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John Wesley's notes on the Gospel: John 3:1-15
Chapter III 

1  A ruler - One of the great council. 

2  The same came - Through desire; but by night - Through shame: We know - Even we rulers and Pharisees. 

3  Jesus answered - That knowledge will not avail thee unless thou be born again - Otherwise thou canst not see, that is, experience and enjoy, either the inward or the glorious kingdom of God. In this solemn discourse our Lord shows, that no external profession, no ceremonial ordinances or privileges of birth, could entitle any to the blessings of the Messiah's kingdom: that an entire change of heart as well as of life was necessary for that purpose: that this could only be wrought in man by the almighty power of God: that every man born into the world was by nature in a state of sin, condemnation, and misery: that the free mercy of God had given his Son to deliver them from it, and to raise them to a blessed immortality: that all mankind, Gentiles as well as Jews, might share in these benefits, procured by his being lifted up on the cross, and to be received by faith in him: but that if they rejected him, their eternal, aggravated condemnation, would be the certain consequence. Except a man be born again - If our Lord by being born again means only reformation of life, instead of making any new discovery, he has only thrown a great deal of obscurity on what was before plain and obvious. 

4  When he is old - As Nicodemus himself was. 

6  That which is born of the flesh is flesh - Mere flesh, void of the Spirit, yea, at enmity with it; And that which is born of the Spirit is spirit - Is spiritual, heavenly, divine, like its Author. 

7  Ye must be born again - To be born again, is to be inwardly changed from all sinfulness to all holiness. It is fitly so called, because as great a change then passes on the soul as passes on the body when it is born into the world. 

8  The wind bloweth - According to its own nature, not thy will, and thou hearest the sound thereof - Thou art sure it doth blow, but canst not explain the particular manner of its acting. So is every one that is born of the Spirit - The fact is plain, the manner of his operations inexplicable. 

11  We speak what we know - I and all that believe in me. 

12  Earthly things - Things done on earth; such as the new birth, and the present privileges of the children of God. Heavenly things - Such as the eternity of the Son, and the unity of the Father, Son, and Spirit. 

13  For no one - For here you must rely on my single testimony, whereas there you have a cloud of witnesses: Hath gone up to heaven, but he that came down from heaven. Who is in heaven - Therefore he is omnipresent; else he could not be in heaven and on earth at once. This is a plain instance of what is usually termed the communication of properties between the Divine and human nature; whereby what is proper to the Divine nature is spoken concerning the human, and what is proper to the human is, as here, spoken of the Divine. 

14  And as Moses - And even this single witness will soon be taken from you; yea, and in a most ignominious manner. Num 21:8,9. 

15  That whosoever - He must be lifted up, that hereby he may purchase salvation for all believers: all those who look to him by faith recover spiritual health, even as all that looked at that serpent recovered bodily health.