Information Processing and Biological Systems


Book Description

Living beings require constant information processing for survival. In cells, information is being processed and propagated at various levels, from the gene regulatory network to chemical pathways, to the interaction with the environment. How this is achieved and how information is coded is still poorly understood. For example, what a cell interprets as information in the temporal level of an mRNA and what is interpreted as noise remains an open question. Recently, information theoretical methods and other tools, developed in the context of engineering and natural sciences, have been applied to study diverse biological processes. This book covers the latest findings on how information is processed in various biological processes, ranging from information processing and propagation in gene regulatory networks to information processing in natural language. An overview is presented of the state-of-the-art in information processing in biological systems and the opinion of current leaders in this research field on future research directions.




Information Processing And Living Systems


Book Description

Information processing and information flow occur in the course of an organism's development and throughout its lifespan. Organisms do not exist in isolation, but interact with each other constantly within a complex ecosystem. The relationships between organisms, such as those between prey or predator, host and parasite, and between mating partners, are complex and multidimensional. In all cases, there is constant communication and information flow at many levels.This book focuses on information processing by life forms and the use of information technology in understanding them. Readers are first given a comprehensive overview of biocomputing before navigating the complex terrain of natural processing of biological information using physiological and analogous computing models. The remainder of the book deals with “artificial” processing of biological information as a human endeavor in order to derive new knowledge and gain insight into life forms and their functioning. Specific innovative applications and tools for biological discovery are provided as the link and complement to biocomputing.Since “artificial” processing of biological information is complementary to natural processing, a better understanding of the former helps us improve the latter. Consequently, readers are exposed to both domains and, when dealing with biological problems of their interest, will be better equipped to grasp relevant ideas.




Information Processing in Biological Systems


Book Description

This volume contains the greater part of the papers submitted to the Information Processing in Biology portion of the 1983 Orbis Scientiae, then dedicated to the eightieth year of Professor P.A.M. Dirac. Before the volume could be published, Professor Dirac passed away on October 20, 1984, thereby changing the dedica tion of this volume, and its companion, on High Energy Physics, to his everlasting memory. The last Orbis Scientiae (as it was often in the past) was shared by two frontier fields - in this case by High Energy Physics and Information Processing in Biology, demonstrating the universality of scientific principles and goals. The interaction amongst scientists of diverse interests can only enhance the fruitfulness of their efforts. The editors take pride in the modest contribution of Orbis Scientiae towards this goal. It is a pleasure to acknowledge the typing of these proceedings by Regelio Rodriguez and Helga Billings, and the customary excellent supervision by the latter. The efficient preparation and organiza tion of the conference was due largely to the skill and dedication of Linda Scott. As in the past, Orbis Scientiae 1983 received nominal support from the United States Department of Energy and the National Science Foundation.




Evolution of Information Processing Systems


Book Description

An interdisciplinary team of scientists is presenting a new paradigm: all existing structures on earth are the consequence of information processing. Since these structures have been evolved over the last five billion years, information processing and its systems have an evolution.This is under consideration in the book. Starting with a basic paper which summarizes the essential hypotheses about the evolution of informaion processing systems, sixteen international scientists have tried to verify or falsify these hypothesises. This has been done at the physical, the chemical, the genetic, the neural, the social, the societal and the socio-technical level. Thus, the reader gets an insight into the recent status of research on the evolution of information processing systems. The papers are the result of an interdisciplinary project in which scientists of the classical disciplines have been invited to collaborate. Their inputs have been intensively discussed in a workshop. The book is the output of the workshop. The first goal of the bookis to give the reader an insight into basic principles about the evolution of information processing systems. This, however, leads directly to a very old and essential question: who is controlling the world, "matter" or an "immaterial intelligence"? Several authors of the papers are arguing that there is a basic concept of information processing in nature. This is the crucial process, which, however, needs a material basis. The reader has a chance to understand this paradigm as an approach which is valid for all levels of inorganic, organic and societal structures. This provocative concept is open to debate.




Biological Processes in Living Systems


Book Description

Biological Processes in Living Systems is the fourth and final volume of the Toward a Theoretical Biology series. It contains essays that deal in detail with particular biological processes: morphogenesis of pattern, the development of neuronal networks, evolutionary processes, and others. The main thrust of this volume brings relevance to the general underlying nature of living systems. Faced with trying to understand how the complexity of molecular microstates leads to the relative simplicity of phenome structures, Waddington-on behalf of his colleagues-stresses on the structure of language as a paradigm for a theory of general biology. This is language in an imperative mood: a set of symbols, organized by some form of generative grammar, making possible the conveyance of commands for action to produce effects on the surroundings of the emitting and the receiving entities. "Biology," he writes, "is concerned with algorithm and program." Among the contributions in this volume are: "The Riemann-Hugoniot Catastrophe and van der Waals Equation," David H. Fowler; "Differential Equations for the Heartbeat and Nerve Impulse," E. Christopher Zeeman; "Structuralism and Biology," Rene Thom; "The Concept of Positional Information and Pattern Formation," Lewis Wolpert; "Pattern Formation in Fibroblast Cultures," Tom Elsdale; "Form and Information," C. H. Waddington; "Organizational Principles for Theoretical Neurophysiology," Michael A. Arbib; "Stochastic Models of Neuroelectric Activity," Jack D. Cowan. Biological Processes in Living Systems is a pioneering volume by recognized leaders in an ever-growing field.




Information and Living Systems


Book Description

The informational nature of biological organization, at levels from the genetic and epigenetic to the cognitive and linguistic. Information shapes biological organization in fundamental ways and at every organizational level. Because organisms use information--including DNA codes, gene expression, and chemical signaling--to construct, maintain, repair, and replicate themselves, it would seem only natural to use information-related ideas in our attempts to understand the general nature of living systems, the causality by which they operate, the difference between living and inanimate matter, and the emergence, in some biological species, of cognition, emotion, and language. And yet philosophers and scientists have been slow to do so. This volume fills that gap. Information and Living Systems offers a collection of original chapters in which scientists and philosophers discuss the informational nature of biological organization at levels ranging from the genetic to the cognitive and linguistic. The chapters examine not only familiar information-related ideas intrinsic to the biological sciences but also broader information-theoretic perspectives used to interpret their significance. The contributors represent a range of disciplines, including anthropology, biology, chemistry, cognitive science, information theory, philosophy, psychology, and systems theory, thus demonstrating the deeply interdisciplinary nature of the volume's bioinformational theme.




Biological Information--new Perspectives


Book Description

In the spring of 2011, a diverse group of scientists gathered at Cornell University to discuss their research into the nature and origin of biological information. This symposium brought together experts in information theory, computer science, numerical simulation, thermodynamics, evolutionary theory, whole organism biology, developmental biology, molecular biology, genetics, physics, biophysics, mathematics, and linguistics. This volume presents new research by those invited to speak at the conference. The contributors to this volume use their wide-ranging expertise in the area of biological information to bring fresh insights into the explanatory difficulties that biological information raises. Going beyond the conventional scientific wisdom, which attempts to explain biological information reductionistically via chemical, genetic, and natural selective determinants, the work represented here develops novel non-reductionist approaches to biological information, looking notably to telic and self-organizational processes. Several clear themes emerged from these research papers: 1) Information is indispensable to our understanding of what life is. 2) Biological information is more than the material structures that embody it. 3) Conventional chemical and evolutionary mechanisms seem insufficient to fully explain the labyrinth of information that is life. By exploring new perspectives on biological information, this volume seeks to expand, encourage, and enrich research on the nature and origin of biological information.




The Science and Applications of Synthetic and Systems Biology


Book Description

Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.




Molecular Mechanisms of Autonomy in Biological Systems


Book Description

This book presents a novel molecular description for understanding the regulatory mechanisms behind the autonomy and self-organization in biological systems. Chapters focus on defining and explaining the regulatory molecular mechanisms behind different aspects of autonomy and self-organization in the sense of autonomous coding, data processing, structure (mass) formation and energy production in a biological system. Subsequent chapters discuss the cross-talk among mechanisms of energy, and mass and information, transformation in biological systems. Other chapters focus on applications regarding therapeutic approaches in regenerative medicine. Molecular Mechanisms of Autonomy in Biological Systems is an indispensable resource for scientists and researchers in regenerative medicine, stem cell biology, molecular biology, tissue engineering, developmental biology, biochemistry, biophysics, bioinformatics, as well as big data sciences, complexity and soft computing.




Data Processing Handbook for Complex Biological Data Sources


Book Description

Data Processing Handbook for Complex Biological Data provides relevant and to the point content for those who need to understand the different types of biological data and the techniques to process and interpret them. The book includes feedback the editor received from students studying at both undergraduate and graduate levels, and from her peers. In order to succeed in data processing for biological data sources, it is necessary to master the type of data and general methods and tools for modern data processing. For instance, many labs follow the path of interdisciplinary studies and get their data validated by several methods. Researchers at those labs may not perform all the techniques themselves, but either in collaboration or through outsourcing, they make use of a range of them, because, in the absence of cross validation using different techniques, the chances for acceptance of an article for publication in high profile journals is weakened. - Explains how to interpret enormous amounts of data generated using several experimental approaches in simple terms, thus relating biology and physics at the atomic level - Presents sample data files and explains the usage of equations and web servers cited in research articles to extract useful information from their own biological data - Discusses, in detail, raw data files, data processing strategies, and the web based sources relevant for data processing