RationalWiki:Kitzmiller v. Dover annotated transcript/P011

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Day 3 (28 Sept 2005): Morning Session - Direct of Robert Pennock

Section 1 THE COURT: Be seated, please. Be seated. All right, we commence Day 3, and we remain in the plaintiff's case. Mr. Rothschild, you look most eager, so you apparently are going to take charge as we start Day 3. MR ROTHSCHILD: Good morning, Your Honor. Plaintiffs are here to call Robert Pennock to the stand. (Dr. Robert Pennock was called to testify and was affirmed by the courtroom deputy.) COURTROOM DEPUTY: Thank you very much. Please state your name and spell your name for the record. THE WITNESS: It's Robert T. Pennock, P-E-N-N-O-C-K.	Section 1 notes
Section 2 DIRECT EXAMINATION BY MR ROTHSCHILD: Q. Good morning, Dr. Pennock? A. Good morning. Q. I have placed before you a notebook of exhibits that we may use today. In addition certain of the exhibits will also appear on the screen and on the monitor before you. Where do you live? A. I live in East Lansing, Michigan. Q. And what do you do? A. I'm a professor at Michigan State University. I teach in the Lyman Briggs School of Science, in the department of philosophy, and the department of computer science. Q. Matt, could you pull up Exhibit P-319? Dr. Pennock, do you recognize this document? A. Yes. This is an earlier version of my CV. Q. And when you say earlier, is it accurate as of the date on the CV? A. As of January that's accurate. There's been some changes. I am now a full professor and not an associate professor anymore. Q. And where do you teach? A. At Michigan State University. I'm appointed in several departments. My primary appointment is in the Lyman Briggs School of Science, which is in the college of natural sciences. I'm also in the department of philosophy, and I'm also in the college of engineering and the computer science and engineering department, and also in the graduate program in ecology, evolutionary biology, and behavior. Q. And what subjects do you teach at Michigan State? A. Primarily courses in the philosophy of science, things having to do with confirmation theory, philosophy of biology in particular. I also teach courses in artificial life, evolutionary computation, and issues, related to ethics in science. Q. If I could ask you just to speak up a little bit more for the benefit of the court reporter. What degrees do you hold? A. I hold a bachelors, BA, from Earlham College, a double major in biology and philosophy, and my graduate work was in history and philosophy of science at the University of Pittsburg, Ph.D. Q. Did you write a dissertation? A. Yes, I did. Q. And what was the topic of that dissertation? A. My dissertation was on the nature of scientific evidence in the philosophy of science, the area known as confirmation theory. The specific topic had to do with the nature of what's known as the evidence relationship, what's the notion of relevance between hypothesis and the evidence that tests it. That's the specific area that I was writing about.	Section 2 notes
Section 3 Q. Can you explain what philosophers of science do? A. Many people ask that question. What philosophers of science do is analyze the basic concepts, assumptions, practices of science and scientists. It's like any other philosophical practice, focused on the nature of the concepts in particular. So philosophy of those subjects, and there are a whole range of them, deals with the concepts, assumptions of that area. So philosophy of science deals with the areas within science. There are subspecialties of philosophy of biology, philosophy of physics, philosophy of psychology, and so on, and each of those cases what we do is look at what scientists say, what they write, the practices that they engage in, to try to understand the concepts that are behind it, and try to in our terms explicate them, which is to say take concepts that may not be systematic, but to try to make them systematic, try to make them rigorous. Q. How do philosophers of science distinguish between science and non-science? A. Philosophers of science focus on what scientists do. If one does philosophy of art, then one looks at what artists do. So our primary starting point is the practices, the concepts of science. So we'll look at the nature of evidence for example, the basic characteristics that we expect to find that we will start with is that science is a practice that deals with examining questions about the natural world, giving explanations about the natural world in terms of natural law, and offering hypotheses that can be tested against the natural world. Q. Have you focused your research and writing on any particular subjects? A. As I said, my general topic of interest is the nature of evidence in science, and the particular case study that I have most focused on over the years has been creationism, and more particularly intelligent design creationism as a way of looking at those issues.	Section 3 notes
Section 4 Q. When you use the term creationism, what do you mean? A. Creationism as I use it in its general sense is a rejection of evolution as science understands it and a positing instead of that some sort of supernatural non-material intervention. There are many different kinds of creationists, but that's the generic notion when I use it. I also try to be specific about what particular time I'm referring to. It doesn't necessarily have to be a Christian. There are non-Christian creationists. So one has to be specific about the type. Q. And what are the types of creationism that you commonly find in the United States? A. A whole range. Probably the stereotypical notion is what's known as young earth creationism, a view that says one can from scripture perhaps calculate how old the earth is and come to a conclusion that says six to ten thousand years. Other creationists say well, we can accept something much more along scientific lines, you can interpret scripture to allow geological time. So those would be older creationists. Within the camps you then have other differing views regarding other topics such as whether there was a global universal flood that was catastrophic that shaped the world and its land forms. Others would say the flood was local or tranquil. So as I got into researching this topic I very quickly learned that there are many different factions among creationists and that the stereotypical view that we have today, the young earth, ten thousand year old one, is actually just one, though obviously dominant view, but just one of many different views. The old earth creationist's view is actually more somewhat of an earlier view that continues to hold. In the Scopes trial obviously we can think of that as the key example of a creationist's view, but that was the old earth view. It was not a young earth view that Bryan held.	Section 4 notes
Section 5 Q. Are you familiar with the term special creation? A. Yes. Q. What does that mean? A. Special creation is another general term that's focusing on the issue that the intervention from the creator the designer is periodic. It's a series of special creations, a particular one. The term actually gets used in different ways, and in some cases historically there's a connection that says that special refers to the creation of species. So that it was individual creations of species themselves, special in that sense. But the term is used somewhat inconsistently. Q. What is intelligent design? A. Intelligent design creationism is a movement that attempts to unite these various factions. I think it's best described as a strategy to take disparate views such as the ones that I have mentioned and to unite them against a common enemy. Nancy Pearcey in her recent book on "Total Truth" actually explains this very well. She says that intelligent design is a way for Christians who might be young earth creationists, old earth creationists, progressive creationists, theistic evolutionists, to come together, she mentions how Phillip Johnson specifically created that strategy to allow them to come together to then oppose the naturalist world view of evolution. Q. Is intelligent design creationism? A. Yes. It's a form of creationism. Q. And is it a form of special creationism? A. Yes. They hold that you cannot have a natural explanation of biological complexity and you need to have some special intelligence, non-natural intelligence that intervenes to produce this.	Section 5 notes
Section 6 Q. I take it from your answers that you have researched intelligent design extensively? A. I've been following this from pretty much the beginning of the movement really for the last fifteen years focusing on intelligent design, but my work on creationism really started before that when it was called creation science, and I sort of watched in part as the transition and language occurred from creation science to abrupt appearance to intelligent design. Q. Describe how you go about you research on these topics. A. My early work was actually inspired in part by a student coming in with the book "Pandas and People," it was in Texas, and it was going to be proposed to be introduced in her school district, and she was concerned about this. It was the first time I had looked at the book. I had also seen Phillip Johnson, I believe the pioneer of the intelligent design movement, give a talk in the early, early parts of this movement, and wrote an article based upon one of his early articles his early book. I was present at a very important conference that they held at Southern Methodist University where many of the current big names came together to articulate some of the meetings for the first time. I read many of their books. I have a large shelf of that, and probably hundreds of their articles. I have attended their talks. So that's the process by which I have come to know them quite well.	Section 6 notes
Section 7 Q. Who is Phillip Johnson? A. Phillip Johnson is a retired law professor, and he's thought of as like a pioneer most credited with bringing this movement together and crafting a strategy. Q. Not a scientist? A. No. Q. This conference at Southern Methodist University, do you remember who was in attendance? A. It was on the occasion of Phillip Johnson's book "Darwin on Trial," something that was organized around the publication of that book. Some of the names that we now recognize where there are William Dembski, Stephen Meyer, I believe Michael Behe as well. Q. And these are all people involved in the intelligent design movement? A. That's right. Those are the core, among the core leaders of the movement. Q. And they continue to be to this day? A. That's right.	Section 7 notes
Section 8 Q. Have you written on the subject of intelligent design? A. Yes. I have written probably a dozen articles in various journals, and a book, and I have edited an anthology. Q. What is that book called? A. The book is called "Tower of Babel: The Evidence Against the New Creationism." Q. Could you pull up Exhibit 339 on the screen? Is that the cover of the book? A. Yes. Q. Can you tell us what it's about? A. What it does is look at the arguments of creationism both in its creation science form and in its intelligent design form, mostly focusing on the second, showing what they argue, and, you know, what is wrong with it. So it's a critical analysis of the movement.	Section 8 notes
Section 9 Q. Did you in this book discuss how intelligent design arguments compare to prior creation arguments? A. That's one of the things that I do in comparison there is show how really, although the terminology is different, the basic concepts underlying it are straightforwardly connected to the earlier view. Q. You also said you edited an anthology? A. The anthology was called "Intelligent Design Creationism and Its Critics: Philosophical, Scientific, and Theological Perspectives." Q. And could you pull up Exhibit 627? Is that the cover of the anthology you edited? A. Yes, that's right. Q. And what's contained in that anthology? A. The goal in that was to have a source book as complete as possible of representative articles from the intelligent design group itself and critical assessments thereof. I focused on articles that they published, and on the critical side some previously published articles, and in some cases new articles that I commissioned for the volume.	Section 9 notes
Section 10 Q. Have you done any scientific research on the subject of evolution? A. Yes. Some of my current research is on testing evolutionary hypotheses making use of evolving computer organisms. Q. Can you describe in general terms what that research is? A. Sure. The idea is to make use of a system that essentially is an evolutionary system whereby the Darwinian mechanism is implemented in the computer and using that to form experiments to test evolutionary hypotheses. Essentially one is able to watch evolution happen and in replicable controlled experiments test particular evolutionary hypotheses. Q. Has this research been published in a peer reviewed scientific journal? A. Yes, in Nature. Q. Matt, could you pull up Exhibit P-330? Is this the first page of that article in Nature? A. Yes, that's right. Q. And Ken Miller plugged Nature repeatedly in his testimony, but I'll give you the chance as well. Is Nature one of the more prestigious scientific journals? A. Nature, together with Science and PNAS, Proceedings of the National Academy of Science are really considered the top three journals within science.	Section 10 notes
Section 11 Q. And obviously peer reviewed? A. Peer reviewed journals, that's right. Q. You didn't write this article by yourself? A. This was a collaborative project. My collaborators in this case were two of my colleagues at Michigan State, Richard Lenski, who is an evolutionary biologist. He's most known for his work on experimental evolution using bacteria. He's had lines of bacteria evolving for the last fifteen years that allows one to do experiments to test evolutionary hypotheses in that kind of system. He got very excited about this new system that allows one to test evolutionary hypotheses in a way where things are even faster. Charles Ofria is another colleague at Michigan State. He's in the department of computer science, and he together with Christoph Adami, the last name there, are the two originators of the platform known at Evita. Adami is a theoretical physicist. He's most known currently for his work solving a problem that Steven Hawkings was trying to work on regarding black holes, but he works in this area as well. He at the time was at Tech. Q. At where? A. At Tech Research Institute out in California.	Section 11 notes
Section 12 Q. I'm going to ask you the same question here that I have asked you in our private meetings, which is these are computer organisms. They're not biological organisms. What can they possibly show about biological evolution? A. They show us how the Darwinian mechanism works. The key thing about them is that it's a model where you have the laws that Darwin discovered, the mechanism of random variation that's heritable, that then can be naturally selected, can be seen, manipulated, experimented with in just the same way, it works in just the same way that it works in the biological case. These organisms, computer viruses if you will, evolve. And so one can set up experiments to watch them evolve and test hypotheses about how the Darwinian mechanism works. Q. Now, these organisms, computer organisms, they didn't arise by themselves, correct? There was a programmer involved? A. Yes. That would have been Charles Ofria particularly, writing we called the Ancestor Program. The Ancestor is simply a self-replicator, an organism that has instructions to allow it to replicate itself, but otherwise is just a series of blank instructions. That's the basic part that, was hand coded. Q. So with that, you know, fact of a human designer, a programmer, how can this teach us anything about evolution in the natural world? A. Our investigations are not about the origin of life. Like Darwin we're not really interested in that particular question. We're interested in as Darwin said the origin of species, the origin of complexity, the origin of adaptations, and what we're able to do in this system is examine essentially what Darwin examined. We're not investigating how life began itself. We're investigating how once that happens, things evolve, evolve complex traits. Q. So just to make sure I understand, this research wouldn't be valuable in any way to coming up with a natural explanation for how the first biological life arose? A. No. It's not at all aimed at that.	Section 12 notes
Section 13 Q. Does the designer, the programmer, play any role in the development of these computer organisms, like their evolution after that? A. The wonderful thing about this is that we can essentially sit back and watch evolution happen. We'll set up an environment, set up a system, put in place the Ancestor, put in place the original organism, and then within the experimental set-up, depending on what one wants to investigate you'll set it up differently, but essentially at that point we're not going to go in and hand code anything. We're not going to manipulate the code. What happens at the end, if they've evolve some new functional trait, that something that happens by virtue of the Darwinian mechanism. They randomly evolve, they randomly vary, that variation is inherited, and the natural selection then does its work. Q. What advantages does this computer model have over doing research on the subject of evolution with biological organisms? A. It has the advantage of speed primarily, and precision. It allows us to do what you really can do with natural organisms. Lenski's work with E. coli lets one do experimental evolution so one can test hypotheses in that way. It's taken fifteen years, E. coli are pretty fast replicators, but even so, four generations or so a day still is a long time, and your graduate students would never get out and get jobs if you had to wait for that whole process to go through, and what this does is let one watch it happen much more quickly, and then set up very controlled circumstances so that you can really do replications. A controlled experiment is now possible in a way that allows very precise comparison of groups and then statistically significant results.	Section 13 notes
Section 14 MR ROTHSCHILD: Your Honor, at this time I'd like to move qualify Dr. Pennock as an expert in the philosophy of science, in the history of science, in intelligent design, the subject of intelligent design, and in his research on the evolution of computer generated organisms. THE COURT: All right. Subject to the stipulation of the parties it's my understanding that you are agreeable to that, although I'll certainly give you the opportunity to conduct any voir dire that you may want to. MR. GILLEN: You're correct, Your Honor. We've stipulated to the qualifications of all the experts with one exception you're aware of. THE COURT: As noted previously, so if you have no questions on qualifications we'll admit this witness for the purpose stated by Mr. Rothschild, and you may proceed then with your direct examination.	Section 14 notes
Section 15 BY MR ROTHSCHILD: Q. Do you have an opinion about whether intelligent design is science? A. Yes, I do. Q. And what is that opinion? A. My opinion is that it does not qualify as science. Q. Why not? A. As scientists go about their business, they follow a method. Science is probably most characterized by its way of coming to conclusions. It's not so much the set of specific conclusions that it comes to, but the way in which it reaches them. In philosophy we talk about this as epistemology, it's a way of knowing, and science has limits upon itself. It follows a particular method. It has constraints. It requires that we have testable explanations. It gives natural explanations about the natural world. Intelligent design, creationism specifically, wants to reject that. And so it doesn't really fall within the purview of science. Q. Is there a name or term of art for this rule of science that it must look for natural explanations for natural phenomena? A. Scientists themselves may not use the term. This is something that philosophers of science use, but the term is methodological naturalism, and the idea is that this is a form of method that constrains what counts as a scientific explanation.	Section 15 notes
Section 16 Q. In his opening defense counsel used the term philosophical naturalism. Is that a term you're familiar with? A. Yes. Philosophical naturalism is one term that's used. Some other terms that one finds include metaphysical naturalism. I've used the term ontological naturalism. The key notion there is a philosophical one about the nature of ultimate reality, the metaphysical notion, and that's not part of science itself. Q. If one were a philosophical naturalist or a metaphysical naturalist, what conclusions does that lead one to? A. A philosophical naturalist would be someone who says the world as it is in its ultimate reality, its metaphysical reality, is nothing but material natural processes, and there is no supernatural, there is no god, there is nothing beyond. A philosophical position, sometimes with subtleties, one might call it a metaphysical naturalist or metaphysical materialist position, but it's a statement about the ultimate nature, the metaphysical nature of reality. Q. And a statement of that nature is not a scientific statement? A. That's right. Science is not in the business of making philosophical metaphysical claims. Q. Some scientists may make those statements, but that doesn't make it science? A. That's right.	Section 16 notes
Section 17 Q. How did science adopt this rule of methodological naturalism? A. As I said, the term itself is something that philosophers have used. So one really has to go back and sort of see how that method, that concept arose, and it really arose in fits and starts. It's not as though one can point to a particular time, but it's a change that one can really trace back even to the pre-Socratics, we sometimes point to Hippocrates for example as one of the early glimmers of this type of view with regard for example to the nature of disease. An earlier view would have said that a disease is the result of some perhaps possession by some supernatural, divine, or demonic being. Q. Can you give us an example of that? A. Yes. Epilepsy was the example that Hippocrates dealt with. It was called the sacred disease. The idea was that it was kind of divine possession when one went into an epileptic seizure. Hippocrates suggested that we should not think of it in that way but just think of it as a normal illness and try to find a normal, natural way of curing it. As he talked about epidemics, again epidemics would have been things that under some non-scientific ways of thinking about it they're the result of displeasure of God perhaps, and Hippocrates said we should try to find by cataloging natural regularities try to find causes for epidemics. So that's sort of an early inkling of this, and it's not as though this then set root and established everything. One go through really century by century before one finds these things being teased apart. So for example really in the 13th through 15th century one finds alchemists, people doing supernatural magic, trying to think that one can find ways of overcoming the laws of nature by appeal to supernatural entities and so on. And a switch that kind of happened of the same sort where people suggested well, maybe there are just hidden regularities that we don't yet know about that are actually natural explanations for these apparent magical things. So they talked about the natural magic, and the idea then was let's think about what these might be. Now, it's not as though they got things right. Facchino was one 15th century natural magic proponent who thought that influences from the planets of particular sorts could explain events on earth. He wasn't thinking of these as supernatural. He thought of them as natural, but that they could be controlled by other material, talismans for example. So there you're getting this notion of a method that assumes natural regularities and appeal to those as coming out. Really this gets much more firmly established then in enlightenment and scientific revolution. That's probably what's most characteristic of the scientific revolution, rejecting appeal to authority and saying we will appeal just to nature itself. We'll appeal just to the evidence, the empirical evidence.	Section 17 notes
Section 18 And it's very clear at that point then that when one does science, one is setting aside questions about whether the gods or some supernatural beings had some hand in this. A classic example had to do with meteorological phenomenon, lightning. It would have been thought or that lightning perhaps would have been an expression of God's displeasure, right? That God by design would send lightning somewhere, and it was one of the founding fathers, Benjamin Franklin of course, who investigated lightning under this assumption of methodological naturalism and said you can have a natural explanation of lightning, it's electricity. And that's an example of this shift, a shift as saying we're not going to say what God may or may not be doing with sending lighting bolts. We'll simply say let's examine this as part of the natural laws of nature. Today this is just firmly entrenched. Several month ago I did a literature search to see if I could find whether scientists might be reintroducing the supernatural, the transcendent into their work, and I did find the supernatural in there in one sense. It was considered by folks who were doing work, research on medicine, and wondering about how we could better get patients to follow a medical regimen, follow their medications, and it turned out that the beliefs that patients had about the supernatural played a role. And so in that sense they had to consider it, people believed this, and so they had to understand that in order to help them better follow their therapies for example. The single case where I found, though, where it was proposed as the supernatural should be introduced in some way was in an alternative medicine journal, and in that case the author specifically said, "But to do so of course would be to take this out of the realm of science, and I'm not proposing that."	Section 18 notes
Section 19 Q. So methodological naturalism is basic to the nature or science today? A. As I said, I could not find an exception to that. Q. And the rule is well accepted in the scientific community? A. That's right. Q. Why is this methodological rule important for science? A. Well, it's important in the sense that I just described that it's part of what it means now to be a scientist. If one were to start appealing to the supernatural, one would immediately get the reaction from one's colleagues this is no longer part of what it is to be a scientist. So part of it is just essential to the notion. Philosophically it's important in the sense that it's relevant to the justification of conclusions, of scientific conclusions. What one expects in science is that one is going to be testing hypotheses against the natural world, and what methodological naturalism does is say we can't cheat. We can't just call for quick assistance to some supernatural power. It would certainly make science very easy if we could do that. We're forced to restrain ourselves to looking for natural regularities. That's part of what it means to be able to give evidence for something. You've undermined that notion of empirical evidence if you start to introduce the supernatural. And then the second part of that is it's important because it makes a difference. Okay? That then allows you to practically apply the results of scientific inquiry. When you discover these natural regularities, these causal regularities, you're then able to use them in pathology and so on, and to just take it back to the example of Franklin, Franklin's naturalistic, let's say methodological naturalistic understanding of lightning then led him to be able to invent the lightning rod, which then was a very practical way of stopping buildings from being hit by lightning. So that’s a sense in which this is crucial, because it makes a difference. It lets us apply the conclusions, the discoveries that scientists make.	Section 19 notes
Section 20 Q. Is the theory of evolution an example of utility of methodological naturalism? A. I actually recommend that science teachers use evolution as a great exemplar of the application of scientific method. It's a well confirmed interlinked series of hypotheses. It's not just one hypothesis, but a whole range of them, that have been tested and well confirmed, and in the same way that I was describing before, it has practical utility. One can make use of evolutionary knowledge, as scientists do in a range of fields, to social utility. One needs to know it with regard to medicine, and even with regard to engineering applications, now one can make use of Darwin's mechanism to allow engineering designs to evolve. So there's practical applications to evolution right now. You can get a job at Google if you know something about evolution. They're looking for people who know about this. Q. And the theory of evolution has been able to come up with explanations and useful conclusions without appeal to the supernatural? A. That's the basic presumption. That's the way evolution works, the way science works generally. Evolution is not exceptional in this case. It's really exactly the same as any other sort of science. We test it in the same way, and we can apply it in the same way. Q. Do leaders of the intelligent design movement agree that science as it is currently practiced includes the rule of methodological naturalism? A. They do, except that it includes methodological naturalism, and really their primary goal is to try to overturn that.	Section 20 notes
Section 21 Q. Are you familiar with someone named William Dembski? A. William Dembski is one of the intelligent design leaders that I have mentioned and researched. He's someone who is very much at the forefront of this movement. Q. And is he one of the people who has asserted this position that intelligent design needs to overturn the rule of methodological naturalism? A. Yes, he has. In a number of different places he's explicitly discussed the importance of this and how intelligent design has to be able to overturn this in order to move forward. Q. And I'm going to show you some of Dr. Dembski's writings. And have you highlighted particular portions of those writings that emphasize this point? A. What I did was just take a representative selection to try to indicate the way in which he describes this. Q. Could you pull up Exhibit P-343 please, Matt? And do you recognize this cover here? This is a cover from one of William Dembski's several books, "The Design Revolution: Answering the Toughest Questions about Intelligent Design." And is this a book you have read? A. Yes.	Section 21 notes
Section 22 Q. Could you turn to page 19 of this book please, Matt? And could you just illuminate the passage that Dr. Pennock highlighted? Could you read that into the record? A. So this is Dembski writing, "Nonetheless," he says, "there is good reason to think that intelligent design fits the bill as a full scale scientific revolution. Indeed not only is it challenging the grand idol of evolutionary biology, Darwinism, but it is also changing the ground rules by which the natural scientists are conducted. Ever since Darwin the natural sciences have resisted the idea that intelligent causes could play a substantive empirically significant role in the natural world. Intelligent causes might emerge out of a blind evolutionary process, he says, "but they were in no way fundamental the operation of the world. Intelligent design challenges this exclusion of design from the natural sciences, and in doing so promises to remake science in the world." Q. Could you now go to Exhibit 341, Matt? Do you recognize this cover page here? A. This is another one of William Dembski's books, "Intelligent Design: The Bridge Between Science and Theology." Q. And have you read this book? A. Yes. Q. Could you turn to page 224 of this book please, Matt? Could you illuminate the passages that Dr. Pennock has highlighted? Could you read this statement into the record? A. Here Dembski writes, "The scientific picture of the world championed since the Enlightenment is not just wrong, but massively wrong. Indeed entire fields of inquiry, including especially the human sciences, will need to be rethought from the ground up in terms of intelligent design." Essentially he’s telling us that we need to reject what it means to be scientists and start over.	Section 22 notes
Section 23 Q. And just one more exhibit on this point. Could you pull up Exhibit 359, please? And if you could illuminate the title and author? Do you recognize this document? A. Yes. This is an article from, by William Dembski, "What Every Theologian Should Know About Creation, Evolution, and Design." Q. And have you read this article? A. Yes. Q. Could you turn to page 7 of the document, Matt, and illuminate the passage that Dr. Pennock has highlighted? And could you read that highlighted passage into the record? A. Dembski writes, "The view that science must be restricted solely to purposeless naturalistic material processes also has a name. It's called methodological naturalism. So long as methodological naturalism sets the ground rules for how the game of science is played, is to be played, IDT has no chance," Hades, I assume no chance in Hades. Q. What do you understand Dr. Dembski to be conveying in that passage? A. What he's saying here is pretty clear, that if you take science as science, that intelligent design theory has a snowball's chance, and they need to change the ground rules. They need to change what science is, that, you know, science is hard. It requires that one test things. One always says as the scientists know, where's the beef, show us the evidence. It's I suppose hot in the kitchen, and I guess what they're saying is if it's too hot and they won't survive in the kitchen, and one might say well, if the kitchen too hot, go elsewhere. Q. Specific reference to a hot kitchen there. A. Exactly.	Section 23 notes
Section 24 Q. Could you turn to page 8 of the article? And again highlight the passage? And could you read that highlighted passage into the record? A. Here he writes, "In the words of Vladimir Lenin, 'What is to be done?' Design theorists aren't at all bashful about answering this question. The ground rules of science have to be changed." Q. And I have to admit I didn't know until I read that that Vladimir Lenin was part of the intelligent design movement, but putting that aside these passages summarize the position that intelligent design takes about scientists' rule of methodological naturalism? A. They're quite clear. They admit that these are the ground rules of science, and what they want to do is revolutionize that. They want a theistic science. Q. What would it mean for science if intelligent design's project of overturning methodological naturalism was successful? A. Essentially what this would be, what this would mean if they were to succeed in this project would be that it would turn back us to an earlier era, a pre-Enlightenment era, an era that I was speaking about before, before we had teased apart these differences, and that would be a really radical change. It would be a number of steps backwards. Q. Are there any other reasons besides this rejection of methodological naturalism that intelligent design does not, the intelligent design argument does not qualify as science? A. I point to one other particularly important one which is connected to the first and one that I have already mentioned indirectly, which is the importance of testing. Intelligent design needs to have for it to be a science a way of offering a specific hypothesis that one could then test in an ordinary way. They failed to do that, and so they really don't get off the ground with regard to science.	Section 24 notes
Section 25 Q. Well, doesn't intelligent design have some arguments like irreducible complexity and specified complexity? A. The notions of irreducible complexity, specified complexity, or as it's sometimes called complex specified information, these are characteristic terms. In a way there's, they're new terms for old concepts. Creation scientists had similarly made criticisms of the possibility of evolution to produce complex features. The particular challenges from irreducible complexity or specified complexity are challenges to evolution and its ability to produce adaptations to produce complexities of certain sorts. Their claim is evolution can't do it. Systems that are "irreducibly complex" or have specified complexity are supposed to be by them impossible to produce through Darwinian mechanisms, or indeed any natural mechanism. So it's a challenge to evolution. Q. Is it a positive argument in favor of intelligent design? A. It's like the creation scientists before in attempt to say here's something that you can't do. It's an attempt to poke holes in evolution itself. Q. And what's wrong with that as a way of demonstrating the proposition you support? A. One would expect as someone who is offering a particular hypothesis, if one were to do that, that you would give evidence directly in support of that rather than simply trying to knock down one's opponent with the hope that one would be left standing. The way in which this was done in the earlier iteration of creationism was to propose that there were two views. In that sense it was called creation science. Evolution science, and creation science has said here are some things that science can't explain, that evolution can't explain, with the hope of casting doubt upon evolution. What would then be left standing, well, there's would be, you wouldn't have to say anything positive about that. Now the terminology has changed. Now it's intelligent design theory versus Darwinism, but the logic of the argument is exactly the same. It's here's what's wrong with you, here's something that purportedly you can't explain, and we're going to be the ones then to be left standing.	Section 25 notes
Section 26 Q. And is there a logical problem with that kind of argument? A. It's an example of a false dichotomy. It's an example of in the previous iteration we called it the dual model argument, as though there are only two positions, and that by knocking down one the other is left over. But of course it's a false dichotomy. There are many other positions besides Darwinism, and there are certainly many other positions besides intelligent design. Q. Are irreducible complexity and specified complexity associated with particular individuals in the intelligent design movement? A. Irreducible complexity is most associated with Michael Behe. Specified complexity is most associated with William Dembski. These are interrelated concepts though. Specified complexity is the more general form. Dembski directly though says that irreducible complexity is a type of, a case of specified complexity.	Section 26 notes
Section 27 Q. Does your work on computer organisms address these arguments of irreducible complexity and specified complexity? A. Yes, it does. Q. Can you just describe for us briefly how it does that? A. Sure. The claims that are made with regard to these two concepts are as follows. Systems that exhibit or that purportedly exhibit irreducible complexity or specified complexity, actually at this point let me just focus on irreducible complexity, because since it’s an example of specified complexity, any conclusion that we can get with regard to irreducible complexity would also deal with specified complexity. So we can just focus on that. So the claim is any system, Behe's example is a mouse trap, so it doesn't have to be a specifically biological system, just a very general argument, any system that is irreducibly complex, thus to say has interacting parts that are well matched to introduce a function, such that if you remove any of those parts, it breaks, stops functioning, doesn't produce that basic function, is an irreducibly complex system, and such systems the claim is couldn't have been evolved through a Darwinian mechanism. What our system shows is that's just wrong. We can observe digital organisms evolving by the Darwinian mechanism, starting with an organism that cannot produce some effect, cannot fulfill a function, doesn't have this possibility, and later on evolve to the point where it can, some complex trait that we can then examine. The nice thing about this system is it lets one look at it very precisely, we can look inside and see does it fulfill the definition? In fact, it does. We can test to see, remove the parts, does it break? In fact, it does. And we can say here at the end we have an irreducibly complex system, a little organism this can produce this complex function. But the nice thing about the system is that we can look back and see in fact it did evolve. We can watch it happen. So it's a direct refutation of that challenge to evolution.	Section 27 notes
Section 28 Q. Is that point addressed, put forward in the Nature paper? A. It's not. The Nature paper itself is meant just to be a test of a general evolutionary hypothesis, examining how it is that complex features arise. Darwin had specific things to say about that. What we were doing was simply looking into that, testing it in a way. It just turns out that it also applies to this case. Q. Still on the subject of Michael Behe, but in a slightly different way, if you could pull up Exhibit 602? This is the expert report by Michael Behe that was provided to plaintiffs in this case. And could you turn, Matt, to -- actually if you could display both pages 9 and 10 of the report, and highlight the language that I asked you to last night? In this report Dr. Behe lists five claims for the theory of evolution made by the renowned biologist Ernst Meyer. Evolution as such, common descent, multiplication of species, gradualism, and natural selection. And if you could now turn to page 11, and highlight the underlined language in the report? Dr. Behe asserts, "Intelligent design theory focuses exclusively on the proposed mechanism of how complex biological structures arose. In other words, intelligent design focuses exclusively on the fifth claim of Darwinism, natural selection, in Ernst Meyer's list on the preceding page and does not concern any of the other claims." Is that an accurate characterization of the claims of intelligent design? A. I would say not at all. I'm very surprised to seeing something put in that way. Intelligent design creationists have written about and explicitly dealt with far more than just the proposed mechanism, the Darwinian mechanism. They have claims rejecting a range of biological theses from evolution, including common descent, and really things from physics, cosmology as well. So they focus far more than just this point.	Section 28 notes
Section 29 Q. On the issue of common descent, do you know what position the book "Of Pandas and People" takes on that topic? A. "Pandas and People" quite explicitly says that we should not take common descent, it's not accepted. So it's rejecting that. Q. Just we got quite a biology lesson and evolution lesson from Dr. Miller over the past couple of days, but what do you mean by the term common descent? A. Common descent is sometimes talked about in terms of the metaphor of the tree of life, the idea that the organisms, the species that we see today are the result of common ancestors. So they descend through a pathway that has common points of origin. Q. And as William Dembski taken a position on whether common descent is a valid proposition? A. Dembski is one of the design theorists who has rejected that.	Section 29 notes
Section 30 Q. And let me just ask, Matt, to pull up Exhibit 323, and I think we looked at this article earlier, but could you turn to page, and this is the article "What Every Theologian Should Know About Creation, Evolution, and Design," would you turn to the page Bates stamped R-214 and highlight the language Dr. Pennock asked you to highlight? Could you read that passage into the record from Dr. Dembski's article? A. Dembski writes, "Yes, I do believe that organisms have undergone some change in the course of natural history, though I believe that this change has occurred within strict limits and that human beings were specifically created." This is really language that is exactly the same really as from the creation science literature, excepting small changes within strict limits, sort the micro-evolution, but requiring a rejection of common descent in speciation for example. Q. If human becomes were specially created, at least in their case there was no common descent? A. That's correct. Q. Does intelligent design make claims about the age of the earth? A. Intelligent design as I mentioned before is often claimed to accept the scientific age of the earth, but that's not correct. Intelligent design as I mentioned before as Nancy Pearcey described it and as you see from the literature is a view that unites young earth creationists and old earth creationists, and so individual folks who would identify themselves as themselves design theorists, some of them would take a young earth view, some of them would take an old earth view. So it's not correct to say intelligent design is old earth if it accepts that, and they have explicitly written about this in many cases but agreed to set that aside temporarily until the initial proposition that organisms were designed, that they were created, is put into place. Phillip Johnson talked about how after we established that, after we've gotten the thin edge of the wedge in, then we can have a great time talking about how old the earth is, and that together with common descent is something that they have explicitly said should be appropriate to be considered in public school science classes under the heading of intelligent design.	Section 30 notes
Section 31 Q. And just on this point of Phillip Johnson, if you could pull up Exhibit 338? And this is an article in the magazine "Christianity Today," if you could first turn to the article, do you recognize this document? A. Yes, this is an interview with Phillip Johnson. Q. And could you turn to page RP-184 and highlight that passage that Dr. Pennock asked you to? And could you read that into the record? A. So the introductory paragraph says, "In spite of the division between religious believers, University of California law professor Phillip Johnson, whose books critique Darwinism, says Christians should set aside internally divisive issues and focus on establishing the credibility of a theistic world view. Johnson told CT," that's to say Christianity Today, "people of differing theological views should learn who's close to them, form alliances, and put aside divisive issues until later." He says, "I say after we have settled the issue of a creator, we'll have a wonderful time arguing about the age of the earth." Q. From a scientific perspective does this agnosticism towards the age of the earth, is that problematic for intelligent design? A. It's an example of a general problem with the view to say we just won't say is the earth six thousand, ten thousand years old, or 4.5 billion. You know, that's a big difference. And one can't remain neutral on that. The sciences are interconnected, and hypotheses, biological hypotheses, in order to test them have to rely upon what we've learned from other sciences as well. We make use regularly in biology to information that we get from geologists to information that we get from physicists, and vice versa as well. One can't just set aside the issue of this huge difference between six thousand and 4.5 billion and say well, we just don't take a stand on that. You have to be able to say here's is what we can take from what geologists have discovered and then make use of with regard to testing, confirming biological hypotheses. Young earth creationists are of course pretty much concerned that you could quickly reject evolution. They like this idea if there's only six to ten thousand years old, then of course that would reject the possibility of evolution. That would falsify it right away. You couldn't get the Darwinian mechanism in that short time to produce this. The strategic silence on this issue is a sign of just how far this is removed from the ordinary basic practice of what one has to deal with science. Science is interconnected.	Section 31 notes
Section 32 Q. Darwin's theory of evolution with small incremental steps is somewhat more plausible or tenable if there were 4.6 billion years to act than six thousand years? A. It's sometimes said by creationists that evolution itself can't be tested, can't falsified, and of course this is an example to show just why that's wrong. If the world is really only six thousand years old, that would falsify evolution. Q. But that's not what the geological record says? A. But that's not the case. Q. Is intelligent design a religious proposition? A. Yes, I believe it is. Q. Why? A. Really for the same reason here that by insisting upon this basic proposition that the features of the natural world are produced by transcendent, immaterial, non-natural being, that's by itself a supernatural, a religious proposition.	Section 32 notes
Section 33 Q. Have intelligent design leaders actually described intelligent design as a religious proposition? A. In many different ways they have. As I said, the terminology has shifted over time, and it also shifts depending upon who intelligent design creationists are talking to. If they're talking to the press they will say one thing, but if they're talking to a church group they will be more explicit. The terms have varied. Now we most hear intelligent design theory, but at other times it's been talked about not as the design hypothesis but as the creation hypothesis or even the God hypothesis. So there are lots of examples of that. Q. Could you pull up Exhibit 332, Matt? Do you recognize this document? A. This is an article from Stephen Meyer, "The Return of the God Hypothesis." Q. And who is Stephen Meyer? A. Meyer is one of the core intelligent design leaders. He's currently at the Discovery Institute directing the center for science and culture. He was also one of the "Pandas and People" authors. Q. And this article is obviously called "The Return of the God Hypothesis"? A. And what he does here is describe how it is that this new movement is able to bring this back, the God hypothesis.	Section 33 notes
Section 34 Q. Call you pull up Exhibit 328? Do you recognize this document? A. This is a review essay from Phillip Johnson of a book, "The Battle of Beginnings: Why Neither Side is Winning the Creation Evolution Debate," by Dell Ratzsch. Q. And could you turn to page RP-63 in the document and highlight the passage Dr. Pennock asked you to? And could you read that passage into the record? A. Here's Phillip Johnson describing intelligent design. He says, "My colleagues and I speak of 'theistic realism, ' or sometimes mere creation, as the defining concept of our movement." That's to say of the intelligent design movement. "This means that we affirm that God is objectively real as creator, and that the reality of God is tangibly recorded in evidence accessible to science, particularly in biology." Q. Is intelligent design a universal religious view, or is it hostile to some religious views? A. In some sense it's generic enough that some other religious traditions can accept it under the umbrella where we will speak about other things later, but intelligent design is also explicitly hostile to other particular religious views. It takes a stand for example rejecting what philosophers sometimes call theistic evolution, a compatibilist position that allows that evolution is true as science has discovered it, but also accepts belief in God. They reject that position. Q. Are there particular individuals who have rejected that? A. One can find many such examples from a range of folks. William Dembski in particular has quite explicitly said intelligent design theorists are no friends of theistic evolution.	Section 34 notes
Section 35 Q. And just to be clear, is theistic evolution a scientific proposition? A. No, and that's actually important to say. Science is neutral with regard to these sorts of issues, and this isn't something that one would teach or discuss in a science class. Whether or not something is compatible with a particular religious view, that's a theological view. You might talk about that in a theology class or a comparative religion class, but that's not part of science itself. Q. Proponents of intelligent design claim that intelligent design is not religious because it does not name the designer or describe how or why it carried out the design. Why doesn't that rebut your argument that intelligent design is religious? A. It's always important in philosophy to focus upon the concepts rather than simply the terms that are used, and even if one doesn't explicitly say God, although as we have seen they do indeed say God directly in many cases, but even if one were to leave out that word and simply say we're speaking of a transcendent non-natural being or power, that by itself is what we would call a direct description. It identifies a religious concept. Even if one doesn't exactly say the name, one still has the concept there. It's like saying well, I didn't say Valerie Plame Wilson. I simply said Ambassador Wilson's wife. That's a direct still identification of an individual. THE COURT: To use a popular example. A. Just as an example.	Section 35 notes
Section 36 Q. Another argument that we hear from the intelligent design movement is that, and if you could pull up "Pandas," which is Exhibit 11, and actually turn to page 7 of the book, is that -- you see the writing "John loves Mary" in the sand on the page of "Pandas" there, that writings like "John loves Mary" or something like the statue of Mt. Rushmore or an archaeological object is regularly concluded that those things were designed, and we're just doing the same thing here for biological organisms. Why isn't that argument valid? A. This is a pretty common misunderstanding about what science does. It's not the case that you don't speak about design in science. We do so quite regularly. Archaeologists will unearth artifacts, and by looking at them and examining them will try to draw some conclusions about the civilization that created them. Forensic scientists will look at evidence and say, you know, here's who done it. So this is very common to draw those ordinary sorts of design inferences in science and just in ordinary life. But that's of course not what's at issue. We do that through ordinary means under the presumptions of methodological naturalism. That's not what is at issue here. That's very, very different from drawing the conclusion about a transcendent supernatural being. We really don't have any grasp upon that. Q. So when we do that for example, for a stone object that an archaeologist is trying to determine is this something that was the product of erosion or is it a tool, do archaeologists make some conclusion about who did that? A. In ordinary cases that would be one of the first things that one would ask. In examining an artifact we're able to draw conclusions about when it was created. We're able to draw some conclusions perhaps about who did it, what civilization it was, something about why they did it perhaps. These are pretty standard questions one would ask. In fact, they're natural questions one would ask with regard to ordinary notions of design, natural notions of design, under the normal presumptions of methodological naturalism. Again there's nothing unusual about that, but that's not what's being posited by intelligent design theory. This is something that's removing those constraints. Q. And in the case of an archaeological object we also draw some conclusions about how it was done? A. That's right. We know something about other human beings, we know something about their motives, we know something about their interests, we know something about their causal properties. We know lots of background information that allows us to say here's what we can conclude about who did it, when, where, why, how, those natural sorts of questions that we would ask.	Section 36 notes
Section 37 Q. And all those questions which all the media in the audience ask every day. Who, when, where, why, are those questions that intelligent design answers? A. They'll explicitly say design can tell us nothing about who the designer was or anything about the designer's characteristics or motives, and that's really just a sign of how disparate this concept is from the basic scientific notion where those would be among the first things that one would offer and then get evidence for. Q. Intelligent design also argues that their work is similar to the SETI project, the Search For Extraterrestrial Intelligence. Are you familiar with SETI? A. Yes, this is a topic that I sometimes used as a case study in some of my courses. Q. Do you know how the SETI project works? A. What SETI scientists attempt to do is see if they can find evidence of extraterrestrial beings, that is to say beings on other planets. They search for signals from other planets that might be an indication that there are beings there who would be sending such a signal. Q. And what kind of signal are they searching for? A. I have got this information secondhand, I'm not a SETI scientist myself, but in talking to SETI scientists, particularly a SETI scientist who was addressing the question about whether their work was like intelligent design, explain that they don't do anything like is claimed of them. They're not looking for Pi to be found and so on. They're looking for a very simple signal, they sometimes describe it as a whistle. The key thing is it's an artificial signal, something that we produce ourselves, that we know something about, a radio signal that's focused in a certain way. And they quite explicitly said this isn't at all like is being claimed of us by intelligent design theorists.	Section 37 notes
Section 38 Q. One more question. During his opening argument defendant's counsel argued that the Dover policy which presents intelligent design as a scientific concept in the science class is the essence of liberal education. Do you agree with that assertion? A. I don't. Q. Why not? A. It's true only in the sense that, and as a philosopher I'm actually happy with this sense, the classic liberal arts includes philosophy, it includes theology, and in that sense certainly this is a part of that. We talked about the design argument in its classical theological sense, arguments for the existence of God, very regularly in a philosophy class or in a theology class or a comparative religion class. So in that sense, sure, it's part of a classical liberal education. But the liberal arts and sciences as we understand them now differentiate that aspect of the liberal arts from the sciences. The sciences has its own characteristic method, and to take these sorts of arguments, which properly belong in this other area, and claim that it's science I think really undermines the very notion of a discipline. There is a rigor that's important to careful thought, and that's what the liberal arts attempts to instill, a kind of systematic way of thinking, and it says there's something about a discipline that's critical that should be respected. This could certainly be respected within those other kinds of classes. I regularly talked about them. This is actually a very common thing to discuss in the philosophy class, theology class, comparative religion class, but not a science class. In that sense it would not at all be a liberal education. MR ROTHSCHILD: Thank you, Dr. Pennock. I have no further questions. THE COURT: All right. Thank you, Mr. Rothschild. This would be a good time to take our customary mid-morning break for at least twenty minutes. We'll do that now, and we'll stand in recess and we'll pick it up with the cross examination of Dr. Pennock. (Recess taken at 10:17 a.m. Trial proceedings resumed at 10:45 a.m.)	Section 38 notes

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