_rpd comments on If there IS alien super-inteligence in our own galaxy, then what it could be like? - Less Wrong
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The superintelligence could have been written to value-load based on its calculations about an alien (to its creators) superintelligence (what Bostrom refers to as the "Hail Mary" approach). This could cause it to value the natural development of alien biology enough to actively hide its activities from us.
...Think of the Federation's "Prime Directive" in Star Trek.
Or we are an experiment (natural or artificial) that yields optimal information when unmanipulated or manipulated imperceptibly (from our point of view).