Evolution and Theological Arguments

My interest in the theory of evolution started about 25 years ago when I read the article Evolution as Fact and Theory by Stephen Jay Gould. Prior to that reading I had no particular interest in evolution one way or the other. I learned it in high school biology, did well on the biology Regents, and that was that.

What caught my interest in Gould's article was the form of argument he used. In particular, the following paragraph fascinated me:

"Evolution lies exposed in the imperfections that record a history of descent. Why should a rat run, a bat fly, a porpoise swim, and I type this essay with structures built of the same bones unless we all inherited them from a common ancestor? An engineer, starting from scratch, could design better limbs in each case. Why should all the large native mammals of Australia be marsupials, unless they descended from a common ancestor isolated on this island continent? Marsupials are not 'better', or ideally suited for Australia; many have been wiped out by placental mammals imported by man from other continents. This principle of imperfection extends to all historical sciences. When we recognize the etymology of September, October, November and December (seventh, eighth, ninth, and tenth), we know that the year once started in March, or that two additional months must have been added to an original calendar of ten months." [Italics in original]

Now this argument may be perfectly sound. But whether it is sound or not, it is not scientific in the ordinary sense of the word; it is theological. Its premise is that we know what God - if there is one - would do in creating life: He would create to a standard of perfection; at least He would do a better job than has apparently been done. Since the life we find does not measure up to the standard we suppose God must create to, God could not have done it. 

How is it that a scientific theory rests on a purely theological argument? I've been trying to find the answer to this question for these past decades to no avail. I'm not the only or the first one to make the point; the despised intelligent design advocates and creationists make it repeatedly but apparently to no effect. For example, last weekend's Boston Sunday Globe contains a review of Jerry Coyne's new book "Why Evolution is True", which the reviewer says "lays out an airtight case that Earth is unspeakably old and that new species evolve from previous ones." I don't doubt that the Earth is old, but what is so unspeakable about it? It's about 4.5 billion years old, right? What's so hard about saying that, especially when we have no problem speaking about 850 billion dollar stimulus packages?

Anyway, among the mountains of undeniable scientific evidence that proves that evolution is "far more than a scientific theory", "it is a scientific fact", which evidence is selected for presentation in the review? Why, our old friend the theological argument:

"Why, " he asks, in a typical example, "would a creator use exactly the same bones in flying and flightless wings, including the wings of swimming penguins?"

The answer is: I have no idea. Does Jerry Coyne? How does he have any idea - let alone a scientific idea - what a putative Creator might or might not do? What sort of scientific theory offers as evidence speculations about divine creative methods and purposes? I don't remember Newton relying on his knowledge of God's purposes to argue for his three laws of motion.

Why is it considered terribly vulgar and reactionary merely to ask this question?