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Some have mistakenly used this verse as proof that an individual is not born again until he is composed of spirit. However, Jesus is not considering a person's bodily composition at all. A Bible student can be misled by abruptly abandoning Jesus' use of spiritual imagery and returning to a literal interpretation. Like the rest of the context, verse 6 must be understood spiritually and figuratively.
The verse states why the new birth is necessary. Flesh can continue to give birth only to what it has always produced: flesh. Yet, Jesus states clearly in John 6:63, "The flesh profits nothing." In John 8:15, He accuses the Jews of judging Him according to the flesh rather than using God's Word—which is Spirit—as their evidence. In both of these cases, Jesus is also speaking figuratively.
In Greek, "flesh" is sarx (Strong's #4561). Jesus and Paul commonly use the term as a metaphor for sinful man's nature, sometimes also described as "carnal." Used in this way, sarx is morally negative, even though by creation a person's flesh is not intrinsically negative. Figuratively, it symbolizes the unregenerate moral and spiritual state of man that almost continuously generates sinful acts. "Flesh," then, represents the inward, carnal inclination rather than muscle, skin, and bones—disposition rather than composition.
Paul writes in Romans 7:18, "I know that in me (that is, in my flesh) nothing good dwells," meaning nothing good spiritually. Later, in verse 25, he admits that his "flesh [serves] the law of sin." In Galatians 5:15-17, he positions the Holy Spirit as the opposite of the flesh, declaring that these two are at war:
But if you bite and devour one another, beware lest you be consumed by one another! I say then: Walk in the Spirit, and you shall not fulfill the lust of the flesh. For the flesh lusts against the Spirit, and the Spirit against the flesh; and these are contrary to one another, so that you do not do the things that you wish.
Biblically, the term "born" or "birth" is used, not only to indicate coming from the womb as in mammalian birth, but also to describe the source or beginning of a thing, an event, or series of events. For example, we speak of the birth of a nation, an institution, or a concept. The "womb" of those births was an event or series of events that triggered the inception of a new direction, manner of life, activity, or thought.
This is how Jesus is using "born" or "birth" in John 3. He is not speaking of the birth of a human child but the birth of a new nature. The events triggering this birth are the calling of God, repentance from sin, justification through faith in Christ's death, and the receipt of God's Holy Spirit. All of these are effects of the acts of the spiritual God.
Conversely, human nature gives birth to more human nature and thus more of human nature's sinful works. It cannot do otherwise. As Job 14:4 says, "Who can bring a clean thing out of any unclean? No one!" Paul makes the same point theologically:
For to be carnally minded is death, but to be spiritually minded is life and peace. Because the carnal mind is enmity against God; for it is not subject to the law of God, nor indeed can be. So then, those who are in the flesh cannot please God. (Romans 8:6-8)
The flesh expresses itself, produces, and gives birth to the works of the flesh and thus to immorality, impurity, sensuality, idolatry, and other evils, as Galatians 5:19-21 details. Though the flesh is capable of doing some good things (Matthew 7:11), in relation to God and His way, the evil will always dominate. The natural, fleshly condition of man will always exhibit the same propensities. In contrast, the Holy Spirit gives birth to and is expressed by the fruit of the Spirit: love, joy, peace, etc. (Galatians 5:22-23). Therefore, a change must take place from a life dominated by the natural human heart to one motivated by God's Spirit—or a person will never be prepared for the Kingdom of God.
John W. Ritenbaugh
Born Again or Begotten? (Part Two)