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The author misses the interpretation given in the passage by the Lord Himself. One must go beyond John 3:5 and read all the way to John 3:6 to the interpretation of verse 5. Here they are together:
John 3:5 Jesus answered, Verily, verily, I say unto thee, Except a man be born of water and of the Spirit, he cannot enter into the kingdom of God. 6 That which is born of the flesh is flesh; and that which is born of the Spirit is spirit.
Born of water is physical birth: born of the flesh. Not washed by Scripture nor sprinkled with “holy water”.
Born of the Spirit is just that: born a new creature in Christ (2 Cor 5:17) by the power of the Holy Spirit, having been dead in sins (Ephesians 2).
No need to make it seem obscure nor allegorical.
This is spin; if Jesus wanted to say "physical birth" He would refer to "womb", just like Nicodemus does in his question. He would not respond with a riddle forcing Nicodemus to figure out that womb=water. The entire reference to borth of the water and spirit is a plain reference to baptism which combines these two elements precisely.
I have always believed this was the best interpretation. All the other interpretations read into the text what they want to find, this explanation is purely inductive which is how all scripture should be interpreted.