Baker was an undergraduate at New College of Florida, later doing his PhD research on humpback whales at the University of Hawaii, Manoa.

Starting in 1994, he became a regular delegate to the Scientific Committee of the International Whaling Commission for New Zealand or the USA, and a member of the Cetacean Specialist Group of the IUCN.

In 1993-94, Baker conducted molecular genetic surveys of whale products sold in Japan and South Korea for Earthtrust.

[3][4][5] The methods for molecular identification of whales, dolphins and porpoises used in these surveys have been implemented in the web-based program DNA-Surveillance.

[6][7] In 2001, Baker was awarded the Bronze Medal in Science and Technology from the Royal Society of New Zealand for his work in applied conservation genetics.