Biological Evolution And Statistical Physics

This set of lecture notes gives a first coherent account of a novel aspect of the living world that can be called biological information. The book presents both a pedagogical and state-of-the art roadmap of this rapidly evolving area and covers the whole field, from information which is encoded in the molecular genetic code to the description of large-scale evolution of complex species networks. The book will prove useful for all those who work at the interface of biology, physics and information science.

This set of lecture notes gives a first coherent account of a novel aspect of the living world that can be called biological information. The book presents both a pedagogical and state-of-the art roadmap of this rapidly evolving area and covers the whole field, from information which is encoded in the molecular genetic code to the description of large-scale evolution of complex species networks. The book will prove useful for all those who work at the interface of biology, physics and information science.

Analyzes approaches to the study of complexity in the physical, biological, and social sciences.

This concise primer (based on lectures given at summer schools on complex systems and on a masters degree course in complex systems modeling) will provide graduate students and newcomers to the field with the basic knowledge of the concepts and methods of statistical physics and its potential for application to interdisciplinary topics. Indeed, in recent years, statistical physics has begun to attract the interest of a broad community of researchers in the field of complex system sciences, ranging from biology to the social sciences, economics and computer science. More generally, a growing number of graduate students and researchers feel the need to learn some basic concepts and questions originating in other disciplines without necessarily having to master all of the corresponding technicalities and jargon. Generally speaking, the goals of statistical physics may be summarized as follows: on the one hand to study systems composed of a large number of interacting ‘entities’, and on the other to predict the macroscopic (or collective) behavior of the system considered from the microscopic laws ruling the dynamics of the individual ‘entities’. These two goals are, to some extent, also shared by what is nowadays called ‘complex systems science’ and for these reasons, systems studied in the framework of statistical physics may be considered as among the simplest examples of complex systems—allowing in addition a rather well developed mathematical treatment.

This book for physicists, biologists, computer scientists, economists or social scientists shows in selected examples how computer simulation methods which are typical to statistical physics have been applied in other areas outside of physics. Our main part deals with the biology of ageing, while other examples are the functioning of the immune system, the structure of DNA, the fluctuations on the stock market, theories for sociology and for World War II. Are leaky water faucets similar to our heartbeats? Throughout the book we emphasize microscopic models dealing with the action of individuals, whether they are cells of the immune system or traders speculating on the currency market. Complete computer programs are given and explained for biological ageing. The references try to introduce the expert from the covered other fields to the relevant physics literature; and they also show the physicists the way into the biological literature on ageing.

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.

This authored monograph introduces a genuinely theoretical approach to biology. Starting point is the investigation of empirical biological scaling including their variability, which is found in the literature, e.g. allometric relationships, fractals, etc. The book then analyzes two different aspects of biological time: first, a supplementary temporal dimension to accommodate proper biological rhythms; secondly, the concepts of protension and retention as a means of local organization of time in living organisms. Moreover, the book investigates the role of symmetry in biology, in view of its ubiquitous importance in physics. In relation with the notion of extended critical transitions, the book proposes that organisms and their evolution can be characterized by continued symmetry changes, which accounts for the irreducibility of their historicity and variability. The authors also introduce the concept of anti-entropy as a measure for the potential of variability, being equally understood as alterations in symmetry. By this, the book provides a mathematical account of Gould's analysis of phenotypic complexity with respect to biological evolution. The target audience primarily comprises researchers interested in new theoretical approaches to biology, from physical, biological or philosophical backgrounds, but the book may also be beneficial for graduate students who want to enter this field.

Market: Those in economics, especially thermodynamics, statistical mechanics, cybernetics, information theory, resource use, and evolutionary economic behavior. This book presents an innovative and challenging look at evolution on several scales, from the earth and its geology and chemistry to living organisms to social and economic systems. Applying the principles of thermodynamics and the concepts of information gathering and self- organization, the author characterizes the direction of evolution in each case as an accumulation of "distinguishability" information--a type of universal knowledge.