Q. So science doesn't -- these rules don't just apply in the United States?
A. No, sir, they don't. I think science might be the closest thing we have on this planet to a universal culture, and these rules apply everywhere.
Section 31 notes
Section 32 
Q. Why are these rules important?
A. These rules are important because if you don't have these rules, you don't have science. The entire -- human beings are fallible, and I mentioned that science is a human activity. It's a systematic search for natural explanations for natural phenomena.
And if you invoke a non-natural cause, a spirit force or something like that in your research and I decide to test it, I have no way to test it. I can't order that from a biological supply house, I can't grow it in my laboratory. And that means that your explanations in that respect, even if they were correct, were not something I could test or replicate, and therefore they really wouldn't be part of science.
Section 32 notes
Miller says that you can't test for the supernatural, and it is therefore not science.
Section 33 
Q. So supernatural causation is not considered part of science?
A. Yeah. I hesitate to beg the patience of the Court with this, but being a Boston Red Sox fan, I can't resist it. One might say, for example, that the reason the Boston Red Sox were able to come back from three games down against the New York Yankees was because God was tired of George Steinbrenner and wanted to see the Red Sox win.
In my part of the country, you'd be surprised how many people think that's a perfectly reasonable explanation for what happened last year. And you know what, it might be true, but it certainly is not science, it's not scientific, and it's certainly not something we can test. So, yes, those rules certainly apply.
Section 33 notes
It might be true that God influences the outcomes of sporting events, but that wouldn't be scientific.
Section 34 
Q. Does science consider issues of meaning and purpose in the universe?
A. To be perfectly honest, no. Scientists think all the time about the meaning of their work, about the purpose of life, about the purpose of their own lives. I certainly do. But these questions, as important as they are, are not scientific questions.
If I could solve the question of the meaning of my life by doing an experiment in the laboratory, I assure you I would rush off and do it right now. But these questions simply lie outside the purview of science. It doesn't say they're not important, it doesn't say that any answer to these is necessarily wrong, but it does say that science cannot address it. It's a reflection of the limitation of science.
Section 34 notes
Section 35 
Q. Could you briefly tell us, how is it that scientists do their work? How is it that you approach a particular problem?
A. There are probably as many ways to approach scientific problems as there are scientists. But I think one of the key questions, one of the key aspects of this is thinking of a question. Now, that's, in many ways, the hardest thing to do. But what we try to do is to look at the natural world and try to narrow down a specific question from the point of view that we can develop a very specific testable hypothesis about that question.
And in many ways, that's the greatest art of being a scientist, because no one tells you how you come up with good questions. But a good question is one that is important, the result will be interesting to other people, other scientists, as well, it will shed light on a natural biological or physical or chemical process, and we can phrase a hypothesis about it in a way that we can actually devise a test.
And once we frame that really good hypothesis, we do an experiment, we go into the field, we look for evidence, we do measurements, we make observations, and we try to gather the data that will be sufficient to confirm or refute the hypothesis. And if we confirm it, we don't consider it to be proven, you never prove anything in science, but we consider it to be supported, and then very often we go on and ask another tough question about the same hypothesis. If the hypothesis is refuted, we discard it, go back, think of a better idea. That's as close as I can come to a good description.
Section 35 notes
Section 36 
Q. So after you have the hypothesis, after you've gone and done the experimentation or observation, is there something you do with the data after that?
A. Oh, excuse me, I'm talking about the work of an individual scientist. And if you think you either have the data that refutes an important hypothesis or data that tends to support and confirm an important hypothesis, if you think this will be of interest to other people in the scientific community, you then gather up your methods, your procedures, your experimental data, might be photographs, might be diagrams, results, tables, gels that we run in the laboratory, something along those lines, and you put them into a scientific publication. You write a paper and you send that paper to a reputable, hopefully a prestigious, if you think it's important work, scientific journal, and you immediately subject it to peer review and criticism by your colleagues.
Section 36 notes
Section 37 
Q. Now, is this peer-review process important? Tell us a little bit of how it works.
A. It's exquisitely important. You don't have science without it. And the way in which it works is, for example, I will write up my research in the manner that I have just described and send it off, perhaps, to Nature or the Journal of Cell Biology or something along those lines.
An editor at the other end will read my work, will consult, perhaps, with other editors, try to find three or four experts in the field who are knowledgeable about the kind of work I'm doing and the questions I'm asking, send it out for review. Those people will then examine the paper. They'll look for methodological flaws. Perhaps I used the wrong reagent, perhaps I used the wrong reaction temperature. They'll look for logical flaws. Perhaps the experimental results I got don't really mean what I think they mean. And they'll also look for novelty.
And by novelty, if the work I'm doing just confirms a hypothesis that has already been abundantly confirmed, nobody really cares, and that's what I mean about novelty. They will then decide if my paper is absolutely fabulous and should go right into the journal or if it can be accepted in the journal if I make a few changes, corrections, do another experiment, or basically if I should be sent back to the drawing board saying, this is not worthy of publication in our journal.
The Journal of Cell Biology, for which I served a term as editor, had a rejection rate of about 60 percent, which meant that six papers out of ten were simply sent back saying, we're not going to publish this.
Section 37 notes
Many papers are rejected from journals because they're just bad: in the case of the Journal of Cell Biology the rejection rate is around 60%.
Section 38 
Q. So unless a theory meets these rules of science and has gone through these procedures of science, can it be accepted as a scientific theory?
A. Well, you've actually jumped from sending a scientific paper in to what constitutes a theory and how can a theory be accepted. I have never done any research so grand that I would have described in any of those papers a new theory that I have. Hypotheses, yes, but theories are a whole other level of understanding.
Theories are broad, useful, powerful generalizations that explain and unite a broad range of facts. Theories have to make testable predictions, because otherwise they're not useful as theories. If a theory is enunciated to explain a natural process, it has to make predictions that lead to testable hypotheses so that people can go into the laboratory, can make those tests, and can tend to confirm or refute the theory.
Q. But if a theory does not meet these ground rules of science, testability, observability, they are not considered scientific?
A. It's just not a scientific theory, that's correct. And my tongue-in-cheek explanation of the baseball playoffs last year falls into exactly that category. It's not a theory because it's not scientific and it's not testable.
Section 38 notes
Section 39 
Q. Now, this nonscientific theory, does that mean its wrong?
A. Oh, of course not. I also said, again, thinking about that silly example, a lot of people in my part of the country think that's absolutely true. Explanations that lie out of science can be true, but they're not scientific. And I think that applies to the sort of theory that you were talking about.
Section 39 notes
If it's not scientific it's not necessarily wrong.
Section 40 
MR. WALCZAK: Your Honor, I know, has indicated that we'll take periodic breaks, and this is actually a good breaking point for us.
THE COURT: Yes, I think it's an opportune time for us to break. Let's break for a reasonable interval. We'll see what we'll do as far as the duration of the breaks as we go, but we'll probably take at least 20 minutes, I would say, so that people can have an ample break. We may take longer if we need to. So this will be our midmorning break, and we'll stand in recess.
Section 40 notes
Thye take a 20min break.
Section 41 
THE COURT: Mr. Walczak, you may continue.
MR. WALCZAK: Thank you, Your Honor.
DIRECT EXAMINATION (continued) BY MR. WALCZAK:
Q. Dr. Miller, I want to shift gears. We just talked about the science and the nature of science, and I want to now move to the topic of evolution. What is evolution?
A. You always ask good questions.
Q. Thank you.
A. Most biologists would describe evolution as a process of change over time that characterizes the natural history of life on this planet.
Section 41 notes
Miller defines evolution as "change over time."
Section 42 
Q. And are there certain core propositions to evolutionary theory?
A. Yeah, I think there are, and I think basically there are three. And the first one is the observation that life really has changed over time, that the life of the past is different or was different from the life of the present, and that the natural history of this planet is characterized by a process of change over time.
The second thing, the second core element, I guess, is the principle of common descent, and that is the notion that living things are united by a core of common ancestry, that living things, if you trace them back far enough, show common ancestors that gave rise to the many forms of life today.
And the third core proposition and I think probably the simplest way to state it is the process that drove that change through time from common ancestors and common descent is driven by forces and principles and actions that are observable in the world today. And the key, therefore, is that we can understand how evolution works by looking at what's happening in the world around us today.
Q. And is there a name for that force that drives the change?
A. The force that drives the change, actually, there are many individual forces and processes. Many of them are united under the term of "natural selection."
Section 42 notes
Evolution is based on the following core propositions:
One of these forces—though not the only one—is natural selection.
Section 43 
Q. Now, there's a gentleman named Charles Darwin who played some role here. I was wondering, who was Charles Darwin?
A. Charles Darwin was a British naturalist who was born on February 12th, 1809. If memory serves me well, that's a better-than-average day for the history of humankind because Abraham Lincoln was born on exactly the same day.
He lived in Great Britain, he studied natural history and studied theology, became a naturalist, traveled around the world on a British ship called the Beagle, made a number of very interesting observations during that trip and came back from that trip to think, to write, critique his ideas for many years, and then wrote a series of books which are the foundation of what we consider to be modern evolutionary theory.
Section 43 notes
Section 44 
Q. And what was Darwin's contribution to evolution?
A. Well, one of the -- I think the most interesting and oftentimes overlooked aspects is that the first core proposition of evolution, which is that life has changed over time, was actually appreciated well before Darwin was born.
The great French naturalist Cuvier recognized that the fossils told a record of life in the past and that that record was a record of change, and that as life changed into the present, new organisms appeared and old organisms went extinct. So the process of change, what we sometimes today simply call the process of evolution, that was understood well before Darwin.
What Darwin did for the first time was to propose a plausible, workable, and ultimately testable mechanism for the processes that drove that change, and that is the mechanism of natural selection.
Section 44 notes
Darwin did not invent the whole of the theory of evolution, and certainly not without historical precedent. Cuvier—who in fact opposed evolution in the sense that one fossil form could change into another, but recognised that fossil organisms existed for a period and then were replaced—did his work around the turn of the 19th century, around fifty years before On the Origin of Species was published.
Section 45 
Q. And has evolutionary theory stood still since Darwin's time or has it evolved?
A. It has -- nothing in science stands still, and that's true of evolutionary theory, as well. Charles Darwin lived and worked and wrote at a time when, for the most part, scientists were unaware of the existence of genes, of macromolecules, certainly of DNA, and a host of other tools and techniques by which we study biology today.
And to me, as a scientist, the most remarkable thing about evolutionary theory is that as the science of biochemistry has developed, as the science of cell biology, genetics, molecular biology, and other elements of science have developed, all of these have fit beautifully into the general framework described by Darwin almost 150 years ago.
Section 45 notes
Evolutionary theory has not stood still since Darwin either, with new discoveries and techniques adding to the theory.
Section 46 
Q. So the evolutionary theory draws on many branches of science?
A. Yes, it does.
Q. How has the emergence of modern genetics and molecular biology affected scientists' views of evolution?
A. Well, genetics really is the first one and I think in some historical respects the most interesting within. Charles Darwin, towards the end of his life, was worried about something, and what he was worried about was that favorable characteristics that might appear in organisms might be blended away as they had to mate to reproduce.
So if an individual showed up with a really good characteristic that could be favored by natural selection, its offspring might only have half of that characteristic because Darwin thought that the inheritance of organisms blended in their offspring, and the next generation a quarter and the next generation an eighth, and after a while, no matter how favorable the variation was, it would be gone.
Well, the discovery of genetics, beginning with Gregor Mendel in the 1850s, suddenly answered Darwin's most profound concern because it showed that genetics, inheritance, is particulate. And what I mean by that sort of a jargon term in science is that our inheritance is controlled by individual units called genes which are passed from one generation to the next.
And that solved Darwin's problem because it showed that inheritance is not really a blending and that these favorable characteristics can actually be preserved. So modern genetics, basically, we might say, came to the rescue of a potential problem in evolutionary theory.
Things got better when molecular biology added the dimension of DNA and RNA, because for the first time we could understand how evolution could work right down to the level of the molecule. And in every respect, it provided a dramatic confirmation to that general framework.
Section 46 notes
You may note that Mendel discovered genetics before Origin was actually published—how then could this have been a concern for Darwin? The cause is twofold:
First, Darwin sat on his ideas for a long time, being prompted to publish only when he discovered that Alfred Russel Wallace had independently come to many of the same conclusions as he. Secondly there was also a lengthy period before Mendel's own discoveries were widely known, as it was not until a number of other researchers stumbled upon the same results around 1900—some years after the deaths of both Mendel and Darwin—that Mendel's discovery that inheritance does not blend was widely accepted.
Miller's point is that new discoveries have had the effect of plugging potential holes in the theory rather than fundamentally challenging it, analogous to the discovery of new elements fitting neatly into the periodic table.
Section 47 
Q. I think maybe we should take a step back and maybe I can ask you to explain the whole concept of natural selection. What are we talking about here?
A. Well, Darwin and other people were impressed at how much plant and animal breeders could influence the ultimate characteristics by selecting individuals from a breeding population, let's say of horses or rabbits that had a particular characteristic the breeder wanted and allowing them to breed. Plant breeders have done the same thing for years. This was the methodology of Luther Burbank when he developed all sorts of beneficial strains of plants.
And Darwin was enough of a naturalist to realize that the same process of selection actually happens in nature. Darwin pointed out there's a struggle for existence, whether we like to admit it or not, and not all organisms are able to pass their genes on to the next generation. Those that do the best in that struggle for existence -- and it's not just a struggle to survive, it's a struggle to find mates, to reproduce, and to raise those offspring. So in many respects things that are very cooperative are important in this struggle.
Darwin realized that those organisms that had the characteristics that suited them best in that struggle, those were the ones that were going to leave their characteristics in the next generation, and he realized that's pretty much what plant and animal breeders do, and therefore over time the average characteristics of a population could change in one direction or another and they could change quite dramatically. And that's the essential idea of natural selection.
Section 47 notes
Section 48 
Q. And what Darwin didn't understand was exactly how that happened because he wasn't -- he didn't have the benefit of genetics at the time?
A. The entire process depends scientifically on what that mechanism of inheritance is. Darwin didn't know it. He couldn't have known it. Nobody knew it at the time. And therefore you might say that when modern genetics came into being by the rediscovering of the work of Gregor Mendel, everything in Darwin's theory was at risk, could have been overturned if genetics turned out to contradict the essential elements of evolutionary theory, but it didn't contradict them, it confirmed them in great detail.
Q. Now, are you able to give us some examples of how modern genetics has applied to evolutionary theory?
A. Well, I can give you quite a few of examples. Would you like me to use a demonstrative that would be useful to the Court?
Section 48 notes
Section 49 
Q. And you have, at my request, prepared a series of slides that will help you to explain this?
A. Yes, I have, as a matter of fact. I thought that I would start illustrating this by looking at hemoglobin. Hemoglobin is the protein that makes your blood red. It's the oxygen-carrying protein found in red blood cells.
And in the upper right-hand corner of the slide, there is a molecular diagram of hemoglobin. It's made up of four parts. Those parts are called polypeptides, but we can think of them essentially as four subunits. It has two copies of a part called alpha-globin and two copies of a part called beta-globin.
Now, what modern molecular biology has enabled us to do is to look at exactly where the instructions are that specify these. And you'll notice that the beta-globin -- excuse me, the alpha-globin instructions are specified on Chromosome Number 16 and the beta-globin instructions are specified on Chromosome Number 11.
And as our genome does for many genes, we have multiple copies of these, so we have backups. We've got extra copies of the alpha-globin genes and extra copies of the beta-globin genes, and they have very interesting physiological functions, these multiple copies, which are not relevant right now and therefore we won't get into.
Section 49 notes
Section 50 
But there's something very interesting about these, and it enables us to test evolution right down to the level of the molecule. And I want to point that out by looking at the beta-globin genes on Chromosome Number 11.
If you could advance the slide, please. I've zeroed in on the six copies of the beta-globin gene sequence. Each of these copies is a set of instructions for how you build this polypeptide. Five of them work, but one of them doesn't. It's given the Greek letters psi, beta, and then the number one. And the psi-beta-1 sequence isn't a gene. It doesn't work. It's a pseudogene, and a pseudogene is recognized as a gene because it's so similar to the other five in its DNA sequence, but it has some mistakes. It's broken, and it has a series of molecular errors that render the gene non-functional. Now, I'd like to show you exactly what those molecular errors are in the next slide. This is a blow-up of the pseudogene. These are the portions that actually do the coding, if it was coded in red here. And you'll notice that there are six distinct mistakes in this gene.
Now, I don't know if I really want to try the patience of the Court in terms of going into the details of molecular biology, but in a very simple way, the altered initiator means that the signal that exists at the front of the gene that says "copy me" is missing. And therefore RNA preliminaries, the molecule that copies genes, can't bind, and it never gets expressed.
But even if it did get expressed, it has five other errors that would keep this, the RNA copy of this gene, from being translated. It's missing the start signal. It's got stop codons that would cause the synthetic apparatus to grind to a halt. It's just a mess.
Section 50 notes
Section 51 
Now, the reason that this is important in evolution is actually very simple, and that is, these errors appear in a gene, they have no functional purpose. And you might ask yourself, what would I do, what would you do if we were to find another organism that didn't just have similar genes but also had a pseudogene in the same spot and had the same set of errors?
There's no reason why evolution would produce a duplicate set of mistakes in two copies of things. It must mean that these two organisms are descended with modification from another organism that had the same set of mistakes.
And if you go on to the next slide, what I'd like to show you are three organisms, the gorilla, the chimpanzee, and the human being that share the exact same set of molecular mistakes.
Now, why is this significant? One of the core principles of evolution is common descent. One could always argue that because the three species that I've depicted on this slide are all African species, that's where they all come from, they're all primates and they all probably started out living in similar environments, that the functional parts of this gene locus, they might work the same. But you cannot argue that the mistakes should match.
And the fact that all three of these species have matching mistakes leads us to just one conclusion, and that's the same conclusion that Charles Darwin predicted almost a century and a half ago, and that is that these three species share a common ancestor. Matching mistakes are evidence of common ancestry.
Section 51 notes
We have mistakes in our genes—specifically, extra copies that are broken in certain ways. These same mistakes are common to species that are evolutionarily closely related, but not to those that are only distantly related.
Section 52 
Q. And are there other animals that share the same mistakes?
A. Well, we actually don't know, because there are two great apes in which we're waiting on the genome sequence. Those are the orangutan and the Bonobo, pygmy chimpanzee. And if I had to make a friendly bet, I'd bet that they do.
But other primates and other mammals, cats, dogs, horses, they don't have these mistakes. These mistakes are unique to the lineage that shows common ancestry of us and these other organisms.
Section 52 notes
At this time only a quite limited set of animals had been fully sequenced. The Bonobo chimp became the last Great Ape to have its genome sequenced in mid 2012.
Section 53 
Q. Could you give us another example?
A. Sure, I'm very happy to. The next slide, this is another test of the evolutionary hypothesis of common ancestry.
We have, as I'm sure most people know, 46 chromosomes in our human cells. That means we have 23 pairs of chromosomes because you get 23 from mom and you get 23 from dad, so we've all got 46 total. We've got 23 pairs.
Now, the curious thing about the great apes is they have more. They have, as you can see from the slide, 48 chromosomes, which means they have 24 pairs. Now, what that means, Mr. Walczak, is that you and I, in a sense, are missing a chromosome, we're missing a pair of chromosomes. And the question is, if evolution is right about this common ancestry idea, where did the chromosome go?
Now, there's no possibility that that common ancestry which would have had 48 chromosomes because the other three species have 48, there's no possibility the chromosome could have just got lost or thrown away. Chromosome has so much genetic information on it that the loss of a whole chromosome would probably be fatal. So that's not a hypothesis.
Section 53 notes
Section 54 
Therefore, evolution makes a testable prediction, and that is, somewhere in the human genome we've got to be able to find a human chromosome that actually shows the point at which two of these common ancestors were pasted together. We ought to be able to find a piece of Scotch tape holding together two chromosomes so that our 24 pairs -- one of them was pasted together to form just 23. And if we can't find that, then the hypothesis of common ancestry is wrong and evolution is mistaken.
Go to the next slide. Now, the prediction is even better than that. And the reason for that is chromosomes themselves have little genetic markers in their middles and on their ends. They have DNA sequences, which I've highlighted in here, called telomeres that exist on the edges of the chromosomes. Then they have special DNA sequences at the center called centromeres, which I've highlighted in red. Centromeres are really important because that's where the chromosomes are separated when a cell divides. If you don't have a centromere, you're in really big trouble.
Now, if one of our chromosomes, as evolution predicts, really was formed by the fusion of two chromosomes, what we should find is in that human chromosome, we should find those telomere sequences which belong at the ends, but we should find them in the middle. Sort of like the seam at which you've glued two things together, it should still be there. And we should also find that there are two centromeres, one of which has, perhaps, been inactivated in order to make it convenient to separate this when a cell divides. That's a prediction. And if we can't find it in our genome, then evolution is in trouble.
Section 54 notes
We have one fewer pairs of chromosomes than our nearest relatives. Evolution therefore predicts that there must be a human chromosome that shows signs of being a merger of two pre-existing chromosomes.
Section 55 
Next slide. Well, lo and behold, the answer is in Chromosome Number 2. This is a paper that -- this is a facsimile of a paper that was published in the British journal Nature in 2004. It's a multi-authored paper. The first author is Hillier, and other authors are listed as et al. And it's entitled, The Generation and Annotation of the DNA Sequences of Human Chromosomes 2 and 4. And what this paper shows very clearly is that all of the marks of the fusion of those chromosomes predicted by common descent and evolution, all those marks are present on human Chromosome Number 2.
Would you advance the slide. And I put this up to remind the Court of what that prediction is. We should find telomeres at the fusion point of one of our chromosomes, we should have an inactivated centromere and we should have another one that still works.
And you'll note -- this is some scientific jargon from the paper, but I will read part of it. Quote, Chromosome 2 is unique to the human lineage of evolution having emerged as a result of head-to-head fusion of two acrocentric chromosomes that remain separate in other primates. The precise fusion site has been located, the reference then says exactly there, where our analysis confirmed the presence of multiple telomere, subtelomeric duplications. So those are right there.
Section 55 notes
Section 56 
And then, secondly, during the formation of human chromosome 2, one of the two centromeres became inactivated, and the exact point of that inactivation is pointed out, and the chromosome that is inactivated in us -- excuse me, the centromere that is inactivated in us turns out to correspond to primate Chromosome Number 13.
So the case is closed in a most beautiful way, and that is, the prediction of evolution of common ancestry is fulfilled by that lead-pipe evidence that you see here in terms of tying everything together, that our chromosome formed by the fusion from our common ancestor is Chromosome Number 2. Evolution has made a testable prediction and has passed.
Section 56 notes
This prediction has been confirmed, though it is now known that the situation isn't quite as simple as a single straight tip-to-tip merger.
Section 57 
Q. So what you're testifying here is that modern genetics and molecular biology actually support evolutionary theory?
A. They support it in great detail. And the closer that we can get to looking at the details of the human genome, the more powerful the evidence has become.
Q. I'd like you to direct your attention to Plaintiffs' Exhibit 127. Do you recognize this document?
A. Yes, I have seen it before. I believe it's a newsletter produced by the Dover Area School District.
Q. And, Matt, if you could highlight. I've highlighted a passage from the second page of the newsletter, and I would like you to read what has been highlighted.
A. Sure. Quote, In simple terms, on a molecular level, scientists have discovered a purposeful arrangement of parts which cannot be explained by Darwin's theory. In fact, since the 1950s, advances in molecular biology and chemistry have shown us that living cells, the fundamental units of life processes, cannot be explained by chance.
Q. Is that a true statement?
A. I think neither of those two sentences is a true statement. Would you like me to explain why?
Section 57 notes
A copy of this newsletter can be found here, with Miller's quote coming from a section headed "What is the theory of Intelligent Design?." If you think that quote is objectionable, there's plenty more where that came from—e.g. the previous paragraph:
Section 58 
A. Okay. The first point is the purposeful arrangement of parts. Science doesn't really deal with questions of purpose, value, and meaning. So to say that science has discovered a purposeful arrangement of parts puts science on the other side of this divide of empirical knowledge where it doesn't belong, so that certainly is not true.
As I've just mentioned to you, the arrangement of chromosomes in our genome, the existence of molecular errors, actually fits evolutionary theory remarkably well, so that part of the sentence doesn't hold up, either. And then the second sentence, to any scientist who is extremely curious, it says, The fundamental units of life processes cannot be explained by chance. I completely agree. Natural selection is not a chance process. Evolution is not just random chance. And natural selection is the most unchance-like part of evolutionary theory. So stating that you can't explain something by chance is not equivalent to saying you can't explain it by evolution.
Section 58 notes
Science simply doesn't deal with questions of "purpose," while there's much more to evolution than chance processes.
Section 59 
Q. Now, is there research ongoing in this area, molecular biology and genetics?
A. Oh, absolutely. In fact, it's moving so fast that it's difficult to keep up with it.
Q. And, in fact, is there a very recent publication, peer-reviewed publication, that bears on this issue of common descent?
A. Well, the answer to that is, there's more than one. And the one that comes to my mind right away is an issue earlier this month of the scientific journal Nature, which might be the most prestigious scientific journal in the world, which focused on seven or eight papers describing the complete genome analysis of the genome of the chimpanzee.
Q. And if I could direct your attention to what's been marked as Plaintiffs' Exhibit 643, is this the cover of the publication to which you refer?
A. Yes, that is the cover of the September 1st, 2005 issue of the scientific journal Nature. And you can see that the cover story is the chimpanzee genome.
Section 59 notes
Section 60 
Q. Matt, if you could turn to -- I believe it's Page 69. Is this the article to which you are referring?
A. Well, it's one of about seven or eight articles on the genome and its implications to which I refer. But this is the prime article that presents the chimpanzee sequence and points out some of the highlights of the sequence. So if one article in this large journal was said to be the cover story, the key article, this is it.
Q. And why is this important?
A. It's important because it introduces an enormous data set, the chimpanzee genome, that we simply didn't have before. And the title of the article I think actually tells you what you're going to find in here.
Initial sequence, because we change these things as we get better data, initial sequence of the chimpanzee genome and in comparison with the human genome. These organisms, as the earlier demonstratives that I presented to the Court show, clearly show a common ancestry with us, but as any observation will tell you, they're not like us. So understanding how we are similar and how we are different from these organisms is a really important and exciting problem in biology.
Section 60 notes
Said article title is "Initial sequence of the chimpanzee genome and comparison with the human genome."
Section 61 
Q. Matt, could you highlight the first sentence. This is the first sentence of the article. Could I ask you to read this, Dr. Miller?
A. Of course. And this is the introductory sentence to the article, and it reads, quote, More than a century ago Darwin and Huxley posited that humans share recent common ancestors with the African great apes. Modern molecular studies have spectacularly confirmed this prediction and have refined the relationships showing that the common chimpanzee, Pan troglodytes, and Bonobo, Pan paniscus or pygmy chimpanzee, are our closest living evolutionary relatives.
Q. It says "spectacularly confirmed." Is that something you routinely find in scientific journals?
A. I think you could read the journal Nature for several years and not see another use of the word "spectacular." It tells you that the authors of this paper are really excited about this data. And, to be perfectly honest, the entire scientific community was excited by the chance to compare this data with our own genome, and that warrants the use of the word "spectacular."
Section 61 notes
Section 62 
Q. Dr. Miller, isn't evolution just a theory?
A. Evolution is just a theory, in the same way that the atomic theory of matter is just a theory, the Copernican theory of the solar system is just a theory, or the germ theory of disease is just a theory. But theories, as I emphasized earlier, are not hunches, they're not unproven speculation. Theories are systems of explanations which are strongly supported by factual observations and which explain whole sets of facts and experimental results.
Q. And how do you distinguish, say, a theory from a fact?
A. A fact is a repeatable, verifiable observation or a result. So, for example, in the earlier demonstratives I showed, it is a fact that there is an altered initiator sequence on the beta-globin pseudogene. It's also a fact that there are five working copies of this gene on Chromosome Number 11. All of these are facts. We can test them, we can verify them, we can put them together. But facts by themselves don't tell us a whole lot. A very famous biologist once said that without theories to tie them together, biology is just stamp collecting. And what they meant by that was that the production of isolated individual facts is unimportant unless you can tie all those facts together in an explanatory framework, and what a theory is is just such a mechanism.
So evolutionary theory takes the sorts of facts that I have pointed out in the last few slides that the Court has looked at and ties them into a coherent whole by common explanation, for example, by the hypothesis of common descent.
Section 62 notes
Miller addresses the "just a theory" argument.
Section 63 
Q. So the term "theory" has a particular meaning within science distinct from everyday usage?
A. Absolutely. And when we're out on the street and we say, I have a theory on what the best way to drive to Pittsburgh is given the traffic or I have a theory on whether or not it's going to rain this afternoon, we mean, in ordinary conversation, a hunch, speculation, a guess.
When we say "theory" in science, we mean a broad, overarching, explanatory explanation that's very strongly supported by fact and by factual evidence and that ties all of this together in an explanatory framework that helps us make testable predictions and testable hypotheses. And if it doesn't do that, it's not a scientific theory.
Q. And is your understanding of theory and fact, as those terms are used in science, reflected by the scientific community?
A. Oh, I think it's fair to say that the understanding that I've expressed here in the Court today is exactly the understanding possessed by the members of the scientific community elsewhere.
Section 63 notes
Section 64 
Q. I'd like to direct your attention to Plaintiffs' Exhibit 649. And this is, again, the National Academy of Sciences publication?
A. Yes, sir, it is.
Q. And if you could turn to Page 5. And, Matt, if you could pull up the highlighted passage. Dr. Miller, could you read the highlighted text, please, from Page 5 of this publication?
A. Be glad to. Quote, Ironically, facts in science often are more susceptible to change than theories, which is one reason why the word "fact" is not used very much in science, unquote.
Q. So is evolution a theory or a fact?
A. In English, we often use the word "evolution" to refer to two different things. We often use the word "evolution" to refer to the fact that life has changed over time. And in that respect, evolution is as much of a fact as anything else we know about the natural history of this planet. However, the use of "evolution" as a theory is basically used to describe the mechanisms by which those changes took place. And in that respect, evolution is, indeed, a theory because it is a powerful, useful, and predictive explanation of a whole range of scientific facts.
Section 64 notes
We return to the Teaching About Evolution and the Nature of Science book mentioned above, now on page 5. The full paragraph reads:
In addition, Miller says that evolution is in one sense a "theory," and in another a "fact."
Section 65 
Q. Is evolutionary theory, including natural selection and descent with modification from a common ancestor, generally accepted by the scientific community?
A. It is overwhelmingly accepted by the scientific community.
Q. I'd like to direct your attention, staying on the same publication from the National Academy of Sciences, if we could turn to Page 16. Now, I believe you testified earlier that the National Academy of Sciences is probably the most prestigious scientific association in the country?
A. I think it's probably the most prestigious scientific association in the world.
Q. And have they taken a position on whether evolution is accepted?
A. Yes, they have.
Q. Matt, could you please highlight. Dr. Miller, I'd like you to read the highlighted passage from Page 16, please.
A. Sure. Quote, The concept of evolution through random genetic variation and natural selection makes sense of what would otherwise be a huge body of unconnected observations. It is no longer possible to sustain scientifically the view that living things we see today did not evolve from earlier forms or that the human species was not produced by the same evolutionary mechanisms that apply to the rest of the living world, unquote.
Section 65 notes
Page 16. The quoted paragraph begins by saying that evolution "is the only plausible scientific explanation that accounts for the extensive array of observations summarized above."
Section 66 
Q. I'd like to now direct your attention to Plaintiffs' Exhibit 192. Do you recognize this publication?
A. Yes, I do.
Q. And who publishes this?
A. This is a booklet that was published a few years ago by the National Academy of Sciences.
Q. And is this more recent than the other publication that we were just referring to?
A. I believe it is. I think this was published -- you'll correct me if I'm wrong -- in 1999 or in 2000.
Q. Matt, could you go to Page Roman Numeral VIII, please, and if you could highlight the text. Dr. Miller, I'd like you to read from this National Academy of Sciences publication the highlighted text, please.
A. Sure, I'd be glad to. Quote, The concept of biological evolution is one of the most important ideas ever generated by the application of scientific methods to the natural world. The evolution of all the organisms that live on earth today from ancestors that lived in the past is at the core of genetics, biochemistry, neurobiology, physiology, ecology, and other biological disciplines. It helps to explain the emergence of new infectious diseases, the development of antibiotic resistance in bacteria, the agricultural relationships among wild and domestic plants and animals, the composition of the earth's atmosphere, the molecular machinery of the cell, the similarities between human beings and other primates, and countless other features of the biological and physical world. As the great geneticist and evolutionist Theodosius Dobzhansky wrote in 1973, quote, Nothing in biology makes sense except in light of evolution, unquote.
Q. Do you agree with that, Dr. Miller?
A. I agree with that wholeheartedly.
Section 66 notes
This exhibit is Science and Creationism: A View from the National Academy of Sciences, Second Edition, a booklet published by the NAS in 1999. Page VIII can be read here, and the quote given by Miller continues onto the following page.
Section 67 
Q. You testified earlier that the American Association for the Advancement of Sciences is the largest association of scientists in this country. Do you know whether they have taken a position on whether evolution is accepted in science?
A. Yes, sir, they have taken a position.
Q. I'd direct your attention to Plaintiffs' Exhibit 654. Do you recognize this?
A. Yes, I do. This is an online feature published by the American Association for the Advancement of Science, and it has a series of questions and answers on evolution and intelligent design.
Q. And do you know whether the statements contained in here are supported by the leadership of the American Association for the Advancement of Science?
A. It is my understanding that they are.
Q. Matt, if you could highlight the text, please. The question that's posed is, is there evidence against contemporary evolutionary theory? And, Dr. Miller, if you could read the answer from the American Association for the Advancement of Science.
A. Sure. The answer reads, quote, No, there are still many puzzles in biology about the particular pathways of the evolutionary process and how various species are related to one another. However, these puzzles neither invalidate nor challenge Darwin's basic theory of descent with modification, nor the theory's present form that incorporates and is supported by the genetic sciences. Contemporary evolutionary theory provides the conceptual framework in which these puzzles can be addressed and points towards a way to solve them.
Q. End quote?
A. End quote. Thank you, Counsel.
Section 67 notes
The exhibit is a webpage on the AAAS website, called "Q & A on Evolution and Intelligent Design." Miller reads one of the sections.
Section 68 
Q. Are there other associations or organizations of scientists that have taken a similar view on the acceptance of evolution?
A. Yes, there are, literally scores of them.
Q. And can you name a few?
A. I certainly can't give you an exhaustive list, but the American Institute of Biological Sciences, the American Society for Cell Biology, the American Society for Biochemistry and Molecular Biology, the Geophysical Society of the United States, and the American Society of Microbiology, just to name a few.
Q. Are you aware of any scientific societies, academies, or organizations that have taken a contrary position and said that evolutionary theory is not firmly established?
A. I have to tell you that to my knowledge, every single scientific society in the United States that has taken a position on this issue has taken a position against intelligent design and in favor of evolution.
Q. Are you aware of any controversy in the scientific community over evolution?
A. Yes, I am. There are controversies in all fields of science, and what I mean by that are points that are held in dispute. For example, the evolution of sex is an enormous and controversial issue in biology.
Q. Sex as in gender?
A. Sex as in gender, as to why, for example, everybody does it, not just talking about us primates, but also oak trees and yeast and all sorts of organisms, as to where gender comes from in terms of sexual reproduction. It's a very important issue within evolutionary theory and certainly not an issue that is solved.
There is also enormous controversy within evolutionary theory on the relative values and weights to give to forces such as natural selection, sexual selection, genetic recombination, horizontal gene transfer, and so forth.
But I think the relevant and the interesting point is that there is no controversy within science over the core propositions of evolutionary theory, there is no controversy over whether or not evolution took place, and there is no controversy with respect to the proposition that evolution provides the most useful and invaluable way in which we can extend our understanding of living organisms.
Section 68 notes
You could spend all day just listing organisations that have taken similar pro-evolution stances, but the list of credible organisations in opposition is short to non-existent.
Miller goes on to talk about scientific controversies: specific controversies exist—Miller talks about the evolution of sex, for example—but evolution itself is non-controversial.
Section 69 
Q. Is evolution just a historical process, or is it still something that's being used today?
A. That's an interesting question, and I've often been approached by people who have told me, well, evolution is a just-so story about our past, and it has no scientific significance in the world today, it's unimportant. I can't think of any statement that I would disagree with more.
Q. Well, let me tell you that an expert for the school district in this case, Professor Scott Minnich, has said that evolution plays little, if any, role in experimental science and that it may actually impede science in the arena of drug-resistant research.
A. I believe, with all due respect, that Dr. Minnich is profoundly mistaken. And drug resistance is a very good example. All of -- any science -- I'm sorry, any physician who develops a specialty in the treatment of infectious diseases had better know about evolution. And the reason for that is, disease therapy, whether it's antibiotic therapy or whether it's antiviral therapy of the sort, for example, that is used to extend the lives of patients with AIDS, any therapy in these infectious diseases is predicated on a profound understanding of the evolutionary processes by which the bacteria or the viruses acquire resistance to the agents that are used against them. And if one doesn't understand the evolution of resistance, one is not going to be a very effective physician. And that's not the only area. Whole areas of drug research and development use what are known as genetic algorithms or evolutionary methods. And what these scientists often do is to set up in a test tube an evolutionary process where they allow incremental changes to be made automatically by an organism, by replicating molecule, to allow a kind of natural selection in the test tube to develop a better drug than anyone could design on their own. So by mimicking Darwinian evolution, people often in the laboratory will use that as a research tool.
It's also worth noting that an understanding of evolution is absolutely essential in other areas, as well. In agricultural, for example, the use of genetically modified crops in areas around the United States -- and much of the food that we eat depends upon genetically modified crops -- the use of the genetically modified crops becomes ineffective if the farmers employing them don't understand the evolutionary mechanisms by which insects can evolve resistance to the insect-fighting proteins which are engineered into the plants. So therefore very careful precautions have to be taken to prevent the process of evolution from taking place.
So I think evolution is at the core of discovering the biological sciences. And there's really no better example of that than that issue of Nature that we highlighted earlier and used as one of the exhibits. Virtually every paper in there uses evolution as a tool to explore what our genome does, what the ape genome does, and how the differences between them make us unique as individuals and organisms. It turns out to be a hard-working theory which is at the core of biological discovery and biological exploration.
Section 69 notes
The idea that evolution has no modern relevance—especially in the case of drug-resistance—would be laughable if it weren't so dangerous.
Section 70 
Q. Is evolution antireligious?
A. I certainly don't think so, and I devoted a whole book to arguing why I didn't think it was.
Q. Don't some scientists invoke evolution in their arguments to say that, in fact, science and evolution is antireligious, it's anti-God?
A. Yes, they do. And I can certainly think of any number of specific examples from distinguished evolutionary biologists like Richard Dawkins or philosophers who have written about evolution like Daniel Dennett or William Paley.
But as I said earlier, it's very important to appreciate that every word that comes forth from the mouth of a scientist is not necessarily science. And every word that one says on the meaning or the importance of evolutionary theory is not necessarily scientific.
Richard Dawkins, for example, has been eloquent in saying that for him, understanding that life and the origin of species has a material cause frees him from the need to believe in a divine being. I don't know if I've been as eloquent as Richard Dawkins, but I have worked very hard in my own way to say that for me, the notion that we are united in a great chain of being with every other living thing on this planet confirms my faith in a divine purpose and in a divine plan and means that when I go to church on Sunday, I thank the creator for this wonderful and bounteous earth and for the process of evolution that gave rise to such beauty and gave rise to such diversity that surrounds us. Those are my sentiments, in the same way that Dawkins' are his. But I'm not speaking scientifically, and I'm not speaking as a scientist, and that's, I think, the critical distinction.
Section 70 notes
Miller doesn't think that evolution is anti-religious, but acknowledges that people on both sides have made that claim. The William Paley mentioned is the same Paley as in the argument of Paley's watch. Just because a person is a scientist, however, doesn't make their pronouncements "science."
Section 71 
Q. So you wrote a whole book exploring this intersection between science and faith?
A. That's correct.
Q. And is any of that kind of discussion found in your high school biology textbook?
A. No, of course not.
A. Because it's not scientific. And I've made the point earlier that just when you say something is not scientific doesn't mean it's not important, doesn't mean it's not true, doesn't mean it doesn't concern something that you really and deeply care about. And I deeply care about my own religious beliefs and my faith, and I also deeply care about science, and I wanted to explain to a general audience how I understand the intersection of those two beliefs, not just to reconcile them, but to confirm and enhance both beliefs.
Now, I believe in that very strongly, but I certainly recognize that my views on this are not science and they are not scientific. My coauthor, Joseph Levine, who also is a religious person, I have to tell you, has different views of faith, belongs to a different faith, and follows a different religious tradition than I do.
Joe and I both have enormous respect for religion. We both believe that the evolutionary theory is fully compatible with our different religious beliefs, but we also recognize that our religious beliefs are not scientific, that they are philosophical, theological, and deeply personal, and, as such, they don't belong in a science curriculum, and they certainly don't belong in a science textbook.
Q. And they're not found in your high school science textbook?
A. Definitely not.
Section 71 notes
Miller may have written a whole book on the issue of science and religion, but none of that is in his textbook. He freely admits that his effort to reconcile scientific thinking with personal faith is "not science".
Section 72 
Q. I want to switch gears here again to the topic of intelligent design. What is intelligent design?
A. As it has been explained to me, intelligent design is the proposition that some features of living things are too complex to have been produced by the process of evolution and therefore they must be attributed to the creative work of a special intelligence or designer who creates these pathways, these genes, and these organisms and operates in ways that stand outside of nature and therefore by mechanisms which cannot be scientifically investigated.
Q. Who is the designer?
A. The advocates of intelligent design, over the last ten years, have refused to say. But I have to tell you that when I debated scientific creationists in the early 1980s, they were very fond of saying that life has a design and that design implies a designer and that designer is the creator, it is God.
Q. I'd like to direct your attention to Plaintiffs' Exhibit 124. Do you recognize this document, Dr. Miller?
A. Well, I recognize the last four paragraphs of the document. The first time I saw the rest of the document was in our pretrial discussions at the law offices yesterday. So now I recognize it. But until yesterday, I hadn't seen the whole document.
Q. And to your knowledge, what are the last four paragraphs there?
A. The last four paragraphs, which I certainly recognize, are the administrative statement which was read to students in Dover High School, I believe earlier this year, in concordance with the school board's intelligent design policy.
Section 72 notes
Their refusal continues to this day, but it is abundantly clear who they think it really is.
Exhibit 124 is the "Administrator’s Biology Statement in Biology Class," i.e. the "four-paragraph statement" from Gillen's opening statement. To refresh, it reads:
Section 73 
Q. Matt, if you could highlight the third paragraph. Could you please read the highlighted text?
A. Sure. Quote, Intelligent design is an explanation of the origin of life that differs from Darwin's view. The reference book Of Pandas and People is available for students who might be interested in gaining an understanding of what intelligent design actually involves, end quote.
Q. Are you familiar with this textbook, Of Pandas and People?
A. Yes, sir, I am.
Q. And, in fact, is that the book you were debating the first time you debated Michael Behe back in 1995?
A. Yes, that is the book.
Q. To your knowledge, is Pandas representative of intelligent design thinking?
A. I believe that it is. It certainly is put forward as an example of a textbook which had advanced the idea of intelligent design. I am sure that there are people within the intelligent design community who might hold slightly different positions on certain isolated issues from Pandas, but I think in general the arguments made in Pandas are representative of intelligent design.
Q. Now, one name that's going to be coming up in this trial, and, actually, the gentleman will be testifying for the school district, is Michael Behe. Are you familiar with his works?
A. Yes, sir, I am.
Q. And are his ideas consistent with what is represented in Of Pandas and People?
A. The answer to that is very much so. In fact, as I read Of Pandas and People, from our experience in the debate, which was in 1995, about a year later a book was published called Darwin's Black Box by Dr. Behe. And when I read through the pages of Darwin's Black Box, I was struck by how many of the arguments used against evolution that are found in Of Pandas and People are also used in Darwin's Black Box. And the one that really stuck in my mind was the discussion of the blood clotting cascade in both Dr. Behe's book and in Of Pandas and People. It struck me as essentially -- the two discussions struck me as essentially identical.
Section 73 notes
Section 74 
Q. We're going to come back to Dr. Behe in a little while. Let's focus now on the book Of Pandas and People that's referred to in the four-paragraph statement. If we could turn to Page 150. And Pandas is Plaintiffs' Exhibit 11. And Page 150 is part of the glossary. I'd like you to read for us the highlighted language, which is the Pandas definition of intelligent design.
A. Sure. Quote, Any theory that attributes an action, function, or the structure of an object to the creative mental capacities of a personal agent, period. In biology, the theory that biological organisms owe their origin to a preexistent intelligence, unquote.
Q. Let's take those sentences one at a time. The first sentence, to your mind, does that accurately describe intelligent design as you understand it?
A. I certainly think that it does. In fact, if one does a library search on intelligent design, it will return a large number of engineering, graphic design, and other articles about the intelligent design, let's say, of the courtroom or the intelligent design of a ventilation system or the intelligent design of a microprocessor.
So it is certainly true that the term "intelligent design" can be used in the context of a human designer designing an apparatus, putting together a message, and so forth. So I think that's a perfectly accurate statement.
Q. How about the second sentence?
A. The second sentence says, In biology -- and I believe this is the context that is important in the courtroom today -- biology, intelligent design is the theory that biological origins owe their -- excuse me, biological organisms owe their origin to a preexistent intelligence.
And I think that is exactly what intelligent design means. So this is a good glossary and this is a very good definition, because it indicates that organisms originated from the creative power of a preexisting intelligence, and that's a classic doctrine which is known as "special creation." By definition, that creative force has to have intelligence, takes intelligence to create, and that's exactly what this glossary definition says.
Section 74 notes
Miller says that Of Pandas and People has a "very good" definition of intelligent design, but this definition is the same as that of "special creation."
Section 75 
Q. What is the argument in Pandas to support this idea of an intelligent designer?
A. Well, I believe the argument in Pandas that supports -- that is used to support the idea of the intelligent designer takes many forums. For example, Pandas looks at the fossil record of natural history of life on this earth, and it says every time we see the sudden appearance of a new or different or novel organisms -- organism, that must be the hand of the designer. That's a classic example of special creation.
Pandas also says anytime we see a complex biochemical system made up of many different interlocking parts, that can only be explained by the actions of an intelligent designer. And Pandas also states that living systems contain complex biological information. And by analogy, since information in the real world -- excuse me, information in human society, in telephone books, in texts, perhaps in the arrangement of transistors in a microprocessor, since that kind of information requires human intelligence, then the information which is in a biological system must have had an intelligence to put it there, too. Those are -- I'm sure there are other detailed arguments, but those are the general categories by which Pandas makes this argument.
Q. And Pandas does address issues of science, issues of biology, does it not?
A. Yes. Pandas, in every one of its six chapters, sections, excursions, deals with biological organisms, with the question of biological origins, and also with life processes. So it's a book about biology, that's correct.
Q. And in your estimation, is the treatment of science, of biology, by Pandas accurate?
A. I think the treatment of biology by Pandas is inaccurate and in many respects downright false in every section of the book.
Q. Are you able to give us some examples about some of the errors that are contained in Of Pandas and People?
A. Sure, I'd be very happy to. My understanding is that you will call some other witnesses who will testify about other errors, but I will certainly be happy to talk about a few that are in my own area of work.
Q. And at my request, have you prepared a couple of slide demonstrations to help you explain these errors in Pandas?
A. Yes, I have.
Section 75 notes
Pandas' evidence for ID is also that which is used for special creation.
Miller also says that while Pandas does indeed discuss matters of science, it is woefully inaccurate about them. He promises to talk about a few of the egregious errors that are within his area of expertise.
Section 76 
Q. If we could have molecular trees in Pandas. Could you tell us what this is, Dr. Miller?
A. Yes. What you see on the slide now is the cover of Of Pandas and People and two quotations from various parts of what is known as Section 6 of Pandas, which is the section on biochemical similarities. And with your permission, with the Court's permission, I'll read both of those.
THE COURT: You may.
THE WITNESS: The first one is a quotation from Page 36. And what it says is, quote, When the measurements of the similarities between proteins are put side by side, the pattern that emerges contradicts the expectations based on Darwinism, unquote. I should add the emphasis, the boldface on this is mine, it's not from the original.
That point of contradicting what it calls Darwinism or Darwinian expectations is made on the next page, Page 37. Quote, Notice that the cytochrome c of this insect, the silkworm moth, exhibits the same degree of difference from organisms as diverse as humans, penguin, snapping turtle, tuna, and lamprey. The reason this finding is so surprising is that it contradicts the Darwinism expectation. And, once again, the emphasis is mine.
So Pandas, on these two pages, says that when you look at the biochemical similarities between organisms, it tells students those similarities contradict the expectations of evolution. In other words, evolution is wrong.
Can we look at the next slide, please? What you see in this diagram is a table, a data table of biochemical similarities from Pandas, and I'm flipping through my own copy so I get the proper reference here. The table appears on Page 37, and I have placed a quotation from Page 37 on the slide.
Section 76 notes
A blog post inspecting chapter 6 can be found at the Skeptical Analysis blog.
Section 77 
And referring to this table of differences between 17 organisms, Pandas tells students, quote, Darwinism would predict a greater molecular distance from the insect to the amphibian than to the living fish, yet greater still to the reptile and greater still than that to the mammal, yet this pattern is not found, unquote. And, again, the emphasis is mine. So what it tells students is, look at the data. That data contradicts the Darwinism expectation. So the message is not subtle, it's very clear, Darwinism is wrong, what it refers to as Darwinism is wrong, and this table tells you something else. That's the message from Pandas, and that's what they tell students.
May we look at the next slide, please? The next slide shows a diagram, and I apologize to the Court for not having this on the slide itself, but the diagram that you see here is from Page 38 of Pandas, and the quotation that I'm using which refers to this phenomena is actually from Pages 139 to 140. And it refers to the same phenomena.
Now, what the diagram shows is the cytochrome c, which is a protein found in all living organisms, essentially -- it's a very important protein -- it compares the sequence of cytochrome c of the carp, of a fish, and it says that the carp cytochrome c differs from that of the bullfrog by percent, by that of the snapping turtle also by percent, carp to the chicken 14 percent, carp to the rabbit 13 percent, carp to the horse 13 percent. In other words, it tells students there's the exact same difference between cytochrome c in a fish and an amphibian, a reptile, a bird, and two representative mammals. In other words, they're all the same distance apart.
Now, why is that a problem for evolution, according to Pandas? The quotation explains that. It tells students to use the classic Darwinian scenario, amphibians are intermediate between fish and other land-dwelling vertebrates, therefore analysis of their amino acid should place amphibians in an intermediate position, but it does not.
Section 77 notes
The problem with the explanation in Pandas is that it is based on the flawed conception of evolution as a linear progression, i.e.
Invertebrate --> Fish --> Amphibian --> Reptile --> Mammal --> Human
Based on this notion they conclude that there should be a larger distance (as measured by comparisons of the same proteins in different species) between the invertebrate and the amphibian than there is between the invertebrate and the fish. But that's not what's observed, and nor is it what evolution predicts. That would look more like this:
Evolution is not a linear process, and instead tends to produce a "tree" radiating from a common ancestor (the point at the top of the diagram). The predicted molecular difference can be imagined as the distance connecting any two points while following the lines. This predicts that the distance from the invertebrate to any other item should be the same, but tracing from other points not on the edge of the diagram the distances should be different. Believe it or not, this is what is observed in nature, and it spectacularly confirms evolution.
Section 78 
In other words, that fish should be closer to the amphibian than it is to the turtle, much closer than to the chicken, and much closer still than that to the horses. That's what Pandas tells students. Yet the fact that they're all the same distance apart means that the Darwinian, the evolutionary expectation, is contradicted by the data. And that is the message that Pandas tells students, any student who might use it.
Go to the next slide, please. This is not an isolated quotation. This is the entire theme of this particular section, which is one-sixth of the book, which is that evolution has it wrong on molecular similarities.
Here I've gone to Page 139, which is in the excursion or the more detailed section of the book. I've reproduced a facsimile of the page. This time it compares the dogfish shark and its cytochrome c to six different organisms. And basically this chart says they're all about the same distance from the shark. And then it says, instead of a progression of increasing divergence, each vertebrate sequence is equally isolated from the cytochrome sequence for the dogfish, unquote, from Page 139.
As a result of all this data, what Pandas then tells students -- and this is a textbook intended to be used in classes -- quote, In this and countless other comparisons, it has proved impossible to arrange protein sequences in a macroevolutionary series corresponding to the expected transitions from fish to amphibian to reptile to mammal, unquote. So, in other words, all these data contradict the prediction of evolution. That is the message of Pandas on page after page and diagram after diagram.
Now, the question that I think anybody using this book might want to consider is, is that true? Is that what the data actually show? Can I have the next slide, please?
Remember the central claim, and this slide reproduces the diagram I have already shown from Page 37 on Pandas. And Pandas claims that finding the same molecular distance between a fish and these organisms contradicts evolution. The reality of the situation is that it does nothing of the sort. Standard evolutionary relationships, which have been known for decades, between these organisms, a mammal, a bird, a reptile, an amphibian, and a fish, actually show that all of these organisms share a common ancestor at an equal molecular distance.
And what that means is, the frog should be just as far removed from that common ancestor as the horse should be. So therefore, when we compare a fish today, the distance from fish to mammal should be the same as the distance from fish to amphibian.
Section 78 notes
Section 79 
Q. I'm sorry, Dr. Miller, could you explain how, on the diagram on the lower right, how do you measure that? How does a biologist or a scientist read that?
A. Fair enough. What this diagram is intended to show is molecular distances between these organisms, in other words, how much their cytochrome c's differ in terms of times since a common ancestor. So in the chart the organisms that are pretty close together are the chicken and the turtle, and they share a recent common ancestor. So we shouldn't be surprised.
Q. I'm sorry, is the common ancestor where you have the Y?
A. Thank you very much for asking that. The common ancestor is at the intersection point right there, which I am now attempting to wave the pointer around. It is at the Y where these two diagrams join. So the relevant comparison here is that all five of these organisms should be, in molecular terms -- all four of these should be equally distant from the fish since the distance all the way down to the common ancestor of all vertebrates predicted by common descent is exactly the same.
And, incredibly, that is what the data actually show, which is an equal distance from the fish for all the other vertebrates, and that actually doesn't contradict evolution, it provides strong support for it. But students using Pandas would misunderstand this point completely.
May I have the next slide? Now, one might ask whether or not, since Pandas is -- I think is -- your opposing counsel might have mentioned in the opening statement -- a little out of date, whether or not Pandas can be forgiven this mistake, because, after all, it was published in 1993, and, as I emphasized, a lot has happened since then. What I have placed on the left-hand side of the slide is my rendering of the proper relationships between these organisms supported by data, and on the right-hand slide I have placed a figure from a paper published by Fitch and Margoliash in 1967, 38 years ago, showing molecular similarities based on cytochrome c.
Now, the Fitch and Margoliash picture, as you can see, is much more detailed than the simple one that I included because it includes more organisms. But you'll also note that the molecular tree formulation of diagram -- of the diagram shows exactly what I have been pointing out, which is that one does not expect a progression from one organism to another, as Pandas tells students, but one expects a deepening molecular tree so that the relationship of a fish to the other organisms, which are highlighted here in little red boxes, should be the same for every one of these organisms to the fish.
Section 79 notes
Miller explains all this, but then comes to an issue: is this a mistake created by the age of Pandas, or should they have known that their conception of evolution was flawed even back when the book was being written in the 1980s? Miller cites a figure out of a paper from 1967 to show that evolutionary trees are old news.
Section 80 
Q. And since 1967, has science contradicted that?
A. Science not only has not contradicted it, but it has confirmed this pattern in one protein and one gene after another. Now, it's worth noting that one of the things that scientists have noticed is that the rate of evolution seems to differ in one gene from another. So sometimes the pace of change is quicker, sometimes the pace of change is slower. But the ultimate pattern of change, with very, very few exceptions, supports the pattern that you see here.
And there's a final point that is worth making. And that is, one might ask, even though this paper appeared 38 years ago and clearly the authors of Pandas should have known about this, is this recent, is this formulation of evolutionary descent, is this something just in the molecular age, that it's brand-new, or is this the core understanding of evolution since the first time the idea was formulated? And the last slide that I have in this series will make that point. This is my formulation of the tree of --
Q. I'm sorry, that's in the upper left-hand corner?
A. Thank you very much. The upper left-hand corner of the slide is my formulation, a very simple diagram of the proper relationships between these species. The right-hand side of the slide shows the molecular tree sketched out from Fitch and Margoliash, the paper published in 1967. And, again, the question I pose before the Court is, is this a new idea of relationships just in the molecular age? I have here a diagram, it's the only figure from the Origin of Species published by Charles Darwin in 1859, and it shows an almost exact match of the tree concept. So any person writing or pretending to teach students about evolution should be aware of the fact that evolution, since its very formulation by Charles Darwin, has held to the idea of the tree as the ancestorial model.
And if you could advance the animation in this slide, whereas what Pandas has done is to argue that a straight line progression like that is actually what is expected. That is a -- either a misunderstanding or a deliberate misinforming of students about the nature of evolutionary theory. And what I wrote on this slide is, Pandas misleads students as to the actual predictions of evolutionary theory by pretending that evolution predicts a linear sequence like that. And as I've shown the Court, going back to Charles Darwin, that isn't what it predicts.
Section 80 notes
Since the publication of the aforementioned paper, the tree pattern has been confirmed in protein after protein. What's more, the same basic structure was arrived at by Darwin himself in On the Origin of Species:
It is therefore incorrect to say that "the pattern that emerges" from the molecular data "contradicts the expectations based on Darwinism"—in reality the data confirms them.
Section 81 
Q. Do you have another example of what we might call an error or a misrepresentation of evolutionary theory that is contained in Pandas?
A. I can certainly point to quite a few. I believe that's the last demonstrative that I have prepared from Pandas. Is that correct, sir?
Q. Yes. If we could have the blood clotting test.
A. Okay. Sorry. I had forgotten that I had prepared these demonstratives. Pandas also, in their discussion of molecular similarities, talks about what is known as the blood clotting cascade. And in this particular case, all of us -- hopefully all of us in the courtroom have blood that clots properly. And what that means, of course, when we cut ourselves, we don't just bleed and bleed and bleed and bleed, but that cut eventually seals with a blood clot.
That's, in many respects, even more important inside our body, because when we get a bruise, that actually is a result of broken blood vessels, and if that didn't close with a clot, we'd be in serious trouble.
Now, blood clotting is, biochemically, an enormously complicated process. And I have placed a diagram of some of the elements of the clotting pathway on the upper left-hand corner of the slide. It's a diagram that I drew from the Internet. It's not from any exhibits in the court here. It's not from Pandas.
It's the sort of slide -- if people in the court are awed by the complexity of this slide, I would assure you that this is a subject that is used to torture biochemistry students at the undergraduate and graduate level. Everyone agrees that this is complicated. In the lower right-hand corner, there is a scanned electron micrograph of a red blood cell caught in a clot. And the action of this pathway produces a crosslink protein known as fibrin, which produces a meshwork which actually stabilizes the clot and helps blood to stop flowing.
Section 81 notes
The next error Miller chooses to talk about is the blood-clot cascade. This is a classic example of what is claimed to be irreducible complexity. While nobody disputes that the cascade is complex—and very much so—Miller will argue that it isn't "irreducible."
Section 82 
Now, I'm going to have to stand up so I can see the slide properly. Is that all right, Your Honor? I'll just talk loud enough so hopefully it will be picked up. Pandas describes this system, and on Page 141, and I quote, it tells students, As we shall see, such interactive systems as illustrated here by the mechanism for a blood clotting are very strong arguments for intelligent design and are virtually impossible to explain in terms of Darwinian evolution, unquote. Now, it's interesting to look into Pandas and say, why is it that this is an argument for design and impossible to explain by evolution?
If you could go to the next slide, please, I'd appreciate it. Here is a page from Pandas describing the blood clotting cascade and a diagram of the cascade and two quotations from Pages 145 and 146. Here is the essence of the argument that students are given in Pandas. From Page 145, quote, Only when all the components of the system are present and in good working order does the system function properly, unquote.
Later in the page and going onto Page 146, it talks about the various proteins in the clotting pathway, and it says, quote, Some of them -- these are the clotting proteins -- share discrete regions of their sequences with some others. Does that mean that they derive from one another? It may. But consider that even if this were the case, all of the proteins had to be present simultaneously for the blood clotting system to function, unquote. And the emphasis here is mine.
So the argument made by Pandas is that the reason this is an example of design is because it's a multi-part system, and all of the parts have to be put together, presumably by a creator/designer before the system will work.
Can I have the next slide, please? Well, that's a scientific statement in the sense that it's a claim that all the parts have to be present for the system to work. And because that is a scientific claim, we can investigate it scientifically and see if it is valid.
What I have placed on this slide is my own representation of the blood clotting cascade, which I blew up a little bit to try to make it large enough for the Court to see and to try to emphasize the points that I need to point out to the Court at this point.
Section 82 notes
Section 83 
A standard and simple and straightforward scientific test of the claim that all parts must be present for this to work is simple. Eliminate one of the parts, see if the blood will clot. If it won't clot anymore, the claim might be right. If it will clot, the claim could be wrong.
Well, fortunately nature has actually done that experiment for us. And if you could advance the slide, I'm going to show right now, essentially here's the pathway, and I'm going to propose an experiment which is that we eliminate one of the important factors known as factor 12. That's right here. So there's my experiment. You can do this very easily on PowerPoint, much easier than you can do in the laboratory.
We have just eliminated factor 12, and the question now before the Court is, will blood clot or will it not? Advance the slide, please. It turns out that whales and dolphins have done this experiment for us already. Whales and dolphins, in 1969, well before Pandas was published, were shown to lack factor 12. And the slide contains a reference to an article by Robins, Kasting, and Aggeler from Science Magazine, Volume 166, Page 1420, 1969. And you will note a quotation from the abstract of this article saying, The dolphin intrinsic cascade lacks factor 12, unquote.
Now, this is from ancient history, as far as we molecular biologists might be concerned today, because 1969 is pre-molecular. So one might wonder, has that result held up?
Also in the lower left-hand corner of the slide I have pointed out that a paper published in 1998 by Semba, et al., confirms using genome analysis, that whale Hageman factor 12 basically is now a pseudogene in the whale genome. That's why it is not produced. It is, indeed, missing from the clotting cascade.
Whales face many problems on this planet. They're overhunted, they're overfished, but they don't have any problems with their blood clotting. So blood clots just fine, despite missing the factor. So the scientific prediction from Pandas turns out to be wrong.
Section 83 notes
If a system is irreducibly complex, then if you remove one part the whole system will fail to function. Miller points to whales and dolphins, who lack what he calls "factor 12" yet still have clotting blood. The cascade is therefore not irreducibly complex, as one of the parts can be removed. This was known in 1969, many years before Pandas was published but also before direct molecular evidence was available. Miller mentions a 1998 paper investigating the underlying genetics to show that the discovery has held up over the decades.
Miller (or the transcriber) does make a slight mistake here: the name of the first author of the 1969 paper was Robinson, not Robins.
Section 84 
Q. And the prediction was -- this was known in 1969 is what you're saying?
A. Absolutely, that's correct. So certainly the people writing it should have known. But interestingly, in recent years, you might say the situation has gotten worse.
Q. I'm sorry, worse in what sense?
A. Worse in the sense that the case that Pandas is trying to make has become even farther removed from scientific reality.
Can I show the next slide, please? Here again is my representation of the various components of the blood clotting cascade. And this time I'd like to propose that we take away not one part, but three. If you'd advance the slide, please. The proposal is that we take away the three parts which are known as the contact phase system. Now, that includes factor 12, which we talked about a second ago, but also factor 11 and also the factor that catalyzes the conversion of 12 to the active form.
Advance the slide, please. Those are the three parts that I propose eliminating. And advance it one more time, please. There they go. They're gone. It turns out these three parts are missing in a vertebrate known as the puffer fish.
And I have placed in the left-hand part of the slide a reference to a paper Jiang and Doolittle, 2003. The title of the paper is, The Evolution of Vertebrate Blood Coagulation as Viewed from a Comparison of Puffer Fish and Sea Squirt Genomes. It appeared in the proceedings of the National Academy of Sciences, a very eminent scientific journal, Volume 100, Page 7527. And the relevant point here is that they are missing three parts of the system and their blood clots perfectly well. Should we -- Go ahead, a question?
Section 84 notes
But it gets worse: Miller talks about another paper (published only a couple of years prior to the trial, and thus some time after Pandas) that looks at species that "are missing three parts of the system and their blood clots perfectly well."
Section 85 
Q. So the prediction in Pandas and what Pandas teaches students has, in fact, been invalidated, refuted by the scientific evidence?
A. It was refuted by the scientific evidence in 1969 that was confirmed by genome studies of the whale, and it has been further refuted by Jiang and Doolittle's study of the contact phase system.
Q. I'd like to go to the third example of what we might consider significant errors or representations contained in Pandas, and that is the concept of new biological information. I was wondering if you could explain what Pandas says about this and then talk a little bit about the science.
A. May I ask the counselor if we have demonstratives on this?
THE COURT: You may, certainly.
THE WITNESS: Do we have a demonstrative on this one?
BY MR. WALCZAK:
Q. We have a copy of Page 7 from Pandas.
A. Okay. That would be just fine. Page 7 from the book Of Pandas and People makes the point that biological information and living things contain abundant amounts of information. There certainly is no argument there. The biological information must come from a designer.
And the way in which Pandas makes this argument is by using an example of information from the nonbiological world. So it tells students, if we walk along the beach and we see something written here that says, John loves Mary, that's an example of information from which we immediately infer the existence of an intelligent designer, a designer who thought of the message, coded it in the sand, and used symbols, symbolic language, in order to get that information across.
What Pandas then says is that biological information meets the same standard. And do we have -- have we highlighted part of the text on this page? Okay.
The patterns in biological information are described in this passage from Page 7 in Pandas. And the passage which I will read begins with the following: Quote, Are natural causes capable of producing these kinds of patterns? To say that DNA and protein arose by natural causes, as chemical evolution does, is to say that complex coded messages arose by natural causes. It is akin to saying John loves Mary, the message written on the beach, arose from the action of the waves or from the interaction of the grains of sand.
And I'd like to skip to the highlighted portion at the bottom of this and say -- and read to the Court that Pandas tells us, quote, If science is based on experience, then science tells us the message encoded in DNA must have originated from an intelligent cause, unquote.
So Pandas basically tells students all information must come from an intelligent cause, there's information in DNA, and therefore it's just like John loves Mary written on the beach, there must have been somebody there to write it.
Section 85 notes
Pandas was wrong before it even existed.
Section 86 
Q. And is that correct?
A. No, sir, I don't think it's correct at all. I think there are logical problems with the analogy, and as an experimental scientist, there is strong scientific evidence that this is simply not the case with respect to biological information.
Q. Let's start with the analogy that they make. What's wrong with this analogy to John loves Mary must have been designed by some intelligent designer?
A. Well, I can think of a lot of things that are wrong with it. The first thing is that the message John loves Mary, which is sitting here in the beach, doesn't have the capacity to replicate as DNA does. It is never passed along in the process of reproduction as DNA is. It can never undergo genetic recombination as DNA can. It can never be subject to natural selection as the organisms and their characteristics coded for by DNA can. In short, that message is not part of a living organism, and the fact that messages in DNA are part of a living organism makes them entirely different.
The second point, however, that the analogy fails is something that any philosopher, any logician would spot in a second. When we look at the John loves Mary sentence, we know, for example, what the -- we know who made that message, and what I mean by that is, we know that a human being made that message because it is the kind of message that human beings make. We also know how that designer, the human being, made that message, probably by scratching a stick or other object into the sand to move the sand apart and create the message. And, finally, from our own ordinary experience, we've seen it happen. So we know the designer, we know the mechanism, and we have observed it happen in our own empirical experience. In the case of inferring a designer for DNA, curiously, the advocates of intelligent design don't meet those standards. They say, we can't tell who the designer is, we cannot know the mechanism, and we also do not know how the designer operated and we've never observed it. Therefore, the comparison between that kind of message and the kind of message in DNA fails even the most basic test of logic.
Section 86 notes
Creationists like drawing analogies between life and manmade objects we know to have been "intelligently designed." Miller says that there are two flaws with such analogies: first, that manmade objects cannot replicate; and second, that we already know that those kind of things are made by humans, but we have no such information about the supposed designer.
Section 87 
Q. Now, has there been scientific research done on this proposition of whether or not there are natural explanations for new biological information?
A. Yes, there has, in fact, a great deal.
Q. And could I direct your attention to Plaintiffs' Exhibit 245. Do you recognize this exhibit?
A. Yes, I do. This is a review article that was written in a very prestigious journal, Nature Reviews Genetics, and it's written by Manyuan Long and several other people. And the title of the article is, The Origin of New Genes, Glimpses From the Young and the Old. It's an article that I read immediately, as many scientists did when it came out, because it describes a number of mechanisms by which new genetic information is developed by the processes of evolution.
Q. When did this article come out?
A. I believe this was published in the year 2003.
Section 87 notes
Exhibit 245 is a paper called "The origin of new genes: glimpses from the young and old," and Miller says that it has some bearing on how new information can arise in the genome.
Section 88 
Q. And how does this contradict what Pandas tells students?
A. Well, it contradicts what Pandas tells students in a number of ways. First of all, you remember that Pandas said that all biological information, by analogy to John loves Mary written on the beach, had to be directly encoded by a designer. And what this paper summarizes, because it's a review paper, is it summarizes dozens of research projects in laboratories around the world on different mechanisms by which new biological information arises through the process of evolution by natural selection.
And if we could advance the slide, please, I prepared a slide showing a table from the second page of this article. And thank you very much for zooming in on the table. And what you see on this table are a series of mechanisms by which new genetic information can arise. You'll notice the top one, the area up here talks about exon shuffling. The next one, gene duplication, then retroposition, mobile genetic elements, lateral gene transfer, gene fusion and fish, and, finally, de novo gene origination. Every one of these is a distinctly different molecular mechanism that results in the generation of new genetic information. None of them requires a designer, curiously.
Now, the other thing that I find, I think, worthy of the Court's attention is that none of these are hypothetical mechanisms. In every case, the specific genes that have been formed by these mechanisms are listed in the third column of the table. And in the fifth column of the table, there are a series of scientific references documenting the studies that have shown how these genes originated by evolutionary processes.
Q. So this is one article, but, in fact, it talks about many other articles that have done the research to support this proposition?
A. That is correct. This references more than three dozen scientific studies showing the origin of new genetic information by these evolutionary processes.
Section 88 notes
"None of these are hypothetical mechanisms." The table Miller is talking about can be viewed here.
Section 89 
Q. Let me ask you, because I'm not a scientist, so I'm going to ask you to pretend that I'm your mother here. This notion of creating new biological information through natural pathways, I mean, is that a big deal that Pandas gets this wrong?
A. I think it is a very big deal that Pandas gets this wrong, because you have to remember that the core argument of Of Pandas and People is that there is abundant evidence in biological systems not only that evolution is wrong, but also that there is a creator/designer who encoded all of this information into biological systems.
Pandas at one point makes a statement that this information was written by the designer into the various types of organisms at the beginning, which is clearly the description of a creative act. And the only way that it can make that statement is by arguing that information cannot arise by natural mechanisms of the sort described abundantly in this review and summary paper.
Q. So Pandas is just dead wrong on this point?
A. Pandas is wrong on this point, but I think it's more important to point out that Pandas is wrong in a most particular way. Anybody can write a book about science and make a few mistakes, and Lord knows I have made my share of mistakes in trying to summarize science. But the error in Pandas in this respect is systematic, and that is, the errors are all intended to point students towards the acts of special creation by the unnamed designer that are designed to encode the information into systems.
So by arguing that studies like this don't exist, that mechanisms like this don't work, Pandas makes the case for the existence of the supernatural special designer or creator.
Section 89 notes
Any textbook can make a mistake, but this one in Pandas is fundamental to their point.
Section 90 
Q. Now, you've discussed with us three errors in Pandas which come within your field of molecular biology. Are there other what you would consider significant errors or distortions of the science in Pandas?
A. Yes, sir, there are.
Q. And we will have another expert, Professor Padian, who will come in and talk about some of these in more detail, but just briefly, if you could just identify what some of those other errors are.
A. Well, I think the principal one that I would identify for the Court is that Pandas completely misstates the character of the fossil record and the nature of natural history. And one element of that -- I know you will have a paleontologist coming in later to go over that in detail for the Court, but one element of that that I find particularly significant is in Pandas' nearly complete omission of any discussion of what causes extinction.
Pandas mentions the fact that -- well, actually, Pandas mentions extinction in a few places. Any paleontologist will tell you that more than 99.9 percent of all organisms that have ever existed on this planet have gone extinct. So just about every organism that has ever appeared is now extinct. Now, evolution, of course, has no problem explaining this because the competition between organisms and continuing genetic change is one of the engines that drives extinction. This is extremely well understood.
But if one proposes to students the existence of an intelligent designer who used his skill and craft and cunning to encode this information and to produce perfectly-designed organisms, the fact that most of them go extinct is an embarrassment. And, in fact, you know, an intelligent designer who designed things, 99.9 percent of which didn't last, certainly wouldn't be very intelligent. And one of the questions that I think any reasonably inquisitive student will have when they open this book is, if an intelligent designer made all these things, why have they all become extinct if he's so intelligent? And Pandas simply does not address the issue, even though it clearly is going to raise it in the mind of any student who uses this book.
THE COURT: Mr. Walczak, I'll tell you that anytime between now and 12:30 that you want to wrap up a line of questioning, you can do so. But I don't want to stop you here if you're in the middle of something.
MR. WALCZAK: Your Honor, I think about five more minutes would be --
THE COURT: That's fine. Let's wrap it up by 12:30, at least.
Section 90 notes
There are many more errors in Pandas than those that Miller has described above, and the plaintiffs have other witnesses that will come in and detail them. As a teaser Miller mentions inaccuracies in the textbooks discussion of the nature of the fossil record, particularly in relation to the mechanisms of extinction.
Section 91 
Q. Dr. Miller, you talked earlier about the core of propositions of evolution. Does Pandas reject those core propositions or argue that, in fact, they are scientifically incorrect?
A. Yes, sir, it does. It rejects all of them. In my opinion, it dances around the proposition that life has changed over time. It sort of -- it maintains what you might call a reserved indifference to that proposition. It certainly rejects common descent, and it profoundly rejects the third proposition, which is that the process of change can be understood by things that we observe happening in the world around us today.
Q. Let me direct your attention to Page 65 of Pandas. Matt, if you could highlight it. Could you read this highlighted passage from Page 65 on Pandas?
A. Of course. Page 65, quote, Adherents of intelligent design assume that in the beginning all basic types of organisms were given a set of genetic instructions that harbored variation but were resilient and stable, unquote.
Q. That's a rejection of natural selection and common descent?
A. It is a profound rejection of this, because basically what it describes is the special creation of all organisms, because it says basic types of organisms, which in earlier parlance might have been referred to as created kinds, were given a set of instructions. In other words, the genetic information was written into them. They couldn't change, they were resilient and stable.
So the picture that any reasonably intelligent student is going to get out of this is that intelligent design means that the designer/creator inserted these instructions into living organisms and they have remained essentially unchanged since that time.
Q. Let me direct your attention now to Pages 99 and 100 of Pandas. I'd ask you to read the highlighted passage.
A. Quote, intelligent design means that various forms of life began abruptly through an intelligent agency with their distinctive features already intact, fish with fins and scales, birds with feathers, beaks, and wings, et cetera.
Q. Is that science?
A. No, not at all. And, in fact, anyone would recognize that in a flash as a form of special creation, because what we have here is intelligent design means the various forms began abruptly, and I might add separately, which is what the previous quote implied, and everything was intact. In other words, organisms were created by an intelligent force instantaneously with all of their features present. Now, I don't know if we have a demonstrative to this, but on Page 99 there is also a graphic that drives home this point in case the verbal -- in case the words are too subtle. Do we have that as a demonstrative?
Section 91 notes
Miller alludes to his three core propositions from above, namely
He says that Pandas rejects all three, even "dancing around" the relatively uncontentious idea that life has changed over time. The rejections of the other two points are much stronger.
Walczak moves on to the issue of how Pandas portrays the fossil record. Miller's quote—"intelligent design means that various forms of life began abruptly through an intelligent agency with their distinctive features already intact, fish with fins and scales, birds with feathers, beaks, and wings, et cetera."—will be seen again later on in the trial when it comes time to discuss the difference between definitions given for creationism and ID in the various drafts of the book, but for now Miller wants to talk about the science. He says that that position is "not science," but instead an example of special creation.
Section 92 
Q. Could you pull up Page 99?
A. I think, actually, that's fine without further enlargement. And what you see now is Page 99, Of Pandas and People, and you can see that what is presented here is Pandas -- or the view of the fossil record and natural history that Pandas wishes to show to students, and that is that every single organism began its existence on earth as a result of a creative process with the information inserted into it, as it says, by an intelligent agent. It lasts for a certain time on earth, and then it vanishes due to extinction. So what we have basically is a series of separate creative events required to bring each individual type of organism into existence. If one wished to understand whether or not Pandas is consistent with the idea of common descent, one look at this graphic tells you huh-uh, because what Pandas clearly shows in this graphic is separate descent of every single basic type of organism.
Q. And is that similar to creation science as it was practiced in the 1980s?
A. It is -- the notion of separate descent is identical to creation science, and the only difference that I can see is that in Pandas the creative events are presumed to be spaced out over time, whereas in creation science, those creative events were presumed to have occurred at the same time or the same six-day period. Other than that, I don't see much to differ them.
MR. WALCZAK: I think, Your Honor, now would be a good time for me.
THE COURT: All right. We'll take a lunch break now. I might be inclined to say class dismissed for the morning. We'll return at 1:45. I'd ask that you be in your seats promptly at that time so that we can start our afternoon session then. I thank you. We'll stand in recess until 1:45.
(A luncheon recess was taken.)
Section 92 notes
The image Miller is talking about can be found at the NCSE website here. The idea being put forward is that specific morphologies appear in the fossil record ex nihilo, exist for a period, and then dissapear without having changed in any significant manner—this is called the "face value interpretation of the fossil record." To Miller, this shows that Pandas rejects common descent in favour of a blatantly creationist view.
With that the court broke for lunch.
Day 1 (26 Sept 2005): Afternoon Session - Direct (continued) of Dr. Kenneth Miller
THE COURT: All right. We welcome you all back from our lunch break. We're two or three minutes later than we wanted to be, but you'll excuse that, I hope, and we'll proceed. Mr. Walczak, back to you.
MR. WALCZAK: Thank you, Your Honor.
DIRECT EXAMINATION (continued) BY MR. WALCZAK:
Section 93 
Q. Dr. Miller, I want to now switch gears from the discussion of the textbook Of Pandas and People to Professor Behe. Who is Michael Behe?
A. Michael Behe, I believe, is a professor of biochemistry at Lehigh University.
Q. And has he done research on intelligent design?
A. Well, to be perfectly honest, I'm not sure that he's done research on intelligent design. I'm aware of some of his published peer reviewed literature and can say that it concerns a wide variety of topics. I believe nucleotide and nucleic acid biogenesis, and most recently, a study on random replacement of neucleoties in genes; in other words, sort of a moving around of the genetic code and see happens to a gene.
Q. So Dr. Behe has published some peer reviewed articles, but these are not on intelligent design?
A. To my reading, none of them actually are on intelligent design. He's published a fair number, good number of peer reviewed articles in leading peer reviewed scientific journals, no question.
Q. What is it that Professor Behe brings to the concept of intelligent design? Does he bring some idea to the table here?
A. Yes, I think he does. And the idea that he brings to the table, as you put it, is that the classic argument from design, which has been around for hundreds, thousands of years, that biological systems are complex and suggest the existence of a designer can also be phrased in terms of biochemistry.
So I believe Dr. Behe's book, Darwin's Black Box, was subtitled the Biochemical Challenge to Evolution, so what he brings to the discussion basically is the old argument from design written up in the new language of biochemistry.
Section 93 notes
Miller discusses Dr Michael Behe, one of the defence's own expert witnesses. He says that while Behe has published "a good number of peer reviewed articles in leading peer reviewed scientific journals," none of them were actually anything to do with ID. A later analysis of Behe's output by Dr. David Lampe contradicts the first part of the above: Behe hasn't actually published a great deal of research of any kind.
According to Miller, all Behe really brings to the table is the classic argument from design "written up in the new language of biochemistry."
Section 94 
Q. Let's take that in a couple of steps. First of all, you mentioned Darwin's Black Box. And I direct your attention to Plaintiff's Exhibit 434. Is this the book to which you refer?
A. Yes, sir, it is.
Q. And is this the book that Professor Behe wrote which explains his idea of irreducible complexity?
A. Yes, sir, it is.
Q. Now let me ask you. Is this a peer-reviewed publication?
A. To my understanding, no. Books like this are subject of what you might call a kind of peer review, which is a discussion between you and the editor and perhaps the copy editor, in the same way that my own box, Finding Darwin's God, was subject to those discussions. But by the standards of science, neither my book nor Dr. Behe's book counts as a peer-review publication.
Q. Now you said a moment ago that Dr. Behe's idea isn't actually new. What do you mean by that?
A. Well, the essential argument that some features of living things are too complex to have been generated in any other way other than by attribution to a designer is an idea that, to my poor understanding of ancient philosophy goes back to the Greeks. And in western culture, very often one would go back to a book called Natural Theology that was written by the Reverend William Paley and published, I believe, in 1802.
And Paley's book had what's probably the best pre-Charles Darwin classical formulation of the idea of intelligent design. Paley was quite a naturalist. And he really understood the complexities of living systems, of living organs. He understood how they work with each other, how delicate the interplay is. And he said that this very complexity argued for the presence and the existence of an intelligent designer who drafted all these organisms and created each of them individually.
Section 94 notes
Behe published Darwin's Black Box (Plaintiff's Exhibit 434) in 1996—since then many of his claims have been refuted. Miller points out that the book is not peer-reviewed (and neither is his own).
Section 95 
Q. And did Reverend Paley use certain examples that we might be familiar with?
A. Yes, he did. Paley used a whole variety of examples. And I believe some of them included the nervous system, the muscular system, the digestive system. And he used them in a variety of different types of organisms. So it was a very interesting book to read, and still is a very interesting book to read. The example of Paley's that I think is remembered the best is the example of the eye.
And he pointed out that the eyes that we humans have -- because among the animal kingdom, we have very good eyes. Very few animals that can surpass the human eye. Our eye is a complex multi-part system. And I can't name all the parts not being an anatomist. But we have the cornea, we have the lens, we have the iris, we have the aqueous humor, the vitreous humor. We have the retina in the back of the eye. And for proper vision, all of these parts have to work together as a coordinated whole. And that was part of Paley's example.
Paley said, for example, what good would a lens be without a retina? And what good would a retina be without a lens? And, therefore, all the parts would have to be assembled together. And, therefore, only a designer could do that.
Q. So his conclusion was that, there could not be a natural explanation for this complex system, the eye, therefore, there was a designer?
A. That is correct.
Q. And did Paley identify the designer?
A. To Reverend William Paley, there was absolutely no doubt as to who the designer was. He said it was God.
Section 95 notes
Section 96 
Q. And so how does Dr. Behe's argument differ from Reverend Paley's?
A. Well, as far as I can tell, it differs in two essential respects. The first respect is that, Dr. Behe, although he praises the arguments of William Paley in several areas of his book, argues that the argument from design, as Paley's argument is known, is made most effectively at the level of the cell, at the level of the molecule. So he basically has attempted to update Paley's argument, not by looking at large organ systems, but by looking at biochemical machines that exist inside individual living cells. And the second way in which his argument differs from Paley is that, Dr. Behe, after coming to the same conclusion, that there had to be an independent designer, a creative force that created these machines, these pathways, and put them into being, Dr. Behe is unwillingly to name the identity of that designer. And I believe he suggests that the designer, of course, could be a divine force, but it could be super intelligent space aliens from Mars or perhaps time traveling cell biologists going into the past from the future and causing the structures to be put together.
Q. And have you actually heard Dr. Behe use these examples?
A. Yes, sir, I have. Dr. Behe and I have discussed and debated this issue a number of times, and these are examples that he has used in those discussions.
Q. Now Dr. Behe advances an idea known as irreducible complexity. Can you explain to us what that idea consists of?
A. Sure. The idea of irreducible complexity starts with the observation that living cells contain complex biochemical systems and machines. They are composed of many parts. He then suggests that, that complexity is irreducible. What he means by irreducible complexity is, if we start to take a few parts away to see if we can make a simpler machine, we very quickly discover that we can't, that a machine stops functioning. Now I've prepared a few demonstratives with quotes from Dr. Behe's work to sort of illustrate this point, if it's all right for the Court to show these.
THE COURT: Yes.
Section 96 notes
Behe differs from Paley in two respects: he uses examples that are much smaller than what was available for Paley (or Darwin) to study, and he outright refuses to specify the designer he has in mind.
Section 97 
BY MR. WALCZAK:
Q. Could we have the bacterial flagellum power point?
A. So this is, in a way, a summary of Dr. Behe's argument. And one of the things that I think is important to make clear to the Court is that, it is absolutely true that there are many, many structures in the living cell, many biochemical pathways for which we don't have a detailed biochemical -- excuse me, a detailed evolutionary explanation. That is a point that all scientists will concede. Do Doctor --
Q. I'm sorry. Is that true just about evolutionary theory or is that true about any science?
A. That's true about anything. In cell biology, for example, I think most people and the court are aware that when a cell divides, the chromosomes that carry the genetic information of a cell are moved apart and separated into the two daughter cells. We have enormous arguments in the field of cell biology as to what the exact mechanism is by which that force is generated. We can all see it happen. Any high school student can watch the separation of chromosomes under a microscope in a high school laboratory. But we still don't know exactly what the motor or the mechanism is that moves these apart. There are many, many other unsolved problems in biology.
Q. I'm sorry. Please continue.
Section 97 notes
Miller begins to talk about the bacterial flagellum, the most famous claim of irreducible complexity. His first point boils down to "just because we don't know exactly how something happens, doesn't mean we don't (or can't) know that it does."
Miller's arguments here were later published in his article The Flagellum Unspun: The Collapse of "Irreducible Complexity".
Section 98 
A. Sure. So it's important to note that Dr. Behe's argument does not say simply, well, there are complex structures within the cell for whom we do not understand the detailed evolutionary origin of, that's absolutely true. But his argument really rises to a different level. What I've shown on this slide is a diagram of the bacterial flagellum. Now bacteria, of course, are very, very simple cells. They're found everywhere in nature. They're found, for example, in our digestive systems. They're found in the skin. They're found on the surface of the table. Some bacteria have little whip like structures called flagellum. You might almost considers them to be outboard motors. And these things whip around at very high rates of speed, and they propel the bacteria through water, or sometimes they pull the bacteria in sort of a screw like motion through the water. So it's marvelous machines. They are acid powdered reversible rotary engines. These are marvelous little machines, and they are made of a whole series of protein parts, some of which are shown in this little diagram here. Now if we can animate this slide a little bit.
Next point. Now what I wrote here is that, Dr. Behe has made very clear in what I think is fairly called his biochemical argument from design, that that argument depends upon a much bolder claim than simply saying, scientists have not completely explained how this structure evolved. And that bolder claim is shown in the next animated section of this slide. And that is that, the evolution of complex biochemical structures cannot even or ever be explained in principle. And, of course, what he means by that is, there is some aspect of this complexity, which means we can say not just, we haven't figured it out yet, but we will never figure it out, and that's where the evidence for design lies. Now if I may advance to the next slide. I'll try to use Dr. Behe's words to explain why he holds this point of view.
Section 98 notes
Irreducible complexity rises beyond simply saying "it's complicated, and we don't know how it came to be." IC demands that we can't know how the feature arose, because it can't have arisen via evolution at all.
Section 99 
The reason that evolution cannot explain, he says, the origin of such structures is because they have a property, which he calls irreducible complexity, or they are irreducibly complex. I thought it best for the Court to read the description of irreducible complexity in Dr. Behe's own words. So in the lower part of the the slide, I have a quotation from page 39 of his book, Darwin's Black Block. And I will read that to the Court. Quote, By irreducibly complex, I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. And now, from my point of view, the key part of the argument, and I'll continue to read. An irreducibly complex system cannot be produced directly by slight, successive modifications of a pre-cursor system -- and that's how evolution would have to produce it -- because any pre-cursor to an irreducibly complex system that is missing a part is by definition non-functional. So his argument is that, if you have a multi-part system, and all the parts are necessary to function, you can't produce that system five parts at a time, six, seven, and gradually build up the complex system, because there is no function possible until the last part is snapped into place. And that's why evolution cannot produce that system.
Now the next slide is another quote of Dr. Behe's that tries to make this point absolutely explicit as to why you need the system to be working. He points out, another quote, Darwin's Black Box, page 39, quote, Since natural selection can only choose systems that are already working -- and if you remember, his contention is, if you're missing a part, you're not working -- then if a biological system cannot be produced gradually, it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act upon, closed quote. And Dr. Behe rightly points out that, to imagine such complex systems arising spontaneously in one fell swoop is something that no serious biologist would argue could happen, and I will not argue either. So his point is, as long as irreducible complexity holds, then any system we can identify as irreducibly complex couldn't have been produced by evolution. It's a very, very coherent argument.
Section 99 notes
Miller defines IC. "It's a very, very coherent argument."
Section 100 
Q. Does he identify some organisms that he calls irreducibly complex?
A. Well, counselor, not so much organisms, but he certainly identifies some machines and some structures that he regards as irreducibly complex, one of which, of course, is the bacterial flagellum. And I pointed out, this slide contains a diagram of the flagellum. And to the right is actually sort of what we call a false color, but an electron micrograph showing a bacterium with several flagellum protruding from one end. So that is one of the principal systems to which he points. Now the next slide, please. And I should also point out, to be a little more responsive than I have been to your question, that Dr. Behe also says, the blood clotting cascade that we talked about earlier as an example of an irreducibly complex system, the eukaryotic cilium, similar system to the flagellum, that's irreducibly complex, the vesicle targeting system that parcels out things in living cells, and also the immune system are all examples of irreducibly complex systems.
Now what I did in this slide was to prepare a graphic to make this point as clear as possible to those of us in court today. And that is to emphasize that complex biochemical machines composed of multiple interacting parts, if they work, they can have a function that's favored by natural selection. The essence of the biochemical argument from irreducible complexity, however, is that the individual parts of that machine have no function of their own. And because they have no function on their own, they cannot be produced by natural selection and, therefore, the impediment, the reason you can't get to here from there, you can't go from individual parts to the machine, is because the individual parts have no functions of their own. Now evolutionary biology has grappled with this problem before. And the next slide shows how evolutionary biologists generally explain the evolution of complex machines.
And that is, they agree, yes, there are such machines. You need all these parts for a particular function. But where these machines come from is, they come from pre-existing machines which have functions of their own, and that the individual parts of these machines originate in components that have different functions. So the way in which evolutionary biology picks up Dr. Behe's challenge is to basically say, you're wrong, that the individual parts of these machines cannot have a function that is favored by natural selection. Now that, of course, in this slide, this is not evidence, of course, in the scientific sense. This is merely an argument. But the reason I like the way that Dr. Behe has put his argument, and I like sort of describing it this way, is because it actually is amenable to a scientific test. Something that most arguments for intelligent design are not. And the next slide.
Section 100 notes
Section 101 
Q. I'm sorry. This is -- is Dr. Behe's argument for irreducible complexity, is that an argument directly for design?
A. That's a good point. The answer is, no, it's not. It really is an argument that says why such systems are not produceable by evolution. So it's a negative argument against evolution. It is in itself not evidence. Even if the argument were correct, it's not evidence of a designer, it's not argument for design, it simply is an argument that the evolutionary mechanism wouldn't work in this case.
Q. So that's why this argument is testable?
A. That is correct. As I mentioned earlier, one of the problems with intelligent design is that it doesn't make any testable predictions. This actually isn't a testable prediction of design either. This is simply an argument as to why evolution wouldn't work. And that can be subjected to a test.
Section 101 notes
Section 102 
Q. Please continue.
A. Thank you. Next slide, please. So what I have done in this slide is to place the graphic summaries of the argument from irreducible complexity that I just made in the upper left-hand corner of the slide, and in the upper right-hand corner, I have basically put the evolutionary explanation using the same graphic convention. And the nature of the test that I or any other scientist would propose is pretty simple. If you animate the slide, you'll see that Dr. Behe's prediction is that the parts of any irreducibly complex system should have no useful function. Therefore, we ought to be able to take the bacterial flagellum, for example, break its parts down, and discover that none of the parts are good for anything except when we're all assembled in a flagellum. If evolutionary theory holds, however, and we can animate again, and we'll show that in the right-hand side, evolution makes an extremely straight forward prediction. And that is, when we look at these irreducibly complex structures, we ought to be able to find parts of those systems that actually do have useful functions within them. So we can do a very straight forward either/or test to distinguish between these two alternatives. So what I'd like to show in the next slide is how such a test can be conducted.
This is a -- in the upper right-hand corner of the slide is a graphic representation from a review article showing some of the proteins involved in the construction of the bacterial flagellum. Now the individual names of the gene products need not concern us. They often begin with FL for flagellum. But as you can see, just as Dr. Behe says, this is a complex multi-part biochemical machine. Now the test that I would propose, we can animate the slide, please, to start with this flagellum. And if Dr. Behe is correct, if we take away even one part, there should be no function. But I'm going to propose that we take away not one, not two, I'm going to propose we take away 30 parts.
Section 102 notes
Section 103 
And what I'm going to propose to do is, take 30 of these proteins away and see what is left. And the slide that I set up is animated, and what we have done is -- actually, could you go back for the animation and then do it again? And let's watch the Court do it, and we'll do the animation now. Thank you. And you can see the parts that I have removed are on the outside and the inside, and what are left are 10 proteins that span the inner and outer membrane. These bacteria, many of them are surrounded by two membranes. These 10 remaining parts are shown in the next diagram, which will come up on the slide. And this is a diagram showing where these 10 parts are. They exist at the very base of the flagellum near one of the cellular membranes.
Now the prediction that is made by Dr. Behe in his book is extremely straight forward, which is, since this was an irreducibly complex machine, and we've taken away most of its parts, what's left behind should be non-functional because, you remember, he wrote, any pre-cursor to an irreducibly complex machine that is missing a part is, by definition, non-functional. This guy is missing 30 parts. Next slide. Well, it turns out that what is actually left behind when we take those parts away is a little structure with those 10 parts, which is known to microbiologists as the type III secretory system. And I can see, Mr. Walczak, you're saying, why, of course, it's the type III secretory system.
Section 103 notes
Section 104 
THE COURT: That certainly was on my mind.
THE WITNESS: Exactly. Now I was expecting a question of, how do you know it's not type II or type IV? The type III secretory system is a little molecular syringe that some of the nastiest bacteria in all of nature have. Yrsinia pestis, for example, which is the organism that causes bubonic plague, is a type III secretor. And what it does is, it gets inside our body, crawls up alongside, and uses this syringe to inject poisons into a human cell. And in the lower left-hand corner of the slide, I have some diagrams showing the operation of a type III secretory system. Now the connection between this and the flagellum is that the type III -- the 10 proteins in the type III system are almost a precise match for the corresponding 10 proteins in the base of the bacterial flagellum. So it's very clear that a subset of those proteins has an entirely different function, a beneficial function, not for us, but for the bacterium, and a function that can and is favored by natural selection.
Can I have the next slide, please? So the summary of this example is really very straight forward. When we take this complex multi-part system, which is the bacterial flagellum, the prediction made by Dr. Behe from irreducible complexity is when we break the parts apart, we should have no useful functions. Anyone missing a part is, by definition, non-functional. We follow that up. We do break it apart. And lo and behold, we find -- actually, we find a variety of useful functions, one of which I have just pointed out, which is type III secretion. What that means, in ordinary scientific terms is that, the argument that Dr. Behe is made is falsified, it's wrong, it's time to go back to the drawing board.
Q. And does Dr. Behe focus on just one type of cell? I'm sorry if I'm using the wrong terms here.
A. No, he doesn't. His arguments extend to a wide variety of cells and a wide variety of systems that he identifies as irreducibly complex.
Section 104 notes
Section 105 
Q. But the reasoning, the analysis that you just went through is -- applies in the same fashion to these other examples, is that correct?
A. Yes, it would. And if I could redirect the Court's recollection to earlier today, one of those systems was, in fact, the blood clotting cascade. And Pandas, and as it turns out, Dr. Behe's book, Darwin's Black Box, makes the same statement, which is that, all of the parts have to be together for blood to clot effectively. The exact quotation, I think, is, if even one part is missing, the system fails and blood does not clot. And I then showed that when we look for, for example, at the genome sequence of the puffer fish, we find that three of the parts are missing and blood still clots perfectly well. That is exactly the same kind of argument, which we just examined, and also found wanting in another of Dr. Behe's chosen examples, which is the flagellum.
Q. I asked you, in preparation, to select a third example, and that was the immune system. What is the immune system?
A. Well, it's a very good question, because we all depend for our very lives on a functioning immune system. It's a system of our body that is widely distributed. We have cells from our immune system sort of engaging in patrol, floating throughout the blood stream and the tissues. And it's a system that enables us to identify, defend against, and to repel foreign invaders. When I was a little boy, for example, it was on vacation, too, which I never really liked very much, I got the chicken pox, and I was very, very sick. And it was during spring vacation, so I had the wonderful experience of being sick during vacation week. But chicken pox is a virus when invades the human body, the immune system recognizes the code proteins on the virus, makes cells that can continue to recognize it, and produces proteins called antibodies that will bind to the surface of the virus. What that meant is, once I had gone through that miserable week with the chicken pox, I could be confident I would never get it again. I would be permanently immune to the chicken box. This is a very important realization for medicine to have because, of course, most of us in this room have received vaccinations designed to stimulate our immunity from diseases far worse than chicken pox such as, for example, polio and diptheria and whooping cough in an effort to stipulate our immune systems to make sure we never get sick from those diseases.
Q. Have you prepared a presentation on the immune system that will help you to explain this?
A. Yes, sir, I have. And if we could show the first slide, I want to start -- and, Your Honor, I may have to stand up to --
THE COURT: That's fine.
Section 105 notes
Section 106 
THE WITNESS: Thanks. I thought I would start by pointing out an essential protein of the immune system. You can't work without it. That essential protein is sometimes -- it is called by researchers an immunoglobulin, but it is more commonly called an antibody. These are the essential molecules of the immune system.
In the upper left-hand corner of the slide, there is a molecular diagram for what an antibody actually looks like. It basically is a little Y shaped molecule with two binding sites. And you'll notice in the slide, those binding sites are labeled foreign particle binding sites. I hope I have antibodies circulating in my bloodstream against chicken pox. So if I get chicken pox virus in my body, that foreign particle binding site on my chicken pox antibody will bind to the surface of the virus. Another one will bind to the other site.
And gradually, the virus will be cross linked into a mesh world, which my immune system recognizes, eliminates from the circulation, and destroys. And that's why, hopefully, I'm not going to get chicken pox again. Now in the lower right-hand is a more diagrammatic view of this molecule. It's made up of four parts.
These are each polypeptides, and they're diagrammed. And you'll notice that part of these -- each of the polypeptides is colored blue, and another part is colored red. The red says, variable region. Now I know some of my own vaccination history, so I've been vaccinated against polio, diptheria, measles, and a number of other diseases.
The antibodies in my body against polio differ from the antibodies I have against diptheria in the variable regions. They have a different shape because the viruses or the bacteria have different molecules on the surface.
Section 106 notes
Section 107 
The genius, if you will, of the immune system, is that it can produce an antibody that will attach to, stick to, identify, and destroy just about anything. So one of the most important things in our immune system is the ability, basically, to produce antibodies against any conceivable molecule that might get inside our body. Can I have the next slide? Now about 20 years ago, a scientist working at MIT named Susumu Tonegawa -- I know I'm going to have to spell that for the court reporter -- determined exactly how antibodies had the ability to produce such diversity. And that is, it turns out to be a system in the genes of cells in the immune system known as a VDJ recombination system.
And this system is not at all unlike a dealer shuffling a deck of cards, and that at a certain point in development, parts of DNA, in a variety of genes, are literally shuffled. They're tossed from one side to another, and they are rearranged to form a final gene. Now some elements of this shuffling are random just like you hope the dealer, when you go to Las Vegas, is shuffling those card randomly so you don't know what you're going to get.
But it's in that random shuffling that our immune system develops the ability to produce an antibody to just about anything. That shuffling is at the heart of why the immune system works. If anything goes wrong with this process, the individual in which it goes wrong loses the ability to make diverse antibodies, they get very sick, and they're in big trouble when they start to see foreign organisms.
Now the next slide. Where did this system come from? That's the question that people interested in evolution always try to answer. About 10 years ago, a number of scientists, including Nobel Prize winner David Baltimore, speculated that this process, which is called VDJ recombination, might actually have evolved from a system known as transposition, a system in which genes jump around.
What I have placed on the slide in addition to this diagram and the reference to the Baltimore group's paper in the proceedings of the National Academy of Sciences is a quotation from this paper illustrating his hypothesis. They, and he means the gene shuffling system, could have been part of retrotransposons and had a DNA rearrangement function this their previous life. It's possible that the ancestors of these genes, they're called RAG genes, may have been horizontally transferred into a metazoan multi-cellular animal lineage at a recent point in evolution.
So he argued, he suggests there might be an evolutionary way to explain where this system came from. It's a very interesting suggestion. And as I wrote in the slide, perhaps the three part system arose from a type of mobile genetic element known as a transposon. It's a hypothesis, but the important point, and the reason it's useful is that, it is a testable hypothesis. Can I have the next slide, please? Now Dr. Behe was aware when he wrote Darwin's Black Box of the speculations of the Baltimore lab.
Section 107 notes
Section 108 
BY MR. WALCZAK:
Q. I'm sorry, what year was Black Box written?
A. That was written in 1996.
Q. And the Baltimore article was?
Q. So Dr. Behe addressed that. And he regarded this as mere speculation. And he also basically told researchers, don't bother. And the reason you shouldn't bother is actually given in the bottom of the slide. On page 130 of Darwin's Black Box, he wrote, and I quote, In the absence of the machine -- that's the gene shuffling machine -- the parts never get cut and joined. In the absence of the signals for where to cut, it's like expecting the machine that's randomly cutting paper to make a paper doll. And, of course, in an absence of the message for the antibody itself, the other components would be useless, closed quote. So he basically argues, because this is a multi-part system and all parts had to be together for it to work ahead of time, you're not going make any progress.
A few pages later, he's even more explicit about that. On page 139, he wrote, quote, As scientists, we yearn to understand how this magnificent mechanism came to be, but the complexity of the system dooms all Darwinian explanations to frustration. Sisyphus himself would pity us. I hope you're up on your classical mythology.
Q. That's what Dr. Behe wrote in his book in 1996?
A. That is correct, sir. He basically told scientists, don't bother to try to investigate the evolution of this because it's irreducibly complex, it's multi-part, you cannot solve it with evolution.
Section 108 notes
Section 109 
Q. So what's happened since then?
A. What's happened since then is, I think, very interesting. Can I have the next slide? This is the quote from Dr. Behe. The complexity of the system dooms all Darwinian explanations to frustration. If you animate the slide, please. In 1996, the same year that Darwin's Black Box came out, very strong biochemical similarities were found between this shuffling process, the VDJ recombination, and the way in which retroviruses shuffle their DNA, very suggestive.
Q. Now when you say, found, where was this found?
A. The -- well, the report is in the journal Science. This particular case, I believe, was found in a prokaryotic system because retroviruses can go into all sorts of systems. But the important point is, these investigators noticed there were biochemical similarities between the way the genes are shuffled in the immune system and the way that retroviruses go into other cells.
Q. This is a publication that has been peer reviewed?
A. That is correct. This is the journal Science, one of the best scientific publications in the United States. And, obviously, this was peer reviewed research.
Section 109 notes
Section 110 
Q. Please continue.
A. Happy to. Two years later in the journal Nature, which I have plugged repeatedly as a great publication, it turns out that the cutting and transposing enzymes that are normally used for these transposable genetic elements can be replaced by the RAG enzymes, which do the cutting and pasting in the immune system. So that's suggested a further biochemical similarity between these two systems published in 1998 in the journal Nature. Also, of course, peer reviewed. Can I have the next element, please?
In 2000, the RAG enzymes were shown to cause transposition in mammalian cells. What this meant was, not only can they shuffle the immune system pieces of DNA, they can shuffle other pieces of DNA as well. So little by little, we're beginning to understand that elements of the Baltimore hypothesis are being born out by published research in peer review journals.
Q. What is Blood? Is that also a peer reviewed publication?
A. Blood is also a peer reviewed journal. This is an original research paper subjected to the usual process of review. Can I have the next slide, please? Once again, the quote that we've been talking about, if you could advance it, in 2003, the VDJ recombinase was shown to cause transposition -- in other words, shuffle DNA around -- not just in mammalian cells, but in human cells as well.
The next animation, please, will show the transposases were discovered in nature not associated with the immune system that are a perfect mimic for the 0 way the immune system gene shuffling machine works in human cells. And this was in the journal Nature. And finally, the last part of this puzzle was put together in the last year, and that is the actual transposic from which these enzymes and insertion sequences evolved were identified by a paper printed in the public library of science, which is a brand new, but very highly regarded peer review journal, and this is Kapitonov & Jurka in 2005.
Section 110 notes
Section 111 
It's worth noting how these researchers described their own work. And the next slide will show a facsimile of the paper, and also has a quotation from the abstract. Now this is absolutely filled with technically latent language, but it shows how thoroughly researchers have explored this particular -- this particular hypothesis.
And what I will do is, I will read, and I'm going to skip parts of this, but I'm going to read, starting at the quotation marks, and I will skip over some of the technical terminology. Quote, The significant similarity between the transib transpases and RAG core, the common structure of these transpases and others, as well as the similar size of these basically catalyzed by these enzymes directly support the 25-year-old hypothesis of a transposon related origin of the VDJ machinery.
And the researchers then point out, there have been other hypotheses that have been considered. Previously, the RAG transposon hypothesis was open to challenge by alternative models of convergent evolution. Because there were no known transpases similar to the gene shuffling ones, the RAG ones found, it could be argued that our gene shuffling enzymes, the RAG1 independently developed some transposon-like properties rather than deriving them from a transposable element encoded transpases. These arguments can now be put to rest.
And they're very straight forward about saying, we have solved the puzzle of where this system came from. It came from evolution. And it came from a transposable element system. Can I have the next slide, please? Okay.
So the summary of what we have just gone through, and this is a tree analysis of these transposons and humans and mammals are right down where it says, mammals, is that the summary is that between 1996 and 05, each element of the transposon hypothesis has been confirmed and, furthermore, when the enzymes that do this gene shuffling are actually put to an analysis to see how closely related they are to see if they themselves match the evolutionary predicted tree, they match that tree perfectly. So we've got it.
Section 111 notes
Section 112 
Q. So what do you tell your mother about what all this means for Dr. Behe's theory?
THE COURT: Or me?
THE WITNESS: I was about to say, my mother and Your Honor, but Your Honor, not being a retired nurse like my mother, my mother is deeply interested in immunity. And I often remind her that the reason I got chicken pox in the first place is because she wanted me to have immunity to it, so she marched me down the street to play with Denny Marsh who had chicken pox at the time to make sure that I would get sick. And she forgot to realize that 10 days later, which is the incubation period, was going to be spring break for me, spring vacation for me.
Your Honor, I've never forgiven my mother for that to this day. So we'll have to take that up. So the important point basically is that, we have, in our immune system, as an essential part of our survival, the ability to shuffle genetic information so as to make it possible for our immune cells to make an antibody to just about anything.
That shuffling ability was proposed 10 years ago to have evolved from sequences known as transposable genetic elements. In 10 years of research, every step of that hypothesis has been confirmed. And we, therefore, do know, as the result of investigation using evolutionary theory, where that came from and how this gene shuffling ability arose. It also means -- could we advance to the next slide, please? Actually, I'm sorry, I forgot that. I'm finished with the slides. It also means that the prediction that Dr. Behe quite confidently made on the basis of intelligent design theory, that this system would not be amenable to Darwinian investigation, that there would be no evolutionary explanation for it, turned out to be wrong, and I am happy to say that fortunately research scientists did not listen to him.
If they had listened to him, they might not have done this research, and we might not have had this fundamental breakthrough in how the immune system works.
Section 112 notes
Section 113 
Q. Did Dr. Behe, in fact, rely on this argument, that the immune system could never be explained by natural selection to argue that, in fact, there must be an intelligent designer?
A. Yes, sir, he did. And this is actually one of several arguments that he raises in Darwin's Black Box to say that, if you cannot, in principle, explain the origin of a complex system by evolutionary means, that is by invoking the negative, that is evidence for an intelligent designer. This is another essential example in his list of irreducibly complex systems.
Q. Let me direct your attention now to Plaintiff's Exhibit 665. And not to be redundant, but, in fact, is there now even more research on the immune system that has come out even this past week?
A. Well, yes, it has. And as I was getting ready to pack up and come to Harrisburg for this trial, I happened to glance over the Internet at the latest issue of the journal Nature, which has actually not yet appeared in print. I'm still waiting for my copy in the mail. But fortunately, you can on look at things on the Internet several days ahead of time.
The VDJ recombination system is not the only important part of the immune system. There is another important part known as the compliment system. And in this case, compliment does not mean, say something nice about somebody. Compliment in this case is a system that compliments or completes part of what's known as the immune response.
And it consists of a series of proteins that target and destroy. And they destroy, in a molecular sense in a most vicious way possible, foreign invaders, especially bacteria and foreign cells. One of the key elements of this is a compliment component now as C.. this article reported, and this is from Jansen et al. It's from a combined Dutch and Scandinavian group. And again, it's in the latest issue of Nature.
They, for the first time, worked out the detailed structure of compliment C. and the structure of compliment C. Immediately told them how this compound must -- how this protein must have evolved. It was made up of a series of modular units of exactly the sort that one would expect to arise by gene duplication, and the molecule had unmistakable sites in which pieces of another gene became recombined with it to produce the complete molecule. Hence, they title this work structures of compliment component C. Provide insights into the function and evolution of immunity. So the entire idea of evolutionary theory is providing a fruitful avenue of investigation into every aspect of the immune system, not just the gene shuffling that I've talked about, but into this other area known as compliment.
Section 113 notes
Section 114 
Q. So Sisyphus isn't that envious?
A. I don't think so.
Q. I'm listening to the arguments that you have described Dr. Behe is making, that these components are irreducibly complex, and that science cannot explain them. And in some cases, he's been shown wrong. But is that essentially the argument, that scientists currently can't explain some aspects of evolution?
A. In essence, that is the argument. It is what a philosopher might call the argument from ignorance, which is to say that, because we don't understand something, we assume we never will, and therefore we can invoke a cause outside of nature, a supernatural creator or supernatural designer.
Q. And is this not a completely negative argument? I mean, it sounds like this is an attack on evolution?
A. This is in every respect a completely negative argument. And if one combs the pages Of Pandas and People or, for that matter, if one looks at Dr. Behe's book or if one looks at the writings of other people who consider themselves to be intelligent design advocates, all that one finds is example after example, argument after argument, as to why evolution couldn't produce this, didn't make that, and doesn't provide an explanation for the following.
I have yet to see any explanation, advanced by any adherent of design that basically says, we have found positive evidence for design. The evidence is always negative, and it basically says, if evolution is incorrect, the answer must be design. Never considers an alternative idea.
Section 114 notes
Section 115 
Q. Now let me just stop you. Just because science today cannot explain something, does that mean it can never be explained?
A. Of course not. And if it did, no one would do scientific research. What attracts scientists to research is the lure of the unknown. There is nothing more dreadful than to wake up one morning and think that all the fundamental problems in your field has been solved. On the day that I think all fundamental problems in cell biology have been resolved, I will retired to Sussex and keep bees, as Sherlock Holmes once said.
You want unsolved problems. You're attracted to them. I'll just give you a very simple example. Proteins are built by hooking together strings of amino acid, almost like beads on a string. The machine that does that building is called a ribosome. We have worked for years to understand the detailed molecular structure of the ribosome.
As a result of work that's been published in the last couple years, we know the internal structure of the ribosome down to the atomic level. We can now look inside it, and we can see the molecular details of how these two amino acids are brought into very close proximity.
But do you know what? There's still an unsolved problem. We still don't understand the chemistry that forges the link between those two beads on a chain. There was a very popular hypothesis that was put forward by Peter Moore at Yale University. But in the last year, a number of experimenters, including Al Dahlberg at my own university, has shown that Moore's ideas are wrong.
So what scientists everywhere realize is, there's a great prize to be won. That's very exciting. To find the mechanism by which these are joined together. What no one is doing is to say, we'll never solve it, we're going to attribute the formation of the bond between amino acids to an unseen outside force operating beyond nature and, therefore, any chemical explanation is doomed to failure.
That's something we never say in science, because if we did, it would be a research stopper. It would tell us, give up, go home, we'll never figure it out.
Section 115 notes
Section 116 
Q. What is Dr. Behe's argument? What evidence does Dr. Behe, and -- well, strike that. Dr. Behe's argument is consistent with the arguments made in Pandas, I believe you testified before?
A. Yes, sir, that's exactly what I testified. The term irreducible complexity, which is a feature of Dr. Behe's book, does not appear in Pandas. But the core idea behind irreducible complexity, which is in these complex systems, all parts must be assembled in order to have function, that is at the heart and soul of the arguments which are in Pandas.
Q. Now what I've heard are these negative arguments about evolution. What is the evidence in Pandas? Let's start with Pandas. What is the affirmative evidence for a designer?
A. I'm not aware that there is any affirmative evidence for a designer anywhere in that book.
Q. And what about in Dr. Behe's work?
A. As far as I can tell, there is no affirmative evidence for a designer in Dr. Behe's book either. Both books rely entirely on negative inferences by saying that, if evolution has problems, if evolution is wrong, if evolution cannot provide complete explanations, then we can go ahead and say it's a designer.
Q. So how do they make that argument? I mean, even if there's no evidence? What's the rationale? What's the reasoning for getting to that designer?
A. Well, with all due respect, I believe I've already answered that question, which is, I don't find there is any reasoning in that area at all. It's the sort of logical fallacy in which you might say, well, I have theory A, and I have theory B. And I can prove theory B by showing theory A is wrong. And in science, you say, excuse me, just a minute.
Besides theory B, there's an infinite number of other possible theories. So you don't, quote, prove one by showing that another one is wrong. If you show another one is wrong, you've shown that it's wrong. All other alternative theories are now equal contenders. So the logic of picking out intelligent design, which is inherently untestable, and saying that any evidence against evolution is evidence for intelligent design employs a logical fallacy that I think most scientists reject.
Section 116 notes
Section 117 
Q. So the argument is that, if science can't explain it, that default is, a designer?
A. That is the argument, as I understand it, and as it is expressed in both of these books.
Q. Has the scientific community taken a position similar to yours about intelligent design not being science?
A. Well, the scientific community, of course, is large and diverse, and I'm sure there are a few people who are enamored of intelligent design. As I mentioned earlier, the largest scientific organization in the United States, the one organization that probably can fairly be said to speak on behalf of the scientific community in this country is the American Association for the Advancement of Science, or AAAS. I know they have indeed taken a position on this issue.
Section 117 notes
Section 118 
Q. Could I direct your attention to exhibit -- Plaintiff's Exhibit 198? Do you recognize this?
A. Yes, sir, I do. This is a board resolution by the governing board of AAAS on intelligent design theory.
Q. If we can highlight the passages. And Dr. Miller, could you read the highlighted text?
A. I'd be glad to. Quote, Whereas ID, intelligent design, proponents claim that contemporary evolutionary theory is incapable of explaining the origin of diversity of living organisms, whereas to date, the ID movement has failed to offer credible scientific evidence to support their claim that ID undermines the current scientifically accepted theory of evolution, wheres as the ID movement has not proposed a scientific means of testing its claim, therefore, be it resolved that the lack of scientific warrant for so-called intelligent design theory makes it improper to include it as a part of science education, closed quote.
Q. That is the official position of AAAS?
A. That is correct, sir.
Q. That is the largest association of scientists in North America?
A. That is absolutely correct. And this is the organization that really speaks on behalf of the scientific community in our country.
Section 118 notes
Section 119 
Q. Now has the National Academy of Science taken a position on intelligent design?
A. Yes, sir, I believe it has.
Q. Could I ask you to take a look at Plaintiff's Exhibit 192? This is the publication we viewed earlier today?
A. Yes, sir, it is.
Q. Could you turn to page 25, please? And could we highlight the third paragraph on that page, please? And this is from the conclusion of this publication, Dr. Miller?
A. Yes, sir, I believe it is.
Q. Could you please read for the record the highlighted text?
A. Quote, Creationism, intelligent design, and other claims of supernatural intervention in the origin of life or of species are not science because they are not testable by the methods of science. These claims subordinate observed data to statements based on the authority, revelation, or religious belief. Documentation offered in support of these claims is typically limited to the special publications of their advocates.
These publications do not offer hypotheses subject to change in light of new data, new interpretations, or demonstration of error. This contrasts with science where any hypothesis or theory always remains subject to the possibility of rejection or modification in the light of new knowledge, close quote.
Q. Are you aware of any scientific organizations that have taken a position that intelligent design is science?
A. I am not aware of any scientific organization that has taken a position that intelligent design is science, not one.
Section 119 notes
Section 120 
Q. Why do you believe that intelligent design, as described in Pandas and by Professor Behe, is a form of, I think as you put, special creationism?
A. I believe that as a proper analysis for the following reason. Each of the systems described by Dr. Behe had their origination, their first appearance at some time in the natural history of this planet. Each of the organisms described in Pandas and People and said to appear suddenly, fully formed in the fossil record had their origin at a particular time in the past. To say that such organisms are designed or such pathways are designed is only to tell part of the story.
Because, for example, if the blood clotting cascade had only been designed, our blood wouldn't clot. That pathway had -- that design had to be executed. It had to be created. It had to be put into physical form. And by any definition, that is an act of creative energy and power.
What that means, for example, the bacterial flagellum perhaps originated a billion years ago. It means the first organism containing that flagellum had to be created. The blood clotting cascade came into existence, we think, about 450 million years ago. The genes, the co-factors, the pathways had to be created. Advocates of intelligent design point to the first appearance of many major animal groups in what is known as the Cambrian period of geologic history.
If one says that those organisms were designed, they also had to be created. So that the natural history of this planet, according to intelligent design advocates, is marked by instance after instance after instance of specific and special creation. Saying that something is designed, as I mentioned, is only part of the story. We won't know about the design unless somebody created it and put it into execution, and that is what makes intelligent design inherently a theory of special creation.
Section 120 notes
Section 121 
Q. Now does intelligent design differ from creation science or scientific creationism what you are debating in the early 1980's?
A. In the early 1980's, the scientific creationist movement proposed a number of essential tenants or doctorates. One of them was that, the earth is about 6 to 10,000 years old. Another one is that, all of the geological column of this planet was formed in a single world wide flood, so that geologists are wrong when they talk about ages in the past; in fact, everything was laid down in about 40 days and 40 nights, that humans and apes have separate ancestory, that biochemical and biological systems show evidence of design, and that the mechanism of evolution does not work.
These are all elements, as I understand them, of the creation science or the creationist or scientific creationism movement. Now the difference between this movement and intelligent design ironically is that intelligent design has withdrawn the testable scientific predictions made by scientific creationists. The statement that the earth is only 6000 years old is a testable scientific statement. They've withdrawn that. The statement that all of the geological formations of this planet were laid down in a 0 day, 40 night flood, that's actually a testable statement. They've withdrawn from that.
The only thing that they have left is an untestable assertion, and that assertion is that the living things on this planet are too complex to have been explained by evolution and, therefore, they must be the work of a supernatural designer creator working outside of the laws of nature unidentifiable and not subject to detection, analysis, or identification. So, as I said, ironically, intelligent design is somewhat less scientific in terms of the prediction it makes than scientific creationism, but it shares that core belief, and that is that design can be attributed to a supernatural designer or creator.
Section 121 notes
Section 122 
Q. I want to switch gears now and bring us back from the classroom, so to speak, to the classroom at Dover, Pennsylvania. I'd like to direct your attention to Plaintiff's Exhibit 124. Again, this is the four paragraph statement that was read to the students in January of 2005.
You indicated earlier that you did not -- you believed that this statement did not promote students' understanding of evolution in particular or science and biology generally. I'm wondering if you could comment a little bit more specifically about your views on this four paragraph statement. And perhaps we want to take it paragraph at a time?
A. Yeah, I was going to -- thank you very much. I was simply going to ask for the whole statement to be put up there. I'd be happy to discuss this statement with you in a number of ways. We could parcel it word by word and line by line, if you had the patience to do that.
But I think it's probably better to take it first a paragraph at a time and basically see what it says. Well, that first paragraph basically says, kids, we have to teach evolution whether we want to or not because the State of Pennsylvania requires us to.
The second paragraph says, oh, by the way, we don't really believe this stuff, it's a theory not a fact. There are gaps. There's no evidence. We're very skeptical of this.
The third paragraph said, by the way, there's another alternative really good idea called intelligent design, and we're going to provide you with curricular material and the book Pandas and People so you can explore it. And I say that because I note that, there's no statement in here that intelligent design is theory not a fact, that it has gaps which cannot be explained. Those are only pointed out for evolution.
The third paragraph says, basically we think this is a pretty good theory, and we're giving it our endorsement. The fourth one basically reminds students basically, go home, discuss this with your families, and reminds them again, oh, by the way, we have to test you on this stuff whether we want to or not because the State of Pennsylvania requires us to.
Now when I read this, and I try to think of how a student will react to this, what it basically tells students who have studied theory after theory and subject after subject and hypothesis after hypothesis in earth science, in physical science, in chemistry and biology, it says, oh, by the way, of all the stuff you studied, we want to warn you about just one of those things. And that one thing is evolution. We have to teach evolution whether we like it or not. We think it's pretty shaky.
There is this other theory called intelligent design which we think is on a very sound footing. Go home, talk it over with mom and dad, and, oh, yeah, remember, we have to test you on evolution.
Section 122 notes
Section 123 
Q. Dr. Miller, I'd like to focus your attention back onto the second paragraph. And this makes various assertions about evolution generally. And maybe we could go through that sentence by sentence.
A. Okay. I'd be glad to do that. The first sentence reads, quote, Because Darwin's theory is a theory, it continues to be tested as new evidence is discovered, closed quote. Well, it certainly is true that the theory of evolution is a theory. That's almost redundant. That's obvious from the terminology. It continues to be tested. All scientific theories are continued to be tested. So to pick out evolution and say, by the way, it's a theory, and we're going to keep testing it, implies to students that really this is the only theory that we have to continue to keep testing. Other theories, they're fine. They're on sound footing. But this one, we have to keep working on.
Q. I'm sorry. From your textbook, evolution is not the only theory that is presented for 9th grade biology?
A. Of course not. And we talk about cell theory and the germ theory of disease. We even talk about the pressure flow hypothesis of phloem transfer. I've never seen a statement in the textbook saying, keep your eye on that special pressure flow hypothesis in phloem transfer.
This is the only theory people seem to be concerned about. The Dover statement, first of all, basically begins in this paragraph by calling special attention to just one part of the curriculum, and that is evolution.
Section 123 notes
Section 124 
Now the second sentence, the theory is not a fact. As far as that reads, that's actually a true statement. No scientific theory is a fact. That's not because we're sure of facts and we're not certain about theories. It's because theory is a higher level of scientific understanding than fact. Theories explain facts.
And if this statement said, no scientific theory is a fact, but rather, theories are based on facts and supported by facts, and theories explain facts, it would be fine. But by saying, the theory is not a fact, it essentially invites students to say, you know what, other theories might be factual, this one isn't. And that implication is incorrect.
The next sentence reads, gaps in the theory exist for which there is no evidence. I continue -- I have to tell you, I have read that statement hundreds of times, and I don't understand what it means by gaps in the theory. There certainly are elements in the natural history of our planet for which evidence is missing.
There are pieces of our natural history that we don't know, just like there are pieces of our political, military, and human history that we don't know. I can only trace one part of my family back to about 1850. I don't know what happened before that.
That doesn't mean I couldn't possibly be here because I don't have any ancestors before 1850. It means, I don't have the whole story. Well, that's true about evolution as well. There are parts of our recent past that are gaps, that are missing, that we don't have the story. But to say that's a gap in the theory strikes me as very very strange. There are missing pieces of evidence but not gaps in the theory. And then the last sentence, a theory is defined as a well-tested explanation that unifies a broad range of observations. Do you know what? That's fine.
And if evolutionary theory had been introduced in this paragraph by saying, evolutionary theory is a well-tested explanation for the origin of life that unifies -- for the origin of species that unifies a broad range of observations, I'd be saying, terrific, that's a very useful thing to tell students.
Section 124 notes
Section 125 
Q. As an author of a textbook, biology textbook for high school students, does this promote sound science education?
A. No, I certainly don't think it does. I think it, in fact, undermines sound scientific education in a number of ways. First of all, it misleads students into the relationship between theory and fact. Secondly, it undermines the scientific status of evolution in a way that it does to no other scientific theory as if to pretend to students, we are certain of everything we're going to teach in biology this year except for evolution.
And that certainly gives students a false understanding of evolution. And I think, as an experimental cell biologist, it gives them a false certainty of the rest of science, which is equally damaging. And then finally, to say that there are gaps for which there are no evidence, once again, is targeting evolution for a very specific purpose, and that is to create doubt and confusion in the minds of students about the scientific status of evolution and evolutionary theory.
Q. I believe you were here for the opening statements this morning?
A. Yes, sir, I was.
Section 125 notes
Section 126 
Q. The School District argues, you know, it takes a minute to read this statement. I haven't timed it. It takes about a minute to read this statement. What's the big deal? What's the harm in reading this to Dover School District students?
A. That's a very interesting point. And if they raised the issue, what is the harm in reading it, one might well turn around and say, well then why read it in the first place, if it makes so little difference, if it is of so little consequence? Then why have you insisted on doing this and why are you in court today?
The only thing I can infer from turning that question around is that the Dover School Board must think this is enormously important to compose this, to instruct administrators to read it, to be willing to fight all the way to the court. They must think that this performs a very important function.
Now turning it around back to my side of the table, do I think this is important? You bet I think this is important for a couple of reasons. One of which, first of all, as I mentioned earlier, it falsely undermines the scientific status of evolutionary theory and gives students a false understanding of what theory actually means. Now that's damaging enough.
Section 126 notes
Section 127 
The second thing is, it is really the first attempt or the first movement to try to drive a wedge between students and the practice of science, because what this really tells students is, you know what, you can't trust the scientific process. You can't trust scientists. They're pushing this theory. And there are gaps in the theory. It's on shaky evidence. You really can't believe them. You should be enormously skeptical.
What that tells students basically is, science is not to be relied upon and certainly not the kind of profession that you might like to go into. And thirdly, that third paragraph that we haven't talked about very much right now points out that intelligent design, which has implicit endorsement in this statement, because we don't hear that it's just a theory, we don't hear that it's being tested, it sounds like it's a pretty good explanation. It's available. It's good stuff. And students will understand immediately, as anybody does who reads Pandas, that the argument is made on virtually every page of Pandas for the existence of a supernatural creator designer.
And by holding this up as an alternative to evolution, students will get the message in a flash. And the message is, over here, kids. You got your God consistent theory, your theistic theory, your Bible friendly theory, and over on the other side, you got your atheist theory, which is evolution. It produces a false duality. And it tells students basically, and this statement tells them, I think, quite explicitly, choose God on the side of intelligent design or choose atheism on the side of science.
What it does is to provide religious conflict into every science classroom in Dover High School. And I think that kind of religious conflict is very dangerous. I say that as a person of faith who was blessed with two daughters, who raised both of my daughters in the church, and had they been given an education in which they were explicitly or implicitly forced to choose between God and science, I would have been furious, because I want my children to keep their religious faith.
I also want my students to love, understand, respect, and appreciate science. And I'm very proud of the fact that one of my daughters has actually gone on to become a scientist. So by promoting this, I think, this is a tremendously dangerous statement in terms of its educational effect, in terms of its religious effect, and in terms of impeding the educational process in the classrooms in Dover.
Section 127 notes
End of Direct examination 
THE COURT: I was going to break about 3:00, Mr. Walczak. Is that good for you. If you want to move onto another line of questioning, this might be a good time to do it.
MR. ROTHSCHILD: I'm done, Your Honor. I would just move the exhibits into evidence.
THE COURT: Is there an objection, first of all, to any of the exhibits?
MR. MUISE: No, Your Honor.
THE COURT: We'll get those in the record when we come back from the break. I think we have a list. Why don't you compare notes with Liz and make sure that we've got a comprehensive roster of the exhibits. We'll take at least a 20 minute break or so. So my friends in the jury box who look like they could use a little caffeine, this will give you ample time to patronize the local establishments and get some caffeine and come back. That not a knock on you, Doctor.
THE WITNESS: I knew I should have shown more slides, Your Honor.
THE COURT: No, it's perfectly all right. We'll see you back here shortly. We'll be in recess.
(Whereupon, a recess was taken at 2:55 p.m. and proceedings reconvened at 3:24 p.m.)
- Peer-Reviewed & Peer-Edited Scientific Publications Supporting the Theory of Intelligent Design (Annotated), Center for Science and Culture, February 1, 2012.
- Claims of Peer Review for Intelligent Design examined … and debunked, Dave Gamble, Skeptical Science, October 7, 2012.
- Discovery Institute: Their Peer-Reviewed Papers, The Sensuous Curmudgeon, 14 February 2012.
- Bonobo Genome Completed: The Final Great Ape to Be Sequenced, ScienceDaily, 13 June 2012.
- The Mystery of the Missing Chromosome (With A Special Guest Appearance from Facebook Creationists), Carl Zimmer, The Loom, 19 July 2012.
- Initial sequence of the chimpanzee genome and comparison with the human genome, Nature, 1 September 2005.
- Quoted in Science and Creationism: A View from the National Academy of Sciences, Second Edition, 1999, page IX.
- Memorandum Opinion by Judge John E. Jones III, wikisource (may contain spoilers).
- Stomping Through Pandas, Skeptical Analysis, 22 January 2012.
- Construction of Phylogenetic Trees, Fitch and Margoliash, Science, 20 January 1967 (pdf).
- Whale Hageman Factor (Factor XII): Prevented Production Due to Pseudogene Conversion, Semba et al., Thrombosis Research, 1 April 1998.
- Hageman Factor (Factor XII) Deficiency in Marine Mammals, A. Jean Robinson, Mona Kropatkin, Paul M. Aggeler, Science, 12 December 1969 (pdf).
- The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes, Jiang and Doolittle, PNAS, 24 June 2003.
- The Discovery Institute provides a list of Pandas quotes, which includes this one ("Quote B").
- The origin of new genes: glimpses from the young and old, Long et al., Nature Reviews Genetics, November 2003 (pdf).
- larger version. The image is from Kevin Padian's slides from later in the trial, which are available online.
- What kind of scientist is Michael Behe? at the Wayback Machine (archived 25 February 2008).