The Tangled Tree
Page 42
a kind of “pabulum”: ibid., 153.
“up to the chemists” to explain: Pollock (1970), 10.
“a bombshell which fell into a fused situation”: Olby (1994), 178.
“had to be practically forced into a taxi”: Pollock (1970), 7.
“There is no consensus of opinion amongst geneticists”: Morgan (1934), 315.
“considered a ‘boring molecule’ or a ‘stupid molecule’ ”: boring: Cobb (2015), 42, 54; stupid: Judson (1979), 59, 63.
“a strange impression” of holy duty seized him: Dubos (1976), 49.
His friends called him “Babe’ ”: ibid., 56.
began to speak of “the transforming principle”: McCarty (1985), 85, 92.
“much more impulsive and impatient”: ibid., 101.
to spray “an invisible aerosol laden with bacteria”: ibid., 104.
no longer “Babe,” far from it, but “the Professor”: Dubos (1976), 4, 62.
“We were not unaware that this idea would be greeted”: McCarty (1985), 143.
“Who could have guessed it?”: Oswald Avery to Roy Avery, May 26, 1943, quoted in Dubos (1976), 218–19.
“This is it, at long last”: McCarty (1985), 171.
“In order that various genes may have the opportunity”: Lederberg and Tatum (1946a), 558.
she detected a system of “sexual compatibility”: Lederberg, Cavalli, and Lederberg (1952), 720; see also “The True History of Fertility Factor F,” Esther M. Zimmer Lederberg Memorial Website,” accessed www.esthermlederberg.com/Clark_MemorialVita/HISTORY52.html, wherein Esther Lederberg asserts her priority of credit.
some sort of “infective hereditary factor”: Lederberg et al. (1952), 729.
alluded likewise to “infective heredity”: Lederberg (1952), 413.
Watanabe called it “an example of ‘infective heredity’ ”: Watanabe (1963), 87.
Its medical significance was “limited to Japan at present”: ibid., 108.
“The discovery of transferable R factors, forty years ago”: Levy (2002), 78–79.
Baker’s team found “intrinsic antimicrobial resistance”: Baker et al. (2014), 1696.
the people of the Solomons were still “an antibiotic virgin population”: Gardner (1969), 774.
a person “from the innermost bush country”: ibid., 775.
“additional VRSA infections are likely to occur”: Miller (2002), 902.
his “great gift” for rubbing people the wrong way: Anthony Tucker, “E.S. Anderson,” Guardian US, last modified March 21, 2006, www.theguardian.com/society/2006/mar/22/health.science.
“is their possible importance in bacterial evolution”: Anderson (1968), 176.
“the temptation is very strong to suggest”: ibid.
“This in turn could favor extremely reticulate modes”: Jones and Sneath (1970), 69.
“It may well be that gene exchange is so frequent”: ibid.
gives the bacterial entity “a huge available gene pool”: Sonea and Panisset (1983), 112.
They called it a “superorganism”: ibid., 8, 85.
Ford Doolittle called it “bold if inchoate”: Doolittle (2004), in Cracraft and Donoghue (2004), 88–89.
“could be evolutionarily significant in promoting trans-kingdom”: Heinemann and Sprague (1989), 205, abstract.
“Can Genes Jump Between Eukaryotic Species?”: Lewin (1982).
an “apparently fanciful and certainly unorthodox” idea: ibid., 42.
“massive” uploads of alien genes: Gladyshev et al. (2008), 1210, 1213.
also found “many hundreds” of foreign genes: Eyres et al. (2015), 1.
“Arguably,” according to one expert, “the spread of Wolbachia represents”: Werren (2005), 299.
“Hundreds of human genes appear likely to have resulted”: Lander et al. (2001), 860.
“the most exciting news” from the Human Genome Project so far: Andersson et al. (2001), 1.
called the Consortium’s claim “at least an overstatement”: Edward R. Winstead, “Researchers Challenge Recent Claim That Humans Acquired 223 Bacterial Genes During Evolution,” Genome News Network, last modified May 21, 2001, www.genomenewsnetwork.org/articles/05_01/Gene_transfer.shtml.
“fresh skirmish in the genome wars”: Nicholas Wade, “Link Between Human Genes and Bacteria Is Hotly Debated by Rival Scientific Camps,” New York Times online, May 18, 2001.
“I was immediately struck by the fact”: quoted in ibid.
PART VI: Topiary
“Dammit, one of these days”: quoted in letter from Hugo Krubsack to Dennis Krubsack, May 13, 1975, cited in “John Krubsack,” Wikipedia, https://en.wikipedia.org/wiki/John_Krubsack.
ignored the crossovers entirely in his “universal phylogenetic tree”: Woese et al. (1990), 4578, fig. 1.
“shattered,” according to one eminent microbiologist: Norman Pace, quoted in Morell (1996), 1043.
“This completes that basic set,” he told Science: ibid.
“you can’t make sense of these phylogenies”: quoted in Pennisi (1998), 2.
“Each gene has its own history”: Robert Feldman, quoted in ibid., 3.
“the last resort of the impoverished imagination”: Doolittle remembers: email to DQ, February 5, 2017.
“Extensive gene transfer,” Brown and Doolittle wrote: Brown et al. (1994), 575.
“The impulse to classify organisms is ancient”: Doolittle (1999), 2124.
He called it the “current consensus” model: ibid., 2125, fig. 2.
“something quite ominous” about these E. coli results: Martin (1999), 101.
He called this one “a reticulated tree”: Doolittle (1999), 2127, fig. 3.
Horizontal gene transfer was “rampant,” he told the readers: Doolittle (2000), 94.
“By swapping genes freely,” he wrote: ibid., 97.
“persuading me of the importance” of HGT: Doolittle (1999), 2128.
They focused on “prokaryote” evolution, using that old word: Gogarten et al. (2002), 2226.
horizontal gene transfer might be the “principal explanatory force”: ibid., 2234.
“too fantastic for present mention in polite biological society”: Wilson (1925), 738–39.
Another . . . discussed the “mosaic” character: Martin (1999), 99.
“quite ominous” to contemplate how HGT must have played out: ibid., 101.
“the tree of 1 percent” of those genomes: Dagan and Martin (2006), 1–2.
what he began calling “the universal phylogenetic tree”: Woese (2000), 8392.
have been called his “millennial series”: Koonin (2014), 197.
“As a cell design becomes more complex and interconnected”: Woese (2002), 8742.
the tree image was “absolutely central” to Darwin’s thinking: Graham Lawton, “Axing Darwin’s Tree,” New Scientist, January 24, 2009.
“There’s a promiscuous exchange of genetic information”: quoted in ibid.
“the uprooting of the tree” as the start of something bigger: ibid.
“What on earth were you thinking”: letter to the editor by Daniel Dennett, Jerry Coyne, Richard Dawkins, and Paul Myers, “Darwin Was Right,” New Scientist, February 18, 2009.
“handing the creationists a golden opportunity”: ibid.
“iconic concept of evolution” that had “fallen on hard times”: Eric Lyons, “Startling Admission: ‘Darwin Was Wrong,’ ” Apologetics Press. www.apologeticspress.org/APContent.aspx?category=23&article=2666.
“turning out to be much more involved”: unsigned editorial in New Scientist, “The Future of Life, but Not as We Know It,” January 24, 2009.
“None of this should give succor to creationists”: ibid.
“the history of life cannot properly be represented”: Doolittle (1999), 2124.
At what point is the “Ship of Theseus”: Doolittle (2004), R176.
It isn’t just an “attractive hypothesis”: Doolittle (2000), 97.
his k
nack with bizarre trees, “I talk to them”: “Axel Erlandson,” Wikipedia, https://en.wikipedia.org/wiki/Axel_Erlandson, quoting from Wilma Erlandson (2001), My Father Talked to Trees, 13.
PART VII: E Pluribus Human
“the ecological community of commensal, symbiotic, and pathogenic”: Lederberg (2001), 2.
“a little white matter, which is as thick”: Leeuwenhoek letter to the Royal Society, September 17, 1683, quoted in “Antony van Leeuwenhoek (1632–1723),” University of California Museum of Paleontology online, www.ucmp.berkeley.edu/history/leeuwenhoek.html.
“Friendship in the kingdom”: the photo appears in Gold (2013), 3206.
“human-associated bacteria”—denizens of the human body: Smillie et al. (2011), 242.
“Taken together, these analyses indicate”: ibid., 242.
“erased the deep ancestral trace” of any uniquely valid: ibid.
called that first ping “the most important email of my life”: Goldenfeld (2014), 248.
“My telephone is 3-9369,” Woese wrote: ibid.
“You may not feel too much at home with biology”: ibid.
“So began a scientific partnership and friendship”: ibid.
The dynamic process involved “non-Darwinian” mechanisms: Vestigian et al. (2006), 10696.
“the coming avalanche of genomic data”: Goldenfeld and Woese (2007), 369.
“Among microbes, HGT is pervasive and powerful”: ibid.
“self-organization” emerging from biological systems: Kauffman (1993), xiii, 22–26.
an “operating system” might have spontaneously taken form: Goldenfeld and Woese (2007), 369.
an “unearthly figure in a full neck brace”: Lewin (2014), 273.
“an unrehearsed statement, a stream of scientific consciousness”: ibid.
Harris Lewin considered himself “an improbable friend”: ibid.
That ended his “isolation” in Morrill: ibid., 275.
“I wanted to do something to honor Carl’s discoveries”: ibid., 276.
“likely to have resulted from horizontal transfer”: Lander et al. (2001), 860.
“an extraordinary trove of information”: ibid.
She called them “controlling elements”: Comfort (2001), 9.
“for her discovery of mobile genetic elements”: ibid., 251, his translation from the Swedish.
“horribly disgusting, to feel numerous creatures”: Keynes, ed. (1988), 315, and n. 1.
“For Carl, winning the Crafoord Prize by himself”: Lewin (2014), 275.
declined to “an engineering discipline”: Woese (2004), 173.
might illuminate “the master plan of the living world”: ibid.
Worse, molecular biology took a “reductionist” perspective: ibid., 174.
“a biology that operates from an engineering perspective”: Woese (2004), 173.
“whose writings I encountered rather late in the game”: Woese (2005), R112.
“jan, you accord darwin so much more substance”: Draft of “Beyond God and Darwin,” in the Woese Archives, University of Illinois, Champaign-Urbana.
“Book 1: Growing Up in Science”: This CVS notebook is in the Woese Archives, University of Illinois, Champaign-Urbana.
“bacteria evolve by leaps and bounds”: Draft of “Beyond God and Darwin,” in the Woese Archives, University of Illinois, Champaign-Urbana.
“The cells that make up our bodies have also not arisen gradually”: ibid.
“Consider too,” Sapp wrote, “that a great percentage of our own DNA”: ibid.
“We made a sort of viral archeology,” Heidmann said: Saib and Benkirane (2009), 4.
genetically modified mice—“knockout” mice: Dupressoir et al. (2005), 730.
clustered regularly interspaced short palindromic repeats: Morange (2015), 221.
These CRISPR-associated genes (cas genes, for short): Jansen et al. (2002), 1565, 1569.
“Modern society knows that it desperately needs”: ibid.
“I rushed to share my out-of-biology experience”: Woese (2007), 4.
“These sequences are sacred scrolls”: Carl Woese to Harry Noller, August 22, 1974; courtesy of Harry Noller.
“obstreperous, petty, and insulting”: Carl Woese to Professor J. Health, May 17, 1988; copy to Harry Noller, which Noller shared with DQ.
“Last night I discovered humor”: Noller (2014), 230.
“Carl was a profoundly creative and fiercely uncompromising scientist”: ibid., 230–31.
“Newly Discovered ‘Missing Link’ Shows”: Rachel Feltman, Washington Post, May 6, 2015.
beware of the “shitkickers” in Section 61: Lewin (2014), 277.
“Sadly, over the next few months”: ibid.
“Species are groups of actually or potentially interbreeding”: Mayr (1942), 120.
often saying “Cut” or “Hold” when he couldn’t summon: These videotapes are available for viewing, with permission, through the Carl R. Woese Institute for Genomic Biology, University of Illinois, Champaign-Urbana.
Bibliography
Acuña, Ricardo, Beatriz E. Padilla, Claudia P. Flórez-Ramos, José D. Rubio, Juan C. Herrera, Pablo Benavides, Sang-Jik Lee, Trevor H. Yeats, Ashley N. Egan, Jeffrey J. Doyle, and Jocelyn K. C. Rose. 2012. “Adaptive Horizontal Transfer of a Bacterial Gene to an Invasive Insect Pest of Coffee.” Proceedings of the National Academy of Sciences 109 (11).
Akanni, Wasiu A., Karen Siu-Ting, Christopher J. Creevey, James O. McInerney, Mark Wilkinson, Peter G. Foster, and Davide Pisani. 2015. “Horizontal Gene Flow from Eubacteria to Archaebacteria and What It Means for Our Understanding of Eukaryogenesis.” Philosophical Transactions of the Royal Society of London (B) 370 (1678).
Albers, Sonja-Verena, Patrick Forterre, David Prangishvili, and Christa Schleper. 2013. “The Legacy of Carl Woese and Wolfram Zillig: From Phylogeny to Landmark Discoveries.” Nature Reviews Microbiology 11 (10).
Amunts, Alexey, Alan Brown, Jaan Toots, Sjors H. W. Scheres, and V. Ramakrishnan. 2015. “The Structure of the Human Mitochondrial Ribosome.” Science 348 (6230).
Andam, Cheryl P., David Williams, and J. Peter Gogarten. 2010. “Natural Taxonomy in Light of Horizontal Gene Transfer.” Biology & Philosophy 25 (4).
Andam, Cheryl P., and J. Peter Gogarten. 2011. “Biased Gene Transfer in Microbial Evolution.” Nature Reviews Microbiology 9 (7).
Andam, Cheryl P., Gregory P. Fournier, and Johann Peter Gogarten. 2011. “Multilevel Populations and the Evolution of Antibiotic Resistance Through Horizontal Gene Transfer.” FEMS Microbiology Reviews 35 (5).
Anderson, E. S. 1968. “The Ecology of Transferable Drug Resistance in the Enterobacteria.” Annual Review of Microbiology, 22.
Anderson, Jan O., Asa M. Sjögren, Lesley A. M. Davis, T. Martin Embley, and Andrew J. Roger. 2003. “Phylogenetic Analyses of Diplomonad Genes Reveal Frequent Lateral Gene Transfers Affecting Eukaryotes.” Current Biology 13.
Anderson, Norman G. 1970. “Evolutionary Significance of Virus Infection.” Nature 227 (5265).
Anderson, O. Roger. 1983. Radiolaria. New York: Springer-Verlag.
Andersson, J. O. 2001. “Lateral Gene Transfer in Eukaryotes.” Cellular and Molecular Life Sciences 62 (11).
Anderson, Jan O., W. Ford Doolittle, and Camilla L. Nesbø. 2001. “Are There Bugs in Our Genome?” Science 292 (5523).
Andersson, Jan O., Asa M. Sjögren, Lesley A. M. Davis, T. Martin Embley, and Andrew J. Roger. 2003. “Phylogenetic Analyses of Diplomonad Genes Reveal Frequent Lateral Gene Transfers Affecting Eukaryotes.” Current Biology 13 (2).
Anon. 1941. “Obituary. F. Griffith, M.B., and W. M. Scott, M.D., Medical Officers, Ministry of Health.” British Medical Journal 1 (4191).
Arbuckle, Jesse H., Maria M. Medveczky, Janos Luka, Stephen H. Hadley, Andrea Luegmayr, Dharam Ablashi, Troy C. Lund, Jakub Tolar, Kenny De Meirleir, Jose G. Montoya et al. 2010. “The Latent Human Herpesvirus-6A Genome Specifically Integrates in Telomeres of Human Chromosomes In Vivo and
In Vitro.” Proceedings of the National Academy of Sciences 107 (12).
Archibald, J. David. 2009. “Edward Hitchcock’s Pre-Darwinian (1840) ‘Tree of Life.’ ” Journal of the History of Biology 42.
Archibald, J. David. 2014. Aristotle’s Ladder, Darwin’s Tree: The Evolution of Visual Metaphors for Biological Order. New York: Columbia University Press.
Archibald, John. 2014. One Plus One Equals One: Symbiosis and the Evolution of Complex Life. New York: Oxford University Press.
Archibald, John M. 2008. “The Eocyte Hypothesis and the Origin of Eukaryotic Cells.” Proceedings of the National Academy of Sciences 105 (51).
____. 2015. “Gene Transfer in Complex Cells.” Nature 524 (7566).
Arkhipova, Irina R., Mark A. Batzer, Juergen Brosius, Cedric Feschotte, John V. Moran, Jürgen Schmitz, and Jerzy Jurka. 2012. “Genomic Impact of Eukaryotic Transposable Elements.” Mobile DNA 3 (1).
Arnold, Michael L. 2007. Evolution Through Genetic Exchange. New York: Oxford University Press.
____. 2009. Reticulate Evolution and Humans: Origins and Ecology. New York: Oxford University Press.
Arnold, Michael L., and Edward J. Larson. 2004. “Evolution’s New Look.” Wilson Quarterly (Autumn).
Arnold, Michael L., and Axel Meyer. 2006. “Natural Hybridization in Primates: One Evolutionary Mechanism.” Zoology 109 (4).
Arnold, Michael L., Yuval Sapir, and Noland H. Martin. 2008. “Genetic Exchange and the Origin of Adaptations: Prokaryotes to Primates.” Philosophical Transactions of the Royal Society of London (B) 363 (1505).
Avery, Oswald T., Colin M. MacLeod, and Maclyn McCarty. 1944. “Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III.” Journal of Experimental Medicine 79 (2).
Azad, Rajeev K., and Jeffrey G. Lawrence. 2011. “Towards More Robust Methods of Alien Gene Detection.” Nucleic Acids Research 39 (9).
Baker, Kate S., Alison E. Mather, Hannah McGregor, Paul Coupland, Gemma C. Langridge, Martin Day, Ana Deheer-Graham, Julian Parkhill, Julie E. Russell, and Nicholas R. Thomson. 2014. “The Extant World War 1 Dysentery Bacillus NCTC1: A Genomic Analysis.” Lancet 384 (9955).