First, it is vital to understand that the answer to this question can come only from the Bible itself. The Bible is the only body of literature of which we can say, "Thus says the LORD" (another issue we could discuss).
Well, what does the Bible say about God's sovereignty? The Bible says that God is completely sovereign (in control), over history, over nature, even over the hearts of men. We see this in Daniel 4:35, where Daniel says, "He [God] does according to His will in the host of heaven and among the inhabitants of earth; and no one can ward off His hand or say to Him, 'What hast Thou done?'" We see his sovereignty over the heart of man in Exodus 3:21, where God causes the Egyptians to have favor upon Israel: "I [God] will grant this people [Israel] favor in the sight of the Egyptians." We see God's sovereignty even over what we call 'luck': "The lot is cast into the lap, but its every decision is from the LORD." Casting the lot was like rolling dice. It was pure chance. But this verse says that every casting of the lot (rolling of the dice) is decided by God. God is completely sovereign.
But what about our actions? Are we free? The Bible says that, while God is in control, we are free to do as we wish. We see this, for example, in Mark 14:7 where Jesus says, "The poor you always have with you, and whenever you wish, you can do them good." As we see from this statement, and other Biblical statements like it, we really do have wishes, and we can act according to what we wish. So, in this sense, we are free -- free to do as we wish (which is what we typically mean by "free will").
Not only does the Bible claim that God is sovereign and that man is free, but it even presents these two together. Concerning his crucifiction, Jesus said, "The Son of Man is to go [to death], just as it is written of Him [God planned it]; but woe to that man by whom the Son of Man is betrayed [man's choosing]! It would have been good for that man if he had not been born [man held responsible for his free choice]." Shortly after the resurrection of Christ, Peter preached this (Acts 2:22): "Men of Israel, listen to these words: Jesus the Nazarene, a man attested to you by God with miracles and wonders and signs which God performed through Him in your midst, just as you yourselves know -- this Man, delivered up by the predetermined plan and foreknowledge of God [God's sovereignty], you nailed to a cross by the hands of godless men [man's choice] and put Him to death." We see this in God's dealing with Pharaoh as well. Throughout Exodus 7-11, the text says that Pharaoh hardened his heart. But in this same text, it also says that God hardened Pharaoh's heart. The Bible claims that God is in control and that man does as he wishes, together in the same texts.
So that's what the Bible says. But, thinking about it philosophically, how can both be true? We first must clear up some common misconceptions. The first misconception is that man's freedom means that man has the ability to do what God has not decreed. If this is what it means for man to be free, then we have a contradiction. For it is not possible for everything to happen according to God's decree and for man to act against that decree. But that is not what the Bible means when it says that man is free. What the Bible means is that man is free to do as he wishes. So, is it contradictory to say that everything God decrees comes to pass and to say that man does as he wishes? No, it is not. It may be mysterious (we may not fully understand it), but it does not lead to a contradiction (something that logically cannot be true).
The second misconception is that God's sovereignty means that we are prevented from doing as we wish, but are simply puppets through which God does as he wishes. This assumes that God's sovereignty is coersive. If this were true, then we would again have a contradiction, for we cannot be coersed and free at the same time. But God does not coerse us. We are not "puppets on a string." We are not creatures who are manipulated to carry out God's decree against our will. We do as we wish -- period. Again, this is mysterious, but not contradictory.
Now that we've addressed the misconceptions, let's actually explain what we can about how God is in control and man is free. To explain it, allow me to make use of an illustration. Not too long ago, Star Wars was on the silver screen again with new scenes. There are several characters in the movie, including Han Solo, Princess Leah, Luke Skywalker, and Darth Vader. Imagine that you are on the Death Star with Vader, watching his every move. As you watch him, ask yourself, "Is Vader free to do as he wishes? Of course he is! But then ask yourself another question: is George Lucas not in control of his every action? Of course he is! Darth Vader is free to do as he wishes because he has the power of choice. Lucas is in control, not because he coerses Vader (Vader does as he wishes), but because he wrote the script of Star Wars. In the same way, we are free because we have the power of choice, but God is in control because he wrote the script of reality. How out of place it would be if you were to watch Vader on that Death Star saying, "It's your fault, Lucas. I did this only because you wrote it in the script"? The fact that Lucas wrote the script does not take away from the fact that Vader is free to do as he wishes in Star Wars and responsible for what he does. He chose it!
When discussing the mystery of divine sovereignty and human freedom, we must be careful to say precisely what the mystery is and what it is not. The mystery is not how these two things can both be true, for they must be true. (If God did not create us free to do as we wish, he would not be the Creator of men, but of robots. If God is not in control of all things, then he is not truly God, but merely some creature more powerful than us.) This is not a foreign concept. God is the Creator and Producer of reality. Since we are created in God's image, we reflect who God is in many ways. One of those ways is by creating and producing. We create and produce movies, books, etc. Of course, we don't reflect God in the sense that we cannot create and produce reality as God does. But just as a producer is in control of a movie, so God is in control of reality.
So what is the mystery, properly defined? The mystery is in precisely how these two things relate with one another. What is the connection between God's sovereignty and human freedom? The connection between these two does not lie within the universe as we know it (it is totally different), just as the relationship between Lucas' control and Vader's choice lies outside the realm of the movie (Vader would not be able to comprehend the connection, even though we who are outside the realm of the movie understand it quite well). So only God, who is the only one outside the realm of reality as we know it, fully understands how divine sovereignty and human freedom are connected. That's the mystery (not the existence of divine sovereignty and human freedom, but the connection between the two)!
So what's the purpose in such a discussion? The main purpose should not be for mere intellectual curiosity. The main purpose should be to learn how we should respond to these facts. How do we respond to the fact that we are free to do as we wish? We should respond by doing as God requires us to do, and to repent and turn to Jesus for salvation when we fail. How do we respond to the fact that God is in control of everything? We should respond by taking comfort in the fact that God is for his people and he has the power to accomplish his purposes. These are the proper responses, and this is why the Bible presents these things, not so we can have intellectual debates, but so we will live right.
So let me recap. God is in control of all things, and man is free to do as he wishes. There is no contradiction between these two. Infact, we see examples of this in life, as we ourselves produce books and movies. There is no mystery in the fact that divine sovereignty and human freedom both exist. The mystery is in their connection. This mystery, however, is just that, a mystery and not a contradiction. The problem is not that they both can't be true, for we have seen that they are both consistent. The problem is that the connection between these two is beyond our understanding. And we should expect that it would be beyond our understanding, for we are talking about the fact that God is totally beyond our universe (as Lucas is totally beyond Star Wars). How can we who are in the universe understand God's sovereignty which operates beyond the universe?
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