Evolution Seen from the Phase Diagram of Life

This book aims to understand biological evolution through a physical approach, focusing on the macroscopic aspects of the biological genome. Readers will discover the connection between genomic information and the harmony of biological systems, a relationship that remains elusive to many researchers in biological sciences.

The most common approach to understanding living organisms with physics is to begin with a single molecule of an organism. In contrast to this bottom-up approach, building from each molecule to the whole, this book takes a coarse-grained approach at the amino acid level to physically understand the macroscopic aspects of the organism. The book presents a system developed by the authors to predict membrane proteins with high accuracy using only physical parameters. Another distinctive perspective of this book is that it proposes the idea of a physical mechanism, other than natural selection, that orchestrates the emergence of order from random processes.The study of macroscopic aspects of living organisms based on this concept has parallels with thermostatistical mechanics for states of matter. Just as random processes create order in matter, there are physical random processes that form order in living organisms. This analogy is the central theme of the book.

Using terms and analogies familiar to physicists, the book bridges the gap between biological and physical sciences. The book focuses on simple principles and is aimed primarily at researchers. While the content of this book is at the boundary area of biophysics, soft matter physics and bioinformatics, it will also be of interest to researchers and graduate students working on any biological topics.

Chapter 1. Organisms viewed from real space and sequence space.- Chapter 2. The relationship between biology and physics.- Chapter 3. Three-dimensional structures of proteins responsible for biological functions.- Chapter 4. Molecular devices that support genome processing.- Chapter 5. Biological membranes and membrane proteins.- Chapter 6. Signal transduction and enzymatic metabolic reactions in living organisms.- Chapter 7. System biology and protein structure prediction by computer.- Chapter 8. Similarities in order formation in matter and organisms.- Chapter 9. Protein distribution analysis by a high-precision prediction system for membrane proteins.- Chapter 10. : Changes in the proportion of membrane proteins by mutation simulation.- Chapter 11. Habitable zone in nucleotide composition space: Phase diagram of life.- Chapter 12. Relationship between the phase diagram of life and protein distribution.- Chapter 13. Definition of species and mysteries of evolution.- Chapter 14.Biological hierarchies and various mutations in genome sequences.- Chapter 15. Analysis of viruses, and the fusion of biology and physics through the phase diagram of life.

Shigeki Mitaku has been a Professor at the Department of Applied Physics, Nagoya University, Japan, since 2003. His research interests lie in the biophysics of proteins, membranes and genome sequences, particularly in their macroscopic properties. His research methods include experiments such as ultrasonic and spectroscopic measurements, as well as computational analysis of amino acid and genomic sequences. He has been a board member of the Physical Society of Japan, since 1997, president of the Biophysical Society of Japan, since 2006, and a visiting fellow of Toyota Physical and Chemical Research Institute, since 2013. His publications include 'Introduction to Molecular Biology' (2002, in Japanese) and 'A Modern Approach to Biological Science' (2015, in Japanese). His translations include 'The Edge of the Unknown' by J. Trefil (1996) and 'How to Write and Publish a Scientific Paper, 6th Edition' by R. A. Day and B. Gastel (2006).

Ryusuke Sawada has been an Assistant professor at the Department of Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Japan, since 2022. His research interests include the biological evolution of genomes and protein sequences, and computational methods for drug development.