(This post was last edited on 21-Jun-12, by reorganizing the list into a more logical sequence. I apologize in advance for the inconvenience this may cause to people who have posted comments or their own articles discussing these.)

As a follow-up to my last post, I compiled a list of my own questions for theists. I’m sure readers will have many of their own to add.

1. The question “Why is there something rather than nothing” presupposes “nothing” as being  the normal state of affairs. Why believe that? Why can’t we flip the question on its head? In other words, why can’t it be the case that the normal state of affairs is for things to actually exist and nothingness itself would be weird?  (HT: Thy Kingdom Come (Undone))
2. Given that the universe has a finite age, why did the universe begin with time rather than in time?
3. Why is so much of our universe intelligible without any appeal to supernatural agency? Why does the history of science contains numerous examples of naturalistic explanations replacing supernatural ones and no examples of supernatural explanations replacing naturalistic ones?
4. Why is the physical universe so unimaginably large?
5. If you believe that visual beauty is evidence of God, why isn’t the universe saturated with auditory, tactile, or other non-visual types of sensory beauty?
6. If you believe the universe is fine-tuned for intelligent life, why isn’t our universe teeming with life, including life much more impressive than human life?
7. Why would God use biological evolution as a method for creation? Do you have any answer that is independent of the scientific evidence for evolution?
8. Why would God desire to create embodied moral agents, as opposed to unembodied minds (such as souls, spirits, or ghosts)? Why is the human mind dependent on the physical brain?
9. Did Australopithecus have a soul? What about homo habilis? Homo erectus? Neanderthals? Why or why not? (HT: Keith Parsons)
10. How do souls interact with physical matter? Do you have any answer that is not tantamount to “I don’t know?” (HT: Keith Parsons)
11. If you believe humans have free will, why would humans have free will if God exists? Why are we able to exercise free will in some situations but not others?
12. Why are pain and pleasure so connected to the biological goals of survival and reproduction, but morally random? Is there some greater good that logically requires (or logically requires risking) that suffering be used to motivate animals to pursue the biological goal of self-preservation? Does some moral end make it desierable for suffering to continue even when it serves no biological purpose? For example, why do sentient beings, including animals which are not moral agents, experience pain or pleasure that we do not know to be biologically useful?
13. Why do only a fraction of living things, including the majority of sentient beings, thrive? In other words, why do very few living things have an adequate supply of food and water, are able to reproduce, avoid predators, and remain healthy? Why would God create a world in which all sentient beings savagely compete with one another for survival? Why do an even smaller fraction of organisms thrive for most of their lives? Why do almost no organisms thrive for all of their lives? 
14. Why is there social evil, i.e., instances of pain or suffering that results from the game-theoretic interactions of many individuals? 
15. Why does God allow horrific suffering (and relatively little glorious pleasure)?
16. Why does horrific suffering often destroy a person, at least psychologically, and prevent them from growing morally, spiritually, and intellectually?
17. Why is there nonculpable (reasonable) nonbelief in God? Why are there former believers, i.e., people who, from the perspective of theism, were on the right path when they lost belief? Why are there so many people who gave their lives to God only to discover there is no God? Why are there lifelong seekers? Why are there converts to nontheistic religions and especially nonresistant believers who arrive as a result of honest inquiry at nontheistic experiences and beliefs? Why are there isolated nontheists, i.e., people who have never so much as had the idea of God?
18. Why do some believers feel there is evidence for God’s existence on which they may rely, but in which God is not felt as directly present to her experience, and may indeed feel absent?
19. Why are there such striking geographic differences in the incidence of theistic belief? Why does
    theistic belief vary dramatically with cultural and national boundaries? For example, why does a population of millions of non-theists persist in Thailand but not in Saudi Arabia? And why has the global incidence of theistic belief varied dramatically over time, i.e., during the existence of the human species?
20. Why do only some people have religious experiences? In particular, why is it that most of the people who do have religious experiences almost always have a prior belief in God or extensive exposure to a theistic religion?
21. For those people who do have religious experiences, why do they pursue a variety of radically different religious paths, none of which bears abundantly more moral fruit than all of the others?
22. Why do so many people report not experiencing God’s comforting presence in the face of tragedies?
23. Why does the the relatively new discipline of cognitive science of religion support the claim that we have a Hyperactive Agency Detection Device (HADD), which causes human beings to naturally form beliefs about invisible agents? Considering HADD’s poor track record of producing true beliefs about invisible agents in general, why should we trust it when it produces a belief about one invisible agent, the God of theism?
24. Why does God allow such confusion or disagreement among people, including theists, about what is morally good or bad and morally right or wrong?
25. Why should we believe that, of the innumerable deities worshipped by human beings over the ages, yours is the one that really exists?  Why believe in Yahweh rather than Zeus, Odin, Marduk, Ishtar, Osiris, Quetzalcoatl, Madame Pele, Ahura-Mazda, etc., etc., etc.? (HT: Keith Parsons)