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The Real Presence is the Holy Spirit

Provocative discussions with a friend about the Eucharist drew me to a careful re-reading of the sixth chapter of the Gospel of John, because it is John 6 which many believe provides a scriptural basis for the doctrine of transubstantiation. It’s the belief that communion involves partaking of the real presence of the body and blood of Jesus. The real presence of Jesus in the wine and bread of the Eucharist is confirmed, some believe, by John 6:51-58, where Jesus says:

But here is the bread that comes down from heaven, which a man may eat and not die. I am the living bread that came down from heaven. If anyone eats of this bread, he will live forever. This bread is my flesh, which I will give for the life of the world. Then the Jews began to argue sharply among themselves, “How can this man give us his flesh to eat?” Jesus said to them, “I tell you the truth, unless you eat the flesh of the Son of Man and drink his blood, you have no life in you. Whoever eats my flesh and drinks my blood has eternal life, and I will raise him up at the last day. For my flesh is real food and my blood is real drink. Whoever eats my flesh and drinks my blood remains in me, and I in them. Just as the living Father sent me, and I live because of the Father, so the one who feeds on me will live because of me. This is the bread that came down from heaven. Your forefathers ate manna and died, but he who feeds on this bread will live forever. (NIV)


“Your forefathers ate manna and died, but he who feeds on this bread will live forever.”


I believe that a careful study of John 6, with a careful focus on the context of John 6, results in an important discovery: The “real presence” in the Gospel of John is not his physical body in the Eucharist. Rather, it’s the presence of the Holy Spirit in our lives. Although this is best explained by Jesus in John 7, especially verses 14-16, let’s first consider the larger context of these passages in the Gospel of John.

Symbols in the Gospel of John

Reading John 6:50-58 as symbolic or spiritual, not literally physical, has a reasonable basis in the text. That is confirmed by the context of the entire chapter and by earlier and later chapters of the Gospel of John.

In the first five chapters of John, there are numerous examples of Jesus speaking “figuratively” (as Jesus expressly acknowledged in John 16), referring to physical realities to make a spiritual point, or to suggest there is a spiritual reality behind the physical.

In John 2:19-21, Jesus references the physical temple to refer to “his body.” In other passages in John (and elsewhere in the Gospels), Jesus uses physical symbols and metaphors to teach spiritual truths. Jesus is spiritual light (3:19; 8:12), spiritual water (John 4:13), and a spiritual vine (John 15: “life on the vine”). For example, notice the wording of John 8:12, in which Jesus refers to himself as spiritual light: “Whoever follows me will never walk in darkness but will have the light of life.” That’s not a promise that we will never walk in physical darkness.


“Jesus uses physical symbols and metaphors to teach spiritual truths.”


Jesus also compares himself to other physical “types”: the manna which came down from heaven (6:31-32; 6:49) and the snake in the desert (3:14). Reading the “bread of life” in John 6 as spiritual, not physical, is consistent with these examples.

So it’s not so surprising that Jesus refers to himself, his body, as spiritual bread (John 6:27, 33, 35, 51, “bread of life”). In fact, there is a direct parallel in his language between “light of life” (8:12) and “bread of life” (6:48).

Confused by Jesus’ Metaphors

It’s also important to note that the metaphors which Jesus employs produce misunderstandings repeatedly among his listeners (see John 2:20, 4:13, 6:51). The first example is the physical and spiritual temple of his body in John 2:19. This produces misunderstanding, which Jesus doesn’t correct (but is explained by the author in 2:21).

In John 4, the Samaritan woman had a similar misunderstanding of Jesus’ statement about “living water.” Jesus starts the conversation by asking her for a drink. He then moves to the spiritual and refers to the gift of “living water.” (4:10) He then contrasts physical water (of which people will be “thirsty again,” see 4:13) with “the water that I will give him,” and if they “drink” of that they “will never be thirsty forever” (4:14). The audiences repeatedly mistake Jesus’ spiritual meaning as physical.


“The audiences repeatedly mistake Jesus’ spiritual meaning as physical.”


The “crowd” that Jesus fed in John 6 found Jesus the next day. There, at the synagogue in Capernaum (6:59), Jesus called them out with a metaphor that frames the rest of John 6: “You are looking for me…because you ate the loaves and had your fill. Do not work for food that spoils, but for food that endures to eternal life, which the Son of Man will give you” (6:27). At this point, Jesus starts to emphasize spiritual food.

The misunderstanding reflected in their question in 6:52 (“How can this man give us his flesh to eat?”)—that Jesus’ statement about spiritual things was meant physically—is reflected in the earlier passage. The misunderstanding of taking physically or literally what Jesus meant spiritually continues in John 8:33 and 8:51.

Three Contextual Themes

In addition to the physical-spiritual misunderstandings preceding John 6, there are three contextual themes we ought to note in John 6: incarnation, sacrifice, and abiding (remaining).

1. Incarnation

In John 3-5, Jesus builds from emphasis on God (e.g., 5:24: “whoever hears my word and believes him who sent me has eternal life”), to speaking in the third person about “the Son of Man” (e.g., John 3:13,14; 5:19-23), to speaking in the first person about himself (6:48: “I am the bread of life”) and his incarnation (“coming down from heaven”) which culminates in John 6, when he says it three times in John 6:50, 51, and 58. The Jews’ question in 6:52 (“How can this man give us his flesh to eat?”) is actually a misunderstanding of what Jesus says in 6:50-51, which, again, is about incarnation.

The crowd grumbled in John 6:41 not because he said “I am bread” but because he said “I came down from heaven”—incarnation. They respond with misunderstanding: “How can he now say ‘I came down from heaven’?” (6:42) It is the personalized focus on Jesus as coming down from heaven (incarnation) that amazes them and causes them to grumble. (See also 5:28: they were “amazed” because the Father has “granted the Son to have life in himself”).

2. Sacrifice

There is also the theme of sacrifice. At the end of v. 51, when Jesus says, “And the bread that I will give for the life of the world is my flesh,” he is talking about sacrificing himself on the cross (cf. Heb. 9:26: “to put away sin by the sacrifice of himself”). John 6 is not the first time that “flesh” appears in John. John 1:14 says, “The Word became flesh and made his dwelling among us.” This is clearly a statement of incarnation.

The Jews in verse 52 then misunderstand sacrifice on the cross (“I will give”) for literally eating flesh. They took to be literal what Jesus meant as spiritual. The most significant word in the Jews’ question in 6:52 is “how.” And the “how” is answered in Jesus’ sacrifice on the cross. Flesh is a vivid way of referring to incarnation and sacrifice, as in “put on flesh.” It is vivid, not literal.


“‘The Word became flesh and made his dwelling among us.’ This is clearly a statement of incarnation.”


3. Abiding

There is a third theme we ought to notice in John 6: abiding. Jesus uses the crowd’s confusion in v. 52 to press the point of feeding/abiding. Jesus can be understood in 6:53-57 as emphasizing flesh and blood in order to intensify or “double-down” on the personal and spiritual, as when he emphasizes food and drink in v. 55. Verse 56 combines feeding and abiding, a major theme developed more in John 8:31 and John 14-17, and in John’s epistles.

The spiritual sense of “feeding” and “drinking” are spiritual references that connect with our need to “abide,” which Jesus first uses in 8:31 and continues in John 15 (and John later emphasizes in 1 John 4). When his “disciples” say in 6:60 “this is hard teaching, who can accept it,” “this” may refer to “whoever feeds on this bread,” but it can also be understood as referring to “came down from heaven” and “will live forever” from the rest of 6:58, or otherwise incarnation and feeding/abiding.

The Power of the Spiritual

Jesus is spiritual water (John 4:13, 6:35), spiritual light (3:19), and spiritual bread (John 6:27, 33, 51). So, it’s not surprising if Jesus refers to his body as spiritual food. And the emphasis on flesh in 6:51 refers to his coming sacrifice and feeding/abiding. This is reaffirmed in Revelation 7:16, which seems to be a quote from Jesus’ words in John 6: “Never again will they hunger; never again will they thirst.”

So, I’m suggesting that the real emphasis in John 6:47ff is more spiritual than physical. And that theme is seen earlier in Jesus’ conversation with Nicodemus: John 3:5 “I tell you the truth, no one can enter the kingdom of God unless he is born of water and the Spirit. Flesh gives birth to flesh, but the Spirit gives birth to spirit.”).


“The emphasis on flesh in 6:51 refers to his coming sacrifice and feeding/abiding.”


The larger point of John 6 is that Jesus came down from heaven to be the way to eternal life and that he would sacrifice himself, his body. Thus, putting emphasis on the body and blood as literal is counter to Jesus’ emphasis on the spiritual in John 6. The crowd emphasizes the literal; Jesus emphasizes the spiritual. John 6 shows the power of the spiritual.

The Power of the Spirit

Taking 6:53-57 as physically eating Jesus’ flesh and blood is also undercut in four additional ways. First, John 6:63 says very specifically, “The Spirit gives life; the flesh counts for nothing. The words I have spoken to you are spirit and they are life.” The spiritual is more powerful than the physical.

Second, it is counter to Jesus’ teaching that he is leaving and that he will send the Holy Spirit. He warned that he was with them “only a short time” and makes the point of his leaving emphatically in 7:33-34. (See also John 8:21; 12:35; 13:1). (In Matthew 9:15, using the metaphor of the bridegroom, Jesus tells them that he will be “taken from them.”)

Third, the Lord’s Supper is never actually mentioned in John 6. There’s a compelling reason for this: Jesus is addressing unbelievers who abandon him. Jesus does not inaugurate the Lord’s Supper until he is alone, later, with the apostles the night before he was crucified.


“Jesus is addressing unbelievers who abandon him.”


Fourth, Jesus introduces them to his leaving (“ascend”) and the coming of the Holy Spirit in John 6:62-63. In John 7:38-39,

Jesus stood up and cried out, “If anyone thirsts, let him come to me and drink. Whoever believes in me, as the Scripture has said, ‘Out of his heart will flow rivers of living water.” Now this he said about the Spirit, whom those who believed in him were to receive.

Here he refers to the Holy Spirit as “living water” as he had earlier referred to himself. Or John 14:15-17: “another advocate to help you and be with you forever—the Spirit of truth…for he lives with you and will be in you.” The real presence Jesus emphasizes over and over is the presence of the Holy Spirit.

The Presence of the Spirit

In John 16, Jesus tells the apostles again that he is not staying but going away and must go away: “It is for your good that I am going away. Unless I go away, the Advocate will not come to you; but if I go, I will send him to you….”

Jesus leaves and sends the Holy Spirit (the Comforter) to be the “real presence” in the believer, a personal presence, a constant presence, a powerful presence. There are more than a dozen passages which emphasize how personally present is the Holy Spirit. Acts 2:38 tells us the process by which the Holy Spirit comes to us: “Repent and be baptized every one of you in the name of Jesus Christ for the forgiveness of your sins, and you will receive the gift of the Holy Spirit” (NIV). If they follow this process, no believer has to doubt that they have the Holy Spirit. It is a promise (Acts 2:39).


“Jesus leaves and sends the Holy Spirit (the Comforter) to be the “real presence” in the believer, a personal presence, a constant presence, a powerful presence.”


Numerous other New Testament passages elaborate on and confirm who the Holy Spirit is and how he is present in the believer’s life.

  • Acts 9:31 – “And walking in the fear of the Lord and in the comfort of the Holy Spirit…”
  • Romans 5:5 – “…God’s love has been poured into our hearts through the Holy Spirit who has been given to us.”
  • Romans 8:26 – “the Spirit himself intercedes for us…. the Spirit intercedes for the saints….”
  • Romans 15:16 – “…sanctified by the Holy Spirit.”
  • 1 Corinthians 6:19 – “…your body is a temple of the Holy Spirit within you….”
  • 1 Corinthians 3:16 – “…that God’s Spirit dwells in you?”
  • 2 Corinthians 1:22 – “…given us his Spirit in our hearts as a guarantee.”
  • Galatians 4:6 calls him “the Spirit of his Son.”
  • Ephesians 3:16 – “…strengthened with power through his Spirit in your inner being….”
  • Ephesians 5:18 – “…be filled with the Spirit”
  • 2 Timothy 1:14 – “By the Holy Spirit who dwells within us….”
  • Titus 3:5-6 – “…by the washing of regeneration and renewal of the Holy Spirit, whom he poured out on us richly through Jesus Christ our Savior….”
  • 1 John 3:24 – “And by this we know that he abides in us, by the Spirit whom he has given us.”

This discussion about John 6 has been ongoing between believers for centuries, but a careful reading of the text of John 6 is rewarding and should encourage us that the Holy Spirit is a constant presence in each believer. It is by the Spirit that Christ abides in us.

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