Nicodemus said to him, “How can these things be?”
– John 3:9 (ESV)
Jesus had just explained the spiritual birds and bees to Nicodemus, and the rabbi was struggling to understand how it all worked. This wasn’t a good thing for someone whom all Israel looked up to for spiritual truth…
Jesus answered him, “Are you the teacher of Israel and yet you do not understand these things?
– John 3:10 (ESV)
This was embarrassing. “How can you teach if you don’t know this?” Wasn’t it obvious that God created the world in such a way that each living thing reproduces itself in kind?
Olive trees only come from olive trees.
Donkeys only come from donkeys.
Humans only come from humans.
And spiritual life only comes from the Holy Spirit. Only the Holy Spirit that gave both physical and spiritual life to man in the beginning (Genesis 2:7) gives spiritual life back to fallen man (John 6:63).
Nicodemus wanted to know how it all worked… the mechanics as it were, before he would believe. Jesus, on the other hand, was concerned only with belief:
Truly, truly, I say to you, we speak of what we know, and bear witness to what we have seen, but you do not receive our testimony. If I have told you earthly things and you do not believe, how can you believe if I tell you heavenly things?
– John 3:11-12 (ESV)
The rabbi acknowledged Jesus to be a teacher from God, and yet was not willing to believe what He said without some kind of logical explanation. This lack of belief was hindering him and his fellow Jews from progressing, not just towards more significant spiritual knowledge: it was keeping them from spiritual life.
Contrast this with the disciples who didn’t understand, and yet believed. Both the disciples and Nicodemus knew that Jesus was from God. The only difference was in their faith.