Hitting Times of Some Critical Events in RNA Origins of Life
Can a replicase be found in the vast sequence space by random drift? We partially answer this question through a proof-of-concept study of the times of occurrence (hitting times) of some critical events in the origins of life for low-dimensional RNA sequences using a mathematical model and stochasti...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-12-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/11/12/1419 |
| _version_ | 1797502934617948160 |
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| author | Caleb Deen Bastian Hershel Rabitz |
| author_facet | Caleb Deen Bastian Hershel Rabitz |
| author_sort | Caleb Deen Bastian |
| collection | DOAJ |
| description | Can a replicase be found in the vast sequence space by random drift? We partially answer this question through a proof-of-concept study of the times of occurrence (hitting times) of some critical events in the origins of life for low-dimensional RNA sequences using a mathematical model and stochastic simulation studies from Python software. We parameterize fitness and similarity landscapes for polymerases and study a replicating population of sequences (randomly) participating in template-directed polymerization. Under the ansatz of localization where sequence proximity correlates with spatial proximity of sequences, we find that, for a replicating population of sequences, the hitting and establishment of a high-fidelity replicator depends critically on the polymerase fitness and sequence (spatial) similarity landscapes and on sequence dimension. Probability of hitting is dominated by landscape curvature, whereas hitting time is dominated by sequence dimension. Surface chemistries, compartmentalization, and decay increase hitting times. Compartmentalization by vesicles reveals a trade-off between vesicle formation rate and replicative mass, suggesting that compartmentalization is necessary to ensure sufficient concentration of precursors. Metabolism is thought to be necessary to replication by supplying precursors of nucleobase synthesis. We suggest that the dynamics of the search for a high-fidelity replicase evolved mostly during the final period and, upon hitting, would have been followed by genomic adaptation of genes and to compartmentalization and metabolism, effecting degree-of-freedom gains of replication channel control over domain and state to ensure the fidelity and safe operations of the primordial genetic communication system of life. |
| first_indexed | 2024-03-10T03:43:15Z |
| format | Article |
| id | doaj.art-b2fd38c5a9e14a91ae5219d6aaaa3807 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-10T03:43:15Z |
| publishDate | 2021-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-b2fd38c5a9e14a91ae5219d6aaaa38072023-11-23T09:15:12ZengMDPI AGLife2075-17292021-12-011112141910.3390/life11121419Hitting Times of Some Critical Events in RNA Origins of LifeCaleb Deen Bastian0Hershel Rabitz1Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ 08544, USAProgram in Applied and Computational Mathematics, Princeton University, Princeton, NJ 08544, USACan a replicase be found in the vast sequence space by random drift? We partially answer this question through a proof-of-concept study of the times of occurrence (hitting times) of some critical events in the origins of life for low-dimensional RNA sequences using a mathematical model and stochastic simulation studies from Python software. We parameterize fitness and similarity landscapes for polymerases and study a replicating population of sequences (randomly) participating in template-directed polymerization. Under the ansatz of localization where sequence proximity correlates with spatial proximity of sequences, we find that, for a replicating population of sequences, the hitting and establishment of a high-fidelity replicator depends critically on the polymerase fitness and sequence (spatial) similarity landscapes and on sequence dimension. Probability of hitting is dominated by landscape curvature, whereas hitting time is dominated by sequence dimension. Surface chemistries, compartmentalization, and decay increase hitting times. Compartmentalization by vesicles reveals a trade-off between vesicle formation rate and replicative mass, suggesting that compartmentalization is necessary to ensure sufficient concentration of precursors. Metabolism is thought to be necessary to replication by supplying precursors of nucleobase synthesis. We suggest that the dynamics of the search for a high-fidelity replicase evolved mostly during the final period and, upon hitting, would have been followed by genomic adaptation of genes and to compartmentalization and metabolism, effecting degree-of-freedom gains of replication channel control over domain and state to ensure the fidelity and safe operations of the primordial genetic communication system of life.https://www.mdpi.com/2075-1729/11/12/1419RNA worldstochastic simulation algorithmrandom counting measuremeasure-kernel-functionordinary differential equationhigh dimensional model representation |
| spellingShingle | Caleb Deen Bastian Hershel Rabitz Hitting Times of Some Critical Events in RNA Origins of Life Life RNA world stochastic simulation algorithm random counting measure measure-kernel-function ordinary differential equation high dimensional model representation |
| title | Hitting Times of Some Critical Events in RNA Origins of Life |
| title_full | Hitting Times of Some Critical Events in RNA Origins of Life |
| title_fullStr | Hitting Times of Some Critical Events in RNA Origins of Life |
| title_full_unstemmed | Hitting Times of Some Critical Events in RNA Origins of Life |
| title_short | Hitting Times of Some Critical Events in RNA Origins of Life |
| title_sort | hitting times of some critical events in rna origins of life |
| topic | RNA world stochastic simulation algorithm random counting measure measure-kernel-function ordinary differential equation high dimensional model representation |
| url | https://www.mdpi.com/2075-1729/11/12/1419 |
| work_keys_str_mv | AT calebdeenbastian hittingtimesofsomecriticaleventsinrnaoriginsoflife AT hershelrabitz hittingtimesofsomecriticaleventsinrnaoriginsoflife |