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The next story that the apostle compiled is a further explanation of Jesus’ first sign regarding turning water into wine. The sign was ultimately about sonship, or how to become sons of God, as set forth earlier in John 1:12 and 13. Turning water into wine is about being transformed from soulish sons of Adam to spiritual sons of God.
Nicodemus was a perfect illustration of this (as we will see shortly), because the conversation he had with Jesus was all about how to become a son of God.
Nicodemus
John 3:1, 2 says,
1 Now there was a man of the Pharisees, named Nicodemus, a ruler of the Jews; 2 this man came to Him by night and said to Him, “Rabbi, we know that You have come from God as a teacher; for no one can do these signs that You do unless God is with him.”
Nicodemus stands in contrast to those in John 2:23 who believed openly at first but who later denied Jesus by siding with the chief priests in their condemnation of Him. Nicodemus started out believing in secret but in the end proved that his faith was genuine, for history tells us that Nicodemus was ultimately expelled from the Sanhedrin for his faith in Jesus.
John himself tells us that when Joseph of Arimathea claimed Jesus’ body after His crucifixion, Nicodemus brought spices in which to wrap His body (John 19:39, 40). These two Sanhedrin members thus openly showed their disagreement and disapproval of the verdict against Jesus. The stoning of Stephen (Acts 7) was the main turning point where they knew that they leave the city of Jerusalem.
In those early days, when the persecution of Christians came primarily from Jerusalem, Caesarea was the obvious place for a Christian to find refuge in the persecutions taking place in Jerusalem. Caesarea was a Roman city, specifically built for and named for “Caesar” by Herod the Great from 25-13 B.C. It was an administrative center for the Judean Province in the Roman Empire, and during the time of Jesus’ crucifixion and afterward, the centurion in charge of the Roman troops was Cornelius (Acts 10:1).
Cornelius may have been converted by Philip, who went there after his encounter with the Ethiopian eunuch (Acts 8:40). In fact, Philip lived and ministered in Caesarea for many years, providing a refuge for Christians fleeing Jerusalem (Acts 21:8). Paul himself was later taken to Caesarea for his own protection (Acts 23:23, 24).
Nicodemus himself spent some time in Caesarea after leaving Jerusalem. John W. Taylor writes on page 63 of his book, The Coming of the Saints,
“At Caesarea we find (according to the ‘Recognitions’) St. Joseph of Arimathea, Nicodemus, St. Lazarus, St. Zaccheus, and the ‘Holy Women’—probably St. Salome, the mother of St. James, St. Mary, the wife of Cleopas, St. Martha, and St. Mary Magdalene. Such appears to have been, so far as we can gather, the earliest disposition of the disciples after the persecution which arose about St. Stephen.”
The Recognitions reference in the above quotation are the known as the Recognitions of Clement (bishop of Rome from 88-99 A.D.). Some historians doubt that Clement of Rome was the actual author of these books, but their value as history is in no way diminished.
http://www.essene.com/Recognitions/index2.htm
The point is that the Apostle John had known Nicodemus very well in the early years of the church. Hence, he knew Nicodemus’ story firsthand and included it in his gospel to give us Jesus’ own teachings on sonship and to show how these teachings supported the first sign—turning water into wine.
When Nicodemus came to Jesus by night, he was not alone in believing in Jesus. He said, “we know that You have come from God as a teacher.” Nicodemus was just one of those who knew. Yet he stopped short of believing that Jesus was the Messiah, for it was too early in Jesus’ ministry for this to be revealed.
The Heart of the Message
Nicodemus and Jesus must have talked about many things, but the apostle focuses on one particular part of their conversation: sonship. John 3:3 says,
3 Jesus answered and said to him, “Truly, truly, [“amen, amen”] I say to you, unless one is born again [gennao anothen], he cannot see the kingdom of God.”
The term “born again” is a common evangelical term used today to describe a genuine believer in Christ. The Greek words used here are gennao and anothen. As I have explained earlier, gennao has a double meaning, depending on whether it is applied to a man or a woman. When applied to a man, it means “to beget.” When applied to a woman, it means “to give birth.”
In John 3:3 it is unclear how to translate it. John may have been speaking of the process including both conception and birth. We know that sonship is not simply a matter of being begotten by the Spirit, for many are begotten who later miscarry through neglect of the word or who deliberately abort by renouncing Christ. To be a son of God ultimately requires birthing as well.
Conception is achieved through the feast of Passover; growth and development comes through Pentecost by following the leading of the Spirit; birthing comes through the feast of Tabernacles.
The second term, anothen, means “from above, from a higher place.” Only rarely does it mean “repetition” or “again.’
https://www.blueletterbible.org/lang/Lexicon/Lexicon.cfm?strongs=G509&t=NASB
This word implies conception through seed that is heavenly, rather than earthly. In John 3:31 the apostle quotes John the Baptist, who uses this word anothen, who says,
31 He who comes from above [anothen] is above all, he who is of the earth is from the earth and speaks of the earth. He who comes from heaven is above all.
As we see, coming “from above” is equated to coming “from heaven.” So “born again” seems to strain the meaning and is probably based on the translators’ lack of sonship understanding. Hence, in my view Jesus was telling Nicodemus, “unless one is begotten from above, he cannot see the kingdom of God.”
Nicodemus’ Ignorance
John 3:4 gives us Nicodemus’ response:
4 Nicodemus said to Him, “How can a man be born when he is old? He cannot enter a second time into his mother’s womb and be born, can he?”
Though he was a respected rabbi leader and a member of the Sanhedrin, he did not understand how to become a son of God. He knew only about earthly conception and birth, and he knew also that it was not possible to do this twice. Until Mary was impregnated by the Holy Spirit to bring forth the Son of God, spiritual birth was not known or revealed. It was prophesied in certain Old Testament writings, but it was veiled and hidden through types and shadows.
Fleshly and Spiritual Birth
It is therefore likely that when the apostle penned Jesus’ words in John 1:12, 13, he was laying the foundation for the story of Nicodemus. Perhaps the apostle was paraphrasing Jesus’ own conversation with Nicodemus. Most likely, Jesus confided to His disciples what He had told Nicodemus in private. Whatever the case, the apostle did not see fit to repeat those precise words. His explanation to Nicodemus is summarized in John 3:5-7,
5 Jesus answered, “Truly, truly, I say to you, unless one is born of water and the Spirit, he cannot enter into the kingdom of God. 6 That which is born of the flesh is flesh, and that which is born of the Spirit is spirit. 7 Do not marvel that I said to you, “You must be born again.”
This is a further explanation of what Jesus had told Nicodemus earlier. To be “born of water” is the equivalent of being “born of the flesh.” To be “born of the Spirit” is obviously not a fleshly process, whether being begotten or being born.
It was known that an embryo lives in water. Today we call it amniotic fluid, but it was water to Nicodemus. Water always accompanied a baby’s birth. Being born of the Spirit was qualitatively different, Jesus told him.
Seeing and Entering the Kingdom
In John 3:3 Jesus spoke of seeing the Kingdom, but in John 3:5 He spoke of entering the kingdom. Both ideas are inherent in this process, but the difference appears to tie in with the two meanings of gennao. After conception, one sees the evidence of pregnancy as the woman’s belly grows, but only at birth does the baby enter the outside world as such.
One may also view it in reverse, of course. At conception, a baby enters the world, and at birth the baby is seen visibly. However we view this, it is clear that it is a two-step process not only in the natural but also in the spiritual.
Moses, for instance, saw the Promised Land (kingdom) but did not enter it (Deuteronomy 34:4). In that way, Moses represented the Old Covenant, which can show men the kingdom of God but cannot give anyone entrance. Moses leads us to the kingdom, but Joshua (Jesus) must lead us into the kingdom through the New Covenant.
This is also seen in the name of Moses himself, for he was so named because he was drawn from water (Exodus 2:10). In the biblical types and shadows, Moses had been placed in an ark and put into the Nile River so that he might picture natural childbirth as he was “born of water.” This takes us back to John 1:17, where we read that “the Law was given through Moses; grace and truth were realized through Jesus Christ.”
When John and Paul speak of “the law,” they often mean the Old Covenant, which is based upon the will of man and man’s ability to fulfill his vow of obedience in order to attain “life.” Such fleshly vows are incapable of imparting immortality, for men are unable to keep their vows, regardless of their sincerity. Immortal life, then, must come by grace (the will of God) and truth, that is, believing truth, which is the basis of genuine faith.
Water and Wind
John 3:8 says,
8 The wind blows where it wishes and you hear the sound of it, but do not know where it comes from and where it is going; so is everyone who is born [gennao] of the Spirit.
Even as water represents natural, fleshly begetting and birthing, so also does wind represent spiritual begetting and birthing. Wind is pneuma in Greek and ruach in Hebrew. Ruach can be translated either as wind, breath, or spirit. One may observe a river and see its source and where it ends, but one cannot do the same with the wind.
When one is begotten by the Holy Spirit (“wind”), it is through faith that comes through hearing the word (Romans 10:17). One is begotten through the ear, and the seed of the word that is implanted in one’s heart is not readily observable apart from spiritual discernment.
This entire passage is designed to show us the contrast between natural and spiritual childbirth. Many do not understand the difference even today, for they still maintain that men are chosen by bloodline, or that men are saved by their own will, or that men are saved by the pronouncements and declarations of men. John clearly opposes such teaching, both in John 1:12, 13 and again in John 3:5, 6.