So, as LOST is getting all the nearer to it's end, some people are dazzled and confused about all the Egyptian stuff. Where did it all come from? This isn't a proper theory like all the others, this just me trying to connect the dots.
Okay, let's start at Across The Sea. Let's imagine that just after the creation of Smokie and Jacob's turn to godliness some Egyptians came to the island. On their boats they had tons of stones and boulders. Somehow they ended up on the island through some strange time and space travel. They started a society on the island. Then when their pregnant women started dying, they got mighty worried and with all the stones and boulders they built the statue of Taweret. It didn't really fix anything, so as their group slowly started dying off they ventured of into the jungle building all kinds of things. Like the temple. They also build the tunnels underneath the temple. There they encountered the light we saw in Across The Sea - however it was tainted and out came the smoke monster. Believing this was an angry god, they prepared a little altar for sacrificing stuff.
As the Egyptians eventually started dying, the MIB became all the more bitter about the human race, and entered into a heated argument against Jacob. Jacob claimed that a human being is inherently good, whilst MIB claimed the opposite. Thus Jacob started with his lighthouse bring all these people to the island just to prove MIB wrong. And perhaps as a way not be bored.
One day he saw how a group of scientist managed to get to the island through the Hanso family. These people were the kinda, "we're scientists, but we're totally not square man"-type of scientists. They went around the island looking for whatever could help them in their research. They encountered the temple with all of the hostile. They made a deal not to cross the hostile land and keep to themselves.
Now, as the Dharma continued on studying the island, they must've encountered the Egyptian stuff sooner or later. Perhaps they came to associate it with the electromagnetism. So, when making the Swan, a natural, if not slightly stoned, way of showing "oh, something's bad going to happened" was to have the timer turn into scary hieroglyphs.
As I said, I'm just trying to connect the dots through stuff we've been told. And that just seems logical. We don't need to be told how it happened when we've been giving the tools and the clues to figure it out by ourselves.