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Walter Gilbert was born in Boston, Massachusetts, on March 21, 1932, the son of Emma (Cohen), a child psychologist, and Richard V. Gilbert, an economist. He was educated at the Sidwell Friends School, and attended Harvard University for undergraduate and graduate studies, earning a baccalaureate in chemistry and physics in 1953 and a master's degree in physics in 1954. He studied for his doctorate at the University of Cambridge, where he earned a Ph.D in Physics under the mentorship of Nobel laureate Abdus Salam in 1957.

Gilbert returned to Harvard in 1956 and was appointed assistant professor of physics in 1959; in 1964 he was promoted to associate professor of biophysics and promoted again in 1968 to professor of biochemistry. In 1969, he was awarded Harvard's Ledlie Prize. In 1972 he was named American Cancer Society Professor of Molecular Biology.

He is a co-founder of the biotech start-up companies Biogen and Myriad Genetics, and was the first chairman on their respective boards of directors. He is also a member of the Board of Scientific Governors at The Scripps Research Institute. Gilbert is currently the chairman of the Harvard Society of Fellows.

Together with Allan Maxam, Gilbert developed a new DNA sequencing method. His approach to the first synthesis of insulin lost out to Genentech's approach which used genes built up from the nucleotides rather than from natural sources.

Gilbert first proposed the existence of introns and exons and explained the evolution of introns in a seminal 1978 "News and Views" paper published in Nature. In 1986, Gilbert proposed the RNA world hypothesis for the origin of life, based on a concept first proposed by Carl Woese in 1967.

In 1979, Gilbert was awarded the Louisa Gross Horwitz Prize from Columbia University together with Frederick Sanger. That year he was also awarded the Gairdner Prize and the Albert Lasker Award for Basic Medical Research.

Gilbert was awarded the 1980 Nobel Prize in Chemistry, shared with Frederick Sanger and Paul Berg. Gilbert and Sanger were recognized for their pioneering work in devising methods for determining the sequence of nucleotides in a nucleic acid.

Gilbert has also been honored by the National Academy of Sciences (US Steel Foundation Award, 1968); Massachusetts General Hospital (Warren Triennial Prize, 1977); the New York Academy of Sciences; (Louis and Bert Freedman Foundation Award, 1977), the Academie des Sciences of France (Prix Charles-Leopold Mayer Award, 1977). Gilbert was made a Foreign Member of the Royal Society of London in 1987.