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1. The game of Senet was given to MIB by Mother. Senet was a popular board game in ancient Egypt and may possibly be one of the ancestors of Backgammon. People of all levels of ancient Egyptian society played it and some believe it had religious meaning. Senet was the favorite pastime of king tut and in fact his mother in-laws name "Nefertiti" can be traced to one of the symbols on the game board. She likely found this on the island.
2. Time flash on island when the well disappeared and Sawyer was left holding the rope, which had traveled in time with him because he was holding it during the flash, the statue of Taweret was seen. Since the well is not there and appears to have not been built yet but the statue is seen this is a strong argument for the ancient Egyptians being on the island before Jacob and MIB.
3. The Romans conquered the city of Carthage (in ancient Tunisia) 2nd century BC. This clue was also mentioned by Charlotte as she was near death during the time flashes when she said, "I know more about ancient Carthage than Hannibal himself." This was a clue, I believe, that Charlotte gave us as to the ancient history and mythology of the island. Tunisia is the location that the person turning the wheel winds up in.
4. Egypt became a province of the Roman Empire in 30 BC. This is long before we see Mother, Claudia, and the birth of Jacob and MIB. The ancient ruins, wheel room, the Statue of Taweret, the temple basement, the underground tunnels all were ancient Egyptian and had glyphs.
5. The wheel room was only discovered and unearthed by MIB while digging the well, which was right next to the wheel room. When Locke meets Christian in there you can clearly see that they are two different places but next to each other. This well is the one by the Orchid Station. The wheel room had glyphs on the pillars, which show that it was built by the Egyptians, although they did not attempt to harness the source, the exotic matter, with the wheel.
I can safely presume that when the Dharma Initiative was building all of the stations and doing so much excavating on the island, that they discovered many if not all of the ancient Egyptian influences such as the ruins and the glyphs. I think that it was for this very simple reason that they used glyphs on the count down clock in the Swan.