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Every cell, tissue, organ and organism is competent to use signs to exchange information reaching common coordinations and organisations of both single cell and group behavior. These sign-mediated interactions we term biological communication. The regulatory system that works in development, morphology, cell fate and identity, physiology, genetic instructions, immunity, memory/learning, physical and mental disease depends on epigenetic marks. The communication of cells, persistent viruses and their defectives such as mobile genetic elements and RNA networks ensures both the transport of regulatory instructions and the reprogramming of these instructions. But how are the different states of the epigenome orchestrated? The epigenetic pathways respond to various signaling cues such as DNA methylation, histone variants, histone modifications, chromatin structure, nucleosome remodeling, and epigenetic interactions. Epigenetic signals are responsible for the establishment, maintenance and reversal of transcriptional states that are fundamental for the cell's ability to memorize past events, such as changes in the external environment, socio-sphere or developmental cues. External signals trigger changes in the epigenome, allowing cells to respond dynamically. Internal signals direct activities that are necessary for body maintenance, and repairing damaged tissues and organs. With the emergence of epigenetic memory, organisms can fix historical and context dependent impressive experiences. Evolution from now on learnt to learn. Learning means organisms can avoid reproduction of always the same. This is key to adaptation. However, inheritance of acquired characteristics is only one of the many examples of the explanatory power of epigenetics. Behavioral epigenetics demonstrates the way in which environmental and social experiences produce individual differences in behaviour, cognition, personality, and mental health. This book assembles experts to outline the various motifs of all kinds of epigenetic regulation of cells throughout their lives.

Title in English: Limits to Darwinism Darwinism claims to be a complete theory of biological life, including human life. It has a significant effect on the self-concept of contemporary humans and their worldview. In his unique book, Professor Emeritus of Masaryk University, physician and philosopher Jiří Vácha summarizes the current scientific critique of Darwinism, and also expands the whole problem by the notion of'consciousness'as the most specific feature of live beings. In addition to the evolving physical aspect of organisms, their experiential aspect has evolved too, and Darwinism does not take that sufficiently into account. Modern natural science, following in the footsteps of Descartes'mechanism, has a priori closed the door to this fundamental problem and has had to make way for philosophy and its interpretation. Despite its broad scientific scope, the book is surprisingly readable, the author explains complex things in clear and simple language.

Biodiversity and Evolution includes chapters devoted to the evolution and biodiversity of organisms at the molecular level, based on the study of natural collections from the Museum of Natural History. The book starts with an epistemological and historical introduction and ends with a critical overview of the Anthropocene epoch. - Explores the study of natural collections of the Museum of Natural History - Examines evolution and biodiversity at the molecular level - Features an introduction focusing on epistemology and history - Provides a critical overview

Now in its third edition and supplemented with more online material, this book aims to make the'new'information-based (rather than gene-based) bioinformatics intelligible both to the'bio'people and the'info'people. Books on bioinformatics have traditionally served gene-hunters, and biologists who wish to construct family trees showing tidy lines of descent. While dealing extensively with the exciting topics of gene discovery and database-searching, such books have hardly considered genomes as information channels through which multiple forms and levels of information have passed through the generations. This “new bioinformatics” contrasts with the'old'gene-based bioinformatics that so preoccupies previous texts. Forms of information that we are familiar with (mental, textual) are related to forms with which we are less familiar (hereditary). The book extends a line of evolutionary thought that leads from the nineteenth century (Darwin, Butler, Romanes, Bateson), through the twentieth (Goldschmidt, White), and into the twenty first (the final works of the late Stephen Jay Gould). Long an area of controversy, diverging views may now be reconciled.

The power of Darwin's theory of natural selection is beyond doubt, it explains how useful adaptations are preserved over generations. But evolution's biggest mystery eluded Darwin: how those adaptations arise in the first place. Can random mutations over a 3.8 billion years be solely responsible for wings, eyeballs, knees, photosynthesis, and the rest of nature's creative marvels? And by calling these mutations ‘random', are we not just admitting our own ignorance? What if we could now uncover the wellspring of all biological innovation? Renowned evolutionary biologist Andreas Wagner presents the missing piece in Darwin's theory. Using cutting-edge experimental and computational technologies, he has found that adaptations are in fact driven by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take. Consider the Arctic cod, a fish that lives in waters cold enough to turn the internal fluids of most organisms into ice crystals. And yet the Arctic cod survives by producing ‘natural anti-freeze', proteins that lower the freezing temperature of its body fluids. The invention of those proteins is an archetypal example of nature's enormous powers of creativity. Meticulously researched, carefully argued, and full of fascinating examples from the animal kingdom, Arrival of the Fittest offers up the final puzzle piece in the mystery of life's rich diversity.

The Logic of Chance offers a reappraisal and a new synthesis of theories, concepts, and hypotheses on the key aspects of the evolution of life on earth in light of comparative genomics and systems biology. The author presents many specific examples from systems and comparative genomic analysis to begin to build a new, much more detailed, complex, and realistic picture of evolution. The book examines a broad range of topics in evolutionary biology including the inadequacy of natural selection and adaptation as the only or even the main mode of evolution; the key role of horizontal gene transfer in evolution and the consequent overhaul of the Tree of Life concept; the central, underappreciated evolutionary importance of viruses; the origin of eukaryotes as a result of endosymbiosis; the concomitant origin of cells and viruses on the primordial earth; universal dependences between genomic and molecular-phenomic variables; and the evolving landscape of constraints that shape the evolution of genomes and molecular phenomes.'Koonin's account of viral and pre-eukaryotic evolution is undoubtedly up-to-date. His'mega views'of evolution (given what was said above) and his cosmological musings, on the other hand, are interesting reading.'Summing Up: Recommended Reprinted with permission from CHOICE, copyright by the American Library Association.

A reappraisal of Lamarckism—its historical impact and contemporary significance.In 1809—the year of Charles Darwin's birth—Jean-Baptiste Lamarck published Philosophie zoologique, the first comprehensive and systematic theory of biological evolution. The Lamarckian approach emphasizes the generation of developmental variations; Darwinism stresses selection. Lamarck's ideas were eventually eclipsed by Darwinian concepts, especially after the emergence of the Modern Synthesis in the twentieth century. The different approaches—which can be seen as complementary rather than mutually exclusive—have important implications for the kinds of questions biologists ask and for the type of research they conduct. Lamarckism has been evolving—or, in Lamarckian terminology, transforming—since Philosophie zoologique's description of biological processes mediated by'subtle fluids.'Essays in this book focus on new developments in biology that make Lamarck's ideas relevant not only to modern empirical and theoretical research but also to problems in the philosophy of biology. Contributors discuss the historical transformations of Lamarckism from the 1820s to the 1940s, and the different understandings of Lamarck and Lamarckism; the Modern Synthesis and its emphasis on Mendelian genetics; theoretical and experimental research on such'Lamarckian'topics as plasticity, soft (epigenetic) inheritance, and individuality; and the importance of a developmental approach to evolution in the philosophy of biology. The book shows the advantages of a'Lamarckian'perspective on evolution. Indeed, the development-oriented approach it presents is becoming central to current evolutionary studies—as can be seen in the burgeoning field of Evo-Devo. Transformations of Lamarckism makes a unique contribution to this research.

James A. Shapiro proposes an important new paradigm for understanding biological evolution, the core organizing principle of biology. Shapiro introduces crucial new molecular evidence that tests the conventional scientific view of evolution based on the neo-Darwinian synthesis, shows why this view is inadequate to today's evidence, and presents a compelling alternative view of the evolutionary process that reflects the shift in life sciences towards a more information- and systems-based approach in Evolution: A View from the 21st Century. Shapiro integrates advances in symbiogenesis, epigenetics, and saltationism into a unified approach that views evolutionary change as an active cell process, regulated epigenetically and capable of making rapid large changes by horizontal DNA transfer, inter-specific hybridization, whole genome doubling, symbiogenesis, or massive genome restructuring. Evolution marshals extensive evidence in support of a fundamental reinterpretation of evolutionary processes, including more than 1,100 references to the scientific literature. Shapiro's work will generate extensive discussion throughout the biological community, and may significantly change your own thinking about how life has evolved. It also has major implications for evolutionary computation, information science, and the growing synthesis of the physical and biological sciences.

I wrote this book for biologists and those who are interested in both biological affairs in general and perspectives which integrate a large number of specialised biological disciplines. The theory of biocommunication presented herein investigates signal transd- tion processes among cells, tissues, organs and organisms in bacteria, animals (corals and bees), fungi and plants in the light of the current available empirical data. Because life is the central focus of the life sciences, this theory will also focus on typical features of life as opposed to inorganic matter. Because this eld of investigation is based on the methodological primacy of a pragmatic action theory, the book may also be of interest to researchers of lingu- tics, communication sciences and sociology (e.g. plant sociology, animal sociology) who would welcome an overview of these highly specialised biological disciplines. Current molecular biology as well as cell biology investigates its scienti c object by using key terms such as genetic code, code without commas, misre- ing of the genetic code, coding, open reading frame, genetic storage medium DNA, genetic information, genetic alphabet, genetic expression, messenger RNA, ce- to-cell communication, immune response, transcription, translation, nucleic acid language, amino acid language, recognition sequences, recognition sites, protein coding sequences, repeat sequences, signalling, signal transduction, signalling codes, signalling pathways, etc.

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.

For over half a century, we have been in the thrall of the double-helicaln structure of DNA, which, in an instant, revealed that information can be transferred between generations by a simple rule, A pairs with T, G pairs with C. In its beautiful simplicity, this structure, along with the table of codons worked out in the following decade, had entranced us into believing that we can fully understand the information content of a DNA sequence, simply by treating it as text that is read in a linear fashion. While we have learned much based on this assumption, there is much we have missed. Far from a passive tape running through a reader, genomes contain information that appears in new forms which create regions with distinct behavior. Some are'gene rich', some mobile, some full of repeats and duplications, some sticking together across long evolutionary distances, some readily breaking apart in tumor cells. Even protein-coding regions can carry additional information, taking advantage of the flexible coding options provided by the degeneracy of the genetic code. The chapters in this volume touch on one or more of three interconnected themes; information can be implied, rather than explicit, in a genome; information can lead to focused and/or regulated changes in nucleotide sequences; information that affects the probability of distinct classes of mutation has implications for evolutionary theory.

This concise, entry level text provides an introduction to the importance of genetic studies in conservation and presents the essentials of the discipline in an easy-to-follow format, with main points and terms clearly highlighted. The authors assume only a basic knowledge of Mendelian genetics and simple statistics, making the book accessible to those with a limited background in these areas. Connections between conservation genetics and the wider field of conservation biology are interwoven throughout the book. Worked examples are provided throughout to help illustrate key equations and glossary and suggestions for further reading provide additional support for the reader. Many beautiful pen and ink portraits of endangered species are included to enhance the text. Written for short, introductory level courses in genetics, conservation genetics and conservation biology, this book will also be suitable for practising conservation biologists, zoo biologists and wildlife managers.