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This may be a reach but what if the Smoke Monster is the Electromagnetic Energy. It has been theorized before that it has something to do with it. What if it is emitted when MiB speaks and sort of scrambles your brain and thus comes the phrase: "If you let him talk to you, it is already too late." Or when Claire says Jack is following Locke because he let him talk to you. Bear with me here, what if when jacob was on the Island he could balance out this power, these emissions and now that he is gone, only someone special like Desmond and maybe Dogan etc can withstand this energy. Maybe that is what Whitmore was testing Desmond for and when he passed he saw that it was safe to send Desmond.
Now lets say if you are not effected by the EM energy than you can see things clearly....like the Boy! So in saying that, perhaps James is able to withstand the EM as well.
Maybe everyone who survived the Swan site explosion can also withstand this energy except for Sayid because he was in a weakened state...Maybe they already went through the same type of test.
Perhaps that is why Desmond is unafriad because he sees him for who he is and is not "mystified" by the smoke, the EM. what do you think?