It is notable that when St. Thomas argues for the existence of God he does not point to seeming exceptions to the laws of nature and ask, "Why are there exceptions to the rules?" That's because he knows the work of the sciences is to discover why there are seeming exceptions to the rules of Nature. The person whose faith rests on exceptions to the rules today ("If there is no God, then explain lightning, or disease.") will find that faith in ruins when the exception is explained with static electricity and germs.

Instead, what Thomas does is begin, not *against* the sciences, but for them. Science is nothing other than the enterprise of learning the rules of nature (and how to exploit them for our benefit). It is the measurement of the metric properties, of time, space, matter and energy. It begins with the purely faith-based assumption that a) there are rules governing these things and b) the three-pound piece of meat behind our eyes can understand these rules. Without those purely faith-based assumptions, you can have no science. Thomas then asks a metaphysical, not scientific, question: "Why are there rules?" And he concludes "There are rules because there is something beyond Nature that is a Rulegiver. And that is what everybody means by God." It's not a question science can answer, since it is a faith statement science must assume in order to function at all. Little demonstrations of the order inherent in the structure of things, such as this one...

 delight both the Thomist and the scientist for similar reasons. One loves the One who invested the universe with order. The other loves the order with which the universe is invested. It's a shame the latter ever thought there was a quarrel.  And it's an even greater shame when any Catholic buys into the idea that the quarrel is real.  The Faith has absolutely nothing to fear from the Sciences for the very good reason that the Author of the world is also the Author of revelation.

Indeed, the Sciences were born in Latin Catholic Europe as a side benefit of two articles of Catholic faith.  The first was that God was a God of reason, the ordering Word who is the Logos.  Cultures that believed the gods were a quarrelsome and capricious bunch had trouble getting the sciences off the ground for the very good reason that they had no trust the universe made sense.  So what was the point of trying to make sense of it?  Oh sure, a few pioneers played with trying to order things as a hobby.  But no organized scientific enterprise was undertaken in pagan antiquity. (And before you say it, no, mathematics and engineering are not Science.  Science is the systematic measurement of the metric properties of time. space, matter, and energy.  Mathematics is an important element of this project and the language of what would become the sciences.  And engineering is a practical expression of mathematics that clever humans soon figured out how to use to make pyramids and calculate the seasons.  But the project of trying to make sense of the universe and understand how an why it behaved as it did was not something that many ancients did, because most ancients were not at all convinced that the universe was anything other than magical and capricious.  It's easy to understand why, when you lived in world like Mesopotamia, where floods and catastrophes randomly swept through and death was a constant companion.  

But with the rise of Christian culture, the came with it the conviction of the Faith that the universe was the creation of a just and orderly God who is the Logos: the ordering principle behind the universe.  That was the first thing needed for the rise of the sciences: a fundament belief that the search for order in the universe would not be a waste of time.

The second thing needed was something unique to the Judeo-Christian tradition (and something Islam failed to ultimately accept, though there were voices in medieval Islam who tried to advance the idea).  This was the concept of "secondary causes".  That is, the belief that God has invested in creatures their own powers and potencies and that creatures can therefore act upon each other.  In short, while everything happens according to God's providential will, it is not Christian (or Jewish) faith that creatures are all robots and everything they do is done because God is exerting total control to *make* them act or, even worse, denying them any actual power of causation in order to preserve his own Glory.  

Let me explain.  Westerners are used to living in a world where the explanation for why a piece of paper burns when you touch a lit match to it is that the flame is consuming the carbon, hydrogen, and oxygen in the paper and turning them in water and carbon dioxide.  The creature called "fire" is acting on the creature called "paper".  Both exist because God wills they exist, but these creatures also interact with each other.

Now, suppose you hold a theology which says that it is blasphemous to say that any action of a creature can effect change in another creature since that would deny God the glory of being truly God.  Suppose, following from this notion, you declare that fire does not burn paper, but that God sovereignly wills to turn paper black where flame touches it.  There is, in this theory, no actual connection between the flame and the burning paper.  God is doing everything.  And God is utterly inscrutable and may not be questioned.  It just happens.  Accept it.

This, in brief, is how things fell out in the Islamic world.  And as a result, the sciences ended up stillborn in the Islamic world while they took off in Latin Europe.  Because science is totally founded upon the assumption, not only that the universe is orderly, but that the order involves the action of creatures upon one another and that we can interrogate that order and understand it.  It is founded, in fact, on the a theological belief that "It is the glory of God to conceal a matter and the glory of kings to search a matter out" (Proverbs 25:2).