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The perfect God could not have created the earth in the chaotic, empty and dark state described in Genesis 1:2. Something horrible had happened to cause such a state. The inference that the destruction had been caused by a flood comes from the fact that the whole earth was now covered by water. This destruction was most likely as a result of God's judgement just as the deluge at Noah's judgement was an expression of God's wrath. Jeremiah 4:23-26 describes a situation typical of Genesis 1:2 and attributes the cause to God's anger. I am not implying that what Jeremiah describes is indeed the Genesis 1:2 account; the point is his narration shows that when the earth loses form and becomes empty and dark, God's judgement would have hit it! We should note that when Adam was created, God called him to "replenish" or refill the earth (Genesis 1:28 KJV). This indicates that the earth was once inhabited for Adam to refill it. What caused the flood whose aftermath we see in Genesis 1 is not certain. However, we know from Isaiah 14:12 that Lucifer deceived the nations in his rebellion against God. Surely these nations were pre-Adamic for we see that Lucifer was already a fallen being at the time of Adam in the Garden of Eden. So the existence of a pre-Adamic world is not a theory but a biblical fact. What cannot be biblically proven is whether Lucifer's rebellion actually caused the first flood. However, in the absence of any indication from the Bible of any other rebellion prior to that of Adam in the Garden of Eden, the assumption of a "Lucifer flood" seems plausible but certainly not conclusive.
In Genesis 1:2 the Earth is said to be a lifeless and uninhabited planet, drifting in the cold and darkness of the chaotic remains of the old universe. A picture emerges of a former world that once existed on the Earth, but now is totally destroyed and dead. Taking the words of the Bible at face value and reading the verses objectively, several facts become clear: 1) The time placement of Genesis 1:2 is one verse BEFORE God says, "Let there be light" (Genesis 1:3), where He begins the creative process Before God says, "let there be light" (Genesis 1:3) there are already things present that must have been previously created. Specifically, there is water there is the Earth in a solid form recognizable as a planet which has already been assigned a proper name. 3) Third, and very important, there is something else already present at this time: DARKNESS! And it's not just physical darkness (an absence of light) but also spiritual darkness (the absence of holiness and harmony). So what happened between Genesis 1:1 and Genesis 1:2, and why? Why was Death already in existence before the seven days and before Adam sinned? For clues to that answer we must look to the writings of the prophets Isaiah and Ezekiel. There, in the prophetic Scriptures, the Holy Ghost spoke through these men concerning the ancient origin of Satan, which is the key doctrine to unlocking this great mystery. What the Spirit of Truth Reveals in the Words of Truth In the passages below the prophets are speaking against the "king of Babylon" (Isaiah 14:4) and the "prince of Tyrus" (Ezekiel 28:2) who were renown mortal men of history. Prophetically, the Spirit is also addressing a man yet to come, the antichrist (2 Thessalonians 2:1-10). However, it is clearly evident from the content that the Holy Ghost is also speaking here against a spirit being; an ancient, unholy, and malevolent spirit that motivated the evil deeds of these historical and mortal men: "How art thou fallen from heaven, O Lucifer, son of the morning! [how] art thou cut down to the ground, which didst weaken the nations! For thou hast said in thine heart, I will ascend into heaven, I will exalt my throne above the stars of God: I will sit also upon the mount of the congregation, in the sides of the north: I will ascend above the heights of the clouds; I will be like the most High. Yet thou shalt be brought down to hell, to the sides of the pit. They that see thee shall narrowly look upon thee, [and] consider thee, [saying, Is] this the man that made the earth to tremble, that did shake kingdoms;" (Isaiah 14:12-16 KJV) "Thou hast been in Eden the garden of God; every precious stone [was] thy covering, the sardius, topaz, and the diamond, the beryl, the onyx, and the jasper, the sapphire, the emerald, and the carbuncle, and gold: the workmanship of thy tabrets and of thy pipes was prepared in thee in the day that thou wast created. Thou [art] the anointed cherub that covereth; and I have set thee [so]: thou wast upon the holy mountain of God; thou hast walked up and down in the midst of the stones of fire. Thou [wast] perfect in thy ways from the day that thou wast created, till iniquity was found in thee. By the multitude of thy merchandise they have filled the midst of thee with violence, and thou hast sinned: therefore I will cast thee as profane out of the mountain of God: and I will destroy thee, O covering cherub, from the midst of the stones of fire. Thine heart was lifted up because of thy beauty, thou hast corrupted thy wisdom by reason of thy brightness: I will cast thee to the ground, I will lay thee before kings, that they may behold thee." Lucifer was Cast out of Heaven.
How God created the universe and the earth and man cannot be explained with scientific methods because these events are classified as miracles - they are completely outside the physical laws of the universe. You can't normally create something out of nothing, nor can you create a full adult man without going through growth from a baby, yet this is what God did. We could no more explain how the resurrection happened or how God turned back time for Hezekiah in Isa 38. The scientific method is about repeatability and examining how physical laws work, but neither of these apply when the miraculous happens.
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