The conscience is what God gave us so we know right from wrong. It is the part of us that is most like God (Genesis 3:22). When we say we want a clear conscience, we want purity, holiness, and absolution from the mistakes, or sins, we have made.
The Good News is that God has provided a way for us to have just that. "Therefore, brothers, since we have confidence to enter the holy places by the blood of Jesus, by the new and living way that he opened for us through the curtain, that is, through his flesh, and since we have a great priest over the house of God, let us draw near with a true heart in full assurance of faith, with our hearts sprinkled clean from an evil conscience and our bodies washed with pure water" (Hebrews 10:19–22).
When we try to create a clear conscience ourselves, we fail. We cannot become pure, nor remain pure, based on willpower, trying harder, or being good. Only God will separate us from our sin (Hebrews 8:12; Psalm 103:12).
When we sin—fall short of God's absolute holiness or rebel against Him and His ways in our spirits—we are acting against God. Even when we hurt another person or cause harm to others, it is God who ultimately is offended because He created us to be in harmony with each other and with Him.
Adam and Eve were the first humans and they sinned against God when they decided to disobey Him (Genesis 3:6). They were created to have a relationship with God and each other. So were we. But their sin got in the way, and so does ours. Adam and Eve passed down a sinful nature to all their descendants. We all disobey God and also experience separation from God and from one another. The Bible says that we are "dead" in our sins (Ephesians 2:1–3). There is nothing we can do to save ourselves.
But God makes a way for us to be in a right relationship with Him (Ephesians 2:4–5). For Adam and Eve, God killed an innocent animal and made clothes for them (Genesis 3:21). They were covered physically and spiritually. This was a sort of preview of what God had in store for the rest of humanity. God promised a future Messiah who would redeem all of humanity (Genesis 3:15).
Though men and women have devised various ways to atone for their mistakes, to be right before God—to clear their consciences—none work except the way God intends (John 14:6). He provides for us through the death of a perfect and innocent Being (Exodus 12:5; Leviticus 9:3; 1 Peter 1:18–19). That perfect sacrifice was His own Son, Jesus Christ, who is Messiah. "For God so loved the world, that he gave his only Son, that whoever believes in him should not perish but have eternal life. For God did not send his Son into the world to condemn the world, but in order that the world might be saved through him" John 3:16–17).
Jesus went to the cross willingly, taking all of our sins with Him to atone for them (1 Peter 2:24). His death was the result of all of God's wrath against us and our sin (Isaiah 53:6; John 3:36).
When we recognize the truth of who Jesus is and the truth of His sacrifice for us and accept it by faith to atone for our sins rather than pay for them ourselves in an eternity separated from God, then we can truly begin to pursue righteousness, purity, and a clear conscience (Romans 6:18). Of course, we will continue to fall short of the perfect fellowship God desires for us, but God took care of that, too. "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).
Our clear consciences come when we are in a right relationship with God. We must have faith that Jesus' sacrifice was for our own punishment and that He defeated even death by His resurrection from the dead. This puts us in a position to be in relationship with God. Then we grow in that fellowship with God—keeping our consciences clear, choosing to live for Him, seeking the things of God rather than of the world (Matthew 6:33), and continuing to confess our sins when we fall short, trusting that He is always faithful to forgive. A clear conscience is freedom. Jesus said, "So if the Son sets you free, you will be free indeed" (John 8:36).
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