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One thing I like most about Lost is how it manages to make ideas like good and evil into material things, in order to discuss the ideas in a different way. The Monster is Evil (whether the Man in Black is evil or not, the Monster has come to symbolize evil on the Island), bringing death, fear and destruction. Dogen was Good, and so protected the Temple. The Spring is Good, and so can heal and give life.
Except the Spring doesn't do that anymore. Not since Jacob died. And, as I've said before, I think it's due to the Infection starting to leak through the cork.
So, what if the energy pockets are the Infection? Yes, they have side effects which include Purple Skies and Time Travel, they involve electromagnetism; but they are actually just the Infection being held back by the Island. What would happen if a hole were to be, um, I don't know, drilled into the Island? Might the Infection start to leak out?
That begs the question: what about the crater Jughead must have left, which the DI covered with concrete and, ultimately, the Swan? Holding back evil by pressing the button so it couldn't build up and break the cork. But it might also mean a bit of the Infection was leaking out all the time.
Could this be why the pregnant women kept dying in childbirth? If conception happens on the Island while the Infection is slowly permeating things, could it be the fetus grows without a "soul" (which would, like the pockets of energy, be represented as electromagnetism or some other such physical thing), but instead are Infected to the point they kill their mothers from the inside?
Once again, this is just for the purposes of Lost and the story. I'm not talking about reality. But in this context, could it be a bit of an answer? Jacob wouldn't really have cared about whether people could give birth or not on the Island, as he brought whomever he wished there without effort. But he certainly wanted the Swan built. The Infection spreading a little and causing women to die in childbirth might be another of Jacob's necessary evils, something he accepted for the greater good. Might it also be why we've yet to see the actual aftermath of the Incident in the past? I mean, a blast of that magnitude would not go unnoticed by the Others, and they might have needed to inform the DI at that point what the energy pockets actually were. Maybe that's why Richard said he saw the Losties die. Jacob might have told him he needed to observe the Incident so he could make sure the Swan was built. He probably would have said it differently - he obviously left Richard in the dark a lot - but it sounds like a mission Jacob would send Richard on.
All speculation, but what do you think?