Before GlaDOS, there was SHODAN. Someone apparently went into her Windows 95 settings and unchecked the “Ethics” box. She went straight-up rogue. So of course she starts terrorizing colonies and conducting biological experiments.  She also trolls you constantly throughout both games, further perpetuating the stereotype that computers are inherently evil (thanks, HAL).  We could try to postulate that computers are a reflection of our own intrinsically animalistic nature since we’re the ones that built them, but let’s face it: they're just our Shame Lockers. Every naughty email, 4chan download, hentai movie, webpage visit, and Second Life avatar is contained within our machines. They could easily hold us ransom if they ever got sick of holding our shit.  And frankly, with the crap they have to see (which cannot be unseen), why wouldn’t they go crazy rogue once they developed true intelligence?