Waffle, 'In the beginning' , refers to the time when something or someone began to be present. God had no beginning, so it cannot be referring to him.
I'm afraid it does, Mr Gordon, it refers to the changeless state of G.d as a beginning. Think of it as a reference point. Now you and I both know that it is not a literal, "beginning" but it does refer to the eternal condition that exists, existed before physical Creation. Because as you well know it could be argued from both science and religion that nothing had a beginning as nothing can be derived from absolute nothingness.
Even life itself has no beginning, if existence has a beginning then we have to contemplate the emergence of existence from non-existence and it would seem that non-existence is impossible. So think of "In the beginning" as a baseline and remember this is a work for minds and concepts of several thousand years ago.
"This makes it clear that the one that began was the Word." I don't much is clear at all, otherwise Christianity would not be in such a disunited mess.
