That's an interesting question, I look forward to seeing what sort of responses you get.
The only books I could think to recommend would be some science biographies/histories... the one that popped into my mind first is "The Double Helix." Oh, also that book about Barbara McClintock... "A Feeling for the Organism" I think it's called. That one would probably be more what you're asking for, since her method of doing science is a major focus of the book, as it was pretty unique. (I haven't read any science/philosophy books outside of the field of biology in yeeeears so those are the only specific books I can recommend, heh.)
My husband insists that the reason he's a scientific super-genius (my words, not his) is from learning computer programming at an early age. He was pretty much grounded from ages 10-16 so he spent all that time programming in his room. I don't know if that's what did it, but that guy LIVES the scientific method and logical thinking. Makes me jealous. =]