Brooks seems particularly inclined to find evidence of our machine nature at the level of biomolecules. Since he never tells us why these molecules should be regarded as machinery, there isn't much to quarrel with. But a couple of extremely brief comments may prove useful.
Two of the most longstanding and fundamental questions about living things are, first, How does the organism sustain its order and resist decay? That is, how is matter "caught up" in the organism's living processes in a way that suddenly and dramatically ceases when the organism dies and the inevitable processes of putrefaction and decay take over? Or again: what is the difference between the state of the same physical body shortly before and shortly after death? And second, How is the distinctive form of every organism brought into being and maintained?
Both these questions have tended to fade from view as biology has transformed itself from a discipline about organisms to a discipline about molecules. Researchers seem to believe (if they think about the matter at all) that if they can just get a handle on the molecular "machinery" of the cell and organism, the larger questions will somehow answer themselves.
What has actually been happening provides an ironic counterpoint to this expectation. It is less that the lower "mechanisms" are answering the larger questions than that the larger questions are simply reasserting themselves at the lower level. In particular, the problem of order and resistance to decay stares microbiologists in the face regardless of where they look. As Lenny Moss (who is both a cell biologist and a philosopher) puts it, when we look at the molecular dynamics within the cytoplasm of the cell, what we see suggests that "biological resistance to thermodynamically driven entropic heat decay obtains all the way down to the most basic fabric of living matter" (Moss 2003, p. 91). Moss is one of many researchers looking at the complex chemical dynamics of the cell as a whole, and noting that there is no one-way chain of cause and effect determining the cell's order. This order (which is passed from one generation to the next) is irreducibly manifested in the cell as a whole, with each part (including the DNA) being effect as well as cause. There are no one-directional causal mechanisms sitting at the bottom and explaining the maintenance of living order.
As to the other problem, that of organic form, one need only point to the decisive issue of protein folding. This is opening up into a complex and massive question of form that mirrors, and is organically inseparable from, the question of overall form in the organism. Harvard biologist Richard Lewontin, after citing some of the many factors affecting protein folding (and therefore protein functioning), continues:
These understandings, however, have not penetrated into the main structure of biological explanation.... What is needed is to move the issue of structure from the peripheral realm of a few special cases to a central concern of investigation at the molecular level. (Lewontin 2000, pp. 115-17)
Given that these two fundamental questions about life the question of order and the question of form simply reappear as questions at the molecular level, rather than being explained at that level, what sense does it make to say, as Brooks does, that the living organism is now understood and explained as merely a collection of biomolecules? Certainly the new questions will, to the mechanistically inclined, appear to demand standard mechanistic solutions. But by the same token, to the researcher who was willing to see the qualitative (and therefore non-mechanistic) unity of the organism as a whole, the new problems at the molecular level will appear as verifications of that original view rather than as refutations of it.