Disclaimer: my field of specialization is experimental tests of fundamental physics. I’m not an expert on string theory nor GR. But let’s take Patrick’s example of quantum mechanics, or to be more precise and up-to-date, the Standard Model (SM) of particle physics. The SM is a framework that incorporates three of the four kinds of forces we know in the universe: electromagnetism, strong, and weak forces. The SM gives some meaning to the fundamental particles we know of in the universe (e.g. electron, muon, 6 types of quarks that make up protons and neutrons) as well as the particles that mediate forces (photons, gluons, and gauge bosons). It is completely harmonized with quantum mechanics (QM) and special relativity (SR). But It does not say anything about gravity or General Relativity, the theory which we use to describe gravity.
Now does the SM contradict evidence? Yes and no. Patrick is right in that the SM has passed almost every experimental test that we’ve thrown at it.* The Higgs boson was discovered in 2012, the last piece of the SM. Since then the Large Hadron Collider (LHC) has kept running at higher energies and so far we’ve not discovered any new, exotic particles not predicted by the SM. The most precise measurement in all of physics is predicted by quantum electrodynamics (QED), a part of the SM: the magnetic moment of the electron. In this case, theory and experiment have been shown to agree at 12 decimal places. (Incidentally, the experiment to show this was done downstairs in my lab at Harvard.) Because of this incredible robustness, one can say that the SM is the crowning achievement of decades of particle physics from the 1950s to 2012.
But there are several problems with the SM. One of the biggest ones: according to the SM, the universe as we know it shouldn’t exist. The reason is because the SM doesn’t explain what makes antimatter different from matter. They are perfect opposites of each other. Thus, the Big Bang should’ve produced equal amounts of matter and antimatter, resulting in the two annihilating each other, giving us a bath of photons: no atoms, stars, galaxies, or planets. No us. Now is that an “empirical observation”? I surely think so. This problem is called baryogenesis: by what mechanism does nature produce the asymmetry of baryons verses antibaryons? Questions like these are what makes many particle physicists continue to test the SM, looking to see if it fails in any way. My own experiment is one of those. It looks to find something called CP violation which is not predicted by the SM, which might be the key to explaining baryogenesis. I’ve written more about this in my blog before, if anyone is interested to read it: Why CP Violation Might Explain Everything About the Universe.
So to sum up, while the SM has indeed passed most of the laboratory tests we’ve thrown at it, it fails to explain certain basic features of the Universe. All particle physicists desperately hope that the SM is false at some level. In fact some would go as far as to say we know it cannot be all there is, because of these issues.
- Caveat: Neutrino oscillations are not covered by the SM, and we know they exist. Because of that the people who discovered it got Nobel Prizes. But neutrino oscillations are not the smoking gun that will guide us into figuring out what is wrong with the SM, because one can incorporate them into the SM by a very simple extension to the model. In other words, it’s not weird enough. There was a recent neutrino result regarding sterile neutrinos which might make my statement outdated (and I am not a neutrino expert), but that experimental result has not been unanimously accepted by the community, AFAIK.