SiennaTheGr8 said:
we can talk about an absolute "amount" of rest energy. We're not limited to talking about differences in energy here. But if we can't say the same for the potential energy within the system (that contributes to the system's "absolute" rest energy), then isn't there a contradiction?
No, but there is a need to be very careful about describing the actual physics involved.
First, the concept of "potential energy" only applies to a stationary system--roughly, one whose properties as seen from far away don't change with time. So we are not talking about a completely general concept; we're only talking about a particular class of systems.
Second, for that class of systems, the rest energy is "absolute"--i.e., the rest energy itself is a meaningful number, not just differences in it--only in the sense that, as seen from far away, the system as a whole has a 4-momentum vector with an invariant length, which is the rest energy. But this rest energy is not, in general, the sum of rest energies of components of the system. It's not an absolute "amount of stuff" contained in the system. It's just an external property the system has.
Third, you are correct that, for this special class of systems, the potential energy contributes to the rest energy--but
only if we define the "zero point" of potential energy properly. The proper definition is that potential energy goes to zero at spatial infinity, i.e., very far away from the system, which must, on this view, be confined to a finite region of space. Only on this definition does potential energy make a (negative, classically--but see below for some complications when quantum effects are brought in) contribution to the system's rest energy as seen from far away.
It might help to consider a concrete example. Suppose we have a huge cloud of matter that collapses gravitationally into a small spherical object. The cloud starts out spread out over a very large region of space, with each individual piece of matter in the cloud at rest relative to all the others. The spherical object that is the endpoint of the collapse also has all individual pieces of matter at rest, and is at zero temperature, i.e., all possible energy that can be radiated away has been radiated away to infinity. However, no matter escapes during this process; all of the matter particles that were in the initial cloud are in the final spherical object. We can then define a "rest frame" for this entire process (the frame in which both the initial cloud and the final spherical object are at rest), and in this frame, the initial mass ##M_i## of the cloud will be larger than the final mass ##M_f## of the spherical object. The difference ##M_i - M_f## is the "binding energy" of the object, and is also the energy that must have been released as radiation to infinity during the collapse process. (Whether we define the sign of the binding energy as positive or negative is just a convention; either way the physical fact that ##M_i > M_f## is the same.)
SiennaTheGr8 said:
I've read that about 99% of the mass of a proton comes from the kinetic and potential energy "within" it. Is this potential energy not binding energy, and thus negative (or to be subtracted)?
This case is a bit more complicated than the example I gave above, because now we are allowing for individual constituents of the system to move (as seen in the rest frame of the system as a whole). Also, there is a terminology issue here (not yours but in the pop science descriptions) regarding "potential energy".
Allowing for the motion of individual constituents is easy to add to the model, because, as above, we have a rest frame defined for the entire system, so all we have to do is calculate the relativistic energy of each constituent in that frame, i.e., we calculate ##\gamma m## for each constituent, where ##m## is the constituent's rest mass and ##\gamma## is its relativistic gamma factor as evaluated in the system rest frame.
Allowing for "potential energy" in the sense I defined it above--where it goes to zero at infinity--for each constituent is also easy to add to the model, because we can treat each constituent as being in a bound orbit in the system's rest frame, and any such bound orbit has a well-defined sum of kinetic and potential energy. In the simplest case the orbit is circular and the kinetic and potential energies are both constant (the first positive and the second negative), so we can consider them separately; but even for elliptical orbits we can consider their sum, which is a constant of the motion (and will be positive if we include the constituent's rest mass as above).
(Note that in the case of a nucleon, the "orbits" are not classical orbits but ground state quantum energy levels; but the underlying principle is the same.)
However, the term "potential energy" in the case of nucleons does not refer to a simple attractive potential as we have been discussing so far (where potential energy is zero at infinity and gets more and more negative as you get closer and closer to the center of mass of the system). The exact potential function for the strong interaction is not known, but it is known that it becomes repulsive at very short range, which means the "potential energy" of a quark inside a nucleon can actually be positive, not negative, for certain portions of its "orbit", which is actually, as above, a ground state quantum energy level--a more precise way of saying what I just said is that the quark has an amplitude to have a positive potential energy as well as a negative one. Even this is still a highly heuristic description; but the key point is that, when we are dealing with quantum systems of this sort, terms like "potential energy" and "binding energy" become fuzzy, and there can be contributions to the total rest energy of the system, as seen from far away, that have no simple classical interpretation such as we have been discussing.