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Since these discussions tend to quickly become ad hom discussions, I'll say first, if you care, that I'm a Christian who thinks the universe is designed but I have no sympathy for the ID arguments I've seen on FR, as they seem to be intellectually weak.

I say that to get to this specimen of weak thinking: ...Roughly, a metaphysical naturalist claims that [1] the world per se is roughly the way that the world is portrayed in the natural sciences. The first, but not principle advantage, of naturalism is its profoundly elegant simplicity; at its heart rests [2] the intuition that the world simply is the way that it seems to be.

(The numbers I added).

The writer seems to think his [1] and [2] are the same thing. But they are the same thing only if you ASSUME that "...portrayed in the natural sciences.." is equivalent to "...seems to be...". They may be equivalent, but this is an epistemological assumption the writer seems to be unaware of. Of course, we all have the hardest time seeing OUR OWN assumptions as anything other than axioms.

Or maybe he realizes he is working with an epistemological assumption, which he is calling an "intuition" -- an intuition which he says is at the "heart" of naturalism.

So, it goes like this: I "intuit" the universe is just the way it "seems" to be, and I then follow that intuition and investigate the universe by the methods of natural science, and argue that anyone who says the universe is not, or more, than what it 'seems" has the burden of proof -- and why? Because, at the heart of my thought is an "intuition", and mine is better than yours.

You may actually operate like this and be a great scientist (which is fine, actually), but this is not rigorous philosophy.