My conclusion stems from an attempt by Mooney to argue for why atheists should sit down and shut up when it comes to their ideas for why science undermines traditional theism and religion. To be fair, Chris Mooney is only quoting Barbara Forrest (via Barfefoot Bum and Saint Gasoline) and these aren't his own original, nonsensical thoughts, but since he quotes thme so approvingly (even concluding with an "amen"), he can be held accountable for their faults:
1. Etiquette. Or as Forrest put it, “be nice.” Religion is a very private matter, and given that liberal religionists support church-state separation, we really have no business questioning their personal way of making meaning of the world. After all, they are not trying to force it on anybody else.
Since when is being "nice" more important than intellectual challenge, criticism, and engagement? I'll bet Barbara Forrest and Chris Mooney don't recommend this sort of "strategy" with any other subject, which means this is nothing more than the same sort of special pleading we see so often from religious apologists: religion is so special and delicate that it just can't stand up to any sort of critical scrutiny from atheists.
Beyond that, though Barbara Forrest is lying — yes, lying. So is Chris Mooney by extension because he agreed with her. Both Barbara Forrest and Chris Mooney have to know that religion is not just a "very private matter." Religion plays a significant role in the public square both directly and indirectly. Liberal religious believers do not shy away from bringing their religious beliefs up in public; Barack Obama, to cite just one prominent example, has started public lectures and meetings with prayers far more often than even George W. Bush did.
What does it say about Barbara Forrest and Chris Mooney that they have to engage in such an obvious and blatant lie in order to argue that atheists shouldn't criticize religion? Well, at the very least it says that they not only don’t have a sound position but know that they don't have a sound position. Sadly, their argument actually gets worse.
2. Diversity. There are so many religions out there, and so much variation even within particular sects or faiths. So why would we want to criticize liberal Christians, who have not sacrificed scientific accuracy, who are pro-evolution, when there are so many fundamentalists out there attacking science and trying to translate their beliefs into public policy?
This brings us back to their lie about religion being a "very private matter." It would help to point to the context for Chris Mooney's admission of scientific illiteracy (coming up): a review by Jerry Coyne of books by Kenneth Miller and Karl Giberson — books all about reconciling religion and science (specifically, evolution). This is part of why we know Forrest and Mooney are liars: the very context of these arguments is an atheist's response to liberal Christians making their religious beliefs something other than a "very private matter."
Forrest and Mooney are going further than just lying, though: here they are specifically arguing that regardless of what a liberal Christian says about their religion or what implications science might have for their beliefs, atheists shouldn't respond. It doesn't matter whether the liberal Christians say things that are unreasonable, illogical, false, or even presumably outright lies — atheists shouldn't criticize. Atheists can, however, criticize fundamentalists who are attacking science. Why is that?
It looks to me like Barbara Forrest and Chris Mooney are rejecting the principle that ideas should be accepted or criticized based on their merits; instead, they seem to be arguing that criticism should be predicated entirely on whether or not one agrees with the political agenda of the person expressing those ideas. Liberal Christians support church/state separation and science, so we shouldn’t be critical of anything they say; fundamentalists oppose church/state separation and science so it's OK to criticize their writings.
It should be pretty obvious that such a principle is a violation of just about any reasonable intellectual and ethical value. You shouldn't refrain from criticizing ideas just because political allies of yours like them. You shouldn't refrain from challenging opinions merely because your friends hold those opinions. You shouldn't refrain from questioning claims solely because they are made by people you agree with on other issues. This is in fact an important intellectual principle in science and Chris Mooney is basically throwing it out the window, but that's still not the worst...
3. Humility. Science can’t prove a negative: Saying there is no God is saying more than we can ever really know empirically, or based on data and evidence. So why drive a wedge between religious and non-religious defenders of evolution when it is not even possible to definitively prove the former wrong about metaphysics?
I just want to be sick. I usually see this "we can't prove a negative" claptrap from creationists and religious apologists who have completely lost every argument they've trotted out and so are now resorting to the idea that they can't be proven absolutely wrong, therefore it's reasonable for them to continue believe that they are right (despite the mountains of evidence contradicting them). It's a pathetic argument and one that can only be offered sincerely by someone who either doesn't understand science or who is deliberately misrepresenting science for an ideological agenda — an option we can't ignore when dealing with people who decide whether or not to challenge claims based on the other person's ideological agenda.
Can science "prove a negative"? Yes, to the extent that science can prove anything (remembering that "prove" has a variety of meanings and doesn't carry the same sense of absoluteness in science that it can in the vernacular). Science can't prove any old negative that comes along; instead, science can only prove a negative when the context and problem are defined clearly enough. Science can prove the nonexistence of alleged entities to the same extent that it can prove the existence of alleged entities.
Can we say "there is no God"? Yes, if "God" is defined clearly enough. If undefined, the statement is meaningless. So, yes, it is possible to prove that religious theists are wrong about their metaphysics if their metaphysics is defined clearly and coherently enough. If their metaphysics is incoherent or undefined, that's criticizable as well. Either way, religious theists cannot be claimed to be immune to challenges, questions, or critiques. Every attempt to so do reduces to what we see from Barbara Forrest and Chris Mooney: misrepresentations, lies, falsehoods, and sheer nonsense.
What I think I find most telling about all this is the fact that if Chris Mooney were to take any of his ideas or principles seriously, he would have to apply them to his own treatment of atheists. His insistence at behaving towards atheists in exactly the manner he argues atheists shouldn't be behaving towards theists communicates not only his own pervasive hypocrisy, but also the fact that everything he's saying is being said in pursuit of an ideological agenda rather than due to principle or sincere belief. A person who will say or argue anything, no matter how baseless, contradictory, or hypocritical for the sake of an ideological agenda, is not a person who can be trusted and is certainly not any sort of ally.
Update: Chris Mooney responds, after a fashion. Apparently criticism of him is a "waste our limited energy and resources on the narcissism of petty differences," but his criticism of atheists is really appropriate and good. Criticism of Chris Mooney runs the risk that we "won’t have the strength left to forge a better, more scientifically literate country," but that isn't a problem when Chris Mooney criticizes atheist scientists.
Funny how my closing comments above are all about how Mooney doesn't apply his standards to himself. Hypocrisy? A lack of self-reflection? Who knows.
What's most noteworthy, though, is the complete absence of any attempt to actually and substantively disagree with any of my arguments. It's also absent from any of the comment there, with the one exception of Erasmussimo who came here to try to do that. Since Erasmussimo is here, I'll just comment on this:
If rational people cannot agree among themselves, then rationalism isn’t a very reliable way to think, is it?
Uh, that conclusion doesn't follow from that premise. Not at all. Rational people disagree all the time; what separates rational people disagreeing from irrational people disagreeing is that rational people should, in principle, have rational, reliable means for working through their disagreements. For example, rational people should approve of using evidence in arguments and this is a good means for working through disagreements. Irrational people don't care so much about evidence. Be rational does not, cannot, and never will imply universal agreement among rational people on all things.
What's more, I think that it's implied at a couple of points that Mooney is not approaching this in a genuinely rational manner. For example, insisting that others should abide by standards which you do not accept for yourself is not rational. Another example is Mooney's attempt to argue that his way of doing things is so much better than others' without supplying evidence for this. Where's his evidence that articles like Coyne's will drive Christians away from science? It doesn't exist; he's just guessing.