Some persons labor under the delusion that the success of the natural sciences to explain the material reality we inhabit in some way lends credence to the doctrine of metaphysical naturalism, according to which the material reality and its empirically detectable aspects are all there is; nothing else outside of these exists. See my friend Bill's recent posting on this matter.
It should be obvious that this is a very poor argument, one that anyone who pretends to be a philosopher should be able to see right through from the start.
The method of the natural sciences is limited a priori to the investigation of only those aspects of reality which have certain qualities -- e.g., they are quantifiable, they are testable and repeatable, etc. Now insofar as every material object has aspects of these sorts, it is in principle guaranteed that a natural-scientific account may be given of every event within history which has a material substratum. If to be material implies having qualities such as these, it is obvious that every event involving material reality will be capable of being understood along these lines.
This says exactly zero about whether there are not other elements of reality, however. If I limit myself ahead of time to the investigation of only that which is quantifiable, then naturally I am not going to be proffering explanations of what I find in the world in non-quantifiable terms. This does not mean that everything can be quantified, or that there are no non-quantifiable elements of the very things I am investigated. I am cut off from them from the start by my own decision; my subsequent research does nothing to confirm or negate the "hypothesis" that all that exists is quantifiable, or that non-quantifiable realities are illusions.
Beyond that it should be obvious that the success of the natural sciences presupposes the existence of a number of things which are not themselves subject to scientific scrutiny. For instance, we make statements about the qualities and attributes of atoms, even though our research has only ever dealt with an extremely small proportion of them. The only justification for doing this is the supposition that atoms have universal natures, an essence that defines them as atoms and which is always the same. But already we have moved from empirical science to metaphysics, that ancient and most glorious of the classical sciences.
This shows us that our scientific practices presuppose certain metaphysical commitments, they presuppose certain substantial claims about reality that go beyond the empirically verifiable and quantifiable. The success of the natural sciences, if anything, disproves metaphysical naturalism, since essences and the like are clearly not natural things. They are not quantifiable or testable or repeatable or anything of the sort; they are the necessary presuppositions of having and investigating a reality that is quantifiable and the rest.