Evolution: The Triumph of an Idea

To Grace

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 muta…