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One of the complaints was that the colonel advocated total war against Islam. Mr. Thompson said the charge is untrue. A guest lecturer talked of war as one scenario should radical Islamists obtain nuclear weapons.

The university’s faculty handbook states that students and teachers may express opinions “free of limitations, restraints or coercion by the University or external environment,” and that “no subject or issue is considered taboo.”

Mr. Thompson said Col. Dooley is pursuing an administrative appeal inside the Army. If that fails, his grievance will be decided in federal court.

Col. Dooley’s latest officer evaluation, based on his work at Fort Eustis, awarded him the highest rating — “best qualified” — for promotion to colonel.

“I rank Matt #1 of the 5 lieutenant colonels I rate,” his supervisor wrote. “Leveraging his superb leadership skills, tactical expertise and attention to detail, LTC Dooley quickly established himself a consummate expert on key lethality capabilities in the Army and across the Joint community.”