As I hope to show in my upcoming essays, most of naturalism's "nature" is terribly impoverished, anemic even. By exalting nature beyond its dignity as a creature, naturalism ends up honoring nature in the breach, leaving her without both a proper character of her own and any 'supremacy' over man apart from his arbitrary manipulations of her resources. Leeching nature of metaphysics is naturalism's greatest assault on nature. Without finality, for instance, natural laws have no proper connection between cause and effect. Likewise, without essence, there are no fermions and bosons all the way down, as Rosenberg puts it, since such things are either are what they are in essence, and this is discoverable by humans, or they are void of any essential character, in which case they are mere constructivist nomenclators which, as a result, can't be said to define the rest of reality. Rosenberg's précis is rather long, and Dr. Feser's analysis is only as short as it ought to be, but I highly recommend reading both posts in full. For my part, at this juncture, I will only note three oddities, from among many, in Rosenberg's essay. As Dr. Feser's analysis shows, Rosenberg's (or any committed naturalist's) metaphysical problem is trying to have his cake for later and eat it now too.
First example. When Rosenberg says, "What science has discovered about reality can’t be packaged into whodunit narratives about motives and actions. … Our demand for plotted narratives is the greatest obstacle to getting a grip on reality", he does so in a paragraph that tells us a story about the world and man's place in it. Once upon a time, humans believed in purpose, magic, and divine realities, but along came the Light of Science and now humans are free (free, that is, from the illusion that they are free). For good measure, in his best nanny-voice, Rosenberg adds a moral for all you younguns still hankering after narrative coherence: "It’s also what greases the skids down the slippery slope to religion’s 'greatest story ever told.' Scientism helps us see how mistaken the demand for stories instead of theories really is." The End. To Rosenberg's claim that concrete organized complexity could not possibly have come about in any other way than by Darwinian "passive envrionmental filtration," I can only retort that our sense of the world cannot come about in any other way than in a narrative mode. So if the apparent conceptual ineluctability of the former is proof of its truth, then the performative ineluctablity of narrative metaphysics is proof of its truth, in which case the former can't cut against the latter as Rosenberg wants it to do.
[A year or two ago I wrote a lengthy post about the irreducibly aesthetic-narrative nature of human existence, and how this points to God. Cf.  below for a key quotation from that post in which Bertrand Russell anticipates Rosenberg's narrative anti-narrativism.]
Second example. In his third paragraph, Rosenberg alludes to the methodological fallibility of science, but then brushes it aside so he can get on with his nihilistic narrative. He says one reason more scientists don't draw radically nihilistic, eliminative conclusions from their research is because "science is fallible and scientists are taught never to be definitive even about their own conclusions; the persistent questions are so broad that no scientist’s research program addresses them directly, and few are prepared to stick their necks out beyond their specialty when they don’t have to." Einstein quipped that the man of science makes a poor philosopher, but at least the way Rosenberg portrays them makes them brilliant thinkers. Scientists aren't prepared to stick their necks out––while Rosenberg is quite willing to stick his neck out and up and then lower his nose––about sweeping metaphysical nihilism most likely because they instinctively grasp how destructive naturalistic nihilism would be for their actual work. You can't very well choose to pursue a new line of research, or persist in an old one, if the cosmos literally has no beliefs, desires, purposes, or wills.
Even so, Rosenberg tries to ride over the main difficulty under a cloak of philosophical synthesis. There is an inverse ratio between scientific certainty and scientific rigor. One of the most cherished aspects of science for "scientismatics" (my term of art for devotees of scientism) is its relentless self-correcting process, especially in contrast to dogmatism, revelation, etc. That being so, it is impossible for a scientismatic––a term which Rosenberg would gleefully embrace for himself––to endorse any reigning scientific account of the world as "the final word," since doing so makes a scientific Weltbild into a dogma or revelation. As such, all the weight Rosenberg et alii put on the account of the world according to current science should literally only be taken ex hypothesi. But then how can a hypothesis ground an entire worldview? Indeed, how can the cosmos as a whole, much less the eternal existence of the cosmos, be ascertained by scientific means? As Stanley Jaki has argued in numerous places, the cosmos, as a single coherent whole, is an object of scientific belief, not a rational deliverance of science itself. Likewise, how does one "test for" causality without assuming it? Or how does one "test for" the law of identity if there are no 'minds' over against brute matter to which that law can appear as "self-evident"? It follows that scientism's ideological security devolves to the quality of its metaphysics, but, alas, since physics is the structure of nature, metaphysics has no place in scientism. Basically, then, Rosenberg wants to subsume metaphysics to sheer science, but he can only do so by a metaphysical inflation of "science as we know it" to "the way the world really is." In any case, the foregoing doesn't even touch the problem, raised so acutely by Dr. Feser in this post et alias, as to what a scientific "theory" can even mean (that word again!) in naturalism.
Third example of Rosenberg's eat-cake-have-cake modus operandi. In the third section of the essay, Rosenberg gingerly piles on against finality, purpose, and design by showing how Darwinian natural selection provides a wholly mechanistic account of organized complexity as "the inevitable result of" the second law of thermodynamics. I first encountered Rosenberg's "a priori Darwinism" (my term of art) reading some lectures he gave at Duke a few years ago about Darwinism as "the only game in town." In this latest essay he espouses the same thing by saying Darwinian natural selection follows deductively (and thus irreformably) from the second law of thermodynamics: "Any explanation of the very existence of even the slightest adaptation must be Darwinian. … [G]iven the 2d law, the only possible source of adaptations in the universe that was originally bereft of them is the process Darwin discovered." A trenchant narrative, to be sure, but how is this any longer science? A scientific theory should be falsifiable, but by saying that Darwinism is a logical necessity, Rosenberg pretty much makes Darwinism an axiom of reason. Are we seriously to believe that Darwin's meticulous pondering over mounds and mounds of biological data, after centuries of similar pondering by great explorers, only resulted in a virtual law of logic? I think Darwin would be nonplussed about the supposed obviousness of his insight.
Why does Rosenberg insist Darwinism is the only possible account of organized complexity? I quote:
Scientism, and for that matter science too, needs an explanation of adaptation in general that starts from the complete absence of any. Otherwise, we have not explained how even the simplest, most minimal sliver of adaptation could have emerged in a world with zero adaptation. Since the process of adaptational evolution is, unlike the basic processes in physics, a one-way past to future process, it can only be driven by the 2d law of thermodynamics, since that is the source of all irreversible processes in the universe.
Leaving aside the historically naive hubris which such an account displays––since the history of science is strewn with the corpses of past "final theories" which turn out to be but limiting cases of some higher law––Rosenberg subtly contradicts his a priori Darwinism with reference, in the first section of the essay, to the "fundamental laws of nature [as] mostly timeless mathematical truths that work just as well backwards as forward…." All the biological and organic design we seem to see in the world is "just the foresightless play of fermions and bosons producing, in us conspiracy-theorists, the illusion of purpose." Moreover, "if physics fixes all the facts, it could not have turned out any other way." By coupling "timeless mathematical laws" to temporal 'design' in a rigorously Darwinian way, however, Rosenberg faces two problems. First, what could "trigger" timeless mathematical laws to instantiate temporal sub-mathematical phenomena? Stephen Hawking and, I believe, John Wheeler noted that, for all their beauty and simplicity, the laws of physics lack the ability to breath life into their own content, to give flight to their amazing idealized designs. As Nancy Cartwright has argued in several places, "natural law" requires a lawgiver, which makes Rosenberg's surprisingly blithe reliance on such a Platonic idea as timeless, immaterial, abstract forms a strong pointer toward an eternal lawgiver.
The second problem is that if, somehow, timeless, mindless, and volitionless mathematical laws could make the real world real, and if the result as we now find it "could not have happened in any other way," then the world as we now see it is also a timeless reality, a mere derivation of those timeless mathematical laws. For the timelessness of the most basic mathematical laws, combined with their mysterious but deterministic 'fruition' in the irreversible world as we know it, entails that the irreversible world is necessarily a function of reversible laws. If that were true, however, the basic laws would not be reversible, since their actual operations necessarily result in irreversible phenomena, and do so in a timelessly (eternally). So, the universe is either the way it is from all time, in which case responsible scientific thinkering succumbs to sheer a priori idealism, or the world could have developed other than it actually did so, and scientismatic necessitarianism is false. So, in turn, is Rosenberg's naturalism false.
 Yeah, I just made that word up. Entation. It means the act of something actually existing, or a case thereof. Meh. I like it.
 From my post, "The center of the circle…":Physics has demonstrated time and again the irreducibly specific nature of the material universe, a specificity that shouts contingency. For, anything that is one way specifically could exist another way specifically. And this 'could' is the essence of contingency. The universe demonstrates quantifiable specificity on every level, in every nook and cranny, and this is because it is the farthest thing from an eternal, infinite, homogeneous, undifferentiable, nonspecific pantheistic eternal cosmos. From another perspective, however, the universe is a great light show for children. Are they wrong to see faces in the heavens when physicists are busy seeing the heavens in our faces? (We are all stardust…) Is the poet wrong to see the world as a great symphony of light when the physicist is busy seeing the world as a cacophony of dark matter? Neither one is right or wrong in their proper modes of perception. Only when they impose their aesthetic lens on someone using a different lens, will their be a dispute. Only when the poet tries to strangle the physicist's vision with a glistening portrait of Mother Nature, or the physicists tries to explode the poet's vision with a humming portrait of the unified filed theory, will there be a clash. The thing that unites them is not their specific vision of the cosmos (i.e., how big its circumference is or what its texture is), but their bedrock commitment to the idea that the cosmos has a shape at all. Just as no section of the circle can escape the omnipresent primacy of the invisible center
Consider the Ecclesiastes-like somberness of Bertrand Russell's words in "A Free Man's Worship" (1902):…even more purposeless, more void of meaning, is the world which Science presents for our belief. Amid such a world, if anywhere, our ideals henceforward must find a home. That Man is the product of causes which had no prevision of the end they were achieving; that his origin, his growth, his hopes and fears, his loves and his beliefs, are but the outcome of accidental collocations of atoms; that no fire, no heroism, no intensity of thought and feeling, can preserve an individual life beyond the grave; that all the labors of the ages, all the devotion, all the inspiration, all the noonday brightness of human genius, are destined to extinction in the vast death of the solar system, and that the whole temple of Man’s achievement must inevitably be buried beneath the debris of a universe in ruins—all these things, if not quite beyond dispute, are yet so nearly certain, that no philosophy which rejects them can hope to stand. Only within the scaffolding of these truths, only on the firm foundation of unyielding despair, can the soul’s habitation henceforth be safely built.
There are at least two great ironies here. One is that these words are surely among the more immortal words penned by man, though they are driven by a consuming vision of the mortality of all man's words and works. (Methinks he protests too much!) Art, including beautiful rhetoric, is hoisted as a flag of protest against the futility and finality of the world. Art repudiates doom. Art is created as a lasting sign of the human trace upon the world. So even when it accentuates or, as the case may be, glorifies, the frailty of all human efforts, it is intended to outlast the passing flux and be a lasting marker of the unlasting, an intransigent icon of the transient, a feud with futility. (I explored this topic in my story, "From the Forest Itself", if you care to brave the telling of that tortu(r)ous tale.)
In any case, the second irony in Russell's is what really concerns us. Even by painting such a grim picture of the world, Russell did just that––painted a picture. He took a heap of meaningless debris and formed it into a coherent collage of despair. Even when he said the universe is meaningless, he ascribed to it a total meaning, namely, utter meaninglessness. I could just as easily imagine an artist taking a heap of garbage and calling it "Life". It may strike hard against hope and good cheer, but it still strikes artistically, meaningfully, 'shapefully'. We simply cannot escape giving a larger coherent shape to the world as we experience it, even when we say the world shape is ugly, erratic, and pointless. And this is a crucial inevitability. For to live as creatures that inevitably and automatically give a shape to our experience, is to live as beings inevitably and automatically confronted by the point of origin in the same way every segment of a circle is confronted with its central point. The reason the world inevitably takes on a shape in our eyes, is because the world is radically contingent on God as its shapeless shaper, as the uncreated creator. This, then, is what the cosmological argument is getting at: even if the world seems like bad art (as criticisms of the design argument would have it), it still seems like art, and ineluctably so, because it depends for its existence on God in the same way a circle cannot help but be shaped by its center.
The aim of science is to give a coherent picture of the world. But if science cannot account for its own 'shaping' tendency, it falls to religion to give that ultimate level of order and aesthetic depth to the world. Believing in the universe––an empirical object which we can never observe––is necessary for understanding it and admiring it as one 'piece'. Likewise, believing in the Creator, and beholding the world as one 'piece', is even more crucial for knowing and admiring nature's beauty. Dostoevsky is right: The world will be saved by beauty. The world can only be called 'the world' if it is beheld in the mind's eye as one thing with one ultimate shape. And that shape is nothing other than a shape-transcending abstractness as incense vessel, shining mirror, rocking cradle for the glory of God among us. Just as the specific events in the flux of spacetime all depend on God as their uncaused cause, so the entire structure of the cosmos depends for God as its absolute index of shape.