The Spirit in John’s Gospel


If you have your Bible, please turn with me to the Gospel of John, chapter 1.

Since the beginning of last year I’ve been doing a series of messages on the Holy Spirit or Spirit of the Lord in the Bible. I want you to understand better the last Person in the Holy Trinity. Holy Spirit takes the humblest role with the least authority of the Godhead. Yet He is the One entrusted to wield the power of God and craft the works of God in the lives of men and women. Holy Spirit, if you will, is the Master Craftsman of the lives of every person and every society on earth.

He is also the Master Storyteller. He shapes the universe around us to tell a story of the glory of God. He reveals wisdom through the behaviors and character qualities of every living thing that we can learn and reflect upon. But the greatest stories He is telling are in the lives of people. We are the only creatures on earth, or in the universe that we know about, that are capable of telling and vicariously experiencing life stories, and thus perceiving some of the glory of God.

Every one of you is a unique and unrepeatable miracle of God; and your life story is a masterpiece of creation. It may not seem like that to you, because you’re surrounded by people who are not unlike you. We’re all connected inescapably to a much greater society that makes us all feel small in comparison. But behind us all is One infinitely greater who finds you immeasurably interesting. He has watched your life develop from an act of love that caused a single sperm cell to mate with a female egg. Thus began the most extraordinary work in all of creation – the development of a human child, a creature capable of being an image bearer of God. We’re the one creature chosen by God to be a holy receptacle, or temple, of God’s Holy Spirit. And there is nothing in all of creation, now and forevermore, like the human race. And there is no temple of God quite like you. And God, the Author of all things, takes immense pleasure in every one of you because of that.

God knows everyone’s life story in infinite detail, from beginning to end, because He lives and acts beyond space and time to shape the Creation as He sees fit. He works in and around every person’s free choices to shape their destiny to guide the destiny of this world. Yet He does so without violating our freedom to make choices.

If you care to believe it, every human being’s stories are immeasurably precious to God – even the stories of those who fail and ultimately end up in hell. Their stories will only be remembered by God, who both loved them and judged them faithfully. Every one of us could be dead and lost in hades right now, contemplating all the opportunities we failed to take to know the living God so that we could pursue selfish pleasure.

Instead, I declare by faith, God has appointed every one of you to triumph over this sin-scarred life and end up in heaven. You will come there with a life full of stories – some good and some bad – wherein God’s Spirit secretly worked to ensure that your eternal destiny is good. You are doing your part to position yourself for heaven by coming to church and hearing God’s word preached to you. You are saved through persevering in faith in Christ.

You always have the freedom to turn away from God and return to your base impulses. But Romans 6:21 asks each of us, “What benefit were you deriving from the things of which you are now ashamed? For the outcome of those things is death.” It’s the Spirit who makes you want to be good and godly for the glory of God. You only get there by submitting to His gentle nudges to turn in the right direction in the right way at the right time. This is the miracle of sanctification – turning sinners towards God in order to make us more holy and pleasing to God.

The Apostle John was likely the youngest of Jesus’ twelve apostles. John lived nearly to the end of the first century; so he was a witness to both the beginning and establishing of the early Christian faith. By the time John died, two or three generations of Jewish and Christian believers in Jesus had come to life through the gospel. Christianity was on its way to becoming a movement that would ultimately transform the Roman Empire. Then it expanded throughout Europe, and now the world, through the gospel of our Savior, Jesus Christ.

John’s first description of the Holy Spirit came through the words of John the Baptist, “I have seen the Spirit descending as a dove out of heaven, and He remained upon Him.” The dove represents gentleness and peace; and the dove descending clearly points to the falling of the Spirit from heaven upon people for regeneration and healing. Under the old covenant, the turtledove could be substituted by the poor for lambs in sin offerings. So there is a connection between Jesus, the Lamb of God, and the Holy Spirit, represented by the turtledove.

Most importantly, as John 1:33 says of the Baptist, “I did not recognize Him, but He who sent me to baptize in water said to me, ‘He upon whom you see the Spirit descending and remaining upon Him, this is the One who baptizes in the Holy Spirit.’” The baptism in the Holy Spirit is one of the chief reasons Jesus came to earth. Spiritual regeneration is accompanied by the indwelling of the Holy Spirit. This is the initial immersion in the Spirit.

I come from a vein of Christianity – Pentecostalism and Charismatic faith – that affirms a second baptism in the Spirit subsequent to our salvation. This is not the initial entry of the Spirit, but a subsequent work of empowerment for works of service. Jesus clearly had the Spirit within Him from earliest childhood; but His immersion in water, and subsequent immersion in the Holy Spirit was the initiating act of His anointing with power to be a prophet of God.

We next see the Spirit in John’s Gospel, chapter three. A leader among the Pharisees, and member of the Jewish high court or Sanhedrin, named Nicodemus came to see Jesus by night. Even at this early stage of Jesus’ ministry, Nicodemus was afraid to be publicly associated with Jesus. Such was Jesus’ impact on the Jewish religious community that He aroused almost immediate opposition.

Nicodemus said to Jesus, “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.” Jesus answered and said to him, “Truly, truly, I say to you, unless one is born again he cannot see the kingdom of God.” Nicodemus understood that Jesus’ miracles were proof that He was anointed by God. But Jesus replied that he needed something more than just acknowledging Jesus was a teacher sent by God. He needed a spiritual rebirth. Without it, it’s impossible to see the ways and heart of God in this world, or enter His eternal kingdom thereafter.

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?” 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. That which is born of the flesh is flesh, and that which is born of the Spirit is spirit.”

Nicodemus couldn’t see that Jesus was speaking about the realm of the Spirit. His mind gravitated to this natural world, and saw rebirth as an impossible reentry into a mother’s womb. Jesus replied that there are two births that must occur to enter God’s kingdom. You must be born both of water – that is through natural birth – and of the Spirit.

So what is spiritual birth? Jesus said that anything coming from the natural body, “the flesh”, is natural; but spiritual birth produces spirit life. As I have said before, the realm of the spirit is imperceptible to our natural senses. It exists, properly, in a different dimension of reality; yet it intersects the natural dimension.

The human race is the only race of creatures in creation that is both natural and spiritual. Other animals are merely natural, and their “breath of life” is exactly that, physical breath. But human beings interact with both the physical and spiritual realms of reality. The physical realm is impermanent; it has a beginning and an end point. But the spiritual realm is never-ending.

Once you enter eternity after natural death, your spiritual condition is fixed forever. There is no purgatory for those who are lost in hades after death. Nor is there a purgatory for souls redeemed through Christ’s death. Those who are born of the Spirit are regenerated with the life of God. They retain their spiritual life and imputed righteousness throughout this life, even though they may defile their spirit with sin.

Spiritual birth is necessary, because we enter the natural world with an imputed sin nature, which the Bible says is the legacy of Adam’s fall from grace. I do not understand how a sin nature is transmitted to children at childbirth; but it is. No one has to teach little children how to be selfish, lie, steal, throw temper tantrums or hate. It just comes to them. “Foolishness is bound up in the heart of a child” says Proverbs 22:15. Earthly discipline helps children mature into those who can restrain their basest impulses; but only regeneration can remove the core sin nature from a person’s spirit.

Spiritual birth, or regeneration, is the miraculous transformation of a human’s inner nature that removes the sin nature and replaces it with the nature of Christ by the indwelt Holy Spirit. With this nature comes imputed righteousness and the ability to perceive the truth of the gospel by faith. The result of belief in the gospel of Christ is justification – a declaration of innocence by God, where God’s judgment against sin is satisfied and sin is completely removed or expiated. The Bible also calls this “the remission of sin.”

When we can see our true spiritual condition apart from Christ, and its terrible consequences – bondage to sin and hell as our final destination, we can clearly appreciate the benefit of the gospel. This is one benefit of seeing the kingdom of God that Jesus spoke about to Nicodemus. 1 Peter 3:18 says, “For Christ also died for sins once for all, the just for the unjust, so that He might bring us to God, having been put to death in the flesh, but made alive in the spirit.”

Salvation from the penalty of sin is the benefit of justification. Being saved from the present power of sin is called sanctification, that is, being made more holy. Holiness in this instance is the character of God’s integrity expressed through us. Our rebirth sanctifies us forever in heaven. But it also releases the grace of God to sanctify us presently so we can overcome the sins that cause us and others the most harm.

Another benefit of spiritual regeneration is the ability to appreciate the beauty of our God and Savior Jesus Christ. Seeing the kingdom of God means seeing Jesus at work in your life and that of others, and being able to commune with Him by faith. Christ died for our sins to bring us to God in a vital fellowship and life of faith we call communion. This communion will continue forever. When we appreciate the beauty of God’s character and His wisdom, we are positioned to glorify God and enjoy Him forever.

John Piper, in his renowned work Desiring God, reworks the words of the Westminster Confession to state “The chief of end of man is to glorify God by enjoying Him forever.” Being born again enables us to glorify God by giving us joy at being part of His eternal kingdom. When we do this, we enter into the heart of God’s kingdom, because as Piper notes, “The chief end of God is [also] to glorify God and enjoy Himself forever.” And I would add “with His creation.” For God gets the most joy when we enjoy Him for His intrinsic beauty, His glory.

When we enter the kingdom of God through faith in the King, Jesus Christ, we experience eternal joy. There we find our highest and purest pleasures in knowing God and sharing in His super-bountiful kingdom. His is a living realm that will continue forever with a whole race of redeemed people as His royal priesthood and vice-regents. And, of course, the greatest benefit of being born again is the immortality of the soul that will be raised to eternal life at the resurrection of the dead.

Jesus then continued in chapter 3:7-8, “Do not be amazed that I said to you, ‘You must be born again.’ 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 of the Spirit.” When you are born of the Spirit, you are liberated to experience life on a different plane. You become like the wind, Jesus said, where you can come and go in new ways that others cannot predict or determine. You are led by God’s Spirit, and His ways are unfathomable and unpredictable. Your potential is implicitly unshackled when you are reborn by God’s Spirit.

John uses John the Baptist’s final words as His mouthpiece for celebrating the Spirit’s work in and through Jesus in ch.3:33-34, “He who has received His testimony has set his seal to this, that God is true. 34 For He whom God has sent speaks the words of God; for He gives the Spirit without measure.” Jesus had the Spirit without measure in His ministry on earth; but I don’t think this statement was exclusively meant for Jesus. Jesus’ salvation brings the reception of the Holy Spirit. God gives His Spirit without measure to the Church.

Those who speak the words of God can also experience the Spirit given without measure. Jesus clearly alluded to this later in John’s gospel when he said, “Truly, truly, I say to you, he who believes in Me, the works that I do shall he do also. And greater works than these shall he do, because I go to the Father.”

So what are the words of God that John the Baptist, and John the Evangelist, knew could release the Spirit without measure? The Baptist’s final remarks were that “The Father loves the Son and has given all things into His hand. 36 He who believes in the Son has eternal life; but he who does not obey the Son will not see life, but the wrath of God abides on him.”

God the Father’s love for His Son is the driving force behind God’s work of redemption. The Spirit works so that Christ might have a mighty kingdom of redeemed people who love Him. This love relationship goes on forever; so everything the Spirit of God does is a celebration of the Father’s love for the Son and for His creation. Thus our ultimate purpose is also to celebrate the Father’s love for the Son, and vice versa.

The next mention of Holy Spirit in John’s gospel is in chapter 4, where Jesus encountered a Samaritan woman at a well. This unusual meeting fleshed out what Jesus said about those born of the Spirit being led by God’s wind not others’ expectations. Jesus walked directly north from Judea to Galilee. He avoided the indirect route across the Jordan River that most Jews used to avoid the despised Samaritans. For God’s Spirit had other plans for Messiah.

He came to a Samaritan town called Sychar around noon, and found an unmarried woman fetching water from the well. Noon wasn’t the time respectable women went to the well to fetch water. Water buckets are heavy; so carrying one in the heat of noon day was wearying. But this woman came at noon – probably to avoid the scorn of village women who regarded her as a harlot. Jesus later revealed to the woman that she had five previous husbands and was now living unmarried with a man. Yet this was a precious soul whom God loved, and Messiah was sent to redeem her.

Jesus simply asked the woman for a drink, provoking surprise from her that a Jewish man would ask a favor of a Samaritan woman. Reading on from v.10: “Jesus answered and said to her, “If you knew the gift of God, and who it is who says to you, ‘Give Me a drink,’ you would have asked Him, and He would have given you living water.” 11 She said to Him, “Sir, You have nothing to draw with and the well is deep; where then do You get that living water? 12 You are not greater than our father Jacob, are You, who gave us the well, and drank of it himself and his sons and his cattle?” 13 Jesus answered and said to her, “Everyone who drinks of this water will thirst again; 14 but whoever drinks of the water that I will give him shall never thirst; but the water that I will give him will become in him a well of water springing up to eternal life. 15 The woman said to Him, “Sir, give me this water, so I will not be thirsty nor come all the way here to draw.”

Notice the sublime irony in this encounter. Jesus, who was physically thirsty in the heat of day, asked this Samaritan woman for a drink. But Jesus turned the conversation away from the natural toward the spiritual, provoking a spiritual thirst in her that would become a well of living water. She, however, was still focused on natural water.

That’s when Jesus asked her to call her husband. She admitted she had none, and Jesus divulged her past without an air of stern condemnation. I envision his words and tone toward her were gentle, compassionate and caring. The woman perceived he was a prophet and started engaging in a religious dialogue about the proper place of worship – Jerusalem or Mt. Gerizim in northern Israel. But Jesus redirected her to the focus of true worship – the Heavenly Father.

“Woman, believe Me, an hour is coming when neither in this mountain nor in Jerusalem will you worship the Father. 22 You worship what you do not know; we worship what we know, for salvation is from the Jews. 23 But an hour is coming, and now is, when the true worshipers will worship the Father in spirit and truth; for such people the Father seeks to be His worshipers. 24 God is spirit, and those who worship Him must worship in spirit and truth.”

In just a few minutes, Jesus was able to reveal her sinful condition, awaken her need for salvation, and redirect her to worshipping the Father in spirit and in truth. For God is spirit. He can only be worshipped by those whose spirits are awakened to the truth of who He is. For we are made in the image of God to worship Him through our spirits.

The Samaritan woman was taken in by Jesus’ revelation and was now spiritually thirsty. “The woman said to Him, “I know that Messiah is coming (He who is called Christ); when that One comes, He will declare all things to us.” 26 Jesus said to her, “I who speak to you am He.” In the original Greek, Jesus simply says, “I who speak to you am.” This is the first of the I AM statements by Jesus in John’s Gospel that definitively affirm that Jesus knew He was Messiah, God incarnate.

Faith in Jesus now captivated her heart rather than physical thirst. She left her waterpot at the well and returned to Sychar where she spoke to anyone with excitement. ‘“Come, see a man who told me all the things that I have done; this is not the Christ, is it?” They went out of the city, and were coming to Him.’ Through this one encounter the whole village turned out to hear Jesus teach. The beautiful irony here is that the town harlot that no one wanted to associate with was the person who led her village to Christ. She left her fear of public reproach, the burden of guilt and shame, and returned to her village with childlike wonder to tell everyone that Messiah had come.

The next episode of the Holy Spirit in John’s gospel is in chapter six, where Jesus revealed His divinity more explicitly and connected it to consumable bread. In John 6:35, Jesus said, “I am the bread of life; he who comes to Me will not hunger, and he who believes in Me will never thirst.” In John 6:41, He said, “I am the bread that came down from heaven.” And then in v.48, He repeated, “I am the bread of life.” And again, in v.51, “I am the living bread that came down out of heaven; if anyone eats of this bread, he will live forever; and the bread also which I will give for the life of the world is My flesh.” These are four more “I am” statements where Jesus connected His divine life as essential for nurturing the lives of His followers.

This passage explicitly affirms that Jesus had a eucharistic understanding of his life and death as feeding the world’s hunger and thirst for God. Yet He refused to see this Eucharist or thanksgiving gift in physical terms. When many of His followers abandoned Him for telling them His blood was true drink, He then stated in v. 63, “It is the Spirit who gives life; the flesh profits nothing; the words that I have spoken to you are spirit and are life.”

The wonderful truth in this passage is how each person of the Triune God plays a critical role in our salvation. It is the Father who offered His Son as a living sacrifice for our sins. He was in the role of the priest who offered animal sacrifices to atone for the sins of the people. It is Jesus who freely offered Himself, like Isaac, as a living sacrifice. Thus he became our Savior and Redeemer, and the Church’s first love. Finally, it is the Holy Spirit who imparts life by regenerating those who believe in Jesus’ death and resurrection. His atonement satisfied once and for all time God’s justice against sin.

The Spirit of God imparts life to our souls and nurtures us in the life of God. He comes to those who entrust themselves to Jesus Christ as their personal Lord and Savior. He works imperceptibly among us to shape our lives and destinies so that we, too, can impart life-giving words and assurance as Jesus did. His beautifully creative love works in ways that are always surprising and refreshing for those who perceive it. The Holy Spirit wants to shape your journey of life into a journey of love to the heart of the Father who called you to believe in His Son.

I can still recall how my journey of love with Christ began. I was raised in a family of atheists. My dad, now 99, is a renowned biochemist – a brilliant man who was my highest authority as a child. He told my brother and me, “There is no God;” so I believed him. But later as a teenager I wasn’t so sure; I could see darkness in the world that social programs could never cure. By the time I reached college I called myself an agnostic – one who doesn’t know. An agnostic is an atheist who is too timid to admit it, and too lazy to seek God!

But years later, as a lonely second lieutenant in Fort Sill, Oklahoma, I went through a difficult first year on active duty. My Lance Missile platoon flunked a major field test and I was transferred up to battalion headquarters. I felt like a failure – trapped and adrift in my job – with 2½ more years to go in my commitment.

On November 23, 1977, I found myself weeping alone saying, “I’m so bitter, and there’s nothing I can do about it!” I sat down at my desk to write a letter to my former college girlfriend; and I broke down in tears. But then I remembered what my former driver, SPC Steven Ellis told me: “I believe Jesus will touch everyone at least once in their life.”

So I did something I’d never done before. In tears I said, “Jesus, if you’re really there, help me! Help me!” Instantly, I heard something within like a “whoo!”, and felt something drop in me and I suddenly calmed down. I sat there wondering was that really Jesus or something psychosomatic. I didn’t know; but I knew that if Jesus was real I wanted to follow Him. I believe at that moment I experienced regeneration. I had a new spirit within me that wanted to know the Truth about Jesus.

That weekend, I saw a movie called “The Late, Great Planet Earth” based on the best-selling book by Hal Lindsay. My Christian neighbor went to the movie with me, and he was really praying for me. He just happened to have that book. Over three days, I slowly read the book and looked up every Bible verse in it. The biblical prophecy about Jesus persuaded me He had to be Messiah, the Son of God. So on November 30, 1977, I got on my knees and read the sinner’s prayer in the back of that book; and I’ve never looked back. My bitterness was replaced with forgiveness; and my love and knowledge of Jesus has only increased. I know that I know that He’s the true Son of God, and I will live forever with Him and His people, the Redeemed.

You are a unique and unrepeatable miracle of God; and the Spirit who is the miracle-worker wants to make the miracle of your life even more beautiful. For the beauty of your life as an image bearer of God reflects the glory of God.

The joy of the Spirit is taking lives that are barren of divine beauty and steadily and purposefully imparting the graces and character of Christ to it. That is what God finds beautiful. He sees the struggles you have to master your sin nature, but He still loves you. And the Father directs the Holy Spirit to make you a member of Christ’s bride, the Church, without spot or blemish at His coming.

Therefore, I charge you as a minister of the gospel of Jesus Christ, to surrender to the wise and purposeful influence of the Holy Spirit. Let Him nudge your spirit and will to be a more faithful, willing and teachable child of God. It starts with a willing surrender to the Lordship of Christ. And then you launch into a lifelong journey, as free as the wind, being guided by the invisible hand of the Almighty towards heaven and eternal rewards for your glad obedience.

Let us pray.