At this point I would like to jump ahead to Harris's chapters 2, the Mystery of Consciousness. I'll come back to the intervening parts later (or maybe not).
In chapter 2, Harris struggles with coming to terms with the fact and nature of consciousness in terms of modern materialist philosophy.
And the question of how consciousness relates to the physical world remains famously unresolved... Whatever the ultimate relationship between consciousness and matter, almost everyone will agree that at some point in the development of complex organisms like ourselves, consciousness seems to emerge. This emergence does not depend on a change of materials, for you and I are both of the same atoms as a fern or a ham sandwich. Instead, the birth of consciousness must be the result of organization. Arranging atoms in certain ways appears to bring about an experience of being that very collection of atoms. This is undoubtedly one of the deepest mysteries given to us to contemplate.
Harris's perplexity is a function of the materialist philosophy he takes for granted. This philosophy, having its origin in the Enlightenment, holds that reality is composed of bits of brute matter (or energy fields or whatever) banging together, the "clockwork universe" thought to have been implied by Newton's discoveries. What's important here is that one of the points of this philosophy was to banish Aristotle's formal and final causes from nature. These causes are fundamental to our experience of consciousness. My thoughts are "directed" at their object as an arrow to a target (an example of final causality). And I can understand why the angles of a triangle must add to 180 degrees (which is to understand the formal causality of a triangle). Aristotle thought this "directedness" was a basic feature of nature itself, which was why consciousness did not seem to him the scandal that it is to modern philosophy. Fire is "directed" to heat, acorns are "directed" to grow into oak trees, and minds are "directed" to understanding. And our ability to understand formal causality is simply a reflection of the fact that formal causality is part of nature itself.
But how are such experiences to be understood in the clockwork universe of the materialist? As Edward Feser's pithy expression puts it, formal and final causality were "swept under the rug of the mind." The directedness of nature is not something we discover in nature but is rather read into nature by the mind. This creates a problem, however, when we try to understand the mind itself in terms of the clockwork universe. For our experience of the mind just is those experiences of formal and final causality that were banished in principle from the materialist universe. This makes the mind more than merely a mystery for the materialist; it makes it a scandal. The difference being that a scandal is not in principle solvable in terms of the fundamental principles of a philosophy, while a mystery is in principle intelligible, even if practically it may never be fully illuminated.
The temptation in the face of scandal is to deny its basis, and this has been done by some modern philosophers who simply deny the reality of the mind (e.g. Daniel Dennett), dismissing it as an illusion of the material brain (a position that does not make sense - more on that later). Harris, to his credit, is unwilling to simply dismiss the significance of our experience of consciousness: "Consciousness is the one thing in this universe that cannot be an illusion."
The next few pages of Waking Up consist of Harris further wrestling with the incongruity of consciousness in a materialist universe:
First there is a physical world, unconscious and seething with unperceived events; then, by virtue of some physical property or process, consciousness itself springs, or staggers, into being. This idea seems to me not merely strange but perfectly mysterious... To simply assert that consciousness arose at some point in the evolution of life, and that it results from a specific arrangement of neurons firing in concert within an individual brain, doesn't give us any inkling of how it could emerge from unconscious processes, even in principle.
Harris, again to his credit, refuses to accept the empty answer that time, genetic mutation and natural selection are responsible for consciousness. Even if they are, no light has been shed until it is explained how they account for it. It is like claiming that gravity is responsible for the movement of the planets without providing any theory that accounts for planetary orbits in terms of gravity (e.g. Newton's theory of gravitation).
I am sympathetic with those who, like the philosopher Colin McGinn and the psychologist Steven Pinker, have suggested that perhaps the emergence of consciousness is simply incomprehensible in human terms. Every chain of explanation must end somewhere - generally with a brute fact that neglects to explain itself. Perhaps consciousness presents an impasse of this sort.
When brute facts are invoked, you know you are at the point of a philosopher waving the white flag. A chain of explanation that ends in a brute fact isn't really a chain of explanation at all, since you might as well have invoked the brute fact at the start of the explanation as at the end. In any case, if Harris's first sentence is amended to "... perhaps the emergence of consciousness is simply incomprehensible in materialist terms" he might be on the way to a breakthrough, or at least a breakout, from the materialist prison in which finds himself without realizing it.
One of the charges against philosophy is that it makes no progress. Philosophers have been arguing over the same basic questions that they always have. While this is true, it is not true that this eternal philosophical conversation is fruitless. For it is a good clue that a particular philosophical school is fundamentally mistaken when it gives up attempting to account for something after having struggled with it for a long time. Materialist philosophers have been trying to find a place in their philosophy for the fact of consciousness - a fact, Harris concedes, that is undeniable - for a long time, with little success even by their own lights. They are now at the point of simply giving up on the project. The alternative to giving up on explaining consciousness, of course, is to abandon the philosophy that makes such an explanation impossible and go in search of another one.