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In 'Not in Portland', Karl is found at the Hydra Station in Room 23 being subjected to what appears to be brainwashing. According to the Lost podcast, Dharma was doing experiments on animals here but what is it being used for now?
When Richard takes young Ben from Kate, he asks if she's sure as Ben will 'be one of us' and 'loose his innocence'. It's as if Ben will go in as one person, have an experience, and come through it quite different than when he went in. Could that experience be similiar to brainwashing? Could Ben, who quite possibly has trapped Jacob, be using Room 23 to replicate the type of experience someone has when the are taken to the Temple? In essence circumventing the process that makes them loyal to the Island and replacing it with one that makes them loyal to him?