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The following is an excerpt from The MacArthur New Testament Commentary on 1 John 3.
We will know by this that we are of the truth, and will assure our heart before Him in whatever our heart condemns us; for God is greater than our heart and knows all things. (3:19–20)
Every human being is born with the law of God written in the heart and with a conscience to accuse or excuse, depending on how the person acts in regard to that law:
For when Gentiles who do not have the Law do instinctively the things of the Law, these, not having the Law, are a law to themselves, in that they show the work of the Law written in their hearts, their conscience bearing witness and their thoughts alternately accusing or else defending them. (Rom. 2:14–15)
This means every person has some degree of self-knowledge and some innate ability to recognize right and wrong.
Those who are Christians have embraced the truth of Scripture, by which they were regenerated (1 Peter 1:23) and are being sanctified (John 17:17). They desire to know and obey the Word (cf. 1 John 2:3–6; 3:6–10). And when believers obey the Word of God, their consciences inform them that they did the right thing (Rom. 9:1), giving them joy and godly confidence (2 Cor. 1:12). Similarly, if they sin, their consciences indict them on account of their wrong thoughts, words, or actions (John 8:9). If believers persist in sin, implicitly the conscience will make them fearful, depressed, and insecure (cf. Pss. 32:3–4; 38:1–8; 40:11–12). They will then begin to question the genuineness of their profession of faith, on account of their prolonged disobedience. While they cannot lose their salvation (if they are truly saved), they can begin to lose the assurance of that salvation due to a plaguing conscience that accuses them. Until they properly deal with their sin, their conscience, empowered by true, Spirit-aided knowledge of the scriptural standards for holiness, will continue to painfully remind them of the blatant discrepancy between what they profess and what they practice.
The conscience then is God’s guilt-producing warning device, given to every person to confront sin. In the same way that pain is a physical warning mechanism that tells people they have a bodily injury or illness, the conscience is a spiritual warning mechanism that alerts of conduct dangerous to the soul. Of course, to function effectively, the conscience must be informed by the right standards, because it is only a reactor to the person’s convictions about right and wrong. If ill-informed by falsehoods and lies, the conscience will still react to those untruths that govern an individual’s beliefs (e.g., Muslim suicide bombers).
Conscience is thus not in itself an independent system of morality. Rather, it operates based on whatever knowledge and belief system that informs it, and in response to the cultural conditions surrounding it. If the level of moral and spiritual knowledge is drawn from any other source than Scripture, the conscience (like that of the Islamic suicide bomber who is convinced he is doing God’s work) will function in response to those false ideas. It can be silenced not only by being misinformed, but by being constantly ignored or overridden, until it is scarred and unresponsive (1 Tim. 4:2).
That is why it is crucial to know God’s law accurately (Pss. 19:7–9; 119:1–8; Luke 11:28; John 8:31–32; James 1:21–25) and allow it to properly inform the conscience. It is the law of God empowered by the Spirit that awakens people to their sinful condition and need of salvation (cf. John 16:8–11; Rom. 7:9–10). The sinner, seeing his true wretchedness as one guilty before God, is then faced with the reality of divine wrath and judgment against him, offset by the offer of mercy and deliverance through faith in the Lord Jesus Christ (cf. Luke 18:13).
In salvation, by the work of Christ on the cross, the wrath of God is propitiated and the guilt of sin removed from the forgiven sinner who then comes to enjoy the exhilarating, heartfelt deliverance of heavenly grace (cf. Eph. 2:1–9; Col. 2:11–14; 3:9–10). One of salvation’s most gracious gifts is a cleansed conscience (cf. Heb. 10:19–22), meaning it ceases to accuse. Just before salvation it accuses most intensely, but afterward the accusation stops and the believer goes from fear to joy, dread to hope, and anxiety to peace. The writer of Hebrews refers to this work of God when he writes: “How much more will the blood of Christ, who through the eternal Spirit offered Himself without blemish to God, cleanse your conscience from dead works to serve the living God?” (Heb. 9:14). In Hebrews 10:22 he speaks of “having our hearts sprinkled clean from an evil conscience” in salvation.
Still the apostle John understood that at times true believers can struggle with their assurance. Some of his readers may have been so overwhelmed by the memory of their past sins and awareness of present ones that they found the thought of God’s forgiveness nearly impossible to accept. Their overactive consciences, beleaguering them with their own shortcomings, perhaps made it difficult for them to have a settled confidence in their right standing before God. So John wrote to encourage those believers and enable them to accurately evaluate their own spiritual condition. In so doing, he sought to solidify their conviction, rightly inform their conscience, and strengthen their assurance with a true understanding of their transformation and its evidences. (For a fuller discussion of the human conscience, see my book The Vanishing Conscience [Dallas: Word, 1994], 35–75, 229–55.)
The phrase we will know translates a form of the common Greek verb ginosko, which means “to know,” “to learn,” “to find out,” or “to realize.” John’s use of the future tense indicates that what his readers would eventually grasp was not something intuitive or indefinite, but a promise based on an existing reality. This point is strengthened by the next short phrase by this, which most naturally refers back to verse 18’s admonition for brotherly love. When believers know they have sincere love for one another, they can be certain that they are of the truth (the phrase literally reads, “out of the truth we exist”). Only those who have been genuinely converted through the supernatural work of God possess the sacrificial love that John describes in verses 14–18, which issues in the submissive obedience that John delineates in verses 4–12.
The truth in view here is the written truth of Scripture (Ps. 119:160; John 17:17), which encompasses the truth incarnate in the Lord Jesus Christ (John 1:9, 14; 7:18; 14:6; 1 John 5:20). Belief in the truth marks all who repent and believe (2 Thess. 2:10, 12–13; 1 Tim. 3:15b).
Believers enjoy an assurance based not only on what Scripture promises to those who believe (Ps. 4:3; Phil. 1:6; 2 Tim. 1:12), but, on a practical level, based on the presence of a serving love for fellow believers (cf. vv. 13–18) and a desire to live in holiness (cf. vv. 4–12). These qualities, because they come from God, cannot exist in a person who is still unregenerate. Assure comes from the future active indicative of the verb peitho and means “will persuade.” Some lexicographers give “to tranquilize” as a possible definition, which could have an interesting connotation in this context. Even though believers stand before Him, in the awesome, intimidating presence of the absolutely holy God (Ex. 15:11; 1 Sam. 2:2; Rev. 15:4), they can have a calm, tranquil, confident heart and an affirming conscience (Acts 23:1; 24:16; 2 Cor. 1:12; 1 Tim. 1:5; 3:9; 2 Tim. 1:3).
Being in the presence of God terrified even the noblest of saints. Moses “hid his face, for he was afraid to look at God” (Ex. 3:6). The prophets Isaiah (Isa. 6:1–5) and Ezekiel (Ezek. 1:26–28) also felt great fear as they stood in the presence of holiness. After witnessing one of His miracles, the apostle Peter “fell down at Jesus’ feet, saying, ‘Go away from me Lord, for I am a sinful man, O Lord!’ ” (Luke 5:8). He and fellow apostles James and John were traumatized on the Mount of Transfiguration (Matt. 17:1–8), as was John when he saw the glorified Christ (Rev. 1:12–18). Although believers are no longer slaves to sin but to righteousness (Rom. 6:16–18), the remaining sin within their unredeemed humanness (cf. Rom. 7:14–25) could make God’s holy presence very frightening were it not for the gracious gift of assurance.
Those who have been justified by faith are at peace with God (Rom. 5:1) and enjoy the peace of God (Phil. 4:7). Nevertheless, a believer may experience unnecessary guilt as his heart condemns him. But there is a higher court than the human heart, for God is greater than our heart and knows all things. If He has declared believers righteous in Christ, then they are righteous. Thus Paul wrote, “Therefore there is now no condemnation for those who are in Christ Jesus” (Rom. 8:1). And no one can ever separate them from the saving love of God in Christ (8:31–39). He sees believers’ greatest, most profound failures, and He knows far more about their weaknesses than even their consciences do (Pss. 1:6; 103:14; 139:1–6; Prov. 24:12; Heb. 4:13). Yet God has forgiven those who by faith in Christ have been adopted into His family (Rom. 8:14–17). Moreover, He is at work in their hearts, continuing to cleanse them from the sin that still lingers there (cf. Phil. 2:12–13). He looks beyond the remaining sin and sees the holy affections He has planted in them that demonstrate the transformed natures of His children. Therefore even when overwhelmed by their sinfulness believers can say with Peter, “Lord, You know all things; You know that I love You” (John 21:17; cf. Rom. 7:14–25).