OP, this has nothing to do with mystery, and everything to do with dehumanization. It's offensive to think that we're being classified as experiments or non-human creatures by people who are ingorant about 99% of reality. In the end, it makes it easier for people to treat us like crap because they can justify it to themselves that we're "not human".
People that make this sh*t up have absolutely no basis for their "theories", no scientific understanding of autism (or anything else for that matter) whatsoever, and half of them probably do most of their "research" by going to backwater sites that have even more people with even less knowledge than the person who made up the "theory", sites that have at best, circumstantial evidence that may or may not be real at all, and at worst some of the most screwed up ideas in human history. And what makes it worse is... people are dumb enough to believe it over real facts.
I have a conspiracy theory of my own: Conspiracy theorists make up stuff that will anger certain people into taking certain action against other certain people, by giving circumstantial evidence that may or may not be completely fictional or relevant, in order to control the masses and thereby controlling applicable law that may come as a result of violence.
Makes it easier to hate conspiracy theorists? Absolutely (if you believe it). Based in reality by way of circumstantial evidence (what conspiracies suggest, how they suggest it, etc)? Yes, by circumstantial evidence alone. Accurate? Probably not.
See my point? In the theory I presented (which is total fiction, mind you), I made conspiracy theorists the poster child for mass control and violence and given how gullible people are, a lot might even believe it and thereby start hating conspiracy theorists because of it, rationalizing any violence against them (even a bunch of insults/spam/etc on the net) as being justified because they are branded as having a dark agenda.
It's no different with conspiracies about autistics being non-human in some way, people use said "theory" to dehumanize us and justify any negative emotion or action toward us, and it's because they're ignorant screws who believe some guy with a "theory" more than real, established fact.
So, yes, it's offensive, it's damaging to us (and only us), and it's not something that should be allowed to occur. These kinds of conspiracy theories are no different than printing libel and frankly, we should have the right to force a retraction and public apology, or sue for the very real damaging effects that said theories cause.
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Writer. Author.