Fleming on the Dark Side of the Enlightenment is great, I agree. But I wouldn't say his book is trying to separate the dross of ridiculous belief from the gold of "true" science or philosophy. What I take away from that book is a to me more interesting claim that Enlightenment ideals and methods have always been entangled with varieties of magical beliefs, be they utopian idealism or alchemy or (in a contemporary context) transhumanism. I wrote about this at more length in an article about the history of drugs that appeared in Aeon magazine a few months ago, if you're interested: http://aeon.co/magazine/altered-states/yesterdays-drugs-are-...
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Welcome to HN, by the way!
Aeon and The Appendix have both been sources of some excellent posts here. We'd like to see more such material—the more in-depth, the better. I'm excited to see what you do with The Appendix. There's a crying need for more substantive general-interest articles online.
HN has a largely technical orientation, but its mandate is for intellectual diversity and we're a little low on historical nutrients these days.