The Evolution of the Chemoton

Abstract: Tibor Ganti proposed the chemoton as the minimal system capable of open-ended evolution, consisting of three stoichiometrically coupled autocatalytic systems, a metabolism, a membrane and a template replicating system. Our models show that an autocatalytic metabolic system could evolve only if chemical and physical niches could be discovered that limited the extent of tapping side-reactions. After that, selection at the protocell level would have favored those containing clean template replication rather than messy polymerization. Template length could additionally confer a weak Lamarkian inheritance mechanism. We propose a mechanism for the origin of long template replication. Although unlimited nucleic acid elongation is possible at low temperatures, elongation out-competes replication for limited monomer resource. However, in a reactor with a low temperature baseline, with denaturation spikes, the minimal functionality required of an RNA motif capable of self-replication is that it can `cut itself out' of an elongating strand, and accept oligomers upon renaturation. No ligase function or processivity is necessary, or possible. Several artificial ribozymes were designed and tested. Such a restriction ribozyme function is readily observed in extant RNAs, may have been selected for, and is an ideal mechanism for dealing with elongation side-reactions.

Supplementary software is available.

 

Chapter 1: The Origin of Metabolism.

i. Mathematica (Cellerator) files describing ecologies of autocatalytic particles in re-cycling systems.

ii. Mathematica (Cellerator) files analysing conditions for co-existence in competitive cycles (Click here for Numerical Simulatiion) (Click here for analysis).

ii.i. Mathematica (Cellerator) files for analysing co-existence in parabolic replicators, with and without inactive component decay.

iii. Mathematica (Cellerator) files analysing conditions for co-existence in predator-prey cycles.

iv. Mathematica (Cellerator) files analysing the origin of mutualism by assimilation of environmental re-cycling capacities.

Chapter 3: Stochastic Model of Template Replication.

A validation of the stochastic model is carried out here. It is necessary to check the predictive value of the model by comparing it to deterministic kinetic equations. Work in progress on these validations is shown in full here.

i. Mathematica (Cellerator) file showing ODE models of replicator dynamics.

ii. Models of Tidal Cycling (Supplementary material for Tidal Cycling Paper).

iii. From Elongation to Replication. The transformation of self-assembly into distributed self-replication (19th June, 2006).

 

Download Revised Thesis Pdf (Version from 1st October, 2006).

Download pdf. (Version from 27th September 2005).

Download pdf.zip (27th Sept. 2005).

 

Old Preparatory Notes and References.

 

1. Introduction.

2. Background.

3. Theory.

4. Methodology.

5. Whole Chemoton Models.

6. Stochastic Models of Non-Enzymatic Template Replication.

7. Stochastic Models of the Evolution of Metabolism.

8. Discussion.

9. Conclusion.

10. Glossary of Terms.