I will also make my replies, given my limited time at the moment, based on what I know rather than do any new research or provide links, I certainly can substantiate any of these positions, if prompted for the right reasons.
"Atheism, by definition, holds that there is no God and nothing beyond this world of matter, space, time, and energy."
"Atheism, by definition, holds that there is no God and nothing beyond this world of matter, space, time, and energy."
Well atheism does apply to the first clause but the second clause is an additional position, not held by all atheists and is a version of naturalism. Since I prefer the label naturalist this is not an issue for me, however let us note that many atheists would not agree to this second clause.
"Consistent with this viewpoint come a large number of necessary truths and the problems relating to them."
We can begin to see why Pruett needed to confuse atheism with naturalism as without doing this there is no worldview he could be addressing and all his questions can be answered in quite different ways depending on the worldview of the atheist. So really Pruett is asking 10 questions for Naturalists. What he means by "necessary truths" may or may not be a problem, we will see.
"Atheism is not made rational merely by the rejection of the evidences for God; it has its own wares to sell and difficulties to overcome."
Here is another question, the supposition that atheism is made rational. It is quite possible for people to be atheist for irrational or unconsidered reasons, due to where they were born, the worldview of their parents and their peers and so on, in much the same way as many theists and the accompanying worldview they have received, also hold such on an irrational or unconsidered basis. Still we can grant he is addressing naturalists who have considered their position.
"Here is a sampling of the kinds of issues which atheism is obliged to address."
This is another questionable supposition, are atheists obliged to address any of these issues. I will address them as a naturalist but also see if they are the type of issue that atheists are indeed obliged to answer.
The overwhelming consensus of science is that the entire cosmos (including space and time) came into existence at a finite point in the past. All of our observations, equations, and physical laws testify to a point of origin for this universe. In light of the troubling evidence for a beginning, and that we may not even be able to find a natural cause in principle, what explanation is given to the questions, "Why is there something rather than nothing?" and "Where did it all come from?"
Are atheists obliged to answer this? Many Buddhists do not think so. When asking a Buddhist about the origins of the universe, they could reply "I don't know, ask a scientist" and as for a being claiming to be a creator god, they would say that such a being is deluded and not a creator god. Interestingly, many of the same said Buddhists are not naturalists, contrary to Pruett's categorisation in his introduction, however some neo-Buddhism can and does reject all supernatural aspects, including the idea of 12 planes of existence, where such beings that could claim to be creator gods are meant to exist. Still this does not invalidate the Buddhist "Argument from Delusion" as a criticism of anyone who thinks there is a being who created the universe - how does anyone know that whatever the being has told or demonstrated to them, it is not deluded? Which is more likely, that such a being did create the universe or that they are deluded? Giving a positive answer to Pruett's question might settle the likelihood of this question just asked.
Why is this evidence "troubling"? The knowledge we have obtained, through our systematic empirical investigation of the universe we inhabit, is far beyond the simplistic and woefully inadequate and, often absurd, imaginings of any of the creation myths of any religion. We already know far, far more about the universe through such methods than any religion has been remotely able to provide. A key element of being able to do this was not accepting any question as settled, leaving it open to challenge in the light of new evidence, and seeking better answers given such new evidence.
So we do not currently know what happened before Plank time, we do know as best we can provisionally that there was a Big Bang and the age of the universe we inhabit - which is not the same as the cosmos, which Pruett also used in his question, and which I anyway reserve for everything including other universes, in parallel or prior to our one.
Much of this is speculation of course, however coherent it is extrapolated from what we do know in the pragmatic sense. We also know that Occam's Razor has sound statistical and probabilistic support from many tests of it within fields of empirical inquiry. So the simple answer is we do not know, but if one desires to attempt to answer we can say the hypothesis of a creator god is both on coherence and Occam principles well near the bottom of the pile of candidate answers. I have no need to dwell on this question any further as it is also incredibly unlikely that any answer would make the remotest substantive difference to my life. I have bigger questions to examine that might bear more significance to me as an atheist and as a naturalist.
The past several decades have added profoundly to our knowledge of chemistry, physics, and cosmology. It has become increasingly clear that we live in a universe finely tuned for the support of complex life. This fact is so universally acknowledged that even secular scientists have coined the term "Anthropic Principle" to describe it.Pruett puts many implicitly troubling biases in his question. Is this universe fine-tuned for life? Here we are on a particular type of small planet within a narrow orbit band where life could get started 10 billion years after the Big Bang, circling one of 100 billion stars out of 100 billion galaxies. I think it is likely there is other life on the universe but it certainly does not remotely look like it is finely tuned for life. So I disagree with Pruett's supposition here, it certainly does not look like an orderly and hospitable universe, since as far we can tell the range where the type of life we know could occur and survive is an incredibly minute portion of the universe.
How is it that we live in such an exquisitely fine-tuned universe? Even assuming that the universe could have popped out of nothingness, why should it have been such an orderly and hospitable one? Is there a scientific, testable answer for this question that does not simply appeal to imagination?
There are other issues with the question of "finely tuned" universal constants, we have no idea of what range of values they could take and so cannot derive any probabilities from this, we have no idea what type of universes could occur with different constants only that they would be radically different from ours but this tells us nothing about whether the equivalent of life is more or less likely in those other universes.
An additional and very brief illustration of the problems that Pruett fails to address is based on a pack of cards.If you shuffle a pack of cards and you take one hand out of it, you can look at the hand and calculate the probability of it occurring and this might be astronomically low. But the same would occur for whatever hand you did this calculation. The same applies to us looking at the this univese we inhabit. It might appear to be incredibly unlikely but the same would apply to any sentient being asking this question in their universe. So what?
Pruett is right be concerned with an appeal to imagination, on this we can agree. And claiming that some god set these constants to such values is such an appeal to imagination and following what is implicit in Pruett's question, we should certainly reject such an argument.
Update: Question 3 really belongs with the previous two so I have republished this post with the addition of my answer to question 3.
The problem of abiogenesis (the origin of the first lifeform) is one of the thorniest and most intractable issues in chemistry. Our increasing knowledge of microbiology and earth history has only added to the complexity of what needs to be explained. The simplest life is equivalent to modern bacteria, which is loaded with complex activity, information, and molecular "machines." The fossil record does not give evidence that there was a "prebiotic soup," or that there were any biological precursors to the first organisms, or that the atmosphere was the ideal mix to yield the necessary molecules, or that there was the expected long period of time between when the Earth could support life and when it actually appeared. Evolutionists regularly segregate the abiogenesis problem from the issue of evolution because (1) it is a challenge they'd rather not be saddled with, or (2) it is the most logical point for possible divine intervention. However, for the atheist there is no escaping this issue; they are obliged to seek out some purely natural explanation. What hope for an explanation do you have? Are you satisfied to have problems like this that are unanswered, or even unanswerable? In telling the tale of life on earth science writers often unconsciously use the word "miracle" for the appearance of the first organisms. What kind of evidence is needed before we are to actually accept that something like this really is a miracle?
Really, how on earth does the fossil record tell us anything about the prebiotic soup? In saying this Pruett displays a deep ignorance of this topic. Some evolutionary biologists do separate origins from the evolution of life but simply because their speciality is the evolution of life, abiogensis is not what they study. There are other skills and specialisations required to study the origins of life, of which insights from evolutionary biology can provide data, ideas and challenges. This does not stop evolutionary biologists being interested, if they choose, in this question and even getting involved in it or at least following the literature and having an opinion on which theory is more likely correct. Pruett seeks to manufacture a problem or an issue which does not really exist here.
Now is it the thorniest and most intractable problem, I don't think so. The fact that Pruett asks this is indicative that he really does not comprehend the nature of the work in this field. Is it one of the most interesting questions, surely yes. As for intractable it is not like we have no idea of the origins of life, indeed it is the opposite, we already have too many theories! For example of a few more than just possible but plausible explanations we have Kaufmann's Autocatalysis, Maturana and Varela's autopoesis, Eigen's hypercyles, Cairn-Smith's clay and genetic takeover theory, iron-sulfur world theory and these are the ones that just sprang to mind, there are quite a few others. Of course we do not know which one is correct and all the current ones have some shortcomings but there is nothing to indicate that this is work in progress with much of great interest we are still likely to find. It most certainly is not at all intractable.
Are these current unanswered, yes to any degree of objective inter-subjective agreement although we have plenty of interesting and fascinating hypotheses coherent and consistent with what else we know. Ara these unanswerable? Not at all! Well, they are certainly not answerable in the way that any questions of a supposed creator are!
What hope is there for an answer, in this case it is surely far higher than resolving what happened before Planck time and far, far higher than the demonstration of any miraculous origin of life. Maybe scientists have used this word but so what? No scientist practising in this field, such as those I listed above, as far as I know uses this term and, even if they did, this is not preventing them seeking an answer from nature as to how life came about. Pruett might be happy with a non-explanation and a non-answer such as miracle but no-one who is truly interested in finding out would find that acceptable.
I am beginning to see a pattern here in the biased presumptions Pruett brings to his questions. If we had settled for the comforting falsehoods of religious explanations we - and Pruett himself - would have known far less about the origins and order of the universe and abiogenesis. It was only by questioning and rejecting those comforting explanations and seeking the truth in answers in nature that we now know what we know. Pruett seems to have this upside down, we have the latest and best answers to these age old questons. The knowledge upon which Pruett - however inadequately and biased he forms his questions - are the answers that any naturalist would provide.
Part 2 tomorrow.