Microcosm: E. Coli and the New Science of Life

In Microcosm, Zimmer has eloquently condensed a century of scientific study surrounding Eschericia coli into an accurate and flowing story readable by anyone with even just a modest understanding of biology. As Zimmer points out, E.coli has held a central role in microbiology since its first description by German pediatrician Theodor Escherich in the 19th century. This simple bacterium and its various strains have always been there since we first started looking for the microbes involved in human disease. E.coli's normal and pathological roles in the animal body have taught us volumes about the inventive potential of life. The theme running throughout is that E.coli is a microcosm for understanding all of life. Zimmer reinforces this theme with repeated mention of a Jacques Monod quote, "What is true for E.coli is true for the elephant. Most pointedly, E.coli populations offer clues into the nature of cooperation and competition, altruism and spite. And of course no book on E.coli would be complete without re-tracing its role in molecular biology. A long series of discoveries, made with E.coli as the experimental system, have elucidated the mechanisms of DNA replication and transcription, regulation of gene expression, and basic metabolism. Even genetic engineering techniques were pioneered in E.coli, which Zimmer describes in the chapter on "Playing Nature" - a nice twist on the old saying "Playing God," that is actually more appropriate. Then there's the story of E.coli's vast evolutionary potential - from antibiotic resistence to immune evasion tactics, the simple and rapid replication cycle of bacteria have enabled natural selection, ecological niches, and population divergence to be studied over the course of tens of thousands of generations. In the process of his story, Zimmer explains how the bacterial genome is more of a palimpsest rather than an instruction manual - a book that's been written and re-written many, many times. It's that palimpsest that serves as both a history book of how it has been modified from its ancestors, but also as an example of "Open Source" text available to modification by its descendents and accessible to horizontal gene transfer. My only complaints with this book are the obvious: This book presents one perspective, focused on one type of microbe. As such, it misses out on much of bacteriology in favor of molecular genetics, barely mentioning Pasteur and Robert Koch not at all. If Zimmer had included those items in his history lesson, it wouldn't be subtitled "*E.coli* and the New Science of Life" then, would it?

With the trained eyes of a scientist and the soul of poet, eminent science writer Carl Zimmer takes us on an all too brief, yet fascinating, trek into contemporary biology, as seen from the perspective of the bacterium Escherichia coli, in his latest book, "Microcosm: E. coli and the New Science of Life". More than a mere recounting of decades of elegant scientific research from the likes of Joshua Lederberg and Salvador Luria, among others, "Microcosm" is truly a book about contemporary biology itself, tying in almost every facet of it, from systematics to population genetics and ecology, and even, paleobiology. But it is a book that takes such an in-depth exploration of biology from the unique perspective of a rather most unassuming organism - or at least what readers might think - the bacterium E. coli, whose ubiquitous habitats include the intestinal tracts of humans and other mammals. Indeed, E. coli is truly a wonderful organismal metaphor for describing all of biology in its totality, as evidenced, for example, in one of Zimmer's terse chapters devoted to the evolution of cooperation amongst organisms via mechanisms such as natural selection and kin selection; an elegant experimental analogue to the types of selective pressures operating on other, more complex, organisms, including us. Indeed, "Microcosm" ought to be regarded as "Macrocosm", since Zimmer has offered an elegant, often poetic, exploration of all of biology, by demonstrating E. coli's scientific relevance to humanity. If there is indeed one important underlying theme to "Microcosm", then perhaps it is the prevalence of sex in this single-celled organism, and its importance as a key ingredient in understanding evolution, which was recognized decades ago by a young Joshua Lederberg. Zimmer describes how E. coli has demonstrated the veracity of Darwin's concept of natural selection, via an elegant "slot machine" experiment designed by Salvador Luria, and culminating now in the ongoing experiment by microbial ecologist Richard Lenski; Zimmer's engaging account of which is among the most important highlights of this book (Yet as a brief aside, I am surprised Zimmer did not mention that Lenski's research is offering experimental proof of evolutionary stasis, as defined by paleontologists Niles Eldredge and Stephen Jay Gould in their theory of punctuated equilibrium; a point emphasized in a relatively recent paper co-authored by Lenski, Eldredge and others.). Zimmer also devotes ample time touching on other aspects of E. coli's evolutionary ecology from a public health perspective, tracing the origins of epidemics caused by toxic strains of this otherwise benign prokaryote. There is also, regrettably, ample discussion too of creationist interest in E. coli as an example of an organism created by an "Intelligent Designer"; Zimmer notes correctly that creationists were interested in its flagellum years before the bacterial flagellum became important "proof" supporting leading Intel

Inside your gut are maybe a hundred trillion cells. The number is an interesting one, because these cells sitting in your digestive tract outnumber the neurons, muscle cells, and other cells that make "you" by ten to one. In other words, by the numbers, your own cells are a machine that exists to keep a huger number of cells alive in your intestines. Among those trillions of cells is a small population of _Escherichia coli_, one of the world's most important and most studied bacteria. They may be tiny, but they are numerous and they are not simple, and the lessons within _Microcosm: E. coli and the New Science of Life_ (Pantheon) by science writer Carl Zimmer are that there is a complex cosmos of activity within _E. coli_, and there are relationships between one _E. coli_ and its fellow _E. coli_ and the other microbes churning in our guts, and there are relationships between _E. coli_ and the bigger animals that carry it. It is all as complicated as can be; we have come a long way in understanding some of these mysteries, but mysteries still abound. Zimmer's wonderful book keeps us from taking these humble bacteria for granted; as products of the same evolutionary processes that produced us, they have much in common with us. Scientists make _E. coli_ a particular subject of investigation; it was one of the first microbes whose genome was fully mapped (1997). A few strains have toxins, but usually our own _E. coli_ are quietly going about their business and are a help to us. The intricacies of just one cell are astounding. An _E. coli_ has sixty million molecules which have to act just so to keep the bacterium living, and Zimmer examines a few of the intricate feedback systems involved. A team of microbiologists has succeeded in programming a computer with information on 1,260 of its genes and 2,077 of its chemical reactions; a huge program can predict what _E. coli_ will do, for instance, if starved for oxygen, and the model gets it right. But little _E. coli_ has been getting it right for ages. One of its pieces Zimmer pays special attention to is its flagellum, its means of mobility. Zimmer, in several pages devoted to flagella and Intelligent Design, tells again the story of the Dover, Pennsylvania, court decision that Intelligent Design had only religion going for it, not science, and thus could not be taught in public schools. A lawyer at the trial said, "We could probably call this the Bacterial Flagellum Trial", since the flagellum was discussed in detail, and was shown not to be "irreducibly complex", the supposed hallmark of designed systems that cannot be made any simpler and still remain operational. The ID proponents have only an "It's too wonderful not to have a designer" attitude, not experiments or evidence. Zimmer shows how there is within _E. coli_ molecular evidence that flagella are related to other bacterial systems, and that hypotheses built on this evidence show how natural selection was indeed sufficient t

This is an outstanding book. In each chapter, Zimmer exposes a fascinating aspect of biological science, revolving around the study of and lessons learned from E. Coli. This microbe, often maligned in the press, is made an interesting and compelling protagonist in this highly readable book. Some of the descriptions of experiments may be a bit confusing to the lay reader (putting things into centrifuges and seeing what spins out, and how it proves one or another particular theory), but with a bit of concentration those will become clear as well. Highly recommended.

You didn't possess a single one when you were born. Now, there are trillions of them, mostly enjoying the warm hospitality of your gut. If you are recently born, they may have been put into you on purpose. They are the famous/infamous Escherichia coli microbes of our inner selves - billions of them residing peacefully in each of our intestinal tracts. Carl Zimmer has added yet another gem in his crown as North America's premier science writer with this comprehensive and insightful account. Zimmer's talent lies in taking up serious science that deals with complex issues, and then putting it down in a way that seizes and holds your interest. More importantly, he informs you on topics relevant to your daily life - and prompts you to think about future decisions. While the subject may seem off-beat or esoteric, rest assured that "Microcosm" is aptly titled, with a host of life's secrets tucked away in how this microbe lives. The microbe was first identified in 1885 by Theodore Escherich, who was struck by the "massive, luxurious growth" it could achieve. He dubbed it "a common bacteria of the colon", having no idea of its prowess or future role. Renamed Escherichia coli in the following century, the microbe entered an unexpected role in research - from medicine to evolutionary biology. Zimmer stresses this role and its importance in science, technology, business and even government through this account. Understanding those roles is fundamental to understanding the importance of this fine book - and why it's important for you to read it. E. coli long played an enigmatic role in science - it was "discovered" more than once. Microbiology, not unlike palaeoanthropology, was once divided between the "splitters" and the "lumpers". Was each similar but distinct new organism a new species or just a variation on a theme. In E. coli's case, the "lumpers" prevailed and Zimmer explains clearly about "strains" of E. coli and their significance to us. The "K-12" strain is the one chiefly used as a standard for biological research. It's considered harmless to humans - as one researcher demonstrated by drinking a water glass filled with it. On the other hand, not long after Escherich's discovery, a Japanese scientist who was trying to fathom an outbreak of dysentery, isolated a bacterium resembling the German's find. Thinking it a different species, they named it "Shigella". It wasn't a new species, it was a strain of E. coli. That strain "O157:H7" plays a large role in this book because it is a serious disrupter of the human gut. And we brought it into existence. The ubiquitous nature of E. coli and the various strains identified rendered it the workhorse of biological research laboratories. It is easy to modify by changing conditions like food supplies, temperature and assaulting it with viruses or chemicals all provide answers to how it works. In so doing, it also explains to us how life works, and how it likely worked in the past. Adva