The Mystery of the Word made Flesh

Text: John 1:1-18

John 1:1-18 (ESV)

The Word Became Flesh
v.1 In the beginning was the Word, and the Word was with God, and the Word was God. v.2 He was in the beginning with God. v.3 All things were made through him, and without him was not any thing made that was made. v.4 In him was life, and the life was the light of men. v.5 The light shines in the darkness, and the darkness has not overcome it.

v.6 There was a man sent from God, whose name was John. v.7 He came as a witness, to bear witness about the light, that all might believe through him. v.8 He was not the light, but came to bear witness about the light.

v.9 The true light, which gives light to everyone, was coming into the world. v.10 He was in the world, and the world was made through him, yet the world did not know him. v.11 He came to his own, and his own people did not receive him. v.12 But to all who did receive him, who believed in his name, he gave the right to become children of God, v.13 who were born, not of blood nor of the will of the flesh nor of the will of man, but of God.

v.14 And the Word became flesh and dwelt among us, and we have seen his glory, glory as of the only Son from the Father, full of grace and truth. v.15 (John bore witness about him, and cried out,This was he of whom I said, ‘He who comes after me ranks before me, because he was before me.’”) v.16 For from his fullness we have all received, grace upon grace. v.17 For the law was given through Moses; grace and truth came through Jesus Christ. v.18 No one has ever seen God; the only God, who is at the Father’s side, he has made him known.


From time to time I sense the Lord leading me to pray about what the New Testament calls

the mystery
, this “mystery” is certainly related to Christmas but not in a way we find naturally attractive.

Unlike the culturally appealing baby in the manger theme the mystery leads directly to the cross.

In a concise way Paul expounds the mystery in a way which was extremely counter cultural to the spirituality of his day; “the great mystery of our faith, was manifested in the flesh” (1 Tim 3:16).

John’s Gospel shares this testimony, “the Word became flesh and dwelt among us, and we have seen his glory, glory as of the only Son from the Father” (John 1:14).

Whenever the Church has a fresh revelation of the Word made flesh it experiences the radiance of the Father’s glory and matures in Christ. This is the revelation we need if we are to be spiritually prepared for the tough times that lie ahead in a culture where biblical Christianity is increasingly unpopular.

The place we need to turn today is John 1:1-18.

Popular preachers love to tell stories about how God helps people, but in John 1 God tells his own story. The story of the Word made flesh is a statement as to how in reshaping his own identity the Son of God reshapes ours.

Often the way Christians casually talk about the Lord trivialises the dignity of his person.

As you don’t share your heart with anyone so God does  not share his mysteries with shallow people. This becomes very clear when we notice a profound connection between what John 1:18 says about Jesus and how the apostle John describes his own relationship with Christ;

John 1:18 reads literally, “No one has ever seen God; the only God, who is in the bosom of Father, he has made him known.”, and John 13:23 says, “Now there was leaning on Jesus’ bosom one of his disciples, whom Jesus loved.” (John 13:23).

In a physical sense “bosom” means the centre of the human chest but symbolically it means strength of feeling, intimacy and fellowship.

Only someone who enjoys rich intimacy with Jesus, only a “bosom buddy” of Christ can be spiritually connected with his deep intimacy with the Father and receive a revelation of the mystery of God. John 1:1-18 confronts us with this challenge today.

Eternal Word

By starting his Gospel with “In the beginning was the Word”, or more literally, “When the beginning began the Word already was.” John takes us back not only to “the beginning” of creation in Genesis 1:1 but into the backdrop of eternity.


The Greek term we translate “Word” is Logos.

For ancient people the world made sense.

When John’s Greek readers saw the word Logos

they thought of the blueprint for the universe and the powerful cosmic presence holding everything together.

For the Jews the Word was the agent of creation and God’s mode of communication through law and prophets 

Yesterday I was listening to a friend share his testimony of how reading through twentieth century Western literature at university plunged him into a deep depression.

Any society which abandons faith in the Word and commits to an atheistic evolutionary view that sees the world as ultimately irrational will fall into spiritual, moral and mental darkness.

When John says “the Word was with God, he uses a Greek term that conveys a dynamic interconnection between the Word and God which flows into his next expression “and the Word was God”.

The text does not say that the Word was divine or that the Word was a little “g” God, it says the

Word was God….in the beginning with God” (1:1-2); there never was a time when the Word was not God.

Creation through the Word

John now scales down from eternity to the Word’s creation of space and time. 

JOHN 1: v.3 All things were made through him, and without him was not any thing made that was made.(cf. Heb 1:2-3)

Creation by the Word sets the stage for illumination by the Word.


JOHN 1: v.4 – v.5 v.4 In him was life, and the life was the light of men. v.5 The light shines in the darkness, and the darkness has not overcome it.

As life and light were paired in creation’s beginning so now the life of the Word is the source of all spiritual enlightenment.

In John’s Gospel the life and light do things; as “the resurrection and the life” Jesus raises Lazarus from the dead (11:25, 43-44), as “the light of the world” he gives light to blind eyes (8:12; 9:5-7).

As the first act of creation dispelled physical darkness so the spiritual light of the Word dispels spiritual darkness. In John 3 Jesus speaks of darkness as a power that hates him, “v.19 the light has come into the world, and people loved the darkness rather than the light because their works were evil. v.20 For everyone who does wicked things hates the light and does not come to the light, lest his works should be exposed.” (John 3:19-20 cf. Matt 13:13; John 13:27-30). Not everyone hated the light.

John the Baptist appears briefly in this section of the Gospel as a witness of the Word.

JOHN 1: v.6 – v.9 & v.15 | “v.6John. v.7cameto bear witness about the light, that all might believe through him. v.8 …. v.15 (John bore witness about him, and cried out, “This was he of whom I said, ‘He who comes after me ranks before me, because he was before me.’”)

In the other Gospels the Baptist is the greatest of all “born of women” but in John his status is solely as a witness. To share in this spirit of witness which directs all attention to Jesus is God’s call on all our lives.

Born Again

JOHN 1: v.9 v.9 The true light, which gives light to everyone, was coming into the world.

Any religious, political or philosophical system that does not have Christ at its centre is a false light and a satanic lie
(Ps 24:4; Isa 44:20; Amos 2:4; Rom 1:25; 2 Cor 11:14).

Back in the 70’s we encountered a group on the streets of Adelaide who experienced a mystical initiation through “taking knowledge” (Divine Light Mission). In this ritual a flashing light went off in the head of the disciple and powerfully convinced them their guru rather than Jesus was the Light of the world.

If there is counterfeit mysticism there are true mystical experiences.

Some years ago in prayer I had an encounter with the most intense WHITE light that powerfully and spontaneously moved me to worship God through Christ (1 John 1:6ff.). In my prayer diary I wrote the words, “before the purity of this light we will worship forever” (cf. 1 Tim 6:16). This is the light of the Word which enlightens the world.

When the light of the Word enters into our hearts (Ps 119:130; 2 Cor 4:4) it gives us a new identity.

Jesus said if we believe in him we would “become sons of light” (John 12:35-36; 1 Thess 5:5 cf. Ps 36:9; Eph 5:8).

Seeing things through God’s light, which as we will see ultimately means the light of the cross, reshapes the way we see everything.

A university friend had an experience of the light of the Lord and shortly after went into a lab and looked through the microscope at a plant section (cotyledon); he could only describe what he saw as “beautiful”.

In the light of Christ all the children of God are radiantly beautiful; I have had powerful experiences of this myself. No child of God should ever see themselves as fundamentally dark, depraved or sinful (cf. Rom 13:12, 14) but called to be alive with the light of the Lord bringing illumination to those in the darkness (cf. Matt 5:16)

I was listening to a former gay activist talking about homosexuality recently and he stressed all his hundreds of relationships with other men were based on getting things from the lives in a fruitless attempt to become whole. He was like a “black hole” where things go in but nothing comes out. The narcissistic pattern of relating which is fast becoming the norm in our society is an inevitable consequence of its rejection of the light of the Word.

JOHN 1: v.10 – v.11 v.10He was in the world, and the world was made through him, yet the world did not know him.In John’s writingthe worldis humanity in its alienation from God. How painfully horrible it must have been for the Creator-Word to live amongst his beloved creatures unrecognised.v.11 He came to his own, and his own people did not receive him.

The Jews saw the Torah/O.T. as the world’s light, but when Torah appeared in human form they rejected him.

More positively however:

JOHN 1: v.12 – v.13 v.12But to all who did receive him, who believed in his name, he gave the right to become children of God, v.13 who were born, not of blood nor of the will of the flesh nor of the will of man, but of God.

To believe in his name is to accept him as having God’s authority to adopt you as his child (3:18; 13:33; 20; 31; 21:5).

If the sonship enjoyed by Adam in the first creation was lost by a fall into darkness adoption into God’s family through the Word means becoming part of a new creation (Luke 3:38; Rom 1:21). How this mysterious transaction takes place is about to be expounded; the Word that had forever been with God became “flesh” so that those naturally born from flesh might be born from God.

The Triumph of the Flesh

JOHN 1: v.14 v.14 And the Word became flesh and dwelt among us, and we have seen his glory, glory as of the only Son from the Father, full of grace and truth.

In various religions divine messengers visit the earth but uniquely in our faith God has become one of us.

When “the Word became flesh” humanity was added to deity so that Jesus was 100% God and 100% human.

Even more amazing than God becoming a human being is what sort of human nature he took on.

In John’s Gospel “flesh” is what needs to be regenerated; “That which is born of the flesh is flesh, and that which is born of the Spirit is spirit….you must be born again” (John 3:6-7). Jesus teaches that “flesh” is useless when it comes to perceiving spiritual truth; “It is the Spirit who gives life; the flesh is no help at all.” (John 6:63).

Throughout scripture “flesh” is that dimension of our sinful humanity that makes us stubborn, prideful, independent of God and resistant to God’s Spirit (Gen 6:2ff; Rom 8:5-8; Gal 5:16-17).

Flesh is a place where darkness dwells; flesh means weakness and finally death. As the Word become flesh Jesus walked the earth experiencing hunger, thirst, tiredness, sadness, grief, suffering, temptation and death (Luke 4:1-4; 22:43-44; John 4:6; John 19:34; Heb 2:14).

Today the radical reality of the fleshly humanity of Christ the Word is commonly ignored by popular pastors who have no appetite for “mystery”.

It was not so in previous generations. 450 years ago (1563) one of the Reformation Confessions (Heidelberg Catechism) summed up the life of the Word- as-flesh like this; “during his whole life on earth, but especially at the end, Christ sustained in body and soul the wrath of God against the sin of the whole human race.”

This is not saying that the Father was ever angry with the Son but that in becoming “flesh” God the Word voluntary deprived himself of the infinite bliss of heaven to be immersed in our  groaning world handed over for our sins to weakness, suffering and death (Rom 8:22).

Even sincere Christians sometimes feel that God does not understand their perplexity and pain; but the most common emotion attributed to Jesus in the Gospels is..?.. compassion.

The extreme compassion drawn out of Jesus in seeing men and women in distress flowed from his personal sharing in the “flesh and blood” nature of lost humanity (Matt 9:36; 14:14; Heb 2:14-15). He knew for himself what it was like to be a frail human being! The climax of the enfleshment of the Word is however the cross.

In carrying our condemned flesh to its ultimate fate Jesus must endure the perplexity and pain of our lostness.

The cry from the cross, “My God…why have you forsaken me?” is certainly a cry from perishing flesh (cf. 1 Pet 2:24), but there is something radically different here in the suffering of this man’s flesh.

Instead of stubbornly turning away from God, or trying to bribe or beg for favour, Jesus’ flesh is fully turned towards the Lord. In Paul’s radical language about the humiliation of the cross “by sending his Son in the likeness of sinful flesh…(God) condemned sin in the flesh” (Rom 8:3).

In the God-centred character of the flesh of Christ our self-centred flesh has been condemned and destroyed. This is a great mystery.

The cross is the place in God’s plan where in the maximum impotence of mortal flesh the Word is fully surrendered to his Father’s love; ““Father, into your hands I commit my spirit!”” (Luke 23:46). These words are especially powerful to me because on the one occasion I felt sure I was dying I found myself praying them over and over in my heart.

It is Jesus’ weak flesh fully surrendered to the Father that lights the way to God. To emphasise this John employs Old Testament language. In saying that the enfleshed Word “dwelt amongst us” he literally describes the “tabernacling” of the Word. As God indwelt and showed his glory in the wilderness the Word “tabernacled” amongst us (Ex 33; 40:34).

The testimony “we have seen his glory” involves a seeing of divine splendour in the fleshly humanity of Christ (11:45; 14:7, 9 cf. 1 John 3:6; 3 John 11). This is “glory as of the only Son of the Father”. In the theology of John the ultimate reason why Jesus emptied himself of the glories of heaven to become “flesh” and died is that this brought glory to his Father. (Phil 2:7)?

In its fixation with being loved, in its unsanctified fleshliness, popular Christian spirituality usually fails to grasp the inner glory of the cross.

There’s a catchy song about the sacrifice of Jesus which ends with, “Like a rose trampled on the ground you took the fall, and thought of me above all.” The ending of this chorus is hopelessly self-centred (anthropocentric), in dying Jesus didn’t think of me above all, he thought of me in the Father, he saved me, and you to bring glory to the Father.

In John’s Gospel “glory” comes through the cross and what it brings. Jesus prays, ““v.27 Now is my soul troubled. And what shall I say? ‘Father, save me from this hour’? But for this purpose I have come to this hour. v.28 Father, glorify your name.” Then a voice came from heaven: “I have glorified it, and I will glorify it again.”… Jesus said “v.32 And I, when I am lifted up from the earth, will draw all people to myself.v.33 He said this to show by what kind of death he was going to die.”  (John 12:27-28, 32 cf. John 12:12:16; John 12:13:31-32; John 12:21:19).

Flesh on fire with sacrificial love for a world whose deep depravity he has personally endured unveils a God whose love is so great that he can only be called “Father”. 

To see the dying Jesus is to see the invisible Father (John 14:9-10). This is the pure light of a sinless humanity which fully illuminates the truth of God; this is the triumph of the humanity of the Son of God.

Some insight into this glory came through an experience I had in Cambodia a few years ago. Here are some things I wrote at the time; “As I was praying in my filthy street in Phnom Penh it was if I could see in the Spirit what the Father saw when he looked at the cross, I could see that he did not look at the cross so much as look through the cross, through the absolute purity of heart (cf. Matt 5:8) of the sacrificial Son dying for the world, and what he saw was himself, he saw the fullness of his own glory perfectly imaged without any defect, distortion, corruption or stain (Col 1:15)”.

Knowing this is “the glory of the (unique) only Son” (cf. Gen 22:2; Ex 4:22; Jer 31:9) multiplies the pathos of his sacrifice for us [1]John 3:16.  As “full of grace and truth” Jesus brings to fulfilment the partial revelation of God’s covenant love and faithfulness in the Old Testament (Ex 34:6). The “grace upon grace”[2]v.16 he imparts means he is an inexhaustible supply of blessing (Eph 2:7; 3:8).

JOHN 1:17 v.17For the law was given through Moses; grace and truth came through Jesus Christ.

In its time and place the law was good, but now that Jesus has obeyed the commandments of God in his own flesh on our behalf the law has no place in our salvation. Deliverance is in Jesus alone (John 14:6; Acts 4:12). We have reached the climax of our passage.

JOHN 1:18 v.18 No one has ever seen God; the only God, who is in the bosom of the Father, he has made him known.

The Old Testament common remarks, “no one can see God and live” (Ex 33:20 etc.) but in Jesus God has stepped out of eternity into time through the enfleshment of the Word. In John’s language Christ is “the only God…in the bosom of the Father”. This is the most accurate translation of this text but it may also be reasonably translated “near to the Father’s heart” or “in the lap of the Father”. For a number of years I was involved with extensive prayer retreats called Prayer Summits. Early in the retreat we would place a chair in the centre of a circle and invite anyone who felt led to come and receive prayers from others. This was called “sitting in the Father’s lap”, and to be quite honest at first I thought this expression was somewhat “mushy”, but year after year “sitting in the Father’s lap” proved for many people to be their most powerful encounter with the love of God, and theologically it is exactly what John 1:18 is teaching.

Where John commenced his account in John 1:1 with language about “God” he consummates it in 1:18 with calling God “Father”, the final revelation of “God” is not “God” but “Father”. The Spirit communicates the warm and tender relationship between Jesus and his Father to us; “God has sent the Spirit of his Son into our hearts crying, “Abba! Father!” (Gal 4:6).

When John says the one “in the bosom of the Father” “has made him known” he means that the mystery of who God is has been laid bare for all to see in the person of Jesus. The invisible God has become visible the hidden God has appeared in unsurpassable form (John 5:37; 6:46; 1 Tim 1:17; 6:16 cf. 1 John 4:12, 20). The great mystery which has puzzled wise men and sages over millennia has been fully and finally revealed through the flesh of the Son of God.

Application and Conclusion

This revelation of the deep things of God speaks directly to many of the confusions of the Church in Australia today. Western Christianity has long been suffering from a self-confidence that is the exact opposite of the humble flesh of the Word of God. If intellectual arrogance was introduced into theology by ‘Enlightened’ Europeans, Church as-a-business has been learned from the Americans.

In speaking of that terrible pride of unsanctified flesh which is the exact opposite of the humility of Christ the KJV uses the word “vainglory”. Unlike our vainglorious and stubborn fleshliness the flesh of Jesus always turned in loving obedience to the Father. The key question is how do we become more like Jesus?

We need to bring together the insights of John 1 with the teaching of Paul.

Remember it was Paul who taught us that “the great mystery of our faith/godliness, was manifested in the flesh” (1 Tim 3:16).

We share in the godliness of Jesus when by grace our naturally useless flesh is united with the flesh of the Word in his constant turning to the Father.

When in our daily sufferings as enfleshed people we are united with the human Jesus is his dependence on God we share in his resurrection power (1 Cor 15:31; Phil 3:10).

This sort of deep connection never happens in comfortable circumstances.

One of the missionaries we support is down from Indonesia at the moment and she shared with me during the week how it was only when she was in hospital with typhoid that the Lord was able to speak to her clearly about a critical situation in her team.

The Word is most real when our flesh acknowledges its weakness.

Often I have heard people cry, “If only we had more signs and wonders we would have revival.” These folk are sincerely confused. They fail to understand that it was only as Jesus, Paul and every other godly figure I can think of, turned to heaven in consciousness of their enfleshed weakness that power came from above.

Only a Church immersed in the godliness of the enfleshed weakness of the Word will turn in his lowly obedience to the Spirit of God for acts of extreme power, receive them in abundance and persevere in maturity and continuous revival.

The renewal of the power of the Word in the Church will only come when we have a revelation of the fullness of the weakness God the Word embraced for us.

Paul lived out this mystery; “lest the cross of Christ be emptied of its power…..I was with you in weakness and fear and much trembling….Who is weak, and I am not weak?” (1 Cor 1:17; 2:3; 11:29).

All who live in the light of the Word made flesh will through him light the way to the Father.

If we know we are living with Jesus “in the bosom of the Father” the invisible God will become visible through us (John 14:21-23; 16:16-19, 22; 20:18, 25 cf. Col 3:1-3).

This is the key to a revolution in witnessing.

In John’s Gospel the word “witness” is a legal term for a counter-witness against the world’s false witness against Jesus.

When I was a child no media outlet at Christmas time would dare challenge the claims of Christ to be the way to the Father; those times are well gone.

We are in a season when it is becoming increasingly difficult to be a Christian and the Lord is calling us back to the revelation of the mystery of his own humble enfleshed life.

The mystery of God the Word made flesh is too great to be grasped by any human being, but we can be grasped by it so that we are constrained to communicate it

(Acts 4:20; 2 Cor 5:14ff.)

The revelation of the mystery of the glory of God comes in only one way, through intentional focussed and sustained prayer. This is a priority the Lord has set for my life in 2016 and I am sure he has set it for his whole Church.


1 John 3:16
2 v.16

John Yates

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