The pattern of misunderstanding is charachterized by the following elements: (1) Jesus makes a statement, (2) it is misunderstood and (3) he or the narrator in turn must decipher the meaning of what has been said. The pattern itself suggests its function.
In his book the Anatomy of the Fourth Gospel, R. Alan Culpepper notes that the misunderstandings blatantly instruct readers on how they should read the gospel.
The misunderstandings call
attention to the gospel’s metaphors, double-entendres, and
plurisignations as well as guide the reader by interpreting some of
these and ruling out the literal, material, worldly, or general
meanings of such references. Readers are therefore oriented to the
level on which the gospel’s language is to be understood and warned
that failure to understand identifies them with the characterization
of the Jews and the others who cannot interpret the gospel’s language
correctly.”
The misunderstanding in the temple cleansing, for instance, calls attention to Jesus word for temple. Before Jesus says, "destroy this temple" both the narrator and the Jews have used the Greek word hieron. Hieron is only ever used in the New Testament for the physical temple. But Jesus calls them to "destroy this naos", a word that can refer to either a literal temple or a figurative one. For instance in the New Testament it is the word naos which is used in reference to believers as the temple of the Holy Spirit (1 Corinthians 6:19-20). When Jesus uses the word naos the Jews have a decision to make. They can interpret in its literal sense or they can interpret it spiritually. Its the later which Jesus appears to intend.
When Jesus tells Nicodimus he must "be born again" it is the word again which possess two different meanings. In English "again" only means a “second time.” But the Greek word anothen, which Jesus uses here, can mean both "a second time" and “from above.” Once again we find that Nicodimus errors in choosing the more physical or earthly meaning. Jesus is not speaking about a second physical birth but rather a new heavenly birth from above.