Hello all, long time since I wandered into this den of vipers!

I recently read
this book and it prompted me to have a chat with you guys.
Presumably the atheists among you would hold a naturalistic/materialistic worldview, meaning that all of reality consists of nothing but physical matter and energy. OK so far?
If this is the case, I'm wondering how you would deal with questions such as the following:
- How can matter produce consciousness? Is the quark self-aware?
- Where does the faculty of reason come from and how do we know we can trust it if it has a physical origin? So how do we know that chemical/electrical interactions produce coherent, logical, rational thoughts? Is our rationality an illusion?
- Do we have free-will or is it just a convincing illusion?
How do you guys deal with these questions?
Thanks.