From 1957 to 1966, Ellis Kerley was employed at the Armed Forces Institute of Pathology (AFIP) in Washington, DC. Kerley worked in the Orthopedic Pathology section under the supervision of Lent C. Johnson, MD. As the only staff anthropologist at the AFIP, he lectured, conducted research, and consulted on forensic cases. His best-known research completed during these years was the osteon aging technique. He also conducted research and lectured on paleopathology and skeletal identification. Kerley's AFIP experience aided him in pursuing a distinguished career as a forensic scientist, within both academia and the federal government.
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