{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T19:47:36Z","timestamp":1785181656013,"version":"3.55.0"},"reference-count":50,"publisher":"MIT Press","issue":"1","content-domain":{"domain":["direct.mit.edu"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2024,2,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>It is very important to model the behavior of protocells as basic lifelike artificial organisms more and more accurately from the level of genomes to the level of populations. A better understanding of basic protocell communities may help us in describing more complex ecological systems accurately. In this article, we propose a new comprehensive, bilevel mathematical model of a community of three protocell species (one generalist and two specialists). The aim is to achieve a model that is as basic\/fundamental as possible while already displaying mutation, selection, and complex population dynamics phenomena (like competitive exclusion and keystone species). At the microlevel of genetic codes, the protocells and their mutations are modeled with Turing machines (TMs). The specialists arise from the generalist by means of mutation. Then the species are put into a common habitat, where, at the macrolevel of populations, they have to compete for the available nutrients, a part of which they themselves can produce. Because of different kinds of mutations, the running times of the species as TMs (algorithms) are different. This feature is passed on to the macrolevel as different reproduction times. At the macrolevel, a discrete-time dynamic model describes the competition. The model displays complex lifelike behavior known from population ecology, including the so-called competitive exclusion principle and the effect of keystone species. In future works, the bilevel model will have a good chance of serving as a simple and useful tool for studying more lifelike phenomena (like evolution) in their pure\/abstract form.<\/jats:p>","DOI":"10.1162\/artl_a_00463","type":"journal-article","created":{"date-parts":[[2024,12,24]],"date-time":"2024-12-24T16:59:46Z","timestamp":1735059586000},"page":"2-30","update-policy":"https:\/\/doi.org\/10.1162\/mitpressjournals.corrections.policy","source":"Crossref","is-referenced-by-count":2,"title":["Modeling the Mutation and Competition of Certain Nutrient-Producing Protocells by Means of Specific Turing Machines"],"prefix":"10.1162","volume":"31","author":[{"given":"Rich\u00e1rd","family":"Kicsiny","sequence":"first","affiliation":[{"name":"Hungarian University of Agriculture and Life Sciences, Institute of Mathematics and Basic Science, Department of Mathematics and Modelling. kicsiny.richard@uni-mate.hu"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Levente","family":"Hufnagel","sequence":"additional","affiliation":[{"name":"John Wesley Theological College, Research Institute of Multidisciplinary Ecotheology"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lajos","family":"L\u00f3czi","sequence":"additional","affiliation":[{"name":"ELTE Faculty of Informatics, Department of Numerical Analysis"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L\u00e1szl\u00f3","family":"Sz\u00e9kely","sequence":"additional","affiliation":[{"name":"Hungarian University of Agriculture and Life Sciences, Institute of Mathematics and Basic Science, Department of Mathematics and Modelling"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zolt\u00e1n","family":"Varga","sequence":"additional","affiliation":[{"name":"Hungarian University of Agriculture and Life Sciences, Institute of Mathematics and Basic Science, Department of Mathematics and Modelling"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"281","published-online":{"date-parts":[[2025,2,25]]},"reference":[{"key":"2025022519462490500_bib1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-84882-530-7","volume-title":"Artificial life models in hardware","author":"Adamatzky","year":"2009"},{"issue":"11","key":"2025022519462490500_bib2","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1016\/S0300-9084(02)00035-4","article-title":"Genetically modified bacteria in agriculture","volume":"84","author":"Amarger","year":"2002","journal-title":"Biochimie"},{"key":"2025022519462490500_bib3","volume-title":"MATLAB: A practical introduction to programming and problem solving","author":"Attaway","year":"2019"},{"issue":"11","key":"2025022519462490500_bib4","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1016\/j.tics.2003.09.012","article-title":"Artificial Life: Organization, adaptation and complexity from the bottom up","volume":"7","author":"Bedau","year":"2003","journal-title":"Trends in Cognitive Sciences"},{"key":"2025022519462490500_bib5","volume-title":"Computability and unsolvability","author":"Davis","year":"1982"},{"key":"2025022519462490500_bib6","first-page":"95","article-title":"Mesoscopic analysis of self-evolution in an artificial chemistry","volume-title":"Artificial Life VI","author":"Dittrich","year":"1998"},{"issue":"3","key":"2025022519462490500_bib7","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1162\/106454601753238636","article-title":"Artificial chemistries\u2014a review","volume":"7","author":"Dittrich","year":"2001","journal-title":"Artificial Life"},{"key":"2025022519462490500_bib8","volume-title":"An introduction to difference equations","author":"Elaydi","year":"2005","edition":"3rd ed."},{"issue":"6","key":"2025022519462490500_bib9","doi-asserted-by":"publisher","first-page":"Article 061901","DOI":"10.1103\/PhysRevE.77.061901","article-title":"Evolutionary model with Turing machines","volume":"77","author":"Feverati","year":"2008","journal-title":"Physical Review E"},{"issue":"1","key":"2025022519462490500_bib10","doi-asserted-by":"publisher","first-page":"e1000292","DOI":"10.1371\/journal.pbio.1000292","article-title":"Evolution of adaptive behaviour in robots by means of Darwinian selection","volume":"8","author":"Floreano","year":"2010","journal-title":"PLoS Biology"},{"key":"2025022519462490500_bib11","doi-asserted-by":"publisher","DOI":"10.1117\/12.669679","article-title":"Foundations of evolutionary computation","volume-title":"Proceedings of SPIE 6228","author":"Fogel","year":"2006"},{"key":"2025022519462490500_bib12","volume-title":"Algorithmic chemistry","author":"Fontana","year":"1990"},{"key":"2025022519462490500_bib13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/BF02458289","article-title":"\u201cThe arrival of the fittest\u201d: Toward a theory of biological organization","volume":"56","author":"Fontana","year":"1994","journal-title":"Bulletin of Mathematical Biology"},{"issue":"1","key":"2025022519462490500_bib14","doi-asserted-by":"publisher","first-page":"Article e01151\u201320","DOI":"10.1128\/mSystems.01151-20","article-title":"Identifying potentially beneficial genetic mutations associated with monophyletic selective sweep and a proof-of-concept study with viral genetic data","volume":"6","author":"Furuse","year":"2021","journal-title":"mSystems"},{"key":"2025022519462490500_bib15","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1016\/j.jtbi.2017.06.025","article-title":"Ecological monitoring in a discrete-time prey-predator model","volume":"429","author":"G\u00e1mez","year":"2017","journal-title":"Journal of Theoretical Biology"},{"key":"2025022519462490500_bib16","doi-asserted-by":"crossref","DOI":"10.1093\/acprof:oso\/9780198507260.001.0001","volume-title":"The principles of life","author":"G\u00e1nti","year":"2003"},{"issue":"2","key":"2025022519462490500_bib17","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1007\/s10340-014-0609-z","article-title":"A new multistage dynamic model for biological control exemplified by the host\u2013parasitoid system Spodoptera exigua-Chelonus oculator","volume":"88","author":"Garay","year":"2015","journal-title":"Journal of Pest Science"},{"issue":"1400","key":"2025022519462490500_bib18","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1098\/rspb.1998.0391","article-title":"When will a sexual population evolve to an ESS?","volume":"265","author":"Garay","year":"1998","journal-title":"Proceedings of the Royal Society B"},{"issue":"7","key":"2025022519462490500_bib19","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/j.jtbi.2012.06.021","article-title":"Optimal nutrient foraging strategy of an omnivore: Liebig\u2019s law determining numerical response","volume":"310","author":"Garay","year":"2012","journal-title":"Journal of Theoretical Biology"},{"issue":"4","key":"2025022519462490500_bib20","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1242\/jeb.9.4.389","article-title":"Experimental studies on the struggle for existence: 1. Mixed population of two species of yeast","volume":"9","author":"Gause","year":"1932","journal-title":"Journal of Experimental Biology"},{"issue":"3","key":"2025022519462490500_bib21","doi-asserted-by":"publisher","first-page":"391","DOI":"10.1162\/artl_a_00324","article-title":"Self-organization and Artificial Life","volume":"26","author":"Gershenson","year":"2020","journal-title":"Artificial Life"},{"issue":"3409","key":"2025022519462490500_bib22","doi-asserted-by":"publisher","first-page":"1292","DOI":"10.1126\/science.131.3409.1292","article-title":"The competitive exclusion principle","volume":"131","author":"Hardin","year":"1960","journal-title":"Science"},{"key":"2025022519462490500_bib23","doi-asserted-by":"publisher","DOI":"10.1017\/9781139029117","volume-title":"Biological control: Ecology and applications","author":"Heimpel","year":"2017"},{"key":"2025022519462490500_bib24","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9781139173179","volume-title":"Evolutionary games and population dynamics","author":"Hofbauer","year":"1998"},{"key":"2025022519462490500_bib25","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-84882-285-6","volume-title":"Artificial Life models in software","author":"Komosinski","year":"2009"},{"issue":"3","key":"2025022519462490500_bib26","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1093\/biomet\/33.3.183","article-title":"On the use of matrices in certain population mathematics","volume":"33","author":"Leslie","year":"1945","journal-title":"Biometrika"},{"issue":"1","key":"2025022519462490500_bib27","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1016\/j.biosystems.2006.03.005","article-title":"Monitoring in a Lotka-Volterra model","volume":"87","author":"L\u00f3pez","year":"2007","journal-title":"Biosystems"},{"key":"2025022519462490500_bib28","volume-title":"Complexity of algorithms","author":"Lov\u00e1sz","year":"2014"},{"key":"2025022519462490500_bib29","doi-asserted-by":"publisher","first-page":"154096","DOI":"10.1109\/ACCESS.2019.2949286","article-title":"Black-box vs. white-box: Understanding their advantages and weaknesses from a practical point of view","volume":"7","author":"Loyola-Gonzalez","year":"2019","journal-title":"IEEE Access"},{"key":"2025022519462490500_bib30","doi-asserted-by":"publisher","DOI":"10.1007\/978-981-10-6955-0","volume-title":"DNA replication: From old principles to new discoveries","author":"Masai","year":"2018"},{"issue":"4","key":"2025022519462490500_bib31","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1162\/106454600300103674","article-title":"John von Neumann and the evolutionary growth of complexity: Looking backward, looking forward","volume":"6","author":"McMullin","year":"2000","journal-title":"Artificial Life"},{"issue":"1","key":"2025022519462490500_bib32","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1016\/j.biosystems.2011.08.003","article-title":"Mutation-selection dynamics and error threshold in an evolutionary model for turing machines","volume":"107","author":"Musso","year":"2012","journal-title":"Biosystems"},{"issue":"20","key":"2025022519462490500_bib33","first-page":"57","article-title":"Empirical aspects of computability theory","volume":"7","author":"Mycka","year":"2004","journal-title":"Studies in Grammar, Logic, and Rhetoric"},{"key":"2025022519462490500_bib34","volume-title":"A novel approach to point mutation","author":"Norman","year":"2015"},{"key":"2025022519462490500_bib35","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1007\/BF00184645","article-title":"Automata, repeated games and noise","volume":"33","author":"Nowak","year":"1995","journal-title":"Journal of Mathematical Biology"},{"issue":"7","key":"2025022519462490500_bib36","doi-asserted-by":"publisher","first-page":"a010108","DOI":"10.1101\/cshperspect.a010108","article-title":"Principles and concepts of DNA replication in Bacteria, Archaea, and Eukarya","volume":"5","author":"O\u2019Donnell","year":"2013","journal-title":"Cold Spring Harbor Perspectives in Biology"},{"issue":"929","key":"2025022519462490500_bib37","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1086\/282586","article-title":"A note on trophic complexity and community stability","volume":"103","author":"Paine","year":"1969","journal-title":"American Naturalist"},{"issue":"4","key":"2025022519462490500_bib38","doi-asserted-by":"publisher","first-page":"962","DOI":"10.1046\/j.1523-1739.1995.09040962.x","article-title":"A conversation on refining the concept of keystone species","volume":"9","author":"Paine","year":"1995","journal-title":"Conservation Biology"},{"key":"2025022519462490500_bib39","doi-asserted-by":"publisher","DOI":"10.1038\/d41586-018-05476-4","article-title":"Genetically modified bacteria enlisted in fight against disease","author":"Reardon","year":"2018","journal-title":"Nature"},{"issue":"4","key":"2025022519462490500_bib40","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1016\/j.plrev.2009.08.001","article-title":"Evolutionary game theory: Temporal and spatial effects beyond replicator dynamics","volume":"6","author":"Roca","year":"2009","journal-title":"Physics of Life Reviews"},{"key":"2025022519462490500_bib41","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-50151-7","volume-title":"The golden age of theoretical ecology: 1923\u20131940","author":"Scudo","year":"1978"},{"key":"2025022519462490500_bib42","volume-title":"Formal modelling for population dynamics","author":"Setiawan","year":"2015"},{"key":"2025022519462490500_bib43","volume-title":"Some dynamical properties of Turing machine dynamical models","author":"Torres Avil\u00e9s","year":"2016"},{"issue":"42","key":"2025022519462490500_bib44","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1112\/plms\/s2-42.1.230","article-title":"On computable numbers, with an application to the entscheidungsproblem","volume":"2","author":"Turing","year":"1937","journal-title":"Proceedings of the London Mathematical Society"},{"key":"2025022519462490500_bib45","doi-asserted-by":"publisher","first-page":"1139","DOI":"10.1007\/978-3-642-56478-9_59","article-title":"The Turing machine paradigm in contemporary computing","volume-title":"Mathematics unlimited\u20142001 and beyond","author":"van Leeuwen","year":"2001"},{"key":"2025022519462490500_bib46","volume-title":"Le\u00e7ons sur la th\u00e9orie math\u00e9matique de la Lutte pour la vie","author":"Volterra","year":"1931"},{"key":"2025022519462490500_bib47","volume-title":"Theory of self-reproducing automata","author":"von Neumann","year":"1966"},{"key":"2025022519462490500_bib48","doi-asserted-by":"publisher","DOI":"10.7551\/mitpress\/4660.001.0001","volume-title":"The MIT encyclopedia of the cognitive sciences","author":"Wilson","year":"1999"},{"key":"2025022519462490500_bib49","volume-title":"A new kind of science","author":"Wolfram","year":"2002"},{"key":"2025022519462490500_bib50","doi-asserted-by":"publisher","first-page":"Article 10","DOI":"10.1186\/s12896-017-0337-6","article-title":"A novel point mutation in RpoB improves osmotolerance and succinic acid production in Esherichia coli","volume":"17","author":"Xiao","year":"2017","journal-title":"BMC Biotechnology"}],"container-title":["Artificial Life"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/direct.mit.edu\/artl\/article-pdf\/31\/1\/2\/2487214\/artl_a_00463.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/direct.mit.edu\/artl\/article-pdf\/31\/1\/2\/2487214\/artl_a_00463.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,25]],"date-time":"2025-02-25T19:46:39Z","timestamp":1740512799000},"score":1,"resource":{"primary":{"URL":"https:\/\/direct.mit.edu\/artl\/article\/31\/1\/2\/125952\/Modeling-the-Mutation-and-Competition-of-Certain"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2,25]]},"references-count":50,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,2,25]]},"published-print":{"date-parts":[[2024,2,25]]}},"URL":"https:\/\/doi.org\/10.1162\/artl_a_00463","relation":{},"ISSN":["1064-5462","1530-9185"],"issn-type":[{"value":"1064-5462","type":"print"},{"value":"1530-9185","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025]]},"published":{"date-parts":[[2024,2,25]]}}}