I figured I'd start answering some of the questions. I will try to answer them from a Clarkian perspective (on my other blog here).
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.
When it is said, “things actually exist” in what manner do they exist? Do they exist contingently or necessarily? I do not believe there is any possible world, or state of affairs in which nothing could exist, since God is a necessary being, He exists in all possible worlds and states of affairs. But for the naturalist, he must affirm the necessary existence of the, parts or whole, universe or multi-verse.
Given that the universe has a finite age, why did the universe begin with time rather than in time?
If time were infinite, then, there would be an actual infinite series of events. Events can simply be moments of time or temporal parts; in any case, an actual infinite series of events are impossible. Since an actual infinite series of events would require an infinite series of events to elapse before this present moment. But if an actual infinite series of events occur before this present event, then this present event will never occur. With the existence of this present moment we properly conclude that time, like space and matter, is finite.
But if we assume time is eternal then are we not thereby committed to the eternality of space and matter? But this still pushes the fundamental question back further. Is time contingent or necessary? We obviously can imagine a state of timelessness so time cannot be thought of as necessary.
Christians can account for time either way. Presentists can either affirm time necessarily is an attribute of God or part of contingent creation. Eternalists argue God eternally created time, hence it’s a contingent property. In what way does the naturalist account for time?
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?
Intelligibility presupposes God. Presuppositionalists have been pointing this out for years. The very laws of logic, mathematics, knowledge, consciousness, induction, intentionality and freedom all have been taken as examples of the general principle that human thought and experience presupposes God. Science assumes God exists from the very start so it is unnecessary for the discipline to explain things in terms of God’s direct providence. Instead, it is to explain things in terms of God’s indirect providence as secondary causes.
Why is the physical universe so unimaginably large?
It is to bring glory to God. It is ostensive to God’s majesty.
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?
Who says it doesn’t? Many sensations in themselves are forms of beauty. Maybe the film Equilibrium illustrates this point well. Moreover, it does not logically follow that if God created beauty in the world God must create the whole world beautiful. Nor does such a view take into account God’s purposes.
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?
Who is to say it isn’t? Impressive by whom? This wasn’t God’s chief end in creation.
Why would God use biological evolution as a method for creation?
Who said he did? But even if we grant that he did, He could have sufficient reasons for doing so.
Why would God desire to create embodied moral agents, as opposed to unembodied minds (such as souls, spirits, or ghosts)?
God wanted to create humans to accomplish His will.
Why is the human mind dependent on the physical brain?
We have brains we use to think. Much like a musician uses an instrument to play music. It makes us physical. But we are not merely physical we are also spiritual. Five reasons can be given for this. First, our brains are affected by our thoughts. Second, if we think of a physical object, say, like a toaster, and a neurosurgeon opens up our brains, there would be no object in it. Third, our brains change but our minds do not. Forth, the only people that have access to their own thoughts are themselves. People have to ask what others are thinking. There is no way to know what a person is thinking without asking her. Fifth, we can think “about” things. We can think about what we want. So if the mind is merely the brain then there is no freedom. Actions, thoughts, and beliefs (including the belief that the mind is the brain) are a byproduct of chemical processes in the brain.
Did Australopithecus have a soul? What about homo habilis? Homo erectus? Neanderthals? Why or why not? (HT: Keith Parsons)
If they didn’t they were robots.
How do souls interact with physical matter? Do you have any answer that is not tantamount to “I don’t know?” (HT: Keith Parsons)
Well, before I can adequately answer the question I must ask, how does a person lift his arm? Is it chemicals in the brain that force him/her to lift it? Or is it simply, the person chooses to lift his arm? If you grant the possibility that a person can lift his arm by simply willing it, I see no logical reason to not think also God could create humans with souls that can command their bodies to perform actions. What is the natural mechanism that allows the body and mind to interact? This question rides on a category mistake. But why even think there must be a mechanism for them to interact? If a mechanism must be given, which I don’t see why logically it must, certainly if God sustains the universe, He can sustain the interaction between the body and soul. Perhaps Parson’s wants to know precisely how God sustains both. God has not revealed this, nor is it clear we could even understand with our limited finite minds. But God’s providence is a sufficient general explanation for how the body and mind interact. Parson’s begs the question if he thinks my account is insufficient, since it does not fit his naturalistic criteria of what, he thinks, is an adequate explanation.
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?
It depends on what is meant by “free will”? If by it one means the ability to choose what one most desires, then yes, we have freedom. It is the kind of freedom that is compatible with God’s providence. We can exercise freedom in some cases and not others because we are sinful in a fallen world.
Why are pain and pleasure so connected to the biological goals of survival and reproduction, but morally random?
Biological goals? If naturalism is true there is no goals in nature. It is all random chance. Pain and pleasure can have different moral statuses based on the commandments of God.
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?
Are animals and humans intrinsically valuable? Do they have moral worth? God created us intrinsically valuable with instincts such as self-preservation.
Does some moral end make it desierable for suffering to continue even when it serves no biological purpose?
Biological purpose? Notice you are borrowing teleological language. If God has a morally sufficient reason, which I believe he does, it is reasonable to think there is.
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?
Why is there social evil, i.e., instances of pain or suffering that results from the game-theoretic interactions of many individuals?
Why does God allow horrific suffering (and relatively little glorious pleasure)?
Why does horrific suffering often destroy a person, at least psychologically, and prevent them from growing morally, spiritually, and intellectually?
See my post God, why is there evil?
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?
This is fallacious. It begs the question, makes a hasty generalization, and fails to discredit the belief in question on the grounds of its origin.
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)
Well, there are no good reasons for me to believe in Zeus, Odin, Marduk, Ishtar, Osiris, Quetzalcoatl, Madame Pele, or Ahura-Mazda. However, I have good reasons to believe Christianity is true (e.g. common objections). Furthermore, to ask such a question is to falsely make a hasty generalization.