I think the word "son" is a metaphor, in that the word inadequately expresses the relationship, just as all language inadequately describes God. However, there are many things about the concept of Son that help us to understand God/Jesus. He is not a son in the biological sense since Jesus was not conceived in the ordinary biological sense, and since Jesus predates his incarnation. "He was in the beginning with God." But our own experience of the closeness of our children, help us to get a handle on the closeness of God the Father and God the Son.