Easily the most challenging aspect of Gates' career as secretary of defense was the changing technologies of weapons and weapons delivery systems. The advances in nuclear weaponry exposed a new need for continental and constant defense systems.
During his period in office, nuclear weapons delivery systems were being researched, and the "strategic triad" of weapons delivery was completed with the development of the submarine launched ballistic missile (SLBM), used in conjunction with manned bombers and ICBM's. Much of this development was in response to Russia's development of land based ICBM's as well as their surprise success with Sputnik.
One of the primary concerns about nuclear weapons was the potential for a "missile gap", the worry that Russia's missiles were longer range, and thus a threat. However, Gates recognized that one of the primary results of this race for nuclear weaponry was the United States' development of small lightweight warheads which could be carried within smaller missiles. Because of the ability to use mobile systems to place and launch the missiles (via submarines and aircraft), the United States did not feel threatened by the Soviet Union's longer range, but ground based nuclear delivery systems.
When Kennedy was elected in 1960, many expected that Gates would continue as Secretary of Defense as many expected Kennedy to include a republican within his staff, however Kennedy appointed Robert S. McNamara, and Gates left office on January 20, 1961.
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