As a reviewer facing an avowed attempt at brutalization, perhaps I will be forgiven a touch of bluntness. When, using the characteristic language of the insecure reductionist ("we are nothing more than"), Brooks refers to molecular interactions and says emphatically, "That is all there is," he is engaged in a startlingly transparent argument from ignorance.
"That is all there is." What is all there is? Brooks makes the statement in order to intimidate, but is unwilling or unable to tell us anything at all about the brute, underlying, mechanistic reality he is pretending to beat us with. If there is one thing no respectable physicist since the mid-twentieth century would claim to do, it is to describe some sort of ultimate physical machine, let alone a well-understood physical machine. The entire movement of physics has been away from concrete machine models and, indeed, away from models altogether. Theories at the lowest level no longer even describe particular things or events that might be modeled. So when, with an air of settling matters for good, Brooks says "That is all there is," what hard reality is he shoving in front of our faces?
His general idea seems to be that there is some "mere" machine-stuff down at a lower level of explanation, and everything above it is "nothing more than" the compounded articulations of this mechanistic reality. Explanation proceeds from below upward. Our nature is fixed by the foundation on which it rests. "We are machines."
But if explanation proceeds from below, then you need to start with whatever is at the bottom. Your primary explanatory apparatus, in other words, is quantum weirdness. And the one place in science where you absolutely cannot find a machine is amid the scarcely utterable perplexities of the quantum realm. Nevertheless, there is where Brooks would apparently nail down our determining and limiting nature the reality we are "nothing more than." Does he care to tell us a little about this reality?
Certainly not in Flesh and Machines. Moreover, even if he could extract something of our essential nature from the sphere of quantum effects, and even if he could demonstrate the machine-like character of this nature, there would remain the difficulty facing all bottom-up expositors of the human being: where is the bottom, since not one iota of evidence within physics suggests we have reached it, and no one even seems to know what it might mean for there to be a bottom or what would be its distinguishing features.
Physicist Steven Weinberg (2001, pp. 99-100) informs us that some of the unknown, "deeper" structures pointed to by currently accepted theory "are much smaller than the smallest structures we have studied so far not by a factor of a hundred or thousand or ten billion, but by a factor of a million billion." In other words, it is much further from the atomic nucleus to these unknown structures than it is from the scale of ordinary life to the atomic nucleus. If the idea of explanatory levels makes any sense at all (it doesn't), and if our nature is determined by whatever constitutes the bottom, then so, too, the nature of atoms and molecules must be determined by the same inaccessible bottom.
But still, in his happy ignorance about whatever is "down there," Brooks can find satisfaction in the effort to whip us into submission with a phantom: "That is all there is." One wonders what he pictures in his own mind as he says "that." Here I have a nothing-more-than conjecture of my own: his idealized bit of ultimate matter is nothing more than a projection of the machines he builds; his imagined molecule is a kind of minuscule robot-homunculus.
Brooks might reply that, at some higher level of explanation, quantum weirdness (and the unknowns lying beneath it) manage to even themselves out, leaving us with the hope of identifying neat mechanisms at this higher level. But if he is not appealing to determination from a well-understood bottom if he claims to discern our mereness at some higher level what saves his choice of levels from arbitrariness? Why should we not, for example, take the living organism, or consciousness, as most fundamental and most revelatory for any explanation of the world? If we really want to understand the sustaining powers, the living energies, presented in the world, doesn't it make most sense to look for our understanding where those powers and energies are most fully developed and most explicitly manifest? In any case, whatever level Brooks chooses, he needs to demonstrate, rather than simply assert, both its fundamental and its essentially mechanistic nature. He doesn't seem interested in the task.
If he had been interested, he might have begun by listening to the physicists. When Werner Heisenberg can say that atoms are not things, and when Steven Weinberg can say that "particles are just bundles of field energy," and when Richard Feynman confesses that "in physics today, we have no knowledge of what energy is" well, then, the natural question to put to Brooks is, Where's the beef? Show us your grand, microcosmic machine! And tell us what makes it merely a machine.