While I'm thinking of it, I want to briefly explain (I want to explain briefly, but it doesn't look like it will be all that brief) one way I see that what I'll call "theistic scientism" can cause bad theology.
First to define "theistic scientism." Scientism proper, in the words of the blessed John Paul II,
is the philosophical notion which refuses to admit the validity of forms of knowledge other than those of the positive sciences; and it relegates religious, theological, ethical and aesthetic knowledge to the realm of mere fantasy. [Fides et Ratio, n. 88]
Theistic scientism, as I'm using the term, backs off from the "realm of mere fantasy" bit, but privileges positive scientific knowledge far above all other forms of knowledge.
The process I have in mind, by which this attitude leads to bad theology, goes like this:
Positive science is, in very rough terms, the search for natural causes of natural effects. Supernatural causes and effects are explicitly outside its scope. If a physicist were trying to measure the dielectric constant of a synthetic crystal, and his guardian angel appeared in the middle of one experiment and made the dielectric constant vary over three orders of magnitude, as a physicist he would have to throw out the data from that experiment. True or false, "Angels can change the physical properties of matter" is not a statement of scientific knowledge.
Scientists assume, for the purposes of physics, that angels aren't messing around with their experiments. More precisely, they assume that, if repeating a test yields the same result, they're observing the same physical cause; if the results are different, they assume there's some variation in physical causes they haven't accounted for. Science is only interested in the part of reality that is scientifically perceivable.
So far so good; this insistence on limiting the scope of science has proven very useful.
But what I think happens next in this process is not so good. It is that people forget that the assumptions required for the scientific method to work are assumptions; they forget its limited scope, and take the part of reality that science studies for the whole.
Under scientism, what is scientifically perceivable exists; what is not scientifically perceivable does not. Theistic scientism modifies this somewhat, in that what is not scientifically perceivable may exist, but it does not act on what is scientifically perceivable (else it would itself be perceivable).
But wait: What is scientifically perceivable? By construction, by assumption, science looks at only natural causes and effects (actually, only repeatable, natural causes and effects). Is it any wonder, then, that supernatural causes and effects aren't scientifically perceivable? But it doesn't follow that, because they aren't -- practically by definition -- scientifically perceivable, they don't exist. If you purposely don't include something, the fact that you don't wind up including it isn't evidence that it isn't there. It's like saying, "Not counting me, there are no humans in this room. Therefore, there are no humans in this room."
Such theistic scientism results in both a false dualism and a false fideism. The dualism opposes the natural and supernatural on the basis of science's exclusion of the supernatural. It holds that natural causes are absolutely sufficient to explain natural effects, to the degree that if a natural cause is found, there is no supernatural cause.
The fideism is the medium in which the tensions between theism and scientism are resolved: We believe in all sorts of things that aren't scientifically perceivable. Why? Well, we just do. Such belief is not true (i.e., scientific) knowledge, and must be prepared to adapt itself to whatever new natural causes science might uncover. Still, a belief can be true without us really knowing that it's true.
Theistic scientism uses physics as its metaphysics, then allows for religious faith to fit around it as best it can. This basic error of taking the part for the whole, one perspective for the objectively normative perspective, can lead to all sorts of nonsense, from the functional Deism of certain Catholic scientists to the suggestion that the immediate creation of the human soul is "crude creationism" to the whacked-out neopaganism of the New Universe Story and similar idiocies that fall afoul of Spong's Law of Theophysical Asininity.