The first professor of Natural History at the Massachusetts Agricultural College, Henry James Clark, had one of the briefest and most tragic tenures of any member of the faculty during the nineteenth century. Born in Easton, Mass., on June 22, 1826, the son of Rev. Henry Porter and Abigail Jackson (Orton) Clark, Henry was raised primarily in Brooklyn, N.Y. After graduating from the City University of New York in 1848, Clark took a job teaching in White Plains. Already interested in the local flora, his wife recalled that he contacted the great botanist at Harvard, Asa Gray, after discovering a flower that he thought might be new to science. With Gray's encouragement, Clark resumed his studies in 1850, working under both Gray and Louis Agassiz, and graduating from the Lawrence Scientific School at Harvard in 1854.

At Harvard, Clark's interests gradually shifted from flora to fauna, and he became fascinated with the then-fashionable questions of the nature of the cell and the nature of protoplasm. After graduation, he remained in Cambridge for several years, working as an assistant to Agassiz, and from June 1860 to 1865, as an adjunct professor at the Museum of Comparative Zoology. A talented microscopist and keen observer, he published a series of widely-regarded works in histology and on the structure of flagellate protists, sponges, and the coelenterate Haliclystus auricula. He is sometimes credited with being the first to identify the choanoflagellates and he produced important works on flagellae in sponges and the nature of individuality in animals.

Clark's longest and most philosophical work, Mind in nature (1865), explored the origins and organization of life, grappling with larger concepts such as spontaneous generation (of which he was a strong advocate), symmetry, development and form, and the relationship of natural history to natural theology. Without referencing Charles Darwin, Clark staked out a position similar to Richard Owen on the evolution of life forms. Clark earned election to the American Academy of Arts and Sciences in 1856, and enjoyed membership in the Boston Society of Natural History (1857), American Microscopical Society (1865), and the National Academy of Sciences (1872).

Leaving Cambridge in 1866, Clark passed through academic appointments on the faculty of the Agricultural College of Pennsylvania (now Penn State) and the University of Kentucky (1869-1872). Already diagnosed with tabes mesenterica (tuberculosis), he accepted a position at the relatively new Massachusetts Agricultural College in February 1872. His disease, however, progressed rapidly, and on July 1, 1873, he succumbed, leaving behind his wife, Mary, whom he had married in 1854, and seven of their eight children.