Within days of being born, we are infected with billions of E. coli. They will inhabit each and every one of us until we die. E. coli is notorious for making people gravely ill, but engineered strains of the bacteria save millions of lives each year.
Despite its microscopic size, E.coli contains more than four thousand genes that operate a staggeringly sophisticated network of millions of molecules.
Scientists are rebuilding E. coli from the ground up, redefining our understanding of life on Earth.
In the tradition of classics like Lewis Thomas's Lives of a Cell, Carl Zimmer has written a fascinating and utterly accessible investigation of what it means to be alive. Zimmer traces E. coli's remarkable history, showing how scientists used it to discover how genes work and then to launch the entire biotechnology industry. While some strains of E. coli grab headlines by causing deadly diseases, scientists are retooling the bacteria to produce everything from human insulin to jet fuel.
Microcosm is the story of the one species on Earth that science knows best of all. It's also a story of life itself--of its rules, its mysteries, and its future.
When most readers hear the words E. coli, they think tainted hamburger or toxic spinach. Noted science writer Zimmer says there are in fact many different strains of E. coli, some coexisting quite happily with us in our digestive tracts. These rod-shaped bacteria were among the first organisms to have their genome mapped, and today they are the toolbox of the genetic engineering industry and even of high school scientists. Zimmer (Evolution: The Triumph of an Idea) explains that by scrutinizing the bacteria's genome, scientists have discovered that genes can jump from one species to another and how virus DNA has become tightly intertwined with the genes of living creatures all the way up the tree of life to humans. Studying starving E. coli has taught us about how our own cells age. Advocates of intelligent design often produce the E. coli flagellum as Exhibit A, but the author shows how new research has shed light on the possible evolutionary arc of the flagellum. Zimmer devotes a chapter to the ethical debates surrounding genetic engineering. Written in elegant, even poetic prose, Zimmer's well-crafted exploration should be required reading for all well-educated readers. (May 6) Copyright 2008 Reed Business Information. -- PUBLISHERS WEEKLY.
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May 05, 2008
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Excerpt from Microcosm by Carl Zimmer
I GAZE OUT A WINDOW, a clear, puck-shaped box in my hand. Life fills my view: fescue and clover spreading out across the yard, rose of Sharon holding out leaves to catch sunlight and flowers to lure bumblebees. An orange cat lurks under a lilac bush, gazing up at an oblivious goldfinch. Snowy egrets and seagulls fly overhead. Stinkhorns and toadstools rudely surprise. All of these things have something in common with one another, something not found in rocks or rivers, in tugboats or thumbtacks. They live.
The fact that they live may be obvious, but what it means for them to be alive is not. How do all of the molecules in a snowy egret work together to keep it alive? That's a good question, made all the better by the fact that scientists have decoded only a few snips of snowy egret DNA. Most other species on Earth are equally mysterious. We don't even know all that much about ourselves. We can now read the entire human genome, all 3.5 billion base pairs of DNA in which the recipe for Homo sapiens is written. Within this genetic tome, scientists have identified about 18,000 genes, each of which encodes proteins that build our bodies. And yet scientists have no idea what a third of those genes are for and only a faint understanding of most of the others. Our ignorance actually reaches far beyond protein-coding genes. They take up only about 2 percent of the human genome. The other 98 percent of our DNA is a barely explored wilderness.
Only a few species on the entire planet are exceptions to this rule. The biggest exception lives in the plastic box in my hand. The box-a petri dish-looks lifeless compared with the biological riot outside my window. A few beads of water cling to the underside of the lid. On the bottom is a layer of agar, a firm gray goo made from dead algae and infused with sugar and other compounds. On top of the agar lies a trail of pale gold spots, a pointillistic flourish. Each of those spots is made up of millions of bacteria. They belong to a species that scientists have studied intensely for a century, that they understand better than almost any other species on the planet. I've made this species my guide-an oracle that can speak of the difference between life and lifeless matter, of the rules that govern all living things-bacteria, snowy egret, and curious human. I turn over the dish. On the bottom is a piece of tape labeled "E. coli K-12 (P1 strain)."
I got my dish of Escherichia coli on a visit to Osborne Memorial Laboratories, a fortress of a building on the campus of Yale University. On the third floor is a laboratory filled with nose-turning incubators and murky flasks. A graduate student named Nadia Morales put on purple gloves and set two petri dishes on a lab bench. One was sterile, and the other contained a cloudy mush rich with E. coli. She picked up a loop-a curled wire on a plastic handle-and stuck it in the flame of a Bunsen burner. The loop glowed orange. She moved it away from the flame, and after it cooled down she dipped it into the mush. Opening the empty dish, she smeared a dollop across the sterile agar as if she were signing it. Morales snapped the lid on the second dish and taped it shut.
"You'll probably start seeing colonies tomorrow," she said, handing it to me. "In a few days it will get stinky."
It was as if Morales had given me the philosopher's stone. The lifeless agar in my petri dish began to rage with new chemistry. Old molecules snapped apart and were forged together into new ones. Oxygen molecules disappeared from the air in the dish, and carbon dioxide and beads of water were created. Life had taken hold. If I had microscopes for eyes, I could have watched the hundreds of E. coli Morales had given me as they wandered, fed, and grew. Each one is shaped like a microscopic submarine, enshrouded by fatty, sugary membranes. It trails propeller-like tails that spin hundreds of times a second. It is packed with tens of millions of molecules, jostling and cooperating to make the microbe grow. Once it grows long enough, it splits cleanly in two. Splitting again and again, it gives rise to a miniature dynasty. When these dynasties grow large enough, they become visible as golden spots. And together the spots reveal the path of Morales's living signature.
E. coli may seem like an odd choice as a guide to life if the only place you've heard about it is in news reports of food poisoning. There are certainly some deadly strains in its ranks. But most E. coli are harmless. Billions of them live peacefully in my intestines, billions more in yours, and many others in just about every warm-blooded animal on Earth. They live in rivers and lakes, forests and backyards. And they also live in thousands of laboratories, nurtured in yeasty flasks and smeared across petri dishes.