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Simulation of pre-biotic formation of metabolic networks with the appearance of heritable catalysts of random specificity
Thesis (MSc)--Stellenbosch University, 2025.
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Stellenbosch : Stellenbosch University
2025
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| _version_ | 1867613802478960640 |
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| access_status_str | Open Access |
| author | Du Plessis, Anna Christina |
| author2 | Patterton, Hugh-George |
| author_browse | Du Plessis, Anna Christina Patterton, Hugh-George |
| author_facet | Patterton, Hugh-George Du Plessis, Anna Christina |
| author_sort | Du Plessis, Anna Christina |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MSc)--Stellenbosch University, 2025. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/132142 |
| institution | Stellenbosch University (South Africa) |
| last_indexed | 2026-06-10T12:41:56.100Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/132142 Simulation of pre-biotic formation of metabolic networks with the appearance of heritable catalysts of random specificity Du Plessis, Anna Christina Patterton, Hugh-George Muro, Enrique Stellenbosch University. Faculty of Science. Centre for Bioinformatics & Computational Biology. Prebiotics Life -- Origin Hydrothermal vent ecology Systems biology -- Simulation methods Python (Computer program language) -- Data processing Catalysts UCTD Thesis (MSc)--Stellenbosch University, 2025. Du Plessis, A. C. 2025. Simulation of pre-biotic formation of metabolic networks with the appearance of heritable catalysts of random specificity. Unpublished masters thesis. Stellenbosch: Stellenbosch University [online]. Available: https://scholar.sun.ac.za/items/2e781722-c758-408f-8cbd-d5a0f30e29a5 ENGLISH ABSTRACT: The origin of life on Earth remains a fundamental scientific question, as recreating early Earth conditions without direct evidence is virtually impossible. A central unresolved question in this field is whether catalysts or replicators emerged first. This study seeks to address this debate by exploring the effects of introducing heritable catalysts of undefined specificity into hypothetical systems and quantifying their resulting "suitability". Building on the premise that energy, information, and a barrier separating a living system from its environment are essential components of life, we hypothesized that systems possessing these features would develop preferentially. These hypothetical systems are simulated on the premise that life could have originated in an alkaline hydrothermal vent system, with the simulated systems conceptualized as pores in such a vent. To investigate this scenario, a Python-based simulation was developed, incorporating reactions from the minimal organism JCVI syn3A into hypothetical systems to observe the evolution of the reaction networks. A novel fitness metric was designed, quantifying the total Shannon Information Entropy of all metabolites within the system while penalizing the total number of metabolites present. This approach assessed the potential for protometabolic networks to emerge under specific conditions, assuming the presence of all required metabolites. The simulations produced reaction networks resembling those in JCVI syn3A. The results demonstrated that the stochastic addition of catalysts, guided by minimal metabolic rules, can lead to the emergence of reaction networks resembling that of JCVI syn3A. While the parameters do not perfectly replicate early Earth conditions, the findings suggest that metabolic networks could form spontaneously under specific conditions following the evolution of replication mechanisms. AFRIKAANSE OPSOMMING: Geen opsomming beskikbaar. Masters 2025-05-27T12:26:16Z 2025-05-27T12:26:16Z 2025-03 Thesis https://scholar.sun.ac.za/handle/10019.1/132142 Stellenbosch University vii, 75 pages : illustrations application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Prebiotics Life -- Origin Hydrothermal vent ecology Systems biology -- Simulation methods Python (Computer program language) -- Data processing Catalysts UCTD Du Plessis, Anna Christina Simulation of pre-biotic formation of metabolic networks with the appearance of heritable catalysts of random specificity |
| title | Simulation of pre-biotic formation of metabolic networks with the appearance of heritable catalysts of random specificity |
| title_full | Simulation of pre-biotic formation of metabolic networks with the appearance of heritable catalysts of random specificity |
| title_fullStr | Simulation of pre-biotic formation of metabolic networks with the appearance of heritable catalysts of random specificity |
| title_full_unstemmed | Simulation of pre-biotic formation of metabolic networks with the appearance of heritable catalysts of random specificity |
| title_short | Simulation of pre-biotic formation of metabolic networks with the appearance of heritable catalysts of random specificity |
| title_sort | simulation of pre biotic formation of metabolic networks with the appearance of heritable catalysts of random specificity |
| topic | Prebiotics Life -- Origin Hydrothermal vent ecology Systems biology -- Simulation methods Python (Computer program language) -- Data processing Catalysts UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/132142 |
| work_keys_str_mv | AT duplessisannachristina simulationofprebioticformationofmetabolicnetworkswiththeappearanceofheritablecatalystsofrandomspecificity |