Preparing the theory of natural selection for publication

Darwin now had the framework of his theory of natural selection "by which to work",as his "prime hobby". His research included animal husbandry and extensive experiments with plants, finding evidence that species were not fixed and investigating many detailed ideas to refine and substantiate his theory^.
For fifteen years this work was in the background to his main occupation of writing on geology and publishing expert reports on the Beagle collections.
When FitzRoy's Narrative was published in May 1839, Darwin's Journal and Remarks was such a success as the third volume that later that year it was published on its own. Early in 1842, Darwin wrote about his ideas to Charles Lyell, who noted that his ally "denies seeing a beginning to each crop of species".
Darwin's book The Structure and Distribution of Coral Reefs on his theory of atoll formation was published in May 1842 after more than three years of work, and he then wrote his first "pencil sketch" of his theory of natural selection. To escape the pressures of London, the family moved to rural Down House in September. On 11 January 1844 Darwin mentioned his theorising to the botanist Joseph Dalton Hooker, writing with melodramatic humour "it is like confessing a murder".Hooker replied "There may in my opinion have been a series of productions on different spots, & also a gradual change of species. I shall be delighted to hear how you think that this change may have taken place, as no presently conceived opinions satisfy me on the subject."

Darwin's "sandwalk" at Down House was his usual "Thinking Path".

By July, Darwin had expanded his "sketch" into a 230-page "Essay", to be expanded with his research results if he died prematurely.In November the anonymously published sensational best-seller Vestiges of the Natural History of Creation brought wide interest in transmutation. Darwin scorned its amateurish geology and zoology, but carefully reviewed his own arguments. Controversy erupted, and it continued to sell well despite contemptuous dismissal by scientists.
Darwin completed his third geological book in 1846. He now renewed a fascination and expertise in marine invertebrates, dating back to his student days with Grant, by dissecting and classifying the barnacles he had collected on the voyage, enjoying observing beautiful structures and thinking about comparisons with allied structures. In 1847, Hooker read the "Essay" and sent notes that provided Darwin with the calm critical feedback that he needed, but would not commit himself and questioned Darwin's opposition to continuing acts of creation.
In an attempt to improve his chronic ill health, Darwin went in 1849 to Dr. James Gully's Malvern spa and was surprised to find some benefit from hydrotherapy. Then in 1851 his treasured daughter Annie fell ill, reawakening his fears that his illness might be hereditary, and after a long series of crises she died.
In eight years of work on barnacles (Cirripedia), Darwin's theory helped him to find "homologies" showing that slightly changed body parts served different functions to meet new conditions, and in some genera he found minute males parasitic on hermaphrodites, showing an intermediate stage in evolution of distinct sexes. In 1853 it earned him the Royal Society's Royal Medal, and it made his reputation as a biologist. He resumed work on his theory of species in 1854, and in November realised that divergence in the character of descendants could be explained by them becoming adapted to "diversified places in the economy of nature".