Now, Collins' piece is short and more than a little hand-wavy, and even the bits that can be fairly construed as arguments aren't very good arguments. But PZ is just being disingenuous when he does things like this (emphasized text Collins'; ellipses PZ'):
... I see DNA, the information molecule of all living things, as God's language, and the elegance and complexity of our own bodies and the rest of nature as a reflection of God's plan.
This is an empty tautology. He sees something as a product of a god, therefore he believes in a god…but he offers no reason to see it as a god-product in the first place. If the reason for that is "elegance and complexity", then he is making the intelligent design argument. We know, however, that complexity is a consequence of accumulating randomness, and that elegance is honed out of the noise by selection. No gods are required for either, this is not a reason to believe.
Yes, if this is an argument, it's a crappy version of IDers already crappy arguments. But it's not meant to be an argument. Let's fill in those ellipses.
As a believer, I see DNA, the information molecule of all living things, as God's language, and the elegance and complexity of our own bodies and the rest of nature as a reflection of God's plan.
He's just explaining how he personally reconiciles his faith with something that's supposedly incompatible with faith. PZ is right that no gods are required, but Collins is just claiming consistency.
Collins actually does have a philosophical argument: `science alone' can't answer questions like `What is the meaning of life?' and `If the universe had a beginning, who created it?' Again, not a great argument. But the way to address it is not to play logical postivist. (And a very sloppy logical positivist at that.)
Some of those questions are nonsense ("What is the meaning of life?" There is no meaning beyond what you give to it), some are more tautologies ("Who created the universe?" Why assume it was a who?), and some have been answered or can be answered by science ("Why do humans have a moral sense?" Look up the word "altruism" in an evolution text, buddy.)
Most damning of all, though, why would an inability to answer a question cause one to turn from science to an alternative, religion, that is spectacularly unqualified to answer any of the questions posed? Religion cannot tell you what happens after you die in any meaningful way. The religious have no answers, nothing that someone trained to think scientifically can trace back to the evidence — they have assertions, and every one seems to make a different claim.
Verificationism -- the idea that every claim ought to or can be traced back to empirical evidence -- doesn't work. Consider statistical mechanics. Statistical mechanics models the thermodynamic properties of a gas by representing the gas as a collection of tiny, billiard ball-like objects bouncing off each other in some closed, finite space. It's an extremely well-accepted theory. And of course no-one has ever been able to look and see that ordinary gases have this composition. We can't see individual molecules, at least molecules of that size. The best we can do is take the assumptions of the theory, draw out inferences about what will happen when we perform a given experiment, and check and see that those conclusions actually do occur. Other theories would be just as good at predicting the outcomes of experiments, leaving us with several different and incompatible assertions about the microstructure of gases. What the other theories lack are the other so-called epistemic virtues, including simplicity, explanatory power, and unity with other branches of science (in this case, the dynamics of macroscopic solid objects).
Arguably, religion still doesn't make any experimental predictions, and still falls short. But once we allow the other epistemic virtues to play some role in guiding scientific theory choice, it's begging the question to claim the theist cannot use them to argue for theism. Presumably theists think they have a very elegant explanation for all of Collins' questions.
I don't think the theist's account is ultimately successful -- in particular, the combination of natural disasters and divine foreknowledge is going to wreck its purported elegance and simplicity -- but, in any case, evaluating this is more a job for philosophy than science, and also not something to be done in a couple of paragraphs in a blog post.
The problem I have with atheists of the stripe PZ/Dawkins stripe is, I think, the same one John Wilkins has:
I think rational people can hold a range of views so long as they are self-consistent, and I think a theist can be self-consistent (and can also accept science). That is not compelling to a nonbeliever because to find theism compelling you need to be inside that particular hermeneutic bubble, but all I argue is that we can, as nonbelievers, allow that theists can be rational in their own way. It's a simple plea for tolerance and respect. Why this is problematic eludes me.
PZ, Dawkins, et al, seem to think, not just that theism is theoretically unacceptable compared to atheism or strict deism, but that theism is morally or politically dangerous. The only way this last makes any sense to me is if you think theism is, or is generally, or is popularly, the same thing as theocracy. And that's just silly. I'll grant that there's a lot of religious discrimination tied into popular theism, but I think that will fade over the next few decades, and we're seeing a Renaissance of progressive theism in American politics right now which is decidedly anti-theocratic.