John Calvin Commentary Hebrews 12:9

"Furthermore, we had the fathers of our flesh to chasten us, and we gave them reverence: shall we not much rather be in subjection unto the Father of spirits, and live?" — Hebrews 12:9 (ASV)

Furthermore, we have had fathers of our flesh, etc. This comparison has several parts:

1. That if we showed so much reverence to the fathers from whom we have descended according to the flesh, submitting to their discipline, much more honor is due to God who is our spiritual Father.
2. That the discipline which fathers use toward their children is only useful for the present life, but God looks further, intending to prepare us for eternal life.
3. That men chastise their children as it seems good to them, but God regulates His discipline in the best manner and with perfect wisdom, so that there is nothing in it but what is properly ordered.

He then, in the first place, makes this distinction between God and men: that men are the fathers of the flesh, but God is of the spirit. On this distinction he elaborates by comparing the flesh with the spirit.

But it may be asked: Is not God the Father also of our flesh? For it is not without reason that Job mentions the creation of human beings as one of the chief miracles of God; therefore, on this account also, He is justly entitled to the name of Father. If we were to say that He is called the Father of spirits because He alone creates and regenerates our souls without the aid of man, it might be said in response that Paul glories in being the spiritual father of those whom he had begotten in Christ by the Gospel.

To these things I reply that God is the Father of the body as well as of the soul; and, properly speaking, He is indeed the only true Father. This name is applied to men only by way of concession, as it were, both in regard to the body and of the soul. However, since in creating souls He uses the instrumentality of men, and since He renews them in a wonderful manner by the power of His Spirit, He is peculiarly called, preeminently, the Father of spirits.

When he says, and we gave them reverence, he refers to a feeling implanted in us by nature, so that we honor parents even when they treat us harshly. By saying, in subjection to the Father of spirits, he intimates that it is only just to concede to God the authority He has over us by the right of a Father. By saying, and live, he points out the cause or the end, for the conjunction “and” is to be rendered that, — “that we may live.” Now we are reminded by this word live, that there is nothing more ruinous to us than to refuse to surrender ourselves in obedience to God.