The University of Southampton
University of Southampton Institutional Repository

Avenues for emergent ecologies

Avenues for emergent ecologies
Avenues for emergent ecologies
In this work, we present some fascinating behaviour emerging from a simple synthetic chemistry model. The results of Ono and Ikegami (2001) demonstrated the spontaneous formation of primitive, self-reproducing cells from a random homogeneous mixture of chemical components. Their model made use of a simple, artificial reaction network. Discrete particles were placed on a triangular lattice and the dynamics consisted of the following particle transitions: translation over one lattice spacing and chemical transformation. The primary particle types were membrane-forming particles, catalysts and water. The membrane particles formed structures akin to lipid bilayers. Their synthesis was stimulated by the catalyst particles, which were also capable of template self-replication using precursors. The system readily exhibits protocell formation from a random initial condition. These protocells form, grow, divide and eventually decay in a continuous cycle. Such emergent dynamics were an illuminating result given that the simulation itself only defines local interactions between particles and a set of physical transition rules. The protocell structures are not explicitly represented or built into the model. Hence it demonstrated a basic physical logic wherein the concepts of self-maintenance and self-reproduction could arise spontaneously from a set of simpler, lower level rules. In essence, it was an in silico realisation of the principle of autopoiesis.

We decided to extend this work by augmenting the particle species repertoire. An additional catalyst was added, which did not stimulate the synthesis of membrane particles, but rather stimulated their decay. It was expected that this would reduce the rate of protocell formation. However a surprising dynamic was uncovered with this new system. As one might expect the protocells did not arise in abundance as in the original model. Instead they formed in small, isolated colonies since this was the only means by which they could avoid the destructive effects of the new catalyst. However because this toxic particle was also autocatalytic (like the other, constructive catalyst), its concentration rose sharply in regions confined by membrane particles since the membranes slowed their outward diffusion. Thus membranes actually created a niche for the toxic catalyst. This in turn produced a predator-prey dynamic with clouds of the toxic particle growing near protocells and protocells being forced to grow in the opposite direction to avoid the destructive effects of the new particle. These results reveal that high level, ecological phenomena can manifest themselves even in simple physico-chemical systems. They demonstrate that ideas of natural selection and fitness are intimately bound with the basic principle of free energy minimisation. We have also now enhanced the model further by adding a second reaction network. It is similar, but independent to the first and allows for two "species" of protocell. It is also possible for hybrids to form, comprised of mixtures of the membrane particles from the two reaction networks. Results from this new version are currently being gathered and analysed
Bartlett, Stuart
d6942368-4dbc-4111-bce0-1867f4c60a89
Bullock, Seth
2ad576e4-56b8-4f31-84e0-51bd0b7a1cd3
Bartlett, Stuart
d6942368-4dbc-4111-bce0-1867f4c60a89
Bullock, Seth
2ad576e4-56b8-4f31-84e0-51bd0b7a1cd3

Bartlett, Stuart and Bullock, Seth (2013) Avenues for emergent ecologies. Emergence in Chemical Systems 3.0, United States. 17 - 22 Jun 2013.

Record type: Conference or Workshop Item (Poster)

Abstract

In this work, we present some fascinating behaviour emerging from a simple synthetic chemistry model. The results of Ono and Ikegami (2001) demonstrated the spontaneous formation of primitive, self-reproducing cells from a random homogeneous mixture of chemical components. Their model made use of a simple, artificial reaction network. Discrete particles were placed on a triangular lattice and the dynamics consisted of the following particle transitions: translation over one lattice spacing and chemical transformation. The primary particle types were membrane-forming particles, catalysts and water. The membrane particles formed structures akin to lipid bilayers. Their synthesis was stimulated by the catalyst particles, which were also capable of template self-replication using precursors. The system readily exhibits protocell formation from a random initial condition. These protocells form, grow, divide and eventually decay in a continuous cycle. Such emergent dynamics were an illuminating result given that the simulation itself only defines local interactions between particles and a set of physical transition rules. The protocell structures are not explicitly represented or built into the model. Hence it demonstrated a basic physical logic wherein the concepts of self-maintenance and self-reproduction could arise spontaneously from a set of simpler, lower level rules. In essence, it was an in silico realisation of the principle of autopoiesis.

We decided to extend this work by augmenting the particle species repertoire. An additional catalyst was added, which did not stimulate the synthesis of membrane particles, but rather stimulated their decay. It was expected that this would reduce the rate of protocell formation. However a surprising dynamic was uncovered with this new system. As one might expect the protocells did not arise in abundance as in the original model. Instead they formed in small, isolated colonies since this was the only means by which they could avoid the destructive effects of the new catalyst. However because this toxic particle was also autocatalytic (like the other, constructive catalyst), its concentration rose sharply in regions confined by membrane particles since the membranes slowed their outward diffusion. Thus membranes actually created a niche for the toxic catalyst. This in turn produced a predator-prey dynamic with clouds of the toxic particle growing near protocells and protocells being forced to grow in the opposite direction to avoid the destructive effects of the new particle. These results reveal that high level, ecological phenomena can manifest themselves even in simple physico-chemical systems. They demonstrate that ideas of natural selection and fitness are intimately bound with the basic principle of free energy minimisation. We have also now enhanced the model further by adding a second reaction network. It is similar, but independent to the first and allows for two "species" of protocell. It is also possible for hybrids to form, comprised of mixtures of the membrane particles from the two reaction networks. Results from this new version are currently being gathered and analysed

PDF
emcs_poster.pdf - Other
Download (2MB)

More information

Published date: June 2013
Venue - Dates: Emergence in Chemical Systems 3.0, United States, 2013-06-17 - 2013-06-22
Organisations: Agents, Interactions & Complexity

Identifiers

Local EPrints ID: 361438
URI: https://eprints.soton.ac.uk/id/eprint/361438
PURE UUID: 65f8c122-5903-4828-972d-a217e385f4f2

Catalogue record

Date deposited: 23 Jan 2014 12:20
Last modified: 18 Jul 2017 03:02

Export record

Contributors

Author: Stuart Bartlett
Author: Seth Bullock

University divisions

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of https://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×