Comment by terminalbraid

> decoherence

This has a specific meaning and is not a word I would use here. For something to be "decoherent" the particle phases would need to be "uncorrelated" or "random", but given the internal wavelengths, masses, and strength of the interaction of the particles involved against the spatial dimension of the proton this is not the case under quantum field theory.

In some ways the problem of this being "complicated" is because it's intractably coherent with a fluctuating large number of particles interacting via three "colors" of self-interacting charge (very different from electric charge and not just "three" independent charges) to consider. I'd put money on any decoherence would likely simplify the problem.

> Normally, the universe only asks protons the question: "are you a proton?" and it's like "Yep I'm a proton." (What's your baryon number? What's your charge? etc)

Protons have internal structure (the quarks and gluons) and size. Those are relevant to its interactions. To consider a proton "by itself" and just reduced to quantum numbers is not "normal" if by "normal" you mean "protons at a scale in nature you deal with every day". Those protons are bound in nuclei and are modified by the fact they are bound. These effects have been explicitly measured and documented, the EMC effect being one of them. The "new questions" you are referring to are in fact relevant questions at low energies and are not "new". They are a large active area of research typically referred to as "medium energy" (despite the fact it extends into "low" energy traditional nuclear physics and high energy QCD physics).

Even in a hydrogen atom, the internal structure of the proton modifies the chemistry by small changes in the electronic shell energies, in particular contributions to the lamb shift which has been used to measure the radius of the proton.

Maybe most directly, if what you described were the case you wouldn't have so many decimals in atomic mass numbers of nuclei.

> So having different answers based on how you look is really answering different questions, just like asking an electron: What's your momentum? What's your location?

The problems of looking at quarks and gluons at different energy scales are also endemic to other forces (e.g. electromagnetic) and all particles (for example, look up the running of coupling constants and renormalization theory). Saying they are "different" questions is more akin to comparing questions of skyscraper engineering and concrete dust mechanics. They are not orthogonal as I would consider momentum and location. They're questions of scale and things like emergent effects at different scales.

There are orthogonal questions of internal structure to be considered, though. Deep inelastic scattering processes at high energies tend to ask the "what are the momentum" questions. Elastic nucleon form factors ask more the "location". They both exist in a unified framework of "generalized parton distributions".