The testimony of Kevin Padian in Kitzmiller v. Dover

Edited by Nick Matzke, National Center for Science Education
Version 1.1

This web page contains the testimony given by U.C. Berkeley paleontologist Kevin Padian during his appearance as an expert witness in the 2005 Kitzmiller v. Dover case. Padian is also the president of the board of directors of the National Center for Science Education. Padian's exhibit slides are included in the transcript, and are also available separately.

Sections:
Background (by Nick Matzke)
Copyright and Reproduction Information
Expert Qualifications
Direct Examination
     Introduction
     Classification, Ancestors, And Relationships
     Creationism and the Fossil Record
          I. "Irreducible Complexity" and the evolution of major adaptations
          II. The "Cambrian Explosion"
          III. How vertebrates gained land (the "fish-amphibian" transition)
          IV. The Origin of Birds
          V. Fossil Mammals
               The Evolution of the Ear in Mammals
               The Origin of Whales
     Creationist misrepresentations of Homology and Analogy
          Pandas on homology: the real wolf and Tasmanian "wolf"
          IDCers prefer the explanation of special creation over descent
Cross Examination
     Cross Examination (continued)
Redirect
Acknowledgements



Background (by Nick Matzke)

Kevin Padian testified on Friday, October 14, 2005, in the courtroom of Judge John Jones III, located in the federal courthouse in Harrisburg, Pennsylvania. This was Day 9 of the 21-day Kitzmiller v. Dover case. Kitzmiller was a district-level court case, held in the Middle District of Pennsylvania. The complaint was filed on December 14, 2004, and the decision was issued on December 20, 2005. Padian was one of six expert witnesses who testified for the victorious plaintiffs. For more information on the Kitzmiller case, including transcripts, legal filings, and the decision, see the relevant pages at NCSE and TalkOrigins.org. The original PDF transcripts are available in the transcripts directory of the NCSE Kitzmiller documents archive.

The courtroom transcript was taken by Lori A. Shuey in the morning and Wesley J. Armstrong in the afternoon. In addition to Padian, the major speaker is Vic Walczak of the ACLU of Pennsylvania, who conducted the direct examination of Padian for the plaintiffs. Robert Muise of the Thomas More Law Center conducted the cross-examination for the defense.

Padian's slides were introduced into evidence in the case as plaintiffs' exhibit P-855. The slides were assembled by Padian and the graduate students in his lab (see Acknowledgements). The captions for the slides were added by me in early 2007. New scientific developments that took place after the October 2005 trial are noted in some captions. Any errors that remain in the captions are mine. A few slides received minor corrections, and in a few cases graphics from an unknown source were replaced with similar public domain graphics (e.g. the dolphin). The original court transcript was spellchecked to correct typos and phonetic spellings of technical terms, but some errors may remain in this version. We have decided not to attempt other corrections, e.g. grammar and punctuation -- this would be a very large job, and would move the text further from the original court transcript. There will be inevitable difficulties in any written transcript of a spoken conversation. In most cases a confusing sentence will make sense if you imagine someone speaking it rather than writing it. Please send corrections and comments to me at matzke(AT)ncseweb.org.

-- Nick Matzke, National Center for Science Education




Copyright and Reproduction Information

Notes on copyright: All slides are copyright 2005 by Kevin Padian and reproduced with permission. However, many of the slides contain images from copyrighted sources; see individual slides for references and, where possible, permissions (primarily journals and museum specimens). Many slides also contain fair use material, such as small graphics of book covers, or quotes from exhibit material that is receiving academic criticism during the court testimony; the citation information is typically given within the slide.

Notes on reproduction: The slide material produced by Kevin Padian and his lab may be reproduced on the web and in presentations (e.g. Powerpoint) and handouts, for nonprofit or educational purposes, as long as Kevin Padian and the NCSE-hosted webpage are acknowledged. Contact NCSE if you are interested in reproduction for a printed publication (higher-resolution versions of the slides are available). However, for copyrighted material held by others we have only acquired permission for reproduction on the NCSE website. Further reproduction of those materials should fit within the parameters of academic fair use, or the individual copyright holders should be contacted. Many of the images come from sources that grant blanket permission for nonprofit educational reproduction, e.g. Wikipedia (under e.g. a Creative Commons license), the public domain (e.g., U.S. government websites), the websites of whale evolution researchers Thewissen and Gingerich, or journal articles from the Proceedings of the National Academy of Sciences (see the PNAS Rights and Permissions page). The journal Nature typically auto-grants permission for nonprofit educational reproduction of images; obtaining this permission requires that the user register on Nature's permissions website and fill out a web form for each image. Other sources should be contacted via their permissions departments, e.g. Science or Wiley.




Expert Qualifications

[On Friday, October 14, 2005, a previous witness, plaintiff Steve Stough, had to finish testifying before Kevin Padian took the stand.]

THE COURT: All right. Sir, that concludes your testimony. You may step down. Thank you. Exhibits --

MR. HARVEY: Your Honor, may I make a suggestion before you begin that?

THE COURT: Yes.

MR. HARVEY: That is that we have an expert witness, Dr. Padian --

THE COURT: And you're going to tell me you want to get moving?

MR. HARVEY: That's a dangerous thing to say to the Court.

THE COURT: No, that's fine. I know you have an expert and you want to get moving on the expert. So you want to reserve the argument on the exhibits until later?

MR. HARVEY: Exactly, Your Honor.

THE COURT: I'll rely on you then to remind me so that we get those in, and let's take your witness.

MR. WALCZAK: Your Honor, plaintiffs call Dr. Kevin Padian.

KEVIN PADIAN, Ph.D., called as a witness, having been duly sworn or affirmed, testified as follows:

THE CLERK: If you could state and spell your name for the record.

THE WITNESS: My name is Kevin Padian, P-a-d-i-a-n.

THE COURT: You may proceed.

DIRECT EXAMINATION

BY MR. WALCZAK:

Q. Good morning, Dr. Padian.

A. Good morning, Mr. Walczak.

Q. Where do you live?

A. I live in Berkeley, California.

Q. What do you do there?

A. I am Professor of Integrative Biology at the University of California and a curator in the Museum of Paleontology.

Q. I'd like to direct your attention to what's been marked as Plaintiffs' Exhibit 292. Matt, could you put that up. Do you recognize this document?

A. It looks like my CV.

Q. Is this a reasonably accurate representation of your professional experience?

A. I believe that's a recent one, yes.

Q. I'd first like to focus on your educational background. And you have a bachelor's of arts degree from Colgate University?

A. Yes, sir.

Q. And you have a master's of arts in teaching. Is that correct?

A. That is right.

Q. What does that mean?

A. It means that I have permanent certification in the State of New York and several other states to teach life science in grades 7 - 12. And for this training, you take postgraduate courses in education and your subject major, whatever it happens to be, and you do intern teaching and you're certified to teach.

Q. And what was your subject major?

A. I majored in natural sciences at Colgate, and so I'm certified with life sciences.

Q. And have you ever used that degree to teach elementary or secondary school biology?

A. Yes. I've taught seventh-grade life science and biology, and I've taught two years of sixth-grade process science.

Q. And when was that?

A. That would be in the years '72 to '75.

Q. And after that, did you go back to school to get your Ph.D.?

A. I went to Yale for my Ph.D. after that, which I got in biology in 1980.

Q. And did you write a dissertation for your Ph.D.?

A. I did. That's required.

Q. And what was the topic of your dissertation?

A. The topic of my dissertation was on the evolution of flight and locomotion in the flying reptiles called pterosaurs, which lived during the age of dinosaurs.

Q. And where was your first professional appointment after graduating?

A. I went to Berkeley right after that as an assistant professor, and I've been there ever since.

Q. And what's your position there now?

A. I am a professor and curator, so a professor in the Department of Integrative Biology and curator in the Museum of Paleontology there.

Q. And what do you teach, Professor Padian?

A. I teach a variety of courses over 25 years. Some I don't teach anymore because the curriculum changes, but currently I teach and coordinate half of our upper division junior/senior courses in evolution. I teach an upper division course in the evolution of vertebrates. I teach a number of freshman seminars usually on dinosaurs. I teach a number of graduate seminars on topics that range from macroevolution to the history of evolutionary thought. Currently we're doing Darwin's Origin of Species.

Q. And you said a moment ago that your background and expertise is in evolutionary biology and paleontology. Could you tell us what those specialties involve?

A. Sure. Evolutionary biology is a broad field that ranges from the study of the changes through time of molecules to the changes in time of the whole history of life as it relates to the changes of the planet Earth through time, the whole solar system. And my specialty in this is what we call macroevolution. Within that, I focus principally on how major new adaptations begin in evolution.

Q. When you say "major new adaptations," what do you mean?

A. Well, about things like flight or how, for example, dinosaurs took over the earth. That's a great big change in evolution that happened about 225 million years ago. I work on problems like that.

And I also work on problems involving dinosaurs and general things about reading their footprints, their locomotion, again, how the age of dinosaurs got started. And I'm interested in the history of evolutionary thought, how people have conceived of the idea of evolution and how it's developed over time in the past 200 years.

Q. And is some aspect of what you just talked about paleontology?

A. Paleontology is the study of life of the past, generally put. And so when I say that I work on macroevolution, these are large changes that happened at a scale above the population level. So we usually have to look at them through time.

Q. And do you look at something called the fossil record?

A. The fossil record is where I spend a lot of my time.

Q. And what is the fossil record?

A. The fossil record is the record in the rocks of the remains of organic beings through time. It can take the form of bone, shells, footprints, trace fossils, all sorts of things.

And what we do is, we don't -- I mean, when you look at television documentaries, it normally focuses on people going out in the field and parking the truck and walking out in the Badlands and, you know, stumbling over bones someplace and finding that it's interesting in digging up and getting a skeleton and putting it in plaster and taking it back to the lab.

That's the first stage of what we do, but that's just the beginning of the science. The science is asking the questions about how life evolves, how the changes in life have happened through time.

Q. It sounds like you have to have knowledge in many different fields.

A. Well, my department is called integrative biology for a reason, that we actually look at problems in a rather integrative way. That is, my work involves physiology, bone histology, which is the tissue form of bones and mechanics of growth, as well as fossils and geologic change through time.

So, yeah, the questions you ask could be pretty complex and integrative, and different kinds of evolutionary biologists and paleontologists work on different aspects of these problems.

Q. And are you still involved in research?

A. Oh, yes. Berkeley is a premiere research institution like Harvard or Yale or Penn State, and basically most of what we do is research and teaching. So as part of my job, I'm expected to produce a lot of peer-reviewed articles and books and things on a regular basis.

Q. And you've been doing research for 30 years now?

A. Yeah, roughly.

Q. And this is all on evolution and paleontology and the fossil record?

A. Oh, yes.

Q. And you mentioned that you've --

(White noise.)

MR. WALCZAK: Is that a hint, Your Honor?

THE COURT: No. Inadvertent button push.

BY MR. WALCZAK:

Q. You mentioned that you've published peer-reviewed research. Let me direct your attention to the top of Page 2 of your curriculum vitae, or I guess about a third of the way down. Now, it says there, Publications. What do you mean by that?

A. These are -- the list that I enclose with my CV here includes what we call peer-reviewed publications. And so these would be publications that have been sent out to our professional journals and, in some cases, to books that are edited by professionals again.

I don't know if you've gone through the concept of peer review much in the court, but by "peer review" we mean that if you publish -- if you have some research that you've produced and you want to get it published, you send it to a journal in the field, and the editor, who is an expert in the field, takes your manuscript and sends it to several experts that you can't choose and you don't know who they are. And --

Q. So you, as the author, don't know who is reviewing your articles?

A. That's correct. This is the anonymity of peer review. Ordinarily you don't know who these commentators are.

Q. What's the purpose of that?

A. Well, it's basically so that they can give a frank appraisal of what you're writing without worrying about whether they're going to offend you and, if you're a senior scientist, whether you're going to get mad at them or something. I don't know. But it's been a habit that's always been the case in the scientific field, certainly.

And the reviewers who look at your papers then decide whether you've followed the right procedures for going about the science, whether the methods you use are up to date, whether you've cited all the literature that's relevant, whether you've inferred or speculated on more than you should, or whether it's basically within the grounds of what is acceptable science.

And they will propose changes, major or minor. If they don't think that your paper is very good, they'll suggest it be rejected, and the editor takes that into consideration.

Q. And so is everything that is submitted to a peer-review journal published?

A. Oh, no. A lot submitted to peer-review journals isn't published. It depends on the journal. On the journals on which I've been an editor, you have an acceptance rate of anywhere from 50 percent upwards or downwards to 30 percent, for example, in the ones I'm familiar with.

Q. And is there a -- what you might consider a hierarchy of journals for publication?

A. Yes, there are certain journals that pretty much every scientist in the world reads every week. Two of them in particular are Nature, which is published in London by Macmillan Journals, and Science, which is published in Washington every week by the American Association for the Advancement of Science, which is our sort of central public science organization in America.

Everybody reads those journals because they contain good review articles, but mainly the hottest sort of new research in all fields. They will also include news about new scientific developments not just in science but in education, industry, technology, even this court case, for example.

Q. And do they have a high rejection rate?

A. Oh, yes, they have a very high rejection rate. No more than about 10 percent of what's submitted to them even gets considered for publication.

Q. Now, is there something called -- is it an impact factor?

A. Yeah, there's a -- the Institute for Scientific Information produces a measure of how important journals are basically to the fields. Journals like Nature and Science have a very high impact factor. But they're general journals that everybody reads, and they're highly selective.

Some fields are smaller fields, they don't have much of an impact because they're not cited very much simply because the fields are small, but within the fields they might be very important. So you could have an impact factor that is relatively low, but in the field it's high because it's cited a lot for that field.

Q. And the way they measure this impact factor is to see how many times an article from that publication is cited thereafter?

A. That's basically it.

Q. And what journals have you published in?

A. Well, I've published in a lot of journals. My colleagues and I try to -- you know, you always try to go for the best journal in the field that you're writing for the people who would be the most interested in the research.

Sometimes I'm writing about dinosaur footprints, and I might try to publish in a journal that publishes a lot of footprint work. Other times, for example, when we've done our work on how fast dinosaurs grow, learning about this from the fine structure of their bone tissues, we've gone to Nature, we've gone to Paleobiology, we've gone to Journal of Vertebrate Paleontology, again, sort of the best journals in the field that we can target, depending on the scope and interest of what we're trying to do.

Not all the papers are gems, not all are Nobel prize quality. Sometimes they are very general, and sometimes they're a very specific interest.

Q. Now, I note that by my count, you've got eight pages of peer-reviewed publications listed here in your curriculum vitae. Do you know how many peer-reviewed publications you are either an author or coauthor on?

A. It's 80 to 100. I don't keep a correct count.

Q. And have you included in this curriculum vitae non-peer reviewed publications?

A. I believe the copy that I gave the Court may have only the peer-reviewed ones. I have about another eight or ten pages of things like book reviews and popular articles, things in Scientific American and stuff like that. But I didn't include all those here. I may have included some of the books that I've authored or edited.

Q. Let's turn to -- I believe it's Page 9. And you've got a heading on books. And you are either the author or the editor or a contributor to these nine books?

A. Yes.

Q. And just pick one. Tell us about your contribution to, for instance, the Encyclopedia of Dinosaurs, and what is that book?

A. The Encyclopedia of Dinosaurs was published by Academic Press, I guess in 1997. It's a standard reference work for the field. And my job, along with Phil Currie, my coeditor, was to organize and solicit the contributions to make sure all the relevant entries were covered, to read the manuscripts when they came in from the authors, if they needed changes, to suggest them or to make them.

And, in fact, as it turns out, I wound up writing about a sixth or a seventh of the book before publication just because of filling in the parts that were needed, as inevitably happens with reference works.

Q. And this is a book that would be found in your public library or your school library as a reference text on dinosaurs?

A. Yes. This book is cited by other scientists in their publications. It is in libraries for ordinary people to read. We tried to write it at a level that somebody that would have a general understanding of dinosaurs would do it. And then for the dino fans and freaks, they're going to pick it up, too, and enjoy it as much as the rest of us.

Q. Now, does something become science or accepted in science because it's published in a book?

A. Well, it depends on the book. When books are published, they may have a seminal influence, but simply because something is published in a book doesn't mean that it's science. I think that that's a question of its reception by the scientific community.

If somebody writes a book and nobody reads it, is it influential? And the answer would be no. And if somebody writes a book but claims it's science and it's not cited by scientists, it doesn't stimulate scientific research and the ideas in it are never brought to peer review, then the answer is probably not much, because we depend on peer-review discussion of ideas and research results in order to further the progress of science.

Q. So anybody can write a book and proclaim that they have a new scientific theory, but the test really is whether it's ultimately accepted by a large part of the scientific community?

A. Yes. And here I think the term "theory," again, has to be looked at the way scientists consider it. A theory is not just something that we think of in the middle of the night after too much coffee and not enough sleep. That's an idea. And if you have a hypothesis, it's something that's a testable proposition, you can actually find some evidence that will help you to weigh it one way or the other.

A. A theory, in science, as maybe it's been pointed out in court, I don't know, in science means a very large body of information that's withstood a lot of testing. It probably consists of a number of different hypotheses, many different lines of evidence. And it's something that is very difficult to slay with an ugly fact, as Huxley once put it, because it's just a complex body of work that's been worked on through time.

Gravitation is a theory that's unlikely to be falsified even if we saw something fall up. It would make us wonder, but we'd try to figure out what was going on there rather than just immediately dismiss gravitation.

Q. Is the same true for evolution?

A. Oh, yes. Evolution has a great number of different kinds of lines of evidence that support it from, of course, the fossil record, the geologic record, comparative anatomy, comparative embryology, systematic, that is, classification work, molecular phylogenies, all of these independent lines of evidence.

Q. We're going to talk a little bit more in detail about some of those concepts in just a couple of minutes. Your expertise has been recognized by professional societies and scientific journals in a sense that you have been an officer or a committee chair on a number of prominent scientific associations?

A. Yes, if that's a measure. My work is published in the organs of scientific societies, their professional journals. I've served as an officer in a couple of societies and committee member, and I've been on the editorial board of a number of peer-reviewed journals in our field.

Q. Matt, if you could turn back to the first page of Dr. Padian's CV under Professional Service. Now, it appears that you've been an editor on the editorial board of more than a half a dozen journals. Can you tell us what it means to be an editor of a journal?

A. It generally means that when manuscripts come in, the chief editor will send them to you either for review yourself or for deciding whether they should be reviewed by people. Or if you send them out to review, you might gather the reviews from the referees and determine the merits of the manuscript in question.

Often, of course, with general editorial meetings you're looking at where the journal wants to go, what kinds of papers and research it wants to solicit, sort of things like that.

Q. And I note that you've had a couple of stints as editor of the Journal of Vertebrate Paleontology. Is that a prestigious journal in your field?

A. That is, in our field of just those paleontologists that run around the rocks and look for the remains of old animals with backbones, yes, that's our primary international scientific organization. Paleobiology is probably the premiere journal in the field of paleontology that works on macroevolution, which is one of the things that interests me.

Q. And you were the editor of Paleobiology for six years?

A. I was one of the editors on the editorial committee, yes.

Q. And you were also on the editorial board of Geology and the Proceedings of the Royal Society of London?

A. Yes.

Q. Dr. Padian, have you had any experience with high school or elementary school curriculum development and teacher training?

A. Yes. Since I've been in California, since the mid 1980s, I've worked in several capacities for the State Department of Education in California on various panels and committees.

Notably, I guess, I was one of the people who wrote and edited the state science framework for K-12 schools in 1990. And this is the central document that embodies science education for the state. It's the document against which districts and other organizations will develop their curricula locally.

And my role there was to write about guidelines for the -- explaining what science is, the nature of science, explaining the goals for K12 in the life sciences and for some of the earth sciences and several other parts of that.

In addition, I guess I've served three times on what we call the instructional materials evaluation panel as a scientific member. California is an adoption state, which means that it's one of 23 states for which the state actually selects which textbooks can be used by local districts and for which state funds can be spent.

And so it's kind of a quality control that educators and content area specialists like scientists or historians or mathematicians will get together and evaluate textbooks and things submitted. And then the question is whether these are -- which ones pass muster and which ones don't, and that's what you can use state funds to buy.

Q. And you've been involved in that for several years?

A. Three times.

Q. And do you have familiarity with creationism and intelligent design?

A. Yes.

Q. And just tell us a little bit about that. What's your history of involvement?

A. Well, California has an interesting history with respect to the creationist movement, I guess we might call it creation science and related fields.

The Institute for Creation Research in Southern California has been very active since the early 1980s and various kinds of legal and social processes that have come out of objections to the teaching of evolution in California have mirrored what's happened in other states, as well.

And so early on in the 1980s I was one of a number of scientists who were involved in trying to clarify evolution and related science to the public and to advise the Department of Education and other bodies about it and to talk generally to the public about what evolution was.

And these organizations and sort of committees of correspondence, as they were called then, eventually morphed into what became the National Center for Science Education which I've been president of for some years.

Q. I'm sorry, you said you're president of the National Center for Science --

A. National Center for Science Education.

Q. Dr. Padian, can you tell us a little bit about the history of paleontology and its importance to evolution?

A. Sure. Paleontology, the idea that you're finding rocks that have the remains of ancient life in it, has been around actually in some form or another since the 1500s and 1600s when people first started to understand that these were actually the remains of organisms that were dead and not simply sports of nature or some kind of sculptural-looking accident.

The understanding of fossils really began to mature in the late 1700s when people realized that these were the remains of dead creatures that were not coming back, they were extinct. And the upshot of this meant that ideas about the philosophy of nature began to change as the enlightenment developed.

By 1800, you had people in both England and France developing systems of looking at the order of the rocks through time, moving up through a section, that could be correlated from one area to another. The same sequences of rocks were appearing. These were used in England, for example, by civil engineers to dig canals and to show them where reliably they could find the right rocks to dig canals through.

Part of these indications were by the fossils that they contained which also went up in the same sequence every time. And this resulted in the first real geologic map of England, which was produced in about 1800. So we're already talking about using fossils in a very forensic sense, that is, to help dig canals, but using them as an index for mapping geologic -- we call them strata or outcrops all over England. A similar development of the idea was taking place in France at the time and also in Germany.

So the idea that there was a progression of fossils in rocks from the oldest to the youngest going up through a section of rocks is really quite old. And it was developed, in a sense, that had nothing to do with any ideas about evolution. It was just seen as the progression of fossils through time.

And then ultimately in the early 1800s people began to understand that this reflected an idea of common ancestry change through time and the fact that in the past the world was not like it is now.

Q. And so what you've just told us about is taking place before Charles Darwin published his Origin of Species?

A. Oh, yes. Darwin doesn't publish the Origin of Species until 1859. The geologic map of England is being done by 1801, and already by 1846 they have a pretty good idea of the diversity of fossils through time.

Q. So was Darwin trying to explain the history of life or the fossil record?

A. No, he really wasn't. Other people were doing that at the time, including people like Richard Owen. What Darwin was doing was proposing a mechanism for how change through time could occur in a lineage of organisms, and he called that natural selection.

He made an analogy with what he called artificial selection, which is what breeders do every day in selecting plants and animals for the characteristics that we admire or want to use for various purposes.

Q. Now, we've had, I guess, testimony in this case where people seem to be using terms in different ways. Could you distinguish for us the way science uses the term "natural selection" from "evolution of life"? I mean, is there a distinction?

A. Yes. "Evolution," of course, refers to change through time in a general sense. Darwin's own definition is descent with modification, which is probably still the best one.

Natural selection is a mechanism, a process that accounts for a lot of that change, but it needs to be distinguished from evolution, per se, because there are a number of mechanisms, as Darwin noted, including sexual selection, which is another term he invented, a concept that he invented, as he did so many things, and it's just one mechanism for life to change. It's not the whole thing. Darwin was very clear on that in his writings.

Q. And can you distinguish evolution of life, the term "evolution of life," from the term "origin of life"?

A. Sure. And that's a common conflation in popular parlance. Evolution of life is essentially the whole enchilada. It's everything from the first organisms that appeared right up until the organisms that are alive today. That whole procession of things, all the patterns and processes that are involved in it, we would call the evolution of life.

"Origins" is a trickier phrase. The origin of life we expect, as Darwin said in 1859 -- the last paragraph of The Origin of Species refers to one or a few forms being the original embodiment of life. But today we look at the genetic material, DNA, RNA, and its genetic components, and scientists reason from this that they are so complex and so similar that they must have had a common origin. And this is the origin of life question.

That's separate if you talk about, like, origin of birds or origin of mammals or origin of the middle ear. Those things are part of the progression of life that's already established. They aren't something new that happens all over again that's, in other words, abruptly or specially put in there. They're just part of something that's already happening that now is modified to become something else.

Q. So as scientists would use "origin of life," that would be sort of first life?

A. Exactly.

Q. Now, it seems that genes and molecules are getting much of the attention today when you're talking about evolution. Is it still important to study comparative anatomy, fossils, geology, paleontology? I guess another way to say it, are you still relevant?

A. I'm a fossil like everybody else. No, genes and molecules get a lot of press, and deservedly so. The research on them has been amazing over the past half century. The new discovery has just come at an incredible rate. They're just revealing all sorts of new things about the world we never could have imagined. We could have hoped we could have known, but we wouldn't have known how.

But, oddly enough, the most recent great advances in biology are coming with the integration of this new molecular evidence with what we already know from comparative anatomy, from fossils, and from geology.

An example I could give you is like the hottest area in biology today is called evo-devo or evolutionary developmental biology. Evo-devo is not a rock group. And the thing about it is that the whole premise of evo-devo is that we are now understanding a lot more about the genes that actually code for the development of organisms. That is, we know the genes that make you line up in a front-to-back axis and make your limbs sprout and make you have wings instead of hoofs or whatever it happens to be.

These are under the command of a relatively well-organized system of genes that are universal among a great many organisms. And you can even transplant parts of these into other organisms, and they'll work properly, which is really amazing.

And why paleontology and evolutionary biology is relevant to this is because, for one thing, in the fossil record we see a lot of forms that are not present in any kind of shape today. Configurations of hands and wings and skulls that we can see by examination of the genetic structure and functions of development actually are produced in certain ways and they mimic what we see in the past.

So, oddly enough, paleontology, evolutionary biology are coming back front and center to be integrated in this very hot new area.

Q. So is it fair to say that molecular biology today reinforces what you find in paleontology or integrative biology?

A. Oh, yes. The molecular biology of the 1960s and '70s was very strongly what we would call reductionist. That is, they were looking for the little, tiny workings, because they were able to do so, of genes and structures in the cells and chromosomes, and that was really amazing.

But, you know, in a sense, all that work is figuring out how the carburetor goes, you know, what are all the parts here. But they don't lose sight of and it doesn't change the importance of, you know, how you drive the car, what the purpose of the car is in terms of running down the road and operating on the internal combustion engine. And that's where the evolution comes in.

Q. I want to ask you one other question coming back to natural selection, and you said that is a mechanism for driving evolution.

A. Yes.

Q. And is that a mechanism that is widely supported by the scientific community?

A. Oh, yes. Darwin proposed it at the same time that Alfred Russel Wallace came up with it in 1858. And since then natural selection has been tested in the wild and in laboratory populations by a great number of scientists. And there are many books written that summarize this research, and the understanding of natural selection is primary to understanding population biology and evolution.

Q. Now, next week an expert for the school district, Dr. Behe, are you familiar with him?

A. Yes.

Q. He's going to testify. And Dr. Behe has claimed that it is not possible to observe natural selection in the fossil record. And is that true, and, if so, is the fossil record relevant to evolution?

A. Dr. Behe and some of the ID proponents characterize evolution, Darwinism evolution, as they call it, as random mutation and natural selection alone. And natural selection is important, but it's not the only process. Random mutation is a whole other problem in language. But natural selection can be observed in the fossil record in a different way than we'd see it in populations.

When Darwin developed his idea of natural selection, he's looking at individuals running around out there. He's saying that an individual horse is going to be able better to escape a lion than another horse. That horse is going to live longer, produce more offspring with the same characteristics, and those will be passed on to the next generation. So this is an idea about individuals.

Now, the problem is, when we go out to the fossil record, if we have a nice fossil deposit here of snails or clams or whatever it happens to be and you've got, you know, many local fossils, fossil deposits which you can find things like this, you know, we can't tell whether a particular fossil clam was better adapted than the guy who is dead next to him. We can't measure how many successful offspring he had. We just simply don't know. We don't know anything about the reproduction of fossils, individual organisms. And so in that sense, we're not looking at that level of natural selection.

But as everybody knows, we have a concept in evolution called "adaptation," which is sort of the main thing that drives the origination of new sort of types of organisms, the way that they get around in the world. And this notion of adaptation, by definition, is shaped by natural selection.

And my job is to look at macroevolution, and I focus on how new adaptations get going. So I study natural selection all the time in its ramifications for the development and improvement of all these complex adaptations that click in piece by piece in fossil animals and are shaped and preserved by natural selection.

Q. So the fossil record, in fact, helps to support the whole concept of natural selection?

A. In fact, it's indispensable to it, because we could look at natural selection in populations today, but our compass for looking at populations today is on the order of years, maybe decades, in some cases centuries.

A. A trend that we see today might reverse itself. It might be just sort of a drift or a random fluctuation, a temporary change, but in the fossil record, you see change through the big time. This is deep time, we call it. This is like mega history.

MR. WALCZAK: Your Honor, I was thinking about taking a break now. It might be an opportune time.

THE COURT: Why don't we do that. Let's take a shorter break than we've been taking so that we can keep moving with this witness. We'll take a 15-minute break at this point, and we'll return with Mr. Walczak's continued direct examination of this witness. We'll be in recess.

(Recess taken.)




Direct Examination

THE COURT: All right, Mr. Walczak, you may continue.

MR. WALCZAK: Thank you, Your Honor.

BY MR. WALCZAK:

Q. Dr. Padian, what is intelligent design?

A. As I understand the definition, intelligent design is the proposition that there are some things, natural phenomena in the world that could not have come to being by natural means and that the design of these structures has a certain complexity and certain features that implies that they must have been produced by what is called an intelligent designer by which is understood to mean possibly some kind of unknown forces or a supernatural being.

Q. And how is intelligent design different from creation science?

A. Well, it has some similarities, and it has some differences. Creation science is a movement that flowered mostly in the 1960s and 1970s. And creation science was an attempt by certain conservative Christian people with some science or engineering degrees to attempt to explain Bible stories or to find scientific evidence for Bible stories or explain them in scientific terms, that is, to attempt to justify them on scientific grounds.

Intelligent design doesn't have as its objective to validate Bible stories or any particular religious or creation stories, but what it shares with creation science, in part, is the insistence that things were designed and could not have evolved. And so over 90 percent of the corpus of intelligent design work has to do with basically trying to undermine the evidence for evolution and the concepts associated with evolution and related sciences.

Q. And we're going to spend a good bit of time talking about the undermining attempt, the undermining of the evolutionary science.

As I understand it, the affirmative argument for design, not the criticism of evolution, but the affirmative argument for design is that it looks designed or it's so complicated we can't imagine that it couldn't have been designed. Is that your understanding?

A. That's my understanding, in an informal sense, that that's what they mean.

Q. What's wrong with this appearance of design analysis from a scientific standpoint?

A. Well, it's not particularly rigorous. Lots of things look designed, but they may not necessarily be designed. Intelligent design looks a lot like science in some respects, but it's only superficial. It doesn't operate according to the principles of science, so the resemblances are superficial.

And appearances can be deceiving. For all the world, it looks like, you know, to us normal people, that the sun goes around the Earth. And for most people, it wouldn't make a difference whether the sun went around the Earth or it went around the moon, as Sherlock Holmes famously said to Watson. But when the renaissance scholars understood, found out that, in fact, the sun does not go around the Earth but the Earth and the planets go around the sun, it changed the way we look at the whole natural world in a very important and fundamental way.

And so part of the process of science is to discover things that will make a difference to our understanding of the natural world and not simply to reinforce appearances that are very difficult to test in an objective or testable sense.

Q. Let's begin to talk about the problems that you have with how intelligent design represents science, and I want to focus on the areas of science within your expertise. What is wrong with the intelligent design arguments against evolution?

A. Well, there are a number of systemic problems with the arguments about intelligent design.

Q. I'm sorry, Professor Padian, have you prepared an exhibit to help you explain this?

A. Yes. At your request, I've done some demonstratives that I hope may be of use in illustrating some of these things.





Slide 001
Slide 1: Summary of why "intelligent design" is a form of creationism.
(Right-click to download pdf.)

Introduction

Q. Matt, would you put up the first slide, please.

A. There are certain systemic problems with the way that intelligent design represents the scientific findings of the scientific community. And in a sense, it is really just standard anti-evolutionist special creationism. I will explain why it's special creationism in the course of things.

The ways that scientists have problems with intelligent design literature is, first of all, that it provides some misleading definitions of evolution. In doing so, it sets up a straw man. It also distorts some commonplace scientific concepts, and, as a result, it sows doubt in the minds of students who would understandably be confused, as I am, by their treatment of certain fairly standard ideas. When they --

Q. What kind of concepts do they sow doubt about?

A. Well, they begin -- if you want to begin with definitions of evolution, they define micro and macroevolution in different terms. Microevolution they're fine with. That's evolution in populations. It's just genetic variation. And creation scientists didn't have a problem with that stuff, either.

But when we study evolution, we actually look at it on several discrete levels. Microevolution is what happens in populations at the gene level and among individuals in populations within a species.

But then when populations diverge from each other geographically and genetically to the point where they become different species, different lineages that are not going to have a mixed history anymore but separate histories and diverge further and make more new species, we call this process speciation, and it's a different level of consideration than simply what happens in populations, because now you see we have the situation where we're no longer exchanging genes with each other in a population, we're actually looking at two separate or more separate entities that will be that way historically for the future.

Once we start looking at how these new lineages, new species and new species that they give rise to, interact in the environment, how they change further through time, how they adapt more to changing environmental conditions, we're now at the level that's called macroevolution. And the reason we call it macroevolution is it's just on a bigger level. We're no longer dealing with populations.

Q. And by "populations," you mean, like, people or horses or --

A. Well, like just groups of organisms. Individual organisms within a species are different populations. You can have a population in this valley, a population in that state, whatever it happens to be.

The way that scientists regard this is much like economists look at microeconomics and macroeconomics. Microeconomics is how you run the corner grocery store, you know, what the economic balance is in the small town's economy, how a company works. But macroeconomics has more to do with things like the Federal Reserve, the international balance of trade. The common thing that -- the thread between this is, of course, money. It's all about currency. It's cash at some level.

And with evolution, we've got genes that are very similar because everything is hereditary. It's transmitted. And the genetic transmission of this works one way within populations when organisms can exchange genes, but when you get above the species level, they're no longer exchanging genes. We're working at different species disporting themselves through time. And then you get the whole process of the evolution of new adaptations and major groups of animals and plants.

And the intelligent design people define macroevolution as a major change that has to happen to make a major group, and they say that this is a completely different process than what happens at the microevolutionary level. And scientists just don't think so.

Q. And are some of the other concepts that they don't quite represent accurately homology and cladistics and classifications?

A. Yes, the basic principles of classification, the principles also by which you can compare organisms in order to say things in comparative biology are very problematic for intelligent design creationists. They have a hard time explaining these in the terms that scientists use. And so a lot of what they do is to try to cast doubt on the very legitimacy of the basis of doing these things as scientists understand them.

Q. I'm sorry, continue. I believe you were on Number 3.

A. One of the problems with the ways that intelligent design creationists present scientific evidence is that they present only part of it. They present the part that might suit their cause, but they really leave out an awful lot of important research. And in so doing, they say that scientists don't know this or they can't know this. And this creates the sense of ridicule for students.

Now, you know, we'll be the first people to admit that science doesn't know everything and can't know everything. But on the other hand, we would like a fair and accurate representation of what we do know.

I would also like to show in the course of explaining some of these things today that most of the claims that the ID proponents make are directly inherited from the old-time scientific creationism claims in the evolution bashing that they do. Many of the same arguments are used, the same kinds of evidence are used.

And, finally, the conclusion that is raised is that if you can mount some kind of alleged evidence against evolution, which is most of what the ID proponents do, as the scientific creationists did, then this is evidence for intelligent design. In so doing, they set up this false dichotomy or contrived dualism of religion and science that is disturbing to scientists who have religious backgrounds, as well as to those who don't have religious backgrounds because it isn't part of science to do that.

Slide 002
Slide 2: Pandas on macroevolution.
(Right-click to download pdf.)

Q. Now, you said that ID proponents mischaracterize evolution as just a starting point. Matt, could you put up the next slide.

A. Yes, calling macroevolution the origin of new types, this is not a definition that scientists would recognize. Macroevolution, as I mentioned, is looking at the patterns and processes of organisms above the level of species.

So we're trying to figure out a lot of the major patterns of evolutionary change, but the origin of new types, again, that word "origins" comes in, and scientists just don't talk about origins in that sort of cataclysmic sense.

The proponents of intelligent design, as you see here embodied in these quotes from Of Pandas and People, claim that it's a mistake to claim from macroevolution the status of fact. And, again, this confuses for students what facts mean in science.

In contrast, from Pandas, again from Page 99 to 100, they state, quote, that intelligent design means that various forms of life begin abruptly through an intelligent agency with their distinctive features already intact. And this tells you two things, first of all, that everything was already the way it was when things first appeared, so there's no transitions, and that an intelligent agency did this.

Now, that's a perfectly fine idea, but it's not scientific to claim this in advance of any kind of evidence that could be adduced to the contrary.

Q. But in order for this to be true, you have to show that evolution is false?

A. Yes, or at least you have to exclude the possibility of considering it in advance, which is a philosophical rather than an empirical consideration.

Slide 003
Slide 3: Summary of speciation and macroevolution.
(Right-click to download pdf.)

Q. If we could go to the next slide. You say that there are other definitions that intelligent design proponents confuse.

A. Yes. I would just like to clarify what we mean when we talk about speciation, macroevolution, which really differs from how it's treated in texts like Pandas. We call speciation what happens when new lineages are formed. They diverge from parent populations. That is, from old species new species bud off, if you will.

And this can happen in many different ways. You can have changes in behavior, in structure, in ecological adaptation, in physiology, in geography, and all these things may lead to the historical differentiation of these lineages. That's how we get new species. It's been happening ever since life was first running around on the planet.

Intelligent design proponents claim, for example, in Pandas that when speciation occurs, it actually limits variation, and so it's really unlikely that the kinds of changes we see in populations can actually lead to speciation.

I find this statement surprising because there's no evidence that I know of that when a new species forms, that genetic variability is necessarily reduced. It doesn't seem to be the case. Species that are closely related to each other, you don't find one with a lot less genetic variability than another that has ascribed to this process.

And so we regard speciation, in fact, as the raw material for the big changes through time. It's like births in a population are the starting point for populational change and development and the way that new species are formed. Without new species, we wouldn't get any kind of new developments in evolution.

Q. And that's contrasted with macroevolution how?

A. Well, the macroevolution -- then the speciation becomes the raw material for macroevolution, because macroevolution would be the study of what happens to those species after they're formed and as they deploy themselves through time, space, and ecology.

Slide 004
Slide 4: ID says there are strict limits to evolutionary change.
(Right-click to download pdf.)

Q. And, Matt, if you could turn to the next slide. And you're familiar with the textbook Of Pandas and People?

A. Yes.

Q. And do you believe that Pandas is a good representation of intelligent design theory or thinking?

A. I think it is. And I believe that the ID proponents also attest to this.

Q. And here we have a slide. We pulled out a passage from Page 85. This is what they say about speciation?

A. Yes.

Q. And could you read the highlighted passage?

A. The whole thing?

Q. Please.

A. It says, Does speciation fit with the theory that species were originally designed? If the intelligent design explanation is true, there may be species on the face of the earth that have undergone no substantial change since their beginning. On the other hand, the idea of intelligent design does not preclude the possibility that variation within species occurs or that new species are formed from existing populations as illustrated by the previous discussion of squirrels. The theory of intelligent design does suggest that there are limits to the amount of variation that natural selection and random change mechanisms can produce.

Q. So according to intelligent design, speciation is what?

A. Well, speciation is, for them, mostly unlikely on the basis of the kind of genetic variation that occurs. They're happy with genetic variation occurring within species. That's perfectly okay with them. That doesn't lead to much of anything. They say that speciation can occur, but it doesn't involve new innovations and that some species have not changed since their beginning. Now, we'll have to examine what we mean by "some."

But they do state that the known natural mechanisms are too limited to account for the important biological change and the adaptive diversity that we see through time.

Q. And if science's concept of speciation is, in fact, accurate, then that would mean that there's no abrupt appearance of organisms already intact?

A. Well, it certainly would mean that we are not finding new complex adaptations appearing all at once in major groups of organisms with no possibility of their evolution step by step from other kinds of creatures out there, and that's a point on which books like Pandas is quite adamant. They consistently say this does not occur.

Q. And is this argument from Pandas and by intelligent design proponents similar to the argument that creation scientists made?

A. Yes. It's quite similar in its ramifications.

Slide 005
Slide 5: Scientific creationist Duane Gish also claimed limits to evolutionary change.
(Right-click to download pdf.)

Q. Could you put up the next slide, please, Matt. Could you tell us what this is, Professor Padian?

A. The slide is some text from a publication from the Institute for Creation Research called Impact Number 43 by Duane Gish. Duane Gish is vice president of the Institute for Creation Research, a famous creation scientist speaker who has been giving presentations against evolution for several decades now.

And what I'd like to show by this quotation included in the record is that the ideas of intelligent design reflect exactly what special creationists, what scientific creationists, so-called, were saying decades ago.

Here, for example, outlined in yellow on the top paragraph, Duane Gish says that natural selection would be powerless to generate increasing complexity and to originate something new or novel and thus powerless to change one kind of animal into another.

Now, by that is understood, at least, the basis of speciation, and this is very close to what the Pandas text says, and I think the idea really conveys the same message. In the bottom paragraph, Mr. Gish notes that such a process could only produce variance within an established kind and could never produce new and novel structures.

Q. I want to start talking about some of the areas of evolutionary biology and evolution that Pandas discusses and get your understanding of whether they are accurate representations of current scientific thought.

I've asked you to pick several examples out of Pandas where you believe that they do not accurately represent the science. And does the first one involve something called cladistics?

A. Yes. I wanted to talk a bit to explain, if I could, the basis for classification in science.



Slide 006
Slide 6: Beginning section on modern classification, cladistics, and how evolutionary relationships are reconstructed.
(Right-click to download pdf.)

Classification, Ancestors, And Relationships

Q. And when you say "classification," what do you mean by that?

A. I mean precisely how we study the relationships of organisms. The basis of classification, since Darwin, has been the relationships that organisms have to each other.

And the concepts of how classification is done, how we, in other words, understand and construct the tree of life, the whole idea of who ancestors and what ancestors are and the relationships of organisms to each other are problems that works such as Pandas really do not reflect accurately the way that science understands these processes, procedures and methods.

Q. And have you prepared a demonstrative exhibit to help explain this?

A. Yes. I'd like to do just a basic showing of what some of the principles are, if I could have the next slide to talk about that. In their texts, intelligent design proponents either do not understand or they don't accept how scientists establish relationships among organisms because most of this is left out of what their discussions are.

Despite a lot of popular impression, when we try to establish relationships among living and extinct organisms, it's not a never-ending search for direct ancestors. We don't go out in the fossil record, I don't go out looking for dinosaurs or whatever I'm doing in the summer in the field season looking for the ancestor of something else I know. I don't expect to find a direct ancestor of anything. The chances of that are really small. But I want to show you what we do try to look for.

Slide 007
Slide 7: Summary of what ID proponents do not understand about phylogeny reconstruction.
(Right-click to download pdf.)

Paleontologists, in other words, are not searching the rocks for the missing links. Instead, when we, like all biologists, establish organisms, living and extinct, whether we work on bacteria or mosses or hoofed animals, it doesn't matter, we all do this according to the same methods in biology, and it doesn't matter whether we use molecules or fossils.

What we do is we look for shared characteristics. These are uniquely shared characteristics shared by certain organisms and not others. And by identifying these characteristics, we identify the pathway of evolution, that is, the order, the sequence, the genealogy of evolution. We want to find out who is most closely related to whom.

And the reasoning is that if an organism acquires a new trait and passes it on to its descendents, then those descendents will be more closely related to each other because they possess that new trait than anybody else in the world will be. And that's the principle that we use.

And this is a fairly simple concept to get across, and it's revolutionized the way that people do what we call systematics or to assemble the tree of life. But, in fact, this began in the 1960s and 1970s, and so for decades it's been the standard.

There are two concepts of ancestry that are important to point out here. One is lineal, and the other is called collateral. Lineal ancestors are the ones that are directly in your path, that is, your parents, your grandparents, your great grandparents, your great, great, great, and all the times you can say great, those are your direct ancestors.

But collateral ancestors are a little broader than that. They would include your aunts and uncles, your great aunt, your cousin twice removed on your mother's side, and that guy with the funny hat in the civil war picture on the wall in the dining room, whatever it happens to be. These are what we call collateral ancestors. They are individuals who are not directly in your ancestral line, but they still share so many of your features that they can tell us a lot about who you were -- who you are.

Slide 008
Slide 8: Two kinds of ancestry, lineal and collateral. Collateral ancestor "is a legal term referring to a person not in the direct line of ascent, but is of an ancestral family" (Encyclopedia of Genealogy). Parents are lineal ancestors; siblings are collateral ancestors. Padian's point is that both are informative about ancestry - you share 1/2 of your genome with your mother, but also share 1/2 with your sister. Similarly, you share 1/4 of your genome with both your grandparent and your cousin. Creationists claim that paleontologists must find direct ancestors to document common ancestry, but this can be done equally rigorously with cladistic methods that identify "sister" and "cousin" groups on the basis of shared characters.
(Right-click to download pdf.)

Credits: Graphic by Liz Perotti, U.C. Berkeley. Reproduced with permission.

If you know, for example, that your family came from Sweden in the 1800s, you can return to Sweden to the approximate place where they came. Maybe you can't find their bones in the church yard, but you can find the relics and the remains and the museum's evidence for many other aspects of their culture and their biology. You know what they ate, you know what they wore, you know the language they spoke. You may know from photographs and drawings what they looked like, what their features were. You may be able to recognize your ancestral features, as well. All these things are properties of collateral ancestors, not just lineal or direct ancestors.

So when we look to assemble the relationships of organisms, we don't have to find every direct ancestor. In fact, in the fossil record, it's really hard to say that somebody was anybody's direct ancestor, as I mentioned before with the fossil clams. We don't know what offspring any individual left. It's too hard for us to figure out. But we can still tell a great deal about it. And this is how we assemble the tree of life.

The next slide I have here is a preparation of a kind of diagram that we call a cladogram. And it's very similar to a phylogenetic tree, that is to say a tree of relationships. But the logic of this, I want to point out, is not something that's arbitrary. It's not simply assembled by art or by anything that's subjective. Rather, it is a diagram that reflects the grouping of organisms according to these new evolutionary features, these shared characteristics I mentioned before.

And if you can see the red marks along this -- the basic spine of the hat rack running from the lower left to the upper right -- these things always look like hat racks to me. I don't know what else you'd describe them as. But each one of those red bars represents a feature that was a new evolutionary feature that we reasoned was a new evolutionary feature because it suddenly is something that now all the animals above it share and the animals below it do not share.

So, for example, at the top here, the human and gorilla are united by a great many features, and we've only listed a few here because it would just really crowd things, and I think it's fairly obvious. Things that the human and gorilla share are a prehensile hand and a large brain. That is not the case for the cow, the lion, the marsupials, and the other animals on this slide.

We reason that on the basis of this and many other shared characteristics that these features were inherited from a common ancestor. It's the best natural explanation we can come up with. And as we go down this diagram even more, what we find is that at each juncture -- and if we can just stop it there for a second -- we find an increasing number of things that all these groups have.

And so if you look at the level put here on the chart that's indicated, there's a shared feature called an amnion, which is a property of one of the membranes of the egg around the embryo, that is shared by birds, marsupials, and placental mammals, but frogs and sharks and fishes don't have it. And so these hierarchically nested sets of features are the logical structure by which scientists establish the relationships of life.

Slide 009
Slide 9: A vertebrate cladogram showing a few of the many characters that unite major groups. This is just an educational example; actual research cladograms incorporate hundreds of characters. Using large datasets allows researchers to quantify the statistical support for a given phylogenic hypothesis.
(Right-click to download pdf.)

Credits: Graphic by Liz Perotti, U.C. Berkeley. Reproduced with permission.
Slide 010
Slide 10: A few of the characters shared by humans and apes.
(Right-click to download pdf.)

Credits: Graphic by Liz Perotti, U.C. Berkeley. Reproduced with permission.
Slide 011
Slide 11: Primates are closer relatives of cows than lions, based on the shared character of a stirrup-shaped ear bone.
(Right-click to download pdf.)

Credits: Graphic by Liz Perotti, U.C. Berkeley. Reproduced with permission.
Slide 012
Slide 12: All placental mammals are united by a placenta.
(Right-click to download pdf.)

Credits: Graphic by Liz Perotti, U.C. Berkeley. Reproduced with permission.
Slide 013
Slide 13: All mammals are united by several characters, including hair, mammary glands, and a synapsid opening in the skull (synapsids have one opening on the side of the skull behind each eye; diapsids (birds and most "reptiles") have two.
(Right-click to download pdf.)

Credits: Graphic by Liz Perotti, U.C. Berkeley. Reproduced with permission.
Slide 014
Slide 14: All amniotes (all tetrapods except for amphibians) are united by the amnion (a membranous sac which surrounds and protects the embryo).
(Right-click to download pdf.)

Credits: Graphic by Liz Perotti, U.C. Berkeley. Reproduced with permission.
Slide 015
Slide 15: Birds and dinosaurs like Tyrannosaurus rex are united by the shared character of a hole in the hip socket.
(Right-click to download pdf.)

Credits: Graphic by Liz Perotti, U.C. Berkeley. Reproduced with permission.
Slide 016
Slide 16: All tetrapods are united by a four-legged ancestor. Some tetrapods (such as snakes and whales) have lost limbs, but they descended from legged ancestors.
(Right-click to download pdf.)

Credits: Graphic by Liz Perotti, U.C. Berkeley. Reproduced with permission.
Slide 017
Slide 17: Vertebrates with jaws form a related group that excludes jawless fishes such as lampreys.
(Right-click to download pdf.)

Credits: Graphic by Liz Perotti, U.C. Berkeley. Reproduced with permission.
Slide 018
Slide 18: All vertebrates share a vertebral column.
(Right-click to download pdf.)

Credits: Graphic by Liz Perotti, U.C. Berkeley. Reproduced with permission.

Q. I'm sorry, Professor Padian. Matt, if you could go back just a couple of slides. So you talked about how -- and I guess we read from left to right up the line is how you read this?

A. Well, all we can say is this is a depiction of how all these organisms are related. We don't look on this as a ladder of life. We don't look at it as fish give rise to frogs which give rise to birds. It's not like that.

Q. But, for instance, where you have the stirrup-shaped ear bone --

A. Yes.

Q. -- and you have that line, so it would be the organisms above that that share that particular feature?

A. That's correct. That would be something that unites them to the exclusion of all the other critters on the slide. And that's the logic of cladograms, pure and simple.

I'd like to stress that we can use physical features like this, we can use them on fossils or on living animals, we can use them on molecules or we can use them on skeletal features or egg shell proteins or anything else that we want to do. Whatever works, we use. It's very practical.

Q. And is this a -- could you say it's a universal approach used by scientists?

A. Since the 1960s, it has become the dominant form of understanding relationships in the scientific community around the world.

I would go so far as to say that if you were going to apply to the National Science Foundation to ask for money to work on the classification of a group of organisms, whether it was dinosaurs or a group of bacteria or mosses or liverworts, you would have to show the review panel that you understood the principles that I'm discussing here and that you were going to use this kind of analysis in your work if you wanted to convince them that you knew what you were doing.

Q. And is this method somehow validated quantitatively or statistically?

A. Yes. And I'm glad you raised that point, because I've only put a couple of the features on this chart. But, in fact, there are hundreds that are represented in this analysis. And it's obviously too many for us to arrange by hand.

And so all the characters that we're talking about and all the animals that we're trying to analyze, we have ways of putting these into a data matrix and asking the computer essentially to sort this out for us to produce the simplest to the most, basically, complicated trees that you could possibly get. And we try to start with the simplest trees for further work, which is a principle in science called parsimony.

Q. And do intelligent design proponents use this type of cladogram?

A. I haven't seen them use any type of analysis like this in any of their works.



Slide 019
Slide 19: Figure 4-4 from page 99 of Pandas (1993) alleges that the fossil record shows only sudden origin followed by stasis.
(Right-click to download pdf.)

Creationism and the Fossil Record

Q. And if you could advance to the intelligent design slide. Is this a copy of a chart found in Of Pandas and People?

A. Yes. This is Figure 4 from Pandas, second edition.

Q. And can you tell us what this is?

A. Well, the caption says that it's the pattern of phylogenetic origins, according to the face value interpretation of the fossil record.

Q. And can you make heads or tails of this?

A. I have trouble. I'm not sure -- I guess I understand that time is the axis from top to bottom. That's perfectly fine, although there are no particular periods listed. I understand that they're looking at variation in morphology, and that's perfectly fine. But there are no names of organisms there, so I don't know exactly what they're talking about.

Also, the presence of these bars as straight bars without variation suggests quite strongly that organisms suddenly appear quite recognizable as what they are and do not vary in morphology all the way up through the geologic column until they peter out.

Q. So this chart would show that there's abrupt creation and then there's no change in those organisms throughout their lifetimes?

A. That would be the face-value interpretation that they say the fossil record shows. Now, I just want to point out that this implies that there is no substantial change in any fossil lineages because they have drawn only bars that go straight up with no change, no diversification, no anything.

Q. And if you represented a classification system in a grant application to the National Science Foundation like this, you don't believe you would get a grant?

A. Well, no, but, of course, this is not meant to represent any kind of research, it's meant to be a didactic device for teaching. I should also note that if we're talking about phylogeny in relationships, this wouldn't qualify because it doesn't draw any lines between those lines. It doesn't admit the possibility that any of those lines evolved from any of the others.


I. "Irreducible Complexity" and the evolution of major adaptations

Q. I'm going to talk about the use of the term "irreducible complexity" and "adaptational packages" as it's used by intelligent design proponents.

Can you explain to us how Pandas uses the term "adaptational packages"?

A. Well, the last slide showed you lineages of organisms that seem to have a sudden appearance and no substantial change during their histories and of no relationship to any other lineages in this diagram.

This suggests quite strongly, and the Pandas authors are making this point, that organisms that they regard as major types of organisms suddenly appear with all their major features intact and that they do not change. These are characterized in works like Pandas as adaptational packages, which they say cannot be separated into simpler components without destroying the functional advantage that they provide to the organisms that have them.

And so these adaptational packages for ID proponents represent the concept called irreducible complexity, which means that they can't evolve by known natural means, they're too complex to do so, and so they must be specially created by a designer.

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Slide 20: Padian argues that Behe's "irreducible complexity" argument, if not the exact term, is clearly found in both the first (1989) and second (1993) editions of Pandas, and that the fossil record can speak to this argument.
(Right-click to download pdf.)
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Slide 21: Pandas argues that "adaptational packages" have multiple required parts, therefore could not have evolved gradually, and thus must have been intelligently designed (specially created) all at once. This is the same argument as Behe's "irreducible complexity."
(Right-click to download pdf.)
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Slide 22: Behe's claim that the "irreducible complexity" argument applies only at the molecular level is contradicted by Pandas, which applies the argument to whole organs and organisms.
(Right-click to download pdf.)

Q. Now, that term "irreducible complexity," is that one, to your knowledge, that's found in Pandas?

A. To my knowledge, the exact words are not found in Pandas. I believe the first place where that is really brought out as a major term is in Michael Behe's book Darwin's Black Box in 1996. But in 1993, when I believe Professor Behe was working on the second edition of Pandas, these concepts are brought out in the second edition of that text.

Q. So Dr. Behe's concept of irreducible complexity is contained in Pandas even though that term is not used?

A. Yes. And before, even in the first edition, these adaptational packages are represented. They are essentially one of these ideas that, again, has a long pedigree, that there are such complex forms out there they couldn't possibly have evolved. We've heard these arguments since the 1800s, so they do have a long history.

Q. Perhaps you could help explain to us these adaptational packages and irreducible complexity.

A. Well, there seems to be some conflict among the ID proponents about this. Dr. Behe claims that irreducible complexity applies only to cells and molecules, and that's his specialty, of course, he's a biochemist, and that it does not apply to adaptive features in organs or to major groups of organisms.

But if you look at the whole corpus of intelligent design work, including Pandas, on which Dr. Behe worked, the implications of irreducible complexity are extended time and time again to large-scale tissue and organ adaptations and, indeed, to whole organisms.

And so if we're going to accept this, we have to accept that Dr. Behe had no knowledge that his coauthors were going to take his concept above the cell and molecular level, or irreducible complexity is, in fact, not only a molecular concept and we cannot accept Dr. Behe's view on that point.

Q. And have you identified an example to show how this irreducible complexity does apply above the molecular level?

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Slide 23: Examples of Pandas making the IC argument above the molecular level, at the organismal level.
(Right-click to download pdf.)

A. Yes. I'll give a number of them from Pandas just to show that they actually are there. The next slide, I believe, shows several quotations from Pandas that indicate that it applies to levels above simply molecules. A quote from Page 72 indicates that multi-functional adaptations where a single structure or trait achieves two or more functions at once. This is not restricted to the cell level.

A quote from Page 71 talks about, quote, the total engineering requirements of an organism like the giraffe, unquote. So here they are talking about the whole organism, a giraffe, not simply a cell or a molecule.

The quote from Page 66 says, quote, It has not been demonstrated that mutations are able to produce the highly-coordinated parts of novel structures needed again and again by macroevolution.

Now, recall here that macroevolution, to intelligent designers, is the origin of new types of organisms, not of new cells, not of new molecules. So they are really looking at the large-scale structural tissue, organ, individual organism level. And, finally, the quotation from Page 25, which I believe is maybe even repeated more or less on Page 99 --

Q. So that's not an error, that is on Page 25?

A. Oh, yes, it's 25, as well.

Q. And this is from the introduction, overview of the book?

A. Yes, it's from the overview of the book. It says, quote, that design theories suggest that various forms of life began with their distinctive features already intact, fish with fins and scales, birds with feathers, beaks, and wings, et cetera. So they are talking about various forms of life, not molecules, not cells.

And here's an example, just to show you a page from Pandas, that does this with respect not to the giraffe as a whole, I've already showed you how they've dealt with the consummate engineering requirements of the giraffe as a whole, but this is just a set of structures in the giraffe's head, neck, and brain.