Mustard Seed Theory by JMP

At the conclusion of "The End", Jack tells Flocke that he is nothing like his friend John Locke and that if John Locke were there he would tell him that he was right all along. I think what Jack was referring to is that John Locke, the man of faith, was right to believe as the island represents a place where faith dominates science.

The "light" at the center of the Island was whatever you wanted it to be provided that you truly believed. For instance, Jacob thought that if you entered the light you would experience a fate worse than death. Consequently, when he tossed his brother into the cavern what came out was malevolence reincarnate. Jack believed that the light would provide him with an opportunity to kill Flocke, which it did. Flocke believed that the light would cause the island to be submerged in water, which it was in the process of doing until Jack killed Flocke. Desmond believed that entering the light would allow Desmond and his Island buddies to enter a world where everyone lived happily ever after [the alternate universe]. When he entered the light, this is exactly what happened, but it didn't happen immediately. [note: I think Desmond could have just dreamed up this heavenly world when whitmore zapped him with the magnetic force - otherwise you get stuck in one of those chicken or the egg conundrums].

Jacob was "special" b/c he was a believer. He believed that he could make Richard immortal and therefore he could. He believed he couldn't kill the smoke monster [b/c that's what his mother told him] and so he couldn't - but he also believed the smoke monster couldn't kill him. I guess he believed if he put Dogan in the temple and touched him that he could put of a sort of force field around the temple, and that is exactly what happened.

The "faith" over "science" thing isn't limited to the Island's
protector [notice Desmond and Flocke mentioned earlier] as John Locke was also "secial" b/c he was a believer. This explains the cabin incident. Jacob hadn't lived in the cabin for a long time, but Ben knew the cabin was his old resting place [maybe Richard told him]. He took Locke to the cabin and told him Jacob was there. Locke believed there was some ghost in the room and what he got is what you or I would imagine if we believed we were in the room with a ghost. Ben told Lock there was a "magical box" where you could get anything you desire and Locke's faith in this allowed him to bring his father [Anthony Cooper] to the island.

There are countless other examples,but the other one that sticks out to me is when Locke told Walt to picture the dagger hitting the tree in his "mind's eye". [note: I think walt was special in a similar way, but his anger at his father may have sent him down a different path].

I am sure there are holes in this theory, but I believe this is what the Island is all about. In the real world Locke was seen as a loser for being so gullable [similar to Jacob], but on a place like the Island he would be rewarded for his faith.

Anyway this doesn't explain everything on the island, but its a start and the good news is that with just a little faith, you will be able to see that there is an answer to your questions about the show. Well....at least some of your questions.