The Art of Theoretical Biology PDF Download

Author: Franziska Matthäus
Publisher: Springer Nature
ISBN: 3030334716
Category : Science
Languages : en
Pages : 152

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Book Description
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.

Author: Brian Munsky
Publisher: MIT Press
ISBN: 0262347113
Category : Science
Languages : en
Pages : 729

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Book Description
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

Author: Daniel S. Brooks
Publisher: MIT Press
ISBN: 0262045338
Category : Technology & Engineering
Languages : en
Pages : 337

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Book Description
Scientific philosophers examine the nature and significance of levels of organization, a core structural principle in the biological sciences. This volume examines the idea of levels of organization as a distinct object of investigation, considering its merits as a core organizational principle for the scientific image of the natural world. It approaches levels of organization--roughly, the idea that the natural world is segregated into part-whole relationships of increasing spatiotemporal scale and complexity--in terms of its roles in scientific reasoning as a dynamic, open-ended idea capable of performing multiple overlapping functions in distinct empirical settings. The contributors--scientific philosophers with longstanding ties to the biological sciences--discuss topics including the philosophical and scientific contexts for an inquiry into levels; whether the concept can actually deliver on its organizational promises; the role of levels in the development and evolution of complex systems; conditional independence and downward causation; and the extension of the concept into the sociocultural realm. Taken together, the contributions embrace the diverse usages of the term as aspects of the big picture of levels of organization. Contributors Jan Baedke, Robert W. Batterman, Daniel S. Brooks, James DiFrisco, Markus I. Eronen, Carl Gillett, Sara Green, James Griesemer, Alan C. Love, Angela Potochnik, Thomas Reydon, Ilya Tëmkin, Jon Umerez, William C. Wimsatt, James Woodward

Author: Tobias Uller
Publisher: MIT Press
ISBN: 0262039923
Category : Science
Languages : en
Pages : 361

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Book Description
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

Author: Charissa Terranova
Publisher: Routledge
ISBN: 1317419502
Category : Architecture
Languages : en
Pages : 761

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Book Description
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.

Author: Snait B. Gissis
Publisher: MIT Press
ISBN: 0262036851
Category : Science
Languages : en
Pages : 433

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Book Description
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

Author: Werner Callebaut
Publisher: MIT Press
ISBN: 9780262033268
Category : Computers
Languages : en
Pages : 480

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Book Description
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

Author: Jan Spitzer
Publisher: MIT Press
ISBN: 0262362597
Category : Science
Languages : en
Pages : 249

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Book Description
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.

Author: Matthew Rampley
Publisher: Penn State Press
ISBN: 0271079002
Category : Art
Languages : en
Pages : 201

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Book Description
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.

Author: Sarah P. Otto
Publisher: Princeton University Press
ISBN: 1400840910
Category : Science
Languages : en
Pages : 745

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Book Description
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