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The Surgeon General ran the day-to-day activities of Starfleet Medical, directing medical research and handing out duty assignments to the varied types of medical officers which served within the division. (TOS - My Brother's Keeper novel: Constitution)
The Surgeon General also had the authority to relieve starship medical officers who were judged to be incompetent. In 2269 the Surgeon General, with cooperation with Starfleet Command, relieved Doctor Arthur Coleman for "administrative incompetence" and "flagrant medical blunders". (TOS episode: "Turnabout Intruder")