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Alicorn comments on Rationality Quotes September 2012 - Less Wrong
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There was a (flimsy) historical reason - there had been wars about "augments" in the past; the anti-augments won (somehow), determined the war was about "people setting themselves above their fellow humans", and discouraged more people augmenting themselves/their children in this way by (ineffectively) making it a net negative.
Heck, anti-fascism beat fascism, it's not always the stronger-seeming ideology that comes out on top.
Anti-fascism is perhaps more usefully described as pro-something else. In the event, communism.
I read somewhere that, in Star Trek land, genetic engineering of intelligent beings is highly correlated with evil, either because it's being done for an evil purpose to begin with or because the engineered beings themselves end up as arrogant, narcissistic jerks with a strong tendency toward becoming evil. The latter implies that there's a technical problem with the genetic engineering of humans that hasn't been solved yet, which Bashir was lucky to have avoided.
It might not be a technical problem. It might merely be that most augments are raised by people who keep telling them that they're genetically superior to everyone else and therefore create in them a sense of arrogance and entitlement. Which is only made worse by the fact that they actually are stronger, healthier and smarter than everyone else (but not by as big a margin as they tend to imagine).