Published In

Journal of Systems Chemistry

Document Type

Article

Publication Date

4-2014

Subjects

Catalytic RNA, Life -- Origin, Molecular evolution

Abstract

Background: The concept of an autocatalytic set of molecules has been posited theoretically and demonstrated empirically with catalytic RNA molecules. For this concept to have significance in a realistic origins-of-life scenario, it will be important to demonstrate the evolvability of such sets. Here, we employ a Gillespie algorithm to improve and expand on previous simulations of an empirical system of self-assembling RNA fragments that has the ability to spontaneously form autocatalytic networks. We specifically examine the role of serial transfer as a plausible means to allow time-dependent changes in set composition, and compare the results to equilibrium, or "batch" scenarios.

Results: We show that the simulation model produces results that are in close agreement with the original experimental observations in terms of generating varying autocatalytic (sub)sets over time. Furthermore, the model results indicate that in a “batch” scenario the equilibrium distribution is largely determined by competition for resources and stochastic fluctuations. However, with serial transfer the system is prevented from reaching such an equilibrium state, and the dynamics are mostly determined by differences in reaction rates. This is a consistent pattern that can be repeated, or made stronger or weaker by varying the reaction rates or the duration of the transfer steps. Increasing the number of molecules in the simulation actually strengthens the potential for selection.

Conclusions: These simulations provide a more realistic emulation of wet lab conditions using self-assembling catalytic RNAs that form interaction networks. In doing so, they highlight the potential evolutionary advantage to a prebiotic scenario that involves cyclic dehydration/rehydration events. We posit that such cyclicity is a plausible means to promote evolution in primordial autocatalytic sets, which could later lead to the establishment of individual-based biology.

Description

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© 2014 Hordijk et al.; licensee Chemistry Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

DOI

10.1186/1759-2208-5-4

Persistent Identifier

http://archives.pdx.edu/ds/psu/11356

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