UNIVERSITIES EXIST to pose tough questions, promote critical thinking, and generally challenge complacency and prejudice. When he became president of Harvard five years ago, Lawrence H. Summers determined that the university was not living up to this mission: It was infected by its own complacencies and prejudices, and he did not shrink from saying so. This outspokenness won Mr. Summers support across the university: A new online poll conducted by the Harvard Crimson found that 57 percent of undergraduates supported him -- only 19 percent thought he should resign -- and the deans of several faculties praised his leadership. But Mr. Summers alienated a vocal portion of the Arts and Sciences faculty, which pressed last year for a vote of no confidence in him and recently forced a second such vote on to the schedule for next week. Yesterday Mr. Summers preempted that second vote by announcing that he would step down in the summer. Because of the prestige of Harvard, his defeat may demoralize reformers at other universities.

Mr. Summers fought several well-publicized battles with Harvard's establishment. He refused to rubber-stamp appointees chosen by the faculties, blocking candidates who seemed insufficiently distinguished and pressing for diversity in political outlook. This prompted complaints that he was acting like a corporate chief executive -- as though there were something wrong with that. Next, Mr. Summers had the temerity to suggest that Cornel West, a professor of Afro-American studies, produce less performance art and more scholarship. This plea for academics to do academic work was construed as racist. After the terrorist attacks of Sept. 11, 2001, Mr. Summers criticized Harvard's hostility to the U.S. armed forces and called attention to the cultural gap between elite coastal campuses and mainstream American values. The fact that these commonsensical positions alienated people at Harvard speaks volumes about the cultural gap that troubled Mr. Summers.

Perhaps most explosively, Mr. Summers raised the possibility that the underrepresentation of women in science and engineering faculties might reflect innate gender differences in ability. His claim was not that women were less intelligent on average, but rather that fewer women than men might be outstandingly bad or outstandingly good at math, with the result that the pool of math geniuses from which universities recruit is disproportionately male. "I would far prefer to believe something else, because it would be easier to address what is surely a serious social problem if something else were true," he noted. But he was immediately branded a sexist.

Mr. Summers can be undiplomatic, as he acknowledged in his resignation letter. But university professors, of all people, should not require mollycoddling; they should be willing to embrace leaders who ask hard questions about how well they are doing their jobs. The tragedy is that the majority at Harvard seems to have known that. But, in university politics as elsewhere, loud and unreasonable minorities can trump good sense.