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Fritz Allhoff
Philosophies of the Sciences Philosophies of the Sciences A Guide Edited by Fritz Allhoff A John Wiley & Sons, Ltd., Publication This edition first published 2010 © 2010 Blackwell Publishing Ltd Blackwell Publishing was acquired by John Wiley & Sons in February 2007. Blackwell’s publishing program has been merged with Wiley’s global Scientific, Technical, and Medical business to form Wiley-Blackwell. Registered Office John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, United Kingdom Editorial Offices 350 Main Street, Malden, MA 02148-5020, USA 9600 Garsington Road, Oxford, OX4 2DQ, UK The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK For details of our global editorial offices, for customer services, and for information about how to apply for permission to reuse the copyright material in this book please see our website at www.wiley.com/wiley-blackwell. The right of Fritz Allhoff to be identified as the author of the editorial material in this work has been asserted in accordance with the Copyright, Designs and Patents Act 1988. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs and Patents Act 1988, without the prior permission of the publisher. Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic books. Designations used by companies to distinguish their products are often claimed as trademarks. All brand names and product names used in this book are trade names, service marks, trademarks or registered trademarks of their respective owners. -
Framing Major Prebiotic Transitions As Stages of Protocell Development: Three Challenges for Origins-Of-Life Research
Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research Ben Shirt-Ediss1, Sara Murillo-Sánchez2,3 and Kepa Ruiz-Mirazo*2,3 Commentary Open Access Address: Beilstein J. Org. Chem. 2017, 13, 1388–1395. 1Interdisciplinary Computing and Complex BioSystems Group, doi:10.3762/bjoc.13.135 University of Newcastle, UK, 2Dept. Logic and Philosophy of Science, University of the Basque Country, Spain and 3Biofisika Institute Received: 16 February 2017 (CSIC, UPV-EHU), Spain Accepted: 27 June 2017 Published: 13 July 2017 Email: Kepa Ruiz-Mirazo* - [email protected] This article is part of the Thematic Series "From prebiotic chemistry to molecular evolution". * Corresponding author Guest Editor: L. Cronin Keywords: functional integration; origins of life; prebiotic evolution; protocells © 2017 Shirt-Ediss et al.; licensee Beilstein-Institut. License and terms: see end of document. Abstract Conceiving the process of biogenesis as the evolutionary development of highly dynamic and integrated protocell populations provides the most appropriate framework to address the difficult problem of how prebiotic chemistry bridged the gap to full-fledged living organisms on the early Earth. In this contribution we briefly discuss the implications of taking dynamic, functionally inte- grated protocell systems (rather than complex reaction networks in bulk solution, sets of artificially evolvable replicating molecules, or even these same replicating molecules encapsulated in passive compartments) -
Chapter 9. NATURAL SELECTION and BIOLOGICAL EVOLUTION
Chapter 9. NATURAL SELECTION AND BIOLOGICAL EVOLUTION Which beginning of time [the Creation] according to our Chronologie, fell upon the entrance of the night preced- ing the twenty third day of Octob. in the year of the Julian Calendar, 710 [i.e. B.C. 4004]. Archbishop James Ussher (1581—1656) The Annals of the World1 (1658:1) “How stupid not to have thought of that!” Thomas Huxley (1825-1895), about Darwin’s theory of Evolution by Nat- ural Selection. I. Introduction A. Classical Discoveries of Biology From the mid 18th Century to the early part of the 20th, a large fraction of biologists’ efforts went into two massive collective discoveries, the discovery of biotic diversity, and the discovery of evolution. Over the period from 1750 to 1950 the careful descriptive analyses of Swedish biol- ogist Karl von Linné and his followers showed there to be on the order of 10 million or so different types of living organisms. The differences in biotas in different parts of the world came to be appreciated, the amazing diversity of the tropics was documented, and previ- ously unimagined major groups of organisms were discovered, including microorganisms and the biota of odd habitats like the oceanic plankton. The sometimes bizarre and always impressive adaptation of organisms to their habitats and ways of life greatly impressed the early scientific naturalists, who argued that it proved the existence of an All Seeing Design- er. Similarly, paleontologists described a huge variety of fossil plants and animals. The succession of forms, and the presence of many detailed structural similarities between liv- ing and extinct forms, as well as structural parallels between living forms, strongly suggest- ed that living and ancient forms of life were connected by branching lines of descent. -
Uniting Micro- with Macroevolution Into an Extended Synthesis: Reintegrating Life’S Natural History Into Evolution Studies
Uniting Micro- with Macroevolution into an Extended Synthesis: Reintegrating Life’s Natural History into Evolution Studies Nathalie Gontier Abstract The Modern Synthesis explains the evolution of life at a mesolevel by identifying phenotype–environmental interactions as the locus of evolution and by identifying natural selection as the means by which evolution occurs. Both micro- and macroevolutionary schools of thought are post-synthetic attempts to evolution- ize phenomena above and below organisms that have traditionally been conceived as non-living. Microevolutionary thought associates with the study of how genetic selection explains higher-order phenomena such as speciation and extinction, while macroevolutionary research fields understand species and higher taxa as biological individuals and they attribute evolutionary causation to biotic and abiotic factors that transcend genetic selection. The microreductionist and macroholistic research schools are characterized as two distinct epistemic cultures where the former favor mechanical explanations, while the latter favor historical explanations of the evolu- tionary process by identifying recurring patterns and trends in the evolution of life. I demonstrate that both cultures endorse radically different notions on time and explain how both perspectives can be unified by endorsing epistemic pluralism. Keywords Microevolution · Macroevolution · Origin of life · Evolutionary biology · Sociocultural evolution · Natural history · Organicism · Biorealities · Units, levels and mechanisms of evolution · Major transitions · Hierarchy theory But how … shall we describe a process which nobody has seen performed, and of which no written history gives any account? This is only to be investigated, first, in examining the nature of those solid bodies, the history of which we want to know; and 2dly, in exam- ining the natural operations of the globe, in order to see if there now actually exist such operations, as, from the nature of the solid bodies, appear to have been necessary to their formation. -
Reproduction of a Protocell by Replication of Minority Molecule in Catalytic Reaction Network
APS/123-QED Reproduction of a Protocell by Replication of Minority Molecule in Catalytic Reaction Network Atsushi Kamimura1 and Kunihiko Kaneko2, 3 1Department of Applied Physics, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan. 2Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo 153-8902, Japan 3Complex Systems Biology Project, ERATO, JST, Tokyo, Japan. (Dated: October 31, 2018) Abstract For understanding the origin of life, it is essential to explain the development of a compartmen- talized structure, which undergoes growth and division, from a set of chemical reactions. In this study, a hypercycle with two chemicals that mutually catalyze each other is considered in order to show that the reproduction of a protocell with a growth-division process naturally occurs when the replication speed of one chemical is considerably slower than that of the other chemical. It is observed that the protocell divides after a minority molecule is replicated at a slow synthesis rate, and thus, a synchrony between the reproduction of a cell and molecule replication is achieved. The robustness of such protocells against the invasion of parasitic molecules is also demonstrated. arXiv:1005.1142v1 [q-bio.CB] 7 May 2010 PACS numbers: 87.17.-d, 05.40.-a, 82.39.-k 1 Filling a gap between just a set of catalytic reactions and a reproducing cell is a difficult problem; however, it is essential to fully understand this relationship to unveil the origin of life, to establish a theory for a living state, and to experimentally synthesize protocells[1]. -
Stephen J. Gould's Legacy
STEPHEN J. GOULD’S LEGACY NATURE, HISTORY, SOCIETY Venice, May 10–12, 2012 Organized by Istituto Veneto di Scienze, Lettere ed Arti in collaboration with Università Ca’ Foscari di Venezia ABSTRACTS Organizing Committee Gian Antonio Danieli, Istituto Veneto di Scienze, Lettere ed Arti Elena Gagliasso, Sapienza Università di Roma Alessandro Minelli, Università degli studi di Padova and Istituto Veneto di Scienze, Lettere ed Arti Telmo Pievani, Università degli studi di Milano Bicocca and Istituto Veneto di Scienze, Lettere ed Arti Maria Turchetto, Università Ca’ Foscari di Venezia Chairpersons Bernardino Fantini, Université de Genève Marco Ferraguti, Università degli studi di Milano Elena Gagliasso, Sapienza Università di Roma Giorgio Manzi, Sapienza Università di Roma Alessandro Minelli, Università degli studi di Padova and Istituto Veneto di Scienze, Lettere ed Arti Telmo Pievani, Università degli studi di Milano Bicocca and Istituto Veneto di Scienze, Lettere ed Arti Maria Turchetto, Università Ca’ Foscari di Venezia Invited speakers Guido Barbujani, Università degli studi di Ferrara Marcello Buiatti, Università degli studi di Firenze Andrea Cavazzini, Université de Liège Niles Eldredge, American Museum of Natural History, New York T. Ryan Gregory, University of Guelph Alberto Gualandi, Università degli studi di Bologna Elisabeth Lloyd, Indiana University Giuseppe Longo, CNRS; École Normale Supérieure, Paris Winfried Menninghaus, Freie Universität Berlin Alessandro Minelli, Università degli studi di Padova and Istituto Veneto di Scienze, Lettere ed Arti Gerd Müller, Konrad Lorenz Institute, Vienna and Istituto Veneto di Scienze, Lettere ed Arti Marco Pappalardo, McGill University, Montreal Telmo Pievani, Università degli studi di Milano Bicocca and Istituto Veneto di Scienze, Lettere ed Arti Klaus Scherer, Université de Genève Ian Tattersall, American Museum of Natural History, New York May 20, 2012 will be the tenth anniversary of Stephen Jay Gould’s death. -
According to Science Ramy Brustein Ben-Gurion University of the Negev
The Creation of the World – According to Science Ramy Brustein Ben-Gurion University of the Negev How was the world created? People have asked this ever since they could ask anything, and answers have come from all sides: from religion, tradition, philosophy, mysticism….and science. While this does not seem like a problem amenable to scientific measurement, it has led scientists to come up with fascinating ideas and observations: the Big Bang, the concept of inflation, the fact that most of the world is made up of dark matter and dark energy which we cannot perceive, and more. Of course scientists cannot claim to know the definitive truth. But we can approach the question from a scientific viewpoint and see what we find out. How do we do that? First, we look to the data. Thanks to modern technology, we have much more information than did people of previous ages who asked the same question. Then we can use scientific methods and techniques to analyze the data, organize them in a coherent way and try and extract an answer. This process and its main findings will be described in the lecture. The Ghosts in the (Primitive) Soup: A Review of Some of the Debates that Shaped Early Discussions on the Origin and Nature of Life Antonio Lazcano Universidad Nacional Autónoma de México The heterotrophic origin of life proposed by Oparin and Haldane in the 1920’s was part of a Darwinian framework that assumed that living organisms were the historical outcome of a gradual transformation of lifeless matter. This idea was strongly opposed by the geneticist H. -
Evolution, Development, and the Units of Selection (Epigenesis/Modern Synthesis/Preformation/Somatic Embryogenesis/Weismann's Doctrine) LEO W
Proc. Nat. Acad. Sci. USA Vol. 80, pp. 1387-1391, March 1983 Evolution Evolution, development, and the units of selection (epigenesis/Modern Synthesis/preformation/somatic embryogenesis/Weismann's doctrine) LEO W. Buss Department of Biology and Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06511 Communicated by G, Evelyn Hutchinson, December 17, 1982 ABSTRACT The "Modern Synthesis" forms the foundation of those working with the comparative embryology of vertebrates, current evolutionary theory. It is based on variation among indi- saw strong evidence for Weismann's scheme in the sequestering viduals within populations. Variations within individuals are be- of germ cells during early embryology. Finally, several inves- lieved to hold no phylogenetic significance because such variation tigators studying wound-healing had clearly illustrated that many cannot be transmitted to the germ line (i.e., Weismann's doctrine). somatic cells were, in fact, incapable of regeneration. Weismann's doctrine, however, does not apply to protists, fungi, Support for Weismann's doctrine was by no means universal. or plants and is an entirely unsupported assumption for 19 phyla Botanists were Weismann's earliest critics (5). Debate over the of animals. This fact requires that the Modern Synthesis be reex- issue was central in the development of the continuing rift be- amined and modified. tween botanists and zoologists despite the commonality of their interests (G. E. Hutchinson, personal communication). Al- The Darwinian notion of evolution as a process directed by se- though Weismann's doctrine was the subject of two very critical lection acting upon heritable variation has not been challenged reviews in the 20th century (6, 7), these criticisms fell on deaf seriously since Darwin first articulated it. -
Adaptationism and the Logic of Research Questions: How to Think Clearly About Evolutionary Causes
Biol Theory (2015) 10:343–362 DOI 10.1007/s13752-015-0214-2 ORIGINAL ARTICLE Adaptationism and the Logic of Research Questions: How to Think Clearly About Evolutionary Causes Elisabeth A. Lloyd1 Received: 20 March 2015 / Accepted: 29 May 2015 / Published online: 9 July 2015 Ó Konrad Lorenz Institute for Evolution and Cognition Research 2015 Abstract This article discusses various dangers that popular methods, despite its benign reputation. In ‘‘The accompany the supposedly benign methods in behavioral Spandrels of San Marco and the Panglossian Paradigm,’’ evolutionary biology and evolutionary psychology that fall Gould and Lewontin (1979) drew attention to several under the framework of ‘‘methodological adaptationism.’’ dangers in using this method. In this article, I present a A ‘‘Logic of Research Questions’’ is proposed that aids in framework for analysis that makes their worries clearer. I clarifying the reasoning problems that arise due to the also warn of further risks of this methodological frame- framework under critique. The live, and widely practiced, work, expanding on the dangers it poses to scientific rea- ‘‘evolutionary factors’’ framework is offered as the key soning in evolutionary biology. At the same time, I comparison and alternative. The article goes beyond the emphasize that I am not attacking the notion of looking for traditional critique of Stephen Jay Gould and Richard C. adaptations in evolutionary studies: I am not anti-adapta- Lewontin, to present problems such as the disappearance of tion. The issues concern which framework is most appro- evidence, the mishandling of the null hypothesis, and priate and fruitful. failures in scientific reasoning, exemplified by a case from As evolutionary biology is usually taught and con- human behavioral ecology. -
Stephen Jay Gould Papers M1437
http://oac.cdlib.org/findaid/ark:/13030/kt229036tr No online items Guide to the Stephen Jay Gould Papers M1437 Jenny Johnson Department of Special Collections and University Archives August 2011 ; revised 2019 Green Library 557 Escondido Mall Stanford 94305-6064 [email protected] URL: http://library.stanford.edu/spc Guide to the Stephen Jay Gould M1437 1 Papers M1437 Language of Material: English Contributing Institution: Department of Special Collections and University Archives Title: Stephen Jay Gould papers creator: Gould, Stephen Jay source: Shearer, Rhonda Roland Identifier/Call Number: M1437 Physical Description: 575 Linear Feet(958 boxes) Physical Description: 1180 computer file(s)(52 megabytes) Date (inclusive): 1868-2004 Date (bulk): bulk Abstract: This collection documents the life of noted American paleontologist, evolutionary biologist, and historian of science, Stephen Jay Gould. The papers include correspondence, juvenilia, manuscripts, subject files, teaching files, photographs, audiovisual materials, and personal and biographical materials created and compiled by Gould. Both textual and born-digital materials are represented in the collection. Preferred Citation [identification of item], Stephen Jay Gould Papers, M1437. Dept. of Special Collections, Stanford University Libraries, Stanford, Calif. Publication Rights While Special Collections is the owner of the physical and digital items, permission to examine collection materials is not an authorization to publish. These materials are made available for use -
Individuality and Adaptation Across Levels of Selection: How Shall We Name and Generalize the Unit of Darwinism?
Individuality and adaptation across levels of selection: How shall we name and generalize the unit of Darwinism? Stephen Jay Gould*† and Elisabeth A. Lloyd‡ *Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138; and ‡History and Philosophy of Science, Indiana University, 130 Goodbody Hall, Bloomington, IN 47405 Contributed by Stephen Jay Gould, June 2, 1999 Two major clarifications have greatly abetted the understanding and none more pressing than learning how to think about the viscerally fruitful expansion of the theory of natural selection in recent years: unfamiliar (and in many ways counterintuitive) supraorganismal the acknowledgment that interactors, not replicators, constitute the levels of organization and selection. (Given the reductionist tradi- causal unit of selection; and the recognition that interactors are tions of Western science, we are naturally more comfortable with Darwinian individuals, and that such individuals exist with potency at suborganismal units of genes and cell lineages.) We claim that several levels of organization (genes, organisms, demes, and species evolutionists have generally not appreciated the importance of in particular), thus engendering a rich hierarchical theory of selection higher levels, particularly the species level of selection, because in contrast with Darwin’s own emphasis on the organismic level. But species-individuals may not build many adaptations of their own. a piece of the argument has been missing, and individuals at levels False emphasis on adaptation therefore leads biologists to down- distinct from organisms have been denied potency (although granted grade the species level as only weakly operative in the processes of existence within the undeniable logic of the theory), because they do selection. -
Adaptationism and the Logic of Research Questions: How to Think Clearly About Evolutionary Causes
Biol Theory (2015) 10:343–362 DOI 10.1007/s13752-015-0214-2 ORIGINAL ARTICLE Adaptationism and the Logic of Research Questions: How to Think Clearly About Evolutionary Causes Elisabeth A. Lloyd1 Received: 20 March 2015 / Accepted: 29 May 2015 / Published online: 9 July 2015 Ó Konrad Lorenz Institute for Evolution and Cognition Research 2015 Abstract This article discusses various dangers that popular methods, despite its benign reputation. In ‘‘The accompany the supposedly benign methods in behavioral Spandrels of San Marco and the Panglossian Paradigm,’’ evolutionary biology and evolutionary psychology that fall Gould and Lewontin (1979) drew attention to several under the framework of ‘‘methodological adaptationism.’’ dangers in using this method. In this article, I present a A ‘‘Logic of Research Questions’’ is proposed that aids in framework for analysis that makes their worries clearer. I clarifying the reasoning problems that arise due to the also warn of further risks of this methodological frame- framework under critique. The live, and widely practiced, work, expanding on the dangers it poses to scientific rea- ‘‘evolutionary factors’’ framework is offered as the key soning in evolutionary biology. At the same time, I comparison and alternative. The article goes beyond the emphasize that I am not attacking the notion of looking for traditional critique of Stephen Jay Gould and Richard C. adaptations in evolutionary studies: I am not anti-adapta- Lewontin, to present problems such as the disappearance of tion. The issues concern which framework is most appro- evidence, the mishandling of the null hypothesis, and priate and fruitful. failures in scientific reasoning, exemplified by a case from As evolutionary biology is usually taught and con- human behavioral ecology.