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.
The other parallel universes join through the dimensions, which are essentially "phase" vibrations of different orders. Places where they touch in a more basic sense with relation to our universe, are the places where they create the subatomic particles that are the basis for our electrons, protons and neutrons.
In the sense that Jesus is forever unchanging, and that those who believe in Him are in Him, and that He is in the Father - the essence of "Godness" - you might say that we had a hand in creating the beginning. Yet, in a practical sense, it was the Father Who created through Jesus, even though we might have been allowed to modify a little.
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.
Part of the reasoning for this is found in descriptions of the power of the devil in Ezekiel 28. Part is in the word was - "and the earth was formless and void." "Was" can be translated "became." Another thought about this is that God doesn't do anything uselessly. So why would He create something that was a simple chunk of water - plus the chemicals, so that it was more like a thin mud - and the heavens? Also, the idea in the Revelation that the tail of the dragon (devil) swept a third of the stars out of the sky, shows the power of the devil to destroy a third of the laws of the universe. (The word "stars" is considered by Bible scholars to be angels, and when you consider the many descriptions of the angels and other living, heavenly beings, you can see that they are the laws of the universe... living, powerful laws.)
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.
God hovering over the waters was Him getting right in there to do His work of creation, which might actually have been, in part, re-formation and re-creation.
Putting all this together, we can see that the physics of the universe was extremely different in the past, even in the recent past. Because of this, much (most?) of the timing of things that modern science says is billions of years, etc., is simply what could be described as an upheaval in physics of the past. If things had been a completely smooth operation right back to what scientists call the Big Bang, scientists might be right. Yet, because they are leaving out the descriptions in the Bible, they are missing out on multitudes of things.
EDIT: Part of the reason that people of thousands of years ago - or even hundreds - didn't become as advanced as we, technologically, is that the changing physics of the universe made it very difficult for them determine from one year to the next how to use the sciences. The reason that things have settled down in the last couple thousand years has to do with a slowing of the rate of entropy. You know how a hot piece of iron transfers a lot of its heat to a cold piece of iron, very rapidly, at the beginning of the time when the two come in contact. Then, as the temperature of both approach a happy medium, the exchange rate of heat transfer slows down. This is why the changing physics of the universe isn't changing nearly as rapidly as it did in the past. And, because of it, we are able to examine and use what we have observed though science.
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