James Hannam has a fairly nice little article at the Guardian's "Comment is free" space on the conflict thesis. One of the nice things about it is that it recognizes the fundamental issue of the conflict thesis: namely, that it does not depend on one's personal philosophical views of the nature of religion or, for that matter, the nature of science, but on the evidence to which those philosophical views must be held: the actual history of science. The importance of this is not to be downplayed. It's still not utterly impossible to argue for a conflict thesis historically, and perhaps never will be, given just how much work has to go into thorough refutation of views of history; the argument for it at this point, however, would have to be extraordinarily complex, because all routes to a simple conflict thesis have been pretty thoroughly blocked since the days of White and the like. Any version of the conflict thesis that is seriously put forward will have to deal with this fact, that virtually every major historical advance in the field has shown itself problematic for the conflict thesis: this or that particular religious doctrine understood this or that particular way may conflict with this or that particular scientific conclusion at this or that particular stage of scientific inquiry, but the historical evidence that one proves to be a serious obstacle to the other has steadily grown weaker over time. The evidence suggests the rather weaker conclusion that people can force a conflict when they want to, and here and there can back themselves into corners they can't see a way out of, but that's the whole of the conflict. There is no monolith Religion opposed to a monolith Science, however much we may reify them. You can have conflicts between them here and there that can be put in terms of something religious conflicting with something scientific, just as you can have conflicts between particular claims made by politicians and particular scientific conclusions, but the evidence for the two is about the same, and a general conflict thesis for Religion and Science is no more reasonable, on the historical evidence, than a general conflict thesis for Politics and Science.
It's important to recognize for another reason. You can still find people citing White's 1874 book as proof of the conflict thesis as if the discipline of history. That's lag -- there's folk history as well as folk science, and it can be harder to stamp out, and there will probably be people fifty years from now still citing White as if historical research were incapable of moving beyond him. But it's also become easier to challenge, and as proponents of various versions of the conflict thesis have found history less and less amenable to their point, they have slowly begun to vacate the historical ground and argue that there is a general philosophical opposition in their 'spirit' or 'approach'. Thus the grounds for the conflict thesis become ethereal: it is irrelevant (the argument goes) whether scientists have been religious, or religious people have been scientific, or if there have been times when scientists were inspired to scientific discovery by this or that philosophical view, or if there have been reasonable people who saw no conflict. All irrelevant. What matters is that they are somehow conceptually opposed: if you try to put them together you get an inconsistency. This way of arguing, like the other, runs up against the monolith problem again: we have no good reason to think that there is One Universal and True Account of What Religion Is, and no good reason to think that there is One Universal and True Account of What Science Is, and certainly no good reason to think that the conflict theorists have them. Indeed, 'religion' is just a colloquial term whose meaning changes massively depending on context, and 'science' was coined not to describe a unified field but a vast array of very different fields of philosophy that happened to make distinctive use of what were seen as 'inductive' or 'experimental' methods; it would be astonishing if conceptual analysis could boil them down so straightforwardly, as if we had magically hit on the natural classification, and carved nature perfectly at the joints, our first time at bat. But even if they did have the magic accounts that could show the conceptual incompatibility, they could only show that they did by looking at the historical evidence that shows what, in fact, people have said, believed, and done religiously and scientifically, and showing that Religion and Science as they understand them do in fact describe what people like Max Planck and others were doing. As I always tell people (but being a historian of philosophy myself, I am perhaps oversensitive to the point), that there is no avoiding the actual evidence of history even by abstract philosophy. Evidence: you can't really do without it. And while this particular topic is one where the evidence is especially complicated and tangled, and where the history runs right up to the present time, and thus is continually accumulated (sometimes in surprising ways), it's to the history that we have to go for evidence. Moving to philosophical territory does not make the argument simpler; quite the reverse, in fact.
Thus, as conflict theorists have increasingly had to resort to begging the question and making things up, it is important to nail their arguments to the actual evidence. And while the CiF space doesn't give much room for doing this, Hannam does a fair job in the limited space available.
I do have one criticism; it's a conflation that Hannam is actually carrying over from Coyne and others, which I think would be helpful to resolve into distinctions. Coyne builds his anti-accommodationism on a conflict thesis and has not, at least as far as I have seen, taken the trouble to distinguish them. In fact, accommodationism is not a thesis about science and religion but a thesis about the best practical policy for some end -- in the current context, the debate has been about the ends of scientific pedagogy (especially with regard to evolution). It is possible to accept the conflict thesis but also accept accommodationism in this context (e.g., if you think that the only alternative is the collapse of scientific education, or if you think in fact it is unavoidable in our current culture); and it is possible to reject the conflict thesis but reject accommodationism (e.g., if you think that as a practical matter organizations like the NCSE, whatever their intentions, are only likely to make things worse in cases where conflicts occur or are perceived to occur). The two are relevant to each other -- most of the anti-accommodationists stake their claim on some form of the conflict thesis, and likewise most of the accommodationists stake their claim on the rejection of it -- but the argument would be more illuminating and fruitful if we took the trouble to distinguish the two up front. There are forms of anti-accommodation that are not tied to the conflict thesis, and forms of accommodation that are not tied to its rejection. But for those cases where there is a clear tie, it's good to hold the conflict thesis to the actual evidence.