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Darwin began his schooling as a physician in Edinburgh in 1825, at the age of 16. His father, Robert, and grandfather Erasmus had both been physicians, and both had been trained at Edinburgh. They chose Edinburgh because it had a larger and stronger medical program than Cambridge, and it was home to a more radical and cosmopolitan faculty and student body. Edinburgh itself was a relatively liberal, cosmopolitan city where the Darwins and the Wedgwoods had many friends.

Charles's brother Erasmus came to Edinburgh in 1825 for a hospital residency after completing his course work at Christ's College in Cambridge. Charles and Erasmus stayed in a hotel at first, but quickly found a boarding house at eleven Lothian Street. At first they were both enthusiastic about learning if not about lectures, checking out more books from the library than all the other students combined. But Erasmus stayed in Edinburgh for only four months, after which he returned to Shrewsbury to assist his father, leaving Charles to face the trials of medical training alone. Edinburgh was the best choice for medical school for Charles, but unfortunately medical school proved not to be something for which he had any particular enthusiasm. Although he had spent the summer of 1825 in Shropshire helping his father treat the local poor, and found it satisfying, he found little to like at Edinburgh. While he found the lectures "intolerably dull," even those on what was to become his life-long passion, zoology, he did start to make a few tentative steps into the world of science, including becoming a member of the Royal Medical Society. He found the anatomy sessions disgusting; he attended two surgeries, both done without anesthesia. After the second, a particularly gruesome surgery on a small child, he swore never to return the operating room. Charles spent the summer of 1826 hiking through North Wales with friends, and then went to Maer, the Wedgwood estate, to hunt rabbits, birds, and foxes.

In his second year, 1826–1827, Charles was just as dissatisfied with his classes and had lost his enthusisam for the library. He did, however, become a friend of Dr. Robert Grant, a physician and lecturer at Edinburgh with a particular interest in marine biology. Grant took him to meetings of the Wernerian Society, where he heard lectures by the master bird-watcher John Audubon and others. During the two years at Edinburgh Darwin almost certainly heard about the idea of evolution for the first time. But the evolution he heard about remained a vague, mysterious process that depended on unknown mechanisms. It was starting to seem clear to some that all living beings were related, but as of yet it was difficult to say how they were related. Darwin became an active member of the Plinian Society, a society of students and some faculty and community members that met to present and discuss scientific papers. Darwin himself presented, at the beginning of 1826, a short paper on oyster larvae that he had conducted with advice from Dr. Grant.

Unfortunately, hunting was capturing his attention far more than the prospect of becoming a physician, as was a new hobby: beetle collecting. The combination of his lack of interest in the medicine with his absolute squeamishness at the prospect of surgery boded ill for his success in the profession. His father scolded him for his "indolent" lifestyle. After Charles's second year at Edinburgh, Robert Darwin, realizing that Charles would not follow in his footsteps, encouraged him to seek another occupation. Darwin considered the possibilities over the course of the summer of 1827, carefully reading books on divinity to see if he might make a place for himself as a clergyman.

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