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I think that the point of this verse, or what it is meant to emphasize, is that, even in the dark, chaotic conditions that existed before God began His creative work (that is, from eternity past), God (as represented by His Spirit) was present, and "in control" of the situation. The creative process was thus not a series of random events, but was from its very beginning the work of an eternal God that was carried out in accordance with His defined plan, and for His intended purpose.
Excellent question. God took the initial conditions ("formless and empty") and from Genesis 1:3 onward designed the universe for His ultimate purposes, ending with Man and Woman, created in His image and likeness, ruling over the earth where He created them. On the first three days He "formed" the: heavens, the seas, and the earth, and on days four through six He "filled" the heavens, the seas, and the earth. The initial conditions ("formless and empty") were transformed by His creative Word to become "formed and filled." When His creative work, culminating in the creation of Adam and Eve, was complete, He pronounced all things "very good,"
Why did God’s Spirit hover over the dark waters of the earth? (Genesis 1:2) The Spirit’s activity appears strange in this context. What was he doing there? I personally like John Gill’s (1697-1771) explanation where he says “ This same Spirit "moved" or brooded (u) upon the face of the waters, to impregnate them, as an hen upon eggs to hatch them, so he to separate the parts which were mixed together, and give them a quickening virtue to produce living creatures in them.” When John Gill wrote this in the 1700’s, he had no idea that life had already been evidenced to be present in the waters at that early date. Science today has found chemical signatures in the oldest rocks that indicate organic life was present in the waters. It didn’t take billions or even millions of years for life to form. It was present just as soon as the waters cooled enough to support it. This is a recent discovery so how did John Gill know that the Spirit “brooded upon the face of the waters, to impregnate them,... “ It was because the language used by Moses implied this without any awareness that we would one day come to discover their hidden truth. In my opinion, I believe the text is telling us that the holy Spirit was already working by creating and caring for life growing in the oceans. This should serve as a testimony to the Bible’s insightful accuracy and encourage us today to follow its commands. Only God would have known that life on earth was present from the very beginning.
Water is symbolized in the Bible as many people. When there was no people yet only spirits because in each element of the earth, there is God's spirit. If you also observe water it is formless, and chaotic. God's spirit, hovering, organizing, gathering, and creating the laws of heaven and earth from the waters or the elements of the chaotic universe.
In my opinion, the Spirit hovered or moved (KJV) to search and find the most appropriate place for the dry land called "earth" to appear out of the waters. The location would not have been the polar or tropical regions where life for Adam would be too much of a challenge. The temperate region was considered best as Adam's ultimate home. The basic idea is that the earth was created for Adam, and Adam was created for God. God's divine plan was thus in effect even before any dry land had appeared The dry land of Day 3 wasn't mostly dry - it would be completely dry due to the total absence of rain (until Noah's flood). Any land coming up subject to rain or snow wouldn't be properly termed "earth." So Day 3 doesn't describe all the land existing on our planet. Today we only have an approximation to the original earth before the Flood with the example of oases found in desert or wilderness areas.
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