ALPHABETICAL BRAIN™ VOCABULARY
HUMANIST GALAXY
OF SECULAR SCIENCE STARS
CARL ZIMMER

August 31, 2021

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MICROCOSM:
E. Coli and the new science of life
by Carl Zimmer
Vintage Books, 2009
(243 pages)

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    Quote = "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?" (By the author of the book, Carl Zimmer, from Chapter 1, Signature, page 3)

    Quote = "That is 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 do not 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." (By the author of the book, Carl Zimmer, from the Chapter 1, Signature, page 3)

    Quote = "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." (By the author of the book, Carl Zimmer, from the Chapter 1, Signature, page 3)
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BOOK OUTLINE
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note = Numbers in parentheses refer to pages

1) SIGNATURE (3-5)

2) E. COLI AND THE ELEPHANT (6-31)

3) THE SYSTEM (32-49)

4) THE E. COLI WATCHER'S FIELD GUIDE (50-63)

5) EVERFLUX (64-79)

6) DEATH AND KINDNESS (80-96)

7) DARWIN AT THE DRUGSTORE (97-112)

8) OPEN SOURCE (113-124)

9) PALIMPSEST (125-156)

10) PLAYING NATURE (157-192)

11) N EQUALS ONE (193-199)

ACKNOWLEDGMENTS (201)

NOTES (203-212)

SELECTED BIBLIOGRAPHY (213-228)

INDEX (229-243)

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AUTHOR NOTES, SUMMARY
AND BOOK DESCRIPTION

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AUTHOR NOTES = Carl Zimmer writes about science for The New York Times , and his work also appears in National Geographic , Scientific American , and Discover , where he is a contributing editor. He won a 2007 National Academies Communication Award, the highest honor for science writing. He is the author of five prevcious books, including Evolution: The Triumph of an Idea and Parasite Rex , for which he has earned fellowships from the John Simon Guggenheim Memorial Foundation and the Alfred P. Sloan Foundation. Zimmer also writes an award-winning blog, The Loom. He lives in Connecticut with his wife and children.

SUMMARY = A Best Book of the Year Seed Magazine by Granta Magazine, The Plain-Dealer. In this fascinating and utterly engaging book, Carl Zimmer traces E. coli 's pivotal role in the history of biology, from the discovery of DNA to the latest advances in biotechnology.

BOOK DESCRIPTION = Zimmer reveals the many surprising and alarming parallels between E. coli 's life and our own. And he describes how E. coli changes in real time, revealing billions of years of history encoded within its genome. E. coli is also the most engineered species on Earth, and as scientists retool this microbe to produce life-saving drugs and clean fuel, they are discovering just how far the definition of life can be stretched.

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EDITORIAL BOOK REVIEWS
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PUBLISHER'S WEEKLY REVIEW = 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.

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EXCERPT
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Chapter 1 Signature (pages 3-5)

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 is 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 do not 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 have 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 will 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...

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