The Beagle survey took five years, two-thirds of which Darwin spent exploring on land. He studied a rich variety of geological features, fossils and living organisms, and met a wide range of people, both native and colonial. He methodically collected an enormous number of specimens, many of them new to science. This established his reputation as a naturalist and made him one of the precursors of the field of ecology, particularly the notion of biocoenosis. His extensive detailed notes showed his gift for theorising and formed the basis for his later work, as well as providing social, political and anthropological insights into the areas he visited.

On the voyage, Charles Darwin read Charles Lyell's Principles of Geology, which explained geological features as the outcome of gradual processes over huge periods of time, and wrote home that he was seeing landforms "as though he had the eyes of Lyell": he saw stepped plains of shingle and seashells in Patagonia as raised beaches; in Chile, he experienced an earthquake and noted mussel-beds stranded above high tide showing that the land had been raised; and even high in the Andes, he was able to collect seashells. He theorised that coral atolls form on sinking volcanic mountains, an idea he confirmed when the Beagle surveyed the Cocos (Keeling) Islands.

In South America he discovered fossils of gigantic extinct mammals including megatheria and glyptodons in strata which showed no signs of catastrophe or change in climate. At the time, he thought them similar to African species, but after the voyage Richard Owen showed that the remains were of animals related to living creatures in the same area. In Argentina two species of rhea had separate but overlapping territories. On the Galápagos Islands Darwin found that mockingbirds differed from one island to another, and on returning to Britain he was shown that Galápagos tortoises and finches were also in distinct species based on the individual islands they inhabited. The Australian marsupial rat-kangaroo and platypus were such strikingly unusual animals that on 19 January 1836, in
New South Wales, he recorded this in his journal:


He puzzled over all he saw, and, in the first edition of The Voyage of the Beagle, he explained species distribution in light of Charles Lyell's ideas of "centres of creation". In later editions of this Journal he foreshadowed his use of Galápagos Islands fauna as evidence for evolution: "one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends."

Three native missionaries were returned by the Beagle to Tierra del Fuego. They had become "civilised" in England over the previous two years, yet their relatives appeared to Darwin to be "miserable, degraded savages". Within a year, the missionaries had reverted to their harsh previous way of life, yet they preferred this and did not want to return to England. This experience, his detestation of the slavery he saw elsewhere in South America, and other problems he found about such as the effect of European settlement on aborigines in New Zealand and Australia, persuaded him that there was no moral justification for the mistreating of others based on the concept of race. He now thought that humanity was not as far removed from animals as his clerical friends believed.

While on board the ship, Darwin suffered from seasickness. In October 1833 he caught a fever in Argentina, and in July 1834, while returning from the Andes down to Valparaíso, he fell ill and spent a month in bed. From 1837 onwards Darwin was repeatedly incapacitated with episodes of stomach pains, vomiting, severe boils, palpitations, trembling and other symptoms. These symptoms particularly affected him at times of stress, such as when attending meetings or dealing with controversy over his theory. The cause of Darwin's illness was unknown during his lifetime, and attempts at treatment had little success. Recent speculation has suggested he caught Chagas disease from insect bites in South America, leading to the later problems. Other possible causes include psychobiological problems and Ménière's disease.

While Darwin was still on the voyage, Henslow carefully fostered his former pupil's reputation by giving selected naturalists access to the fossil specimens and printed copies of Darwin's geological writings. When the Beagle returned on 2 October 1836, Darwin was a celebrity in scientific circles. He visited his home in Shrewsbury and his father organised investments so that Darwin could become a self-funded gentleman scientist. Darwin then went to Cambridge and persuaded Henslow to work on botanical descriptions of modern plants he had collected. Afterwards Darwin went round the London institutions to find the best naturalists available to describe his other collections for timely publication. An eager Charles Lyell met Darwin on 29 October and introduced him to the up-and-coming anatomist Richard Owen. After working on Darwin's collection of fossil bones at his Royal College of Surgeons, Owen caused great surprise by revealing that some were from gigantic extinct rodents and sloths. This enhanced Darwin's reputation. With Lyell's enthusiastic backing, Darwin read his first paper to the Geological Society of London on 4 January 1837, arguing that the South American landmass was slowly rising. On the same day Darwin presented his mammal and bird specimens to the Zoological Society. The Mammalia were taken on by George R. Waterhouse. Though the birds seemed almost an afterthought, the ornithologist John Gould revealed that what Darwin had taken to be wrens, blackbirds and slightly differing finches from the Galápagos were all finches, but each was a separate species. Others on the Beagle, including FitzRoy, had also collected these birds and had been more careful with their notes, enabling Darwin to determine from which island each species had come.

In London, Darwin stayed with his freethinking brother Erasmus and at dinner parties met inspiring savants who thought that God preordained life by natural laws rather than ad hoc miraculous creations. His brother's lady friend Miss Harriet Martineau was a writer whose stories promoted Malthusian Whig Poor Law reforms. Scientific circles were buzzing with ideas of transmutation of species controversially associated with ''Radical'' unrest. Darwin preferred the respectability of his friends the Cambridge Dons, even though his ideas were pushing beyond their belief that natural history must justify religion and social order.



On 17 February 1837, Lyell used his presidential address at the Geographical Society to present Owen's findings to date on Darwin's fossils, noting particularly the unexpected implication that extinct species were related to current species in the same locality. At the same meeting Darwin was elected to the Council of the Society. He had already been invited by FitzRoy to contribute a Journal based on his field notes as the natural history section of the captain's account of the Beagles voyage. He now plunged into writing a book on South American Geology. At the same time he speculated on transmutation in his Red Notebook which he had begun on the Beagle. Another project he started was getting the expert reports on his collection published as a multivolume Zoology of the Voyage of H.M.S. Beagle, and Henslow used his contacts to arrange a Treasury grant of £1,000 to sponsor this. Darwin finished writing his Journal around 20 June when King William IV died and the Victorian era began. In mid-July he began his secret "B" notebook on transmutation, and developed the hypothesis that where every island in the Galápagos Archipelago had its own kind of tortoise, these had originated from a single tortoise species and had adapted to life on the different islands in different ways.

Under pressure with organising Zoology and correcting proofs of his Journal, Darwin's health suffered. On 20 September 1837 he suffered "palpitations of the heart" and left for a month of recuperation in the country. He visited Maer Hall where his invalid aunt was being cared for by her spinster daughter Emma Wedgwood, and entertained his relatives with tales of his travels. His uncle Jos pointed out an area of ground where cinders had disappeared under loam and suggested that this might have been the work of earthworms. This led Darwin to the idea for a talk which he gave to the Geological Society on 1 November, on the unusually mundane subject of worm casts. This work is considered to be the first scholarly treatment of soil forming processes. He had avoided taking on official posts which would have taken up valuable time, but by March William Whewell had recruited him as Secretary of the Geological Society. Illness prompted Darwin to take a break from the pressure of work and he went "geologising" in Scotland. In glorious weather he visited Glen Roy to see the phenomenon known as "roads" which he (incorrectly) identified as raised beaches.



Fully recuperated, he returned home to Shrewsbury. Scientifically pondering his career and prospects he drew up a list with columns headed "Marry" and "Not Marry". Entries in the pro-marriage column included "constant companion and a friend in old age ... better than a dog anyhow," while listed among the cons were "less money for books" and "terrible loss of time." The pros won out. He discussed the prospect of marriage with his father then went to visit his cousin Emma on 29 July 1838. He did not get around to proposing, but against his father's advice he told her of his ideas on transmutation. While his thoughts and work continued in London over the autumn he suffered repeated bouts of illness. On 11 November he returned and proposed to Emma, once more telling her his ideas. She accepted, but later wrote beseeching him to read from the Gospel of St. John a section on love and following the Way which also states that "If a man abide not in me...they are burned". He sent a warm reply which eased her concern, but she would continue to worry that his lapses of faith could endanger her hope that they would meet in afterlife.

Darwin considered Malthus's argument that human population increases more quickly than food production, leaving people competing for food and making charity useless. He later formulated this in the terms of his biological theory as: "Man tends to increase at a greater rate than his means of subsistence; consequently he is occasionally subjected to a severe struggle for existence, and natural selection will have effected whatever lies within its scope." (Descent of Man, Ch.21) He related this to the findings about species relating to localities, his enquiries into animal breeding, and ideas of Natural "laws of harmony". Towards the end of November 1838 he compared breeders selecting traits to a Malthusian Nature selecting from variants thrown up by "chance" so that "every part of newly acquired structure is fully practised and perfected", and thought this "the most beautiful part of my theory" of how species originated. He went house-hunting and eventually found "Macaw Cottage" in Gower Street, London, then moved his "museum" in over Christmas. He was showing the stress, and Emma wrote urging him to get some rest, almost prophetically remarking "So don't be ill any more my dear Charley till I can be with you to nurse you." On 24 January 1839 he was honoured by being elected as Fellow of the Royal Society and presented his paper on the Roads of Glen Roy.

Darwin's book set off a public controversy which he monitored closely, keeping press cuttings of thousands of reviews, articles, satires, parodies and caricatures. Reviewers were quick to pick out the unstated implications of "men from monkeys", though a Unitarian review was favourable and The Times published a glowing review by Huxley which included swipes at Richard Owen, leader of the scientific establishment Huxley was trying to overthrow. Owen initially appeared neutral, but then wrote a review condemning the book.

The Church of England scientific establishment including Darwin's old Cambridge tutors Sedgwick and Henslow reacted against the book, though it was well received by a younger generation of professional naturalists. Then Essays and Reviews by seven liberal Anglican theologians declared that miracles were irrational (and supported the Origin), distracting attention away from Darwin.

The most famous confrontation took place at a meeting of the British Association for the Advancement of Science in Oxford. Professor John William Draper delivered a long lecture about Darwin and social progress, then Samuel Wilberforce, the Bishop of Oxford, argued against Darwin. In the ensuing debate Joseph Hooker argued strongly for Darwin and Thomas Huxley established himself as "Darwin's bulldog" – the fiercest defender of evolutionary theory on the Victorian stage. The story is that on being asked by Wilberforce whether he was descended from monkeys on his grandfather's side or his grandmother's side, Huxley muttered: "The Lord has delivered him into my hands" and replied that he "would rather be descended from an ape than from a cultivated man who used his gifts of culture and eloquence in the service of prejudice and falsehood" (this is contested). The story spread around the country: Huxley had said he would rather be an ape than a Bishop.

Many people felt that Darwin's view of nature destroyed the important distinction between man and beast. Darwin himself did not personally defend his theories in public, though he read eagerly about the continuing debates. He was frequently very ill, and mustered support through letters and correspondence. A core circle of scientific friends – Huxley, Hooker, Charles Lyell and Asa Gray – actively pushed his work to the fore of the scientific and public stage, defending him against his many critics in this key scientific controversy of the era, and helping to gain him the honour of the Royal Society's Copley Medal in 1864. Darwin's theory also resonated with various movements at the time and became a key fixture of popular culture. The book was translated into many languages and went through numerous reprints. It became a staple scientific text accessible both to a newly curious middle class and to "working men", and was hailed as the most controversial and discussed scientific book ever written.

Charles Darwin's theory that evolution occurred through natural selection changed the thinking of countless fields of study from biology to anthropology. His work established that "evolution" had occurred: not necessarily that it was by natural or sexual selection (this particular recognition would not become fully standard until the rediscovery of Gregor Mendel's work in the early 20th century and the creation of the modern synthesis). Others before him had outlined the idea of natural selection: in his lifetime Darwin acknowledged the earlier writings of William Charles Wells and Patrick Matthew which he (and practically all other naturalists) had been unaware of when publishing his theory. However, it is clear that Darwin was the first to develop and publish a scientific theory of natural selection, and that the alleged predecessors did not contribute to the development or success of natural selection as a theory in science.

Darwin's work was very controversial at the time he published it and many during his time did not take it seriously. Evolution by natural selection proved to be a significant blow to notions of divine creation and intelligent design prevalent in 19th-century science, specifically overturning the Creation biology doctrine of "created kinds". The idea that there was no line to be drawn between human beings, races, and animals would forever make Darwin a symbol of iconoclasm who removed humanity's privileged place in the universe. To some of his detractors, Darwin would be "the monkey man", often depicted as part ape. His ideas also stood in opposition to the more common beliefs at the time that the human races had developed separately or that one race was superior by virtue of biology than another.