A point that I perhaps didn't make clear enough in my original post on the quantum challenge: the challenge comes primarily from the quantum phenomena themselves, and only secondarily from the theory of quantum mechanics. Regardless of what the theory says about the electron transitions that produce line spectra, the very existence and pattern of those transitions is what the Thomist must reconcile with his metaphysical views. Since Feser's response is directed at the theory of quantum mechanics and how it answers different questions than the metaphysical ones, that response is to some extent missing the point.
As an analogy, suppose someone were to discover a kind of pebble that behaves in every way like an ordinary pebble, except that, at some time during its existence, it suddenly turns into a puddle of goo. No external cause can be found for this strange transition. So, we look for an internal cause: some sort of internal structure that could explain the change. But slicing the pebble open reveals no such structure: the pebble seems to have a very simple composition. So we look deeper: perhaps there is some chemical change going on? But no such chemical changes can be found. And as time goes on, scientists continue to be unable to identify any cause of the change.
My claim is that the existence of a class of pebbles like these would call into question the principle "Whatever changes is changed by something else." And this would be the case regardless of any theoretical description of the puddling pebbles that scientists were able to work out. One could always hold out hope that an explanation of the change would someday be found. Or one could attempt to subsume the phenomenon under the principle by, for instance, pushing the "something else" that causes the change back to whatever brought the pebble into existence in the first place. But you can't claim that these pebbles are irrelevant to the principle.
My second point is that, whatever you make of the connection between natural laws and causes, it can't be true that the former is irrelevant to the latter, as Feser claims. This is clear even from his own book: every example of causation that Feser gives is implicitly or explicitly dependent on laws of nature.
For example, on p.54 he considers a rubber ball that becomes gooey when heated, and says that the heat is what actualizes the potential gooeyness of the ball.
This makes no sense unless we already know a natural law to the effect that "rubber becomes gooey when heated." For consider: suppose I place the ball on a hot plate and simultaneously wave my magic wand over it. After a while, it becomes gooey. Now, if natural laws are irrelevant to the question of causes, then it makes just as much sense to say that waving the wand was the cause, as it does to say the heat of the hot plate was the cause. In fact, it makes just as much sense to say that the flapping of a butterfly's wings was the cause, or the position of Jupiter in the sky. Without natural laws, we can have no conception of cause and effect.
I could continue to cite examples - breaking the glass with a brick (p.68: laws of force and fracture), the train pulling out of the station (p.95: laws of motion) - but I think you get the idea. In his latest post, Feser cautions against confusing illustrations of philosophical ideas with empirical evidence for them. The question remains: how can we know how causality works unless from our experience of actual causal sequences?
And if inertial motion is irrelevant to the First Way, then why does Michael Augros spend ten pages of this paper (PDF) dealing with the "problem" of inertial motion, and why is Feser himself writing a paper about it?
(One way to make the connection between laws and causes - if you'll forgive me getting technical for a bit - is via Hempel's deductive-nomological model of scientific explanation. On the DN model, a scientific explanation of a particular situation is a list of laws of nature, L1, L2, ... and a list of conditions, C1, C2, ... that guarantee the laws apply in this situation. Then the causes of the phenomenon can be identified as just the conditions, C1, C2, .... In the melting ball example, we would need (at least) a law of melting and a law of heat transfer. The conditions would include the contact between the ball and the hot plate, and the length of time they were in contact. Then we can clearly identify the hot plate as a cause of the ball's gooeyness - and likewise rule out the wand as a cause, as there is no natural law that would allow it to bring about the melting.
In this model the relationship between laws and causes is clear and explicit. This model has problems of its own, of course; it's just an example of the kind of account that Feser needs to give to make his position coherent.)
To be sure, Feser clearly realizes that there is a connection between our experience of the world and our concept of causality. In his first response, he wrote
Oerter ends his latest post with the remark that “It seems that physics is not, after all, irrelevant to metaphysics.” Well, I don’t think I ever said that it is irrelevant.
And in this recent follow-up, he writes
Though metaphysics takes us well beyond the natural world, then, its concepts have a foundation in our empirical knowledge of that world -- to be sure, not necessarily in the knowledge of the specifics of the empirical world that natural science gives us, but in the knowledge of what must be true of any empirical world in general, which the philosophy of nature gives us.
Now for the Aristotelian no less than for the empiricist, all of our concepts and all knowledge must ultimately derive from experience.In that post, he promises another response to my objections. Perhaps he will clarify how our concept of causation can be derived from experience, and yet the experience of quantum phenomena be irrelevant to that concept.
Thirdly, Feser writes.
No, laws are not formal causes.
Good. Now will people please stop telling me that "the laws of quantum mechanics are the cause of electron transitions"? (This remark is directed at those commenters who made that claim, not at Dr. Feser.)
Finally, Feser writes
Now, along the same lines, we might say that the hydrogen atom also behaves as it does “spontaneously,” simply by virtue of having the substantial form it does. Why do the electron transitions occur in just the pattern they do? Because that’s the sort of thing that happens in anything having the substantial form of a hydrogen atom, just as gravitational attraction is the sort of thing that naturally happens in anything having a substantial form of the sort typical of material objects. What is the efficient cause of this pattern? The efficient cause is whatever brought a particular hydrogen atom into existence, just as the efficient cause of gravitational attraction is whatever brought a particular material object into existence. That is one way, anyway, of giving an Aristotelian interpretation of QM phenomena of the sort cited by Oerter, and it is intended only as a sketch made for purposes of illustration rather than a completely worked out account. But it shows how QM can be naturally fitted into the Aristotelian framework using concepts that already exist within the latter.
This is actually very similar to what a physicist would say about the electron and its transitions. But it is a disaster for Feser's position. For, if spontaneous changes of state (with the emission of a photon) are just "the sort of thing that naturally happens" from time to time, then it is clearly not true that "Whatever changes is changed by something else." And so the First Way collapses.
I am not planning any more posts on The Last Superstition (which Prof. Feser will be glad to hear, I'm sure). Any further questions I have for him I'll post on the comments to his blog. Thanks to all of you who have taken part in the discussion, and biggest thanks to Prof. Feser for engaging my questions.