1 Introduction

Autopoiesis is a term coined by the biologists Humberto Maturana and Francisco Varela to denote a form of system organisation where the system as a whole produces and replaces its own components, and discriminates itself from its surrounding environment, on an on-going basis (Maturana & Varela 1973). The concept was inspired by the abstract organisation of relatively simple biological organisms, such as bacteria. It is intended to capture the essential organisational distinction between such an organism and a mere un-organised aggregation of the same molecular components.

Note that an autopoietic system is, by definition, collectively autocatalytic; but it differs from, or goes beyond, simply being collectively autocatalytic in that it must establish and maintain a boundary which contains and separates the reactions comprising the autopoietic system from the rest of its environment.

In an effort to present this concept in the most clear and concrete manner possible, Varela et al. developed a ``minimal'' abstract or model chemistry that would be capable of supporting autopoietic organisation. Furthermore, they used this as a basis for developing a computer simulation (realisation?) of this model chemistry, in which autopoietic organisations would be expected to spontaneously emerge and persist (Varela et al. 1974). The computer implementation thus served to test the claim that this particular model chemistry is indeed sufficient to support autopoietic organisation. More generally, such computerised models are open to detailed observation and experiment in ways that are currently impractical for real biological organisms.

Varela et al. (1974) presented a detailed algorithm for the computer implementation of their model chemistry. The current report presents a critical re-presentation and review of that algorithm, from the point of view of internal consistency and completeness, and also external consistency with the experimental runs illustrated in the original paper. A number of problems regarding the detailed interpretation of the algorithm will be identified. As far as possible, I shall also suggest ``reasonable'' resolutions for such problems, which may be helpful to anyone intending to re-implement the model.

I am greatly indebted to Francisco Varela for making available previously unpublished documentation and a source code listing associated with the original model, and for giving his permission to include these as an Appendix to this report. These materials are somewhat fragmentary, and it is not possible to be sure exactly how they relate to the version of the model actually presented in (Varela et al. 1974). Nonetheless, they provide a very important source of additional information, and allow some of the most difficult problems of interpretation of the original published description to be resolved. This general description of the model referred to it as PROTOBIO. The source code listing apparently comes from one single specific version or run of the model, labeled EXP29.FOR.

Note that this report will not attempt any detailed review of the actual phenomenology to be expected from this class of model--that is deferred for a subsequent companion report.

Fragments from the original paper (Varela et al. 1974) will be quoted verbatim here, where appropriate. However, to fully follow the detailed discussion in the current report it will generally be helpful to have a copy of that original paper to hand, for reference purposes.

2 Overview of the Model Chemistry

Computational Autopoiesis: The Original Algorithm

Computational Autopoiesis: The Original Algorithm

Document: Computational Autopoiesis: The Original Algorithm

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