An autopoietic machine is a machine organized (defined as a unity) as a network of processes of production (transformation and destruction) of components that produces the components which:
Maturana & Varela
(1973, pp. 78-79)
This is the canonical definition of autopoiesis offered by Maturana and Varela. In the specific case of molecular autopoiesis, it seems clear that the ``components'' should be interpreted as individual molecules, and the ``processes of production'' are essentially chemical reactions. It is not quite so clear what it means for these molecules to ``continuously regenerate and realize the network of processes that produced them''. Elsewhere, the following qualification is offered:
Consider for example the case of a cell: it is a network of chemical reactions which produce molecules such that
Varela et al. (1974, p. 188)
Still, it is not clear what is the force of the phrase ``generate and participate recursively''. Specifically, is ``generating'' a chemical reaction a distinct thing from ``participating'' in one?
Having reference to the (highly schematic) computer model presented by Varela et al. (1974), it seems plausible to interpret ``participating'' in a reaction as meaning simply to be a reactant; whereas ``generating'' a reaction might mean to catalyse it. Catalysts are also, of course ``reactants''; but their special property is that they emerge unchanged from the catalysed reaction, while drastically increasing the reaction rate. In the limiting case, the un-catalysed reaction may occur with negligible rate, whereas, in the presence of catalyst, it may occur at a rate which has significant manifestations in the system. In such a case, it seems reasonable to say that the catalyst ``generates'' the reaction (given the availability of the other reactants).
So the first condition for molecular autopoiesis is that the reaction network which characterizes the organization of the system must produce all the species of molecular component which are considered to materially constitute the system, and these components must themselves generate the reaction network, in the sense of catalysing some (or all?) of the reactions (which would otherwise occur at negligible rate).
There are still some significant ambiguities here. How, for example, do we determine which components materially ``constitute'' the system? In the computer model of molecular autopoiesis there is one component, performing a specifically catalytic function, which is not itself produced by any reaction in the network--so should it not be regarded as a material component of the system? There are also ``substrate'' particles which are not--or at least, not necessarily--produced through the constituent reactions of the system (i.e., they may be produced by the reaction network, but may alternatively ``drift'' in from the external ambience). Also in this model there are two reactions (``concatenation'' and ``disintegration'') which are not catalysed at all--and thus arguably not ``generated'' by the system.
I should note that Varela et al. (1974) do present a 6-point ``key'' for determining whether or not a specific system should be regarded as autopoietic. This seems to suggest, for example, that it is acceptable for some of the components not to be produced by reactions in the system, provided that they ``participate as necessary permanent constitutive components in the production of other components''. This may account for the case of the catalytic component in the model system--though I would suggest that the meaning is still less than precise.
In any case, let us now move on to the second defining condition for autopoiesis. This is that the system itself must specify ``the topological domain of its realization''. The essential idea here seems to be that the same network of chemical processes which is used to identify the system as such, must also have the effect of locating or demarcating the system in space. The system must, in other words, establish some sort of boundary between ``itself'' and the rest of the universe in which it is embedded.
In the specific case of biological cells, this boundary is manifested in the external membrane of the cell. In the simplified computer model (which exists in a two dimensional universe), this boundary consists of a closed linear chain of molecules. It seems that, in the case of molecular autopoiesis, the boundary performs at least the function of limiting or controlling the spatial diffusion of the molecules constituting the system. This is presumably necessary because, in the absence of such control on diffusion, the reactant concentrations may dilute to the point where one or more of the defining reactions effectively ceases to operate, and the whole self-sustaining reaction network then breaks down.
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