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Darwinian Detectives: Revealing the Natural History of Genes and Genomes/Norman A DARWINIAN DETECTIVES This page intentionally left blank DARWINIAN DETECTIVES Revealing the Natural History of Genes and Genomes Norman A. Johnson 1 3 Oxford University Press, Inc., publishes works that further Oxford University’s objective of excellence in research, scholarship, and education. Oxford New York Auckland Cape Town Dar es Salaam Hong Kong Karachi Kuala Lumpur Madrid Melbourne Mexico City Nairobi New Delhi Shanghai Taipei Toronto With offices in Argentina Austria Brazil Chile Czech Republic France Greece Guatemala Hungary Italy Japan Poland Portugal Singapore South Korea Switzerland Thailand Turkey Ukraine Vietnam Copyright © by Oxford University Press, Inc. Published by Oxford University Press, Inc. Madison Avenue, New York, New York www.oup.com Oxford is a registered trademark of Oxford University Press 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, electronic, mechanical, photocopying, recording, or otherwise, without the prior permission of Oxford University Press. Library of Congress Cataloging-in-Publication Data Johnson, Norman A., – Darwinian detectives: revealing the natural history of genes and genomes/Norman A. Johnson. p. ; cm. Includes bibliographical references and index. ISBN –––– . Evolutionary genetics. Natural history. Molecular genetics. I. Title. [DNLM: . Selection (Genetics) . Evolution. Genetics. Genomics. Natural History. QU Jd ] QH.J .’—dc Printed in the United States of America on acid-free paper Dedicated to Julie Froehlig, just for being This page intentionally left blank Foreword Imagine that the theory of evolution had never been discovered. Suppose that we are at the start of the twenty-first century without it. Biology remains based on some type of creationism, as it was before Darwin published his theory of evolution, but all of modern biotechnology is in place. A bizarre fossil is discovered in an Ethiopian desert, bones that no one has seen before, part way between a chimpanzee and a human. The skull is small, smaller than that of any grown human, but the rest of the skeleton suggests that this man-ape monstrosity could walk upright with ease. An ayatollah declares it a creation of a Satan, a long dead minion of evil. Sub-Saharan African children die of sickle-shaped red blood corpuscles in great numbers, but there is no contagious disease that explains the disorder, not even the endemic parasite Plasmodium that causes malaria. Molecular biologists work out that the sickling is usually due to a single amino acid change in the string of amino acids that makes up part of the hemoglobin molecule, but they have no idea why it is so frequent. An ancient curse is suspected by practitioners of voodoo. It has been established that all known cases of inheritance are due to nucleic acids, overwhelmingly deoxyribonucleic acid (DNA), but sometimes its close chemical cousin, ribonucleic acid (RNA). The pope declares that the efficiency of these molecules shows God’s Providence at work in the world. A world where biologists only document the details of God’s Creation has no mysteries. Every feature of life can be attributed to the action of this unknown, but supremely powerful, gaseous vertebrate. Yes, biologists will viii Foreword still work on the details, but whatever these details turn out to be, the “guilty party” is always the same: God. Now imagine a scientific field that is devoted to finding other causes for the panoply of life, a field that invokes material causation in place of an all-powerful Creator. Then there are mysteries. How could organs so much like video cameras have been placed on the front of our faces, giving almost all members of the species Homo sapiens binocular color vision? Why is there so much variation in the amino acids making up important proteins? Why are the genes that code for proteins interrupted by noncoding DNA, of no apparent purpose? Why is more than of the human genome apparently noncoding junk DNA? Why do some genes hop around, while others stay in the same place? We can either suppose God to be perverse or look for other guilty parties. If we choose the latter alternative, further choices arise. Perhaps the causes of living diversity are secular instruments of a more subtle Creator, or the work- ings of a Godless universe. We don’t need to decide that question right away, as biologists. But if we suppose that the living world conforms to decipherable laws, beyond those of physics and chemistry alone, though not in violation of them, then we have to work out these laws. Having worked out these lawful mechanisms, we will perforce seek out their applications to the particulars of the living world, in part to understand that living world better and in part to test these laws of life themselves. Then and only then can we consider biologists scientists in their own right, rather than the “natural historians” of God’s Creation, or the less intelligent handmaidens to chemists and physicists. It is this challenge that has been taken up by evolutionary biologists above all other biologists. Exploring secular forces behind the machinery of life is a relatively new enterprise. For the general public, this endeavor is less than years old, even though the natural history of life is one of mankind’s earliest interests. And this natural history work continues at a steadily accelerating pace. Most of molecular and cellular biology is that natural history project continuing down to the level of organic chemistry, with new facts of life discovered every hour in a laboratory somewhere around the globe. But they are only creating new mysteries to be solved. For all their dazzling machinery, most cell biologists are the policemen on the beat, arresting the obvious “perps” and discovering the dead bodies, sequencing the genes and showing how the proteins fold and interact. It is the evolutionary biologists who are the detectives, the Columbos, the Miss Marples, often older or eccentric, driving ancient vehicles and muttering to themselves about things that the cops on the molecular biology beat find baffling. This engaging volume introduces Darwinian detective work, how we go about unraveling the guilty parties that remain behind the scenes until they are apprehended. Foreword ix Many people have little interest in this enterprise. Others question its validity. Sometimes our work turns up little or nothing at first. Cases go cold, sometimes for decades. Then a new piece of evidence is turned up by a cell biology patrolman or a fossil bounty hunter, and we have a new theory explaining a mystery of life. Sometimes this theory is shot down soon after it is proposed, the victim of some ugly fact. But we work on, convinced that there has to be some underlying cause, some explanatory key that would have tickled Darwin himself, our first great evolutionary detective, and still an unrivaled master at the level of pure intuition. But our detective work has been greatly aided by new quantitative tools, tools to which Darwin did not have access. Unbeknownst to many cursing statistics students in college, the variances and regressions that they struggle with are tools of data analysis first brought to maturity in pursuit of evolu- tionary mysteries. Quantitative analysis of data has grown in tandem with evolutionary biology. Now much of the evolutionary genetics that Norman Johnson describes for us is based on massive computation. (I have myself donated a successful doctoral student in evolutionary theory, Michel Krieber, to the world of stock market analysis, a forbiddingly sophisticated application of mathematics.) Modern-day evolutionary biologists can solve problems that Darwin couldn’t, because our field has advanced far beyond the solid foundations that he hammered into the ground of biology; it is the most dauntingly mathematical part of biology. But not to fear. You will be spared mathematical heavy-lifting here. There is a literal intersection of criminology and Darwinian detective work: genetic forensics. My closest colleague, Larry Mueller, serves as an expert witness in cases that involve the use of DNA from blood, semen, and other crime-scene tissues. The very fact that this technology has value in courts of law is one of the mysteries that evolutionists have been most inter- ested in: the abundant genetic variation within our species, and most others. Without copious genetic variation, forensic DNA would be of little value. The riddle of that variation is one of the most important themes of this book. As in many other respects at this moment in history, Western civilization has a choice between an increasingly awkward obscurantism and science. You can suppose that global warming is fanciful, that God made our bodies in His Image, that one or another ancient book contains all that a decent person should know. Or you can embrace a world that has many obscure secular causes, a world with real mysteries that take some care to figure out. Many people accept the triumphant working out of the great mysteries of physics, though there are still those who believe that the Sun revolves around the Earth, as the Bible proposes. Most people also already accept that the Earth is ancient, though few have an intuitive sense of its enormous age. It is now time for reasonably informed people to add biological evolution to their repertoire of general knowledge. Norman Johnson introduces the educated reader, one who knows perhaps a smattering of science, to some of the most exciting mysteries in biology, x Foreword mysteries that only evolutionary biologists have the hubris to try to solve. Like the cosmologists of physics or the theorists of quantum mechanics, evolutionary biologists delight in paradoxes and puzzles, organisms that shouldn’t exist, and genes that seem to defy reason.
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