Shoemaker was born in Los Angeles, and received his undergraduate degree at Caltech at the age of 19. A year later, in 1948, the Cold War had directed geological exploration activity in the United States towards identifying uranium deposits in Colorado and Utah. Shoemaker joined this effort as an employee of the US Geological Survey (USGS). But while studying the volcanic rocks of the southwest, Shoemaker became interested in the question of whether the craters on the Moon were volcanic or caused by impacts of asteroids and comets (a question that was only finally answered upon the return of lunar samples by the Apollo programme). After his first visit to Meteor Crater, Arizona, in 1952, he became convinced that both it and lunar craters had been formed by impacts.
In 1956, Shoemaker was assigned to map craters formed by nuclear explosions at the Nevada test site. He discovered that the nuclear craters and Meteor Crater had the same overturned flap with inverted stratigraphy, ejected from the craters, and that these craters had transiently been deeper cavities, partly filled by fall-back ejecta. This work, described in his PhD thesis (1960) and in The Planets (ed. G. Kuiper, Univ. Chicago Press, 1962), first defined many features of the impact process.
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