To me, *of course* naturalism denies non-natural predicates as real ‘in themselves’ - as distinct and independent in any way from natural predicates.
I think before making the accusation you will need to unpack what that odd expression “in themselves” is supposed to mean.
Is a house real “in itself”, even though it is made up only of bricks and mortar?
Is a hydrogen atom?
Okay, I will bite at this a *bit*.
My moves are in summary first to state the issue of reducing chemistry to QM and show that QM fails to ‘even approximately’ reproduce the periodic table and thus reduce atomic concepts to QM ones. Then, I apply this a fortiori to any other reductive enterprise like it. (If we can’t even do the first, simplest step, then the whole project has a foundation of sand.) In the second part, I take dougsmith’s claim that we need to allow for a handful of irreducible *natural* sciences. Then, I take this as automatically a failure of the spirit of reduction: we were supposed to have a *single, unified, master* science - Science! - and if that project is claimed to be a failure, why stop at a cluster of natural levels: we might as well give up reduction as a failure and go ahead and posit non-natural entities and properties as needed. Okham’s Razor is not our problem here: the right alternative isn’t a *bloated* ontology of spooks and orbiting invisible teapots: only that sometimes our observations *are* better explained by a distinct and irreducible field of concepts. And so while moral facts, or beauty, or even God isn’t *proved* just by this argument, but the reductionist argument that we don’t ‘need’ irreducibly non-natural entities and predicates does fail to have bite.
This first part is derived from papers by the chemist and philosopher Scerri, especially ‘Has Chemistry Been at Least Approximately Reduced to Quantum Mechanics?’ (PSA: Proceedings of the Biennial Meeting of the Philosophy of Science Association, Volume 1994, Issue Vol. 1, Contributed Papers, 1994, pp.160-70). I’m not claiming he’d endorse my use of it, btw.
 Leave the article aside for a moment. ‘Hydrogen atom’ is a chemical notion. Sure, it’s *made of* something, in the sense that a house is made of bricks etc. But just as the notion house is not defined by its materials, so chemical atom is not defined by its materials. There’s no *conceptual* bar to hydrogen being made of other unconceived materials. So the idea of hydrogen atoms isn’t fully, or even well analyzed by ‘made of such-and-such’ without unpacking exactly what those somethings are.
 But that’s too abstract even for my tastes. What about the subatomic theory we have now: Aren’t hydrogen atoms well analyzed by subatomic physics? Okay, maybe that’s too stringent - I don’t want to scotch reductionism in chemistry just because insufficient work has been done. So are chemical atoms at least *approximately* analyzed into subatomic physics? One might think of this as taking quantum mechanical theory and ‘turning the crank’ of it to produce ersatz observations: given QM, here pops out the hydrogen atom with its properties, and next comes helium, then lithium, and so on.
From the introduction:
“I follow most authors . . . by starting . . . with Nagel (Nagel 1961) . . . he stipulates two formal conditions, namely connectabiity and derivability should be fulfilled in order to say that reduction of theory T2 to theory T1 has occurred. In addition . . . a non-formal condition, that the primary or reducing science should be supported by experimental evidence.
“Furthermore . . . reductions occur in two main varieties . . . . In homogeneous reduction the terms used by the reducing theory are also common to the theory to be reduced. . . . Newton’s theory of mechanics absorbed or reduced both [Galilean and celestial mechanics]. . . . no new concepts are needed to describe motion. In heterogeneous reduction the distinctive traits of some subject matter are assimilated into those of a set of quite different traits. Nagel see this type of reduction as problematical and worthy of analysis unlike homogeneous reduction. . . . for example . . . the concept of a chemical bond [one of the most important ideas in chemistry] cannot be found in [quantum mechanical] calculations. . . .”
Okay, I realize this is really a paper. Allow this to be just an introduction to the direction i will take - or *would* take, if you decide this will get much too long. Anything here we can concentrate on? My method is a bit Goedelian: take a fragment of our ‘total’ language; if our analysis turns up as P, then we expand to P* as applying generally.
Sorry - after asking you to go first, i jumped through the doorway!