There's a dilemma for intellectual skeptics of neo-Darwinism like Thomas Nagel and Noam Chomsky. Their philosophical naturalism commits them to excluding the solution of God.

http://www.firstthings.com/web-exclusiv ... our-office is a commentary. It states “On the new view of nature inaugurated by Galileo and Descartes, the material world is comprised of nothing more than colorless, odorless, soundless, meaningless, purposeless particles in motion, describable in purely mathematical terms… Thomas Nagel [takes] the bizarre implications of materialism … to constitute a compelling reason to reject materialism and look for an alternative way to formulate naturalism. Hence the subtitle of his new book Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False. Nagel does not reject evolution per se , but only the standard reductionist interpretation of evolutionary processes. But neither does he embrace theistic evolution. (His atheism seems as firm as it was in his earlier book The Last Word… the possibility of a teleology or directedness that is inherent to the natural order [means] … consciousness in turn cannot easily be explained in reductive terms…. Value, Nagel insists, is a real feature of the world rather than a projection of our subjective desires or sentiments… for phenomena like life, consciousness, rationality, and value to arise in the later stages of the history of the universe, we have to suppose they were somehow “latent in the nature of things” from the beginning… an effect must in some way be contained in its total cause…

“Nagel extends his attack on materialistic reductionism—which he describes as the thesis that physics provides a complete explanation of everything—well beyond the mind-body problem. He argues that evolutionary biology is fundamentally flawed and that physics also needs to be rethought—that we need a new way to do science. Nagel’s new way is teleological—scientific explanations need to invoke goals, not just mechanistic causes… aspects of the mind are, therefore, forever beyond the reach of physical explanation… evolutionary theory taken on its own (without the philosophical add-on) is incomplete. Incompleteness means that the theory cannot fully explain important biological events… A complete account of consciousness must show that consciousness was “something to be expected.” Nagel thinks that evolutionary theory as we now have it fails in this regard… consider the more global fact that the universe contains life and intelligence and consciousness at some time in its total history. What’s the probability of that, given the universe’s initial state?... When a theory says that X was improbable, this does not mean that the theory says that X is unintelligible: the final result could be improbable even though each step in the process was highly likely…
Charles Darwin and Alfred Russel Wallace disagreed about how the human capacity for abstract theoretical reasoning should be explained. Darwin saw it as a byproduct. There was selection for reasoning well in situations that made a difference for survival and reproduction, and our capacity to reason about mathematics and natural science and philosophy is a happy byproduct. Wallace, on the other hand, thought that a spiritualistic explanation was needed. Nagel finds Darwin’s side effect account “very far-fetched,” but he does not say why.
For Nagel, the statement that causing suffering is bad is like the statement that the Rocky Mountains are more than 10,000 feet tall—both are true independently of whether anyone thinks they are true. Nagel thinks “moral realism is incompatible with a Darwinian account of the evolutionary influence on our faculties of moral and evaluative judgment.” He resolves the conflict as follows: “since moral realism is true, a Darwinian account of the motives underlying moral judgment must be false.”.. Darwin argued that moral norms enjoining altruistic behavior are now widespread in human societies because groups that internalized and complied with these norms outcompeted groups that did not. Whether it is true that we ought to act altruistically isn’t something that Darwin or more recent biologists need to take a stand on… Nagel’s reason for thinking that there is a conflict between evolutionary theory and moral realism [is] evolutionary theory underwrites a parsimony argument against moral realism.
Nagel’s answer is that science should go teleological: concepts of goal and purpose need to be used in new scientific theories. This suggestion conflicts with the dominant scientific tradition of Galileo, Newton, and their successors. Teleology is the most radical idea in Nagel’s book. Nagel says that teleology means that “things happen because they are on a path that leads to certain outcomes.” Suppose that X caused Y and that Y then caused Z. A teleological explanation of Y will say that it occurred because it was on the path from X to Z. This explanation of Y cites Z, which occurs later than Y… Nagel also says that conventional (non-teleological) physics describes “how each state of the universe evolved from its immediate predecessor,” but a teleological science will be different: “teleology requires that [some] successor states . . . have a significantly higher probability than is entailed by the laws of physics alone.”.. Nagel’s thesis is not just that there are true teleological statements about the emergence of life, mind, and consciousness, but that these statements cannot be explained by a purely causal/materialistic science. Only then does his teleology go beyond what materialistic reductionism allows… it would help if Nagel identified some modest phenomenon that clearly has that sort of explanation. He never does.”

Nagel doesn’t deliver.
Not only doesn’t Nagel deliver: he strikes out three times, with three distinct arguments as to why we should reject natural selection in its current, materialist form. Each of the book’s three main thrusts – involving consciousness, theoretical knowledge, and morality – begets a unique species of error.
In Mind and Cosmos, Nagel claims that the failure of a materialist reduction of mind to matter has implications for science in general, including natural selection. Since the brain does not adequately explain consciousness, neither can natural selection, even if it adequately explains the brain. The mind-body problem becomes the mind-evolution problem. Nagel supplements his argument from consciousness with two others, to the effect that natural selection is incompatible with the possibility of theoretical knowledge and the objectivity of ethical judgments. But he also more generally entertains the notion that natural selection is too implausible to explain much of anything.
Nagel’s argument from consciousness suggests to him that the problem with natural selection is its materialism. And so his solution is to amend natural selection to incorporate a non-materialist explanation in which mind is a basic feature of the universe.
Nagel’s teleological principle works such that the available mutations upon which natural selection operates must be determined in part by a pre-existing tendency of the universe – itself not reducible to physics or chemistry or another other causal explanation afforded by materialist natural science – to produce beings that are capable of consciousness, theoretical knowledge, and objective judgments of value.
when it comes to choosing between admitting to the intractability of the mind-body problem and modifying natural selection with a teleological principle, however strange that might seem, teleology wins the day.
Nagel is worried that materialist natural selection undermines moral realism, or the view that moral propositions (for example “murder is wrong”) purport to objectively describe the world… because there is no adaptive value to recognizing evaluative truths
Where Street takes this incompatibility of natural selection and moral realism a reason to reject moral realism, Nagel takes it as a reason to reject natural selection in its materialist form,
The charge of circularity that Nagel levels in his argument from cognition is based entirely on the kind of misunderstanding that is surprising for a philosopher of his caliber. It is not circular to argue that logical judgments have adaptive value via an evolutionary account that depends on the accuracy of logical judgments.

pure snark. "The shoddy reasoning of a once-great thinker," Steven Pinker tweeted. The Weekly Standard quoted the philosopher Daniel Dennett calling Nagel a member of a "retrograde gang" whose work "isn't worth anything—it's cute and it's clever and it's not worth a damn."
The critics have focused much of their ire on what Nagel calls "natural teleology," the hypothesis that the universe has an internal logic that inevitably drives matter from nonliving to living, from simple to complex, from chemistry to consciousness, from instinctual to intellectual.
According to orthodox Darwinism, nature has no goals, no direction, no inevitable outcomes. Jerry Coyne, an evolutionary biologist at the University of Chicago, is among those who took umbrage. When I asked him to comment for this article, he wrote, "Nagel is a teleologist, and although not an explicit creationist, his views are pretty much anti-science and not worth highlighting. However, that's The Chronicle's decision: If they want an article on astrology (which is the equivalent of what Nagel is saying), well, fine and good."
N agel didn't help his cause by (a) being a philosopher opining on science; (b) being alarmingly nice to intelligent-design theorists; and (c) writing in a convoluted style that made him sound unconvinced of his own ideas
he is an atheist and has no truck with supernatural gods. He views the ID crowd the way a broad-minded capitalist would sum up Marx: right in his critique, wrong in his solutions. But ID, he says, does contain criticisms of evolutionary theory that should be taken seriously.
Dawkins writing sentences like, "I have described atonement, the central doctrine of Christianity, as vicious, sadomasochistic, and repellent. We should also dismiss it as barking mad. ..." In that climate, saying anything nice at all about religion is a tactical error.
Kevin Kelly, founding editor of Wired, made the case for teleology as clearly as could be in his book What Technology Wants: "Evolution ... has an inherent direction, shaped by the nature of matter and energy." That is, there may be laws of nature that push the universe toward the creation of life and mind. Not a supernatural god, but laws as basic and fundamental as those of thermodynamics. Robert Wright said much the same in Nonzero: The Logic of Human Destiny: "This book is a full-throated argument for destiny in the sense of direction."
biologists usually argue that when you do get progress, it came about by accident.
When you have millions of species taking random walks through the wilds of genetic variation and natural selection, some will, by the luck of the draw, become more complex and more capable.
some scientists think that increases in complexity also happen "actively," that is, driven by physical laws that directly favor increases in complexity. As a group, these scientists have no sympathy for intelligent design. However, they do see reasons to think that seen as a whole, life does go from simple to complex, from instinctual to intellectual. And they are asking if there are fundamental laws of nature that make it happen.
a "zero-force evolutionary law," which posits that diversity and complexity will necessarily increase even without environmental change… life exhibits "dynamic kinetic stability," in which self-replicating systems become more stable through becoming more complex—and are therefore inherently driven to do so.
"functional information," which measures the number of functions and relationships an organism has relative to its environment.
energy-rate density against the emergence of new species, the clear result is an overall increase in complexity over time.
"He's done so little serious homework," says Michael Ruse. "He just dismisses origin-of-life studies without any indication that he's done any work on it whatsoever."
Nagel's goal was valid: to point out that fundamental questions of origins, evolution, and intelligence remain unanswered, and to question whether current ways of thinking are up to the task. A really good book on this subject would need to be both scientific and philosophical: scientific to show what is known, philosophical to show how to go beyond what is known.