True, there is a likeness between the two – but just as the likeness between artificial leather and leather does not make the first a sort of leather, neither does the likeness between methodological naturalism and Naturalism make the first a sort of Naturalism.
The crucial difference is that Naturalism is essentially a claim about all explanations while methodological naturalism is not. Naturalism is a claim that no rational explanation can appeal to a supernatural reality; methodological naturalism need not mean anything more than, say “organic chemistry treats the universe as a closed system” – a claim which not only has nothing to say about all rational explanations, but even has nothing to say about every possible account of organic molecules. Similar things apply to any mode of discourse: If, for example, you wanted to study and learn Euclid’s Elements you have to be “methodologically Euclidian” but this in no way commits you to Euclidianism, i.e. the claim that Lobachevsky’s or Reimann’s geometries were false; if you want to explain classical physics then you have to be “methologically Newtonian”, even if you think that Newtonianism is false.
The attempt to bootstrap from methodological naturalism to Naturalism is therefore a category mistake – the first is not an unrealized and practical Naturalism that is looking for its theoretical completion in full-blown Naturalism, rather, methodological naturalism provides no information at all about Naturalism and is even compatible with its falsity or impossibility. The Naturalist can forget about appealing to methodological naturalism to prove his beliefs are likely – he can’t even appeal to it to show his beliefs are possible.
Just Thomism 