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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. Advances in technologies not only provided maps of E. coli's genome, it was found the genome could be tampered with successfully. Genes could be removed and inserted. So long as the basic life-support genes were left unscathed, E. coli would merrily perform for the scientists. Viruses might be resisted or even ousted after an infection. More astonishing to early researchers, it was seen that E. coli could pick up genes from a virus or other microbes and change its own genome. Today, there are those contending viruses inserting genes into DNA have driven evolution itself. Why do we have over 3 billion base pairs in a genome with only 18 thousand working genes? Invading viruses in our ancestors - and those of E. coli - have left traceable remnants.

The author doesn't confine himself to accounts of laboratory research and analyses. E. coli research has led to numerous social and even legal questions. The latter is best revealed in a lively account of the recent trial in Dover, Pennsylvania. There, a school board insisted on biology teachers reading a challenge to Darwin's theory of evolution by natural selection. The board demanded the adding of elements of the "intelligent design" proposal to the course. Zimmer's account of the testimony and witness exchanges resulted in the presiding judge dismissing "ID" as based on fallacious assumptions and bearing no scientific credibility. The social questions are broader and of greater concern. Forty years ago, as the potential for E. coli as a working tool to manipulate genetic information emerged, public outcry and researchers' own reflections on possibilities led to a brief interruption in "genetic engineering" efforts. With various safeguards in place, Zimmer explains, advances continued. He notes that fears about things like "Frankenfood" are generally baseless, given the long history of Nature's own tinkering with genetic processes. An informed, reasoned approach is required to determine which claims for benefits are possible and which threats, if any, need further addressing. He even manages to address issues in "exobiology", the prospect of either finding life on another planet, or introducing it there.

The wide sweep of topics, thoroughly and effectively addressed by this author make this book a treat to read and an asset to retain. It's Pulitzer or Aventis Prize material and deserves the highest recognition. [stephen a. haines - Ottawa, Canada]
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HALL OF FAMEon July 2, 2008
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 Intelligent Design advocate Michael Behe's concept of "Irreducible Complexity", and how this "proof" was demolished effectively by prominent Intelligent Design critic Ken Miller during the 2005 Kitzmiller vs. Dover Area School District trial.
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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 to build flagella. Scientists can't say for sure that flagella were built in one certain way, but if the proposed steps of building reasonably come from the data, there is no reason to think that a deity somehow took pity on immobile bacteria and miraculously equipped them with motors.

"I look at life through a lens made of _E. coli_," writes Zimmer, and writes convincingly about how biologists are doing the same. Not only was the _E. coli_ genome among the first to be completely deciphered, they have been used to help understand how genes switch on and off. They are a foundation point for the study of molecular and now synthetic biology. They do a lot of the things we do. They sense nutrition molecules and go for them; they sense unattractive chemicals and run from them. They cooperate with other _E. coli_ and have a social life; they are not the loners scientists had originally thought, but can build their own microbial city. They have a type of chemical warfare that they deploy against enemies. They have a sex not in the way we do, but in their own way. They fight viruses and have virus-injected coding on their DNA just as we do. Zimmer frequently refers to the famous remark of biologist Jacques Monod, who said, "What is true for _E. coli_ is true for the elephant." There is hyperbole there, of course, but in one example after another, Zimmer's clear and enthusiastic prose beautifully demonstrates a biological and evolutionary universality.
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on May 26, 2008
It would have been easy to make this book very dry, and the author did an excellent job of balancing scientific detail with a good narrative. It includes just enough components of history and science to be complete without over-doing either area.

The author takes us from the isolation of E. coli in 1885 to, for example, current debates over how some mutations help bacteria survive environmental stress. Between these two benchmarks the author weaves a well-written story that covers what is known about E. coli and other bacteria. More importantly, he also explains why we know what we know. Of perhaps the greatest worth is the book's coverage of why natural selection is such an important scientific concept, using drug resistance as one of many examples.

A nice read for either the interested layperson or the professional.
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on May 21, 2008
The word and the organism, E. coli, can strike fear in the hearts of many. Food poisoning outbreaks! Drug resistance! Of course the organism is also a necessary part of human life. Without the colonization of "good" E. coli, our bodies could well be overrun by pathogens. But even removing those two sides of the equation, there is still so much more to this little microbe than being either the death or salvation of us. This single-celled organism is more like us than most people imagine and has provided insight into many of life's mysteries.

What we know about DNA basically originated in studies of E. coli. What we know about mutations and adaptations we first learned in E. coli. What we know of drug resistance began in E. coli. Protein folding, viruses, the internet and "noise" each have an understanding somewhat due to E. coli. We can even get E. coli to make stuff for us that it has no reason to make other than we told it to. Who knows, it may soon be the cure for cancer. That's one impressive creature.

Microcosm is a well-written and fascinating look at a creature that has a bad rap, considering all it has taught us. Zimmer does an awesome job of storytelling the history behind each of the discoveries, and part of the book, particularly the beginning of each chapter, are very easy to read. However there are often details that I found hard to follow, which surprised me considering I studied and did research with E. coli for several years.

I almost wonder if my history did more to hinder my reading and if someone with less knowledge on the subject matter would enjoy the book more. He also leans heavily towards the old-earth Darwinian point of view, so people hypersensitive to evolutionary beliefs might want to be aware of that. In my experience, though, people of faith in the sciences have mostly learned to take evolutionary discussion in stride, and his approach isn't "in your face" so much as "matter of fact." Whether readers want to agree with his fact is up to them.

Armchair Interviews agrees.
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on August 12, 2008
First, Carl Zimmer is an excellent writer. He seems to have done his homework thoroughly. The book is rich and rewarding, and much appreciated.

I will make two suggestions. One, a glossary would be very helpful. The lay reader (his intended audience) is not very familiar with the arcane biological types that are continuously bantered about. A glossary would not be difficult to produce, or too lengthy to add. I'm really curious as to why a glossary was not added because it seems such an obvious thing to do.

Two, along the same lines, a chart or diagram to display major kinds of microcosms, maybe a sort of tree branching. It would let a lay reader visualize the different branches of bacteria, viruses, e-coli and variations (perhaps evolutionary branching, and a time scale - that would be wonderful), etc.

I write this review after having read about 90% of the book, but continue to be frustrated by the above two absences.

Nevertheless, a very worthwhile book. I highly recommend it, especially if Mr. Zimmer and his publisher would make the two additions on the next printing.Microcosm: E. coli and the New Science of Life
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on February 25, 2009
Hi, this is Joanne, a bioengineering instructor at the University of Illinois. I read science books and review them. [...]

As someone who teaches high level biology courses at a University, I wondered what I could possibly learn from a book like this....What I learned is that everything it took me many years to learn could be explained succinctly and beautifully in less than 200 pages. Amazing!
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on August 17, 2008
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?
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on May 23, 2008
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.
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on January 26, 2014
This book is a fascinating story about how we have learned about how genetics and cells work within our own bodies by studying one of the simplest forms of life, a bacteria called E, Coli. This bacteria is present in all of us and by studying it, we are learning about ourselves. As other reviewers have said, this could be a very boring and dry account of science, but it is far from it. It gives the history of mankind's study of the bacteria, what we have learned from it, and how we have applied that knowledge to other fields of study.

This is the kind of science book that should come out every 5 to 10 years to help keep the lay person up to date on what is going in the fields of scientific discovery, particularly the life sciences, to see what we are discovering and how it applies to us as persons. This is the type of book which explains the field so the common person can understand without having to have a college degree in life sciences.

I would recommend this book to anyone who enjoys reading about science and is curious about how all the microorganisms that are contained in our bodies work. Also the discussion about how scientists determined how genes affect certain traits and how this was determined is good for those interested in genetics.
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