5 comments about Biological Thermodynamics.

1. I teach a course in thermodynamics for college students in biology, as such, I thought the book could be useful, perhaps the new textbook for my course.
   Possitive things:
   * you will find real thermodynamics, biology and also historical notes in the book.
   * there are not too many books that blend biology and thermodynamics in forms acceptable to biologist and physicists, this one does.
   * it has an interesting selection of subjects

   Problems:
   * most of the time it has TOO many words, for those that like concise presentations, it is a problem. There are no evident forms to distinguish essential from accesory
   * there is a bias towards bio-chemistry that introduces some additional difficulties for people with other backgrounds

   My recommendation to the students
   Main text: Kondepudi and Prigogine. Modern Thermodynamics
   (extremely clear, concise and with historical notes but little biology)
   Second text: Biological Thermodynamics by Haynie




2. For people with little insight (but interest) in thermodynamics this book is mandatory. For me personally it has been a quick way to freshen up the concepts of thermodynamics. The book is in large parts well written with many easy to understand examples of otherwise diffucult topics.



3. As someone who has used the book during his graduate studies in biophysical chemistry (the field of biopolymer conformational dynamics), I warmly recomend this book to any student/researcher interested in learning more about this field. The book offers a solid foundation to those interested in exploring the field in greater details.



4. I found this text replete with misconceptions and mistakes. An interesting attempt, but it should have had a critical editor who knew something about thermodynamics. Clearly, this was not the case.
   
   I sought elsewhere, and I suggest you do too.



5. For neophytes to this field, like me, a more descriptive title for this book would be some jaw-breaker like "Thermal Physical Biochemistry". I'd picked the book up because I was interested in, e.g., the thermodynamic aspects of plant and animal physiology and morphology -- such as the shapes of leaves, snouts, beehives, etc. You won't find any of those subjects here, nor even any discussion of the thermodynamic differences between warm-blooded and cold-blooded animals other than a reference in a problem set. The book's scope is not really biology, but rather biochemistry. (According to an email I received from the author after posting an earlier version of this review, there is a professional society for "biological thermodynamics" that indeed focuses primarily on biochemistry. But if, like me, you're not a pro, you might be surprised to learn that the title phrase has such a narrow meaning. The author also tells me that there isn't enough material for a book about leaves, snouts, etc. at the undergraduate level; nonetheless, if that's what you're interested in, you should know it's not here.)
   
   On the plus side, the book does have some down to earth explanations of concepts like entropy and free energy. It's also good at explaining why, for example, sometimes you want to use enthalpy and other times free energy. Most thermo textbooks just rattle off various combinations of variables, state functions and partial derviative relationships, without giving you any practical feel for when you'd use one or the other. In keeping with its emphasis on clarifying basic concepts, this book avoids calculus, and actually is better for it in many places.
   
   That said, its approach is not purely thermodynamic. Thermo is based on macroscopic phenomena, even when discussing concepts like entropy. But this book's discussion of entropy is based on the statistical mechanics point of view from the get-go (even though stat mech isn't formally introduced until much later). It is not historically correct to say that "The Second Law is about the tendency of *particles* [emphasis in the original] to go from being concentrated to being spread out in space" (@60); the particle-based conception of the law followed the the law's discovery by several decades. The author's focus on particles fits in with the book's interest in chemistry. But the macroscopic point of view can give you many insights, too. (See, e.g., DeHoff's "Thermodynamics in Materials Science" for a non-biological example; ditto, in fact, for most engineering textbooks that deal with thermo.)
   
   The book doesn't have any self-contained hints or solutions to any of the exercises. (The author tells me that those interested in solutions should write to him or the publisher for a solution set. I appreciate this, and I hope that news benefits you if you read the book; but in future editions this would be more helpful if stated on a website or in a preface.) There are also rather more typos, awkward phrases and awkward analogies than one would like to see in a 2nd edition. E.g., @73 the description of protein denaturation mixes up "decreases" with "increases"; there are too many negative signs in Table 4.1; a reaction is described as "cooperative" @ 97, even though this term is never defined in the text, leaving one to be mystifed by the glossary entry for "cooperativity" ("the degree of 'concertedness' of a change in conformation or arrangement of particles in a system," @402). (The author tells me that he will try to correct some of these problems in the next printing.) An explantion of the First Law analogizing energy to money is kind of OK in the limited context (@6), but the analogy is generally misleading, since money is not a conserved quantity even in economics theory. The author also has a tiresome and fitful quirk of mentioning the occupations of the fathers of many, though not all, of the scientists he names in the text.
   
   Maybe the 3rd edition of this book will become a classic, but this edition isn't quite there yet.

No comments about Protein Crystallography: A Concise Guide.

3 comments about Biological Physics of the Developing Embryo.

1. The book by Forgacs and Newman on one hand introduces important biological concepts for physicists with interest in development, covering properties of isolated cells and principles of their regulation, the interaction between cells and cell and their environment, the formation of tissues by morphogenesis, principles underlying organogenesis, and evolutionary aspects important in development.
   On the other hand the book also presents the complex interplay of physical processes under genetic control during development. It introduces fundamental physical concepts from point and continuum mechanics, thermodynamics and statistical mechanics (including critical phenomena), dynamical systems theory and reaction-diffusion systems. A major strength of the book is that physics is introduced through fundamental biological processes, thus using a framework familiar to biologists (and not the other way around, as in most texts on biophysics). The selection of examples captures many stages and processes during development.
   The model description does not stop at the level of purely qualitative text description but includes the basic equations and their analysis, although this is done at an elementary level, requiring minimal knowledge of calculus (and the more complicated concepts are discussed in special "Boxes"). In this way the book also contains a short course in mathematical model formulation written for biologists. It does not aim at replacing existing books on developmental biology or biophysics but fits into the gap between both. It builds an interface between physicists and biologists in embryonic development and thereby should facilitate the reading of the more specialized books on developmental biology by physicists as well as the better understanding of physical principles and mathematical models and the role these play in biological systems, by biologists.



2. While the course of embryological development is extremely complex, many of the component processes that go into shaping an embryo are strongly reminiscent of simpler physical phenomena which occur in nonliving materials. Some of these analogies are exact, the same physics applies in both cases. However, often the analogy is inexact or even misleading. Thus, while physical analogies can be extremely useful in understanding development, they also need to be approached with caution. Until now, no book-length overview has reviewed the many successes and pitfalls of a biological-physics approach to development and the material available in technical articles has been dispersed and often written in a technical jargon inaccessible to its target audience. Biological Physics of the Developing Embryo, fills this niche in a style that is easily comprehensible by advanced undergraduate biologists and physicists (and assumes minimal background on either side), while containing enough material that even senior researchers in development will learn a great deal. I've been working in the area for 15 years and found many ideas and references that were both new and valuable. The biological illustrations and examples are well chosen and cover almost every aspect of development in a clear, logical sequence. The consistent philosophy and approach of the two writers, one a physicist and bioengineer and the other a developmental biologist, helps organize an apparently heterogeneous collection of models and developmental mechanisms into a coherent story.
   
   Because of its novelty and breadth, the book contains a number of minor errors, which will doubtless be corrected in a future edition. Overall, this is a path-breaking book, which I am recommending to all of my own students and to any colleagues interested in the question "What does physics have to say about development?"



3. "Biological Physics of the Developing Embryo" is a remarkable causal description of embryonic development as controlled by the interplay of physical and biomolecular processes. Based on their expertise in both theory and experiment (Forgacs is a condensed matter physicist and Newman was trained in physical chemistry, and each currently directs a program in cell and tissue biology), the authors present an engaging and original view of cell-cell interactions and multicellular morphogenesis and pattern formation. They offer a paradigm within which spatiotemporal cell behavior is explained by the concerted action of "generic" physical principles and specific genetic factors. Reading the book is made easy for both the physical and life scientist by the logic of its presentation: early development is presented according to the major stages familiar to the biologist in a clear fashion that also provides a short introduction to each event or process (cleavage, differentiation, gastrulation, segmentation, several kinds of organogenesis, fertilization) for the physicist. The physical modeling of each developmental episode is then discussed, making a smooth transition that is not overwhelming for the biologist. Each chapter ends with a short "perspective" which epitomizes the main conceptual lessons of the chapter resulting from the synthesis of experimental facts and relevant physical models. Books of this kind are rare, although badly needed, due to the large accumulation of facts. Not to be lost in the sea of data, an atheoretical descriptive analysis is no longer an option. Experimental results must be supplemented by systematic modeling for useful interpretations to emerge. The book by Forgacs and Newman teaches us how to accomplish this.

5 comments about Signal Transduction.

1. Anyone who has surveyed the collection of existing textbooks on signal transduction realizes that they come in two basic flavors - those that cover alot of ground in an extremely superficial fashion, and those that delve in depth into a few narrow area while leaving vast tracts of the subject untouched. In addition, most texts are written on a chapter-by-chapter basis by different authors, leaving these texts more a collection of essays than a comprehensive review.
   Gomperts, Kramer and Tatham's book has suceeded dramatically where most of the others have failed. The text is strikingly comprehensive, covering nearly all major areas of signal transduction including receptors, G proteins, calcium signaling, protein and lipid kinases and phosphatases, growth factors and cell adhesion. It is the first book I have seen that integrates historical, pharmacological, and physiological findings in these areas with the biochemistry and fine molecular detail of the molecules involved. Written with a single voice, the chapters integrate elegantly with one another, and provide the reader with both broad and comprehensive viewpoints - one sees the forest AND the trees! Remarkably current and up-to-date, the book promises to be a core text for graduate and advanced undergraduate courses in cell signaling and molecular cell biology, and a valuable reference book for all scientists whose work involves mechanisms of cell communication.



2. 5 stars - give me a break, that book hasn't been written yet! By comparison with the other [stuff]hat's out there, like the abysmal Hancock book from a few years ago or the equally execrable Helmreich text, this one DOES stand out like a overexpressed GFP-kinase. One thing that is definitely better is the illustrations (not credited remarkably enough) most of which are well done. It is a pretty good undergrad text and I used it in a course to generally good reviews. The format is entirely conventional, however, and follows a predictable sequence. One is not going to learn much new, if already in the field. Old Gomp et al do get nostalgic with their historical sidelines and overdo it in some places - e.g. the abstruse tale of who really discovered insulin - but in general the use of sidebars (very reminiscent of the new Nature review journals in format) is well done.

   There are several problems that are difficult to work out in teaching signalling to undergrads these days. One is how to incorporate enough physiology of specific organs such that the tissue-specific signalling that makes them work is comprehensible. Another is how to incorporate the newer structural information so that it actually adds to understanding, as opposed to being just a superficial take on structural biology. I don't think the text solves either of these problems particularly well, but it does make a worthwhile stab at it.

   All in all a good buy. One awaits the paperback so that the [money]tag is not such a hurdle to purchase.




3. My research group used a previous edition of this text in a seminar series during our weekly group meetings as a review text. It is very good at introducing the subject matter or serving as a refresher for students. The background info adds a nice touch. The ample illustrations help convey the information for the visual learners among us.



4. This book is a very good introduction to the subject. Depth and breadth of coverage is in general well balanced and the abundant diagrams help understanding quite a bit. The topics choosen by the authors are informative and put together an ok picture of signaling processes. There is one main areas that have been omited and I think prevent the book from giving a "very good" (as opposed to just ok) picture of the field, namely: spatio-temporal dynamics of signaling cascades and mathematical modeling of this processes. In my opionion, understanding the spatio-temportal organization of the signaling machinery is fundamental to understand signaling and the authors do not present the subject adequately (if at all). The second failure is in the area of "systems thinking". The book fails to convey the complexity of the multiple levels of feedback and other forms of regulation that make these systems work. Spatio-temporal organization and dynamics are a fundamental part of signaling pathways and you can't get a realistic picture of what is going on without them.
   
   The field is advancing at warp speed and a new edition may be in order. Perhaps the new edition could include a couple of chapters about spatial organization and a more "holistic" view of signaling systems.



5. The authors intended this book for students and professionals. I don't fall into either group but I enjoyed it and learned from it, so I'm reviewing it for other similarly inclined non-scientists.
   
   Cell-to-cell communication is of supreme importance to multicellular organisms and so it is of interest from many points of view. For example, I am very interested in its role in evolutionary developmental biology. Other people will be more interested in hormones, nerve signaling, et al. Signal Transduction is that part of communication that happens inside the cell, between the signal and the DNA. Thus it doesn't include neurotransmitters which activate ion channels in the membrane, nor does it include steroids, which pass through the membrane and into the nucleus. Nevertheless, it covers most cell communication. In particular, there is a lot of material on G-protein-coupled receptors, which make up a majority of the receptors, and tyrosine kinase receptors, which are also plentiful.
   
   As the authors describe it, chapters 1-9 are on the "nuts and bolts" of transduction. This includes a very brief introduction to intercellular signaling molecules (such as hormones and neurotransmitters) and receptors, followed by some details about the internals, including calcium ions and phosphate exchange. In the second part, "attention is concentrated on transduction processes set in action by growth factors and adhesion molecules". There is also a short section on insulin. This part fills in the chains from the receptors to the DNA and describes the processes which regulate the chains and switch them off after they've done their jobs.
   
   The choice of emphasis in the second part allows the authors to spend some time on cancer. Failure in the growth factor pathways can cause cells to proliferate out of control; failure in cell adhesion can result in metastasis. Accordingly, there are sections on the cell cycle, the transformations of cancer cells, and apoptosis.
   
   (For more details, click above on "See all Editorial Reviews".)
   
   I said that I am not a scientist, but that doesn't mean that Signal Transduction is a book for beginners. The reader must have some experience with molecular biology diagrams in which symbols stand for molecules that are interacting with each other. Some biochemistry is required, though not a lot. The reader will need to know what amino acids, lipids, and nucleotides are. If you're unsure if this is the level for you, it might help you to click on my name above and read the "In My Own Words" part of my profile and to click on "Read all my reviews" to get some idea of what I've been reading. Signal Transduction isn't the most advanced book that I've read, but it's more advanced than most.
   
   The book jacket calls this book a "text reference" and a "valuable resource". That is the right way to see it; I have already used it to help me understand some articles on the Internet. But I also recommend that you read the book at least once all the way through, both to get the lay of the land and to enjoy this fine book.
   
   I mentioned that cell signaling is very important in evolutionary developmental biology ("Evo-Devo"). For any reader interested in that subject, I highly recommend Sean Carroll's From DNA to Diversity. If you are interested in evolution, note in Signal Transduction how enormous complexity comes about through duplication and modification of genes; indeed, whole transduction chains can be regarded as modules that are duplicated with modification.
   
   If you want to know more about what happens at the other end of the chain, at the DNA, I recommend Molecular Biology of the Gene by Watson, et al. If you want to know more about cancer, there is an excellent elementary book, Molecular Biology of Cancer, by Lauren Pecorino; this book helped prepare me for Signal Transduction.

2 comments about Physics and the Art of Dance: Understanding Movement.

1. The question of how a knowledge of the science behind the movement of the human body helps students of dance learn to dance better is always discussed. Like the author, I too am both a physicist and a ballet dancer. I have found that the most important thing to learn in ballet is the imagery that works for you, and sometimes science can actually get in the way. Take walking for example: if we had to analyze ever movement in walking we would never be able to move. I should also point out that science still does not thoroughly understand walking, let alone dancing! Still, it is helpful in some places to understand, at least a little, what is happening in a movement or static pose. This book does a surprisingly fine job of covering most of the pertinent topics and some topics you would not have thought of asking about. I liked the fact that the author does not over simplify some topics, which is often done in elementary explanations. Science usually tries to abstract and simplify in order to explain phenomena, but this can lead to problems. Take, for example, the case of static balance on a point. If you approximate the human body as a rigid body, it is impossible to explain stable equilibrium on a point. Rigid bodies can only achieve unstable equilibrium over a point. But human beings are not rigid! In ballet, we can achieve stable balance over a point for an indefinite period of time(it is very difficult and rarely seen in performance but often in ballet class). This book actually mentions this and explains how it is done. It even includes a discussion of how much a cushioned floor will reduce shock to the dancer's joints. Many illustrations and photos are also included. This is the best book available on this subject, and for those who want to explore this topic further, this is the best place to start.



2. I am a teenaged ballet student. I LOVED THIS BOOK. It helped me in my study of ballet in so many ways: understanding, balancing, executing movements, creating the illusions, improving my technique, and on and on. I love how the book is written, because it is easy to understand even if you are not a Physicist (but it also has Scientific material and some pages with the math and physics illustrated in equations, etc., as well). The chapters engage you with a question or puzzle that you have to solve. This makes you want to hurry up to get to the end of each chapter to see if your guesses were correct. You will learn how to create the illusion of floating in your grand jetes. You will learn how dancers suspend their movement that receives a 'gasp' from the audience that happens whenever something is held beyond what seems possible or expected. It is a book I needed in order to get beyond my limits as a dancer.

2 comments about Self-Organizing Maps.

1. The material is presented clearly and comprehensively from the unique perspective of the SOM originator himself. The inclusion of exhaustive references is particularly useful for the prospective researcher, but, at the risk of sounding ungrateful, I'm curious as to why paper titles were not included in the citations? Overall though, a very good reference.



2. This is a wonderfully written, and excellent book. It assumes only minimal background knowledge but imparts a great deal of insight. I love the way that the author describes this area and the connections with deep and beautiful mathematics.

2 comments about Principles of Regenerative Medicine.

1. In the history of scientific literature, especially in the life sciences, there have been a few books that have endured. One was Wilson's Cytology, the other was Dan Mazia's book that established cell biology. The third is this one. Atala and his gang have conspired to compose a dazzling array of facts and factoids about the recurrent problem of biological strategies for healing tissues. While that odious term "stem cells" as opposed to the less emotional "multipotent progenitor cells or MPC" is used with abandon, the purpose of the book is to establish regenerative medicine as a legitimate endeavor. The authors have completed a monumental feat in getting so many contributors to deliver manuscripts on time, and for managing to cover a vast amount of the scientific landscape. Of course. the wary reader will find items of oversight eg, endogenous retroviruses in human and mouse cells, or rigid cytological characterization of the so called "stem cell lines" promoted by a high official who has never studied biology, even at Yale.
   I recommend this hefty book to almost any one who has ever wondered about regrowing an amputated thumb or who actually did study biology.



2. Who would have believed that you could capture the state of this (art) science so well in just 1,448 pages? But that is exactly what the contributors to this book have pulled off. What's more, the editors did a profoundly apt job of mixing the basic biology, biomaterials science and (stem) cell therapy aspects of regenerative medicine. Indeed, the reader is provided a well-integrated vision of this multi-disciplinary field. In terms of star power, well, most everyone who is anyone in this area was a contributor to the work. The book touches on tissue engineering of systems you would expect (Genitourinary, Cardiac and Alimentary systems etc) and some you haven't even thought of lately and in its completeness, there is even a section on Regulations and Ethics. While this book would not be accessible to a medical neophyte, anyone with a working knowledge of anatomy and cell physiology will be able to work out any gaps in understanding with some effort. Let's just say I had to hit Wikipedia a few times while working through this excellent book.
   
   Stephen Quinn, CEO
   Ratner BioMedical Inc.

5 comments about Mathematical Biology II.

1. I thoroughly enjoyed this book. Although a tough read, it is well worth your time and effort. The sections on spots and stripe formation are excellent and quite interesting. An excellent book!



2. A few decades ago mathematical biology consisted mostly of evolutionary and predator-prey models. This has changed dramatically in recent years with the advent of computational biology and gene sequencing projects. The applications of mathematics to biology are now exploding and this book is an excellent example of that. The book could best be described as the application of nonlinear dynamical systems and reaction-diffusion partial differential equations to biology structures and processes. Readers with background in these areas of mathematics will find their ideas applied beautifully in this book. The best sections of the book for me were the discussions of synchronized insect emergence, models of testosterone secretion control, insect dispersal models, calcium waves on amphibian eggs, mammalian coat patterns, models of hallucination patterns in the brain, and modeling the transmission dynamics of HIV. Numerous exercises end each chapter, and the mathematical algorithms can easily be coded in Mathematica or some other high level language. This is a fine addition to the literature on mathematical biology and for the price it is a real bargain.



3. Many reviews here are about the old edition of Mathematical Biology (the softcover one volume, 2nd ed). Recently J.D. Murray split the second edition in two hardcover volumes. Volume 1 discusses mainly models that use Ordinary Differential Equation, while slightly more complicated Math is required for Volume 2. These new books have added topics (modelling of marital interaction, temperature-dependent sex determination, wolf territoriality, etc). While sometimes the model is still very simple and in its inital stages (e.g. marital interaction model), the books show how much biology and applied mathematics intersect, and they make very interesting read.
   There is a certain lack of analysis of the nonlinear cases, so for those who need examples of amplitude equations, different ways of perturbing a linear model, these books are not so good. These books might be too complicated for a bio person with not much mathematical background, but it is very accessible to those with some math background, and are certainly easy for Math or Physics people who want to know more applications to biology.



4. This product was in fabulous condition and was shipped quickly--I recommend the company to all.



5. I bought part I a few years ago. I am an economist interested in using examples from biology to explain and model commercial markets, more as a hobby than as a professional. I recently worked on Lotka-Volterra predator prey models and competitive models (a grey squirrel competing a brown squirrel out of business). I hope to find patterns in time series that are similar to patterns in economic time series. Book I covers this but most of the subject is in book II. With help of the Mathematica package I played with the examples in the book and it worked fine. It is a high level mathematical book and although the approach is pragmatic and well written, this book is primarily written for specialized mathematicians which I am not. However I like these two books very much just because of the mathematical depth. Normally the author decides how deep I will dig into matters, here I can decide myself.

No comments about Quantum Aspects of Life.

5 comments about Life in Moving Fluids.

1. "Life in Moving Fluids" is a well-written and entertaining, as well as technically accurate, introduction to the behavior of fluids. It explains many of the concepts of fluid dynamics in terms of biological examples, and is my first choice of book to recommend to biologists who want to understand the design and behavior of a wide range of plants and animals that live, as most do, in moving air or water -- our two most common fluids.

   That would be quite enough distinction for a book, but the utility of Vogel's book goes farther: it is one of the best introductions to the subject of fluid dynamics for those interested in physics, such as the nature of lift and drag, or the design of buildings or wind tunnels (sometimes the same thing). It also is helpful in physical chemistry where diffusion and convection must be understood -- to say nothing of how fluids move through the pipes and junctures of our equipment.

   I was inspired to write this review because I had just recommended the book to a colleague who was designing a wind tunnel to work at Reynolds numbers in the 10,000 range and whose previous sources were from aerodynamicists, whose designs are generally not appropriate at this scale. If you don't know what a Reynolds number is or why it is interesting, this book has the best explanation I've seen. It does not assume that you remember much, it teaches what you need as it goes along.

   Many are the times I've recommended "Life in Moving Fluids" to students and co-workers, and in each case, I have been warmly thanked. This review allows me to thank Dr. Vogel in a practical manner for his outstanding book. He also has a penchant for the occasional pun and keeps a light tone throughout, which makes the book suitable as pleasure reading for those who enjoy the popular science magazines, but don't mind a bit more depth.

   If you work in fields where fluid dynamics counts (see the section on prairie squirrels), or just fly model planes, the book is also a handy refresher/reference work. It'll blow you away.




2. This is a great book to start with when getting in to the field of bio-fluid dynamics. Not only does it explain the basic concepts of fluid dynamics, but it also illustrates a large number of cases where the life different plants and animals are affected by the fluids of their environment and their interior.



3. This is really an excellent book for understanding basic fluid mechanics and physics. Profesor Vogel is a gifted writer and provides a real understanding of the various parameters and equations in fluid flow such as viscosity and turbulance. He writes in a very readable and fun style that makes it much more interesting to read then any standard textbook. And of course his insights into how animals and insects have evolved to take advantage of various fluid environment is the strength of the book. I think if this this book was used in more introductory physics classes that more kids would be turned on to physics because they see the application in the natural world. I highly recommended.



4. I bought this book for my personal collection after frequently using an older edition my professor had. Once I got my copy I was rather dissapointed to realize the section on measuring flow and thermistor construction (the section I REALLY wanted the book for) was not included. There was basically a brief statement saying it could be found in the older edition, but was not included in this one. Bummer.



5. I needed this book for a class. This book is rich in biology and fluid mechanics that it was way over my head. My professor explained things that we needed to know much simplier than this book did.