'Artificial Cell Research As a Field That Connects
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Prebiological Evolution and the Metabolic Origins of Life
Prebiological Evolution and the Andrew J. Pratt* Metabolic Origins of Life University of Canterbury Keywords Abiogenesis, origin of life, metabolism, hydrothermal, iron Abstract The chemoton model of cells posits three subsystems: metabolism, compartmentalization, and information. A specific model for the prebiological evolution of a reproducing system with rudimentary versions of these three interdependent subsystems is presented. This is based on the initial emergence and reproduction of autocatalytic networks in hydrothermal microcompartments containing iron sulfide. The driving force for life was catalysis of the dissipation of the intrinsic redox gradient of the planet. The codependence of life on iron and phosphate provides chemical constraints on the ordering of prebiological evolution. The initial protometabolism was based on positive feedback loops associated with in situ carbon fixation in which the initial protometabolites modified the catalytic capacity and mobility of metal-based catalysts, especially iron-sulfur centers. A number of selection mechanisms, including catalytic efficiency and specificity, hydrolytic stability, and selective solubilization, are proposed as key determinants for autocatalytic reproduction exploited in protometabolic evolution. This evolutionary process led from autocatalytic networks within preexisting compartments to discrete, reproducing, mobile vesicular protocells with the capacity to use soluble sugar phosphates and hence the opportunity to develop nucleic acids. Fidelity of information transfer in the reproduction of these increasingly complex autocatalytic networks is a key selection pressure in prebiological evolution that eventually leads to the selection of nucleic acids as a digital information subsystem and hence the emergence of fully functional chemotons capable of Darwinian evolution. 1 Introduction: Chemoton Subsystems and Evolutionary Pathways Living cells are autocatalytic entities that harness redox energy via the selective catalysis of biochemical transformations. -
Artificial Cell Research As a Field That Connects Chemical, Biological and Philosophical Questions
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2016 Artificial cell research as a field that connects chemical, biological and philosophical questions Deplazes-Zemp, Anna Abstract: This review article discusses the interdisciplinary nature and implications of artificial cell research. It starts from two historical theories: Gánti’s chemoton model and the autopoiesis theory by Maturana and Varela. They both explain the transition from chemical molecules to biological cells. These models exemplify two different ways in which disciplines of chemistry, biology and philosophy canprofit from each other. In the chemoton model, conclusions from one disciplinary approach are relevant for the other disciplines. In contrast, the autopoiesis model itself (rather than its conclusions) is transferred from one discipline to the other. The article closes by underpinning the relevance of artificial cell research for philosophy with reference to the on-going philosophical debates on emergence, biological functions and biocentrism. DOI: https://doi.org/10.2533/chimia.2016.443 Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-135057 Journal Article Published Version Originally published at: Deplazes-Zemp, Anna (2016). Artificial cell research as a field that connects chemical, biological and philosophical questions. CHIMIA International Journal for Chemistry, 70(6):443-448. DOI: https://doi.org/10.2533/chimia.2016.443 NCCR MoleCulaR SySteMS eNgiNeeRiNg CHIMIA 2016, 70, No. 6 443 doi:10.2533/chimia.2016.443 Chimia 70 (2016) 443–448 © Swiss Chemical Society Artificial Cell Research as a Field that Connects Chemical, Biological and Philosophical Questions Anna Deplazes-Zemp* Abstract: This review article discusses the interdisciplinary nature and implications of artificial cell research. -
Are Living Beings Extended Autopoietic Systems? an Embodied Reply
Article Adaptive Behavior 1–11 Ó The Author(s) 2019 Are living beings extended autopoietic Article reuse guidelines: sagepub.com/journals-permissions DOI: 10.1177/1059712318823723 systems? An embodied reply journals.sagepub.com/home/adb Mario Villalobos1,2 and Pablo Razeto-Barry2,3 Abstract Building on the original formulation of the autopoietic theory (AT), extended enactivism argues that living beings are autopoietic systems that extend beyond the spatial boundaries of the organism. In this article, we argue that extended enactivism, despite having some basis in AT’s original formulation, mistakes AT’s definition of living beings as autopoietic entities. We offer, as a reply to this interpretation, a more embodied reformulation of autopoiesis, which we think is nec- essary to counterbalance the (excessively) disembodied spirit of AT’s original formulation. The article aims to clarify and correct what we take to be a misinterpretation of ATas a research program. AT, contrary to what some enactivists seem to believe, did not (and does not) intend to motivate an extended conception of living beings. AT’s primary purpose, we argue, was (and is) to provide a universal individuation criterion for living beings, these understood as discrete bodies that are embedded in, but not constituted by, the environment that surrounds them. However, by giving a more expli- citly embodied definition of living beings, AT can rectify and accommodate, so we argue, the enactive extended interpre- tation of autopoiesis, showing that although living beings do not extend beyond their boundaries as autopoietic unities, they do form part, in normal conditions, of broader autopoietic systems that include the environment. -
Learning and Complex Adaptive Systems
LEARNING AND COMPLEX ADAPTIVE SYSTEMS (Article by Diana Stirling, Associate Researcher, Learning Development Institute) EDITORIAL NOTE The following article on Learning and Complex Adaptive Systems by LDI Associate Researcher Diana Stirling was first published in a translated version in Japanese. It appears here for the first time in English, the language in which it was originally written. For citation purposes, the English version should reflect access via this site and should read as follows (MLA style): Stirling, Diana. "Learning and Complex Adaptive Systems." Learning Development Institute. 31 May 2014. Web. The reference for the originally published paper in Japanese is: Stirling, Diana. "Learning and Complex Adaptive Systems." Aichi Universities English Education Research Journal. 30 (2013): 183-226. Trans. Mitsuo Kondo. Print. We thank the Aichi Universities English Education Research Journal for permission to publish this paper on the learndev.org site in accordance with an agreement made with the author. Learning Development Institute, June 1, 2014 JV Learning and Complex Adaptive Systems Diana Stirling Part 1: Complex Adaptive Systems Introduction to Complex Adaptive Systems The science of complexity and complex adaptive systems has engendered a view of the beauty of self-organization which arises as a result of continual transformation, via nonlinear interactions, within and between co-creating systems. Through this lens, learning is seen as a continuous dynamic, the inevitable actualization of an innate biological potential. When the human individual is viewed as a complex adaptive system and learning is seen as an essential dynamic on which the system depends for survival, conscious learning is recognized as the tip of the learning iceberg. -
Towards Autopoietic SB-AI
Towards Autopoietic SB-AI Luisa Damiano1 and Pasquale Stano2 1IULM University, Milan, Italy 2University of Salento, Lecce, Italy [email protected]; [email protected] Abstract that dynamically embed them in environments (e.g., Pfeifer Downloaded from http://direct.mit.edu/isal/proceedings-pdf/isal/33/51/1930006/isal_a_00430.pdf by guest on 29 September 2021 This programmatic paper continues a series of works that we and Scheier, 1999). This development, as such, reoriented AI are dedicating to introduce a novel research program in AI, back towards its cybernetic origins and, more precisely, which we call Autopoietic SB-AI to indicate two basic toward the original cybernetic project: structuring a unified elements of its procedural architecture. (1) The first element is study of biological systems and machines, and this way the innovative methodological option of synthetically studying attempting to overcome the divide between the inorganic and the cognitive domain based on the construction and the organic world (Damiano and Stano, 2018). experimental exploration of wetware –i.e., chemical – models of cognitive processes, using techniques defined in the field of If until now EAI focused on the implementation of Synthetic Biology (SB). (2) The second element is the embodied agents as hardware robots, new possibilities have theoretical option of developing SB models of cognitive been recently prepared by the second of the scientific processes based on the theory of autopoiesis. In our previous advancements we mentioned. This is the constitution, at the works we focused on the epistemological and theoretical beginning of the 2000s, of SB, a sci-tech research domain, at groundings of Autopoietic SB-AI. -
From L'homme Machine to Metabolic Closure Steps Towards
Journal of Theoretical Biology 286 (2011) 100–113 Contents lists available at ScienceDirect Journal of Theoretical Biology journal homepage: www.elsevier.com/locate/yjtbi 50th Anniversary Year Review From L’Homme Machine to metabolic closure: Steps towards understanding life Juan-Carlos Letelier a, Marı´a Luz Ca´rdenas b, Athel Cornish-Bowden b,Ã a Departamento de Biologı´a, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile b Unite´ de Bioe´nerge´tique et Inge´nierie des Prote´ines, Centre National de la Recherche Scientifique, 31 chemin Joseph-Aiguier, 13402 Marseille Cedex 20, France article info abstract Available online 12 July 2011 The nature of life has been a topic of interest from the earliest of times, and efforts to explain it in Keywords: mechanistic terms date at least from the 18th century. However, the impressive development of Origin of life molecular biology since the 1950s has tended to have the question put on one side while biologists (M,R) systems explore mechanisms in greater and greater detail, with the result that studies of life as such have been Autopoiesis confined to a rather small group of researchers who have ignored one another’s work almost Chemoton completely, often using quite different terminology to present very similar ideas. Central among these Self-organization ideas is that of closure, which implies that all of the catalysts needed for an organism to stay alive must be produced by the organism itself, relying on nothing apart from food (and hence chemical energy) from outside. The theories that embody this idea to a greater or less degree are known by a variety of names, including (M,R) systems, autopoiesis, the chemoton, the hypercycle, symbiosis, autocatalytic sets, sysers and RAF sets. -
Phenotypic Diversity and Chaos in a Minimal Cell Model
ARTICLE IN PRESS Journal of Theoretical Biology 240 (2006) 434–442 www.elsevier.com/locate/yjtbi Phenotypic diversity and chaos in a minimal cell model Andreea Munteanua,Ã, Ricard V. Sole´a,b aICREA-Complex Systems Lab, Universitat Pompeu Fabra (GRIB), Dr. Aiguader 80, 08003 Barcelona, Spain bSanta Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA Received 4 April 2005; received in revised form 10 October 2005; accepted 12 October 2005 Available online 5 December 2005 Abstract Ga´nti’s chemoton model (Ga´nti, T., 2002. On the early evolution of biological periodicity. Cell. Biol. Int. 26, 729) is considered as an iconic example of a minimal protocell including three key subsystems: membrane, metabolism and information. The three subsystems are connected through stoichiometrical coupling which ensures the existence of a replication cycle for the chemoton. Our detailed exploration of a version of this model indicates that it displays a wide range of complex dynamics, from regularity to chaos. Here, we report the presence of a very rich set of dynamical patterns potentially displayed by a protocell as described by this implementation of a chemoton-like model. The implications for early cellular evolution and synthesis of artificial cells are discussed. r 2005 Elsevier Ltd. All rights reserved. Keywords: Protocell; Origins of life; Chemoton; Cellular networks; Chaos 1. Introduction pursued in the experiments. For the latter, no intentional implications concerning the birth of primordial cells are Cells are the basic building blocks of all life on our sought and its proper functioning is based on present planet. They are the minimal systems able to self-replicate biogenic and/or abiogenic chemistry. -
Second Order Cybernetics 31/08/2008 10:08
SECOND ORDER CYBERNETICS 31/08/2008 10:08 Search Print this chapter Cite this chapter SECOND ORDER CYBERNETICS Ranulph Glanville, CybernEthics Research, UK and Royal Melbourne Institute of Technology University, Australia Keywords: actor, analogy, argument, automata, autopoiesis, behavior, biology, Black_Box, causality, circularity, coding, cognition, communication, computation, concept, consciousness, control, conversation, cybernetics, description, design, distinction, ecology, education, environment, epistemology, error, ethics, feedback, form, function, generosity, goal, homeostasis, idea, identity, individual, information, interaction, internet, knowing, language, learning, logic, management, mathematics, meaning, mechanism, memory, meta-, metaphor, moment, mutualism, network, object, observe, organizational_closure, oscillation, person, phenomenon, philosophical, physics, positivist, (post-)_modernism, praxis, process, program, psychology, purpose, quality, reality, reason, recursion, relative, responsibility, science, second_order_cybernetics, (self-)_reference, semiotics, social, structure, subject, support, system, theory, thinking, time, truth, understanding, variety, whole_(and_part) Contents 1. Introduction: What Second Order Cybernetics is, and What it Offers 2. Background—the Logical Basis for Second Order Cybernetics 3. Second Order Cybernetics—Historical Overview 4. Theory of Second Order Cybernetics 5. Praxis of Second Order Cybernetics 6. A Note on Second Order Cybernetics and Constructivism 7. Cybernetics, Second Order -
Life Before LUCA∗
Life before LUCA∗ Athel Cornish-Bowden and María Luz Cárdenas Aix Marseille Univ, CNRS, BIP, IMM, Marseille, France AUTHORS’ CONTACT INFORMATION email [email protected] [email protected] telephone + 33 491 16 41 38 ARTICLE INFO Keywords: Lynn Sagan, Lynn Margulis, LUCA, cenancestor, last universal common ancestor, origin of life, definition of life NOTE. This file is printed from the final accepted version of the paper. The PDF file typeset by the Journal will be available later. ABSTRACT We see the last universal common ancestor of all living organisms, or LUCA, at the evolutionary separation of the Archaea from the Eubacteria, and before the symbiotic event believed to have led to the Eukarya. LUCA is often implicitly taken to be close to the origin of life, and sometimes this is even stated explicitly. However, LUCA already had the capacity to code for many proteins, and had some of the same bioenergetic capacities as modern ∗This paper is dedicated to the memory of Lynn Sagan (Margulis), and especially of her paper “On the origin of mitosing cells”. 1 organisms. An organism at the origin of life must have been vastly simpler, and this invites the question of how to define a living organism. Even if acceptance of the giant viruses as living organisms forces the definition of LUCA to be revised, it will not alter the essential point that LUCA should be regarded as a recent player in the evolution of life. 1. Introduction In general I avoid the last 3 million years of evolution and any other studies that require detailed knowledge of mammalian, including human, biology. -
Contrasting Theories of Life: Historical Context, Current Theories
BioSystems 188 (2020) 104063 Contents lists available at ScienceDirect BioSystems journal homepage: www.elsevier.com/locate/biosystems Review article Contrasting theories of life: Historical context, current theories. In search of an ideal theory Athel Cornish-Bowden <, María Luz Cárdenas Aix Marseille Univ, CNRS, BIP, IMM, Marseille, France ARTICLEINFO ABSTRACT Keywords: Most attempts to define life have concentrated on individual theories, mentioning others hardly at all, but here Autocatalytic sets we compare all of the major current theories. We begin by asking how we know that an entity is alive, and Autopoiesis continue by describing the contributions of La Mettrie, Burke, Leduc, Herrera, Bahadur, D'Arcy Thompson and, Chemoton especially, Schrödinger, whose book What is Life? is a vital starting point. We then briefly describe and discuss Closure (M, R) systems, the hypercycle, the chemoton, autopoiesis and autocatalytic sets. All of these incorporate the Hypercycle Metabolic circularity idea of circularity to some extent, but all of them fail to take account of mechanisms of metabolic regulation, (M, R) systems which we regard as crucial if an organism is to avoid collapsing into a mass of unregulated reactions. In Origin of life a final section we study the extent to which each of the current theories can aid in the search for a more Self-organization complete theory of life, and explain the characteristics of metabolic control analysis that make it essential for an adequate understanding of organisms. Contents 1. General introduction -
Niklas Luhmann Neosystemic Theory and the Notion of Communicative Autopoiesis in Organizational Studies
A teoria neosistêmica de Niklas Luhmann e a noção de autopoiese comunicativa nos estudos organizacionais Josep Pont Vidal Universidade Federal do Pará / Núcleo Altos Estudos Amazônicos, Belém – PA, Brasil Resumo Na teoria dos sistemas autorreferenciais, de Niklas Luhmann, a análise das organizações ocupa lugar de destaque, mas tem sido objeto de inúmeras controvérsias. Nos últimos anos, vêm sendo produzidos um diálogo e um cruzamento com os representantes da filosofia social pós-estruturalista, em particular, com aspectos referentes às possibilidades autorreferenciais das comunicações e da linguagem. Na atuali- dade, são diversos os pontos de vista teóricos que convergem para uma autodefinição construtivista, ecológica e sistêmica. Como possibili- dade alternativa às limitações autopoiéticas na observação das organizações, propõe-se a ideia de autopoiese reflexiva. Palavras-chave: Teoria de sistemas autorreferenciais. Pós-estruturalismo. Teoria organizacional. Autopoiese reflexiva. Niklas Luhmann neosystemic theory and the notion of communicative autopoiesis in organizational studies Abstract The analysis of organizations stands out in Niklas Luhmann’s theory of self-referential systems. However, this analysis has been subject of controversies. In recent years, a dialogue and an exchange of opinions with representatives of poststructuralist social philosophy have been in place, particularly regarding self-referential possibilities of communication and language. Currently there are several theoretical viewpoints converging to a constructivist, -
Autopoiesis and a Biology of Intentionality∗
Essay 1 Autopoiesis and a Biology of Intentionality∗ Francisco J. Varela CREA, CNRS—Ecole Polytechnique, Paris, France. ∗Parts of this text have been published in (Varela 1991). 4 Biology of Intentionality Francisco J. Varela 1.1 Introduction enumeration of properties. But what is this basic process? Its description must be situated at a very As everybody here knows, autopoiesis is a neolo- specific level: it must be sufficiently universal to al- gism, introduced in 1971 by H. Maturana and my- low us to recognize living systems as a class, without self to designate the organization of a minimal living essential reference to the material components. Yet system. The term became emblematic of a view of at the same time it must not be too abstract, that the relation between an organism and its medium, is, it must be explicit enough to allow us to see such where its self constituting and autonomous aspects dynamical patterns in action in the actual living sys- are put at the center of the stage. From 1971, until tem we know on earth, those potentially to be found now much has happened to reinforce this perspec- in other solar systems, and eventually those created tive. Some of the developments have to do with the artificially by man. As stated by the organizer of a notion of autopoiesis itself in relation to the cellular meeting on artificial life: “Only when we are able to organization and the origin of life. Much more has view life-as-we-know-it in the larger context of life- to do with the autonomy and self-organizing qual- as-it-could-be will we really understand the nature ities of the organism in relation with its cognitive of the beast” (Langton 1989b, p.