We are all used to seeing changes of state. When the state of a system changes; say, with an animal having offspring, there is no change in the system, only in the state of the system. But when that offspring mutates into a new species, the change is to the system itself. At the human time horizon, we do not get to see changes of system like this unless we tease, using reason, the knowledge from a set of individually less meaningful observations. Thus you can't learn about a change in the system without deducing it. It's not plain, and we have to use our memories and our intelligence to do the job consciously.
Science as a whole is like this. When a theory of great explanatory power is derived by knocking down false theories, its history appears shifted toward its eventual enshrinement. This is a change of system, and it is happening now with the quantum. Quantum physics is not a new science; it is a new kind of thing, a kind of substratum of science. So quantum mechanics is more fundamental than classical science itself.