Adam and Eve?
Could Adam and Eve, the two skeletons disovered by the caves in Season 1, be earlier incarnations of Jacob and MIB? I realize that one of the skeletons they found was a female, but fLocke did say that Jacob stole his body, so maybe that body was a female body? Or maybe Jacob was female at some point and took over a man's body and some point in history.
This would explain the black and white stones that were found with Adam and Eve - an inside joke that has gone on for hundreds or maybe thousand of years. May also explain maybe why Smokey/Christian led Jack to the caves in White Rabbit - he wanted Jack to find the bodies.