From cell division to heartbeat, clocklike rhythms pervade the activities of every living organism. The cycles of life are ultimately biochemical in mechanism but many of the principles that dominate their orchestration are essentially mathematical.
The Geometry of Biological Time describes periodic processes in living systems and their non-living analogues in the abstract terms of nonlinear dynamics. Enphasis is given in phase singularities, waves, and mutual synchronization in tissues composed of many clocklike units. Also provided are descriptions of the best-studied experimental systems such as chemical oscillators, pacemaker neurons, circadian clocks, and excitable media organized into biochemical and bioelectrical wave patterns in two and three dimensions. No theoretical background is assumed; the required notions are introduced through an extensive collection of pictures and easily understood examples. This extensively updated new edition incorporates the fruits of two decades' further exploration guided by the same principles. Limit cycle theories of circadian clocks are now applied to human jet lag and are understood in terms of the molecular genetics of their recently discovered mechanisms. Supercomputers reveal the unforeseen architecture and dynamics of three-dimensional scroll waves in excitable media. Their role in life-threatening electrical aberrations of the heartbeat is exposed by laboratory experiments and corroborated in the clinic. These developments trace back to three basic mathematical ideas.
1980 Preface 1999 Preface 1999 Acknowledgements Introduction 1 Circular Logic 2 Phase Singularities (Screwy Results of Circular Logic) 3 The Rules of the Ring 4 Ring Populations 5 Getting Off the Ring 6 Attracting Cycles and Isochrons 7 Measuring the Trajectories of a Circadian Clock 8 Populations of Attractor Cycle Oscillators 9 Excitable Kinetics and Excitable Media 10 The Varieties of Phaseless Experience: In Which the Geometrical Orderliness of Rhythmic Organization Breaks Down in Diverse Ways 11 The Firefly Machine 12 Energy Metabolism in Cells 13 The Malonic Acid Reagent ('Sodium Geometrate') 14 Electrical Rhythmicity and Excitability in Cell Membranes 15 The Aggregation of Slime Mold Amoebae 16 Numerical Organizing Centers 17 Electrical Singular Filaments in the Heart Wall 18 Pattern Formation in the Fungi 19 Circadian Rhythms in General 20 The Circadian Clocks of Insect Eclosion 21 The Flower of Kalanchoe 22 The Cell Mitotic Cycle 23 The Female Cycle References Index of Names Index of Subjects
From the reviews:
"This book is a wonderful exposition about his life's work and is presented with such clarity that the reader gains an insight into details of his manner of thinking...the reader is taken on a quest to solve biological mysteries and travels from the intricate beginnings of formulating the questions, through the apices and troughs of analyzing, and on to the discovery of the holy grail, that which yields biological predictions and answers. One leaves with a sense of understanding that hopefully can be applied to one's own work...this book could easily serve a dual purpose. First, through the introduction of basic mathematical concepts such as topology combined with modeling, the book serves as an introduction helping the non-applied reader to see the beauty of mathematical modeling. Second, because Winfree explains the modeling process very thoroughly, instead of just presenting equations, the book can serve as a medium for the medical professional to acquire an understanding of the modeling process. A wonderful accomplishment...I am proud to have this book on my shelf and consider it...a seminal text in mathematical modeling. This is a text that every first year graduate student should look at in some detail." (Mathematical Reviews)
"The new edition of The Geometry of Biological Time is a fascinating update of the delightful original. This new edition contains thoughtful commentary on new developments in the field, adding a historical and sociological dimension to the original book's elegant and unifying treatment of biological problems involving processes that repeat themselves regularly, i.e. involve 'rhythmic return through a cycle of change.' The book is an enjoyable page-turner, even for those readers with only a passing interest in biology, and demonstrates well the synergistic effect between biology and mathematics. ...
The term 'page-turner' may seem unusual in mathematics; however, it is appropriate here. Not only is the reader continually tantalized by the figures appearing on the ensuing pages, but the new commentary lends a mystery-novel feeling to the book. This second edition was created by inserting new text boxes into the original, mostly intact, edition. This style leads to a fascinating historical picture. For example, the text, '(...In the latter cases the periodicity approximation gets worse closer to the pivot. I wish here to sweep such matters under the rug (in 1978))' is followed by a new text box that begins, 'The bulge under the rug grew and grew...', continuing with a description of developments over the last two decades. The plot continues even now, with descriptions of the last twenty years often followed in the book by descriptions of current puzzles. In summary, the original book is good and the second edition is even better; the historical commentary is fascinating, and there are also a few reorganized and new chapters presenting additonal biological examples." (MAA Online)
1980 Preface * 1999 Preface * 1999 Acknowledgements * Introduction * 1 Circular Logic * 2 Phase Singularities (Screwy Results of Circular Logic) * 3 The Rules of the Ring * 4 Ring Populations * 5 Getting Off the Ring * 6 Attracting Cycles and Isochrons * 7 Measuring the Trajectories of a Circadian Clock * 8 Populations of Attractor Cycle Oscillators * 9 Excitable Kinetics and Excitable Media * 10 The Varieties of Phaseless Experience: In Which the Geometrical Orderliness of Rhythmic Organization Breaks Down in Diverse Ways * 11 The Firefly Machine 12 Energy Metabolism in Cells * 13 The Malonic Acid Reagent ("Sodium Geometrate") * 14 Electrical Rhythmicity and Excitability in Cell Membranes * 15 The Aggregation of Slime Mold Amoebae * 16 Numerical Organizing Centers * 17 Electrical Singular Filaments in the Heart Wall * 18 Pattern Formation in the Fungi * 19 Circadian Rhythms in General * 20 The Circadian Clocks of Insect Eclosion * 21 The Flower of Kalanchoe * 22 The Cell Mitotic Cycle * 23 The Female Cycle * References * Index of Names * Index of Subjects
Dealing with dynamics of processes that repeat themselves regularly, this revised and updated edition extends the thread from 1980 to the present day, concentrating on areas of interest where there will be much activity in the future. This involves going through spatial biochemical, electrophysiological, and organismic dynamical systems and patterns that were discovered by pursuing the theme of phase singularities introduced in the original book. In particular the work on excitability in cell membranes will be thoroughly updated as will the references throughout the book.
This is an update of a classic mathematical biology book by an author who is a leader in the field. It deals with dynamics of processes that repeat themselves regularly. This cycle of change is an ubiquitous principle of organization in living systems. In this new edition the author addresses areas that have come to fruition since 1980 and also concentrates on areas which he personally feels will see much activity in future.