Earlier quoted context omitted.
> Evidence for atoms and protons was already there before they were "invented". Right, and there is also evidence for dark matter.
I think arenaninja is saying that the theoretical models predicted those things, then empirical experiments later confirmed them. (I don't know if this is actually the case) This gives the theories credibility as being predictive. In this case we have a theoretical mode, but we later notice our empirical data doesn't match this. Both MOND and dark matter are an attempt to patch up our existing theory to explain what…
General relativity might be wrong, but it's probably not over-fitted because it's quite simple as far as theoretical constructs go.
And it has a pretty good track record. Both black holes and gravity waves were "invented" because the theory seemed to indicate that they should exist, even though there was no evidence yet. Both were spectacularly confirmed last year.
That said, we know there is some shortcoming in either GR or quantum mechanics (or both), because they don't agree under certain conditions. Dark matter, being a gravitational phenomena that seems like it might be a new kind of particle, is potentially in that same area.