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Froese T, Weber N, Shpurov I, Ikegami T. From autopoiesis to self-optimization: Toward an enactive model of biological regulation. Biosystems 2023:104959. [PMID: 37380066 DOI: 10.1016/j.biosystems.2023.104959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/08/2023] [Accepted: 06/15/2023] [Indexed: 06/30/2023]
Abstract
The theory of autopoiesis has been influential in many areas of theoretical biology, especially in the fields of artificial life and origins of life. However, it has not managed to productively connect with mainstream biology, partly for theoretical reasons, but arguably mainly because deriving specific working hypotheses has been challenging. The theory has recently undergone significant conceptual development in the enactive approach to life and mind. Hidden complexity in the original conception of autopoiesis has been explicated in the service of other operationalizable concepts related to self-individuation: precariousness, adaptivity, and agency. Here we advance these developments by highlighting the interplay of these concepts with considerations from thermodynamics: reversibility, irreversibility, and path-dependence. We interpret this interplay in terms of the self-optimization model, and present modeling results that illustrate how these minimal conditions enable a system to re-organize itself such that it tends toward coordinated constraint satisfaction at the system level. Although the model is still very abstract, these results point in a direction where the enactive approach could productively connect with cell biology.
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Affiliation(s)
- Tom Froese
- Embodied Cognitive Science Unit, Okinawa Institute of Science and Technology Graduate University, Tancha, Okinawa, Japan.
| | - Natalya Weber
- Embodied Cognitive Science Unit, Okinawa Institute of Science and Technology Graduate University, Tancha, Okinawa, Japan
| | - Ivan Shpurov
- Embodied Cognitive Science Unit, Okinawa Institute of Science and Technology Graduate University, Tancha, Okinawa, Japan
| | - Takashi Ikegami
- Theoretical Sciences Visiting Program, Okinawa Institute of Science and Technology Graduate University, Tancha, Okinawa, Japan; Ikegami Lab, Department of General Systems Studies, University of Tokyo, Komaba, Tokyo, Japan
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Roca-Rada X, Souilmi Y, Teixeira JC, Llamas B. Ancient DNA Studies in Pre-Columbian Mesoamerica. Genes (Basel) 2020; 11:E1346. [PMID: 33202852 PMCID: PMC7696771 DOI: 10.3390/genes11111346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/04/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
Mesoamerica is a historically and culturally defined geographic area comprising current central and south Mexico, Belize, Guatemala, El Salvador, and border regions of Honduras, western Nicaragua, and northwestern Costa Rica. The permanent settling of Mesoamerica was accompanied by the development of agriculture and pottery manufacturing (2500 BCE-150 CE), which led to the rise of several cultures connected by commerce and farming. Hence, Mesoamericans probably carried an invaluable genetic diversity partly lost during the Spanish conquest and the subsequent colonial period. Mesoamerican ancient DNA (aDNA) research has mainly focused on the study of mitochondrial DNA in the Basin of Mexico and the Yucatán Peninsula and its nearby territories, particularly during the Postclassic period (900-1519 CE). Despite limitations associated with the poor preservation of samples in tropical areas, recent methodological improvements pave the way for a deeper analysis of Mesoamerica. Here, we review how aDNA research has helped discern population dynamics patterns in the pre-Columbian Mesoamerican context, how it supports archaeological, linguistic, and anthropological conclusions, and finally, how it offers new working hypotheses.
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Affiliation(s)
- Xavier Roca-Rada
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (Y.S.); (J.C.T.)
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (Y.S.); (J.C.T.)
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (Y.S.); (J.C.T.)
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (Y.S.); (J.C.T.)
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
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Gershenson C, Trianni V, Werfel J, Sayama H. Self-Organization and Artificial Life. ARTIFICIAL LIFE 2020; 26:391-408. [PMID: 32697161 DOI: 10.1162/artl_a_00324] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Self-organization can be broadly defined as the ability of a system to display ordered spatiotemporal patterns solely as the result of the interactions among the system components. Processes of this kind characterize both living and artificial systems, making self-organization a concept that is at the basis of several disciplines, from physics to biology and engineering. Placed at the frontiers between disciplines, artificial life (ALife) has heavily borrowed concepts and tools from the study of self-organization, providing mechanistic interpretations of lifelike phenomena as well as useful constructivist approaches to artificial system design. Despite its broad usage within ALife, the concept of self-organization has been often excessively stretched or misinterpreted, calling for a clarification that could help with tracing the borders between what can and cannot be considered self-organization. In this review, we discuss the fundamental aspects of self-organization and list the main usages within three primary ALife domains, namely "soft" (mathematical/computational modeling), "hard" (physical robots), and "wet" (chemical/biological systems) ALife. We also provide a classification to locate this research. Finally, we discuss the usefulness of self-organization and related concepts within ALife studies, point to perspectives and challenges for future research, and list open questions. We hope that this work will motivate discussions related to self-organization in ALife and related fields.
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Affiliation(s)
- Carlos Gershenson
- Universidad Nacional Autónoma de México, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Centro de Ciencias de la Complejidad.
- ITMO University
| | - Vito Trianni
- Italian National Research Council, Institute of Cognitive Sciences and Technologies.
| | - Justin Werfel
- Harvard University, Wyss Institute for Biologically Inspired Engineering.
| | - Hiroki Sayama
- Binghamton University, Center for Collective Dynamics of Complex Systems.
- Waseda University, Waseda Innovation Laboratory
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Modeling collective rule at ancient Teotihuacan as a complex adaptive system: Communal ritual makes social hierarchy more effective. COGN SYST RES 2018. [DOI: 10.1016/j.cogsys.2018.09.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Carballo DM, Feinman GM. Cooperation, collective action, and the archeology of large‐scale societies. Evol Anthropol 2016; 25:288-296. [DOI: 10.1002/evan.21506] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Indexed: 11/08/2022]
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Jennings J, Earle TK. Urbanization, State Formation, and Cooperation: A Reappraisal. CURRENT ANTHROPOLOGY 2016. [DOI: 10.1086/687510] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abstract
Norenzayan et al. suggest that Big Gods can be replaced by Big Governments. We examine forms of social and self-monitoring and ritual practice that emerged in Classical China, heterarchical societies like those that emerged in pre-Columbian Mesoamerica, and the contemporary Zapatista movement of Chiapas, and we recommend widening the hypothesis space to include these alternative forms of social organization.
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