Diffusive Growth And Noisy Replication

The bulk of this dissertation consists of three separate research projects. Each of them involves models of multi-locus evolution in the context of finite population size, genetic linkage, and both beneficial and deleterious mutations. Each project employs stochastic computer simulations and numerical solutions to equations which approximate a full stochastic model. The first project, presented in chapter two, was conceived as a problem in the field of non-equilibrium statistical physics known as "front propagation'' and was published in Physical Review E. The connection to biological evolution is due to my advisor, Herbert Levine, and his colleagues who pointed out an analogy between diffusive fronts propagating through physical space and a mutating population evolving through fitness space. The second project, presented in chapter three and published in Genetics, is more biologically oriented than the first project. It concerns the evolutionary pressures acting on the rate at which organisms produce spontaneous mutation. Our results agree with experimental data and also make testable predictions. The mathematical methods used are familiar from non-equilibrium statistical physics, but are quite distinct from those used in the first project. The third project, presented in chapter four, is currently being prepared for publication. It concerns the evolutionary advantage of "competence'' for genetic transformation in bacteria, which is conceptually similar to sex. Thus, issues related to the evolution of sex have bearing on this project, and vice versa. A puzzling feature of competence in many species is that normal, vegetatively growing cells stochastically switch in and out of the competence phenotype. We believe that this project provides a novel explanation for this puzzling "mixed strategy.'' A common theme in this dissertation is the drastic effect of having a finite population size N. In each project, the system behaves qualitatively differently in the infinite N limit than for any finite N. Thus, although "mean field theory'' provides helpful approximations in many areas of physics and stochastic processes, it should be used cautiously in evolutionary problems or those with a similar mathematical structure.

During the past decade interest in the formation of complex disorderly patterns far from equilibrium has grown rapidly. This interest has been stim ulated by the development of new approaches (based primarily on fractal geometry) to the quantitative description of complex structures, increased understanding of non-linear phenomena and the introduction of a variety of models (such as the diffusion-limited aggregation model) that provide paradigms for non-equilibrium growth phenomena. Advances in computer technology have played a crucial role in both the experimental and theoret ical aspects of this enterprise. Substantial progress has been made towards the development of comprehensive understanding of non-equilibrium growth phenomena but most of our current understanding is based on simple com puter models. Pattern formation processes are important in almost all areas of science and technology, and, clearly, pattern growth pervades biology. Very often remarkably similar patterns are found in quite diverse systems. In some case (dielectric breakdown, electrodeposition, fluid-fluid displacement in porous media, dissolution patterns and random dendritic growth for example) the underlying causes of this similarity is quite well understood. In other cases (vascular trees, nerve cells and river networks for example) we do not yet know if a fundamental relationship exists between the mechanisms leading the formation of these structures.

Managing Without Growth offers a compelling argument for the need for a new policy focus in the rich nations. Peter Victor argues that it is time for our obsession with economic growth to end. A new focus on human well-being must replace our more is better philosophy. Brett Dolter, Briarpatch Magazine Peter Victor clearly presents the arguments as to why already relatively rich countries may have to manage low or no growth in their economies if they wish to address rather than continue contributing to global environmental problems. His modelling suggests that managing without growth need not be the economic disaster that is so often assumed. This is a lucid book that provides an excellent introduction to this important but neglected area. Paul Ekins, King's College London, UK At last, Managing Without Growth, a book that puts economics in its proper place within the real world and points the direction we must go in confronting the ecological crisis of the planet. As an economist, environmental studies professor Peter Victor is eminently qualified for the task. He examines some of our most fundamental assumptions and beliefs about the market, pricing, free trade and growth, prosperity and happiness that too often preclude a serious consideration of the environment and economy. His book couldn t be a more timely and important analysis of the destructive consequences of aspiring to endless growth and downloading the costs onto nature itself. He makes a powerful case for the need to work deliberately towards a steady state economy where the real world of the biosphere should set the limits to our activity. Victor s book should be at the basis for our discussion of these critical issues today. David Suzuki, broadcaster and activist Peter Victor analyses the critical policy question of our time, how to manage our economy equitably and efficiently without growing beyond biophysical limits. He reasons carefully and rigorously, yet pulls no punches in drawing conclusions that some will consider radical. A superb book! Herman E. Daly, University of Maryland, US Overcoming our addiction to economic growth is one of the most important challenges for the 21st century. Peter Victor s masterful summary of the history and fallacies of this particularly pervasive and increasingly dangerous addiction will be a great help in getting over it. A sustainable and desirable future requires clearly differentiating between bigger and better and a recognition that in the overdeveloped West these two have parted ways. Peter Victor s book will help us slow down by design, not disaster, and understand how that slowing down will in fact increase our quality of life. Robert Costanza, The University of Vermont, US Peter Victor s book is a carefully crafted argument for managing without growth . It is not only an up-to-date survey of the latest thinking on energy, climate, and population, it offers practical policy responses to these challenges. This book is a must read for academics and policymakers concerned with environmental integrity and human wellbeing. John Gowdy, Rensselaer Polytechnic Institute, US Peter Victor challenges the priority that rich countries continue to give to economic growth as an over-arching objective of economic policy. The challenge is based on a critical analysis of the literature on environmental and resource limits to growth, on the disconnect between higher incomes and happiness, and on the failure of economic growth to meet other key economic, social and environmental policy objectives. Shortly after World War II, economic growth became the paramount economic policy objective in most countries, a position that it maintains today. This book presents three arguments on why rich countries should turn away from economic growth as the primary policy objective and pursue more specific objectives that enhance wellbeing. The author contends that continued economic growth worldwide is unrealistic due to environmental and

The first comprehensive general resource on state-of-the-art protocell research, describing current approaches to making new forms of life from scratch in the laboratory. Protocells offers a comprehensive resource on current attempts to create simple forms of life from scratch in the laboratory. These minimal versions of cells, known as protocells, are entities with lifelike properties created from nonliving materials, and the book provides in-depth investigations of processes at the interface between nonliving and living matter. Chapters by experts in the field put this state-of-the-art research in the context of theory, laboratory work, and computer simulations on the components and properties of protocells. The book also provides perspectives on research in related areas and such broader societal issues as commercial applications and ethical considerations. The book covers all major scientific approaches to creating minimal life, both in the laboratory and in simulation. It emphasizes the bottom-up view of physicists, chemists, and material scientists but also includes the molecular biologists' top-down approach and the origin-of-life perspective. The capacity to engineer living technology could have an enormous socioeconomic impact and could bring both good and ill. Protocells promises to be the essential reference for research on bottom-up assembly of life and living technology for years to come. It is written to be both resource and inspiration for scientists working in this exciting and important field and a definitive text for the interested layman.

All papers in this proceedings volume were peer reviewed. The purview of this third conference was shifted toward biology and medicine. Among the topics covered were: the constructive role of noise in the central nervous system, neuronal networks, and sensory transduction (hearing in humans, photo- and electroreception in marine animals), encoding of information into nerve pulse trains, single molecules and noise (including single molecule detection and characterization by nanopores - molecular "Coulter counting"), concepts of noise in neurophysiology (randomness and order in brain and heart electrical activities under normal conditions and in pathology), the role of noise in genetic regulation and gene expression, biosensors, etc.

Publishes papers that report results of research in statistical physics, plasmas, fluids, and related interdisciplinary topics. There are sections on (1) methods of statistical physics, (2) classical fluids, (3) liquid crystals, (4) diffusion-limited aggregation, and dendritic growth, (5) biological physics, (6) plasma physics, (7) physics of beams, (8) classical physics, including nonlinear media, and (9) computational physics.

Using simple models this book shows how we can gain insights into the behavior of complex systems. It is devoted to the discussion of functional self-organization in large populations of interacting active elements. The authors have chosen a series of models from physics, biochemistry, biology, sociology and economics, and systematically discuss their general properties. The book addresses researchers and graduate students in a variety of disciplines.

Beginning with the germ theory of disease in the 19th century and extending through most of the 20th century, microbes were believed to live their lives as solitary, unicellular, disease-causing organisms . This perception stemmed from the focus of most investigators on organisms that could be grown in the laboratory as cellular monocultures, often dispersed in liquid, and under ambient conditions of temperature, lighting, and humidity. Most such inquiries were designed to identify microbial pathogens by satisfying Koch's postulates.3 This pathogen-centric approach to the study of microorganisms produced a metaphorical "war" against these microbial invaders waged with antibiotic therapies, while simultaneously obscuring the dynamic relationships that exist among and between host organisms and their associated microorganisms-only a tiny fraction of which act as pathogens. Despite their obvious importance, very little is actually known about the processes and factors that influence the assembly, function, and stability of microbial communities. Gaining this knowledge will require a seismic shift away from the study of individual microbes in isolation to inquiries into the nature of diverse and often complex microbial communities, the forces that shape them, and their relationships with other communities and organisms, including their multicellular hosts. On March 6 and 7, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats hosted a public workshop to explore the emerging science of the "social biology" of microbial communities. Workshop presentations and discussions embraced a wide spectrum of topics, experimental systems, and theoretical perspectives representative of the current, multifaceted exploration of the microbial frontier. Participants discussed ecological, evolutionary, and genetic factors contributing to the assembly, function, and stability of microbial communities; how microbial communities adapt and respond to environmental stimuli; theoretical and experimental approaches to advance this nascent field; and potential applications of knowledge gained from the study of microbial communities for the improvement of human, animal, plant, and ecosystem health and toward a deeper understanding of microbial diversity and evolution. The Social Biology of Microbial Communities: Workshop Summary further explains the happenings of the workshop.

An integrative approach linking the causes of migration to genetic consequences for human evolution.