The philosophical doctrine of methodological naturalism holds that, for any study of the world to qualify as "scientific," it cannot refer to God's creative activity (or any sort of divine activity). The methods of science, it is claimed, "give us no purchase" on theological propositions--even if the latter are true--and theology therefore cannot influence scientific explanation or theory justification. Thus, science is said to be religiously neutral, if only because science and religion are, by their very natures, epistemically distinct.
Methodological naturalism is the most consistent example of a modern metaphysics. Immanuel Kant ended pre-modern metaphysics with his Critique of Pure Reason. (In case you missed the joke, the title of this blog comes from his work, A Prolegomena to Any Future Metaphysics That Will Be Able to Present Itself as a Science.) Kant essentially divided reality into two parts--the "phenomenal" aspect of things, which can be seen and touched and measured, and the "noumenal" aspect, involving the "thing in itself" rather than its observable categories. Since Kant, modernism has ignored the noumenal and devoted itself exclusively to the phenomenal world.
The methodological naturalists treat "God" as a non-concept, an "ERROR" that corrupts every function that references that cell in their secular spreadsheet. Any future metaphysics will have to do better that if it claims the legacy of Kant. Kant treated "God" and "free will" as fundamental albeit unproveable principles that were essential to his version of "practical reason."