Publications

Paper and poster for the "Extending the Darwinian Framework: New levels of selection and inheritance" workshop at ECAL 2007, 9th European Conference on Artificial Life

Abstract: Network dynamics may have played a key role in the Origin of Life. 'Smart' molecules such as template replicators and enzymes may not have been necessary in the first evolving entities. Instead, a process of natural selection between chemical networks operating in different organisms may have been the key evolutionary mechanism. This paper shows such a process using the SimSoup artificial chemistry simulation. The context and conceptual background for SimSoup is first outlined. The model is then described, and differences with other models are highlighted. SimSoup has network elements that correspond directly to the unimolecular and bimolecular elementary reaction schemes of physical chemistry. These network elements can be combined in very general ways to produce 'compound interactions' which can be catalytic. The model includes mass conservation, reaction rates based on considerations of energy and thermodynamics, and cycle detection. A run of the model is presented showing an evolutionary process in which a metabolic network is modified at periodic intervals, and the modification is accepted or discarded according to whether or not it results in higher metabolic activity. The network includes a large number of cyclic flows. It evolves through a series of persistent states, each of which can be regarded as a different 'species'.

Presentation to the New Approaches to Modelling Evolution/Ecosystems) group (NAME) at Sussex University - 1 August 2007

Paper outlining the SimSoup model, and presenting results of an initial investigation into the relationship between network connection density and network activity. It is shown that persistent states in SimSoup networks can exist for long periods. It is also shown that in some cases they can have an oscillating behaviour.

Presentation to the Artificial Chemistry workshop at ECAL 2005 - VIIIth European Conference on Artificial Life in September 2005.

Paper presented to the Artificial Chemistry workshop at ECAL 2005 - VIIIth European Conference on Artificial Life in September 2005.

Abstract: The mechanism for evolution in the first lifeforms is a key question that must be addressed by any explanation of the Origin of Life. The SimSoup artificial chemistry model is described, and it is shown how catalytic reactions can be represented as 'compound interactions'. A possible mechanism for inheritance in metabolic networks is outlined using graphical notation developed for SimSoup. Preliminary results from computer simulations are presented; it is demonstrated that a SimSoup network has multiple persistent states and that transitions between these states can occur as a result of perturbations or random fluctuations. It is argued that this may have relevance to understanding the mechanism of evolution in early lifeforms.

Presentation to Alergic group at Sussex University, UK.

The presentation provides an outline and background to the problem of the Origin Of Life, and presents a case for adopting the view that life had a metabolic origin. It includes a simple example of a metabolism based inheritance mechanism. This is illustrated using the SimSoup artificial chemistry simulator.