Lord, thank you for making the universe simple enough that we can understand the principles of how it works, from the smallest atom to the largest galaxy; that could have been otherwise. But thank you also for making the working out of those principles so wonderfully complex and beautiful; that could also have been otherwise.
Two of the more disturbing books I've read are China Miéville's Perdido Street Station and Iron Council. They give me a peculiarly strong impression of a world where there is no underlying order --- where real science is impossible. They're wonderful stories though --- highly recommended :-).
(Yes, I need to locate The Scar...)