I have now with the exception of some Zoological papers on the lower marine animals completed all which I shall ever attempt on the materials collected during the voyage-These lower marine animals referred to were barnacles (Cirripedia), and the same day as writing this letter, Darwin began his barnacle work which continued through 1854. He remarked in his autobiography:
In October, 1846, I began to work on Cirripedia. When on the coast of Chile, I found a most curious form, which burrowed into the shells of Concholepas, and which differed so much from all other Cirripedes that I had to form a new sub-order for its sole reception. Lately an allied burrowing genus has been found on the shores of Portugal. To understand the structure of my new Cirripede I had to examine and dissect many of the common forms: and this gradually led me on to take up the whole group. I worked steadily on the subject for the next eight years, and ultimately published two thick volumes, describing all the known living species, and two thin quartos on the extinct species. I do not doubt that Sir E. Lytton Bulwer had me in his mind when he introduces in one of his novels a Professor Long, who had written two huge volumes on Limpets.From Today in Science History:
Although I was employed during eight years on this work, yet I record in my diary that about two years out of this time was lost by illness. On this account I went in 1848 for some months to Malvern for hydropathic treatment, which did me much good, so that on my return home I was able to resume work. So much was I out of health that when my dear father died on November 13th, 1847, I was unable to attend his funeral or to act as one of his executors.
My work on the Cirripedia possesses, I think, considerable value, as besides describing several new and remarkable forms, I made out the homologies of the various parts—I discovered the cementing apparatus, though I blundered dreadfully about the cement glands—and lastly I proved the existence in certain genera of minute males complemental to and parasitic on the hermaphrodites. This latter discovery has at last been fully confirmed; though at one time a German writer was pleased to attribute the whole account to my fertile imagination. The Cirripedes form a highly varying and difficult group of species to class; and my work was of considerable use to me, when I had to discuss in the Origin of Species the principles of a natural classification. Nevertheless, I doubt whether the work was worth the consumption of so much time.
In 1846, ten years after his voyage on the Beagle, Charles Darwin began his study of barnacles, which was to appear in four volumes on living and fossil Cirripedes (barnacles). For his observations, he had a single lens microscope made to his own design. Intended to be more practical, it did not fine focusing and had a larger stage than the Beagle microscope to take shallow dishes for aqueous dissections.Living Cirripedia and Fossil Cirripedia on Darwin Online.
Alan C. Love, "Darwin and Cirripedia prior to 1846: Exploring the origins of the barnacle research," Journal of the History of Biology 35 (2002): 251-89.
Abstract: Phillip Sloan has thoroughly documented the importance of Darwin's general invertebrate research program in the period from 1826 to 1836 and demonstrated how it had an impact on his conversion to transformism. Although Darwin later spent eight years of his life (1846–1854) investigating barnacles, this period has received less treatment in studies of Darwin and the development of his thought. The most prominent question for the barnacle period that has been attended to is why Darwin ``delayed'' in publishing his theory of evolution. A related but distinct question concerns the variety of earlier events and influences that led Darwin to the study of Cirripedia in 1846, apart from its role in the trajectory that led to On the Origin of Species (1859).Rebecca Stott, Darwin and the Barnacle: The Story of One Tiny Creature and History's Most Spectacular Scientific Breakthrough (New York: W.W. Norton, 2003).
In this paper I focus on four specific episodes prior to 1846 that inform a picture of why Darwin had an antecedent interest in barnacles: (1) the orientation to collecting strange and curious invertebrate organisms, as well as the strong affinities of Darwin's invertebrate collecting on the Beagle voyage with the work of John Vaughan Thompson; (2) the critical role of marine invertebrate fossils in Darwin's geological reasoning aboard the Beagle and exemplified in his Geological Observations of South America; (3) the strange absence of a Zoology of the Beagle volume on invertebrates and Darwin's original intent to publish some of the descriptions himself;and (4) the noteworthy presence of barnacles in Darwin's transformation theorizing between 1837 and 1839. There is a wealth of support for the thesis that Darwin had a strong interest in cirripedes prior to the formal barnacle research, blunting arguments that it was psychological aversion or a feeling of inferiority about his taxonomic abilities that drove Darwin to the cirripedes.