I don't know if it's the same thing, but it feels like an analogy:
Protein structure prediction is now considered to be "solved," but the way it was solved was not through physics applied to what is clearly a physics problem. Instead it was solved with lots of data, with protein language modeling, and with deep nets applied to contact maps (which are an old tool in the space), and some refinement at the end.
The end result is correct not because physics simulations are capable of doing the same thing and we could check Alphafold against it, but because we have thousands of solved crystal structures from decades of grueling lab work and electron density map reconstruction from thousands of people.
We still need that crystal structure to be sure of anything, but we can get really good first guesses with AlphaFold and the models that followed, and it has opened new avenues of research because a very very expensive certainty now has very very cheap mostly-right guesses.
When it comes to very complicated things, physics tends to fall down and we need to try non-physics modeling, and/or come up with non-physics abstraction.
Protein folding is in no way "solved". AlphaFold dramatically improved the state-of-the-art, and works very well for monomeric protein chains with structurally resolved nearest neighbors. It abjectly fails on the most interesting proteins - just go check out any of the industry's hottest undrugged targets (e.g. transcription factors)
> When it comes to very complicated things, physics tends to fall down and we need to try non-physics modeling, and/or come up with non-physics abstraction.
"When things are complicated, if I just dream that it is not complicated and solve another problem than the one I have, I find a great solution!"
Joking apart, models that can help target potentially very interesting sub phase space much smaller than the original one, are incredibly useful, but fundamental understanding of the underlying principles, allowing to make very educated guesses on what can and cannot be ignored, usually wins against throwing everything at the wall...
And as you are pointing out, when the complex reality comes knocking in it usually is much much messier...
I have your spherical cow standing on a frictionless surface right here, sir. If you act quickly, I can include the "spherical gaussian sphere" addon with it, at no extra cost.
It’s interesting that we do essentially the same thing in all of non-physics science.
Everything is nuclear physics in the end, but trying to solve problems in, say, economics or psychology by solving a vast number of subatomic equations is only theoretically possible. Even in most of physics we have to round up and make abstractions.