Shut Up and Calculate
The main thesis is that the universe is a mathematical universe, i.e. mathematics does not describe a universe, they are the universe (a possible answer to [the-unreasonable-effectiveness-of-mathematics-in-the-natural-sciences]).
When we derive the consequences of a theory, we introduce new concepts — protons, molecules, stars — because they are convenient. It is important to remember, however, that it is we humans who create these concepts; in principle, everything could be calculated without this baggage.