Many people become Christians thinking that salvation means that they will be free from the struggle with sinful behaviors or destructive ways of thinking. How can Christ live in us while at the same time we have un-Christlike thinking and actions? If the Bible tells us that we are victorious, why do we still experience things like depression, fear, and doubt? In Escaping the Matrix, Greg made the follow observations:
In God’s design, the core of our being—our “spirit” (Heb. 4:12)—is to submit to him. God is to be the ultimate authority telling us as spirit-beings who we are. We are then to have authority over our minds, which includes our thoughts and emotions. Our minds are then to have authority over our bodies, telling them to act out the truths we believe. And through our bodies we are to have authority over our physical environment. We are created to have dominion over the earth (Gen. 1:26-28). We are to be partners with God’s loving lordship and are to work with God to see his will done “on earth as it is in heaven.” (Matt. 6:10).
The god of this age seeks to reverse God’s wonderful arrangement, and he’s largely successful in this fallen world. Satan literally “perverts” it (from the Latin perversio, meaning “to turn upside down”). He uses the world to impact our bodies—all that we experience with our senses—to lie to our minds about what is true. And our spirits submit to this! “That’s just the way I am, “ or, “That’s just the way I see things,” we often hear people say. And God is basically out of the picture. …
We might say that whereas God’s design has us defined from the top down (God >>> spirit) and from the inside out (spirit >>> body >>> world), Satan attempts to define us from the bottom up (Satan >>> world) and from the outside in (world >>> body >>> mind >>> spirit). He wants us to be merely robotic extensions of the people and events we’ve experienced and thereby conformed to the pattern of the world he is over.
Now when we in our innermost being (“spirit”) are submitted to God, the proper order of things is restored in terms of the God >>> spirit relationships. The spirit of the regenerate person genuinely wants to live in relationship with God and to do his will. All that God says is true about us in Scripture is true on this level. We are in our innermost being identified with Christ and are holy, blameless, filled with all the fullness of God, etc. But the proper spirit >>> mind relationship is not automatically restored. On the contrary, because they are rooted in our physical neural-nets, our thoughts and emotions continue on in their autopilot fashion, however they’ve been programmed to run, for good or for ill. This is why we don’t automatically experience the truth of who we truly are in Christ. …
The gap between our regenerate spirits and our largely unregenerate minds explains why we can genuinely want to do God’s will in the core of our being and yet find that we experience desires, motivations, emotions, and behaviors that are completely out of sync with God’s will. We are defined by the top down in terms of the God >>> spirit relationship the moment we truly surrender to Christ. But we are still largely defined from the bottom up in body >>> soul >>> spirit relationship.
This also explains why the New Testament locates the central place of spiritual warfare in the mind. It is here that God’s design and Satan’s design most directly clash. Christ is at work in us, empowering us to bring about our liberation in the mind. But we must assert our God-given authority over our brains and work with him to experience this liberation. (Escaping the Matrix, 82-84)