Microcosm

by Carl Zimmer

JOHN CAIRNS, THEN AT HARVARD: Cairns, Overbaugh, and Miller, 1988.

  SUSAN ROSENBERG OF BAYLOR COLLEGE OF MEDICINE: Ponder, Fonville, and Rosenberg, 2005.

  NATURAL SELECTION, TENAILLON PROPOSES: Tenaillon, Denamur, and Matic, 2004.

  ANTIBIOTICS MAY ALSO DRIVE THE RISE OF HIGH MUTATORS: Denamur et al., 2005.

  WHEN NOTHING OF THE SORT HAS TAKEN PLACE: Roth et al., 2006.

  SUSAN LINDQUIST OF THE WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH: Queitsch, Sangster, and Lindquist, 2002.

  ICHIRO MATSUMURA, A BIOLOGIST AT EMORY UNIVERSITY: Patrick et al., 2007.

  OTHER SPECIES MAY DEPEND ON THE SAME POTENTIAL: Francino, 2005.

  SOME OF THESE EXTRA GENES: Myllykangas et al., 2006; Roth et al., 2006.

  FEW SCIENTISTS OUTSIDE JAPAN: Watanabe, 1963.

  IN A SURVEY OF E. COLI LIVING IN THE GREAT LAKES: Bartoloni et al., 2006.

  EIGHT: OPEN SOURCE

  AND IN HIS INTESTINES: Fricker, Spigelman, and Fricker, 1997.

  LAWRENCE AND OCHMAN ESTIMATED: J. G. Lawrence and Ochman, 1998.

  IN 2006, OCHMAN AND SEVERAL OTHER COLLEAGUES: Wirth et al., 2006.

  SCIENTISTS COULD THEN COMPARE IT: Perna et al., 2001.

  HORIZONTAL GENE TRANSFER MIGHT HAVE IMPORTED A FEW GENES: Wirth et al., 2006.

  OF ALL THE E. COLI GENES SCIENTISTS HAD NOW IDENTIFIED: Welch et al., 2002.

  THE LIST OF GENES SHARED: Binnewies et al., 2006; Chen et al., 2006.

  IT’S UP TO 11,000 GENES NOW: David Ussery, personal communication.

  VIRUSES IN THE OCEAN TRANSFER GENES TO NEW HOSTS: Sullivan and Baross, 2007.

  OPEN-SOURCE EVOLUTION: Frost et al., 2005.

  JUST AS IMPORTANT AS THE GENES SHIGELLA GAINED: Casalino et al., 2005.

  SCIENTISTS WHO STUDY E. COLI O157:H7: Wick et al., 2005.

  THEY SPECULATE THAT O157:H7’S TOXINS STIMULATE: Ferens, Cobbold, and Hovde, 2006.

  WHEN PROTOZOANS ATTACK E. COLI COLONIES: Meltz Steinberg and Levin, 2007.

  THEY FOUND GENES FOR CELL-KILLING FACTORS: Hejnova et al., 2005.

  IT’S POSSIBLE THAT THE BACTERIA BENEFIT: Gamage et al., 2003, 2004, 2006; Shaikh and Tarr, 2003; Zhang et al., 2006.

  ICHIZO KOBAYASHI, A GENETICIST AT THE UNIVERSITY OF TOKYO: Kobayashi, 2001.

  NINE: PALIMPSEST

  “THE COMPLETE GENOME SEQUENCE OF E. COLI K-12”: Blattner et al., 1997.

  MY FAVORITE IS AN OLD BATTERED BOOK: Chong, 2006.

  CARL WOESE, A BIOLOGIST AT THE UNIVERSITY OF ILLINOIS: Woese and Fox, 1977.

  W. FORD DOOLITTLE, A BIOLOGIST AT DALHOUSIE UNIVERSITY: Doolittle, 2000.

  THE TREE OF LIFE STILL STANDS: Ge, Wang, and Kim, 2005.

  HOWARD OCHMAN CAME TO THIS CONCLUSION: Lerat et al., 2005.

  AT THE CENTER OF THE WHEEL IS THE LAST COMMON ANCESTOR: Ciccarelli et al., 2006.

  CHRISTOS OUZOUNIS AND HIS COLLEAGUES: Ouzounis et al., 2006.

  FOUR BILLION YEARS AGO, EARTH WAS REGULARLY DEVASTATED: Battistuzzi, Feijao, and Hedges, 2004.

  OTHERS LIVE ON THE SIDES OF UNDERSEA VOLCANOES: Hou et al., 2004.

  BUT SOME SPECIES, INCLUDING THE ANCESTORS OF E. COLI: Raymond and Segre, 2006.

  TODAY E. COLI CAN STILL SWITCH BACK AND FORTH: Tomitani et al., 2006.

  TODAY BACTERIA HAVE AN IMPRESSIVE RANGE OF DEFENSES: Matz and Kjelleberg, 2005; Matz et al., 2005.

  THE FEDERAL COURTHOUSE IN HARRISBURG: My account of Kitzmiller v. Dover is based on several sources, including Humes, 2007; Talbot, 2005; and TalkOrigins Archive, 2006.

  “WE WOULD PREDICT THAT WE’D SEE”: Bliss, 1981.

  “TO THE MICROMECHANICIANS OF INDUSTRIAL RESEARCH AND DEVELOPMENT OPERATIONS”: Lumsden, 1994.

  BIOLOGISTS AND MATHEMATICIANS ALIKE: Van Till, 2002.

  “SUCH SYSTEMS SIMPLY DEFY DARWINIST EXPLANATIONS”: Hartwig, 2002.

  “A SINGLE SYSTEM COMPOSED OF SEVERAL WELL-MATCHED, INTERACTING PARTS”: quotations from Behe, 1996, p. 39.

  “IF IT LOOKS DESIGNED, MAYBE IT IS”: quoted in “Intelligently Designed Apparel and Merchandise,” CafePress.com, http://www.cafepress.com/accessresearch/982234; accessed June 27, 2007.

  IN 2005, MARK PALLEN OF THE UNIVERSITY OF BIRMINGHAM: Ren et al., 2005.

  PALLEN AND NICHOLAS MATZKE: Pallen and Matzke, 2006.

  E. COLI’ S CONTROL NETWORKS HAVE AN ANCIENT HISTORY OF THEIR OWN: Cosentino Lagomarsino et al., 2007.

  IN 2006, M. MADAN BABU, A BIOLOGIST AT THE UNIVERSITY OF CAMBRIDGE: Babu and Aravind, 2006.

  ONE OF THE SIMPLEST MEANS: Zinser and Kolter, 2004.

  E. COLI’ S NETWORK GREW IN A SIMILAR WAY: Zhou, Carlson, and Doyle, 2005.

  “THE RNA WORLD”: Gesteland, Cech, and Atkins, 2006.

  IN THE 1990S, RONALD BREAKER, A BIOCHEMIST AT YALE: Barrick and Breaker, 2007.

  HE PROPOSES THAT THE PROFOUND SPLIT: Zimmer, 2006.

  TEN: PLAYING NATURE

  A $75 BILLION INDUSTRY: S. Lawrence, 2007b.

  NOW 250 MILLION ACRES OF FARMLAND: S. Lawrence, 2007a.

  A NEW KIND OF GENETIC ENGINEERING CALLED SYNTHETIC BIOLOGY: Baker et al., 2006.

  BIOTECHNOLOGY WAS BORN MANY TIMES: Bud, 1993.

  THE FIRST NEOLITHIC BIOTECHNOLOGISTS WERE MANIPULATING MICROBES: Mira, Pushker, and Rodriguez-Valera, 2006.

  BY BOMBARDING THE MOLD THAT MAKES PENICILLIN: Adrio and Demain, 2006.

  J.B.S. HALDANE INDULGED IN SOME SCIENCE FICTION: Haldane, 1923.

  AND THOSE TOOLS WOULD EVENTUALLY BE USED: My account of the history of genetic engineering is based mainly on Hall, 2002; Jackson and Stich, 1979; Krimsky, 1982; Rogers, 1977; Singer, 2001; Wade, 1977; Watson and Tooze, 1981; Wright, 1994; and Zilinskas and Zimmerman, 1986.

  SOMEONE HAD ISOLATED GENES: Shapiro et al., 1969.

  “THE STEPS DO NOT EXIST NOW”: quoted in Reinhold, 1969.

  “ARE WE WISE ENOUGH TO BE TAMPERING”: quoted in Krimsky, 1982, p. 35.

  “I DIDN’T WANT TO BE THE PERSON”: quoted in Krimsky, 1982, p. 31.

  “NEW STRAINS OF LIFE—OR DEATH”: Cavalieri, 1976.

  “IT WAS NEVER THE INTENTION”: Watson and Tooze, 1981, p. ix.

  “SCIENTISTS ALONE DECIDED TO IMPOSE A MORATORIUM”: quoted in Jackson and Stich, 1979, p. 101.

  “BY THE YEAR 2000 VIRTUALLY ALL THE MAJOR HUMAN DISEASES”: quoted in Dutton, Preston, and Pfund, 1988, p. 200.

  IN 1977, THE NATIONAL ACADEMY OF SCIENCES HELD A PUBLIC FORUM: National Academy of Sciences, 1977.

  “FROM THE POINT OF PUBLIC HEALTH”: quoted from Cavalieri, 1976.

  “AN IRREVERSIBLE ATTACK ON THE BIOSPHERE”: Chargaff and Simring, 1976.

  “NIGHTMARISH AND DISASTROUS”: Berg and Cohen quoted in Watson and Tooze, 1981, p. 389.

  “WE WERE JACKASSES”: Watson and Tooze, 1981, p. 437.

  “I’M AFRAID THAT BY CRYING WOLF”: Watson and Tooze, 1981, p. 155.

  HUMULIN, ITS MICROBE-PRODUCED INSULIN: Figure from Eli Lilly and Company, “Humulin,” http://www.lillydiabetes.com/product/humulin_family.jsp?reqNavId=5.3; accessed June 27, 2007.

  “THE FIRST SYNTHETIC LIFE FORM”: Service, 2003, p. 640.

  SCIENTISTS HAVE ADDED OVER THIRTY MORE UNNATURAL ACIDS: Wang, Xie, and Schultz, 2006.

  MICHAEL ELOWITZ AT CALIFORNIA INSTITUTE OF TECHNOLOGY: Elowitz and Leibler, 2000.

  THE SECOND REPORT CAME FROM THE LABORATORY OF JAMES COLLINS: T. S. Gardner, Cantor, and Collins, 2000.

  IN 2004, STUDENTS AT THE UNIVERSITY OF TEXAS AND THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO: Levskaya et al., 2005.

  THE DRUG, KNOWN AS ARTEMISININ: M. C. Chang and Keasling, 2006.

  SINCE 2001, DREW ENDY AND THOMAS KNIGHT OF MIT HAVE BEEN BUILDING: Endy, 2005.

  GEORGE CHURCH AND HIS COLLEAGUES HAVE DRAWN UP A LIST: Forster and Church, 2006.

  ALBERT LIBCHABER TOOK AN EVEN SIMPLER APPROACH: Noireaux et al., 2005.

  “BIOTECH HAS ALREADY IGNITED WORLDWIDE PROTESTS”: quoted in ETC Group, 2006.

  THEY FOUND THAT THE BACTERIA RAPIDLY DISAPPEARED:
Bogosian and Kane, 1991; Heitkamp et al., 1993.

  STUDIES SUGGEST THAT EVEN IF AN ALIEN GENE GAVE BACTERIA A COMPETITIVE ADVANTAGE: Nielsen and Townsend, 2004.

  THE INCIDENCE OF TYPE 2 DIABETES HAS DOUBLED: Statistics from U.S. Department of Health and Human Services, Centers for Disease Control and Prevention, “Diabetes Data & Trends,” http://www.cdc.gov/diabetes/statistics/prev/national/figpersons.htm; accessed June 27, 2007.

  CASES OF DIABETES WORLDWIDE HAVE INCREASED TENFOLD: World Health Organization, Media Centre, “Diabetes,” http://www.who/int/mediacentre/factsheets/fs312/en/’ accessed June 27, 2007.

  E. COLI HAS PROVIDED INSULIN: Eli Lilly Company, “Humulin,” http://www.lillydiabetes.com/product/humulin_family.jsp?reqNavId=5.3; accessed June 27, 2007.

  THAT SUGAR COMES INCREASINGLY FROM HIGH-FRUCTOSE CORN SYRUP: Crabb and Shetty, 1999.

  THE COMPANY HAD TO PAY $50 MILLION TO SETTLE CHARGES: Nordenberg, 1999.

  WE MUST RESIST EMPTY FEAR AND EMPTY HYPE: Avise, 2004.

  “THE AFFLUENT NATIONS CAN AFFORD”: Borlaug, 2000, p. 489.

  GOLDEN RICE, A STRAIN OF RICE ENGINEERED: Babili and Beyer, 2005.

  “THIS RICE COULD SAVE A MILLION KIDS A YEAR”: Nash, 2000.

  “IN FIGHTING AGAINST ‘GOLDEN RICE’ REACHING THE POOR”: Potrykus, 2001, p. 1160.

  IT MAY NOT BRING MUCH BENEFIT AT ALL: Krawinkel, 2007.

  VITAMIN A HAS TO BE CONSUMED ALONG WITH DIETARY FAT: Schnapp and Schiermeier, 2001.

  ABOUT 80 PERCENT OF ALL THE TRANSGENIC CROPS: Service, 2007.

  STUDIES INDICATED THAT FARMERS WHO GREW THE TRANSGENIC CROPS: Raney, 2006.

  FARMERS BEGAN TO NOTICE HORSEWEED AND MORNING GLORY: Owen and Zelaya, 2005.

  AND ONCE THE WEEDS EVOLVED THEIR RESISTANCE: Zelaya, Owen, and VanGessel, 2007.

  THEY HAD ENGINEERED PLANTS WITH GENES THAT MAKE THEM RESISTANT: Behrens et al., 2007.

  FARMERS CAN RESORT TO OLD-FASHIONED METHODS: Sandermann, 2006.

  “WE CAN NOW TRANSFORM THAT EVOLUTIONARY TREE”: quoted in Jackson and Stich, 1979, p. 97.

  THE MIT BIOLOGIST JONATHAN KING DECLARED: quoted in Hall, 2002, p. 51.

  “THE GENETIC STRUCTURES OF LIVING BEINGS”: Silver, 2006, p. 287.

  “LET THE EARTH BRING FORTH GRASS”: Gen. 1:11-24 (King James version).

  “THOU SHALT NOT LET THY CATTLE”: Lev. 19:19 (King James version).

  “NEITHER SHALT THOU LIE”: Lev. 18:23 (King James version).

  “USING HUMAN PROCREATION”: Jones, 2006.

  “REPUGNANCE MAY BE THE ONLY VOICE LEFT”: Kass and Wilson, 1998, p. 19.

  PRESIDENT BUSH CALLED FOR A BAN: Bush, 2006.

  “RESPECT FOR HUMAN DIGNITY AND THE INTEGRITY OF THE HUMAN SPECIES”: U.S. Congress, 2005.

  “A THING EITHER IS OR IS NOT A WHOLE HUMAN BEING”: George and Gomez-Lobo, 2005, p. 202.

  E. COLI STARVES AND SUFFERS: Chou, 2007.

  EACH KIND HAS ITS OWN ESSENCE: Gelman, 2004.

  “THE THING IS AN ABOMINATION”: Wells, 1896.

  CONSIDER A GENE CALLED MICROCEPHALIN: Evans et al., 2006.

  “IN A WORLD WHOSE ONCE-GIVEN NATURAL BOUNDARIES”: Kass, 1997.

  AND SOME CHIMERAS WILL PROBABLY BE BANNED: Scott, 2006.

  ELEVEN: N EQUALS 1

  “BUT ITS DOMAIN HAS BEEN LIMITED”: Lederberg, 1963.

  “INVASION FROM MARS? MICROBES!”: Los Angeles Examiner, March 20, 1960.

  “THESE QUESTIONS MIGHT BE ANSWERED IN TWO WAYS”: Lederberg, 1963.

  “WE CAN DEFER OUR CONCERN”: Lederberg, 1960, p. 394.

  NASA AGREED: Dick, 1998.

  “THAT’S THE BALL GAME”: quoted in Dick and Strick, 2004.

  “WE CAN NO LONGER BE CONFIDENT”: quoted in McElheny, 1976.

  SYNTHETIC BIOLOGY BLURS INTO ASTROBIOLOGY: Benner, Ricardo, and Carrigan, 2004.

  PLANETS MAY TRADE BITS OF THEMSELVES: Gladman et al., 2005; Warmflash and Weiss, 2005.

  THE MOST EXTREME FORM OF PANSPERMIA: Napier, 2004.

  IT FLOATS INSIDE THE BODIES OF THE ASTRONAUTS: La Duc et al., 2004.

  “THE FIELD IS HAUNTED BY THINKING”: quoted in Clarke, 2001, p. 248.

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