During World War II he was a physicist at the Berkeley Radiation Laboratory and at Oak Ridge, Tennessee as part of the Manhattan Project. He was the first director of Lawrence Livermore National Laboratory from 1952 to 1958. After leaving the laboratory in 1958, he held numerous positions in both government and academia, including Chief Scientist of the Advanced Research Projects Agency, and Director of Defense Research and Engineering.
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York was Director Emeritus of the Institute on Global Conflict and Cooperation at UC San Diego and served as chairman of the university's Scientific and Academic Advisory Committee, which oversees activities at both Livermore and Los Alamos National Laboratories. He also served on the board of the Council for a Livable World, a non partisan arms control organization in Washington, D.C. York occasionally guest lectured for the University of California San Diego and other institutions.
Herbert York died 19 May 2009 in San Diego at age 87