Download or read book The Art of Theoretical Biology written by Franziska Matthäus and published by Springer Nature. This book was released on 2020-04-16 with total page 162 pages. Available in PDF, EPUB and Kindle. Book excerpt: This beautifully crafted book collects images, which were created during the process of research in all fields of theoretical biology. Data analysis, numerical treatment of a model, or simulation results yield stunning images, which represent pieces of art just by themselves. The approach of the book is to present for each piece of visualization a lucid synopsis of the scientific background as well as an outline of the artistic vision.
Download or read book Quantitative Biology written by Brian Munsky and published by MIT Press. This book was released on 2018-08-21 with total page 729 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to the quantitative modeling of biological processes, presenting modeling approaches, methodology, practical algorithms, software tools, and examples of current research. The quantitative modeling of biological processes promises to expand biological research from a science of observation and discovery to one of rigorous prediction and quantitative analysis. The rapidly growing field of quantitative biology seeks to use biology's emerging technological and computational capabilities to model biological processes. This textbook offers an introduction to the theory, methods, and tools of quantitative biology. The book first introduces the foundations of biological modeling, focusing on some of the most widely used formalisms. It then presents essential methodology for model-guided analyses of biological data, covering such methods as network reconstruction, uncertainty quantification, and experimental design; practical algorithms and software packages for modeling biological systems; and specific examples of current quantitative biology research and related specialized methods. Most chapters offer problems, progressing from simple to complex, that test the reader's mastery of such key techniques as deterministic and stochastic simulations and data analysis. Many chapters include snippets of code that can be used to recreate analyses and generate figures related to the text. Examples are presented in the three popular computing languages: Matlab, R, and Python. A variety of online resources supplement the the text. The editors are long-time organizers of the Annual q-bio Summer School, which was founded in 2007. Through the school, the editors have helped to train more than 400 visiting students in Los Alamos, NM, Santa Fe, NM, San Diego, CA, Albuquerque, NM, and Fort Collins, CO. This book is inspired by the school's curricula, and most of the contributors have participated in the school as students, lecturers, or both. Contributors John H. Abel, Roberto Bertolusso, Daniela Besozzi, Michael L. Blinov, Clive G. Bowsher, Fiona A. Chandra, Paolo Cazzaniga, Bryan C. Daniels, Bernie J. Daigle, Jr., Maciej Dobrzynski, Jonathan P. Doye, Brian Drawert, Sean Fancer, Gareth W. Fearnley, Dirk Fey, Zachary Fox, Ramon Grima, Andreas Hellander, Stefan Hellander, David Hofmann, Damian Hernandez, William S. Hlavacek, Jianjun Huang, Tomasz Jetka, Dongya Jia, Mohit Kumar Jolly, Boris N. Kholodenko, Markek Kimmel, Michał Komorowski, Ganhui Lan, Heeseob Lee, Herbert Levine, Leslie M Loew, Jason G. Lomnitz, Ard A. Louis, Grant Lythe, Carmen Molina-París, Ion I. Moraru, Andrew Mugler, Brian Munsky, Joe Natale, Ilya Nemenman, Karol Nienałtowski, Marco S. Nobile, Maria Nowicka, Sarah Olson, Alan S. Perelson, Linda R. Petzold, Sreenivasan Ponnambalam, Arya Pourzanjani, Ruy M. Ribeiro, William Raymond, William Raymond, Herbert M. Sauro, Michael A. Savageau, Abhyudai Singh, James C. Schaff, Boris M. Slepchenko, Thomas R. Sokolowski, Petr Šulc, Andrea Tangherloni, Pieter Rein ten Wolde, Philipp Thomas, Karen Tkach Tuzman, Lev S. Tsimring, Dan Vasilescu, Margaritis Voliotis, Lisa Weber
Download or read book Evolutionary Causation written by Tobias Uller and published by MIT Press. This book was released on 2019-09-03 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive treatment of the concept of causation in evolutionary biology that makes clear its central role in both historical and contemporary debates. Most scientific explanations are causal. This is certainly the case in evolutionary biology, which seeks to explain the diversity of life and the adaptive fit between organisms and their surroundings. The nature of causation in evolutionary biology, however, is contentious. How causation is understood shapes the structure of evolutionary theory, and historical and contemporary debates in evolutionary biology have revolved around the nature of causation. Despite its centrality, and differing views on the subject, the major conceptual issues regarding the nature of causation in evolutionary biology are rarely addressed. This volume fills the gap, bringing together biologists and philosophers to offer a comprehensive, interdisciplinary treatment of evolutionary causation. Contributors first address biological motivations for rethinking evolutionary causation, considering the ways in which development, extra-genetic inheritance, and niche construction challenge notions of cause and process in evolution, and describing how alternative representations of evolutionary causation can shed light on a range of evolutionary problems. Contributors then analyze evolutionary causation from a philosophical perspective, considering such topics as causal entanglement, the commingling of organism and environment, and the relationship between causation and information. Contributors John A. Baker, Lynn Chiu, David I. Dayan, Renée A. Duckworth, Marcus W Feldman, Susan A. Foster, Melissa A. Graham, Heikki Helanterä, Kevin N. Laland, Armin P. Moczek, John Odling-Smee, Jun Otsuka, Massimo Pigliucci, Arnaud Pocheville, Arlin Stoltzfus, Karola Stotz, Sonia E. Sultan, Christoph Thies, Tobias Uller, Denis M. Walsh, Richard A. Watson
Download or read book Origination of Organismal Form written by Gerd B. Muller and published by MIT Press. This book was released on 2003-01-03 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: A more comprehensive version of evolutionary theory that focuses as much on the origin of biological form as on its diversification. The field of evolutionary biology arose from the desire to understand the origin and diversity of biological forms. In recent years, however, evolutionary genetics, with its focus on the modification and inheritance of presumed genetic programs, has all but overwhelmed other aspects of evolutionary biology. This has led to the neglect of the study of the generative origins of biological form. Drawing on work from developmental biology, paleontology, developmental and population genetics, cancer research, physics, and theoretical biology, this book explores the multiple factors responsible for the origination of biological form. It examines the essential problems of morphological evolution—why, for example, the basic body plans of nearly all metazoans arose within a relatively short time span, why similar morphological design motifs appear in phylogenetically independent lineages, and how new structural elements are added to the body plan of a given phylogenetic lineage. It also examines discordances between genetic and phenotypic change, the physical determinants of morphogenesis, and the role of epigenetic processes in evolution. The book discusses these and other topics within the framework of evolutionary developmental biology, a new research agenda that concerns the interaction of development and evolution in the generation of biological form. By placing epigenetic processes, rather than gene sequence and gene expression changes, at the center of morphological origination, this book points the way to a more comprehensive theory of evolution.
Download or read book The Routledge Companion to Biology in Art and Architecture written by Charissa Terranova and published by Routledge. This book was released on 2016-08-12 with total page 761 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Routledge Companion to Biology in Art and Architecture collects thirty essays from a transdisciplinary array of experts on biology in art and architecture. The book presents a diversity of hybrid art-and-science thinking, revealing how science and culture are interwoven. The book situates bioart and bioarchitecture within an expanded field of biology in art, architecture, and design. It proposes an emergent field of biocreativity and outlines its historical and theoretical foundations from the perspective of artists, architects, designers, scientists, historians, and theoreticians. Includes over 150 black and white images.
Download or read book Landscapes of Collectivity in the Life Sciences written by Snait B. Gissis and published by MIT Press. This book was released on 2018-01-12 with total page 433 pages. Available in PDF, EPUB and Kindle. Book excerpt: Broad perspective on collectivity in the life sciences, from microorganisms to human consensus, and the theoretical and empirical opportunities and challenges. Many researchers and scholars in the life sciences have become increasingly critical of the traditional methodological focus on the individual. This volume counters such methodological individualism by exploring recent and influential work in the life sciences that utilizes notions of collectivity, sociality, rich interactions, and emergent phenomena as essential explanatory tools to handle numerous persistent scientific questions in the life sciences. The contributors consider case studies of collectivity that range from microorganisms to human consensus, discussing theoretical and empirical challenges and the innovative methods and solutions scientists have devised. The contributors offer historical, philosophical, and biological perspectives on collectivity, and describe collective phenomena seen in insects, the immune system, communication, and human collectivity, with examples ranging from cooperative transport in the longhorn crazy ant to the evolution of autobiographical memory. They examine ways of explaining collectivity, including case studies and modeling approaches, and explore collectivity's explanatory power. They present a comprehensive look at a specific case of collectivity: the Holobiont notion (the idea of a multi-species collective, a host and diverse microorganisms) and the hologenome theory (which posits that the holobiont and its hologenome are a unit of adaption). The volume concludes with reflections on the work of the late physicist Eshel Ben-Jacob, pioneer in the study of collective phenomena in living systems. Contributors Oren Bader, John Beatty, Dinah R. Davison, Daniel Dor, Ofer Feinerman, Raghavendra Gadagkar, Scott F. Gilbert, Snait B. Gissis, Deborah M. Gordon, James Griesemer, Zachariah I. Grochau-Wright, Erik R. Hanschen, Eva Jablonka, Mohit Kumar Jolly, Anat Kolumbus, Ehud Lamm, Herbert Levine, Arnon Levy, Xue-Fei Li, Elisabeth A. Lloyd, Yael Lubin, Eva Maria Luef, Ehud Meron, Richard E. Michod, Samir Okasha, Simone Pika, Joan Roughgarden, Eugene Rosenberg, Ayelet Shavit, Yael Silver, Alfred I. Tauber, Ilana Zilber-Rosenberg
Download or read book Modularity written by Werner Callebaut and published by MIT Press. This book was released on 2005 with total page 480 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modularity—the attempt to understand systems as integrations of partially independent and interacting units—is today a dominant theme in the life sciences, cognitive science, and computer science. The concept goes back at least implicitly to the Scientific (or Copernican) Revolution, and can be found behind later theories of phrenology, physiology, and genetics; moreover, art, engineering, and mathematics rely on modular design principles. This collection broadens the scientific discussion of modularity by bringing together experts from a variety of disciplines, including artificial life, cognitive science, economics, evolutionary computation, developmental and evolutionary biology, linguistics, mathematics, morphology, paleontology, physics, theoretical chemistry, philosophy, and the arts. The contributors debate and compare the uses of modularity, discussing the different disciplinary contexts of "modular thinking" in general (including hierarchical organization, near-decomposability, quasi-independence, and recursion) or of more specialized concepts (including character complex, gene family, encapsulation, and mosaic evolution); what modules are, why and how they develop and evolve, and the implication for the research agenda in the disciplines involved; and how to bring about useful cross-disciplinary knowledge transfer on the topic. The book includes a foreword by the late Herbert A. Simon addressing the role of near-decomposability in understanding complex systems. Contributors: Lee Altenberg, Lauren W. Ancel-Meyers, Carl Anderson, Robert B. Brandon, Angela D. Buscalioni, Raffaele Calabretta, Werner Callebaut, Anne De Joan, Rafael Delgado-Buscalioni, Gunther J. Eble, Walter Fontana, Fernand Gobet, Alicia de la Iglesia, Slavik V. Jablan, Luigi Marengo, Daniel W. McShea, Jason Mezey, D. Kimbrough Oller, Domenico Parisi, Corrado Pasquali, Diego Rasskin-Gutman, Gerhard Schlosser, Herbert A. Simon, Roger D. K. Thomas, Marco Valente, Boris M. Velichkovsky, Gunter P. Wagner, Rasmus G. Winter Vienna Series in Theoretical Biology
Download or read book An Introduction to Systems Biology written by Uri Alon and published by CRC Press. This book was released on 2006-07-07 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt: Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits. The textavoids specialist terms, focusing instead on several well-studied biological systems that concisely demonstrate key principles. An Introduction to Systems Biology: Design Principles of Biological Circuits builds a solid foundation for the intuitive understanding of general principles. It encourages the reader to ask why a system is designed in a particular way and then proceeds to answer with simplified models.
Download or read book The Theoretical Biologist s Toolbox written by Marc Mangel and published by Cambridge University Press. This book was released on 2006-07-27 with total page 323 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematical modelling is widely used in ecology and evolutionary biology and it is a topic that many biologists find difficult to grasp. In this new textbook Marc Mangel provides a no-nonsense introduction to the skills needed to understand the principles of theoretical and mathematical biology. Fundamental theories and applications are introduced using numerous examples from current biological research, complete with illustrations to highlight key points. Exercises are also included throughout the text to show how theory can be applied and to test knowledge gained so far. Suitable for advanced undergraduate courses in theoretical and mathematical biology, this book forms an essential resource for anyone wanting to gain an understanding of theoretical ecology and evolution.
Download or read book Levels of Organization in the Biological Sciences written by Daniel S. Brooks and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: "This book addresses basic and advanced questions surrounding the idea of levels or organization in the biological sciences"--
Download or read book The Major Transitions in Evolution Revisited written by Brett Calcott and published by MIT Press. This book was released on 2011-04-22 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: Drawing on recent advances in evolutionary biology, prominent scholars return to the question posed in a pathbreaking book: how evolution itself evolved. In 1995, John Maynard Smith and Eörs Szathmáry published their influential book The Major Transitions in Evolution. The "transitions" that Maynard Smith and Szathmáry chose to describe all constituted major changes in the kinds of organisms that existed but, most important, these events also transformed the evolutionary process itself. The evolution of new levels of biological organization, such as chromosomes, cells, multicelled organisms, and complex social groups radically changed the kinds of individuals natural selection could act upon. Many of these events also produced revolutionary changes in the process of inheritance, by expanding the range and fidelity of transmission, establishing new inheritance channels, and developing more open-ended sources of variation. Maynard Smith and Szathmáry had planned a major revision of their work, but the death of Maynard Smith in 2004 prevented this. In this volume, prominent scholars (including Szathmáry himself) reconsider and extend the earlier book's themes in light of recent developments in evolutionary biology. The contributors discuss different frameworks for understanding macroevolution, prokaryote evolution (the study of which has been aided by developments in molecular biology), and the complex evolution of multicellularity.
Download or read book A Biologist s Guide to Mathematical Modeling in Ecology and Evolution written by Sarah P. Otto and published by Princeton University Press. This book was released on 2011-09-19 with total page 745 pages. Available in PDF, EPUB and Kindle. Book excerpt: Thirty years ago, biologists could get by with a rudimentary grasp of mathematics and modeling. Not so today. In seeking to answer fundamental questions about how biological systems function and change over time, the modern biologist is as likely to rely on sophisticated mathematical and computer-based models as traditional fieldwork. In this book, Sarah Otto and Troy Day provide biology students with the tools necessary to both interpret models and to build their own. The book starts at an elementary level of mathematical modeling, assuming that the reader has had high school mathematics and first-year calculus. Otto and Day then gradually build in depth and complexity, from classic models in ecology and evolution to more intricate class-structured and probabilistic models. The authors provide primers with instructive exercises to introduce readers to the more advanced subjects of linear algebra and probability theory. Through examples, they describe how models have been used to understand such topics as the spread of HIV, chaos, the age structure of a country, speciation, and extinction. Ecologists and evolutionary biologists today need enough mathematical training to be able to assess the power and limits of biological models and to develop theories and models themselves. This innovative book will be an indispensable guide to the world of mathematical models for the next generation of biologists. A how-to guide for developing new mathematical models in biology Provides step-by-step recipes for constructing and analyzing models Interesting biological applications Explores classical models in ecology and evolution Questions at the end of every chapter Primers cover important mathematical topics Exercises with answers Appendixes summarize useful rules Labs and advanced material available
Download or read book How Molecular Forces and Rotating Planets Create Life written by Jan Spitzer and published by MIT Press. This book was released on 2021-02-09 with total page 249 pages. Available in PDF, EPUB and Kindle. Book excerpt: A reconceptualization of origins research that exploits a modern understanding of non-covalent molecular forces that stabilize living prokaryotic cells. Scientific research into the origins of life remains exploratory and speculative. Science has no definitive answer to the biggest questions--"What is life?" and "How did life begin on earth?" In this book, Jan Spitzer reconceptualizes origins research by exploiting a modern understanding of non-covalent molecular forces and covalent bond formation--a physicochemical approach propounded originally by Linus Pauling and Max Delbrück. Spitzer develops the Pauling-Delbrück premise as a physicochemical jigsaw puzzle that identifies key stages in life's emergence, from the formation of first oceans, tidal sediments, and proto-biofilms to progenotes, proto-cells and the first cellular organisms.
Download or read book The Seductions of Darwin written by Matthew Rampley and published by Penn State Press. This book was released on 2017-01-12 with total page 201 pages. Available in PDF, EPUB and Kindle. Book excerpt: The surge of evolutionary and neurological analyses of art and its effects raises questions of how art, culture, and the biological sciences influence one another, and what we gain in applying scientific methods to the interpretation of artwork. In this insightful book, Matthew Rampley addresses these questions by exploring key areas where Darwinism, neuroscience, and art history intersect. Taking a scientific approach to understanding art has led to novel and provocative ideas about its origins, the basis of aesthetic experience, and the nature of research into art and the humanities. Rampley’s inquiry examines models of artistic development, the theories and development of aesthetic response, and ideas about brain processes underlying creative work. He considers the validity of the arguments put forward by advocates of evolutionary and neuroscientific analysis, as well as its value as a way of understanding art and culture. With the goal of bridging the divide between science and culture, Rampley advocates for wider recognition of the human motivations that drive inquiry of all types, and he argues that our engagement with art can never be encapsulated in a single notion of scientific knowledge. Engaging and compelling, The Seductions of Darwin is a rewarding look at the identity and development of art history and its complicated ties to the world of scientific thought.
Download or read book The Convergent Evolution of Agriculture in Humans and Insects written by Ted R Schultz and published by MIT Press. This book was released on 2022-02-22 with total page 339 pages. Available in PDF, EPUB and Kindle. Book excerpt: Contributors explore common elements in the evolutionary histories of both human and insect agriculture resulting from convergent evolution. During the past 12,000 years, agriculture originated in humans as many as twenty-three times, and during the past 65 million years, agriculture also originated in nonhuman animals at least twenty times and in insects at least fifteen times. It is much more likely that these independent origins represent similar solutions to the challenge of growing food than that they are due purely to chance. This volume seeks to identify common elements in the evolutionary histories of both human and insect agriculture that are the results of convergent evolution. The goal is to create a new, synthetic field that characterizes, quantifies, and empirically documents the evolutionary and ecological mechanisms that drive both human and nonhuman agriculture. The contributors report on the results of quantitative analyses comparing human and nonhuman agriculture; discuss evolutionary conflicts of interest between and among farmers and cultivars and how they interfere with efficiencies of agricultural symbiosis; describe in detail agriculture in termites, ambrosia beetles, and ants; and consider patterns of evolutionary convergence in different aspects of agriculture, comparing fungal parasites of ant agriculture with fungal parasites of human agriculture, analyzing the effects of agriculture on human anatomy, and tracing the similarities and differences between the evolution of agriculture in humans and in a single, relatively well-studied insect group, fungus-farming ants.
Download or read book Complex Population Dynamics written by Peter Turchin and published by Princeton University Press. This book was released on 2003-02-02 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt: Why do organisms become extremely abundant one year and then seem to disappear a few years later? Why do population outbreaks in particular species happen more or less regularly in certain locations, but only irregularly (or never at all) in other locations? Complex population dynamics have fascinated biologists for decades. By bringing together mathematical models, statistical analyses, and field experiments, this book offers a comprehensive new synthesis of the theory of population oscillations. Peter Turchin first reviews the conceptual tools that ecologists use to investigate population oscillations, introducing population modeling and the statistical analysis of time series data. He then provides an in-depth discussion of several case studies--including the larch budmoth, southern pine beetle, red grouse, voles and lemmings, snowshoe hare, and ungulates--to develop a new analysis of the mechanisms that drive population oscillations in nature. Through such work, the author argues, ecologists can develop general laws of population dynamics that will help turn ecology into a truly quantitative and predictive science. Complex Population Dynamics integrates theoretical and empirical studies into a major new synthesis of current knowledge about population dynamics. It is also a pioneering work that sets the course for ecology's future as a predictive science.
Download or read book Rethinking Cancer written by Bernhard Strauss and published by MIT Press. This book was released on 2021-04-27 with total page 433 pages. Available in PDF, EPUB and Kindle. Book excerpt: Leading scientists argue for a new paradigm for cancer research, proposing a complex systems view of cancer supported by empirical evidence. Current consensus in cancer research explains cancer as a disease caused by specific mutations in certain genes. After dramatic advances in genome sequencing, never before have we known so much about the individual cancer cell--and yet never before has it been so unclear what to do with this knowledge. In this volume, leading researchers argue for a new theory framework for understanding and treating cancer. The contributors propose a complex systems view of cancer, presenting conceptual building blocks for a new research paradigm supported by empirical evidence. The contributors first discuss the new research framework in terms of theoretical foundations and then take up the relevance of a systems approach, reviewing such topics as nonlinearity, recurrence after treatment, the cellular attractor concept, network theory, and non-coding DNA--the "dark matter" of our genome. They address the temporality of cancer progression, drawing on evolutionary theory and clinical experience. Finally, they cover the dominant role of the tissue microenvironment in cancer, analyzing topics including altered metabolic pathways, the disease-defining influence on metastasis, and the interconnectedness of different environmental niches across levels of organization.
