Devotional 36: The Remains of Corruption in Believers: The Flesh Wars Against the Spirit

The Confession Read

This corruption of nature, during this life, doth remain in those that are regenerated; and although it be, through Christ, pardoned and mortified; yet both itself, and all the motions thereof, are truly and properly sin.

— Westminster Confession of Faith, Chapter 6, Section 5

Introduction

There is a moment in the Christian life that every sincere believer knows, though few are warned of it in advance. You have been converted, perhaps for some years. The old habits have been broken. The old companions have been left behind. Prayer, once a duty, has become a delight. The Word, once dry, now speaks with living voice. You have tasted that the Lord is gracious, and the taste is sweet. And then, in the quiet of a Tuesday afternoon or in the press of a temptation you thought long dead, you feel it stir again. The old anger rises hot and sudden. The old lust whispers its familiar invitation. The old pride swells at a compliment and sulks at a slight. And a cold dread settles over you: If I were truly saved, surely this would not still be here. If Christ were really in me, how could such darkness remain? The question is as old as the Christian church, and the Westminster divines answer it in a single sentence that has steadied more trembling consciences than any other section of the Confession. They tell us something the natural man would never guess and the immature Christian finds hard to believe: regeneration is not eradication. The corruption of nature that Section 4 described as the fountain of all actual sin — that same corruption outlasts the new birth. It is not removed or annihilated when Christ enters; it is contested and dethroned. The poison remains in the bloodstream, though the antidote has been administered. The enemy garrison still occupies outposts of the city, though the rightful King has planted His standard in the citadel. This is not a defect in God's saving work but the design of it — a design whose wisdom we shall trace through Scripture, through the fathers, and into the daily life of every believer who has ever cried with the Apostle, "O wretched man that I am." The Confession has brought us through dark terrain: the fall of Adam, the total corruption of human nature, the imputation of guilt, and the ceaseless production of actual sin. Now Section 5 turns to the regenerate. The same original sin that damns the unbeliever dwells in the believer — pardoned, yes; mortified, yes; but present and active, and still in its every motion, truly and properly sin. This doctrine is heavy, but it is also the key to Christian honesty and Christian hope. For if we do not know what sin remains, we shall not know how to fight it. And if we do not know that it is pardoned, we shall despair.

Scripture Foundation

The doctrine that original corruption remains in the regenerate is not a deduction from the logic of theology; it is the plain testimony of Holy Scripture, and nowhere more vividly than in the Apostle Paul's own spiritual autobiography. Turn with me to the seventh chapter of Romans, a passage that has been the battleground of interpreters but whose plain sense is the experience of every man and woman in whom the Spirit of God has kindled new life. Hear Paul's confession, written in the present tense by an apostle who had walked with Christ for decades: "For we know that the law is spiritual: but I am carnal, sold under sin. For that which I do I allow not: for what I would, that do I not; but what I hate, that do I" (Romans 7:14-15). The verbs are present — I am, I do, I hate, I would. This is not Paul remembering his pre-conversion days with a retrospective shudder but describing his present experience as a mature believer. The regenerate Paul does what he hates and fails to do what he loves. If this were the experience of an unregenerate man, it would be extraordinary — for the unregenerate man does not hate his sin, does not delight in the law of God after the inward man, does not cry out in anguish over the chasm between what he loves and what he does. This is the regenerate man discovering what the Confession teaches: regeneration implants a new principle of life, but it does not extract the old principle of death. The two coexist in the same soul, locked in warfare until death parts them. Paul's conclusion rings through the centuries: "So then with the mind I myself serve the law of God; but with the flesh the law of sin" (Romans 7:25). The flesh here is sarx — not the physical body merely, but the whole fallen human nature, the corruption inherited from Adam that clings to the regenerate as ivy clings to a wall. The ivy has been cut at the root but not yet stripped away. Paul's cry at the climax is the cry of every honest Christian: "O wretched man that I am! who shall deliver me from the body of this death?" (Romans 7:24). The body of death probably alludes to a Roman punishment in which a corpse was bound to a living prisoner, the living forced to carry the dead until he perished from the putrefaction. So Paul feels about indwelling corruption — strapped to him, inseparable in this life, a weight he longs to be free of. Yet his cry is not despair but the prelude to thanksgiving: "I thank God through Jesus Christ our Lord" (Romans 7:25). The deliverance is certain, though not yet complete. For now, the struggle continues — but the struggle itself is evidence that the new man lives, for dead men do not wrestle. Turn next to Galatians, where the same truth is set forth as universal principle. "For the flesh lusteth against the Spirit, and the Spirit against the flesh: and these are contrary the one to the other: so that ye cannot do the things that ye would" (Galatians 5:17). Paul is writing to believers in whom the Spirit dwells, yet he describes a conflict, not a truce. The flesh lusts against the Spirit; the Greek verb epithumei is the same word James uses for the craving that conceives sin. It is military language: two armies on the same field, each seeking the other's defeat. The Spirit wars against the flesh; the Holy Ghost does not negotiate with indwelling sin. The result is that "ye cannot do the things that ye would" — the renewed will desires holiness, but the remaining corruption obstructs and sometimes overpowers it. This is not an excuse for sin but an explanation of the battle every Christian fights daily. The Apostle John adds his witness: "If we say that we have no sin, we deceive ourselves, and the truth is not in us" (1 John 1:8). The "we" is emphatic: John includes himself. He is the aged apostle who leaned on Jesus' breast at the Last Supper, who had seen the transfigured Christ and the resurrected Lord. If any man might be thought to have outgrown indwelling sin, it would be John. And yet he does not say, "If you say you have no sin" but "If we say." He sharpens the point: "If we say that we have not sinned, we make him a liar, and his word is not in us" (1 John 1:10). The claim to sinlessness is not merely an error; it calls God a liar. The proper response is not to deny remaining sin but to confess it — and to trust the provision God has made: "the blood of Jesus Christ his Son cleanseth us from all sin" (1 John 1:7). Here is the confessional balance: sin remains, but it is pardoned; corruption lingers, but it is mortified through Christ. Finally, Paul's command to the Romans assumes the ongoing presence of sin that must be actively put to death. "For if ye live after the flesh, ye shall die: but if ye through the Spirit do mortify the deeds of the body, ye shall live" (Romans 8:13). The verb "mortify" — thanatoute in Greek — means to put to death, to kill, to execute. It is an ongoing imperative, not a completed action. The believer is commanded to be constantly putting sin to death. Why? Because sin is not dead. Because the flesh still produces deeds that must be executed one by one. The great Puritan John Owen would later distill this verse into his famous aphorism: "Be killing sin, or it will be killing you." The presence of the command proves the presence of the enemy. You do not command a man to kill what is already dead. The very fact that we are told to mortify the deeds of the body means that the body of sin is still producing deeds, that the corruption of nature is still active, that the motions of sin still require daily execution. And the instrument of this mortification is "the Spirit" — not our own resolve, not our own willpower, but the indwelling Holy Ghost who alone has power to overcome the indwelling flesh. These four passages — Romans 7, Galatians 5, 1 John 1, and Romans 8 — establish the confessional claim beyond reasonable dispute. Original corruption remains in the regenerate. It is not silent; it speaks. It is not passive; it wars. It is not imaginary; it produces real sins that require real mortification. The man who denies this is not more spiritual than Paul; he is less honest. The woman who claims to have transcended the struggle is not more sanctified than John; she has merely stopped listening to the witness of Scripture and the testimony of her own heart.

What the Divines Meant

The Westminster Assembly drafted this section with a precise theological purpose, and every phrase carries the weight of controversy as well as the balm of pastoral care. Let us weigh each clause. "This corruption of nature." The Confession picks up the thread from Section 4 without a break. The "corruption of nature" is the same original sin that the previous sections have defined: the loss of original righteousness, the total defilement of every faculty, the positive bent toward evil that has been transmitted from Adam to all his posterity by ordinary generation. The divines do not introduce a new concept here; they bring the old concept into the regenerate state and ask: what happens to this corruption when a man is born again? Their answer upsets every expectation that natural religion might entertain. "During this life." The temporal qualification is essential. The divines are not teaching that original corruption remains forever. They are teaching that it remains throughout the course of earthly existence and is only finally removed at death or at the return of Christ. Later, in Chapter 13 on sanctification, they will speak of sanctification as being "throughout, in the whole man; yet imperfect in this life, there abiding still some remnants of corruption in every part." And in Chapter 9 on free will, they will teach that "the will of man is made perfectly and immutably free to good alone, in the state of glory only." The corruption that dogs the believer's steps from conversion to the grave will not cross the threshold of heaven. But until that threshold is crossed, it remains a live-in enemy. "Doth remain in those that are regenerated." The verb is present and active. Corruption does not merely leave a residue; it remains, abides, dwells. And it dwells in "those that are regenerated" — not the merely baptized or professing, but the genuinely born again. The most regenerate soul on earth — the apostle caught up into the third heaven, the martyr singing in the flames, the saint who spent eighty years in communion with God — carries the corruption of nature to the grave. There is no perfectionism in the Confession, only honest biblical realism that looks at Romans 7 and says: this is the normal Christian life. "And although it be, through Christ, pardoned and mortified." Here the divines balance the dark truth with the bright gospel. The corruption that remains is not untouched by grace. It is "pardoned": the guilt of it is covered by Christ's blood, so that the believer is not condemned for the indwelling sin that defiles him. It is "mortified": its power is being broken by the Spirit. The corruption is like a snake whose head has been crushed but whose body still writhes. The death blow has been struck, the writhing continues for a season. Both pardon and mortification are "through Christ": His blood pardons, His Spirit mortifies. And the two are never separated. "Yet both itself, and all the motions thereof, are truly and properly sin." This is the clause that drew the sharpest line in the Reformation era, and it remains the most demanding part of the section for the Christian conscience. The divines are asserting that original corruption — the concupiscentia, the disordered desire, the bent toward evil — is not a misfortune, a weakness, or a mere tendency to sin, but sin itself in the fullest and most proper sense. And not only the corruption itself but "all the motions thereof" — every stirring of pride, every flicker of lust, every surge of anger, every impulse of envy, every inclination toward unbelief — every one of these motions is truly and properly sin, even when it does not issue in a deliberate act, even when it is resisted, even when it is hated and grieved over. This was aimed directly at the Council of Trent, which had decreed in its fifth session that concupiscence in the baptized "is not truly and properly sin" but is only called sin because it comes from sin and inclines to sin. Rome taught that baptism so cleanses the soul that the remaining disordered desire, though it remains as a punishment and an occasion for struggle, does not have the nature of sin in the regenerate. Against this, the Reformed churches insisted that whatever is contrary to the law of God is sin, regardless of whether it dwells in a regenerate or unregenerate heart. The standard is not our spiritual state but God's holy law. What transgresses that law is sin — always, everywhere, and in whomever it is found. This has profound pastoral implications. If the motions of sin in the believer are not truly sin, then what are they? Misfortunes? Excusable weaknesses? And if they are not sin, why grieve over them, confess them, seek pardon for them? The Roman position tends to lower the believer's sensitivity to the evil within. If my disordered desire is not really sin, I need not be so troubled. The Reformed position sharpens the conscience to its finest point. Every motion of envy is sin. Every fleeting lust is sin. And because it is sin, it must be confessed as sin, hated as sin, mortified as sin, and covered by the blood of Christ as sin. The believer who understands this lives with a tender conscience — sensitive to the smallest stirrings, quick to repent, quick to flee to Christ. The believer who does not understand it may drift into comfortable carelessness about the inner life, content that his outward conduct is decent while his heart remains a half-tended garden of weeds he no longer calls weeds. The divines were also answering enthusiasts and antinomians who taught that the regenerate person is so united to Christ that his sins are no longer his own — that only the old man sins, for which the believer bears no responsibility. Against this, the Confession insists that the corruption and its motions are the believer's own. He cannot disown them as though they belonged to someone else. They arise from his own heart, and he is responsible for them, even while not condemned for them because of Christ. The simul iustus et peccator — at once righteous and a sinner — is not a division of the person into two agents but a description of the one person who is, in Christ, perfectly righteous by imputation, and in himself, still a sinner by remaining corruption. Both are true of the same man at the same moment.

Theological Depth

The Reformed tradition has explored this doctrine with the care of a surgeon mapping the chambers of the human heart. Let us draw near to several of its witnesses. Samuel Rutherford, the Scottish commissioner to the Westminster Assembly whose letters breathe the very fragrance of Christ, wrote with particular tenderness about the believer's remaining corruption precisely because he felt it so keenly himself. In his letters from Aberdeen, where he was exiled for his fidelity to the crown rights of King Jesus, Rutherford describes his own heart as a "lodging house" where Christ and corruption dwell under the same roof. He writes to a correspondent: "I find the old man, that besieging enemy, still shooting arrows at my soul. But I rejoice that the Captain of my salvation is in the castle, and He will not yield the keys to the adversary." For Rutherford, the presence of remaining sin was not a cause for doubting his salvation but an occasion for clinging more tightly to Christ. He saw that the believer's corruption drives him out of himself: if all were well within, we should be content to remain within. But because the heart is a battleground, we are forced to look outward and upward for peace. Rutherford's letters are filled with this two-beat rhythm: honest confession of the sin that remains, followed by joyful flight to the Christ who pardons. He never minimized the corruption — he called it "the devil's brat that I nursed in my bosom" — but he never let the sight of it drive him from the cross. Rather, the worse he saw himself, the nearer he drew to Christ. That is the confessional logic lived out in a human soul. Robert Traill, a Scottish Presbyterian minister whose sermons on justification and the throne of grace are among the richest treasures of Puritan literature, addresses remaining corruption from a different angle. Traill is concerned to guard the doctrine of justification from corruption by the doctrine of sanctification — not that sanctification is unimportant, but that our standing before God must never be grounded in the imperfect holiness that we possess, only in the perfect righteousness of Christ that is imputed. In his sermon on 1 Peter 1:21, Traill writes that the believer "hath sin in him, but no sin on him; sin dwells in him, but it doth not reign over him." The corruption remains, but the guilt of it is transferred to Christ, and the dominion of it is broken by the Spirit. Traill warns against two equal errors: the error of those who make light of indwelling sin because they are justified, and the error of those who doubt their justification because indwelling sin remains. The first error leads to carelessness; the second leads to despair. The right path lies between them: take your remaining sin with the utmost seriousness — mourn over it, confess it, wage war against it — but never let the sight of it shake your confidence in the righteousness of Christ. That righteousness is perfect, and it is yours by faith, and no corruption within you can diminish it by a single degree. Traill's word to the trembling believer is this: the sin you feel is real sin, but the righteousness you have is real righteousness, and the righteousness is greater. Thomas Boston, whose Human Nature in Its Fourfold State we have consulted before, gives the most systematic treatment of the state of grace — the third of his four states, between the state of nature and the state of glory. Boston describes the regenerate man as one in whom a new principle of grace has been implanted, but the old principle of corruption has not been eradicated. He likens the soul to a house into which a new tenant has moved, while the old tenant refuses to leave. The new tenant has the title deed and the rightful possession; the old tenant is a squatter with no legal claim. And yet the old tenant remains, making noise in the upper rooms and contesting every inch of ground. "The two principles," Boston writes, "are contrary the one to the other, and so there is a continual conflict betwixt them. This war is a sure sign of a gracious state; for in the unregenerate, all is quiet, because the strong man armed keepeth the house." He goes on to make a crucial pastoral distinction: the remaining corruption is in the believer, but it is not the believer. The true self, the "I" of the regenerate man, is the new nature, the inner man that delights in the law of God. The sin that remains is an alien presence, a usurper — present in the soul, active in the members, but not constitutive of the person's true identity in Christ. This is why Paul can say, "It is no more I that do it, but sin that dwelleth in me" (Romans 7:17). Boston's pastoral counsel is gentle and wise: hate the sin, but do not despise yourself. Wage war on the corruption, but do not conclude that you are not a child of God because the war continues. The war is the proof that you have been invaded by grace. These three witnesses — Rutherford's pastoral warmth, Traill's doctrinal clarity, and Boston's systematic precision — together paint a picture of the Christian life that is at once sobering and hopeful. The corruption remains; that is sobering. But it is pardoned, mortified, and destined for destruction; that is hope. And in the meantime, the struggle itself, painful as it is, is the surest sign that the Spirit of God is at work within.

Puritan Application

The doctrine that original corruption remains in the regenerate is not an item for the theological syllabus alone. It is a lens through which every believer must learn to view his own soul, struggles, and daily walk with God. Here are five applications. First, let this doctrine deliver you from the shock of remaining sin. One of the most common snares in the Christian life is the expectation that conversion will produce an immediate and comprehensive holiness. New believers, full of the joy of their first love, often imagine that the old temptations will simply fall away, that the old tempers will evaporate, that the inner life will become a calm lake untroubled by the storms of lust and pride. And then, when it does not happen — when the old anger flares, when the old lust whispers, when the old vanity preens — they are thrown into confusion. "If I were truly converted," the thought runs, "this would not be." The enemy of souls seizes the moment: "You see? It was all a delusion. You are the same person you always were." The Confession answers this snare with clarity. Regeneration is not eradication. The new birth implants a new nature; it does not extract the old. The Spirit comes to dwell in a heart that is still, in its remaining corruption, hostile to Him. The fact that you feel the war is not evidence that you are unconverted; it is evidence that the Spirit has invaded territory that was previously content under a single sovereign. The unregenerate heart is a totalitarian state where sin rules without opposition. The regenerate heart is a civil war. That war is painful, but it is the pain of life, not the stillness of death. When next you are surprised by a surge of sin from within, do not conclude that you have never been born again. Conclude rather that the corruption the Confession describes is real, that it remains in you as it remained in Paul, and that its stirring is not the defeat of grace but the occasion for grace to do its deeper work. Be not shocked that the old man still breathes; be shocked only if he breathes and you do not fight. Second, make no peace with the corruption that remains. The fact that indwelling sin is pardoned does not make it permissible. The fact that it is inevitable does not make it excusable. The Confession teaches that the corruption and its motions are "truly and properly sin" — and sin, wherever it is found, is to be hated, resisted, and mortified. The believer who reasons, "Well, I will always have this lust, so there is no point fighting it," has misunderstood the doctrine entirely. The corruption remains, but it does so as an enemy, not as a tolerated guest. The command of Scripture is not "learn to live with your sin"; it is "mortify the deeds of the body." The verb is violent. It speaks of execution, not accommodation. Consider the practical outworking. If you know that pride is your particular corruption, do not merely manage your pride — keep it from becoming too obvious, too offensive, too damaging to your reputation. Kill it. Identify its motions the moment they arise — that swell of satisfaction at praise, that sting of resentment at criticism, that secret comparison with others that always places you a little higher — and bring each motion to the Spirit for execution. If you know that lust is your particular corruption, do not merely avoid gross outward acts. Kill the first stirring, the lingering glance, the entertained imagination. The Puritan Thomas Brooks, whom we met in our study of Section 4, taught that sin is most easily killed at the level of the thought, harder at the level of the desire, and hardest of all at the level of the act. The wise Christian strikes early. The corruption cannot be eradicated in this life, but its motions can be — and must be — mortified one by one. The Spirit who dwells in you is the Spirit of holiness, and He will not share His habitation with a tolerated lust. Third, let the presence of remaining sin drive you daily to Christ for pardon. The Confession teaches that the corruption is "through Christ, pardoned." The pardon is not a past event with no present relevance. It is an ongoing reality, a fountain that never runs dry, a mercy that is new every morning. The believer who understands the doctrine of remaining corruption will be a believer who confesses sin daily — not in a general and perfunctory way, but specifically and earnestly. John writes that "if we confess our sins, he is faithful and just to forgive us our sins, and to cleanse us from all unrighteousness" (1 John 1:9). The present tense — "if we confess" — implies a continuing practice, not a once-for-all transaction. The pardons we need today are for the sins that arose today, the motions of corruption that stirred in the quiet hours of the morning, the sharp word spoken before breakfast, the vain imagination entertained in the idle moment, the resentment nursed over a remembered slight. None of these will condemn the believer, for there is no condemnation to them that are in Christ Jesus. But all of them require confession, for the relationship between the believer and his God is a filial relationship, and children who sin against a loving Father do not hide their sin; they bring it to Him for forgiveness. The blood of Christ is not a static deposit made once in the past; it is a living reality, a cleansing stream into which the believer may plunge every hour. Let remaining corruption drive you to the cross, not away from it. The worst response to indwelling sin is to avoid the face of God out of shame. The best response is to run toward Him, confessing all, trusting the Advocate who ever lives to intercede. Fourth, let the struggle humble you and kindle a longing for glory. The knowledge that original corruption remains should end every impulse toward spiritual pride. When you are tempted to look down on a brother who has fallen into some sin you have avoided, remember that the seed of that same sin lies in your own heart. The circumstances have not aligned, the temptation has not been suited to your corruption, the restraining grace of God has held you back — but the material is there. Before the cross, there are no elite Christians who have moved beyond the common struggle. There are only sinners — pardoned, justified, regenerated, but sinners still — clinging to the same grace and waging the same war. And let the weariness of that war kindle in you a longing for the glory where it will cease forever. The Confession teaches that this corruption remains "during this life" — but it does not remain beyond it. The day is coming when the body of death will be torn away, when the old man will be not merely dethroned but destroyed. There will be no more civil war in the soul, no more confession, no more mortification — because there will be no more sin. Paul's cry, "who shall deliver me?" is answered by the promise that Christ shall deliver. Let every failure, every stumble, every secret shame turn your eyes from the present battlefield to the coming kingdom where the battle is over and the victory complete. The corruption that wearies you today will not weary you forever. The sin that clings so closely will one day be stripped away, and you will stand before the throne, conformed fully to the image of Christ.

Prayer

O most holy God, whose eyes are too pure to behold iniquity, we bow before Thee in the knowledge of what we are. Thy Word declares that the corruption of our nature remains in us even after the new birth, and our own consciences bear witness that it is true. We confess, with the Apostle, that the good we would do, we do not, and the evil we would not, that we do. The motions of sin stir within us daily — pride, lust, anger, envy, unbelief — and we know that every one of them is truly and properly sin, an offense against Thy majesty. We do not excuse ourselves. We call it what it is: rebellion against a holy God, and we are ashamed. Yet we bless Thee that Thou hast not left us to despair. We thank Thee for Jesus Christ, in whom this corruption is fully pardoned. The guilt that would sink us is laid upon our Substitute. We thank Thee for the Holy Spirit, by whom this corruption is daily mortified. The power that would enslave us is broken, sin's motions put to death one by one. We are pardoned and purified, and both are Thy work alone. Grant us the grace to live in the light of this truth. When sin rises within, steady our hearts with the knowledge that regeneration is not eradication, that the war we feel is evidence of life. When we are tempted to make peace with some tolerated lust, sharpen our hatred of sin and strengthen our hands for mortification. When we are tempted to despair because progress seems small, lift our eyes to Christ, who will complete the work He has begun. Keep us from false comfort that minimizes our corruption, and from false fear that minimizes our redemption. Let the sight of remaining sin drive us to the cross, and let the righteousness of Christ be our only peace. For Thy people who struggle this day — the man who fights a secret lust, the woman who battles a bitter spirit, the soul weary of its own corruptions — grant the comfort of Thy presence. Tell them in the depths that they are Thine, that the corruption they hate will not have dominion, that the day of full deliverance draws near. Sustain them in the interval. And when the last motion of sin is stilled, receive them into that kingdom where Thy servants serve Thee with undivided hearts, world without end. Until that day, we rest in the finished work of Christ, who loved us and gave Himself for us, in whose name we pray. Amen.