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Darwin chose to start his argument not on the remote Galápagos Islands, not in the murky depths of the oceans among coral reefs, but in ordinary, comfortable English life. He talked about the many forms that animals and plants could assume in the hands of breeders. Pigeon breeders had doubled the normal allotment of feathers on the fantail; they had turned the neck feathers on the Jacobin into a hood. These were the sorts of traits that could set off a bird as a species of its own, and yet the breeders had created them in only a few generations.

Darwin acknowledged that no one really understood how heredity allowed breeders to work these miracles. Breeders simply knew that different traits tended to be inherited with each other. Cats with blue eyes, for instance, are invariably deaf. But while heredity might be a mystery, at least it was clear that parents produced offspring that tended to be like them—although each generation came with a certain amount of variability.

If you came across a fantail and a Jacobin in the wild, you might think they were different species, yet, strangely, they could still mate and produce fledglings. In fact, Darwin pointed out, it is very hard to distinguish between species and varieties in the wild. Biologists argue about whether certain kinds of oak trees belong to the same species. Darwin suggested that the confusion stemmed from the fact that varieties have some of the same characteristics as species. And that is because varieties are often incipient species themselves.

How could an incipient species become a full-blown one? Here Darwin brought Malthus into the argument. Even a slow-breeding species like a human or a condor can double its numbers in 20 or 30 years, easily overrunning the planet in a few millennia. But plants and animals are regularly wiped out in staggering numbers. Darwin recalled how four-fifths of the birds around Down House died one year in a cold snap. The tranquil surface of nature hid a massive slaughter from view.

Some members of a species survived these challenges thanks to luck, while others had certain qualities that made them less likely to die. The survivors would reproduce, while the badly adapted ones would die. Nature, in other words, was a breeder of its own, and a far superior one to humans. A human might breed pigeons for only one trait, such as tail feathers, while nature bred for countless ones—not just traits of flesh and blood, but of instincts as well. “She can act on every internal organ, on every shade of constitutional difference, on the whole machinery of life,” Darwin wrote. “Man selects only for his own good; Nature only for that of the being which she tends.”

And whereas breeders can do their work only over the course of years or decades, nature has at its disposal a vast expanse of time. “It may be said that natural selection is daily and hourly scrutinizing, through the world, every variation, even the slightest,” Darwin wrote. “We see nothing of these slow changes in progress, until the hand of time has marked the long lapses of ages.”

If natural selection worked on a variety long enough, it would turn it into a new species of its own. After a thousand generations, a single species of bird made of two varieties might end up as two distinct species. Just as individuals of a given species struggle with one another, they also struggle with members of other species. And the competition between two similar species would be most intense. Eventually one of them might be driven out of existence. This, Darwin argued, accounted for all of the fossils of animals that could no longer be found on Earth. They had not simply disappeared—they had been obliterated by other animals.

To help his readers understand this process, Darwin drew the one illustration that appeared in his book. At the bottom were a few original species, which rose like limbs on a tree, dividing over time into new branches. Most of these branches were nothing more than twigs—varieties or species that became extinct—but some of them branched their way all the way to the top of the page. Life was not a Great Chain of Being, said Darwin, but a bushy tree.

Origin of Species is a deeply defensive book, written by a man who had quietly listened for years to other scientists scoff at evolution, and had imagined them scoffing at him as well. He addressed their objections one by one. If old species gradually turned into new species, then why were animals so distinct from one another? Darwin’s answer was that competition between two similar species would tend to drive one of them extinct, so that the animals alive today would be only a scattered selection of all the species that had ever lived.

But shouldn’t we be able to see these intermediate forms as fossils? Darwin reminded his readers that fossils, by their nature, could provide only a few fragments of life’s history. In order to become a fossil, a carcass had to be properly buried in sediment, turned to rock, and then avoid destruction by volcanoes or earthquakes or erosion. Those chances are abysmally low, and so a species, which once included millions of individual animals, might be known from a single fossil. Gaps in the fossil record shouldn’t be a surprise—they should be the rule. “The crust of the earth is a vast museum,” Darwin wrote, “but the natural collections have been made only at intervals of time immensely remote.”

How could natural selection create complex organs, or entire bodies, that were made of so many interdependent parts? How, for instance, could it make a bat or an eye? Fossils couldn’t be expected to tell the whole story. Instead, Darwin turned to living animals as analogies to show at least that such a transformation wasn’t impossible. For bats, he pointed to squirrels. Many tree-living squirrels have four ordinary legs and a slender tail. But there are also some species that have flattened tails and loose skin. Then there are squirrels that have broad flaps stretching between their legs and even their tail and can parachute out of trees. Then, Darwin pointed out, there are gliding mammals known as flying lemurs, which have elongated fingers and a membrane that stretches from jaw to tail.

Here was a relatively smooth gradation from an ordinary four-legged mammal to a creature with almost a batlike anatomy. It was possible that the ancestors of bats went through this evolutionary sequence and then went one step farther, evolving the muscles necessary for true flight.

Likewise, there was no need for an eye to pop out of an animal’s head all at once. Invertebrates such as flatworms have nothing more than nerves with endings coated in light-sensitive pigments. Some crustaceans have eyes that consist of little more than a layer of pigment coated by a membrane. Over time, this membrane could separate from the pigment and begin to act like a crude lens. With small alterations, such an eye could turn into the precise telescopes that birds and mammals use. Because a little eyesight is better than none at all, each new step along the way would be rewarded by natural selection.

With his discovery of natural selection, Darwin turned back to the ideas of other scientists and showed how they made more sense as parts of his own theory. As a young man Darwin had admired Paley, but now he showed how natural designs could come into being without a designer’s direct control. Karl von Baer had demonstrated how embryos of different animals resembled one another early on and grew more particular. For Darwin, this was a sign of the common heritage of animals, and the differences in their development came after their ancestors had diverged.

And Darwin even absorbed Owen’s archetype. “I look at Owen’s Archetypes as more than ideal, as real representation as far as the most consummate skill & loftiest generalization can represent the parent of the Vertebrata,” he once wrote to a colleague. To Owen, the homology between a bat wing and a manatee paddle showed how the mind of God worked. But to Darwin, the homology was a sign of inheritance.