Mathematical Hierarchies and Biology


Book Description

Twenty-four articles from the November 1996 workshop investigate the reconstruction of trees or ranking hierarchies from dissimilarity or entity-to-character data, the use of hierarchies for modeling evolution and other processes, and the combining of gene trees. Included are mathematical treatments of hierarchies in the frameworks of set systems, linear subspaces, graph objects, and tree metrics in their analyses. Such current applications as learning robots, intron evolution, and the development of language are addressed. Annotation copyrighted by Book News, Inc., Portland, OR.




The Hierarchical Genome and Differentiation Waves


Book Description

Over the past few decades numerous scientists have called for a unification of the fields of embryo development, genetics, and evolution. Each field has glaring holes in its ability to explain the fundamental phenomena of life. In this book, the author shows how the phenomenon of cell differentiation, considered in its temporal and spatial aspects during embryogenesis, provides a starting point for a unified theory of multicellular organisms (plants, fungi and animals), including their evolution and genetics. This unification is based on the recent discovery of differentiation waves by the author and his colleagues, described in the appendices, and illustrated by a flip movie prepared by a medical artist. To help the reader through the many fields covered, a glossary is included.This book will be of great value to the researcher and practicing doctors/scientists alike. The research students will receive an in-depth tutorial on the topics covered. The seasoned researcher will appreciate the applications and the gold mine of other possibilities for novel research topics.




Evolutionary Theory


Book Description

The natural world is infinitely complex and hierarchically structured, with smaller units forming the components of progressively larger systems: molecules make up cells, cells comprise tissues and organs that are, in turn, parts of individual organisms, which are united into populations and integrated into yet more encompassing ecosystems. In the face of such awe-inspiring complexity, there is a need for a comprehensive, non-reductionist evolutionary theory. Having emerged at the crossroads of paleobiology, genetics, and developmental biology, the hierarchical approach to evolution provides a unifying perspective on the natural world and offers an operational framework for scientists seeking to understand the way complex biological systems work and evolve. Coedited by one of the founders of hierarchy theory and featuring a diverse and renowned group of contributors, this volume provides an integrated, comprehensive, cutting-edge introduction to the hierarchy theory of evolution. From sweeping historical reviews to philosophical pieces, theoretical essays, and strictly empirical chapters, it reveals hierarchy theory as a vibrant field of scientific enterprise that holds promise for unification across the life sciences and offers new venues of empirical and theoretical research. Stretching from molecules to the biosphere, hierarchy theory aims to provide an all-encompassing understanding of evolution and—with this first collection devoted entirely to the concept—will help make transparent the fundamental patterns that propel living systems.




Biological Neural Networks: Hierarchical Concept of Brain Function


Book Description

This book is devoted to a novel conceptual theoretical framework of neuro science and is an attempt to show that we can postulate a very small number of assumptions and utilize their heuristics to explain a very large spectrum of brain phenomena. The major assumption made in this book is that inborn and acquired neural automatisms are generated according to the same func tional principles. Accordingly, the principles that have been revealed experi mentally to govern inborn motor automatisms, such as locomotion and scratching, are used to elucidate the nature of acquired or learned automat isms. This approach allowed me to apply the language of control theory to describe functions of biological neural networks. You, the reader, can judge the logic of the conclusions regarding brain phenomena that the book derives from these assumptions. If you find the argument flawless, one can call it common sense and consider that to be the best praise for a chain of logical conclusions. For the sake of clarity, I have attempted to make this monograph as readable as possible. Special attention has been given to describing some of the concepts of optimal control theory in such a way that it will be under standable to a biologist or physician. I have also included plenty of illustra tive examples and references designed to demonstrate the appropriateness and applicability of these conceptual theoretical notions for the neurosciences.




Phylogenetic Supertrees


Book Description

This is the first book on "phylogenetic supertrees", a recent, but controversial development for inferring evolutionary trees. Rather than analyze the combined primary character data directly, supertree construction proceeds by combining the tree topologies derived from those data. This difference in strategy has allowed for the exciting possibility of larger, more complete phylogenies than are otherwise currently possible, with the potential to revolutionize evolutionarily-based research. This book provides a comprehensive look at supertrees, ranging from the methods used to build supertrees to the significance of supertrees to bioinformatic and biological research. Reviews of many the major supertree methods are provided and four new techniques, including a Bayesian implementation of supertrees, are described for the first time. The far-reaching impact of supertrees on biological research is highlighted both in general terms and through specific examples from diverse clades such as flowering plants, even-toed ungulates, and primates. The book also critically examines the many outstanding challenges and problem areas for this relatively new field, showing the way for supertree construction in the age of genomics. Interdisciplinary contributions from the majority of the leading authorities on supertree construction in all areas of the bioinformatic community (biology, computer sciences, and mathematics) will ensure that this book is a valuable reference with wide appeal to anyone interested in phylogenetic inference.




The Mathematical Biology of Diatoms


Book Description

THE MATHEMATICAL BIOLOGY OF DIATOMS This book contains unique, advanced applications using mathematics, algorithmic techniques, geometric analysis, and other computational methods in diatom research. Historically, diatom research has centered on taxonomy and systematics. While these topics are of the utmost importance, other aspects of this important group of unicells have been increasingly explored in the biological sciences. While mathematical applications are still rare, they are starting take hold and provide an extensive avenue of new diatom research, including applications in multidisciplinary fields. The work contained in this volume is an eclectic mix of analytical studies on diatoms. Mathematical treatment of the various biological disciplines covered in this book range from implicit, but succinct studies to more elaborate detailed computational studies. Topics include growth models, nanostructure, nanoengineering, cell growth, araphid diatoms, valve ontogeny, diatom metabolism, diatom motility, synchronization, diatom kinematics, photonics, biogenic sensors, photochemistry, diatom light response, colony growth, siliceous unicells, algal kinetics, diatom structure, diatom imaging, functional morphology, geometric structure, biomineralization, high-resolution imaging, non-destructive imaging, and 3D structure. This wide-ranging volume provides an introductory as well as an advanced treatment of recent interests in diatom research. The mathematical research in this volume may be applicable to studies of other unicells, biomechanics, biological processes, physio-chemical analyses, or nanoscience.




Combinatorial Pattern Matching


Book Description

The refereed proceedings of the 14th Annual Symposium on Combinatorial Pattern Matching, CPM 2003, held in Morelia, Michoacán, Mexico in June 2003. The 28 revised full papers presented were carefully reviewed and selected from 57 submissions. The papers are devoted to current theoretical and computational aspects of searching and matching strings and more complicated patterns, such as trees, regular expressions, graphs, point sets, and arrays. Among the application fields addressed are computational biology, bioinformatics, genomics, the Web, data compression, coding, multimedia, information retrieval, pattern recognition, and computer vision.




Bioconsensus


Book Description

This volume is based on two DIMACS working group meetings on ''Bioconsensus''. It provides a valuable introduction and reference to the various aspects of this rapidly developing field. The meetings brought together mathematical and biological scientists to discuss the uses in the biological sciences of methods of consensus and social choice. These two lively meetings contributed much toward establishing the new field of ''bioconsensus''. Yet this book is much more than just a report of two meetings. It includes some historical background, as well as a substantial introduction to the axiomatic foundations of the field of bioconsensus and some practical applications of consensus methods to real data. Also included are contributed papers from experts who were not at the meetings. The book is intended for mathematical biologists, evolutionary biologists, and computer scientists.




Models and Methods for Biological Evolution


Book Description

Biological evolution is the phenomenon concerning how species are born, are transformed or disappear over time. Its study relies on sophisticated methods that involve both mathematical modeling of the biological processes at play and the design of efficient algorithms to fit these models to genetic and morphological data. Models and Methods for Biological Evolution outlines the main methods to study evolution and provides a broad overview illustrating the variety of formal approaches used, notably including combinatorial optimization, stochastic models and statistical inference techniques. Some of the most relevant applications of these methods are detailed, concerning, for example, the study of migratory events of ancient human populations or the progression of epidemics. This book should thus be of interest to applied mathematicians interested in central problems in biology, and to biologists eager to get a deeper understanding of widely used techniques of evolutionary data analysis.




Mathematical Reviews


Book Description