He was really telling a Jew who didn't want anyone to know he was talking to Jesus in private, that he was going to have to make a public confession and have a change of heart before he could enter the kingdom of God.[ or become a part of it]
Public confessions to attach ones self to a religion came in the form of public baptism. A cleansing from one unto the other, washing away the past and taking on the new.
Then this Jew acted like he didn't know what Jesus was talking about by replying with a stupid question like, can I enter into my mothers womb again? Da!!
So Jesus sat him straight by saying, That which is flesh is flesh and that which is spirit is spirit.
Man I have heard this taught and preached so many ways. It's a simple message of, turn from the old covenant and follow me in this new covenant. Confess me before all if you really believe in your heart that I am the messiah sent from God.
Nicodemus knew what Jesus was talking about the first time he said it. He didn't want to come down from his position in the temple and in the community and make a public change. He like so many thought he could receive this teaching from Jesus and hold it privately, just like people do today.
Salvation by works.
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Hebrews 13:23 Know ye that our brother Timothy is set at liberty