Download or read book Reconstructing the Past written by Elliott Sober and published by MIT Press. This book was released on 1991-02-05 with total page 298 pages. Available in PDF, EPUB and Kindle. Book excerpt: Reconstructing the Past seeks to clarify and help resolve the vexing methodological issues that arise when biologists try to answer such questions as whether human beings are more closely related to chimps than they are to gorillas. It explores the case for considering the philosophical idea of simplicity/parsimony as a useful principle for evaluating taxonomic theories of evolutionary relationships. For the past two decades, evolutionists have been vigorously debating the appropriate methods that should be used in systematics, the field that aims at reconstructing phylogenetic relationships among species. This debate over phylogenetic inference, Elliott Sober observes, raises broader questions of hypothesis testing and theory evaluation that run head on into long standing issues concerning simplicity/parsimony in the philosophy of science. Sober treats the problem of phylogenetic inference as a detailed case study in which the philosophical idea of simplicity/parsimony can be tested as a principle of theory evaluation. Bringing together philosophy and biology, as well as statistics, Sober builds a general framework for understanding the circumstances in which parsimony makes sense as a tool of phylogenetic inference. Along the way he provides a detailed critique of parsimony in the biological literature, exploring the strengths and limitations of both statistical and nonstatistical cladistic arguments.
Download or read book Reconstructing Evolution written by Olivier Gascuel and published by OUP Oxford. This book was released on 2007-06-28 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: Evolution is a complex process, acting at multiple scales, from DNA sequences and proteins to populations of species. Understanding and reconstructing evolution is of major importance in numerous subfields of biology. For example, phylogenetics and sequence evolution is central to comparative genomics, attempts to decipher genomes, and molecular epidemiology. Phylogenetics is also the focal point of large-scale international biodiversity assessment initiatives such as the 'Tree of Life' project, which aims to build the evolutionary tree for all extant species. Since the pioneering work in phylogenetics in the 1960s, models have become increasingly sophisticated to account for the inherent complexity of evolution. They rely heavily on mathematics and aim at modelling and analyzing biological phenomena such as horizontal gene transfer, heterogeneity of mutation, and speciation and extinction processes. This book presents these recent models, their biological relevance, their mathematical basis, their properties, and the algorithms to infer them from data. A number of subfields from mathematics and computer science are involved: combinatorics, graph theory, stringology, probabilistic and Markov models, information theory, statistical inference, Monte Carlo methods, continuous and discrete algorithmics. This book arises from the Mathematics of Evolution & Phylogenetics meeting at the Mathematical Institute Henri Poincaré, Paris, in June 2005 and is based on the outstanding state-of-the-art reports presented by the conference speakers. Ten chapters - based around five themes - provide a detailed overview of key topics, from the underlying concepts to the latest results, some of which are at the forefront of current research.
Download or read book Mathematics of Evolution and Phylogeny written by Olivier Gascuel and published by OUP Oxford. This book was released on 2005-02-24 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book considers evolution at different scales: sequences, genes, gene families, organelles, genomes and species. The focus is on the mathematical and computational tools and concepts, which form an essential basis of evolutionary studies, indicate their limitations, and give them orientation. Recent years have witnessed rapid progress in the mathematics of evolution and phylogeny, with models and methods becoming more realistic, powerful, and complex. Aimed at graduates and researchers in phylogenetics, mathematicians, computer scientists and biologists, and including chapters by leading scientists: A. Bergeron, D. Bertrand, D. Bryant, R. Desper, O. Elemento, N. El-Mabrouk, N. Galtier, O. Gascuel, M. Hendy, S. Holmes, K. Huber, A. Meade, J. Mixtacki, B. Moret, E. Mossel, V. Moulton, M. Pagel, M.-A. Poursat, D. Sankoff, M. Steel, J. Stoye, J. Tang, L.-S. Wang, T. Warnow, Z. Yang, this book of contributed chapters explains the basis and covers the recent results in this highly topical area.
Download or read book Ecological Niches and Geographic Distributions MPB 49 written by A. Townsend Peterson and published by Princeton University Press. This book was released on 2011-11-20 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: Terminology, conceptual overview, biogeography, modeling.
Download or read book Tangled Trees written by Roderic D. M. Page and published by University of Chicago Press. This book was released on 2003 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, the use of molecular data to build phylogenetic trees and sophisticated computer-aided techniques to analyze them have led to a revolution in the study of cospeciation. Tangled Trees provides an up-to-date review and synthesis of current knowledge about phylogeny, cospeciation, and coevolution. The opening chapters present various methodological and theoretical approaches, ranging from the well-known parsimony approach to "jungles" and Bayesian statistical models. Then a series of empirical chapters discusses detailed studies of cospeciation involving vertebrate hosts and their parasites, including nematodes, viruses, and lice. Tangled Trees will be welcomed by researchers in a wide variety of fields, from parasitology and ecology to systematics and evolutionary biology. Contributors: Sarah Al-Tamimi, Michael A. Charleston, Dale H. Clayton, James W. Demastes, Russell D. Gray, Mark S. Hafner, John P. Huelsenbeck, J.-P. Hugot, Kevin P. Johnson, Peter Kabat, Bret Larget, Joanne Martin, Yannis Michalakis, Roderic D. M. Page, Ricardo L. Palma, Adrian M. Paterson, Susan L. Perkins, Andy Purvis, Bruce Rannala, David L. Reed, Fredrik Ronquist, Theresa A. Spradling, Jason Taylor, Michael Tristem
Download or read book Reconstructing Earth written by Braden Allenby and published by Island Press. This book was released on 2013-04-15 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Earth's biological, chemical, and physical systems are increasingly shaped by the activities of one species-ours. In our decisions about everything from manufacturing technologies to restaurant menus, the health of the planet has become a product of human choice. Environmentalism, however, has largely failed to adapt to this new reality. Reconstructing Earth offers seven essays that explore ways of developing a new, more sophisticated approach to the environment that replaces the fantasy of recovering pristine landscapes with a more grounded viewpoint that can foster a better relationship between humans and the planet. Braden Allenby, a lawyer with degrees in both engineering and environmental studies, explains the importance of technological choice, and how that factor is far more significant in shaping our environment (in ways both desirable and not) than environmental controls. Drawing on his varied background and experience in both academia and the corporate world, he describes the emerging field of "earth systems engineering and management," which offers an integrated approach to understanding and managing complex human/natural systems that can serve as a basis for crafting better, more lasting solutions to widespread environmental problems. Reconstructing Earth not only critiques dysfunctional elements of current environmentalism but establishes a foundation for future environmental management and progress, one built on an understanding of technological evolution and the cultural systems that support modern technologies. Taken together, the essays offer an important means of developing an environmentalism that is robust and realistic enough to address the urgent realities of our planet. Reconstructing Earth is a thought-provoking new work for anyone concerned with the past or future of environmental thought, including students and teachers of environmental studies, environmental policy, technology policy, technological evolution, or sustainability.
Download or read book In the Light of Evolution written by National Academy of Sciences and published by . This book was released on 2007 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Arthur M. Sackler Colloquia of the National Academy of Sciences address scientific topics of broad and current interest, cutting across the boundaries of traditional disciplines. Each year, four or five such colloquia are scheduled, typically two days in length and international in scope. Colloquia are organized by a member of the Academy, often with the assistance of an organizing committee, and feature presentations by leading scientists in the field and discussions with a hundred or more researchers with an interest in the topic. Colloquia presentations are recorded and posted on the National Academy of Sciences Sackler colloquia website and published on CD-ROM. These Colloquia are made possible by a generous gift from Mrs. Jill Sackler, in memory of her husband, Arthur M. Sackler.
Download or read book Reconstructing Reason and Representation written by Murray Clarke and published by MIT Press. This book was released on 2004-06-11 with total page 200 pages. Available in PDF, EPUB and Kindle. Book excerpt: A study of the philosophical implications of evolutionary psychology, suggesting that knowledge is a set of natural kinds housed in the modules of a massively modular mind. In Reconstructing Reason and Representation, Murray Clarke offers a detailed study of the philosophical implications of evolutionary psychology. In doing so, he offers new solutions to key problems in epistemology and philosophy of mind, including misrepresentation and rationality. He proposes a naturalistic approach to reason and representation that is informed by evolutionary psychology, and, expanding on the massive modularity thesis advanced in work by Leda Cosmides and John Tooby, argues for a modular, adapticist account of misrepresentation and knowledge. Just as the reliability of representation can be defended on the basis of an account of the proper function of cognitive modularity, misrepresentation can be explained through an appeal to the "gap theory," by noting the divergence between the proper and actual domains of cognitive modules in a massively modular mind. Clarke argues for an externalist, modular reliabilism by suggesting that evolution has equipped us with generally reliable inferential systems even if they do not always produce true beliefs. He argues that reliable deductive and inductive inference occurs only when cognitive modules deal with actual domains that are sufficiently similar to their proper domains. This psychologically informed, naturalized adapticism leads to the suggestion that knowledge is a set of natural kinds housed in the modules of a massively modular mind. Typically, the proper function of these cognitive modules is to provide us with truths that enable us to satisfy our basic biological needs. Beyond reasoning modules, other cognitive modules discussed include the ability to orient ourselves in space, and our abilities with language, numbers, object reasoning, and social understanding. Clarke also defends Cosmides and Tooby's massive modularity hypothesis against such critics as Jerry Fodor by demonstrating that these critics consistently misrepresent Cosmides and Tooby's position.
Download or read book Molecular Evolution written by Roderick D.M. Page and published by John Wiley & Sons. This book was released on 2009-07-14 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of evolution at the molecular level has given the subject of evolutionary biology a new significance. Phylogenetic 'trees' of gene sequences are a powerful tool for recovering evolutionary relationships among species, and can be used to answer a broad range of evolutionary and ecological questions. They are also beginning to permeate the medical sciences. In this book, the authors approach the study of molecular evolution with the phylogenetic tree as a central metaphor. This will equip students and professionals with the ability to see both the evolutionary relevance of molecular data, and the significance evolutionary theory has for molecular studies. The book is accessible yet sufficiently detailed and explicit so that the student can learn the mechanics of the procedures discussed. The book is intended for senior undergraduate and graduate students taking courses in molecular evolution/phylogenetic reconstruction. It will also be a useful supplement for students taking wider courses in evolution, as well as a valuable resource for professionals. First student textbook of phylogenetic reconstruction which uses the tree as a central metaphor of evolution. Chapter summaries and annotated suggestions for further reading. Worked examples facilitate understanding of some of the more complex issues. Emphasis on clarity and accessibility.
Download or read book Reconstructing the Tree of Life written by Trevor R. Hodkinson and published by CRC Press. This book was released on 2006-12-26 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: To document the world's diversity of species and reconstruct the tree of life we need to undertake some simple but mountainous tasks. Most importantly, we need to tackle species rich groups. We need to collect, name, and classify them, and then position them on the tree of life. We need to do this systematically across all groups of organisms and b
Download or read book Ancestral Sequence Reconstruction written by David A Liberles and published by OUP Oxford. This book was released on 2007-05-31 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ancestral sequence reconstruction is a technique of growing importance in molecular evolutionary biology and comparative genomics. As a powerful tool for testing evolutionary and ecological hypotheses, as well as uncovering the link between sequence and molecular phenotype, there are potential applications in a range of fields. Ancestral Sequence Reconstruction starts with a historical overview of the field, before discussing the potential applications in drug discovery and the pharmaceutical industry. This is followed by a section on computational methodology, which provides a detailed discussion of the available methods for reconstructing ancestral sequences (including their advantages, disadvantages, and potential pitfalls). Purely computational applications of the technique are then covered, including whole proteome reconstruction. Further chapters provide a detailed discussion on taking computationally reconstructed sequences and synthesizing them in the laboratory. The book concludes with a description of the scientific questions where experimental ancestral sequence reconstruction has been utilized to provide insights and inform future research. This research level text provides a first synthesis of the theories, methodologies and applications associated with ancestral sequence recognition, while simultaneously addressing many of the hot topics in the field. It will be of interest and use to both graduate students and researchers in the fields of molecular biology, molecular evolution, and evolutionary bioinformatics.
Download or read book DE EVOLUTION written by Jeff Frank and published by Page Publishing Inc. This book was released on 2016-12-22 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: A large sophisticated telescope complex sits atop a dormant volcano in one of Earth's most remote locations. Some incredibly bright but fiercely independent folks operate it much of the time. They detect, map, and perform threat analysis of near-Earth objects. Shortly after the world narrowly escapes an extinction event, they start collecting pieces of a related cosmic puzzle. When they've connected enough of them, an intriguing and disturbing picture emerges. Yet the most revealing pieces don't reveal themselves until after all life on Earth already has begun marching in lockstep toward possible oblivion.
Download or read book Understanding Evolution written by Kostas Kampourakis and published by Cambridge University Press. This book was released on 2014-04-03 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bringing together conceptual obstacles and core concepts of evolutionary theory, this book presents evolution as straightforward and intuitive.
Download or read book Biological Evolution and Statistical Physics written by M. Lässig and published by Springer. This book was released on 2008-01-11 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: This set of lecture notes gives a first coherent account of a novel aspect of the living world that can be called biological information. The book presents both a pedagogical and state-of-the art roadmap of this rapidly evolving area and covers the whole field, from information which is encoded in the molecular genetic code to the description of large-scale evolution of complex species networks. The book will prove useful for all those who work at the interface of biology, physics and information science.
Download or read book Molecular Evolution and Phylogenetics written by Masatoshi Nei and published by Oxford University Press. This book was released on 2000-07-27 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: During the last ten years, remarkable progress has occurred in the study of molecular evolution. Among the most important factors that are responsible for this progress are the development of new statistical methods and advances in computational technology. In particular, phylogenetic analysis of DNA or protein sequences has become a powerful tool for studying molecular evolution. Along with this developing technology, the application of the new statistical and computational methods has become more complicated and there is no comprehensive volume that treats these methods in depth. Molecular Evolution and Phylogenetics fills this gap and present various statistical methods that are easily accessible to general biologists as well as biochemists, bioinformatists and graduate students. The text covers measurement of sequence divergence, construction of phylogenetic trees, statistical tests for detection of positive Darwinian selection, inference of ancestral amino acid sequences, construction of linearized trees, and analysis of allele frequency data. Emphasis is given to practical methods of data analysis, and methods can be learned by working through numerical examples using the computer program MEGA2 that is provided.
Download or read book The Meaning of Evolution written by Robert J. Richards and published by University of Chicago Press. This book was released on 2009-02-02 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: Did Darwin see evolution as progressive, directed toward producing ever more advanced forms of life? Most contemporary scholars say no. In this challenge to prevailing views, Robert J. Richards says yes—and argues that current perspectives on Darwin and his theory are both ideologically motivated and scientifically unsound. This provocative new reading of Darwin goes directly to the origins of evolutionary theory. Unlike most contemporary biologists or historians and philosophers of science, Richards holds that Darwin did concern himself with the idea of progress, or telos, as he constructed his theory. Richards maintains that Darwin drew on the traditional embryological meanings of the terms "evolution" and "descent with modification." In the 1600s and 1700s, "evolution" referred to the embryological theory of preformation, the idea that the embryo exists as a miniature adult of its own species that simply grows, or evolves, during gestation. By the early 1800s, however, the idea of preformation had become the concept of evolutionary recapitulation, the idea that during its development an embryo passes through a series of stages, each the adult form of an ancestor species. Richards demonstrates that, for Darwin, embryological recapitulation provided a graphic model of how species evolve. If an embryo could be seen as successively taking the structures and forms of its ancestral species, then one could see the evolution of life itself as a succession of species, each transformed from its ancestor. Richards works with the Origin and other published and archival material to show that these embryological models were much on Darwin's mind as he considered the evidence for descent with modification. Why do so many modern researchers find these embryological roots of Darwin's theory so problematic? Richards argues that the current tendency to see evolution as a process that is not progressive and not teleological imposes perspectives on Darwin that incorrectly deny the clearly progressive heart of his embryological models and his evolutionary theory.
Download or read book The Phylogenetic Handbook written by Marco Salemi and published by Cambridge University Press. This book was released on 2009-03-26 with total page 750 pages. Available in PDF, EPUB and Kindle. Book excerpt: A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.
