Since the content of Nagel's article is off-topic, I won't discuss it further in this post. Except to say that it may indirectly suggest why some of us, frustrated by the inadequacies of Reductionism, Materialism, and Naturalism, have labeled the ultimate origins of Mind, Consciousness, and Language as a poetic mystery, instead of a topic for scientific analysis.: — Gnomon
Agree with your analysis and glad you found that essay worthwhile. The bottom line is naturalism is essentially defined against what it denies: most obviously ‘the supernatural’. Which, in effect, is taken to mean religion - and not only that, but ideas associated with religion, which are a very broad palette of ideas. Nagel, commenting on Peirce’s platonist musings, says that Peirce’s idea of the ‘inward sympathy’ with nature is alarming to many people:
The reason I call this view alarming is that it is hard to know what world picture to associate it with, and difficult to avoid the suspicion that the picture will be religious, or quasi-religious. Rationalism has always had a more religious flavor than empiricism. Even without God, the idea of a natural sympathy between the deepest truths of nature and the deepest layers of the human mind, which can be exploited to allow gradual development of a truer and truer conception of reality, makes us more at home in the universe than is secularly comfortable. The thought that the relation between mind and the world is something fundamental makes many people in this day and age nervous. I believe this is one manifestation of a fear of religion which has large and often pernicious consequences for modern intellectual life.
That is the preamble to the famous and frequently-quoted passage on the fear of religion:
In speaking of the fear of religion, I don't mean to refer to the entirely reasonable hostility toward certain established religions and religious institutions, in virtue of their objectionable moral doctrines, social policies, and political influence. Nor am I referring to the association of many religious beliefs with superstition and the acceptance of evident empirical falsehoods. I am talking about something much deeper--namely, the fear of religion itself. I speak from experience, being strongly subject to this fear myself. I want atheism to be true and am made uneasy by the fact that some of the most intelligent and well-informed people I know are religious believers. It isn't just that I don't believe in God and, naturally, hope that I'm right in my belief. It's that I hope there is no God! I don't want there to be a God; I don't want the universe to be like that.
My guess is that this cosmic authority problem is not a rare condition and that it is responsible for much of the scientism and reductionism of our time. One of the tendencies it supports is the ludicrous overuse of evolutionary biology to explain everything about life, including everything about the human mind. Darwin enabled modern secular culture to heave a great collective sigh of relief, by apparently providing a way to eliminate purpose, meaning, and design as fundamental features of the world. Instead they become epiphenomena, generated incidentally by a process that can be entirely explained by the operation of the non-teleological laws of physics on the material of which we and our environments are all composed. — Thomas Nagel
I've observed it countless times in over 12 years of online debates of just these kinds of questions. There is an undercurrent, a kind of firewall, against such ideas as 'inward sympathy' or 'eternal verities'
because they're associated with religion or at least with philosophical spirituality (which is the same thing for most people.)
So, this is the sense that 'fear of religion' drives a good deal of philosophical discussion, including naturalism about the mind. That is why I introduced it: not out of ‘finger pointing’ but because it is a real and potent undercurrent in debates about mind and cosmos.
Here Nagel turns to an analysis of the notion that reason itself has a naturalistic explanation, namely as a product of evolutionary adaptation - something which I’m sure nearly everyone accepts without questioning. It seems commonsense to say that ‘reason evolved in the service of survival’. He says, however, that
Unless it [this analysis] is coupled with an independent basis for confidence in reason, the evolutionary hypothesis is threatening rather than reassuring. It is consistent with continued confidence only if it amounts to the hypothesis that evolution has led to the existence of creatures, namely us, with a capacity for reasoning in whose validity we can have much stronger confidence than would be warranted merely from its having come into existence in that way. I have to be able to believe that the evolutionary explanation is consistent with the proposition that I follow the rules of logic because they are correct--not merely because I am biologically programmed to do so. But to believe that, I have to be justified independently in believing that they are correct. And this cannot be merely on the basis of my contingent psychological disposition, together with the hypothesis that it is the product of natural selection. I can have no justification for trusting a reasoning capacity I have as a consequence of natural selection, unless I am justified in trusting it simply in itself -- that is, believing what it tells me, in virtue of the content of the arguments it delivers. — Thomas Nagel
So notice here that Nagel rejects the idea that the faculty of reason can be seen as a product of adaptation - because to do so, is to undermine the sovereignty of reason. Which, one would hope, would be the last thing a philosopher would wish for.