Harry Potter and the Methods of Rationality
A blur was coming over Harry's vision, as his brain started to comprehend what had just broken. The whole idea of a unified universe with mathematically regular laws, that was what had been flushed down the toilet; the whole notion of physics. Three thousand years of resolving big complicated things into smaller pieces, discovering that the music of the planets was the same tune as a falling apple, finding that the true laws were perfectly universal and had no exceptions anywhere and took the form of simple math governing the smallest parts, not to mention that the mind was the brain and the brain was made of neurons, a brain was what a person was -
And then a woman turned into a cat, so much for all that.