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If the Smoke Monster is a mutation of electro-magnetism then perhaps it wouldn't be able to hurt Desmond. Unless of course he was in John Locke form and shot him. But if you look back at that conversation that Desmond and Flock had, Desmond made sure that Flock new that he was immune to electro-magnetism (for the most part). Here's a question, and forgive me if i'm forgetting something...but has Desmond ever encountered the Smoke Monster before?