The episode "Ab Aeterno" certainly answers many questions that we LOST fans have been searching for. It also opens up whole new twists and turns. Principal concepts behind this episode include two ideas that are often points of argument among theologians; mainly that of "Free Will versus Predestination" and "Total Depravity."
As a disclaimer, I myself am a Christian who is theologically a Calvinist. I couldn't help but notice that Jacob's own view regarding the depravity of man and the role of free will stand diametrically opposite of the Calvinist perspective. So much so that I have to wonder if this opposition is more than just a coincidence. I really think that the show is going out of it's way to intentionally criticize a particular viewpoint on the nature of God.
Calvinism teaches that mankind is totally depraved. From the Wikipedia article regarding Total Depravity we read, "The doctrine of total depravity asserts that people are by nature not inclined or even able to love God wholly with heart, mind, and strength, but rather all are inclined by nature to serve their own will and desires and to reject the rule of God."
This statement is the antithesis of Jacob's own perspective. In fact, it would appear that the Man in Black is a Calvinist and Jacob is on a mission to prove the Man in Black wrong.
Additionally, Jacob seems obsessed with maintaining the free will of all those who arrive on the Island. He doesn't want to directly intercede with them in order to direct their actions into doing "the right thing."
Calvinism is usually broken down into five key doctrines. They are:
1. Total Depravity
2. Unconditional Election
3. Limited Atonement
4. Irresistible Grace
5. Preservation of the saints
All five of these doctrines are based in the idea that mankind lacks any "free will" ability to save himself or to please God. Calvinism teaches quite the opposite: Mankind has been flawed since Adam and Eve and cannot save himself. God himself must intervene in the lives of men to save them. Those whom God saves are saved through no action of their own doing, it's all the work of God on their behalf.
This is very non-Jacob. Jacob seems to believe that humankind can, in fact, do the right thing and pull themselves up by their own bootstraps, so to speak.
It's interesting to note that Carlton Cuse himself was raised Roman Catholic and the ideas expressed in Calvinism were among those that led to the split of Protestantism from Roman Catholicism. In fact, those Christian Churches which still prescribe to the doctrines of Calvinism remain the most vocal opponents to the Roman Catholic institution today, so it may not be too much of a stretch to imagine that LOST is intentionally criticizing a viewpoint that many Christians find to be either heretical or blasphemous.