Perhaps the most important thing you can say to him is that you still love him, even if you disagree with him. Arguing, I suspect, will only make him more close-minded and determined to stick to his ideas. The Bible wisely says, “A gentle answer turns away wrath, but a harsh word stirs up anger” (Proverbs 15:1).
At the same time, I hope you’ll encourage him to keep an open mind and heart. His teacher’s arguments have been around for hundreds of years, and for hundreds of years Christians of great ability have been answering them. Your local Christian bookstore can suggest some reading if he’s interested. As the Bible says, “There is nothing new under the sun” (Ecclesiastes 1:9).
I also hope your son will realize how many things we accept every day as true, even though we can’t put them in a test tube or prove them scientifically. Can you prove scientifically that love exists? Or beauty? Or goodness, or evil, or jealousy, or contentment? We see their effects and we know they exist, but we can’t put them under a microscope. In a far greater way, the same is true with God.
God has revealed Himself to us in many ways — through the wonders of His creation, for example. But most of all, we know He exists because He became a man and lived among us in the person of Jesus Christ. Pray for your son, and urge him to look at Christ.