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Semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry

We present a novel stringmol-based artificial chemistry system modelled on the universal constructor architecture (UCA) first explored by von Neumann. In a UCA, machines interact with an abstract description of themselves to replicate by copying the abstract description and constructing the machines...

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Detalles Bibliográficos
Autores principales: Clark, Edward B., Hickinbotham, Simon J., Stepney, Susan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454285/
https://www.ncbi.nlm.nih.gov/pubmed/28515326
http://dx.doi.org/10.1098/rsif.2016.1033
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author Clark, Edward B.
Hickinbotham, Simon J.
Stepney, Susan
author_facet Clark, Edward B.
Hickinbotham, Simon J.
Stepney, Susan
author_sort Clark, Edward B.
collection PubMed
description We present a novel stringmol-based artificial chemistry system modelled on the universal constructor architecture (UCA) first explored by von Neumann. In a UCA, machines interact with an abstract description of themselves to replicate by copying the abstract description and constructing the machines that the abstract description encodes. DNA-based replication follows this architecture, with DNA being the abstract description, the polymerase being the copier, and the ribosome being the principal machine in expressing what is encoded on the DNA. This architecture is semantically closed as the machine that defines what the abstract description means is itself encoded on that abstract description. We present a series of experiments with the stringmol UCA that show the evolution of the meaning of genomic material, allowing the concept of semantic closure and transitions between semantically closed states to be elucidated in the light of concrete examples. We present results where, for the first time in an in silico system, simultaneous evolution of the genomic material, copier and constructor of a UCA, giving rise to viable offspring.
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spelling pubmed-54542852017-06-05 Semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry Clark, Edward B. Hickinbotham, Simon J. Stepney, Susan J R Soc Interface Life Sciences–Engineering interface We present a novel stringmol-based artificial chemistry system modelled on the universal constructor architecture (UCA) first explored by von Neumann. In a UCA, machines interact with an abstract description of themselves to replicate by copying the abstract description and constructing the machines that the abstract description encodes. DNA-based replication follows this architecture, with DNA being the abstract description, the polymerase being the copier, and the ribosome being the principal machine in expressing what is encoded on the DNA. This architecture is semantically closed as the machine that defines what the abstract description means is itself encoded on that abstract description. We present a series of experiments with the stringmol UCA that show the evolution of the meaning of genomic material, allowing the concept of semantic closure and transitions between semantically closed states to be elucidated in the light of concrete examples. We present results where, for the first time in an in silico system, simultaneous evolution of the genomic material, copier and constructor of a UCA, giving rise to viable offspring. The Royal Society 2017-05 2017-05-17 /pmc/articles/PMC5454285/ /pubmed/28515326 http://dx.doi.org/10.1098/rsif.2016.1033 Text en © 2017 The Author(s). http://creativecommons.org/licenses/by/4.0/ Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.
spellingShingle Life Sciences–Engineering interface
Clark, Edward B.
Hickinbotham, Simon J.
Stepney, Susan
Semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry
title Semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry
title_full Semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry
title_fullStr Semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry
title_full_unstemmed Semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry
title_short Semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry
title_sort semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry
topic Life Sciences–Engineering interface
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454285/
https://www.ncbi.nlm.nih.gov/pubmed/28515326
http://dx.doi.org/10.1098/rsif.2016.1033
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