In March of 2001 the Gallup News Service reported the results of their survey that found 45 percent of Americans agree with the statement “God created human beings pretty much in their present form at one time within the last 10,000 years or so,” while 37 percent preferred a blended belief that “Human beings have developed over millions of years from less advanced forms of life, but God guided this process,” and a paltry 12 percent accepted the standard scientific theory that “Human beings have developed over millions of years from less advanced forms of life, but God had no part in this process.”
Well, if “the standard scientific theory” is that “God had no part” in the process of evolution — not just that human beings developed in a particular way, but that God didn’t guide this — then it seems to me that the theory of evolution is a challenge to many people’s deeply held religious convictions. And that’s so not just as to the young-earthers who believe the Earth was created several thousand years ago, but also to people who are willing to embrace the scientific evidence but see the guiding hand of God in the process.
What’s more, how exactly do scientists come to the conclusion that “God had no part in this process”? What’s their proof? That’s the sort of thing that can’t really be proved, it seems to me — which makes it sound as if scientists, despite their protestations of requiring proof rather than faith, make assertions about God that they can’t prove.
I think Quinean ontological principles can help us properly understand Shermer's statement, and avoid what seems to me to be a confusion on Eugene's part.
Quine says that to exist is to be the value of bound variable in the formal statement of our best explanatory theory of the world. That is, if your best theory of something requires you to posit some entity or property in order to state it, then you are ontologically committed to that entity or property; you're saying it exists. The best explanatory theory of the emergence of life and the development of biological variety is the theory of evolution by natural selection. The statement of this theory does not require us to quantify over, or commit to, any supernatural properties. That “God had no part in the process” is straightforwardly implied by the fact that the theory does not mention God or God-properties. The “proof” that God is no part of the process is simply the statement of the theory, and the fact that the theory is the best, whatever our criteria for “best” are. You can tell that something has no part in the process by checking the list of things one is ontologically committed to by dint of accepting the theory. If it isn't on the list, it plays no part. Surely Eugene would agree that God is not on the ontological list we would compile by scouring the formulation of the standard theory of evolution to see the kinds of things it quantifies over. But that is, I think, all Shermer is saying.
Now, the fact that the theory of evolution by natural selection doesn't quantify over God-properties does not, by itself, “challenge” the conviction that god exists, unless that conviction is based on the explanation of biological phenomena. If no part of our OVERALL best theory (or collection of theories) of the world requires God-properties, than that is a challenge to the conviction that God exists, because commitment to God's existence just is the belief in the claim that Godmaking properties figure in to the best overall theory of the world. If he doesn't figure in, then he isn't listed in the catalog of things we have reason to believe in.
It seems that Eugene almost flirts with Meinongian nonsense, where not existing is a property something can have, just like existing, so that something's not existing requires that it exist, in a superspecial not-existing way, in order for there to be something that is doing all that not-existing. In that case, the claim that something doesn't exist (or does) is substantive, since one is attributing a property to it, and it makes sense to ask for evidence that it does have that property. But to say that something doesn't exist is not in fact substantive. It is simply to point out a formal absence, like the fact that there is no 'p' in 'beer'. (If you're lucky!)