I think the New York Times is being rather conciliatory on the issue of intelligent design, and in doing so illustrates what I believe to be the flaw in the entire discussion. I don't necessarily think, as some do, that the problem with intelligent design is that it fails to confine religion and science to their proper spheres. For one thing, religion defies nearly every sort of definition, since its nature and extent are determined solely by the whims of its founders and adherents. It irritates me, therefore, when the self-proclaimed arbiters of such things take the attitude that religion should be confined to affairs of the spirit, and science to the natural world--a sort of you-play-in-your-half-of-the-sandbox compromise that politicians might broker, but which is antithetical to the boundless claims of religion. I think, rather, that it is the purpose of science that has been misapprehended by most in the controversy. In particular, I take issue with the assertion that science's purpose is to "explain" things.
The issue of scientific explanation is touched on by the latest post at Querencia. The post itself concerns the relationship between art and science, and I won't comment on it. But it quotes a passage from one of Wendell Berry's more recent works, in which, characteristically, the author gets worked up about the inability of science to explain certain things, like art and other good stuff. Although Berry is never one for nailing down his terms, it seems from the context that by "explanation" he means something like reducing things to their elements. That is, he seems to think of scientific explanation as a process in which a multiplicity of things are reduced to their common principles, a very Peripatetic view of the scientific enterprise. He is terribly worried that just because we can discover the principles of certain things we will think we can do the same with all things, which grates on his artistic cum agrarian spiritual sensibilities. But I would advise him not to get his knickers in such a twist over science itself. The project of science since the renaissance has never been to explain things in the sense of discovering their fundamental nature. Indeed, the very success of science over the past several hundred years is entirely a consequence of its limited scope. Science's sole purpose, by definition and necessity, is to order phaenomena.
Science, as such, has only been concerned with one thing: predicting what we will perceive (there is, from an epistemological perspective, a potential disjunct between what one person and another might perceive, but science has given up on this issue long ago). That is to say, the only purpose of science is to order phenomena in the most comprehensive way possible, with the success of that project being determined only by how neatly the new phenomena fit into the old classifications. Thus, for example, the purpose of astronomy is to classify the movements of celestial bodies, and a good astronomer can predict eclipses. If he takes to imagining what the heavens tell him about the nature of God, he becomes a mere astrologer. The animating force behind scientific discovery is always a search for the power to predict, and often the power to manipulate what we see. This assertion is true even of sciences such as paleontology and evolutionary biology: even they can only be confirmed or disconfirmed by their ability to predict present phaenomena--the rest is woolgathering.
The problem arises when the statements made of phaenomena are construed to be statements about some thing, that is, that there's a world beyond the phaenomena out there that has some significance beyond the perceptions we have of it. To ascribe mysterious significance to phenomena is all very groovy, of course, and is what religions mostly concern themselves with: but science can't care about such claims. To the extent that it does care, it ceases to be able to make the unequivocal statements that it must. The purported controversy between actual science and theology is therefore strictly manufactured. To the extent that religious doctrine conflicts with what scientific observations imply about the "things" that are conceived to underlie them, it is quarreling with a straw man, since science can make no claims on this score. I, as a Humean, might scoff at the notion that we can ever "pretend to know body otherwise than by those external properties, which discover themselves to the senses"*; but everyone's entitled to his opinion. When one's receiving the Eucharist at a protestant church, I can assure you that the portions handed out in clear plastic receptacles, with none of the surreptition employed by papists, gives ample assurance from all five senses that one is consuming nothing but grape juice and crackers, yet it is in the refusal to believe these sensory impressions that religion resides. Furthermore, to the extent people actually deny the sensory impressions themselves, they are simply lying (or else, as mentioned above, there is no commonality of experience, and we all have much bigger problems).
I therefore contend that the N.Y. Times article spends an unnecessary lot of argument dithering over various definitions of the scientific method, in order to make the assertion that by removing the requirement that explanations be "natural" from the definition of science, the Kansas Board of Education has altered the fundamental traditions of scientific philosophy, as defined by a designated list of pointy-heads. The flaw in both definitions is that they both claim science explains things, though it does nothing of the kind. I find particularly muttonheaded the parting shot about how science is not incompatible with religion because both are ways to "understand the divine." Any remarks Galileo may have made to that effect assuredly derived from his and his audience's undue familiarity with Aristotle, and consequent inability to penetrate entirely the intellectual fog of the dark ages. As an example of science's true allegiance and purpose, witness that Galileo himself was not a cleric, but calculated gunnery tables for a living. I don't by any means wish to say that one cannot seek the divine by perceiving the natural world (as opposed to classifying one's perceptions of it), but that's a rather different subject.
* David Hume, A Treatise of Human Nature 64 (L.A. Selby-Bigge ed., 2d ed., 1978).