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Kitzmiller v. Dover Area School District

Trial transcript: Day 10 (October 17), PM Session, Part 2


THE COURT: Be seated, please. You can pick it up where you left off, Mr. Muise.


Q. Thank you, Your Honor. Dr. Behe, before we broke we were talking about how proteins aren't simply colored squares or hexagons, that they are far more complex than that, including what makes them stick together in any particular order, and I want to return back to that. We put up a slide which has some indication I believe of proteins, and I'd like you to explain what you meant, that they're more complex than just these colored hexagons.

A. Yes, sure. Let me preface my explanation by saying this, that in talking about these matters there's kind of, an intelligent design proponent and a Darwinian theorist who have different goals.

A Darwinian wants to persuade his audience that evolution isn't all that difficult, it's doable, and so will not always attend to all the complexity of a system, whereas in order to show the difficulties for undirected unintelligent processes, an intelligent design proponent has to show all of the very severe complexity of systems, and that's often times hard to do because people often times don't have the patience to attend to it, but I apologize in advance but I have to attend to some of the complexities here.

So on this slide there are three figures taken from a biochemistry textbook by Voet and Voet of the protein, of the same protein, a protein named hemoglobin. Hemoglobin is the protein that binds oxygen and carries it from your lungs and dumps it off in peripheral tissues such as your fingers and so on. Now, this is a rendering of the structure of hemoglobin, and actually this rendering itself does not show the full complexity of hemoglobin. Let's focus --

Q. You're referring to Figure 8-63 on this slide?

A. Yes, that's correct. Let's focus on this yellow glob here. You'll notice a number of circles. They represent atoms in one of what are called the protein chains of hemoglobin, but the amino acids in that protein chain are actually different. So if it was actually rendered in more detail you would see a lot of different colors of atoms, indicating different groups and so on, and the identity of all these amino acids is also frequently very critical to the function of a protein.

Hemoglobin itself consists an aggregate of four proteins designated here by the blue and the green and the light blue colors, and it is the aggregate of the four protein chains, that is the active molecular machine in this cell that carries oxygen from your lungs to your tissues. Nonetheless, a drawing like this of such a complex system is often times bewildering to students, and so artists with the proper purpose of getting across some conceptual points to students will draw simplified renditions of the same figure.

For example, in the lower left here this is also supposed to be a rendition of the same protein hemoglobin. But in here the only atoms that are represented are things called the alpha carbons of each amino acid, and the artist has kind of shaded it to show the different directions in which the protein chain is heading. One can also to make a legitimate point to students simplify the drawing even further, and here's another rendering of hemoglobin in Voet and Voet.

Here each very, very complex protein chain is rendered as a simple square, and the O sub 2 represents the oxygen that each protein is supposed to be carrying. Now, all of these are legitimate renderings of the protein hemoglobin, but when we discuss these matters and we discuss difficulties with evolution and we discuss arguments for intelligent design, we have to keep in mind that this is the actual protein, this is the actual machine in the cell, and so these are the things that we have to deal with.

Q. Again that last figure you're referring to is 8-63?

A. That's right, uh-huh.

Q. And the two previous, the one just previous to that was Figure 10-37 and the one prior to that 10-13?

A. That's correct. Now, let's consider a further point. We have this yellow conglomeration of circles representing the atoms of the protein chain, with this blue one and this green one and this light blue one. Why do they stick together? Why don't they just float away? How come they are in the arrangement they are? Why don't we have the yellow one over here? The green one down here?

Well, it turns out that proteins arrange themselves. Molecular machines are actually much more sophisticated than the machines of our common experience, because in our common experience with things like say outboard motors, an intelligent agent assembles the parts of those machines. But in the cell the molecular machines have to assemble themselves. How do they do that? They do it by having surfaces which are both geometrically and chemically complementary to the proteins to which they're supposed to bind, and I think --

Q. Do you have a slide to demonstrate that for us?

A. Yes, I do. I think it's the next one. Okay, remember here's another little cartoon version which gets rid of some complexity of the system in order to make an important point to students. This is also a figure taken from the biochemistry textbook Voet and Voet. This is meant to convey why two molecules, why two proteins bind to each other specifically in the cell. This one up here is supposed to represent one protein. The second one is supposed to be this greenish area, and it's supposed to have a depression in it in which the yellowish protein binds to and sticks.

Now, let me point out a couple of things. You'll notice that the shapes of the proteins are matched to each other. They're geometrically complementary, kind of like a hand in a glove. But not only are they geometrically complementary, they're also chemically complementary. You see these little circles and NH and this thing here? Well, these are chemical groups on the surface of the two binding proteins, and they attract each other. Certain groups attach other groups.

I think the easiest to understand is the one right here, there's a red circle marked with a minus sign in it. That indicates an amino side chain of a protein that has a negative charge. When it binds to the larger one, notice that on the surface of the larger protein there's this blue circle with a plus sign in it. That is taken, that is meant to indicate an amino acid side chain with a positive charge. Negative and positive charges attract. So therefore these guys stick together.

If this were a negative charge these two proteins would not stick together. They would float away from each other. It's not sufficient to have just one group in the protein be complementary to another group in a protein. Usually proteins have multiple amino acids that stick together and cause them to bind to each other. For example, look up here, this little circle labeled H. H is supposed to stand for something called hydrophobic, which essentially means oily. It doesn't like to be in contact with water.

It lines up with another H on the green protein so that the two oily groups can stick together and avoid water. So it's kind of like oil, you know, oil and water, they don't mix. If they're in this configuration the two oily groups can stick together and be away from water, and there are other groups, too, which I won't go into which exhibit things call hydrogen bonding which also help the proteins stick together.

So in molecular machines, in aggregates of proteins, all of the proteins which are sticking together have to have all these complementary surfaces in order for them to bind their correct partners. If they do not have the complementary surface, they don't bind and the molecular machine does not form. Now, interestingly, remember Darwin's theory says that evolution has to proceed in small steps, tiny steps.

Well, one way something like this might form is by, you have to have mutations that might produce each of these interactions at a time. For example, I think there's a quotation from an article in Nature which kind of make this point, and I'll explain it after I quote it, it's from an article by a man named John Maynard Smith, who is a very prominent evolutionary biologist who died about a year ago I believe, and he wrote in a paper called Natural Selection and the Concept of a Protein Space, which was published in Nature in 1970, "It follows that if evolution by natural selection is to occur, functional proteins must form a continuous network which can be traversed by unit mutational steps without passing through nonfunctional intermediates," and by unit mutational steps, we mean each of those pluses, each of those H's, each of those OH's and so on that I showed you in that little cartoon drawing on the previous slide.

If for example a mutation came along that changed a positive into a negative charge and disallowed an interaction that needed to occur, that would be a detrimental one. John Maynard Smith is saying that we need to proceed, you know, one step at a time. So the point is that those little colored squares are enormously complex in themselves, and further the ability to get them to bind specifically to their correct partners also requires much more additional information. It is not a single step phenomenon. You have to have the surfaces of two proteins to match.


A difficulty of getting two changes at once?

A. Yes, that's exactly right. If you can do this one tiny, tiny step at a time, then Darwinian evolution can work. If you need to make several changes at once, two, three, four, there were multiple interactions that were required for those two proteins to bind. If you need multiple interactions, the plausibility of Darwinian evolution rapidly, rapidly diminishes.

Q. And have other scientists made similar observations?

A. Yes. On the next slide an evolutionary biologist by the name of Allen Orr, who's at the University of Rochester, published an article in a journal called Biology entitled A Minimum on the Number of Steps Taken in Adaptive Walks in which he makes this similar point. He says, "Given realistically low mutation rates, double mutants will be so rare that adaptation is essentially constrained to surveying and substituting one mutational step neighbors. Thus, if a double mutant sequence is favorable, but all single amino acid mutants are deleterious, adaptation will generally not proceed," and translating that into more colloquial English it means that you have to change again those groups one at a time, and if you need to change two at a time in order to get a favorable interaction, then you are running into a big roadblock for Darwinian processes.

Q. Now, have you done any writing or research that emphasizes this particular point?

A. Yes. On the next slide I believe is a copy of an article that I published with David Smoke which was published last year in the journal Protein Science, which is entitled Simulating Evolution by Gene Duplication of Protein Features that Require Multiple Amino Acid Residues, and in this paper we were addressing exactly that problem. What happens if you need to change a couple of amino acids before you get a selective effect?

And the gist of the conclusion is if you need to change two at once or three at once, then again the expectation that that will happen at a probability becomes much smaller, the length of time one would have to wait for such a mutation to show up is much longer, the population size of a species would have to be much, much longer to have an expectation of such a mutation occurring.

Q. And this particular article, the one you wrote with David Smoke, you testified to previously?

A. Yes, that's the same one.

Q. I believe we have a diagram to further make this point?

A. Yes. Here again is a little simplified cartoon version of how proteins might interact, simply to point out the problem that is not apparent in the earlier drawings. Now I've made the shapes of those colored proteins, I've altered the shapes. Now the A is a circle and what's that, a C, the C is a rectangle, and the other proteins have other shapes. How do we get those to bind into a conglomerate molecular machine?

In order to get them to bind to each other we have to alter their surfaces to be geometrically and chemically complementary, and that is a large and long, tall evolutionary order. As a matter of fact, it's so tall that one can reasonably conclude that something like this would not be expected to occur. So the point I want to make here is that even if one was to have parts in the cell which if they could develop binding sites to bind to each other, and if that binding together would produce a new selectable property, that still does not help in Darwinian processes, because you still have the problem of adjusting many, many different things before you get the final result.

Q. And this diagram is a figure from the chapter that you wrote in Debating Design, is that correct?

A. Yes. That's Figure 2.

Q. And that's the chapter that you've already testified to previously?

A. Yes, that's correct.

Q. And I believe we have a slide with the figure legend?

A. Yes, that's right. I make this point exactly in my article in that book Debating Design. Let's just look at the bold and underlined text. It's says, "Thus, the problem of irreducibility remains even if the separate parts originally had individual functions." So even if the parts can do something on their own, that does not explain how one can get a multipart molecular machine in a cell.

Q. I just want to point out that that figure legend in the figure is from pages 352 to 370 in your chapter?

A. No, that's the whole chapter. The figure legend is on one of those pages.

Q. As well as that previous diagram?

A. Yes, that's correct.

Q. Dr. Behe, if I understand you correctly, so even if there are similar separate parts are in the cell, that doesn't explain irreducible complexity?

A. That's correct.

Q. Dr. Miller testified about something called the Type 3 secretory system, the TTSS, and he said that that showed that the flagellum was not irreducibly complex, do you agree with that assessment?

A. No, I disagree. That's a mischaracterization.

Q. Why do you disagree?

A. Well, I think we have some slides from Professor Miller's presentation, and he said that, let us start with the bacteria flagellum, and he has a drawing of the flagellum from a recent paper. Let me just make another similar point. You see these little three, four-letter abbreviations all over here? Each one of those is of the complexity of a hemoglobin molecule that I showed on an earlier slide. Each one of those has all the sophistication, all the needs to have very complex features to bind together that hemoglobin had.

Can you press the slide again to advance the figure on this same thing of Professor Miller's? Professor Miller says that well, okay, you start with the bacterial flagellum, and if you remove the pieces, then he says, press again, please, he says, "That leaves just ten," and he says, his characterization, his mischaracterization of my argument is that what's left behind should be non-functional.

And if we go to the next slide of Professor Miller's, he says, "But it's not. Those ten parts are fully functional as a protein secretion system," but again I tried to be very careful in my book to say that we are focusing on the function of the system, of the bacterial flagellum, and while a subset of the flagellum might be able to be used as something else, if you take away those parts it does not act as a rotary motor. So it is irreducibly complex as I tried to carefully explain. I'm sorry.

Q. So is it fair to say that Dr. Miller makes a misrepresentation of what your claim is by his representation?

A. This is a mischaracterization, yes, that's correct, and I think I pointed that out on the next slide. I pointed this out, as I said earlier we've debated this back and forth for a while. I pointed it out recently in my book chapter. I write, "Miller asserted that the flagellum is not irreducibly complex because some proteins of the flagellum could be missing, and the remainder could still transport proteins perhaps independently.

"Again he was equivocating, switching the focus from the function of the system to act as a rotary propulsion machine to the ability of a subset of the system to transport proteins across a membrane. However, taking away the parts of flagellum certainly destroys the ability of the system to act as a rotary propulsion machine as I have argued. "Thus, contra Miller, the flagellum is indeed irreducibly complex."

Q. Dr. Behe, even if that is true, doesn't the Type 3 secretory system help us to explain the flagellum, the development of the flagellum?

A. No, it does not help in the least. And that may be surprising to some people, so let me take a second to explain. Most people when they see an argument such as Professor Miller presents will naturally assume that well, perhaps this part, this system that had fewer parts, the Type 3 secretory system, maybe that was a stepping stone, maybe that was an intermediate on the way to the more complex bacterial flagellum.

But in fact a number of scientists have said that's not true, and perhaps we could see the next slide. Yes, thank you. For example, in a paper published by Nguyen, et al. five years ago they investigated the Type 3 protein secretion system, and they said the following, "We suggest that the flagellar apparatus was the evolutionary precursor of Type 3 protein secretion systems."

In other words, they're saying that from their investigation it looked like the more complex type or more complex flagellum came first, and then the system with fewer parts, the Type 3 secretory system came second and perhaps was derived from that. Exactly what the opposite of what one might first expect.

Q. Have scientists reached different conclusions?

A. Yes, and it turns out that other groups have reached different conclusions from those of Nguyen at all. For example, in a paper published by Gophna, et al. recently in 2003 in the journal Gene they write, "The fact that several of the Type 3 secretory system proteins are closely related to flagellar export protein has led to the suggestion that the TTSS has evolved from flagella. Here we reconstruct the evolutionary history of four conserved Type 3 secretion proteins and their phylogenetic relationships with flagellar paralog." And then they say, "The suggestion that Type 3 secretory system genes have evolved from genes and coding flagellar proteins is effectively refuted." In other words. They say that the conclusion of the first group was incorrect. Instead they suggest that the Type 3 secretory system and the flagellum developed independently of each other, perhaps from the same precursor gene. And I think on the --

Q. We have another study on this issue, correct?

A. Yes. I think that's right. In the year a man named Milton Sayer, who was the one of the authors, the senior author actually on the study by Nguyen, et al. that I referred to a couple of slides ago, wrote an article in a journal called Transient Microbiology called Evolution of Bacterial Type 3 Protein Secretion Systems, he says the following, "It is often not possible to prove directionality of an evolutionary process. At present, too little information is available to distinguish between these possibilities with certainty. As is often true in evaluating evolutionary arguments, the investigator must rely on logical deduction and intuition.

"According to my own intuition and the arguments discussed above, I prefer pathway for the Type 3 system deriving from the flagellum. What's your opinion?" So I think you can see from this the very tentative nature of the results regarding the Type 3 secretory system and the flagellum that in fact what is going on is very much up in the air.

Q. And again I believe we have another result from --

A. Yes. Let me apologize that again this is a complex subject, and so you really have to delve into it to come to a firm conclusion. This is a quotation from a review article by a man named Robert Macnab who was a professor of biology at Yale University who died in the year 2003, and this article was actually published posthumously. It's entitled Type 3 Flagellar Protein Export and Flagellar Assembly. It was published in journal Biochemica Biophysica Acta, and I underlined words that emphasized the tentativeness and the speculative nature of discussions on this topic.

Robert Macnab wrote, "It has been suggested that the Type 3 virulence factor secretion system evolved from the Type 3 flagellar protein export system since flagella are far more ancient, existing in very diverse genre than the organisms which are targets for Type 3 virulence systems. However, it is possible that the original targets were other bacteria. Also, the possibility of lateral gene transfer cannot be ruled out.

"Finally, one could argue that evolution from a less complex structure, the needle complex, to a more complex one, the flagellum, is more probable than the other way around," and he continues I think on the next slide, and I think I'll pass over much of this quotation and just go to the last line of his article, and he says, "As the above discussion indicates, there is much about the evolution of Type 3 systems that remains mysterious."

So let me point out that in the past couple of years we've had investigators suggest that in fact the flagellum came first and the Type 3 secretory system came after it. We've had other investigators suggest that the Type 3 secretory system came first and the flagellum came after it. We've had other investigators suggest that the Type 3 secretory system and the flagellum arose independently, perhaps from similar genes, so --

Q. Dr. Behe, so what do these widely different opinions mean?

A. Well, maybe we could go to the next slide. To me it means this. We see the little cartoon drawing of the flagellum here, and this is a cartoon drawing of the Type 3 secretory system.

Q. I'm sorry, this is one of Dr. Miller's slides?

A. I'm sorry, yes. This is Dr. Miller's slide. Science knows a lot of information about the structure of the Type 3 secretory system, a lot of information about the structure and function of the flagellum. It knows the sequences of proteins of the flagellum. It knows the sequences of the proteins of the Type secretory system. It sees many similarities between them, both in the amino acid sequence and function, and it still can't tell how one arose or whether one arose first, the other second, or whether they arose independently.

So this to me drives home the point that such information simply does not come out of Darwinian theory. Much like our discussion of Haeckel's embryos earlier in the day, Darwinian theory can live with any result that experimental science comes up with on this question and then goes back and tries to rationalize the results afterwards post hoc, and so to a person like myself this exemplifies the fact in fact these results have nothing to do with Darwinian theory. They are no support at all for the claim that natural selection could have produced them. Quite the contrary.

Q. I just need to backtrack for one moment. If I may approach the witness, Your Honor?

THE COURT: You may.

Q. Dr. Behe, I handed you what's been marked as Defendant's Exhibit, 238 correct?

A. Yes.

Q. Is that the study from Nguyen that you referenced in your testimony on the section of the Type 3 secretory systems?

A. Yes, that's correct.

Q. It was inadvertently left out of your book, but I just wanted to make sure you identified it as an exhibit. You can just keep that with you and I'll retrieve it later.

A. Thank you.

Q. I want to see if I can get you correct, Dr. Behe. It's your opinion that this also shows that even knowledge of the structure and sequences of two systems doesn't necessarily give a clue as to how these systems might have arisen, is that true?

A. That's exactly right.

Q. And could you explain that further? And I believe we have some additional slides for that.

A. Yes, I think some text with actually Professor Padian wrote as part of his expert report illustrates this problem, and I'd like to quote you several sections from that report. On the next slide Professor Padian said the following. He said that, "Darwin's main concern, however, was with the mechanism of natural selection, which cannot be observed directly in the fossil record."

So to me this means you cannot see natural selection. You see fossils, and how you classify those fossils and what explanations you come up with them is not based directly on the evidence. Rather, it's provided by your theory. And I think we have a further quote from Professor Padian. He said the following, and this is a long quote, so --

Q. If you could read it a little bit slower for our court reporter when you are reading these quotes, please? Thank you.

A. Okay. "Molecular biology has produced tremendously powerful tools to compare the DNA sequence of all manner of living organisms, and a few extinct ones, and so help to derive their evolutionary relationships. However, molecular systematics can say nothing about the relationship or role of fossil organisms to each other or to living lineages," and he gives an example.

"For example, several recent molecular analyses agree that whales and hippos are each other's closest relatives. From this conclusion some authors have suggested that because both kinds of animals spend time in the water, their common ancestors would have been aquatic. Only the fossil record could show that this inference is incorrect. Therefore, hippos and whales, even if they are each other's closest relatives among living animals, did not have a common ancestor that lived in the water, but that was terrestrial. Only paleontological research and materials could demonstrate this."

And let me make a point about this. Professor Padian is saying that molecular studies of DN A sequence of whales and hippos suggested or led to the suggestion that both animals had aquatic ancestors. But they didn't. They had terrestrial ancestors. That means that the molecular information is compatible with either result, with the ancestors being aquatic or the ancestors being terrestrial.

That means that the molecular information can't decide what the ancestors were and therefore it can't tell what the selective pressure was or other factors of what might have caused an ancestor of those organisms to produce what we see in the modern world. So that means that does not speak to Darwin's claim that natural selection drove evolution, okay? Well, molecular data can't decide the question.

But nonetheless, Professor Padian told us that paleontology did. Paleontology discovered what seemed to be ancestor of both hippos and whales, and saw that they are terrestrial organisms. So can paleontology tell us whether it was natural selection that drove the evolution of these organisms? Well, no. On the previous slide he said explicitly natural selection is not shown directly in the fossil record.

That means that there is nothing that can show from the fossil record or from molecular data that current organisms derive by a process of natural selection from organisms in the past or how such a thing might have happened. That means that in fact the inference that such a thing did is simply a theoretical construct in which we try to fit that data into our current theory. The current theory either predicts it, does not predict it, and may be consistent with such evidence, but a lot of theories might be consistent with the same evidence.

And I think that, bring it back to the flagellum, I think that's illustrated in the flagellum and Type 3 secretory system 2. We know all the molecular data, we know lots of structural and functional studies, and yet we still can't tell how natural selection could have produced them.

Q. So are you saying then at best the evidence, and you were talking about sequence comparisons and in particular the fossil record, at best they may be consistent with natural selection but they also may be consistent with any number of mechanisms that might be derived?

A. That's exactly right. Perhaps intelligent design, perhaps complexity theory, perhaps something else. But consistent does not, is not the same thing as evidence for a theory.

Q. And the next slide we have is another quote from Dr. Padian that I'd like you to comment about.

A. I think this also throws light on this topic. Professor Padian said in his expert statement, he said, "Darwin was not talking about how major new adaptive change took place. He was talking about how minor variations could be selected. He was really talking about the baby steps of evolution. He made only the most passing references to how new major adaptive types might emerge," and I could comment that no one disputes or certainly no one I'm aware of disputes that Darwinian processes, Darwinian mechanism, can explain some things in life. And certainly nobody disputes that baby steps could be explained by random mutation and natural selection. It is exactly the new major adaptive types and new molecular systems for myself as a biochemist that is the focus of dispute.

Q. So again though when you say nobody refutes, is that saying that intelligent design does not refute this notion of baby steps that Dr. Padian is referring to?

A. That's right. It is very happy to say that Darwinian processes are consistent with those.

Q. Here I believe is a continuation of that particular statement from his report.

A. Yes, this is Professor Padian continued, referring to Darwin, he said, "Though he was convinced that would happen in the course of time," and let me just comment on that. Well, that's interesting that he was convinced that would happen, but another way of saying that is that Darwin assumed that these small changes would add up to larger changes, or to major new adaptive features, but that is exactly the point of contention. And for a point of contention an assumption is not evidence, let alone proof. So I see this as very pertinent to the question of things like the flagellum Type 3 secretory system and other things as well.

Q. So is it clear, I guess in summarizing you think that the flagellum is in fact irreducibly complex, correct?

A. Yes, that's right.

Q. Does that affect necessarily the positive argument for intelligent design?

A. Well, yes. Let's perhaps we can look at another slide here that I just wrote out some text to make this point clear. It's this. For the past number of, past hour or so we've been talking about the argument against Darwinian processes, but I want to re-emphasize to say that it is important to keep in mind that the positive inductive argument for design is in the purposeful arrangement of parts.

Irreducible complexity, on the other hand, is an argument to show that Darwinism, the presumptive alternative to design, is an unlikely explanation. However, one also has to be careful to remember that Darwinism isn't positively demonstrated by attacks on the concept of irreducible complexity. Darwinism can only be positively supported by convincing demonstrations that it is capable of building the machinery of the degree of complexity found in life. In the absence of such convincing demonstration it is rationally justified to think that design is correct.

Q. So an argument against irreducible complexity is not necessarily an argument against design?

A. An argument against irreducibly complexity is not an argument against design, and more importantly it's not an argument in favor of Darwinian evolution.

Q. Have other scientists agreed that Darwinian theory has not yet explained complex biochemical systems?

A. Yes. I recall there on that slide that I say Darwinism can only be positively supported by convincing demonstrations, and almost everybody agrees that such demonstrations have not yet been forthcoming. For example, on the next slide these are quotations taken from a number of reviews of my book Darwin's Black Box, most of these are by scientists. The first one James Shreeve, a science writer, but all of them making the point that we do not yet have Darwinian explanations for such complex structures.

For example, James Shreeve, the science writer, writing the New York Times said, "Mr. Behe may be right that given our current state of knowledge, good old Darwinian evolution cannot explain the origin of blood clotting or cellular transport," and James Shapiro, who is a professor of microbiology at the University of Chicago, wrote in a review that, "There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system, only a variety of wishful speculations."

Jerry Coyne, who's a professor of evolutionary biology at the University of Chicago wrote in a review of the book in the journal Nature, "There is no doubt that the pathways described by Behe are dauntingly complex, and their evolution will be hard to unravel. We may forever be unable to envisage the first protopathways."

And Andrew Pomiankowski, who is an evolutionary biologist I believe at the University College London, wrote in a review in New Scientist, "Pick up any biochemistry textbook and you will find perhaps two or three references to evolution. Turn to one of these and you will be lucky to find anything better than 'evolution selects the fittest molecules for their biological function.'"

So this is a sampling of writings by scientists agreeing with the point that no, we do not have these demonstrations yet that Darwinian processes can produce complex biological systems.

Q. And these were scientists, and in one case a science writer, who are commenting on your particular book, correct?

A. Yes.

Q. And have scientists in other contexts made similar claims?

A. Yes, another good comment on this was by Franklin Harold, who I mentioned before, he's an emeritus professor of biochemistry at Colorado State University, and in his book The Way of the Cell published by Oxford University Press in 2001 he kind of echos James Shapiro. He says, "We must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical system, only a variety of wishful speculations," and perhaps I might add that besides these people one can add also complexity theorists, who also like Stuart Kauffman who also deny that such things have been explained in Darwinian theory.

Q. Sir, have some scientists argued that there is experimental evidence that complex biochemical systems can arise by Darwinian processes?

A. Yes, there have been a total of two such arguments which I regard to be very important, because these were claims that there had been experimental demonstrations, not just speculations, not just stories, but experimental demonstrations that either irreducible complexity was incorrect or that complex systems could be built by Darwinian processes.

Q. And one of those claims was raised by Dr. Miller, is that correct?

A. That's correct. I think on the next slide we see that he wrote in his book Finding Darwin's God ,which was published in 1998, he said, " A true acid test used the tools of molecular genetics to wipe out an existing multipart system and then see if evolution can come to the rescue with a system to replace it."

So here he was making the point well, here one test of this claim of irreducible complexity and the ability of Darwinian processes to make complex systems, well, is to find a complex system in a cell, destroy it, and then see if random mutation and natural selection can come back and replace it. And I have to say I agree that's an excellent test of that claim. However, I disagree with Professor Miller's further comments and conclusions.

Q. What was the particular system that he was looking at?

A. Well, he was referring to what is shown in a little cartoon version on the next slide. This is a figure again taken from that biochemistry textbook by Voet and Voet discussing a system called the lac operon. Now, an operon is a little segment of DN A in a bacteria which codes for a couple of genes, and genes code for proteins, and the proteins usually have related functions or function as a group, and one of them is called the lac operon which is used to, the proteins of which are necessary for the bacterium Escherichia coli to metabolize a sugar called lactose, which is a milk sugar.

And it consists of a number of parts. No, let's go back one slide, please, I'm sorry. All these little squares here, this little green thing represents a very complex protein called a repressor, which will bind to the DNA, and when it binds there it stops another protein called an RN A prelimerase from binding to the same spot, and therefore the information carried by these genes is not expressed, and that's important because the sugar lactose is usually not present in the bacteria's environment, and making proteins that metabolize lactose in the absence of that sugar would be wasting energy.

So the bacterium wants to keep that turned off until lactose is around. So the repressor turns off the operon, and that means that the genes for these three proteins here are not turned on, not expressed. This first one, which is labeled Z, codes, is the gene for a protein called a beta galactosidase, okay? That's actually the enzyme which chops up lactose. We don't have to go into the detail of how that happens.

This little thing marked Y codes for something called a permease. Now, a permease it turns out is a protein who is job it is to allow the lactose to enter the bacterial cell. The bacterial cell is surrounded by a membrane which generally acts as a barrier to largish molecules, and there's this specialized protein, this specialized machine called a permease which, when lactose is around, grabs the lactose from outside the cell, turns it around, and allows it to enter to the inside of the cell.

In the absence of that permease the lactose might be present in abundance in the bacteria's environment, but it can't get inside the cell. And so the bacterium can't use it. One other detail of this before I go on is that this repressor kind of sticks to the beginning of the gene and turns it off, but when lactose is present in the environment a small molecule which is a derivative of lactose can bind to the repressor, and that, and again start thinking in terms of the complex shape and structure of hemoglobin, when that happens it interacts in specific ways in order and causes the shape of the repressor to change, and that changed shape makes it now no longer geometrically and chemically complementary to the site that it bound on the lac operon, and it falls off. So in the presence of the inducer the repressor falls off, this prelimerase can come along and those proteins get made in the cell.

Q. Would you like the next slide?

A. Yes, thank you. Now I'm going to simplify, after that discussion I'm going to try to simplify nonetheless. So let me just list some parts of the lac operon. There's the galactosidase, the repressor, the permease, all three of which are proteins, and something that I've written IPTG/allolactose. That is the small molecule which can bind to the repressor and cause to it fall off of the operon, allolactose is something, is a metabolite of lactose itself, and that's the substance which usually binds to the repressor in the cell, but there's also an artificial chemical called IPTG, which stands for isopropyl thiogalactoside, which is sold by chemical supply companies, which mimics the action of the allolactose, and when a scientist comes and dumps some IPTG into the beaker, that binds to the repressor and causes those genes to be expressed, to be turned on.

Okay, those are the parts of the lac operon. Now, for purposes of further illustration let me just mention that in E. coli there are thousands of genes, and many of them are grouped into operons. Unbeknownst to the experimenter, whose name is Barry Hall, there also existed in the E. coli another operon called the EBG operon, which he called it that because it stands for evolved beta galactosidase. He thought this protein evolved in response to the selective pressure that he put on it, and it turns out that that operon also codes for a galactosidase, another galactosidase and another repressor as well.

Q. So this was the system that Dr. Miller was talking about in --

A. Yes, I'm afraid this is the background for the system that he started to discuss in his book.

Q. Which he sees it as experimental evidence to refute the irreducible complexity claim?

A. Yes, that's right, and if you look on the next slide you'll see the part of his book where he discusses that. He says of the system, he says, "Think for a moment. If we were to happen upon the interlocking biochemical complexity of the re-evolved lactose system, wouldn't we be impressed by the intelligence of its design. Lactose triggers a regulatory sequence that switches on the synthesis of an enzyme that then metabolizes lactose itself.

"The products of that successful lactose metabolism then activate the gene for the lac permease, which ensures a steady supply of lactose entering the cell. Irreducible complexity, what good would the permease be without the galactosidase? No good of course." And he continues that same discussion on the next slide, he continues, "By the very same logic applied by Michael Behe to other systems, therefore, we can conclude that this system had been designed, except we know that it was not designed. "We know it evolved, because we watched it happen right in the laboratory. No doubt about it, the evolution of biochemical systems, even complex multipart ones, is explicable in terms of evolution. Behe is wrong."

Q. Is Dr. Miller right?

A. No. Dr. Miller is wrong. Now, Professor Miller is always enthusiastic and he always writes and speaks with great excitement, but I say that when you examine his arguments closely, under close inspection they simply don't hold up and this is enormously exaggerated, and the results of researcher Barry Hall that he is describing here I would happily have included as an example of irreducible complexity in Darwin's Black Box.

So let me please try to explain why I say that. Reading Professor Miller's prose one would get, and I certainly did get when I first read it, the impression that this system was completely knocked out in that it completely came back under the experiments that Barry Hall conducted. But it turns out of this multipart system, only one part, the protein beta galactosidase, was knocked out by experimental method.

Everything else, the repressor, the permease, and we'll see later IPTG, and importantly as well other proteins which did very, very similar jobs in the cell, were left behind. And the worker Barry Hall himself was always very careful to say that he was only knocking out that one protein.

Q. The galactosidase?

A. Yes, that's correct. I think on the next slide he makes that point. This is a quotation from a paper by Professor Hall recalling his experiments that he did earlier on the lac operon. He says the following, "All of the other functions for lactose metabolism, including lactose permease and the pathways for metabolism of glucose and lactose, the products of lactose hydrolysis, remain intact. Thus, reacquisition of lactose utilization requires only the evolution of a new," and this should be a beta, "beta galactosidase function."

So let me point out that what he did in his laboratory was to take an E. coli bacterium and using molecular biological methods to knock out or destroy the gene for that one part of the loc operon, the beta galactosidase. He left the permease intact, he left the repressor intact, everything else was intact. He just had to get one more component of the system.

And what he saw was that he did get bacteria that were again able to use lactose. And when he did the experiments in the 1970's, that's all he saw. He saw he had bacteria that could grow when they were fed lactose. But years later after methods had developed and after he had the ability to do so, he asked himself what protein was it that took over the role of the beta galactosidase, and he named it EBG, evolved beta galactosidase.

But when he looked at it further he found it to be a very similar protein to the one that he had knocked out. Essentially it was almost a spare copy of the protein that had been destroyed. So this slide makes a couple of points. Let me just point to a couple. The EBG protein that took the place of the beta galactosidase is homologous to lac proteins. That's a technical term, that means they're very similar. Their protein structures, their sequences are pretty similar, and odds are good that they have the same sort of activity.

What's more, after further investigation Professor Hall showed that even the unmutated, even the EBG galactosidase before he did his experiment, the unmutated galactosidase could already hydrolyze, although it was inefficient. So again this was almost a spare copy of the protein, and I think on the next slide, I'll skip that last point on the next slide to drive home the point I want to show you what are the amino acid sequences of the area around what's called the active site of the protein, which is kind of the business end where the lactose binds and where the chemical groups reside which will cause it to be hydrolyzed into two component parts.

Notice this. Look at these sequence of letters. Now, I know that they don't mean much to most people in here, but notice the sequence of letters, these are the amino acid sequences, abbreviations for the amino acid sequence of various beta galactosidase enzymes found in E. coli and a related species. Notice here, let's start in here, there's an R here, HEHEMYEHW. Look up top, there's RHEHEMYEHW, the same thing on the lower one, too. They're active sites, their business ends are almost identical. Like I said, these are essentially spare copies of each other.

Q. So in fact it wasn't a new evolved element to this system. It was a spare part that was already existing?

A. Well, it was there and it did undergo small changes. But nobody, nobody denies that Darwinian evolution can make small changes in preexisting systems. Professor Miller was claiming that a whole new lactose utilizing system had been evolved in Barry Hall's laboratory, and that's, you know, that's very, very greatly exaggerated.

Q. Again do you have additional slides to emphasize the point?

A. Yes. This might be hard to explain, but Professor Hall says in one of his papers that, "The evidence indicates that either AS-92 and sys trip 977," these are the same of some amino acids, "are the only acceptable amino acids at those positions, or that all of the single based substitutions that might be on the pathway to other amino acid replacements at those sites, are so deleterious that they constitute a deep selective valley that have not been transversed in the two billion years since those proteins emerged from a common ancestor." Now, translated into --

Q. Yes, please into English.

A. -- more common language, that means that that very similar protein could only work if it became even more similar to the beta galactosidase that it replaced, and if you then also knock out that EBG galactosidase, no other protein in Professor hall's experience was able to substitute for the beta galactosidase. So the bottom line, the bottom line is that the only thing demonstrated was that you can get tiny changes in preexisting systems, tiny changes in preexisting systems, which of course everybody already had admitted.

Another interesting point, another interesting point is shown on that figure from Voet and Voet, the inducer, this little red dot, this little red dot actually stands for this chemical that binds to the repressor which changes its shape which causes it to fall off of the operon and allow the prelimerase to come in and transcribe that information. Well, it turns out that the EBG operon, this place in the DN A and E. coli that had that spare beta galactosidase, did not have a spare permease.

So the system was stuck, because it didn't have its own permease. When the repressor binds to this operon, the normal lac operon, if there weren't any lactose around then the repressor would be essentially stuck there indefinitely. And even if lactose were present outside the cell, it had no way to get inside the cell. So what Barry Hall did to allow his experiment to continue was that he added the inducer. He added that artificial chemical IPTG that he can buy from a chemical supply house, and he took some and sprinkled it in the beaker for the specific purpose of allowing the bacteria to survive so that it could take these small little steps to produce a new beta galactosidase.

Q. You have a slide to demonstrate that?

A. Yes. And Barry Hall was always very careful to explain exactly how these experiments were performed, and he brought it directly to the attention of readers when he described his system. For example he writes, "At this point it is important to discuss the use of IPTG in these studies. Unless otherwise indicated, IPTG is always included in media containing lactose," and that italics is Barry Hall's emphasis. He wanted to make sure his reader understood exactly what he was doing.

"The sole function of the IPTG is to induce synthesis of the lactose permease and thus to deliver lactose to the inside of the cell. Neither constitutive nor the inducible of all strains grew on lactose in the absence of IPTG." In other words, if this intelligent agent, Barry Hall, had not gone to the store and gotten some IPTG to help the bacteria survive, they would not have lived. This would not have occurred in the wild. This tells us virtually nothing about how Darwinian evolution could produce complex molecular systems.

Q. So again this system would not have worked in nature but for Barry Hall interjecting the IPTG to make this system work?

A. Yes. I should point out that Professor Miller does not mention this aspect of Barry Hall's experiments in his discussion, in his book Finding Darwin's God.

Q. Is that a significant oversight?

A. Well, I certainly would have included it.

MR. MUISE: Your Honor, we're about to move into the blood clotting system, which is really complex.

THE COURT: Really? We've certainly absorbed a lot, haven't we?

MR. MUISE: We certainly have, Your Honor. This is Biology 2. It's a quarter past, and if we're going to go until 4:30, it's probably not worthwhile to start up on the blood clotting because it's fairly complex and heavy and a lot of it is going to be --

THE COURT: Well, we don't have an issue as to his availability through the day tomorrow I assume?

MR. MUISE: He's available, Your Honor, for as long as we need him.

THE COURT: Any objection if we --

MR. ROTHSCHILD: No. He started it.

THE COURT: I was just waiting to see what you'd say.

MR. MUISE: We've gone from Biology 101 to advanced biology. So this is where we get.

THE COURT: We will recess then for today, and we'll reconvene at 9:00 tomorrow and we will pick up with Mr. Muise's direct examination at that time. So have a pleasant good evening, and we'll see you tomorrow.

(Court was adjourned at 4:15 p.m.)


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