Autocatalytic sets

Kauffman SA, Autocatalytic sets of proteins, J. Theor. Biol., 119 1-24, 1986. 

Kauffman, S. A. Autocatalytic sets of proteins. Journal of Theoretical Biology, 119 (1986), 1-24. 

The Theory of Collectively Autocatalytic Sets and the Origin of Molecular Reproduction... 

The fifth theory is that of collectively autocatalytic sets, first proposed for peptides by myself (7-/0) and Freeman Dyson 11). The theory however, is broader than peptides alone, and might include a variety of polymers and metabolites (70, 72). 

A collectively autocatalytic set is a set of molecules, say A and B, both say polymers, where A catalyzes the formation of B out of B fragments, while B catalyzes the formation of A out of A fragments. It is important to stress that in such a system, no molecule catalyzes its own formation. The set as a whole achieves catalytic closure , such that each molecule in the system whose formation requires catalysis, has a last step in its synthesis catalyzed by some member of the set. 

Thus, collectively autocatalytic sets have been demonstrated experimentally for DNA and peptide systems. The next point to make is that a cell is a collectively autocatalytic set as a whole, and achieves catalytic closure as a whole. No molecule in a cell reproduces itself, the cell as a whole reproduces. 

The more general theory of autocatalytic sets is based on several general ideas (10, 12) ... 

Figure 2. A typical autocatalytic set, built up from a food set, concentric ellipses, consisting in the monomers, a and b, as well as the dimers aa and bb. Catalysis is shown by the dotted lines leading from the catalyst to the reaction box, here reduced to a node, representing each of the ligation reactions. (Reproduced with permission from reference 9. Copyright 2000 Oxford University Press.)...

It should be always very important to remember that self-organising processes have to be considered at least on three scales the one of interest, the upper (constraint) one and the lower one (significance). If some components of an autocatalytic set are excluded, the system will appear as linear. It is what happens to the classical theory of succession, because e.g. the landscape is never considered as a basic parameter. Therefore, in landscape bionomic the importance of ecological succession as linear and divided into primary and secondary phases is drastically reduced. 

In 1972, Field, Koros, and Noyes (FKN group investigated the kinetic details which characterized the entire aspects of BZ reaction, illuminating the essential constiments of reaction and their roles in oscillations [31, 53]. The kinetic model composed three consecutive reaction processes as, (A), (B), and (C). The process A is a fast reaction step, the process (B) is an autocatalytic set of reaction, and C is the process where (Br ) ions are consumed. The oxidation of metal catalyst ions has also been taken place in the processes (A) and (B), respectively. A recovery step (process C) involves for the reduction of metal catalysts and regenerates the necessary reactant (Br ) ions for re-initiating the oscillatory-phase reaction from beginning. A schematic model for description of the chemistry of BZ reaction is shown in Fig. 1.3. 

In the literature many frameworks potentially able to explain the emergence of autocatalytic sets of molecules are described in all these frameworks the formation of these assemblies is highly probable, provided that an high enough molecular diversity is present. Nevertheless, it seems that finding these structures in the lab is extremely difficult. 

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