There were many stories being told of Larry Summers when I was in Harvard last week. Last month he resigned as president of the university in the run-up to a second no-confidence vote in 11 months in a stand-off with disaffected faculty members. (He lost the first, which was over his remark that women had less “intrinsic aptitude” than men for science.) The resignation propelled the world’s most feted university into opinion columns and blogs worldwide. Gossip in Harvard Yard was about only one thing.

Of the many stories told, here is one. Summers had been invited to a dinner party by a member of the Harvard faculty. As was his wont, he dominated the conversation. But as the evening reached its closing stages, he seemed to grow bored. Clasping his hands behind his neck, he lowered his face to the table - and stayed that way.

Apocryphal or not, the tale exposes what the wise men and women of the university seem to think of him. They think he blew it. However intelligent he is, however good his plans, however right his determination to raise Harvard’s game, make war on its inefficiencies and be the scourge of its academic free-riders, he didn’t have the one thing needed to run an American university in the 21st century. He did not take the oath which people in his position must: “Do no harm.” He did the worst kind of harm, short of a crime, which leading figures can do in a university. He challenged moral certainties. He picked up icons, held them up to the light and let them smash to the floor.

The result of one of Summers’ earliest icon-breaking moments illustrates the point - and shows how a great university works. Early in his period of office, he challenged the prominent African American studies professor Cornel West about the latter’s lack of recent academic work. He called West to account about his enthusiasm for popular music and his rap lyrics and musicals, and his high-profile political stance. Harvard’s African and African American studies department is the most famous of its kind in the US; it is led by Henry Louis Gates, a writer and scholar. Although some others share Summers’ concerns about African American studies, he is the only person of his rank to wade into waters others thought too deep. In the US, departments devoted to studying black America are the Academy’s way of recognising the obscenity of slavery, and the excision of African Americans from their country’s history. Its moral purpose is as important as its academic one, so its standards cannot be conventionally challenged.

Yet Summers did. West left for a job at that other great Ivy League institution, Princeton. But Summers had to pay for his folly: the department received tens of millions in extra funding. In The Harvard Crimson, the student newspaper, Gates commented on the irony that one of Summers’ legacies was a stronger African and African American studies department.

Gates played the academic game with subtlety - perhaps the only way it can be played. He and his colleagues saw a weakness and exploited it: Summers had attacked a morally impregnable institution and didn’t have the force to win the battle. Universities are honeycombs of departments, academic centres, research labs, special chairs and programmes. Some will be wonderful, some less than that; but all are united in a desire to be left alone by higher authority. Private sector corporations have bosses with power; professors have tenure.

Summers wanted a university with fewer weak parts. At a meeting in London last year he made it clear that his mission was to make sure all students had good teaching, and to end the lottery in which, even in top-flight colleges, bad teachers teach unchallenged. Characteristically, he said no one but himself would take on this fight.

The conclusion I now hear from the wise men and women of Harvard is that here was a man in the wrong job. Whatever his formidable strengths - of mind, argument and character - they are also his weaknesses. Presidents should woo donors, talk up the university and give speeches full of high purpose and transcendent ideas. Finding fault and making controversial statements are not in the job description.

The Harvard faculty wisdom is that, as president, you will never do all you want, but you may move in the right direction. Had Summers been more of a politician - though ironically he was a politician, occupying high posts throughout both Clinton administrations - he would have grasped that. Instead, his argumentative, opinionated nature drove him to speak out on just the two areas most calculated to cause offence: racial and sexual politics.

Yet almost everyone who has commented on the issue with any degree of seriousness admits that Harvard, and universities in general, need fixing. Peter Beinart of The New Republic wrote that graduates emerge from Harvard “without the kind of core knowledge you would expect from a good high school student”. Nicholas Lemann, dean of the Columbia University Graduate School of Journalism and an expert on academic testing, commented that the faculty members had “an incentive to spend as little time as possible designing and teaching undergraduate courses”.

It remains a shame that Larry Summers has gone. He may not have been hired to break icons. But even if he was wrong, insensitive and naive in doing so - a view I find hard to accept, given universities’ role in speculation and debate - that must be set against his achievements. The vigour of his leadership, his concern for standards, his willingness to use his presidency as a pulpit to warn of the intellectual incoherence afflicting the Academy, all speak against his fate. The scales are weighed against those who have punished him. And the consequences will run beyond Harvard Yard.

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