Spiritual elements in a science-fiction novel
Does using unexplained spiritual elements (soul, "spiritual"/non-physical beings, afterlife, God, etc.) in a story with a futuristic setting make it science fantasy rather than science fiction?
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That's a question of definitions that one could debate endlessly. Definitions are invented by people, often indirectly by simply using words with a certain meaning in mind without necessarily spelling out a definition. On subtleties like this, different dictionaries will often have different details to the definition.
So really, I agree with @temporary_user_name's comment: Who cares? Just write a good story.
To actually answer the question: I don't see how referring to God or the soul would of itself make a story not science fiction. If a character in a realistic adventure novel said, "It was a miracle that we escaped", and in context it was apparent that he meant that literally, I don't think that would make this now a "religious story" and not an "adventure story".
Or more to the point, suppose someone wrote a story where a character invents a machine that can detect and measure a soul. I'd think that is practically the essence of science fiction: postulating a new and extraordinary technology and exploring the implications. The fact that the technology overlaps a subject that has historically been thought of as "religious" would to my mind make it, at least potentially, more interesting science fiction, not non-science fiction.
And in real life, genres intersect all the time. I've read science fiction murder mysteries and spy thrillers set in fantasy worlds. Almost any genre can include romance subplots. Etc. To say that a story might have elements of science fiction and also elements of religion is an unremarkable assertion.
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There are a few ways to answer this. Which answer you use depends on what you want to achieve - something lacking in the original question. Does the work already exist and you're just trying to categorize it? Or are you in the planning stages?
For this answer, I'm assuming that there are deities or other spiritual elements explicitly in your story.
If there are deities:
Deities of any sort are fantasy, and we should all grow up and acknowledge this. This is the prototypical hardline-atheist answer. Your book will be looked at as such.
Deities may seem unlikely, but what if "god" is really just a powerful energy being? Arthur C. Clarke did this, as did Star Trek. It's a way to have gods in your fiction, still have it be science fiction (maybe), and avoid disrespecting religion.
"Pagan" gods are, of course, fantasy. The god I worship is real, so that makes this sci-fi. That would make your book religious fiction. I'm not aware if religious science-fiction exists or not, so you'd either be joining an existing genre or creating a new one.
If there are no deities, but there are spirits or ghosts, that would probably make your book a fantasy, or possibly what's now called a "paranormal" book.
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Does using unexplained spiritual elements (soul, "spiritual"/non-physical beings, afterlife, God, etc.) in a story with a futuristic setting make it science fantasy rather than science fiction?
If they are treated as real then yes. If we just have a scifi MC that believes in God and souls and ghosts, then no.
I would also classify Star Wars as a Science Fantasy; but Star Trek as science fiction, despite the tendency of many characters in Star Trek to refer to "life essence" or whatnot.
Of course most science fiction takes on fantasy elements. Star Trek uses FTL travel, Time Travel, Transporters, all of which violate the laws of physics as we know them.
But the pretense in Star Trek is that all of this is technology and nothing but. It can coexist with religion, but there is no magic, no ghosts, no God making decisions about what happens next. Even their God-like figures (Q for example) are explicitly alien and using alien technology, Q can be killed.
That is not the pretense in Star Wars; they are explicitly on the spiritual side, an unexplained magical Force that transcends space and can be used only by an elite. The Force is not strong in most people. That they supplement that with technology does not make it science fiction.
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