EASy Thesis
From Ben Shirt-Ediss
Submitted in fulfillment of the Evolutionary and Adaptive Systems MSc, University of Sussex, 2009. Supervised by Dr. Ezequiel Di Paolo.
Forging the Road Toward Autonomy: Explorations with a Stochastic Protocell Model
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Abstract
This thesis is concerned with the re-implementation and continued development of a recent computational ’protocell’ model driving a vibrant new line of research into the origins of life. The protocell model is a physically plausible representation of what was probably the very first instance of cellular organisation on this planet: a fatty-acid vesicle structure acting as a selective membrane enclosing an internal chemical reaction system. Pioneers of the model - a research group centred at the University of the Basque Country in San Sebastian, Spain - are currently testing the dynamical properties of more elaborate variants of the protocell system (utilising, for example, more complex membrane processes/properties coupled to more complicated internal reaction networks) with the ultimate goal of identifying the structural changes which could transform a purely reactive vesicle compartment into an autonomous cellular unity capable of complex, adaptable self-maintaining behaviour. Investigating the minimal origin and then graded appearance of autonomy in the cellular system dynamics is one major conceptual theme with this approach. This work hopes to contribute to the accelerating protocell research avenue on an analytical and experimental level. Firstly, dynamical systems analysis is performed on the protocell lipid compartment to fill gaps in the mathematical base of the model. This effort forges a complete explanation for the early published simulation results and additionally reveals how a bare lipid compartment can undergo an interesting bifurcation in behaviour when ’osmotic buffer’ becomes added to the cellular system. Secondly a further experiment is performed on the lipid-peptide variant of the protocell model. Fluctuating environmental conditions are used to assess what beneficial effects membrane peptide channels can have on cellular stability in a wider context, when a protocell is more realistically immersed in a constant ’wash’ of other external processes. Whilst Maturana and Varela’s Autopoiesis originally inspired this work, this study actually begins by arguing that making models of autopoiesis may not be the best start when making models of autonomous cellular systems.
Keywords
Autonomy, protocell dynamics, stochastic chemical simulation, Gillespie Method, peptide channel, lipid vesicle, origins of life, phase portrait, autopoiesis
Reference As
Blundell, B.J. (2009). Forging the Road Toward Autonomy: Explorations with a Stochastic Protocell Model. Unpublished MSc thesis. Brighton: University of Sussex.
Supplementary Material
- Dynamical Systems Analysis of a Protocell Lipid Compartment - This paper was accepted as a full talk at the 10th European Conference on Artificial Life, Budapest, September 13-16, 2009, and is a condensed version of the analysis presented in Part IV of the thesis.
- Thesis poster: Exploring the fundamental processes of life (PDF)
- Some of my notes on Gillespie's derivation of the Stochastic Simulation Algorithm (PDF)
- Slides I gave for a presentation in Barcelona on the Gillespie SSA algorithm (PDF)
- The original skeleton (PDF) I wrote for the project
