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John 6:16-21

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Now when evening came, His disciples went down to the sea, [17] and after getting into a boat, they started to cross the sea to Capernaum. And it had already become dark, and Jesus had not yet come to them. [18] And the sea began to be stirred up because a strong wind was blowing. [19] When therefore they had rowed about three or four miles, they beheld Jesus walking on the sea and drawing near to the boat; and they were frightened. [20] But He said to them, "It is I; do not be afraid." [21] They were willing therefore to receive Him into the boat; and immediately the boat was at the land to which they were going. 

This miracle also appears in the gospel of Mark (6:47-52) and in the gospel of Matthew (14:24-33). Both gospels contribute to a better understanding of what took place. Mark's gospel explains why they were afraid when they saw Jesus walking on the water-they thought he was a ghost. Matthew, on the other hand gives a much fuller picture of the event.

In Mark's as in John's version, Jesus identified himself by saying, "It is I; do not be afraid," and the disciples calmed down and welcomed Jesus in the boat. Matthew gives additional information. "And Peter answered Him and said, "Lord, if it is You, command me to come to You on the water." (Matthew 14:28 NASB)

Peter's fear of the voice on the water was so deep that he would rather go to the voice, even if it meant leaving the safety of the boat, than to let the person in the boat with them. I don't know about you, but I'd prefer to take my chances letting someone in the boat with me than to step out of the boat on a stormy sea.

But not Peter. Why?

Well, the text already answers that question-he was afraid. It doesn't say he was rational, it says he was afraid. Is fear ever rational?

Well, yes. It is rational to be afraid to jump off a bridge with nothing but a bungee cord tied to your feet. It is irrational, not to be afraid. 

As Matthew's version of the miracle goes, Peter stepped out onto the water and began to walk toward Jesus, but when he became aware of his fears again, his faith flickered and he began to sink into the water. In a moment of sheer desperation, he cried out, "Lord save me." (Matt. 14:30) Though his faith flickered, it didn't fail him, and neither did Jesus. Jesus reached out His hand and saved him.

John gives a much shorter version of the miracle. Peter, the star of Matthew's version, isn't even mentioned by John. Why? I believe it is because the drama of Peter's encounter with Jesus would muddle his point rather than illustrate it. 
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