opposable thumbs placenta hair amniotic egg digits jaws figure 2. A phylogeny (evolutionary tree) of vertebrates, showing how evolution produces a heirarchical grouping of features, and thus of species containing these features. The dots indicate where on the tree each trait arose.

Actually, the nested arrangement of life was recognized long before Darwin. Starting with the Swedish botanist Carl Linnaeus in 1635, biologists began classifying animals and plants, discovering that they consistently fell into what was called a "natural" classification. Strikingly, different biologists came up with nearly identical groupings. This means that these groupings are not subjective artifacts of a human need to classify, but that they tell us something real and fundamental about nature. But nobody knew what that something was until Darwin came along, and showed that the nested arrangement of life is precisely what evolution predicts. Creatures with recent common ancestors share many traits, while those whose common ancestors lay in the distant past are more dissimilar. The "natural" classification is itself strong evidence for evolution.

Why? Because we don't see such a nested arrangement if we're trying to arrange objects that haven't arisen by an evolutionary process of splitting and descent. Take cardboard books of matches, which I used to collect. They don't fall into a natural classification in the same way as living species. You could, for example, sort matchbooks hierarchically beginning with size, and then by country within size, color within country, and so on. Or you could start with the type of product advertised, sorting thereafter by color and then by date. There are many ways to order them, and everyone will do it differently. There is no sorting system that all collectors agree on. This is because rather than evolving, so that each matchbook gives rise to another that is only slightly different, each design was created from scratch by human whim.

Matchbooks resemble the kinds of creatures expected under a creationist explanation of life. In such a case, organisms would not have common ancestry, but would simply result from an instantaneous creation of forms designed de novo to fit their environments. Under this scenario, we wouldn't expect to see species falling into a nested hierarchy of forms that is recognized by all biologists.2

Until about thirty years ago, biologists used visible features like anatomy and mode of reproduction to reconstruct the ancestry of living species. This was based on the reasonable assumption that organisms with similar features also have similar genes, and thus are more closely related. But now we have a powerful new and independent way to establish ancestry: we can look directly at the genes themselves. By sequencing the DNA of various species and measuring how similar these sequences are, we can reconstruct their evolutionary relationships. This is done by making the entirely reasonable assumption that species having more similar DNA are more closely related—that is, their common ancestors lived more recently. These molecular methods have not produced much change in the pre-DNA-era trees of life: both the visible traits of organisms and their DNA sequences usually give the same information about evolutionary relationships.

The idea of common ancestry leads naturally to powerful and testable predictions about evolution. If we see that birds and reptiles group together based on their features and DNA sequences, we can predict that we should find common ancestors of birds and reptiles in the fossil record. Such predictions have been fulfilled, giving some of the strongest evidence for evolution. We'll meet some of these ancestors in the next chapter.

The fifth part of evolutionary theory is what Darwin clearly saw as his greatest intellectual achievement: the idea of natural selection. This idea was not in fact unique to Darwin—his contemporary, the naturalist Alfred Russel Wallace, came up with it at about the same time, leading to one of the most famous simultaneous discoveries in the history of science. Darwin, however, gets the lion's share of credit because in The Origin he worked out the idea of selection in great detail, gave evidence for it, and explored its many consequences.

But natural selection was also the part of evolutionary theory considered most revolutionary in Darwin's time, and it is still unsettling to many. Selection is both revolutionary and disturbing for the same reason: it explains apparent design in nature by a purely materialistic process that doesn't require creation or guidance by supernatural forces.

The idea of natural selection is not hard to grasp. If individuals within a species differ genetically from one another, and some of those differences affect an individual's ability to survive and reproduce in its environment, then in the next generation the "good" genes that lead to higher survival and reproduction will have relatively more copies than the "not so good" genes. Over time, the population will gradually become more and more suited to its environment as helpful mutations arise and spread through the population, while deleterious ones are weeded out. Ultimately, this process produces organisms that are well adapted to their habitats and way of life.

Here's a simple example. The wooly mammoth inhabited the northern parts of Eurasia and North America, and was adapted to the cold by bearing a thick coat of hair (entire frozen specimens have been found buried in the tundra).3 It probably descended from mammoth ancestors that had little hair—like modern elephants. Mutations in the ancestral species led to some individual mammoths—like some modern humans—to be hairier than others. When the climate became cold, or the species spread into more northerly regions, the hirsute individuals were better able to tolerate their frigid surroundings and left more offspring than their balder counterparts. This enriched the population in genes for hairiness. In the next generation, the average mammoth would be a bit hairier than before. Let this process continue over some thousands of generations, and your smooth mammoth gets replaced by a shaggy one. And let many different features affect your resistance to cold (for example, body size, amount of fat, and so on), and those features will change concurrently.

The process is remarkably simple. It requires only that individuals of a species vary genetically in their ability to survive and reproduce in their environment. Given this, natural selection—and evolution—are inevitable. As we shall see, this requirement is met in every species that has ever been examined. And since many traits can affect an individual's adaptation to its environment (its "fitness"), natural selection can, over eons, sculpt an animal or plant into something that looks designed.

It's important to realize, though, that there's a real difference in what you expect to see if organisms were consciously designed rather than if they evolved by natural selection. Natural selection is not a master engineer, but a tinkerer. It doesn't produce the absolute perfection achievable by a designer starting from scratch, but merely the best it can do with what it has to work with. Mutations for a perfect design may not arise because they are simply too rare. The African rhinoceros, with its two tandemly placed horns, may be better adapted at defending itself and sparring with its brethren than is the Indian rhino, graced with but a single horn (actually, these are not true horns, but compacted hairs). But a mutation producing two horns may simply not have arisen among Indian rhinos. Still, one horn is better than no horns. The Indian rhino is better off than its hornless ancestor, but accidents of genetic history may have led to a less than perfect "design." And, of course, every instance of a plant or animal that is parasitized or diseased represents a failure to adapt. Likewise for all cases of extinction, which represent well over 99 percent of species that ever lived. (This, by the way, poses an enormous problem for theories of intelligent design. It doesn't seem so intelligent to design millions of species that are destined to go extinct, and then replace them with other, similar species, most of which will also vanish. ID supporters have never addressed this difficulty.)

Natural selection must also work with the design of an organism as a whole, which is a compromise among different adaptations. Female sea turtles dig their nests on the beach with their flippers—a painful, slow, and clumsy process that exposes their eggs to predators. Having more shovel-like flippers would help them do a better and faster job, but then they couldn't swim as well. A conscientious designer might have given the turtles an extra pair of limbs, with retractable shovel-like appendages, but turtles, like all reptiles, are stuck with a developmental plan that limits their limbs to four.

Organisms aren't just at the mercy of the luck of the mutational draw, but are also constrained by their development and evolutionary history. Mutations are changes in traits that already exist; they almost never create brand-new features. This means that evolution must build a new species starting with the design of its ancestors. Evolution is like an architect who cannot design a building from scratch, but must build every new structure by adapting a preexisting building, keeping the structure habitable all the while. This leads to some compromises. We men, for example, would be better off if our testes formed directly outside the body, where the cooler temperature is better for sperm.4 The testes, however, begin development in the abdomen. When the fetus is six or seven months old, they migrate down into the scrotum through two channels called the inguinal canals, removing them from the damaging heat of the rest of the body. Those canals leave weak spots in the body wall that make men prone to inguinal hernias. These hernias are bad: they can obstruct the intestine, and sometimes caused death in the years before surgery. No intelligent designer would have given us this tortuous testicular journey. We're stuck with it because we inherited our developmental program for making testes from fish-like ancestors, whose gonads developed, and remained, completely within the abdomen. We begin development with fish-like internal testes, and our testicular descent evolved later, as a clumsy add-on.

So natural selection does not yield perfection—only improvements over what came before. It produces the fitter, not the fittest. And although selection gives the appearance of design, that design may often be imperfect. Ironically, it is in those imperfections, as we'll see in chapter 3, that we find important evidence for evolution.

This brings us to the last of evolutionary theory's six points: processes other than natural selection that can cause evolutionary change. The most important is simple random changes in the proportion of genes caused by the fact that different families have different numbers of offspring. This leads to evolutionary change that, being random, has nothing to do with adaptation. The influence of this process on important evolutionary change, though, is probably minor, because it does not have the molding power of natural selection. Natural selection remains the only process that can produce adaptation. Nevertheless, we'll see in chapter 5 that genetic drift may play some evolutionary role in small populations and probably accounts for some nonadaptive features of DNA.

These, then, are the six parts of evolutionary theory.5 Some parts are intimately connected. If speciation is true, for instance, then common ancestry must also be true. But some parts are independent of others. Evolution might occur, for example, but it need not occur gradually. Some "mutationists" in the early twentieth century thought that a species could instantly produce a radically different species via a single monster mutation. The renowned zoologist Richard Goldschmidt, for example, once argued that the first creature recognizable as a bird might have hatched from an egg laid by an unambiguous reptile. Such claims can be tested. Mutationism predicts that new groups should arise instantly from old ones, without transitions in the fossil record. But the fossils tell us that this is not the way evolution works. Nevertheless, such tests show that different parts of Darwinism can be tested independently.

Alternatively, evolution might be true, but natural selection might not be its cause. Many biologists, for instance, once thought that evolution occurred by a mystical and teleological force: organisms were said to have an "inner drive" that made species change in certain prescribed directions. This kind of drive was said to have propelled the evolution of the huge canine teeth of saber-toothed tigers, making the teeth get larger and larger, regardless of their usefulness, until the animal could not close its mouth and the species starved itself to extinction. We now know that there's no evidence for teleological forces—saber-toothed tigers did not in fact starve to death, but lived happily with oversized canines for millions of years before they went extinct for other reasons. Yet the fact that evolution might have different causes was one reason why biologists accepted evolution many decades before accepting natural selection.

So much for the claims of evolutionary theory. But here's an important and commonly heard refrain: evolution is only a theory, isn't it? Addressing an evangelical group in Texas in 1980, presidential candidate Ronald Reagan characterized evolution this way: "Well, it is a theory. It is a scientific theory only, and it has in recent years been challenged in the world of science and is not yet believed in the scientific community to be as infallible as it once was believed."

The keyword in this quote is "only." Only a theory. The implication is that there is something not quite right about a theory—that it is a mere speculation, and very likely wrong. Indeed, the everyday connotation of "theory" is "guess," as in, "My theory is that Fred is crazy about Sue." But in science the word "theory" means something completely different, conveying far more assurance and rigor than the notion of a simple guess.

According to the Oxford English Dictionary, a scientific theory is "a statement of what are held to be the general laws, principles, or causes of something known or observed." Thus we can speak of the "theory of gravity" as the proposition that all objects with mass attract each other according to a strict relationship involving the distance between them. Or we talk of the "theory of relativity," which makes specific claims about the speed of light and the curvature of space-time.

There are two points I want to emphasize here. First, in science, a theory is much more than just a speculation about how things are: it is a well-thought-out group of propositions meant to explain facts about the real world. "Atomic theory" isn't just the statement that "atoms exist": it's a statement about how atoms interact with one another, form compounds, and behave chemically. Similarly, the theory of evolution is more than just the statement that "evolution happened": it is an extensively documented set of principles—I've described six major ones—that explain how and why evolution happens.

This brings us to the second point. For a theory to be considered scientific, it must be testable and make verifiable predictions. That is, we must be able to make observations about the real world that either support it or disprove it. Atomic theory was initially speculative, but gained more and more credibility as data from chemistry piled up, supporting the existence of atoms. Although we couldn't actually see atoms until scanning-probe microscopy was invented in 1981 (and under the microscope they do look like the little balls we envision), scientists were already convinced long before that atoms were real. Similarly, a good theory makes predictions about what we should find if we look more closely at nature. And if those predictions are met, it gives us more confidence that the theory is true. Einstein's general theory of relativity, proposed in 1915, predicted that light would be bent as it passed by a large celestial body. (To be technical, the gravity of such a body distorts space-time, which distorts the path of nearby photons.) Sure enough, Arthur Eddington verified this prediction in 1919 by showing, during a solar eclipse, that light coming from distant stars was bent as it went by the Sun, shifting the stars' apparent positions. It was only when this prediction was verified that Einstein's theory began to be widely accepted.

Because a theory is accepted as "true" only when its assertions and predictions are tested over and over again, and confirmed repeatedly, there is no one moment when a scientific theory suddenly becomes a scientific fact. A theory becomes a fact (or a "truth") when so much evidence has accumulated in its favor—and there is no decisive evidence against it—that virtually all reasonable people will accept it. This does not mean that a "true" theory will never be falsified. All scientific truth is provisional, subject to modification in light of new evidence. There is no alarm bell that goes off to tell scientists that they've finally hit on the ultimate, unchangeable truths about nature. As we'll see, it is possible that despite thousands of observations that support Darwinism, new data might show it to be wrong. I think this is unlikely, but scientists, unlike zealots, can't afford to become arrogant about what they accept as true.

In the process of becoming truths, or facts, scientific theories are usually tested against alternative theories. After all, there are usually several explanations for a given phenomenon. Scientists try to make key observations, or conduct decisive experiments, that will test one rival explanation against another. For many years, the position of the Earth's landmasses was thought to have been the same throughout the history of life. But in 1912, the German geophysicist Alfred Wegener came up with the rival theory of "continental drift," proposing that continents had moved about. Initially, his theory was inspired by the observation that the shapes of continents like South America and Africa could be fitted together like pieces of a jigsaw puzzle. Continental drift then became more certain as fossils accumulated and paleontologists found that the distribution of ancient species suggested that the continents were once joined. Later, "plate tectonics" was suggested as a mechanism for continental movement, just as natural selection was suggested as the mechanism for evolution: the plates of the Earth's crust and mantle floated about on more liquid material in the Earth's interior. And although plate tectonics was also greeted with skepticism by geologists, it was subject to rigorous testing on many fronts, yielding convincing evidence that it is true. Now, thanks to global positioning satellite technology, we can even see the continents moving apart, at a speed of 2 to 4 inches per year, about the same rate that your fingernails grow. (This, by the way, combined with the unassailable evidence that the continents were once connected, is evidence against the claim of "young-Earth" creationists that the Earth is only 6,000 to 10,000 years old. If that were the case, we'd be able to stand on the west coast of Spain and see the skyline of New York City, for Europe and America would have moved less than a mile apart!)

When Darwin wrote The Origin, most Western scientists, and nearly everyone else, were creationists. While they might not have accepted every detail of the story laid out in Genesis, most thought that life had been created pretty much in its present form, designed by an omnipotent creator, and had not changed since. In The Origin, Darwin provided an alternative hypothesis for the development, diversification, and design of life. Much of that book presents evidence that not only supports evolution but at the same time refutes creationism. In Darwin's day, the evidence for his theories was compelling but not completely decisive. We can say, then, that evolution was a theory (albeit a strongly supported one) when first proposed by Darwin, and since 1859 has graduated to "facthood" as more and more supporting evidence has piled up. Evolution is still called a "theory," just like the theory of gravity, but it's a theory that is also a fact.

So how do we test evolutionary theory against the still popular alternative view that life was created and remained unchanged thereafter? There are actually two kinds of evidence. The first comes from using the six tenets of Darwinism to make testable predictions. By predictions, I don't mean that Darwinism can predict how things will evolve in the future. Rather, it predicts what we should find in living or ancient species when we study them. Here are some evolutionary predictions:

• Since there are fossil remains of ancient life, we should be able to find some evidence for evolutionary change in the fossil record. The deepest (and oldest) layers of rock would contain the fossils of more primitive species, and some fossils should become more complex as the layers of rock become younger, with organisms resembling present-day species found in the most recent layers. And we should be able to see some species changing over time, forming lineages showing "descent with modification" (adaptation).

• We should be able to find some cases of speciation in the fossil record, with one line of descent dividing into two or more. And we should be able to find new species forming in the wild.

• We should be able to find examples of species that link together major groups suspected to have common ancestry, like birds with reptiles and fish with amphibians. Moreover, these "missing links" (more aptly called "transitional forms") should occur in layers of rock that date to the time when the groups are supposed to have diverged.

• We should expect that species show genetic variation for many traits (otherwise there would be no possibility of evolution happening).

• Imperfection is the mark of evolution, not of conscious design. We should then be able to find cases of imperfect adaptation, in which evolution has not been able to achieve the same degree of optimality as would a creator.

• We should be able to see natural selection acting in the wild.

In addition to these predictions, Darwinism can also be supported by what I call retrodictions: facts and data that aren't necessarily predicted by the theory of evolution, but make sense only in light of the theory of evolution. Retrodictions are a valid way to do science: some of the evidence supporting plate tectonics, for example, came only after scientists learned to read ancient changes in the direction of the Earth's magnetic field from patterns of rocks on the sea floor. Some of the retrodictions that support evolution (as opposed to special creation) include patterns of species distribution on the Earth's surface, peculiarities of how organisms develop from embryos, and the existence of vestigial features that are of no apparent use. These are the subjects of chapters 3 and 4.

Evolutionary theory, then, makes predictions that are bold and clear. Darwin spent some twenty years amassing evidence for his theory before publishing The Origin. That was over 150 years ago. So much knowledge has accumulated since then! So many more fossils found; so many more species collected and their distributions mapped around the world; so much more work in uncovering the evolutionary relationships of different species. And whole new branches of science, undreamt of by Darwin, have arisen, including molecular biology and systematics (the study of how organisms are related).

As we'll see, all the evidence—both old and new—leads ineluctably to the conclusion that evolution is true.

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