(Genesis 2:7:  And the Lord God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul.)

The Lord God formed man of the dust of the ground: This refers to the human body. "The breath of life" was blown into the nostrils, which is the human spirit. "The Living soul" means the human soul. A complete man, thus, consists of three parts: spirit, soul and body.

(Hebrews. 4:12-13: For the word of God is living and active. Sharper than any double-edged sword, it penetrates even to dividing soul and spirit, joints and marrow; it judges the thoughts and attitudes of the heart. Nothing in all creation is hidden from God’s sight. Everything is uncovered and laid bare before the eyes of him to whom we must give ACCOUNT.)  Some people view the soul and body interchangeably, while others think the soul and spirit are the same. But it’s more accurate to think of them as separate components.  Our soul is the conscious part of us, composed of mind (intellect), will, and emotions.   It makes choices and controls our behavior by giving orders to the body. Our spirit is the subconscious part, an internal adviser to the conscious soul.  It’s our conscience. (Corinthians 2:11:  For what man knows the things of a man except the spirit of the man which is in him? Even so no one knows the things of God except the Spirit of God.)

Both our soul and our spirit are intangible and eternal and are housed in our body which is tangible and temporal. Our body is designed for use in this life, and when we die we leave it behind. Paul described our body as our earthly dwelling and spoke of how we long to be clothed with our heavenly dwelling.  Believers don’t desire so much to be rid of our earthly bodies, he said, as to receive our heavenly ones. He said RECEIVING our heavenly body is the very purpose for which we were created, and that’s why God gave us the Holy Spirit at the first moment of our belief. He is a deposit guaranteeing what is to come, which is the exchange of our earthly dwelling for our heavenly one. (2 Cor. 5:1-5:  For we know that if the earthly tent we live in is destroyed, we have a building from God, an eternal house in heaven, not built by human hands. ² Meanwhile we groan, longing to be clothed instead with our heavenly dwelling, ³ because when we are clothed, we will not be found naked. ⁴ For while we are in this tent, we groan and are burdened, because we do not wish to be unclothed but to be clothed instead with our heavenly dwelling, so that what is mortal may be swallowed up by life. ⁵ Now the one who has fashioned us for this very purpose is God, who has given us the Spirit as a deposit, guaranteeing what is to come.)

It Wasn’t Always Like That

I believe Adam and Eve were created with a heavenly alignment of body, soul, and spirit.  Their body was submissive to their soul which was submissive to their spirit which was one with the Spirit of God.  But at the fall this alignment was perverted and through Satan’s INFLUENCE the soul began to assert itself over the spirit. Both were contaminated by sin and the direct link to God was broken. In the time after the fall the soul became more assertive as man entered the period between Adam and Noah that some call the Dispensation of Conscience. Man was left to decide for himself what was right but because of the misalignment that came with the fall, things got progressively worse until God had to wipe the slate clean and start over. This experience has been repeated again and again. Even the time of Israel’s dominance in the world, when the communication link with God was formally re-opened, ended in failure. During that period Prophets were appointed to speak to the people for God and Priests to speak to God for the people. But it wasn’t enough.

The problem was that the spirit of unsaved man is confused and uncertain because of the effects of sin and often gives bad advice to his soul, which is also contaminated by sin, making it impossible for him to please God.

The cross changed all that. Now, when we are born again our spirit becomes one with the Spirit of God (1 Cor. 6:17: But whoever is united with the Lord is one with him in spirit.) and the confusion and uncertainty clears up. Our spirit again knows right and wrong as absolutes, and as our conscience it begins to serve as a reliable guide to our soul, which is still sin infested. (Titus 3: 5-7:  He saved us, not because of righteous things we had done, but because of his mercy. He saved us through the washing of rebirth and renewal by the Holy Spirit, ⁶ whom he poured out on us generously through Jesus Christ our Savior, ⁷ so that, having been justified by his grace, we might become heirs having the hope of eternal life.. That we may be called by his grace, righteousness, can become heirs with the hope of eternal life.)

The difference that being born again makes in us is so profound that we can only understand God’s word after we become believers. The natural man cannot comprehend it. (1 Cor 2:14: The person without the Spirit does not accept the things that come from the Spirit of God but considers them foolishness, and cannot understand them because they are discerned only through the Spirit.) This explains why the Lord’s disciples were often confused about His teaching, and failed to understand much of it. They didn’t RECEIVE the Holy Spirit until the night of His resurrection. (John 20:22: And with that he breathed on them and said, “Receive the Holy Spirit.)

This is also why Jesus told us that our righteousness has to surpass that of the Pharisees and the teachers of the law.  Not being born again, their efforts at keeping the law were acts of will and were often in conflict with what their spirits were advising them to do. In other words, it was still a matter of their soul asserting itself over their spirit. They just knew the law well enough to know when their spirits were giving them bad advice.  In Isaiah 29:13 the Lord had said, “These people come near to me with their lips (governed by the soul), but their hearts (spirits) are far from me.” Jesus accused them of looking like whitewashed tombs, beautiful on the outside, but inside full of dead men’s bones and everything unclean (Matt. 23:27:  “Woe to you, teachers of the law and Pharisees, you hypocrites! You are like whitewashed tombs, which look beautiful on the outside but on the inside are full of the bones of the dead and everything unclean.) Their obedience to the law was only intellectual assent backed up by will power. Their spirit was still infested with sin.

Back To Hebrews 4

But the Lord pays special attention to the motives of our heart and judges us on our intentions, not our actions. This is what the writer to the Hebrews meant when he said that the word of God can divide soul (behavior) and spirit (motive). He is not fooled by man’s attempts at good behavior. He knows the thoughts and attitudes of our heart. Nothing is hidden from His sight. Commenting on ceremonial cleanliness He said that it’s not what goes into us that makes us unclean, but what comes out of us. (Matt. 15:17-19: “For out of the heart come evil thoughts, murder, adultery, sexual immorality, theft, false testimony, slander.”)  Jeremiah wrote that the heart of man is deceitful above all things and beyond cure. (Jere. 17:9: The heart is deceitful above all things    and beyond cure.    Who can understand it?) After sinning with Bathsheba, David prayed that God would create in him a pure heart, and renew a steadfast spirit within him. (Psalm 51:10: Create in me a pure heart, O God, and renew a steadfast spirit within me.)  This is what happens when we’re born again and the Holy Spirit unites with our spirit. It renews a steadfast spirit with in us.  It’s what David longed for, but it couldn’t happen before the cross. (John 7:39: By this he meant the Spirit, whom those who believed in him were later to 

RECEIVE. Up to that time the Spirit had not been given, since Jesus had not yet been glorified.)

In effect, the Holy Spirit works through our spirit to repossess our soul from its bondage to sin. But since it’s not the conscious part of us, our spirit can only WORK to INFLUENCE our decisions. Our soul must choose to heed the advice of our spirit, in whose “ear” the Holy Spirit is whispering. This is what Paul meant when he told us to be transformed by the renewing of our minds (soul) (Romans 12:2: Do not conform to the pattern of this world, but be transformed by the renewing of your mind. Then you will be able to test and approve what God’s will is—his good, pleasing and perfect will.) This transformation consists of consciously choosing to allow the Holy Spirit to become the primary influence in determining our actions. This is the heavenly alignment again. God’s Spirit to our spirit, to our soul, and to our body. This is why the Pharisees were criticized. God’s Spirit was not within them, and so their obedience was a product of their intellect, their soul. Their spirit remained unregenerate. It looked good on the outside, but inside it was all out of order. It was form without substance, and it produced self-righteousness, not humility.

The biggest problem we have is that our soul is still struggling with its bondage to sin, and therefore must constantly choose to submit to our renewed spirit. Remember the soul is where our behavioral decisions are made. Our spirit is one with the Spirit of God, but can only advise. Paul described our dilemma poignantly in Romans 7:14-25: We know that the law is spiritual; but I am unspiritual, sold as a slave to sin. ¹⁵ I do not understand what I do. For what I want to do I do not do, but what I hate I do. ¹⁶ And if I do what I do not want to do, I agree that the law is good. ¹⁷ As it is, it is no longer I myself who do it, but it is sin living in me. ¹⁸ For I know that good itself does not dwell in me, that is, in my sinful nature. For I have the desire to do what is good, but I cannot carry it out. ¹⁹ For I do not do the good I want to do, but the evil I do not want to do—this I keep on doing. ²⁰ Now if I do what I do not want to do, it is no longer I who do it, but it is sin living in me that does it. ²¹ So I find this law at WORK: Although I want to do good, evil is right there with me. ²² For in my inner being I delight in God’s law; ²³ but I see another law at WORK in me, waging war against the law of my mind and making me a prisoner of the law of sin at WORK within me. ²⁴ What a wretched man I am! Who will rescue me from this body that is subject to death? ²⁵ Thanks be to God, who delivers me through Jesus Christ our Lord! So then, I myself in my mind am a slave to God’s law, but in my sinful nature a slave to the law of sin, saying that he had the desire to do good but could not carry it out. His spirit was one with God, but his soul sometimes rebelled. Inwardly he could delight in God’s Law, but outwardly he would sometimes conform to the law of sin and death. (John 16: 7-8: But very truly I tell you, it is for your good that I am going away. Unless I go away, the Advocate will not come to you; but if I go, I will send him to you. ⁸ When he comes, he will prove the world to be in the wrong about sin and righteousness and judgment.)

It’s actually the opposite of the Pharisees’ problem. They looked good on the outside but were full of evil thoughts and intentions. While the Lord condemned them, he directs no condemnation toward us (Romans 8:1: Therefore, there is now no condemnation for those who are in Christ Jesus.) because although our soul often betrays us, our spirit is one with God. He goes so far as to separate the behavior from the believer saying that it’s not we who sin, but the sin nature that dwells within us. (Romans 7:20: Now if I do what I do not want to do, it is no longer I who do it, but it is sin living in me that does it.) (Romans 8: 5: For those who live according to the flesh set their minds on the things of the flesh, but those who live according to the Spirit, the things of the Spirit.)

In fact, after our rebirth from the Holy Spirit, we become the temple of God with the indwelling of the Holy Spirit. (1 Corinthians 3:16-17: Don’t you know that you yourselves are God’s temple and that God’s Spirit dwells in your midst? ¹⁷ If anyone destroys God’s temple, God will destroy that person; for God’s temple is sacred, and you together are that temple.) And the body is the outer court, the soul the Holy Place and the spirit, the Holy of the Holies.

In the outer court, we offer our bodies, as well as the lust of the flesh, the lust of the eyes, and the pride of life (1 John 2:15-16 :  Do not love the world or anything in the world. If anyone loves the world, love for the Father is not in them. ¹⁶ For everything in the world—the lust of the flesh, the lust of the eyes, and the pride of life—comes not from the Father but from the world. ) as a living sacrifice. (Romans 12:1: 12 Therefore, I urge you, brothers and sisters, in view of God’s mercy, to offer your bodies as a living sacrifice, holy and pleasing to God—this is your true and proper worship.)

Then we can proceed to the Holy Place where we offer our souls (Psalm 25:1: To You, O Lord, I lift up my soul.) and receive the light of God from the golden lamp stance and are cleansed by the Word of God. (John 15:3: You are already clean because of the word I have spoken to you.) And then we can leave behind the carnal state )(1 Corinthians 3:3:  for you are still carnal. For where there are envy, strife, and divisions among you, are you not carnal and behaving like mere men?) and enter the Holy of Holies in the spiritual state where we meet God face to face. (Romans 8: 5: For those who live according to the flesh set their minds on the things of the flesh, but those who live according to the Spirit, the things of the Spirit.)

Will This Ever End?

This is a process of sanctification that leads to glorification as Paul prays in 1 Thessalonians 5:23: “May the God of peace himself sanctify you completely, and may your whole spirit and soul and body be kept blameless at the coming of our Lord Jesus Christ”. Paul speaks of Christ as “the hope of glory” (Colossians 1:27) and links the glorious appearing of Christ to our personal glorification: “When Christ, who is your life, appears, then you also will appear with him in glory” (Colossians 3:4). This glorified state will be our ultimate separation from sin, a total sanctification in every regard. “We know that when Christ appears, we shall be like him, for we shall see him as he is” (1 John 3:2).

Sanctification is a translation of the Greek word hagiasmos, meaning “holiness” or “a separation.” In the past, God granted us justification, a once-for-all, positional holiness in Christ. Now, God guides us to maturity, a practical, progressive holiness. In the future, God will give us glorification, a permanent, ultimate holiness. These three phases of sanctification separate the believer from the penalty of sin (justification), the power of sin (maturity), and the presence of sin (glorification).

When we die or are raptured, our transformation will be complete, and the Holy Spirit’s WORK of repossessing our soul will be finished. The heavenly alignment will be permanently restored, our regenerated soul in perpetual submission to our spirit which is one with God. Only then will we be ready for our resurrection bodies. It will no longer occur to us to behave in a manner contrary to God’s will, and we’ll finally be fit to dwell with Him forever.

The new body we receive will compare to the old one only in physical CHARACTERISTICS. The old one is corrupt and doomed to perish. The new one will be incorruptible and will never perish. (1 Cor. 15:53: For the perishable must clothe itself with the imperishable, and the mortal with immortality.) We’ll recognize each other and will know God as we are known by Him. (1 Cor.13:12:  For now we see only a reflection as in a mirror; then we shall see face to face. Now I know in part; then I shall know fully, even as I am fully known.) No longer will things be hidden from our understanding or beyond our comprehension because our soul, where understanding and comprehension take place, will finally be freed from the bondage of sin. The immeasurable creative capacity with which the human mind was created will finally be unleashed for our eternal use and enjoyment. The tiny nuggets of talent and ability in the arts and sciences that we can only faintly glimpse now will become rich veins to be mined for all eternity.

And best of all, we’ll finally achieve our heart’s true desire, to be one with our Creator, body, soul, and spirit. 

A Bible study by Insight based on a study by Brother Jack Keller @Gracethrufaith.com