God could have created sufficient light to make Day constant and universal, but he chose not to do so. He left some darkness, reducing it by half at least. He had plans for the remainder. He made it serve his system that he imposed upon the darkened, deluged earth of verse two. Why? Scripture, as Genesis bears out chapter three, will tell us. Before we turn to his making use of darkness in a special way, redemptively (used in regard to the process and the final result, not in regard to the evil that arose from the choices of free moral agents and a certain tempter), we see in verses six and seven that God created a "firmament" or atmosphere, dividing the waters that enchained the world, and made a lower waters and an upper waters through this division.
This makes little sense, perhaps, to human conception, but this is what God did. An atmosphere, clearly, was necessary to a restored earth--that we can see. Also, it demonstrated God's power over the waters as well. Where before they enchained the world, now they were broken in power and divided by a layer of atmosphere, or "firmament". This firmament God called "heaven."
Meanwhile, the system of Day and Night still operated upon the earth and its new firmament, while the waters now were divided, with the lower waters lying, presmably, upon the earth, and the others lying above the firmament. As for the earth, with perhaps half the waters, if not gone, at least diminished in depth considerably. For, verse nine, "God said, Let the waters under the heaven (firmament: atmosphere) be gathered together unto one place, and let the dry land appear: and it was so." God not only subdued the waters, but separated them, and then went on to further containment and use of them. Now waters were a form of destruction and disaster (and, clearly, evil). Yet God demonstrated in these verses just how he could make them useful (and even productive) servants. From uncontrolled monster-forces he turned the waters into obedient servants, just as he made the darkness, in part and in whole, subservient to Him in preceding verses.
"Exodus: Types of Christ in Moses, the Tabernacle, and the Passover Lamb," by Ronald Ginther
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