The Bible says that Jesus was “conceived by the Holy Spirit.” Therefore he cannot be the son of the Father. How does this work?
My first question is this: Does this really matter to our daily lives as Christians? This seems to be parsing out a very unimportant difference.
My second point is this: We need to ask what is the meaning of the phrase “what is conceived in her is from the Holy Spirit.” (Matthew 1:20).
To answer this, we need to do two things:
a. Look at relevant parallel passages.
b. Ask what it might mean in light of related but not parallel passages.
The directly parallel passage is Luke 1:35. “The Holy Spirit will come on you, and the power of the Most High will overshadow you. So the holy one to be born will be called the Son of God.”
It is fairly clear that the Luke passage gives us more information and should be used to help explain the Matthew passage.
As for b. I would add John 1:14 and John 3:16. For the sake of brevity, I will only quote John 1:14. “The Word became flesh and made his dwelling among us. We have seen his glory, the glory of the one and only Son, who came from the Father, full of grace and truth.”
Given the two John passages (and many, many others….) I believe that the Son submits to the Father, not to the Holy Spirit and that he was sent (exactly what that means I cannot say) by the Father, not by the Holy Spirit. The Luke passage is easily interpreted in this way. To be honest, the Matthew passage is a difficult one, and can be seen, in isolation, to support your conclusion, but given the parallel passage which is more ambiguous, and given the many, many other relevant passages, I believe that this is the correct understanding of Matthew 1:20:
Jesus was conceived by the Father in Mary through the working of the Holy Spirit.
This is clearly a possible interpretation of Matthew 1:20, and I believe that this interpretation is demanded by the other passages (most of which I am not quoting here, to be honest, but you can do your own research. Jesus did exactly what the Father said, If you have seem me, you have seen the Father, and so forth…)