[3] He preferred to explore the Atlantic coast in search of shells and snails, or go to the field to study the fauna and flora.

[4] Despite his lack of formal education, his collections soon earned him the visit of eminent scientists from Boston, Washington and even the United Kingdom.

As a young man, it enabled him to be employed as a mechanical draughtsman at the Portland Locomotive Company and later preparing wood engravings for natural history publications.

Morse was recommended by Philip Pearsall Carpenter to Louis Agassiz (1807–1873) at the Museum of Comparative Zoology at Harvard University for his intellectual qualities and talent at drawing.

After completing his studies he served as Agassiz's assistant in charge of conservation, documentation and drawing collections of mollusks and brachiopods until 1862.

[9][10] During the American Civil War, Morse attempted to enlist in the 25th Maine Infantry, but was turned down due to a chronic tonsil infection.

His combination of broad knowledge, speaking skill, and ability to draw quickly on the blackboard with both hands made him a popular presenter.

[15] Modern taxonomy agrees with the first of these propositions, but not the second, classifying molluscs, brachiopods and annelids as three separate phyla within the superphylum Lophotrochozoa.

[21] Helen Muir-Wood has given an account of the history of the classification of the brachiopods that places Morse's work in its historical context.

Though the school only operated for a few years, several of its students went on to distinguished careers, including David Starr Jordan.

He argued that the persistence of animals such as Lingula (a brachiopod) over immense periods of time, from the Silurian to the present day, with little change was "a fatal objection to the theory of gradual development".

[28] A clear statement of Morse's position on evolution is found in his address, as vice-president (Natural History) of the American Association for the Advancement of Science at its Buffalo NY meeting in August 1876 (reprinted under the title of What American Zoologists have done for Evolution)[29][30] He adopts a clear selectionist position, in contrast, for example, to Hyatt, who was a neo-Lamarckian.

He did not only express these views in a western context, but was subsequently the first to bring Darwin's theory of evolution to Japan.

His visit turned into a three-year stay when he was offered a post as the first professor of Zoology at the Tokyo Imperial University.

He went on to recommend several fellow Americans as o-yatoi gaikokujin (foreign advisors) to support the modernization of Japan in the Meiji Era.

He devised the term "cord-marked" for the sherds of Stone Age pottery, decorated by impressing cords into the wet clay.

[34] He brought back to Boston a collection amassed by government minister and amateur art collector Ōkuma Shigenobu, who donated it to Morse in recognition of his services to Japan.

Morse would occasionally journey to the Lowell Observatory in Flagstaff, Arizona, during optimal viewing times to observe the planet.