LOST Answers

The light underneath the island was a hole in our universe which allowing matter / antimatter from elsewhere to seep in. The rock was a wedge that kept the hole open just enough for some of this matter to get into our universe. This was used to usurp our realities and laws of physics, such as shifting the island in space / time, etc. This wedge kept the gap open just enough, but not enough to cause it to seal itself back up again. This gap was also doused in running water to help keep it under control, with the side effect of the water containing special healing properties.

Removing the rock allowed the light to go out and matter / antimatter to enter our universe. This began to destroy the island. If left open, it would have eventually destroyed our universe too. Jack had to put the plug back in place to stop this. This was illustrated by Jacob himself with the cork in the bottle of wine.

The smoke monster was an entity from outside the universe, possibly made of carbon atoms and loose covalent bonds that had to take the form and memories of a dead person to interface with this reality. Desmond went inside the cave but was not turned into a smoke moster simply because he was alive when he entered. Jacob’s brother however was thrown into the cave and died when he hit the ground. Desmond found skeletons lying inside the cave, possibly from other people who had tried to enter and died.