Following the inception of Charles Darwin's theory of natural selection in 1838, the development of Darwin's theory to explain the "mystery of mysteries" of how new species originated was his "prime hobby" in the background to his main occupation of publishing the scientific results of the Beagle voyage. He was settling into married life, but suffered from bouts of illness and after his first child was born the family moved to rural Down House as a family home away from the pressures of London.
The publication in 1839 of his Journal and Remarks (now known as The Voyage of the Beagle) brought him success as an author, and in 1842 he published his first major scientific book, The Structure and Distribution of Coral Reefs, setting out his theory of the formation of coral atolls. He wrote out a sketch setting out his basic ideas on transmutation of species, which he expanded into an "essay" in 1844, and discussed his theory with friends as well as continuing with experiments and wide investigations. In the same year the anonymous Vestiges of the Natural History of Creation brought wide public interest in evolutionary ideas, but also showed the need for sound evidence to gain scientific acceptance of evolution.
In 1846 he completed his third geological book, and turned from supervising the publication of expert reports on the findings from the voyage to examining barnacle specimens himself. This grew into an eight-year study, making use of his theory to find hitherto unknown relationships between the many species of barnacle, and establishing his expertise as a biologist. His faith in Christianity dwindled and he stopped going to church. In 1851 his treasured daughter suffered a long illness and died. In 1854 he resumed his work on the species question which led on to the publication of Darwin's theory.