{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T04:28:40Z","timestamp":1772252920812,"version":"3.50.1"},"reference-count":165,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2017,3,6]],"date-time":"2017-03-06T00:00:00Z","timestamp":1488758400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002322","name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","doi-asserted-by":"publisher","award":["10313\/88-2"],"award-info":[{"award-number":["10313\/88-2"]}],"id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]},{"name":"PCI\/LNCC, Brazil","award":["several"],"award-info":[{"award-number":["several"]}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["097820\/Z\/11\/B"],"award-info":[{"award-number":["097820\/Z\/11\/B"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004586","name":"Funda\u00e7\u00e3o Carlos Chagas Filho de Amparo \u00e0 Pesquisa do Estado do Rio de Janeiro","doi-asserted-by":"publisher","award":["several"],"award-info":[{"award-number":["several"]}],"id":[{"id":"10.13039\/501100004586","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004586","name":"Funda\u00e7\u00e3o Carlos Chagas Filho de Amparo \u00e0 Pesquisa do Estado do Rio de Janeiro","doi-asserted-by":"publisher","award":["101.261\/2014"],"award-info":[{"award-number":["101.261\/2014"]}],"id":[{"id":"10.13039\/501100004586","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Systems"],"abstract":"<jats:p>Warren Weaver, writing about the function that science should have in mankind\u2019s developing future, ideas and ideals, proposed to classify scientific problems into \u2018problems of simplicity\u2019, \u2018problems of disorganised complexity\u2019, and \u2018problems of organised complexity\u2019\u2014the huge complementary class to which all biological, human, and social problems belong. Problems of simplicity have few components and variables and have been extensively addressed in the last 400 years. Problems of disorganised complexity have a huge number of individually erratic components and variables, but possess collective regularities that can be analysed by resourcing to stochastic methods. Yet, \u2018problems of organised complexity\u2019 do not yield easily to classical or statistical treatment. Interrelations among phenomenon elements change during its evolution alongside commonly used state variables. This invalidates independence and additivity assumptions that support reductionism and affect behaviour and outcome. Moreover, organisation, the focal point in this complementary class, is still an elusive concept despite gigantic efforts undertaken since a century ago to tame it. This paper addresses the description, representation and study of phenomena in the \u2018problems of organised complexity\u2019 class, arguing that they should be treated as a collection of interacting organisations. Furthermore, grounded on relational mathematical constructs, a formal theoretical framework that provides operational definitions, schemes for representing organisations and their changes, as well as interactions of organisations is introduced. Organisations formally extend the general systems concept and suggest a novel perspective for addressing organised complexity phenomena as a collection of interacting organisations.<\/jats:p>","DOI":"10.3390\/systems5010023","type":"journal-article","created":{"date-parts":[[2017,3,9]],"date-time":"2017-03-09T06:56:43Z","timestamp":1489042603000},"page":"23","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["From Systems to Organisations"],"prefix":"10.3390","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2205-9981","authenticated-orcid":false,"given":"Maur\u00edcio","family":"Kritz","sequence":"first","affiliation":[{"name":"National Laboratory for Scientific Computation, Av. Get\u00falio Vargas, 333, 25651-075 Petr\u00f3polis, RJ, Brazil"}]}],"member":"1968","published-online":{"date-parts":[[2017,3,6]]},"reference":[{"key":"ref_1","first-page":"536","article-title":"Science and Complexity","volume":"36","author":"Weaver","year":"1948","journal-title":"Am. Sci."},{"key":"ref_2","unstructured":"Miller, J.G. (1978). Living Systems, McGraw-Hill Book Co., Inc."},{"key":"ref_3","first-page":"2673","article-title":"Boundaries, Interactions and Environmental Systems","volume":"29","author":"Kritz","year":"2010","journal-title":"Mec. Comput."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Mohler, R.R., and Ruberti, A. (1978). Recent Developments in Variable Structure Systems, Economics and Biology, Springer. Lecture Notes in Economics and Mathematical Systems.","DOI":"10.1007\/978-3-642-45509-4"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Junk, W.J. (1997). The Central Amazon Floodplain: Ecology of a Pulsating System, Springer.","DOI":"10.1007\/978-3-662-03416-3"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"De Ruiter, P.C., Wolters, V., and Moore, J.C. (2005). Dynamic Food Webs : Multi-species Assemblages, Ecosystem Development, and Environmental Change, Elsevier.","DOI":"10.1016\/B978-012088458-2\/50002-3"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Pascual, M., and Dunne, J.A. (2006). Ecological Networks: Linking Structure to Dynamics in Food Webs, Studies in the Sciences of Complexity, Santa Fe Institute, Oxford University Press.","DOI":"10.1093\/oso\/9780195188165.002.0002"},{"key":"ref_8","unstructured":"Rosen, R. (1991). Life Itself: A Comprehesive Inquiry into the Nature, Origin, and Fabrication of Life, Columbia University Press."},{"key":"ref_9","unstructured":"Hofmeyr, J.H.S. (2007). Systems Biology: Philosophical Foundations, Elsevier B.V."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/bs.3830170102","article-title":"Living Systems: The Organization","volume":"17","author":"Miller","year":"1972","journal-title":"Behav. Sci."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Harold, F.M. (2001). The Way of the Cell: Molecules, Organisms and the Order of Life, Oxford University Press.","DOI":"10.1093\/oso\/9780195135121.001.0001"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1086\/286778","article-title":"Living Systems and Non-living Systems","volume":"9","author":"Lillie","year":"1942","journal-title":"Philos. Sci."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/j.ecocom.2004.07.003","article-title":"On the nature of ecodynamics","volume":"1","author":"Ulanowicz","year":"2004","journal-title":"Ecol. Complex."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1128\/MMBR.69.4.544-564.2005","article-title":"Molecules into Cells: Specifying Spatial Architecture","volume":"69","author":"Harold","year":"2005","journal-title":"Microbiol. Mole. Biol. Rev."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Alon, U. (2007). An Introduction to Systems Biology: Design Principles of Biological Circuits, Mathematical and Computational Biology, Chapman & Hall\/CRC.","DOI":"10.1201\/9781420011432"},{"key":"ref_16","unstructured":"Boogerd, F.C., Bruggeman, F.J., Hofmeyr, J.H.S., and Westerhoff, H.V. (2007). Systems Biology: Philosophical Foundations, Elsevier."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.jtbi.2011.01.051","article-title":"The challenges and scope of theoretical biology","volume":"276","author":"Krakauer","year":"2011","journal-title":"J. Theor. Biol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1002\/cplx.20049","article-title":"Evolution in complex systems","volume":"10","author":"Anderson","year":"2004","journal-title":"Complexity"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Roberts, A.J. (2015). Model Emergent Dynamics in Complex Systems, Mathematical Modeling and Computation, SIAM, Society for Industrial and Applied Mathematics.","DOI":"10.1137\/1.9781611973563"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1142\/S0218339008002514","article-title":"Extended Critical Situations: The Physical Singularity of Life Phenomena","volume":"16","author":"Bailly","year":"2008","journal-title":"J. Biol. Syst."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1086\/394374","article-title":"Biological Organization","volume":"6","author":"Watson","year":"1931","journal-title":"Q. Rev. Biol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Mesarovi\u0107, M.D. (1968). System Theory and Biology, Springer.","DOI":"10.1007\/978-3-642-88343-9"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Klir, G.J. (2001). Facets of Systems Science, Plenum Press. [2nd ed.].","DOI":"10.1007\/978-1-4615-1331-5"},{"key":"ref_24","unstructured":"Balescu, R. (1975). Equilibrium and Non-Equilibrium Statistical Mechanics, A Wiley-Interscience Publication, John Wiley & Sons."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/0025-5564(75)90108-X","article-title":"On interactions between dynamical systems","volume":"27","author":"Rosen","year":"1975","journal-title":"Math. Biosci."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Peixoto, M.M., Rand, D., and Pinto, A.A. (2011). Dynamics, Games and Science II, Springer.","DOI":"10.1007\/978-3-642-14788-3"},{"key":"ref_27","unstructured":"von Foster, H., and Zopf, G.W. (1962). Principles of Self-Organization: Transactions of the University of Illinois Symposium, University of Illinois, Pergamon Press."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1080\/03081077408960769","article-title":"Biological Systems as Organizational Paradigms","volume":"1","author":"Rosen","year":"1974","journal-title":"Int. J. Gen. Syst."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/0303-2647(74)90031-8","article-title":"Autopoiesis: The Organization of Living Systems, Its Characterization and a Model","volume":"5","author":"Varela","year":"1974","journal-title":"Biosystems"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1002\/bs.3830100302","article-title":"Living Systems: Basic Concepts","volume":"10","author":"Miller","year":"1965","journal-title":"Behav. Sci."},{"key":"ref_31","unstructured":"Auger, P. (1961). On Modern Physics, Clarkson N. Potter, Inc. Publisher."},{"key":"ref_32","first-page":"55","article-title":"Living systems","volume":"4","author":"Miller","year":"1971","journal-title":"Curr. Mod. Biol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1146\/annurev.micro.55.1.165","article-title":"Quorum Sensing In Bacteria","volume":"55","author":"Miller","year":"2001","journal-title":"Ann. Rev. Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Stoney, R.A., Ames, R.M., Nenadic, G., Robertson, D.L., and Schwartz, J.M. (2015). Disentangling the multigenic and pleiotropic nature of molecular function. BMC Syst. Biol., 9.","DOI":"10.1186\/1752-0509-9-S6-S3"},{"key":"ref_35","unstructured":"Oyeyemi, O.J. (2016). Modelling HIV-1 Interaction with the Host System. [Ph.D. Thesis, University of Manchester]."},{"key":"ref_36","first-page":"2331","article-title":"Using fly genetics to dissect the cytoskeletal machinery of neurons during axonal growth and maintenance","volume":"126","author":"Prokop","year":"2013","journal-title":"J. Cell Sci."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1264","DOI":"10.1109\/TCBB.2014.2318715","article-title":"Organized modularity in the interactome: Evidence from the analysis of dynamic organization in the cell cycle","volume":"11","author":"Wang","year":"2014","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1276","DOI":"10.1002\/pmic.201200412","article-title":"Quantitative analysis of chaperone network throughput in budding yeast","volume":"13","author":"Brownridge","year":"2013","journal-title":"Proteomics"},{"key":"ref_39","unstructured":"Peacocke, A.R. (1983). An Introduction to the Physical Chemistry of Biological Organization, Clarendon Press."},{"key":"ref_40","unstructured":"Atlan, H. (1986). Entre le Cristal et la Fum\u00e9e. Essay sur l\u2019Organization du Vivant, \u00c9ditions du Seuil."},{"key":"ref_41","unstructured":"Kritz, M.V. (1996, January 9\u201312). Creating Bio-Mathematical Worlds. P&D Report 29\/95, LNCC\/MCT, Petr\u00f3polis, 1995. Proceedings of the 13th European Meeting on Cybernetics and Systems Research, Vienna, Austria."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.pbiomolbio.2013.03.019","article-title":"Theoretical aspects of Systems Biology","volume":"112","author":"Bizzarri","year":"2013","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1080\/03081070701524232","article-title":"High end complexity","volume":"37","author":"Kitto","year":"2008","journal-title":"Int. J. Gen. Syst."},{"key":"ref_44","unstructured":"Waddington, C.H. (1959). Biological Organization, Cellular and Sub-cellular, Pergamon Press."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1063\/1.882934","article-title":"Motile behavior of bacteria","volume":"53","author":"Berg","year":"2000","journal-title":"Phys. Today"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1152\/physrev.00018.2013","article-title":"Actin Dynamics, Architecture, and Mechanics in Cell Motility","volume":"94","author":"Blanchoin","year":"2014","journal-title":"Physiol. Rev."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1111\/j.1469-185X.1933.tb01153.x","article-title":"On the dissociability of the fundamental processes in ontogenesis","volume":"8","author":"Needham","year":"1933","journal-title":"Biol. Rev."},{"key":"ref_48","unstructured":"Rosen, R. (1977). Structural And Functional Considerations in the Modelling of Biological Organization, The Center for Theoretical Biology, SUNY. Technical Report 77 25."},{"key":"ref_49","unstructured":"Schweitzer, F. (1997). Self-Organization of Complex Structures: From Individual to Collective Dynamics, CRC Press, Taylor and Francis Group, LLC."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1126\/science.324.5924.197","article-title":"Proteins in Motion","volume":"324","author":"Vinson","year":"2009","journal-title":"Science"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.pbiomolbio.2012.06.004","article-title":"Is information a proper observable for biological organization?","volume":"109","author":"Longo","year":"2012","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"ref_52","unstructured":"von Bertalanffy, L. (1968). General Systems Theory, Allen Lane The Penguin Press."},{"key":"ref_53","unstructured":"Casti, J.L., and Karlqvist, A. (1996). Boundaries and Barriers, Addison-Wesley Publishing Company, Inc."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1016\/j.jtbi.2005.07.007","article-title":"Organizational invariance and metabolic closure: Analysis in terms of systems","volume":"238","author":"Letelier","year":"2006","journal-title":"J. Theor. Biol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1016\/j.jtbi.2015.05.015","article-title":"Tibor G\u00e1nti and Robert Rosen: Contrasting approaches to the same problem","volume":"381","year":"2015","journal-title":"J. Theor. Biol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.jtbi.2015.04.036","article-title":"The systems perspective at the crossroads between chemistry and biology","volume":"381","author":"Briones","year":"2015","journal-title":"J. Theor. Biol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.jtbi.2015.02.029","article-title":"Biological Organization as Closure of Constraints","volume":"372","author":"Mossio","year":"2015","journal-title":"J. Theor. Biol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1007\/s11538-006-9130-8","article-title":"Chemical Organisation Theory","volume":"69","author":"Dittrich","year":"2007","journal-title":"Bull. Math. Biol."},{"key":"ref_59","unstructured":"Kauffman, S.A. (1995). At Home in the Universe: The Search for Laws of Self-Organization and Complexity, Oxford University Press."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Kauffman, S.A. (1993). The Origins of Order: Self-Organization and Selection in Evolution, Oxford University Press.","DOI":"10.1093\/oso\/9780195079517.001.0001"},{"key":"ref_61","first-page":"229","article-title":"Life, information theory, and topology","volume":"17","author":"Rashevsky","year":"1955","journal-title":"Bull. Math. Biol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/0022-5193(68)90059-3","article-title":"Application of information theory to the study of the stimulating effects of ionizing radiation, thermal energy, and other environmental factors. Preliminary ideas for a theory of organization","volume":"21","author":"Atlan","year":"1968","journal-title":"J. Theor. Biol."},{"key":"ref_63","unstructured":"Walker, I. (2005). The Evolution of Biological Organization as a Function of Information, Editora INPA."},{"key":"ref_64","first-page":"317","article-title":"Topology and life: In search of general mathematical principles in biology and sociology","volume":"16","author":"Rashevsky","year":"1954","journal-title":"Bull. Math. Biol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/0022-5193(74)90115-5","article-title":"On a formal definition of organization","volume":"45","author":"Atlan","year":"1974","journal-title":"J. Theor. Biol."},{"key":"ref_66","unstructured":"Pahl-Wostl, C. (1995). The Dynamic Nature of Ecosystems, Chaos and Order Entwined, John Wiley & Sons."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1006\/ijhc.1974.0304","article-title":"The Organization of the Living: A Theory of the Living Organization","volume":"51","author":"Maturana","year":"1999","journal-title":"Int. J. Hum. Comput. Stud."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1007\/s10516-005-4203-0","article-title":"(M,R)-Systems and their Realizations","volume":"16","author":"Louie","year":"2006","journal-title":"Axiomathes"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1007\/s10516-011-9154-z","article-title":"Relational Science: A Synthesis","volume":"21","author":"Kineman","year":"2011","journal-title":"Axiomathes"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1080\/03081079.2012.728406","article-title":"On structure and organization: An organizing principle","volume":"42","author":"Baas","year":"2013","journal-title":"Int. J. Gen. Syst."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1080\/03081079.2015.1118095","article-title":"On higher structures","volume":"45","author":"Baas","year":"2016","journal-title":"Int. J. Gen. Syst."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1080\/03081079.2015.1123708","article-title":"The Animate\u2014Inanimate Relationship","volume":"45","author":"Hellerman","year":"2016","journal-title":"Int. J. Gen. Syst."},{"key":"ref_73","unstructured":"Schweitzer, F. (1997). Self-organisation of Complex Structures: From Individual to Collective Dynamics, CRC Press."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/131457a0","article-title":"Light and Life","volume":"131","author":"Bohr","year":"1933","journal-title":"Nature"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1086\/392768","article-title":"The Concept of Information in Biology","volume":"67","year":"2000","journal-title":"Philos. Sci."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.plrev.2004.01.002","article-title":"Information theory in molecular biology","volume":"1","author":"Adami","year":"2004","journal-title":"Phys. Life Rev."},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Feltz, B., Crommelinck, M., and Goujon, P. (2006). Self-Organization and Emergence in Life Sciences, Springer.","DOI":"10.1007\/1-4020-3917-4"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/0048-9697(95)04969-X","article-title":"Ecosystem dynamics viewed from an endoperspective","volume":"183","author":"Hauhs","year":"1996","journal-title":"Sci. Total Environ."},{"key":"ref_79","unstructured":"Jablonka, E., and Lamb, M.J. (2005). Life and Mind: Philosophical Issues in Biology and Psycology, A Bradford Book, The MIT Press."},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Roederer, J.G. (2005). Information and its Role in Nature, Springer. The Frontiers Collection.","DOI":"10.1007\/3-540-27698-X"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1080\/03081079.2013.776206","article-title":"On creativity of slime mould","volume":"42","author":"Adamatzky","year":"2013","journal-title":"Int. J. Gen. Syst."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1145\/1247047.1247052","article-title":"To a Mathematical Definition of \u2018LIFE\u2019","volume":"4","author":"Chaitin","year":"1970","journal-title":"SIGACT News"},{"key":"ref_83","unstructured":"Levine, R.D., and Tribus, M. (1979). Maximum Entropy Formalism, M.I.T. Press."},{"key":"ref_84","unstructured":"Langton, C. (1989). Artificial Life, Addison-Wesley Publishing Company, Inc."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1007\/BF02458575","article-title":"The cellular computer DNA: Program or data","volume":"52","author":"Atlan","year":"1990","journal-title":"Bull. Math. Biol."},{"key":"ref_86","first-page":"1","article-title":"The Computational Notion of Life","volume":"9","author":"Emmeche","year":"1994","journal-title":"Theoria"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1086\/392891","article-title":"Genetic Information: A Metaphor in Search of a Theory","volume":"68","author":"Griffiths","year":"2001","journal-title":"Philos. Sci."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1086\/344621","article-title":"Information: Its interpretation, its inheritance, and its sharing","volume":"69","author":"Jablonka","year":"2002","journal-title":"Philos. Sci."},{"key":"ref_89","unstructured":"Thaller, B. (2005). Advanced Visual Quantum Mechanics, Springer Science+Business Media Inc."},{"key":"ref_90","unstructured":"Scott Kelso, J.A. (1999). Dynamic Patterns: The Self-Organization of Brain and Behaviour, The MIT Press, A Bradford Book."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1080\/0951508021000041996","article-title":"BioComplexity: A pluralist research strategy is necessary for a mechanistic explanation of the \u201clive\u201d state","volume":"15","author":"Bruggeman","year":"2002","journal-title":"Philos. Psychol."},{"key":"ref_92","first-page":"377","article-title":"Counting Isomers and Isomerizations","volume":"Volume 576","author":"Capobianco","year":"1989","journal-title":"Graph Theory and Its Applications: East and West, Proceedings of the First China_USA International Graph Theory Conference, Jinan, China, June 9\u201320, 1986"},{"key":"ref_93","first-page":"347","article-title":"The chiral graph theory","volume":"73","author":"Dobrowolski","year":"2015","journal-title":"MATCH Commun. Math. Comput. Chem."},{"key":"ref_94","doi-asserted-by":"crossref","unstructured":"Barwise, J. (1975). Admissible Sets and Structures, Springer.","DOI":"10.1007\/978-3-662-11035-5"},{"key":"ref_95","unstructured":"Kritz, M.V. (1991). On Biology and Information, LNCC\/MCTI. P&D Report 25\/91."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"C47","DOI":"10.1038\/35011540","article-title":"From molecular to modular cell biology","volume":"402","author":"Hartwell","year":"1999","journal-title":"Nature"},{"key":"ref_97","unstructured":"Berge, C. (1973). Graphs and Hypergraphs, North-Holland."},{"key":"ref_98","doi-asserted-by":"crossref","unstructured":"Schmidt, G., and Str\u00f6hlein, T. (1993). Relations and Graphs: Discrete Mathematics for Computer Scientists, Springer. EACTS Monagraphs on Theoretical Computer Science.","DOI":"10.1007\/978-3-642-77968-8"},{"key":"ref_99","doi-asserted-by":"crossref","unstructured":"Klamt, S., Haus, U.U., and Theis, F. (2009). Hypergraphs and Cellular Networks. PLoS Comput. Biol., 5.","DOI":"10.1371\/journal.pcbi.1000385"},{"key":"ref_100","unstructured":"Mondaini, R., and Dil\u00e3o, R. (2006). Proceedings of the International Symposium on Mathematical and Computational Biology (BIOMAT 2005), E-papers Servi\u00e7os Editoriais Ltda."},{"key":"ref_101","unstructured":"Manna, Z. (1974). The Mathematical Theory of Computation, McGraw-Hill Co."},{"key":"ref_102","unstructured":"Bailly, A. (1963). Dictionnaire Grec Fran\u00e7ais, Librairie Hachette. [26th ed.]. (1e \u00c9dition, 1894)."},{"key":"ref_103","doi-asserted-by":"crossref","unstructured":"Arnol\u2019d, V.I. (1978). Mathematical Methods of Classical Mechanics; Vol. 60, Graduate Texts in Mathematics, Springer.","DOI":"10.1007\/978-1-4757-1693-1"},{"key":"ref_104","unstructured":"Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., and Walter, P. (2002). Molecular Biology of the Cell, Garland Science. [4th ed.]."},{"key":"ref_105","first-page":"153","article-title":"On Relations between i-graphs and Data Structures","volume":"39","author":"Kritz","year":"1996","journal-title":"Logique Analyse"},{"key":"ref_106","first-page":"89","article-title":"Biological Organizations","volume":"Volume 2","author":"Mondaini","year":"2005","journal-title":"Proceedings of the IV Brazilian Symposium on Mathematical and Computational Biology (BIOMAT IV)"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1038\/nature08112","article-title":"Adaptive prediction of environmental changes by microorganisms","volume":"460","author":"Mitchell","year":"2009","journal-title":"Nature"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1038\/nature14237","article-title":"Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity","volume":"519","author":"Lee","year":"2015","journal-title":"Nature"},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"aac7341","DOI":"10.1126\/science.aac7341","article-title":"Genetic circuit design automation","volume":"352","author":"Nielsen","year":"2016","journal-title":"Science"},{"key":"ref_110","doi-asserted-by":"crossref","unstructured":"Stonier, T. (1990). Information and the Internal Structure of the Universe, Springer.","DOI":"10.1007\/978-1-4471-3265-3"},{"key":"ref_111","unstructured":"Schweitzer, F. (1997). Self-organisation of Complex Structures: From Individual to Collective Dynamics, CRC Press."},{"key":"ref_112","unstructured":"Shannon, C.E., and Weaver, W. (1949). The Mathematical Theory of Communication, University of Illinois Press."},{"key":"ref_113","unstructured":"Hoath, S.B. (1997, January 18\u201321). Considerations on the Role of the Skin as the Boundary of an Autopoietic System. Proceedings of the Biology, Language, Cognition and Society: International Symposium on Autopoiesis, Belo Horizonte, Brazil."},{"key":"ref_114","doi-asserted-by":"crossref","unstructured":"Santra, T., Kolch, W., and Kholodenko, B.N. (2014). Navigating the multilayered organization of eukaryotic signaling: A new trend in data integration. PLoS Comput. Biol., 10.","DOI":"10.1371\/journal.pcbi.1003385"},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1080\/03081070903453685","article-title":"Anticipation and dynamics: Rosen\u2019s anticipation in the perspective of time","volume":"39","author":"Nadin","year":"2010","journal-title":"Int. J. Gen. Syst."},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"1416","DOI":"10.1016\/j.bpj.2012.08.041","article-title":"Mechanical activation of cells induces chromatin remodeling preceding MKL nuclear transport","volume":"103","author":"Iyer","year":"2012","journal-title":"Biophys. J."},{"key":"ref_117","unstructured":"Gerritsen, V.B. (2003). Moody wallpaper. Protein Spotlight, 33, Available online: http:\/\/citeseerx.ist.psu.edu\/viewdoc\/download?doi=10.1.1.616.8546&rep=rep1&type=pdf."},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1016\/j.bmcl.2008.12.016","article-title":"Insight into the effects of chiral isomers quinidine and quinine on CYP2D6 inhibition","volume":"19","author":"Ai","year":"2009","journal-title":"Bioorg. Med. Chem. Lett."},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1007\/BF01073624","article-title":"The Pheromone Activity of Chiral Isomers of Trogodermal for Male Khapra Beetles","volume":"67","author":"Levinson","year":"1980","journal-title":"Naturwissenschaften"},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1016\/j.molcel.2014.03.011","article-title":"CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity","volume":"54","author":"Barrangou","year":"2014","journal-title":"Mol. Cell"},{"key":"ref_121","unstructured":"Simon, H.A. (1996). The Sciences of the Artificial, The MIT Press. [3rd ed.]."},{"key":"ref_122","unstructured":"Lenneberg, E.H. (1984). Biological Foundations of Language, Robert E. Krieger Publ. Co.. [reprint ed.]. (Original edition and copyright: John Wiley & Sons, Inc., 1967.)."},{"key":"ref_123","doi-asserted-by":"crossref","unstructured":"Casti, J.L., and Karlqvist, A. (1986). Complexity, Language, and Life: Mathematical Approaches; Vol. 16, Lecture Notes in Biomathematics, Springer.","DOI":"10.1007\/978-3-642-70953-1"},{"key":"ref_124","unstructured":"Weinberg, G.M. (2001). An Introduction to General Systems Thinking, Dorset Hause Publishing."},{"key":"ref_125","unstructured":"Bosch, O., Maani, K., and Smith, C. (2007). Systems Thinking\u2014Language of Complexity for Scientists and Managers, The University of Queensland."},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.jtbi.2015.02.002","article-title":"\u201cSynergistic selection\u201d: A Darwinian frame for the evolution of complexity","volume":"371","author":"Corning","year":"2015","journal-title":"J. Theor. Biol."},{"key":"ref_127","unstructured":"Zurek, W.H. (1990). Santa Fe Institute Studies in the Sciences of Complexity, Perseus Publishing."},{"key":"ref_128","unstructured":"Watkins, J.J. (2014). Number Theory: A Historical Approach, Princeton University Press."},{"key":"ref_129","doi-asserted-by":"crossref","unstructured":"Hartnett, W. (1977). Systems, Approaches, Theories, Applications, D. Reidel Publishing Co.","DOI":"10.1007\/978-94-010-1239-3"},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"E2595","DOI":"10.1073\/pnas.1504837112","article-title":"Mechanical stimulation induces formin-dependent assembly of a perinuclear actin rim","volume":"112","author":"Shao","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1016\/j.bpj.2012.12.044","article-title":"There is More Than One Way to Model an Elephant. Experiment-DrivenModeling of the Actin Cytoskeleton","volume":"104","author":"Ditlev","year":"2013","journal-title":"Biophys. J."},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1007\/s11538-013-9844-3","article-title":"Multiscale Stochastic Reaction\u2013Diffusion Modeling: Application to Actin Dynamics in Filopodia","volume":"76","author":"Erban","year":"2013","journal-title":"Bull. Math. Biol."},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"782","DOI":"10.1529\/biophysj.104.056515","article-title":"The physics of filopodial protrusion","volume":"89","author":"Mogilner","year":"2005","journal-title":"Biophys. J."},{"key":"ref_134","doi-asserted-by":"crossref","unstructured":"Santiago, O.L., da Silva-Neto, A.J., and Silva, G. (2016). Modeling and Computational Intelligence in Engineering Applications, Springer.","DOI":"10.1007\/978-3-319-38869-4"},{"key":"ref_135","unstructured":"Callebaut, W., and Rasskin-Gutman, D. (2005). Modularity: Understanding the Development and Evolution of Natural Complex Systems, The MIT Press."},{"key":"ref_136","first-page":"467","article-title":"The Architecture of Complexity","volume":"106","author":"Simon","year":"1962","journal-title":"Proc. Am. Philos. Soc."},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1126\/science.132.3420.115","article-title":"Organelle Systems and Biological Organization","volume":"132","author":"Ehret","year":"1960","journal-title":"Science"},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1038\/nbt1492","article-title":"A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology","volume":"26","author":"Swainston","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"1021","DOI":"10.1111\/j.1467-8659.2011.01951.x","article-title":"Pathway Preserving Representation of Metabolic Networks","volume":"30","author":"Lambert","year":"2011","journal-title":"Comput. Graph. Forum"},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1016\/j.jtbi.2010.04.026","article-title":"Organizing Metabolic Networks: Cycles in Flux Distribution","volume":"265","author":"Kritz","year":"2010","journal-title":"J. Theor. Biol."},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1126\/science.aaf1647","article-title":"A unifying model of epigenetic regulation","volume":"351","author":"Keung","year":"2016","journal-title":"Science"},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"3810","DOI":"10.1073\/pnas.0510070103","article-title":"Dissecting toxin immunity in virus-infected killer yeast uncovers an intrinsic strategy of self-protection","volume":"103","author":"Breinig","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1038\/nrmicro1347","article-title":"Yeast viral killer toxins: Lethality and self-protection","volume":"4","author":"Schmitt","year":"2006","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"1822","DOI":"10.1128\/AEM.02501-10","article-title":"A new wine Saccharomyces cerevisiae killer toxin (Klus), encoded by a double-stranded rna virus, with broad antifungal activity is evolutionarily related to a chromosomal host gene","volume":"77","author":"Maqueda","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_145","unstructured":"Zadeh, L.A., and Polak, E. (1969). System Theory, Vol. 8, Inter-University Electronics Series, TATA McGraw-Hill Publishing Co. Ltd."},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1080\/03081079.2011.622088","article-title":"Anticipation in (M,R)-systems","volume":"41","author":"Louie","year":"2012","journal-title":"Int. J. Gen. Syst."},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"590","DOI":"10.3390\/systems2040590","article-title":"Postmodern Fuzzy System Theory: A Deconstruction Approach Based on Kabbalah","volume":"2","author":"Burstein","year":"2014","journal-title":"Systems"},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1080\/03081079.2015.1032525","article-title":"Anticipatory dynamics of biological systems: From molecular quantum states to evolution","volume":"44","author":"Igamberdiev","year":"2015","journal-title":"Int. J. Gen. Syst."},{"key":"ref_149","unstructured":"Kritz, M.V. (2009). Biological Information and Knowledge, LNCC\/MCT. Relat\u00f3rio de P&D 23\/2009."},{"key":"ref_150","first-page":"012617","article-title":"Biological Organization, Biological Information, and Knowledge","volume":"2014","author":"Kritz","year":"2014","journal-title":"bioRxiv"},{"key":"ref_151","first-page":"21","article-title":"A Theory of Stars in Complex Systems","volume":"Volume 16","author":"Casti","year":"1986","journal-title":"Complexity, Language, and Life: Mathematical Approaches"},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/S0303-2647(98)00034-3","article-title":"Metabolism and the problem of its universalization","volume":"49","author":"Bergareche","year":"1999","journal-title":"BioSystems"},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s11424-006-0001-z","article-title":"Studying complex adaptive systems","volume":"19","author":"Holland","year":"2006","journal-title":"J. Syst. Sci. Complex."},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1016\/j.jtbi.2011.06.033","article-title":"From L\u2019Homme Machine to metabolic closure: Steps towards understanding life","volume":"286","author":"Letelier","year":"2011","journal-title":"J. Theor. Biol."},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1075\/pc.15.3.06emm","article-title":"A Bio-semiotic Note on Organisms, animals, machines, Cyborgs, and the Quasi-autonomy of Robots","volume":"15","author":"Emmeche","year":"2007","journal-title":"Pragmat. Cogn."},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.jtbi.2009.11.010","article-title":"Closure to efficient causation, computability and artificial life","volume":"263","author":"Letelier","year":"2010","journal-title":"J. Theor. Biol."},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"837","DOI":"10.3390\/life4040837","article-title":"Growth and Division in a Dynamic Protocell Model","volume":"4","author":"Villani","year":"2014","journal-title":"Life"},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"1934","DOI":"10.1093\/bioinformatics\/btg277","article-title":"The fiction of function","volume":"19","author":"Shrager","year":"2003","journal-title":"Bioinformatics"},{"key":"ref_159","unstructured":"Brownlee, J. (2007). Complex Adaptive Systems, Complex Intelligent Systems Laboratory, Centre for Information Technology Research. CIS Technical Report 070302A."},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1093\/bib\/2.3.258","article-title":"Systems biology: The reincarnation of systems theory applied in biology?","volume":"2","author":"Wolkenhauer","year":"2001","journal-title":"Brief. Bioinform."},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.jtbi.2015.04.037","article-title":"Founder of systems chemistry and foundational theoretical biologist: Tibor G\u00e1nti (1933-2009)","volume":"381","year":"2015","journal-title":"J. Theor. Biol."},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/S1535-6108(02)00133-2","article-title":"Can a biologist fix a radio?\u2014Or, what I learned while studying apoptosis","volume":"2","author":"Lazebnik","year":"2002","journal-title":"Cancer Cell"},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1080\/0951508021000042012","article-title":"Inter-level relations in computer science, biology, and psychology","volume":"15","author":"Boogerd","year":"2002","journal-title":"Philos. Psychol."},{"key":"ref_164","unstructured":"Mayr, E. (1997). This Is Biology: The Science of the Living World, Belknap Press\/Havard University Press."},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"541","DOI":"10.3390\/systems2040541","article-title":"A Contextualised General Systems Theory","volume":"2","author":"Kitto","year":"2014","journal-title":"Systems"}],"container-title":["Systems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-8954\/5\/1\/23\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T18:29:51Z","timestamp":1760207391000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-8954\/5\/1\/23"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,3,6]]},"references-count":165,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,3]]}},"alternative-id":["systems5010023"],"URL":"https:\/\/doi.org\/10.3390\/systems5010023","relation":{"has-preprint":[{"id-type":"doi","id":"10.20944\/preprints201611.0026.v1","asserted-by":"object"}]},"ISSN":["2079-8954"],"issn-type":[{"value":"2079-8954","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,3,6]]}}}