The Self-Organization of Cyberprotest
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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. -
Quasispecies Theory in Virology
JOURNAL OF VIROLOGY, Jan. 2002, p. 463–465 Vol. 76, No. 1 0022-538X/02/$04.00ϩ0 DOI: 10.1128/JVI.76.1.463–465.2002 Copyright © 2002, American Society for Microbiology. All Rights Reserved. Quasispecies Theory in Virology Holmes and Moya claim that quasispecies is an unnecessary ular sort. Darwinian principles in connection with quasispecies and misleading description of RNA virus evolution, that virol- have been explicitly invoked by theoreticians and experimen- ogists refer to quasispecies inappropriately, and that there is talists alike (11, 13, 16, 35). little evidence of quasispecies in RNA virus evolution. They What is the evidence of quasispecies dynamics in RNA virus wish to look for other ideas in evolutionary biology and to set populations, and why is quasispecies theory exerting an influ- down an agenda for future research. I argue here that real virus ence in virology? The initial experiment with phage Q which quasispecies often differ from the theoretical quasispecies as provided the first experimental support for a quasispecies dy- initially formulated and that this difference does not invalidate namics in an RNA virus (14, 17) has now been carried out with quasispecies as a suitable theoretical framework to understand biological and molecular clones of representatives of the major viruses at the population level. groups of human, animal, and plant RNA viruses, including In the initial theoretical formulation to describe error-prone immunodeficiency viruses and hepatitis C virus, both in cell replication of simple RNA (or RNA-like) molecules, quasispe- culture and in vivo (11). Support for quasispecies has also cies were defined as stationary (equilibrium) mutant distribu- come from studies on replication of RNA molecules in vitro tions of infinite size, centered around one or several master (4). -
Dynamics of a Discrete Hypercycle
Treball final de grau GRAU DE MATEMÀTIQUES Facultat de Matemàtiques i Informàtica Universitat de Barcelona Dynamics of a Discrete Hypercycle Autor: Júlia Perona García Directors: Dr. Ernest Fontich, Dr. Josep Sardanyés Realitzat a: Departament de Matemàtiques i Informàtica Barcelona, June 27, 2018 Abstract The concept of the Hypercycle was introduced in 1977 by Manfred Eigen and Peter Schuster within the framework of origins of life and prebiotic evolution. Hypercycle are catalytic sets of macromolecules, where each replicator catalyzes the replication of the next species of the set. This system was proposed as a possible solution to the information crisis in prebiotic evolution. Hypercycles are cooperative systems that allow replicators to increase their information content beyond the error threshold. This project studies the dynamics of a discrete-time model of the hypercycle consider- ing heterocatalytic interactions. To date, hypercycles’ dynamics has been mainly studied using continuous-time dynamical systems. We follow the Hofbauer’s discrete model [13]. First, we introduce some important and necessary mathematical notions. Then, we also review the biological concept of the hypercycle and some criticisms that it has received. We present a complete proof of the fact that the hypercycle is a cooperative system. Also, we present an analytic study of the fixed point in any dimension and its stability. In particular, in dimension three we prove that fixed point is globally asymptotically stable. In dimension four we have obtained a stable invariant curve for all values of the discreteness parameter. 2010 Mathematics Subject Classification. 37C05, 37N25 Acknowledgements I would like to thank my directors, Ernest and Josep, to support me throughout this project. -
The Molecular Underpinnings of Genetic Phenomena
Heredity (2008) 100, 6–12 & 2008 Nature Publishing Group All rights reserved 0018-067X/08 $30.00 www.nature.com/hdy SHORT REVIEW The molecular underpinnings of genetic phenomena N Lehman Department of Chemistry, Portland State University, Portland, OR, USA Epiphenomena are those processes that ostensibly have no whole organisms and populations may have their ultimate precedent at lower levels of scientific organization. In this evolutionary roots in the chemical repertoire of catalytic review, it is argued that many genetic processes, including RNAs. Some of these phenomena will eventually prove to be ploidy, dominance, heritability, pleiotropy, epistasis, muta- not only analogous but homologous to ribozyme activities. tional load and recombination, all are at least analogous to Heredity (2008) 100, 6–12; doi:10.1038/sj.hdy.6801053; biochemical events that were requisite features of the RNA published online 29 August 2007 world. Most, if not all, of these features of contemporary Keywords: RNA; ploidy; pleiotropy; epistasis; heritability; recombination Introduction Below are discussed seven well-known genetic pro- cesses for which a clear molecular basis can be The history of life, if traced with perfect detail, would postulated. By ‘molecular basis’ it is meant that a reveal a long and gradual expansion of networks of chemical property of biopolymers, usually RNA, can be chemical reactions. If viewed in less detail, a series of identified as a direct forbearer of the higher-order plateaus would be seen, each representing a discrete property observed in whole organisms. Again, an advancement in complexity (Fontana and Schuster, 1998; important aspect of this is the idea that many of these Hazen et al., 2007). -
Markets Not Capitalism Explores the Gap Between Radically Freed Markets and the Capitalist-Controlled Markets That Prevail Today
individualist anarchism against bosses, inequality, corporate power, and structural poverty Edited by Gary Chartier & Charles W. Johnson Individualist anarchists believe in mutual exchange, not economic privilege. They believe in freed markets, not capitalism. They defend a distinctive response to the challenges of ending global capitalism and achieving social justice: eliminate the political privileges that prop up capitalists. Massive concentrations of wealth, rigid economic hierarchies, and unsustainable modes of production are not the results of the market form, but of markets deformed and rigged by a network of state-secured controls and privileges to the business class. Markets Not Capitalism explores the gap between radically freed markets and the capitalist-controlled markets that prevail today. It explains how liberating market exchange from state capitalist privilege can abolish structural poverty, help working people take control over the conditions of their labor, and redistribute wealth and social power. Featuring discussions of socialism, capitalism, markets, ownership, labor struggle, grassroots privatization, intellectual property, health care, racism, sexism, and environmental issues, this unique collection brings together classic essays by Cleyre, and such contemporary innovators as Kevin Carson and Roderick Long. It introduces an eye-opening approach to radical social thought, rooted equally in libertarian socialism and market anarchism. “We on the left need a good shake to get us thinking, and these arguments for market anarchism do the job in lively and thoughtful fashion.” – Alexander Cockburn, editor and publisher, Counterpunch “Anarchy is not chaos; nor is it violence. This rich and provocative gathering of essays by anarchists past and present imagines society unburdened by state, markets un-warped by capitalism. -
Error Propagation in the Hypercycle
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by CERN Document Server Error propagation in the hypercycle P. R. A. Campos and J. F. Fontanari Instituto de F´ısica de S˜ao Carlos, Universidade de S˜ao Paulo Caixa Postal 369, 13560-970 S˜ao Carlos SP, Brazil P. F. Stadler Institut f¨ur Theorestische Chemie, Universit¨at Wien W¨ahringerstraße 17, A-1090 Wien, Austria The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe NM 87501, USA some pathological, discontinuous replication landscapes We study analytically the steady-state regime of a net- [4], the coexistence problem seems to be more pervasive, work of n error-prone self-replicating templates forming an as it is associated to the form of the growth functions in asymmetric hypercycle and its error tail. We show that the the chemical kinetics equations [5,6]. existence of a master template with a higher non-catalyzed In order to circumvent the aforementioned limitations self-replicative productivity, a, than the error tail ensures the of the quasispecies model, Eigen and Schuster proposed stability of chains in which m<n 1 templates coexist with the master species. The stability of− these chains against the the hypercycle [7], that is, a catalytic feedback network error tail is guaranteed for catalytic coupling strengths (K) whereby each template helps in the replication of the next of order of a. We find that the hypercycle becomes more sta- one, in a regulatory cycle closing on itself. This model ble than the chains only for K of order of a2. -
Full Analysis of Small Hypercycles with Short-Circuits in Prebiotic Evolution
Full Analysis of Small Hypercycles with Short-circuits in Prebiotic Evolution Josep Sardany´es,1, 2, ∗ J. Tom´asL´azaro,3, 4 Toni Guillamon,4, 5 and Ernest Fontich4, 6 1ICREA-Complex Systems Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain 2Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Mar´ıtim de la Barceloneta 37, 08003 Barcelona, Spain 3Departament de Matem`atiques,Av. Diagonal, 647 (Universitat Polit`ecnica de Catalunya) 08028, Barcelona, Spain 4Barcelona Graduate School of Mathematics BGSMath 5Departament de Matem`atiques,Av. Gregorio Mara~n´on44-50 (Universitat Polit`ecnica de Catalunya) 08028, Barcelona, Spain 6Departament de Matem`atiquesi Inform`atica (Universitat de Barcelona), Gran Via de les Corts Catalanes 585, 08007 Barcelona, Spain (Dated: November 25, 2016) It is known that hypercycles are sensitive to the so-called parasites and short-circuits. While the impact of parasites has been widely investigated for well-mixed and spatial hypercycles, the effect of short-circuits in hypercycles remains poorly understood. In this article we analyze the mean field and spatial dynamics of two small, asymmetric hypercycles with short-circuits. Specifically, we analyze a two-member hypercycle where one of the species contains an autocatalytic loop, as the simplest hypercycle with a short-circuit. Then, we extend this system by adding another species that closes a three-member hypercycle while keeping the autocatalytic short-circuit and the two-member cycle. The mean field model allows us to discard the presence of stable or unstable periodic orbits for both systems. We characterize the bifurcations and transitions involved in the dominance of the short-circuits i.e., in the reduction of the hypercycles' size. -
The Anarchist Aspects of Nietzsche's Philosophy- Presentation
The Anarchist Aspects of Nietzsche’s Philosophy- Presentation The core of my hypothesis is that Friedrich Nietzsche’s philosophy promotes basic anarchist notions. Hence, what I am intending to show is the existence of a bond between the anarchist tradition and the German philosopher. My main idea is to review Nietzsche’s work from an anarchist angle. This means I will try to re-examine basic concepts of the Nietzschean philosophy by comparing them to the notions of prominent anarchists and libertarians together with using these concepts in order to give a Nietzschean interpretation to certain anarchistic historical incidents like those of the Schism of the 1st International, the Spanish Revolution, May ’68, and even the Revolt of December 2008 in Athens-Greece. The importance of such a connection lies in highlighting the elective affinity between Nietzsche and the anarchists and, actually, the whole research is based on this elective relationship. When I say elective affinity I mean “a special kind of dialectical relationship that develops between two social or cultural configurations, one that cannot be reduced to direct causality or to „influences‟ in the traditional sense”.1 This is Michael Lowy’s definition of elective affinity in his essay on Jewish libertarian thought,2 and that’s the way I am going to follow it. Elective affinity is not something new in Nietzschean scholarship. Almost every dissertation on Nietzsche makes references to the direct or indirect influence the German philosopher had on his contemporaries and successors and therefore, elective affinity is present to most, short or extended, relevant works. -
Leaving the Left Behind 115 Post-Left Anarchy?
Anarchy after Leftism 5 Preface . 7 Introduction . 11 Chapter 1: Murray Bookchin, Grumpy Old Man . 15 Chapter 2: What is Individualist Anarchism? . 25 Chapter 3: Lifestyle Anarchism . 37 Chapter 4: On Organization . 43 Chapter 5: Murray Bookchin, Municipal Statist . 53 Chapter 6: Reason and Revolution . 61 Chapter 7: In Search of the Primitivists Part I: Pristine Angles . 71 Chapter 8: In Search of the Primitivists Part II: Primitive Affluence . 83 Chapter 9: From Primitive Affluence to Labor-Enslaving Technology . 89 Chapter 10: Shut Up, Marxist! . 95 Chapter 11: Anarchy after Leftism . 97 References . 105 Post-Left Anarchy: Leaving the Left Behind 115 Prologue to Post-Left Anarchy . 117 Introduction . 118 Leftists in the Anarchist Milieu . 120 Recuperation and the Left-Wing of Capital . 121 Anarchy as a Theory & Critique of Organization . 122 Anarchy as a Theory & Critique of Ideology . 125 Neither God, nor Master, nor Moral Order: Anarchy as Critique of Morality and Moralism . 126 Post-Left Anarchy: Neither Left, nor Right, but Autonomous . 128 Post-Left Anarchy? 131 Leftism 101 137 What is Leftism? . 139 Moderate, Radical, and Extreme Leftism . 140 Tactics and strategies . 140 Relationship to capitalists . 140 The role of the State . 141 The role of the individual . 142 A Generic Leftism? . 142 Are All Forms of Anarchism Leftism . 143 1 Anarchists, Don’t let the Left(overs) Ruin your Appetite 147 Introduction . 149 Anarchists and the International Labor Movement, Part I . 149 Interlude: Anarchists in the Mexican and Russian Revolutions . 151 Anarchists in the International Labor Movement, Part II . 154 Spain . 154 The Left . 155 The ’60s and ’70s . -
Statistical Properties and Error Threshold of Quasispecies on Single-Peak Gaussian-Distributed Fitness Landscapes
Statistical properties and error threshold of quasispecies on single-peak Gaussian-distributed fitness landscapes Duo-Fang Li a, Tian-Guang Cao a, Jin-Peng Geng a, Jian-Zhong Gu b, Hai-Long Ana,Yong Zhan a* a Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin 300401, China b China Institute of Atomic Energy, P. O. Box 275 (10), Beijing 102413, China Abstract: The stochastic Eigen model proposed by Feng et al. (Journal of theoretical biology, 246 (2007) 28) showed that error threshold is no longer a phase transition point but a crossover region whose width depends on the strength of the random fluctuation in an environment. The underlying cause of this phenomenon has not yet been well examined. In this article, we adopt a single peak Gaussian distributed fitness landscape instead of a constant one to investigate and analyze the change of the error threshold and the statistical property of the quasi-species population. We find a roughly linear relation between the width of the error threshold and the fitness fluctuation strength. For a given quasi-species, the fluctuation of the relative concentration has a minimum with a normal distribution of the relative concentration at the maximum of the averaged relative concentration, it has however a largest value with a bimodal distribution of the relative concentration near the error threshold. The above results deepen our understanding of the quasispecies and error threshold and are heuristic for exploring practicable antiviral strategies. Keywords: quasispecies; error threshold; single peak fitness; Gaussian distribution; randomization 1. Introduction The researches on the species evolution have been a focus for a long time. -
Evolutionary Virology at 40
| PERSPECTIVES Evolutionary Virology at 40 Jemma L. Geoghegan* and Edward C. Holmes†,‡,§,**,1 *Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia and †Marie Bashir Institute for Infectious Diseases and Biosecurity, ‡Charles Perkins Centre, §School of Life and Environmental Sciences, and **Sydney Medical School, The University of Sydney, New South Wales 2006, Australia ORCID IDs: 0000-0003-0970-0153 (J.L.G.); 0000-0001-9596-3552 (E.C.H.) ABSTRACT RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus–host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. -
Post-Anarchism in Grant Morrison's the Invisibles
4. “A Thought Thinking Itself:” Post-anarchism in Grant Morrison’s The Invisibles Lewis Call* Grant Morrison’s The Invisibles (1994-2000) tells the tale of a diverse band of anarchist freedom fighters. Morrison’s narrative follows the adventures of a cell within a centuries-old revolutionary organization called the Invisible College. The leader of this cell is King Mob, a bald, pierced fetishist, who resembles Morrison more than a little. Three of King Mob’s fellow “Invisibles” present as women: the cross-dressing Brazilian shaman Lord Fanny, a slightly insane time-travelling redhead called Ragged Robin, and an African-American former cop who calls herself Boy. The cell’s newest recruit is Jack Frost, a foul-mouthed working-class punk from Liverpool. Together these Invisible revolutionaries fight against an interdimensional authoritarian conspiracy called the “Outer Church.” This Outer Church works towards a world in which political, economic and religious institutions unite to create a system of total authority. Meanwhile, the Invisible College works towards the opposite end: a left- libertarian world based upon individual freedom, inclusive diversity, and universal access to the means of happiness (including sex, drugs, and magic). The Invisibles can thus be read as an inspirational story of anti-authoritarian rebellion: a strange, beautiful, anarchist fairy tale. Yet, The Invisibles is much more than that. Morrison’s comic is also a post-anarchist cultural artifact. Post-anarchism is a radical form of anarchist theory that first emerged in the 1980s. It draws on twentieth century post-structuralism and post- modernism to extend anarchism’s critical power beyond its traditional targets, capitalism and the state.