Look at this, I found an interesting theory on the internet, it explains the black smoke. Look at this book: http://en.wikipedia.org/wiki/Prey_%28novel%29
It’s about some nanorobots that escaped and formed a black smoke….

And thats what I found on that wiki page at the bottom:

It has been said[attribution needed] that the swarm in Prey is the inspiration for the mystical monster on Lost, though nanobots have been officially denied as the nature of the creature.[1][2] However, Damon Lindelof has said (in the 4/30/07 podcast), “Basically anything that appears in a Michael Crichton novel - dinosaurs, nanobots, time travel — they’re all in play.”