John 3:6

6. Flesh… Spirit Flesh is not synonymous with body. The word is used in the Old Testament to designate the entire transient, perishable, fallen, and corrupt nature of man, both in body and soul. Hence the meaning of the first clause of this first verse is: That which is generated of fallen and depraved humanity, is itself fallen and depraved humanity. Like produces like. Through all the productive, procreative kingdoms, whether animal or vegetable, no offspring is of a higher species than its parentage. On the other hand, Spirit here refers to the Holy Spirit as so operating upon the human spirit, and so changing its nature, as to be said to beget it anew. For as generation is a modifying of substance or being, imparting to it a new principle of life, conforming it, as living being, to the likeness of the generator, so regeneration is a modification of the human spirit by the Holy Spirit, conforming the temper of the human to the Holy.

Is spirit As flesh signifies a depraved nature, so spirit in this verse signifies a pure nature.

For it is a pure and holy Spirit which is the generator, and it must be a pure and holy spirit which is generated. The whole text then is: As a depraved nature generates a depraved nature, so the holy nature generates a holy nature. And as we are first born of a depraved nature, and therefore depraved, so we must be born (or rather begotten) from a holy nature, and so be renewed.