[Insert poop joke here]

It's rare for me to be reading just one book at a time. Usually I bounce back and forth between at least two—one that I read at my desk or on the couch, and one that I read in my "inner sanctum". It's an unusual book that has me so interested that I'm willing to go searching for it every time I want something to read (or need to use the can). Yet for the time it took to read it, Carl Zimmer's Microcosm: E. Coli and the New Science of Life was essentially glued to my hand. Perhaps it would have been more appropriate, given the subject matter, to only read it on the throne, but it was just too good to be read in mere 15-minute snippets.

First isolated from baby diapers by a German physician in the 19th century, Escherichia coli (and its Mr. Hyde, Shigella) is most famous today for making people sick. Inside our bodies E. coli is a pioneer—one of the first species of bacterium to set up shop inside us, though hardly the last, and in normal circumstances it can provide a protective effect. At the heart of this seeming contradiction is the fact that E. coli has enormous diversity. Much of the fun in reading Microcosm lies in coming to understand how that could be so, given that this lowly microbe mostly reproduces by binary fission.

As a structural biologist, I frequently use liters of E. coli—primarily a strain called BL21(DE3). One thing Zimmer notes is that E. coli is absolutely essential to modern molecular bioscience. Its ability to produce the DNA and proteins we need for research makes this lowly bacterium one of our greatest investigative tools. Biomolecular NMR as we know it owes as much or more to the humble microbe (and its willingness to grow thickly in nutrient-poor media) as it does to men like Wüthrich and Bax.

Those who, like myself, primarily know E. coli as a tool for bioscience will recognize several names along this little tour, and learn a great deal about how it came to be such a powerful resource for us. Many will be surprised to learn how controversial some activities we take for granted (transfection of exogenous genetic material into bacteria, for example) were 20-30 years ago. Readers who have very little biology background need not fret, of course. Carl Zimmer is an excellent writer who introduces all the material carefully. Only some very basic knowledge about DNA, proteins, and bacteria is necessary. Zimmer will carry you the rest of the way, from bacteriophages and flagella all the way to synthetic biology, GM crops, and gene circuits.

Whether you work with E. coli every day or just cringe when you hear those words on the evening news, Microcosm will be an engaging, rewarding, and informative read.

While you wait for a chance to go to the bookstore (or for delivery, if like me you use Amazon all the time) check out Carl Zimmer's blog, The Loom, at ScienceBlogs.

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Arieh Ben-Naim's Mystifying Decisions

I recently read Arieh Ben-Naim's book Entropy Demystified, a book I feel would have benefitted greatly from being more somewhat more focused on the task of explaining entropy than it actually was. While Ben-Naim, as promised, does a good job of reducing the second law of thermodynamics to "plain common sense", he makes confusing decisions to include arguments better meant for experts and diatribes that serve nobody. As a result I feel the book, though largely useful, may ill-serve the lay audience for which it is apparently intended, especially as regards the areas where non-scientists are most likely to encounter the concept of entropy.

In my view, the purpose of a popular book on a scientific subject is twofold. First, it should provide readers with enough good science to understand the subject as it appears (if it appears) in their lives. Second, it should provide the lay reader with a framework that allows him to interpret the words of experts. That is, the reader should come away with an understanding of what scientists mean by (in this case) entropy. Thus, popular books on any subject are not a reasonable platform to argue for paradigm shifts. First of all, you're not talking to your target audience (i.e. experts) when you do this. Second of all, the lay readers that agree with you will now be thinking of the subject in a very different way than most of the scientists they will encounter. So not only do you fail at what you're intending to do in terms of serving your new paradigm, you also fail at one basic task of the popular science book. The unfortunate thing with Ben-Naim's book is that it fails at the second task and ends up with mixed results on the first, for no real reason. He could have done just as good a job explaining entropy without introducing the new paradigm at all.

Entropy, despite its importance, is not a topic that lay people encounter very often. The transfer of heat from warmer to cooler bodies is a common example, as is the diffusion of dye in a liquid, or the mixing of two liquids or gases. Ben-Naim does an excellent job of explaining the role of entropy in these processes, building up from relatively simple dice games to complex discussions about temperature and gaseous mixtures. However, he does not do any job at all of explaining the role of entropy in reactions. Consequently, he fails to explain how apparent counteractions to entropy occur. A layman reading this book will understand why a gas expands, but not why it was possible to compress it in the first place. Also, Ben-Naim's approach and focus on mixtures and the like will also leave the reader utterly unprepared to encounter discussions of entropy in connection to the hydrophobic effect. Could the framework here introduced be extended to explain micelle formation and protein folding? I don't doubt that this is so, but Ben-Naim doesn't do it, to the detriment of the book and its readers.

What's Ben-Naim doing with all this space that he's not using on talking about the role of entropy in chemical reactions? Well, he's arguing for a view of entropy based on information, specifically defining entropy in terms of "missing information". Although this position has some merits, this book is an entirely inappropriate place to make the case for it. Why? The most pervasive popular misuse of the second law of thermodynamics is in creationist canards about the thermodynamic impossibility of evolution. These misinterpretations often rest on ideas related to information (as colloquially used) or distortions of information theory. Although Ben-Naim repeatedly states (correctly) that information has a precise scientific meaning, he never graces his readers with it. I fear this leaves them more vulnerable to creationist distortions than before they started reading. That Ben-Naim says little to emphasize the meaning of "closed system" or the other parts of thermodynamics exacerbates the problem. The discussion of information was not strictly necessary to his overall point—his excellent introduction of probability would have sufficed—and it is easily misread and misused. In my opinion, he should have held his tongue here and allowed his book targeted at the academic audience (A Farewell to Entropy: Statistical Thermodynamics Based on Information) to make the case.

Ben-Naim also devotes pages and pages to complaints about other authors' (Atkins particularly comes in for criticism) presentations of entropy. These sections contain a few good ideas, but on the whole read like petulant complaints about more popular writers. That these pages serve any real purpose at all is debatable; that they weaken Ben-Naim's case is certain. No matter how much he disagrees with these authors it would be better for him to disregard them and focus on constructing his own case than deconstructing their books. I agree with him that science writers are too eager to portray entropy as mysterious, but clearing up the mystery is sufficient. His detailed rebuttals of their language are unnecessary.

It's a pity, because Ben-Naim really does pack in some useful and important concepts. Strip away the unnecessary information theory, and his book does an excellent job of reducing the law of entropy to common sense. Entropy Demystified explains what entropy actually means for certain physical systems, and excels at building this picture up from very simple games that anyone can intuitively understand and model. That said, Ben-Naim does not tie entropy into real processes nearly as well as he could, and his insistence on representing entropy in a way that has not yet gained mainstream acceptance may mitigate his readers' ability to apprehend what scientists are saying about the subject. Moreover, the fact that this alternative presentation is "entropy as missing information" is more likely to perpetuate misunderstandings about entropy (especially with regard to evolution) among the lay audience than to clear those misunderstandings up. As such, I cannot recommend this book, despite its virtues.

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