Naturalism is a scientific metaphysics, but metaphysics is a study of what is and science is a bewildering, disorganized discourse on what is. I don’t mean the obviously false claim that scientific topics are disorganized but that its existential and predicative discussions of what is are. For a metaphysician reading scientific literature, it is often impossible to tell how scientists want “is” claims to be taken. Here are the first half-dozen possibilities:
1.) The reductive. This is the familiar one: the subject is nothing but the predicate, and the one stands to the other as the unreflective to the precise sense of a term. Uncontroversially, in this sense sunrise is the westward spin of the earth.*
2.) The equivalent. In this sense a dollar is 63 rubles, 32F is 0C, etc. This sense is often connected to…
3.) The causal or potential. Malaria is a parasite carried by mosquitoes and a gallon of gas is 114K BTU’s.
4.) The idealized. This sense of “is” identifies a thing with something ideal and frequently impossible. C is the speed of light, inertial bodies travel in straight lines, X is the rate of attraction for a test particle.
5.) The mathematically defined. GTR is Riemannian, sinusoidal functions are complex numbers, etc. This is a hybrid claim since existence claims in mathematics are justified by proving the absence of contradiction in an idea but this does not suffice to justify an existence claim for a physical thing. Attempts to get beyond the hybrid character of the claim can easily lead to…
6.) The simple or utilitarian. In this sense a thing is the simplest way to calculate it.
While there are a few clear examples of each “is”, most uses are foggy and all but unassignable. In what sense is matter energy, or kinetic energy so much potential energy, or is one light cone intersecting with another, etc? To make things worse, any given scientific argument or term might be formed from any number of these senses, which leads to a further bewilderment of what to do with the hybrids formed by the combinations. Can something be causal (3) if part of its definition is from (4) or (5)? What scientific definition doesn’t avail itself of (4) or (5)? Can (6) be the foundation of any meaningful ontology? What criteria will divide (1) from (2) and (3), and which is more commodious to the de rigueur idea of “emergence”?
I doubt these problems are tractable or even easy to contain. Science is probably better understood as systematic indifference to metaphysics than as proto-metaphysics.
*That said, reduction is itself a fuzzy idea, as is clear from this brief introductory summary in the SEP:
The term ‘reduction’ as used in philosophy expresses the idea that if an entity x reduces to an entity y then y is in a sense prior to x, is more basic than x, is such that x fully depends upon it or is constituted by it. Saying that x reduces to y typically implies that x is nothing more than y or nothing over and above y.
But everything in the first sentence is a description of God and creatures or the soul and the body! It is only the second sentence that says things inconsistent with this.