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Kitzmiller v. Dover Area School District

Trial transcript: Day 1 (September 26), AM Session, Part 2


THE COURT: Mr. Walczak, you may continue.

MR. WALCZAK: Thank you, Your Honor.


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.

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."

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.

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.

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.

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.

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.

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?

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.

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.

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.

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.

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.

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.

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.

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 led-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.

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?

Q. Please.

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.

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.

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.

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."

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Q. Why?

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.

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.

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.

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.

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.

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.

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 13 percent, by that of the snapping turtle also by 13 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.

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.


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.

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.

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.

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.

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.

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?

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?


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.

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.

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.

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.

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.

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.


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?

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: 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.)


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