People who question who Cain's wife was are usually thinking along this line: "Incest is wrong. So Adam and Eve must have been merely a next step in evolution, surrounded by other primitives that could interbreed but, because they were not descended from Adam and Eve, had no soul." Although, from a young-earth creationist point of view, the bulk of that concept is easily rejected, not many realize that the core of the issue is the primary assumption. In and around the beginning of the world, incest between siblings was not wrong.
When God created Adam and Eve, they were genetically perfect. God looked at them and called His creation "very good" (Genesis 1:31). Although they had the genetic potential to give birth to all the different ethnicities we see today, even that capacity was perfect. They had no genetic defects, no congenital faults—no allergies, cleft palate, club feet, not even early hair loss. Once they were expelled from the Garden of Eden and the Earth was cursed, it's likely they were exposed to DNA-damaging radiation, but the effect was minimal on them and their children. As one generation removed from perfection, Cain was physically almost as perfect as his parents. There would be no genetic problem with him marrying a close relative.
About 2000 years later, the Flood occurred. The Earth's mantle ruptured, probably releasing radiation from the rock. It's likely that the atmosphere changed as well, letting in more cosmic radiation. This radiation would have caused progressive alterations to the DNA of the people. Although God apparently had no qualms about Abraham marrying his half-sister (Genesis 20:12), by the time of Moses, populations were already witnessing genetic damage, particularly in the Egyptian royal family. The Egyptian Pharaohs were so protective of their bloodline that marriages were generally only between close relatives, so much so that it's thought King Tutankhamen's deformities and early death were attributable to his incestuous heritage. To prevent this from occurring to His chosen people, God gave Moses new laws regarding marriage with close relations (Leviticus 18, 20).
But there was another reason for the strict incest laws given in Leviticus. Because, in and amongst the list of close blood-relatives, the law prohibits a man from marrying his aunt or sister-in-law or two women who are closely related. This might indicate the law was given to encourage the strength of the family and respect for its members as much as genetic concerns. Jacob certainly learned that marrying two sisters made for a less than peaceful household (see: Genesis 30).
Another problem people have with the marriage of Cain is that he and Abel and Seth are the only children of Adam and Eve that are mentioned. But just because they are the only ones mentioned doesn't mean they are the only ones in existence. The story of their altercation related to Cain and Abel alone; it's understandable if no other players are brought into the picture. Adam and Eve, perfect and perfectly fertile, had enough offspring to ensure the population of the world. Josephus, the Jewish historian who lived around the time of Christ, claimed they had thirty-three sons and twenty-three daughters. Some of these had apparently moved away and settled east of Eden, in Nod, where Cain and his wife moved to.
Who was Cain's wife? Not a Neanderthal that was nearly human but had no soul. She was probably his sister. Possibly his niece. Since they were physically almost perfect, they would have no need to worry about genetic deformities. And because they were of the first few generations born on Earth, they wouldn't have to worry too much about family power dynamics.
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