Bowdoin may have met Benjamin Franklin as early as 1743, and the two became frequent collaborators and correspondents on scientific subjects. During his Harvard years, he was educated in the sciences by John Winthrop, and developed an interest in electricity and astronomy. In 1750 Bowdoin traveled to Philadelphia to meet with Franklin. Bowdoin was interested in Franklin's experiments on electricity, and Franklin solicited his advice on papers he prepared for submission to the Royal Society. Through the offices of Franklin, some of Bowdoin's letters were read to the Society. Bowdoin was instrumental in gaining support in the provincial assembly for an expedition to Newfoundland to observe the 1761 transit of Venus across the sun, and in the same year published a treatise suggesting improvements to the telescope. In 1785 he published a series of memoirs arguing against Isaac Newton's theory that light was transmitted by "corpuscles", citing both natural observations and Scripture.