Beyond Belief
by E.H. ‘Jack’ Sequeira

Chapter 15 – Spirit, Soul, and Body

In the previous chapter, we saw that spiritually we are made up of three components — spirit, soul, and body.  Each of these has a specific work in the spiritual well-being of the whole, but each is also closely related to the others.  In this chapter, we will look at each of these components and their relationship to the Holy Spirit’s work in our lives.  Then we will examine the Spirit’s work in the life of the church.

The First Component — The [Human] Spirit

The following texts clearly teach that each of us, as created by God, possesses a spirit:

God is spirit [see John 4:24], so when He said, “Let us make mankind in our image, in our likeness” [Genesis 1:26], it was primarily this aspect of our being — our spirit — that He had in mind.  This spirit is not our breath, our soul, or the Holy Spirit.  It is the component in us that, above all else, distinguishes us from the animals and makes us spiritual beings accountable to God.  It is because human beings have a spirit that we find even the most primitive people worshiping in some form.  The human spirit wants to commune with the spiritual world just as our bodies interact with the physical world and our minds (soul) interact with other minds.  We are spiritual, physical, and social beings because we are made up of spirit, body, and soul.

God formed in us this spiritual component in order that it might be His point of contact with us — His dwelling place in us.  Through our spirits, He would direct our minds (our souls), which in turn would control our bodies [see Colossians 2:19].  Thus, the entire person, living in total dependence on God, would reflect His character of selfless love [see 1 John 4:7-8].  This was God’s original plan for us when He created our first parents.

Sad to say, sin marred God’s plan.  When Adam and Eve sinned, the Holy Spirit left them, leaving their spirits vacant for Satan to occupy.  Selfishness replaced unselfish love, and their lives were darkened spiritually [see 2 Peter 2:19].  This is the nature with which all their children have been born; we come into the world without the indwelling Spirit of God, slaves to the devil and sin.  Everyone is born into this world uninhabited by God’s Spirit, and can, therefore, walk only “follow[ing] the ways of this world and of the ruler of the kingdom of the air, the spirit who is now at work in those who are disobedient” [Ephesians 2:2].

But we have not been left without hope.  The plan of redemption, formulated in God’s mind “before the creation of the world” [Ephesians 1:4], was designed to recover us fully from our fallen state and restore in us the image of God.  In His humanity, Christ prepared this restoration for each of us, and the work of the Holy Spirit now makes it available to us.

Before conversion, our spirit is not indwelt by God’s Spirit.  Except for the conviction the Holy Spirit brings to us from without, we can hardly feel our spirit’s function in the life.  Therefore, prior to the new birth, we are dominated by the soul, or mind, and its preoccupation with self — or by the body with its lusts.  At conversion, our spirit is made alive because the Holy Spirit comes and dwells in us.  Our spirit becomes God’s dwelling place and the seat of His will in our lives.  This is the new-birth experience that is absolutely essential to justification and that is the prerequisite to sanctification, the process by which God’s character is reproduced in us.

When we experience the new birth, we receive the life of Christ in the person of the Holy Spirit.  Scripture describes such a person as an infant in Christ [see 1 Corinthians 3:1].  We are saved from the guilt and punishment of sin; we are accounted righteous, but we still have to learn to “walk by the Spirit” [Galatians 5:16] just as a newborn baby has to learn to walk on its feet.

Two things will be manifested as the Holy Spirit increases in strength in our lives.  First, our characters will begin to reflect more and more the character of Christ.  Second, we will begin to be able to distinguish between that which proceeds from our spirit and that which comes from the self-life of the soul.  Hebrews 4:12 speaks of this as the separation between soul and spirit that the Word produces.

God regenerates us, teaches us, and leads us into His rest through our spirits.  But, sad to say, because of long years of bondage to the self-life of the soul, many of us know very little of the “Spirit who gives life” that dwells in us and is able to make us “free from the law of sin and death” [Romans 8:2].  We need to earnestly ask God daily to teach us what is spiritual and what proceeds merely from the emotions of the soul.  Even in our Bible study, we tend to rely more on our mental ability than on letting the Spirit guide us into all truth [see 1 Corinthians 2:12-14; John 16:13].

The Second Component — The Soul

The soul is the component that makes us human.  It includes the ability to think and learn and choose, our ideals, love, hate, feelings, discernment, etc.  The seat and essence of our personality is found in the soul; here is where we find the faculties of the mind [see Job 7:15], the will [see Proverbs 2:10, 19], knowledge [see 2 Samuel 5:8; Job 10:1; John 12:27], and the emotions.  For this reason, we often find both the Old and New Testaments using the word soul to refer simply to a human being, a person [see Genesis 14:21; Exodus 1:5; Deuteronomy 10:22; Acts 2:41; 7:14; Romans 13:1].

Since the soul is the seat of our personalities, it is the seat of the real “I.”  That is why Scripture often uses the word soul as a personal pronoun, i.e., I, you, me [see Genesis 12:13; Deuteronomy 23:24; Mark 14:34].  Our soul, then, is simply our self [see Leviticus 11:43; Esther 9:31].  Thus, everything that originates from the soul is polluted with self, which the Bible equates with iniquity.  That is why the judgment condemns self-righteousness acts as works of iniquity [Matthew 7:21-23].

The soul, with its life of self, is our natural life.  The Bible also calls this “the flesh” [see Galatians 3:3; Romans 8:4].  We inherit this life at birth; it is the only life the unconverted person can live.  Nothing we can do of ourselves can change this life — not even education or culture.  This is also the life of the carnal believer — the one who professes Christ, but who lives in contradiction to Christ and the life of the Holy Spirit.

In the one who is sanctified, however, the self-life of the soul is crucified through the cross of Christ [see Galatians 5:24].  That which proceeds from the soul (the mind) and also the behavior of the body is now under the direction of the Holy Spirit as He dwells in the believer’s spirit.  Such a life is actually the life of Christ reproduced in the believer.

This brings us to the main point — the Holy Spirit’s work in the life of the believer.  The Holy Spirit dwells in the believer’s spirit, but it is in the soul, or mind, that He operates.  In the Old Testament sanctuary, God dwelt in the Most Holy Place (representing our spirits) but directed His people through the ministry of the Holy Place (representing our soul or mind).  The same parallel exists in the human temple.  God’s Spirit dwells in our spirits, but He operates through our souls or minds.  Philippians 2:5 calls this having the “same mindset as Christ Jesus.”

Our bodies and, therefore, our behavior, are never directly controlled by the Holy Spirit.  He controls our bodies through our souls, or minds.  Again, the parallel exists in the Old Testament sanctuary.  It was impossible for God to communicate from the Most Holy Place (our spirits) to the courtyard (our bodies) except through the Holy Place (our souls).

To see how this actually works, we need to look at the life of Christ, for He is our prototype and example.  His humanity was identical in every point to ours [see Hebrews 2:17] so the body He received through Mary was a body of sin [see Galatians 4:4; Romans 1:3], dominated by the law of sin [see Romans 8:2-3].  This is how He could be (and was) tempted in all points as we are [see Hebrews 4:15].

However, Christ was also born of the Spirit from His very conception [see Luke 1:35].  So from the very beginning of His life on earth, Christ’s mind, or soul, was under the full control of the Holy Spirit, who dwelt in His human spirit.  “And the child grew and became strong; he was filled with wisdom, and the grace of God was on him” [Luke 2:40; cf. Luke 4:1].

Christ’s temptations came to Him the same way ours come to us — through the sinful (selfish) desires of the flesh.  It was through bodily wants that Satan tempted Him in the wilderness to use His divine power to satisfy self, independently of His Father’s will [see Luke 4:2-4].  It was His natural fear of death (self-love of the flesh) that led Jesus three times to plead with His Father to remove the bitter cup of the cross [see Mark 14:34-41].

But the self-centered desires of the flesh cannot be satisfied without the consent of the mind.  Temptation, in and of itself, does not become sin until the mind consents to the temptation.  “Then, after desire has conceived [in the mind], it gives birth to sin” [James 1:15].  Since Christ’s mind was under the full control of the Holy Spirit, His response to every temptation was “No!”  “Not my will [self], but yours [God’s] be done” [Luke 22:42].  Therefore, sin had no part in His life [see John 6:38].  Instead, He condemned sin (the law of sin) in the flesh [see Romans 8:2-3].

Christ’s flesh, being our corporate sinful flesh, lusted after sin.  But His mind, being spiritual, never yielded to sin, and, thus, He conquered sin in the flesh through the power of the Spirit [see Luke 4:13-14].  Likewise, if we have the mind of Christ, if we put on the Lord Jesus Christ, we will “not think about how to gratify the desires of the flesh” [Romans 13:14].

Hebrews 2:18 reads, “Because He [Christ] Himself suffered when he was tempted, he is able to help those who are being tempted.”  Every time Christ was tempted, He suffered.  We know that Christ was tempted as we are; otherwise, His being able “to help those who are being tempted” would be meaningless.  But the question we must ask is:  Where did Christ suffer being tempted?  The answer is found in 1 Peter 4:1.  “Therefore, since Christ suffered in his body, arm yourselves also with the same attitude, because whoever suffers in the body is done with sin” (emphasis supplied).  Please note that the suffering Peter is talking about here has to do with Christ’s victory over sin; it is not limited to His suffering on the cross.  Being tempted in the flesh, Christ suffered in the flesh [see Hebrews 2:10], but His victory was in the mind.  So also, says Peter, if we arm ourselves with the mind of Christ (the mind of the Spirit), sin will cease in our lives, but the flesh will suffer.  This, as we will see later in this chapter, is because the nature of the flesh cannot change; it will always desire to sin and must, therefore, suffer if not satisfied.

So it is in the mind, or the soul, that Christ gives us victory over sin through His indwelling Spirit.  As Paul said, “I myself in my mind am a slave to God’s law, but in my sinful nature a slave to the law of sin” [Romans 7:25].  Also, he tells us, “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” [Romans 12:2].

In the unbeliever, perfect harmony exists between the soul (the mind) and the body; both are equally under the dominion of sin.  Paul reminded the Ephesian Christians of their life before conversion, which was “gratifying the cravings of our flesh and following its desires and thoughts” [Ephesians 2:3].  In the unconverted person, the life of the soul is also the life of the body.  Both are contaminated through and through with self.

In the carnal believer, who is born of the Spirit but is still walking after the flesh (the life of self), the mind may desire to do God’s will but the body remains subject to the law of sin [see Romans 7:22-23].  Unaided by the Holy Spirit, the mind cannot overcome the law of sin in our members.  Such a life is, therefore, also marred by sin, although the sins may not be as grievous as those in the life of the unbeliever.

But the spiritual Christian is not only born of the Spirit, he or she is also, by faith, absolutely surrendered to the Spirit.  Such a person has the mind of Christ, so that “the old man” no longer lives in him; Christ lives in him through His Spirit.  Thus, “the righteous requirement of the law might be fully met in us, who do not live according to the flesh but according to the Spirit” [Romans 8:4].

The Third Component — The Body

As created by God, the body was to be the servant of the soul.  The soul, in turn, was to be under the direction of God’s Spirit dwelling in man’s spirit.  Thus the desires of the body, such as sex, hunger, love, etc., would be controlled by God through man’s soul; man’s behavior would reflect God’s character.

When man sinned, he separated himself from God’s authority and became independent.  The natural desires of the body, now polluted with self, became lust; their purpose became self-satisfaction rather than pleasing God.  Man’s nature was perverted so that the lust of the flesh became the controlling factor in his life.  The life of fallen man came into harmony with the principle of self originated by Satan.

Scripture refers to our bodies in their sinful conditions as “the body ruled by sin” [Romans 6:6].  This is not because the body is sinful in and of itself, but because the principle of sin has permeated its every member [see Romans 7:23].  The self-life that motivates the body is sinful and makes our flesh sinful.  And this life of sin is beyond repair.  That is why we look forward to the second coming, when our sinful bodies will be redeemed [see Romans 8:23; Philippians 3:20-21; 1 Corinthians 15:50-54].  Until then, the principle of the cross, the principle of self-denial, must daily be applied to our sinful lives through the Holy Spirit [see Luke 9:23].

Sinful human beings are under the power of self, both body and soul, so that even at their very best they are totally self-seeking without God.  “We all, like sheep, have gone astray, each of us has turned to our own way” [Isaiah 53:6; cf. Philippians 2:21; 2 Timothy 3:1-2].  The natural life of mankind is the life of the flesh, made up of the self-life of the soul and body.  It is the life we receive at birth [see John 3:6], and we cannot live any other apart from God.  We may educate ourselves and become highly cultured, but without the Holy Spirit, we will still live the life of the flesh.  Selfishness, in one way or another, will be the controlling factor of our lives.  The unconverted person is powerless to fulfill any of God’s will because he is “weakened by the flesh” [Romans 8:3].

In fact, the flesh is hostile to God, and will not, cannot, truly submit to His law [see Galatians 5:17; Romans 8:7].  We need to realize that the corruption of the flesh is beyond repair [see 1 Corinthians 15:50-53].  Even God Himself, great as His power is, will not transform the flesh into something that is pleasing to Him.  The flesh belongs to the realm of Satan, and God has condemned all that belongs to that realm to destruction.  This is why Christ crucified the flesh at the cross [see Hebrews 10:19-20].

Unbelievers, and also many Christians who do not understand God’s Word, are always trying to reform or improve the flesh.  The flesh can appear good on the surface (it is deceitful, after all, because it is sinful), but within it is “full of hypocrisy and wickedness” [Matthew 23:28].  All attempts to improve the flesh, either by punishing the body or by making promises and resolutions, are bound to fail.

“Flesh gives birth to flesh,” Jesus said [John 3:6], and it will always remain so.  God Himself recognizes the impossibility of changing the flesh because its originator, the devil, cannot change.  So in saving us, God doesn’t try to change the flesh.  Instead, He has put it to death through the cross and gives us a new life, the life of His Spirit.  The flesh must be crucified in order to realize the salvation from the power of sin [Galatians 5:24]!

The behavior of the flesh can be manifested in two different ways.  The first is sinful acts, which proceed from the desires of the body; you will find a list of these in Galatians 5:19-21 referred to as “the acts of the flesh.”  The second is self-righteous acts, which proceed from the soul.  Outwardly, these appear quite different from the works of the flesh; they are commendable, often religious, acts.  The self-righteous acts of Paul before his conversion are a good example [see Philippians 3:4-6].

From our human point of view, we highly value self-righteous acts.  But God condemns both of these manifestations of the flesh as evil [see Isaiah 64:6; Matthew 7:22-23].  The desires of the body make self the center and elevate self-will above God’s will.  The soul may serve God, but only according to its will — not God’s.  It may even try with all its might to keep God’s law, yet self never fails to be at the heart of every activity.  In 1 Corinthians 3:1-3, the apostle Paul divides all believers into two classes:  (1) spiritual Christians in whom the indwelling Spirit of God controls the whole person — spirit, soul, and body; and (2) carnal Christians who have experienced the new birth [see verse 16], but who are still dominated by the life of flesh.

The major problem facing the Christian church today is the problem of carnality.  Churches are filled with babies in Christ, even though the believers are “old” Christians.  This was the problem in the Corinthian and Galatian churches of New Testament times, and it is still the problem of the church today.  Every believer needs to learn that there can be no partnership between the flesh and the Spirit, that the only formula for the Christian life is “Not I, but Christ.”

Victory over the flesh should be our deep longing in these last days.  And this victory is gained through the deeper work of the cross as the Holy Spirit daily brings it to bear upon us.  Once we have reckoned ourselves crucified with Christ [see Romans 6:11], we must allow God’s Spirit to put this crucifixion into effect, putting to death daily the self of the flesh.  Each time self raises its ugly head, the Spirit will bring conviction.  Our reaction must be — not to defend or excuse self — but to surrender self to the cross of Christ.  When self is completely crucified in us, then the splendor of God’s glory will shine forth through our mortal bodies [see Romans 8:11-14].  We will then be ready to meet the Lord without dying.

The deeper work of the cross is to crucify self so that the Spirit may reproduce in us the character of Christ.  The Bible often speaks of this process as fiery ordeals and discipline [see Hebrews 12:5-11; 1 Peter 4:12-13].  Though painful to the flesh at the time, “later on, however, it produces a harvest of righteousness and peace for those who have been trained by it” (Hebrews 12:11).  Even for Christ, it was only through suffering in the flesh that He was able to produce righteousness in sinful flesh [see Hebrews 2:10, 18; 5:8-9].  “Whoever suffers in the body is done with sin” [1 Peter 4:1].

In examining the work of the Holy Spirit in the life of the believer, it is clear that no aspect of the Christian life in independent of the Spirit’s influence.  God intends our total lives to be guided and controlled by His Spirit [see Proverbs 3:5-6].  The Holy Spirit is the One who liberates us from the self-life of sin [see 2 Corinthians 3:17, 19]; is the means of our sanctification [see 2 Thessalonians 2:13; 1 Peter 1:2]; guides us into all truth [see John 16:13]; makes our prayers meaningful [see Romans 8:26; Jude 20]; and gives us the power to witness to the gospel [see Luke 24:49; Acts 1:8].  This is His work in the life of every believer.

The Spirit’s Work in the Life of the Church

The Holy Spirit’s work doesn’t stop with the individual believer; it also involves the life of the whole church.  The indwelling Spirit becomes the link that unites all believers together to form the body of Christ — the church.  “For we were all baptized by one Spirit so as to form one body — whether Jews or Gentiles, slave or free — and we were all given the one Spirit to drink” [1 Corinthians 12:13].  The new birth not only puts us into Christ, it also identifies us with His body so that “in Christ we, though many, form one body, and each member belongs to all the others” [Romans 12:5; cf. 1 Corinthians 10:17; 12:12].

According to the New Testament, the church is a closely knit body of believers with no distinctions whatsoever of race, color, sex, or status [see Galatians 3:26-28].  It is a fellowship of men and women who are all one in Christ, by faith, and who are to be perfected united for the purpose of manifesting the life of God in the same way that Christ manifested it in His human body when He was on earth [see John 14:9; 1 Timothy 3:16].

Sad to say, the Christian church has miserably failed to do this; the world has not really had an opportunity to see, in the church, what God is like.  We must realize that salvation in Christ is more than just a personal way to escape eternal damnation.  Every person saved in Christ is saved “to do good works” [Ephesians 2:10; cf. Matthew 5:16; Colossians 1:10; 1 Peter 2:12].  And these good works are to be carried out in the framework of the church, which is to be as salt and light in the world.  Until we who call ourselves Christians are willing to be instruments in the hands of God’s Spirit, the world that is more than 75 percent non-Christian will never really witness the power of the gospel.

The apostle Paul makes it clear that every member of the church has a specific function in relationship to the body, as allotted by the Holy Spirit [see Romans 12:5-8; 1 Corinthians 12:14-26; Ephesians 4:11-15].  These texts indicate that every believer has been endowed with one or more gifts of the Spirit.  These gifts are to be used to minister to the church itself, and they are also the means by which the church, as Christ’s representative, is to witness of Him to the world.  The church, as Christ’s body, is to manifest God in the flesh.

No individual member can fully display Christ completely for the simple reason that no individual member is the total body of Christ.  Only through the church as a whole, living in perfect coordination and conformity to the direction of the Holy Spirit, can the life of Christ be fully displayed.  This will take place before Christ comes.  The Bible calls this “the mystery of God” that will be accomplished “just as he announced to his servants the prophets” [Revelation 10:7; cf. Colossians 1:25-27].

Obviously, then, the Holy Spirit has an important work to do in the church as well as in the life of the individual believer.  First, the Holy Spirit bestows gifts on the church for the purpose of developing the body of Christ until it grows “to the whole measure of the fullness of Christ” [Ephesians 4:13].  Second, the Spirit bestows gifts on the church in order that it may demonstrate and witness to the power of God to a lost world.

Sadly, after almost two thousand years, the church has neither grown into the fullness of Christ, nor has it fully displayed the life of God in the flesh.  Should we not, here in the twentieth century, come to God in humility and repentance for our failure?  After all, the fault does not lie with God, but with us.  It is we who have distorted the truth of the gospel and have put self above the cause of Christ.

Speaking of the last days, Joel proclaimed, “And afterward, I will pour out my Spirit on all people” [Joel 2:28].  He goes on to say,

“Even now,” declares the Lord, “return to me with all your heart, with fasting and weeping and mourning.” Rend your heart and not your garments.  Return to the Lord your God....  Let the priests, who minister before the Lord, weep between the portico and the altar.  Let them say, “Spare your people, Lord.  Do not make your inheritance an object of scorn, a byword among the nations.  Why should they say among the peoples, ‘Where is their God?’ ”  Then the Lord was jealous for his land and took pity on his people.  [Joel 2:12-13, 17-18]

This is the deep, heartfelt repentance that God is patiently waiting to hear from His people.  “Those whom I love I rebuke and discipline.  So be earnest and repent” [Revelation 3:19].  When the church realizes this, then God will pour out His Spirit, and the earth will be “illuminated by his splendor” [Revelation 18:1].


Key Points in Chapter 15
• Spirit, Soul, and Body •
  1. God intended for the spiritual component in mankind — our spirits — to be His points of contact with us, His indwelling place in us.  Through our spirits, He intended to direct our souls (our minds), which in turn would control our bodies.

  2. Because of Adam’s sin, we are all born without the Holy Spirit dwelling in us — slaves to Satan and sin.  This is our nature before conversion.  When we experience the new birth, we receive the life of Christ in the person of the Holy Spirit, who lives in us.

  3. The soul (the mind) is the component in our makeup that enables us to think, learn, choose; it is the area that includes our ideals, love, hate, feelings, and emotions.  The Bible often uses the term soul to refer simply to a human being [see Genesis 14:21; Exodus 1:5; Acts 2:41; Romans 13:1].

  4. The soul, with its life of self, is our natural life.  The Bible calls it “the flesh,” meaning the human sinful nature.

  5. Temptation comes to us (and came to Christ) through the sinful desires of the flesh.  But the self-centered desires of the flesh cannot be satisfied without the consent of the mind.

  6. Christ’s mind, or soul, being spiritual, never yielded to sin; thus He conquered sin in the flesh through the power of the Spirit [see Luke 4:13-14].  Likewise, if we have the mind of Christ, we will “not think about how to gratify the desires of the flesh” [Romans 13:14].  It is in the mind, or soul, that Christ gives us victory over sin through His indwelling Spirit.

  7. The Bible refers to the third component of our humanity — the body — as “the body ruled by sin” [Romans 6:6].  This is not because the body is sinful in and of itself, but because the principle of sin has permeated its members.

  8. In saving us, God doesn’t try to change the flesh.  Instead, He has put it to death through the cross and has given us a new life — the life of His Spirit.

  9. The flesh manifests itself in two ways:  sinful acts and self-righteous acts.  God condemns both as evil.


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