The question seems a bit loaded. I thought I was going to get an opportunity to react to the Polkinghorne interview. But to briefly respond, I think I experience the universe by making pictures, models as a physicist would put it, of the universe in my mind, on paper and in computers. The pictures are as closely based on my sense experience as I can make them. I often find this quite exhilarating, though sometimes distressing.
Now to turn to Dr. Polkinghorne and your interview, with all respect for his capabilities as a physicist, and as a physicist of modest achievement myself, I find him somewhat embarrassing. It seems to me that science has a distinctly different process for determining what is true than religion does. And in fact, in the most coherent account of the scientific process which I have encountered (attributed to Karl Popper), science never claims to have found a final truth but only hypotheses which are consistent with phenomena which have been observed so far.
If one attempts to treat the hypotheses of religion in this scientific way, by comparing their predictions with observations, then most of them fail. Everyone,including Dr. Polkinghorne, knows this. It is the origin of the "problem of evil" which you briefly discussed: It is contradictory to experience to hypothesize that God is omnipotent in the world and good in the human sense. Polkinghorne talks around such contradictions but in the end they remain. I also think it's disingenuous to suggest that the statistical character of quantum mechanics and the indeterminacy of classical physics in chaotic systems provides much help with the problem of free will.
Finally the remarks about the mathematical beauty in physics are both misleading and quite irrelevant the relation of science to religion: The current "standard model" of elementary particle physics is generally agreed to be a mathematically ugly construction. Nature does not always choose a beautiful arrangement of things, at least to human view. Certainly nature is full of surprises and not easy to understand, but I do not think that Polkinghorne's rather amateurish and clearly theologically biased musings add much to that understanding.
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