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Jacob and Esau
For the purposes of this theory, the question of whether Jacob and Esau (or whatever name you prefer to call his nemesis) are literally God and Satan is irrelevant. What matters is that these are the roles they function as in the show. Jacob possesses all of the traditional attributes of God (all knowing, all powerful, perfectly good, etc.) with the possible exception of being the creator of all things. It very well could be that Jacob and Esau were once mortal humans and only gained what abilities they possess through unknown scientific or spiritual means. Regardless, Jacob now functions as God in the narrative.
As for the inclusion of a God-like character such as Jacob, consider this: it always seemed as if an unknown force had been working throughout the survivors lives, causing them to cross paths in unexpected ways and eventually bringing them all to the Island with a purpose. With Jacob we realize that this is not merely an impersonal force such as destiny though, but a personal being with a will of his own, which adds all the more depth to the show.
Esau is not Jacob’s brother or equal in any way; rather, Esau relates to Jacob as Satan relates to God in the book of Job. Jacob has all the power, and Esau cannot commit any deed with Jacob knowing or permitting it beforehand. While Esau freely and willingly does commit truly evil acts, Jacob is able to ultimately work the outcome of these to his good purpose, as will be made evident at the “end” to which he refers. This is not the end of time, but rather the end of the war between Jacob and Esau, when the latter is finally proven wrong.
There debate, however, is not whether human nature is fundamentally good or evil, as some have speculated. Jacob would actually agree with Esau that, left to their own devices, humans will always fall into corruption. Thus the debate is over whether or not Jacob is capable of intervening in the corruption which Esau sees playing out whenever humans visit the Island, and which Esau even has a hand in. However, Esau does not see the subtlety with which Jacob works, or the way in which he prefers to work through human being rather than overtly impose his will upon their actions. Thus, Esau perceives their battle as being cyclical in nature, where humans prove him right time and time again. Jacob, in his foreknowledge of the end, possesses an eschatological view, and is already certain of his victory; not only that, he is achieving this victory by using Esau’s own deceptions against him.
The ultimate example of this is the loophole which Esau discovered which finally allowed him to kill Jacob. This loophole was necessary not because a set of established rules existed between the two, but because it simply was not possible for Esau to kill the infinitely more powerful Jacob. However, he did know of Jacob’s respect for the free will of humans, and exploited that knowledge by manipulating Ben. Jacob allowed himself to be killed, as Esau anticipated he would, but Jacob is still capable of taking this most heinous act of evil and bringing about his victory from it.
The Smoke Monster
If Jacob and Esau are to be understood through God and Satan in the book of Job, the Smoke Monster is likewise analogous to the Angel of Death in the book of Exodus. Just as this angel is distinct from Satan, so too is the Smoke Monster distinct from Esau. Additionally, the Smoke Monster is still bound by Jacob to its original purpose of enacting diving judgment, though it at the same time a malevolent agent of Esau’s in rebellion with him against Jacob.