Hello there! I hope my input here is helpful to what you were wondering.
I grew up Christian (not Catholic) in the US and several years ago I had a journey of realizing that I had a love for science and figuring out how that fit into this faith, since many see a problem between them. I felt some doubt, but ultimately I didn’t let go of my faith; there was too much value in it and my experience with it just rang true.(Of course, it’s still a journey and I’m not saying I have all the answers). The general conclusion I’ve come to is that to have faith you do not need to sacrifice anything intellectually. Science should pose no threat to belief in God since he is the Creator, so whatever we discover in the natural world, he put it there.
On your mention of having a hard time reconciling supernatural things in the Bible, I would say that in a way they just demonstrate God’s sovereignty over nature. Miracles are not scientific things, but rather, I suppose, exceptions to science. And if anyone can make exceptions to the laws of science, it would be the maker of science himself. That’s what makes them miracles. It seems like an insult to God to suggest that he cannot perform “supernatural” acts, that he is bound by scientific laws himself, when in reality he is greater than them. Giving miracles a scientific explanation seems to discredit their significance.
With reconciling science and faith, my main resource and inspiration was Biologos itself, which my dad introduced me to, and reading Francis Collins’ book The Language of God was interesting too. Sometimes I visit this forum to see other people’s perspectives and thoughts, and there are for sure some varying opinions here.
Also, I feel like I’ve gotten the sense that there is definitely some difference between Europe and the US regarding religious culture, but I haven’t actually visited Europe and I don’t know too much on that. My experience in the US is much like you said. I grew up in a non-denominational church that is still thriving and definitely has an inclusive, helpful community.
Lastly, I definitely urge you to continue to talk with your friend and ask him about his journey in his faith, especially since you’ve had such similar experiences. I’m glad you are reaching out for help and I hope you continue to explore your questions.
“The Son is the image of the invisible God, the firstborn over all creation. For in him all things were created: things in heaven and on earth, visible and invisible, whether thrones or powers or rulers or authorities; all things have been created through him and for him. He is before all things, and in him all things hold together.”Colossians 1:15-17 NIV