Holmes earned his bachelor's degree in biology from Massachusetts Institute of Technology (MIT) in 1954 and then began graduate study in the history department of Harvard University, where he graduated with MA in 1958. His graduate study was interrupted by two years of service in the United States Air Force and when he returned to Harvard he transferred to the department of the history of science, graduating with PhD in 1962 with thesis Claude Bernard and the concept of internal environment. For his dissertation, he reconstructed Claude Bernard's path of discovery of basic physiological functions, such as those of the liver, on the basis of Bernard's laboratory books from the 1840s. Mirko Grmek referred the laboratory books to Holmes. He then spent two years at MIT as a postdoc. At Yale University he became in 1964 an assistant professor and in 1968 an associate professor of the history of science. In 1972 he became a professor at the University of Western Ontario and head of his department. In 1979 he returned to Yale as a full professor and chair from 1979 to 2002 of the Section of the History of Medicine in the Yale School of Medicine.
He became Avalon Professor in 1985, and from 1982 to 1987 was Master of Jonathan Edwards College. He became a leading force in building the history of science and medicine at Yale. He initiated an undergraduate major in the history of science/history of medicine and in 1986 a graduate program in the history of medicine and the life sciences. In 2002 he helped establish a new Program in the History of Medicine and Science.
Holmes was the author of more than sixty papers and several books on the history of medicine and the biological sciences. For his two-volume work on Hans Adolf Krebs and the discovery of the citric acid cycle, Holmes not only evaluated Krebs's lab books, but also conducted detailed interviews with Krebs. Holmes won several prizes and was a leading contributor to the history of medicine and the biological sciences for two generations.
During the final months of his life, he was intent on attempting to finish his study of Seymour Benzer and molecular biology, and those who visited him at the Yale Health Service Clinic recall a room filled with books, papers, a laptop, and a scholar eager to talk about ideas. He completed the final chapter two weeks before his death ...
He and his wife Harriet Vann Holmes (d. 2000) had three daughters.