Today we continue looking at the questions posed in this article - now for the questions 1 through 6.
1.What caused the universe to exist?
Here's our first loaded question (and merely pointing out that I'm pointing this out, doesn't invalidate the assertion). It's presuming the universe began to exist. I'm not even sure I buy that. The current state of the universe, as far as we can tell, began.
In either case, I haven't the faintest clue.
Why are you asking atheists, and and not physicists? My atheism also can't tell you how geckos stick to glass - but why would you ask atheists that?
Whatever I may or may not come to accept as true about that will be due to sufficient quantities of standards-qualifying evidence (at least to the best of my abilities). I'm fine with saying "I don't know" when there's insufficient data.
2.What explains the fine tuning of the universe?
Again, this is loaded. It's presuming that the universe is "finely tuned". When the vast (vast) majority of the universe - and even the majority of our own planet - is uninhabitable to human life without gobs of technology, the phrase "finely tuned" doesn't appear to apply.
What we have is a universe that barely supports life. To phrase that as "finely tuned" is assuming the conclusion, as "finely tuned" implies agency (who tuned it? But apologies if that's not the implication here).
The next question is - how or why do the mechanisms of the universe support life? (a much more unassuming question) To that, I don't know. Whatever we accept as the answer should be supported with sufficient positive evidence.
As an aside, the "God" answer doesn't make a lot of sense. It's almost self-refuting, to a degree. Why would the god need to "tune" the universe at all? Wouldn't that imply imperfection? You'd think the universe would be perfect out of the box. Why do we need air, water and food? Why do we need a sun that pumps out UV radiation, that the ozone layer then (mostly) filters out, in order to get just the good bits of the EM spectrum?
The hallmark of design is simplicity - clean, streamlined solutions. Heavily convoluted mechanisms show the lack of design.
Like with the "problem of unnecessary suffering", a limited god aligns with reality more than an omnipotent one.
3.Why is the universe rational?
I'm not sure I even understand the question. My best interpretation is asking, "Why is there order in the universe?"
I don't know. I'd love to know the answer to that question. "There's an invisible guy who wanted it that way" isn't a very satisfying answer, I must say.
Again, I'm not sure why this is being asked of atheists instead of physicists. Whatever the answer it is, it'd be rational to base it off sufficient amounts of positively supporting evidence, and not just "well, we don't know how else it could have happened."
He's right, though. There's a lot of these that we don't have answers to. And, if we're requiring demonstrably true answers, the author doesn't have the answers either.
4.How did DNA and amino acids arise?
For amino acids, please look up the Miller-Urey Experiments. At least for that one, we have some actual reproducible experiments that show that some kinds of amino acids can arise. (which is much more than theists can say for any of their claims)
For the specific ones that we have for modern life - unknown, still looking into it.
Don't ask physicists about this one - wrong field.
As for DNA... again, don't ask physicists... or atheists.
5.Where did the genetic code come from?
Presumably, if we figure out #4, we'll know this one too. Perhaps combine it with evolution and/or molecular evolution, and there's the beginnings of a specific organism's genetic code.
6.How do irreducibly complex enzyme chains evolve?
Again, loaded. Irreducible complexity isn't real. You may as well be asking me to explain the existence of fairies.
In the Dover Trial (2005), every example that was presented of irreducible complexity was shot down. It's an artificially manufactured "problem" that depends on arbitrary restrictions, like disallowing changes-of-function. An example is that infamous bacterial flagellum - once the change of function is factored in (a syringe instead of a "motor"), there's no longer a problem of "irreducible complexity".
What we've seen is the prior truckloads of supposed examples being all refuted - all the while - the creationists ignore that fact and continue looking for new examples that then shortly thereafter refuted, showing that - yet again - this new example also isn't irreducible.
So, what is this new example of yours?
I may be wrong about our state of knowledge about these questions. I'm being conservative about them. They're dense topics outside of my field of study. Let's just say that I'm unwilling to spend hours doing this homework for a person who can't even ask the right crowd for the information - especially when failing to have those answers does nothing to advance the author's case (whatever it may be).
It's okay to not know. That doesn't mean we have to default to magic for the answers.