No amount of appealing to the (apparent) practices of scientists can render affirming the consequent logically valid. That alone should tell you that any rational reconstruction of scientific inference which says “Hey, guess what – affirming the consequent actually works!” is doomed at the start.
The history of science is replete with failures of affirming the consequent. Take the Copernican Revolution, for instance:
What was the problem here? Besides affirming the consequent, defenders of the Aristotelian / Ptolemaic geometry missed what UC-Irvine philosopher of science Kyle Stanford called an “unconceived alternative,” namely, that the stars were MUCH farther away from Earth than anyone realized.
Scientific inference is very messy and hard to model using propositional logic. If I had to lay money on it, however, I’d say that most problems arise (or, conversely, successes occur) when either (a) the majority misses an unconceived alternative, or, worse, insists it doesn’t exist, OR (b) someone is brave or just crazy enough to search for and find a true unconceived alternative. The discovery of H. pylori as the causative agent of ulcers is a beautiful example.
But these are cases involving the truth of empirical premises, and their possible existence, not logical form.
I think what you (mean to) appeal to, Josh, is what’s known as “convergent realism.” On some mornings, I am a convergent realist. Blood really does circulate. The core and mantle of the Earth really are hotter than its crust, and so on.
On other mornings, I am an anti-realist curmudgeon, and follow Larry Laudan (1981, p. 45):
…ever since antiquity critics of epistemic realism have based their scepticism upon a deep-rooted conviction that the fallacy of affirming the consequent is indeed fallacious. When Sextus or Bellarmine or Hume doubted that certain theories which saved the phenomena were warrantable as true, their doubts were based on a belief that the exhibition that a theory had some true consequences left entirely open the truth-status of the theory. Indeed, many non-realists have been non-realists precisely because they believed that false theories, as well as true ones, could have true consequences.
The first thing I learned from my atheist mentor Adolf Grünbaum, as an undergrad in the philosophy of science program at Pitt, is that one can infer true conclusions from false premises. That is just about the most liberating insight one can take away from the entire corpus of the philosophy of science.
Larry Laudan, “A confutation of convergent realism,” Philosophy of Science 48 (1981):19-49.