EVOLUTION: The First Four Billion Years

EVOLUTION The First Four Billion Years E D I T E D BY

MICHAEL RUSE J O S E P H T R AV I S W I T H A F O R E WO R D BY

E DWA R D O. W I L S O N

THE BELKNAP PRESS OF HARVARD UNIVERSITY PRESS CAMBRIDGE, MASSACHUSETTS LONDON, ENGLAND 2009

Copyright © 2009 by the President and Fellows of Harvard College All rights reserved Printed in the United States of America Library of Congress Cataloging-in-Publication Data Evolution : the first four billion years / edited by Michael Ruse, Joseph Travis ; with a foreword by Edward O. Wilson. p. cm. Includes bibliographical references and index. ISBN 978-0-674-03175-3 (alk. paper) 1. Evolution (Biology) I. Ruse, Michael. II. Travis, Joseph, 1953– QH366.2.E863 2009 576.8—dc22 2008030270

Contents

Foreword Edward O. Wilson

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Introduction Michael Ruse and Joseph Travis

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The History of Evolutionary Thought Michael Ruse

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The Origin of Life Jeffrey L. Bada and Antonio Lazcano

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Paleontology and the History of Life Michael Benton

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Adaptation Joseph Travis and David N. Reznick

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Molecular Evolution Francisco J. Ayala

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Evolution of the Genome Brian Charlesworth and Deborah Charlesworth

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The Pattern and Process of Speciation Margaret B. Ptacek and Shala J. Hankison

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Evolution and Development Gregory A. Wray

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Social Behavior and Sociobiology Daniel I. Rubenstein

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Human Evolution Henry M. McHenry

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Evolutionary Biology of Disease and Darwinian Medicine Michael F. Antolin

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Beyond the Darwinian Paradigm: Understanding Biological Forms Brian Goodwin

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Philosophy of Evolutionary Thought Kim Sterelny

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Evolution and Society Manfred D. Laubichler and Jane Maienschein

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Evolution and Religion David N. Livingstone

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American Antievolutionism: Retrospect and Prospect Eugenie C. Scott

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Alphabetical Guide

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Contributors

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Illustration Credits

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Index

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Introduction Michael Ruse and Joseph Travis

The discovery of evolution is one of the greatest intellectual achievements of Western thought, ranking with the calculus and general and specific relativity among scientific discoveries that changed indelibly how we see our world. From seeing nature as fixed forever in form and composition to seeing it as forever changing, we have been transformed utterly by discovering and understanding evolution. In science the word evolution is used to express three different but related ideas. First, there is the fact of evolution. This is the realization that all organisms, living and dead, including humans, are the end products of a long natural process of change through which each species is descended from other, different ones. Although protoevolutionary ideas date back to the time of the ancient Greeks, only in the eighteenth century did the claim that organisms evolved really start to gain currency. However, the idea was not considered a basic element of scientific knowledge until after Charles Darwin published his On the Origin of Species in 1859. Darwin argued that all the organisms on the planet emerged through a single, straightforward process that operated relentlessly from the dawn of life and that continues to shape the natural world. An enormous amount of scientific research, from paleontology to molecular biology, has provided the compelling and overwhelming evidence that evolution is indeed a fact. Second, evolution is often used to refer to the path of life’s history on this globe. This can refer to the history of a group of existing species, as in the evolution of orchids, or the path through which particular traits emerged, such as the evolution of the middle ear of mammals from small bones in the reptile jaw. Evolutionary histories are reconstructed from a wide variety of evidence that ranges from sequences of species and forms in the fossil record to similarities and differences in the DNA of existing organisms. The evolution of some features, such as the hooves of ungulates, is very well understood, while the evolution of others, particularly very old features like the organelles of cells, is less well understood. The third idea is the theory of evolution. This refers not to a suggestion that evolution has not occurred or that the history of particular features cannot ix

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be reconstructed but to our ideas about the forces that drive evolutionary change. In the Origin Darwin proposed what today is almost universally considered the major force in organic change, natural selection. But natural selection is not the only important evolutionary force; natural selection operates on the variation in shapes, sizes, and forms of organisms created by mutations in their genes, and the rate and magnitude of the changes that are driven by natural selection are governed by how those genes control development. An enormous amount of observation and experiment has documented the action of natural selection and some of the genetic responses to selection. But modern discoveries in genetics and development have raised many new questions and guided us toward some surprising answers about how all these forces combine to drive evolution. Outside science the word evolution refers to a natural process considered the inspiration for a host of sociological, literary, political, philosophical, and religious ideas. From writers exploring the animal nature of humans to psychologists searching for the origin of human behavior in evolutionary history to theologians grappling with the implications of evolution for our understanding of the Divine, the influence of evolution outside science far exceeds that of any other scientific discovery ever made. And as modern controversies in the schools illustrate, particularly in the United States, it provokes reactions almost as strong as issues surrounding the beginning and end of human life. In this book we explore all these facets of evolution. Our authors present the evidence for evolution as fact from the fossil record to genomics, illustrate the history of groups from bacteria to birds, and describe our current ideas about how these histories and this evidence came to be. Our authors also explore the influence of evolution on philosophy, religion, sociology, psychology, and many other areas and address the current controversies about the teaching of evolution in schools. The book covers the historical discoveries, such as homology, that opened the path for discovering evolution; the phenomena, such as industrial melanism, that played major roles in inspiring experimental studies of evolution; the applications of evolutionary principles to areas seemingly far afield, such as computer science; and the contributions of the major figures who shaped the history of evolutionary science and the discipline as it exists today. Perhaps most important, this book presents evolutionary science as a modern, dynamic discipline. All too often discussions of evolution outside the science itself give the impression that the subject became fossilized in the nineteenth century. This is particularly so when the suitability of evolution as a subject for secondary-school students is being argued. The irony is that the discoveries of modern science, from molecular biology to computational innovation, have provided compelling evidence that Darwin could only dream of seeing. From those discoveries have also come applications that Darwin might never have imagined, such as Darwinian medicine. Principles of evolution are being applied to a wide variety of scientific problems, from understanding senescence to strategies for conservation to explaining human

Introduction

behavior. There are few topics in science with so many exciting new facets, which reveal that despite all we have learned, there is much more to be discovered. Not that there is further need to substantiate evolution as fact; rather, there is much more to be done to trace the evolution of groups of species or features, particularly complex features at the cellular and molecular levels, and to refine our theory of evolution to account more fully for the astonishing diversity of life as we continue to discover it. The essays in this book show not only how far we have come but where the scientific horizons lie and how we might move toward those horizons. This book is organized into two parts. The first part contains long essays on the overarching themes in evolution. From the history of evolutionary thought to the controversies over education, from the fossil record and the origin of life to the process of adaptation, the long essays offer primers on the major features of evolution. Many of them offer close looks at particular areas like molecular evolution, genomic evolution, and Darwinian medicine. The second part contains a large number of shorter essays on more specific topics. These include essays on major groups of organisms with which most people are familiar, topics that are important facets of evolution, major figures in the discovery and shaping of evolutionary science, and the critical books that recount the history of discovery, development, and maturation of a discipline. This organization allows the reader to explore evolution according to his or her interests and background. The reader who wishes to be immersed in the science can focus on the major scientific themes, while the reader who is interested in the intellectual history and influence of the subject away from science can enter through a separate set of essays. A reader interested in very specific topics or historical figures can find the appropriate entries, along with essays on related topics. Our goal was to provide an exciting and compelling introduction to evolution along with a basic reference work that could point the way toward a deeper study of individual issues. The essays include bibliographies, which serve as guides to further and deeper reading. Although we hope that our fellow scholars enjoy these essays, we want this volume to inform, educate, and excite readers who are not professional scholars. We find evolution in all of the word’s meanings to be a provocative, interesting, and indeed awe-inspiring topic, and we want our readers to emerge with the same feeling. But beyond the excitement of studying evolution, it is important to understand and appreciate it. Evolution explains the challenge of antibiotic-resistant pathogens and the scourge of novel infectious diseases, it shows us what we can expect climate change and our own alterations of habitat to do to the natural world, and it may offer profound explanations of who we are and why we behave as we do. It also challenges many of our closely held beliefs about man’s, and woman’s, place in nature. The last of these issues is perhaps the foundation of why evolution has proven so controversial. Survey after survey shows that fewer than 50% of people in the United States accept that evolution is responsible for the diversity of life on earth. It is unclear how much of that opposition is based on a poor

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understanding of evolution and the evidence about it and how much is based on the challenges that it offers. Yet opposition to evolution by religious people, especially by Christians, is by no means inevitable; some of the most distinguished believers have accepted evolution without many qualms. We are convinced that the Christian—with the Jew and Muslim and other religious believers—should be at the head of the queue of those who welcome evolutionary ideas. Finding the idea, building and elaborating upon it, and looking at its influence and importance are, as the contributors to this volume show again and again, truly the best of proofs that we are made in the image of God, celebrating creation in all its wonderful manifestations. This book is a testament to one of mankind’s greatest discoveries, a discovery that offers unparalleled insight into what creation really is. We love evolution, and if we and our fellow contributors can inspire you even in a small way with our enthusiasm, then we shall be happy indeed.

The History of Evolutionary Thought Michael Ruse

The idea that all organisms (including humans) are generated by natural means from other forms has ancient roots. Aristotle tells us that Empedocles (fifth century b.c.e.) toyed with such thoughts. However, it was not until the eighteenth century and the Enlightenment that evolution (as we now call this idea of natural development) really started to gain a serious number of supporters. There are reasons both for the long delay and why the idea finally began to gain momentum.

The Early Days The Greeks had no great religious objection to evolution, but their world picture did not have a place for any kind of significant developmental processes. Specifically, the Greeks thought that they had irrefutable reasons to reject ongoing, incremental organic change. They—particularly the philosophers Plato and Aristotle—thought that the world (especially the world of organisms) showed order and intention and, as such, was not something that could simply have appeared through blind, ungoverned processes of law. It certainly was not something that could have grown from simple beginnings to the complexity of today. Plato used human fingernails as an example of order and design: “Sinew, skin and bone were interwoven at the ends of our fingers and toes. The mixture of these three was dried out, resulting in the formation of a single stuff, a piece of hard skin, the same in every case.” Plato then went on to put things in context. Now these were merely auxiliary causes in its formation—the preeminent cause of its production was the purpose that took account of future generations: our creators knew that one day women and the whole realm of wild beasts would one day come to be from men, and in particular they knew that many of these offspring would need the use of nails and claws or hoofs for many purposes. This is why they took care to 1

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include nails formed in a rudimentary way in their design for humankind, right at the start. This was their reason, then, and these the professed aims that guided them in making skin, hair and nails grow at the extremities of our limbs. (Timaeus, 76d–e, in Cooper 1997, 1277) In an incredibly influential discussion, Aristotle in De partibus animalium (1984) identified the factors at work here as “final causes.” These are causes that occur not just to produce or do something (the finger parts dry and make nails) but for the sake of some kind of purpose (the nails protect the finger ends). They show some kind of forethought or intention. For this reason, final causes cannot be reduced to blind, unguided law, as is demanded in evolution. The world, particularly the world of organisms, must in some sense have been designed rather than just produced under its own steam by natural processes. (Sedley 2008 is the definitive study.) The Jews, and following them the early Christians, had religious reasons for the rejection of evolution. It goes against the creation stories of the early chapters of Genesis, which portray a world created miraculously by God and then peopled by him through divine fiat over a short time span. But do not think that religion as such was then and always an absolute bar to evolutionism. The church fathers (the major Christian theologians of the early centuries) worked toward an understanding of the biblical text that would allow interpretation, particularly in the face of advances of science. Saint Augustine was eager not to let ancient creation accounts stand in the way of modern thought. He himself, believing that God stands outside time, speculated in a kind of protoevolutionary fashion that the Divine had formed seeds of life that then sprang into full being when they were placed here on earth. However, one should not read too much into any of this. Like the Greeks, the Jews and Christians were simply not looking in the direction of evolution and would have thought final causes an unanswerable objection to significant developmentalism. As is well known, these kinds of causes became a foundation of one of the major proofs of God’s existence, the Argument from Design, which moves from design here on earth to the existence of the divine artificer. Why, then, did evolution start its rise in the eighteenth century? The answer is simple. It was at this time that people started to challenge the Christian picture of world history—a providential picture of a world created by God, where humans are made in his image but have fallen and are able to achieve salvation only through his undeserved grace. Some began to argue that perhaps humans held their fates in their own hands and could progressively improve their own lots. It was this idea of progress— the belief that the world and its denizens are on a trajectory upward and that this upward rise is made possible by (and only by) the unaided efforts of the world’s human inhabitants—that gave rise to the idea of organic evolution (Ruse 1996). Enthusiasts for progress extended their thinking into nature and developed the idea of evolution—progressive change upward from the simple to the complex. They then read this idea back into

The History of Evolutionary Thought

human thought and social practice as confirmation of their beliefs about progress. The British physician and man of science Erasmus Darwin (grandfather of Charles) was a paradigm who hymned in verse life’s upward rise to humankind: Imperious man, who rules the bestial crowd, Of language, reason, and reflection proud, With brow erect who scorns this earthy sod, And styles himself the image of his God; Arose from rudiments of form and sense, An embryon point, or microscopic ens! (E. Darwin 1803, 1: Canto I, lines 309–314) This is all the end product of the progressive development of human intelligence, which causes and is reflected in humans’ scientific achievements: How loves and tastes, and sympathies commence From evanescent notices of sense; How from yielding touch and rolling eyes The piles immense of human science rise! (Canto III, lines 43–46) Similar ideas were to be found elsewhere, most notably in France. In his Philosophie zoologique (1809), the taxonomist Jean-Baptiste de Lamarck produced the first full-blown evolutionary theory—a picture of upward rise to our own species from the most primitive forms of life, which in turn had been produced from mud and slime through the actions of heat and electricity and other natural forces. Although the metaphysical idea of progress was the main factor behind the rise of evolutionary ideas, it is not true that there was no pertinent empirical evidence. Aristotle had noted that organisms of very different species seem to share common patterns or structures—what today are known as homologies— and the evolutionists were ready to interpret these as signs of common ancestries (Figure 1). Likewise, the successes of animal and plant breeders did not go unnoticed (Figure 2). But generally the evidence took a very secondary position. The fossil record, something that today many (if not most) people would invoke first as the proof of developmental origins, was less than helpful. As a systematic proof of progressive change, the gleanings from the rocks were meager indeed. In any case, counting against the empirical side was the fact that no one had any great understanding of what might have caused evolution. Most assumed some kind of vague, upwardly thrusting force or forces, but little more. Generally, everyone was committed to the folk belief that characteristics acquired in one generation could be transmitted immediately to the future generations—Lamarck was so enthused by this process that the inheritance of acquired characteristics has since become known as Lamarckism—but beyond this was silence.

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The ideology of progress was what counted, and it was for this reason that most people around 1800 would have regarded evolutionism less as a real science and more as a pretender, somewhat like animal magnetism (mesmerism) and the reading of character from skull shape (phrenology). Even judged by the standards of that time, evolution was what may fairly be called a pseudoscience. Obviously, Christian opponents of evolution disliked intensely the antiprovidential underpinnings of the doctrine. But evolution was not associated with total nonbelief, atheism, or even what later in the nineteenth century Thomas Henry Huxley was to call agnosticism. Most evolutionists were deists who believed in God as unmoved mover, a being who had set the world in motion and now let it unfurl without need of miraculous intervention. For the deist, indeed, evolution was proof of God’s power and intention rather than disproof. Everything was planned beforehand and went into effect through the laws of nature. In Erasmus Darwin’s words: “What a magnificent idea of the infinite power of the great architect! The cause of causes! parent of parents! ens entium!” (1801, 2: 247). There is a link here, especially in England, with the Industrial Revolution. People were harnessing the forces of nature—water, coal, and others—to produce goods through machines rather than by hand. The god of the deist was the ultimate

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divine industrialist as he harnessed the forces of nature to produce the goods of the world through law rather than miraculously or by hand. Critics of evolution, notably the great French comparative anatomist Georges Cuvier, made reference to empirical problems. Cuvier cited the mummified bodies of humans and animals brought back by Napoleon’s army from Egypt. Although they were very old, their forms were identical to contemporary forms and hence counted against ongoing organic change. But as with the positive case for evolution, in the negative case it was the ideology that really counted. Above all, for Cuvier, there was hatred of progress— hatred of a doctrine that had led humans to think that they could do more than they could do and had led ultimately to the terrors of the French Revolution, when opponents of the existing state had tried to change all that had proved true and safe for many generations. Combined with this, for Cuvier, as for every other opponent of evolution, was the still-unsolved problem of final cause. The Frenchman emphasized that this was something that could not be ignored; indeed, it was the most important distinguishing feature of life. The key to understanding the organism lay in the fact that it was not

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simply subject to the physical laws of nature but was organized. The parts were directed to the end of the functioning whole, and each individual feature played its role in the overall, purpose-directed scheme of things: Natural history nevertheless has a rational principle that is exclusive to it and which it employs with great advantage on many occasions; it is the conditions of existence or, popularly, final causes. As nothing may exist which does not include the conditions which made its existence possible, the different parts of each creature must be coordinated in such a way as to make possible the whole organism, not only in itself but in its relationship to those which surround it, and the analysis of these conditions often leads to general laws as well founded as those of calculation or experiment. (Cuvier 1817, 1: 6) Cuvier’s point simply was that the organism is far too integrated—organized and complex—to allow significant change in any direction. It is certainly too integrated to allow change from one species to another. Organisms at midpoint would be literally neither fish nor fowl and hence would simply be unable to exist or survive. Evolution was in some sense a theoretical impossibility, as well as empirically unfounded. Religion was involved too. Progress goes against the Christian doctrine of Providence. Nevertheless, although Cuvier thought that there was evidence of Noah’s flood, neither he nor other serious scientists wanted to make the case by simple reference to Genesis. Indeed, by the beginning of the nineteenth century, all were starting to realize that the earth’s history must be far older than the traditional 6,000 years that one can work out from the genealogies given in the Bible. It is not that the Bible is false, but rather that it needs interpretation. Some solved the problem by thinking of the six days of creation as six long periods of time; others solved it by supposing that there were long, unmentioned gaps between the biblical days. God’s creation therefore was a long, drawn-out process, but it was not evolutionary. The controversy was at an impasse, and not much had changed by the middle of the nineteenth century. On the one side were the evolutionists, committed to progress and ardent in their belief that organic development was the perfect complement to this ideology, with enthusiasm outstripping empirical knowledge. Confirming this pattern, in 1844 the Scottish publisher Robert Chambers wrote (anonymously) a highly popular work on evolution, Vestiges of the Natural History of Creation, in which he argued that everything was in a state of upward becoming and that what happened in the social world mirrored what happened in the biological world: The question whether the human race will ever advance far beyond its present position in intellect and morals, is one which has engaged much attention. Judging from the past, we cannot reasonably doubt that great advances are yet to be made; but if the principle of development be admitted, these are certain, whatever may be the space of time required for their realization. A progression resembling development may be traced

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in human nature, both in the individual and in large groups of men . . . Now all of this is in conformity with what we have seen of the progress of organic creation. It seems but the minute hand of a watch, of which the hour hand is the transition from species to species. Knowing what we do of that latter transition, the possibility of a decided and general retrogression of the highest species towards a meaner type is scarce admissible, but a forward movement seems anything but unlikely. (Chambers 1846, 400–402) On the other side were the opponents, committed to Providence, vocal about the significance of final cause, and accepting that Genesis must be modified but thinking that this could be readily done. David Brewster, general man of Scottish science and biographer of Newton, could see the dangers: “It would auger ill for the rising generation, if the mothers of England were infected with the errors of Phrenology: it would auger worse were they tainted with Materialism.” The problem, Brewster gloomily concluded with reflections that still find much support in many circles today, stemmed from the slackness of schools and universities: “Prophetic of infidel times, and indicating the unsoundness of our general education, ‘The Vestiges . . .’ has started into public favour with a fair chance of poisoning the fountains of science, and of sapping the foundations of religion” (Brewster 1844, 503). (Interestingly, this kind of attack seems to have confirmed Chambers in his views. Although, from the start, progress was the leitmotif of his book, he felt the need to make his point ever more explicit. The passage just quoted above is from the fifth edition of Vestiges and replaces a passage that gives more credit to the Creator. [Figure 3]) Of course, neither side was really satisfactory. Ideology is no substitute for real evidence, and final cause can be ignored but does not go away. Referring all to miracle may be socially and psychologically comforting, but it is not a good scientific solution. The time had come for a significant step forward.

Charles Darwin Charles Robert Darwin (1809–1882) was sent to Edinburgh University to train in the family tradition of medicine (Figure 4). After two years he dropped out, bored with the lectures and revolted by the operations. Yet already Darwin had started to mix with scientists, especially naturalists interested in the living world. One of his acquaintances was Robert Grant, an anatomist and an avowed evolutionist. So, quite apart from his grandfather’s work (the young Charles read Erasmus’s major treatise, Zoonomia), evolution was an idea to which Darwin was introduced at an early age. It seems, nevertheless, that the youthful Darwin accepted in a fairly literal form the whole of Christianity, including the early chapters of Genesis, and that this was a factor in his redirected choice of a career: to be an ordained minister in the established Church of England. To achieve this end one needed a degree

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