I'm jumping into the middle of this one, but permit me to make a few observations. First, evidence of the senses (sometimes enhanced by instruments) is pretty much all we have to go on in scientific work. True, we can sometimes see a mirage. But ultimately it's sensory evidence that reveals the mirage for what it is.
As for physics being primarily about theories, I think that's wrong. The theories are explanations of data -- and the data are derived from sensory evidence. Once created, a theory can be used for deductive work, but ultimately the theory survives or falls based on whether it jibes with the evidence of the objectively observable world. In other words, sensory evidence rules.
Swamis and such are always attempting to cause doubts about sensory evidence. When they're successful, their followers are left with only their faith in the swami. So they take a ride on the comet. Not a successful career path.
I can agree with you here, PH, but only up to a certain point. FWIW. For one thing, crudely put, it seems to me that physics is more geared to see what it's doing as inviting falsification of theory, where for biology, the main point is to prove, or justify, a theory. Theory and observational data are implicit in both physics and biology. Yet it seems their respective expectations may differ.
Secondly, I think it's worth noting that physics is more "speculative" than biology. For instance, Einstein didn't come up with general relativity by conducting numerous empirical experiments, and them summing up the data to give him a theory. Instead, he received a "gestalt" of an idea in graphical form, and then realized he was challenged to find a language that could represent what he had received. He found that language in Reimannian geometry. The theory then being formalized, next was to subject it to experimental falsification, the result being the predictions of the theory continue to hold up till this day.
In short, there's a lot more "intuition" involved in theorizing in physics than methodological naturalism seems to allow for. JMHO FWIW
Thank you so much for writing, PH!
My response would be the same as betty boop's at post 589. Physics is always looking at the theory. If the theory is good, the data will establish it over time. OTOH, if the data contradicts, then it is time to revisit the theory itself. In any case, the theory must stand on its own merit subject to falsification.
The standard model is already being spoken of in past tense or as subordinate to supersymmetry for that very reason - and both are being captured by geometric physics (extra dimensionality).