To play devil’s advocate, the same thing can be said of Catholics. A Protestant can’t figure out why Catholics take John 6 literally when Jesus says that his words are “spirit and life” and that the flesh is of no consequence? Yet they believe “I am the vine” to be symbolic. It goes both ways. Sorting out metaphor from reality in Scripture is a full-time job!
The Real Presence have been interpreted in the literal sense since the birth of the Church. Jesus himself taught it. You have to read the entire chapter of John 6 and not pick the ones you think makes sense to you.
When questions of biblical interpretation are raised, it is beneficial to read in context the entire passage that is in dispute. The bread of life discourse begins in John 6:22, and the first point to address is the discussion of the heavenly bread. Jesus makes the point that as the Father sent manna from heaven for the physical nourishment of the Israelites, he has sent Jesus for the spiritual nourishment of the world. When Jesus announced this (6:41), the Jews murmured because he said that he had come down from heaven, not because he said that he was like bread. They understood his symbolic statement regarding the origin of the manna, and were scandalized by what it implied: “Is this not Jesus, the son of Joseph, whose father and mother we know? How does he now say, ‘I have come down from heaven?’” (6:42).
Beginning in verse 43, Jesus replies to these objections. At the completion of his answer (6:51), he speaks of a bread that he is yet to give. The Jews’ understand that he is now speaking in a literal sense, and so they object, “How can this man give us his flesh to eat?” So the Jews first objected because of what Jesus’ initial words meant symbolically, and now they object to what his second statement means literally. Had Jesus been speaking in a metaphorical sense here, this would be the perfect point to clarify his intentions.
Matthew 16:5–12 is one such example where Jesus’ listeners thought that he was speaking in a literal sense, and he had to correct them. In this passage, Christ was warning the disciples of the leaven of the Pharisees and Sadducees. The disciples concluded that he was speaking of the bread they had forgotten to bring for their journey. In seeing their confusion, Jesus had to reiterate that he was not speaking literally of bread.
Keeping this in mind, look how Jesus answers the Jews’ objections in John 6:53–58: “Truly, truly, I say to you, unless you eat the flesh of the Son of man and drink his blood, you have no life in you. . . . For my flesh is food indeed, and my flesh is drink indeed.” These words would hardly quell the Jew’s fear that Jesus spoke literally. Following this, many of his disciples said, “This is a hard saying; who can listen to it?”(6:60). At this point, we witness the only place in Scripture where anyone leaves Jesus for a doctrinal reason. Had Jesus been speaking metaphorically, what would have been so hard for the disciples to accept?
One last passage worth considering is John 10:9, where Jesus says, “I am the door.” Some say that this is the sense in which Jesus’ words in John 6 should be taken. However, no one understood Jesus to be speaking literally when he said that he was a door. The narrative does not continue, “And his disciples murmured about this, saying, ‘How can he be a door? Where are his hinges? We do not see a doorknob.’ Jesus answered them, ‘Amen, Amen, I say to you, I am a door, and my chest is real wood, and my hips are real hinges.’” This is absurd, but it illustrates how shocking Jesus’ words were when he said that his flesh was real food and his blood real drink.
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