Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding
We recently observed that errors in gene replication and translation could be seen qualitatively to behave analogously to the impedances in acoustical and electronic energy transducing systems. We develop here quantitative relationships necessary to confirm that analogy and to place it into the cont...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-10-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/19/7392 |
| _version_ | 1797551611821686784 |
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| author | Peter R. Wills Charles W. Carter |
| author_facet | Peter R. Wills Charles W. Carter |
| author_sort | Peter R. Wills |
| collection | DOAJ |
| description | We recently observed that errors in gene replication and translation could be seen qualitatively to behave analogously to the impedances in acoustical and electronic energy transducing systems. We develop here quantitative relationships necessary to confirm that analogy and to place it into the context of the minimization of dissipative losses of both chemical free energy and information. The formal developments include expressions for the information transferred from a template to a new polymer, I<sub>σ</sub>; an impedance parameter, Z; and an effective alphabet size, n<sup>eff</sup>; all of which have non-linear dependences on the fidelity parameter, q, and the alphabet size, n. Surfaces of these functions over the {n,q} plane reveal key new insights into the origin of coding. Our conclusion is that the emergence and evolutionary refinement of information transfer in biology follow principles previously identified to govern physical energy flows, strengthening analogies (i) between chemical self-organization and biological natural selection, and (ii) between the course of evolutionary trajectories and the most probable pathways for time-dependent transitions in physics. Matching the informational impedance of translation to the four-letter alphabet of genes uncovers a pivotal role for the redundancy of triplet codons in preserving as much intrinsic genetic information as possible, especially in early stages when the coding alphabet size was small. |
| first_indexed | 2024-03-10T15:47:39Z |
| format | Article |
| id | doaj.art-371a6bbfa07e4f8eb7db1353529cd92e |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T15:47:39Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-371a6bbfa07e4f8eb7db1353529cd92e2023-11-20T16:16:58ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-10-012119739210.3390/ijms21197392Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic CodingPeter R. Wills0Charles W. Carter1Department of Physics and Te Ao Marama Centre for Fundamental Inquiry, University of Auckland, PB 92019, Auckland 1142, New ZealandDepartment of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7260, USAWe recently observed that errors in gene replication and translation could be seen qualitatively to behave analogously to the impedances in acoustical and electronic energy transducing systems. We develop here quantitative relationships necessary to confirm that analogy and to place it into the context of the minimization of dissipative losses of both chemical free energy and information. The formal developments include expressions for the information transferred from a template to a new polymer, I<sub>σ</sub>; an impedance parameter, Z; and an effective alphabet size, n<sup>eff</sup>; all of which have non-linear dependences on the fidelity parameter, q, and the alphabet size, n. Surfaces of these functions over the {n,q} plane reveal key new insights into the origin of coding. Our conclusion is that the emergence and evolutionary refinement of information transfer in biology follow principles previously identified to govern physical energy flows, strengthening analogies (i) between chemical self-organization and biological natural selection, and (ii) between the course of evolutionary trajectories and the most probable pathways for time-dependent transitions in physics. Matching the informational impedance of translation to the four-letter alphabet of genes uncovers a pivotal role for the redundancy of triplet codons in preserving as much intrinsic genetic information as possible, especially in early stages when the coding alphabet size was small.https://www.mdpi.com/1422-0067/21/19/7392assignment catalysisaminoacyl-tRNA synthetasesstandard genetic codedissipative processesNTP hydrolysisfree energy transduction |
| spellingShingle | Peter R. Wills Charles W. Carter Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding International Journal of Molecular Sciences assignment catalysis aminoacyl-tRNA synthetases standard genetic code dissipative processes NTP hydrolysis free energy transduction |
| title | Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding |
| title_full | Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding |
| title_fullStr | Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding |
| title_full_unstemmed | Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding |
| title_short | Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding |
| title_sort | impedance matching and the choice between alternative pathways for the origin of genetic coding |
| topic | assignment catalysis aminoacyl-tRNA synthetases standard genetic code dissipative processes NTP hydrolysis free energy transduction |
| url | https://www.mdpi.com/1422-0067/21/19/7392 |
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