Major Cases


Epperson v. Arkansas

In 1968, in Epperson v. Arkansas, the United States Supreme Court invalidated a 1928 Arkansas statute that prohibited the teaching of evolution. The Court held the statute to be an unconstitutional attempt to advance a particular religious viewpoint:
The law's effort was confined to an attempt to blot out a particular theory because of its supposed conflict with the Biblical account, literally read. Plainly, the law is contrary to the mandate of the First, and in violation of the Fourteenth Amendment to the Constitution."
This case established the precedent that a state curriculum could not "be tailored to the principles or prohibitions of any religious sect or dogma." This case brought to an end the enforcement of "Scopes era" laws or the passage of new ones prohibiting the teaching of evolution.



Related Off-Site Material


(Epperson v. Arkansas (1968) 393 U.S. 97, 37 U.S. Law Week 4017, 89 S. Ct. 266, 21 L. Ed 228

McLean v. Arkansas

In 1982, in McLean v. Arkansas Board of Education, a United States federal court held that an Arkansas "balanced treatment" statute violated the Establishment Clause of the U.S. Constitution. The Arkansas statute required public schools to give balanced treatment to "creation-science" and "evolution-science". In a decision that gave a detailed definition of the term "science", the court declared that "creation science" is not, in fact, science. The court also found that the statute did not have a secular purpose, noting that the statute used language peculiar to creationist literature.

The ruling was not technically binding outside the court's district, but the case was considered by the United States Supreme Court in Edwards v. Aguillard, which came to a similar decision.



Related Off-Site Material


(McLean v. Arkansas Board of Education (1982) 529 F. Supp. 1255, 50 U.S. Law Week 2412) Decision by U.S. District Court Judge William R. Overton

Edwards v. Aguillard

In a landmark ruling in 1987 in Edwards v. Aguillard, the U.S. Supreme Court held that the state of Louisiana's "Creationism Act" was unconstitutional. This statute prohibited the teaching of evolution in public schools, except when it was accompanied by instruction in "creation science". The Court found that, by advancing the religious belief that a supernatural being created humankind, which is embraced by the term "creation science," the act impermissibly endorsed a particular religious viewpoint. In addition, the Court found that the provision of a comprehensive science education is undermined when it is forbidden to teach evolution except when creation science is also taught. Some creationists responded to this decision by refashioning "creation science" to avoid any explicit references to the Bible, to God, or to the beliefs of a particular religious sect. This version of creationism re-emerged as part of the "intelligent design" movement in the 1990s.


Related Off-Site Material


Edwards v. Aguillard (1987) 482 U.S. 578

Dean Kenyon affidavit

Talk Origins FAQ on Edwards v. Aguillard

Freiler et al. v. Tangipahoa Parish Board of Education et al.

On April 19, 1994, the school board of Tangipahoa Parish, Louisiana voted to require its teachers to read a "disclaimer" before discussing the subject of evolution. This disclaimer read:

It is hereby recognized by the Tangipahoa Board of Education, that the lesson to be presented, regarding the origin of life and matter, is known as the Scientific Theory of Evolution and should be presented to inform students of the scientific concept and not intended to influence or dissuade the Biblical version of Creation or any other concept.

It is further recognized by the Board of Education that it is the basic right and privilege of each student to form his/her own opinion and maintain beliefs taught by parents on this very important matter of the origin of life and matter. Students are urged to exercise critical thinking and gather all information possible and closely examine each alternative toward forming an opinion.

Three parents of Tangipahoa students filed suit, and on August 8, 1997, District Judge Marcel Livaudais ruled that the disclaimer was unconstitutional. The school board appealed, but a Fifth Circuit appeals panel upheld the district ruling on August 13, 1999 and the circuit denied a petition for rehearing en banc on January 24 of the following year. The Supreme Court declined to review the case on June 19, 2000; Justices Rehnquist, Scalia and Thomas dissented from this decision.

All the legal documentation available to us for this case is provided at the bottom of this page. It is arranged in chronological order.

LeVake v. Independent School District #656

On May 24, 1999, Minnesota Independent School District #656 was sued by one of its science teachers, Rodney LeVake. When LeVake taught high school biology for the 1997-1998 school year without covering the required curriculum sections on evolution, the district had asked LeVake to prepare a position paper on his teaching practices. LeVake stated in this paper that he would only teach evolutionary theory if he could also teach "the difficulties and inconsistencies of the theory." In response, the district reassigned him to a ninth-grade general science course. LeVake sued to recover his prior teaching position, alleging that the reassignment violated his right to free exercise of religion, free speech, due process, and academic freedom. He also sought damages and legal costs, and a declaratory judgment that the district's teaching assignment policy was illegal under the United States and Minnesota Constitutions.

On June 28, 2000, District Court Judge Bernard E. Borene ruled against LeVake on all counts. LeVake appealed at all levels, but a Minnesota Court of Appeals panel upheld Judge Borene's ruling on May 8, 2001. The Minnesota Supreme Court refused to review LeVake's case on July 24, and the United States Supreme Court followed suit on January 27, 2002.

Key legal documents for this case are provided at the bottom of this page. They are arranged in chronological order.



Related NCSE Articles


RNCSE: A New Tactic for Getting "Creation Science" Into Classrooms?

RNCSE: Minnesota Teacher Sues District Over Evolution

News: Rodney LeVake Appeals

News: LeVake "Arguments Against Evolution" Case Fails

RNCSE: Rodney LeVake Loses Appeal

News: Rodney LeVake Appeals to Supreme Court

News: LeVake Case Denied by Supreme Court

Peloza v. Capistrano USD

In September of 1991, a biology teacher named John E. Peloza sued the Capistrano Unified School District (Orange County, California) for forcing him to teach evolution as scientific fact, and for prohibited him from discussing his religious beliefs with students during instructional time. Represented by the Rutherford Institute, Peloza claimed that these policies, and an alleged conspiracy among his administrators and fellow teachers to harass and defame him, violated his freedom of speech, freedom of religion, and rights to due process and equal protection. As part of his case, he argued that "evolutionism" was part of the "religion of secular humanism."

On January 17, 1992, District Judge David Williams dismissed the entirety of Peloza's claims. The court later determined that Peloza's complaint was "frivolous and unreasonable and was filed without adequately researching the subject," and accordingly ordered Peloza to pay the district's legal fees. The Court of Appeals for the Ninth Circuit reversed the latter decision, finding that Peloza's claim was "not entirely frivolous." However, the appeals court affirmed the district court's dismissal of his claims. Upon further appeal, the United States Supreme Court declined to review the case.

Key legal documents for this case are provided below. They are arranged in chronological order.

Segraves et al. v. State of California et al.

(Full Title: Kasey Segraves, Jason Segraves and Kevin Segraves, minors under 14 years of age, by their Guardian ad litem, Kelly Segraves, William Dannemeyer, Michael D. Antonovich, Eugene N. Ragle and Creation Science Research Center, Plaintiffs,
vs.
State of California, Board of Education of the State of California, Department of Education of the State of California, Department of General Services, Wilson Riles, Kenneth Cory, Jessie Unruh and DOES 1 through 50, inclusive, Defendants.
)

On January 19, 1979, Kelly Segraves sued the State of California on behalf of his three children. Segraves, cofounder and then-director of the Creation-Science Research Center, argued that his family's right to free exercise of religion was violated by the discussion of evolution in their public school.

On March 6, 1981, Superior Court Judge Irving Perluss ruled that the teaching of evolution did not violate the Segraves' rights, but that the State Board of Education's 1972 anti-dogmatism teaching policy should be provided to all organizations, institutions and persons receiving a copy of the science curriculum framework.

All the legal documentation available to us for this case is provided at the bottom of this page. It is arranged in chronological order.



Related NCSE Articles


Creation/Evolution Journal: New Creationist Bills, Resolutions, and Court Cases Appear Nationwide

Creation/Evolution Journal: News Briefs

Selman v. Cobb County: The Textbook Disclaimer Case

Summary of the case

In March 2002, the Cobb County School District in Georgia voted to insert the label below on the inside front cover of biology and other science textbooks.


  • In November 2004, Jeffrey Selman and 3 other parents brought suit against the school district on constitutional grounds.
  • In January 2005, Federal District Court Judge Clarence Cooper ruled that the disclaimers are unconstitutional.
  • In April, Cobb County School District filed an Appeals brief with 11th Circuit Court of Appeals
  • In June 2005, Selman et al. filed a brief with 11th Circuit Court of Appeals
  • In June 2005, NCSE submitted an amicus brief along with 7 others urging the Appeals Court to uphold the District Court ruling.
  • In December 2005, a 3-judge panel heard oral argument in the appeal
  • In May 2006, the Appeals Court remanded the case to the district court for clarification of the evidentiary record.
  • On December 19, 2006, the lawsuit reached a settlement; the Cobb County School District agreed not to disclaim or denigrate evolution either orally or in written form.

All the legal documentation available to us for this case is provided at the bottom of this page. It is arranged in chronological order.

For key documents and articles associated with each phase of the case, please see the following pages:

Initial Trial

Appeal

Retrial and Settlement


Related Off-Site Material


Kenneth Miller, writing in the Boston Globe: Remove stickers, open minds

Nick Matzke, at The Panda's Thumb: History and Cobb County

Webster et al. v. New Lenox School District et al.

(Full title: Ray Webster and Matthew Dunne, by and through his parents and next best friends, Philip and Helen Dunne, Plaintiffs, v. New Lenox School District No. 122 and Alex M. Martino, and as Superintendent of New Lenox School District No. 122, Defendants)

In 1987, Ray Webster and Matthew Dunne sued the New Lenox School District of Illinois, as well as Alex Martino, the district superintendent. Webster was a junior high school social studies teacher in that district, and Dunne was one of his students. After complaints about proselytizing in his class, Webster had been advised by the district to refrain from religious advocacy in his teaching, and in particular to refrain from teaching creation science. In the suit, Webster argued that he had a first amendment right to determine his own teaching curriculum, and that it was necessary to teach creation science in order to balance pro-evolution statements in the social studies textbook. Dunne, for his part, argued that he had the right as a student to hear about creation science in school.

On May 25, 1989, US District Judge George Marovich dismissed their complaint, ruling that Webster could not teach creation science without violating the first amendment, and that the district had a right to require Webster to teach within its established curriculum framework. Marovich also ruled that Dunne's desires to learn about creation science in school were outweighed by the district's interest in avoiding the violation of the estalishment clause or other students' first amendment rights. Webster appealed, but on November 6, 1990, the Seventh Circuit Court of Appeals upheld the district court decision.

All the legal documentation available to us for this case is provided at the bottom of this page. It is arranged in chronological order.

Kitzmiller v. Dover: Intelligent Design on Trial

en español

In the legal case Kitzmiller v. Dover, tried in 2005 in a Harrisburg, PA, Federal District Court, "intelligent design" was found to be a form of creationism, and therefore, unconstitutional to teach in American public schools.

As the first case to test a school district policy requiring the teaching of "intelligent design," the trial attracted national and international attention. Both plaintiffs and defendants in the case presented expert testimony over six weeks from September 26 through November 4, 2005). On December 20, 2005, Judge John E. Jones issued a sharply-worded ruling in which he held that "intelligent design" was, as the plaintiffs argued, a form of creationism.

NCSE served as a pro bono consultant for the plaintiffs and assisted the legal team in choosing and preparing expert witnesses and in helping the lawyers deal with the scientific and technical material. A special issue of the Reports of the National Center for Science Education, (vol. 26, no. 1-2), covers several aspects of the Kitzmiller case. This article by former NCSE staff member Nicholas J. Matzke describes NCSE's role in the Kitzmiller case.

As the first trial over "intelligent design," the case received national media attention and has since been the subject of several books.

NCSE provides access to the public legal documents in this case, articles by participants, podcasts, and more.

Highlights from the Kitzmiller Case

Kitzmiller v. Dover Timeline

  • June 2004

    Dover Area School District (DASD) begins the process of selecting biology textbook. The town of Dover (population 1800) is located near York, Pennsylvania in the south-central part of the state. The DASD serves about 40,000 residents. Dover Senior High School has about 1000 students.

  • August 2, 2004
    After acrimonious debate, DASD school board votes 5-3 to select the widely used textbook Biology: The Living Science, by Kenneth Miller and Joseph Levine, as recommended by science teachers.
  • October 2004
    50-60 copies of the "intelligent design book" Of Pandas and People donated anonymously to DASD
  • October 18, 2004
    By a 6-3 vote, DASD school board passes first segment of its “intelligent design” curriculum policy. Two school board members resign in protest.
  • November 19, 2004
    DASD issues press release explaining how policy is to be implemented.
  • December 14, 2004
    11 Dover parents filed suit in Federal District Court against the DASD on the grounds that these policies violate the First Amendment. They were represented by the Pennsylvania ACLU, Americans United, and Pepper Hamilton LLP. Initial Complaint (pdf)
  • January 2, 2005
    Defense files answer to complaint
  • January 2005
    DASD Letter to Parents regarding the Biology curriculum
  • February 2005
    DASD Biology Update Newsletter
  • Expert witnesses announced and statements filed

  • May 23, 2005
    Foundation for Thought and Ethics (FTE) files “application to intervene.”
  • August 8, 2005
    Plaintiffs file for summary judgment
  • September, 13 2005
    Judge denies plaintiff's motion for summary judgment, sending the suit to trial.
  • September 26, 2005
    Bench trial before Judge John E. Jones begins in United States Federal District Court in Harrisburg, PA.
  • November 4, 2005
    Closing arguments given and trial concludes
  • December 20, 2005
    Judge Jones issues 139 page opinion finding that the DASD "intelligent design" policy violates the United States Constitution because "intelligent design" fundamentally represents a religious belief.
  • February 21, 2006
    DASD votes to pay more than $1 million toward legal fees incurred in course of the trial.

Expert Witnesses

Background

In a trial involving expert witnesses, a series of events occur according to an agreed upon schedule. In Kitzmiller, each side named six expert witnesses on March 1, 2005. On April 1, expert reports were produced by each expert. Rebuttal experts were then named, and rebuttal expert reports, if any, were filed on May 15. Depositions were scheduled between May and August.

The purpose of an expert report is to disclose the opinions of the expert, and the evidence upon which he or she will rely. This report is used by opposing counsel for preparation for depositions and trial testimony. At trial, experts are qualified to testify only about their specific topics of expertise, and their testimony is supposed to be restricted to the approximate content of the expert report.

Expert witnesses for Plaintiffs

Barbara Forrest, PhD
Professor of Philosophy, Southeastern Louisiana University
Expert on the ID movement's goals and history
Expert Report: 2005-04-01
Supplemental Report: 2005-07-29. Appendix A to Forrest's report, showing direct text parallels between "intelligent design" and "creationist" drafts of Pandas.

John F. Haught, PhD
Theology Professor, Georgetown University
Theology/religion expert
Expert Report: 2005-04-01

Kenneth R. Miller, PhD
Professor of Biology, Brown University
Biology expert
Expert Report: 2005-03-30

Brian Alters, PhD
Associate Professor of Education, McGill University
Education/pedagogy expert
Expert Report: 2005-03-30

Kevin Padian, PhD
Professor of Integrative Biology, University of California, Berkeley
Curator, Museum of Paleontology, University of California, Berkeley
Paleontology/evolution expert
Expert Report: 2005-03-30

Robert Pennock, PhD
Associate Professor of Science and Technology Studies and Associate Professor of Philosophy, Michigan State University
Philosophy of science expert
Expert Report: 2005-03-31

Rebuttal expert for Plaintiffs

(Rebuttal experts are named after the initial set of expert reports are filed)
Jeffrey Shallit, PhD (deposed, but did not testify at trial due to Dembski's withdrawal)
Professor of Computer Science, University of Waterloo, Ontario
Rebuttal of Dembski: 2005-05-16

Expert witnesses for Defendants

Michael Behe, PhD
Professor of Biochemistry, Lehigh University
DI fellow, biochemistry/intelligent design expert
Expert Report: 2005-03-24
Rebuttal of Miller: 2005-05-15
Rebuttal of Padian: 2005-05-15

John Angus Campbell (withdrew before deposition)
Professor, Department of Communication, University of Memphis
DI fellow, education/rhetoric of science
Expert Report: 2005-03-29

Dick M. Carpenter II, PhD (deposed, but did not testify at trial)
Assistant Professor of Educational Leadership, University of Colorado
Defense education expert, Focus on the Family guest
Expert Report: 2005-3-24
Rebuttal of Alters and Padian: 2005-5-16

William Dembski (withdrew before deposition)
Associate Research Professor, Baylor University (at time of report)
DI fellow, biochemistry/intelligent design expert
Dembski has posted his withdrawn expert and rebuttal reports on his website
Rebuttal of five of the first six plaintiff experts (all but Alters): 2005-05-14

Scott Minnich, PhD
Associate Professor of Microbiology, University of Idaho
DI fellow, microbiology/intelligent design expert
Expert Report: 2005-03-31

Warren A. Nord, PhD (deposed, but did not testify at trial)
Director, Program in the Humanities and Human Values, University of North Carolina, Chapel Hill
Lecturer in Philosophy, University of North Carolina, Chapel Hill
religion/education expert
Expert Report: 2005-03-29

Rebuttal experts for Defendants

(Rebuttal experts are named after the initial set of expert reports are filed)
Steve Fuller, PhD
Professor of Sociology, University of Warwick
Rebuttal of first six plaintiff experts: 2005-05-13

Stephen Meyer (withdrew before deposition)
Director, Discovery Institute Center for Science and Culture (the "intelligent design" program at Discovery Institute)
Rebuttal of Pennock, Forrest, Alters and Padian: 2005-05-16

Notes

1. Barbara Forrest filed a supplemental expert report analyzing documents produced in a subpoena to the Foundation for Thought and Ethics, including unpublished creationist drafts of the "intelligent design" textbook Of Pandas and People.

2. During the trial in October 2005, the Discovery Institute attempted to include Meyer's expert report in a Discovery Institute amicus brief filed with the court. Because Meyer had been withdrawn from the case and his testimony would therefore not be subject to cross-examination, the judge ordered that the amicus brief be stricken. The Discovery Institute then submitted a second amicus which does not include Meyer's expert report.

Kitzmiller Trial Transcripts

Below are links to complete transcripts of testimony at the Kitzmiller v. Dover trial.

Day

Date

Witnesses

Transcripts

Day 1

9/26/05

AM: Opening statements, Kenneth Miller
PM: Kenneth Miller
Day 1 AM (174k PDF)
Day 1 PM (222k PDF)
Day 2 9/27/05 AM: Ken Miller, Tammy Kitzmiller
PM: Aralene "Barrie" Callahan, Bryan Rehm
Day 2 AM (188k PDF)
Day 2 PM (227k PDF)
Day 3 9/28/05 AM: Robert Pennock
PM: Robert Pennock, Christy Rehm, Beth Eveland

Day 3 AM (157k PDF)
Day 3 PM (218k PDF)

Day 4 9/29/05 AM: Carol "Casey" Brown
PM: Carol "Casey" Brown, Jeffrey Brown, Frederick Callahan
Day 4 AM (116k PDF)
Day 4 PM (312k PDF)
Day 5 9/30/05 No morning session
PM: John Haught

Day 5 PM (197k PDF)

Day 6 10/5/05 AM: Barbara Forrest
PM: Barbara Forrest
Day 6 AM (174k PDF)
Day 6 PM (276k PDF)
Day 7 10/6/05 AM: Barbara Forrest, Jennifer Miller
PM: Jennifer Miller, Bertha Spahr
Day 7 AM (328k PDF)
Day 7 PM (234k PDF)
Day 8 10/8/05 AM: Bertha Spahr, Brian Alters
PM: Brian Alters, Cnythia Sneath, Steven Stough
Day 8 AM (173k PDF)
Day 8 PM (312k PDF)
Day 9 10/14/05 AM: Steven Stough, Kevin Padian
PM: Kevin Padian, Joel Leib
Day 9 AM (288k PDF)
Day 9 PM (187k PDF)
Day 10 10/17/05 Defense Begins

AM: Michael Behe
PM: Michael Behe

Day 10 AM (245k PDF)
Day 10 PM (149k PDF)

Day 11 10/18/2005 AM: Michael Behe
PM: Michael Behe
Day 11 AM (259k PDF)
Day 11 PM (189k PDF)
Day 12 10/19/05 AM: Michael Behe
PM: Michael Behe
Day 12 AM (234k PDF)
Day 12 PM (133k PDF)
Day 13 10/20/05 No morning session
PM: Richard Nilsen

Day 13 PM (217k PDF)
Day 14 10/21/05 AM: Richard Nilsen
PM: Richard Nilsen, Michael Baksa
Day 14 AM (245k PDF)
Day 14 PM (201k PDF)
Day 15 10/24/05 AM: Steve William Fuller
PM: Steve William Fuller
Day 15 AM (268k PDF)
Day 15 PM (228k PDF)
Day 16 10/27/05 AM: William "Bill" Buckingham
PM: William "Bill" Buckingham, Heather Bernhard-Bubb
Day 16 AM (164k PDF)
Day 16 PM (287k PDF)
Day 17 10/28/05 AM: Heather Bernhard-Bubb, Joseph Maldonado
PM: Heather Geesey, Michael Baksa
Day 17 AM & PM (354k PDF)
Day 18 10/31/05 AM: Alan Bonsell
PM: Alan Bonsell
Day 18 AM (167k PDF)
Day 18 PM (196k PDF)
Day 19 11/2/05 AM: Alan Bonsell
PM: Sheila Harkins, Michael Baksa
Day 19 AM (309k PDF)
Day 19 PM (280k PDF)
Day 20 11/3/05 AM: Michael Baksa
PM: Scott Minnich
Day 20 AM (136k PDF)
Day 20 PM (190k PDF)
Day 21 11/4/05 AM: Scott Minnich
PM: Closing arguments
Day 21 AM (298k PDF)
Day 21 PM (228k PDF)


The "Pandas" Drafts

An excerpt from Nicholas Matzke's article Design on Trial: How NCSE Helped Win the Kitzmiller Case. Reports of the National Center for Science Education 26(1-2), 37-44.

(Some HTML links have been added, otherwise the text is original.)

Barbara Forrest was the expert who would have to make the connection between the ID movement and creationism. She had, of course, coauthored Creationism's Trojan Horse, which discussed the origins and history of the Discovery Institute, the "Wedge document", and the leaders of the ID movement. However, the Discovery Institute only established the Center for the Renewal of Science and Culture in 1996. Of Pandas and People, which is the first book to use the terms "intelligent design" and "design proponents" systematically, and which presents all of the modern ID arguments, was published in 1989. The creationist origin of Pandas and the "intelligent design" phraseology was not covered in detail in previous works on the history of ID, so my job was to dig up everything we could possibly find on the origin of Pandas and "intelligent design". The NCSE archives contain several files on Pandas and on the publisher of the book, the Foundation for Thought and Ethics (FTE).

Links to Dr. Forrest's testimony on the Pandas drafts, and further discoveries made after the trial, are provided below.

Forrest's Testimony: "Creationism" and "ID"

Here are the now-famous word-count charts used by Barbara Forrest in her testimony in Kitzmiller v. Dover. These charts showed that the words "creation" and "creationist" were systematically changed to "intelligent design" and "design proponent" in the drafts for the book Of Pandas and People, in the aftermath of the 1987 Supreme Court case Edwards v. Aguillard .

Click the images for an enlarged view:

[img_assist|nid=110|title="Creation" to "Design"|desc=|link=popup|align=left|width=0|height=]

[img_assist|nid=112|title="Creationis_" to "Intelligent Design"|desc=|link=popup|align=right|width=0|height=]


Please note: These images may be freely used for nonprofit educational use as long as the source page is cited.

The exhibits that accompanied Dr. Forrest's testimony are available below.

"Cdesign Proponentsists"

For years, "intelligent design" (ID) proponents denied that ID is just a new label for creationism. However, it is now well-known that the first intelligent design "textbook," Of Pandas and People, is just a revised version of a classic "two-model' creationism vs. evolution book named Creation Biology. As Barbara Forrest showed during her testimony in Kitzmiller v. Dover, Pandas was remade into an intelligent design textbook in 1987, in a few months after the Supreme Court ruling against creation science in Edwards v. Aguillard came down.

The most striking example of the transition was discovered by Dr. Forrest as she compared the drafts of Creation Biology and Of Pandas and People. Not only had "creationism" and "creationist" literally been replaced, apparently via a word processor, with "intelligent design" and "design proponent" in passages that were otherwise unchanged, but she even found a transitional form between the two labels!

Scanned images of this passage, in its various versions, are shown below.


Creation Biology (1983), p. 3-34:



Biology and Creation (1986), p. 3-33:



Biology and Origins (1987), p. 3-38:



Of Pandas and People (1987, creationist version), p. 3-40:



Of Pandas and People (1987, “intelligent design” version), p. 3-41:


Padian's Expert Testimony

Kevin Padian's testimony and slides in the Kitzmiller case

The expert witness testimony given by paleontologist Kevin Padian was a highlight of the Kitzmiller v. Dover trial. His testimony and the slides he showed to the court are now available here, via the links at the bottom of his page.

Padian's testimony was cited several times in the court's legal decision (PDF) in the case. For example, "A series of arguments against evolutionary theory found in Pandas involve paleontology, which studies the life of the past and the fossil record. Plaintiffs' expert Professor Padian was the only testifying expert witness with any expertise in paleontology. His testimony therefore remains unrebutted. Dr. Padian's demonstrative slides, prepared on the basis of peer-reviewing scientific literature, illustrate how Pandas systematically distorts and misrepresents established, important evolutionary principles." The judge also noted that "Padian bluntly and effectively stated that in confusing students about science generally and evolution in particular, the disclaimer makes students 'stupid.'"

Author Edward Humes wrote in his book about the Kitzmiller trial, Monkey Girl (Ecco 2007), "Kevin Padian, Berkeley paleontologist and curator of his university's Museum of Paleontology, entertainingly brought the bone hunter's perspective to the courtroom, the sort of character on whom the fossil-hunting hero of the film Jurassic Park was based. Padian happily showed slides of his 'critters,' as he tended to call the ancient fossils and bones he used as a window on the past. ... Padian, with evident fierce joy, debunked the often repeated claim that the absence of 'transitional fossils' was a problem for evolution and an argument for creation or intelligent design."

Padian is Professor in the Department of Integrative Biology at the University of California, Berkeley, Curator of Paleontology at the University of California Museum of Paleontology, and president of NCSE's board of directors.

(Transcript prepared for web publication by Nicholas Matzke and other NCSE staff.)

Cross Examination

Cross Examination

CROSS EXAMINATION BY MR. MUISE:

Q. Good afternoon, Dr. Padian.

A. Mr. Muise.

Q. Sir, you just testified that you believe that this reading of this one-minute statement will clearly cause a great division in students?

A. Did I say those words exactly?

Q. I believe it was --

A. Something to that effect?

Q. -- something to that effect, is that correct?

A. Well, I don't know without looking at the transcript or what my exact words were.

Q. Is it similar to those words?

A. I think what I would say is it would cause great confusion among students.

Q. You've never interviewed any students, is that correct?

A. I've talked to my own students. I have not talked to Dover students.

Q. None of the students who may have heard this statement?

A. Not the students that may have heard that statement.

Q. But it's your opinion that this would cause students to ask questions such as what good is prayer?

A. Yes.

Q. And why is there suffering?

A. Yes.

Q. From reading this one-minute statement?

A. Yes.

Q. And that's your expert opinion?

A. Well, it has a lot to do with it.

Q. Sir, you're not a microbiologist, correct?

A. No, sir.

Q. You're not an expert probability theory?

A. No, sir.

Q. As a paleontologist is it accurate to say that what you are doing is essentially reconstructing the life of the past by accumulating data concerning patterns and then trying to infer processes that account for the change of life through time? Would that be an accurate description?

A. That's a reasonably good statement.

Q. It's reasonably based on comparative evidence, is that correct?

A. Yes, sir.

Q. For example, you know what the function of the feathers of different shapes are in birds today, and you would look at those same structures in fossils animal and then infer that they were used for a similar purpose in the fossil animal? Is that the sort of reasoning you apply?

A. They might be, yes. That would be one line of evidence. There may be others.

Q. But that's the sort of reasoning that you apply as a paleontologist?

A. That's part of it, yes.

Q. And you heard a lot about feathers in hair-like features. With the case of hair-like feathers that cover the body or the whole body of fossils, you infer that they are de facto insulation, correct?

A. Yes.

Q. And they would have to be insulation because they wouldn't simply exist on the body and not have something to do with warming or cooling, is that fair?

A. And this is because they trap air.

Q. And you conclude that they're used for insulation based on what we know about hair and feathers today, correct?

A. Yes.

Q. And that's scientific reasoning?

A. That's part of it, unless we have evidence to the contrary from some other source.

Q. So paleontologists make reasoned inferences based on the comparative evidence? Is that correct?

A. We do our best.

Q. But not all reasoned inferences made by paleontologists are correct?

A. I certainly wouldn't claim that.

Q. For example, your dissertation advisor John Ostrom at one point reasoned that there was an intermediate state for the first wing used for flying and, that stage involved the use of these wing-like features to chase down insects, and he called it the insect hypothesis, correct?

A. He suggested that as a hypothesis, that's correct.

Q. And that was based on his reasoned inference from the evidence?

A. Yes.

Q. Now, a few scientists had another reasoned inference based on that same evidence, correct?

A. Yeah.

Q. And that involved moving the prey catching function from the hands to the mouth and then they're relying on these wing-like features for balance and lift, is that correct?

A. Yes.

Q. So that seemed to work better, correct?

A. Yes, it surmounted a problem of balance.

Q. So you had scientists looking at the same evidence and drawing different reasoned conclusions?

A. Sequentially.

Q. Is the approach to paleontology similar to how scientists consider the structural similarity in embryology?

A. In what sense?

Q. The same sort of reasoned inferences from structural similarities.

A. Yes, with the difference that we can observe how individual embryos develop, but it's really hard to do that with fossils because you have a single specimen which is at one stage of death, and whereas in embryos of living animals we can do a lot of comparative work.

Q. The sort of comparative work that was done with the Haeckel embryos, are you familiar with the Haeckel embryos?

A. Somewhat. It's not exactly my field of the specialization history of science. I have a little familiarity with the case, yes.

Q. And those were drawings that had appeared in biology textbooks for many years?

A. Some versions of those drawings appeared in biology texts for many years, yes.

Q. And they were subsequently determined to be fraudulent, is that correct?

A. I don't know if I'd use the word fraudulent. I would say that they were certainly inaccurate. It's not clear to me that Haeckel intended to show anything fraudulently, but as with the situation of the insect wing or the insect net hypothesis, when we get more evidence we get better answers, and John Ostrom as soon as he heard the insect net hypothesis was, actually had a big problem with it surmounted by these guys in Arizona who very cleverly postulated what would happen with the upset of balance. He said the insect net hypothesis is dead. It did its job. And in the same way, when we get better drawings of embryos, if we know about them we'll try to use them.

Q. Now, with regard to those embryos, is it your understanding they were fudged in some respect? Because you said you don't want to use the word fraudulent because --

A. Yeah, I don't know the details, Mr. Muise. I'm not an embryologist.

Q. Thank you.

A. I haven't studied those, I'm sorry.

Q. Sir, Darwin was not the first to propose the concept of evolution, correct?

A. Correct.

Q. And I want to be clear on this. When we're using the term evolution in this sense, we're talking about changes over time. Life as changed over time. Is that accurate?

A. That's part of it. There's also in there common ancestry of all organisms, which is a separate consideration of evolution that comes and goes, yes.

Q. When we generally use the term evolution, you're saying common ancestry is similar to the general term of evolution?

A. Change through time is a good one for a general explanation of evolution to be more specific. Other individuals, including Darwin, have a more precise or different definition. Darwin's I believe for example is descent with modification.

Q. And that would be a reference to change over time?

A. Yes, sure.

Q. And I believe you testified he was preceded by others I believe it was by as much as two centuries?

A. Yes. Locke, Buffon, many of the previous, Lamarck had a theory of evolution very different from his.

Q. But Darwin's evidence though persuaded people to accept evolution as an explanation for the diversification of life, is that correct?

A. It was, even though as noted before his book was about natural selection.

Q. And I believe as you have noted before, he used artificial selection as an analogy for natural selection, correct?

A. Yes, I did. Yes.

Q. And artificial selection is what for example a dog breeder would use to breed a variation of a particular dog, correct?

A. That's correct.

Q. So when Darwin was writing he was not talking about how major new adaptive changes took place. He was talking about how minor variations could be selected upon by natural forces, correct?

A. Because he wanted to get people to accept the baby steps, and then he would let the bigger ones take care of themselves.

Q. Right. You used that term baby steps in your report as well. That's what Darwin was taking about?

A. Relatively speaking, yes.

Q. And I believe you stated that he made only passing reference as to how new major adaptive types might emerge, is that correct?

A. That's correct.

Q. So Darwin's main concern in his writing was with the mechanism of natural selection?

A. That was what his book was about, that first book.

Q. Now, this mechanism of natural selection, isn't it true that it cannot be observed directly in the fossil record?

A. As I mentioned when Mr. Walczak asked me, there are two ways to look at natural selection. Darwin's view of looking at individuals replacing individuals in populations is at one level, but natural selection also figures very importantly in the evolution of adaptations, and if you know that the cause of adaptation is natural selection, which by definition it is, then you can watch adaptations emerging in the fossil record, then scientist would conclude from this that they are looking at natural selection doing this, and the way we tell it's natural selection rather than something that's random is that we're looking at functional improvement, the change of functions from one thing to the other with the emergence of new types of organisms and organs.

Q. Do you remember in your report you wrote a statement, "His main concern," referring to Darwin, "however was with a mechanism of natural selection, which cannot be observed directly in the fossil record."

A. In his sense, yes. But as of looking at individuals and telling this fossil clam was more fit than that fossil claim or how many offspring it left.

Q. Are you saying in his sense of natural selection that you can't observe that directly in the fossil record?

A. In his sense of natural selection it's very difficult.

Q. And I want to see if I'm following what your argument is. Is it the use of the demonstration of adaptation as a proxy for natural selection that you claim that you can observe it in the fossil record, is that correct?

A. Rather than a proxy I would say it's an effect of natural selection.

Q. I'm sorry, I didn't hear --

A. It's an effect of natural selection at the individual level, exactly what Darwin was talking about, but rather than seeing it at the individual level, we're seeing its effects in the wholesale transformation of lineages over time.

Q. Now, is it that these effects, what you're concluding, are the result of natural selection?

A. That is the standard interpretation of evolutionary biologists, because adaptation is defined as being produced by natural selection.

Q. Now, you're familiar with, I'm not sure if it's a term or a concept, of punctuated equilibrium?

A. Yes, sir.

Q. And did that pose a significant challenge to the theory of evolution?

A. No.

Q. Or did it not challenge the notion, which was the prevailing notion, that the pattern of evolution is slow and yet gradual?

A. That's an interesting question. When Darwin uses the word gradual, and we all accept that Darwin accepted gradual evolution, we have to remember that words meant different things in Darwin's time than they do today. The meanings of words have changed. So for example when Darwin was on the Beagle, fresh out of Cambridge, and he's traveling around the world for five years, and he goes to Chile in the course of collecting specimens on some of the days that he's off the boat, and he gets up in the mountains and he's around Concepcion, and at that time there's a violent earthquake that shakes the whole coastline.

It throws buildings down, ruins the city, hundreds of people are dead. The coastline is jacked up about twenty feet in some places, leaving putrefying sea creatures clinging to the rocks, Darwin in his journal describes this as a gradual change. If you told anyone in California that earthquakes are gradual, they'd think you ought to be taken out and shot. But in that, gradual means step-like, and when Darwin was talking about gradual change, he meant equally step-like as well as proceeding slowly and steadily.

So it's very difficult sometimes to interpret Darwin just by reading him through today's lenses. Punctuated equilibrium is I think you're exactly right, is a different idea than there is really tiny, tiny, tiny changes that are constantly, constantly, constantly, constantly changing like this, but it amounts to the same thing, because punctuated equilibrium is a statement about how morphology in a lineage changes through time, and the empirical evidence that Niles Eldredge and Steve Gould, who proposed this in 1972, they proposed that for most of the time in the fossil record of each species, that is individuals of a particular species, not whole groups of marsupials or whole groups of whales, are going to remain static.

Rather, that within an individual lineage alone that there's not going to be this, that is gradual change toward from one point to point

A in a very slow and stately fashion, but rather that it's going to be pretty much business as usual, and then a fairly rapid change to another form that then becomes progressively more stable, and in the intervening years this indeed has been confirmed by a number of paleontological studies.

Q. I'll let you take a look at this for reference if you'd like. In your deposition you said, "Punctuated equilibrium challenge that notion that the prevailing pattern of evolution is slow and gradual. That's a huge challenge. It was regarded as such. In fact, it was regarded as a greater challenge than his proponent suggested."

A. That's right. It was regarded this way not because it challenged the paleontologists, they were happy with it, and one of the interesting things that Eldredge and Gould did when they proposed this is that they didn't say to the population biologists and the speciation biologists, they didn't say, you know, guys, look, you got the completely wrong model here. You've been thinking about this slow steady thing.

Instead what they said was we've been paying attention to the wrong model in evolution because Ernst Mayr in the 1940's and 50's proposed that actually probably what's happening is you have a whole big species range, and then there's this little population on the fringe in which evolution can evolve very -- I'm sorry, in which genes and the genetic constitution can evolve much more likely than it can through the whole range of population, and that here evolution may be very fast.

This may be where the new species comes in, and Eldredge and Gould said maybe now it's just coming back and taking over the ancestral range. They thought that the evolutionary biologist would be happy with this, the people that worked at the population levels and studied speciation. Instead they were apoplectic. They really didn't think that this was a mechanism. They just never had studied stasis before because, you know, if you are going to write a grant for research to study evolution, you say I want to study how things don't change, they'd think you were nuts.

And so no one had really looked at it this way. So they turned the whole study on its head, and that's pretty much how it led to decades of inquiry by different kinds of scientists about it, and we're still talking about what is making these populations states of static through time. It's a great, great question.

Q. So again just following up on this punctuated equilibrium question, and I think this is how you referenced it in your deposition, you said, "Basically scientists don't know whether it applies to 90 percent of the cases or 40 cases of the cases," but in either case whether you have a punctuated pattern or a gradual pattern you surmise that selection could still be working within those patterns," is that --

A. Yes.

Q. Basically summarizing what you had just described?

A. Selection is not excluded from working at any of those levels. It's just all this is a statement about what we'd say is morphology through time really.

Q. And again you cannot observe the selective process in the fossil record, you observe what you believe to be its effects in that first selection?

A. And in the case of punctuation --

Q. Is that yes? I'm not sure --

A. Yes, I'm sorry, it is a yes, but in the case of punctuation where morphology is static, population biologists, population geneticists have said that the reason that these morphologies stay stable in time is exactly because of selection, and the term they use is a certain kind of selection which is called stabilizing selection. It's a form of natural selection that weeds out the extremes that are produced in a population and canalizes the middle. So as far as population biologists were concerned, and it surprised me, they felt that they could see population processes, individual and individual, in these fossil sequences. Now, whether that's the case is not for me so say.

Q. Is natural selection responsible for punctuated equilibrium?

A. That's a great question. We're not really sure what happens in the transition, and as I said even in keeping a morphology static, that can be a kind of selection that we know very well from populations occurring today.

MR. MUISE: This may be a good time to take a break, Your Honor.

THE COURT: All right, then why don't we do that. We'll break for fifteen minutes, take our afternoon recess, and we'll return with continued cross examination by Mr. Muise after that.

(Recess taken at 2:33 p.m. Trial proceedings resumed at 2:55 p.m.)



Cross Examination (continued)

THE COURT: Be seated, please. All right, Mr. Muise, we continue with cross examination.

MR. MUISE: Thank you, Your Honor.

THE COURT: Mr. Gillen has returned.

MR. GILLEN: My pleasure, Your Honor. There's just not enough of me to go around.

THE COURT: Don't lie to me, Mr. Gillen.

(Laughter in courtroom.)

CONTINUED CROSS BY MR. MUISE:

Q. Dr. Padian, you testified on direct about the Cambrian explosion, correct?

A. Yes.

Q. I want to ask you if you think this is an accurate statement. "It is this relatively abrupt appearance of living phyla that has been dubbed the Cambrian explosion."

A. Yes.

Q. Do you know where that statement is from?

A. No. It's a reasonable one.

Q. I can represent to you, and you can check as well, it's from the article that you cited on your direct testimony by Mr. James Valentine.

A. Valentine.

Q. Entitled Fossils, Molecules, and Embryos: New Perspectives on the Cambrian Explosion.

A. Okay.

Q. So other scientists use the term "abrupt appearance" in different context, correct?

A. Other scientists use the term "abrupt appearance" in different context?

Q. Well, there's been a lot of testimony so far, and you as well, referring to the use of the term "abrupt appearance" in Pandas, and I'm just -- I mean, you acknowledge that abrupt appearance appears if the literature in other contexts?

A. Oh, may I say it means two different things?

Q. I believe you just said it.

A. That abrupt appearance means two different things? Yes. One thing to scientists and another thing to intelligent design proponents.

Q. Let me ask you this. This was I'll represent to you a statement by Stephen Gould found in Natural History. It says, "The fossil record, with its abrupt transitions, offers no support for gradual change. All paleontologists know that the fossil record contains precious little in the way of intermediate forms. Transitions between major groups are characteristically abrupt." Do you believe that, do you agree with that statement?

A. I think that Steve is talking about two different things. So I would say I would agree with his overall statement in context with that article, which I think it comes from a 1980 paper? Am I right about that?

Q. 1986, correct?

A. 86, okay, yes.

Q. I'm sorry. June/July 1977?

A. 77, okay. This is in Paloeobiology?

Q. Natural History?

A. Natural History. Okay, I'm getting close. I'll keep at it. Yeah, Steve was talking about two levels of understanding. One is the transition we talked about before from one species to the next which is abrupt in the shift of morphology in a lineage, and another which he says there is that in that sometimes we have transitions in the fossil record that are abrupt, and there are abrupt changes for some lineages. That is an abrupt appearance in the sense of it appears to be abrupt as opposed to abrupt appearance with no possibility of an intermediate. So we would certainly agree that we haven't worked out transitional stages for all organisms. That's absolutely true.

Q. Let me ask you about this statement, "paleontologists have long..." -- strike that. "Paleontologists had long been aware of a seeming contradiction between Darwin's postulate of gradualism and the factual findings of paleontology. Following phyletic lines through time seemed to reveal only minimal gradual changes, but no clear evidence for any change of a species into a different genus or for the gradual origin of an evolutionary novelty. Anything truly novel always seemed to appear quite abruptly in the fossil record," and I'll represent to you that's from Mayr in his one long argument Charles Darwin and the Genesis of Modern Evolutionary Thought.

A. Yes, Ernst Mayr there is paraphrasing Steve Gould's findings and he's talking about species levels. In other words, the level at which punctuated equilibrium applies to single lineages of one species moving to the next as we talked about before. I think he's not actually talking about the origin of things like I showed in the slides here.

Q. So he's not talking about the origin of a news fossil type?

A. He's not talking about things like the origins of birds and feathers and whales and getting land creatures out of that. Or I should say I can't, because I don't know all the rest of the context in question, but Ernst Mayr was not a paleontologist and did not familiarize himself with the date of the fossil record, and he was not familiar with most of the evidence I talked about today.

Q. And so it's the abrupt appearance of what that they're referring to?

A. In the case of what Gould is talking about with punctuated equilibrium, he's really talking about just new morphological changes that bring us new kinds of species, individual species from a lineage that was already present to a lineage that then appears in the fossil record, and he's talking about that change being relatively rapid, which Mayr would have had no problem with because we know that rapid change can happen in evolution. That's not a problem. The whole question was the lack of gradual change in the slow and steady sense.

Q. And one more statement, and again I want to see if you agree with this. "The Cambrian explosion refers to the seemingly abrupt appearance of diverse metazoan groups representing a number of extent phyla as well as some problematic clades during the Cambrian period."

A. That's sounds like a fair description.

Q. And this is from an article I believe entitled Lower Cambrian Vertebrates from South China.

A. Okay.

Q. Author E.G. -- or excuse me, Shu, S-H-U?

A. Okay.

Q. Are you familiar with that author?

A. No.

Q. But that's an accurate statement?

A. It's made sense to me.

Q. Now, is it the case -- let me back up. Do you see the Cambrian explosion as mainly a problem of fossil preservation?

A. I see it largely as a problem of fossil preservation, although the people that work on the problem more closely than I do and I accept what their findings are about it certainly say that there's a lot of evolution going on in the period of millions to tens of millions of years.

Q. Are with regard to the fossil preservation, the problem is that obviously you have to read the life of the past from the preserved rocks, correct?

A. Yes.

Q. And obviously longer the rocks lay around, the less chance you have of finding what you're looking for in those rocks?

A. That's exactly right.

Q. And so there are increasingly more gaps in the fossil record the further back we go?

A. As a general matter of course that's true, because the rocks on the crust of the earth are continually eroded as you pointed out, and also subducted by geological processes, destroyed inside the earth.

Q. Is it the case that fossil evidence suggests that many of the animal phyla which first appeared without, that first appear without evident precursors during the five to ten million areas in the Cambrian rocks?

A. I think it depends on what you mean by evident precursors. You're correct that at that great distance in time it's harder and harder for us to find rocks of exactly the right age for every integral that we would love to have, but the fact is as I showed that in pre-Cambrian rocks there are already complex metazoan animals going back in some cases to as many as ninety million years before the Cambrian explosion was over. So metazoans in a sense are there. We would call them precursors.

Q. So it's your understanding that there are multicellular precursors to the Cambrian fauna which are the metazoans?

A. In the pre-Cambrian, yes.

Q. Are there scientists who felt that these are ancestral to the pre-Cambrian fauna?

A. What do you mean by the word "ancestral".

Q. That they are precursors to the fauna that found in the Cambrian period.

A. Well, if somebody says that they are not directly ancestral or we can't establish that they are directly ancestral but might be collateral ancestors, I think most paleontologists would be fine with that statement. The reason being that many of these animals the preservation is not great, they don't give us a lot of characteristics to work with, all those shared features that I talked about as being the scientific basis on which we read classifications.

So we might see a little curly thing in the fossil record with maybe some shell associated with it, but is that really a snail when it's like a millimeter long and, you know, typical snails, you know, are bigger. I mean, are we going to call that a snail or are we going to say well, maybe that's just like some little wormy guy that lived in a tube. So we don't know all the timing, without enough characteristics we're going to look for really derived, you know, unusual characters of snails before we start hanging the label snail or direct snail ancestor on a little piece of Cambrian or pre-Cambrian shell.

Q. Is that the, I don't know if I'm saying it right, the Ediacaran fauna?

A. Idiacrin fauna is the soft body at the time, I'm sorry, and it's a tough thing, and these are, Idiacrin is normally a fauna of the remains of soft bodied organisms, many of which don't look at all like creatures we find much later in the record.

Q. Are they considered by some scientists as ancestors to the Cambrian fauna?

A. Most of the critters we fined in the Idiacrin fauna are just weird. They seem to represent early metazoan, like the word experiments is often trotted out, but it's a misleading thing, but they are animals that diverged and had a nice run, and they basically, you know, played out their string and they didn't leave many descendant for very long and finally there's nobody left, but the question of whether they contained the ancestors of the Cambrian fauna is often difficult to say. Again without proper characters we don't really know, and we can't for the ancestors of a particular group to be found. Could I give you a different example that might clarify?

Q. Well, we're talking about pre-Cambrian and Cambrian fauna and the relationship, I'm trying to establish, because my understanding is that some of the work by Stephen J. Gould and Simon Conway Morris called into doubt whether or not these multicellular precursors of the metazoans were actually ancestral to the Cambrian fauna. Is that, are you familiar with that?

A. To the specific animals within the Cambrian fauna, I believe they had a disagreement about parts of that. Part of what they're talking about is when you find these really weird Cambrian, pre-Cambrian forms, can you shoe horn them into existing groups or relatives of existing groups, or were they simply early lineages that simply resembled them in some respects but then became extinct, and that's again a case by case assessment by people, and the only way to find out is roll up your sleeves and go look for these characters who shared derived features by which you can establish relationships.

It's really difficult to tell. For example, in the famous Burgess shale of the Cambrian, as Steve Gould has pointed out once, you know, we have a little animal there that looks like it's an ancestral chordate, and chordates are animals that include vertebrates, and if that little animal, pychea, he said if that animal had been snuffed without any relatives to continue on, whether or not it's the direct ancestor or just a close personal friend of the animal that eventually became chordates, the whole tape would have ended right there for us, but do we know about these critters? Well, you know, we just happened to find that one and that one happened to survive. So we can't always choose what we're going to find in the records when we write about the vagaries of preservation.

Q. I believe you called a Cladogram?

A. Cladogram, yes, sir.

Q. Would it be possible to construct one of those with the metazoans to the Cambrian fauna?

A. Yes.

Q. But there would be a lot of questions in-between to make that connection, is that accurate?

A. Well, there would be questions as to the relationship of many of the specific animals found in the pre-Cambrian, that's exactly right.

Q. What would allow you then to make that connection between the pre-Cambrian fauna and the Cambrian with all of these questions?

A. Because in the Cambrian fauna, in addition to animals that we're not sure what they are or who they're related to, we do have animals that we know at least are metazoans, and some of the animals that I talked about included the trace fossils, which means the kind of tracks that animals make when they wiggle along or burrow or walk. These traces well before the Cambrian show us that these animals are proceeding in this specific front to back direction, forward progression, and that therefore that their sides are symmetrical.

So they're what call bilateral, they're bilaterians, and bilaterians are a subgroup of metazoans. So because we have bilaterian traces in the pre-Cambrian we can understand that metazoans were present. In the same with the embryos that I described from way, tens of millions of years before the Cambrian boundary, have the characteristics of metazoan embryos. That tells us that metazoans are present, but maybe not specifically brachiopods or clams or snails, but that some kind of metazoan is there. And unfortunately we're all sorry about it, we don't have better records of these.

Q. Getting back to the writings by Gould and Morris, do they question that connection between the metazoans and the Cambrian fauna?

A. That there are metazoans in the pre-Cambrian.

Q. That they're ancestral. I know you used that term --

A. Oh, that these specific animals that are found in the pre-Cambrian fauna are directly ancestral to the metazoans of the Cambrian?

Q. Yes.

A. I think we all question that, yes. I don't remember their particular words, but many of them are clearly not directly ancestral.

Q. Is that based on fossil evidence and/or the molecular systematics? Is there a molecular systematics claim to that at all?

A. The molecular evidence can't tell you a lot about things. The molecular evidence is mostly used to tell you about what the approximate divergence times is of living groups of organisms and their ancestors. The fossils are pretty much what we depend on for those things you mentioned.

Q. So would it be accurate to say that molecular systematics can say anything nothing about the relationships or roles of fossil organisms to each other or to living lineages?

A. If you can't get molecules out of a fossil you can't assess its relationships to other fossils or to living organisms. So for example ichthyosaur were denizens of the oceans during the age of dinosaurs. They're not related closely to any known animals, but no one has gotten any DN A out of an ichthyosaur yet. So how an ichthyosaur is related to a plesiosaur or a dinosaur or how it's related to a turtle of today we really don't know.

Q. Poor court reporter. There's been several I guess recent molecular analyses which would agree that whales and hippos are each other's closest relatives, correct?

A. Yes. Living relatives.

Q. And from this conclusion some scientists have suggested that because both kinds of animals spend time in the water that their common ancestor would have been aquatic?

A. There were a couple of molecular biologists who suggested that hypothesis.

Q. And the fossil records show that this inference was incorrect, is that accurate?

A. The fossil record shows that that inference is apparently incorrect.

Q. According to the fossil record the first hippos were terrestrial and not amphibious, is that correct?

A. That is what we understand now, and furthermore that they evolved from a terrestrial group called anthracoceres that reach back to the Eocene when we have the whales first evolving.

Q. And the fossil record shows that whales were fully aquatic some 35 million years before the first hippos evolved?

A. That's what the fossil record tells us.

Q. And that the whales, too, evolved from animals that were entirely terrestrial?

A. As we showed.

Q. So even if the whales and hippos are each other's closest relatives among living animals, they didn't have a common ancestor that lived in the water but rather was terrestrial?

A. That is what we understand.

Q. So based on this, the fossil evidence was more important than the molecular evidence for showing the common ancestor? Is that accurate?

A. No. For showing the ecological condition of the common ancestor. The molecular evidence was wonderful because it showed us that hippos and whales share molecular characteristics that nobody else has, and on this basis scientists accepted that whales and hippos were each other's closest relatives.

Q. But the inferences that were drawn from the molecular evidence which these molecular biologists concluded that the common ancestors had been aquatic was actually shown to be not true through the fossil --

A. Yeah, they made an inference, a hypothesis, that they just hadn't looked at the fossils, and when we were able to assess the fossil evidence and to determine as a post-doctoral student and his team did in the laboratory across from mine at Berkley that hippos actually came from anthracoceres, these other terrestrial animals from earlier, about the time when the whales were first getting started, that it was really quite clear that these animals had independent origins into water, and the hippos never become fully aquatic as far as we know.

Q. And that was something that could not be determined from the molecular evidence?

A. Because the molecular evidence won't tell you about the lifestyles of the old and extinct.

Q. I believe you testified something to the effect that the fossil record provides strong support for evolution and has since the mid 1800's?

A. Yes.

Q. And again when you use the term "evolution" here, you're referring to the change over time, life has changed over time?

A. The progression of life, in that sense. And increasingly through the 1800's, the idea of common ancestry. In the middle of the 1800's it was quite possible to talk about the early records of birds and reptiles and other animals in very, very old rocks from the Mesozoic era and so forth if that's what you mean.

Q. Is it your understanding that intelligent design refutes the claim that life has changed over time?

A. I don't think intelligent design refutes anything in science that I'm aware of.

Q. Would you think ID, intelligent design, proponents don't agree with the notion that life has changed over time?

A. Oh, I think as the quotes from Pandas shows, they're typical, I think that they accept some limited change within lineages. However, the diagram that I showed that for them represents the face value interpretation of the fossil record, that diagram shows straight lines from the bottom to the top without much change if any.

Q. You testified about irreducible complexity, the concept of it, correct?

A. I did talk about that.

Q. And your characterization of irreducible complexity is that it applies beyond the molecular level of biology?

A. I testified that Mr. Behe says that they don't, but that the other IDC proponents indicate quite clearly that it does.

Q. And I believe with the slides that you showed, the term "irreducible complexity" wasn't used in any of those slides, correct?

A. Instead the term "adaptational packages" was used, which are indications that they cannot be disassembled without not working, and that is the same concept as irreducible complexity.

Q. Dr. Behe rebutted such an application in a journal article he wrote in Biology and Philosophy. Are you aware of that?

A. No.

Q. Is it your opinion that it's impossible to test the concept of irreducible complexity?

A. No, it's possible.

Q. Is it your belief that the evidence has falsified the claim of irreducible complexity?

A. If the claim of irreducible complexity is made as a blanket statement, it's not possible to falsify every instance until every instance is tested. What I showed here was many instances where the examples given in Pandas which seem to suggest that evolution of complex structures such as are claimed for irreducible complexity can be tested, they have been shown that in fact we can show transitions, and that the irreducible complexity in these features is not shown.

Q. In your report you reference to some study or evidence on the flagella as demonstrating Dr. Behe's claim of irreducible complexity was falsified.

A. As a principle. In principle that the question of whether, of how, whether the bacterial flagellum could evolve or not is a testable question.

Q. I believe from your report, this is one of the conclusions you reached, "The reasonable conclusion is that the structure we call flagella at first served the secretory purpose (and before this perhaps other purposes) and only later changed behaviorally and structurally to work in propulsion." Do you recall making that conclusion?

A. Yes.

Q. Would that conclusion be consistent with what Darwin's theory would predict?

A. I don't think Darwin's theory would predict a specific outcome in every case. My statement simply says that if you could take one function of a flagellum in a simpler form and have that flagellum acquire a second function and become more complex in the process, much like the wing of a bird became more complex as it evolved flight, then that would be a testable proposition and it would be reasonable to conclude that's one way it could happen.

Q. And is that your conclusion that that falsified based on what I just read?

A. Oh, no, I don't know whether that's the way it went or not. I say it's a reasonable way to say it.

Q. Do you know researchers who work on this flagellum have concluded that the flagellum came first and that the TTS was actually later derived from the flagellum?

A. Some researchers have concluded that, but some researchers have concluded the opposite I believe, but again it's not my field of expertise.

Q. But your reasonable conclusion, the term you use, would be the opposite of what some of researchers actually --

A. The opposite would also be a reasonable conclusion, and the question is if you test it with enough evidence maybe you'll come to a good one.

Q. Two of the main concepts that intelligent design proponents advance, one is the irreducible complexity that we talked about and the other one is specified complexity, is that correct?

A. Specified complexity, correct.

Q. That was a concept that was advanced by Dr. William Dembski?

A. Yes.

Q. Do you know Dr. Dembski?

A. Personally? I've met him.

Q. Do you know of him?

MR. ROTHSCHILD: Your Honor, I'm going to object. It's beyond the scope of the direct.

MR. MUISE: Your Honor, I'm not going to go into the details. One of the points I want to bring out, he testified that they haven't published any of their works, and I'm just going to go into some of the details of what Dr. Dembski actually published without going into the details of specified complexity.

MR. ROTHSCHILD: I would object to that characterization. I don't believe that Dr. Padian has testified he hasn't published in any other works, but he published in lots of books and magazines, but he hasn't published in peer reviewed publications in his field of expertise.

THE COURT: Restate the purpose, Mr. Muise, of the line of questioning.

MR. MUISE: Your Honor, the way I understand his testimony is that they have not, they haven't published any credible materials advancing their claims in peer reviewed --

THE COURT: They?

MR. MUISE: Intelligent design proponents.

THE COURT: Okay.

MR. MUISE: In peer reviewed literature.

THE COURT: All right. I'll allow it for that limited purpose. I'll overrule the objection.

BY MR. MUISE:

Q. Sir, do you know that Dr. William Dembski holds a Ph.D. in mathematics from the University of Chicago?

A. He does.

Q. Do you understand that his ideas were published in a book call The Design Inference?

A. I do.

Q. And that was an academic monograph which was part of a monograph series with the academic editorial board at Cambridge University?

A. I know that.

Q. And the name of the series that it was published in Cambridge Studies and Probability Induction and Decision Theory, are you aware of that?

A. Yes.

Q. Are you aware that this book was published -- strike that. Cambridge University conducts peer reviews of the books they publish, isn't that correct?

A. In some sense, yes.

Q. And his book would have been one that was peer reviewed by Cambridge University?

A. I do not know.

Q. Does intelligent design require adherence to the claim that the earth is no older than six to ten thousand years old?

A. Intelligent design as a, as sort of a dogma as it is, does it postulate a six thousand year old earth?

Q. As a theory does it require adherence to the notion that the earth is no older than six to ten thousand years old?

A. Wow. I don't know of any theory that requires adherence to a, certainly not a scientific theory, but I would agree with you that I think intelligent design is about special creation of things, not about the age of the earth.

Q. Do you think intelligence design requires adherence to the six-day creation event that's the literal interpretation of the Book of Genesis?

A. I don't believe it requires that. Individual proponents may agree with it or not.

Q. Does intelligent design require adherence to the flood geology point of view advanced by creationists?

A. I don't know if it requires that or not.

Q. It's your understanding that intelligent design requires the action of a supernatural creator?

A. I think that this is entailed because they eliminate natural forces, and if you eliminate natural forces then the supernatural is left. Now, whether they are talking always about supernatural that couldn't possibly be natural forces, that would be an item that perhaps is under disagreement by intelligent design proponents.

Q. Let me ask you it this way then. Is it your understanding that intelligent design rules out all natural explanations for design?

A. Well, as you saw from some of the statements that we quoted there from Pandas, they are removing natural cause explanations, they're taking them off the table and positing creative intelligence as explaining these things. In that sense I think I would have to agree with that statement that they really do require a supernatural intelligence doing that and the denial or removal of natural causes that can be discovered by conventional scientific means.

Q. If I understand your testimony correctly, it's your understanding that intelligent design doesn't make any positive argument for design, only a negative argument against evolution?

A. About 90 percent or more of their argument is certainly about criticism of evolutionary theory, much like creation science was. There is this bit about irreducible complexity and there is this bit about specified complexity, but there's been very little work done on it. For example, I don't know whether Mr. Behe -- sorry, Mr. Dembski has elicited a single natural example, a case where specified complexity is an explanation of a particular biological incidence in the record.

Q. You said 90 percent is negative to evolution. Is that, I'm assuming that there's at least 10 percent of the argument that demonstrates a positive argument for design?

A. Up to 90 if I were being charitable, I'm trying to, but I really don't see that there's very much here. If you look at Of Pandas and People there's very little evidence for a designer. It's all evidence against conventional biological concepts.

Q. Have you ever read Darwin's Black Box?

A. I have looked at parts of it.

Q. The parts you looked at, was Dr. Behe citing scientific evidence?

A. For intelligent design?

Q. Correct.

A. Not that I can recall.

(Brief pause.)

Q. Now, when you referred to supernatural agency in your deposition you said it means, "Causes, mechanisms, processes, and influences that are not part of the normal behavior of the natural world as we know it. Things that suspend or override these processes or disrupt them or otherwise influences them in extraordinary ways." Do you still adhere to that definition of supernatural?

A. I believe that would have to be supernatural as opposed to natural.

Q. Would you agree that forces could exist in the natural world that we have not yet discovered, for example thermonuclear fusion, at one time we didn't know what was the force that powered the sun, but then later science discovered this force known as thermonuclear fusion?

A. Sure, and now the front page in the New York Times several years ago is an article about a fifth force in gravity which is still under discussion.

Q. So those examples might not be normal behavior of the natural world as we know it today?

A. Well, would we say that it might be according to the natural laws and processes consistent with those, or would we have to say it would be inconsistent with those?

Q. Well, I'm just asking you, that was your definition. I want to see if it fits that definition. Would those examples be considered a normal behavior of the natural world as we know it?

A. Well, those, these words you say come from my deposition, and that could be if I wanted to think about it a really sort of best crafted definition I could make that would be clear to everyone, maybe some words in that definition might be confusing or ambiguous to people, but by and large I would say that's a generally good description.

Q. Would you agree that this is a good general definition of a theory in science, " A theory is defined as a well tested explanation that unifies a broad range of observations"?

A. Yes.

Q. Would that properly define Darwin's theory of evolution?

A. Yes.

Q. You would agree that Darwin's theory continues to be tested as new evidence is discovered?

A. Yes.

Q. You would agree that Darwin's theory of evolution is not an absolute truth?

A. I don't think anything in science is an absolute truth.

Q. And that would include Darwin's theory of evolution?

A. I don't use the word truth in science.

Q. Some scientists do?

A. Yes, they do.

Q. Is it true that all -- strike that. Is it true that scientists still debate questions such as how new species arise?

A. Yes.

Q. And they still debate the question why species become extinct?

A. Yes.

Q. Would you agree that the origin of life is an unsolved scientific problem?

A. There's always more to find out, yes.

Q. Would you agree that this is an area of which there is little direct fossil evidence?

A. Yes.

Q. Would you agree that Darwin's theory of evolution continues to change as new data are gathered and new ways of thinking arise?

A. Yes.

Q. Would you agree the fossil records are incomplete?

A. Yes.

Q. Would you agree that Darwin's theory of evolution is complete?

A. By Darwin's theory do you mean what Darwin said in 1859, or do you mean the current corpus of evolutionary theory?

Q. I think some of it has been called the neo-Darwinian synthesis?

A. Oh, the neo-Darwinian synthesis. Yeah, the modern synthesis. Yes, it is incomplete, certainly.

Q. And even Darwin's theory as he postulated back in the 1800's would be incomplete as well?

A. In the sense of natural selection not being a good process to account for a lot of evolution or that there's more to natural selection or that we haven't found all the processes yet?

Q. Well, when you answered that the neo-Darwinian synthesis is incomplete, the same standard that you're applying there, would that apply to --

A. Oh, it didn't solve all the problems of course, sure.

Q. I want to see if you agree or disagree with this national science education standard, "In areas where data or understanding are incomplete, such as the details of human evolution or questions surrounding global warming, new data may well lead to changes in current ideas to resolve current conflicts."

A. That's certainly true.

Q. So you would agree that our understanding of the data are incomplete with regard to the details of human evolution?

A. They're incomplete with regard to virtually everything in evolution, as with everything else in science.

Q. That would include human evolution as those standards identify?

A. I would think so, judging by my understanding of the human fossil record, sure, we've got lots more to learn.

Q. Would you agree that the leap from non-life to life is the greatest gap in scientific hypotheses of earth's early history?

A. I'm not sure, because I'm not an expert on earth's early history before life. There may be lots of other big problems we don't know about.

Q. Do you disagree with that statement or you just don't know?

A. I don't know that I would agree with it because I'm just not that familiar with protozoic earth evolution.

Q. Now, Pandas was published in 1993 I believe, is that correct?

A. Second edition.

Q. Second edition, correct?

A. Yes, sir.

Q. And that's the one you were citing to today?

A. Yes, sir.

Q. Is it your opinion that there's been no new original thoughts by intelligent design proponents since that book was published?

A. Oh, I think there has been. Different works by intelligent design proponents have been published since 1993.

Q. Now, those -- did you call it a cladogram?

A. Cladogram.

Q. Cladogram, are those essentially a phylogenetic tree?

A. They're structurally a little bit different, but they're logical precursors, sure.

Q. And I believe you testified that they reflect a grouping based on shared characteristics?

A. Yes, sir.

Q. Would those be described also, I heard the term a tree of life, would those be considered a tree of life?

A. Insofar as they show relationships, the metaphor for this is tree of life. Sometimes it's shown by that, yes. In fact, there's a great web site --

Q. I'm sorry?

A. There's a big web site where people are trying to assemble all the biological cladograms they have, linking them all into a great tree of life.

Q. I believe you testified that no one in science thinks that a trout gave rise to a frog I think was the example you used, is that correct?

A. Correct.

Q. I believe you said that their histories are quite separate?

A. Since about the Devonian or even earlier, sure. So for 400 million years or so.

Q. Is there then just one tree of life or could there be multiple trees of life?

A. Well, if we have only one reality and if we have a history to life, then it's follows it seems to me that there would be only one tree of life, but whether we can discover it in all its ramifications is probably a never ending process.

Q. I want to see if you agree with this statement, sir. "The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches. The rest is inference, however reasonable, not the evidence of fossils."

A. Steve Gould said that some years ago.

Q. That's correct. Do you agree with that statement?

A. No. Steve didn't know what he was talking about. On a lot of areas of paleontology he was one of our greatest scientists and thinkers and scholars as I think any of this goes, but what he knew was not perfect. Steve studied snails, and if you asked me to try to give you a full phylogeny of snails, I ain't going to be able to do it and neither is Steve. But that doesn't mean that we can't do it for other organisms or that we don't find transitions. This was just one of the things that Steve didn't focus on very closely. He was -- his trade secret is really applying to this punctuated equilibrium level of the one species and then the next species that seems to arise or split off from it.

Q. Isn't the late Stephen Gould, wasn't he touted as one of the prominent Darwinian evolutionists?

A. Yes, he was, the whole century. Ernst Mayr was, too, but Ernst Mayr didn't know beans about fossils, and he didn't work on macroevolution. By contrast I don't work on population genetics. I'm not going to tell you about, you know, balanced and stabilizing selection of things. That's not my area, but I think that Steve would be the first to, and Ernst Mayr would certainly say that he would acknowledge what he hadn't worked on. Ernst Mayr worked on birds.

Q. Well, that quote was published in an article that was published in Natural History. Is Natural History a peer reviewed journal?

A. No. And Steve was notorious. He was a great writer, but no one could take a pen to his prose. His columns were put in there, and if you touched them he was going to have a fit. So nobody edited a word. I know this from personal experience working with Steve. He was a great man, he was a great writer, but he worked on an old typewriter, didn't do drafts, he typed it out, and that was it, and he never used a computer in his life.

Q. Let me see if you agree with this statement. "The most striking features of large scale evolution are the extremely rapid divergence of lineages in the time of the origin, followed by long periods in which basic body plans and ways of life are retained. What is missing are the many intermediate forms hypothesized by Darwin and the continual divergence of major lineages into the morpho space between distinct adaptive types," and that was written by Robert Carroll.

A. Yes. Bob wrote that in about it was `89.

Q. In an article entitled Toward the New Evolutionary Synthesis, published January of 2000?

A. Okay. Yes, I think I would disagree in detail on that. Bob in some regards is restating a principle that we have understood since, well, at least the 1940's with George Gaylord Simpson, and that is that the major groups of animals seemed to diverge first. Obviously you have to the higher levels, like phylums appearing before the classes and the orders and the individual families all appear, but these things appear and then they seem to move quickly into a variety of ecological niches. There's sort of an explosion if you will, and then it starts winnowing things out, and you get less diversity as you go on through time and less production of types. That's a pattern that's been noted for many different kinds of animals through the fossil record, and I can't tell you so much about plants.

Q. A couple of more quotes I want to see if you agree with. "Paleobiologists flocked to these scientific visions of the world in a constant state of flux and add mixture. Instead of finding the slow, smooth, and progressive changes Lyell and Darwin had expected, they saw in the fossil records rapid bursts of change, new species simply appearing out of nowhere, and then remaining unchanged for millions of years, patterns hauntingly reminiscent of creation." And that is from Oxford zoologist Mark Pagel writing in Nature magazine.

A. Can you tell me what, from the context perhaps what years he's talking about that these scientists are experiencing this?

Q. In 1999. And as I said in 1999 writing in Nature?

A. I'm sorry, I mean of the -- when he's talking about the paleontologist, the paleontologists of which era is he talking about, do you know?

Q. I don't know. And he's referring to paleobiologists. I don't know if that's --

A. Okay. I don't know either. I mean because I think it's quite possible that in the early days of paleontology that would be probably a more acceptable pattern than it would be later on, but I don't know.

Q. And here's one in 2001 written by Ernst Mayr. "Wherever we look at the living phyata [phyla? biota?], discontinuities are overwhelmingly frequent. The discontinuities are even more striking in the fossil record. New species usually appear in the fossil suddenly, not connected with their ancestors by a series of intermediates." Do you agree with that statement?

A. Well, let's parse it, there's a long, if you unpack it just a little bit, it's a long statement, and he's talking first about, if I heard you right he was talking about the living biota and how it's disconnected by forms, we don't have all the transitional forms living today. Mayr is simply restating one of the most important basic conclusions of Darwin's Origin of Species, which is that you get a branch or a bush like that, but through time selective extinction does its work and it removes all those intermediate forms, leaving those that then create artificial gaps between species, and so this was a basic, a very, very important principle of Darwin's work. In fact, the only illustration that Darwin has of the Origin of Species is a scheme, a tree of life where he's showing exactly this principle in schematic form.

So as far as that applies to living biota, that's a perfectly ordinary statement that everybody knows is true. Where then Ernst changed his attention to the fossil record, then he's talking about the progression of intermediates from one form to another, that you have something progressing through the record and then there's not a lot of intermediate and then there's another form progressing through the record.

If I heard you right there's a perfect description of punctuated equilibrium, which actually Gould and Eldredge took pains to credit Mayr with when they first developed as sort of being incipient in his work. So I think what he's saying there is just basic understood stuff, not anything radical.

Q. In your direct testimony when you were talking about Pandas, and I believe one of the points you were talking about was the origin of feathers?

A. Yes.

Q. And the evidence that you cited was evidence that had come out subsequent to the publication of Pandas, is that correct?

A. That's correct.

Q. Now, you testified about the one minute statement that's read to the students, but I just want to explore your understanding about what may or may not actually be happening in the biology class. Is it your understanding that the theory of evolution will be taught in the ninth grade biology class at Dover pursuant to the state standards?

A. I understand it's required to be taught.

Q. Is it your understanding that the state standards that require students to learn about Darwin's theory evolution take a test which would include aspects of evolution?

A. I gather that that is the requirement or that's the expectation for students.

Q. Do you know that the book that was purchased for use in the ninth grade biology class is a 2004 version of the Miller and Levine biology book?

A. That eventually this was purchased, yes.

Q. And that the book Pandas that you've been testifying about today is going to be placed in the library?

A. Was it originally placed in the library or in the classroom?

Q. What's your understanding?

A. I'm not sure. I believe I know that, or I'm given to understand that it's now in the library.

Q. Is it your understanding that it's a required text for the class?

A. My understanding is that no, it was rejected as a required text. I believe the teachers did not want to use it.

Q. So in terms of how it's going to be applied or used in the ninth grade biology class, it's you're understanding that it's been put in the library and it's only there if students want to voluntarily go to it?

A. They are recommended to go to it to learn more about other ideas about origins.

Q. Is your understanding that whether or not the students will be tested on any of the concepts of intelligent design?

A. I'm not aware that they will be.

Q. Are you familiar with the 2004 biology book by Miller and Levine?

A. No.

Q. Do you know who Dr. Miller is?

A. Oh, yes.

Q. Do you have an understanding that the biology book covers evolution in a manner that's consistent with his status in the scientific community?

A. I trust that it is. I know that Ken has always been very strong about including evolution in his book.

Q. Would you, based on what you know about Dr. Miller and what he does with his science books, will you conclude that the treatment of the fossil record in the biology book would be one that would be consistent with what you believe the scientific evidence shows in the fossil record?

A. Not having reviewed it I wouldn't be prepared to tell you that specifically, I'm sorry.

Q. Would you have any measure of confidence based on the fact that you know Dr. Miller as the co-author?

A. I think Ken would be the first person to say he's not an expert on fossils. I hope he's getting good evidence and good reviews from other people, but I haven't seen that part of the book.

Q. Are you the president of the National Center for Science Education?

A. Yes, sir.

Q. And directors include Dr. Brian Alters, is he one of your directors?

A. Yes.

Q. And Dr. Barbara Forrest?

A. Yes.

Q. And Dr. Miller is considered one of the supporters of the National Center for Science Education?

A. I believe he's on our letterhead as a supporter, scientific supporter.

Q. Is the National Center for Science Education a political advocacy organization?

A. No, it's not.

Q. Are you familiar with the web site of the organization that you're a president of?

A. Well, I must say I don't look at it every day, and I should explain that the role of the president is not to superintend the daily activities of the staff of the center, but rather to preside over the board of directors.

Q. Do you have any familiarity with your web site?

A. I do consult it, but I don't have anything to do with its production and I haven't memorized its contents or have I say a great familiarity with what's up there at the moment.

Q. Do you know if it has a page entitled "25 Ways to Promote Science Education"?

A. I do not know that.

Q. Do you know if your web site encourages individuals when there's a controversy in the community of evolution to hold press conferences with colleagues, record public opinion announcements, send letters or editorials supporting evolution education to local newspapers, are you aware that your web site makes those representations?

A. I don't think I've read that particular page.

Q. Now, plaintiffs' experts in this case and I gather from your testimony as well have criticized intelligent design proponents for not having their ideas published in peer reviewed journals. Do you share their criticism?

A. In the appropriate fields, yes.

Q. Do you know who Dr. Richard Von Sternberg is?

A. I don't believe so.

Q. Sir, do you know if the U.S. Office of Special Counsel conducted a preliminary investigation of a complaint made by this individual that he was, that reprisals were made against him for actually publishing an intelligent design article written by Dr. Steven Meyer in the Proceedings of the Biological Society of Washington, are you aware of that controversy?

THE COURT: All right, go ahead.

MR. WALCZAK: It's way beyond the scope of direct, and the witness has testified that he didn't know who Dr. Sternberg is.

MR. MUISE: I asked him about the controversy, Your Honor, as follow-up.

THE COURT: I guess if he doesn't know him on that basis, the second question might be objectionable. He can't identify him, so how would he know?

MR. MUISE: He may be aware of the controversy surrounding an article that was not published in the Proceedings, and I see the witness is nodding his head right now. So chances are he probably does have some understanding of the controversy.

THE COURT: All right, I'm going to give you some latitude. I'll overrule the objection.

THE WITNESS: I recognized the name when you started to explain the circumstances. Sorry, I don't mean to give you a false impression.

BY MR. MUISE:

Q. So you're familiar with the controversy surrounding the publication of this, what was purported to be an article on intelligent design written by Dr. Steven Meyer?

A. Well, I'm familiar that there is a controversy.

Q. The U.S. Office of Special Counsel conducted a preliminary investigation, and let me read you a portion of this.

THE COURT: I'm going to sustain the objection now. I don't, I think that's beyond the scope.

MR. MUISE: Your Honor, if they're going to complain that intelligent design proponents are not publishing articles, and his organization was identified in a preliminary investigation as placing undue pressure and influence on an organization because he accepted an article, an intelligent design article, that clearly goes to the bias, and you know, there's one thing for them to criticize and it's another thing for them to just take every effort, use all their political clout they can to prevent these articles from being published in peer reviewed journals.

MR. WALCZAK: I think we've got a hearsay problem here, too, Your Honor.

THE COURT: Well --

MR. WALCZAK: And it's way beyond the scope of --

THE COURT: The purpose of the question then, Mr. Muise, is to, if I understand it, and I'm not sure that I do, but help me out, you are embarking on a line of questioning that stems from a complaint that was initiated by the witnesses, by the entity, by the group that the witness is the president of.

MR. MUISE: No. The complaint was, this individual Dr. Richard von Sternberg, was an editor of a peer reviewed journal in which an intelligent design article was submitted for review. He as the editor agreed to accept it. He was then, reprisals were then taken against him for doing so to the point where he initiated a complaint to the U.S. Office of Special Counsel. The U.S. Office of Special Counsel conducted a preliminary investigation, and part of the investigation revealed that his organization, the National Center for Science Education, was involved in creating, in helping the strategy to get, for the reprisals against Mr. Von Sternberg.

THE COURT: Well, you can establish that by testimony I suppose. I think it's not an inappropriate line of questioning, but I guess the, ostensibly I guess it goes to bias on the part of this witness. I think I'd ask the question a more focused way, what does he know about that.

MR. MUISE: And I was going to read a section of the report and see --

THE COURT: And/or what did he have to do with it.

MR. MUISE: Your Honor, I think the section of the report I was going to read was going to provide the foundation for those, or the basis for those follow-up questions, whether he knows this is true, whether he had any part in that.

THE COURT: Well, you've read that. I mean, by the dialogue we've just had you've gotten that in. I think it's clear now the area that you seek to get into. So I think you can hone your questions based on the dialogue that we just had, because it really goes to what he knows and what if anything he did. Isn't that what you're trying to get?

MR. MUISE: Correct, Your Honor, but the dialogue we had was between the court and myself. Not between the --

THE COURT: We didn't put the cone of silence over him while we had the dialogue. I assume he heard it. So why don't you narrow your questions as according to that. I mean, everybody understands now what we're talking about. Ask him what he knows about that, and if anything what he, what part he had in it or what he did. Mr. Walczak, what do you want to say?

MR. WALCZAK: If we might see what the document is that Mr. Muise allegedly is pointing to, we have no idea whether he's accurately characterizing the situation or not here.

THE COURT: Well, I don't think you have to yet. I'm going to let Mr. Muise proceed. That may be necessary and maybe he's going to do that, but go ahead and see --

MR. MUISE: Your Honor, I was going to say if he doesn't believe I have a good faith basis for my question on cross examination, I have a copy of the letter from the U.S. Office of Special Counsel, I'll be happy to show opposing counsel --

THE COURT: Do you want to see that now?

MR. WALCZAK: I'm not imputing that he's got a good faith basis. I do not know as I sit here whether his characterization of what that document says is fair and accurate.

THE COURT: Well, that may or may not be an issue depending on the answers we get. So go ahead and --

MR. MUISE: That's partly the reason why I was going to read that one paragraph, Your Honor, so there wasn't any misrepresentation about what the basis of the question was.

THE COURT: What do you say about that?

MR. WALCZAK: It appears to be a multipage document. Reading one paragraph out of there again I don't know whether that's taken out of context or --

THE COURT: Well, you'll have him on redirect. So why don't you share, do you have a copy, Mr. Muise? Mr. Gillen looks like he's looking for a copy.

MR. GILLEN: I believe that we do, Your Honor. It's Defendant's Exhibit 282.

THE COURT: All right. Then Mr. Muise, your point is well taken. Why don't you go ahead and read that at this point and I'll give you some latitude, and then proceed with your questions on that point, and at the same time plaintiffs' counsel is then alerted to the exhibit number and they can check it. Go ahead.

BY MR. MUISE:

Q. And just so the record is clear the acronyms that will be used, when I use the acronym SI I'm referring to the Smithsonian Institution, and the acronym NMNH is referring to the National Museum of Natural History, and I just want to read you a portion from this preliminary investigation, sir. "Of great import is the fact that these same SI and NMNH employees immediately aligned themselves with the National Center for Science Education, NCSE. Our investigation shows that NCSE is a political advocate organization dedicated to defeating any introduction of ID," meaning intelligent design, "creationism, or religion into the American education system.

"In fact, members of NCSE worked closely with SI and NMNH members in outlining a strategy to have you investigated and discredited within the SI. Members of NCSC furthermore e-mailed detailed statements of repudiation of the Meyer article to high level NMNH officials. In turn, they sent them to the society. There are e-mails that are several pages in length that map out their strategy.

"NCSE recommendations were circulated within the SI and eventually became part of the official public response of the SI to the Meyer articles. OSC, Office for Special Counsel, is not making a statement on whether the SI or NMNH was wrong or right in aligning with the NCSE, although OCS questions the use of appropriated funds to work with on outside advocacy group for this purpose.

"This is only discussed to show that the actions taken on the part of SI employees clearly had a political and religious component. Therefore, it may lend credence to your allegations that your religion and political affiliations were investigated and made a part of the actions taken against you," and the you referring to is the Dr. Richard Von Sternberg whom this was directed to. Sir, are you aware as the president of the NCSE whether or not the NCSE had taken any of the actions that were identified that I just read to you in this preliminary investigation?

A. I was not personally involved in any of those actions.

Q. Do you have any knowledge of any of those actions actually taking place?

A. Well, I am not sure that -- let me put it this way. I expect that there may have been communication. I was not copied on any of the communication between NCSE and anyone in the Smithsonian, but it's common for agencies as well as individuals to consult NCSE, which by the way is a tax exempt organization, not a political advocacy group as the paragraph states, when there is a question about the propriety of introduction of creationist material into for example scientific curricula or such ideas. My understanding is that Mr. Von Sternberg, is his name von Sternberg or Sternberg?

Q. It's Von Sternberg. People refer to him as Mr. Sternberg as well.

A. Mr. Sternberg, okay. That he was an editor for the Proceedings of the Biological Society of Washington, is that an organ of the Smithsonian Institution or the National Museum of Natural History?

Q. You don't know or are you --

A. I don't know. I'm asking.

Q. Well, it doesn't work that I answer questions. If you don't know, that's fine.

A. Then I probably can't help you any farther, I'm sorry. That's all I know about NCSE's part in it.

Q. Do you know if anyone within NCSE sent e-mails to any of members of the SI?

A. I don't have any personal knowledge of specific e-mails.

Q. Is Genie Scott, is she a member of the NCSE?

A. She is our executive director.

Q. Do you know if she just happened to be out giving a lecture on October 12th at the University of Idaho arguing against the teaching of intelligent design?

A. I don't know where she was on that date, sorry.

Q. Do you know Dr. Scott Minnich?

A. Personally no.

Q. Do you know who he is?

A. I think he's going to be deposed in this case, and I think he has submitted an expert report.

Q. Do you know he's a professor at the University of Idaho?

A. I believe I'm aware of that. Is it Idaho or Idaho State? Idaho, okay.

MR. MUISE: No further questions, Your Honor.

THE COURT: Mr. Walczak, redirect?

Direct Examination: Classification, Ancestors, and Relationships

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.


Direct Examination: Creationism and the Fossil Record

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.

Slide 020
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.)
Slide 021
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.)

Slide 022
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?

Slide 023
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.

Slide 024
Slide 24: Pandas used the giraffe as an example of an adaptational package (pp. 69-70).
(Right-click to download pdf.)

Credits: Giraffe from Pandas Figure 2-3, p. 70. ©1993 by Foundation for Thought and Ethics, Richardson, TX 75083-0721

Q. And could you identify the figure and page number?

A. Oh, yes, I'm sorry. This is Figure 2.5 from Pages 69 and 70.

Q. And that's in Pandas?

A. In Pandas, second edition. And so they are talking about an adaptational package in the caption that protects the giraffe from hemorrhaging in the brain. And this is all perfectly reasonable. Pressure sensors along the arteries, muscle fibers in the artery walls, heavily valved veins, and the arteries that approach the head they say correctly branch into what's called rete mirabile, which is a network of capillaries that prevents the brain from exploding when it gets a flood of blood coming up to it suddenly.

These are correctly understood by physiologists as part of an adaptation of the giraffe, but I just want to point out here that this is not a discussion of cells and molecules, this is a discussion of tissues and organs.

Q. Now, I want to turn to the fossil record, and I've asked you to identify from the book Of Pandas and People various examples where they claim that certain types of organisms could not have evolved naturally.

Can you show us where you believe that Pandas misrepresents the science? I believe you want to start with the Cambrian explosion?

A. Well, I'd like to start with a few examples that are of some concern to scientists because the representation of the science in these pages is really quite different from what scientists understand and understood when Pandas was written.

The next slide, I guess, starts with several quotations from Pandas about the Cambrian explosion. Now, I should explain that what is meant by the Cambrian explosion is a sudden appearance of organisms that are shelled marine organisms within a geologically rapid time, relatively speaking, 10 to 30 million years as the smallest possible increment, which seems like a long time to us as humans. If my testimony goes very long, I think it's going to seem like several million years, but --

THE COURT: You're doing fine so far.


Slide 025
Slide 25: Padian addresses the "Cambrian Explosion," a favorite argument of creationists/ID proponents.
(Right-click to download pdf.)

II. The "Cambrian Explosion"

THE WITNESS: You know, time to paleontologists means something quite different than it means to ecologists and normal people. But these organisms appear over 500 million years ago. And we find records mainly of these shelled sea creatures, marine invertebrates we call them, snails and clams and their relatives back in that time.

Before this the record is a bit more difficult. It preserves different kinds of fossils that are a little bit harder to suss out. And this has been a really interesting area of study for paleontologists, biologists, geochemists, geophysicists for many, many years.

The way that Pandas treats this is to say that organisms appear with these adaptational packages intact at the Cambrian boundary, multicellular life first flowers here. No evidence whatsoever of fossil ancestors.

BY MR. WALCZAK:

Q. Now, I'm sorry, is that a direct quote from Pandas?

A. This is a direct quote from Pandas, Page 71 and 72. They go on to infer directly that only an intelligent designer could do this. They state, on Page 94 and 95, that the great majority of these animal phyla, by which is meant sort of these major groups of invertebrates, the arthropods and the annelids and the echinoderms and the mollusks and so forth, brachiopods, appear in a remarkably brief period of time, again, 10 to 30 million years.

We'll have recourse to that 10 to 30 figure in a second. But they say they're not connected by evolutionary intermediates, and there's an unexpected lack of fossils bridging the evolutionary distance between these phyla to document evolutionary origins for them.

Q. What does that mean?

Slide 026
Slide 26: Assertions from Pandas on the origin of phyla at the beginning of the Cambrian.
(Right-click to download pdf.)

A. I'm not sure. There are some code words there. I would agree that the fossil record is not complete. It will never be complete. On the other hand, how many intermediates do you need to suggest relationships, and what do you accept as intermediate?

And in the previous paragraph, there is some text that's even more worrisome because they say that these are adaptational packages that appear at the Cambrian boundary, by which they mean the boundary between the pre-Cambrian and the Cambrian. They say that multicellular life first flowers there, whatever that means, but they say there's no evidence whatsoever of fossil ancestors.

Q. And is that true?

A. Well, I think the record will show us something different. Before we go to the next slide, however, I want to point out at the bottom that after talking about phyla, groups of phyla, these major divisions of animals that are apparently having no bridges between them and no ancestors, they then go on to say that categories of classification are largely artificial human groupings.

I would agree with that, but it contradicts what they say in the previous passages, because if you treat phyla as somehow real entities that you cannot bridge, then how can you also say that these categories are largely artificial?

The next slide shows a bit of this pedigree, again from scientific creationism. A quote here from Henry Morris, who is head of the Institute for Scientific Creationism outside San Diego, from his textbook of more than three decades ago claiming that all of these kingdoms, phyla and classes unchanged since life began, that things appear suddenly, no incipient forms leading up to them. There may have been changes within kinds, but they haven't varied since the beginning except for those that have become extinct.

Slide 027
Slide 27: Henry Morris, the founder of scientific creationism and co-founder of the Institute for Creation Research, made the same argument.
(Right-click to download pdf.)

Q. And that's what Henry Morris said?

A. That's what Henry Morris said as a scientific creationist. This language is, I think, identical to what you see in Pandas. And, again, the statement from Pandas that I just read is below that.

Q. And that's from Page 71 and 72 of Pandas?

A. Yes.

Q. And is that accurate?

A. Is it an accurate representation of science?

Q. Yes.

A. I believe it's a little more complex than that. The next slide is another quotation from Duane Gish, who we've seen before as the vice president for the Institute for Creation Research. Duane Gish is talking about the Cambrian geological strata, a sudden great outburst of fossils, and he says that what is found in rocks supposedly older than the Cambrian, that is, in the so-called pre-Cambrian rocks, he says not a single indisputable fossil, unquote. This is very reminiscent of the language we've just seen in Pandas where they say there aren't any ancestors.

And if I could show the next slide. This quotation, also from Pandas, implies quite directly that there are no chains of fossils leading from lower organisms to higher ones. They stress that we can only accept evolution if we assume that only natural causes were at work to explain these things.

But then they say there's another possibility that science leaves open to us, and that is that an intelligent cause made fully formed and functional creatures which later left their traces in the rocks. This is as close a definition as I could come to special creation. I don't see how else you could interpret that as the possibility that natural processes could have gotten you from one form to another.

Q. And you are just quoting from Pages 25 and 26 of Pandas?

Slide 028
Slide 28: Duane Gish also makes the Cambrian Explosion argument in an ICR publication.
(Right-click to download pdf.)
Slide 029
Slide 29: Pandas claims there is no fossil evidence for common ancestry, only naturalistic philosophy, and argues for special creation ("an intelligent cause made fully-formed and functional creatures, which later left their traces in the rocks").
(Right-click to download pdf.)

A. This is Pages 25-26 of Pandas.

Q. And what is this slide, Professor Padian?

Slide 030
Slide 30: This figure from Pandas attempts to depict the Cambrian "Explosion," but leaves out crucial data such as the time scale and Precambrian fossils.
(Right-click to download pdf.)

Credits: Cambrian Explosion figure from Pandas Figure 4-2, p. 95. ©1993 by Foundation for Thought and Ethics, Richardson, TX 75083-0721

A. This diagram comes from Page 95 of the second edition of Pandas. It's Figure 4.2. I can best describe it by the caption provided, their own caption, which says, This is a generalized schematic of the fossil record that's designed to show the Cambrian origins of nearly all animal phyla. Dotted lines represent the presumed existence of phyla, not the fossil record.

Again, I'm not sure what this chart is meant to represent, because what students are not being shown here or, indeed, any readers, there's no real time scale on here, so the implication clearly is that the vast majority of these things appeared all at once at the Cambrian/pre-Cambrian boundary. Boom, there they are. And if you look at that line below the Cambrian, where it says pre-Cambrian, there is no record whatsoever. There are no fossils as far as they're concerned.

They say in the caption this is a generalized schematic of the fossil record. They don't tell you which animal groups they're talking about, and they don't give you any idea that there could be any possible relationships among these organisms.

And so the question of whether that's an accurate depiction of the fossil record may be illustrated by this diagram from Kevin Peterson and his colleagues in Paleobiology earlier this year.

Q. I'm sorry, what is that text?

A. Paleobiology is a peer-review journal in our field.

Q. And that's 2005?

A. 2005. What the authors have done here is essentially to turn the rock column on its side, so time is now going from the lower left to the lower right as we move up into the Cambrian early and late. And you can see the boundary here between the Cambrian and the Ediacaran period right before that.

Q. Professor Padian, you have a pointer, a laser pointer there. It might be helpful to show that.

A. Okay. We'll see if it works. I can see that there. Okay, I can kind of see it myself. I'm not sure if that's visible to you.

Slide 031
Slide 31: This figure, from a 2005 paper in Paleobiology, shows the data that Pandas ignored, including Precambrian fossils, and the fact that even on a narrow definition based on the appearance of clear bilaterian fossils, the "explosion" took at least 30 million years. The chart also shows that fossil diversity (the blue and yellow bars) increased relatively rapidly, but not all at once.
(Right-click to download pdf.)

Credits: Diagram from Figure 2, page 4 of: Peterson, Kevin J.; McPeek, Mark A.; and Evans, David A. D. (2005). "Tempo and mode of early animal evolution: inferences from rocks, Hox, and molecular clocks." Paleobiology 31(2_Suppl), 36-55. (DOI) Copyright 2005, the Paleontological Society. Reproduced with permission.

THE COURT: We can see it.

THE WITNESS: Okay. The dark bars here, the dark black bars, are the actual fossil records of organisms. The gray bars you see here, these are cases where there are fossils that are supposed to be this old, but they haven't been verified yet.

The lighter colored black bars here are inferred existences that are inferred by a different line of evidence. These red boxes with numbers in them are dates by which scientists estimate when the divergences between -- that is, the separations between lines like this took place, the annelids and the mollusks.

You may ask, how is this done? And the answer is, well, molecular biology looks at the configurations of genes on chromosomes. By lining up the genes, the sequences of the genes are homologized and matched up with each other, and the closest matches and the more derived similarities, the unusual features of evolution, tell us which groups are most related to which.

Now, in the Pandas diagram, all of the names on the right-hand side in these various colors, the names of the major groups of organisms were not given, and there was no indication that we had any idea that these lines could be related to each other.

But, in fact, we had morphological ideas based on fossils, on embryology, and on the shells and tissues of these animals. Molecular biology has now come through with a whole other wealth of data. And this is --

BY MR. WALCZAK:

Q. I'm sorry, in the red boxes, those are dates?

A. The red boxes are numbers that are estimated dates of when each of the lines in question would have separated from each other based on how much their molecules differ or resemble each other.

Q. So that would be the age of the fossils?

A. That would be the age of the splits of the lineages. The fossils may not extend back that far. Sometimes they get nearly that far, and sometimes they don't.

The fossils are represented by the little purple boxes below the slide here. There you see the purple boxes at the bottom. And, for example, here at about 600, we have listed the oldest metazoans. Metazoans are multicellular animals with several distinct tissue layers, so they would include actually all the animals here on this slide except the bottom two, and the bottom two, as their names suggest, are sponges.

And it turns out that the molecular date shows a divergence time at about 604 years. The oldest metazoans are dated, estimated in the fossil record at this date, as well.

Slide 032
Slide 32: Fossils spanning the late Precambrian and early Cambrian. The early Cambrian was preceded by Ediacaran fossils, the tracks and burrows of wormlike fossils, and the beginning of the "small shelly" fauna, which increases rapidly in diversity in the early Cambrian, mostly before recognizable body fossils (e.g. trilobites) are found.

(Note: A 1998 paper in Nature claimed that fossils in the Doushantuo formation in China were early-stage metazoan (animal) embryos (Xiao et al., 1998). This would push fossil evidence of animal life back to perhaps 590 million years ago as shown in the slide. However, this interpretation was questioned by another paper in Nature, published in January 2007, which made a substantial case for the idea that the "embryos" are actually clumps of giant sulphur bacteria (Bailey et al.). This interpretation has some issues as well, since a recent Science paper has claimed that nuclei can be observed in some of the fossils, which would indicate that they are not bacteria (Hagadorn et al. 2006). See Donoghue's (2007) summary in Nature for a semi-technical overview of the issues.)
(Right-click to download pdf.)

Credits:

Trilobite (Olenoides serratus) and oncychophoran (Aysheaia) reproduced with permission from Pamela Gore's Burgess Shale Page.

Primitive arthropod (Fuxianhuia protensa) from Figure 1, p. 4 of: Babcock, Loren E.; Zhang, Wentang; Leslie, Stephen A. (2001). "The Chengjiang Biota: Record of the Early Cambrian Diversification of Life and Clues to Exceptional Preservation of Fossils." GSA Today, 11(2), 4-9. (DOI) Reproduced with permission.

Small shellies from: Figure 8, page 272 of: Steiner, M.; Li, G.; Qian, Y.; and Zhu, M. (2004). "Lower Cambrian Small Shelly Fossils of northern Sichuan and southern Shaanxi (China), and their biostratigraphic importance." Geobios, 37(2), 259-275. (DOI) Copyright 2004 Elsevier. Reproduced with permission.

Ediacaran 'vendobiont' (Dickinsonia) courtesy of Lisa-Ann Gershwin and the UC Museum of Paleontology (source page). Reproduced with permission.

Precambrian embryo from Figure 5g, page 556 of: Xiao, Shuhai; Zhang, Yun; Knoll, Andrew H. (1998). "Three-dimensional preservation of algae and animal embryos in a Neoproterozoic phosphorite." Nature 391(6667), 553-558. (DOI) Reprinted by permission from Macmillan Publishers Ltd., copyright 1998.

Q. I'm sorry, you said 604 years. That's 604 million years?

A. Million years, yeah. The next slide I think will give an indication of not so much the relationships of these organisms, but of the fact that, indeed, before the so-called Cambrian explosion, there was a lot of evolution.

For example, the Cambrian explosion listed here in yellow -- and I'm not sure if I can make this -- yeah. The Cambrian explosion here of skeletonized animals is seen by scientists as really mostly a preservational artifact, although a lot of evolution is going on. But this is the point in history in which a lot of skeletons begin to be preserved, where before this we're not getting that much.

So the Cambrian explosion here is occurring along this yellow bar from about the Cambrian boundary well up into over 520 million years ago. It's not a single abrupt process but rather it's a process that takes quite a long time.

Even after this so-called Cambrian explosion, there are amazing preservations of fossils, soft-bodied critters that show us remains that we don't find earlier just because they're not preserved. It's very difficult to preserve fossils.

And at this Cambrian boundary where, according to works like Pandas, there are no fossils before that, there are no transitions, there are no possible ancestors, well, one of the things I pointed out before is that, you know, we're not always looking for direct ancestors, we're finding things that have the same features as the organisms that we're trying to understand the relationships of.

And so this pre-Cambrian record is actually quite interesting. We have fossilized animal burrows, and the burrows of these animals go in sort of all sorts of curvy lines and wavy lines that indicate that the animals were proceeding front to back, so they were what we call bilaterian, that is, two-sided things like us, like snails, like worms, like things that are -- have a left and a right side. This is the way they walk.

So even though we didn't have their shells or other remains of them, we have their burrows that could only have been made by complex metazoans that were also bilaterians, that is, two-sided animals. We can even go back --

Q. I'm sorry, and those have been dated before the Cambrian boundary?

A. Oh, yes. Everything that you see at the Cambrian boundary is over 540 million years old, and these are things that are still older than that.

Q. And on the right-hand side of this slide, there are several photographs. Can you tell us what those are?

A. These are photographs of the actual fossils. This is the actual fossil evidence that is preserved. These are taken from, in some cases, peer-reviewed books and journals and in some cases Web sites where the specimens are well known from other sources.

I want to point out that at about 590 million years there's a little dot there where it says "fossil metazoan embryos" at the bottom of the slide, and there's a picture of one of them.

This is a really amazing find because it shows us that some 50 million years before the Cambrian boundary and even longer before some of the Cambrian explosion took place, we have evidence of metazoan embryos. By that we mean the embryos of organisms that belong to one of the groups I showed in the previous slide.

How do we know this? We know this because the embryos themselves have characteristics of metazoans. They are not simply one-celled organisms. And if there are these embryos then, then there are metazoans present. That doesn't mean that there are full-blown trilobites and snails and brachiopods and so forth, but it does mean that there was some kind of metazoan life.

Q. And is this well established in science?

Slide 033
Slide 33: Recently published advances in research on the origin of phyla.
(Right-click to download pdf.)

A. Oh, yes. It's the subject of countless articles and books and papers. And a few of them just are here, along with a recent book by Jim Valentine, who is emeritus professor in my department, member of the National Academy of Science, and one of the four or five most important paleobiologists of the last century, and he treated this problem and all its ramifications in depth.

Q. And if you could just read the titles and the journals from which they came into the record.

A. The top one is, Fossils, Molecules, and Embryos: New Perspectives on the Cambrian Explosion. This comes from a journal called Development.

Now, Development is about developmental biology. Would you expect to see fossils in developmental biology? Well, as I said before, this is the new age of integrative biology. Fossils are really important to all kinds of evolutionary study. They're incredibly indispensable to this sort of work.

A. A paper below that from Integrative and Comparative Biology, which is, again, not a paleontological journal, by Nick Butterfield called, Exceptional Fossil Preservation and the Cambrian Explosion, because we see this as a problem of preservation, not just of quick evolution. Both things are going on here.

And, finally, below in a journal called Molecular Phylogenetics and Evolution, again, not a journal you'd think the average rock hound would be publishing in, but we have Current Advances in the Phylogenetic Reconstruction of Metazoan Evolution, a New Paradigm for the Cambrian Explosion?

And these are all journals and articles that show the integration of molecular techniques with the fossil record, with developmental biology, and this is why it's one of the most exciting areas you'll find.

Q. And so the statements you've read to us a few minutes ago about the way Pandas characterizes the Cambrian boundary and says that there are no fossil ancestors before that boundary, that's not supported by the state of science today?

A. Well, as we can see, there are some metazoans that appear well before the Cambrian boundary. If you are looking for direct ancestors, if you insist on an unbroken stream of intermediate fossils to document a case, I'm afraid that that's going to be difficult to get under any circumstances, but it's also equally impossible for the historical record of humans.

If we had to come up with evidence of every one of our direct linear or collateral ancestors and know everything about them, it would be impossible, yet we don't question the parentage of our friends and neighbors because they can't do that.


III. How vertebrates gained land (the "fish-amphibian" transition)

Q. Now, we talked about the evolution of invertebrates. Can you talk to us about how Pandas portrays the evolution of vertebrates?

 
Slide 034
Slide 34: Padian will now cover the origin of tetrapods -- the first vertebrates to walk on land. In traditional classification, this was known as the "fish-amphibian" transition. This terminology is problematic in cladistics because technically tetrapods are just a subgroup of "fish" and thus are "fish," cladistically speaking.
(Right-click to download pdf.)
Slide 035
Slide 35: Pandas, p. 22, asserts that no transitional fossils exist between fish and something else.
(Right-click to download pdf.)

A. Yes, I would like to talk a bit about some of the major transitions that are discussed in Pandas that relate to backboned animals, which are closer to home, as far as we're concerned, because we belong among the backboned vertebrates. The text from Pandas says that fossil types are --

Q. I'm sorry, are you quoting?

A. I'm quoting from Page 22. Fossil types are fully formed and functional when they first appear in the fossil record. For example, we don't find creatures that are partly fish and partly something else leading to today's fish.

They say, Instead, fish have all the characteristics of today's fish from the earliest known fish fossils, reptiles in the record have all the characteristics of present-day reptiles, and so on. This is, again, the abrupt appearance theory, sudden appearance complex adaptive packages, irreducible complexity argument.

Q. So this says fish were formed intact?

A. Yeah, pretty much, yep. Here is their treatment of amphibians.

Q. And this is a slide from Page 104 of Pandas?

A. Page 104, yes. They say at the upper left column, Darwinists believe that the first amphibians evolved from early fish. "Darwinists believe," that's problematic language. It suggests to students that these are just matters of faith without any evidence. And for myself, I'd prefer to reserve matters of belief and faith for things that are not tested empirically.

The Pandas authors say in the next paragraph that if Crossopterygians, by which they mean the fish-like things, really did evolve into amphibians, by which they mean the first animals that came on land, tremendous changes must have taken place. Fins must have been transformed into four limbs, the skull had to change from two parts to a single solid piece. The hipbones had to enlarge and become attached to the backbone. Numerous changes must also have occurred in other soft tissues and so on.

They say in the next paragraph, How many different transitional species were required to bridge the gap? Hundreds even thousands? We don't know, but we do know that no such transitional species have been recovered.

Slide 036
Slide 36: Pandas, p.104, claims that "two large gaps" exist, one on each side of crossopterygians (lobe-finned fishes related to tetrapods).
(Right-click to download pdf.)
Slide 037
Slide 37: Pandas, p. 103, compares Ichthyostega and Eusthenopteron.
(Right-click to download pdf.)

Credits: Image #: 3211693, Drawing by: Helen Ziska. American Museum of Natural History Library - Special Collections. Reproduced with permission.

Q. The next slide, is this a diagram from Pandas?

A. This is a diagram from Pandas of two forms from the fossil record. Eusthenopteron, which they take to be a fish, and Icthyostega, which they take to be an amphibian. Eusthenopteron doesn't look much like any fish you know. Neither does Icthyostega look much like any living amphibian. But in naming them like this, the editors, authors of Pandas are really giving them assignments to different whole groups of organisms and suggesting that the transition between them would be very difficult to achieve.

Slide 038
Slide 38: A series of fossils with transitional features exist between "fish" and modern tetrapods. Padian lists a number of the claims Pandas makes (pp. 103-104) and compares them with the fossils.
(Right-click to download pdf.)

Credits:

Neoceratodus modified from p. 135 of Long, J. (1995). The Rise of Fishes, Johns Hopkins University Press. Original photo credit: Dr. Alex Ritchie, Australian Museum.

Panderichthys, Tulerpeton, phylogeny, modified from p. 58 of: Clack, Jennifer A. (2004). "From Fins to Fingers." Science 304(5667), 57-58. (DOI) Art by Emese Kazar -- http://www.emesekazar.com/, reproduced with permission.

Acanthostega (2005 reconstruction) from Figure 1c, page 137 of: Ahlberg, Per Erik; Clack, Jennifer A.; Blom, Henning (2005). "The axial skeleton of the Devonian tetrapod Ichthyostega." Nature, 437(7055), 137-140. (DOI) Reprinted by permission from Macmillan Publishers Ltd., copyright 2005.

Ichthyostega (2005 reconstruction) from Figure 1a, page 137 of: Ahlberg, Per Erik; Clack, Jennifer A.; Blom, Henning (2005). "The axial skeleton of the Devonian tetrapod Ichthyostega." Nature, 437(7055), 137-140. (DOI) Reprinted by permission from Macmillan Publishers Ltd., copyright 2005.

Greererpeton from Figure 1a, p. 77 of: Godfrey, S. J. (1989). "The Postcranial Skeletal Anatomy of the Carboniferous Tetrapod Greererpeton burkemorani Romer, 1969." Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 323(1213), 75-133. Reproduced with permission of the Royal Society and Stephen Godfrey.

Ensatina salamander photo © 2005 Tom Devitt, U.C. Berkeley Department of Integrative Biology and Museum of Vertebrate Zoology. Reproduced with permission.

Thunnus modified from this image at the Monterrey Bay Aquarium.

Certainly there are differences between these two skeletons. There are differences in the way they're drawn, as well as many features of their specimens that we find in the fossil record. And the next slide --

Q. I'm sorry, and that was from Page 103 of Pandas?

A. Yes. We've prepared some slides that show a bit more accurately the way that scientists understand this fossil record. What we've done here is to take the text from Pandas on Pages 103 and 104, but to illustrate our illustration of some of the major fossil animals that are known that move from aquatic, fish-like critters, up into the first animals that appear on land.

We're including in this Eusthenopteron, which is the second guy from the bottom left, and Icthyostega, which is three more guys up to the right from him, which are the two animals you saw in the last slide in Pandas. Pandas is giving you two animals and inviting you to draw contrasts between them. What we'd like to do is show the evidence that scientists have to show comparisons and to show the transitional features that the Pandas authors say do not exist.

So, for example, the text in the upper left taken again from Pandas insists in blue that no transitional species have been recovered.

Q. Could you read that please, that quote?

A. It says, How many different transitional species were required to bridge this gap? We don't know, but we do know that no such transitional species have been recovered.

Now, here, of course, we're going to focus on what are you defining as a transitional species? Does it have to be a direct ancestor, does it have to be intermediate in all features? Do you have to know that it had the same genetic antecedent composition and therefore could only have been the great, great, great, great, great, great grandfather of the next animal along the way?

That seems like a very difficult standard of evidence to live up to. We can't do that with humans most of the time, and I'd be surprised if we could do it with animals that are 350, 400 million years old.

The next slide looks a lot like the one you just saw. The Pandas authors say in blue that there are two large gaps in the fossil record that we're talking about here. One is between ordinary fish and Crossopterygians, what they would regard as the organisms that are closest to the land animals, and an even larger second gap between these lobed-finned fish and amphibians, again, the transition to life on land.

This slide just points out where the ray-finned fish are on the left. Ray-finned fish include the 25,000-odd species of fish that live today that we would all think of as fish, that is, tunas, trout, salmon, monkfish, angler fish, catfish. It would not include sharks, for example, which are cartilaginous animals. And it doesn't include any of the animals you see running along the right side of this slide. No one thinks that an animal like a trout directly gave rise to an animal like a frog.

Q. When you say "no one," no one in science?

A. No one in science, but I don't think any creationist obviously wouldn't think so, either. But scientists don't think this. Rather, we find that ray-finned fishes, this great radiation of 25,000 species today reaching back into the remote past, have a long history that's independent from the other watery creatures, so to speak. And, in fact, their histories are quite separate.

The two little crosses below the ray-finned fish and the two little crosses to the left of the lungfish are representations of two pairs of fossil species are that listed on the right-hand side. We call them stem taxa because they are ancient relatives. Their names here, just for a couple of examples, Moythomasia and Howqualepis. The names are really unimportant. And on the other side, Psarolepis and Achoania. Again, the names are unimportant.

Slide 039
Slide 39: Pandas' claim about "two large gaps" in the fossil record of the fish-amphibian transition, one on each side of the crossopterygian Eusthenopteron, is challenged. Panderichthys and Acanthostega fill in the gap on the tetrapod side (they were joined by Tiktaalik in 2006), and fossils in the stem groups of both lobe-finned and ray-finned fishes fill in the gap to "ordinary fish."
(Right-click to download pdf.)

But it just goes to show you that we have extinct relatives outside the lungfish. We have extinct relatives outside the ray-finned fishes that indicate that the ray-fins are not directly ancestral to the lungfish and all the other animals on the right side. They are rather a separate evolutionary branch, and they have been since way back in the Devonian, 400 or so million years ago.

The next slide talks a bit about another transition here where the Pandas authors note that fins must have transformed into four limbs, which is certainly fair enough, but they say that no such transitional species have been recovered.

Well, again, here is this cladogram that you see here. And I want to stress, as I did before, that the cladogram in question, that is, the way that we have -- the way that we have developed the relationships of the lungfish, the Eusthenopteron, Panderichthys, and all the other animals on this slide are not just based on a couple of features, they're based on dozens and dozens and dozens of skeletal characters of which we're only going to show a few. But this is backed up by a lot more evidence in peer-reviewed publications that I'll show you at the end of this.

The Pandas authors say that no such transitional species have been recovered, but, in fact, we have indications here, beginning with Eusthenopteron, of a limb that is a very interesting limb with branching bones in it.

Q. I'm sorry, the photograph just below the blue text on Pandas there, what is that?

A. That's a photograph of a limb of Eusthenopteron. And you'll have to excuse me, I'm showing you some Paleozoic road-kill. That's the best way I can describe it. It's pretty ugly. But I wanted to show you the actual fossils so you could see that we have them and then to show you next to that a drawing of what these bones actually are.

This doesn't look much like an arm of any animal today, but scientists have been able to compare the elements, which we've put here in the same colors, by the process of homology, which I'll talk to you about later. And there really is no dispute about the fact that these are, in fact, the precursors of limbs that we see in animals today, the same kinds of structures, the humerus here in yellow, the radius, and ulna, which are, I guess, in green, and then some of the features that become parts of the hand and the other digits in a darker color there.

Slide 040
Slide 40: The fossils show transitional features specifically in the limbs, where Pandas' figure 4-9 claims there is a gap.
(Right-click to download pdf.)

Credits:

Phylogeny, forelimbs, Panderichthys, Tulerpeton modified from p. 58 of: Clack, Jennifer A. (2004). "From Fins to Fingers." Science 304(5667), 57-58. (DOI) Art by Emese Kazar -- http://www.emesekazar.com/, reproduced with permission.

Fin/forelimb figure from Pandas Figure 4-9, p. 104. ©1993 by Foundation for Thought and Ethics, Richardson, TX 75083-0721

Greererpeton forelimb from Figure 26b, p. 118 of: Godfrey, S. J. (1989). "The Postcranial Skeletal Anatomy of the Carboniferous Tetrapod Greererpeton burkemorani Romer, 1969." Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 323(1213), 75-133. Reproduced with permission of the Royal Society and Stephen Godfrey.

You can also see that in the course of evolution, animals that begin having eight digits, such as Acanthostega here, reduce to seven digits, to six digits, and to five digits. I don't know how we could find anything more in the way of transitional forms or features unless we went to six and three-quarters or five and a half digits. But, I mean, that may be as good as we'll get in the fossil record in terms of a transition.

So we do have a very clear change, not just in the reductions of digits, but you'll also notice that they look a lot more digital-like the closer you get to the animals that we recognize as living amphibians and so forth.

In contrast, above, when Pandas teaches this to students, it gives them two animals and invites them to draw contrasts. It essentially does not identify any of the bones, does not indicate that you could have any identification between those two bones, places them in different positions, reconstructs an outline for them that may not be unreasonable, but it's certainly in a different orientation.

And its function, the cumulative effect is really to sort of confuse students, and certainly I'm confused looking at it about what I'm supposed to take out of a diagram like this, except the fact that, boy, these are different, and I don't see how we could get from one way to the other. It would have been so much nicer if they had used a diagram like the one at the bottom or acknowledged that we did at least have some transitional features that we could discuss.

Q. And that's Figure 4.9 from Pandas at the top of the slide?

A. That is Figure 4.9. The next slide is another feature. The Pandas authors, as noted before, said the skull had to change from two parts to a single solid piece, but, again, no such transitional species have been recovered.

Q. And, I'm sorry, that's what Pandas authors say?

A. That's what Pandas says, yeah. But as you can see, on this slide we can go easily from two mobile parts to two immobile parts to two parts that are fused and lack a ventral gap, that is, a one-part skull, to all the remaining vertebrates which have a one-part skull. This is a perfectly reasonable transition, morphologically and physically, and it's difficult to see how you could become any more transitional than this.

Q. So these are transitional fossil forms that have --

A. These are drawings of actual specimens and reconstructions of them from the scientific literature.

The next slide I think will indicate that although the Pandas authors say that the hipbones had to enlarge and become attached to the backbone, no such transitional species have been recovered, according to the Pandas authors.

Slide 041
Slide 41: Pandas also claimed a gap between the two-part skull of fishes and the one-part skull of tetrapods. These fossils are also transitional in this feature, where the skull shifts from two mobile parts, to two immobile parts, to two fused parts, to finally the "one part" skull of early tetrapods.
(Right-click to download pdf.)

Credits:

Eusthenopteron neurocranium from: Jarvik, E. (1980). Basic Structure and Evolution of Vertebrates, vol. 1, Academic Press.

Panderichthys neurocranium from Figure 2a, page 62 of: Ahlberg, Per E.; Clack, Jennifer A.; Luksevics, Ervins (1996). "Rapid braincase evolution between Panderichthys and the earliest tetrapods." Nature, 381(6577), 61-64. (DOI) Reprinted by permission from Macmillan Publishers Ltd., copyright 1996.

Ichthyostega neurocranium from Figure 3c, page 68 of: Clack, J. A.; Ahlberg, P. E.; Finney, S. M.; Dominguez Alonso, P.; Robinson, J.; Ketcham, R. A. (2003). "A uniquely specialized ear in a very early tetrapod." Nature, 425(6953), 65-69. (DOI) Reprinted by permission from Macmillan Publishers Ltd., copyright 2003.

Slide 042
Slide 42: The fossils also show how the rear fins first became attached to the backbone via the sacral rib, and how this attachment was enlarged. Panderichthys specimens, in press in October 2005, filled in an additional piece of this transition in December (see Boissert 2005 in Nature).
(Right-click to download pdf.)

Credits:

Eusthenopteron pelvis from: Jarvik, E. (1980). Basic Structure and Evolution of Vertebrates, vol. 1, Academic Press.

Acanthostega pelvis from Figure 1c, page 137 of: Ahlberg, Per Erik; Clack, Jennifer A.; Blom, Henning (2005). "The axial skeleton of the Devonian tetrapod Ichthyostega." Nature, 437(7055), 137-140. (DOI) Reprinted by permission from Macmillan Publishers Ltd., copyright 2005.

Ichthyostega pelvis from Figure 1a, page 137 of: Ahlberg, Per Erik; Clack, Jennifer A.; Blom, Henning (2005). "The axial skeleton of the Devonian tetrapod Ichthyostega." Nature, 437(7055), 137-140. (DOI) Reprinted by permission from Macmillan Publishers Ltd., copyright 2005.

But we can see, moving from Eusthenopteron up through Acanthostega and Icthyostega, that, in fact, you can go from small, unattached hind limbs and hipbones to become somewhat larger as you can see in Acanthostega and attached to the backbone by what we call a sacral rib. Our sacroiliac is the human equivalent of that.

And as you can see in Icthyostega and other animals, it gets even larger, expanded and attached to the backbone as these animals begin to use their limbs more in support of the skeleton. And as they come out on land, this will be even more important, as it is, of course, in the living animals which -- almost all of which have at least two sacral ribs attaching to their backbones.

Slide 043
Slide 43: A number of the important papers published on the fish-amphibian transition.
(Right-click to download pdf.)

So I think the next slide is just a depiction of some of the references from the scientific peer-reviewed literature from which the slides I've just shown you have given us the information.

Q. Could you just maybe read a couple of the titles into the record, please?

A. Yes. Fins to Limbs, What the Fossils Say, that appeared in Evolution & Development. Again, you can see where paleontology and developmental biology are seeing a great cooperation and a great number of new insights. From Fins to Fingers, again, a paper published in Science by Jenny Clack, who is a paleontologist at Cambridge. Fish-Like Gills and Breathing in the Earliest Known Tetrapod. So we can actually find fossil evidence even of some soft tissues which tell us a bit about these sorts of things. And I'd like to point out that these works are published in Nature, in Science, in the Bulletin of the British Museum of Natural History, and in the Philosophical Transactions of the Royal Society of London, among other publications.

Q. Dr. Padian, I note that some of these articles appear to be pretty old, for instance, Fins to Limbs appears to have been published in 1969, Bulletin of the British Museum is 1984. These were published before Pandas was written.

A. Yes.

Q. So the fact that there were, in fact, transitional fossils is something that was known to scientists at the time Pandas was being written and was published?

A. Yes. There were many fossils that had transitional features that were available in the scientific literature, as scientists understood them. And so for whatever reason, these were not included by the authors of Pandas. Perhaps they didn't accept it as evidence.

Q. And do you know why in Pandas they would misrepresent, it seems, or not accurately portray the state of scientific knowledge at the time?

Slide 044
Slide 44: The famous quote from Pandas, pp. 99-100, which said that intelligent design "means that various forms of life began abruptly," including "birds with feathers, beaks, and wings," which Padian will cover in the next section. This quote also explicitly contrasts ID with "natural cause" explanations
(Right-click to download pdf.)

A. Well, the Pandas book, as noted, promotes the view of intelligent design, which they state here means that various forms of life began abruptly through an intelligent agency with their distinctive features already intact, fish with fins and scales, birds with feathers, beaks, and wings, et cetera. I believe this is from maybe Page 99.

Q. That's right. And what you've just shown us is an evolutionary pathway?

A. Well, this is sort of worrisome, because scientists would interpret this as an evolutionary pathway, and intelligent design seems to be excluding the possibility that you can actually get those pathways. Now, we should note that as you pointed out, some of those publications I just showed were available when Pandas was written and some of them appeared afterward.

But it worries me that students would be told that they have to make a conclusion in advance of all the evidence that you can't get from A to B, essentially, by natural means. This quotation from Pandas says, Should we close our minds to the possibility that the various types of plants and animals were intelligently designed? This alternative suggests that a reasonable natural cause explanation for origins may never be found and that intelligent design best fits the data.

And so the question I would have is, what is a kid supposed to think when you tell him that you can't get from Point A to Point B and then evidence is uncovered that shows that, well, in fact, it looks pretty conceivable you can get from Point A to Point B and we're not making up this stuff.

Is a student supposed to say, well, gee, I guess there's no designer? Or is the student supposed to say, well, I guess the methods of intelligent design are really not very good? Or is he supposed to conclude something else? The intelligent design proponents provide no guidance on this.

Q. So when Pandas asserts that fish must have been created abruptly intact with fins and scales, really science has refuted that proposition?

Slide 045
Slide 45: Again on p. 100, Pandas contrasts ID with natural causes, saying that ID "suggests that a reasonable natural cause explanation for origins may never be found."
(Right-click to download pdf.)

A. Yes.

Q. And in the passage which I think virtually every expert witness has focused on in this trial, Page 99 to 100, when they talk about fish being formed abruptly and the other animal that's mentioned there is birds with wings, feathers, and beaks already intact, can you talk to us about whether or not there is an evolutionary pathway, natural explanation for the evolution of birds?

 


 

IV. The Origin of Birds

A. Well, I'd be delighted to, if I can look at the next slide. As it turns out, when I went to graduate school, my advisor there, John Ostrom, is the person who actually established the origin of birds from carnivorous dinosaurs. And this became very well accepted over the next several years. We are now 30 years on into that, and it is one of the great achievements of 20th Century paleontology and that kind of science.

And I did work on this myself in the course of 30 years of research, the origin of birds and the origin of flight and of feathers. And so I'd like to show a little bit about what science has understood about this.

The next slide, I believe, gives you two quotes from Pandas, along with a picture of Archaeopteryx, which is the first known bird. It's about 150 million years old. It comes from Germany. It's a beautiful fossil. This is the Berlin specimen. It's known from a number of specimens, seven or eight now.

And as you can see, it's got beautiful wings, feathers, look very modern in their appearance, and yet Archaeopteryx has a long bony tail, its skull still has teeth, it's got various configurations of bones that we don't find in birds today. Many of the bones of its hand and foot are not fused like the bones of living birds. And so it's been known since its discovery in the 1860s, the time of the Civil War, right after Darwin published the Origin of Species, that scientists have accepted this as an animal that shows a lot of intermediate characteristics between birds and other animals, particularly certain kinds of reptiles.

Q. And what does Pandas say about this?

A. Well, Pandas says that there is no gradual series of fossils that lead from fish to amphibians or from reptiles to birds, rather these animals are fully formed.

Q. And you were quoting from Page 106 of Pandas?

Slide 046
Slide 46: Padian will now discuss the origin of bird from dinosaurs, and the origin of feathers.
(Right-click to download pdf.)
Slide 047
Slide 47: Pandas takes note of Archaeopteryx (the famous Berlin specimen is shown at right), but complains "[i]f only we could find a fossil showing scales developing the properties of feathers" then "we would have more to go on." "But," concludes Pandas, "the fossil record gives no evidence for such changes."
(Right-click to download pdf.)

Credits: Photo author unknown (various versions widespread on the web). This is the famous Archaeopteryx Berlin Specimen, Museum fuer Naturkunde, Berlin, Germany. See the museum website for the Berlin specimen.

A. 106, yeah. And that's one problem that they come up with. And a second problem that they talk about on Page 22 is that -- is their bemoaning the lack of fossils that show scales developing the property of feathers. They say, then we would have more to go on, but the fossil record gives no evidence for such changes.

I've picked out these two quotes because I want to emphasize that in the first case, there was very good evidence for the evolution of birds from dinosaurs when they wrote Pandas. And in the second case, they were right at the time, we did not have very many fossils that showed anything about the origin of feathers.

But in the past decade, we've had a bunch of remarkable fossils that have. And so this raises the question again of, if you tell children that you can't get there from here and then evidence is found, what are you going to do?

Slide 048
Slide 48: A number of recent discoveries of fossil dinosaurs -- with feathers -- published in Nature in the last ten years.
(Right-click to download pdf.)

The next slide, I believe, talks about some of the -- this is really just a montage of a few, I mean, it's just a very few of the papers about feathered dinosaurs, dinosaurs that are not birds, they didn't fly, but they had various kinds of very rudimentary feathers.

And these have been discovered in a remarkable deposit in Northeastern China, the first one in 1996, so this was after Pandas was written. And so we wouldn't expect those authors to know anything about these discoveries, but it just goes to show that there are some really interesting things that crop up.

Q. And could you just read into the record the titles of some of these?

A. An Exceptionally Well-Preserved Theropod Dinosaur from the Yixian Formation of China. This is a dinosaur with feathers. The next one is Two Feathered Dinosaurs from Northeastern China. Another one here is Branched Integumental Structures in Sinornithosaurus and the Origin of Feathers.

Q. In what type of journals were these published in?

A. These happen to be taken all from the journal Nature, which is one of those two magazines that I noted that all scientists are going to read every week. They're the most prestigious journals to publish in.

Q. And what you're going to show us now about the evolution of feathers is taken based on these peer-reviewed --

A. These and many others, yes. In the next series of slides, if I may, I'd like to show you three things going on at once, because I want to tell you that this is not simply a matter of speculation or of isolated observation and inference, that this comes from independent lines of evidence, not just the fossil record.

What I've done in this series of slides is to take, on the left, one of those hat rack cladograms that show you the relationships of organisms, and again I've turned it on its side. So you can see that Archaeopteryx and modern birds are on the bottom, and that successively the groups above them are various dinosaur groups that are closely related to them.

Slide 049
Slide 49: Padian will show a number of feathered dinosaur fossils, showing where cladistic analysis places them in the phylogeny. The phylogeny allows the ancestral states (the stages, marked in red on the phylogeny) to be reconstructed. Here, a compsognathid fossil (Sinosauropteryx) with hairlike protofeathers down its back. This is exactly what Pandas demanded, a fossil "developing the properties of feathers."
(Right-click to download pdf.)

Credits:

Feather drawing by Patricia J. Wynne. From pp. 90-91 of: Prum, R. and Brush, A. (2003). "Which Came First, the Feather or the Bird?" Scientific American, 288(3), 84-93.

Sinosauropteryx neck/head/feathers from Figure 2a, page 148 of: Chen, Pei-Ji; Dong, Zhi-Ming; Zhen, Shuo-Nan (1998). "An exceptionally well-preserved theropod dinosaur from the Yixian Formation of China." Nature, 391(6663), 147-152. (DOI) Reprinted by permission from Macmillan Publishers Ltd., copyright 1998.

I want to stress that this scheme of relationships, again, is based on dozens and dozens of characteristics that are not controversial to any extent in the scientific community, and whereas we do have uncertainties about some of the minor relationships among these animals, this is the scheme that is generally accepted by paleontologists.

On the upper right, I want to show you a series of pictures that were taken from an article in Scientific American that reflects the work of Rick Prum at Yale and Alan Brush and Scott Williamson and their coauthors on the development of feathers, that is, how feathers develop in living birds.

And the reason for doing this is to couple this with a series of slides I'm going to show you on the bottom, which are of fossils of feathered dinosaurs, that is, dinosaurs that are not birds but that have feathers or some structures that are rudimentary feathers.

And what I want to show you is that as we proceed on the left up the tree leading to birds, we will also see that the feathers that are found in these little carnivorous dinosaurs in the lower right are becoming more and more complex and that they are reflecting the complexification of feather structure seen in the series of diagrams in the upper right as feathers develop embryologically.

So we're actually looking at phylogeny or relationships on the left, we're looking at fossils on the right, and we're looking at developmental structures and embryology on the upper left -- upper right, I mean. Fair enough? Okay.

Then in this stage, we see a little animal in the lower right, and that black fuzz that seems to be going along its backbone is recognized as the most basal traces of things that are going to become feathers. And these structures are hair-like. They look like the structures in the upper right. There has been observation suggesting that they are even hollow in their structure. And we find these at that point in the cladogram noted at Stage 1 on the left-hand side.

The next slide should show us Stage 2. Now we've just jumped up a notch in the cladogram. And here we're beginning to find not just these single filamentous features, but also feathers that begin to branch and begin to have different kinds of tufts involved with them. The specimen on the lower right I realize is a road-kill and it's difficult to interpret, but let me see if I can just give you a sense of -- there we go. Down here we have bones of the backbone, tail. And these black and white marks up in here are remnants of these branched, feathery structures that appear in these dinosaurs.

The next slide shows a further complexification of feathers in the next step up on the cladogram toward birds in which we have a gaggle of feathers there in the center. These are just a group of feathers that have, as you might be able to see, a central sort of stalk where you can see all these things gather in the middle. You can see this happening in the early development of a feather in the upper right. And then you see the feather differentiating into veins along a central stalk, just like you see in the next stage of the development of a feather in a bird that lives today.

Slide 050
Slide 50: Protofeathers become more complex with a branching structure, represented in the tyrannosaurid Dilong. The "stages" come from the evo-devo work of Richard Prum and Alan Brush.
(Right-click to download pdf.)

Credits:

Feather drawing by Patricia J. Wynne. From pp. 90-91 of: Prum, R. and Brush, A. (2003). "Which Came First, the Feather or the Bird?" Scientific American, 288(3), 84-93.

Dilong feathers from Figure 3a, page 683 of: Xu, Xing; Norell, Mark A.; Kuang, Xuewen; Wang, Xiaolin; Zhao, Qi; Jia, Chengkai (2004). "Basal tyrannosauroids from China and evidence for protofeathers in tyrannosauroids." Nature, 431(7009), 680-684. (DOI) Reprinted by permission from Macmillan Publishers Ltd., copyright 2004.

Slide 051
Slide 51: The next stage is the development of a central vein, or "rachis," in the protofeather. These structures are symmetrical and not aerodynamic.
(Right-click to download pdf.)

Credits:

Feather drawing by Patricia J. Wynne. From pp. 90-91 of: Prum, R. and Brush, A. (2003). "Which Came First, the Feather or the Bird?" Scientific American, 288(3), 84-93.

Protarchaeopteryx feather from Figure 3a, page 756 of: Qiang, Ji; Currie, Philip J.; Norell, Mark A.; Shu-An, Ji (1998). "Two feathered dinosaurs from northeastern China." Nature, 393(6687), 753-761. (DOI) Reprinted by permission from Macmillan Publishers Ltd., copyright 1998.

Slide 052
Slide 52: In stage 4, barbules link the barbs together. Still symmetrical. Representative: Caudipteryx.
(Right-click to download pdf.)

Credits:

Feather drawing by Patricia J. Wynne. From pp. 90-91 of: Prum, R. and Brush, A. (2003). "Which Came First, the Feather or the Bird?" Scientific American, 288(3), 84-93.

Caudipteryx feathers from Figure 8b, page 760 of: Qiang, Ji; Currie, Philip J.; Norell, Mark A.; Shu-An, Ji (1998). "Two feathered dinosaurs from northeastern China." Nature, 393(6687), 753-761. (DOI) Reprinted by permission from Macmillan Publishers Ltd., copyright 1998.

Slide 053
Slide 53: In dromaeosaurs like Microraptor -- still phylogenetically basal to Archaeopteryx and more modern birds -- asymmetrical feathers have developed with aerodynamic properties.
(Right-click to download pdf.)

Credits:

Feather drawing by Patricia J. Wynne. From pp. 90-91 of: Prum, R. and Brush, A. (2003). "Which Came First, the Feather or the Bird?" Scientific American, 288(3), 84-93.

Microraptor feather from Figure 3c, p. 338 of: Xu, X.; Zhou, Z.; Wang, X.; Kuang, X.; Zhang, F.; and Du, X. "Four-winged dinosaurs from China." Nature 421(6921), 335-340. (DOI) Reprinted by permission from Macmillan Publishers Ltd., copyright 2003.

The next slide, again, at this stage we also see another kind of feather that is a feather that is organized very well into veins on each side. And these veins are very well organized along the central stalk. In this fossil I've shown you in the middle, you can see perhaps faintly the outline of these black and white structures radiating off along this white stripe, which is the central axis of the feathers.

And so these are several feathers from the tail of one of these animals that are just bunched up right next to each other in one of these fossils. And, again, this is mirrored also in the progress of development from the feather from a single follicle bud up to a complete feather that we'd see today.

The final stages I want to show you as we get closer to birds is a feather in which the veins are asymmetrical, that is, one side of the feather is bigger and the other side is smaller. And this is seen in birds today, but it's also seen in some of the other carnivorous dinosaurs that are close to birds, but not in all of them.

So, again, what we're seeing is as we move up the cladogram towards birds, we go from the simplest filamentous feathers up to more complex structures that are then gathered and around a central stalk that produce veins. These are interlocked by barbs and barbules, and they eventually become the aerodynamic structures that birds use in their wings.

Slide 054
Slide 54: What good is half a wing? Feathers have many known functions besides flight.
(Right-click to download pdf.)

But I'd like to point out, if I can, in the next slide that the obvious question is, what are they doing with these feathers before they're flying? And the evidence that we found in the fossil record in the last ten years indicates beyond any reasonable question that feathers did not evolve for flight. Flight was an afterthought for birds. They somehow acquired that adaptation later on.

What do we know about those first little hairy feathers that we're looking at? Well, one thing we know is, if you put a fur coat on somebody, they're going to stay warmer. And this little covering of dense fibers is going to give you insulation. That tells us something about the metabolic status of these animals even then.

Another thing is, you may have noticed some dark and light color patterns on those feathers. The fossils preserve this. What good are color patterns? Well, on these animals, they could serve as camouflage, as display, or even to help them recognize species.

I'm going to show you another function in a second that indicates that these animals were also using the feathers to shelter the eggs as they brooded their young. And these are all examples of what we call exaptation and evolution. And by that I mean that a structure evolves for one purpose, but it's selected, in turn, to acquire a second purpose, without, of course, losing the first one instantly. It will retain the first one.

And as it develops the second one, because it has the ecological opportunity or the pressure to do so, that second structure, that second function, may become more and more important to the structure, it may be selected to change more to accommodate this new function. And this is how exaptation works to change one kind of function into another through evolution.

Q. You have at the top there, What good is a half wing? What do you mean by that?

A. Well, if you just -- this is the question that has always been asked of evolutionists. St. George Mivart asked this of Darwin in the 1870s, what good is half a wing?

And the answer is, well, if you don't think of it as something you have to use to fly with, you can find out other functions if you just let the evidence tell you. And these are some of the lines of evidence. I will briefly show, if I may, a couple of these other functions.

Slide 55a: The pattern of digits in groups sister to birds. Digits were lost progressively -- first V, then IV.
(Right-click to download pdf.)

The next slide provides some additional evidence of the other problem we talked about, not so much feathers, but the question of the evolution of birds. We have tremendous evidence on this, but one line of evidence comes from the hand itself. If you look at the hand of crocodiles, they have got five fingers. If you go all the way over to the left, you see Archaeopteryx, the first bird, that has only three.

Well, again, here's a cladogram of relationship diagrams of how these organisms are related based on many, many characteristics. And as we move up from the crocodiles through the various kinds of dinosaurs, we see that the fourth and the fifth finger, first the fifth and then the fourth, become reduced and finally lost, until, when you get up to animals like Allosaurus, Deinonychus, and Archaeopteryx, they have only three fingers, and those are the first three fingers. The second finger is the longest, and you can see that through time, these fingers and the hand bones become even longer and more gracile.

Those three fingers that you see in Archaeopteryx at the end are still separate fingers, but in birds today, they're fused up. You would know them better as the pointy part of the wing in the Kentucky fried chicken.

So if you were to dissect your Kentucky fried chicken, which I don't recommend, but I can tell you about turkeys and Thanksgiving, which is a lot of fun, you will find that you can get to the individual hand bones, we can watch the bird develop, and these are individual bones that later become fused. And this is because the bird is no longer using its hand for anything except flight. It's not using its fingers to pick up things or claw or scratch anymore.

And early in the evolution of birds, when they dedicated themselves to flying with the four limbs and very little else, there was no further need to use these fingers for anything, and it made more sense to fuse them into position rather than use muscles to hold them there. And this is the evidence that we have of how these organs evolve.

Slide 55b: The fossil record preserves not only bones -- sometimes it even preserves behavior. This 1995 Nature paper shows an Oviraptor sitting on a nest.
(Right-click to download pdf.)

Credits: Oviraptor from Figure 1a and Figure 2, page 775 of: Norell, Mark A.; Clark, James M.; Chiappe, Luis M.; Dashzeveg, Demberelyin (1995). "A nesting dinosaur." Nature, 378(6559), 774-776. (DOI) Reprinted by permission from Macmillan Publishers Ltd., copyright 1995.

The next slide, I believe, will give us one more thing about feathers and behavior, too. This is a dinosaur, an extraordinary ostrich dinosaur relative. It's an Oviraptor dinosaur. The name isn't important. But one thing you can see about this specimen, which is very beautiful, it comes from the Cretaceous of Mongolia, is that in the photograph at the top, I'm going to show you, here is the right arm, here is the humerus, the bones of the forearm, and three clawed fingers of the right hand. Moving over to the other side, the arm comes out here, and here are the three clawed fingers of the left hand.

These white objects you see in this specimen are eggs. And here is the hind limb and the foot on the left side. Here is the hind limb and foot of the right side. Here is part of the tail. And the animal's rib cage is in here. There are more eggs underneath this animal. This critter was brooding its eggs in exactly the same position that hens brood their eggs today.

Furthermore -- well, one thing to draw from this is that some behaviors that we associate with birds did not evolve with birds, they actually apparently were already present in the dinosaurian relatives of birds, and they simply were passed on to birds as they evolved.

But the other thing this shows is a funny thing. The fingers, you'll notice, are spread so as to cover the eggs. And in the fossil relatives of this particular dinosaur, not this specimen because they aren't preserved, but we have feathers in other Oviraptor dinosaurs that come off the fingers that are long and gracile. And if this particular dinosaur had preserved its feathers, it would have been using them to shelter the eggs as it brooded them. This is evidence of behavior, not just of structure, that we can find very anciently in the fossil record.

Slide 55c: Another example of behavior preserved in the fossil record. This 2004 Nature paper shows a small troodontid dinosaur, Mei long, displaying "the earliest recorded occurrence of the stereotypical sleeping or resting behaviour found in living birds." The head is tucked under the wing.
(Right-click to download pdf.)

Credits: Mei long from Figure 1c-1d, page 839 of: Xu, Xing; Norell, Mark A. (2004). "A new troodontid dinosaur from China with avian-like sleeping posture." Nature, 431(7010), 838-841. (DOI) Reprinted by permission from Macmillan Publishers Ltd., copyright 2004.

The next slide, I believe, shows an equally extraordinary find. And this is of a dinosaur, not a bird. He looks a lot like a bird, but he's in a sleeping position. And what is unusual about this critter is that here's its skull here with its big eye right here, and here's its little beak and its tail, bones like this. Up here are the arm bones of the left arm. And what this animal is doing -- his tail end is back this way and his front end is really to the left, but he's tucked his head and neck underneath his left arm. In other words, he's sleeping like a bird does. This is not a bird. This is a little carnivorous dinosaur that's close to birds.

So, again, there is remarkable evidence that not just the structures of birds, but the behaviors of birds can sometimes be found in the fossil record and they precede birds. They actually are more general. They apply to the fossil record of many dinosaurs, as well.

Q. And, again, this is all based on peer-reviewed research?

A. The paper you see there is from Nature.

Q. And so do scientists today understand that, in fact, birds evolved and were not created abruptly?

A. In fact, that they evolved from small carnivorous dinosaurs sometime in the middle or late Jurassic period about 150 million years ago.

MR. WALCZAK: You Honor, I know there have been a number of references to food here. I have one more very short topic that I'd like to cover with Professor Padian, and that will be a good place to break.

THE COURT: After that point?

MR. WALCZAK: Yes.

THE COURT: That's fine. I thought we'd go to about no later than 12:15, but if it takes longer than that, that's fine. Let's break at whatever point you think is logical so that we don't break up the testimony unnecessarily.

BY MR. WALCZAK:

Q. Professor Padian, you talked about this change of function, and I think you used the term "exaptation."

A. Yes.

Q. Is that a biological concept that's well established?

A. Yes, it is.

Q. And how do intelligent design proponents deal with exaptation?

A. Well, as far as I can tell, they don't really. It's very difficult for them to deal with exaptation because it implies that you can take a structure and change its function to a new function. And the whole purpose of intelligent design is to identify structures and functions that are too complex to have changed naturally from an antecedent state to a new state.

I believe that the evidence that I'm providing here is trying to show that we have, piece by piece, assembly of major adaptations. I believe that we've shown that with the transition of swimming animals up into the animals that came onto land, for example, a very good transition of features step by step by step, and that it isn't like an adaptational package of land animals that had to be assembled abruptly, but rather that structures are changed in their function.

So, for example, the fin of a fish moves up and down and helps it to negotiate the water, that is, to push water, pass it or to steer and do things like that in a medium that's a thousand times denser than air.

How do you get from that to an animal that puts its limbs under its body and stands on this limb? Well, as we've seen, what happens in the evolution of limbs from basic fins is that these bones become stouter and stronger. Their articulations change. They begin to be able to be much more able to support weight, and they change from having a lot of those individual sort of rays that you see in any fish fin to a fewer number of things that are covered by flesh. In fact, these are the fleshy fins that we have, our hands. They're exactly the same structures.

And we saw from the slides that these structures, the numbers of fingers, how they articulate, change in a very step-like pattern, not in an abrupt way at all. So the answer is that intelligent design proponents, this is the last thing they want to hear, because it would indicate to them that there are ways of getting from Point A to Point B when they want to talk about abrupt appearance and irreducible complexity.

MR. WALCZAK: I'd like to end abruptly now so we could get some lunch.

THE COURT: I don't know if there will be a run on chicken. But we'll break here until -- how are you proceeding time-wise?

We could take an abbreviated lunch, take an hour rather than the longer lunch, or we can go to 1:30, which might be a little bit more reasonable. I'll give you a crack at that because you know how much more you have on direct and you want to save time -- I know you don't want to bring this witness back -- you want to save time, reserve time for appropriate cross.

MR. WALCZAK: I'm guessing an hour, maybe a little bit more. We've got mammals, we've got whales.

THE COURT: Mr. Muise, if we stopped at 2:30 or if we gave Mr. Walczak until 2:30, if we reconvened at 1:30, would that give you enough time to cross-examine?

MR. MUISE: 2:30 and stop at 4:00, Your Honor?

THE COURT: Well, no, we'd stop at 4:30-ish. That would give you two full hours. But if you don't think that that's going to be enough, I want to try to regulate what we're doing here.

MR. MUISE: It's always hard to judge, Your Honor, you know, for cross-examination, depending on, you know, how the responses come, obviously.

THE COURT: Well, I'm saying I would hold Mr. Walczak, because I know there's an issue -- this witness has come a great distance. I would hold him to 2:30. You've got to keep it within two. Now, you may not use two, but I'm saying, is that enough? Now, if you want a little over, that's fine. I'm just trying to get a fix on --

MR. MUISE: Let's do an abbreviated lunch since we want to make sure we get done.

THE COURT: Let's take precisely an hour. We'll come back at 1:15. And then why don't you have a conversation during the lunch break about how you want to carve up the afternoon, because I think that's the appropriate thing to do.

So, Mr. Walczak, if you don't go too deeply into the afternoon and not give Mr. Muise enough time, in the interest of not bringing this witness back -- which I think is what you're striving to do. Am I correct?

MR. WALCZAK: That's right, Your Honor.

THE COURT: So as a courtesy, make sure he's got enough time. All right?

MR. WALCZAK: Yes, Your Honor.

THE COURT: We'll be in recess until 1:15.

(A luncheon recess was taken.)

 



 

V. Fossil Mammals

THE COURT: Be seated, please. All right, Mr. Walczak, you'll continue with the direct examination.

MR. WALCZAK: Your Honor, one of the things we did not do was formally move Professor Padian's as an expert, and I know that defendants have stipulated to his expertise.

THE COURT: Why don't you put the, I understand that, and I could refer back to this but it's easier for you to do it, state the exact purpose for which his testimony is being offered in the expert realm.

MR. WALCZAK: We would proffer Dr. Kevin Padian as an expert in paleontology, evolutionary biology, integrated biology, and macroevolution.

THE COURT: And then pursuant to the stipulation I assume you have no objections, Mr. Muise, is that correct?

MR. MUISE: That's correct, Your Honor.

THE COURT: All right. Then he's admitted obviously for that purpose nunc pro tunc. So let me ask you before you start your questioning, do you have an agreement as to how long you're going to go in order to reserve --

MR. WALCZAK: Oh, I'm guessing we have an hour to an hour and fifteen. As I told Mr. Muise, if we have to bring Professor Padian back on Monday, then it's not the end of the world and we certainly don't want to cut them short on their cross.

MR. MUISE: And I'll do my best to get it done before the end of the day.

THE COURT: All right. Well, we'll work with that, and you may proceed.

CONTINUED DIRECT BY MR. WALCZAK:

Slide 056
Slide 56: Padian will now address the origin of mammals. In classical taxonomy, the ancestors of mammals were called the "mammal-like reptiles," but so many fossils with transitional features are now known drawing a line between mammals and "reptiles" became arbitrary. In cladistic classifications, mammals and their fossil relatives are called therapsids.
(Right-click to download pdf.)

Q. When we finished we were talking about the evolution of birds, and just one last point I want to make on that before we move on to mammals. On page 99 to 100 of Pandas it makes the statement there that I think has been read previously in this trial that, "Intelligent design means that various forms of life began abruptly through an intelligent agency with their distinctive features already intact," and it says, "birds with feathers, beaks, and wings, etc." Now, in fact does the fossil record show whether birds evolved with those features intact?

A. You have a thing about the birds today. Dinosaur for lunch? To answer your question, it definitely doesn't show that these features evolved all at once intact, but rather in a step-like progression of features.

Q. So did the birds at first have just feathers and then the other features evolved?

A. We saw the simplification, we saw from a very simplified picture of all the feature that evolve in birds, but they start with very simple filamentous hair-like structures that are feathers, but if I had shown all the features of birds evolving we would have seen the wishbone appear very early before birds evolved and become a very boomerang shaped structure well before birds evolved or take flight. So that evolved for completely different purposes anyway, but birds do use the wishbone today as an anchor of some of the flight muscles. That wasn't the case originally for birds. There's just lots of features like that we could go through, sure.


The Evolution of the Ear in Mammals

Q. Let's talk about mammals. One of the examples that's referenced in Pandas is the mammalian ear, inner ear. Could you talk to us about how Pandas discusses the mammalian ear and what science shows about that? And you've prepared a demonstrative for this?

A. I put a couple of slides together about the transition in the evolution of the mammal ear, which is unusual compared to all the other vertebrates. The next slide I think shows a bit about this. This is going to get a little complex anatomically, but I hope it will only hurt for a minute. The bones of the middle ear, mammals have three of them. You might have heard of them as the hammer, the anvil, and the stirrup.

Slide 057
Slide 57: The mammalian middle ear contains three tiny bones: the stapes, the incus, and the malleus (popularly analogized with a stirrup, an anvil, and a hammer). Other vertebrates have only the stapes in middle ear, but anatomical consensus for over 100 years has been that the incus and malleus are homologous to the quadrate and articular, bones found in the jaw of the other vertebrates. Pandas denies that this amazing transition is documented in the fossil record.
(Right-click to download pdf.)

The stirrup is a bone that's always in the ear, but the mammals have this anvil and hammer thing which are just outside that stirrup bone. These anvil and hammer bones actually correspond to bones that previously made up the upper and lower jaw joint in all the other animals, not just reptiles or anything like them, but everybody pretty much. So the Pandas authors claim that to make this correspondence is really stretching it, because they said there's no fossil record of this amazing process.

Consider, that to make this change one of these bones had to cross the hinge from the lower jaw into the middle ear region of the skull. Again this is from Pandas page 121. So they're saying there's no record of this process and it would be an amazing thing to have to change. The next slide shows that there are actually many sources going back several decades that differ, and there are just a few of them there.

The first one was actually an article by Romer, who was the dean of American vertebrate paleontology for half the century, about a cynodont that has an incipient mammalian jaw articulation, and I'll show you what that is in a minute. That comes from the journal Science in 1969. Here's a somewhat later paper by Edgar Allen of Madison, and now it's Chicago, on the evolution of the mammalian middle ear, and then a third one I put there is very recent piece, a little piece in Science by Thomas Marin from Germany and Zhe-Xi Luo, who's curator at the Carnegie museum here in Pittsburgh just a few hours away, one of the great museums in the country, and they are talking about the evolution of these bones in the middle ear something that is uncontroversial as a principle in comparative anatomy of vertebrates in paleontology.

Q. Now, I note that first article I believe was from 1969.

A. Was.

Q. So this isn't a new development?

A. Oh, no. Oh, no. It's been known for decades.

Slide 058
Slide 58: A 1969 paper by the famous paleontologist Alfred Romer describes the existence of a fossil with just such transitional features.
(Right-click to download pdf.)
Slide 059
Slide 59: A paper by Edgar Allen also discusses the evolution of the mammalian middle ear.
(Right-click to download pdf.)
Slide 060
Slide 60: A third paper suggests that one step in the evolution of the middle ear -- separation of the bones from the mandible -- may have even happened twice, in two related lineages.
(Right-click to download pdf.)
Slide 061
Slide 61: Three early therapsid skulls, plus a modern possum skull, show the changes that occurred in the quadrate (blue, "q") and articular (red, "art") bones. As the quadrate and articular decrease in size, the squamosal (yellow, "sq") and dentary (purple, "d") bones will take over the function of jaw joint.
(Right-click to download pdf.)

Credits: Skulls modified from: Carroll, R.C. (1987). Vertebrate Paleontology and Evolution. W. H. Freeman and Co., New York.

Q. So what you're going to show us is something that was known 25 years before Pandas was published?

A. Yes, and they discuss it. Sure. The next slide I think gives some detail of what's going on here. Trying to make this as painless as possible, there are essentially two sets of bones that are involved in one animal or another in the hinge between the upper and the lower jaw, and outlined in different colors in the skull on top I think you can see an orange bone and maybe a purplish type bone, and in the lower jaw you can see a red one and a blue one.

Now, this is an animal that is not a mammal. It's an ancient relative of mammals, and the jaw joint in this animal is formed by two bones, that blue one marked by a "Q" in the top jaw and the red one, which is called the articulator, in the lower jaw. So the quadrate and the articular are the two bones that in all other animals except mammals make up the jaw.

Slide 062
Slide 62: The skulls in phylogenetic arrangement. Probainognathus and Morganucodon document exactly the transitional stage that Pandas claimed was undocumented. These fossils have jaws in which quadrate-articular and dentary-squamosal joints function simultaneously.
(Right-click to download pdf.)

The next image is of a critter called Probainognathus, which again is not a mammal. It's a little bit closer to mammals than the first guy is, and in this animal you will see that now not only do we have the articulation between the Q bone and the art bone, which is the quadrate and the articular in the upper and lower jaws, but also there is an articulation between the bone in the lower jaw marked with a "D" called the dentary and the squamosal in the skull, and this can be seen perhaps if I can rouse it, sort of in this area here where the dentary and the squamosal would meet right next to the quadrate and the articular.

So these animals actually have what we call a dual jaw joint of two pairs of bones that are actually articulating next to each other on the upper and lower sides of the skull. The next slide is of Morganucodon, which is another animal, again slightly closer to mammals, that also shares this dual jaw joint of the two bones, and the top of the two bones with the bottom I won't bother with the details, and finally the fourth slide is of a typical garden variety, garbage pail variety possum, which has now changed this articulation so that only the dentary and the squamosal bones are connected.

The quadrate and the articular are no longer part of the jaw joint. So we have gone from a quadrate articular joint in which the dentary and squamosal don't participate to two animals, the second and third I showed, there are others like Diarthrognathus I could have shown, in which you have two pairs of bones sitting next to each other and articulating, making that jaw joint, to a situation in mammals, the possum is an example, but many, many mammals in the fossil record would do as well as all the mammals today in which just the new articulation the dentary squamosal is made.

So you might ask what happened to the quadrate and the articular bones, and the next slide shows that actually in the course of time you can see that, again just to summarize this, this transition, the next indication is of the original condition of the quadrate articular joint only to the next condition of having both the quadrate articular and the dentary squamosal joints which is present in these two animals to only the dentary squamosal joint, and this is the way that scientists understand this transition to have taken place.

Slide 063
Slide 63: Another mistake in Pandas. At top, Figure 5-7, p. 121 of Pandas says that "according to Darwinian theory" the quadrate and articular jawbones were relocated as the incus and stapes. But examination of a near-identical figure in Carroll's Vertebrate Paleontology and Evolution shows that it is actually the incus and the malleus that correspond to the quadrate and articular.
(Right-click to download pdf.)

Credits:

Middle ear from Pandas Figure 5-7, p. 121. ©1993 by Foundation for Thought and Ethics, Richardson, TX 75083-0721

Middle ear, scientific version from: Carroll, R.C. (1987). Vertebrate Paleontology and Evolution. W. H. Freeman and Co., New York.

The next slide gives you a sense of what this anatomy is on the inside of the ear. Now what you're looking at in the top is a depiction of the ear bones in some of early mammals. Now, if you can see where the pointer is pointing here on this upper right diagram, this long structure here with a big hole in the middle is called the stapes, and this is an ear bone that connects up to the eardrum in the inner ear, this little funny snail shaped thing, this bone, the stapes, has been in animals ever since they came out on land.

In fact, even the watery ancestors of land animals have this in one form or another. Next to this you'll see a little "Q" and a little "A" which are the quadrate and the articular. These are the two parts that usually that before just made up the jaw joint, but now they are making up part of the ear bone. They are connecting up to it. On the bottom when you look at this, here is this stirrup shaped bone here which we would call the stirrup next to a bone marked by an "I", which is the anvil, and the bone next to it marked by an "M", which is the malleus, or hammer.

So malleus and the incus, or the hammer and the anvil, are actually the quadrate and the articular that used to be in the jaw joint, and now they are hooked up to the stapes here of the ear. They always were connected to the stapes, but now they are moved so that the hammer, or the articular, is now moved into the skull rather than being part of the lower jaw.

Now, Pandas says this is a very difficult transition to make, and yet we see it embryologically and we see this in the fossil record in the transition of the jaw joints. I think the next indication on the slide will give you a picture if I may, the next I think indication is the Pandas version of this, which identifies these bones as the incus and the stapes. The stapes as I have already shown is the stirrup. That's always been in the ear.

I'm not really sure why they call this a relocation as the incus and the stapes when it's been there when actually what is relocated is really the articular bone which used to be in the lower jaw and now is in part of the ear. So the anatomy here is a little bit confused, and I'm sure they didn't mean to do this purposely, but again if they get this wrong, how much else is wrong that we don't know about or that is not being shown to students or has not been obviously corrected in the second edition or in any subsequent work as far as I know?

I think the next slide shows where the stapes is in both things. That's just so you can see where the stapes is the comparable structures. They may look different. One is much more stirrup shaped than the other, which is more rod shaped, but they're the same bone. They hook up to the same structures.

Q. So again here the point that Pandas makes is that there cannot be and have not been natural processes that account for this evolution?

A. And this is just an example of the kind of argumentation that's made to try to say that these transitions are difficult to make and we have no evidence for them, but as I have shown and as you have seen there has been fossil evidence going back decades that show us animals with dual pairs of bones in the jaw joints which is perfect intermediate form. It's kind of like if you had a cup in this hand and you want to transfer it to this hand, well, you could go like that, just toss it from one to the other. But if you take it in both hands and then move it this way, but for a while you've got it in both hands. That's sort of what the mammal jaw was doing.

Q. Now, you've pointed out that what you have just testified about was well known 25 years before Pandas was written. I mean, that those articles were from the late 1960's. Are you familiar with qualifications or backgrounds of the authors of Pandas?

A. I know them as the authors of Pandas. I know very little else about them from firsthand experience.

Q. So that would be Dean Kenyon, Percival Davis, Nancy Pearcey, and Charles Thaxton. Have you ever encountered them at any meetings, paleobiology, evolutionary biology, seen any peer reviewed publications? What can you tell us about these authors?

A. I can say that none of those authors or the other people I know as consulting people on their masthead, I have never seen them at scientific meetings in my fields as far as I know. I've never known them to give papers at those meetings. I've never known them to publish in the peer reviewed literature of any of the fields related to evolutionary biology or paleontology if you want to go to specifics or anything else in related fields, and I haven't seen their work cited by scientists in those fields when discussing advances in science.

Q. Let me ask you the same question about two experts who will be testifying in the coming weeks for the school district. One is Michael Behe, and the other is professor Scott Minnick. Same question, are these folks who are recognized in the field?

A. Not in any of the fields in which I'm familiar, but it would hold they, like the authors of Pandas, may be qualified in other fields, but as far as I understand their experience, accomplishments in the fields related to evolutionary biology, I know of no particular work that they have done that would provide expertise.

Q. So you haven't seen any peer reviewed publications from these individuals involving evolutionary biology or paleontology?

A. Not in those fields, no. Although I don't doubt in their own field they might produce perfectly good work.

Slide 064
Slide 64: Padian moves on to the origin of whales. Pandas claims "there are no clear transitional fossils linking land mammals to whales." (pp. 101-102)
(Right-click to download pdf.)


The Origin of Whales

Q. Let's take one, just more example of the evolution of mammals, and one that Pandas identifies as not being able to evolve naturally is whales, and I'm wondering if, you've prepared a demonstrative to show us how Pandas treats the whales and then explain what science knows about the evolutionary process?

A. I would like to discuss this a bit if I may have the next set of slides. In Pandas, here on page 101 and 102 --

Q. Could you read that passage?

A. The whole passage?

Q. Yes, please.

A. "The absence of unambiguous transitional fossils is illustrated by the fossil record of whales. The earliest forms of whales occur in the rocks of the Eocene age, dated some fifty million years ago, but little is known of their possible ancestors. By and large, Darwinists believe that whales evolved from a land mammal. The problem is that there are no clear transitional fossils linking land mammals to whales. If whales did have land dwelling ancestors it's reasonable to expect to find some transitional fossils."

Q. End quote?

A. End quote.

Slide 065
Slide 65: Recent journal articles on fossil whales with legs.
(Right-click to download pdf.)

Q. And in fact what does the science show?

A. Well, some of the disturbing things about that quote is apparently that the evolution of whales is something that Darwinists believe, and again it's sort of a faith based proposition that seems to have no real evidence. The Pandas authors then go on to say that there are no clear transitional fossils. It raises the question of what they might accept as a transitional fossil, but what I'd like to show you is what some of the evidence is accepted by fossils in ways of making these transitions of features.

Again on the screen here you saw some peer reviewed publications from Nature, Science, and the Proceedings of the National Academy of Science of the US A.

Q. Could you just read a couple of the titles and journal articles into the record?

A. A title here is Skeletons of Terrestrial Cetaceans, which are whales, and The Relationship of Whales to Artiodactyls, which are the hoofed mammals.

Q. And what publication is that from?

A. That comes from Nature I believe. Another article here from Science is called Origin of Whales From Early Artiodactyls, which again are the hoofed mammals, Hands and Feet of Eocene Protoceditae, which is an early group of whales from Pakistan. Those are couple of examples.

Q. So now the testimony you're about to give about whales, does this come from this and other peer reviewed studies?

Slide 066
Slide 66: As with birds and mammals, Padian will display the fossil relatives of modern whales and dolphins (cetaceans) in their phylogenetic context. The origin of whales was long debated, but in recent years molecular and fossil data converged to support the hypothesis that whales evolved within the artiodactyl group. Traditionally, the artiodactyl group included the even-toed ungulates (hoofed animals) -- animals like goats, cows, and hippos. These animals are large, herbivorous, and have thick hooves, but some fossil artiodactyls were small, with small hooves, and omnivorous (as are modern pigs). Shown in the slide are Diacodexis, the first artiodactyl (about the size of a rabbit) and an oreodont, another early artiodactyl.
(Right-click to download pdf.)

Credits:

Diacodexis reconstruction from Figure 1, page 259 of: de Muizon, Christian (2001). "Walking with whales." Nature, 413(6853), 259-260. (DOI) Reprinted by permission from Macmillan Publishers Ltd., copyright 2001.

Reproduced with permission of the UC Museum of Paleontology. Source: http://www.ucmp.berkeley.edu/mammal/artio/artiofr.html.

A. Yes. If I could have the next slide I can show you a bit about this. Once again we're going to use this hat rack cladogram relationship diagram, and again it's turned on its side so that you've got living cetacea, whales, on the bottom in blue. That group of whales and dolphins has a bunch of fossil relatives. The closest one are called basilosaurids. Outside them are protocetids, and there's a couple of forms from the Eocene called Ambulocetus and Pakicetus, and outside that are hippos, which are the closest living relatives of whales, and outside of that we've just listed some early Eocene artiodactyls, or hoofed mammals, from which we have recognized certain characteristics that are shared between hippos and whale, as odd as it might seem.

The skeletons you see there are some fossils from the Eocene of hoofed mammals, members of the group artiodactyl, the ones with the even toes, and we just put them up there to show that we do have fossils of such things.


Slide 067
Slide 67: Hippos are the closest living relatives of cetaceans. This relationship was indicated by molecular evidence in the 1990s, and confirmed by key morphological features shared between anthracotheres (the fossil ancestors of hippos) and early whales in 2005.
(Right-click to download pdf.)

Credits:

Photo by Aaron Logan (source: http://en.wikipedia.org/wiki/Image:Lightmatter_hippo.jpg), licensed under Creative Commons Attribution 2.0).

Photo by Paul Maritz (source: http://en.wikipedia.org/wiki/Image:Hippo_pod_edit.jpg), available under the GNU Free Documentation License.

The next slide gives you a sense of hippos, which no one needs any introduction to,...


Slide 068
Slide 68: Pakicetus is a whale from Pakistan, sharing key skull features with fully aquatic whales.
(Right-click to download pdf.)

Credits: Pakicetus skulls from Figure 3, page 279 of: Thewissen, J. G. M.; Williams, E. M.; Roe, L. J.; Hussain, S. T. (2001). "Skeletons of terrestrial cetaceans and the relationship of whales to artiodactyls." Nature, 413(6853), 277-281. (DOI) Reprinted by permission from Macmillan Publishers Ltd., copyright 2001.

...so we'll pass to the next slide, which is a particularly interesting set of photographic views of a skull, or a partial skull and brain case of an animal called Pakicetus, the critter in the yellow, well, orange or whatever that is, outlined term, that is again closer to whales of today than hippos and the other Eocene artiodactyls are.

This is a another of some of the oldest whales which come from Pakistan, India, Egypt, that area of the world, which once was the edge of an ancient sea in the early part of the Tertiary period, fifty, sixty million years ago when all this was happening. The images on the right are photographs of one of the brain cases and skulls of Pakicetus, and the reason for showing this is just to let you know, although I won't go into any detail, that what Pakicetus shares with whales that live today are not that it has a blow hole or flukes or anything like that, but that it has an ear region with features that are only found in whales.


Slide 069
Slide 69: However, Pakicetus was a whale with legs.
(Right-click to download pdf.)

Credits:

Pakicetus and Ichthyolestes reconstruction from Hans Thewissen's whale evolution page, http://www.nature.com/nature/journal/v413/n6853/fig_tab/413277a0_F2.html (public access granted)

Pakicetus attocki fossil in the collection of: Northeastern Ohio Universities College of Medicine c/o Howard University - Geological Survey of Pakistan Collection. Photograph from http://www.researchcasting.ca/pakicetus.htm, reproduced with permission.

And by this we infer that they share a common ancestor with the first whales. That would be fairly tenuous evidence if we didn't have other evidence, but the next slide will show you that the evidence of this animal does not make it look a lot like a whale either. It's obviously a four-legged critter. It is happy running around on the ground. It looks like a garden variety quadruped, four-footed critter that runs around doing its business, whatever it does, and except for this funny ear region you might not really get a sense of its relationship to whales.


Slide 070
Slide 70: Oxygen isotope ratios from the tooth enamel of fossils indicates that Pakicetus probably fed in the shallow Tethys sea and its estuaries.
(Right-click to download pdf.)

Credits: Figure 4, p. 15467, from: Bajpai S.; Gingerich, P.D. (1998). "A new Eocene archaeocete (Mammalia, Cetacea) from India and the time of origin of whales." Proceedings of the National Academy of Sciences, 95(26), 15464-15468. (PNAS) Reproduced with permission. Copyright 1998 National Academy of Sciences, U.S.A.

And so we note that they are quadrupedal, or four-legged, but the next slide shows you something interesting about them. That stop slide has now changed to just admit a little bit of the insights that we get from isotopes. These are isotopes of oxygen, and oxygen comes in different kind of molecular forms, and the percentage of those forms varies between terrestrial and aquatic horizons, environments, so that when we find bones that are made with oxygen elements that contain this isotopic signal, we can get an idea of whether these animals were primarily terrestrial or aquatic.

In the next slide there's a little indication on this slide there, you can see that the isotopes for Pakicetus demonstrates that it falls in the fresh water marine kind of realm. So we think if this evidence is correct that this animal was spending at least part of its time in water, including brackish or marine water. So it's already getting out there somewhere, but it's still a quadrupedal critter.


Slide 071
Slide 71: Ambulocetus was fully aquatic or nearly so, but still had reduced limbs.
(Right-click to download pdf.)

Credits:

Ambulocetus reconstruction from Hans Thewissen's whale evolution page, http://web.neomed.edu/web/anatomy/Thewissen/whale_origins/index.html (public access granted)

Ambulocetus fossil in the collection of the Northeastern Ohio Universities College of Medicine. Photograph from http://www.researchcasting.ca/ambulocetus.htm, reproduced with permission.

Ambulocetus fossil photo modified from Hans Thewissen's whale evolution page, http://web.neomed.edu/web/anatomy/Thewissen/whale_origins/index.html (public access granted)

The next slide I think is going to give you a sense of Ambulocetus, which means walking whale. Again it still has legs, and as the restoration at the top shows it looks like it's perfectly okay getting around on land,...


Slide 072
Slide 72: The hands and feet are large and paddle-like.
(Right-click to download pdf.)

...but the next indication on this slide will show you that the limbs are large and paddle like. So the hands and the feet are clearly already being broadened and are apparently some use to the animal in getting around in the water, and these are actual skeletons again from the Eocene.


Slide 073
Slide 73: Top and middle: Rodhocetus reconstruction and Artiocetus clavis skull. The bottom photo shows the ankle bones of Rodhocetus, a modern pronghorn antelope, and Artiocetus.
(Right-click to download pdf.)

Credits:

Rodhocetus from Figure 3, p. 2241 of: Gingerich, P. D.; M. Haq; I. S. Zalmout; I. H. Khan; and M. S. Malkani (2001). "Origin of Whales from Early Artiodactyls: Hands and Feet of Eocene Protocetidae from Pakistan." Science 293(5538), 2239-2242. (DOI) Reproduced with permission.

Artiocetus clavis photograph from Philip Gingerich's whale evolution page. ©2001 Philip Gingerich. Reproduced with permission.

Protocetid ankles from Philip Gingerich's whale evolution page. Photograph ©2001 Philip Gingerich. Reproduced with permission.

The next slide shows you protocetids, which are ancient whale relatives that are a little bit closer than the last one was to the whales of today, and protocetids are kind of interesting.


Slide 074
Slide 74: In the protocetids, the hips are decoupled from the backbone. They definitely were not running animals.
(Right-click to download pdf.)

If you, the next indication I think will show that the hips on these animals have been decoupled from the backbone. That is they are no longer connected to the spinal column.

Why this would be might be difficult to fathom, pardon the pun, except that these animals are probably using their backbone, moving it up and down the way whales swim in the water, and if you have your limbs encumbered to your backbone it's just going to be that much more difficult to do it.


Slide 075
Slide 75: Artiocetus clavis skull. The nose is still at the front of the skull, unlike modern whales.
(Right-click to download pdf.)

Credits: Artiocetus skull from Figure 1, p. 2240 of: Gingerich, P. D.; M. Haq; I. S. Zalmout; I. H. Khan; and M. S. Malkani (2001). "Origin of Whales from Early Artiodactyls: Hands and Feet of Eocene Protocetidae from Pakistan." Science 293(5538), 2239-2242. (DOI) Reproduced with permission.

This may be part of the reason why the decoupling is there, and yet these animals, as you'll see from the next indication, still have skulls in which they're getting some increasingly whale-like characteristics, including the nostrils, which are beginning to move backward along the skull.


Slide 076
Slide 76: The drawing shows the astragalus of Artiocetus (A) and full ankle of Rodhocetus balochistanensis (C) (astragalus bone near the top). Rodhocetus's foot was certainly a swimming flipper, but still retained small hooves.

The photo shows three ankles, respectively those of Rodhocetus, a modern pronghorn antelope, and Artiocetus. Remarkably, all three show a "double-pulley" astragalus. The astragalus is the bone with the deep, rounded groove in it (imagine a rope fitting into the groove of a pulley wheel). This groove, called a trochlea, fits another bone to form a sliding joint. The artiodactyl astragalus -- in both the modern pronghorn and these ancient swimming whales -- has the unique feature of having two trochleas, one on each end. This is the "double-pulley." These protocetid whales were definitely not runners, but they retain a clear mark of their ancestry as hoofed running animals. See Gingerich's website and paleos for more details.
(Right-click to download pdf.)

Credits: Protocetid hindlimb/ankle reconstructions from Figure 2, p. 2241 of: Gingerich, P. D.; M. Haq; I. S. Zalmout; I. H. Khan; and M. S. Malkani (2001). "Origin of Whales from Early Artiodactyls: Hands and Feet of Eocene Protocetidae from Pakistan." Science 293(5538), 2239-2242. (DOI) Reproduced with permission.

As you know, in whales the blow hole is right up close to the eyes. The next slide I think shows that even though these animals are quite aquatic and have a lot of whale features, they still have ankle bones that are very much like the ankle bones in the hoofed mammals from which they evolved, including ankles with a double pulley joint and a lever arm off the end.


Slide 077
Slide 77: Mounted skeleton of Dorudon atrox, a basilosaurid, and Basilosaurus isis fossil excavation in Egypt. Basilosaurus was first discovered in the southern U.S. in the early 1800s and was originally thought to be a reptile (thus the "saurus").
(Right-click to download pdf.)

Credits:

Dorudon from Philip Gingerich's whale evolution page. Photograph ©1998 Philip Gingerich. Reproduced with permission.

Basilosaurus in situ from Philip Gingerich's whale evolution page. Photograph ©2005 Philip Gingerich. Reproduced with permission

Even though these animals are spending more and more time in water, they can still deal okay on lands. The next slide I think will show a basilosaurid, which is the next step toward living whales, and this is quite a different proposition.


Slide 078
Slide 78: In the basilosaurids, the nostrils have moved further back along the skull.
(Right-click to download pdf.)

The next indication will show you where the nostrils are, they're moving even farther up along the skull,...


Slide 079
Slide 79: The hind limbs of the basilosaurids were vestigial. These whales were fully aquatic and could not even drag themselves onto a beach.
(Right-click to download pdf.)

... and the next indication shows you about the hind limb bones, which are again the next indication is a close-up of this, the hind limbs are now not just decoupled from the back bone, they've become extremely reduced.


Slide 080
Slide 80: Incredibly, the hind limbs still retain the "double-pulley" astragalus in the ankle.
(Right-click to download pdf.)

Credits: Basilosaurus hindlimb from Philip Gingerich's whale evolution page. Photograph ©1991 Philip Gingerich. Reproduced with permission.

But as you'll notice, right in the middle of that slide is that pulley shaped bone with a little hook off it. That is the ankle. And so the ankle is still like the ankle of a terrestrial animal, a hoofed mammal, from which they evolved, even though this animal couldn't any more walk on land than it could fly.


Slide 081
Slide 81: In living dolphins and whales, the nostrils are at the top of the skull, and they have completely lost their hind limbs, except for rare atavisms.
(Right-click to download pdf.)

Credits:

Dolphin is a public domain image from NOAA, source: http://en.wikipedia.org/wiki/Image:Common_dolphin.jpg

Humpback whale reproduced under the Creative Commons Attribution ShareAlike License v. 2.5. Source: http://en.wikipedia.org/wiki/Image:DSC_7334.JPG

So what we're seeing here is the progression of features more and more whale-like from animals that are terrestrial and conventional land going animals through some really minor features beginning in such odd regions as the ear, which you might not expect to be one of the first things that would change, all the way down to this, the final thing we have here is the living cetacean, which looks, you know, very much like the whales of today because they are the whales of today, and they've almost completely lost the hind limbs. So this is the situation as paleontologists know it in a kind of a, you know, very vague general nutshell.

Q. And this is completely contradictory to which Pandas has said?

A. Well, you look at the treatment that they've given us and that we've just seen, they've told us that there are no clear transitional fossils and that the fossil record of whales is a poster child for the absence of unambiguous transitional fossils, but we think the transition is pretty good.

Q. Now, most of these fossils that you have just pointed to were in fact discovered after the publication of Pandas in 1993?

A. Many of them were. Some of them were still around. Basilosaurids, the last, second to last guys I showed, have been known since the Civil War.

Q. Does the fact that Pandas suggests that there are no transitional fossils and kind of insert an intelligent designer as the cause because of that, what's the implication of finding new evidence where Pandas asserts a designer?

A. Well, again I think it sets a very confusing message to students as well as to everybody, the public included, that I don't know what you're supposed to think from this. Either there is no designer or the methods of intelligent design are very badly flawed, but in each case it confuses rather than advances the educational purpose.

Q. Well, does it also not show up a flaw in the logic of intelligent design, so the fact that we don't have transitional fossils today means the only other possibility is there must have been a designer, whereas in fact what we have now found is now, there are other possibilities we may actually find natural causes for?

A. And so the fallacy is that if we don't have enough evidence for evolution, we must therefore conclude that these things had a supernatural origin.

 

Direct Examination: Creationist Misrepresentations of Homology and Analogy

Slide 083
Slide 83: In the final section, Padian turns to homology and analogy, fundamental concepts in comparative biology. Chapter 5 of Pandas attempts to overturn the idea that homology is strong evidence for common ancestry.
(Right-click to download pdf.)

Creationist misrepresentations of Homology and Analogy

Q. What's homology? Last concept, Your Honor.

A. Homology is the central concept of comparative biology. It's the idea that allows you to compare structures in different animals, the kinds of structures that enable you to say that the bone you have here that we call a humerus is a humerus in a human, it's a humerus in a bat or a goat or a bird or a frog, and this is a very old concept. The notion of homology, the ability to compare comparable parts among organisms, goes back to the 1700's. Goethe was one of the first people who developed this concept in vertebrates as well as in plants because he was besides being the author of Faust and a great poet he was also a great morphologist.

He worked on plants and animals and was a great contributor to these ideas of morphology. Goethe, many of the other German scholars who worked with him, some of French scholars in days, and many of the scholars in Britain at this same time, contributed to this, including notably Sir Richard Owen, who was a little bit older than Darwin but really contemporary with him, but a complete anti-Darwinist in the sense of not accepting natural selection and not accepting the possibility of change from one species to the others in ways that Darwin and the evolutionists proposed.

What is so interesting about the presentation of homology by intelligent design advocates as with creation science, scientists and so on, is that they take a concept that isn't even evolutionary and they manage to completely destroy the fundamental basis on which it's built. Let's go back to the thinking of Richard Owen. In 1846 and 1848 a man who is Darwin's bitterest enemy, he is the only man that Darwin was ever said to have hated, so he's not exactly a big fan, these guys do not form a mutual admiration society, but Owen is a cosmic morphologist, he's the greatest paleontologist and comparative anatomist of his generation, and Owen said look, we have to be able to compare structures, and we can do it on a number of different criteria.

And he's not talking about evolution as saying look, this bone is a humerus because it connects to the same bones in all the animals we're looking at. Connects to the shoulder joint on the one hand, on the one arm, and it connects to the forearm bones on the other side, and that's the way we find it and that's how we can tell that this is a humerus, and this is the same in a goat.

So it's in the same position, that's the first thing. The second thing is it's made of the same stuff, it's bone, and this bone -- so it's not muscle or it's not glass, it's not anything else. It's made from the same stuff, and that's another way you can tell it's the same thing. Another criterion he used is that it develops in the same way. So for example it develops along the arm primordium and it's first beginning to be formed in cartilage and the cartilage is largely replaced by bone as the bone develops in its place.

So you have criteria of position, of what it's made of, and how it develops, and these are only a few of the criteria that people use. This is before people talk about evolution in connection to homology. Now, what Darwin did by publishing The Origin of Species, many more people accepted that organisms had common ancestors, that common ancestry explained the diversity of life. And now homology had a second dimension to it. That is that homology, the resemblances that Owen had talked about and many other morphologists had talked about, why were they similar? Because they were inherited from common ancestors. So common ancestry is not the rationale for homology. It's an explanation of the similarities that we see that is, that were actually established in pre-Darwinian terms by most classical scholars that we have.

Q. And so homology is a very well established concept within biology?

A. Yeah, and when I started by talking about how we classify things, how we make up these cladograms, we have to make sure that we're using homologous features, this is features that actually be compared and not just random features that aren't correlated to each other. Otherwise our classification systems would be invalid.

Q. And what you're talking about is something that's been established not just for a few years but for a really long time?

A. Hundreds of years.


Slide 084
Slide 84: Figure 5-2 of Pandas (p. 117) compares the skulls of a domestic dog (Canis lupus familiaris, a wolf (Canis lupus) and the marsupial "wolf" (also known as the Tasmanian wolf/Tasmanian tiger, or thylacine; scientific name: Thylacinus cynocephalus), a dog-sized marsupial carnivore. The standard evolutionary phylogeny says that the thylacine is more closely related to a kangaroo than a dog, and dogs and wolves are more closely related to humans and other placental mammals (whales, bats, etc.) than to any marsupial. Pandas says this relationship is doubtful and arbitrarily determined, claiming that the skulls of thylacines and wolves are more similar to each other than to their allegedly marsupial and placental relatives.
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Credits: Dog/wolf/thylacine skulls modified from Pandas Figure 5-2, p. 117. ©1993 by Foundation for Thought and Ethics, Richardson, TX 75083-0721

Pandas on homology: the real wolf and Tasmanian "wolf"

Q. And what does Pandas do with homology?

A. It's really weird. If I can give you an example, this one here comes from their figure 5-2. This is their drawing of a dog, a wolf, and an animal called the Tasmanian wolf, which is considered by all scientists to be a marsupial and not a placental mammal. Marsupial are animals like possums and kangaroos and phalangers and koalas and wombats that are a quite a different branch from the placental mammals, humans, primates, bats, wolves, things like that.

The caption here seems to make very little of the similarity between the dog and the wolf and a lot of the supposed identity between the Tasmanian wolf on the bottom, which they say in the caption is allegedly only distantly related to it. If I could have the next slide, this is what they're talking about in making these comparisons.

Q. And now this is from page 29 of Pandas?

A. It is. It says, "Despite these close parallels, because the two animals, that is the Tasmanian wolf and the conventional wolf, differ in a few features, the standard approach is to classify them in widely different categories." So the wolf with the dog and Tasmanian wolf with the kangaroo as a marsupial. Okay, and they're saying if similarity is the basis for classification, what do we do when these similarities conflict?

The marsupial wolf is strikingly similar to the placental wolf in most features. Yet it's like the kangaroo in one significant feature, by which they mean the pouch. Upon which similarity do we build our classification scheme? Should we use the pouch or should we use everything else they're saying. So in other words, they're trying to say that the resemblances between the wolf and the dog are simply superficial, and that just because those other marsupials have pouches doesn't mean we should always classify them together.

I don't think there's ever been any doubt about this since marsupials were discovered. I don't think that there has been mass confusion about marsupials versus placentals. But the next slide I think I would, if I may I would like to show you how a morphologist would look at this question.

Q. I'm sorry, are those these photos taken from Pandas?

A. No. These are photos taken from literature.

Q. And are these reasonable depictions of what these animals look like?

Slide 085
Slide 85: Pandas claims that the similarity of the "wolf" skulls shows that biologists cannot objectively distinguish homology (similarity due to common ancestry) and analogy (similarity not due to common ancestry), and therefore common ancestry and phylogenetic reconstruction are dubious concepts.
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Slide 086
Slide 86: Pandas claims that the skull of a wolf is more similar to that of a Tasmanian "wolf" than to a dog skull. Looking at a photo of a live Tasmanian "wolf" shows that they are substantially different from any wolf or dog.
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Credits: The sources for these photos are unknown, they seem to be stock photos. See: http://www.naturalworlds.org/thylacine/index.htm for many thylacine photos.

A. Yes. I think as mug shots they're okay. The Tasmanian wolf, the last one died in a zoo in the 1930's. I don't think we know of any living population since then. The dogs and the North American wolf of course are still around. The Tasmanian wolf is a very strange animal. You can see its stripes, its funny ears, its snout and so forth, but superficial similarities as we have seen are not the basis on which we establish science. Let's take a look at next set of slides. What we've done here is to take actual skulls from our museum. Here's a dog and a wolf.

Q. And this is how scientists, real scientists would make these comparisons?

Slide 087
Slide 87: Unlike creationist argumentation, comparative biology is a rigorous science. Rather than just "eyeballing" similarity as creationists do, biologists systematically identify specific characters. Padian shows five of the standard skull features that dogs and wolves share. For example, tooth formulas are a standard feature used for classifying mammals. Dogs and wolves both have two molars in the upper jaw.
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Credits: Photos by Andrew Lee, U.C. Berkeley. Skulls from the U.C. Museum of Paleontology and the Museum of Vertebrate Zoology. Reproduced with permission.
Slide 088
Slide 88: A direct comparison of a North American wolf and a Tasmanian "wolf," on the other hand, shows that these two species differ in each of these characters. For example, the tasmanian wolf has four molars instead of two.
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Credits: Photos by Andrew Lee, U.C. Berkeley. Skulls from the U.C. Museum of Paleontology and the Museum of Vertebrate Zoology. Reproduced with permission.

A. Oh, yeah, and in each case we have taken features of the jaws and teeth just to show you the comparability among them. I don't need to run through all the features. I just want you to take a look and see that on this slide the no's and the yes's and the numbers line up pretty well between the dog and the wolf. Do you want me to go through the similarities? Okay, it's close enough for government work.

Then the next one here is the North American wolf and the so-called Tasmanian wolf, and in these features again every one of them is opposite, where you get no's, you get yes's, the numbers are wrong, and the carnassial tooth we see in the wolf above is missing in the Tasmanian wolf. So in these features they're completely different.

Let's go to the next slide, just looking at it the front way, which was not shown in Pandas, but the dog and the wolf, just to show that they both have nasal bones that are narrow or pinched in shape, with three incisors. The next slide contrasts the wolf with the Tasmanian wolf. The Tasmanian wolf has wide nasals and it has four incisors, which you wouldn't see from the side shot that the Pandas authors showed.

Slide 089
Slide 89: Dogs and wolves both have pinched nasals and three incisors on one side of the jaw.
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Credits: Photos by Andrew Lee, U.C. Berkeley. Skulls from the U.C. Museum of Paleontology and the Museum of Vertebrate Zoology. Reproduced with permission.
Slide 090
Slide 90: On the other hand, the Tasmanian "wolf" has wide nasals and four incisors (another difference in tooth formula).
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Credits: Photos by Andrew Lee, U.C. Berkeley. Skulls from the U.C. Museum of Paleontology and the Museum of Vertebrate Zoology. Reproduced with permission.

The next slide shows you a few of these skulls from underneath. The Tasmanian wolf has holes in the roof of its mouth, or palatal holes, which are lacked by the dog and the North American wolf. And the next slide shows the jawbones of these animals which have an opposite number of molars and premolar teeth between the Tasmanian wolf, and the dog and wolf.

Slide 091
Slide 91: Viewing the skull from below shows the same pattern. Dogs and wolves do not have holes in the center of the palate (the roof of the mouth). The Tasmanian "wolf" does have palatal holes.
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Credits: Photos by Andrew Lee, U.C. Berkeley. Skulls from the U.C. Museum of Paleontology and the Museum of Vertebrate Zoology. Reproduced with permission.
Slide 092
Slide 92: Comparing the lower jaws shows another difference in tooth formula. Dogs and wolves have three molars and four premolars, whereas the Tasmanian "wolf" has the opposite, four molars and three premolars.
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Credits: Photos by Andrew Lee, U.C. Berkeley. Skulls from the U.C. Museum of Paleontology and the Museum of Vertebrate Zoology. Reproduced with permission.

Also you'll see that Tasmanian wolf has a couple of structures at the back of the jaw which we call the reflected lamina. The term is not important, but it's just a significant feature that's not present in the dog and the wolf. Well, let's do our next comparison and look at the Tasmanian wolf as it relates to the kangaroo, which we know is a marsupial.

In all the features that we've been looking at so far the kangaroo and the Tasmanian wolf correspond exactly with one exception, which is that the kangaroo doesn't have three premolars, and it doesn't have three premolars because the front of its face is modified in a way that many plant eating animals are modified. They lose those front cheek teeth and they developed the very most front teeth in the skull into a cropping organism that they use to, a cropping organ that they use to crop grass and other plants. Except for that, the features of the two skulls correspond. The next one, if you like that here's the Tasmanian wolf against the possum, and although --

Slide 093
Slide 93: Now the Tasmanian "wolf" is compared to a kangaroo -- according to modern biology a much closer evolutionary relative. Pandas claims that "the determination of homologies [is] a matter of subjective judgment" (p. 122) and therefore "the determination of relationship rests upon a subjective judgment" (p. 124). If this is true, the comparative biologist should have difficulty finding the homologies that unite the Tasmanian "wolf" with the kangaroo. Padian shows that these two marsupials share the exact characters that were different between the placental wolf and marsupial "wolf." For example, both have four molars in the upper jaw instead of two.
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Credits: Photos by Andrew Lee, U.C. Berkeley. Skulls from the U.C. Museum of Paleontology and the Museum of Vertebrate Zoology. Reproduced with permission.
Slide 094
Slide 94: The same characters are found to be shared between the Tasmanian "wolf" and the common Virginia opossum.
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Credits: Photos by Andrew Lee, U.C. Berkeley. Skulls from the U.C. Museum of Paleontology and the Museum of Vertebrate Zoology. Reproduced with permission.
Slide 095
Slide 95: A front view of the three marsupial skulls. The number of incisors varies, but all three have wide nasals.
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Credits: Photos by Andrew Lee, U.C. Berkeley. Skulls from the U.C. Museum of Paleontology and the Museum of Vertebrate Zoology. Reproduced with permission.
Slide 096
Slide 96: All three marsupials share palatal holes.
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Credits: Photos by Andrew Lee, U.C. Berkeley. Skulls from the U.C. Museum of Paleontology and the Museum of Vertebrate Zoology. Reproduced with permission.

Q. That's another marsupial?

Slide 097
Slide 97: All three marsupials share four molars and reflected laminae.
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Credits: Photos by Andrew Lee, U.C. Berkeley. Skulls from the U.C. Museum of Paleontology and the Museum of Vertebrate Zoology. Reproduced with permission.

A. Another marsupial, yeah, our garden variety possum here, and although we saw that the kangaroo didn't have those first three premolars in front, the possum does. And the possum corresponds in all respects to those features in the Tasmanian wolf. Let's go a little bit further and look at then from the front. In each case all three, the kangaroo, the possum, and the Tasmanian wolf, have wide nasals. They have a different number of incisors, but they don't have three, except the kangaroo, which has very strange front incisors.

The next slide shows these three marsupials from the bottom. So I can just go back one, thank you. Shows these three skulls from the bottom. You can see that they all have palatal holes, holes in the roof of the mouth, which the dog and the wolf don't have. And the next slide I believe shows the jaws of these three animals, which everyone classifies as marsupials, which all have four molars, three premolars, except the kangaroo for reasons explained before, and they all have this reflected lamina in the back of the jaw.

So what are we to conclude from this? As the next slide shows -- oh, there are genetic similarities as well. I should mention that there have been several molecular studies that leave no doubt that marsupials are not just united by the pouch. They're even united by many molecular similarities that have nothing to do with the pouch as far as we can tell.

Q. Can you just read into the record the name of these articles and journals they're from?

A. Sure. One is from Molecular Phylogenetics and Evolution. Its title is, "Nuclear Gene Sequences Provide Evidence that a Monophyly of Australodelphian Marsupials" by which monophyly means that they all come from the same ancestors, the australodelphian marsupials means the guys that we know that are down there in Australia and some South American mammals.

Here's "An Analysis of Marsupial Interordinal Relationships," that means the relationships within the marsupials, "Based on 12S rRNA, tRNA Valine, 16S rRNA, and Cytochrome b Sequences." So here are four different molecules essentially, and this is in the Journal of Mammalian Evolution.

Slide 098
Slide 98: The skeletal similarities shared by marsupials have been known for generations, but recent gene sequence comparisons have confirmed the longstanding view, originally based purely on morphology, that marsupials form a closely-related group separate from placentals.
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Slide 099
Slide 99: Pandas claims that marsupials share only a pouch and supporting bones, but in fact skull anatomy and DNA points in the same direction. Even with only a skull or a blood sample, marsupials can be easily distinguished from placental mammals by competent biologists.
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Here's a paper from the Royal Society of London on mitochondrial genomes. Again these are DN A that comes out of the mitochondria of cells, on a bandicoot, a brush tailed possum, confirm the monophyly of australodelphian marsupials once again.

Q. Are these just a representative sample of the peer reviewed literature that's out there?

A. Yes.

Q. So there's many more than this?

A. Yes.

Q. So --

A. I think the next slide might give us an indication that in summary it's not just the pouch. It's all these similarities here that link the Tasmanian wolf to the other marsupials and exclude them from the placentals, and that probably should be brought out to students. I believe the next slide gives us an indication of --

Q. Well, let me just stop you there. So from what you have just explained to us, this homology is used to kind of systematically compare animals?

A. Yes. It's a method as I said that goes back to the 1700's, looking for unusual similarities, listing all of them, putting them all together, and seeing which array of features makes the most sense.

Q. And is this widely accepted in science?

A. Yes. As I noted before, it's the basis by which we can do classification. Those shared features that we use for classification would not be anywhere if we didn't use the concept of homology.


Slide 100
Slide 100: Pandas (p. 125) argues against common ancestry because the authors clearly prefer special creation as an explanation for homology, even though they can answer none of the obvious questions raised by this notion.
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IDCers prefer the explanation of special creation over descent

Q. And as we saw, Pandas seems to suggest that the classification and comparisons are arbitrary. How does Pandas use this misrepresentation of homology?

A. I think the next slide might give some indication of that. It seems quite clear from their text that they prefer the explanation of special creation over descent. The highlighted passages here from page 125 of Pandas ask if there is any alternative explanation. They say yes, another theory is that marsupials were all designed with these reproductive structures.

An intelligent designer they say might reasonably be expected to use a variety, if a limited variety, of design approaches to produce a single engineering solution. They say that even if we assume that an intelligent designer had a good reason for all these decisions, it doesn't follow that such reasons will be obvious to us. That's a perplexing statement, because it means that even though we have not been able to find a convincing pattern, and even though we do not know what the overarching plan is, we can still conclude that something was designed and could not have evolved.

They go on to say that, "These questions can nevertheless generate research in areas we might never investigate." I think as a scientist I'd be very concerned about how you can generate research questions when you have closed off an empirical avenue of, a very conventional empirical avenue of investigation, which is that these similarities are the result of common ancestry and provide no program for analyzing what intelligent design is, what the nature of the designer is, what the rules of design are by that designer, and this is I think classically a science stopper, especially when you tell students that these ideas should be considered but then you forbid discussion, you forbid questions.

Q. Now, it says in there that intelligent design should generate research. Are you aware of a significant body of scientific research on intelligent design?

Slide 101
Slide 101: Pandas claims that using homology to support common ancestry is circular reasoning, again ignoring that marsupial homologies extend far beyond just the pouch, and that DNA sequences have independently confirmed the longstanding conclusion of the morphologists.
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A. Well, before I left I checked our electronic database in biology that's available through our library that surveys thousands of peer reviewed scientific journals, and I looked for intelligent design in the field of biology and all I could find were instances where humans had for example designed ergonomic chairs. And they wanted this to be intelligent design. Okay? But they didn't say anything about a creator or that these had evolved, and obviously we don't think chairs have evolved, we know that they are designed by humans.

Other instances referred to for example DN A splicing, where people are designing DNA if you will. They want to do it intelligently. Things like that, but I never saw a single instance where intelligent design had been used as a research program or even as a scientific concept. And similar studies made by other people have I believe turned up the same lack of stimulation of research in any scientific field.

Q. So we hear intelligent design proponents claim that some of their propositions are testable. How do you square that?

A. Well, they began by claiming that intelligent design should be considered on the same playing field with conventional science. They've had a couple of decades now to show that it should be. They don't seem terribly interested in producing reports, peer reviewed literature that will actually document that and change the scientific paradigm. So I'm not really sure what efforts they're trying to make to change the science.

Q. I guess what I'm asking about is that intelligent design makes claims that are testable, and those are claims that they have made about evolution.

A. I don't think any scientific society that's weighed in on this has accepted intelligent design as testable. Speaking for myself, I don't regard intelligent design as a testable idea scientifically. I regard it as a proposition of things that can't be tested scientifically but you recourse to when scientific explanations have failed. Parts of the things that are alleged to make up intelligent design or that are associated with it, such as irreducible complexity, may be a testable proposition, but let's take a look at that.

Irreducible complexity on its face is a simple statement about a machine or some kind of structure that has several parts. If you take away one of those parts, then it stops functioning. Well, any 8-year-old with a broken bicycle chain knows that he can't ride around anymore with a broken bicycle chain, if that part is broken it's not going to work. No one's got a Nobel prize for that proposition. This only makes sense in the context of intelligent design when irreducible complexity is invoked as a way to assert that no structure could have evolved by natural means.

Therefore, it is irreducibly complex. And as we've seen in cases where works like Pandas have asserted this, we've often found that there is evidence to the contrary that we can produce transitional sequences of things, or that the intelligent design advocates have simply left out a lot of the information probably because they do not accept it.

Q. So an essential component of the intelligent design argument is that evolution doesn't work?

A. That's correct.

Q. And they've given a number of examples involving the fossil record, involving your fields of expertise, whether it's no pre-Cambrian ancestors or the inability of fish to have evolved or birds to have evolved or we saw whales to have evolved, and in fact what has science done with all of the scientific predictions or those assertions where evolution doesn't work or that Pandas comes --

A. Well, they've been tested by the discovery of new evidence such as fossils, such as molecular evidence, such as new evidence in developmental biology, and in a great many cases we found that the proceeding difficulties or absences of evidence have disappeared. It's an important principle in philosophy that absence of evidence is not evidence of absence.

Q. But in fact the examples that Pandas has given to show that in fact evolution doesn't work have been refuted by the scientific community?

A. I believe that would be the interpretation of the scientific community, yes.

Q. And in fact the examples that Pandas has selected are only a very few of far more evidence that's out there supporting evolution?

A. Yes.

Q. And they haven't attacked those other bits of evidence?

A. No.

Q. But even those few bits of evidence that they have selected to argue that evolution doesn't work have largely been invalidated by empirical studies?

A. In many cases we would say that we've got a much better resolution to this. I certainly don't want to present we've solved every problem. Otherwise I'd have to go home and retire.

Q. We are going to try to get you home this weekend. Turn to the last slide we have here. Would you say intelligent design is a scientific proposition?

A. I don't think there's anything scientific about intelligent design. As I say, I think it's a sort of idea that you recur to when your scientific explanations fail.

Slide 102
Slide 102: Pandas invokes teleology as the explanation the authors prefer, clearly signaling what they are after.
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Q. Do you think it's a religious proposition? And I direct your attention to page 122 of Pandas, and perhaps if you can read this passage into the record.

A. Well, this concerns me. They say, "For the design proponent, there is another explanation of the origin of analogous features and unrelated groups." They say, "For example, the skulls of marsupial wolves and of placental wolves are similar because one particular skull best suited the requirements of both organisms." We call this idea teleology. That is, they define this as organism that's designed for certain functions or purposes.

Now, when they say an organism is designed, that's maybe a statement, a static statement, it may be in the passive voice, but did someone design it. Again and again in Pandas they say that an intelligent designer has designed this for certain functions or purposes. This indeed is teleology, that things are there for, created for a certain end or purpose, and this is a philosophical and overtly religious notion that is absent from ideas of evolutionary biology.

Q. So teleology is not a scientific term?

A. No, not in the sense they're using it at all.

Q. Dr. Padian, you are familiar with the four-paragraph statement that the Dover school district is reading to students?

A. I've read it before.

Q. I'm not going to ask you to critique it paragraph by paragraph, other witnesses have done that. Let me just ask you, the Dover school district's response has been it's a one-minute statement, students don't have to stay in the classroom to listen to it, you know, what's the big deal? Why are we fighting this? Why are students harmed? Why is anybody harmed by reading this one-minute statement to the students?

A. Well, in my view, having educated students for thirty years, and so at a variety of levels from middle school up to graduate students my sense is that it's very difficult to constrain inquiry just by saying you're going to cut it off, and it's very difficult to say that if you just read a statement it's not going to harm anybody. It's quite clear from the evidence that's been given and from the fact that we're sitting here and by the situation that's developed in Dover, clear from news reports of people arguing with each other, parents arguing with other parents and teachers, teachers arguing with the school board, school board members arguing with each other and quitting, who knows how many bitter conversations have taken place in supermarket aisles and across telephone wires.

MR. MUISE: I'm going to object, Your Honor. This is going far down the road of speculation.

THE COURT: I'll overrule the objection to the extent that I'm not hearing anything that I haven't heard before, but why don't you interject a question at this point.

Q. So as a science educator, as somebody who has educated students for thirty years, why is this statement a problem?

A. It's clearly caused a great division in students, a great confusion. If some students are allowed to -- well, if students are required or allowed to hear a statement that is not read by their teacher, and unlike any other statement in the curriculum they may not ask questions about this and they may not discuss it further, this roping off of this kind of a statement means that it's to be treated differently.

It essentially ostracizes this area of study. It makes students confused, and they do ask questions. My students ask me questions about this kind of thing all the time. I don't think you can say that by cutting off inquiry you're going to stop people from asking questions. There are questions that intelligent design raises for students, and not just about science.

They are going to ask about if we have a situation where certain structures cannot evolve, that the natural processes that were perhaps created by a creator aren't sufficient to accomplish things, then what does this say about the perfection of the creation or the creator? What does this say about the ability of the creator to intervene in natural processes? If the creator can intervene, why doesn't he do so more often to relieve pain and suffering? And if this is a problem, of what good is prayer?

These concern me as someone who educates students in the science realm because they're not just asking questions about science. And if we close off inquiry to students and say that something cannot be anymore discussed in science, just accept it this way, or if we make religious propositions part of the science curriculum, then you cannot prevent them from being scrutinized in ways that are completely inappropriate in my view, in the purview of natural science, which never claims to answer such kinds of questions.

Q. And from your perspective as a scientist, what's the problem with this one-minute statement?

A. I think it makes people stupid. I think essentially it makes them ignorant. It confuses them unnecessarily about things that are well understood in science, about which there is no controversy, about ideas that have existed since the 1700's, about a broad body of scientific knowledge that's been developed over centuries by people with religious backgrounds and all walks of life, from all countries and faiths, on which everyone can understand.

I can do paleontology with people in Morocco, in Zimbabwe, in South Africa, in China, in India, any place around the world. I have co-authors in many countries around the world. We don't all share the same religious faith. We don't share the same philosophical outlook, but one thing is clear, and that is when we sit down at the table and do science, we put the rest of the stuff behind.

MR. ROTHSCHILD: I have no further questions.

THE COURT: Why don't we get started, we've only been at it about an hour. So we can get started with your cross, and then we'll take a break.

MR. MUISE: Thank you, Your Honor.

THE COURT: Why don't we try to break, Mr. Muise, in about fifteen minutes or so. That'll give you some time to get started.

Redirect Examination and Acknowledgments

Redirect

REDIRECT BY MR. WALCZAK:

Q. National Center for Science Education, NCSE, is a nonprofit group?

A. It's a nonprofit tax exempt group.

Q. And what is the mission of the NCSE?

A. The mission of NCSE is to clarify science for the public. Normally major people we clarify it for would be government officials, including education officials and school boards, parents, PTA's, members of the press, and individually concerned parents and community members.

Q. Is it a secret that NCSE has taken a position that creationism is not science?

A. Oh, that's no secret at all.

Q. Is it a secret that NCSE has taken a position that intelligent design is not science?

A. No, in that sense NCSE has aligned itself with the major scientific societies.

Q. And is it a secret that the National Academy of Science has taken a position that intelligent design is not science?

A. They certainly have done.

Q. Mr. Muise asked you about abrupt appearance, and he read a number of quotes from individuals. I believe they talked about, I don't remember the exact language, about relatively abrupt appearance in the Cambrian ear, and at one point you said the use of that abrupt appearance in scientific terms is different than the use abrupt appearance in intelligent design terms. Could you explain that, please?

A. Oh, yes, of course. When we say, if a scientist were to say that a form would evolve abruptly or appear abruptly, I mean it has the appearance, that is it seems as far as our record goes to happen very quickly. But abrupt appearance in going back to creation science parlance means something quite different. Wendell Bird for example, who is a lawyer and a conservative Christian anti-evolutionist attorney, wrote a book a couple of decades ago about abrupt appearance theory.

And so for him I mean it's a code word in the old style creation science, antecedent in many ways to the phraseology and the language that's often used in intelligent design that abrupt appearance means that you get these very complex groups, very distinct appearing at once, with no possibility of intermediates, certainly no evidence of intermediates in the fossil record, so that there's an implication there that there aren't ancestors and they aren't going to be found as opposed to a scientist who simply is making a statement about these things appear to come in just now as opposed to later or how rapidly.

Q. The Cambrian era lasted how long?

A. Oh, a few tens of millions of years.

Q. So when you see a bar on a chart and it starts in the Cambrian era, does that mean it was formed abruptly on a certain minute or day?

A. It means it's the first place where we find it. I should emphasize that the first appearance, the earliest appearance in the fossil record is for us a minimum early appearance because we may always be missing earlier ones, just like the last one is not necessarily the last critter to choke.

Q. But you're talking about many millions of years. So you're not talk about instantaneous appearance. You're talking about in a relatively short period of time which in geological terms is in millions of years?

A. If we look at the appearance in the fossil record of the major groups of marine animals, that appears over a sequence of millions of years.

Q. And in geologic terms that's abrupt?

A. It's really relatively fast. To give you an idea, the asteroid that hit the earth at the end of the Cretaceous period when the last dinosaurs that weren't birds and many other things died out is dated at something like 66.5 million years, plus or minus 40,000 years. That means that at a distance of 65 million years the best we can go is like 40,000 years either way for a determination. Now, 40,000 years is enough the take four ice ages, you know, from now back to the extinction of all the big Pleistocene mastodons and mammoths and Irish elks and things, do it four times and put it either way and collapse it into an instant, and we can't tell. That gives you an idea of somehow what the resolution of dating can often be.

Q. Mr. Muise, asked you about William Dembski.

A. Yes.

Q. And he asked you about a book that Mr. Dembski published or contributed to.

A. Yes.

Q. What book was that?

A. Is it called the Design of Life? I don't remember the --

Q. And that was published by an academic press?

A. Cambridge.

Q. Cambridge Academic Press?

A. The Design Inference. Thank you.

Q. Is that the same thing as the peer reviewed publications you were discussing this morning?

A. Book publishers, even book publishers of scholarly presses publish a variety of different kinds of books. Some of them are very scholarly, some of them are not so. I happen to be on the board of editors of the University of California Press and I know sometimes they publish biographies or reminiscences or cookbooks or things like that, as well as scholarly books in semiotics and sociology and molecular biology or whatever they happen to do.

So just because it's published by a scholarly press doesn't necessarily tell you what the peer review is. Also, you don't know in a specific instance what kind of understanding authors and editors have about who or how something would be reviewed. If someone who is publishing a book in a scholarly press based on my experience with UC Press and many other presses I have worked with is any indication, and an editor at the book company, the press itself, is an acquisitions editor someone who would like to do business with the press.

And so the first concern is to public books that will be read, that will be good for the press to public, because they'll be discussed, one way or another drum up interest in the press, sell other books by the press. They certainly want to get scholarly works in there and they want to get things as right as they can, but you know, you're serving several masters, whereas in a scholarly journal an editor has a lot of submissions coming in, and he doesn't have to worry about selling journals.

If he does he's probably not running a very good journal because people in his field are going to go for it. So he can hold authors to a standard that says well, look, if the reviewers say that you can do it, and he sends them to anonymous reviewers for this reason. Now, I think something should be pointed out here is maybe Mr. Dembski's book was reviewed by people who know about math and probability theory.

I don't have a dog in that fight. I don't care or know anything about that stuff, but I do know that it's not biology. It wasn't published in a biology series, it has nothing to do with evolution biology, and so when someone said this is a peer reviewed contribution that bears on evolutionary biology, we say where's the beef.

Q. So there's a couple of points there. One is that this academic press is not subject to the same peer review as for instance you described that would occur at Nature or Science?

A. Not necessarily at all, right.

Q. And we don't know what the peer review was for that if any?

A. We don't know. I don't know. I have no personal knowledge.

Q. And second, does Dr. Behe have to your knowledge any kind of degree in biology?

A. I don't know what he has in biology. In terms of evolutionary biology or paleontology I mentioned I don't know of any expertise in that regard.

Q. I'm sorry, I'm thinking about Professor Behe already. I mean --

A. Oh, Professor Dembski. No, I'm not aware that he has any credentials in any of the natural sciences. I believe that mathematics and theology maybe, or divinity.

Q. And let me ask you that same question I asked before about the Pandas authors. Have you seen Mr. Dembski at any of the conferences that you attend?

A. No.

Q. Have you ever seen any presentations by Mr. Dembski made at evolutionary biology or paleontology conferences?

A. No. I've never heard of him.

Q. Have you ever seen any publications in your field from Mr. Dembski?

A. No.

Q. Mr. Muise asked you about a number of people, and in fact read you quotes from people. He mentioned Stephen J. Gould?

A. Yes.

Q. And it seems the suggestion was that Stephen J. Gould had some problems with evolution. It seems that you knew Stephen J. Gould?

A. Yes. Well.

Q. And are you familiar with his writings?

A. Oh, yes.

Q. Was he someone who questioned evolution?

A. He certainly questioned the relative importance of various mechanisms and patterns in evolution, but not the idea that evolution had occurred or that organisms were related by common ancestry. That was a great theme of Gould's writing that he was always frustrated that anti-evolutionists were trying to make out that there was question about, among in the scientific community about whether evolution had in fact occurred, when really it was just a question of how important is punctuation versus slow and steady change and questions like that, but the overall fact and pattern of evolution was not in question.

Q. And are you aware of whether Stephen J. Gould ever testified as an expert witness in a case?

A. I believe he testified in McLean vs. Arkansas, was that right?

Q. And would that have been a trial in 1981 about scientific creationism?

A. Presided by Judge Overton I believe, yes.

Q. And was he an expert witness in that trial very much in the way you are an expert witness here today?

A. Yes, except he likes the Yankees and I like the Oakland A's.

Q. And in fact which side of the case did he testify on?

A. The Yankees. I'm sorry, he testified on the evolution side.

Q. And I believe Professor Gould was one of the proponents of punctuated equilibrium?

A. He and Niles Eldredge.

Q. I'm not going ask you to explain it. I know you've explained it to me before. I don't fully understand it, but is that an argument against evolution?

A. Not at all. It's simply an argument about what the pace of change is.

Q. And in fact scientists disagree about a whole lot of things, don't they?

A. Oh, yes.

Q. And they disagree about a lot of things within evolution?

A. Oh, yes.

Q. But that doesn't mean that they don't firmly believe in the basics of evolution?

A. Well, I wouldn't again use the word belief. I'd say that they accept it as the best explanation of things. My friends in the physical community argue about string theory. Some of them think it's good idea, some of them think it's nonsense. I have no idea what it is, but it's obviously something that keeps them going and it has ramifications for important understanding of the natural world.

Q. And Mr. Muise mentioned Ernst Mayr?

A. Yes.

Q. And are you familiar with Mr. Mayr's work?

A. Yes, I knew Ernst Mayr and his work.

Q. Is he a proponent of evolution?

A. Well, I'd say he probably is recognized as one of the foremost evolutionary biologist of the 20th century.

Q. How about Robert Carroll?

A. Bob Carroll is an old friend, he's one of the deans of vertebrate paleontology. He's up at McGill university in Toronto.

Q. And are any of those individuals proponents of intelligent design?

A. No.

MR. ROTHSCHILD: I have no further questions.

THE COURT: All right. Recross, Mr. Muise?

MR. MUISE: I have none, Your Honor.

THE COURT: All right. I thank you for your testimony, and you can have a safe trip back now with the cooperation of counsel getting your testimony in. We'll take up the exhibits in just a moment, but you may step down, sir. We thank you.




Acknowledgements

Thanks to Kevin Padian and his students Jann Vendetti, Liz Perotti, Brian Swartz, Randy Irmis, Jenny McGuire, Nick Pyenson, Alan Shabel, and Andrew Lee for assembling the original presentation, and to Brian Swartz for looking up copyright owners. Thanks also to Mike Hopkins and Alex Wing for help with organization and coding. The HTML coding of the transcripts is modified from the TalkOrigins Kitzmiller pages, formatted by Mike Hopkins. Thanks to Alex Wing, Larry Lerner, Mona Albano, and Kevin Padian for catching typos.

Background, Copyright and Reproduction Information

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: Introduction

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.


Dispatches from Dover: Podcasts about the Trial

This section features podcasts recorded by NCSE staff members and friends in the evenings after sessions of the Kitzmiller trial. These recordings offer descriptions, reflections, and analysis of events in the Kitzmiller trial, just after they occurred.

The Immune System and the Kitzmiller Case

The evolution of the immune system was one of the most significant scientific subjects to the Kitzmiller v. Dover trial. Creationists and ID proponents have long argued that the immune system could not arise by natural means, and the plaintiffs took particular care to demonstrate the scientific absurdity of this claim.

Testimony and analysis related to the immune system are listed below.

Annotated Bibliography on the Evolutionary Origin of the Vertebrate Immune System

Books and articles on the evolution of the immune system. Click to enlarge.

by Nick Matzke

This webpage contains the same articles and books used during the Behe cross-examination that are listed in the Supplementary Material for Bottaro et al. (2006). Here, the citations have been placed in chronological order, and each reference is annotated with a blue box containing a short summary of the significance of the paper, and if relevant, significant quotes from the paper.

Sections:
Introduction
Why the Immune System?
Scientific Background
How the Bibliography was Assembled
The Larger Context
Major Themes
Annotated Bibliography in Chronological Order
Acknowledgements

Introduction

The purpose of this annotated bibliography is to give the nonspecialist reader some sense of the scholarly weight of the evolutionary immunology literature (here is another method). In particular, this bibliography focuses attention on the scientific work that developed, tested, and established the "transposon hypothesis" for the origin of receptor rearrangement in the adaptive immune system. Contrary to the impression one might get from the ID literature, the transposon hypothesis was not idle speculation, it was not thought up yesterday over breakfast, it is not particularly vague, it is not untestable, and it is not scientifically useless. In contrast, by reading through the bibliography in chronological order, we can see that the transposon hypothesis was explicitly proposed and published in top journals, it was carefully and seriously discussed for decades in the professional literature, it has inspired a very productive research program (both experimental and comparative), it has been tested with diverse evidence by researchers working in many different labs, and it has been dramatically confirmed.

In short, it is a classic case of serious, advancing evolutionary science. Without ever getting mentioned in a newspaper article or cable news show, hundreds of PhD scientists have devoted their careers to working out how and why the immune system evolved. Any one of these researchers has quietly produced more research results than the entirety of the intelligent design movement with their collection of op-eds, webpages, in-house publications, books published by InterVarsity Press, one or two books by slightly more rigorous publishers but with dubious peer-review, and one or two review articles slipped into obscure journals. Unlike "intelligent design" proponents, evolutionary immunologists repeatedly published their key work in top journals. For some reason, they have not felt the need to write law review articles, lobby school boards and legislatures to get their view taught, or muck around with state science standards, because they know that scientific hypotheses succeed by convincing other scientists through research.

For more along these lines, see Bottaro et al. (2006) and the

Why the Immune System?

The decision to make the evolution of the immune system a key example in both Kenneth Miller's direct testimony and Michael Behe's cross-examination was based on several factors. First, among the major systems that Behe discusses in Darwin's Black Box, such as the eukaryotic cilium, the bacterial flagellum, the blood-clotting cascade, and the immune system, Behe makes particularly florid claims about the absence of literature on the origin of the immune system -- for example:
As scientists we yearn to understand how this magnificent mechanism came to be, but the complexity of the system dooms all Darwinian explanations to frustration. (Darwin's Black Box, p. 139)
We can look high or we can look low, in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system. (Darwin's Black Box, p. 138)
These are claims crying out for refutation. As it happens, there is probably more scientific literature directly on the evolution of the immune system than on the other three systems put together (we can chalk this up to (1) the long tradition of evolutionary and comparative studies in immunology; (2) the age of the discipline (going back to the 1800's); and (3) the massive amount of medical research money available for studies of the immune system, for obvious reasons). So, while Behe makes various mistakes on the other systems, many also discussed at trial, he is most dramatically wrong about the immune system literature.

Second, although the immune system is very complex, everyone is familiar with (a) its importance, (b) vaccinations and immunity to disease, and (c) many people have heard of antibodies. So it is actually not so difficult for a nonspecialist, such as a lawyer or judge, to realize the importance of immune system research.

Third, those in the community of "creationism watchers" knew that the ID advocates were particularly vulnerable on the immune system, given their past flailings in response to internet challenges. Some of this is mentioned in Bottaro et al. (referencing these Panda's Thumb posts: [1] -- [2]) and Michael Behe's weak response. For an earlier episode often recalled by creationism watchers see this celebrated discussion on an ID bulletin board, where several pro-evolution posters challenged several leaders of the ID movement to admit that Behe's 1996 claim was wrong.

Fourth, Behe's dismissal of several famous articles on evolutionary immunology during his deposition also increased confidence that he was not at all familiar with the literature, and instead would brush off any challenges as not meeting his requirement for infinite detail.

Fifth, plaintiffs' attorney Eric Rothschild had the strength of will to continue with the immune system gambit, despite Nick Matzke's early attempt at explaining the evolution of V(D)J recombination to him on a whiteboard:

The beginnings of the immune system "battle plan" for the Behe cross-examination. Whiteboard drawings from May 2005, NCSE office. Click to see larger images.

Scientific Background

The annotated bibliography will not make much sense without a little background understanding of immunology. If you can understand this basic terminology, you should be well on your way to understanding the transposon hypothesis:

  • Adaptive immune system (AIS): The portion of the immune system that generates receptors that specifically recognize and bind to a particular pathogen. This system has "memory", so that if a pathogen returns, it will be recognized much more quickly the second time around. Vaccines expose a person to a killed or weakened form of a pathogen, or key pieces of a pathogen. This "trains" the immune system to recognize common pathogens such as smallpox or polio, so that immunity can be developed without the person having to catch and fight off the actual disease. The adaptive immune response is restricted to jawed vertebrates (i.e., all vertebrates except lampreys and hagfish), and therefore evolved 450-500 million years ago in the common ancestor of cartilagenous fish (sharks and rays) and other "fish" (bony fish, including tetrapods). (Note: there is increasing evidence of different forms of adaptive responses in other organisms.)

  • Innate immune system: The portion of the immune system that uses general, nonspecific responses to fight pathogens. For example, a receptor molecule called TLR5 recognizes flagellin, the major component of bacteria flagella and a common conserved feature. The innate immune system is the first line of defense, and many of its features are shared between vertebrates and invertebrates

  • Immunoglobulins (Igs), also called antibodies: These are the receptor proteins of the immune system. They have a "Y" shape, where the top of the "Y" recognizes foreign molecules called antigens. The genes that encode immunoglobulins are composed of four basic kinds of segments: V (variable), D (diversity), J (joining), and C (constant). Vertebrates have hundreds of different copies of V, D, and J gene segments. Through a process called V(D)J recombination, different copies of these segments are spliced together, producing billions of different unique immunoglobulin receptors. Most of these receptors will not recognize a particular pathogen, but a few of them will, even if it is a completely novel pathogen.

  • Recombination Activating Gene (RAG): A RAG is a gene that codes for a RAG protein (the names of genes are italicized, and the corresponding proteins are not; sometimes PDF and HTML documents will be missing this formatting however). RAG proteins have the ability to recognize specific DNA sequences at two locations called Recombination Signal Sequences (RSSs), bring the pieces together, and cut the DNA at the RSS sites. DNA repair enzymes then repair the DNA and join the two segments, originally distant from each other, together. In the vertebrate immune system, two RAGs, RAG-1 and RAG-2, cooperate in this process.

  • Transposon: A transposon, or transposable genetic element, is a "jumping gene." The transposon is usually a gene that codes for a protein. This protein, in turn, recognizes certain signal sequences (sound familiar?) in the transposon DNA allowing it to snip out the transposon DNA and transplant it someplace else. There are many different types of transposons with various degrees of relationship to each other, and they are found in all groups of organisms. Mutations can "break" transposons, resulting in "fossil" transposons that are thought to usually be "junk DNA" (although it may play some non-coding, structural role in cells). About 3% of the human genome is composed of the remains of DNA transposons, and about half of the genome is made of various other kinds of copied repetitive DNA.

With that terminology in hand, we can discuss the transposon hypothesis. The transposon hypothesis is based on similarities between transposons and RAGs, and suggests that RAG-1 and RAG-2, and the RSSs, are actually descended from "free-living" transposons. The model states that in an early vertebrate, already equipped with an innate immune system, a transposon inserted into a non-rearranging receptor gene. When this receptor gene was expressed, the transposon was activated, and snipped itself out of the receptor. However, because this excision process was inexact, the resulting receptor would be variable, and therefore some copies of the receptor protein would be better able to recognize new or mutated pathogens. Natural selection would therefore spread this variant. An extended process of gene duplication and diversification would elaborate this basic system into the modern V(D)J recombination system.

The transposon hypothesis suggests a number of specific observations that would corroborate the model if found:

  • sequence similarities between V(D)J RSSs and transposon recognition sequences
  • RAGs should operate by mechanisms similar to transposase mechanisms
  • RAGs might still be able to perform the same functions that transposons perform, such as DNA excision and insertion
  • immunoglobulins should have relatives that are non-rearranging receptors
  • if RAGs are descended from transposons, then "free-living" transposon relatives of RAG might still exist "in the wild"

All of these observations have been published in the last 10 years. The crowning achievements, and the easiest successes to understand, were the identification of transposon relatives of RAG-1 in sea urchins, lancelets, and cnidarians (Kapitonov and Jurka, 2005) and a RAG1-RAG2 homolog serving a non-immune function in sea urchins (Fugmann et al. 2006).

If the above, very short, summary did not completely sink in, other resources are available. For an excellent moderate-length introduction to evolutionary immunology, please see Matt Inlay's online article, "Evolving Immunity." Pay particular attention to the graphics. Next, read our Nature Immunology essay for a brief update on the scientific progress of the transposon hypothesis.

See also these Panda's Thumb blogposts by Matt Inlay or Andrea Bottaro: "New discovery of missing link between adaptive immune system and transposons," "The Revenge of Calvin and Hobbes," and "Behe's meaningless complexity." Once you have given those sources a try, take several minutes to work through Figure 1 and Figure 2 of Lewis and Wu's (2000) commentary article, "The Old and the Restless", published in the Journal of Experimental Medicine. Figure 1 is a model of how receptor rearrangement works in modern organisms. Figure 2 is a model of how it evolved.

Another introductory survey can be found in the immunology textbook, Immunobiology: the immune system in health and disease. The 5th edition, Janeway et al. (2001), is freely available online in PubMed's textbooks collection. Chapter 4 is "The Generation of Lymphocyte Antigen Receptors" (sections 1, 2, 3, 4, 5). The Afterword to the book, "Evolution of the Immune System: Past, Present, and Future", is written by Janeway, and summarizes the state of knowledge as of 2001 on the evolution of the innate immune system and evolution of the adaptive immune response. The transposon hypothesis naturally plays a large role in the latter.

Hopefully, after you have worked through this material you can re-read the above summary and make some headway.


How the Bibliography was Assembled

This bibliography was originally developed for the Behe cross-examination in the Kitzmiller case, discussed in Bottaro et al. (2006). The annotations are based on notes that were taken while the bibliography was being assembled (in an all-night session the weekend before Behe testified, it must be said). The annotations have subsequently been revised and updated.

While assembling the exhibit, it was very important to make sure it was not vulnerable to some of the critiques that can be leveled against lists of articles that are uncomprehendingly culled from automated literature searches. When one searches online databases for publications that involve the keywords "immune system" and "evolution" -- two immense research topics -- one will get results on a wide variety of topics. These include:

  1. the evolution of disease organisms
  2. the evolution of modern populations in response to diseases
  3. the evolution of immune system cells when an organism's adaptive immune response is triggered (such as when someone is vaccinated)
  4. the use of customized antibodies for innumerable biomedical purposes
  5. the "evolution" of chemical reactions or biochemical reactions (this is a nonbiological definition of evolution, for example, the "evolution" of hydrogen gas during hydrolysis)
  6. clinical research on AIDS, allergies, etc.
  7. the evolution of the immune system within closely-related organisms -- e.g., mammals, birds, or tetrapods
  8. "deep" comparative immunology between vertebrates and invertebrates
  9. the selective forces driving immune system evolution and receptor diversity
  10. the origin of the innate immune system
  11. the origin of the adaptive immune system

Only the last four topics directly address the evolutionary origin of the immune system, although many of the other topics can have some relevance. Among these four topics, this bibliography focused mostly on topic #11, and included a smattering of work on topics #8, 9, and 10. Within topic #11, the origin of the V(D)J recombination system was emphasized, as it is widely seen as the "key" system, the most remarkable feature of adaptive immunity, and the biggest evolutionary "puzzle" according to ID advocates.

This bibliography also focused on the review literature rather than the research literature. First, the research literature is mostly opaque to nonspecialists, and the implications of findings are made much clearer in the review literature. Second, at his deposition, Michael Behe expressed the opinion that if scientists had made any progress worth talking about in evolutionary immunology, he would have expected to see it in the review literature. A few of the most famous research articles were included, but most of the articles are articles reviewing the research literature -- many of the review articles cite several hundred other articles.

This literature collection should not be considered comprehensive or complete -- it is merely a sample of the literature on the evolution of the adaptive immune system, focusing on V(D)J recombination, with a small sampling of literature on the evolution of innate immunity, MHC, large-scale comparative immunology, etc. For some idea of how much more scientific literature there is on this topic, see the longer unannotated bibliography.


The Larger Context

Matt Inlay (author of "Evolving Immunity" and coauthor of Bottaro et al. 2006) points out that Michael Behe's book Darwin's Black Box was ironically timed. In 1996, the year Darwin's Black Box was was published, research on V(D)J recombination was in the midst of a dramatic upswing:

Research progress on V(D)J recombination over the last 25 years. Results of a PubMed search on the term "V(D)J recombination", plotted as a function of time (blue dots). Numbers of articles per year are shown on the y-axis, and the years of publication on the x-axis. Publications for 2006 were projected based on Jan-Apr numbers. Major breakthroughs in the transposon model are listed in text boxes. The vertical line denotes 1996, the year Darwin's Black Box was published. The trendline was calculated via moving average with a period of 3.
Graph and caption by Matt Inlay.

Inlay has added to the graph boxes showing the chronology of the major research findings supporting the transposon model. The viewer can see that they came fast and furious after 1996, almost as if on cue.


Major Themes

The story told by this bibliography, and by Ken Miller's testimony in Kitzmiller, and by Bottaro et al. (2006), is basically of the proposal, development, testing, and confirmation of Sakano et al.'s 1979 suggestion in Nature that V(D)J recombination might have emerged when a transposon -- a piece of DNA that codes for a protein that can chop out that piece of DNA and insert it somewhere else -- inserted into the middle of a receptor gene. This hypothesis has been gathering steam for awhile, and really took off in the last ten years.

A subplot in the story is how evolution has played a key role in immunology throughout its development. Sakano et al.'s hypothesis was not born in a vacuum; it occurred in a field where comparative immunology, informed by evolutionary modeling, had been a core part of the discipline for a hundred years, going back to the work of Metchnikoff in the late 1800s.

If one reads chronologically through the bibliography, one will see the researchers themselves telling the same story, and citing the same papers that have been repeatedly cited in the various Behe immune system rebuttals. But you will also see some rather remarkable comments about Sakano et al.'s hypothesis. Some of the best ones will be highlighted.

For example, as the transposon hypothesis began to pick up steam in the mid-1990's, it did attract some critisms. E.g., Lewis and Wu (1997) wrote,
It is nonetheless worth noting that in spite of various similarities, there are fundamental differences between transposition and V(D)J recombination. For one, there are no reports of a transposase (mutant or otherwise) that is able to mediate site-specific inversion. Conversely, it has never been demonstrated that V(D)J recombination can cause the integration of one piece of DNA into another. (Lewis and Wu 1997, p. 162)
However, the very next year, two labs discovered that the RAG proteins actually could cause the integration reaction. In a research article in Nature entitled "Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system", Agrawal et al. write in their abstract,
Here we show that RAG1 and RAG2 together form a transposase capable of excising a piece of DNA containing recombination signals from a donor site and inserting it into a target DNA molecule. [...] The results support the theory that RAG1 and RAG2 were once components of a transposable element, and that the split nature of immunoglobulin and T-cell-receptor genes derives from germline insertion of this element into an ancestral receptor gene soon after the evolutionary divergence of jawed and jawless vertebrates.
In a commentary article in the same issue of Nature, Plasterk (1998) said, "the authors show that the RAG1 and RAG2 proteins (which mediate V(D)J joining) can still catalyse a full transposition reaction. A similar result has been independently obtained by Martin Gellert and co-workers, and is reported in tomorrow's issue of Cell." This second article was Hiom et al. (1998). In 1999, Schatz reviewed the progress of Sakano et al.'s transposon hypothesis and pronounced it a "prophetic hypothesis":
When examined in their germline configuration, the RSSs flanking V and J constitute an inverted repeat, much like that found at the end of transposons, and this realization led to the prophetic hypothesis, in 1979, that insertion of a transposable element into an ancient receptor gene exon was responsible for the generation of split antigen receptor genes during evolution ([Sakano et al., 1979]). (Schatz 1999, p. 170, bold added)
Also in 1999, Susanna Lewis -- the same Lewis as Lewis and Wu (1997) -- engaged in a little prophesy of her own. If the RAGs evolved from transposons, she said, it would be really handy to find one:
It would be extremely useful if a contemporary version of the original RAG transposon could be identified. A distant cousin, with credentials, would greatly facilitate any attempts to reconstruct the lost history between the time the first RAG element took up residence in the vertebrate genome and the emergence of a developmental recombination system. (Lewis 1999, p. 65)
Six years later, exactly this was reported by Kapitonov and Jurka (2005). It is worth pointing out that, apart from the transposon hypothesis, there was no reason whatsoever to suspect that transposons similar to RAG should exist.

Annotated Bibliography in Chronological Order

Burnet, F. M. (1971). "Self-recognition in colonial marine forms and flowering plants in relation to the evolution of immunity." Nature 232(5308): 230-235. (PubMed | DOI | Journal | Google Scholar)

The author of this article, Sir Frank MacFarlane Burnet, won the 1960 Nobel Prize in Medicine for the discovery of acquired immunological tolerance (http://nobelprize.org/medicine/laureates/1960/). He shared the award with Peter Medawar. Burnet wrote widely on the origin and evolution of the adaptive immune system in the 1960's and 1970's. Although he wrote before the molecular mechanism of recombination was understood he made many perceptive suggestions and is still commonly cited.

The 1971 Nature article is an early example of using comparative immunology in the explicit context of proposing and testing evolutionary hypotheses for the origin of the adaptive immune system. Burnet's specific point is that the ability to distinguish self from non-self is useful not just for fending off disease, but also for other purposes, e.g. detecting abnormal cancer cells, battling competing colonies in colonial tunicates, and preventing self-fertilization in flowering plants. The molecular mechanisms of recognition, such as complementary protein receptors on the cell surface, are not particularly difficult to understand. He argues that a basic self/nonself-recognition system could have provided a starting point for the evolution of the much more complex system of receptors used in the vertebrate adaptive immune system.

Burnet (1971) is cited repeatedly in the literature as outlining the subsequent research program on the origin of adaptive immunity. An example of one of Burnet's forward-looking statements:
"Much more extensive comparative studies are called for and in due course analysis of the results should allow a clear evolutionary history to emerge. Whatever form that history eventually takes we can be certain that gene duplication (gene expansion) plays a major part, and that progressive specialization of cell function and phenotypic restriction will be as conspicuous as it is in all other organs and functions." (p. 232)
Citation of Burnet (1971) is sometimes accompanied by the following quote, "Comparative studies which are not made meaningful by use of evolutionary hypotheses are bound to be sterile." This is misattributed to the 1971 article; instead, it is actually the last sentence in a 1973 Nature article by Burnet ("Multiple Polymorphism in Relation to Histocompatibility Antigens," Nature 245(5425), pp. 359-361).

Marchalonis, J. J. (1976). Immunity in Evolution. Cambridge, Mass., Harvard University Press. (Library | Amazon | Google Print)

Early synthesis of knowledge on the evolution of the immune system, published in 1976. The forward, by Frank MacFarlane Burnet, suggests that the book might emerge as "the first definitive statement of the evolutionary origins and development of vertebrate immunity" (p. xx). The author, John Marchalonis, went on to be one of the leaders in the field of immune system evolution (see his articles in this bibliography through 2006).

Chapter 1 briefly reviews the history of evolutionary immunology, which goes back to at least to Metchnikoff in late 1800's. One of the major points that emerges from comparative immunology is that the defining features of mammalian immunity are shared to different degrees with relatives on the phylogenetic tree.

In the conclusion (p. 263), Marchalonis states, "many puzzling developments in human and mammalian immunity are clarified when analyzed in an evolutionary context." His final sentence makes the point that the study of evolution has practical benefit: "The study of the phylogeny of immunity still retains the excitement of new discoveries and contributes directly toward the applied questions of immunology."

Sakano, H., Hüppi, K., Heinrich, G. and Tonegawa, S. (1979). "Sequences at the somatic recombination sites of immunoglobulin light-chain genes." Nature 280(6): 288-294. (PubMed | DOI | Journal | Google Scholar)

Famous article (within the field) that proposed the transposon hypothesis for the origin of the V(D)J recombination system of adaptive immunity. This speculation was based upon the paper's report on the role that RSSs play in the mechanism of V(D)J recombination, a discovery fundamental to modern scientific understanding of the rearrangement mechanism.
"Evolution of light-chain genes

Thus, the V-J joining may well be a reversal of an ancient accidental insertion of an IS-like [IS = insertion sequence] DNA element...."

"Fig. 6 A hypothetical scheme for the evolution of the K-light-chain genes." (p. 294)
As of summer 2005, Sakano et al. (1979) had received an extraordinary 735 citations in the scientific literature, according to the Science Citation Index.

Manning, M. J., ed. (1980). Phylogeny of Immunological Memory. Developments in Immunology. Amsterdam, Elsevier/North-Holland Biomedical Press. (Library | Amazon | Google Print)

Thirty-one chapters by various authors on comparative immunology; Proceedings of the International Symposium on Immunological Memory held at the American Society of Zoologists Meeting in Tampa, Florida, USA, 28-30 December, 1979.

Klein, J. (1986). "Evolution of Mhc." Natural History of the Major Histocompatibility Complex. New York, John Wiley & Sons: 715-762. (Library | Google Print)

This textbook provides an overview of the Major Histocompatibility Complex (MHC), a system of proteins that help distinguish self from non-self. The final chapter, chapter 10, is entitled "Evolution" and gives a review of self-recognition in various animals.

The chapter begins (p. 716):
"I believe it was Dobzhansky who said that in biology nothing makes sense except in the light of evolution. This dictum will undoubtedly apply also to the Mhc. I doubt very much if we will ever fully understand the true function of the Mhc (what purpose does the Mhc serve?), the presence of the class Ib genes in the Mhc region (why do they persist?), or the origin and purpose of the Mhc polymorphism, without exploring the source from which the Mhc sprang.

I have used the future tense in this last sentence because the study of Mhc evolution has hardly begun. Although more and more papers are being published in which the authors use the term evolution to explain this or that observation, it is significant that at the time of writing this book no paper has been published in which the Mhc DNA of a nonmammalian species has been cloned. The following pages can testify how little we know about Mhc evolution. Most of the harvesters in molecular biology have moved on to reap the next field that has ripened and have no time to finish harvesting where they began. For this reason, progress will probably be slow, particularly in these times of profit-making science. The study of evolution makes no promises as far as eliminating cancer or even producing vaccine against AIDS is concerned, and it is not easy to justify in a grant application. True, one can still make headlines by cloning bits of DNA from some extinct animal, but this probably will not last very long. Sooner or later somebody will want to know what the cloning tells us about the animals, or even whether this information is worth knowing in the first place.

The study of Mhc evolution will probably be a slow process, which will not be marked out by spectacular successess. Yet, if we want to comprehend the Mhc, we must conquer this last frontier." (p. 716)
Despite the conservative tone of this introduction, the technical discussion of MHC evolution continues for 45 pages.

Kelsoe, G. and Schulze, D. H., eds. (1987). Evolution and Vertebrate Immunity: The Antigen-Receptor and MHC Gene Families. Austin, University of Texas Press. (Library | Amazon | Google Print)

Twenty-six articles on the evolution of the immune system (71 authors). Very technical.

Síma, P. and Vetvicka, V. (1990). Evolution of Immune Reactions. Boca Raton, CRC Press. (Library | Amazon | Google Print)

Sima & Vetvicka (Preface, p. iv), begin by saying, "The purpose of this book is to reconstruct the history and evolutionary pathways of immunity among the various forms of life." (p. iv) This book is a survey of the field and all the relevant lineages. It is quite technical although the introduction and conclusion are more accessible.
"We presume that, in the next few years, the fields of comparative and evolutionary immunology will provide, not only inspiration for further investigations in biomedicine, but also a number of practical applicable results." (p. vii)

"[I]f comparative immunology is to become an exact science, it must respect the laws and knowledge not only of experimental immunology, but also those of the evolutionary sciences." (p. vii)

"From among the vertebrate taxa, we have selected only the first three classes, the Agnatha, Chondrichthyes, and Ostichthyes, in order to show where and how the morpho-functional basis of the truly adaptive immunity of the endothermic tetrapods gradually evolved." (p. v)

"In spite of the relative youthfulness of comparative immunology as a new vigorous branch of modern immunology, an impressive amount of data in this field has been amassed in many laboratories all over the world. However, our knowledge of the history of immunity is still limited. A precise understanding of how the key steps in immune evolution were achieved needs further sophisticated study and comparative research work. Many gaps still need to be filled in. Nevertheless the overall picture of the evolution of the defense system in the animal kingdom, including that of immunity, is now sufficiently well known to provide an integral overview." (p. 229)

"Evolutionary immunology is by now a continually expanding discipline that promises to provide, in the nearest future, not only new fruitful ideas and new knowledge which will be fully utilized in practice, but also a clue to the principles controlling the defense mechanisms." (p. 230)

Warr, G. W. and Cohen, N., eds. (1991). Phylogenesis of Immune Functions. Boca Raton, CRC Press. (Library | Amazon | Google Print)

Another technical work dealing with immune systems of both vertebrates and invertebrates. The introduction (p. iii) begins by citing Metchnikoff (1882). Page iii continues:
"[I]t can be argued that for a biologist to ignore the evolutionary history either of an organism or a complex system is as much an impediment to comprehending fully that organism or system as it is for a student of society to ignore the history of mankind." (p. iii)

"[W]e have concentrated on areas in which we believe that recent exciting developments have led to new insights and understanding of immunity and its evolution in diverse species." (p. iii)
In chapter 9, "Evolutionary Origins of Immunoglobulin Genes," (pp. 171-189), Litman et al. write:
"While the progressive phylogenetic development of immunoglobulin complexity is well documented, until recently little structural information at either the protein or the gene levels has been available with which to evaluate the mechanisms of evolution involved." (p. 173)
In chapter 14, "Mechanisms of Molecular Evolution in the Immunoglobulin Superfamily," (pp. 295-316), Warr & Dover write:
"Duplications, or much higher order multiplications, are obvious in the Ig family" (p. 305).
Figure 4 of this article gives a "Hypothetical scheme for the evolution of Ig genes" (p. 304). The model is pre-transposon hypothesis.

Dreyfus, D. H. (1992). "Evidence suggesting an evolutionary relationship between transposable elements and immune system recombination sequences." Molecular Immunology 29(6): 807-810. (PubMed | DOI | Journal | Google Scholar)

This paper reports sequence similarities between V(D)J recombination signal sequences, and the termini of Tcl-like transposable sequences found in invertebrates. The authors note that this supports Sakano et al.'s 1979 hypothesis:
"Sakano et al. (1979) have previously proposed that the vertebrate somatic recombination pathway evolved via the insertion of a transposable element into an ancestral gene encoding an antigen binding molecule, thus accounting for the simultaneous appearance of separated gene segments and a recombination mechanism for their reassembly." (p. 807)

"These similarities suggest that the Tcl transposition pathway may share common sequence-specific binding factors with the immunoglobulin somatic recombination pathway." (p. 807)

Síma, P. and Vetvicka, V. (1992). "Evolution of Immune Accessory Functions." Immune System Accessory Cells. Edited by L. Fornusek and P. Síma. Boca Raton, CRC Press: 1-55. (Library | Amazon | Google Print)

Long review of immune system cells across vertebrates and invertebrates. Cites Metchnikoff (1892) on p. 5. Figure 2 (p. 37) depicts the progressive emergence of various aspects of the immune system in the phylogeny of animals.
"The aim of this overview is to attempt to compare the evolutionary emergence of accessory cellular function and the role of various defense cell types in defense reactions in major natural assemblages of metazoan species." (p. 2)
The article begins with a quote from Burnet (1973) in Nature: "Comparative studies which are not made meaningful by use of evolutionary hypotheses are bound to be sterile."

Bartl, S., Baltimore, D. and Weissman, I. L. (1994). "Molecular evolution of the vertebrate immune system." Proceedings of the National Academy of Sciences 91(23): 10769-10770. (PubMed | Journal | JSTOR | Google Scholar)

This is a short (2 pages) review article. In his 1996 book Darwin's Black Box, Behe critiqued it for vagueness, but even in 1996 there were longer review articles available (e.g. Thompson 1995), and despite the shortness, the basic ideas proposed in this article and elsewhere have been dramatically confirmed in the subsequent decade, as detailed in our 2006 Nature Immunology essay.

The last sentences of Bartl et al. (1994):
"It is possible that the ancestors of RAG genes may have been horizontally transferred into a metazoan lineage at some relatively recent point in evolution. The newly introduced RAG genes may have acted, most likely with other proteins, on preexisting recombination signals (which consists of conserved heptamer and nonamer sequences) that may have been present for some other function or by random chance. In that view, the signal sequences captured the ancestors of present day TCR and immunoglobulin gene segments. Such a scenario is highly speculative but if true would imply a startling role for horizontal information transfer as the pivotal event in the evolution of vertebrate immunity." (p. 10770)

Beck, G., Cooper, E. L., Habicht, G. S. and Marchalonis, J. J., eds. (1994). Primordial Immunity: Foundations for the Vertebrate Immune System. New York, The New York Academy of Sciences. (Library | PubMed | Publisher | Amazon | Google Print)

This volume on comparative and evolutionary immunology resulted from a May 3-5, 1993 conference held in Woods Hole entitled "Primordial Immunity: Foundations for the Vertebrate Immune System." It contains 24 articles and 18 poster summaries, mostly examining the immune systems of various phylogenetically basal organisms. Three of the articles focusing on the origin of adaptive immunity are included in the articles list.

In the Preface to Primordial Immunity, editor Gail Habicht writes,
"We know -- but we need to be convincing to others -- that studies of primordial immunity have tremendous importance:
for the clues they give us to higher systems;

for their unique strategies -- some of which may be exploitable for human benefit -- not just in medicine but in agriculture where biological pest control is a desirable alternative to toxic pesticides;

but, most importantly, for their own sake.
The value of maintaining the biodiversity of our planet should be obvious: The gene pool possessed by even the lowliest creatures has the potential for enormous benefit to mankind." (p. xi, emphasis added)

Hoffman, J. A., Janeway, C. A. and Natori, S., eds. (1994). Phylogenetic Perspectives in Immunity: The Insect Host Defense. Austin, R. G. Landes Company. (Library | Amazon | Google Print)

Fifteen chapters on the immune systems of basal vertebrates and arthropods in an evolutionary perspective. Three of the most relevant chapters are:

Chapter 6, by Iwanga et al., "Clotting Cascade in the Immune Response of Horseshoe Crab" (pp. 79-96).

Chapter 11, by Eric H. Davidson, "Stepwise Evolution of Major Functional Systems in Vertebrates, Including the Immune System" (pp. 133-142).

Chapter 12, by Alister Dodds, "Molecular and Phylogenetic Aspects of the Complement System" (pp. 143-155).

Marchalonis, J. J. and Schluter, S. F. (1994). "Development of an Immune System." Primordial Immunity: Foundations for the Vertebrate Immune System. Edited by G. Beck, E. L. Cooper, G. S. Habicht and J. J. Marchalonis. New York, New York Academy of Sciences. 712: 1-11. (Library | PubMed | Publisher | Google Print)

Overview of the distribution and origin of major pieces of the immune system, and some discussion of the selective pressures that may have been in play. The lead author, Marchalonis, has been working on the evolutionary origin of the immune system since the 1970's.

The introductory paragraph highlights some of the practical benefits of understanding the evolution of the immune system.
"There has always been considerable interest in understanding the evolutionary origins of the immune system,1-6 and this quest has recently been given impetus by the application of advanced methods in recombinant DNA technology7-14 and immunochemistry.15-18 An understanding of the genetic mechanisms underlying the capacity of vertebrates to respond to a potentially enormous (greater than 107) set of antigenic markers associated with pathogens or cancers that might never have been presented to the animal during its evolutionary development is of general theoretical importance for the understanding of anticipatory mechanisms19 and of practical value in modulating the immune response in autoimmunity or amplifying it in cases of immunodeficiency."
The article is one of three from the special ANYAS volume Primordial Immunity which were included in the bibliography as particularly relevant to the origin of adaptive immunity. The volume contains dozens of other papers, however, so it is included in the books list as well.

Marchalonis, J. J., Hohman, V. S., Kaymaz, H., Schluter, S. F. and Edmundson, A. B. (1994). "Cell Surface Recognition and the Immunoglobulin Superfamily." Primordial Immunity: Foundations for the Vertebrate Immune System. Edited by G. Beck, E. L. Cooper, G. S. Habicht and J. J. Marchalonis. New York, New York Academy of Sciences. 712: 20-33. (Library | PubMed | Publisher | Google Print)

Review of the origin and dramatic diversification of the various immunoglobulins (Igs).
"Data obtained recently on gene sequences of Igs of sharks, the ancestors of which diverged from those of mammals more than 400 million years ago, allow us to make detailed comparisons regarding the homologies among Ig V and C domains in evolution." (p. 21)

"We will analyze putative evolutionary relationships among canonical Igs and members of the Ig superfamily using highly conserved sequences from light and heavy chains of primitive vertebrates (e.g., the sandbar shark) as prototypes to ascertain similarities between Ig-related molecules of vertebrates and invertebrates." (p. 32)

Ohno, S. (1994). "MHC Evolution and Development of a Recognition System." Primordial Immunity: Foundations for the Vertebrate Immune System. Edited by G. Beck, E. L. Cooper, G. S. Habicht and J. J. Marchalonis. New York, New York Academy of Sciences. 712: 13-19. (Library | PubMed | Publisher | Google Print)

Argues for a relatively late origin of MHC (self-recognition capability), after the origin of adaptive immunity. This bucks the dominant view and the article explicitly takes a "devil's advocate" approach.

Stewart, J. (1994). The Primordial VRM System and the Evolution of Vertebrate Immunity. Austin, R. G. Landes. (Library | Amazon | Google Print)

This book is on the origin of the VRM system (VRM = Variable Region Molecules, see p. 9).

The evolutionary origin of various non-VRM immunity is covered on pp. 10-14 as background.
"[T]he early history of immunology was marked by an outstanding contribution which is a fine model of the methodology capable of rendering an evolutionary approach fruitful. The Russian Metchnikoff was exceptional, not only among the immunologists of his day but (unfortunately) among those of succeeding generations as well, in that his background was neither that of a chemist nor of a medical clinician, but truly that of a theoretically informed biologist." (p. 10)
The book emphasizes duplication and exaptation (e.g., see exaptation reference on p. 10: "redeployment" of single-cell feeding ability ("phagocytosis") to immune system function in multicellular animals), but it does not discuss the transposon hypothesis, even though page 45 seems to be crying out for it. However, the hypothesis only seems to have begun a resurgence in about 1994.

Stewart (1994) is cited by Behe on p. 282, note 7. Stewart is also the author of: Stewart, J. (1992) Immunoglobulins did not arise in evolution to fight infection. Immunology Today 13, 396-399.

Vetvicka, V., Síma, P., Cooper, E. L., Bilej, M. and Roch, P. (1994). Immunology of Annelids. Boca Raton, CRC Press. (Library | Amazon | Google Print)

Ten chapters on the immunology of annelids (earthworms and relatives). This may seem obscure, but the importance of annelids to evolutionary immunology is explained in Chapter 1, "Comparative Immunology: The Value of Annelids."
"[A]ll invertebrates, including annelids, have figured prominently in establishing the field of immunology." (p. 6)

"As long as there are invertebrates like earthworms, oysters, or honey bees to be protected, and others like tapeworms, slugs, and mosquitoes to be destroyed, there will be a utilitarian justification for studying invertebrate paleontology and whatever is equivalent in them to what we study in vertebrates as immunology.... Most contributors are interested mainly in what, if any, light such studies of invertebrates can throw on the evolution of the processes of inflammation and immunity as we see them in humans and the experimental mammals of the laboratory. Since Darwin, much of the 'fun' of biological research has been to interpret what directly interests one in evolutionary terms." (pp. 5-6, quoting Burnet 1971 in Nature)

Thompson, C. B. (1995). "New insights into V(D)J recombination and its role in the evolution of the immune system." Immunity 3(5): 531-539. (PubMed | DOI | Journal | Google Scholar)

A long review article summarizing the early results supporting the transposon model for the origin of adaptive immunity.
"Current evidence suggests that the ability to mount an antigen-specific immune response arose over a relatively short period of time coincident with the development of the first jawed vertebrates. This has raised the question of how a mechanism as complex as V(D)J recombination arose over such a short evolutionary period. Recent advances in V(D)J recombination suggest a resolution to this issue and allow us to reexamine the role of antigen specificity in shaping the evolution of the immune system." (p. 531)

"These observations are already renewing speculation concerning the origins of RAG1 and RAG2." (p. 532).

"Conclusion

Recent advances in our understanding of V(D)J recombination and the distribution of immunoglobulin and TCR genes in vertebrate evolution give support to the hypothesis that the V(D)J recombination arose abruptly during early vertebrate evolution. Current evidence suggests that V(D)J recombination is directed by elements that could have been derived from a transposon. [...] Colonization of the genome of an ancestral vertebrate by a transposon represents a fundamental failure of the defense systems of the organism. It is ironic that the participation of such an element in the evolution of antigen-specific immunity may have played an important role in the evolutionary success of vertebrates." (p. 538)

Bernstein, R. M., Schluter, S. F., Bernstein, H. and Marchalonis, J. J. (1996). "Primordial emergence of the recombination activating gene 1 (RAG1): Sequence of the complete shark gene indicates homology to microbial integrases." Proceedings of the National Academy of Sciences 93(18): 9454-9459. (PubMed | Journal | JSTOR | Google Scholar)

This study compared RAG1 and RAG2 in sharks and mammals, delineating the highly conserved regions. These conserved regions were found to exhibit homology to bacterial recombinases.
"Homology domains identified within shark RAG I prompted sequence comparison analyses that suggested similarity of the RAG I and II genes, respectively, to the integrase family genes and integration host factor genes of the bacterial site-specific recombination system. Thus, the apparent explosive evolution (or "big bang") of the ancestral immune system may have been initiated by a transfer of microbial site-specific recombinases." (p. 9454)
Figure 5 contains a general phylogenetic tree of the prokaryotic relatives of RAG1, and depicts the hypothesized horizontal transfer event.

van Gent, D. C., Mizuuchi, K. and Gellert, M. (1996). "Similarities between initiation of V(D)J recombination and retroviral integration." Science 271(5255): 1592-1594. (PubMed | Journal | JSTOR | Google Scholar)

This study reports close similarities between the mechanism of the formation of DNA hairpins during the cutting and assembly of antibody genes, and the processes that occur when transposons and retroviruses insert into DNA.
"These findings provide support for the speculation that the antigen receptor genes, and the RAG1 and RAG2 proteins that mediate their rearrangement, may have evolved from an ancestral transposon (18). The presence of RSSs facing in opposite directions (the most usual arrangement in the antigen receptor loci) is similar to the inverted repeat architecture of many transposon ends, and the RAG proteins could have developed from genes encoded by the former transposon."
Ref. 18 is Thompson (1995).

Hughes, A. L. and Yeager, M. (1997). "Molecular evolution of the vertebrate immune system." BioEssays 19(9): 777-786. (PubMed | Google Scholar)

Review of the evolution of several key pieces of the immune system (e.g., C3 and the other complement proteins, MHC, RAG & immunoglobulins, etc.), with a focus on the evolutionary mechanisms involved, e.g. various forms of gene duplication vs. block duplication.

Several of the key questions asked here in 1997 have been answered. The discussion of the origin of RAGs is quoted to show what was known then, and what research questions were being asked.
"Some major unanswered questions

(1) The origin of the immunoglobulin superfamily C1 type of domain

[...]

(2) Block duplication vs. functional gene clustering

[...]

(3) Conserved proteins involved in vertebrate adaptive immunity

One of the unique features of the vertebrate immune system is the rearrangement of gene segments to produce expressed Ig and TCR genes. Because these gene segments are short and have evolved rapidly, it may be very difficult to reconstruct their early evolutionary history. It may be possible, however, to obtain clues regarding the early history of Ig and TCR by studying the phylogeny of conserved proteins playing key roles in the process of rearrangement. These include the products of two genes called RAG-1 and RAG-2, which are linked in mammals. Homologues of RAG-1 have been sequenced from mammals, amphibians, bony fishes and shark(63). The RAG-1 protein shows some evidence of homology to the bacterial site-specific recombinases Fim B and Fim E(63), while RAG-2 shows homology to the bacterial recombinases Hin A(63). A phylogenetic analysis (Fig. 5), based on the region of homology between RAG-1, FimB and Fim E, illustrates this relationship. RAG-1 shows homology to eukaryotic proteins involved in such processes as excision repair (yeast RAG16(64) and regulation of gene expression (mouse rpt-1r(65) and to a human acid finger protein (66)). Interestingly, in the phylogenetic tree, RAG-1 clusters closer to the bacterial proteins than it does to any of these eukaryotic proteins (Fig. 5).

The homologies between RAG-1 and RAG-2 and bacterial proteins led Bernstein et al.(63) to suggest that somatic recombination arose in vertebrates as a result of horizontal transfer of a mictobial [sic] recombinase gene. The mere fact of homology between RAG-1 and RAG-2 and bacterial genes, however, is not evidence of horizontal gene transfer, since many vertebrate genes have prokaryotic homologues. [...] Nonetheless, Bernstein et al.(63) are correct in pointing out the potential importance of understanding the origin of this gene, and others involved in the recombination process, for gaining insights into the origin of adaptive immunity." (p. 785)
The cited references in this passage include the familiar Bernstein et al. (1996):
[References]

63 Bernstein, R., Schluter, S.F., Bernstein, H. and Marchalonis, J.J. (1996). Primordial emergence of the recombination activating gene 1 (RAG1): sequence of the complete shark gene indicates homology to microbial integrases. Proc. Natl. Acad. Sci. USA 93, 9454-9459.

64 Bang, D.d., Verhage, R., Goosen, N., Brouwer, J. and van de Putte, P. (1992). Molecular cloning of RAD16, a gene involved in differential repair in Saccharomyces cerevisiae. Nucleic Acids Res. 20, 3924-3931.

65 Patarca, R. et al. (1988). rpt-1, an intracellular protein from helper/inducer T cells that regulates gene express of interleukin 2 receptor and human immunodeficiency virus type 1. Proc. Natl. Acad. Sci. USA 85, 2733-2737.

66 Chu, T.W., Capossela, A., Coleman, R., Goel, V.L., Nallur, G. and Gruen, J.R. (1995). Cloning of a new 'finger' protein gene (ZNF173) within the class I region of the human MHC. Genomics 29, 229-239.

67 Hughes, A.L. (1994). Evolution of the ATP-binding cassette transmembrane transporters of vertebrates. Mol. Biol. Evol. 11, 899-910.

Ji, X., Azumi, K., Sasaki, M. and Nonaka, M. (1997). "Ancient origin of the complement lectin pathway revealed by molecular cloning of mannan binding protein-associated serine protease from a urochordate, the Japanese ascidian, Halocynthia roretzi." Proceedings of the National Academy of Sciences 94(12): 6340-6345. (PubMed | Journal | Google Scholar)

Research paper reporting that key innate immune system genes have been discovered in tunicates, invertebrates related to vertebrates (also known as ascidians or sea-squirts).
"The major developments of the complement system, therefore, seem to have occurred in two stages; first, with the emergence in cyclostomes of the alternative pathway to establish a means of amplification, and second, after the divergence of cyclostomes but before the divergence of cartilaginous fish, the emergence of the classical and lytic pathways. This hypothesis would not only explain the evolution of the complement system, but also may help to reevaluate the activation mechanism of the mammalian alternative pathway." (pp. 6344-6345)

Lewis, S. M. and Wu, G. E. (1997). "The origins of V(D)J recombination." Cell 88(2): 159-162. (PubMed | DOI | Journal | Google Scholar)

Lewis and Wu have authored several reviews on the evolutionary origin of the adaptive immune system. This 1997 review in Cell summarizes the state of the question after several then-recent discoveries. The introductory section, "The Origins of V(D)J Recombination," discusses why the evolutionary question was attracting renewed interest:
"Recently V(D)J recombination has been partially reconstituted in vitro (reviewed in Gellert, 1996), and as a result, has been the subject of intense research. A side effect of these efforts has been renewed speculation regarding evolutionary origins. New information bears upon the possibility that this unusual recombination system could have been a transplant from the procaryotic world (Difilippantonio et al., 1996; Spanopoulou et al., 1996, van Gent et al., 1996a)." (p. 159)
This article reviews "The Case for a Transposon Progenitor" of RAG (section heading, p. 161), e.g.:
"Given that the architecture of a joining signal is transposon-like, this similarity between chemical mechanisms would seem to add weight to the idea that the V(D)J recombination system originally carried out transpositional rearrangements. The transposon theory has in fact been suggested, for various reasons, a number of times over the years." (p. 162)
On the other hand, several similarities were missing in 1997:
"It is nonetheless worth noting that in spite of various similarities, there are fundamental differences between transposition and V(D)J recombination. For one, there are no reports of a transposase (mutant or otherwise) that is able to mediate site-specific inversion. Conversely, it has never been demonstrated that V(D)J recombination can cause the integration of one piece of DNA into another." (p. 162)
Both of these features were soon discovered in lab experiments in following years.
[References]

Difilippantonio, M.J., McMahan, C.J., Eastman, Q.M., Spanopoulou, E., and Schatz, D.G. (1996). Cell 87, 253-262.

Gellert, M. (1996). Genes to Cells 1, 269-276.

Lewis, S.M. (1994). Adv. Immunol. 56, 27-150.

Spanopoulou E., Zaitseva, F., Wang, F.-H., Santagata, S., Baltimore, D., and Panaoytou, G. (1996). Cell 87, 263-276.

van Gent, D.C., Mizuuchi, D., and Gellert, M. (1996a). Science 271, 1592-1594.

van Gent, D.C., Ramsden, D.A., and Gellert, M. (1996b). Cell 85, 107-113.

Schluter, S. F., Bernstein, R. M. and Marchalonis, J. J. (1997). "Molecular origins and evolution of immunoglobulin heavy-chain genes of jawed vertebrates." Immunology Today 18(11): 543-549. (PubMed | DOI | Journal | Google Scholar)

A review of the origins of rearranging immunoglobulins in the light of cartilagenous fish, the most basal vertebrate group possessing classic adaptive immunity. The introduction clearly states the kinds of questions that an evolutionary model must answer.
"A model for the evolution of the immunoglobulins (Igs) must explain two separate but closely related aspects. The first is the genetic mechanisms by which the diversity of the expressed effector molecules is generated1. This would encompass both the enzymatic mechanism of recombination and the genomic organization of the various elements of the Ig genes. The second is the functional duality of the receptor proteins whereby the variable (V) regions form the antigen-binding sites and the effector activities are mediated through the constant (C) regions2. This article will focus on the latter aspect, particularly the molecular evolutionary origins of the gene segments encoding Ig heavy (H) chains." (p. 543)
A model for the origin of the various immunoglobulins is constructed based on the phylogenies reviewed in the paper:
"A model for the evolution of the VH genes

From the evidence discussed above, a model for the evolutionary origins of VH and Ig isotypes is presented in Fig. 4. As originally proposed, the V and C domains arose by duplication of a primordial Ig domain3,13. The C domains duplicated and evolved independently to form the primordial prototype H-chain isotype." (p. 548)

Agrawal, A., Eastman, Q. M. and Schatz, D. G. (1998). "Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system." Nature 394(6695): 744-751. (PubMed | DOI | Journal | Google Scholar)

This study reports a major research finding that supported the transposon hypothesis for the origin of adaptive immunity. The authors found that the rearrangment-activating genes, RAG1+RAG2, could still perform both the excision and the insertion reactions, just like a free-living transposon.

Figure 7 is a nice color graphic of the transposon hypothesis.
"Our results are evidence in favour of the theory that a vital event in the evolution of the antigen-specific immune system was the insertion of a 'RAG transposon' into the germ line of a vertebrate ancestor14,41." (p. 750)

[References]

14. Thompson, C. B. New insights into V(D)J recombination and its role in the evolution of the immune system. Immunity 3, 531-539 (1995).

15. Lewis, S. M. & Wu, G. E. The origins of V(D)J recombination. Cell 88, 159-162 (1997).

41. Sakano, H., Hüppi, K., Heinrich, G. & Tonegawa, S. Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Nature 280, 288-294 (1979).

Plasterk, R. (1998). "Ragtime jumping." Nature 394(6695): 718-719. (PubMed | DOI | Journal | Google Scholar)

Summary of the Nature article Agrawal et al. (1998). While short and nontechnical, it is relevant to some of Behe's "search criteria" as he laid out during his sworn deposition for the Kitzmiller case. During his deposition in May 2005, Behe was quizzed about some of his claims about the immune system, and he was asked how he even knew what was in the literature since he wasn't familiar with the peer-reviewed articles that were presented then. Behe's answers (Behe deposition, pp. 231-233) were basically (1) he relies on other people to email him articles that meet his challenges, (2) articles on the evolution of the immune system would be big news, so he watches out for news articles in major scientific publications, and review articles in review journals and other scientific literature, and (3) he watches out for articles in popular scientific outlets such as the New York Times or Scientific American.

Plasterk's 1998 article in Nature is an example of case #2, which Behe missed. Many of the other articles in this bibliography are also review articles; one is even found in Annual Review of Immunology (Litman et al. 1999), and two are in Immunological Reviews (Cannon et al. 2004, Jones et al. 2004). Although not included in this bibliography, two 1996 articles in Scientific American on the evolution of the immune system are examples of case #3.

The Plasterk article begins:

"Transposons are generally considered the ultimate forms of selfish DNA -- a single gene (or sometimes a set of two or three genes) that spreads simply because it ensures its own replication. Indeed, the ability of transposons to encode one or more proteins that selectively replicate the transposon is enough to explain their existence. But selfish elements may also end up doing something useful for their host, and it has often been speculated that transposon jumping may have generated gene arrangements that opened new avenues in evolution. Examples of this are rare, but a spectacular case has now been discovered. On page 744 of this issue, David Schatz and his colleagues report that we owe the repertoire of our immune system to one transposon insertion, which occurred 450 million years ago in an ancestor of the jawed vertebrates. Vertebrates seem to have tamed this ancient transposon for generation of the immune repertoire, and the authors show that the RAG1 and RAG2 proteins (which mediate V(D)J joining) can still catalyse a full transposition reaction. A similar result has been independently obtained by Martin Gellert and co-workers2, and is reported in tomorrow’s issue of Cell."

[References]

1. Agrawal, A., Eastman, Q. M. & Schatz, D. G. Nature 394, 744-751 (1998).

2. Hiom, K., Melek, M. & Gellert, M. Cell 94, 463-470 (1998).

Vetvicka, V. and Síma, P. (1998). Evolutionary Mechanisms of Defense Reactions. Basel, Birkhäuser Verlag. (Library | Amazon | Google Print)

Vetvicka & Sima systematically review the immune systems of animals, starting with the earliest branches on the animal phylogenetic (sponges), through the various simple and complex invertebrates, the chordate relatives of vertebrates, the early diverging vertebrates such as the lampreys and hagfish, and ending with the "higher" vertebrates and their adaptive immune systems. Highly technical, focuses on immune system organs in addition to the cellular/molecular level. The primary themes are that: (1) immune system evolution must be considered in the context of ecological and morphological change in mammal groups; (2) there is a large degree of diversity in so-called "primitive" organisms, and there are many ways organisms survive without the "required" parts of vertebrate immunity.
"[B]asic research in comparative and evolutionary immunology has substantially contributed in many ways to the exciting progress that immunology has made in recent decades." (p. 187)

Lewis, S. M. (1999). "Evolution of Immunoglobulin and T-Cell Receptor Gene Assembly." Annals of the New York Academy of Sciences 870: 58-67. (PubMed | Journal | Google Scholar)

Another detailed review of the RAG transposon hypothesis by Susanna Lewis. It is a clear example of the increasing confidence that researchers in the field have about the transposon hypothesis. E.g., from the introductory section, entitled, "A transposon origin for V(D)J recombination":
"How such a singular mechanism for somatic cell differentiation arose has long been a puzzle.6 Although a multiplicity of site-specific recombination systems exist in bacteria, yeast, and protozoa, no other example apart from V(D)J recombination is known to operate in vertebrates. One speculation dating back to the time of the first molecular descriptions of immunoglobulin gene rearrangement is that the V(D)J recombination system may have evolved from a mobile element.7 Now, almost 20 years later, biochemical analyses of RAG1 and RAG2 have uncovered solid clues that this indeed may be the case." (p. 58)
Figure 4 contains a summary depiction of the transposon hypothesis. Lewis (1999) is especially noteworthy because it contains an uncannily predictive suggestion in the section suggesting further research avenues:
"THE NEXT STEP

It would be extremely useful if a contemporary version of the original RAG transposon could be identified. A distant cousin, with credentials, would greatly facilitate any attempts to reconstruct the lost history between the time the first RAG element took up residence in the vertebrate genome and the emergence of a developmental recombination system." (p. 65)
Exactly this was discovered six years later, in 2005 (Kapitonov & Jurka, 2005). Another cousin was discovered in 2006 (Fugmann, S. D., Messier, C., Novack, L. A., Cameron, R. A. and Rast, J. P. (2006). "An ancient evolutionary origin of the Rag1/2 gene locus." Proc Natl Acad Sci U S A 103(10): 3728-3733)
[References]

1. Marchalonis, J.J., S.F. Schluter, R.M. Bernstein, S. Shen & A.B. Edmundson. 1998. Phylogenetic emergence and molecular evolution of the immunoglobulin family. Adv. Immunol. 70: 417-506.

2. Gellert, M. 1997. Recent advances in understanding V(D)J recombination. Adv. Immunol. 64: 39-64.

[...]

6. Lewis, S. & G. Wu. 1997. The origins of V(D)J recombination. Cell 88: 159-162.

7. Sakano, H., K. Hüppi, G. Heinrich & S. Tonegawa. 1979. Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Nature 280: 288-294.

Litman, G. W., Anderson, M. K. and Rast, J. P. (1999). "Evolution of antigen binding receptors." Annual Review of Immunology 17: 109-147. (PubMed | DOI | Journal | Google Scholar)

This very long (38 pages) and technical review article cites 171 references, surveying all aspects of the origins of adaptive immunity, focusing on the ancestry and phylogeny of the receptors rather than the transposon hypothesis which is taken as confirmed.
"This review addresses issues related to the evolution of the complex multigene families of antigen binding receptors that function in adaptive immunity. [...] As of yet, homologous forms of antigen binding receptors have not been identified in jawless vertebrates; however, acquisition of large amounts of structural data for the antigen binding receptors that are found in a variety of jawed vertebrates has defined shared characteristics that provide unique insight into the distant origins of the rearranging gene systems and their relationships to both adaptive and innate recognition processes." (p. 109)

"Further clarification of the origins and interrelationships of these putative receptors will come through phylogenetic comparisons between rearranging and nonrearranging antigen binding receptors found in jawed vertebrates. Such analyses will also be significant in terms of designing strategies for identification of related systems in agnathans, lower chordates, hemichordates, and echinoderms. The recent discovery that RAG1 and RAG2 proteins together constitute a transposase, capable of excising a piece of DNA containing recombination signals from a donor site and inserting into a target DNA molecule, has enormous bearing on mechanisms whereby nonrearranging receptors diverged into the rearranging antigen binding receptor genes (171)." (p. 139)

[References]

171. Agrawal A, Eastman QM, Schatz DG. 1998. Transposition mediated by the V(D)J recombination proteins RAG1 and RAG2: implications for the origins of the antigen-specific immune system. Nature 394:744-51

Schatz, D. G. (1999). "Transposition mediated by RAG1 and RAG2 and the evolution of the adaptive immune system." Immunologic Research 19(2-3): 169-182. (PubMed | Google Scholar)

Technical review of the tranposon hypothesis. The abstract summarizes Schatz's main point:
"The hypothesis that RAG1 and RAG2 arose in evolution as components of a transposable element has received dramatic support from our recent finding that the RAG proteins are a fully functional transposase in vitro."
Noteworthy in the article is Schatz's description of Sakano et al. (1979) as advancing a "prophetic hypothesis":
"When examined in their germline configuration, the RSSs flanking V and J constitute an inverted repeat, much like that found at the end of transposons, and this realization led to the prophetic hypothesis, in 1979, that insertion of a transposable element into an ancient receptor gene exon was responsible for the generation of split antigen receptor genes during evolution (5)." (p. 170)

[Reference cited]

5 Sakano H, Hüppi K, Heinrich G, Tonegawa S: Sequences at the somatic recominbation sites of immunoglobulin light-chain genes. Nature 1979;280:288-294.

Schluter, S. F., Bernstein, R. M., Bernstein, H. and Marchalonis, J. J. (1999). "'Big Bang' emergence of the combinatorial immune system." Developmental and Comparative Immunology 23(2): 107-111. (PubMed | DOI | Journal | Google Scholar)

Basic review of the transposon hypothesis. The title and various quotes are the kind of thing that are commonly quote-mined by creationists, e.g., "Thus, the Big Bang must have occurred in the extremely short time of emergence of jawed vertebrates from their ostracoderm ancestors." (p. 107) However, it is worth noting that "extremely short" means about 50 million years in this context. And, the whole point of the article is that the transpson hypothesis, where a prokaryotic transposon jumped into the vertebrate genome, is what explains the "big bang" in question.

For example:
"We [1, 2, 20] and others [6, 8, 33, 34] have hypothesized that the event that catalyzed the explosive burst of the generation of combinatorial immunity (Fig. 1) was the horizontal transfer of genes from microbes and/or fungi enabling site-specific recombination of DNA. Because retroviruses have long been known to insert into mammalian chromosomes and defective pieces of retrotransposons have been found in lower deuterostomes [33, 34], sharks [35], turtles [36] and chickens [37], and retrotransposons are widely distributed among teleost fish [38], we tentatively suggested that retroviruses may have played a role in this transition. However, transposons capable of directly modifying DNA [39, 40] may also play a substantial role. It was first recognized by Thompson [6] that the gene cluster specifying RAG1 and RAG2 resembles a disassociated transposon, thus suggesting a transposon origin for these genes. Direct in vitro experimental support for this hypothesis was recently provided in two reports, Agrawal et al., [41] and Hiom et al.[42]. These groups showed that recombinant RAG1 and RAG2 proteins together could cleave a fragment of DNA flanked by RSS (recombinant signal sequence) sites and mediate its insertion into a plasmid, thus directly demonstrating that RAG proteins can express transposase activity." (p. 108)
Figure 2 gives a depiction of the transposon hypothesis. More evidence for the transposon hypothesis is given on the next pages:
"IHF [Integration Host Factor] binding sites in some transposons (e.g. TnA family) occur adjacent to transposase binding sites, suggesting that the RAGI/RAGII recombination system arose from an ancestral system in a transposon or retrotransposon." (pp. 109-110)

[References]

[1] Marchalonis JJ, Schluter SF, Bernstein RM, Edmundson AB. Phylogenetic emergence and molecular evolution of the immunoglobulin family. Adv. in Immunol. 1998; 70:417-506.

[2] Marchalonis JJ, Schluter SF. A stochastic model for the rapid emergence of specific vertebrate immunity incorporating horizontal transfer of systems enabling duplication and combinatorial diversification. J. Theo. Biol. 1998; 193:429-444.

[3] Marchalonis JJ, Schluter SF. On the relevance of invertebrate recognition and defense mechanisms to the emergence of the immune response of vertebrates. Scand. J. Immunol. 1990;32:13-20.

[4] Klein J. Homology between immune responses in vertebrates and invertebrates: does it exist? Scand. J. Immunol. 1997;46:558-564.

[5] Hughes AL, Yeager M. Molecular evolution of the vertebrate immune system. BioEssays 1997;19:777-786.

[6] Thompson CB. New Insights into V(D)J recombination and its role in the evolution of the immune system. Immunity 1995;3:531-539.

[7] Medzhitov R, Janeway CA. Innate Immunity: The virtues of a nonclonal system of recognition. Cell 1997;91:295-298

[8] Bartl S, Baltimore D, Weissman IL. Molecular evolution of the vertebrate immune system. Proc. Natl. Acad. Sci. USA 1994;91:10769-10770.

[9] Habicht GS. Primordial immunity: foundations for the vertebrate immune system. In: Beck G, Cooper EL, Habicht GS, Marchalonis JJ, editors. Primordial Immunity: Foundations for the Vertebrate Immune System, vol. 712. New York: New York Academy of Sciences, 1994:ix-xi.

[41] Agrawal A, Eastman QM, Schatz DG. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 1998;394:744-751.

[42] Hiom K, Melek M, Gellert M. DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 1998;94:463-470.

Du Pasquier, L. (2000). "The Phylogenetic Origin of Antigen-Specific Receptors." Origin and Evolution of the Vertebrate Immune System. Edited by L. Du Pasquier and G. W. Litman. Berlin, Springer. 248: 159-185. (Library | PubMed | Amazon | Google Print)

Highly technical review of the origin of the receptor genes, starting with Ig homologs in invertebrates, and then looking at the relationships between the various immune system genes within vertebrates.
"Fig. 10. Origin and evolution of Igsf members with V and C1 domains. A hypothesis taking into account the genetic linkages and the homologies presented in this chapter." (pp. 178-179)

"This survey reminds us that V domains are very ancient and exist in the most primitive Metazoa. [...] A model (Fig. 10) is presented accounting for many of the linkages and homologies described." (p. 182)

Du Pasquier, L. and Litman, G. W., eds. (2000). Origin and Evolution of the Vertebrate Immune System. Current Topics in Microbiology and Immunology. Berlin, Springer. (Library | Publisher | Amazon | Google Print)

This edited book in the Current Topics in Microbiology and Immunology series contains 14 articles by 33 contributors on the evolutionary origin of the immune system. It is a thorough survey of the evolution of the major parts of the immune system as of 2000. Most of the articles are very technical. Despite this, the Preface reads,
"This book is by no means comprehensive and can be complemented by reading recent issues of Immunological Reviews (nos. 166, Immune systems of ectothermic vertebrates, and 167, Genomic organisation of the MHC: structure, origin, and function)." (p. vi)

"The quantity of information concerning vertebrate immunity from developmental and molecular perspectives is enormous, and offers an excellent opportunity to study the evolutionary behavior of complex molecular networks. As more sea urchin genes that are homologous to genes of the vertebrate immune system are isolated, it is becoming clear that the phylogenetic position of the echinoderms will truly enable the creation and testing of hypotheses of large scale immune system evolution." (Chapter 1, "New approaches Towards and Understanding of Deuterostome Immunity", p. 5)
Also, from Chapter 1, Section 4, "The Evolution of Complex Systems":
"Subsystems of a complex immune system may evolve independently from one another, and as a first step towards understanding system-wide evolution these points of disjunction must be characterized." (Chapter 1, "New approaches Towards and Understanding of Deuterostome Immunity", p. 12)

Hansen, J. D. and McBlane, J. F. (2000). "Recombination-Activating Genes, Transposition, and the Lymphoid-Specific Combinatorial Immune System: A Common Evolutionary Connection." Origin and Evolution of the Vertebrate Immune System. Edited by L. Du Pasquier and G. W. Litman. Berlin, Springer. 248: 111-135. (Library | PubMed | Amazon | Google Print)

This is one of three articles from the volume, "Origin and Evolution of the Vertebrate Immune System," which were included in the article list. The book itself is listed in the book list. The three articles were included in the article bibliography because they were particularly useful summaries of the evolution of key pieces of adaptive and innate immunity.

This article is a technical review of the evolution of V(D)J recombination and evolution. Section 4, "Origins of Rag1 and Rag2," contains the now-familiar review of the development and confirmation of the transposon hypothesis:
"The genomic organization of the Ig and TCR loci themselves first hinted at a possible link between the V(D)J recombination mechanism and DNA transposition (Sakano et al. 1979). Detailed knowledge of the Rag genes and the biochemical activities of their products strengthened this comparison (Lewis and Wu 1997; Thompson 1995). Recent biochemical data sealed this functional link, strongly suggesting that the Rag genes appeared in the vertebrate genome about 450 MYA as passengers in a transposon. The evidence accumulated to date in favor of the Rag transposon comes from 4 main sources..." (p. 122)
The lines of evidence presented should be familiar at this point; however, the authors highlight the importance of the fourth line of evidence, "DNA transposition by the Rag proteins":
"The most dramatic parallel between DNA transposition and V(D)J recombination was shown recently by two groups (Agrawal et al. 1998; Hiom et al. 1998; reviewed in Plasterk 1998; Roth and Craig 1998). In these studies, the Rag proteins performed not only DNA cleavage at the RSS, but also transpositional insertion of the RSS-containing cleavage products into unrelated target DNA (Fig. 4)." (p. 123)
The authors continue:
"The structure of the antigen receptor loci is itself a compelling argument in favor of a transpositional origin for the immune system (Sakano et al. 1979), with both V(D)J recombination and DNA transposition involving a pair of inverted repeats at the ends of the recombining agent." (p. 123)
On p. 125, Figure 5 shows the "Rag transposon model".
The concluding section of the article reviews what has gone before: "We describe multiple lines of evidence above which suggest that the Rag genes were introduced into the vertebrate genome over half a billion years ago as part of an ancestral transposon." (p. 130)
...and follows it up with a summary of the model.

Lewis, S. M. and Wu, G. E. (2000). "The old and the restless." Journal of Experimental Medicine 191(10): 1631-1636. (PubMed | DOI | Journal | Google Scholar)

Another review paper on the RAG transposon hypothesis from Lewis and Wu. Figure 2 contains a usefully clear figure depicting the hypothesis. The second paragraph sums up the development of the transposon hypothesis:
"As recently as only a few years ago, any real information bearing on the actual genesis of the V(D)J recombination system seemed to be irretrievably lost. However, as more was learned about the molecular genetic and biochemical properties of the V(D)J recombination proteins, termed recombination activating gene (RAG)-1 and RAG-2, tantalizing suggestions of a transposon origin began to emerge. These clues included the following: first, the fact that the genes encoding RAG-1 and RAG-2, which are unrelated in sequence, are tightly linked, and as such share this property with genes that are known to undergo horizontal transfer (4). Second, the chemical mechanism of the recombination reaction, where DNA strand breakage and rejoining is accomplished through one step transesterification reactions, was like that of several well-described mobile elements (5). Finally, a surprising finding further indicated that RAG-1 and RAG-2 might have once been part of a transposon when two groups independently demonstrated that purified RAG-1 and RAG-2 proteins have a latent ability to carry out the transposition of DNA (6, 7)." (p. 1631)

"Thus, the unusual in vitro ability of RAG-1 and RAG-2 to do two quite different things, and in particular to transpose DNA, provided strong support for the original speculation that the V(D)J recombination system used to be a transposable element (3)." (p. 1631)

[References]

1. Marchalonis, J.J., S.F. Schluter, R.M. Bernstein, S. Shen, and A.B. Edmundson. 1998. Phylogenetic emergence and molecular evolution of the immunoglobulin family. Adv. Immunol. 70:417-506.

2. Litman, G.W., M.K. Anderson, and J.P. Rast. 1999. Evolution of antigen binding receptors. Annu. Rev. Immunol. 17:109-147.

3. Sakano, H., K. Huppi, G. Heinrich, and S. Tonegawa. 1979. Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Nature. 280:288-294.

4. Oettinger, M.A., D.G. Schatz, C. Gorka, and D. Baltimore. 1990. Rag-1 and Rag-2, adjacent genes that synergistically activate V(D)J recombination. Science. 248:1517-1523.

5. van Gent, D.C., D. Mizuuchi, and M. Gellert. 1996. Similarities between initiation of V(D)J recombination and retroviral integration. Science. 271:1592-1594.

6. Agrawal, A., Q.M. Eastman, and D.G. Schatz. 1998. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature. 394:744-751.

7. Hiom, K., M. Melek, and M. Gellert. 1998. DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell. 94:463-470.

Nonaka, M. (2000). "Origin and evolution of the Complement System." Origin and Evolution of the Vertebrate Immune System. Edited by L. Du Pasquier and G. W. Litman. Berlin, Springer. 248: 37-50. (Library | PubMed | Amazon | Google Print)

Nonaka regularly authors or coauthors articles reviewing the evolutionary origin of the innate immune system. This article surveys the complement systems of vertebrates and invertebrates and focuses on the origin of the B and C2 proteins which help activate the complement system, and the MASP proteins, mammalian serine proteases which actually have homologs in groups as distant as ascidians.
"This chapter discusses recent progress in understanding the evolution of the complement system mainly in invertebrates and lower vertebrates." (p. 38)

"The hypothetical story of the origin and evolution of the complement system has been composed from data discussed above (Fig. 3). The birth of the complement system is located somewhere during evolution of invertebrate phyla, although the exact stage at which the complement system was established must still be clarified. The original complement system most probably resembled the LeP and AP of the mammalian complement system. Lectin-based recognition by MBL, followed by the activation of MASP, B, and then C3, covalent binding of C3 to foreign particles, and finally phagocytosis of C3-tagged foreign particles by phagocytes with C3 receptors on their surface seem to be the most probable constitution of the original complement system." (p. 46)

Opal, S. M. (2000). "Phylogenetic and functional relationships between coagulation and the innate immune response." Critical Care Medicine 28(9): S77-S80. (PubMed | Journal | Google Scholar)

This article reviews the evolutionary and physiological relationships between the blood-clotting cascade (coagulation) and the the inflammatory cascade which initiates innate immune responses.
"The simultaneous activation of the inflammatory response and the coagulation system after injury is a phylogenetically ancient, adaptive response that can be traced back to the early stages of eukaryotic evolution." (p. S77)

"Concluding Remarks. The coagulation system is integrally related to the innate immune response, and its activation and regulation are dependent on local and systemic immune responses. The simultaneous activation of clotting and the innate immune response is a phylogenetically ancient host response to tissue injury and is a primary survival strategy throughout vertebrate evolution." (p. S79)

Richards, M. H. and Nelson, J. L. (2000). "The Evolution of Vertebrate Antigen Receptors: A Phylogenetic Approach." Molecular Biology and Evolution 17(1): 146-155. (PubMed | Journal | Google Scholar)

This research article explores the phylogeny of somatically rearranging antigen receptors, seeking the most basal groups.
"It is now clear that indirect, MHC-restricted antigen recognition must be a derived characteristic of [alpha][beta] T cells, while [gamma][beta] T cells exhibit the primitive condition of direct antigen binding. This removes a major stumbling block in several schemes for the evolution of vertebrate immune systems (e.g., Stewart 1992), because it shows that the origins of diverse T-cell characteristics, such as antigen recognition and effector functions, may be separate, independent evolutionary events. Continued phylogenetic analysis of TCR and Ig relationships, especially as more suitable outgroup sequences are obtained from organisms such as cyclostomes or sharks, should continue to improve our understanding of immune system evolution." (p. 154)
The reference to Stewart is: Stewart, J. 1992. Immunoglobulins did not arise in evolution to fight infection. Immunology Today 13:396-399. Stewart is also the author of the 1994 book The Primordial VRM System and the Evolution of Vertebrate Immunity.

Roth, D. B. (2000). "From lymphocytes to sharks: V(D)J recombinase moves to the germline." Genome Biology 1(2): 1014.1011-1014.1014. (PubMed | DOI | Journal | Google Scholar)

This article reviews the transposon model for the origin of rearranging receptors, and also explores the impact that the V(D)J recombinase may have had as an evolutionary force.
"Early on, it was suggested that the V(D)J recombination system might have arisen by the fortuitous integration of a transposable element into an ancestral antigen-receptor gene [14]. This hypothesis was strengthened by the discovery that the RAG genes are tightly linked [7], and by the finding that the RAG proteins can act as a transposase. Thus, a plausible model for the acquisition of the V(D)J recombination system during vertebrate evolution is the integration of a transposable element carrying the linked RAG genes into a primordial antigen-receptor gene in an ancestral jawed vertebrate, approximately 450 million years ago (reviewed in [1,11]). Presumably, this initial integration event created the first rearranging antigen-receptor gene; subsequent gene duplication events then created the multiple immunoglobulin and T-cell receptor loci." (p. 1014.2)

[Notable References]

1. Thompson CB: New insights into V(D)J recombination and its role in the evolution of the immune system. Immunity 1995, 3:531-539.

2. Litman GW, Anderson MK, Rast JP: Evolution of antigen binding receptors. Annu Rev Immunol 1999, 17:109-147.

3. Marchalonis JJ, Schluter SF, Bernstein RM, Shen S, Edmundson AB: Phylogenetic emergence and molecular evolution of the immunoglobulin family. Adv Immunol 1998, 70:417-506.

4. Lee SS, Fitch D, Flajnik MF, Hsu E: Rearrangement of immunoglobulin genes in shark germ cells. J Exp Med 2000, 191:1637-1648.

[...]

7. Oettinger MA, Schatz DG, Gorka C, Baltimore D: RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 1990, 248:1517-1523.

[...]

11. Hansen JD, McBlane JF: Origin and evolution of the vertebrate immune system. Curr Topics Microbiol Immunol 2000, 248:111-135.

12. Agrawal A, Eastman QM, Schatz DG: Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 1998, 394:744-751.

13. Hiom K, Melek M, Gellert M: DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 1998, 94:463-470.

14. Sakano H, Huppi K, Heinrich G, Tonegawa S: Sequences at the somatic recombination sites of immunoglobulin light chain genes. Nature 1979, 280:288-294.

Vaandrager, J.-W., Schuuring, E., Philippo, K. and Kluin, P. M. (2000). "V(D)J recombinase-mediated transposition of the BCL2 gene to the IGH locus in follicular lymphoma." Blood 96(5): 1947-1952. (PubMed | Journal | Google Scholar)

The results of this research article give indirect evidence that transposition reactions mediated by RAGs can occur not just in vitro, but within mammalian cells, further supporting the transposon hypothesis.

Du Pasquier, L. (2001). "The immune system of invertebrates and vertebrates." Comparative Biochemistry and Physiology Part B Biochemistry & Molecular Biology 129(1): 1-15. (PubMed | DOI | Journal | Google Scholar)

Review of current comparative immunology. Excellent figures show the variability and repeated themes (due to duplication and combination of genes) in various immune systems. Fig. 3 shows the repeated use of proteins in the immunoglobulin superfamily in invertebrates.

Figure 2 mentions the transposon hypothesis:
"The introduction of what nowadays behaves as a site sensitive to the RAG enzyme is supposed to have occurred via the introduction of a transposon (Rougeon, 1986; Thompson, 1995)." (p. 5)
The text does also:
"It is as if a 'horizontal' acquisition of a transposon had occurred at some point during the history of the vertebrates (Thompson, 1995). The receptor gene structure itself, in the region where the rearrangement takes place, suggests the introduction of a transposon. The recombination signal sequences flank the gene segments (V and J in the light chain for instance) in the same way as the LTR does in a transposon (Hansen and McBlane, 2000). In principle, RAG activity is confined to lymphocytes but the existence of germ-line rearrangements in light chain genes in the shark suggests that RAG (Lee et al., 2000) is still an active force changing the genome in some vertebrates."

[References]

Hansen, J.D., McBlane, J.F., 2000. Recombination-activating genes, transposition, and the lymphoid-specific combinatorial immune system: a common evolutionary connection (In Process Citation). Curr. Top. Microbiol. Immunol. 248, 111-135.

Lee, S.S., Fitch, D., Flajnik, M.F., Hsu, E., 2000. Rearrangement of immunoglobulin genes in shark germ cells (see comments). J. Exp. Med. 191, 1637-1648.

Rougeon, F., 1986. La diversité des anticorps. La Recherche 17, 680-689.

Thompson, C.B., 1995. New insights into V(D)J recombination and its role in the evolution of the immune system. Immunity 3, 531-539.

Nonaka, M. and Miyazawa, S. (2001). "Evolution of the Initiating Enzymes of the Complement System." Genome Biology 3(1): 1001.1001-1001.1005. (PubMed | DOI | Journal | Google Scholar)

Technical review of the origin of the innate (non-adaptive) immune system.

"Figure 2 A proposal for the evolution of the MASP-113, MASP-2, C1r and C1s genes." (p. 1001.3)
"The primitive complement system

As discussed here, the complement system seems to have a more ancient origin in evolution than adaptive immunity; the latter seems to have been established only from jawed vertebrates onwards. The central component of the complement system, the C3 protein on which the three activation pathways discussed here converge, has been identified in jawless vertebrates, the lamprey [13] and hagfish [14], as well as in deuterostome invertebrates, amphioxus (a cephalochordate) [15], ascidian (urochordate) [16] and sea urchin (echinoderm) [17]. Although C3- or complement-like molecules of insects show functional similarity with deuterostome C3, there is no shared derived structural character between them, indicating that the deuterostome C3 and insect C3-like molecules derived independently from their common ancestor, [alpha]2-macroglobulin. Thus, the authentic complement system seems to have been established in the deuterostome lineage; the classical pathway of complement activation was then acquired in the jawed vertebrate lineage, at the time adaptive immunity arose." (p. 1001.4)

Cannon, J. P., Haire, R. N. and Litman, G. W. (2002). "Identification of diversified genes that contain immunoglobulin-like variable regions in a protochordate." Nature Immunology 3(12): 1200-1207. (PubMed | DOI | Journal | Google Scholar)

A key research article finally presenting evidence of a non-rearranging receptor closely related to the vertebrate rearranging receptors, in the lancelet (a cephalochordate which lacks adaptive immunity). This is important because it provides one of the homologs that scientists had been seeking for years. It also shows that even without rearranging receptor capability, selection favored diverse receptors:
"Thus, multigenic families encoding diversified V regions exist in a species lacking an adaptive immune response." (p. 1200)

Kaufman, J. (2002). "The origins of the adaptive immune system: whatever next?" Nature Immunology 3(12): 1124-1125. (PubMed | DOI | Journal | Google Scholar)

In this News & Views article in Nature Immunology, Kaufman expresses wonderment at the results of Cannon et al. (2002).
"Indeed, the initial event that enabled the emergence of the adaptive immune system is thought to have been the insertion of a transposon into a previously undisrupted V-like exon of an Ig domain-containing gene2,3,5. But in which Ig gene did the insertion occur?" (p. 1124)

"The obvious approach to answer these questions is to search for a V-like Ig-containing gene in a jawless vertebrate or a nonvertebrate chordate." (p. 1124)

"The discovery of a V-like Ig multigene family in the protochordate amphioxus provides new insights into the evolution of the adaptive immune response." (p. 1124, summary)

[References]

1. Cannon, J. P., Haire, R. N. & Litman, G. L. Nature Immunol. 3, 1200-1207 (2002).

2. Litman, G. W., Anderson, M. K., & Rast, J. P., Annu. Rev. Immunol. 17, 109-147 (1999).

3. Flajnik, M. F. & Kasahara, M. Immunity 15, 351-362 (2001).

[...]

5. Tonegawa, S. Nature 302, 575-581 (1983).

Krem, M. M. and Di Cera, E. (2002). "Evolution of enzyme cascades from embryonic development to blood coagulation." Trends in Biochemical Sciences 27(2): 67-74. (PubMed | DOI | Journal | Google Scholar)

Article reviews the evolutionary and physiological relationships between the blood-clotting cascade and the complement cascade of the innate immune system.
"Here, it is proposed that a single ancestral developmental/immunity cascade gave rise to the protostome and deuterostome developmental, clotting, and complement cascades. Extensive similarities suggest that these cascades were built by adding enzymes from the bottom of the cascade up and from similar macromolecular building blocks." (p. 67)
Figure 2 (p. 71) shows proposed relationships.
"Fig. 2. Evolutionary changes producing developmental, immune and clotting cascades."

"The emergence of the advanced deuterostome complement system, featuring both the classical and alternative pathways, occurred by duplication of primitive complement proteins and recruitment of new proteases from the pool of ancestral building blocks." (p. 73)

"The modern mammalian clotting cascade was completed by the addition of serine proteases such as factors XI and XII, and cofactors such as factors V and VIII, which conferred additional levels of positive and negative feedback regulation." (p. 73)

Laird, D. J. (2002). "Immune System." Encyclopedia of Evolution. Edited by M. Pagel. Oxford, Oxford University Press. 2: 558-564. (Library | Publisher | Amazon | Google Print)

Basic introduction to the immune system, but in a thoroughly evolutionary context. Figure 4 (p. 563) depicts the progressive aquisition of features as one moves closer to mammals in the vertebrate phylogeny. It is noteworthy that the transposon hypothesis is sufficiently well-accepted, and well-known, to make it into a general encyclopedia on evolution. Furthermore, this is another example of the secondary literature that is readily available to anyone seriously looking into evolutionary immunology.
"Structures of the Vertebrate Immune System. Despite the quantity of immune receptors, signalling molecules, and serum factors that carry out antigen recognition and the accompanying inflammatory response, these structures share much in common. Protein motifs such as the immunoglobulin fold, which appears in Ig, TCR, natural killer (NK) cell receptors, MHC receptors, complement proteins, and adhesion molecules, imply extraordinary recycling and even a common origin during evolution. The hypothesis that a primordial immunoglobulinlike receptor gave rise to the rearranging receptors of lymphocytes has inspired the study of Ig, TCR, and other immune receptors of primitive vertebrates. This section focuses on the evolution of the main components of the adaptive immune system, unique to jawed vertebrates." (p. 559)

"The sudden appearance of RAG in Chondrychthyes, coupled with their peculiar genetic features (they lack introns and are adjacent in most species) suggests their origin as a retrotransposon, or a foreign DNA element introduced by a virus some 500 million years ago." (p. 561)

"The origin of adaptive immunity can be approached from many angles. The genomic approach was first employed by Masanori Kasahara, who hypothesized that genome duplications in vertebrate ancestors paved the way for the molecular experimentation that gave rise to this system. Comparison of MHC loci across vertebrate species provides clues about how and when this chromosomal region of immune and nonimmune genes was assembled. The study of RAG structure and mechanism across vertebrates fuels the theory that receptor genes of the adaptive immune system first arose by transposon-induced shuttling of duplicated segments of DNA. Phylogenetic data estimate the appearance of RAG in a vertebrate ancestor about 500 million years ago, approximately coincidental with the last hypothesized genome duplication and the origins of TCR, Ig, and MHC receptors. Another strategy is the reconstruction of the hypothetical ancestral receptor through discovery of surviving remnants, such as nonrearranging immunoglobulin domain receptors in vertebrates and invertebrates alike. Candidates include the paired Ig-like receptors, whose role as inhibitory and activating receptors for MHC I and MHC I-like molecules in mammals suggests their involvement in ancient self-nonself recognition. A number of other Ig-type nonrearranging receptors, such as the NAR in sharks and the NITR in pufferfish, contribute to our understanding of receptor evolution." (p. 564)

Marchalonis, J. J., Jensen, I. and Schluter, S. F. (2002). "Structural, antigenic and evolutionary analyses of immunoglobulins and T cell receptors." Journal of Molecular Recognition 15(5): 260-271. (PubMed | DOI | Journal | Google Scholar)

Long review of the work of the Marchalonis lab.
"This laboratory has focused upon the structure, function and evolution of antibodies and T cell receptors for more than 25 years." (p. 260)
Evolution played a key role in the lab's study of antigen receptors. The article is interesting because it highlights the interrelationship between structural and evolutionary studies -- homology and phylogeny allow structural knowledge gained in one lineage (e.g., sharks) to be applied to another that is more medically relevant (such as humans). The authors also note that sharks were chosen as the study organisms of choice because any features conserved across the evolutionary distance between sharks and humans is likely to be functionally important:
"We have studied antibodies, antibody production and cellular immunity in representatives of all the vertebrate classes, but we have chosen to concentrate our studies of antibody and T cell receptor structure on a comparison between the genes and molecules of sharks and humans because these two species represent the most evolutionarily divergent organisms to express the complete combinatorial immune system consisting of immunoglobulins, major histocompatability complex antigens, T cell receptors, and recombination activator genes (DuPasquier and Flajnik, 1999; Litman et al., 1999; Marchalonis and Schluter, 1998; Marchalonis et al., 1998a)." (p. 261)

Marchalonis, J. J., Kaveri, S., Lacroix-Desmazes, S. and Kazatchkine, M. D. (2002). "Natural recognition repertoire and the evolutionary emergence of the combinatorial immune system." FASEB Journal 16(8): 842-848. (PubMed | Journal | Google Scholar)

Technical review of several aspects of the origin of adaptive immunity, including the capacity for receptor diversity and its selective value, and the importance of clonal selection during maturation of specific antibodies. The quick review of the transposon hypothesis is quoted below:
"The complete [Combinatorial Immune Response, CIR] ensemble is present in all jawed vertebrates (8-10). The system emerged rapidly and accidentally in evolution (3, 14, 18) probably as the result of horizontal transfer of microbial genes for site-specific recombination (4-6, 18, 19). Ab initio, the CIR was neither a defense mechanism nor part of an internal regulatory system (20), but its unparalleled capacity to generate recognition molecules in real time gave it the potential to function effectively in both contexts. The CIR co-opted preexisting cellular and humoral mechanisms for activation, differentiation, and destruction of bound targets including the NF[kappa]B pathway, the IL-1/TOLL receptor complex, and interaction with more ancient complement components to initiate cytolysis, killing, and trigger inflammation (12-15)." (p. 843)

[References]

3. Marchalonis, J. J., and Schluter, S. F. (1998) A stochastic model for the rapid emergence of specific vertebrate immunity incorporating horizontal transfer of systems enabling duplication and combinatorial diversification. J. Theo. Biol. 193, 429-444

4. Bernstein, R. M., Schluter, S. F., Bernstein, H., and Marchalonis, J. J. (1996) Primordial emergence of the recombination activating gene 1 (RAG1): Sequence of the complete shark gene indicates homology to microbial integrates. Proc. Natl. Acad. Sci USA 93, 9545-9459

5. Hiom, K., Melek, M., and Gellert, M. (1998) DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 94, 463-470

6. Agrawal, A., Eastman, Q. M., and Schatz, D. G. (1998) Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature (London) 394, 744-751

7. Burnet, F. M. (1959) The Clonal Selection, Vanderbilt University Press, Nashville, Tennessee

8. Marchalonis, J. J., Schluter, S. F., Bernstein, R. M., and Hohman, V. S. (1998) Antibodies of sharks: revolution and evolution. Immunol. Rev. 166, 103-122

9. Litman, G. W., Anderson, M. K., and Rast, J. P. (1999) Evolution of antigen binding receptors. Annu. Rev. Immunol. 17, 109-147

10. DuPasquier, L., and Flajnik, M. (1999) Origin and evolution of the vertebrate immune system. In Fundamental Immunology (Paul, W. E., ed) pp. 605-650, Lippincott-Raven, Philadelphia

12. Fearon, D., and Locksley, R. M. (1996) The instructive role of innate immunity in the acquired immune response. Science 272, 50-53

13. Meister, M., Hetru, C., and Hoffman, J. A. (2000) The antimicrobial host defense of Drosophila. Curr. Top. Microbiol. Immunol. 248, 17-36

14. Marchalonis, J. J., and Schluter, S. F. (1990) On the relevance of invertebrate recognition and defense mechanisms to the emergence of the immune response of vertebrates. Scand. J. Immunol. 32, 13-20

15. Medzhitov, R., and Janeway, C. A. (1997) Innate Immunity: The virtues of a nonclonal system of recognition. Cell 91, 295-298

17. Good, R. A., and Papermaster, B. W. (1964) Ontogeny and phylogeny of adaptive immunity. Adv. Immunol. 4, 1-115

18. Schluter, S. F., Bernstein, R. M., Bernstein, H., and Marchalonis, J. J. (1999) 'Big Bang' emergence of the combinatorial immune system. Dev. Comp. Immunol. 23, 107-111

19. Plasterk, R. (1998) V(D)J recombination. Ragtime jumping. Nature (London) 394, 744-751

20. Stewart, J. (1992) Immunoglobulins did not arise in evolution to fight infection. Immunol. Today 13, 396-399

Clatworthy, A. E., Valencia, M. A., Haber, J. E. and Oettinger, M. A. (2003). "V(D)J recombination and RAG-mediated transposition in yeast." Molecular Cell 12(2): 489-499. (PubMed | DOI | Journal | Google Scholar)

This paper showed for the first time that RAG1 and RAG2 can act as a bona fide transposase in eukaryotic (yeast) cells, mediating the integration in the genome of an excised DNA fragment. The results confirmed another long-sought prediction of the transposon hypothesis:
"Here, we show that expression in Saccharomyces cerevisiae of murine RAG1 and RAG2, the lymphoid-specific components of the V(D)J recombinase, is sufficient to induce V(D)J cleavage and rejoining in this lower eukaryote." (p. 489)

Flajnik, M. F., Miller, K. and Du Pasquier, L. (2003). "Evolution of the Immune System." Fundamental Immunology. Edited by W. E. Paul. Philadelphia, Lippincott Williams & Wilkins: 519-570. (Library | Amazon | Google Print)

This 51-page review of evolutionary immunology references 213 citations. Technical, but very useful tables and graphics showing how the major features of the vertebrate immune system are gradually acquired in organisms getting closer in the phylogenetic tree to vertebrates.
"As predicted over 10 years ago by Zasloff (2), it is informative from both intellectual and applied viewpoints to understand how all living things defend themselves; few would argue against the premise that studies of Drosophila humoral immunity has fueled great interest in innate immunity, both for its own sake and in the way it regulates adaptive immunity (R3)." (p. 521)
Regarding the transposon hypothesis for the origin of the Recombination-Activating Genes, RAG1 and RAG2, Flajnik et al. write,
"It seems that a 'horizontal' acquisition of a RAG-laden transposon occurred at some point during the history of the vertebrates (R156, 202). The structure of the receptor gene itself, in the region where rearrangements occur, suggests the introduction of a transposon." (p. 562)
The article also suggests future research directions:
"Further molecular studies in hagfish and lamprey and in non-vertebrate deuterostomes will perhaps permit a better understanding of the events leading to the emergence of the adaptive immune system." (p. 566)
Note that in May 2005, a "free-living" transposon relative of RAG1 was discovered in a tunicate, a non-vertebrate deuterostome (Kapitonov and Jurka, 2005).

Just while this review article was being written, seven new research papers came out which the authors saw fit to mention in an addendum, "Publications Worth Noting."
[References cited]

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R3. Janeway CA Jr, Medzhitov R. Innate immune recognition. Annu Rev Immunol 2002; 20:197-216.]

R156. Hansen, J. D., McBlane, J. F. Recombination-activating genes, transposition, and the lymphoid-specific combinatorial immune system: a common evolutionary connection. Current Topics in Microbiology and Immunology 2000; 248:111-135.

R202. Agrawal A., Eastman Q. M., Schatz D. G. Transposition mediated by RAG1 and RAG2 and its implication for the evolution of the immune system. Nature. 1998; 394:744-751.

Market, E. and Papavasiliou, F. N. (2003). "V(D)J Recombination and the Evolution of the Adaptive Immune System." PLoS Biology 1(1): 24-27. (PubMed | DOI | Journal | Google Scholar)

A short review of recombination, and its evolutionary origin from a transposon. Included in the very first issue (volume 1, number 1) of the journal Public Library of Science: Biology. The entire contents of this journal are available free online.

The article notes that RAGs are indispensable for receptor gene rearrangement -- section heading: "RAGs: Indispensable for V(D)J Recombination" (p. 26)

However, despite the claims of antievolutionists, it is clear that RAGs evolved anyway:
"An Evolutionary Model of V(D)J Recombination

From the discovery of the RAG genes on, investigators have suspected that V(D)J recombination may be the result of the landing of a transposable genetic element (a "jumping gene" or transposon) into the vertebrate genome. The clues were many. Firstly, the compact organization of the RAG locus resembles a transposable element (Schatz et al. 1989). Secondly, RAGs cut the DNA after binding RSSs throughout the BCR and TCR loci (Gellert 2002). RSSs resemble the ends of other transposable elements. Biochemically, the reaction shares characteristics with enzymes found in other transposable elements (Gellert 2002). Finally, these genes appear abruptly in evolution: they are present in the jawed vertebrates (like the shark), but not in more ancient organisms (Schluter et al. 1999).

A current model is that an ancient transposon containing the RAG genes flanked by RSS ends "jumped’" into an area of the vertebrate lineage containing a primordial antigen receptor gene, separating it into pieces. When the transposon lifted off, it left the RSSs behind. Multiple rounds of transposition and duplication eventually gave rise to our TCR and BCR loci." (p. 27)

[References]

Gellert M (2002) V(D)J recombination: RAG proteins, repair factors, and regulation. Annu Rev Biochem 71: 101-132.

Schatz DG, Oettinger MA, Baltimore D (1989) The V(D)J recombination activating gene, RAG-1. Cell 59: 1035-1048.

Schluter SF, Bernstein RM, Bernstein H, Marchalonis JJ (1999) 'Big Bang' emergence of the combinatorial immune system. Dev Comp Immunol 23: 107-111.

Messier, T. L., O'Neill, J. P., Hou, S.-M., Nicklas, J. A. and Finette, B. A. (2003). "In vivo transposition mediated by V(D)J recombinase in human T lymphocytes." The EMBO Journal 22(6): 1381-1388. (PubMed | DOI | Journal | Google Scholar)

Messier and coworkers show that in human T lymphocytes, the excised DNA fragments from VDJ recombination can be reintegrated in genomic DNA, in this case causing disruption of the gene for a metabolic enzyme. Like Clathworthy et al (2003, in this bibliography), this paper provides strong evidence for a role of RAG1/2 as a functional transposase.

Cannon, J. P., Haire, R. N., Rast, J. P. and Litman, G. W. (2004). "The phylogenetic origins of the antigen-binding receptors and somatic diversification mechanisms." Immunological Reviews 200(1): 12-22. (PubMed | DOI | Journal | Google Scholar)

Detailed review of the origin of adaptive immunity. It takes the transposon hypothesis for granted and deals mostly with the "setting" for the transposon insertion -- the ancestral receptors and cells, etc.
"A mechanism that most likely gave rise to the adaptive immune system has been identified (1, 2) and is discussed elsewhere in the text. However, to understand the evolution of vertebrate adaptive immunity in detail, the characteristics of the immune systems of pre-adaptive ancestors must be reconstructed.

[...]

1. Agrawal A, Eastman QM, Schatz DG. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 1998;394: 744-751.

2. Hiom K, Melek M, Gellert M. DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 1998;94:463-470." (pp. 12-13, 21)

Davis, M. M. (2004). "The evolutionary and structural 'logic' of antigen receptor diversity." Seminars in Immunology 16: 239-243. (PubMed | DOI | Journal | Google Scholar)

Article on the evolutionary advantages of immune system receptor diversity. Highly technical.

Eason, D. D., Cannon, J. P., Haire, R. N., Rast, J. P., Ostrov, D. A. and Litman, G. W. (2004). "Mechanisms of antigen receptor evolution." Seminars in Immunology 16: 215-226. (PubMed | DOI | Journal | Google Scholar)

Detailed review of the evolutionary origin of adaptive receptors. All of the figures are useful summaries of various points.

The basic conclusion is that while the exact ancestral (pre-rearranging) receptor has not been found, many close relatives sharing key properties have been discovered.
"Taken together, the results suggest that the adaptive immune system in vertebrates may have been derived in unique ways from different sets of 'primordial' receptors, of which one gave rise to the Ig/TCR, another generated the VLRs, and other receptors provided protective immunity in invertebrates and protochordates, further blurring distinctions between the traditional views of adaptive and innate immunity." (pp. 224-225)

Flajnik, M. F. and Du Pasquier, L. (2004). "Evolution of innate and adaptive immunity: can we draw a line?" Trends in Immunology 25(12): 640-644. (PubMed | DOI | Journal | Google Scholar)

New developments in the study of the evolution of adaptive immunity, especially noting that the lines between "innate" and "adaptive" immunity are becoming blurred as more organisms are studied. Representative quotes:
"Particularly exciting are the discoveries of a new gene rearrangement mechanism in lampreys and a somatic diversification of mollusk immune genes." (p. 640)

"For comparative immunologists, these new sequencing data have turned us into kids in a candy shop and have spawned new insights into the integration of different immune systems." (p. 640)

"The birth of the adaptive immune system is believed to have occurred when an Ig superfamily (Igsf) gene of the variable (V) type was invaded by a transposable element containing RAG1 and RAG2 genes [5,6]. This innovative event, which greatly augmented receptor diversity (and heightened the risk of autoimmunity), must have been crucial for the adaptive immune system, even if it were not truly the initiating event [7] because all of the antigen receptor loci rearrange in a similar fashion (see later). There are several invertebrate Igsf family members having features of Ig or TCR V genes, which could be related to the ancestral gene invaded by the transposon [8-10]." (p. 640, emphases original)

"Already, other V genes with features similar to Ig or the TCR and potentially related to the ancestral Igsf gene invaded by the transposon have been isolated...." (p. 641)

"Every immunology student is taught that the jawed-vertebrate adaptive immune system was grafted onto the innate system, co-opting pre-existing effector mechanisms of defense [27]." (p. 643)

[References]

1 Medzhitov, R. et al. (1997) A human homologue of the Drosophila Toll protein signals activation of adaptive immunity. Nature 388, 394-397

2 Hoffmann, J.A. and Reichhart, J.M. (2002) Drosophila innate immunity: an evolutionary perspective. Nat. Immunol. 3, 121-126

3 G. Koretsky (ed. in chief) (2004) Primitive Immune Systems. (J.A. Hoffman, ed.) Immunol. Rev. 198, 303

4 Flajnik, M.F. et al. (2003) Evolution of the immune system. In Fundamental Immunology (Paul, W.E. ed.), pp. 519-570, Lippincott, Williams & Wilkins, Philadelphia

5 Bernstein, R.M. et al. (1996) Primordial emergence of the recombination activating gene 1 (RAG1): sequence of the complete shark gene indicates homology to microbial integrases. Proc. Natl. Acad. Sci. U. S. A. 93, 9454-9459

6 Agrawal, A. et al. (1998) Transposition mediated by RAG1 and RAG and its implications for the evolution of the immune system. Nature 394, 744-751

7 Erwin, D.H. and Krakauer, D.C. (2004) Evolution. Insights into innovation. Science 304, 1117-1119

8 Azumi, K. et al. (2003) Genomic analysis of immunity in a Urochordate and the emergence of the vertebrate immune system: "waiting for Godot". Immunogenetics 55, 570-581

9 Du Pasquier, L. et al. (2004) Immunoglobulin superfamily receptors in protochordates: before RAG time. Immunol. Rev. 198, 233-248

10 Van den Berg, T.K. et al. (2004) On the origins of adaptive immunity: innate immune receptors join the tale. Trends Immunol. 25, 11-16

Galaktionov, V. G. (2004). "Evolutionary Development of the Immunoglobulin Family." Biology Bulletin 31(2): 101-111. (PubMed | DOI | Journal | Google Scholar)

Reviews the evolutionary origin of immunoglobulins, particularly how the immunoglobulin domain has been reused in many different receptors.
"It is believed that RAG was originally introduced by a retrovirus into the genome of ancestral vertebrates, specifically, into the region occupied by the single V gene." (p. 110)

Gould, S. J., Hildreth, J. E. and Booth, A. M. (2004). "The evolution of alloimmunity and the genesis of adaptive immunity." Quarterly Review of Biology 79(4): 359-382. (PubMed | DOI | Journal | Google Scholar)

A long review article in the prestigious general biology journal Quarterly Review of Biology. Stephen J. Gould (a different one than the famous paleontologist) argues that alloimmunity (recognition of self vs. nonself) evolved first, allowing the slightly later evolution of the hypervariable adaptive immune system (the variability creates the risk of accidentally attacking self-cells, so preexisting alloimmunity would ameliorate this).
"Given that alloimmunity arose more than 550 million years ago, at the dawn of animal evolution, and that adaptive immunity arose approximately 100 million years later at the origin of the jawed vertebrates (Schatz 1999), the most parsimonious explanation for why the two systems share so many features is that adaptive immunity evolved from a preexisting alloimmune system. We propose that hypervariable alloimmunity was exapted for adaptive immune responses soon after its genesis, an evolutionary event that could be selected by virtually any pathogen, even HAAPs." (p. 373)

Holmes, E. C. (2004). "Adaptation and Immunity." PLoS Biology 2(9): 1269-1269. (PubMed | DOI | Journal | Google Scholar)

This short primer article in PLoS Biology discusses the well-known adaptive value of having diverse antigen receptor genes, and the evolutionary arms race between immune system cells attempting to detect pathogens, and the pathogens attempting to avoid detection.
"It is therefore little wonder that the host and pathogen genes that control infection and immunity frequently show high levels of genetic diversity and present some of the best examples of positive selection (adaptive evolution) reported to date (Yang and Bilawski 2000). In particular, rates of nonsynonymous substitution per site (resulting in an amino acid change; dN) often greatly exceed those of synonymous substitution per site (silent change; dS), as expected if most mutations are fixed becuase they increase fitness." (p. 1267)

[Reference]

Yang Z, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15: 496-502.

Jones, J. M. (2004). "The taming of a transposon: V(D)J recombination and the immune system." Immunological Reviews 200(1): 233-248. (PubMed | DOI | Journal | Google Scholar)

Review exploring the diversity of transposon systems and their relationship to V(D)J recombination.
"The study of V(D)J recombination has been continually informed by research into other systems, and it is now apparent that V(D)J recombination shares a particularly close relationship with the family of transposons that includes Ac/Ds. These similarities support the hypothesis that V(D)J recombination evolved from a primordial transposon." (pp. 233-234)

Nonaka, M. and Yoshizaki, F. (2004). "Evolution of the Complement System." Molecular Immunology 40(12): 897-902. (PubMed | DOI | Journal | Google Scholar)

Technical review of the origin of the innate (non-adaptive) immune system.
"Here, we discuss an early evolution of the complement components, both the non-modular C3 family and the other modular components, revealed by recent molecular analysis of possible complement genes from [a] variety of animals and the recently published genome analysis of an ascidian, [a tunicate or sea squirt], Ciona intestinalis." (p. 897)

"Thus, the evolution of the vertebrate complement system could be accomplished by integration of several independent functional units into a single reaction system through making a functional linkage among them." (p. 901)

Pancer, Z., Amemiya, C. T., Ehrhardt, G. R. A., Ceitlin, J., Gartland, G. L. and Cooper, M. D. (2004). "Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey." Nature 430(6996): 174-180. (PubMed | DOI | Journal | Google Scholar)

Evidence of a different system of adaptive immunity in an early-diverging vertebrate, the sea lamprey.
"Different evolutionary strategies were thus used to generate highly diverse lymphocyte receptors through rearrangement of LRR modules in agnathans (jawless fish) and of immunoglobulin gene segments in gnathostomes (jawed vertebrates)." (p. 174)

Rothenberg, E. V. and Pant, R. (2004). "Origins of lymphocyte developmental programs: transcription factor evidence." Seminars in Immunology 16(4): 227-238. (PubMed | DOI | Journal | Google Scholar)

Origins of lymphocytes (vertebrate immune system cells). Highly technical.

Cooption reference:
"Co-option of group C factors from other ancestral roles appears to have been harnessed for control of TCR and Ig gene rearrangement and expression." (p. 234)

"The evidence we have reviewed indicates that the full range of different transcription factor types needed to make lymphocytes were available in the genome at least as early as the emergence of urochordates (e.g., ascidians). In other words, the existence of transcription factors of these general families was not the rate-limiting feature for the evolution of lymphocyte development." (p. 234)

Schatz, D. G. (2004). "Antigen receptor genes and the evolution of a recombinase." Seminars in Immunology 16(4): 245-256. (PubMed | DOI | Journal | Google Scholar)

Reviews the transposon hypothesis for the origin of rearranging receptors. Fig. 3 (p. 250) gives the RAG transposon model. The evidence is also reviewed in detail on p. 250.

The authors make an interesting prediction:
"Hence, one might expect to find in the genome of vertebrates relics of these other jumps, including degenerate versions of pairs of RSSs or of the RAG open reading frames." (p. 251)

Stavnezer, J. and Amemiya, C. T. (2004). "Evolution of isotype switching." Seminars in Immunology 16(4): 257-275. (PubMed | DOI | Journal | Google Scholar)

Long, technical review of the evolution of an aspect of the adaptive immune system (CSR, class switch recombination) apparently restricted to tetrapods (amphibians, reptiles, mammals, birds).
"This chapter will review the evolution of the ability to express antibodies, or immunoglobulins (Igs) of different classes or isotypes." (p. 257)
Figure on p. 258 shows diversity of immune system gene organization.

Zhou, L., Mitra, R., Atkinson, P. W., Hickman, A. B., Dyda, F. and Craig, N. L. (2004). "Transposition of hAT elements links transposable elements and V(D)J recombination." Nature 432: 995-1001. (PubMed | DOI | Journal | Google Scholar)

Discovery of a transposon with mechanistic and sequence similarities to the RAG genes.
"It had been suggested that the V(D)J recombination system may have evolved from an ancient transposable DNA element12, 50. Our findings here of such a close mechanistic relationship between hAT transposition and V(D)J recombination...and the related active sites of hAT tranposases and RAG1 provides strong support for the view that V(D)J recombination evolved from transposable elements." (p. 1000)

[References]

12. Gellert, M. V(D)J recombination: RAG proteins, repair factors, and regulation. Annu. Rev. Biochem. 71, 101-132 (2002).

18. Hiom, K., Melek, M. & Gellert, M. DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 94, 463-470 (1998).

19. Agrawal, A., Eastman, O. M. & Schatz, D. G. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394, 744-751 (1998).

20. van Gent, D. C., Mizuuchi, K. & Gellert, M. Similarities between initiation of V(D)J recombination and retroviral integration. Science 271, 1592-1594 (1996).

50. Lewis, S. M. & Wu, G. E. The origins of V(D)J recombination. Cell 88, 159-162 (1997).

Klein, J. and Nikolaidis, N. (2005). "The descent of the antibody-based immune system by gradual evolution." Proceedings of the National Academy of Sciences 102(1): 169-174. (PubMed | DOI | Journal | Google Scholar)

Argues against the "big bang" model of immune system evolution which asserts that the main features of the immune system came together "suddenly", i.e., in less than 50 million years. Instead, it argues that the processes was more graduated and step-by-step. Given that the research community seems to agree that the introduction of RAG clearly was a key step and would be "sudden" compared to other forms of genetic change, but also agrees that many other more common evolutionary processes and precursors were also involved in the origin of adaptive immunity, it can be argued that debating the "big bang" label is not particularly illuminating. Regardless, in doing so Klein and Nikolaidis re-emphasize some useful points:
"We argue that the AIS [Antibody-based Immune System] has been assembled from elements that have primarily evolved to serve other functions and incorporated existing molecular cascades, resulting in the appearance of new organs and new types of cells." (p. 169)

"In reality, however, the AIS is an example of an organ system that has evolved gradually through a series of small steps over an extended period." (p. 169)
Figure 2 shows how many organisms lack many of the parts found in the most sophisticated systems.

Cannon, J. P., Haire, R. N., Pancer, Z., Mueller, M. G., Skapura, D., Cooper, M. D. and Litman, G. W. (2005). "Variable Domains and a VpreB-like molecule are present in a jawless vertebrate." Immunogenetics 56(12): 924-929. (PubMed | DOI | Journal | Google Scholar)

This paper describes a family of non-rearranging receptors in sea lampreys that are closely related to modern immunoglobulins and, together with papers by Cannon et al (2002, in this bibliography) and Suzuki et al (2005, Journal of Immunology, 174:2885-91) constitutes strong evidence of the existence of multiple, diverse families of immunoglobulin-like proteins predating the rearranging antigen receptors found in jawed vertebrates.
"This is the first indication of a molecule related to the B cell receptor (BCR) complex in a species that diverged prior to the jawed vertebrates in which RAG-mediated adaptive immunity is first encountered." (p. 924)

Kapitonov, V. V. and Jurka, J. (2005). "RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons." Public Library of Science Biology 3(6): e181:0001-0014. (PubMed | DOI | Journal | Google Scholar)

Reports the discovery of homologs of RAG1 in several non-chordate phyla -- this is the direct evidence of a free-living transposon suggested by Lewis in 1999. The summary figure was used by Ken Miller during his trial testimony.
"Even prior to the discovery of RAG1 and RAG2, it had been suggested that the first two RSSs were originally terminal inverted repeats (TIRs) of an ancient transposon whose accidental insertion into a gene ancestral to BCR and TCR, followed by gene duplications, triggered the emergence of the V(D)J machinery [4]. Later, this model was expanded by the suggestion that both RAG1 and RAG2 might have evolved from a transposase (TPase) that catalyzed transpositions of ancient transposons flanked by TIRs that were precursors of RSSs [9]. This model has received additional support through observations of similar biochemical reactions in transposition and V(D)J recombination [10,11]. Finally, it was demonstrated that RAG1/2 catalyzed transpositions of a DNA segment flanked by RSS12 and RSS23 in vitro [12,13] and in vivo in yeast [14]. In vertebrates, in vivo RAG-mediated transpositions are strongly suppressed, probably to minimize potential harm to genome function. So far, only one putative instance of such a transposition has been reported [15]. However, given the lack of significant structural similarities between RAGs and known TPases, the "RAG transposon" model [9,12,13,16] remained unproven. Here we demonstrate that the RAG1 core and RSSs were derived from a TPase and TIRs encoded by ancient DNA transposons from the Transib superfamily [17]." (pp. e181-e182)

[References]
4. Sakano H, Huppi K, Heinrich G, Tonegawa S (1979) Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Nature 280: 288-294.

[...]

9. Thompson CB (1995) New insights into V(D)J recombination and its role in the evolution of the immune system. Immunity 3: 531-539.

10. van Gent DC, Mizuuchi K, Gellert M (1996) Similarities between initiation of V(D)J recombination and retroviral integration. Science 271: 1592-1594.

11. Melek M, Gellert M, van Gent DC (1998) Rejoining of DNA by the RAG1 and RAG2 proteins. Science 280: 301-303.

12. Agrawal A, Eastman QM, Schatz DG (1998) Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394: 744-751.

13. Hiom K, Melek M, Gellert M (1998) DNA transposition by the RAG1 and RAG2 proteins: A possible source of oncogenic translocations. Cell 94: 463-470.

14. Clatworthy AE, Valencia MA, Haber JE, Oettinger MA (2003) V(D)J recombination and RAG-mediated transposition in yeast. Mol Cell 12: 489-499.

15. Messier TL, O'Neill JP, Hou SM, Nicklas JA, Finette BA (2003) In vivo transposition mediated by V(D)J recombinase in human T lymphocytes. EMBO J 22: 1381-1388.

16. Lewis SM, Wu GE (2000) The old and the restless. J Exp Med 191: 1631-1636.

17. Kapitonov VV, Jurka J (2003) Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci U S A 100: 6569-6574.

Du Pasquier, L. (2005). "Meeting the demand for innate and adaptive immunities during evolution." Scandinavian Journal of Immunology 62(s1): 39-48. (PubMed | DOI | Journal | Google Scholar)

Detailed review of the total immune responses across metazoa, focusing on the demands imposed by natural selection, and the evolution of cooperation between adaptive and nonadaptive systems.
"Immunoglobulins and T-cell receptors

The RAG1 and 2 complexes looked so far like the only new component responsible for the adaptive system of vertebrates because no related genes were found in invertebrates. However, the discovery of a RAG2-like product with homologs among metazoa and plants (called 'peas' and showing the same composition in 'kelch' domains as RAG2) and associated with the meiotic chromatin, may force us to revise the hypothesis of a RAG transfer by transposition in the immediate ancestors of gnathostomes [32]. What is in question is perhaps not the transposing-like feature of this enzymatic system but the way it was involved in immunity and its association with RAG1. Could have the lymphocyte RAG2 arisen by duplication of a 'peas'-like gene at the time of genome duplications? Maybe the introduction of RAG1 of which [a] homolog can now be found in Echinoderms [33] was the key step for the adaptive system." (p. 44)

"In the Introduction, the simultaneity and the diversity of the pressures that led to the development of immunity at the beginning of the existence of metazoa were stressed. As a result, independent pathways of immunity functioning on different principles of recognition developed, probably in parallel, each being pushed for diversification during adaptation to the changing environment. Some organisms trusted conservatively the genes devoted to their immune system; other added and allowed some randomness in their expression. In the comparative studies one has observed convergences, mimicry, duplications, dead ends, complementation or even perhaps competitions, with a trend towards individualization of responses to the point where the distinctions between adaptive and innate immunity are uncertain. The diversification of the immune molecules has made the necessary control of their expression a difficult task, demanding the involvement of many other gene families that were recruited alongside in the build up of the integrated immune systems. The individual defense mechanisms do not work in isolation in any organism but instead are part of a coherent whole. In fact, there are many unknown genes expressed during immune responses of the simplest organisms outside vertebrates [54]. In addition to the now more fashionable protochordates and jaw-less vertebrates, it would be important to include the study of arthropods less derived than Drosophila such as the horseshoe crab. One should also include the Cnidaria whose genes’ sequences are surprisingly close to those of deuterostomes and the genome of which could contain a reservoir of interesting information for the immunologist preoccupied with evolutionary issues [55]. In those organisms, examination of the genome and individual studies of the regulations and interactions of the different components of their immune systems may provide information as to how to handle the dysfunctions of what I foolishly dared to call in the introduction our ideal Homo sapiens immune system." (p. 47)

[References]

32 Ohinata Y, Sutou S, Mitsui Y. A novel testis-specific RAG2-like protein, Peas: its expression in pachytene spermatocyte cytoplasm and meiotic chromatin. FEBS Lett 2003;537:1-5.

33 Cannon JP, Haire RN, Rast JP, Litman GW. The phylogenetic origins of the antigen-binding receptors and somatic diversification mechanisms. Immunol Rev 2004;200:12-22.

54 De Gregorio E, Spellman PT, Rubin GM, Lemaitre B. Genomewide analysis of the Drosophila immune response by using oligonucleotide microarrays. Proc Natl Acad Sci USA 2001;98:12590-5.

55 Galliot B, Schmid V. Cnidarians as a model system for understanding evolution and regeneration. Int J Dev Biol 2002;46 (1 Spec No): 39-48.

Janssen, B. J. C., Huizinga1, E. G., Raaijmakers, H. C. A., Roos, A., Daha, M. R., Nilsson-Ekdahl, K., Nilsson, B. and Gros, P. (2005). "Structures of complement component C3 provide insights into the function and evolution of immunity." Nature 437(7058): 505-511. (PubMed | DOI | Journal | Google Scholar)

The authors report the crystal structure of the key innate immunity protein, C3, and deduce certain features of the evolutionary origin of the protein, such as internal domain duplications. This research came out the week before trial and was cited in Kenneth Miller's direct testimony.

Cohn, M. (2006). "What are the commonalities governing the behavior of humoral immune recognitive repertoires?" Developmental and Comparative Immunology 30(1-2): 19-42. (PubMed | DOI | Journal | Google Scholar)

Long review of selection-related issues in the evolution of immunity.
"The evolution of the immune system has been reviewed over the years from several points of view [1-10]. I will try to take a different tack by stressing selectable function rather than structure, genealogy, sequence, homology, gene dynamics, etc., the basic tools of comparative immunologists. This is not to downplay the importance of these analyses, which are, in fact, fundamental and indispensable, but rather to see whether another approach will confirm our present views or, hopefully, give us new insights." (p. 19)

[References]

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[2] Diaz M, Flajnik MF. Evolution of somatic hypermutation and gene conversion in adaptive immunity. Immunol Rev 1998; 162:13-24.

[3] Butler JE. Immunoglobulin gene organization and the mechanism of repertoire development. Scand J Immunol 1997;45:455-62.

[4] Du Pasquier L, Wilson M, Greenberg AS, Flajnik MF. Somatic mutation in ectothermic vertebrates: Musings on selection and origins. Curr Topics Microbiol Immunol 1998; 229:199-216.

[5] Flajnik M, Rumfelt LL. Early and natural antibodies in nonmammalian vertebrates. Curr Topics Microbiol Immunol 2000;252:233-40.

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[8] Flajnik M. Comparative analysis of immunoglobulin genes: Surprises and portents. Nat Rev Immunol 2002;2:688-98.

[9] Marchalonis JJ, Jensen I, Schuluter SF. Structural, antigenic and evolutionary analyses of immunoglobulins and T cell receptors. J Mol Recogn 2002;15:260-71.

[10] Neuberger MS. Antibodies: a paradigm for the evolution of molecular recognition. Biochem Soc Trans 2002;30:341-50.

Marchalonis, J. J., Adelman, M. K., Schluter, S. F. and Ramsland, P. A. (2006). "The antibody repertoire in evolution: Chance, selection, and continuity." Developmental and Comparative Immunology 30(1-2): 223-247. (PubMed | DOI | Journal | Google Scholar)

Massive review with 177 references. Deals with mutation and selection explicitly.
"At the onset, we emphasize that evolution is a stochastic or accidental process building upon the spontaneous generation of mutations followed by natural selection based upon survival to reproduce under external/environmental conditions." (p. 224)

"It has been proposed that the rapid evolutionary emergence of the combinatorial response was catalyzed by the horizontal transfer of RAG genes to an ancestral vertebrate [22-26]. The prokaryotic origin of these genes is buttressed by the lack of introns and by homology to microbial site-specific recombinases [23,27-29]." (p. 224)

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[23] Bernstein RM, Schluter SF, Bernstein H, Marchalonis JJ. Primordial emergence of the recombination activating gene 1 (RAG1): sequence of the complete shark gene indicates homology to microbial integrases. Proc Natl Acad Sci USA 1996;93:9454-9.

[24] Schluter SF, Bernstein RM, Bernstein H, Marchalonis JJ. ‘Big Bang‘ emergence of the combinatorial immune system. Dev Comp Immunol 1999;23:107-11.

[25] Laird D, De Tomaso A, Cooper MD, Weissman I. 50 million years of chordate evolution: seeking the origins of adaptive immunity. Proc Natl Acad Sci USA 2000;97:6924-6.

[26] Plasterk R. V(D)J recombination. Ragtime jumping. Nature 1998;394:718-9.

[27] Banerjee-Basu S, Baxevanis AD. The DNA-binding region of RAG1 is not a homoeodomain. Genome Biol 2002;3:1004.

[28] Schatz DG. Transposition mediated by RAG1 and RAG2 and the evolution of the adaptive immune system. Immunol Res 1999;19:169-82.

[29] Agrawal A, Eastman QM, Schatz DG. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 1998;394:744-51.

Acknowledgements

Thanks to Andrea Bottaro, Matt Inlay, and the Panda's Thumb crew for suggestions and corrections. Any mistakes that remain are my own.

Unannotated Bibliography on the Evolutionary Origin of the Immune System

by Nick Matzke

Sections:
Introduction
How the list was assembled
Quantitative Description
By Year
By Author
By Journal
The Implications
Full Bibliography: Alphabetical
Full Bibliography: Chronological
Acknowledgements

Introduction

This webpage contains contains a bibliography of 357 references specifically on the evolutionary origin of the immune system. This list includes the 70 or so references in the annotated bibliography and several hundred additional articles (and a few more books and book chapters). The purpose of this list is to demonstrate that the shorter list is just a sample of what is in the literature. Some simple statistics will also be used to describe the collection.

How the list was assembled

This list was assembled over several months. Beginning with the annotated bibliography, articles were added to this collection if they were cited an informative way in an article in the evolutionary immunology literature, and if they appeared to be directly on or directly relevant to the evolutionary origins of immune systems. For example, Hiom et al. (1998), unintentionally neglected in the annotated bibliography, is repeatedly referenced in the evolutionary immunology literature. Other articles were included as they were gradually discovered in reference lists and database searches, based on an inspection of the title and/or abstract.

The references that were collected fell into several main groups:

  1. Articles published after the Kitzmiller case
  2. Articles repeatedly referenced by immunologists in the annotated bibliography
  3. Articles by noted evolutionary immunologists that had evolutionary content upon inspection
  4. Articles picked up in "Related Articles" searches on PubMed, starting with articles in the annotated bibliography
  5. A few relevant books and book chapters that were discovered or rediscovered after the annotated bibliography was assembled
Many of the articles in this collection have not been looked up, but the chances of "false positives" should be quite low, as the evolutionary relevance is usually made clear by the title and abstract, or by repeated citation in the literature.

Although this list of publications is much longer, it still cannot be considered complete or representative of the field. Many biases are identifiable:

  1. The collection is still biased towards adaptive immunity and V(D)J recombination, although a great deal more comparative immunology has been included.
  2. The collection is biased towards authors found in the annotated bibliography.
  3. The collection exhibits a "pull of the recent", as recent articles are more likely to be accessible, more likely to be cited, and more likely to be listed in online databases.
  4. Like the annotated bibliography, this collection is biased towards review literature rather than research literature.

Nevertheless, some interesting features emerge when the bibliography is analyzed quantitatively. In 1996, Michael Behe claimed that a thorough search of the scientific literature showed that the evolutionary emperor had no clothes. About the evolution of irreducibly complex systems in general, Behe wrote,
There is no publication in the scientific literature -- in prestigious journals, specialty journals, or books -- that describes how molecular evolution of any real, complex, biochemical system either did occur or even might have occurred." (Darwin's Black Box, p. 185)
This was in a chapter boldly entitled "Publish or Perish," which contains section headings like "The Missing Papers" and "Searching High and Low." Behe made a great show of searching biochemistry textbooks, the university library, and the journals, especially a detailed search through the Journal of Molecular Evolution, which occupies four pages of Darwin's Black Box (pp. 173-177). On p. 179, Behe wrote,
The search can be extended, but the results are the same. There has never been a meeting, or a book, or a paper on the details of the evolution of complex biochemical systems."
Behe's famous assertions about the evolutionary immune system literature were quoted in the annotated bibliography, but it is also worth noting that Behe cited a grand total of five publications on evolutionary immunology in the entire immune system chapter of Darwin's Black Box. They have been marked with an asterisk (*) for the reader's convenience. In his new afterword to the tenth anniversiary edition of Darwin's Black Box, Behe cited exactly one additional immune system paper, Klein and Nikolaidis (2005), also marked with an asterisk in this list. Behe completely misses the point of the article, which is discussed in the annotated bibliography. Behe's critique consists of, first, trumpeting the mere fact that the the authors use words like "probably", as if such qualifiers were not found in virtually every careful scientific publication. Apart from Behe, this juvenile tactic is only commonly found among the least sophisticated internet creationists. Second, Behe doesn't find enough mentions of the words he thinks he should find, cognates of "Darwin", "natural selection", and "mutation" -- Behe made this same trivial critique of several immune system articles at trial, and the problems with it were exposed in short order during Rothschild's cross-examination. Here, we can add that Behe's problem is that the immune system literature is too advanced for him -- general "mutations" are not discussed so much as the specific kinds of mutations relevant to the origin of the immune system, such as -- wait for it -- transposition. Regarding natural selection, entire articles, indeed entire careers (see articles by Cohn, Gould, etc.) have been devoted to studying, and often mathematically modeling, the selection forces that lead to immune systems, the diversity of immune system receptor genes, and the ways that various specific hypotheses can be tested by examining substitution ratios and other evidence. Behe seems to assume that if the first random article he reads doesn't start completely from scratch and educate him personally about everything going on in research labs across the country, then the article is worthless. The reality, on the other hand, is that any article specifically focusing on natural selection and the immune system, that didn't reach the level of sophistication of Cohn's work, wouldn't even be worth publishing.

Finally, Behe says that Klein and Nikolaidis admit themselves that this immune system evolution stuff is just speculation, because they suggest some experiments that have not yet been done, and without them "their scenario would 'remain hopelessly in the realm of mere speculations.'" But let's look at the actual concluding paragraph of the article:
The agnathan [jawless fish] genomes should bear witness to how close they have come to acquiring the AIS [Adaptive Immune System]. The closeness can be determined experimentally in two ways: by introducing agnathan genes into the gnathostome [jawed vertebrate] genome or the other way around. It should be possible to determine which changes are necessary for agnathan genes, such as the PSMB, ATP-binding cassette transporter, or CD45, to replace the functions of their gnathostome counterparts. In the opposite direction, introducing gnathostome genes such MHC, BCR, or RAG, into agnathan cells or animals should reveal to what extent the cells' or animals' physiology is "ready" for some of the functions associated with the AIS. Extant agnathans are, of course, evolutionarily far away from the agnathan-gnathostome ancestors, but this kind of experimental molecular evolution should nevertheless shed light on events that would otherwise remain hopelessly in the realm of mere speculations. (Klein and Nikolaidis, 2005, p. 174)
In context, it is clear that what the authors consider "speculation" is the detail of exactly how close the agnathan genome is to acquiring an adaptive immune system. In figure 2, the authors show that agnathans, which lack the adaptive immune system, nevertheless have 12 of the 16 key components of adaptive immunity that the authors identify, and in the conclusion the authors are simply wondering what would happen if a few more key components of the adaptive immune system were introduced into agnathans. Strangely, Behe doesn't take the time to explain how the "partial" adaptive immune system of agnathans remains functional in the light of his famous claim than "any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional" and therefore "cannot be produced gradually" because "it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on" (Behe 1996, p. 39).

Regardless, Behe writes on p. 270 of his afterword,
Today the situation remains unchanged from what it was ten years ago. As I wrote in Chapter 8:
There is no publication in the scientific literature -- in prestigious journals, specialty journals, or books -- that describes how molecular evolution of any real, complex, biochemical system either did occur or even might have occurred. There are assertions that such evolution occurred, but absolutely none are supported by pertinent experiments or calculations.
(Behe 2006, p. 270)
With this in mind, let us examine the bibliography.


Quantitative Description

This bibliography contains 357 articles, books, and book chapters. Counting up the page numbers in the citations yields about 4,700 pages of material, not including the books which would total another few thousand pages. The citations have been arranged chronologically and alphabetically.

By Year

The number of articles in the bibliography published in each year since 1962 is plotted in the below graph. The number for 2006 was estimated by multiplying by three the number of articles available as of April 2006.

Number of publications per year found in this bibliography. Keeping in mind that the bibliography is probably biased against older articles, the general trend is still suggestive of a rapidly growing research field. The vertical dotted line represents the publication of Behe's 1996 book Darwin's Black Box
The bibliography was divided into two periods, the 34 year period from 1962-1995, and the 11 year period from 1996-2006. Darwin's Black Box was published in early 1996, and it can be seen that this bibliography contains 150 articles on evolutionary immunology published before that date. This is 39% of the collection. This seems to substantially weaken Behe's 1996 claims about the scientific literature. From 1996-2006, a further 236 articles were published, or 61% of the collection. This seems to contradict Behe's re-assertions of his claims in the 2006 edition of Darwin's Black Box.

By Author

The authorship of the articles can also be quantified. Academics know that every academic has a specialty, and that in order to be conversant in a particular field you simply must be familiar with the research and publications of the key people in that subfield. This bibliography contains 192 different first authors, and hundreds of additional secondary authors. Who are some of the leaders in evolutionary immunology? The top ten first authors in the bibliography are listed below, along with the number of times each of these researchers appears as an author anywhere in an article authorship list:

AuthorNo. articles
(first author)
No. articles
(any author)
Gary Litman2249
John Marchalonis2138
Martin Flajnik1323
Louis Du Pasquier1219
Masaru Nonaka1122
L. William Clem714
Sir Frank Macfarlane Burnet66
David Schatz59
J. Oriol Sunyer57
Melvin Cohn46
The top ten first authors in the bibliography. The number of publications in the bibliography that they have first-authored, or coauthored in any fashion, is listed. All of these authors have written many more articles than just the ones listed here; see their linked webpages for publication lists and research descriptions. E.g., Martin Flajnik, "My work is centered on the evolution of the immune system, with the major goal being to understand the origins of adaptive immunity...."
Although the top ten authors constitute only 5.2% of the first authors in this bibliography, they have first-authored 106 (30%) of the articles. Counting articles on which the top ten have been an author in any position, including first, they have coauthored over half of the articles in the bibliography (193, or 52%).

At this juncture, readers should ask themselves: has the ID movement grappled with the work of any of these researchers? Is the ID movement simply hoping that they can keep their supporters ignorant that numerous researchers are, daily, doing the work that the ID movement says doesn't exist? If the reader has followed the "intelligent design" movement for a substantial length of time, but has never heard of these researchers or their work, they should ask themselves if they have ever had a realistic picture of what is actually going on in the scientific community.

By Journal

The top ten journals in the bibliography can be tabulated in a similar fashion:

JournalNo. articles
Proceedings of the National Academy of Sciences27
Developmental and Comparative Immunology25
Immunological Reviews23
Journal of Immunology21
Nature20
Cell12
Journal of Experimental Medicine10
Immunogenetics9
Molecular Immunology8
Science7
The top ten journals in the bibliography. The number of publications in the bibliography that they have appeared in each journal is listed. The top ten journals account for 162 articles, or 45% of the publications in the bibliography.
It is evident that the top ten journals in the list fall into two categories. First, immunology journals read by immunologists. This is not surprising, although it may surprise the reader to know that there is a whole journal devoted to comparative immunology. Of the publications listed in this bibliography, 192 (54%) are published in journals or books with a cognate of "immunity" in the title, while the rest are in a wide array of more general biology and science publications.

The second category found in the top ten list, of course, is prestigious general science journals (Nature, Science, PNAS, or the more specialized Cell, the most prestigious journal in cell biology). The ID movement would kill for just one ID publication in any one of these journals.

It is worth noting that the Journal of Molecular Evolution, the journal that Behe spent four pages of Darwin's Black Box on in a great show of allegedly sincere searching for evolution articles, has only one publication in this entire bibliography. Behe pretends that the Journal of Molecular Evolution must be the primary place one would look for the kinds of articles that he seeks -- after all, "molecular evolution" is right there in the title! But if one understands the subtleties of academic tradition, one realizes that JME has tended to focus on slightly different topics such as gene phylogenies and molecular clocks. It is not necessarily the journal one would go to for everything involving evolution for any system, especially when fields like immunology have a set of their own journals, and save the really revolutionary stuff for Science and Nature.


The Implications

In the new afterword to Darwin's Black Box, Behe told his readers what should be expected "at an absolute minimum" for research on the evolutionary origin of the eukaryotic cilium:
It would take at least as much work to figure out how such a structure could evolve by random mutation and natural selection as it did to figure out how it works in the first place. At an absolute minimum that would be expected to result in hundreds of papers -- both theoretical and experimental -- many reviews, books, meetings, and more, all devoted to the question of how such an intricate structure could have evolved in a Darwinian fashion. (Darwin's Black Box, 2006, p. 267)
Admittedly, this level of research has not been conducted on the evolutionary origin of the cilium yet. Although Behe claims the cilium is well understood because the basic mechanism of microtubule sliding is understood, it is actually still a deeply mysterious structure, fundamentally tied to the centriole and the centriole's role in mitosis. For example, scientists do not understand the actual physical mechanism that produces the famous 9+2 microtubule pattern of cilia or the similar pattern in the centriole template. It is hard to see how detailed an evolutionary account could get with such basic questions unanswered. The blatant contradiction between Behe's lax scientific standards for understanding current cell biology -- on the cilium, he basically says, "The microtubules slide past each other, what else is there to know?" -- and his ridiculous scientific standards for evolution -- basically, "Give me every single mutation and selection pressure in every lineage over the last billion years" -- will have to be explored in more detail elsewhere. Also saved for later is the question of where exactly the ID movement's hundreds of papers are that give detailed accounts of the ID explanation for the cilium, the immune system, etc.

Although there are not hundreds of papers, meetings, books, etc., on cilium evolution, the point of these webpages is -- as the reader has already guessed -- that evolutionary immunology does have this level of research behind it. Will the ID movement ever admit it, or will they just continue to brazenly dismiss the work of hundreds of scientists as "speculation"? Time will tell. In the meantime, unsupported statements about the lack of scientific literature on the evolution of irreducibly complex systems -- even statements from seemingly authoritative sources -- must be treated with skepticism (the ID movement has a small handful of quotes from respected scientists that they wield like talismans against criticism, but there is no evidence that these authorities have any particular familiarity with evolutionary immunology).


Full Bibliography: Alphabetical

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2. Agrawal, A., Eastman, Q. M. and Schatz, D. G. (1998). "Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system." Nature 394(6695): 744-751. (Google Scholar | DOI | Journal | PubMed)

3. Alder, M. N., Rogozin, I. B., Iyer, L. M., Glazko, G. V., Cooper, M. D. and Pancer, Z. (2005). "Diversity and function of adaptive immune receptors in a jawless vertebrate." Science 310(5756): 1970-1973. (PubMed)

4. Al-Sharif, W. Z., Sunyer, J. O., Lambris, J. D. and Smith, L. C. (1998). "Sea urchin coelomocytes specifically express a homologue of the complement component C3." Journal of Immunology 160(6): 2983-2997. (PubMed)

5. Altmann, S. M., Mellon, M. T., Distel, D. L. and Kim, C. H. (2003). "Molecular and functional analysis of an interferon gene from the zebrafish, Danio rerio." Journal of Virology 77(3): 1992-2002. (PubMed)

6. Amemiya, C. T. and Litman, G. W. (1990). "Complete nucleotide sequence of an immunoglobulin heavy-chain gene and analysis of immunoglobulin gene organization in a primitive teleost species." Proceedings of the National Academy of Sciences 87(2): 811-815. (PubMed)

7. Amemiya, C. T., Ohta, Y., Litman, R. T., Rast, J. P., Haire, R. N. and Litman, G. W. (1993). "VH gene organization in a relict species, the coelacanth Latimeria chalumnae: evolutionary implications." Proceedings of the National Academy of Sciences 90(14): 6661-6665. (PubMed)

8. Anderson, M. K., Pant, R., Miracle, A. L., Sun, X., Luer, C. A., Walsh, C. J., Telfer, J. C., Litman, G. W. and Rothenberg, E. V. (2004). "Evolutionary origins of lymphocytes: ensembles of T cell and B cell transcriptional regulators in a cartilaginous fish." Journal of Immunology 172(10): 5851-5860. (PubMed)

9. Anonymous (1971). "A Wise Cell Knows Which its Parent." Nature 232(5308): 219-220. (DOI | Journal)

10. Armstrong, P. B. and Quigley, J. P. (1999). "Alpha2-macroglobulin: an evolutionarily conserved arm of the innate immune system." Developmental and Comparative Immunology 23(4-5): 375-390. (PubMed)

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13. Bang, D. D., Verhage, R., Goosen, N., Brouwer, J. and van de Putte, P. (1992). "Molecular cloning of RAD16, a gene involved in differential repair in Saccharomyces cerevisiae." Nucleic Acids Research 20(15): 3925-3931. (PubMed)

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16. Beck, G., Cooper, E. L., Habicht, G. S. and Marchalonis, J. J., eds. (1994). Primordial Immunity: Foundations for the Vertebrate Immune System. New York, The New York Academy of Sciences. (Library | PubMed | Publisher | Amazon | Google Print)

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18. Beck, G. and Habicht, G. S. (1996). "Immunity and the invertebrates." Scientific American 275(5): 60-63, 66. (Journal)

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45. Cohn, M. (2002). "The immune system: a weapon of mass destruction invented by evolution to even the odds during the war of the DNAs." Immunological Reviews 185: 24-38. (PubMed)

46. Cohn, M. (2005). "The common sense of the self-nonself discrimination." Springer Seminars in Immunopathology 27(1): 3-17. (PubMed)

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54. De Tomaso, A. W., Nyholm, S. V., Palmeri, K. J., Ishizuka, K. J., Ludington, W. B., Mitchel, K. and Weissman, I. L. (2005). "Isolation and characterization of a protochordate histocompatibility locus." Nature 438(7067): 454-459. (DOI | Journal | PubMed)

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56. Diaz, M. and Flajnik, M. F. (1998). "Evolution of somatic hypermutation and gene conversion in adaptive immunity." Immunological Reviews 162: 13-24. (PubMed)

57. Difilippantonio, M. J., McMahan, C. J., Eastman, Q. M., Spanopoulou, E. and Schatz, D. G. (1996). "RAG1 mediates signal sequence recognition and recruitment of RAG2 in V(D)J recombination." Cell 87(2): 253-262. (PubMed)

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