Edward Hitchcock's Pre-Darwinian (1840) ''Tree of Life''
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Taxon Ordering in Phylogenetic Trees by Means of Evolutionary Algorithms Francesco Cerutti1,2, Luigi Bertolotti1,2, Tony L Goldberg3 and Mario Giacobini1,2*
Cerutti et al. BioData Mining 2011, 4:20 http://www.biodatamining.org/content/4/1/20 BioData Mining RESEARCH Open Access Taxon ordering in phylogenetic trees by means of evolutionary algorithms Francesco Cerutti1,2, Luigi Bertolotti1,2, Tony L Goldberg3 and Mario Giacobini1,2* * Correspondence: mario. Abstract [email protected] 1 Department of Animal Production, Background: In in a typical “left-to-right” phylogenetic tree, the vertical order of taxa Epidemiology and Ecology, Faculty of Veterinary Medicine, University is meaningless, as only the branch path between them reflects their degree of of Torino, Via Leonardo da Vinci similarity. To make unresolved trees more informative, here we propose an 44, 10095, Grugliasco (TO), Italy innovative Evolutionary Algorithm (EA) method to search the best graphical Full list of author information is available at the end of the article representation of unresolved trees, in order to give a biological meaning to the vertical order of taxa. Methods: Starting from a West Nile virus phylogenetic tree, in a (1 + 1)-EA we evolved it by randomly rotating the internal nodes and selecting the tree with better fitness every generation. The fitness is a sum of genetic distances between the considered taxon and the r (radius) next taxa. After having set the radius to the best performance, we evolved the trees with (l + μ)-EAs to study the influence of population on the algorithm. Results: The (1 + 1)-EA consistently outperformed a random search, and better results were obtained setting the radius to 8. The (l + μ)-EAs performed as well as the (1 + 1), except the larger population (1000 + 1000). -
John Hill (1714?–1775) on 'Plant Sleep'
Annals of Science ISSN: (Print) (Online) Journal homepage: https://www.tandfonline.com/loi/tasc20 John Hill (1714?–1775) on ‘Plant Sleep’: experimental physiology and the limits of comparative analysis Justin Begley To cite this article: Justin Begley (2020): John Hill (1714?–1775) on ‘Plant Sleep’: experimental physiology and the limits of comparative analysis, Annals of Science, DOI: 10.1080/00033790.2020.1813807 To link to this article: https://doi.org/10.1080/00033790.2020.1813807 © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group Published online: 12 Sep 2020. Submit your article to this journal View related articles View Crossmark data Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=tasc20 ANNALS OF SCIENCE https://doi.org/10.1080/00033790.2020.1813807 John Hill (1714?–1775) on ‘Plant Sleep’: experimental physiology and the limits of comparative analysis Justin Begley Department of Philosophy, History, and Art, University of Helsinki, Helsinki, Finland ABSTRACT ARTICLE HISTORY The phenomenon of ‘plant sleep’–whereby vegetables Received 1 October 2019 rhythmically open and close their leaves or petals in Accepted 18 August 2020 daily cycles – has been a continual source of fascination KEYWORDS for those with botanical interests, from the Portuguese Royal Society; history of physician Cristóbal Acosta and the Italian naturalist botany; John Hill; Prospero Alpini in the sixteenth century to Percy Bysshe experimentation; natural Shelley and Charles Darwin in the nineteenth. But it was history in 1757 that the topic received its earliest systemic treatment on English shores with the prodigious author, botanist, actor, and Royal Society critic John Hill’s The Sleep of Plants, and Cause of Motion in the Sensitive Plant. -
Foucault's Darwinian Genealogy
genealogy Article Foucault’s Darwinian Genealogy Marco Solinas Political Philosophy, University of Florence and Deutsches Institut Florenz, Via dei Pecori 1, 50123 Florence, Italy; [email protected] Academic Editor: Philip Kretsedemas Received: 10 March 2017; Accepted: 16 May 2017; Published: 23 May 2017 Abstract: This paper outlines Darwin’s theory of descent with modification in order to show that it is genealogical in a narrow sense, and that from this point of view, it can be understood as one of the basic models and sources—also indirectly via Nietzsche—of Foucault’s conception of genealogy. Therefore, this essay aims to overcome the impression of a strong opposition to Darwin that arises from Foucault’s critique of the “evolutionistic” research of “origin”—understood as Ursprung and not as Entstehung. By highlighting Darwin’s interpretation of the principles of extinction, divergence of character, and of the many complex contingencies and slight modifications in the becoming of species, this essay shows how his genealogical framework demonstrates an affinity, even if only partially, with Foucault’s genealogy. Keywords: Darwin; Foucault; genealogy; natural genealogies; teleology; evolution; extinction; origin; Entstehung; rudimentary organs “Our classifications will come to be, as far as they can be so made, genealogies; and will then truly give what may be called the plan of creation. The rules for classifying will no doubt become simpler when we have a definite object in view. We possess no pedigrees or armorial bearings; and we have to discover and trace the many diverging lines of descent in our natural genealogies, by characters of any kind which have long been inherited. -
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B. M ü ller, G ü nter P. Wagner, and Werner Callebaut, editors The Evolution of Cognition , edited by Cecilia Heyes and Ludwig Huber, 2000 Origination of Organismal Form: Beyond the Gene in Development and Evolutionary Biology , edited by Gerd B. M ü ller and Stuart A. Newman, 2003 Environment, Development, and Evolution: Toward a Synthesis , edited by Brian K. Hall, Roy D. Pearson, and Gerd B. M ü ller, 2004 Evolution of Communication Systems: A Comparative Approach , edited by D. Kimbrough Oller and Ulrike Griebel, 2004 Modularity: Understanding the Development and Evolution of Natural Complex Systems , edited by Werner Callebaut and Diego Rasskin-Gutman, 2005 Compositional Evolution: The Impact of Sex, Symbiosis, and Modularity on the Gradualist Framework of Evolution , by Richard A. Watson, 2006 Biological Emergences: Evolution by Natural Experiment , by Robert G. B. Reid, 2007 Modeling Biology: Structure, Behaviors, Evolution , edited by Manfred D. Laubichler and Gerd B. M ü ller, 2007 Evolution of Communicative Flexibility: Complexity, Creativity, and Adaptability in Human and Animal Communication , edited by Kimbrough D. Oller and Ulrike Griebel, 2008 Functions in Biological and Artifi cial Worlds: Comparative Philosophical Perspectives , edited by Ulrich Krohs and Peter Kroes, 2009 Cognitive Biology: Evolutionary and Developmental Perspectives on Mind, Brain, and Behavior , edited by Luca Tommasi, Mary A. Peterson, and Lynn Nadel, 2009 Innovation in Cultural Systems: Contributions from Evolutionary Anthropology , edited by Michael J. O ’ Brien and Stephen J. Shennan, 2010 The Major Transitions in Evolution Revisited , edited by Brett Calcott and Kim Sterelny, 2011 Transformations of Lamarckism: From Subtle Fluids to Molecular Biology , edited by Snait B. -
A General Criterion for Translating Phylogenetic Trees Into Linear Sequences
A general criterion for translating phylogenetic trees into linear sequences Proposal (474) to South American Classification Committee In most of the books, papers and check-lists of birds (e.g. Meyer de Schauensee 1970, Stotz et al. 1996; and other taxa e.g. Lewis et al. 2005, Haston et al. 2009, for plants), at least the higher taxa are arranged phylogenetically, with the “oldest” groups (Rheiformes/Tinamiformes) placed first, and the “modern” birds (Passeriformes) at the end. The molecular phylogenetic analysis of Hackett et al. (2008) supports this criterion. For this reason, it would be desirable that in the SACC list not only orders and families, but also genera within families and species within genera, are phylogenetically ordered. In spite of the SACC’s efforts in producing an updated phylogeny-based list, it is evident that there are differences in the way the phylogenetic information has been translated into linear sequences, mainly for node rotation and polytomies. This is probably one of the reasons why Douglas Stotz (Proposal #423) has criticized using sequence to show relationships. He considers that we are creating unstable sequences with little value in terms of understanding of relationships. He added, “We would be much better served by doing what most taxonomic groups do and placing taxa within the hierarchy in alphabetical order, making no pretense that sequence can provide useful information on the branching patterns of trees. This would greatly stabilize sequences and not cost much information about relationships”. However, we encourage creating sequences that reflect phylogeny as much as possible at all taxonomic levels (although we agree with Douglas Stotz that the translation of a phylogenetic tree into a simple linear sequence inevitably involves a loss of information about relationships that is present in the trees on which the sequence is based). -
Synthesis of Phylogeny and Taxonomy Into a Comprehensive Tree of Life
Synthesis of phylogeny and taxonomy into a comprehensive tree of life Cody E. Hinchliffa,1, Stephen A. Smitha,1,2, James F. Allmanb, J. Gordon Burleighc, Ruchi Chaudharyc, Lyndon M. Coghilld, Keith A. Crandalle, Jiabin Dengc, Bryan T. Drewf, Romina Gazisg, Karl Gudeh, David S. Hibbettg, Laura A. Katzi, H. Dail Laughinghouse IVi, Emily Jane McTavishj, Peter E. Midfordd, Christopher L. Owenc, Richard H. Reed, Jonathan A. Reesk, Douglas E. Soltisc,l, Tiffani Williamsm, and Karen A. Cranstonk,2 aEcology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109; bInterrobang Corporation, Wake Forest, NC 27587; cDepartment of Biology, University of Florida, Gainesville, FL 32611; dField Museum of Natural History, Chicago, IL 60605; eComputational Biology Institute, George Washington University, Ashburn, VA 20147; fDepartment of Biology, University of Nebraska-Kearney, Kearney, NE 68849; gDepartment of Biology, Clark University, Worcester, MA 01610; hSchool of Journalism, Michigan State University, East Lansing, MI 48824; iBiological Science, Clark Science Center, Smith College, Northampton, MA 01063; jDepartment of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045; kNational Evolutionary Synthesis Center, Duke University, Durham, NC 27705; lFlorida Museum of Natural History, University of Florida, Gainesville, FL 32611; and mComputer Science and Engineering, Texas A&M University, College Station, TX 77843 Edited by David M. Hillis, The University of Texas at Austin, Austin, TX, and approved July 28, 2015 (received for review December 3, 2014) Reconstructing the phylogenetic relationships that unite all line- published phylogenies are available only as journal figures, rather ages (the tree of life) is a grand challenge. The paucity of homologous than in electronic formats that can be integrated into databases and character data across disparately related lineages currently renders synthesis methods (7–9). -
Some Philosophical Questions About Paleontology and Their Practica1 Consequences
ACTA GEOLOGICA HISPANICA. Concept and method in Paleontology. 16 (1981) nos 1-2, pags. 7-23 Some philosophical questions about paleontology and their practica1 consequences by Miquel DE RENZI Depto. de Geología, Facultad de Ciencias Biológicas, Universidad de Valencia. Burjassot (Valencia). This papcr attempts to objectively discuss the actual state ofpaleontology. The En aquest treball s'ha intentat fer un balanc d'alguns aspectes de I'estat de la progress of this science stood still somewhat during the latter part of the last paleontologia. La historia de la paleontologia mostra un estancarnent a les century which caused it to develop apart from the biological sciences. an area to darreries del segle passac aquest estancament va Fer que la nostra ciencia s'anes which it is naturally tied. As aconsequence, this bruought a long-term stagnation, allunyant cada cop mes de I'area de les ciencies bii~logiques,amb les qualsestava because biology, dunng this century, has made great progress and paleontology lligada naturalment AixO va portar, com a conseqüencia, un important has not During the last 20 years paleontology as a science hasrecuperatedsome endarreriment, car la biologia, durant aquest segle, ha donat un gran pas of this loss, but we as scientists need to be careful in various aspects of its endavant, mentre que aquest no ha estat el cas de lapaleontologia Al nostre pais development -i possiblement a molts d'altres- la paleontologia es, fonamentalment, un estn per datar estrats. Tanmateix, un mal estri, car la datació es basadaen les especies fossils i la seva determinació es fonamenta en el ccncepte d'especie biolbgica; els fossils pero en moltes ocasions, són utilitzats mes aviat com si fossin segells o monedes. -
Leibniz on Whether the World Increases in Perfection
LEIBNIZ ON WHETHER THE WORLD INCREASES IN PERFECTION Lloyd Strickland In a letter to Bourguet written on 5 August 1715, a little over a year before his death, Leibniz suggests that, on the question of the world’s perfection, ‘Two hypotheses can be formed – one that nature is equally perfect, the other that it always increases in perfection.’ (L664)1 He then proceeds to split the second option into two further 1 The abbreviations I use throughout when citing Leibniz are as follows: A = Sämtliche schriften und briefe, ed by Akademie der Wissenschaften, multiple volumes in 6 series, cited by series (reihe) and volume (band) (Berlin, 1923-). AG = Philosophical essays, trans & ed by Roger Ariew & Daniel Garber (Indianapolis, 1989). D = De summa rerum, trans by G. H. R. Parkinson (New Haven, 1992). DM = Discourse on metaphysics, cited by section number, various translations in AG, L, P, W etc. Dn = The philosophical works of Leibnitz, trans & ed George Martin Duncan (New Haven, 1908). E = Opera Philosophica, ed by J. E. Erdmann (Berlin, 1840). G = Die philosophiscen Schriften von Gottfried Wilhelm Leibniz, ed by C. I. Gerhardt, 7 vols (Berlin, 1875-1890). GM = G. W. Leibniz: Mathematische Schriften, ed by C. I. Gerhardt, 7 vols (Berlin, 1962). Gr = Textes inédits, ed by Gaston Grua, 2 vols with successive pagination (Paris, 1948). H = Theodicy, trans by E. M. Huggard (Chicago, 1990). L = Philosophical papers and letters, trans & ed Leroy E. Loemker (Dordrecht, 2ed 1969). Mon = Monadology, cited by section number, various translations in AG, L, P, W etc. NE = New essays concerning human understanding, trans & ed by Peter Remnant & Jonathan Bennett (Cambridge, 1996). -
The Paleontology Synthesis Project and Establishing a Framework for Managing National Park Service Paleontological Resource Archives and Data
Lucas, S.G. and Sullivan, R.M., eds., 2018, Fossil Record 6. New Mexico Museum of Natural History and Science Bulletin 79. 589 THE PALEONTOLOGY SYNTHESIS PROJECT AND ESTABLISHING A FRAMEWORK FOR MANAGING NATIONAL PARK SERVICE PALEONTOLOGICAL RESOURCE ARCHIVES AND DATA VINCENT L. SANTUCCI1, JUSTIN S. TWEET2 and TIMOTHY B. CONNORS3 1National Park Service, Geologic Resources Division, 1849 “C” Street, NW, Washington, D.C. 20240, [email protected]; 2National Park Service, 9149 79th Street S., Cottage Grove, MN 55016, [email protected]; 3National Park Service, Geologic Resources Division, 12795 W. Alameda Parkway, Lakewood, CO 80225, [email protected] Abstract—The National Park Service Paleontology Program maintains an extensive collection of digital and hard copy documents, publications, photographs and other archives associated with the paleontological resources documented in 268 parks. The organization and preservation of the NPS paleontology archives has been the focus of intensive data management activities by a small and dedicated team of NPS staff. The data preservation strategy complemented the NPS servicewide inventories for paleontological resources. The first phase of the data management, referred to as the NPS Paleontology Synthesis Project, compiled servicewide paleontological resource data pertaining to geologic time, taxonomy, museum repositories, holotype fossil specimens, and numerous other topics. In 2015, the second phase of data management was implemented with the creation and organization of a multi-faceted digital data system known as the NPS Paleontology Archives and NPS Paleontology Library. Two components of the NPS Paleontology Archives were designed for the preservation of both park specific and servicewide paleontological resource archives and data. A third component, the NPS Paleontology Library, is a repository for electronic copies of geology and paleontology publications, reports, and other media. -
Staying Optimistic: the Trials and Tribulations of Leibnizian Optimism
Strickland, Lloyd 2019 Staying Optimistic: The Trials and Tribulations of Leibnizian Optimism. Journal of Modern Philosophy, 1(1): 3, pp. 1–21. DOI: https://doi.org/10.32881/jomp.3 RESEARCH Staying Optimistic: The Trials and Tribulations of Leibnizian Optimism Lloyd Strickland Manchester Metropolitan University, GB [email protected] The oft-told story of Leibniz’s doctrine of the best world, or optimism, is that it enjoyed a great deal of popularity in the eighteenth century until the massive earthquake that struck Lisbon on 1 November 1755 destroyed its support. Despite its long history, this story is nothing more than a commentators’ fiction that has become accepted wisdom not through sheer weight of evidence but through sheer frequency of repetition. In this paper we shall examine the reception of Leibniz’s doctrine of the best world in the eighteenth century in order to get a clearer understanding of what its fate really was. As we shall see, while Leibniz’s doctrine did win a good number of adherents in the 1720s and 1730s, especially in Germany, support for it had largely dried up by the mid-1740s; moreover, while opponents of Leibniz’s doctrine were few and far between in the 1710s and 1720s, they became increasing vocal in the 1730s and afterwards, between them producing an array of objections that served to make Leibnizian optimism both philosophically and theologically toxic years before the Lisbon earthquake struck. Keywords: Leibniz; Optimism; Best world; Lisbon earthquake; Evil; Wolff The oft-told story of Leibniz’s doctrine of the best world, or optimism, is that it enjoyed a great deal of popularity in the eighteenth century until the massive earthquake that struck Lisbon on 1 November 1755 destroyed its support. -
Ten Misunderstandings About Evolution a Very Brief Guide for the Curious and the Confused by Dr
Ten Misunderstandings About Evolution A Very Brief Guide for the Curious and the Confused By Dr. Mike Webster, Dept. of Neurobiology and Behavior, Cornell Lab of Ornithology, Cornell University ([email protected]); February 2010 The current debate over evolution and “intelligent design” (ID) is being driven by a relatively small group of individuals who object to the theory of evolution for religious reasons. The debate is fueled, though, by misunderstandings on the part of the American public about what evolutionary biology is and what it says. These misunderstandings are exploited by proponents of ID, intentionally or not, and are often echoed in the media. In this booklet I briefly outline and explain 10 of the most common (and serious) misunderstandings. It is impossible to treat each point thoroughly in this limited space; I encourage you to read further on these topics and also by visiting the websites given on the resource sheet. In addition, I am happy to send a somewhat expanded version of this booklet to anybody who is interested – just send me an email to ask for one! What are the misunderstandings? 1. Evolution is progressive improvement of species Evolution, particularly human evolution, is often pictured in textbooks as a string of organisms marching in single file from “simple” organisms (usually a single celled organism or a monkey) on one side of the page and advancing to “complex” organisms on the opposite side of the page (almost invariably a human being). We have all seen this enduring image and likely have some version of it burned into our brains. -
Scientific BIOGRAPHY and the CASE of GEORGES CUVIER
Hist. Sci.) xiv (1976), 101-137 1976HisSc..14..101O SCIENTIFic BIOGRAPHY AND THE CASE OF GEORGES CUVIER: WITH A CRITICAL BIBLIOGRAPHY Dorinda OutralU University of Reading The purpose of this introduction is to provide some interpretative tools for the reader of the body of secondary literature on Georges Cuvier which is examined in the attached critical bibliography. Criticism and analysis of existing work is therefore emphasized, and the problems in volved in constructing a positive biography of Cuvier are only briefly examined. Not only strictly biographical studies, but also work on all aspects of Cuvier's achievement, have been so strongly informed by pre suppositions about his character, that a knowledge of this bias and its characteristic expressions is nece.<;sary before previous work on Cuvier can be properly interp'reted. This bibliography is thus also intended as a necessary clearing of the ground before further study of Cuvier's career can be undertaken. This is true not only because it is necessary to discover the precise extent of factual inadequacy in our knowledge of Cuvier's life and achievement, but also because we need to increase our awareness of the role which biographical inquiry has played in the history of science, for without this awareness, the full implications of the adoption of the form cannot be assessed. Interest in Georges Cuvier has increased considerably during the last decade, but so far almost no account has been taken of the extraordinary biographical tradition through which we view him. Almost every presen tation of Cuvier since his death in 1832 has been dominated by emphases which were established very soon afterwards, and which have continued to monopolize the attention of historians of the life-sciences until very recently.