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On December 8, 1941, the United States declares war on Japan. By December 11 the nation is at war with Germany and Italy as well. Life soon changes at the Rice Institute when a Navy ROTC unit begins training large numbers of military engineers. Classes meet year-round, and the school holds 2 commencements each year. The student body is half military and half civilian, but among men, sailors outnumber civilians by 2 to 1.

Rice Institute leadership changes significantly during the decade. Edgar Odell Lovett submits his resignation in May 1941 but agrees to remain until the war ends. William Houston, a physicist from the California Institute of Technology, succeeds him as president in 1946. Houston quickly moves to reorganize the curriculum, hire more faculty and increase graduate enrollment and research activity. The Institute Board also is transformed. Captain James A. Baker dies on August 2, 1941, and several other deaths and resignations follow. Younger Houstonians, including George R. Brown and Harry Wiess, assume leadership roles.

The late 1940s are years of football glory. Coach Jess Neely and the Owls win the Orange Bowl in 1947 and are Southwest Conference Champions in 1949.

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