John Calvin Commentary 1 Timothy 1:2

"unto Timothy, my true child in faith: Grace, mercy, peace, from God the Father and Christ Jesus our Lord." — 1 Timothy 1:2 (ASV)

To Timothy my own son This commendation expresses no small praise. Paul means by it that he acknowledges Timothy to be a true and not an illegitimate son, and wishes that others would acknowledge him as such; and he even applauds Timothy in the same manner as if he were another Paul. But how does this agree with the injunction given by Christ, Call no man your father on the earth? (Matthew 23:9).

Or how does it agree with the declaration of the Apostle:

Though ye have many fathers according to the flesh, yet there is but One who is the Father of spirits (1 Corinthians 4:15; Hebrews 12:9).

I reply, while Paul claims for himself the title of father, he does it in such a way as not to take away or diminish the smallest portion of the honor that is due to God (Hebrews 12:9). It is a common proverb, "That which is placed below another is not at variance with it." The name father, applied to Paul with reference to God, belongs to this class.

God alone is the Father of all in faith, because He regenerates us all by His word and by the power of His Spirit, and because He alone bestows faith. But those whom He is graciously pleased to employ as His ministers for that purpose are also allowed to share with Him in His honor, while, at the same time, He parts with nothing that belongs to Himself.

Thus God, and God alone, strictly speaking, was Timothy’s spiritual Father; but Paul, who was God’s minister in begetting Timothy, lays claim to this title by what may be called a subordinate right.

Grace, mercy, peace. So far as relates to the word mercy, he has departed from his ordinary custom in introducing it, moved, perhaps, by his extraordinary affection for Timothy. Besides, he does not observe the exact order, for he places first what ought to have been last, namely, the grace which flows from mercy. For the reason why God at first receives us into favor, and why He loves us, is that He is merciful. But it is not unusual to mention the cause after the effect for the sake of explanation. As to the words grace and peace, we have spoken on other occasions.