Jesus’ conversation with Nicodemus tells us three important truths which we must not allow our opinions, traditions or religiosity to obscure.
First, we must all receive a completely new nature, a new kind of life generated by the Spirit of God from above. Without this, we are mere “flesh” that cannot see or enter God’s realm of eternal reality. This is a solemn and inescapable truth, twice affirmed by Jesus’ double phrase “truly, truly” — literally “amen, amen” (John 3:3-7).
Second, this is a great mystery, for no one can decide to be born. Parents decide to have children, not the other way around. Those born from above are not born by human decision, human effort or human act (John 1:12-13). The Greek word pneuma means breath, wind and spirit/Spirit — all equally unfathomable to the human mind. We see the wind’s effects but its operation is mysterious and invisible. So it is with those who are regenerated from above by God’s Spirit (3:8-11). Do not expect to explain the new birth — it is divine mystery and so it will remain! Jesus declares the necessity of new birth; he does not command anyone to make it happen. That is something only God can bring about.
Third, Jesus is lifted up as Savior and God promises eternal life to anyone who believes in him. Jesus was “lifted up” literally on the cross, where he was also “lifted up” in exaltation as God’s Lamb who takes away the sin of the world (John 1:29; 3:14). Just as God gave life to snake-bitten Israelites in the wilderness who looked in faith at the brass snake Moses had lifted up on a pole (Numbers 21), so God gives eternal life to every person who looks by faith at the atoning Savior making that atoning sacrifice (John 3:15).
Our final destiny will be either to live or to perish (v. 16). God’s heart is love, his desire is to save, his promise is faithful and sure (v. 16-17). Those finally lost will perish because they loved darkness and rejected God’s light (v. 18-21). Anyone who will believe can believe. All who believe must thank God for the new nature that made them willing. Both these statements are true and neither must be allowed to eliminate or to nullify the other. One day we will know fully, even as we are fully known. Until then we embrace the mystery and walk by faith not by sight.