(*) It seems to me that the most natural position for the naturalist to take towards science is the realist position. Seems to me that methodological naturalism even requires it. Take Jerry Fodor's claim about how a naturalist views science as a paradigmatic expression of this:
"...[O]n the one hand, the goals of scientific inquiry include the discovery of objective empirical truths; and, on the other hand, that science has come pretty close to achieving its goals from time to time" (Jerry Fodor, Is Science Biologically Possible?, in Naturalism Defeated: Essays on Plantinga's Evolutionary Argument Against Naturalism, ed. James Beilby, 2002, p. 30).
(**) It also seems to me that the most natural position for the naturalist to take towards ethics is an anti-realist position. Take J.L. Mackie's claim about how a naturalist views ethics (or at least how he should, view ethics), for example:
"If their were objective values, then they would be entities or qualities or relations of a very strange sort, utterly different from anything else in the universe. Correspondingly, if we are aware of them, it would have to be by some special faculty or moral perception or intuition, utterly different from our ordinary ways of knowing anything else" (J.L. Mackie, Ethics: Inventing Right and Wrong, 1977, p.38).
From a naturalist perspective, that seems right to me.
But, with respects to science, one of the main arguments for realism is that the anti-realist cannot adequately explain why science progresses. They can't explain why a theory is said to be improved, or better, if it is not indeed moving closer to, corresponding to, the theory-independent world. How can the anti-realist explain scientific progress, they ask.
But it seems to me that even ethical anti-realists allow for moral reform. That our moral theories are "getting better." That we are "progressing." But why isn't this taken as saying that we are getting closer to stating the truth about the way the world really is? The ethical anti-realist says that we are just stating more useful rules, that we are able to survive better with the new moral than an old one. But this shouldn't be confused with truth.
To the above claims made by the scientific realist, an anti-realist might respond that science does in fact make progress, new theories are more pragmatically useful, to be sure they help us explain more things, make better predictions, allow us to make better technological advances, etc., but this is not to be confused with truthfulness. A theory can be useful, but not true.
But then of course, a good case can be made that naturalists should be anti-realists about science. Naturalists such as Lauden, Quine, Rorty, &c argue for this. Some theists have argued that scientific realism is incompatible with naturalism (see Koons' The Incompatibility of Naturalism and Scientific Realism, in Naturalism: A Critical Analysis, ed. W.L. Craig and J.P. Moreland, 2002, pp. 49-63).
So perhaps the naturalist can embrace anti-realism with respects to both. But this of course has its drawbacks. Scientific and external ethical problems could not be used against theism as defeaters.
It seems that to embrace both (*) and (**) is possibly inconsistent ( of course it would be easier for a theist to embrace the converse of (*) and (**) (i.e., ethical realism and scientific anti-realism), but discussing that takes us past the scope of this entry), or possibly arbitrary.
So perhaps the naturalist embraces realism for both (*) and (**). But of course this, especially realism about (**), is very problematic for the naturalist (and Mackie agrees). Indeed, one could even argue that this move, at the very least, lets a divine foot in the door; and the naturalist can't have that.
At this stage it looks like it is twilight for the naturalist:
It appears that both internalist and externalist theories of warrant are incompatible with naturalism.
It appears that epistemic norms are incompatible with naturalism.
It appears that scientific realism is incompatible with naturalism (see the Koons essay).
It appears that human reasoning is incompatible with naturalism.
It appears that ethical anti-realism is incompatible with naturalism (and, see Mackie &c.).
It appears that holding to either realism or anti-realism for (*) and (**) is problematic for the naturalist too.
It appears that naturalists are growing more eccentric, fly ball, freakish, funny, geeky, goony, idiosyncratic, irregular, kooky, loony, loopy, nutty, odd, oddball, off-center, offbeat, outlandish, peculiar, quaint, queer, quirky, quizzical, screwy, singular, strange, uncommon, unconventional, unnatural, unusual, way out, weird, weirdo, whacko, whacky, whimsical, wild, yo-yo, and flat out bonkers as time progresses.
I think it's time to let this ship of fools sail off into the sunset and search for another alternative worldview to Christianity.