Along with the rest of the lesswrong community, I've been enjoying "Harry Potter and the Methods of Rationality."
I would like to heartily recommend another series with similar themes:
Like HP:MOR, we have a protagonist applying scientific methods to understand "magic". Unlike HP:MOR, this protagonist doesn't have the benefit of an accumulated body of knowledge on science and rationality (the setting is medieval era technology, more or less). Refreshingly and realistically, though, her pursuits are part of a larger collaboration, the "steerswomen", a group devoted to furthering and freely disseminating human knowledge. Unlike HP, the protagonist has to be confused (about things we as readers already know) not just for minutes, but for years. We are painstakingly led through every step and misstep of her reasoning.