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A few quickies here. First, the span of time in the earth's rotation has altered drastically throughout millions of years. It has had several shifts in the magnetic poles. It has changed as recently as a couple of years ago when El Nino was so powerful, that the major jetsreams it created literally slowed the rotation of the planet by about 1/10 of a second. It might not seem like much, but it affacts everything; the tides, the seasons, night and day.
2. Mists and steam rising from the earth IS water in vapor form. A hot core and a cold outer shell couldn't help but produce vapor so moving over the face of the deep would appear to be the depth of cloud cover, which is water, which the spirit also would have moved across. There is no contradiction in either of these things.
3. Chapters 1-5 all happened around the earth, not on it.
And God made the firmament, (heaven,) and divided the waters which [were] under the firmament (mists and vapors rising up from the earth,) from the waters which [were] above the firmament: (*maximum cloud cover which sunlight couldn't breach,) and it was so.
4. TIME did not begin on earth until Chapter 14.
5. These [are] the GENERATIONS of the heavens and of the earth when they were created, in the day that the LORD God made the earth and the heavens,
And began the cycle of life.