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John 3:13 And no man hath ascended up to heaven, but he that came down from heaven, even the Son of man which is in heaven.
Skeptics sometimes misuse the English in this verse, asking how Jesus can be in heaven and on earth at the same time. The understanding of this verse is achieved by noting the allusion to hearing heavenly things in the verse preceding (v. 12), the comparison to Moses immediately following (v. 14), and the echo of Wisdom of Solomon in this passage as a whole. (Witheringon, John commentary, 100).
Let's look at that broader context:
John 3:11-14 Verily, verily, I say unto thee, We speak that we do know, and testify that we have seen; and ye receive not our witness. If I have told you earthly things, and ye believe not, how shall ye believe, if I tell you of heavenly things? And no man hath ascended up to heaven, but he that came down from heaven, even the Son of man which is in heaven. And as Moses lifted up the serpent in the wilderness, even so must the Son of man be lifted up...
The interpretive key is that Jesus seems to be speaking as though he has already ascended into heaven -- and that is indeed what he has done. The allusion to Moses here, who ascended Mount Sinai to receive the covenant revelation, is what tells us what is being referred to.
The "ascent" in question is an ascent like that experienced by Paul (2 Cor. 12:1-7) who also received revelation. As Jesus is here defending his revelatory authority, it is understandable that he makes this appeal to his route to revelation.
That still leaves the matter of the latter part of the verse, which refers to the Son of Man "which is in" heaven -- as in, in the present tense. Modern translations do not read the verse this way; the NIV states, for example, "No one has ever gone into heaven except the one who came from heaven--the Son of Man."
The NRSV does the same -- and for good reason. As all commentators agree (Michaels commentary on John, 61; Moloney, 101; Lindars, 156) this final phrase is a late scribal addition, not found in the best textual witnesses (P66, P75). It was added at a later date, probably by scribes who thought that Jesus had his own ascension in view.