John 3:9-13 meaning

Nicodemus then answered Jesus' explanation of being born again, and said to Him, "How can these things be?" Nicodemus does not argue with Jesus. He just expresses astonishment. He knows Jesus has God with Him, as he stated in verse 2. But now Jesus is telling him things that he apparently does not know how to process. Jesus is telling him he actually doesn't have the eyes to see the kingdom of God unless he is born again.

To the astonished exclamation of Nicodemus, Jesus answered and said to him, "Are you the teacher of Israel and do not understand these things? As a Pharisee, and a member of the Sanhedrin, Nicodemus was a teacher of Israel. Jesus is saying "How can you not understand something that is so elementary?" Jesus is presenting being born again as a foundational truth, and Nicodemus, who is a Bible scholar, is expressing astonishment, and is having a hard time following.

To attempt to put ourselves in the shoes of Nicodemus for a moment, we should first acknowledge that all we know about him here makes it appear he is genuinely seeking to know the truth. He has recognized that God is working through Jesus. He hasn't argued with Jesus, but seems to be trying to understand. Nicodemus would have been intimately familiar with the notion of God's Spirit being like the wind ("ruah" in Hebrew or "pneuma" in Greek). In Genesis and Exodus "ruah" is translated into English as "Spirit," "breath," "mind," and "wind." However, there is nothing in the Old Testament (the Bible Nicodemus would have known) that uses the term "born again." If you search "born again" you will get no Old Testament references. There are many instances where physical birth is spoken of—Nicodemus likely had learned all the lineages and genealogies of his people. But these are all physical rather than spiritual.

Notwithstanding, Jesus clearly thinks it reasonable and expected for Nicodemus to have deduced from scripture that a spiritual rebirth is a necessity in order to be able to see, or enter the kingdom of God. Tracing "ruah" (spirit, or breath) through the Old Testament, you can find many instances where God's Spirit impacted humans. For example, God's Spirit came upon the artisans and craftsmen who built the tabernacle, to give them wisdom and skill. God's Spirit came upon King Saul and King David such that they prophesied. God's Spirit moved on God's prophets, and gave them power to work wonders. And God's Spirit hardened the heart of Pharaoh. It seems that Jesus' expectation was that Nicodemus should have deduced from studying these movements of God's Spirit in the scriptures that without our spirits being reborn by the Spirit of God, we can't really see or enter into the things of God.

Jesus continued with His explanation, saying Truly, truly, I say to you, we speak of what we know and testify of what we have seen, and you do not accept our testimony. Here we discover that Nicodemus had not come to the point to accept the testimony of Jesus. Therefore, we can deduce that Nicodemus is not yet born again, having not believed. Jesus says that He is speaking of what we know. That Jesus speaks in plural form, saying we know, is likely a subtle message to Nicodemus that Jesus is speaking from the position as a member of the three-person Godhead. "We" includes Father, Son, and Holy Spirit. Jesus is the Jewish Messiah, as well as the Son of God.

Nicodemus has not recognized that Jesus is God. But Jesus is God, so is speaking from firsthand knowledge. Things He (as a member of the Godhead) has seen. He speaks of what we (God) know. While Nicodemus, as a teacher of scripture, ought to have been able to discern the need for a spiritual rebirth, Jesus didn't need to deduce that from scripture. Because He is God, He knows it firsthand. Jesus is testifying that He is God, if Nicodemus has the ears to hear, by testifying of His firsthand experience in the spiritual realm.

Jesus now says If I told you earthly things and you do not believe, how will you believe if I tell you heavenly things? Since Nicodemus has had trouble understanding, and did not believe about spiritual rebirth of humans, which are earthly things, then how will Nicodemus believe if Jesus tells him about heavenly things? The heavenly things may refer to the nature and character of Jesus, who is both Messiah and God. There is one God, and three persons: Father, Son, and Holy Spirit. It seems to fit the context to consider Jesus as saying "If you can't understand and believe how God works in people, how are you going to understand that God has become man, and is now speaking with you?"

Jesus now begins to tell Nicodemus of heavenly things, heavenly things that are connected to earthly things. He says No one has ascended into heaven, but He who descended from heaven: the Son of Man. In His earthly ministry, Jesus often referred to Himself as the Son of Man. It can mean "human" which Jesus is, truly. Jesus was fully human, and was tempted in all things, just as we are, but was without sin (Hebrews 4:15). But Son of Man is also a Messianic reference, referring to Daniel 7:13, where the Messiah descends from heaven, and is given dominion over all nations:

"I kept looking in the night visions, And behold, with the clouds of heaven, One like a Son of Man was coming, And He came up to the Ancient of Days, And was presented before Him. "And to Him was given dominion, Glory and a kingdom, That all the peoples, nations and men of every language Might serve Him. His dominion is an everlasting dominion Which will not pass away; And His kingdom is one Which will not be destroyed."
(Daniel 7:13-14)

Jesus likely intended both meanings in His use of Son of Man to refer to Himself. He was a human who came to earth as a servant, and suffered rejection of men, learning obedience, even to death on a cross (Philippians 2:5-11). But He was and is also the One who will rule over the entire earth.

Jesus asserts that He, the Son of Man, descended from heaven. Here Jesus seems to be claiming to be the Son of Man depicted in Daniel 7. Nicodemus would probably have been fluent in the prophecies of Daniel and picked up the reference. If he was amazed before, now he would have been astounded. It is He, the Son of Man, who descended from heaven. He was God in heaven, and left His heavenly abode in order to do the will of His Father (Philippians 2:5-10).

However, Jesus also said He ascended into heaven. This might refer to His station prior to coming to earth. He was in heaven, with His Father. It could also be a prophetic claim, speaking in past tense indicating a future certainty that was fulfilled when Jesus ascended to heaven after He rose from the dead, and testified to many of His resurrection (Acts 1:10).