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Back in season 5, when young Ben is shot by Sayid, he is given to Richard who in return states that he can heal Ben but that he will never be the same. I think this has to do with the revival method used on Sayid and also maybe Claire (temple fountain). If this is so, and if the term "will never be the same" means "infected by darkness" - the affliction affecting Sayid currently in the past season 6 episode - then Ben being infected by darkness makes sense. It also explains why Jacob never acknowledged Ben's presence as a leader and never met with him face to face at all.
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Secondly, what does this mean to be infected. When the head temple other (samurai-looking dude) runs the tests on Sayid to try and find this infection, he throws that gra…