Evolution: The Triumph of an Idea

By Carl Zimmer

“This brilliant book is a virtual Voyage of the Beagle! Carl Zimmer shows, with the benefit of a hundred and fifty years of hindsight, how right Darwin was.” —Steve Jones, author of Darwin’s Ghost

Darwin’s The Origin of Species was breathtaking—beautifully written, staunchly defended, defiantly radical. Yet it emerged long before modern genetics, molecular biology, and contemporary findings in paleontology.

In this remarkable book, a rich and up-to-date view of evolution is presented that explores the far-reaching implications of Darwin’s theory. At a time when controversies surrounding creationism and education are bursting into public consciousness, this book’s emphasis on the power, significance, and relevance of evolution will make it a catalyst for public debate. Evolution marks a turning point in the 150-year debate and will be an indispensable asset to any serious reader with an interest in the life sciences, a passion for truth in education, or a concern for the future of the planet.

“The evolution of life over four billion years is a grand narrative, full of plots, intrigues, surprises and deaths. Carl Zimmer tells the tale with zest and style.” —Matt Ridley, New York Times–bestselling author

“Proceeding from the flurry of preparations for Darwin’s famous voyage, Carl Zimmer leads us off on a journey of our own, tracking the development—and the implications—of one of the most powerful ideas in the biological sciences.” —Scientific American

“Science writer Zimmer does a superb job of providing a sweeping overview of most of the topics critical to understanding evolution, presenting his material from both a historical and a topical perspective.” —Publishers Weekly

“Popular science that will truly be popular.” —Booklist

• Language: English
• Publisher: Open Road Integrated Media
• Release date: Nov 23, 2010
• ISBN: 9780062038234

Carl Zimmer

Carl Zimmer is a popular science writer and columnist, who reports from the frontiers of biology, where scientists are expanding our understanding of life. Since 2013 he has been a columnist at the New York Times. He is a popular speaker at universities, medical schools, museums, and festivals, and he is also a frequent on radio programs such as Radiolab and This American Life. In 2016, Zimmer won the Stephen Jay Gould Prize, awarded annually by the Society for the Study of Evolution to recognize individuals whose sustained efforts have advanced public understanding of evolutionary science. Zimmer has written on subjects ranging from viruses to neuroscience to evolution, including She Has Her Mother's Laugh, focusing on heredity.

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PREFACE

In the history of life, five years is a blink. But for us humans, it’s a major chunk of chronology. When Evolution: The Triumph of an Idea was first published in 2001, life was very different than it is today. Our conversations today are full of words and names – blogs, al-Qaeda – that would have drawn blank stares five years ago. Five years have brought tremendous advances in science as well. We now know much more about the natural world, from stem cells to planets orbiting other stars. We also know much more about how life has evolved, thanks to tens of thousands of new scientific papers that have been published since 2001.

Some of the most exciting new research on evolution has built on the work I wrote about in this book, from the early evolution of life to the causes of mass extinctions, from the coevolution of males and females to the arms race between hosts and parasites. But to me, the most stunning body of work concerns the final part of my book: the evolution of humans. It’s striking because it strikes closest to home.

In 2001 it had become clear that the closest living relatives to humans are chimpanzees and bonobos. This realization emerged from studies carried out in the 1990s on fragments of DNA from humans and other animals. Comparing these fragments allowed scientists to draw an evolutionary tree and determine which branches are closest to our own. Those studies also allowed scientists to estimate when our ancestors diverged from those of other apes. Over millions of years, mutations accumulate in a species’s DNA at a roughly regular pace. As a result, scientists can read a molecular clock by comparing the mutations that have accumulated in species that share a common ancestor. In the case of humans and chimpanzees, scientists estimated that their common ancestor lived five to seven million years ago.

But if the molecular clock was right, it meant that paleoanthropologists had a lot of work to do. In 2001 the oldest known hominid – a species belonging to our own short twig of the evolutionary tree – was a species called Ardipithecus ramidus. The fossil, discovered in Ethiopia, was 4.4 million years old. If the molecular clock was right, it might not actually be all that old. Hominids might have already emerged 2.5 million years earlier.

When Evolution: The Triumph of an Idea was originally published, those 2.5 million years were a vast void. But in just five years, the void has been populated by three different species of hominids. In 2004, the same team that found Ardipithecus ramidus reported the discovery of an older species in the same region of Ethiopia. Ardipithecus kadabba, as they named it, lived 5.7 million years ago. Meanwhile in Kenya, another team of paleontologists found six-million-year-old fossils, which they dubbed Orrorin tugenensis. And in the desolate emptiness of the Sahara desert, a third team unearthed a wonderfully preserved skull of a third species, which they estimate lived some time between six and seven million years ago. They named it Sahelanthropus tchadensis.

These discoveries represent a spectacular case study in how evolutionary biologists create hypotheses and test them. Given the evidence from DNA five years ago, one would have predicted that paleoanthropologists should find hominid fossils dating back between five and seven million years. What’s more, one would have predicted those fossils would be found in Africa. For one thing, all the hominid fossils older than two million years came from there, as do the closest living relatives of humans, chimpanzees, and bonobos. Both preictions turned out to be correct.

Scientific discoveries don’t just confirm old hypotheses, however. They spur fresh debates of their own. Some scientists are arguing that these new hominid fossils are the first hints of an enormous diversity of early species. The hominid branch of the tree of life had a bushy base, these scientists maintain, and many of those shoots were cut short by extinction. Other researchers see things very differently. They argue that hominid evolution was much less extravagant, and they place Ardipithecus, Orrorin, and Sahelanthropus in a single genus. To them, the base of the hominid branch should look like a nearly straight line.

Another tantalizing question the new fossils pose is what the first hominids looked like. Early hominids probably stood about as tall as a chimpanzee and had a chimp-sized brain (about a third the size of ours). But they may have differed from chimpanzees and other living apes in one crucial respect: they may have walked upright. Orrorin’s femur is solidly buttressed, suggesting that it could have supported the weight of a hominid’s upper body. Sahelanthropus is known only from its skull, but it offers its own hints of bipedalism. The clues come from the hole where the spinal cord exits the base of the skull, known as the foramen magnum. In living apes, the position of the foramen magnum reflects how each species walks. Knuckle-walking chimpanzees walk with their backs tipped forward, and so their foramen magnum is located toward the back of their skull. Humans walk upright, with their back directly underneath their heads, and so the human foramen magnum sits at the base of the skull. Sahelanthropus’s foramen magnum is positioned like a human’s, suggesting it held itself upright. In other words, as far back in time as hominid fossils have been found, hominids seem to have been walking. The evolution of walking may thus have been the first major innovation that set hominids off from other apes.

While paleoanthropologists have been searching Africa for fossil clues about our evolution, other scientists have been searching our own DNA. Their search has accelerated dramatically thanks to the publication of the human genome in 2001. Instead of looking at a handful of short fragments of DNA, scientists can now analyze the entire three-billion-letter code. They can also compare the human genome to genomes of hundreds of other species, including rats, chickens, zebrafish, and chimpanzees. Since each of these species belongs to its own branch on the tree of life, scientists can find clues to our genetic history by comparing our genome to theirs.

This new research has made it clearer than ever that chimpanzees are the closest living relatives of humans. For long stretches, the two genomes are practically identical. In some cases, these stretches are genes that carry the codes for producing proteins. Even more remarkable are the broken genes that humans and chimpanzees share.

Some of the most striking examples of these broken genes come from our noses. All mammals carry several hundred genes for producing receptors on nerve endings in the nose. These genes evolved through accidental duplications. When a single gene became two, both genes at first encoded the same receptor. But then a mutation struck one of them, changing the receptor’s ability to catch odors. If the receptor did a worse job with the mutation, natural selection tended to delete the gene. But in some cases the mutation caused the receptor to catch a new odor molecule, expanding the smells the mammal could detect. Over millions of years, this process gave rise to a huge family of odor receptor genes.

In mice, dogs, and other mammals that depend heavily on their sense of smell, almost all the copies of these genes work properly. But in chimpanzees and humans, the majority of odor receptor genes are defective. They can’t make a receptor at all. Scientists generally agree that these mutant genes must have accumulated in our genomes because ancient apes were evolving to rely less on their noses and more on their eyes. As a result, chimpanzees and humans share a strange legacy of our common ancestry: broken genes.

From fossils to genes, the past five years have buried us under a fresh avalanche of evidence that we share a common ancestor with apes – that we are the product of evolution like all other organisms on Earth. But this news apparently has not reached D. Chris Buttars, a state senator in Utah. In 2005, Buttars wrote an opinion piece in USA Today in which he declared, The theory of evolution, which states that man evolved from some other species, has more holes in it than a crocheted bathtub.

Despite all the new fossils of hominids scientists have described in the past five years – not to mention thousands of other hominid fossils discovered in earlier decades – Buttars flatly stated that there has not been any scientific fossil evidence linking apes to man. He did not even bother to mention all the evidence of human evolution stored in DNA. Apparently that was not even worth rejecting.

Buttars came to national attention in 2005 when he launched a campaign to change the way public schools in Utah teach biology. He did not want teachers to present evolution as the only plausible scientific explanation for the diversity of life today. He wanted students to learn as well about something he called divine design.

Buttars hasn’t been very clear about what he means by this phrase. According to the Salt Lake Tribune, Buttars believes God is the creator, but His creations have evolved within their own species.

We get different types of dogs and different types of cats, but you have never seen a ‘dat,’ Buttars said to the newspaper.

Dats notwithstanding, it’s not too hard to figure out what Buttars has in mind. In Evolution: The Triumph of An Idea, I described how in the 1980s creationists were stung by a string of defeats in the courts. Judges recognized that creation science was actually religion and therefore had no place in classrooms. Some creationists set out to repackage many of their old arguments, leaving out explicit mentions of religion, and gave them a new name: intelligent design. In 1989, intelligent design advocates published a book, Of Pandas and People, which they promoted as a textbook for ninth-grade students. Organizations such as the Discovery Institute of Seattle began claiming that intelligent design was a viable alternative to evolution.

In 1999 conservative members of the state board of Kansas took the message seriously and decided to draft changes to the state education standards. The changes would have introduced doubt and uncertainty about evolution. In some cases it simply stripped it out of the standards altogether – along with discussions of the age of the Earth and the Big Bang. Their proposals drew international attention, which may have led to the defeat of several creationist-allied members in 2000.

The story did not end there, however. In the next round of elections the balance of the board shifted back, and the push moved forward again. In October 2005, the Kansas Board of Education finally passed their new education standards. The changes actually extended far beyond evolution, to redefine science itself. Previously, the Kansas standards held that science is the human activity of seeking natural explanations for what we observe in the world around us – a definition that’s supported by every major organization of scientists. But the new standards no longer limit science to the natural. The school board redefined it as a systematic method of continuing investigation that uses observation, hypothesis testing, measurement, experimentation, logical argument, and theory building to lead to more adequate explanations of natural phenomena. Supernatural explanations of the world have a place in science – at least in Kansas.

Over the past five years other states have seen renewed attempts to stop or at least undermine the teaching of evolution in public schools. And in October 2004, a rural school district in Dover, Pennsylvania, went one step further and began to promote intelligent design. The local school board added a new statement to their science curriculum: Students will be made aware of gaps/problems in Darwin’s theory and of other theories of evolution including, but not limited to, intelligent design.

The board of education also demanded the teachers read a second statement aloud to all Dover biology classes. The teachers were required to say that evolution was a theory, not a fact – confusing the nature of both facts and theories. Intelligent design is an explanation of the origin of life that differs from Darwin’s view, the statement continued. "The reference book Of Pandas and People is available for students to see if they would like to explore this view in an effort to gain an understanding of what intelligent design actually involves. As is true with any theory, students are encouraged to keep an open mind."

The Dover science teachers were appalled and refused to read the statement. Administrators had to step in. When students asked what sort of designer was behind intelligent design, the administrators told them to ask their parents.

Two months later, eleven parents in the Dover area school district filed a lawsuit, arguing that this statement violated the First Amendment because it represented the impermissible establishment of religion. The board of education countered that they had nothing of the sort in mind. All the Dover school board did was allow students to get a glimpse of a controversy that is really boiling over in the scientific community, declared Richard Thompson, the chief counsel for the school district.

A few inconvenient facts emerged over the next few weeks, however. Thompson is the president of the Thomas More Law Center in Michigan, which describes itself as dedicated to the defense and promotion of the religious freedom of Christians, time-honored family values, and the sanctity of human life. As early as 2000, lawyers from the Thomas More Law Center had visited school boards around the country to find one that would teach Of Pandas and People in their science classes. As the New York Times reported in November 2005, the lawyers promised that if a board was sued, they would defend it at no cost. In West Virginia, Minnesota, and Michigan, the lawyers were turned down. But in Dover they had better luck. Witnesses at the trial testified how Dover school board members began talking about how they would introduce intelligent design into science classes to bring prayer and faith back into the school.

The trial put to rest any doubts about the origins of intelligent design, thanks to the testimony of Barbara Forrest, a philosopher of science at Southeastern Louisiana University. Forrest compared a draft of Of Pandas and People to the final version. She showed how the authors had used terms like creationism or creation science one hundred fifty times in the draft, and then transformed them all into intelligent design.

The trial proved to be a devastating blow for creationists. Shortly after it ended – and before Judge John E. Jones III had issued his decision – the people of Dover voted out the intelligent design-friendly members of the school board. They were replaced by candidates who had promised to take creationism out of the schools. Seven weeks later, on December 20, 2005, Judge Jones delivered a blistering defeat to the entire intelligent design movement.

We conclude that the religious nature of I.D. would be readily apparent to an objective observer, adult or child, he wrote. On all levels, he ruled, intelligent design failed as a science.

Richard Thompson may have claimed that students should be told about a controversy that is really boiling over in the scientific community, but in fact no such scientific controversy exists. In an actual scientific controversy, both sides publish a string of papers in peer-reviewed journals presenting new evidence from experiments and observations. In an actual scientific controversy, scientists go to major conferences and present their results to their peers, who can challenge their data face-to-face. There’s no shortage of scientific controversies that meet this standard, from debates about the architecture of thought to battles over the causes of cancer.

Intelligent design, on the other hand, comes nowhere close. You will search long and hard through scientific journals to find a paper documenting a new and important discovery about how nature works made possible by intelligent design. In 2004, the Discovery Institute triumphantly announced that one of its fellows, Stephen Meyer, had published the first paper in a peer-reviewed journal about intelligent design. In a review that appeared in the Proceedings of the Biological Society of Washington, Meyer argued that the Cambrian Explosion (a period when many major groups of animals first appeared) could not have been the result of evolution. But this glory was short-lived. The council of the Biological Society of Washington issued a statement that the former editor who had handled Meyer’s paper had violated the journal’s rules for peer review. They stated that "there is no credible scientific evidence supporting I.D. as a testable hypothesis to explain the origin of organic diversity. Accordingly, the Meyer paper does not meet the scientific standards of the Proceedings."

As I explained earlier, human origins is one of the most exciting areas of research in evolution. To understand why scientists find intelligent design so useless, just compare what it has to say about human origins. Of Pandas and People explains that design adherents consider hominids as little more than apes, and point instead to the abrupt appearance of the culture and patterns of behavior which distinguish man from the apes. It does not explain what is intelligent about an intelligent designer that created at least twenty lineages of human-like apes, all of which became extinct. It does not explain why the older lineages are more like apes, with smaller brains and longer arms. It does not explain why younger lineages gradually acquired more traits in common with humans, such as taller bodies, bigger brains, and increasingly sophisticated tools. It does not add anything to our understanding of the vast genetic similarities of chimpanzees and humans, or explain how the differences arose. It does not offer any hypothesis about when Homo sapiens first emerged, or where, or how.

To be fair, the passage in the previous paragraph comes from the most recent edition of Of Pandas and People, which came out in 1993. With all of the findings that have emerged since then, have intelligent design adherents found something more concrete to say about human origins? Hardly. In a 2004 essay on the subject, William Dembski, a mathematician and theologian at Southern Baptist Theological Seminary, kept up the tradition of haziness. There may be good reasons for thinking that humans are redesigned monkeys, he wrote. Even so, a design-theoretic perspective does not require that novel designs must invariably result from modifying existing designs. Hence, there may also be good reasons for thinking that a redesign process didn’t produce humans and that, instead, humans were built [sic] from the ground up. Design theorists have yet to reach a consensus on these matters.

There’s a big difference between being designed from scratch or redesigned from monkeys. One wonders how long we’ll have to wait for them to settle on one or the other.

The contrast between intelligent design and evolutionary biology could not be more clear when it comes to human origins. While intelligent design advocates have wandered in this haze, evolutionary biologists have done more than find new fossils and evidence from DNA linking us to other apes. Since 2001 they’ve made astonishing progress toward understanding the genetic changes that helped to make us uniquely human.

This advance was made possible by some new statistical methods for detecting the fingerprint of natural selection. One common kind of mutation changes a single nucleotide – a letter in the genetic code. This sort of mutation can have one of two effects. Some mutations change the way a cell translates the code of a gene into a protein. Other mutations don’t. Scientists call these mutations non-silent and silent substitutions, respectively.

Non-silent substitutions give rise to new sorts of proteins. Those proteins may be so deformed that they cause devastating diseases. Or they may turn out to help an individual survive. Natural selection may favor beneficial non-silent substitutions, and they may spread until they are carried by every individual in a species. Silent substitutions, on the other hand, have no effect on the structure of proteins. Natural selection cannot drive them into extinction or help them spread. Their fate is a matter of pure chance.

One way to detect natural selection’s fingerprint is to tally up the silent and non-silent substitutions in a human gene. When a gene undergoes strong natural selection, it builds up a number of mutations that change the shape of the protein they make. These non-silent mutations make up a much higher proportion of the differences in the gene, compared to silent ones.

Since 2001, methods like this one have allowed scientists to discover thousands of genes that underwent strong natural selection over the past six million years of hominid evolution. Scientists can even measure the strength of natural selection that has acted on these genes. You might think that the genes at the top of the list would be involved in the things that seem to set us apart most obviously from other animals, such as our oversized brains or our upright posture. But that’s not the case. Instead, sex and disease have had the most intense effects on our DNA.

As I explain in chapters 9 and 10 of Evolution: The Triumph of An Idea, these two factors are huge evolutionary forces throughout the natural world. So it should not be a big surprise that we humans obey the rule. Viruses, bacteria, and other pathogens have been adapting to our bodies for millions of years. The evolution of new defenses against diseases literally meant the difference between life and death for our ancestors. And as soon as our ancestors evolved new defenses, their parasites were evolving new ways to evade them. Locked in this perpetual arms race, disease-related genes have been drastically altered over the past six million years of hominid evolution.

Intense natural selection has also been at work on human genes involved in building eggs and sperm. Studies on animals have revealed how sexual selection can turn into an arms race. Male fruit flies, for example, appear to inject chemicals when they mate that make females less receptive to other males. The females in turn evolve ways to neutralize the chemicals, which spurs the males to evolve even more powerful compounds. Such an unconscious battle between the sexes may have been the cause of some of the intense selection acting on human genes.

Sperm may also be competing with one another. A gene that allows sperm to grow rapidly and ignore the signals that would ordinarily make them stop dividing will produce more sperm carrying that gene. Scientists suspect that it’s no coincidence that some of these fast-evolving genes also become active in cancer cells. What’s good for a fast-dividing sperm cell may also be good for a fast-dividing tumor.

More subtle – but no less important – has been natural selection’s effects on the human brain. Six million years ago, the brains of our ancestors were a third the size of our own. They probably had a mind like other apes. They communicated in grunts and gestures. They could not use fire or make sophisticated stone tools. They could not get a deep understanding of what other individuals were thinking or feeling. In 2001, scientists had yet to identify the fingerprint of natural selection on a single gene active in the human brain. As I write this, they’ve found hundreds.

It is going to take a very long time to assemble these new pieces of research together into a clear understanding of how the human brain diverged from other ape brains. Scientists just don’t know much yet about how genes build brains. But clues are already emerging. Some of the most tantalizing clues come from a gene called ASPM. It first came to the attention of scientists because of the devastating effects that occur when the gene mutates. Children with mutant forms of the gene generally grow very small – or microcephalic – brains. The outer layer of the brain, called the cerebral cortex, is almost entirely missing from microcephalic brains. Clearly, ASPM plays some sort of crucial role in growing brains. And it turns out to have undergone strong natural selection since our ancestors split from other apes. It’s possible that ASPM is part of the answer to how our brains got so big. The evolution of ASPM may have been particularly crucial to the expansion of the cerebral cortex, in which we carry out our most abstract thoughts.

Size is not everything, however. Natural selection has also shaped some human genes that appear to control particular kinds of thought. Take language. As I wrote in 2001, our capacity to learn a language shows some signs of being a hard-wired instinct. That suggested that genes shaped language, and yet at the time scientists didn’t know of a single language-linked gene. Now they have one. It was discovered in a family in London who suffered a hereditary difficulty with both speech and grammar. In 2002 British scientists announced that the family members who had language problems all carried a mutant form of a gene they called FOXP2. Brain scans later revealed that people who carry mutant forms of FOXP2 have less activity in a language-related region of their brain called Broca’s area.

Scientists then compared human FOXP2 to the version carried by other mammals. Obviously, FOXP2 does not produce a capacity for language in other species. But in a 2005 experiment with mice, scientists showed that it influences animal communication. Mouse pups with only one working copy made far fewer cries to their mother. Those without any working copies made no cries at all.

A comparison of silent and non-silent substitutions revealed that FOXP2 has undergone intense natural selection in humans. Scientists were even able to estimate when that natural selection took place: less than two hundred thousand years ago. That just so happens to be around the time our species first emerged. These results hint that full-blown language was a late-arriving skill and has only evolved relatively recently in the hominid lineage.

But natural selection did not stop there. Several new studies have identified genes that have evolved over just the past fifty thousand years. One of these studies, published in March 2006 by scientists at the University of Chicago, proved particularly exciting. They looked for signs of natural selection in just the past few thousand years. The scientists based their search on the way genes get split apart from one generation to the next. Each person carries two pairs of each chromosome. As eggs and sperm form, each chromosome may swap a chunk of genes with its partner. One of the chunks inherited by a child may carry a gene that offers a major reproductive advantage. Over the course of generations, that gene will spread rapidly through the population – along with the surrounding genes in its chunk of chromosome.

The scientists looked for versions of genes that consistently turned up lodged in the same chunk of surrounding DNA. They discovered seven hundred regions of the human genome that contained these fast-spreading genes. The genes influence traits ranging from skin color to digestion. Taste and smell genes have evolved rapidly as well. Many of these genes, which are estimated to have evolved over the past six thousand to ten thousand years, may have been favored as humans began to shift to eating domesticated plants and animals. A few of the still-evolving genes are active in the brain. Could the rise of civilization and rich human culture have driven the evolution of these genes? Check back in five years – at the rate things are going, scientists may have some answers.

These past five years have seen great advances in evolutionary biology, but they’ve also seen the loss of some of its most important thinkers. In 2004, the English biologist John Maynard Smith died at age eighty-four. Maynard Smith realized that he could make sense of evolution by borrowing concepts from mathematics and economics. One of his most fruitful imports was game theory, the study of how different strategies lead players to victory or defeat. Maynard Smith made organisms into players, and their behaviors into strategies. It then became possible to analyze how different strategies would thrive thanks to natural selection or be driven to extinction.

Scientists have found that in many cases several different behaviors can coexist. A male elephant seal may try to gain reproductive success, for example, either by challenging a big male or skulking at the edge of the big male’s harm, mating secretly with a few females. Scientists have found lots of these so-called evolutionarily stable strategies. Evolutionary stable strategies may have a lot to tell us about human behavior as well. Genes have a role in personality, intelligence, and behavior, and there’s obviously a lot of variation in all these factors. It’s possible that these genes have, over millions of years, reached an evolutionarily stable state with one another. And these games may also be a model for how something as peculiar as cooperation evolved in our own species.

In Evolution: The Triumph of an Idea, I describe how a young ornithologist named Ernst Mayr explored Pacific islands in the 1920s and in the process laid the groundwork for the modern understanding of species and how they are born. Mayr died in 2005 at the age of one hundred. He spent the last few decades of his life watching his ideas inspire generations of new biologists, but he enjoyed watching them pushing beyond his own ideas. The new research has one most encouraging message for the active evolutionist, he wrote in an essay shortly before his death. It is that evolutionary biology is an endless frontier and there is still plenty to be discovered. I only regret that I won’t be present to enjoy these future developments.

Sadly, Stephen Jay Gould did not enjoy the longevity of Maynard Smith or Mayr, dying at age sixty in 2002. When his introduction graced my book the year before his death, I had no idea that he would leave us so soon. I was honored then, and I’m even more honored now that now that Evolution: The Triumph of an Idea remains associated with him. Gould achieved greatness both as a scientist and as a writer. He pressed biologists to think about evolution in new ways, whether they were looking at the fossil record or at embryos. And few writers of the past one hundred fifty years could compete with him in bringing the glory of evolutionary biology to the public at large. It is to these three great scientists – and to future evolutionary biologists – that I rededicate this book.

INTRODUCTION

A famous legend (perhaps even true) from the early days of Darwinism provides a good organizing theme for understanding the centrality and importance of evolution both in science and for human life in general. A prominent English lady, the wife of a lord or a bishop (yes, they may marry in the Church of England), exclaimed to her husband when she grasped the scary novelty of evolution: Oh my dear, let us hope that what Mr. Darwin says is not true. But if it is true, let us hope that it will not become generally known!

Scientists invoke this familiar story to laugh at the recalcitrant stodginess of old belief and breeding – especially the risible image of the upper classes keeping a revolutionary fact of nature in the Pandora’s box of their own private learning. Thus, the lady of this anecdote enters history as a quintessential patrician fool. Let me suggest, however, if only to organize the outline of this introduction, that we reconceptualize her as a prophet. For what Mr. Darwin said is clearly true, and it has also not become generally known (or, at least in the United States, albeit uniquely in the Western world, even generally acknowledged). We need to understand the reasons for this exceedingly curious situation.

EVOLUTION AS TRUE

The task of science is twofold: to determine, as best we can, the empirical character of the natural world; and to ascertain why our world operates as it does, rather than in some other conceivable, but unrealized, way – in other words, to specify facts and validate theories. Science, as we professionals always point out, cannot establish absolute truth; thus, our conclusions must always remain tentative. But this healthy skepticism need not be extended to the point of nihilism, and we may surely state that some facts have been ascertained with sufficient confidence that we may designate them as true in any legitimate, vernacular meaning of the word. (Perhaps I cannot be absolutely certain that the earth is round rather than flat, but the roughly spherical shape of our planet has been sufficiently well verified that I need not grant the flat earth society a platform of equal time, or even any time at all, in my science classroom.) Evolution, the basic organizing concept of all the biological sciences, has been validated to an equally high degree, and may therefore be designated as true or factual.

In discussing the truth of evolution, we should make a distinction, as Darwin explicitly did, between the simple fact of evolution – defined as the genealogical connection among all earthly organisms, based on their descent from a common ancestor, and the history of any lineage as a process of descent with modification – and theories (like Darwinian natural selection) that have been proposed to explain the causes of evolutionary change.

Three broad categories of evidence best express the factuality of evolution. First, direct evidence of human observation, guided by an explicit theory since Darwin’s publication in 1859, but buttressed by data on longer periods of breeding for improved crop plants and domesticated animals, provides hundreds of exquisitely documented examples of the small-scale changes that our theories anticipate over such geologically brief periods of time. These include the familiar cases of changing pigmentation in moth wings as an adaptive response to substrates darkened by industrial soot, altered beak shapes in Galápagos species of Darwin’s finches as climates and food resources change, and the development of antibiotic resistance by numerous strains of bacteria. No one – not even among creationists – has denied this overwhelming weight of evidence in the small, but we also need proof that such minor changes can accumulate through geological time into the substantial novelties that build the history of life’s expanding diversity.

We must therefore turn to a second category of direct evidence from transitional stages of major alterations found in the fossil record. A common claim, stated often enough to merit the label of urban legend, holds that no such transitional forms exist and that paleontologists, dogmatically committed to evolution, have either withheld this information from the public or have claimed that the fossil record is too imperfect to preserve the intermediates that must once have existed. In fact, although the fossil record is indeed spotty (a problem with nearly all historical documents, after all), the assiduous work of paleontologists has revealed numerous elegant examples of sequences of intermediary forms (not just single in between specimens) joining ancestors in proper temporal order to very different descendants – as in the evolution of whales from terrestrial mammalian ancestors through several intermediate stages, including Ambulocetus (literally, the walking whale), the evolution of birds from small running dinosaurs, of mammals from reptilian ancestors, and a threefold increase in brain size during the last 4 million years of human evolution.

Finally, a third major category of more indirect, but ubiquitous, evidence allows us to draw a clear inference of change from a different historical past by observing the quirks and imperfections, present in all modern organisms, that make no sense except as holdovers from an otherwise altered (that is, evolved) ancestral state – that is, except as products of evolution. This principle governs the analysis of all kinds of historical series, not just biological evolution. We can infer that an abandoned railroad line once linked a group of well-spaced and linearly ordered towns (that would have no other reason for such an alignment). We can also identify social change from a more rural past by the etymological evidence of many words now used in very different meanings in our modern industrial world (broadcast as a mode of planting by throwing out seeds by the handful; or pecuniary advantages, literally measured in cattle, from the Latin pecus, or cow). In the same manner, all organisms carry useless remnants of formerly functional structures that make no sense except as holdovers from different ancestral states – the tiny vestiges of leg bones, invisibly embedded in the skin of certain whales, or the nonfunctional nubs of pelvic bones in some snakes, surviving as vestiges of ancestors with legs.

EVOLUTION AS NOT GENERALLY KNOWN OR ACKNOWLEDGED

No scientific revolution can match Darwin’s discovery in degree of upset to our previous comforts and certainties. In the only conceivable challenge, Copernicus and Galileo moved our cosmic location from the center of the universe to a small and peripheral body circling a central sun. But this cosmic reorganization only fractured our concept of real estate; Darwinian evolution, on the other (and deeper) hand, revolutionized our view of our own meaning and essence (insofar as science can address such questions at all): Who are we? How did we get here? How are we related to other creatures, and in what manner?

Evolution substituted a naturalistic explanation of cold comfort for our former conviction that a benevolent deity fashioned us directly in his own image, to have dominion over the entire earth and all other creatures – and that all but the first five days of earthly history have been graced by our ruling presence. In evolutionary terms, however, humans represent but one tiny twig on an enormous and luxuriantly branching tree of life, with all twigs interconnected by descent, and the entire tree growing (so far as science can tell) by a natural and lawlike process. Moreover, the unique and minuscule twig of Homo sapiens emerged in a geological yesterday, and has flourished for only an eyeblink of cosmic immensity (about 100,000 years for our species and only 6–8 million years for our entire lineage since our branchlet split from the node of our closest living relative, the chimpanzee. By contrast, the oldest bacterial fossils on Earth arose 3,600 million years ago).

We might mitigate the challenge of these basic facts if we could espouse a theory of evolutionary change that remained congenial to our old comforts about human necessity and inherent superiority – as in the common misconception that evolution implies predictable and progressive pathways of change, and that human origins (however belated) may therefore be viewed as both inevitable and culminating. But our best understanding of how evolution operates – that is, our preferred theory for the mechanism of evolutionary change (as contrasted with the simple factuality of evolution, discussed in the last section) – does not even grant us this ideological comfort. For our favored and well-attested theory, Darwinian natural selection, offers no solace or support for these traditional hopes about human necessity or cosmic importance.

Hence, when I ask myself why evolution, although true by our strongest scientific confidence, has not become generally known or acknowledged in the United States – that is, nearly 150 years after Darwin’s publication, and in the most technologically advanced nation on earth – I can only conclude that our misunderstanding of the broader implications of Darwinism, in particular our misreading of his doctrine as doleful, or as subversive to our spiritual hopes and needs, rather than as ethically neutral and intellectually exhilarating, has impeded public acceptance of our best documented biological generality. Hence, I treat the meaning of Darwinism, or the implications of evolutionary theory (rather than the mere understanding of evolution’s factuality), as my major theme in trying to explicate why such an evident fact has not become generally known.

Public difficulty in grasping the Darwinian theory of natural selection cannot be attributed to any conceptual complexity – for no great theory ever boasted such a simple structure of three undeniable facts and an almost syllogistic inference therefrom. (In a famous, and true, anecdote, Thomas Henry Huxley, after reading Origin of Species, could only say of natural selection: How extremely stupid not to have thought of that myself.) First, that all organisms produce more offspring than can possibly survive; second, that all organisms within a species vary, one from the other; third, that at least some of this variation is inherited by offspring. From these three facts, we infer the principle of natural selection: since only some offspring can survive, on average the survivors will be those variants that, by good fortune, are better adapted to changing local environments. Since these offspring will inherit the favorable variations of their parents, organisms of the next generation will, on average, become better adapted to local conditions.

The difficulties lie not in this simple mechanism but in the far-reaching and radical philosophical consequences – as Darwin himself well understood – of postulating a causal theory stripped of such conventional comforts as a guarantee of progress, a principle of natural harmony, or any notion of an inherent goal or purpose. Darwin’s mechanism can only generate local adaptation to environments that change in a directionless way through time, thus imparting no goal or progressive vector to life’s history. (In Darwin’s system, an internal parasite, so anatomically degenerate that it has become little more than a bag of ingestive and reproductive tissue within the body of its host, may be just as well adapted, and may enjoy just as much prospect of future success, as the most complex mammalian carnivore, wily, fleet, and adept, living free on the savannas.) Moreover, although organisms may be well designed, and ecosystems harmonious, these broader features of life arise only as consequences of the unconscious struggles of individual organisms for personal reproductive success, and not as direct results of any natural principle operating overtly for such higher goods.

Darwin’s mechanism may sound bleak at first, but a deeper view should lead us to embrace natural selection (and a variety of other legitimate evolutionary mechanisms from punctuated equilibrium to catastrophic mass extinction) for two basic reasons. First, truthful science is liberating in the practical sense that knowledge of nature’s actual mechanisms gives us the potential power to cure and to heal when factual matters cause us harm. When, for example, we know how bacteria and other disease-causing organisms evolve, we can understand, and find means to combat, the development of antibiotic resistance, or the unusual mutability of the AIDS virus. Also, when we recognize how recently our so-called human races diverged from a common African ancestry, and when we measure the minuscule genetic differences that separate our groups as a result, then we can know why racism, the scourge of human relations for so many centuries, can claim no factual foundation in any real differences among human groups.

Second, and more generally, by taking the Darwinian cold bath, and staring a factual reality in the face, we can finally abandon the cardinal false hope of the ages – that factual nature can specify the meaning of our life by validating our inherent superiority, or by proving that evolution exists to generate us as the summit of life’s purpose. In principle, the factual state of the universe, whatever it may be, cannot teach us how we should live or what our lives should mean – for these ethical questions of value and meaning belong to such different realms of human life as religion, philosophy, and humanistic study. Nature’s facts can help us to realize a goal once we have made our ethical decisions on other grounds – as the trivial genetic differences among human groups, for example, can help us to understand human unity once we have agreed on the unalienable rights of all people to life, liberty, and the pursuit of happiness. Facts are just facts, in all their fascination, their pristine beauty, and, sometimes, their unfortunate necessity (bodily decline and mortality, as the obvious example), and ethical rectitude, or spiritual meaning, reside within other domains of human inquiry.

When we thought that factual nature matched our hopes and comforts – all things bright and beautiful, and all things made for our superior selves – then we easily fell into the trap of equating actuality with righteousness. But when we sense the different fascination of evolution’s naturalistic ways, and of life’s astonishingly rich diversity and history of change, with Homo sapiens as but one contingent twig on the most luxuriant of all trees, then we finally become free to detach our search for ethical truth and spiritual meaning from our scientific quest to understand the facts and mechanisms of nature. Darwin, in defining the factual grandeur of this view of life (to quote the last line of Origin of Species), liberated us from asking too much of nature, thus leaving us free to comprehend whatever fearful fascination may reside out there, in full confidence that our quest for decency and meaning cannot be threatened thereby, and can emerge only from our own moral consciousness.

Stephen Jay Gould

Museum of Comparative Zoology

Harvard University

PART ONE

Slow Victory:

Darwin and the Rise of Darwinism

ONE

DARWIN AND THE BEAGLE

In late October 1831 a 90-foot coaster named HMS Beagle lay docked at Plymouth, England. Its crew scrambled about it like termites in a nest. They were packing the ship as tightly as they could for a voyage around the world, one that would last five years. They rolled barrels of flour and rum into the hold and crammed the deck with wooden boxes that contained experimental clocks resting on beds of sawdust. The Beagle’s voyage was a scientific one: its crew