With quantum mechanics (and modern experimental technology), we can actually look down below the level of individual particles, and we have found that photons are actually their own particles, not patterns of vibration (or whatever) within other particles.

We knew this before quantum mechanics. Lorentz's aether wasn't matter.

You mean quantum mechanics? Quantum mechanics is very elegant, it's just usually explained badly. See http://www.amazon.com/QED-Strange-Theory-Light-Matter/dp/0691024170.

I've read (indeed, I own) this book. I don't know how to evaluate elegance, but the Standard Model particle zoo isn't simple, at least not in the way Newton or special relativity is simple. I wish you would assume I have some idea what I'm talking about and that my concerns and questions might be well motivated, however alien they seem to you.

Would you care to propose some alternative theory of truth?

I would like too but I haven't really figured out what I think. I'm not particularly radical, but I think the epistemology Eliezer has laid out on Less Wrong has some holes, leaves important questions unanswered etc. Maybe one day I'll write something.

Obviously, but that disagreement should then be resolved by reference to experiment. There is no room for persistent disagreement. In engineering, you can have five different methods, each with their own advantages and disadvantages, and this is a stable state. In science, having five different theories is not a stable state; it needs to be resolved, rather than harden into different factions.

But they aren't always resolved that way! Special relativity beat out Lorentzian Ether Theory even though they are empirically equivalent. Obviously if you have two theories that predict different outcomes of some feasible experiment you can run that experiment and resolve the difference. The question is, what we do when there is no experiment to run? Well we do some math and try to come up with testable hypotheses. Using different theories or different vocabulary seems to affect how easy it is to do the math and generate hypotheses.

"And then once you notice that theories of physics have this nasty habit of turning out false... well then I don't even know what you're using to declare A right and B wrong."

Experimental evidence?

As the sentence immediately following this one was supposed to indicate, usually both theories are wrong in the long run.

What does that even mean? How would you apply that to a theory of physics (past or present)? What "theoretical assumptions" are involved in, say, Special Relativity? Special Relativity makes the assertion that the speed of light is constant regardless of reference frame, but this isn't just a mathematical axiom that you can pick up and discard at will; it is based on a huge pile of experimental evidence.

It isn't based on any experimental evidence that distinguishes it from a theory that says mass contracts in the direction it moves in. But it turns out that if you start from a theory which says's light's speed is constant you can come up with things like the theory of General Relativity. Alternately, you might have two theories that describe totally different phenomena without error but have the potential to describe things about other phenomena and eventually one might be subsumed under the other. But it won't always be obvious which theory is the more fundamental one. I suspect one reason there is a lot of work done trying to incorporate gravity into quantum mechanics rather than the other three fundamental forces into General Relativity is that SR/GR just doesn't have the vocabulary to make hypotheses about particle physics. The former is sort of obvious though "Oh there is another force, there must be this other wavicle: a graviton." That doesn't mean it will be an successful approach but that is part of the reason it is the popular one.