The Rude Atheist at Brooklyn College
There is a good discussion of the case here; an excerpt:
So it's 2005 and this is the academic question that has driven the Daily News and the right-wing New York Sun into apoplectic fits, and caused heartburn all over CUNY: Should Tim Shortell, an atheist, be allowed to assume the chair of the sociology department of Brooklyn College? You know, an atheist--someone who doesn't believe in God. An anticleric. A disrespecter of religion. A mocker of Christianity. Someone like, oh, Diderot ("Man will never be free until the last king is strangled with the entrails of the last priest"). Or Voltaire ("The truths of religion are never so well understood as by those who have lost the power of reasoning"). Or Bertrand Russell ("The Christian religion, as organized in its churches, has been and still is the principal enemy of moral progress in the world")....
Unfortunately, Shortell is no Bertrand Russell....For one thing, Russell was an energetic antireligious propagandist, while Shortell's low opinion of God and his fans is confined to a brief essay, "Religion and Morality: A Contradiction Explained," posted at www.anti-naturals.org, an obscure website with a vaguely Situationist flavor. For another, Russell was a terrific writer, while Shortell's essay is self-satisfied adolescent twaddle....
[S]o what if Shortell's essay is offensive? Brooklyn College is a public, secular institution, not a Bible college. The Sun claimed Shortell's disdain for religion would cloud his judgment of job candidates, but there was never any evidence that this would be the case. No student ever complained about his teaching; his colleagues trusted him enough to elect him to the post; the student work posted on his website is apolitical and bland. Predictions of bias, absent any evidence, are just a backhanded way of attacking his beliefs. You might as well say no Southern Baptist should be chair, since someone who believes that women should be subject to their husbands, homosexuality is evil and Jews are doomed to hell won't be fair to female, gay or Jewish job candidates. Or no Orthodox Jew or Muslim should be chair because religious restrictions on contact with the opposite sex would privilege some job candidates over others.
But nobody ever does say that. As long as a believer ascribes his views to his faith, he can say anything he wants and if you don't like it, you're the bigot. Simplistic as Shortell's essay is, it does raise a useful point: Faith and morality are not only not the same, as Americans like to think, they express contradictory impulses. I believe Kierkegaard said something along these lines in Fear and Trembling in his discussion of Abraham's willingness to sacrifice his son. Or as the physicist Steven Weinberg put it more recently: "With or without religion, you would have good people doing good things, and evil people doing evil things. But for good people to do evil things, that takes religion." Would Weinberg be too "offensive" for CUNY?...
People who believe in academic freedom have got to take these incidents seriously and get active before it's too late. "The perfect case is never going to come along," my old friend the historian Joshua Freeman told me. "Nobody is going to fire their Nobel laureate."
The legal protections, alas, of academic freedom do not include administrative appointments, as we have had occasion to note before.
There is another useful discussion of the case here.

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