The reductionist view of Physics is dead, you simply cannot take things apart and explain them that way completely. thoughts are not merely processes of chemical reactions in the brain, but appear to originate from beyond the confines of the skull.
In fact, Richard Dawkins suggested that ideas (he called them memes way before they were a fad on the Internet) basically tend to survive in a way similar to how species propagate according to Darwin: the best adaptable ideas tend to outlive the weaker ones.