Some of these obviously involve multiple questions…
1. Does the universe have a beginning that requires a cause? If so, what was this cause?
2. Is materialistic determinism compatible with the intrinsically probabilistic nature of quantum mechanics?
3. How do you account for the physical parameters of the universe (the gravitational constant, the strong nuclear force, the mass and charge of a proton, etc.) being finely tuned for the existence of stars, planets, and life?
4. Why is the human mind naturally fluent in the language of mathematics, and how do you explain the eerie, seemingly unreasonable effectiveness of mathematics in describing the laws of nature?
5. Do you believe that DNA repair mechanisms, catalytically perfect enzymes, and phenomena such as substrate channeling are best explained by naturalism? If so, why are rational human scientists and engineers so woefully incapable of imitating the precision and complexity of cellular machinery that (presumably) arose via strictly irrational processes?
6. Do you believe free will to be illusory? If so, can the punishment of crimes be ethically justified (and does the word “ethical” have any real meaning)?
7. Does objective morality exist? If so, what is its source…and how do you define “objective”? If not, do you concede that concepts like “justice”, “fairness”, and “equality” are nothing more than social fads, and that acts of violence and oppression must be regarded merely as differences of opinion?
8. In what terms do you define the value of human life? Is the life of a human child more or less valuable, for example, than that of an endangered species of primate?
9. Much attention has been given to alleged cognitive biases and “wishful thinking” contributing to religious belief. Do you believe that similar biases (for example, the desire for moral autonomy) play a role in religious nonbelief? If not, what specifically makes atheism immune to these influences?
10. Do you believe religion (speaking generally) has had a net positive or a net negative effect on humanity? If the latter, how do you explain the prevalence of religion in evolutionary terms?
11. Is it rational for you to risk your life to save a stranger?*
12. How would you begin to follow Jesus if it became clear to you that Christianity was true? What would be the hardest adjustment you would have to make to live a faithful, public Christian life?*
*Questions 11 and 12 are taken from a similar list on Wintery Knight.
Christians & Theists: If you have additional questions you would have included on this list (or disagreements with anything I’ve included), I invite you to respond in the comments section, or with a post of your own.
Atheists: If you would like to respond to these questions, I also invite you to do so in the comments section, or with a post of your own. In the interest of fairness, I will include on this page a link to any such posts.
UPDATE: I’ve posted a compiled list of answers (n=11) HERE.