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I will welcome comments on any of the papers / presentations below at the following email address:-


2014

Molecules Designed for Chemical Network Memory and Non-Genetic Inheritance

Slides for presentation at the Institute for Complex Systems Simulation at the University of Southampton

Abstract: In this talk I will present a memory system based on an artificial chemistry. This is relevant as a 'proof of concept' for metabolism based Origin of Life theories, and in the field of biological and chemical computing. Each memory unit can be switched between three alternative active states. A unit maintains itself in a particular state using an autocatalytic reaction process. Switching between states occurs when an external stimulus triggers the autocatalytic process for the new state, along with an associated process that inhibits autocatalytic activity for the old state. I will show artificial molecular species with structures that support the autocatalytic and inhibiting processes. I will also present results from the SimSoup artificial chemistry simulator showing the operation of a 5-unit memory system with 243 alternative states (equivalent to just under 8 bits of memory). The design supports systems with more units, but computational requirements to run the simulator increase substantially. I will conclude the talk with a short review of some alternative network architectures for chemical memory and inheritance.

2013

Molecules Designed for Chemical Network Memory and Non-Genetic Inheritance

Slides for and video of presentation to the Alergic Group at Sussex University, 30 October 2013.

The SimSoup Guide - Version 1.2

This document is the SimSoup Guide . It includes: Creative Commons License
The SimSoup Guide by Chris Gordon-Smith is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

Molecules Designed for Switchable Autocatalytic Memory

Paper* and poster for ECAL 2013, the 11th European Conference on Artificial Life

Abstract: A memory system based on an artificial chemistry is presented. This is relevant for metabolism based Origin of Life theories, and in the field of biological and chemical computing. Each memory unit can be switched between three alternative active states. A unit maintains itself in a particular state using an autocatalytic reaction process. Switching between states occurs when an external stimulus triggers the autocatalytic process for the new state, along with an associated process that inhibits autocatalytic activity for the old state. Artificial molecular species with structures designed to support the autocatalytic and inhibiting processes are presented. The SimSoup artificial chemistry simulator is used to show that the structures do indeed produce the memory system behaviour. With the advent of engineering at the molecular level, it may be possible to transfer the concepts from an in silico environment to a chemical environment.

*First published in: Advances in Artificial Life, Proceedings of the 12th European Conference on Artificial Life, MIT Press

2012

Molecules Designed For Network Memory And Evolution

Short paper and presentation for the BioChemIT Workshop at the 11th International Conference for Unconventional Computation and Natural Computation, Orleans, 6 September 2012.

Background and Motivation: A key challenge for BioChemIT is the development of evolvable systems. This requires the implementation of a mechanism for inheritance using components that can be readily constructed and manipulated. Contemporary life-forms use RNA and DNA and associated mechanisms. Origin Of Life research suggests that these mechanisms are too complex to be plausible in a prebiotic environment. The SimSoup project is seeking a simpler inheritance mechanism based on chemical networks. This search is relevant from a BioChemIT perspective, with its need for mechanisms that are sufficiently simple to be implementable. This paper summarises in silico work on an inheritance mechanism using molecular structures designed to produce autocatalytic reaction networks. The motivation is to highlight the potential of this approach for a practical evolutionary mechanism in a BioChemIT context. The paper concludes by identifying key requirements for a BioChemIT implementation of such a mechanism.

2011

Non-Template Molecules Designed For Open-Ended Evolution

Abstract: Theories of the Origin of Life can be categorised as ‘template replication first’ and ‘metabolism first’. A key question for metabolism first theories is whether metabolic systems can support open-ended evolution; this is related to the number of possible persistent states of such a system. Earlier work has demonstrated that artificial chemical systems can have memory; an essential requirement for inheritance. The current paper extends this, taking a ‘proof of concept’ approach to the question of the number of persistent states. It shows an artificial chemical network forming a ‘memory bank’ with many possible states. It also makes the link between chemical network structure and molecular structure, and provides a design for a set of artificial molecular species for the memory bank network. Preliminary simulation results from the SimSoup artificial chemistry simulator are included, confirming the operation of an initial set of ‘memory units’. The work supports the view that open-ended evolution can begin without requiring highly complex template molecules.

*First published in Advances in Artificial Life, ECAL 2011 Proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems

2010

The Origin Of Life: A Network Oriented View

Attractor Based Evolution
Slides and Video for presentation to the Life And Mind Group at Sussex University, 18 June 2010. For the best effect, view the video and the PDF slides in different windows.

This talk:

2009

SimSoup: Artificial Chemistry Meets Pauling

Paper* and poster for ECAL 2009, the 10th European Conference on Artificial Life.

Abstract: Theories of the Origin of Life can be categorised as ‘template replication first’ and ‘metabolism first’. A key question for metabolism first theories is the mechanism for transfer of inherited information. Earlier work presented a mechanism based on catalytic cycles, along with supporting results from the SimSoup artificial chemistry simulator. The current paper presents an enhanced SimSoup model that is closer to real chemistry and more open ended. Molecules and the types of Interactions between them are constructed by the model itself using simple rules based on valence theory. Results of a preliminary run of the model are presented. Most of the Molecules produced are of a few simple types with low molecular weight. There is a ‘long tail’ of many low frequency Molecules, many of which are more complex with high molecular weight.

* First published in Advances in Artificial Life: Proceedings of the Tenth European Conference on Artificial Life (ECAL 2009), Springer

The Origin Of Life: A Network Oriented View

Paper and poster for the Levels of Selection Workshop at ECAL 2009, the 10th European Conference on Artificial Life.

Abstract: Origin of Life theories are in two main categories: ‘template replication first’ and ‘metabolism first’. A network oriented viewpoint is presented, under which properties of metabolic networks played a key role in the origin of the first evolving systems. A mechanism for memory in chemical networks is illustrated. The simplicity of `network memory', especially in comparison with template mechanisms, suggests its plausibility as a prebiotic phenomenon and as a fruitful area for Origin of Life research.

2007

Evolution Without Smart Molecules

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'.

Evolution Without Smart Molecules Presentation

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

2006

Network Dynamics In the SimSoup Artificial Chemistry

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.

2005

SimSoup: An Artifical Chemistry Model for Investigation of the Evolution of Metabolic Networks

Paper and presentation for 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.

The Origin Of Life: An Outline of Key Issues and a Case for the Metabolic View

Presentation to the Alergic group at Sussex University, UK.

The presentation provides an outline of 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.

Copyright Chris Gordon-Smith 2013