Genesis 1:2 - “Now the earth was formless and empty,
darkness was over the surface of the deep,
and the Spirit of God was hovering over the waters.”
The Dark, Formless, Empty Earth
In Genesis 1:1b and zircon crystals, we found agreement between science and scripture that the earth started as a hydrosphere, covered in water and clouds. Genesis 1:2 describes it as "formless and empty... darkness was over the surface of the deep." Psalm 104:6 confirms that the earth was covered in water. Job 38:9 confirms the deep was covered in clouds. Science demonstrates this was 3.9 Ga (billion years ago).
The Holy Spirit
Given this concurrance between scripture and science, was the Holy Spirit hovering over the rain (the waters above), or over the deep (the waters below)? All scripture says is "waters".
Knowing that Jesus was also present (Genesis 1:1a) gives us a guide for determining how Jesus and the Holy Spirit might have appeared together at Creation. Short answer: when both appear visibly in scripture, the Holy Spirit appears as a cloud. Clouds hover, even above other clouds. Was Jesus there, too? Let us look in the scriptures for other examples to see.
The Mount of Transfiguration - Matthew 17:2-5a
2 There he was transfigured before them. His face shone like the sun, and his clothes became as white as the light.
3 Just then there appeared before them
Moses and Elijah, talking with Jesus.
4 Peter said to Jesus, “Lord, it is good for us to be here.
If you wish, I will put up three shelters—
one for you, one for Moses and one for Elijah.”
5 While he was still speaking, a bright cloud covered them
Then, God's voice spoke from the cloud. However, God the Father is always in Heaven when Jesus speaks of Him, so the bright cloud was probably the Holy Spirit. It suggests a similar relationship at Creation... God the Father in Heaven, the Holy Spirit hovering as a cloud, and then Jesus, somehow present with the Holy Spirit, creating, as Proverbs 8:30 records.
We can find confirmation of this interpretation by noticing another interesting detail in Mount of Transfiguration account: the presence of Moses. It turns out that understanding Jesus' inclusion of Moses in this moment on the mountain gives additional insight into Jesus' relationship with the Holy Spirit at Creation, though in a very surprising way. I believe Moses' inclusion on the Mount of Transfiguration was in fulfillment to a request he had made thousands of years before...
Jesus Visits Moses at His Tent - Exodus 33:9-23
9 As Moses went into the tent, the pillar of cloud would come
down and stay at the entrance, while the LORD spoke with Moses.
10 Whenever the people saw the pillar of cloud standing at the entrance to the tent,
they all stood and worshiped, each at the entrance to their tent.
11 The LORD would speak to Moses face to face, as one speaks to a friend.
Could the cloud be the Holy Spirit, and the LORD be Jesus? Be mindful that Moses is seeing God face-to-face. Over the next few verses, Moses expresses some hesitance to lead God's people through the desert, and he asks God for assurance that He will be with them. God promises that the Holy Spirit will be there ("My Presence will go with you"). But Moses was seeing Him "face-to-face" right now. Was a cloud all he could ask for?
18 Then Moses said, “Now show me your glory.”
19 And the LORD said, “I will cause all my goodness to pass in front of you,
and I will proclaim my name, the LORD, in your presence.
I will have mercy on whom I will have mercy, and I will have compassion on whom I will have compassion.
20 But,” he said, “you cannot see my face, for no one may see me and live.”
Notice that God spoke to Moses face-to-face, in his tent, then said Moses could not see His face and live when talking of His glory. In other words, Moses was seeing God face-to-face, but not in his glory. This is much as it was for the Apostles when they were with Jesus... talking face-to-face with God, but not really seeing His face, at least not in His glory (until the Mount of Transfiguration!).
Later, we read that God walked by Moses, in His glory, but only allowed him to see His back. Now go back up to our passage in Matthew, where Moses is there to see Jesus face-to-face... in His glory! From this final fulfillment of Moses' request, we see now that Jesus was in fact in Moses' tent with him back in Exodus 33! And it was Jesus who walked by Moses on the mountain, in His glory... and it was the Holy Spirit who was outside Moses' tent, as a cloud.
It would certainly make for a more compelling case if Jesus and the Holy Spirit were actually recorded together at Creation, instead of piecing it together from such disparate scripture. Well, it turns out they were recorded there together, but not where you might expect!
Jesus and the Holy Spirit Together at Creation
Psalm 104 is a parallel account of Creation. The Creation account begins as follows, matching the perspective of one hovering over the clouds 3.9 Ga...
2 The LORD wraps himself in light as with a garment;
he stretches out the heavens like a tent
3 and lays the beams of his upper chambers on their waters.
He makes the clouds his chariot
and rides on the wings of the wind.
4 He makes winds his messengers, flames of fire his servants.
5 He set the earth on its foundations; it can never be moved.
6 You covered it with the watery depths as with a garment;
the waters stood above the mountains.
Now seriously, consider this. If the Holy Spirit is hovering above the rain clouds, then it still may be dark over the surface of the ocean. But, it is not dark above the clouds! Remember, the Heavens and the Earth were created in verse 1; the heavens are above and the earth (albeit obscured) is below. Jesus, glorying in His work is wrapping Himself in the sunlight, as with a garment. Without a proper atmosphere yet, the stars are brilliant, stretching out above Him like a tent. We also see something interesting... His upper chambers are made of light, not water. This scientifically accurate perspective must have come from the Holy Spirit when this Psalm was inspired!
But, was Jesus really above the upper waters? You bet! He was riding the winds in a cloud... the Holy Spirit, who was hovering. To close out this passage, note verses 5 and 6. The earth's foundations were already set, and it was completely covered in water. Though some believe this passage to be the flood, it fits our Creation account in every detail, and it continues all the way through verse 23, Day by Day. However, the sequence for Days 2 through 6 only work if the verses above are describing the conditions of Day 1.
In short, the scripture confirms the science, and vice versa. It tells us that in Genesis 1:2, the Holy Spirit was hovering over the waters, and Jesus was right there with Him, the Father's master craftsman at work.
09/09/2012 - Added references to Job 38
04/12/2013 - Elaborated a little, to help the flow