Have you read anything by Julian May? Her Pliocene Exile series has dwarves, elves and magic powers. Only the dwarves and elves are really exiles from a dimorphic alien species who came to earth because their sentient ship determined it was biologically compatible, and the magic is psionics.
Then in her Moon series, magical amulets are communications devices made by a sadistic species of energy beings who live, or are, the Aurora Borealis. They call themselves the Greater Lights and you properly greet them in your request for favours by saying "All hail the Cold Light Army".
There is no difference between science fiction and fantasy except for this: science fiction is rationalistic whereas fantasy is mystical. That's why there exists the dichotomy between ray guns, aliens, psionics versus wands, elves, magic. Talking trees? Baah, that's just biotechnology!
No, the real reason why LOTR is fantasy is because of JRR Tolkien's crap about the Maiar, powerful spirits that rule the world. Also because of his feudalism. In a science-fiction context you can portray feudalism, as Julian May does, but you can't say this is how the world should or ought to be.
So when princes win kingdoms in science-fiction, it's because they're smarter, stronger and braver than anyone else. It isn't because they've got any Divine Right To Rule. And when the humans struck down the elves' tyranny in May's Pliocene Exile series, this was a GOOD thing. Not like in LOTR where the humans' defiance of their elvish overlords in the divinely preordained order resulted in them being destroyed.
When Picard the starship captain defies the gods then this is good. When Paksennarion the paladin defies the gods then this is evil. Because in a rationalistic worldview the universe is to be controlled and subjugated, but in a mystical one the universe is to be feared and propitiated.
Given that our civilization is entirely the result of rationalists, it amazes me that we allow the magical thinkers to enjoy the fruits of civilization instead of driving them into the wilds to die of starvation. I remain hopeful this is only because we haven't figured out how to eugenics the mysticism out of human DNA, yet.
No comment on this subject can be complete without reference to David Brin's essay on the romantics now only available at the internet archive from its former URL (http://www.davidbrin.com/tolkienarticle.html). The only non-Romantic mystical writer I know of is Ursula K LeGuin in her Earthsea series.
Oh and the Romantics are still with us today. They're calling themselves Greens now. And they're just as dedicated to anti-industrialism as ever. They've given up the hierarchy bit but have more than made up for it in sheer misanthropy.
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