Hello A-G! It seems you have thrown down the gauntlet: This is a most incisive list of questions designed to challenge the most fundamental assumptions of the metaphysical naturalists out there. Well done!
Of course, not every metaphysical naturalist is an atheist (the theme of this thread). Many are simply agnostic. But if anyone will seriously consider these questions, they may find they are able to broaden their perspectives thereby. To anyone but an atheist, these are not "dangerous questions."
I often wonder about the psychology of atheism, what motivates it, and what atheists hope to achieve/obtain from it. I guess in the end, atheists somehow believe that God is dangerous in some way to their personal well-being (however understood). But this strikes me as being an absolute inversion of natural truth. Still, inverted truth seems to have many champions these days. I wouldn't know how else to explain a Michael Newdow, a Richard Lewontin, a Noam Chomsky, et al., than that they are "inverted" (unnatural) people, trying to invert the world into a "more pleasing shape." (E.g., as much unlike the one God "shaped" as possible.... FWIW
I also think you're right to call atheism a "religion" -- an inverted one, an ersatz one, to be sure; but a religion nonetheless. Methinks it is a religion devoted to the worship, not of God, but of "Me." Thanks for this great post!
> To anyone but an atheist, these are not "dangerous questions."
Nor are they "dangerous" to atheists.
Consider:
Q1: " there was a beginning, an uncaused cause, i.e. God!"
A1: i.e.... somethign entirely else. "I don't know" does not equal God.
Q2: "i.e. a life force"
A2: Scientists ahve made living things (polio virii) from non-living molecular components. No "life force" was injected.
Q3: "Why does the organism have a will to live?"
A3: Because if it didn't, it wouldn't live, and thus wouldn't reproduce.
Q4: "the incredibly delicate physical constants, physical laws ..."
A4: Change the laws, and we become impossible. But change the laws and something *else* becomes possible.
Q5: "why our vision and mind are tuned to a particular selection of four coordinates"
A5: These are the ones that are useful for perception of our environment.
Q6: "He'd have to explain how biological semiosis arose through natural means."
A6: Look up the experiments of Urey, and the follow-on experiments of Fox.
Q7: "i.e. cardiovascular without the lungs, nervous system without the brain"
A7: Lungs and Brains aren't needed for life; note your nearest amoeba.
Q8-a: "explain how eyes developed concurrently across phyla – i.e. vertebrates and invertebrates "
A8-a: Vertebrates evolved from invertebrates after the development of eyes. Look up Pikaia.
Q8-b: "virtually no new body plans since the Cambrian Explosion"
A8-b: Because optimums can be reached. There's a reason why really fast submersibles tend to look like fish, and why subsonic aircraft look like birds or insects (helicopters). Natural forces mean that certain forms function better than others. How effective would a fish shaped like, say, a mastodon be?
Q9: "He’d have to have a natural explanation for qualia "
A9: Without them you die and don't reproduce.
Not a one of these means either that God exists or doesn't exist. The ability to answer does not negate God, the inability to answer does nto make God inevitable.
> I often wonder about the psychology of atheism, what motivates it, and what atheists hope to achieve/obtain from it.
What do you hope to achieve by believing that the world is round, or that the Earh goes round the sun? It makes no difference to the lives of the vast majority of people. You believe things because they are, to your judgement based on the evidence at hand, so.
A better thign to wonder about is the psychology of those who demand that anyone who believes very differently about the supernatural is somehow sick or evil.
I've had a tendency over the years to view atheists by three types: the ordinary atheist who doesn't believe but doesn't mind if you do, the pondering atheist who wants to present his reasoning (as if always reevaluating his own thoughts) and the evangelical atheist who insists that nobody else ought believe in God. IMHO, the Newdow's and Lewontin's are evangelical - using every power at their disposal to influence others.
Would it be too simplistic to posit that the above mentioned characters are the centers of their own universes and that the existence of God spoils such narcissism? Therefore, His existence shall be denied not because it causes Him to not exist, but because it allows self-centered, postmodern universes to temporarily prosper "for a season."