As painful as these questions are, here are some more. As a warning, there are a lot of repeats. This list is a little more vague, but has some merit.
As always, answers in quotes.
1.What caused the universe to exist?
I don’t know. Do you? There are some theories, the most promising is quantum fluctuations. We may never know and ’cause’ is a meaningless question when there is no time.
2.What explains the fine tuning of the universe?
The anthropic principle. I don’t want to explain it all here. Why is a hole the perfect shape of the puddle that resides in it?
3.Why is the universe rational?
I don’t understand the questions. I don’t think it is rational, I can’t begin to pretend to rationalize the universe, as a whole. I have a finite mind.
4.How did DNA and amino acids arise?
This is an area of ongoing research. Amino acids seem to arise as a natural property of the universe. It was probably RNA first, then DNA, possibly much later on. Given enough time and energy, the odds are, it will just happen.
5.Where did the genetic code come from?
See #4.
6.How do irreducibly complex enzyme chains evolve?
I don’t think there is such a thing. Meaningless question.
7.How do we account for the origin of 116 distinct language families?
I am not a linguist. How does different languages prove anything other than migration of early humans? Isolation is a great explanation for the divergence of languages.
8.Why did cities suddenly appear all over the world between 3,000 and 1,000BC?
They did not appear all over the world at that time. Some were as much as 6,000 year ago, in China, and as late as 700 years ago in the Americas. How odd, the cities in China dates before the biblical beginning of the universe?
9.How is independent thought possible in a world ruled by chance and necessity?
Seriously malformed question. I don’t there is something like truly independent thought, most of what we do is driven by chance and necessity.
10.How do we account for self-awareness?
It is either a side effect of really developed temporal lobes or has an evolutionary advantage to be self aware. Natural selection would favor individuals that have that little bit more drive to survive than those who who not self aware. That is my view, but I am not a biologist that specialises in neuroscience. Are you?
11.How is free will possible in a material universe?
Free will is an illusion. All of our actions are reactions to a previous cause or condition.
12.How do we account for conscience?
Another malformed question. As sense of good and evil? Empathy is a great account for it. Other species have these traits as well.
13.On what basis can we make moral judgements?
Empathy and social norms.
14.Why does suffering matter?
Again, empathy. I don’t want to suffer, I don’t want other members of my own species to suffer.
15.Why do human beings matter?
Humans matter because I am a human and I matter to myself and I care about other members of my own species. We want to survive and make the world better for everyone.
16.Why care about justice?
Empathy, empathy, empathy. To advance as a species, we need justice and there are very very strong natural selection pressures to have morality and justice.
17.How do we account for the almost universal belief in the supernatural?
Humans are pattern seekers and have over active agency detection. We want to assign meaning and patterns, even if the patterns are random. We don’t like unknowns. Go read The God Delusion for a more complete answer.
18.How do we know the supernatural does not exist?
Because we are adults and don’t believe in magic. Not a good answer? How about a more reasoned one: anything that violates the laws of the universe can not exist. The supernatural, by definition, violates the laws of the universe and does not exist.
19.How can we know if there is conscious existence after death?
By some sort of two way communication between the living and dead. Conscious existence depends on a living brain, and if the brain stops working, so does consciousness. A broken watch tells no time. A broken brain no longer thinks.
20.What accounts for the empty tomb, resurrection appearances and growth of the church?
People are gullible and want a happy lie and don’t want to cease existing. Simple as that. Jesus didn’t die for our sins. I highly doubt he even existed and the gospels are just a bunch of fairy tales.