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Ok, so I think we've established that Jacob's brother transformed into the Smoke Monster after his encounter with the Source, but there is still inconclusive evidence as to whether Smokey existed before this incident. I believe that there are two likely possibilities...
1. The Smoke Monster's origins are in this event: The fusion of man and intense electromagnetism created this billowing mass of black smoke, or more precisely, the Man in Black was physically transformed from human being to supernatural entity, and his body was disposed of in the process. This made the Man in Black ageless, and we can assume that he has assumed the form of his human self in dialogue with Jacob and Richard, as he vowed revenge on his brother for betraying him and robbing him of his humanity, with his ultimate goal his departure from the Island.
2. The Smoke Monster was the Mother: The Smoke Monster has been protecting the island since the dawn of time, with candidates accepting the role as guardian. Mother's actions at the end were part of a long con. Weary with the responsibility of protecting the island, she provoked her son by causing the village massacre and filling in the well both in her Smoke Monster form, with the result that he would kill her, and thus releasing her of her responsibilities. Part of this theory is that Mother would have pre-empted Jacob's decision to throw his brother into the light, and thus the Man in Black would replace her as the Smoke Monster.
Theory 2 demands that Mother is both the protector of the light and the Smoke Monster, and decided to share the burden of both responsibilities between Jacob and the Man in Black, perhaps not anticipating that the brother would end up antagonistic to each other. Maybe Mother used her Smoke Monster abilities for the good of the Island, and we have several incidents when the Man in Black has killed for the sake of the island ("The Shape of Things to Come") but yet he seems to be of the opinion that the island does not need protecting.
I am leaning towards the possibility that the Smoke Monster was protector of the light up until responsibilities were shared. This is shown in the drawings in the Temple...which seem to originate in Ancient Egyptian times. But Mother split the responsibility between Jacob and MIB because Jacob was considered fundamentally good, while MIB was considered to be "special". MIB, fuelled with vengeance and a desire to leave the island, used his powers for evil for the most part, and has been engineering his plan to leave ever since. This theory however does not mean that the Smoke Monsters through the ages have been one specific deity channeling its way through the human form of others. The Smoke Monster as we know it has the experiences, memories and personality traits of the Man in Black ONLY.
Please share your thoughts as this is a question raised at a very late stage in the game that could have been solved so easily in "Across the Sea" if it wasn't for needless ambiguity on the writers' part. (Unless they are setting us up for a big reveal in upcoming episodes for which I take it back)