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kilobug comments on Harry Potter and the Methods of Rationality discussion thread, part 12 - Less Wrong Discussion
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I would say Voltaire's philosophical tales (Zadig, Candid) apply to that qualification, even if they are more written in order to defend a particular pov than about educating in general.
Hard science-fiction could also qualify, it often contains some valid bits of science. But it's hard to tell the limit between the author's imagination and the real science.
Anyway, I second the question, it would be interesting to have more of those.
I recommend repeating your question as a discussion post so that more people will see it.
There are a couple Charles Sheffield books (the story collection "The Compleat McAndrew" is one; I forget which other(s)) where an appendix essay distinguishes the well-supported science from the scientific community's speculation and from the author's own speculation.
I wouldn't put them in the same category as HPMoR, though - they're clearly written to be exciting stories that happen to teach a little interesting science rather than exciting science that happens to be in the form of an interesting story.