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In a litteral sense, it was early man who discovered that when you cracked someone's skull, there was good eating inside. Should you mean: who first discovered what role the brain played in the functioning of living bodies, it very probably was the ancient Greek Alcmaeon of Croton in the 6th century BC, who first concluded that the brain was the organ where the mind was located. It took two centuries before this view was generally accepted and in the 3rd century BC it was the ancient Greek anatomist Erisistratus, who through further research and experiments proved Alcmaeon's theory right and discovered many details about the working of the brain and the central nervous system.

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