Darwin was now an eminent geologist in the scientific Úlite of clerical naturalists, settled with a private
income, while privately working on his theory. He had a vast amount of work to do, writing up all his findings and supervising
the preparation of the multivolume Zoology, which would describe his collections. He was convinced of the occurrence of evolution,
but for a long time had been aware that transmutation of species was associated with the crime of blasphemy as well as with
Radical democratic agitators in Britain who were seeking to overthrow society; thus, publication risked ruining his reputation.
He embarked on extensive experiments with plants and consultations with animal husbanders, including pigeon and pig breeders,
trying to find soundly based answers to all the arguments he anticipated when he presented his theory in public.
When FitzRoy's account was published in May 1839, Darwin's Journal and Remarks was a great success. Later that
year it was published on its own, becoming the bestseller today known as The Voyage of the Beagle. In December 1839, as Emma's
first pregnancy progressed, Darwin suffered more illness and accomplished little during the following year.
Darwin tried to explain his theory to close friends, but they were slow to show interest and thought that selection
must need a divine selector. In 1842 the family moved to rural Down House to escape the pressures of London. Darwin formulated
a short "Pencil Sketch" of his theory, and by 1844 had written a 240-page "Essay" that expanded his early ideas on natural
selection. Darwin completed his third Geological book in 1846. Assisted by his friend, the young botanist Joseph Dalton Hooker,
he embarked on a huge study of barnacles. In 1847, Hooker read the "Essay" and sent notes that provided Darwin with the calm
critical feedback that he needed.
Darwin feared putting the theory out in an incomplete form, as his ideas about evolution would be highly controversial
if any attention was paid to them at all. Other ideas about evolution — especially the work of Jean-Baptiste Lamarck
— had been soundly dismissed by the British scientific community, and were associated with political radicalism. The
anonymous publication of Vestiges of the Natural History of Creation in 1844 created another controversy over radicalism and
evolution, and was severely attacked by Darwin's friends who stressed that no reputable scientist would want to be associated
with such ideas.
To try to deal with his illness, Darwin went to a spa in Malvern in 1849, and to his surprise found that the
two months of water treatment helped. In his work on barnacles he found "homologies" that supported his theory by showing
that slightly changed body parts could serve different functions to meet new conditions. Then his treasured daughter Annie
fell ill, reawakening his fears that his illness might be hereditary. After a long series of crises, she died and Darwin lost
all faith in a beneficent God.
He met the young freethinking naturalist Thomas Huxley who was to become a close friend and ally. Darwin's work
on barnacles (Cirripedia) earned him the Royal Society's Royal Medal in 1853, establishing his reputation as a biologist.
He completed this study in 1854 and turned his attention to his theory of species.