Thank you for demonstrating taking a verse out of context. You only cited Jn. 3:6, if you had included verses 5;7;8, it gives the context. The passage says, "Jesus answered, “Truly, truly, I say to you, unless someone is born of water and
the Spirit, he cannot enter the kingdom of God. That which has been born of the flesh is flesh, and that which has been born of the Spirit is spirit. Do not be amazed that I said to you, ‘You must be born again.’ The wind blows where it wishes, and you hear the sound of it, but you do not know where it is coming from and where it is going; so is everyone who has been born of the Spirit." So, in short, He's speaking about the conversion of souls.
Back to the topic, the Father, the Son, and the Holy Spirit are the one God. God in His spirit form (the Father) wanted to die for humanity, for He is the perfect sacrifice, but a spirit cannot die physically, so the part of Himself (the Word) became flesh (Jesus), so as to be able to die for humanity. So, Jesus the Son
is God in physical form.
In the original language used, Koine Greek, it says:
"and God was the Word"
"καὶ (
and) θεὸς (
God) ἦν (
was) ὁ (
the) λόγος (
Word)..." (Jn. 1:1)
"And the Word became flesh and dwelt among us"
"Καὶ ὁ λόγος σὰρξ ἐγένετο καὶ ἐσκήνωσεν ἐν ἡμῖν, καὶ ἐθεασάμεθα τὴν δόξαν αὐτοῦ, δόξαν ὡς μονογενοῦς παρὰ πατρός, πλήρης χάριτος καὶ ἀληθείας." "Καὶ (
And) ὁ (
the) λόγος (
Word) σὰρξ (
flesh) ἐγένετο (
became) καὶ (
and) ἐσκήνωσεν (
dwelt) ἐν (
among) ἡμῖν (
us)..." (Jn. 1:14)
Who is the Word that became flesh? Jesus. The Word is
Who Jesus is, the same Word identified as God 13 verses prior in Jn. 1:1: "καὶ θεὸς ἦν ὁ λόγος" (
and God was the Word), and thus
Jesus the Messiah is God Incarnate.
Additionally, Moses said to God that the children of Israel will ask the name of the one who sent him, then asked what name shall he tell them: "Καὶ εἶπε Μωυσῆς πρὸς τὸν Θεὸν, ἰδοὺ ἐγὼ ἐξελεύσομαι πρὸς τοὺς υἱοὺς ᾿Ισραὴλ, καὶ ἐρῶ πρὸς αὐτοὺς, Θεὸς τῶν πατέρων ἡμῶν ἀπέσταλκέ με πρὸς ὑμᾶς: ἐρωτήσουσί με, τί ὄνομα αὐτῷ; τί ἐρῶ. πρὸς αὐτούς; Καὶ εἶπεν ὁ Θεὸς πρὸς Μωυσῆν, λέγων, ἐγώ εἰμι ὃ "Qu: (
I AM THE BEING): καὶ εἶπεν, οὕτως ἐρεῖς τοῖς υἱοῖς Ἰσραὴλ, ὁ Ὧν ἀπέσταλκέ με πρὸς ὑμᾶς (
say to the children of Israel THE BEING has sent me to you)." (Ex. 3:13-14)
Fast forward to the scene of Jn. 8:58, where Jesus claimed to be eternal and to have existed before Abraham, but more importantly, He called himself by the ancient title ascribed only to God Himself: "...πρὶν (before) Ἀβραὰμ (Abraham) γενέσθαι ἐγὼ (
I) εἰμί (
AM)." The Pharisees knew exactly what Jesus meant by this. From their perspective, Jesus said specifically, “I am God”. How do we know this was their interpretations of His words? We know it from their reaction.
They responded by attempting to stone Jesus for claiming to be God (an act of blasphemy they considered worthy of death): "ἦραν (
picked) οὖν λίθους (
stones) ἵνα (
to) βάλωσιν (
throw) ἐπ' (
at) αὐτόν (
him): Ἰησοῦς δὲ ἐκρύβη καὶ ἐξῆλθεν ἐκ τοῦ ἱεροῦ," but He escaped them (Jn. 8:59).
Now, how was Jesus existing before Abraham was born? As He's always existed: as the Word with God (ὁ (
the) λόγος (
Word) ἦν (
was) πρὸς τὸν (
with) θεόν (
God), and at the same time also as God (θεὸς (
God) ἦν (
was) ὁ (
the) λόγος (
Word) (Jn. 1:1), the eternal God "Θεὸς αἰώνιος" (Gen. 21:33), and the Word became flesh and dwelt among us (Jn. 1:14).
In Jn. 10:22-36, again the Pharisees understood Jesus was calling Himself God, and they wanted to kill him for it, for they said: "ἀπεκρίθησαν αὐτῷ οἱ Ἰουδαῖοι, Περὶ καλοῦ ἔργου οὐ λιθάζομέν (
stone) σε (
you) ἀλλὰ περὶ (
for) βλασφημίας (
blasphemy), καὶ ὅτι σὺ ἄνθρωπος ὢν ποιεῖς (
making) σεαυτὸν (
yourself)
θεόν (
God)" (Jn. 10:33), and Jesus didn't deny it because He did as He's God Incarnate.
The same Jesus said to be God by His apostle, Thomas: "ἀπεκρίθη (replied) Θωμᾶς (Thomas) καὶ (and) εἶπεν (saying) αὐτῷ (to), Ὁ κύριός (
Lord) μου (
my) καὶ (and) ὁ
θεός (
God) μου." (Jn. 20:28)
The apostles knew Jesus was God. Even the
Pharisees understood Jesus called Himself God, though they didn't believe Him, which is why they tried to kill Him for blasphemy, and Jesus never denied it when they acknowledged He claimed to be God, because He is. Therefore, how can you deny it?