Investigating self-fabrication in the context of artificial chemistries

Van Niekerk, Christopher (2014-12)

Thesis (MSc)--Stellenbosch University, 2014.

Thesis

ENGLISH ABSTRACT: This thesis gives a broad overview of what artificial chemistries (ACs) are, a brief review of several ACs and their applications, and an in depth analysis of one speci c AC: the four-bit binary string system. The model designed by Banzhaf [1] for in silico examination was recreated using the Python programming language. The initial motivation was to identify an existing AC that could be used to elucidate the sequence-function relationship, which led to the simultaneous investigation of self-organization in AC systems [7]. The interest in sequence-function relationships stems from their importance for self-production of objects [35]. For self-replication to be possible in larger organizations, the components of the organization must be able to continuously produce themselves [3, 7]. We chose the four-bit binary string system for investigation because of its simple design and implementation, its ability to yield complex results from interactions between a small population of objects, and its analogy to the DNA{RNA{protein organisation. When a population of objects are allowed to continuously interact, self-production and self-organization occur, even in simple arti cial systems [7, 8]. The stability of the emergent organizations depends on the interactions of its components, which must be capable of self-production if they are to maintain the organization [27]. Self-production of objects depends on their sequence-function relationship, which determines their rate of replication when interacting with other objects.

AFRIKAANSE OPSOMMING: Hierdie tesis verskaf `n bree oorsig van die algemene aard van artifisiele chemies (ACs), `n kort opsomming van `n paar ACs en hul toepassings, en `n diepgaande analise van een spesifieke AC: die 4-bis binere stringstelsel. Die model wat Banzhaf [1] ontwerp het vir in silico eksperimentering is hier herskep in die Python programmeringstaal. Die aanvanklike motivering was om `n bestaande AC te identifiseer wat gebruik kon word om die sekwens-funksie verwantskap te ontrafel, en dit het gelei tot die gelyktydige ondersoek van self-organisasie in AC stelsels [7]. Ons belangstelling in sekwens-funksie verwantskappe spruit uit hul belang vir die selfproduksie van objekte [35]. Om selfreplisering in meer omvangryke organisasies moontlik te maak moet die komponente in staat wees om hulself eenstryk te produseer [3, 7]. Ons het `n 4-bis stelsel vir hierdie studie gekies omdat die ontwerp en implementering eenvoudig is, omdat interaksies binne `n klein populasie van objekte komplekse resultate gee, en omdat die stelsel se organisasie analoog aan die DNA-RNA-proteien organisasie is. Wanneer `n populasie van objekte toegelaat word om eenstryk op mekaar te reageer vind self-produksie en self-organisasie vanself plaas, selfs in eenvoudige artifsiele stelsels [7, 8]. Die stabiliteit van die emergente organisasies hang af van die interaksies tussen die komponente, wat self die vermoe tot selfproduksie moet he indien hulle die organisasie in stand wil hou [27]. Selfproduksie van objekte hang af van hul sekwens-funsieverwantskap, wat op hul beurt bepaal hoe vinnig hulle repliseer wanneer in interaksie met ander objekte.

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