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Book Review |
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Physics in Molecular Biology Kim Sneppen & Giovanni Zocchi New York, NY: Cambridge Univ. Press, 2005, 319 pp., index, $70.00. ISBN: 0-521-84419-3. Theoretical physicist Kim Sneppen (Niels Bohr Institute) and experimental physicist Giovanni Zocchi (UCLA) have teamed up to produce a textbook on biophysics intended for third- and fourth-year physics students. The book may be viewed as yet another testimony of the vibrant biophysics community which has emerged in Denmark. The book is not aiming at an encyclopedic coverage of biophysics but to teach basic physical ideas relevant to molecular biology via specific examples. Tools are introduced as needed while the elements of statistical physics are summarized in an appendix. Statistical physics is the toolbox of choice since biological systems consists of a large number of interacting molecules. Basically one is looking for the states and configurations which maximize the total entropy Stot (which is equivalent to minimizing the Gibb’s energy G of the system). Also single molecules like proteins may consist of hundreds of subunits interacting with each other and with solvent molecules. It is quite hopeless to approach such systems with quantum mechanical ab initio methods, and furthermore, we are seldom interested in that detailed a description were it even possible. For instance, for proteins we might be interested in various conformational structures. When an “exact treatment” is too forbidding we have to rely on artful simplifications which make calculations feasible while still retaining the essential features of the problem. To succeed in such endeavours is the secret of (bio)physics. One of the basic simplified models is that of a polymer as a chain of more or less randomly oriented units. Sneppen and coworkers have mimicked the effect of hydrogen bonds on polymer folding using such a simplified model by associating every polymer unit with a spin which could be oriented along the x-, y- or z-axis. Making the neighbouring units interact via the oriented “spin” is shown to generate secondary structures (alpha and beta helices). While this model requires simulations, many of the examples discussed in the book are based on back-on-the-envelope type calculations and this applies also to the exercises dispersed throughout the text. The ability to make quick estimates of typical quantities involved in problems is one of the more useful talents to acquire. Biophysical problems can be especially tricky in this respect since we may have many interactions balancing each other (van der Waals forces, salt bridges, H-bonds, hydrophobic forces, disulfide bridges), and whether the balance tips this or that way makes all the difference. A central agent here is the thermal fluctuations whose characteristic energy is kT, or 1/40 eV (at room temperature), to be compared with a typical energy of 1 eV for covalent bonds. From this follows the dramatic influence of an aqueous environment on interactions since it reduces the electrostatic energy by a factor of 80 (the dielectric constant of water) thus amplifying the importance of the fluctuations. One intriguing effect of water is the cold melting of proteins which is described by another simplified model. Discussing the intricate role of hydrophobicity for protein structures the authors remark (p. 89) that “the hydrophobic interaction occupies, in life sciences, a position of importance comparable with any of the four fundamental interactions in the physical sciences. Yet our knowledge is very limited. We do not, for example, really know its range”. So that’s a hint for physicists looking for big challenges! The book focuses on genes, RNA, DNA, proteins, molecular networks and finally evolution including the popular Bak-Sneppen model. The pièce de résistance is chapter 7 devoted to the genetic regulation of the lambda-phage switch which is an example of the functioning of molecular networks which is the subject of the following chapter. The book thus presents an interesting interplay between component biology and systems biology, and demonstrates how semi-quantitative models may facilitate the understanding of how the components fit together in a system. I would recommend it to researchers, and as supplementary reading for students with the proviso that it requires a firm grasp of the elements of statistical physics and thermodynamics. The advantage of the book is that it quickly introduces research topics and the tools to tackle the problems. The book is packed with facts in a condensed monographic style yet the biological details are explained as needed and the book can therefore be considered to be largely self contained. A number of printing errors may however create some traps for the novice (lack of proofreading?). Every chapter ends with full bibliographic references to the original literature. There is also a brief glossary of important concepts at the end. Nevertheless it is advisable to have some general introductory work on biophysics near at hand when reading the book (of recent introductory works I may mention the ones by Rodney Cotterill, Meyer B Jackson and Michel Daune). Frank Borg Univ. of Jyväskylä, Finland |
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Books Received |
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Exercise Biochemistry. Vassilis Mougios. Champaign, IL: Human Kinetics, 2006, 349 pp., illus., index, $79.00. ISBN: 13: 978-0-7360-5638-0. My Other Body. Ann Pai. Overland Park, KS: Sunspot Press, 2006, 332 pp., $15.00. ISBN: 0-9772045-0-2. Nutrition and Clinical Management of Chronic Conditions and Diseases. Felix Bronner, (Editor). Atlanta, GA: CRC Press/Taylor & Francis Group, LLC, 2006, 282 pp., illus., index, $139.95. ISBN: 0-8493-2765-2. Physiology Case Studies in Pharmacy. Laurie Kelly McCorry, Ph.D. Washington, DC: American Pharmacists Association, 2006, 208 pp., index, $35.00. ISBN: 1-58212-089-7. Reflections of a Physician in His Ninety-Seventh Year. David I. Abramson, M.D. Coral Springs, FL: Llumina Press, 2005, 211 pp., illus., $12.95. ISBN: 1595260250. |
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