From Matter to Form: the Evolution of the Genetic Code as Semio-Poiesis

Barbieri, M., 2012. Codepoiesis—the deep logic of life. Biosemiotics 5(3), 297–299.10.1007/s12304-012-9162-4Search in Google Scholar

Barbieri, M., 2015. Code Biology. A New Science of Life. Dordrecht: Springer.10.1007/978-3-319-14535-8Search in Google Scholar

Barbieri, M., 2018. What is code biology? BioSystems 164, 1–10.10.1016/j.biosystems.2017.10.005Search in Google Scholar

Barbieri, M., 2019. A general model on the origin of biological codes. BioSystems 181, 11–19.10.1016/j.biosystems.2019.04.010Search in Google Scholar

Barbieri, M., 2019. Evolution of the genetic code: The ambiguity-reduction theory. Biosystems 185, available at: <https://doi.org/10.1016/j.biosystems.2019.104024>.Search in Google Scholar

Chebanov, S. V., 2019. Steps towards the semiotic awareness of biology: Biosemiotics replacing the role of synthetic theory of evolution. METHOD: Moscow Yearbook of Works from Social Sciences / Russian Academy of Sciences, INION 9. 151–172 (In Russian).Search in Google Scholar

Cоpley et al., 2005. A mechanism for the association of aminoacids with their codons and the origin of the genetic code. Proc. Natl. Acad. Sci 102, 4442–4447.10.1073/pnas.0501049102Search in Google Scholar

Crick, F. H., 1968. The origin of the genetic code. J Mol Biol. 38(3), 367–379. doi:10.1016/0022-2836(68)90392-6.10.1016/0022-2836(68)90392-6Search in Google Scholar

Crick, F., 1981. Life Itself: Its Origin and Nature. NY: Simon & Schuster.Search in Google Scholar

Crick, F. H., Griffith, J. S., Orgel. L. E., 1957. Codes without commas. Proc. Natl. Acad. Sci 43(5), 416–421.10.1073/pnas.43.5.416Search in Google Scholar

Frank-Kamenetsky, M. D., 1980. Genetic codes. Khimiya i Zhizn (Chemistry and Life) 5, 34–41 (In Russian).Search in Google Scholar

Frank, A., Froese, T., 2018. The Standard Genetic Code can Evolve from a Two-Letter GC Code Without Information Loss or Costly Reassignments. Origins of Life and Evolution of Biospheres 48, 259–272. doi: 10.1007/s11084-018-9559-4.10.1007/s11084-018-9559-4Search in Google Scholar

Gimona, M., 2008. Protein linguistics and the modular code of the cytoskeleton. In Barbieri, M., Hoffmeyer, J. (Eds.), Codes of life: The rules of macroevolution. Berlin: Springer, pp. 189–206.10.1007/978-1-4020-6340-4_8Search in Google Scholar

Gusev, V. A., Schulze-Makuch, D., 2004. Physics of Life Reviews 1. pp. 202–229.10.1016/j.plrev.2004.11.001Search in Google Scholar

Higgs, P. G., 2009. A four-column theory for the origin of the genetic code: Tracing the evolutionary pathways that gave rise to an optimized code. Biology Direct 4(1), available at: <https://doi.org/10.1186/1745-6150-4-16>.Search in Google Scholar

Hoffmeyer, J., 2007. Semiotic scaffolding of living systems. In Barbieri, M. (Ed.), Introduction to Biosemiotics: The New Biological Synthesis. Dordrecht: Springer, pp. 149–166.10.1007/1-4020-4814-9_6Search in Google Scholar

Ikehara, K., 2002. Origins of gene, genetic code, protein and life: comprehensive view of life systems from a GNC-SNS primitive genetic code hypothesis. J. Biosci. 27, 165–186.10.1007/BF02703773Search in Google Scholar

Jakobson, R., 1970. Linguistics. In Unesco (Ed.), Main trends of research in the social and human sciences, Part one: Social sciences. The Hague, Paris: Mouton, pp. 419–463.Search in Google Scholar

Jiménez-Sánchez, A., 1995. On the origin and evolution of the genetic code. J Mol Evol 41, 712–716.10.1007/BF00173149Search in Google Scholar

Koonin, E. V., Novozhilov, A. S., 2009. Origin and evolution of the genetic code: the universal enigma. IUBMB Life 61(2), pp. 99–111. doi: 10.1002/iub.146.10.1002/iub.146Search in Google Scholar

Koonin, E. V., Novozhilov, A. S., 2017. Origin and Evolution of the Universal Genetic Code. Annual Review of Genetics 51, 45–62.10.1146/annurev-genet-120116-024713Search in Google Scholar

Kun, A., Radvanyi, A., 2018. The evolution of the genetic code: impasses and challenges. Biosystems 164, 217–225, available at: <doi.org/10.1016/j. biosystems.2017.10.006>.10.1016/j.biosystems.2017.10.006Search in Google Scholar

Kull, K., 2015. Evolution, choice, and scaffolding: Semiosisis changing its own building. Biosemiotics 8, 223–234, available at: <https://doi.org/10.1007/s12304-015-9243-2>.Search in Google Scholar

Kull, K., 2020. Codes: Necessary, but not sufficient for meaning-making. Constructivist Foundations 15(2): 137–139.Search in Google Scholar

Lacková, Ľ., 2018. A Biosemiotic Encyclopedia: an Encyclopedic Model for Evolution. Biosemiotics 11, 307–322, available at: <https://doi.org/10.1007/s12304-018-9325-z>.Search in Google Scholar

Lacková, Ľ., Matlach, V., Faltýnek, D., 2017. Arbitrariness is not enough: towards a functional approach to the genetic code. Theory Biosci 136, 187–191, available at: <https://doi.org/10.1007/s12064-017-0246-1>.Search in Google Scholar

Lane, N., 2009. Life Ascending: The Ten Great Inventions of Evolution. NY: Norton & Co.Search in Google Scholar

Monod, J., 1971. Chance and Necessity.: An Essay on the Natural Philosophy of Modern Biology. Fontana.Search in Google Scholar

Patel, A., 2005. The triplet genetic code had a doublet predecessor. Journal of Theoretical Biology 233(4), 527–532.10.1016/j.jtbi.2004.10.029Search in Google Scholar

Pattee, H., 2005. The necessity of biosemiotics: Matter--symbol complementarity. Journal of Biosemiotics 1(1), 223–238.Search in Google Scholar

Penny, D., 2005. An Interpretive Review of the Origin of Life Research. Biol Philos 20, 633–671, available at: <https://doi.org/10.1007/s10539-004-7342-6>.Search in Google Scholar

Ratner, V. A., 2000. The Chronicle of the great discovery: ideas and persons. Priroda. 6, 22–30 (in Russian).Search in Google Scholar

Rodin, A. S., Szathmáry, E., 2011. On origin of genetic code and tRNA before translation. Biol Direct. 6, 14. doi: 10.1186/1745-6150-6-14.10.1186/1745-6150-6-14Search in Google Scholar

Rumer, Y. B., 1966. About the codon’s systematization in the genetic code. Proc. USSR Acad. Sci. 167, 1393–1394 (in Russian).Search in Google Scholar

Saussure, F. de, 1959[1916]. Course in General Linguistics. Translated, with an introduction and notes by Wade Baskin. New York, Toronto, London: McGraw--Hill Book Company.Search in Google Scholar

Sengupta, S., Higgs P. G., 2015. Pathways of genetic code evolution in ancient and modern organisms. J. Mol. Evol. 80, 229–243. doi: 10.1007/s00239-015-9686-8.10.1007/s00239-015-9686-8Search in Google Scholar

Štambuk, N., Konjevoda, P., Turčić, P., et al., 2018. Genetic coding algorithm for sense and antisense peptide interactions. Biosystems 164, 199-216. doi: 10.1016/j. biosystems.2017.10.009.Search in Google Scholar

Taylor, F. J., Coates, D., 1989. The code within the codons. Biosystems 22(3), 177–187. doi: 10.1016/0303-2647(89)90059-2.10.1016/0303-2647(89)90059-2Search in Google Scholar

Trifonov, E., 2004. The Triplet Code From First Principles. Journal of Biomolecular Structure and Dynamics 22(1), 1–11.10.1080/07391102.2004.10506975Search in Google Scholar

Trifonov, E. N., 2009. The origin of the genetic code and of the earliest oligopeptides. Research in Microbiology 160, 481–486.10.1016/j.resmic.2009.05.004Search in Google Scholar

Wu, Huan-Lin, Bagby, S., Elsen J. M. H., 2005. Evolution of the Genetic Triplet Code via Two Types of Doublet Codons. J Mol Evol 61(1), 54–64. doi: 10.1007/s00239-004-0224-3.10.1007/s00239-004-0224-3Search in Google Scholar

Zolyan, S., 2018. The Genetic code: Grammar, semantics, evolution. METHOD: Moscow Yearbook of Works from Social Sciences / Russian Academy of Sciences, INION 8. 130–184 (In Russian).Search in Google Scholar

Zolyan, S., Zdanov, R., 2018. Genome as (hyper)text: From metaphor to theory. Semiotica 2018(225), 1–18, available at: <https://doi.org/10.1515/sem-2016-0214>.Search in Google Scholar