{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T22:48:20Z","timestamp":1777589300741,"version":"3.51.4"},"reference-count":49,"publisher":"MIT Press","issue":"1","license":[{"start":{"date-parts":[[2024,2,14]],"date-time":"2024-02-14T00:00:00Z","timestamp":1707868800000},"content-version":"vor","delay-in-days":44,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["direct.mit.edu"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2024,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>In the mid-20th century, two new scientific disciplines emerged forcefully: molecular biology and information-communication theory. At the beginning, cross-fertilization was so deep that the term genetic code was universally accepted for describing the meaning of triplets of mRNA (codons) as amino acids. However, today, such synergy has not taken advantage of the vertiginous advances in the two disciplines and presents more challenges than answers. These challenges not only are of great theoretical relevance but also represent unavoidable milestones for next-generation biology: from personalized genetic therapy and diagnosis to Artificial Life to the production of biologically active proteins. Moreover, the matter is intimately connected to a paradigm shift needed in theoretical biology, pioneered a long time ago, that requires combined contributions from disciplines well beyond the biological realm. The use of information as a conceptual metaphor needs to be turned into quantitative and predictive models that can be tested empirically and integrated in a unified view. Successfully achieving these tasks requires a wide multidisciplinary approach, including Artificial Life researchers, to address such an endeavour.<\/jats:p>","DOI":"10.1162\/artl_a_00432","type":"journal-article","created":{"date-parts":[[2024,2,15]],"date-time":"2024-02-15T13:32:10Z","timestamp":1708003930000},"page":"16-27","update-policy":"https:\/\/doi.org\/10.1162\/mitpressjournals.corrections.policy","source":"Crossref","is-referenced-by-count":6,"title":["Information, Coding, and Biological Function: The Dynamics of\n                    Life"],"prefix":"10.1162","volume":"30","author":[{"given":"Julyan H. E.","family":"Cartwright","sequence":"first","affiliation":[{"name":"CSIC-Universidad de Granada, Instituto Andaluz de Ciencias de la Tierra, Department of Chemical Engineering, Instituto Carlos I de F\u00edsica Te\u00f3rica y Computacional"}]},{"given":"Jitka","family":"\u010cejkov\u00e1","sequence":"additional","affiliation":[{"name":"University of Chemistry and Technology Prague. cejkovaj@vscht.cz"}]},{"given":"Elena","family":"Fimmel","sequence":"additional","affiliation":[{"name":"Mannheim University of Applied Sciences, Institute of Mathematical Biology"}]},{"given":"Simone","family":"Giannerini","sequence":"additional","affiliation":[{"name":"University of Bologna, Department of Statistical Science"}]},{"given":"Diego Luis","family":"Gonzalez","sequence":"additional","affiliation":[{"name":"University of Bologna, Department of Statistical Science CNR, Area della Ricerca di Bologna"}]},{"given":"Greta","family":"Goracci","sequence":"additional","affiliation":[{"name":"Free University of Bozen-Bolzano, Institute of Mathematical Biology"}]},{"given":"Clara","family":"Gr\u00e1cio","sequence":"additional","affiliation":[{"name":"Universidade de \u00c9vora, CIMA Faculty of Economics and Management"}]},{"given":"Jeanine","family":"Houwing-Duistermaat","sequence":"additional","affiliation":[{"name":"Radboud University, Department of Mathematics IMAPP"}]},{"given":"Dragan","family":"Mati\u0107","sequence":"additional","affiliation":[{"name":"University of Banja Luka, Faculty of Natural Science and Mathematics"}]},{"given":"Nata\u0161a","family":"Mi\u0161i\u0107","sequence":"additional","affiliation":[{"name":"Research and Development, Institute Lola Ltd."}]},{"given":"Frans A. A.","family":"Mulder","sequence":"additional","affiliation":[{"name":"Johannes Kepler University, Institute of Biochemistry"}]},{"given":"Oreste","family":"Piro","sequence":"additional","affiliation":[{"name":"Universitat de les Illes Balears, Department of Physics Mediterranean Institute for Advanced Studies"}]}],"member":"281","published-online":{"date-parts":[[2024,2,1]]},"reference":[{"issue":"7571","key":"2024102915293146800_bib1","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic\n                        variation","volume":"526","author":"Auton","year":"2015","journal-title":"Nature"},{"key":"2024102915293146800_bib2","doi-asserted-by":"publisher","DOI":"10.7551\/mitpress\/11909.003.0022","article-title":"How life (and death) spring from\n                        disorder","volume":"26","author":"Ball","year":"2017","journal-title":"Quanta Magazine"},{"key":"2024102915293146800_bib3","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1007\/978-3-319-14535-8_10","article-title":"Code biology","volume-title":"Code biology: A new science of life","author":"Barbieri","year":"2015"},{"key":"2024102915293146800_bib4","doi-asserted-by":"publisher","first-page":"104328","DOI":"10.1016\/j.biosystems.2020.104328","article-title":"Quantum-like modeling in biology with\n                        open quantum systems and instruments","volume":"201","author":"Basieva","year":"2021","journal-title":"Biosystems"},{"issue":"7","key":"2024102915293146800_bib5","doi-asserted-by":"publisher","first-page":"2239","DOI":"10.1007\/s11538-019-00603-2","article-title":"The quality of genetic code models in\n                        terms of their robustness against point mutations","volume":"81","author":"B\u0142a\u017cej","year":"2019","journal-title":"Bulletin of Mathematical Biology"},{"issue":"7386","key":"2024102915293146800_bib6","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1038\/482461a","article-title":"Life\u2019s code\n                        script","volume":"482","author":"Brenner","year":"2012","journal-title":"Nature"},{"issue":"7921","key":"2024102915293146800_bib7","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1038\/d41586-022-02083-2","article-title":"\u201cThe entire protein\n                        universe\u201d: AI predicts shape of nearly every known\n                        protein.","volume":"608","author":"Callaway","year":"2022","journal-title":"Nature"},{"issue":"2063","key":"2024102915293146800_bib8","doi-asserted-by":"publisher","first-page":"20150071","DOI":"10.1098\/rsta.2015.0071","article-title":"DNA as information: At the crossroads between biology,\n                        mathematics, physics and chemistry","volume":"374","author":"Cartwright","year":"2016","journal-title":"Philosophical\n                        Transactions of the Royal Society of London, Series A"},{"issue":"1","key":"2024102915293146800_bib9","first-page":"12","article-title":"Current state-of-the-art and future\n                        directions in systems biology","volume":"1","author":"Chen","year":"2014","journal-title":"Progress and\n                        Communication in Sciences"},{"issue":"4","key":"2024102915293146800_bib10","doi-asserted-by":"publisher","first-page":"e2115642118","DOI":"10.1073\/pnas.2115642118","article-title":"Sequence locally, think globally: The Darwin tree of life\n                        project","volume":"119","author":"Darwin Tree\n                        of Life Project Consortium","year":"2022","journal-title":"Proceedings of the National Academy of\n                        Sciences of the United States of America"},{"issue":"2","key":"2024102915293146800_bib11","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1109\/TMBMC.2017.2658058","article-title":"Guest editorial biological applications of information theory\n                        in honor of Claude Shannon\u2019s centennial\u2014Part\n                        II","volume":"2","author":"Dimitrov","year":"2016","journal-title":"IEEE Transactions on Molecular, Biological and\n                        Multi-scale Communications"},{"key":"2024102915293146800_bib12","volume-title":"Information,\n                        Coding, and Biological Function: The Dynamics of Life","author":"Dynalife","year":"2022\u20132026"},{"key":"2024102915293146800_bib13","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1007\/978-3-030-12082-5_11","article-title":"Genetic code modelling from the perspective of quantum\n                        informatics","volume-title":"Advances in Artificial Systems for\n                        Medicine and Education II","author":"Fimmel","year":"2020"},{"key":"2024102915293146800_bib14","doi-asserted-by":"publisher","first-page":"104416","DOI":"10.1016\/j.biosystems.2021.104416","article-title":"Foundations of mathematics and theoretical biology [Special\n                        issue]","volume":"205","author":"Fimmel","year":"2021","journal-title":"Biosystems"},{"key":"2024102915293146800_bib15","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1016\/j.biosystems.2017.09.007","article-title":"Mathematical fundamentals for the noise\n                        immunity of the genetic code","volume":"164","author":"Fimmel","year":"2018","journal-title":"Biosystems"},{"issue":"4398","key":"2024102915293146800_bib16","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1038\/173318a0","article-title":"Possible relation between\n                        deoxyribonucleic acid and protein structures","volume":"173","author":"Gamow","year":"1954","journal-title":"Nature"},{"issue":"2","key":"2024102915293146800_bib17","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1007\/s11538-006-9141-5","article-title":"Information theory in living systems, methods, applications,\n                        and challenges","volume":"69","author":"Gatenby","year":"2007","journal-title":"Bulletin of Mathematical\n                        Biology"},{"key":"2024102915293146800_bib18","doi-asserted-by":"publisher","first-page":"202","DOI":"10.4153\/CJM-1958-023-9","article-title":"Comma-free codes","volume":"10","author":"Golomb","year":"1958","journal-title":"Canadian Journal of\n                        Mathematics"},{"issue":"3\u20134","key":"2024102915293146800_bib19","doi-asserted-by":"publisher","first-page":"143","DOI":"10.6092\/issn.1973-2201\/3553","article-title":"The mathematical structure of the\n                        genetic code: A tool for inquiring on the origin of life","volume":"69","author":"Gonzalez","year":"2009","journal-title":"Statistica"},{"key":"2024102915293146800_bib20","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.biosystems.2014.12.001","article-title":"On models of the genetic code generated\n                        by binary dichotomic algorithms","volume":"128","author":"Gumbel","year":"2015","journal-title":"Biosystems"},{"issue":"1","key":"2024102915293146800_bib21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1741-7007-12-29","article-title":"Models in biology: \u201cAccurate\n                        descriptions of our pathetic thinking.\u201d","volume":"12","author":"Gunawardena","year":"2014","journal-title":"BMC Biology"},{"issue":"2","key":"2024102915293146800_bib22","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1002\/j.1538-7305.1950.tb00463.x","article-title":"Error detecting and error correcting codes","volume":"29","author":"Hamming","year":"1950","journal-title":"Bell System Technical Journal"},{"key":"2024102915293146800_bib23","volume-title":"Globalization, Biosecurity, and the Future of the Life\n                        Sciences","author":"Institute of\n                        Medicine & National Research Council","year":"2006"},{"issue":"3939","key":"2024102915293146800_bib24","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1126\/science.168.3939.1545","article-title":"Information theory in biology after 18 years: Information\n                        theory must be modified for the description of living\n                        things.","volume":"168","author":"Johnson","year":"1970","journal-title":"Science"},{"issue":"7873","key":"2024102915293146800_bib25","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure\n                        prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"issue":"3","key":"2024102915293146800_bib26","doi-asserted-by":"publisher","first-page":"20220063","DOI":"10.1098\/rsfs.2022.0063","article-title":"A third transition in\n                        science?","volume":"13","author":"Kauffman","year":"2023","journal-title":"Interface Focus"},{"key":"2024102915293146800_bib27","doi-asserted-by":"publisher","DOI":"10.1515\/9781503617575","volume-title":"Who wrote the book of life? A history of the genetic code","author":"Kay","year":"2000"},{"issue":"1\u20133","key":"2024102915293146800_bib28","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/S0303-2647(99)00081-7","article-title":"Is there a biology of quantum information?","volume":"55","author":"Matsuno","year":"2000","journal-title":"BioSystems"},{"issue":"1","key":"2024102915293146800_bib29","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1109\/MEMB.2006.1578660","article-title":"Communication theory and molecular biology at the\n                        crossroads","volume":"25","author":"May","year":"2006","journal-title":"IEEE Engineering in Medicine and Biology\n                        Magazine"},{"issue":"5659","key":"2024102915293146800_bib30","doi-asserted-by":"publisher","first-page":"790","DOI":"10.1126\/science.1094442","article-title":"Uses and abuses of mathematics in biology","volume":"303","author":"May","year":"2004","journal-title":"Science"},{"issue":"5","key":"2024102915293146800_bib31","doi-asserted-by":"publisher","first-page":"1161","DOI":"10.1073\/pnas.53.5.1161","article-title":"RNA codewords and protein synthesis,\n                        VII. On the general nature of the RNA code.","volume":"53","author":"Nirenberg","year":"1965","journal-title":"Proceedings of the National Academy of Sciences of the United States of\n                        America"},{"issue":"10","key":"2024102915293146800_bib32","doi-asserted-by":"publisher","first-page":"1588","DOI":"10.1073\/pnas.47.10.1588","article-title":"The dependence of cell-free protein synthesis in E.\n                            coli upon naturally occurring or synthetic\n                        polyribonucleotides","volume":"47","author":"Nirenberg","year":"1961","journal-title":"Proceedings of the National\n                        Academy of Sciences of the United States of America"},{"issue":"7876","key":"2024102915293146800_bib33","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1038\/d41586-021-02480-z","article-title":"Biology must generate ideas as well as\n                        data","volume":"597","author":"Nurse","year":"2021","journal-title":"Nature"},{"key":"2024102915293146800_bib34","doi-asserted-by":"publisher","DOI":"10.5772\/intechopen.86264","article-title":"Introductory chapter: Systems biology\n                        consolidating state of the art genetics and bioinformatics","volume-title":"Systems Biology","author":"Papakonstantinou","year":"2019"},{"key":"2024102915293146800_bib35","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1007\/978-94-007-5161-3_3","article-title":"How does a molecule become a message?","volume-title":"LAWS, LANGUAGE and LIFE: Howard Pattee\u2019s classic papers on\n                        the physics of symbols with contemporary commentary","author":"Pattee","year":"2012"},{"key":"2024102915293146800_bib36","doi-asserted-by":"publisher","first-page":"EBO\u2013S7364","DOI":"10.4137\/EBO.S7364","article-title":"A novel model for DNA sequence\n                        similarity analysis based on graph theory","volume":"7","author":"Qi","year":"2011","journal-title":"Evolutionary Bioinformatics"},{"key":"2024102915293146800_bib37","volume-title":"What is life? The physical aspect of the living\n                        cell and mind","author":"Schr\u00f6dinger","year":"1944"},{"issue":"3","key":"2024102915293146800_bib38","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1002\/j.1538-7305.1948.tb01338.x","article-title":"A mathematical theory of communication","volume":"27","author":"Shannon","year":"1948","journal-title":"Bell System Technical Journal"},{"issue":"2","key":"2024102915293146800_bib39","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1086\/392768","article-title":"The concept of information in biology","volume":"67","author":"Smith","year":"2000","journal-title":"Philosophy of Science"},{"key":"2024102915293146800_bib40","volume-title":"Life\u2019s other secret: The new mathematics\n                        of the living world","author":"Stewart","year":"1999"},{"key":"2024102915293146800_bib41","doi-asserted-by":"publisher","first-page":"k1687","DOI":"10.1136\/bmj.k1687","article-title":"The 100 000 genomes project: Bringing whole genome sequencing\n                        to the NHS","volume":"361","author":"Turnbull","year":"2018","journal-title":"British Medical Journal"},{"issue":"5141","key":"2024102915293146800_bib42","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1038\/218525a0","article-title":"Towards a theoretical biology","volume":"218","author":"Waddington","year":"1968","journal-title":"Nature"},{"issue":"79","key":"2024102915293146800_bib43","doi-asserted-by":"publisher","first-page":"20120869","DOI":"10.1098\/rsif.2012.0869","article-title":"The algorithmic origins of life","volume":"10","author":"Walker","year":"2013","journal-title":"Journal of the Royal Society Interface"},{"key":"2024102915293146800_bib44","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1007\/978-3-319-93584-3_10","article-title":"Network theory in prebiotic\n                        evolution","volume-title":"Prebiotic chemistry and chemical evolution of nucleic\n                        acids","author":"Walker","year":"2018"},{"issue":"4356","key":"2024102915293146800_bib45","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1038\/171737a0","article-title":"Molecular structure of nucleic acids: A structure for\n                        deoxyribose nucleic acid","volume":"171","author":"Watson","year":"1953","journal-title":"Nature"},{"key":"2024102915293146800_bib46","volume-title":"Cybernetics or control and communication in the\n                        animal and the machine","author":"Wiener","year":"1948"},{"key":"2024102915293146800_bib47","volume-title":"Information theory and molecular biology","author":"Yockey","year":"1992"},{"issue":"3\u20134","key":"2024102915293146800_bib48","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1016\/S0020-0255(02)00173-1","article-title":"Information theory, evolution and the origin of\n                        life","volume":"141","author":"Yockey","year":"2002","journal-title":"Information Sciences"},{"key":"2024102915293146800_bib49","volume-title":"Symposium on information theory in\n                        biology","author":"Yockey","year":"1958"}],"container-title":["Artificial Life"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/direct.mit.edu\/artl\/article-pdf\/30\/1\/16\/2477371\/artl_a_00432.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/direct.mit.edu\/artl\/article-pdf\/30\/1\/16\/2477371\/artl_a_00432.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,29]],"date-time":"2024-10-29T15:29:44Z","timestamp":1730215784000},"score":1,"resource":{"primary":{"URL":"https:\/\/direct.mit.edu\/artl\/article\/30\/1\/16\/119531\/Information-Coding-and-Biological-Function-The"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024]]},"references-count":49,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,2,1]]},"published-print":{"date-parts":[[2024,2,1]]}},"URL":"https:\/\/doi.org\/10.1162\/artl_a_00432","relation":{},"ISSN":["1064-5462","1530-9185"],"issn-type":[{"value":"1064-5462","type":"print"},{"value":"1530-9185","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024]]},"published":{"date-parts":[[2024]]}}}