So... prepare for a rant that contains several theoretical arguments and positions.
Let me start with E=mc2. So most scientists have agreed that mass and energy are the same thing, just in different states. We know then that anything and everything made up of either is subjected to the same rules of positive and negative. They are attracted to each other and reach a balance of neutral when they exist in equal amounts. Protons and neutrons seem to have fixed points in space while electrons seem to be able to be in all places at once, wacky as quantum physics can be.
Mass and energy's interactions make up 3 of the 4 fundamental forces. The 4th force, gravity, while it's laws and effects on space and time are well understood, doesn't seem to have an explanation for it's existence and cause.
Some of the most brilliant minds there ever were have tried to create a unified field theory to complete the standard model have all stumbled in the same area, how macro physics ties to quantum physics, and how gravity ties to both of them. The only theory that has even come close is string theory, but is as of yet, unproven.
Then we find the existence of this troubling thing called dark matter. Annoyingly, the only way we even found it was with gravity (which we still don't get). It doesn't react much with our matter and energy, it seems to exist either on it's own standard model, or is part of a bigger model that we have yet to understand. We do know that the thing that ties it all together is gravity.
So there's my rant. Feel free to comment, elaborate, or correct me. I kind of tried to dumb down a lot of complicated subjects, and it's probably full of holes.