The work of the ALife Lab is focussed on exploring the synthesis of basic Autopoietic Agents in Artificial Chemistries, and understanding the interactions between such autopoietic organisation, self-reproduction and evolution.
An Artificial Chemistry is a computer created virtual "world" which instantiates some kind of "chemistry". That is to say, there is a space (typically more or less Euclidean) in which elementary particles can move around. Particles which are adjacent in this space spontaneously engage in reactions whereby new particles or compound molecules may be formed, leading to further reactions.
Unlike conventional chemical or bio-chemical engineering, the designer of an Artificial Chemistry is free to more or less arbitrarily stipulate the nature and characteristics (bonding, reactions etc.) of the elementary particles, and the mechanics of motion (kinetics, thermodynamics etc.) of such a system. The challenge is then to formulate a suitable artificial chemistry to facilitate the embedding of relatively simple Autopoietic Agents.
The following list summarises research projects which have been carried out at the ALife Lab, both current and completed. Further projects will be developed as resources and priorities at the lab permit.
ALife Lab was a partner in an EU funded (Framework 6) project, Evolving Cell Signaling Networks in Silico (ESIGNET). This project investigated the possibility to computationally evolve and simulate artificial cell signaling networks (CSNs) with pre-specified properties by means of Evolutionary Computation methods. This project had a total value of €1.6M.
ALife Lab was a partner in an EU funded (Framework 6) Integrated Project, Programmable Artificial Cell Evolution, or PACE). This project had a total value of over €8.5M, and create the foundation for a new generation of embedded information technology using programmable, self-assembling artificial cells. The project consortium included 13 partners and 2 cooperating groups from 8 European countries, including Switzerland and Lithuania, and several USA organizations. The DCU contribution is primarily documented in section Evolution of Protocell-embedded Molecular Computation of the PACE final report.
The work was carried out in collaboration with the late Prof. Francisco Varela (co-originator, with Humberto Maturana, of the theory of Autopoiesis) and Prof. Chris Langton. It has resulted in the successful recreation of a basic Autopoietic Agent, in a minimal Virtual Chemistry. This was based on a system originally described by Varela et al amost 25 years ago (Varela et al., 1974)--but corrects a substantive defect in the published description of that model which only came to light in the course of this reimplementation. The new implementation, called SCL, is based on the portable Swarm Agent-Based modelling system, originally developed at the Santa Fe Institute. Detailed information on this work is available in a series of working papers (McMullin, 1997b; McMullin & Varela, 1997; McMullin, 1997a).
Prof. John Holland proposed the α-Universes in the early 1970's as an abstract model for the spontaneous--and relatively fast--emergence of stable "genetic decoding" in a very simple Virtual Chemistry (Holland, 1976). This work was, however, entirely analytic rather than experimental. These analytic results were tested at the ALife Lab by implementing a detailed computer model of the Virtual Chemistry. This experimental work revealed that the original analysis had (in the interests of analytic tractability) neglected certain "side-reactions" which, unfortunately, have non-negligable effects. The conclusion was that this particular model for emergence of genetic decoding is flawed (McMullin, 1992b).
An early project of the ALife Lab was to re-evaluate the seminal work of John von Neumann (von Neumann, 1966) on the engineering of "self-reproducing" machines. There has been continuing disagreement in the literature as to the proper evaluation of this work, due in large part to von Neumann's tragically early death, leaving the work uncompleted and available primarily only in a draft manuscript.
This project culminated in a radical re-interpretation of von Neumann's manuscript, arguing that he should be properly regarded as having addressed (and solved) a substantive problem in the evolutionary growth of complexity; and that his design for a class of self-reproducing machines can only be properly understood in the context of solving this problem.
The detailed results from this project are available in (McMullin, 1992a,1994,2000), and were also the subject of an invited address to the International Computer Science Summer School: von Neumann Day, at the Swiss Federal Institute of Technology, July 25th, 1997.