Do we have anomalies accumulating here that indicate the early phase of a scientific revolution in Thomas Kuhn's terminology, that is, a replacement of the standard model/QCD? Or is it still "so far, so good"?
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In the case of NM we happened to have something that is often also computationally simple and efficient so we keep using it, but it is by no means a “correct theory”. just a useful model that is still useful.
i daresay it will continue to be useful for some things even if we eg discover that we are living in a simulation and manage to escape! As long as some part of us will continue to experience this reality it will be useful - the math is simple and gives good approximations in many cases.
EDIT: Like ironically I would say the planetary model has 1 unique utility, which is that for hydrogen-NMR it's useful to just assume that 1 electron is producing a little magnetic field like a Bohr model atom.
Take it or leave it :-)