It seems to me that at the most general level there are two choices for the "what is, "is"" question. Circular (closed loop), or hierarchical. In a circular system the logic that drives the universe is strictly self contained, the means for and basis of phenomena all may be accounted for. In a hierarchical system, there's a point of irreducibility such that the basis of phenomena, the logic of the universe, are reliant on some sort of "external" system we cannot access by viewing our universe at any scale.

Particles (the proton) may be EMR over a certain frequency threshold. This makes quite a bit of sense when you look at the decay of the neutron, and look at how atoms respond to irradiation.