Defenders of "special creation" and of "irreducible complexities" in nature think that divine agency will show up in such gaps of nature. But "gaps" of nature are the provenance of the specialized empirical sciences.
How does the author know this with any degree of certainty? Are miraculous phenomena like miraculous medical cures "gaps of nature"?
In fact, both currents of thought have been represented by the great Church Doctors, perhaps reflecting the two accounts of Creation in Genesis. Augustine saw in the creation of the earth, for example, the potential to bring forth various kinds of life, whereas Aquinas saw the "days" of creation more in terms of defined periods of divine activity (I'm generalizing here).
Providentially, I have been reading through Aquinas' account of Creation recently, and he mentions the various opinions of the Church Fathers throughout his arguments. See The Six Days (Matter).
Divine agency, rather, ought to be seen in the fundamental teleology of all natural things, in the need for a First Mover, and in the complete dependence of all things on God as the source of their existence.
Why must divine agency be reduced to this? I see no obvious reason why, since God regularly performs miracles and creates new souls every day. The author seems to have a pre-disposition towards semi-deism.
St. Basil the Great, whom Aquinas probably quotes in this section, also preached on the Six Days of Creation in his Hexameron, which I'm skimming through right now:
If there is anything in this system which might appear probable to you, keep your admiration for the source of such perfect order, for the wisdom of God. Grand phenomena do not strike us the less when we have discovered something of their wonderful mechanism. Is it otherwise here?