In the Summa Theologica I.33.2, reply to objection 3, Thomas Aquinas writes:
"In human nature the word is not a subsistence, and hence is not properly called begotten or son. But the divine Word is something subsistent in the divine nature; and hence He is properly and not metaphorically called Son, and His principle is called Father."
Aquinas contends that the Logos is a Son "properly" not metaphorically. The implication is that the Word of God literally is God's Son. Thomas clarifies this point by noting that the Father is the Son's "principle" or "origin" (i.e. loosely speaking, the Father is the "cause" of the Son or the one who communicates the divine nature to the Son. Hence, there is no doubt that Thomas thinks of God as a "proper" or literal Father of the Son. I will concede that Aquinas is not imputing the biological status of paternity to God. But what does it mean to say that God the Father communicates the divine nature to God the Son? How does God communicate the divine nature to the Son timelessly or continuously such that God never began to communicate the divine nature nor will God ever cease to communicate the divine nature? Moreover, is this how the earliest Christians understood God's paternity? The argument in my dissertation is that most early Christian writers thought of "Father" as a metaphor; in fact, it was a very familiar metaphor used in Judaism and in writings penned by Greeks and Romans. LSJ and BDAG Greek-English lexica document these uses. It appears to me that Thomas' treatment of the term "Father" raises more questions that it solves. The utilization of divine atemporality just deepens the mystery of eternal generation.