Über die Autorin bzw. den Autor

William Bialek is the John Archibald Wheeler/Battelle Professor in Physics at Princeton University, where he is also a member of the multidisciplinary Lewis-Sigler Institute for Integrative Genomics, and is Visiting Presidential Professor of Physics at the Graduate Center of the City University of New York. He is the coauthor of Spikes: Exploring the Neural Code.

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"This book is full of insights that were new to me. It explores myriad questions that are both deep background themes in biology, and also fascinating to physicists. Bialek is a dean of this field, and an inspiring teacher."--Philip Nelson, University of Pennsylvania

"Bialek's excellent book bears the stamp of both his originality and technical prowess. What I look for when I read a book is something unique that I know I won't find anywhere else. Bialek delivers that in spades on a topic of great interest to scientists of all stripes."--Rob Phillips, California Institute of Technology

"This excellent book covers very original ground, providing an authoritative overview of important problems while linking strongly to the original literature. The topics are taken from real biology but build on the standard knowledge that a physics student should have. This indeed represents a great path to train interdisciplinary scientists--without losing the discipline."--Pietro Cicuta, University of Cambridge

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"This book is full of insights that were new to me. It explores myriad questions that are both deep background themes in biology, and also fascinating to physicists. Bialek is a dean of this field, and an inspiring teacher."--Philip Nelson, University of Pennsylvania

"Bialek's excellent book bears the stamp of both his originality and technical prowess. What I look for when I read a book is something unique that I know I won't find anywhere else. Bialek delivers that in spades on a topic of great interest to scientists of all stripes."--Rob Phillips, California Institute of Technology

"This excellent book covers very original ground, providing an authoritative overview of important problems while linking strongly to the original literature. The topics are taken from real biology but build on the standard knowledge that a physics student should have. This indeed represents a great path to train interdisciplinary scientists--without losing the discipline."--Pietro Cicuta, University of Cambridge

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Biophysics

PRINCETON UNIVERSITY PRESS

Contents

Acknowledgments...................................................ix1. Introduction...................................................31.1 About Our Subject.............................................31.2 About This Book...............................................112. Photon Counting in Vision......................................172.1 A First Look..................................................172.2 Dynamics of Single Molecules..................................512.3 Biochemical Amplification.....................................682.4 The First Synapse and Beyond..................................972.5 Coda..........................................................1153. Lessons, Problems, Principles..................................1174. Noise Is Not Negligible........................................1274.1 Fluctuations and Chemical Reactions...........................1274.2 Motility and Chemotaxis in Bacteria...........................1494.3 Molecule Counting, More Generally.............................1724.4 More about Noise in Perception................................1924.5 Proofreading and Active Noise Reduction.......................2184.6 Perspectives..................................................2455. No Fine Tuning.................................................2475.1 Sequence Ensembles............................................2485.2 Ion Channels and Neuronal Dynamics............................2795.3 The States of Cells...........................................2995.4 Long Time Scales in Neural Networks...........................3295.5 Perspectives..................................................3496. Efficient Representation.......................................3536.1 Entropy and Information.......................................3546.2 Noise and Information Flow....................................3696.3 Does Biology Care about Bits?.................................3956.4 Optimizing Information Flow...................................4216.5 Gathering Information and Making Models.......................4496.6 Perspectives..................................................4677. Outlook........................................................469Appendix Some Further Topics......................................473A.1 Poisson Processes.............................................473A.2 Correlations, Power Spectra, and All That.....................484A.3 Diffraction and Biomolecular Structure........................495A.4 Electronic Transitions in Large Molecules.....................503A.5 The Kramers Problem...........................................512A.6 Berg and Purcell, Revisited...................................521A.7 Maximum Entropy...............................................533A.8 Measuring Information Transmission............................545Annotated Bibliography............................................557Index.............................................................625

Chapter One

When a PhD student in physics picks up a textbook about elementary particles, or cosmology, or condensed matter, there is little doubt about what will be found inside the covers. There are questions, perhaps, about the level and style of presentation, or about the emphasis given to different subfields, but the overall topic is clear. The situation is very different for books or courses that attempt to bring the intellectual style of physics to bear on the phenomena of life. The problem is not just in how we teach, but also in how we do research. The community of physicists interested in biological problems is incredibly diverse, it spills over into more amorphously defined interdisciplinary communities, and individual physicists often are more connected to biologists working on the same system than they are to physicists asking the same conceptual question in other biological systems. None of this is necessarily good or bad, but it can be confusing for students.

1.1 About Our Subject

Ours is not a new subject, but over its long history, "biophysics" or "biological physics" has come to mean many different things to different communities. At the same time, for many physicists today, biophysics remains new and perhaps a bit foreign. There is an excitement to working in a new field, and I hope to capture this excitement. Yet our excitement, and that of our students, sometimes is tempered by serious concerns, which can be summarized by naive questions: Where is the boundary between physics and biology? Is biophysics really physics or just the application of methods from physics to the problems of biology? My biologist friends tell me that "theoretical biology" is nonsense, so what would theoretical physicists be doing if they got interested in this field? In the interaction between physics and biology, what happens to chemistry? How much biology do I need to know to make progress? Why do physicists and biologists seem to be speaking such different languages? Can I be interested in biological problems and still be a physicist, or do I have to become a biologist? Although there has been much progress over the past decade, I still hear students (and colleagues) asking these questions, and so it seems worth a few pages to place the subject of this book into context.

To put things in perspective, we need to have in mind at least a cartoon sketch of the intellectual landscape that we are trying to explore. I am not a sociologist or historian of science, and cartoons can be, by definition, cartoonish, so there are myriad dangers here. Indeed, the dangers are sufficiently great that at least one colleague recommended scrapping this discussion completely. There is a school of thought that says, roughly, "I don't care if it's biology or physics, I just want to do interesting science," and according to this view one need not worry about the place of biophysics in relation to the larger, separate enterprises of physics and biology. This sounds good and hints at a nirvana in which disciplinary boundaries are erased and (by extension) universities have no departments. But this position is not interdisciplinary or multidisciplinary, it's antidisciplinary, and it assumes, implicitly, that the definition of "interesting" is objective, independent of our intellectual backgrounds. I find this very hard to believe. One might hope that we could construct an objective definition of interesting science, but certainly practicing scientists don't automatically subscribe to such a thing. Indeed, faced with the same natural phenomena, my experience is that physicists and biologists (and mathematicians and chemists and engineers) will ask different questions. By the time we find answers, we ought to be able to convince one another that we have accomplished something. But at the stage where we are still formulating questions, I think that any search for unanimity about what is a "good" or "interesting" question would devolve into one group insisting that they alone have the right to determine what is relevant. I believe there really are physics problems motivated by the phenomena of life and that these problems can be different from those that engage our biologist friends—not better or worse, but different. So, with this in mind, let us draw that sketch, cartoonish though it may be.

Academic disciplines can define themselves either by their objects of study or by their style of inquiry. Physics is firmly in the second...