Published 2007 by Prometheus Books Relics of Eden: The Powerful Evidence of Evolution in Human DNA. Copyright © 2007 by Daniel J. Fairbanks. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, digital, electronic, mechanical, photocopying, recording, or otherwise, or conveyed via the Internet or a Web site without prior written permission of the publisher, except in the case of brief quotations embodied in critical articles and reviews. Inquiries should be addressed to Prometheus Books 59 John Glenn Drive Amherst, New York 14228-2119 VOICE: 716-691-0133, ext. 210 FAX: 716-691-0137 WWW.PROMETHEUSBOOKS.COM 11 10 09 08 07 5 4 3 2 1 Library of Congress Cataloging-in-Publication Data Fairbanks, Daniel J. Relics of Eden : the powerful evidence of evolution in human DNA / Daniel J. Fairbanks. p. cm. Includes bibliographical references and index. ISBN 978-1-59102-564-1 [ D N LISMB 1N. E97v8o-l1u-ti6o1n5,9 M2-o0l0e9cu-9la (re. -2b.o Goke)n o1m. Me,o Hleucmulaanr. e3v.o Gluetnioonm. i2c.s E—vhoilsuttoioryn.ary genetics. I. Title. 4. Human Genome Project. QU 475 F164r 2007] QH390.F35 2007 572.8'38—dc22 2007027126 Printed in the United States of America on acid-free paper Preface Introduction Chapter 1 Fusion Chapter 2 McClintock's Masterpiece Chapter 3 Bogus Genes Chapter 4 Solving the Trichotomy Chapter 5 Darwinian DNA Chapter 6 A Spectacular Confirmation Chapter 7 Diversity Chapter 8 The Tree of Life Chapter 9 “When Faith and Reason Clash” Chapter 10 Abandoning the Dichotomy Introduction to the Appendices Appendix 1 The Story of NANOG and Its Pseudogenes Appendix 2 Nine Inversions Appendix 3 From Darwin to the Human Genome: A Brief History Glossary Bibliography Index n recent years, advocates of the creationism and intelligent design I movements have successfully promoted history's most sophisticated and generously funded attack on science, claiming that evolution, human evolution in particular, is “a theory in crisis.” Ironically, during this same period, the Human Genome Project revealed the most powerful evidence of human evolution ever discovered, and other genome projects, especially the chimpanzee and rhesus macaque projects, have substantially augmented that evidence. With the ongoing controversy over intelligent design, people often ask me to recommend a book on the molecular evidence of human evolution. Unfortunately, most popular human evolution books either fail to include DNA evidence, or, if they do, they cover only a few highlights. Instead, they tend to focus on archaeological, geological, anatomical, physiological, and theoretical evidence with little or no discussion of the literally millions of molecular fossils in DNA. These requests, and my dismay at repeated claims of meager and flawed evidence sup porting human evolution, led me to draft the book you are now reading. This book comes at a time when the clash between those who perceive evolution as a threat to religious faith and those who view religious fervor as a threat to science is as intense as it ever has been. The first eight chapters of this book, and the three appendices, focus on pure and solid science. Toward the end, however, the final two chapters address this clash and argue for the middle ground—that science and religion are complementary ways of seeking answers and they need not be at odds. Most of you reading this have varied backgrounds and interests in science, especially in molecular biology. To satisfy these diverse needs, I have chosen to keep the main text of the book as simple and as concise as possible, while still telling the remarkable story the evidence has to offer. For those of you who want additional information, I have written two appendices that explore some of the main topics in the book in more detail and a third appendix that tells the story of how some of history's best scientific minds laid the foundation for the discoveries presented in this book. You will shortly read about evidence discovered by hundds of scientists. I wish first to acknowledge them and their work, and I hope this book does justice to their extraordinary accomplishments. I also wish to acknowledge those who taught me science, the first being my grandfather, Avard T. Fairbanks, who as a professor, human anatomist, and prominent sculptor opened my eyes to the magnificence of both science and art. I also am especially grateful to professors Clayton White and Duane Jeffery, who, when I was an undergraduate student, helped me explore the wonders of evolution. I recorded the very day, January 30, 1979, when during a discussion on evolution in Dr. White's class I discovered a newfound way of thinking as a scientist. Shortly thereafter I met Dr. Jeffery, who personally helped me work through the change in thought required by that discovery. Now, twenty-six years later, his review of the manuscript for this book has been invaluable. I owe special thanks to Cecie Starr, who introduced me to book authorship. I greatly appreciate her extraordinary encouragement and assistance over the years and during the development of this book. The teachings of many other professors and colleagues have inspired my passion for science and are reflected in the pages that follow. To them I likewise am grateful. I also thank the thousands of students who enliven the classes I teach. There is no better profession than being a university professor, and the students make it all worthwhile. Throughout the publication process, the editors and staff of Prometheus Books have exemplified the utmost courtesy and professionalism. I applaud them for their superb work. It should go without saying that the opinions in this book are entirely my own, and in expressing them by no means do I intend to represent the views of my employer, my colleagues, or the publisher. I have scrupulously tried to ensure that there are no errors but have learned from past publishing experience that in spite of my best efforts at eradicating errors, a few inevitably persist. I apologize in advance for any errors and take sole responsibility for them. Finally, to my wife, Dr. Donna Fairbanks, and my children, Jonathan, Aaron, and Michael, I am indebted to you for your patience and support. wise professor of Russian literature once told me that every university A student should take a course in geology. With my love of science, I needed little convincing. It was the spring of 1982, and in a university with over twenty-five thousand students, only three of us enrolled in the course. (To this day I'm still baffled by the lack of interest most students show toward science.) We were the luckiest three students on campus that term. With such a small class, the professor canceled the classroom and we spent most of our time traveling through the mountains studying geological formations. I was astonished at how often we found fossils. For the last week of class, we camped in Capitol Reef National Park, one of the most geologically rich places on Earth. Our professor hadn't told us how he would determine our grades, and we never had any tests, just constant verbal quizzing from him. As we were leaving the park, he pulled the car to the side of the road and told us to climb a nearby hill. “Anyone who finds a fossil gets an A in the class,” he said with a smirk on his face. We dutifully scampered up the hill to find ourselves on a plateau covered with thousands of fossilized oyster shells. We all got our As. That summer I saw abundant evidence that the earth was very old and that it contains countless remnants of long-extinct organisms. I saw how scientists carefully studied the multitude of fossils they found to reconstruct as much as possible the history of life on Earth. The fossils we saw that summer in very ancient rocks were obviously different from any modern organisms; those from more recent rocks looked much more like the animals and plants we see today. The progression of life over time from the strange to the familiar was readily apparent. I then went to graduate school to study genetics and DNA, where I encountered fossils of a different kind: relics buried in the DNA of all organisms, including ours. Those relics tell a fascinating story. To understand how the story goes, let's start with a simple analogy. As often happens in our electronic age, I received not long ago an amusing e-mail message from a friend. This particular message had a list of predicted headlines from the year 2029; “Baby Conceived Naturally, Scientists Stumped,” read one of them. My friend received it from a friend, who received it from a friend, and so on. Before e- mail, people passed on messages like these as photocopied pages. So let's think back to those days and imagine someone photocopying a page with an amusing message and passing it on to several friends, who photocopy their copies and pass them on to their friends who do the same, and so on. Each time someone photocopies the message, specks of dust on the photocopier glass end up leaving marks on the new copy. These marks are preserved on subsequent copies every time that particular page, or a copy of that page, is photocopied. New marks are added with each round of photocopying so that these extraneous marks end up accumulating until the copies are cluttered with them. Each mark is a relic added at some point in the branching chain of photocopying. Now, imagine a good detective who gathers the thousands of copies of this message passed along through photocopying from friend to friend. This detective could reconstruct the branching chain of photocopying by comparing all of the pages and determining how many of the extraneous marks are the same and how many are different. Marks present on a large proportion of the pages must have occurred early in the chain; those on just a few happened later. Furthermore, this detective can hierarchically group the pages to reconstruct the branching chain purely by comparing similar and different marks on the pages, without any information about who had the pages or who received a copy from whom. These marks are relics of photocopying that tell a story about how the message on the page was passed on, even though they have nothing to do with the message itself. Organisms replicate their DNA and pass it on to their offspring in a manner somewhat like this simple photocopying analogy, although the process of inheritance is much more complex. At times, useless bits of DNA creep into the mass of useful information and end up being passed on from one generation to the next. These relics of DNA accumulate generation after generation until there are literally millions of them. Although most of them have no relationship to the message in DNA, cells do not routinely purge them; instead they copy them, over and over, as the cells divide to form more cells. These relics, in a sense, are fossils buried in the DNA of every organism on Earth, waiting for us to uncover them. Like our hypothetical detective, scientists who examine them can decipher the stories they tell about genetic histories. By the time I received my PhD in 1988, studies of DNA had produced powerful evidence of evolution, as powerful as the overwhelming evidence from fossils in rocks. In the ensuing years, the evidence from DNA grew at a rate so astounding that even the most optimistic scientists were stunned. The most massive evidence came from genome projects, especially the Human Genome Project, which deposited enormous amounts of DNA sequence information in computer databases. The Internet made those sequences easily and freely available to anyone in the world with an Internet connection. The opportunity to search DNA for the story of life was never greater. What once was a trickling stream of DNA-based studies on human evolution became a torrent. One study after another showed that our DNA is littered with literally millions of relics of our evolutionary ancestry. In 1998, the National Academy of Sciences, the most prestigious and highly respected group of scientists in the United States, issued a report with this concise and exceptionally wellworded statement: “It is no longer possible to sustain scientifically the view that living things did not evolve from earlier forms or that the human species was not produced by the same evolutionary mechanisms that apply to the rest of the living world.”1 Few biologists question the reality of evolution. The same cannot be said of the general public. Sadly, few people understand modern evolutionary theory and the scientific evidence on which it is founded. Moreover, few have studied the social culture that has fueled a clash between religious beliefs and evolutionary science for more than one hundred and fifty years. For some, scientific ignorance is bliss. But in today's world, where science plays such a vital role in society, a better understanding of evolution is needed. The intent of this book is to present just a fraction, but a very compelling fraction, of the DNA-based evidence of evolution. I have chosen to focus on human evolution because some people are willing to accept the idea that other species have evolved but draw the line with humans, usually for religious reasons. Yet thanks to the Human Genome Project, we now have more evidence of evolution for humans than for any other species. Lest anyone think that my purpose in writing this book is to criticize religion, be assured it is not. Like many of my scientific colleagues, I hold deep religious convictions. However, along with them, I strongly believe that attempts to discredit the powerful evidence of evolution actually harm faith rather than promote it. We'll return to the debate over evolution and religion at the end of this book. For now, we have a fascinating journey ahead of us as we explore some of the many relics of evolution found in the DNA of every person on the planet.