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He played a significant role in certifying the Association of University of New Brunswick Teachers (AUNBT). As president, he helped secure AUNBT’s first collective agreement.

Thompson was one of Canada’s leading experts on academic freedom. He chaired CAUT’s Academic Freedom and Tenure Committee from 1985 to 1988 and received the James B. Milner Memorial Award in 1993.

He led the independent CAUT commission that investigated the suppression of research findings in the academic freedom case of University of Toronto professor of medicine Dr. Nancy Olivieri. He also examined external interference in a York University academic conference on models of statehood for Israel and Palestine. Both landmark reports carry significant weight in debates over academic freedom and institutional autonomy. He served on the Board of the Harry Crowe Foundation.