Despite having a pretty good Pittsburgh education in the philosophy of science, I never before read Ernan McMullin's "A Case for Scientific Realism". I was especially struck by one thing that I had never noticed before, which Fr. McMullin briefly notes in one context: things are different, realism-wise, in regard to fundamental physics and other areas of science. The rest of this post is me, not McMullin.
Observe that the pessimistic meta-induction works a lot better for fundamental physics than for the special sciences. The meta-induction says that past theories have tended to be eventually refuted, and hence so will the present ones be. (It's really hard to make the statement precise, but nevermind that for now.) But it is false that the special sciences' theories have tended to be eventually refuted. Some, like the geocentric and heliocentric theories in astronomy and the phlogiston theory of combustion, have indeed been refuted. But many theories have stood for millenia. Here is a sample of these theories: (a) there are seasons that come in a cycle, and the cycle is correlated with various botanical phenomena; (b) tigers eat humans and deer; deer eat neither tigers nor humans; (c) rain comes from clouds; (d) herbivores run from apparent danger; (e) much of the earth's energy comes from the sun. And so on. We do not think of these as scientific theories any more because they are so venerable and well-confirmed. This means that we sometimes mistakenly assent to the inductive premise of the meta-induction because those venerable scientific theories that have not been refuted have often become common-sense and hence we exclude them from the sample.
Nonetheless, the pessimistic meta-induction seems to have some force in regard to fundamental physics: there, the change is much more rapid, and very little remains of past theories. We do sometimes get results like the "classical limit" theorems for Quantum Mechanics where we can show that the earlier theory's predictions approximated the predictions of the newer theory, but this approximation in prediction does not typically yield the approximate truth of the earlier theory. The one kind of exception we sometimes get is that sometimes a part of what used to be a fundamental theory survives, but no longer as fundamental—atoms, for instance.
Non-fundamental concepts—such as cell or season—can survive significant shifts in fundamental theories, but obviously fundamental concepts like force or particle find it much more difficult to do so. There is a kind of multiple realizability in the concepts of the special sciences (not along the metaphysical but the conceptual dimension of a two-dimensional modal semantics) which makes them more resilient.
Van Fraassen proposes we be realists about the observable claims of science and non-realists about the unobservable. This is, I think, really implausible. Van Fraassen would have us believe in ova but not in sperm, just because the ovum is large enough to be seen with the naked eye while a sperm is not. But I think there is a view in the vicinity that is worth taking seriously: that we should be realists about non-fundamental science and at least somewhat skeptical of fundamental science.