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Lyell had been a lawyer for as long as he could stand it. When he was thirty years old, he abandoned the law for geology, his true passion. He wrote Principles of Geology to advance the “Uniformitarian” view that the Earth has been shaped by the same gradual processes that we observe today, but operating not merely over a few weeks, or a few thousand years, but ages. There were distinguished geologists who held that floods and other catastrophes might explain the Earth’s landforms, but that the Noachic flood wasn’t enough. It would take many floods, many catastrophes. These scientific Catastrophists were comfortable with Lyell’s long time scales But for the biblical literalists Lyell posed an awkward problem. If Lyell was right, the rocks were saying that the Bible’s six days of Creation, and the age of the Earth deduced by adding up the “begats,” were somehow in error It was through this apparent hole in Genesis that the Beagle would sail into history.

Hired mainly as FitzRoy’s companion and sounding board, Darwin was obliged to bear with equanimity the Captain’s politically conservative, racist, and fundamentalist harangues. For most of the voyage, the two men managed to maintain a truce with regard to their philosophical and political differences. However, Darwin was simply unable to let FitzRoy’s opinion on one particular issue go unchallenged:[A]t Bahia, in Brazil, he defended and praised slavery, which I abominated, and told me that he had just visited a great slave-owner, who had called up many of his slaves and asked them whether they wished to be free, and all answered “No.” I then asked him, perhaps with a sneer, whether he thought that the answers of slaves in the presence of their master was worth anything? This made him excessively angry, and he said that as I doubted his word we could not live any longer together.13

Darwin fully expected to be kicked off the ship. But when the gunroom officers heard of the row, they vied with each other for the privilege of sharing their quarters with him. FitzRoy calmed down and actually apologized to Darwin, rescinding the eviction. Possibly, Darwin’s evolutionary views emerged, in part, out of his exasperation with FitzRoy’s inflexible conventionalism, and the necessity of the young man to suppress for five years the counterarguments that were welling up inside him14

Perhaps it was the legacy of his grandfathers that enabled Darwin to detect the inconsistencies and injustices that other members of his social class would not see. At the very beginning of his book, The Voyage of the Beagle, he tells of a place not far from Rio de Janeiro:This spot is notorious from having been, for a long time, the residence of some runaway slaves, who, by cultivating a little ground near the top, contrived to eke out a subsistence. At length they were discovered, and a party of soldiers being sent, the whole were seized with the exception of one old woman, who, sooner than again be led into slavery, dashed herself to pieces from the summit of the mountain. In a Roman matron this would have been called the noble love of freedom: in a poor negress it is mere brutal obstinacy.15

Darwin had been lured to South America by the prospect of discovering new birds and new beetles, but he couldn’t help noticing the carnage the Europeans were inflicting. Colonial arrogance, the institution of slavery, the extirpation of countless species for the enrichment and entertainment of the invaders, the first depredations of the tropical rain forest—in short, many of the crimes and stupidities that haunt us today—troubled Darwin at a time when Europe was confident that colonialism was an unalloyed benefit for the uncivilized, that the forests were inexhaustible, and that there would always be enough egret feathers for every millinery shop until the Day of Judgment. In part because of these sensitivities, in part because Darwin always wrote as clearly and directly as he could—striving to communicate to the greatest number of people—The Voyage of the Beagle is still a stirring and accessible adventure story.

However, this book has watershed status because it was during the course of the expedition it recounts that Darwin began to amass the great body of evidence—not intuition, but data—that makes the case for evolution by natural selection. “At last gleams of light have come,” he was later to write, “and I am almost convinced that species are not (it is like confessing a murder) immutable.”

The Galapagos is an archipelago of thirteen good-sized islands and many smaller ones lying off the coast of Ecuador. If all the species on Earth were immutable, then why did the beaks of the otherwise very similar finches on islands separated by no more than fifty or sixty miles of ocean vary so dramatically? Why narrow, tiny, pointy beaks on the finches of one island and larger, parrot-like curved beaks on the finches of the next? “Seeing this gradation and diversity of structure in one, small intimately related group of birds,” he later wrote in The Voyage, “one might really fancy that, from an original paucity of birds in this archipelago, one species had been taken and modified for different ends.” (These volcanic islands, we now know, are less than 5 million years old.) And it wasn’t just the finches that raised such problems, but the giant tortoises and the mockingbirds, too.

Back in England, Henslow and Sedgwick had been reading Darwin’s letters aloud at meetings of scientific societies. When Darwin returned home in October 1836, he found he had acquired something of a reputation as an explorer and naturalist. His father was now well pleased with him, and all talk of a parsonage ceased. The same month he met the geologist, Lyell, for the first time. Though not without its rough spots, it was to be a lifelong friendship.

Darwin made important contributions to geology. His interpretation of coral reefs—that they mark the locations of slowly subsiding sea-mounts that had once been islands—was substantiated on the Beagle and corresponds to the modern understanding. In 1838 he published a paper arguing that earthquakes, volcanoes, and the thrusting up of islands are all caused by slow, intermittent, but irresistible global motions in the semi-liquid interior of the Earth. This “almost prophetic”16 thesis, as far as it goes, is part and parcel of modern geophysics. In his 1838 Presidential Address to the Geological Society, William Whewell mentioned Darwin’s name (in the context of this work) more than twice as often as any other geologist, living or dead. In geology, following Lyell, as in biology, Darwin championed the idea that profound changes are worked little by little over vast intervals of time.

In 1839, he married his cousin, Emma Wedgwood. Through ten children and more than four decades they shared a deep, loving, and almost entirely harmonious relationship. During their early married life he was writing down, but certainly not for publication, his first tentative sketch for a theory of evolution. Their rare differences were over religion. “Before I was engaged to be married,” he wrote in his autobiography, “my father advised me to conceal carefully my doubts, for he said that he had known extreme misery thus caused with married persons.”17 A few weeks after their wedding, she wrote to him:May not the habit in scientific pursuits of believing nothing till it is proved influence your mind too much in other things which cannot be proved in the same way, and which if true are likely to be above our comprehension?

Years later, Darwin wrote at the bottom of Emma’s letter,When I am dead, know that many times,

I have kissed and cried over this.18

He tried his best to avoid the public version of this domestic tension. Our past was then a dark and shameful secret. To expose it would have been perceived by many as an affront to the prevailing religious norms and as an assault against human dignity. But to suppress it would have been to reject the data because the implications were disturbing. Darwin recognized that if he was to convince anyone he would have to support his argument with a compelling body of evidence.