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After returning from a visiting professorship at the University of California, Berkeley, Alpert accepted a permanent position at Harvard, where he worked with the Social Relations Department, the Psychology Department, the Graduate School of Education, and the Health Service, where he was a therapist.

Perhaps most notable was the work he did with his close friend and associate Timothy Leary.

Leary and Alpert were formally dismissed from the university in 1963.

According to Harvard President Nathan M. Pusey, Leary was dismissed for leaving Cambridge and his classes without permission or notice, and Alpert for allegedly giving psilocybin to an undergraduate.