Who is the Father of Jesus?

Is Jesus the son of Allah? The Qur'an says no. Yet it is also entirely consistent with the Qur'an to consider Allah the Father of Jesus for the following reasons:
1) Allah caused Mary to become pregnant with Jesus
2) Allah determined some of the physical characteristics of Jesus
3) All of the genetic characteristics of Jesus were determined by just two parties: Allah and Mary.

A Muslim might argue "Being a father implies having sex", and therfore Allah cannot be the father. Not necessarily so. Modern science has brought us "test tube babies", which are conceived without any sex. There is nothing to support the idea that if Allah wants a baby, he must resort to normal human means to have one.
Again, a Muslim may say that if we are going to call Jesus the son of Allah, then we should say that Adam is the son of Allah too. No, we cannot compare Adam to Jesus this way because Adam came into existence without a mother.
Let us first review some background material. What does the Qur'an say about how Mary became pregnant with Jesus? In Surah 3:45-49 we read:

The angels said to Mary: "Allah bids you rejoice in a word from him. His name is the Messiah, Jesus the son of Mary. He shall be noble in this world and the hereafter, and shall be favored by Allah. He shall preach to men in his cradle and the prime of manhood, and shall lead a righteous life."
"Lord", she said, "how can I bear a child when no man has touched me?"
He replied: "Such is the will of Allah. He creates whom He will. When He decrees a thing He need only say: 'Be' and it is. He will instruct him in the Scriptures and in wisdom, in the Torah and in the Gospel, and send him forth as an apostle to the Israelites..."

From this passage we can draw the conclusions presented above:
1) Allah caused Mary to become pregnant with Jesus. Muslims infer from this passage and others like it that Jesus was conceived while Mary was a virgin by the word spoken by Allah, and not by a man.
Not that this in itself implies that Allah is the father. When a doctor causes a woman to become pregnant by artificial insemination, he is not considered the father. Hence the following two points:
2) Allah determined some of the physical characteristics of Jesus. 
When Allah said "Be", did he have something specific in mind? Certainly! Allah had a very detailed plan in mind for Jesus. In particular, Allah decided that Jesus would be male. Normally, it is the sperm that decides the gender of the baby. Here Allah made the choice instead.
3) All of the genetic characteristics of Jesus were determined by precisely two parties: Allah and Mary. 
This is clear because they were the only two parties involved. So we conclude that Allah and Mary are the only two possible candidates for the title "Father".
Hence it appears legitimate to call Allah the father of Jesus, at least in a figurative sense. Therefore we are at a loss to explain why the Qur'an spends so much space arguing against this. Certainly more and better justification is needed than what appears in these passages:

Surely they lie when they declare: "Allah has begotten children".
-- Sura 37:151

Where is the "lie" in our reasoning above?

They say: "Allah has begotten a Son". Glory be to Him! His is what the heavens and the earth contain; all things are obedient to Him. Creator of the heavens and the earth! When he decrees a thing, He need only say "Be", and it is.
-- Sura 2:116

Allah made Mary pregnant. What more would Allah have to do if he wanted a legitimate son?

Allah forbid that He Himself should beget a son! When He decrees a thing He need only say "Be," and it is. -- Sura 19:35

So is Allah unable to beget a son by saying "Be"?

Say: "If the Lord of Mercy had a son, I would be the first to worship him". -- Sura 43:82

We would prefer something more convincing from the Qur'an than this.