I only skimmed through your article, but that was primarily because I started out agreeing with your position and my main interest was in Neil's Nonsense.

I've become disillusioned and quite concerned by him lately; in my estimation he's gone from inspiration to exasperation. His positions and arguments are far removed from the spirit of scientific rigor. He would benefit greatly from a course in postmodern thought and an understanding of how everyone, including even the most scientifically-minded of us, are confined by our ideologies.

One of my favorite teachings comes from James Hillman: scientific tools cannot be applied to the realm of thought. Science is the tool for analyzing the objective universe, psychology for the subjective. A lack of understanding of the latter leads to an inability to understand the lens through which we interpret the former. Philosophy is a crucial bridge between the two.