The proteome is a product of the metabolome. Albeit the reverse sentence is rather obvious for everyone, this fact is often neglected and represents a fundamental problem for any theory of biological organization. Cornish-Bowden, Marilú Cárdenas and colleagues have presented in clear and understandable terms the obscure ideas of Robert Rosen on (M,R) systems. The idea of metabolic closure or circularity is central in that model. Enzymes have a finite life and have to be continuously resynthesized from cell’s own components (from inside). This leads us immediately to the inadequacies of comparing organisms and machines. All man-made machines need external agents which design, manufacture and maintain them. In an organism, the replacement of components (and to a large extent, the construction) is an internal function, without any external aid: self-construction and self-repair are definitory properties of any living being. Rosen put it this way: “A material system is an organism if it is closed to efficient causes”. Therefore, an essential difference between agencies and machines should not be ignored in the context of synthetic biology.

Further discussions on defining and synthesizing life: Apuntes CyT 27_2008 (in Spanish).

[Metabolism] has been a major component of teaching biochemistry to medical and life-science students, and has typically been taught as if the whole complicated organization was arbitrary or haphazard, the result of a whole series of accidents […] over the long period of evolution since the origin of life some thousands of millions of years ago. I shall try to convince you that this view is wrong […].

Cornish-Bowden A (2004) The Pursuit of Perfection: Aspects of Biochemical Evolution Oxford University Press