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In John 3:6, it is written,

6 That which is born of the flesh is flesh, and that which is born of the Spirit is spirit. NKJV, 1982

Ϛʹ τὸ γεγεννημένον ἐκ τῆς σαρκὸς σάρξ ἐστιν καὶ τὸ γεγεννημένον ἐκ τοῦ πνεύματος πνεῦμά ἐστιν TR, 1550

What is the meaning of this phrase? Also, is there a particular reason for the usage of the neuter τὸ γεγεννημένον instead of the masculine ὁ γεγεννημένος?

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In His discourse with Nicodemus, Jesus has been emphasizing the importance of spiritual birth over carnal birth. An alternate translation of verse 3 is:

Most assuredly, I say to you unless one is born from above, he cannot see the kingdom of God.

Most modern translations follow Nicodemus response How can a man be born [again] when he is old (John 4:4) and infer that ἄνωθεν should be translated as "again" in verses 3 and 7, but what Jesus was actually trying to convey was that a man should be born "from above". This is explained in a footnote to the recent translation of Theophylact's commentary on the Gospel according to John:

The two basic meanings of the Greek word ἄνωθεν are "from the top, from above"; and "from the beginning." It is frequently used in the New Testament to mean "from heaven." (See verse 31 later in this same chapter: He that cometh from above [Ὁ ἄνωθεν ἐρχόμενος] is above all; he that is of the earth is earthy.) It is clear that Christ is speaking of spiritual birth from above, from heaven, and from God, that Nicodemus misunderstands Him to mean being born physically a second time. In the Gospel text in verses three and seven of this chapter, we have used born from above, which is a literal translation and the meaning intended by Christ. St. John Chrysostom, in his 24th Homily on the Gospel of John says, "The word, ἄνωθεν, in this place, some understand to mean "from heaven," others "from the beginning."

The Explanation of the Gospel of John (trans. Christopher Stade) (Chrysostom Press: 2007), pp. 48-49

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What we have here is not just a bifurcation but actually a dichotomy.

The difference is that a bifurcation just suggests that something has forked into two ways but with a dichotomy the two ways are considered opposite or antithetical. A river splitting into two streams is a bifurcation while good and bad are a dichotomy.

This is one of the oldest and most appealed to dichotomies in scripture. It began in the making of man:

Gen 2:7 And the LORD God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul.

Adam was not a three part being (body, soul, spirit) but rather a two part being (body/flesh/dirt and breath/spirit).

Breath and spirit are synonyms. In the original languages (Hebrew, Greek, Latin, German, Aramaic and even Olde English) there is no distinction).But not the breath you and I know which is just gases. To the ancients the breath was a mysterious, magical force. For example when Yehovah breathed his own breath into the clay status of himself it came alive and had all kinds of mental faculties. He became a living being (aka "soul").

I suggest to you that if you grasp the dichotomy you will be able to understand a great deal of scripture as you never have before. For example, Paul's writings:

Gal 5:16 ISV So I say, live by the Spirit, and you will never fulfill the desires of the flesh. Gal 5:17 For what the flesh wants is opposed to the Spirit, and what the Spirit wants is opposed to the flesh. They are opposed to each other, and so you do not do what you want to do. Gal 5:18 But if you are being led by the Spirit, you are not under the Law. Gal 5:19 Now the actions of the flesh are obvious: sexual immorality, impurity, promiscuity, Gal 5:20 idolatry, witchcraft, hatred, rivalry, jealously, outbursts of anger, quarrels, conflicts, factions, Gal 5:21 envy, murder, drunkenness, wild partying, and things like that. I am telling you now, as I have told you in the past, that people who practice such things will not inherit the kingdom of God. Gal 5:22 But the fruit of the Spirit is love, joy, peace, patience, kindness, goodness, faithfulness, Gal 5:23 gentleness, and self-control. There is no law against such things. Gal 5:24 Now those who belong to the Messiah Jesus have crucified their flesh with its passions and desires. Gal 5:25 Since we live by the Spirit, by the Spirit let us also be guided.

Now modern translators have replaced "flesh" with "carnal nature" and "breath" with "spirit" but it is the same old dichotomy and the terms "carnal nature" and "spirit" are really inappropriate and obscure the original dichotomy evident in the original languages. Here are some more examples:

Joh 6:63 ISV It is the Spirit [breath] who gives life; the flesh accomplishes nothing. The words that I have spoken to you are spirit [breath] and life.

Breath gave life to Adam's flesh. That's why Jesus can say that so confidently.

So back to John:

Joh 3:6 What is born of the flesh is flesh, and what is born of the Spirit [breath] is spirit [breath]. Joh 3:7 Don't be astonished that I told you, 'All of you must be born from above.' Joh 3:8 The wind blows where it wants to. You hear its sound, but you don't know where it comes from or where it is going. That's the way it is with everyone who is born of the Spirit [breath]."

Note that Jesus/John ascribes volition to the wind: "...The wind blows where it wants to..."

The key to verses 6 and 7 is verse 8. That which originates from the flesh profits nothing and is at odds with that which is born from above, which gives life.

Part of this is intended as actual and part is metaphor.

The neuter verb is a participle. Participles have no gender of their own, they just have to agree if there is a noun to attach to.

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Flesh and Spirit

This phrase is part of a larger section discussing the concept of 'two births':

Jesus replied, “I tell you the solemn truth, unless a person is born from above, he cannot see the kingdom of God.” Nicodemus said to him, “How can a man be born when he is old? He cannot enter his mother’s womb and be born a second time, can he?

Jesus answered, “I tell you the solemn truth, unless a person is born of water and spirit, he cannot enter the kingdom of God. What is born of the flesh is flesh, and what is born of the Spirit is spirit. Do not be amazed that I said to you, ‘You must all be born from above.’ The wind blows wherever it will, and you hear the sound it makes, but do not know where it comes from and where it is going. So it is with everyone who is born of the Spirit.” - John 3:3-8 (NET)

Jesus speaks this line in response to Nicodemus' semi-rhetorical question "can a man be born from the womb twice?" He goes on to explain that's not the birth he is talking about. Yes, there is a water birth (What does it mean to be born of water?), but there is also a spirit birth, and this is what Jesus means to communicate.

To reinforce this, he uses the line in question - see the parallel:

v3 unless a person is born from above, he cannot see the kingdom of God

v5 unless a person is born of water and spirit, he cannot enter the kingdom of God

v6 what is born of the flesh is flesh, and what is born of the spirit is spirit

The intended meaning is to communicate firmly that Jesus is talking about two separate births: when you're born physically (of water) you're physically born, and when you're born spiritually (of spirit) you're spiritually born. This must happen in order to see/enter the Kingdom of God. This is seen more literally from Acts (2:4, 10:44) onwards, where those who enter the kingdom of God receive the Holy Spirit and experience a discernible spiritual re-birth.

My Greek isn't strong enough to comment with any real insight on γεγεννημένον vs γεγεννημένος, but given the usage of the two terms in John 3:6 and 3:8 I could only vaguely suspect that the neuter is going with the singular 'thing having been born' (cf. 1 John 5:1, 5:4) whilst the masculine pairs with the plural 'everyone who is born' (cf. 1 John 3:9, 5:18).

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