Keep in mind that 'darkness' is just as transparent as the 'water' and hence, does not exist.

Edit: As for the firmament, would'nt that be the 'bit' where other parallel univere's 'join' which MAY explain where that 'spirit' of god came from?
Truth is guy's, I'd go as far as say, WE created the begining, from nothing more than a thought, an eternal thought, that grew in the abyss of our mind. I see us as looking IN life, as opposed to most who see out..
Space is the universal mind.
There is some slight evidence in the Bible that between the beginning, and the first day, that somewhere in there, the battle between the archangel Michael and the devil mentioned in the Revelation took place.
If there had been the electromagnetic frequencies of things like light and magnetism before the first day, the battle between Micheal and the devil was so violent that it wiped out whole sections of "universal science" so that the earth became as it was explained at the time the Spirit of God hovered over the waters.
Do you believe this bullshit? Archangel Michael and devil are fictional characters of Jewish mythology. Wake up and come back to reality.