Why Methodological Naturalism in Empiriological Sciences?

The basis of modern empiriological sciences, such as experimental and theoretical physics and astronomy, is "naturalized epistemology," called also "methodological naturalism" or "scientific naturalism." This holds that the methods of empiriological sciences should assume that phenomena they study have only natural causes irrespective of whether supernatural agents can or do effect them. This has allowed for scientists to reproduce experiments and verify results regardless of the scientists' non-scientific beliefs. Science has relegated the Why? questions for the How? questions; final causes are no longer addressed. Because we can only know God and other non-physical realities via the physical word (Rom. 1:20), this implies that the immaterial or supernatural order affects the material or natural order.

Let us address these questions:

1. Does the supernatural affect the natural?
2. If so, why should we incorporate their effects into our physical theories?
3. How would we avoid considering "God did it" as a sufficient explanation of a natural effect?
4. How would we know an exception to a natural law due to something supernatural from an exception due to natural causes?

St. Thomas Aquinas provides an answer to questions 1 and 3 in his discussion on how the universe has a rational plan:

Accordingly that God love His own goodness is something necessary, but it does not necessarily follow from this that it should be reflected in creatures, since the divine goodness is perfect without this. Consequently although the divine goodness is the reason why creatures were originally brought into being, yet this depends on the simple will of God. Supposing, however, that God wishes to communicate His goodness to His creatures by way of likeness as far as it is possible, this is the reason why creatures are of divers kinds: although there is no necessity for this diversity being according to this or that degree of perfection, or this or that number of things. And supposing it to be God's will to establish a particular number in things, and to bestow on each thing a particular measure of perfection, this is the reason why a particular thing has such and such a form and such and such matter: and so on in like manner.

It is therefore clear that the dispensations of providence are according to a certain reason, and yet this reason presupposes the divine will.

Accordingly a twofold error is refuted by what we have said. First, there is the error of those who maintained that all things are the result of God's simple will without any reason. This is the error of the Moslem theologians in the law of the Mohammedans, as Rabbi Moses relates (Doct. Perp. iii. 25.), according to whom the sole reason why fire heats rather than chills is because God so wills. Secondly, we refute the error of those who assert that the ordering of causes proceeds from divine providence by way of necessity. Both of which are false, as is clear from what has been said.

There are certain expressions of Scripture that would seem to ascribe all things to God's simple will. But such things are said, not to remove reason from the dispensations of providence, but to show that God's will is the first principle of all things, as we have already shown. Such are the words of the Psalm cxxxiv. 6.: Whatsoever the Lord pleased, He hath done, and of Job ix. 12: Who can say: Why dost Thou so? and of Rom. ix. 19: Who resisteth His will? Augustine likewise says (3 De Trin. iii., iv.): God's will alone is the first cause of health and sickness, reward and punishment, grace and retribution.

Accordingly if we be asked the wherefore of a particular natural effect, we can assign the reason to some proximate cause: provided, however, that we refer all things to the divine will as their first cause. Thus if it be asked: Why was the wood heated at the presence of fire? we reply: Because to heat is fire's natural action: and this, because heat is its proper accident: and this results from its proper form: and so on until we come to the divine will. Hence if we reply to the question Why was the wood made hot? by saying: Because God so willed: we shall answer rightly, if we intend to trace the question back to its first cause, but incorrectly if we intend to exclude all other causes.

—Summa Contra Gentiles, lib. 3 cap. 97 n. 13-17

Hence in empiriological sciences "we intend to exclude all other causes," i.e., we only focus on the natural cause. But, related to the induction hypothesis, what if our repeated observations of the fire in St. Thomas's example conclude only 99.999% of the time that "to heat is fire's natural action?" What if there were another cause, one supernatural, 0.001% of the time? Would this falsify the theory that "to heat is fire's natural action?" No, it would not falsify the natural theory, for in this case it would be a miracle. Determining when a miracle occurs would answer question 4 above. St. Thomas offers some insights into what a miracle is when he says:

These works that are sometimes done by God outside the usual order assigned to things are wont to be called miracles: because we are astonished (admiramur) at a thing when we see an effect without knowing the cause. And since at times one and the same cause is known to some and unknown to others, it happens that of several who see an effect, some are astonished and some not: thus an astronomer is not astonished when he sees an eclipse of the sun, for he knows the cause; whereas one who is ignorant of this science must needs wonder, since he knows not the cause. Wherefore it is wonderful to the latter but not to the former. Accordingly a thing is wonderful simply, when its cause is hidden simply: and this is what we mean by a miracle: something, to wit, that is wonderful in itself and not only in respect of this person or that. Now God is the cause which is hidden to every man simply: for we have proved above that in this state of life no man can comprehend Him by his intellect. Therefore properly speaking miracles are works done by God outside the order usually observed in things.

Of these miracles there are various degrees and orders. The highest degree in miracles comprises those works wherein something is done by God, that nature can never do: for instance, that two bodies occupy the same place, that the sun recede or stand still, that the sea be divided and make way to passers by. Among these there is a certain order: for the greater the work done by God, and the further it is removed from the capability of nature, the greater the miracle: thus it is a greater miracle that the sun recede, than that the waters be divided.

The second degree in miracles belongs to those whereby God does something that nature can do, but not in the same order: thus it is a work of nature that an animal live, see and walk: but that an animal live after being dead, see after being blind, walk after being lame, this nature cannot do, but God does these things sometimes by a miracle. Among these miracles also, there are degrees, according as the thing done is further removed from the faculty of nature.

The third degree of miracles is when God does what is wont to be done by the operation of nature, but without the operation of the natural principles: for instance when by the power of God a man is cured of a fever that nature is able to cure; or when it rains without the operation of the principles of nature.

—Summa Contra Gentiles, lib. 3 cap. 101

If our intellects can abstract the supernatural from the natural in an object under study, why should we worry about the supernatural? Our findings will never contradict the supernatural because God never contradicts nature, Who is the very rational Author of it. But what about question 2? Consider this: Understanding the natural order to the exclusion of the supernatural order is akin to understanding the moon with astronomy to the exclusion of mathematics. Why do that? St. Thomas, on the difference between mathematics and physics, says:

Since, therefore, the objects of mathematics are abstracted from motion according to the intellect, and since they do not include in their intelligibility sensible matter, which is a subject of motion, the mathematician can abstract them from sensible matter. And it makes no difference as far as the truth is concerned whether they are considered one way or the other. For although the objects of mathematics are not separated according to existence, the mathematicians, in abstracting them according to their understanding, do not lie, because they do not assert that these things exist apart from sensible matter (for this would be a lie). But they consider them without any consideration of sensible matter, which can be done without lying. Thus one can truly consider the white without the musical, even though they exist together in the same subject. But it would not be a true consideration if one were to assert that the white is not musical.

—In Physic., lib. 2 l. 3 n. 5

He says: "And it makes no difference as far as the truth is concerned whether they are considered one way or the other." Therefore, if the goal of science is to seek truth, then it would not hurt to consider natural phenomena in the light of supernatural, metaphysical, or immaterial causes. But this would be unnecessary because of what St. Augustine says in Contra Faustum, XXVI, 3: "God the creator and author of all natures, does nothing unnatural: because to each thing, that is natural which is caused by Him from whom is all measure, number and order in nature." Does this imply that a Catholic scientist can consistently practice methodological naturalism without worrying about possibly capricious supernatural influences because even supernatural beings, such as angels, have natures created rationally and according to the Divine Reason?

Yet all these arguments assume a sharp division between supernatural and natural orders. Does such a sharp division exist? Should it exist? Or would the physical empiriological sciences prosper if their formal objects were in both natural and supernatural orders?