Reply to this Apologia with a Counter Argument Coursework

Prompt from Italian Civilization Instructor:
Reply to the apologia below by presenting the counter argument of the Church at the time in order to show which values are in conflict for example it can be: tradition versus innovation or religion versus science etc…
"My work as a scientist has never decreased my faith in the Catholic Church. After many years, I still remain the same faithful catholic that I have always been. I have learned through the teachings of the church as well as from other scientist before me. I study the work of the scientist before me as a guide for my own work. I have study the work of Copernicus, Aristotle, and Kepler. Being a scientist requires cautious observations of the world and nature. Nevertheless, every scientist has his own way of observing the world around them. As a scientist, we must observe, analyze, and test our findings. New discoveries should be taken in as a way to expand our knowledge in what we already know about the world and not as threat to the faith in the Catholic Church. I have always believed that the bible is the true word of God and that its word serves as an important guidance for everyday life. What that bible doesn't include, is a guide for understanding how nature behaves and that's where we as scientist come in. I do not wish to challenge the work of God, nor the church. I just want to share my discoveries and to remind everyone that God gave us eyes to see the world around us, but that God also gave us a brain, not to contradict the church, but analyze and make sense of what our eyes see."
Notes from me the student:
Remember an “Apologia” (a Greek term that means "speaking in defense") is a formal defense of a position or action. In modern usage, apologia describes a formal defense and should not be confused with the sense of the word 'apology' as the expression of regret.
The assignment must be in Times New Roman Font with Size 12 with 1 inch margins all around.