Microcosm

by Carl Zimmer

  If alien life were to prove Earth-like, scientists would be faced with two possibilities: Perhaps the same biology emerged independently on different worlds. Or perhaps it went from one world to another.

  Anaxagoras, a Greek philosopher who lived in the fifth century B.C., declared that all life on Earth originated from seeds that pervaded the cosmos. He called the process panspermia. In the twentieth century, Francis Crick and several other prominent scientists revived panspermia in various forms. They suggested that spores had fallen to Earth billions of years ago and given rise to all life. The panspermians met with skepticism because they had no clear evidence that life existed on other planets or that it could survive an interplanetary journey. Panspermia was unsatisfying as a theory, because it did not explain the origin of life. It just pushed the question back.

  Panspermia still meets with skepticism, but scientists now regularly talk about it at conferences without being laughed off the dais. Early in the history of the solar system, large meteorites were crashing into planets quite frequently, launching material out into space. In some cases, that material could have reached other planets. The path from Mars to Earth is particularly easy because the planets are so close to each other and because Mars has a much weaker gravitational field. Even today an estimated fifteen meteorites from Mars land on Earth each year. Planets may trade bits of themselves over far greater distances. A few Earth rocks could travel all the way to the moons of Saturn and Jupiter. In fact, according to one estimate, a rock from Earth might strike Jupiter’s moon Europa once every 50,000 years. To us 50,000 years may be an unimaginably long time, but in the history of the solar system it’s like the patters of a hailstorm.

  If these studies are correct, it’s possible that some E. coli rode a meteorite into space thousands of years ago. For most microbes this sort of journey would be fatal. Many would be destroyed by the harsh interplanetary radiation from which our atmosphere shields us. Still others would die in their blazing descent to another world. But a few microbes might survive. And as Lederberg and his colleagues recognized, it would take only a few microbes to populate a fertile planet. Some scientists have even suggested that these journeys might have kept life from disappearing from the solar system altogether. A big enough impact could boil off the oceans of Earth, leaving it sterilized. It would take millions of years for the water vapor to rain back down and allow a stable habitat to form. Life could hold out during that time on Mars or in some other refuge.

  The most extreme form of panspermia was proposed in 2004 by William Napier, an Irish astronomer. He argued that some rocks lofted from our solar system might fly out of the solar system altogether. Once safely distant from the sun, the microbes they carried would no longer be harassed by ultraviolet radiation. Some of the rocks might wind up on planets orbiting other stars, and a few of the microbes might find a new place to grow. Of course, those planets would be hit by heavenly bodies as well, and their organisms would be passed on to other solar systems. Napier estimates that this interstellar infection could contaminate the entire galaxy in a few billion years.

  Which brings me back to the dish of E. coli I hold up to the sky. On some nights at some places on Earth you can spot the International Space Station through a telescope. E. coli is up there. It floats inside the bodies of the astronauts, swims in their drinking water, and drifts inside droplets that cling to the space station walls. Has E. coli gotten any farther? Lederberg’s worry about contaminating other planets has not gone away. No matter what measures engineers take as they build unmanned probes, it seems that a few hardy species manage to settle on their surfaces.

  “The field is haunted by thinking you’ve detected life on Mars and finding that it’s E. coli from Pasadena,” Kenneth Nealson, a University of Southern California geobiologist, said in 2001.

  I can see Mars rising tonight, an ocher point in the dark. I ignore probability for a moment and imagine E. coli piggybacking on some early Martian probe—perhaps a Russian orbiter that lost control and crashed to the surface. E. coli would not take over the planet. In the cold, radioactive night, without a high-pressure atmosphere to push back against it, it would die. As I look at the ocher point, I think of Mars as a tiny failed colony of E. coli set against a vast, black petri dish. Escherichia coli helped guide us to an understanding of life on Earth. Now it scouts ahead, into the greater living universe.

  ACKNOWLEDGMENTS

  I am grateful to a number of scientists who have opened their labs, picked up their phones, and replied to my e-mails, all in order to teach me about Escherichia coli. They include Mark Achtman, Adam Arkin, M. Madan Babu, Steven Benner, Howard Berg, Mary Berlyn, Ronald Breaker, Sam Brown, George Church, Carol Cleland, James Collins, John Dennehy, Michael Doebeli, John Doyle, Michael Ellison, Thierry Emonet, Drew Endy, Thomas Ferenci, Finbarr Hayes, Peter Karp, Jay Keasling, Frank Keil, Andrew Knoll, Michael Krawinkel, Jan-Ulrich Kreft, Richard Lenski, Hirotada Mori, Kaare Nielsen, Christos Ouzounis, Mark Pallen, Bernhard Palsson, Arthur Pardee, Robert Pennock, Mark Ptashne, Margaret Riley, John Roth, Dean Rowe-Magnus, Jack Szostak, Phillip Tarr, Fred Tenover, Paul Thomas, Jeffrey Townsend, Paul Turner, David Ussery, Alexander van Oudenaarden, Barry Wanner, Daniel Weinreich, and George Williams.

  I would also like to thank scientists and writers who looked over the manuscript or portions of it, including Mark Achtman, Uri Alon, Michael Balter, M. Madan Babu, Les Dethlefsen, Michael Feldgarden, Kevin Foster, James Hu, John Ingraham, Richard Lenski, Nicholas Matzke, Frederick Neidhardt, Monica Riley, and Eric Stewart. Moselio Schaechter was particularly generous with his time. Any errors that survived their careful scrutiny are entirely mine.

  I wish to thank Doron Weber at the Alfred P. Sloan Foundation, which helped fund my research for this book. Thanks go also to my editors at the magazines and newspapers where I first wrote about some of the topics I revisit here: James Gorman and Erica Goode at The New York Times, Tim Appenzeller at National Geographic, David Grogan, Susan Kruglinski, and Corey Powell at Discover, Laura Helmuth at Smithsonian, Bruce Fellman and Kathrin Lassila at Yale Alumni Magazine, Leslie Roberts at Science, and Ricki Rusting at Scientific American.

  My agent, Eric Simonoff, has never lost his fine power of discriminating between good book ideas and bad ones. When I saw him raise his eyebrows at my brief description of how E. coli swims, I realized I might have a good one. My thanks also go to Martin Asher, my editor at Pantheon, and Tadeusz Majewski, my illustrator.

  Finally, there is my family. I thank my daughters, Charlotte and Veronica, for their indulgence while their father spent so much time writing about “the good germ.” And my wife, Grace, provided the perfect blend of moral support and editorial criticism. Without her there would be no book. There would be no point.

  NOTES

  ONE: SIGNATURE

  AND YET SCIENTISTS HAVE NO IDEA: Paul D. Thomas, personal communication.

  THE OTHER 98 PERCENT: Bird, Stranger, and Dermitzakis, 2006.

  THEY BELONG TO A SPECIES: Karp et al., 2007.

  TWO: E. COLI AND THE ELEPHANT

  IT THRIVED ON ALL MANNER OF FOOD: Dolman, 1970; Escherich, 1989.

  “IT WOULD APPEAR TO BE A POINTLESS AND DOUBTFUL EXERCISE”: Escherich, 1989, p. 352.

  “WE MAY SAY IN PLAIN WORDS”: Delbrück, 1969.

  “FROM THE ELEPHANT TO BUTYRIC ACID BACTERIUM”: quoted in Friedmann, 2004, p. 47.

  BUT BACTERIA SUCH AS E. COLI: Brock, 1990; Judson, 1996.

  MANY RESEARCHERS LOOKED AT BACTERIA: Brock, 1990.

  “THE TERM ‘GENE’ CAN THEREFORE BE USED”: quote from Gray and Tatum, 1944, p. 410; see also Tatum and Lederberg, 1947.

  “THE LONG-SHOT GAMBLE”: Lederberg, 1987, p. 26.

  “HOORAY ”: Lederberg, 1946.

  “BACTERIAL VIRUSES MAKE THEMSELVES KNOWN”: quoted in Judson, 1996, p. 33.

  THEY CALLED THEMSELVES THE PHAGE CHURCH: Stahl, 2001.

  IT WAS SOMETHING CALLED DEOXYRIBONUCLEIC ACID: Avery, MacLeod, and McCarty, 1979.
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  “SO STUPID A SUBSTANCE”: quoted in Judson, 1996, p. 40.

  HERSHEY AND CHASE CONFIRMED HIS CONCLUSION: Hershey and Chase, 1952.

  “A POWERFUL NEW PROOF”: Watson, 1969, p. 119.

  “THE UNTWIDDLING PROBLEM”: quoted in Holmes, 2001, p. 78.

  DELBRÜCK TRIED TO ANSWER THE QUESTION: Delbrück, 1954.

  THE MOST BEAUTIFUL EXPERIMENT IN BIOLOGY: Meselson and Stahl, 1958.

  AT THE CARNEGIE INSTITUTION: R. B. Roberts, 1955.

  “AN ESSENTIALLY UNIVERSAL CODE”: Marshall, Caskey, and Nirenberg, 1967, p. 826.

  “TODAY, WE ARE LEARNING THE LANGUAGE”: Clinton, 2000.

  MANY BIOLOGISTS HAVE SPENT THEIR CAREERS: Echols, 2001; Neidhardt, 1996; Schaechter, Ingraham, and Neidhardt, 2006.

  AN ENORMOUS PRESSURE INSIDE E. COLI: Norris et al., 2007.

  TO UNCOVER ITS PATHWAYS: Sauer, Heinemann, and Zamboni, 2007.

  E. COLI NEEDS IRON TO LIVE: Andrews, Robinson, and Rodriguez-Quinones, 2003; Wandersman and Delepelaire, 2004.

  SUNLIGHT STRIKES THE PLANET: Michaelian, 2005.

  THE FIRST SCIENTIST TO GET A GOOD LOOK: Berg, 2004.

  WHERE THEY ACT LIKE A MICROBIAL TONGUE: Thiem, Kentner, and Sourjik, 2007.

  ASTONISHINGLY TINY CHANGES IN THE CONCENTRATION OF MOLECULES: Bray, Levin, and Lipkow, 2007.

  IT MAY BE MORE LIKE A BRAIN: M. D. Baker, Wolanin, and Stock, 2006.

  WITH SOME LOOSE DNA TOSSED IN LIKE A BOWL OF TANGLED SPAGHETTI: Harold, 2005.

  TO DIVIDE ALL OF LIFE INTO TWO GREAT GROUPS: Sapp, 2005.

  HOW E. COLI ORGANIZES ITS DNA: Higgins, 2005; Thanbichler and Shapiro, 2006; Willenbrock and Ussery, 2004.

  YET E. COLI CAN DO ALL OF THAT: O’Donnell, 2006.

  TWO NEW CHROMOSOMES FORM: Jun and Mulder, 2006; Norris et al., 2007; Thanbichler and Shapiro, 2006; Woldringh and Nanninga, 2006.

  A PROTEIN CALLED FTSZ: Bernhardt and de Boer, 2005; Goehring and Beckwith, 2005; Margolin, 2005.

  INSTEAD, E. COLI SLAMS ON THE BRAKES: D. E. Chang, Smalley, and Conway, 2002; Higgins, 2005; Nystrom, 2004.

  THREE: THE SYSTEM

  ONE DAY IN JULY 1958: Jacob, 1995.

  IT WOULD TAKE YEARS OF RESEARCH: Müller-Hill, 1996.

  IN ANIMALS LIKE OURSELVES: Ben-Shahar et al., 2006.

  SCIENTISTS HAVE CONTINUED TO PAY CLOSE ATTENTION: Alon, 2007.

  IT ACTS AS A NOISE FILTER: Kalir, Mangan, and Alon, 2005.

  FEED-FORWARD LOOPS ARE UNUSUALLY COMMON IN NATURE: Milo et al., 2002.

  HE AND HIS COLLEAGUES BEGAN TO ANALYZE ITS HEAT-SHOCK PROTEINS: Kurata et al., 2006.

  BERNHARD PALSSON, A BIOLOGIST AT THE UNIVERSITY OF CALIFORNIA, SAN DIEGO: Feist et al., 2007.

  WHY DOES IT CHOOSE AMONG THE BEST FEW?: Trinh et al., 2006.

  THE PICTURE THEY SEE: Ma and Zeng, 2003; Sauer, 2006.

  THE BOW TIE ARCHITECTURE IN E. COLI: Csete and Doyle, 2004; Doyle and Csete, 2005; Doyle et al., 2005; Tanaka, Csete, and Doyle, 2005; Zhou, Carlson, and Doyle, 2005.

  DANIEL KOSHLAND, A SCIENTIST AT THE UNIVERSITY OF CALIFORNIA, BERKELEY: Spudich and Koshland, 1976.

  AARON NOVICK AND MILTON WEINER: Novick and Weiner, 1957.

  SOME MICROBES WERE DARK: Elowitz et al., 2002.

  THEY TURN OUT TO BE RESPONSIBLE: Ozbudak et al., 2004.

  THEY SPEND MOST OF THEIR TIME SLIDING UP AND DOWN THE MICROBE’S DNA: Elf, Li, and Xie, 2007.

  E. COLI WILL PULL METHYL GROUPS OFF ITS DNA: Lim and van Oudenaarden, 2007.

  SOME OF THE FACTORS THAT SPIN THE WHEEL: Raser and O’Shea, 2005.

  THE FIRST CLONED KITTEN, WHICH THEY NAMED CC: Shin et al., 2002.

  FOUR: THE E. COLI WATCHER’S FIELD GUIDE

  AN ISLAND VOLCANO CALLED KRAKATAU: For an excellent account of the history and ecology of this eruption, see Thornton, 1996.

  TO MICROBES, A NEWBORN CHILD IS A KRAKATAU: Dethlefsen et al., 2006.

  E. COLI IS A PIONEER: Wolfe, 2005.

  “A ZEN-LIKE PHYSIOLOGY”: J. W. Foster, 2004.

  THE HAIRS BRING E. COLI TO A HALT: Thomas et al., 2004.

  THE WARMTH OF THE GUT: White-Ziegler, Malhowski, and Young, 2007.

  AT LEAST FOR A FEW DAYS: Favier et al., 2002; H. K. Park et al., 2005.

  THIS ECOSYSTEM E. COLI HELPS TO BUILD: Dethlefsen et al., 2006.

  E. COLI MAKES THE GUT RELIABLY COMFORTABLE: Jones et al., 2007.

  WE, TOO, DEPEND ON OUR MICROBIAL JUNGLE: Backhed et al., 2005; Nicholson, Holmes, and Wilson, 2005.

  IN 2003, JEFFRY STOCK AND HIS COLLEAGUES: S. Park et al., 2003.

  SWARMING ALLOWS E. COLI TO GLIDE ACROSS A PETRI DISH: Inoue et al., 2007; Zorzano et al., 2005.

  E. COLI CAN ALSO SETTLE DOWN: Beloin et al., 2004; Domka et al., 2007; Reisner et al., 2006.

  A CLOUDY LAYER OF SCUM ON THEIR FLASKS: Ghannoum and O’Toole, 2004.

  ON THE INNER WALLS OF OUR INTESTINES: Bollinger et al., 2007.

  KNOWN AS COLICINS: Cascales et al., 2007.

  THERE ARE MANY PREDATORS WAITING TO DEVOUR E. COLI: Meltz Steinberg and Levin, 2007.

  OTHERS, SUCH AS THE BACTERIA BDELLOVIBRIO: Lambert et al., 2006.

  THE BACTERIA MYXOCOCCUS XANTHUS RELEASE MOLECULES: Shi and Zusman, 1993.

  LETS IT FEED ON MANY CARBON-BEARING MOLECULES—EVEN TNT: Stenuit et al., 2006.

  IN AUSTRALIA, FOR EXAMPLE: Power et al., 2005.

  E. COLI ALSO COMES IN FORMS THAT CAN SICKEN OR KILL: The best overall recent survey of pathogenic E. coli is Kaper, 2005.

  JOHN BRAY, A BRITISH PATHOLOGIST: Bray, 1945.

  WHEN SCIENTISTS COULD EXAMINE SHIGELLA’ S GENES LETTER BY LETTER: Wirth et al., 2006.

  SHIGELLA ALONE STRIKES 165 MILLION PEOPLE EVERY YEAR: Sansonetti, 2006.

  FOR ALL ITS NOTORIETY: My account of E. coli O 157: H7 is drawn from Elliott and Robins-Browne, 2005; Karch, Tarr, and Bielaszewska, 2005; Naylor, Gally, and Low, 2005; Pennington, 2003; Rangel et al., 2005; Tarr, Gordon, and Chandler, 2005; and Varma et al., 2003.

  IN SEPTEMBER 2006, CONTAMINATED SPINACH: U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, 2006.

  ONCE THEY’VE FORMED A LARGE ENOUGH ARMY: Walters and Sperandio, 2006.

  IT WANDERS: Jennison and Verma, 2004.

  THEY OPEN UP MORE GAPS: Gorvel, 2006.

  FIVE: EVERFLUX

  “ONE MAY PERCEIVE”: Lamarck, 1984, p. xxx.

  AN ITALIAN REFUGEE SAT IN A COUNTRY CLUB: Luria, 1984; Luria and Delbrück, 1943.

  THEY COLLABORATED WITH SCIENTISTS: Luria, Delbrück, and Anderson, 1943.

  BUT WHEN LURIA AND DELBRÜCK FIRST PUBLISHED THE EXPERIMENT: Davis, 2003.

  THE CONTROVERSY DID NOT DIE: Lederberg and Lederberg, 1952.

  THEY SET OUT TO OBSERVE E. COLI: Zimmer, 2007b.

  ONE OF THOSE SCIENTISTS WAS RICHARD LENSKI: The sources for my descriptions of Lenski’s work include Crozat et al., 2005; Elena and Lenski, 2003; Lenski, 2003; Ostrowski, Rozen, and Lenski, 2005; Pelosi et al., 2006; Remold and Lenski, 2004; Rozen, Schneider, and Lenski, 2005; Schneider and Lenski, 2004; Travisano et al., 1995; Woods et al., 2006.

  BERNHARD PALSSON AND HIS COLLEAGUES: Herring et al., 2006.

  A ROUGHLY 1-IN-10,000 CHANCE: Perfeito et al., 2007.

  “YOU PRESS THE REWIND BUTTON”: Gould, 1989, p. 48.

  IN THE EARLY 1990S, JULIAN ADAMS: Adams, 2004; Spencer et al., 2007.

  MICHAEL DOEBELI AND HIS COLLEAGUES: Spencer et al., 2007.

  IN LAKE APOYO: Barluenga et al., 2006.

  SIX: DEATH AND KINDNESS

  IN ORDER TO BE MORAL: Sapp, 1994, p. 21.

  HIS ESSAYS WERE EVENTUALLY PUBLISHED: Kropotkin, 1919, p. 17.

  YET ROBERTO KOLTER OF HARVARD AND A FORMER STUDENT: Vulic and Kolter, 2001.

  GEORGE WILLIAMS, AN EVOLUTIONARY BIOLOGIST: Zimmer, 2004.

  IN HIS 1966 BOOK, ADAPTATION AND NATURAL SELECTION: Williams, 1966.

  ANOTHER YOUNG BIOLOGIST, WILLIAM HAMILTON: Segerstrale, in press.

  E. COLI SUPPORTS THEIR VIEW
OF LIFE: West et al., 2006.

  CHEATERS CANNOT MARSHAL THESE DEFENSES: K. R. Foster, Parkinson, and Thompson, 2007.

  JOAO XAVIER AND KEVIN FOSTER: Xavier and Foster, 2007.

  CONFLICT AND COOPERATION STRIKE AN UNEASY BALANCE: Michod, 2007.

  WE CALL THEIR SUCCESS CANCER: Zimmer, 2007 a.

  IT PAYS FOR THE POPULATION TO HEDGE ITS BETS: Mettetal et al., 2006; Wolf, Vazirani, and Arkin, 2005.

  SCIENTISTS DISCOVERED SO-CALLED PERSISTER BACTERIA: Lewis, 2005, 2007.

  A TEAM OF SCIENTISTS LED BY NATHALIE BALABAN: Balaban et al., 2004.

  THAT’S THE THEORY OF KIM LEWIS: Lewis, 2007.

  FOR THE ENTIRE POPULATION OF E. COLI: Kussell et al., 2005.

  A NASTY SORT OF ALTRUISM: A. Gardner, West, and Buckling, 2004; West et al., 2006.

  AS WITH PERSISTENCE: Mrak et al., 2007; Mulec et al., 2003.

  SPITE, SOME EXPERIMENTS NOW SUGGEST: Kerr et al., 2002; Kirkup and Riley, 2004.

  THE COMMON SIDE-BLOTCHED LIZARD: Sinervo, 2001.

  SOME YEARS HE RAN A LITTLE FASTER: Williams, 1999.

  SCIENTISTS STUDIED THE SOCKEYE SALMON: Morbey, Brassil, and Hendry, 2005.

  ERIC STEWART, A MICROBIOLOGIST NOW AT NORTHEASTERN UNIVERSITY: Stewart et al., 2005.

  IF IT SPENT ALL ITS RESOURCES ON REPAIR: Ackermann et al., 2007.

  SEVEN: DARWIN AT THE DRUGSTORE

  THE ERA OF ANTIBIOTICS BEGAN SUDDENLY: Levy, 2002; Salyers and Whitt, 2005.

  IN 1948, THE YUGOSLAVIAN-BORN GENETICIST MILISLAV DEMEREC: Demerec, 1948.

  TODAY THE WORLD CONSUMES: Wise and Soulsby, 2002.

  MANY FARMERS TODAY PRACTICALLY DROWN THEIR ANIMALS: Graham, Boland, and Silbergeld, 2007.

  TWO NEW MUTATIONS THAT MADE IT RESISTANT: Robicsek et al., 2006.

  AFTER FIVE MONTHS AND TEN DIFFERENT ANTIBIOTICS: Rasheed et al., 1997; Tenover, 2006.

  MICHAEL ZASLOFF, THEN A RESEARCH SCIENTIST: Shnayerson and Plotkin, 2002.

  HE TEAMED UP WITH BELL: Perron, Zasloff, and Bell, 2006.

  E. COLI AND OTHER BACTERIA ARE LOCKED IN AN EVOLUTIONARY RACE: Peschel and Sahl, 2006.

  FLOYD ROMESBERG, A CHEMIST AT SCRIPPS RESEARCH INSTITUTE: Cirz et al., 2005.