Jim Manzi and Alan Jacobs have already commented on Jerry Coyne's brief for the utter incompability of science and religion, and I basically share their view of the difficulties with Coyne's argument. The core problem, it seems to me, is that Coyne wants to contrast scientific rigor with religious fuzziness and only religious fuzziness; he doesn't want to admit that many realms of human thought and argument are more like theology than chemistry, which is to say that they don't come with a "laboratory-tested" seal of approval.
So he sets up the contrast between religion and science as follows:
What, then, is the nature of "religious truth" that supposedly complements "scientific truth"? The first thing we should ask is whether, and in what sense, religious assertions are "truths." Truth implies the possibility of falsity, so we should have a way of knowing whether religious truths are wrong. But unlike scientific truths, religious ones differ from person to person and sect to sect. And we all know of clear contradictions between the "truths" of different faiths. Christianity unambiguously claims the divinity of Jesus, and many assert that the road to salvation absolutely depends on accepting this claim, whereas the Koran states flatly that anyone accepting the divinity of Jesus will spend eternity in hell. These claims cannot both be "true," at least in a way that does not require intellectual contortions.
Assertions about God's nature also differ among faiths. Giberson explains, for example, that "centuries of Christian reflection on the nature of God have highlighted various characteristics of God: justice, love, goodness, holiness, grace, sovereignty, and so forth." But to those of other faiths, God can be vengeful, as Yahweh was in the Old Testament. Jews cannot imagine an incarnated God, the Word made flesh. Hindus, like ancient Greeks, accept multiple gods with different personalities. To deists, god is apathetic, while many theologians in all the monotheistic faiths claim that we cannot know anything about God's attributes. So which of these many characterizations is "true"? Anything touted as a "truth" must come with a method for being disproved--a method that does not depend on personal revelation. After all, thousands of people have had delusional revelations of "truth" with horrifying consequences.
As Manzi notes, "what Coyne is implying here is that scientific truth is the only form of truth; that no other way of knowing anything has any value or worth responds." But that's not what he actually believes, because further down in the essay we have this:
... the most important conflict--the one ignored by Giberson and Miller--is not between religion and science. It is between religion and secular reason. Secular reason includes science, but also embraces moral and political philosophy, mathematics, logic, history, journalism, and social science--every area that requires us to have good reasons for what we believe.
But "reason" and the "scientific method" are not coterminous: One can reason productively about questions that cannot be resolved through falsification tests. If this weren't the case, philosophy departments, historians, polemicists, and many social "scientists" would be out of business in a hurry. Indeed, if you took the two paragraphs quoted above, which dismiss the truth claims of religion, and substituted, say, "political philosophy" for "faith and "religon" throughout, the critique would make just as much sense (and just as little). Political philosophies vary from person to person and sect to sect; there are clear contradictions between the "truth claims" of, say, Locke and Hobbes, let alone Rawls and Plato; assertions about the nature of man differ wildly from philosopher to philosopher; and there's no empirical test one could devise, so far as I know, to disprove the arguments of The Genealogy of Morals.
Now of course religion is not a thing like political philosophy. But there are similarities between the way that belief operates in both religion and in politics. In making their case, an apologist for Christianity and an apologist for, say, liberal democracy are likely to draw on a similarly hodgepodge-ish set of claims - some philosophical, some historical, some scientific, some anthropological and some personal. Which is to say, both political and religious beliefs depend, in part, on an agglomeration of contentions and experiences that persuade, rather than a set of findings and experiments that prove. Obviously this analogy breaks down in crucial respects: Cults of personality aside, there's no direct analogue in politics to the kind of personal experience in which the most intense forms of religious belief are grounded. But where the intellectual case for religion is concerned, the analogy holds up well enough to be worth keeping in mind when confronted with the following argument from Coyne:
In the end, then, there is a fundamental distinction between scientific truths and religious truths, however you construe them. The difference rests on how you answer one question: how would I know if I were wrong? Darwin's colleague Thomas Huxley remarked that "science is organized common sense where many a beautiful theory was killed by an ugly fact." As with any scientific theory, there are potentially many ugly facts that could kill Darwinism ... Since no such facts have ever appeared, we continue to accept evolution as true. Religious beliefs, on the other hand, are immune to ugly facts. Indeed, they are maintained in the face of ugly facts, such as the impotence of prayer. There is no way to adjudicate between conflicting religious truths as we can between competing scientific explanations. Most scientists can tell you what observations would convince them of God's existence, but I have never met a religious person who could tell me what would disprove it. And what could possibly convince people to abandon their belief that the deity is, as Giberson asserts, good, loving, and just? If the Holocaust cannot do it, then nothing will.
But of course people move in and out of religions all the time, based on experiences they've had, polemics they've read, and so forth. The belief in God is no more impervious to argument, alteration or abandonment than a belief in Randian objectivism or Rawlsian liberalism. Pace Coyne, the problem of theodicy does, in fact, persuade some people to abandon their belief in God - just as the sense that they've encountered God in prayer does, in fact, persuade some spiritually-inquisitive agnostics to take up a religion. Some religions' claims about the world look more implausible than others; some religions (like some political ideologies) lose adherents because their predictions don't come true; some religions clash directly with the current scientific consensus and some do not. (Even Coyne, who I think wildly overstates the conflict between Christianity and science, allows that "pantheism and some forms of Buddhism" are potentially compatible with scientific truth.) It's true that I can't think of a single one-off experiment that would disprove my belief in God once and for all, but I can think of all kinds of experiences and discoveries that would weaken that belief. And I'm pretty sure that Mother Teresa doubted the truth claims of Christianity more frequently than, say, Howard Dean has ever doubted the truth claims of the Democratic Party.
None of this means that Coyne is wrong to argue that science is more empirically-rigorous than religion, and thus worth favoring, provisionally at least, whenever a scientific claim conflicts directly with a religious one. But the standards of scientific rigor simply aren't the only standards that there are for holding warranted beliefs. And if you applied Coyne's "method of disproof" standard to every important question in life, you'd end up paralyzed by indecision - you'd never cast a vote or marry a woman, let alone choose which God to worship, or whether to worship one at all.