Theoretical

The concept of autocatalytic sets was introduced in 1971 by Stuart Kauffman [1], and further developed in the 80’s and 90’s [2,3]. The notion of catalysis plays a central role in this concept. A catalyst is a chemical element that significantly speeds up the rate at which a reaction happens, without being used up in that reaction. Catalysis is essential for life: without it, the necessary reactions would not happen fast enough and not be synchronized sufficiently for life to exist.

Given a set of chemical reactions and the molecules involved in them, an autocatalytic set is now defined as a subset S of reactions and molecules such that:

  1. each reaction in the subset S is catalyzed by at least one molecule from S itself, and
  2. each molecule in S can be produced from a basic food set using only reactions from S.

This definition formally captures the functionally closed (1.) and self-sustaining (2.) properties of living systems. The concept of autocatalytic sets has been formalized more rigorously and studied both mathematically and computationally as RAF theory [4]. Also, several efficient computer algorithms have been developed to detect and analyze autocatalytic sets in general reaction systems [5].

A simple example of an autocatalytic set.

A simple example of an autocatalytic set. Dots represent molecule types, with green dots comprising the food set. Boxes represent reactions. Solid arrows indicate reactants going into and products coming out of a reaction. Dashed arrows indicate catalysis. From [5]

Although much progress has been made over the past several years in developing the theory of autocatalytic sets, many important questions remain to be investigated. Some of these aspects are being studied in more detail in the current collaboration, such as:

  • how to include and deal with inhibition (an important factor in biological regulation),
  • how autocatalytic (sub)sets can evolve into larger and more complex networks [6],
  • possible extensions of RAF theory beyond chemistry (e.g., to entire ecologies or even social networks).

References
[1] S. Kauffman. Cellular homeostasis, epigenesis and replication in randomly aggregated macromolecular systems. Journal of Cybernetics 1: 71–96, 1971.
[2] S. Kauffman. Autocatalytic sets of proteins. Journal of Theoretical Biology 119: 1–24, 1986.
[3] S. Kauffman. The Origins of Order: Self-Organization and Selection in Evolution. Oxford University Press, 1993.
[4] W. Hordijk. Autocatalytic sets: From the origin of life to the economy. BioScience 63(11): 877–881, 2013.
[5] W. Hordijk, J. I. Smith and M. Steel. Algorithms for detecting and analysing autocatalytic sets. Algorithms for Molecular Biology, in press, 2015.
[6] V. Vasas, C. Fernando, M. Santos, S. Kauffman and E. Szathmáry. Evolution before genes. Biology Direct 7: 1, 2012.