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I think that maybe Jacob is the fly in the island's ointment. Smokey has constantly been reffered to as a protector of the island, the glyphs on the Dharma Village egyptian chamber read "to summon protection" It seems to live in the catacombs underneath the temple. So why would the other other others be frightened of it? If there was an island with properties like we have seen, I would rather no human set foot on it too! Smokey is right on the money when he says it always ends the same. He seems to be taking the responsible role here. Jacob mentioned things only ending once, and that everything else is progress towards an end. Sounds more fatalistic than anything. Not to mention the horror Jacob has subjected the survivors to and the horrors he has sanctioned. Smokey showed real empathy towards Locke's condition, whereas Jacob hasn't really ever shown any recognisable emotion.
Just a thought