1. What caused the universe to exist?This presumes an agency, which is a natural way our mind works, but not necessarily true. Our assumption that something causes something else is also due to our pattern-seeking mind. I am currently reading Michael Shermer's The Believing Brain and he addresses the question of why we ask these questions and come up with the answers we do. Basically, we are programmed by evolution to seek patterns even if those patterns are wrong because the cost of not finding a true pattern (e.g., being bit by a predator rustling in the grass) is much greater than the cost of having a false positive (running when we hear a rabbit rustling in the grass).
2. What explains the fine tuning of the universe?There is no fine tuning of the universe. It is a figment of some believers' imagination. We are the center of our own little universes, and when we contemplate the greater universe we want to extend that sense of specialness, even though it's totally wrong. If a Christian really wants to know how people counter that silly argument, they don't have to look far.
3. Why is the universe rational?It's not. Nothing is rational without a prefrontal cortex.
4. How did DNA and amino acids arise?From smaller pieces of matter that got stuck together in bigger and bigger bundles as time went on.
5. Where did the genetic code come from?See the answer to #4
6. How do irreducibly complex enzyme chains evolve?Irreducibly complex anything is a figment of the Christian imagination. Even if there were such a thing, that would not imply a God or any kind of agent or rational entity tinkering with the chemicals. Notice that anti-science Christians never argue that crystals form according to God's plan, only chemicals that happen to be inside the human body. I have windows that have very poor insulation. In the winter crystals form on them every night. They are beautiful even though they are a sign that my landlord is a cheapskate. How does water form crystals on windows in such beautiful patterns? Because of the chemical structure and nature of water. Ditto, everything else.
7. How do we account for the origin of 116 distinct language families?By the spread of humans all across the globe into separate cultural groups. Having one core language group would have been much more of an argument for a God. Language families have family trees that linguists have deduced by studying the relationships amongst the languages. I have never heard this idiotic question before. Kind of makes me wonder if Christians are giving up on trying to out-science everyone with their ignorant arguments.
8. Why did cities suddenly appear all over the world between 3,000 and 1,000BC?This is not true. Mohenjo Daro appeared in India in ca. 5,000 BC and Chinese cities als predate the earliest Middle Eastern Cities. But... the human race is about the same age everywhere, so if we learn from our elders and experiment and adapt our behaviors to various environments, it's kind of inevitable that the same species will do the same behaviors at about the same time in different places.
9. How is independent thought possible in a world ruled by chance and necessity?Ahhh the questions get stupider by the number. Thinking is possible because our brains are adapted for thinking. Not all of use do it very well, as evidenced by this list of questions.
10. How do we account for self-awareness?Neurologists are answering more and more of these things all the time. We have brains that recognize ourselves, but amazingly don't recognize that the brain is what makes it possibe for us to do it. Did Teri Schiavo have self awareness after her brain turned to slush? No. There's your answer.
11. How is free will possible in a material universe?Check out the debate between Jerry Coyne and Richard Carrier (and possibly a few others) on this matter. Our "will" is only as free as our brain allows it to be. And since your "will" is a function of your brain, which is a material object, I think the question is kind of stupid. (Bud, what's the word for this kind of stupidity?)
12. How do we account for conscience?Brains.
13. On what basis can we make moral judgements?On the basis of the moral code that we get from our culture, or that we make up ourselves. Richard Dawkins makes this point very clearly in The God Delusion. Throughout the history of the Judeo-Christian "law" there has been very little relationship between the written word and the morality of the peoples who professed to believe in it.
14. Why does suffering matter?It matters to the being that's suffering because suffering hurts. Owie. We are programmed by evolution to want to live, and to avoid things that hurt. Duh. In a group of beings that are attached by a social bond, the suffering of others matters to us because 1) we have mirror neurons that give us the ability to empathize and 2) the survival of the group depends on the survival of individuals.
15. Why do human beings matter?We don't, except to ourselves and our pets.
16. Why care about justice?Because we live in a social group, and social groups work better when there's a system of justice to punish selfish individuals. Even non-human primates believe in justice, and I swear my smarter cocker spaniel keeps track of how many treats she gets compared to my other dogs.
17. How do we account for the almost universal belief in the supernatural?Michael Shermer to the rescue again. We see patterns because of our neurology, and we also attribute agency to things because not to do so when there's actually an agent would put us at an evolutionary disadvantage. Even Christians know this at heart. It's the basis for Pascal's Wager: being wrong about the supernatural is harmless if we believe in something false, but not believing in it if it's real could be dangerous. It's the snake vs. bunny in the grass wager again.
18. How do we know the supernatural does not exist?You can't absolutely 100% prove a negative in this case, because there could be a supernatural agent on some other planet we can't ever observe. But... so far on this planet things that seem to be supernatural because of some trick of our minds have 100% turned out to be explainable in natural terms, or have not been proved not to be natural.
19. How can we know if there is conscious existence after death?We can't, but it's a safe bet there isn't. If we can be "brain dead," then we're already not conscious. There also isn't conscious existence when we're asleep or under anesthesia. Babies The fact that it can be suspended pretty much points to it being a natural, 100% worldly, phenomenon attributable to the way our brains work. When the brain dies, we die. When others' brains die, they die, but our brains still hold their images and can play tricks on us.
20. What accounts for the empty tomb, resurrection appearances and growth of the church?Empty tomb: here are a few possible explanations. 1) Christ cheated death, 2) it's a made-up story to make Christ seem more supernatural in order to persuade bronze age people who would have expected a story like that of a godlike being, 3) his body was stolen, 4) he wasn't really dead and his pals helped him out of there, 5) he didn't exist, 6) his death was faked and he was never in the tomb.
One of those explanations is supernatural. Five of them are ordinary and fairly prosaic explanations. Why choose to believe the one supernatural one?
Resurrection appearances: You mean how Elvis appeared to his fans for years after his death? Dunno. I never got that one.
Growth of Christianity: prosletyzing, forced conversions, and making up stories that would appeal to the people being prosletyzed to. Other religions have grown too. Believing in agency, the supernatural, authority figures, etc. predispose us to believe in the fairy tales of our elders and to be converted when we are vulnerable. Add to this the tendency of kings and emperors to dictate which religion the people have to follow, and you get mass conversions like crazy. The Africans who came to the U.S. as slaves were pantheists who believed that they were captured because their god wasn't as strong as their captors' god, so they switched to the team with the better pitcher. Now there are millions of African-American Christians who are their descendents. So the spread of Christianity is pretty easily explainable by anyone who has bothered to read a basic world history textbook.
Well, that was fun. Some Christian really thought these questions were unanswerable? Makes you wonder if they have ever tried to find out alternate answers on their own. Most of them aren't even aware of the ways that other religions answer their deep questions. Certainly the spread of Christianity has been documented well enough that they could learn about their own religion. For someone to add that last question shows an appalling level of ignorance.