Somewhat recently I’ve become aware of two seemingly distinct arguments in favor of the idea that the conjunction of evolution and naturalism is prima facie more probable than the conjunction of evolution and theism. The first argument comes from Paul Draper who claims that the brutality of natural selection provides strong evidence against theism.
“For a variety of biological and ecological reasons, organisms compete for survival, with some having an advantage in the struggle for survival over others; as a result, many organisms, including many sentient beings, never flourish because they die before maturity, many others barely survive, but languish for most or all of their lives, and those that reach maturity and flourish for much of their lives usually languish in old age; in the case of human beings and some nonhuman animals as well, languishing often involves intense or prolonged suffering… [This] is extremely surprising given theism. It is not what one would expect to find in a living world created by a perfect God.” 
Natural selection, Draper argues, appears to cause large quantities of unnecessary suffering and hence is not a mechanism that a theistic God (i.e. an all-knowing, all powerful, all-good being) would have employed in creating the biological diversity and complexity we presently observe.
The second argument comes from Peter Milikan who argues that it is puzzling why a theistic God would utilize evolution if substance dualism (which is sometimes taken to be a necessary commitment of theism) were true.
“Most religions, including Christianity, would have us believe that our thoughts can exist quite independently of the brain, unimpaired, even enhanced after the brain and the whole body have been completely destroyed. Now, if this were true, that our mental capacities could exist quite independently of the physical brain, then one has to wonder what on earth has been going on during evolutionary history. The human brain has been growing larger and larger, demanding huge quantities of calories and nutrients to be developed and maintained, and expanding even to the extent of making childbirth seriously dangerous for human mothers. Yet if our thoughts takes place in immaterial soul, which can function perfectly well independently of the physical brain, then it’s utterly mysterious why this expensive and dangerous evolutionary progression should have taken place at all.” 
Milikan seems to be arguing two things here: (1) evolution’s application of selection pressures upon increasing neurological complexity over the course of evolutionary history provides grounds for believing that materialism is likely true, and hence that substance dualism is likely false, and (2) since theism (generally speaking, though not always) is seen as committed to the truth of substance dualism, that theism is likely false as well.
With all of that said, what are people’s thoughts? Do people think that the above two arguments are actually distinct? And if they are distinct, do they provide prima facie evidence for atheism? And finally, what do people think might be some compelling theistic objections that could be given in response to them?