There are a couple of examples here of teaching that Jesus gives that is not fully understood until way later: 2:18-22, and 3:1-12. What Jesus says in 3:1ff is not understood: "how can a man" do this and that, "can he?", and "how can these things be?" However, when it comes to God versus our knowledge, Jesus has a very refreshing thing to say, especially to those with pride in their knowledge and those who have to know all about something before they can believe it: that is verse 8. It's part of the nature of the knowledge, not only of God, who is Spirit, but of everyone else born of God, that knowledge of them is incomplete: "so is everyone who is born of the Spirit" (3:8). They're like the wind; it is manifestly true of the wind, that we do not know where it is going, or where it comes from.
This is the reason Jesus gives for telling Nicodemus "do not be amazed that I said to you, 'You must be born again'" (3:7). It's the best part of knowledge, to know that it stops, and not to be amazed that it does.
The second and final comment of Nicodemus here (3:9)is not a real question, but a remonstrance regarding the topic. He doesn't understand how everyone born of the Spirit is like the wind blowing where it wishes, no one knowing its origin or destination. The rest of the chapter expands on the "everyone" of 3:8. Nicodemus, "the teacher of Israel" -- this is not a slam, but an honorific, which makes the irony even stronger! -- should know about the filial status of Israel, in places like Is 1:2-4 and Hosea 11:1, yet there being at that time only hints about eternal life. Like the people shining like stars in Daniel 12,
So Jesus goes back to the Old Testament to explain more about the means of eternal life: "As Moses lifted up ... so must the Son of Man be lifted up ... so that whoever believes" (3:14-15). That's the means.
The giving by God of His Son, the Son being "lifted up," so that people who believe will "have eternal life," is compared for its similarity to when Moses lifted a serpent up onto a pole in Numbers 21:9. The serpent is a symbol of what was cursed back in the garden. It was lifted up for the Israelites to "look to" and be healed! Jesus uses the event to explain a part of His future ministry: through his death ('Christ became a curse for us', Paul says in Gal 3), and resurrection, He was lifted up so that everyone who believed in Him would have, not just a healing limited by time, but eternal life. Nicodemus, who came secretly, by night, to be taught (3:1), got some teaching.
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