Very interesting! I liked it a lot, and I only have two comments (and I apologize if these points have been brought up before):
1.)"...because if an argument is caused naturally, we have no way of knowing whether or not it is really grounded logically."
&
"On the other hand, if my reason has a source outside the interlocking cause-and-effect chain of events called Nature, then it may in fact be capable of true insights."
&
"Thus, in a roundabout sense science provides compelling evidence for the existence of God; not by the performance of a series of experiments in controlled conditions, but by our confidence in the validity of science itself."
I grant the first two, be reject the second; the first two show that it is necessary to make assumptions, but you do not show that I must choose belief in God as my assumption, and only then would this necessity of assumptions support the Supernaturalist world view. An assumption in keeping with the common viewpoint of the Naturalist is, for example, that my impressions of the world are valid, and that logical arguments are valid. Those two assumptions immediately get us out of that "terrible problem," without having to concede anything more than we were already assuming anyway. It's simply a matter of saying it up front: "I don't REALLY know if this is true, but it sure seems like it. I'm just going to assume its true."
My second problem is the final paragraph, where you say thinking "is a connection point with something beyond Nature, and its very ability to do what it is supposed to do rests upon the fact of the existence of that ‘beyond’." While this appears to be obviously true, I would point out that neurological research to date hasn't unearthed anything regarding the soul that I know of, but we have some basic ideas of how the brain works; with the current body of neurological research in hand, what are you claiming is happening in the brain that is supernatural? What I'm trying to say is, that scientists have a fairly good idea of how brains reach decisions, and so there is (probably) nothing supernatural about thinking. The function and influence of the soul (which I am in no way disputing the existence of) must be much more subtle than as a computational device.
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