Life's Greatest Secret
Page 46
79.New York Times, 3 June 2003.
80.Ezkurdia et al. (2014).
81.Britten and Davidson (1969).
82.Morange (2008).
83.Morris and Mattick (2014).
84.RIKEN et al. (2005).
85.Corden et al. (1980).
86.Keller (2000), Gerstein et al. (2007).
87.See Chapter 9.
88.Pearson (2006).
89.Coyne (2000), Wain et al. (2002).
90.Kishida et al. (2007).
91.Doolittle and Sapienza (1980).
92.Fechotte and Pritham (2007).
93.Sasidharan and Gerstein (2008).
94.Cornelis et al. (2014).
95.Thomas (1971), Gregory (2001).
96.Palazzo and Gregory (2014).
97.http://judgestarling.tumblr.com/post/64504735261/the-origin-of-junk-dna-a-historical-whodunnit.
98.ENCODE Project Consortium (2012). See http://www.nature.com/encode/ and http://blogs.discovermagazine.com/notrocketscience/2012/09/05/encode-the-rough-guide-to-the-human-genome. Birney’s own view: http://genomeinformatician.blogspot.co.uk/2012/09/encode-my-own-thoughts.html.
99.Pennisi (2012); New York Times, 5 September 2012; The Guardian, 5 September 2012.
100.Eddy (2012). Probably the most outspoken critic has been Dan Graur: http://judgestarling.tumblr.com, Graur et al. (2013), Bhattacharjee (2014). See also Doolittle et al. (2014) and Larry Moran’s blog, http://sandwalk.blogspot.co.uk. Germain et al. (2014) are supportive of ENCODE’s approach from a philosophical point of view.
101.ENCODE Project Consortium (2012), p. 57.
102.Eddy (2013).
103.White et al. (2013).
104.http://thefinchandpea.com/2013/07/17/using-a-null-hypothesis-to-find-function-in-the-genome/.
105.Kellis et al. (2014).
Chapter 13
1.Crick (1957), pp. 198–200.
2.Anonymous (1970), p. 1198.
3.Watson (1965), Keyes (1999a). In the final chapter of his book, Watson discussed the possibility that cancer might involve exceptions to the central dogma; this was noted at the time, but seems to have been forgotten since (Sonneborn, 1965).
4.Crick (1970), p. 562.
5.Temin (1971), p. iv.
6.Crick (1970), p. 562. In a letter to Temin, Crick said that his classification of the various kinds of information transfer, including the apparent special exceptions, was ‘tentative, and may need revision from time to time’. Crick to Temin, 3 August 1970. http://profiles.nlm.nih.gov/ps/access/SCBBMG.pdf.
7.Keyes (1999b), Morange (2007a).
8.Prusiner (1982).
9.Hunter (1999), Prusiner and McCarty (2006). For a more nuanced view, see Morange (2007a).
10.Prusiner (1998).
11.Manuelidis et al. (2007).
12.Supattapone and Miller (2013).
13.Bremer et al. (2010).
14.Keyes (1999b).
15.Morange (2008).
16.Denenberg and Rosenberg (1967).
17.Lockyer (2014).
18.Shama and Wegner (2014).
19.Arai et al. (2009).
20.Francis et al. (1999), Carey (2011).
21.Burkeman (2010), Danchin (2013), Jablonka and Lamb (2006), Noble (2013) and Shapiro (2009) all consider that we are in the midst of a revolution. Maderspacher (2010) is not so convinced. For a point-by-point rebuttal of Noble’s views see http://whyevolutionistrue.wordpress.com/2013/08/25/famous-physiologist-embarrasses-himself-by-claiming-that-the-modern-theory-of-evolution-is-in-tatters/
22.See Chapter 11.
23.Guo et al. (2014), Smith et al. (2014).
24.Radford et al. (2014).
25.Hüdl and Basler (2012).
26.Petruk et al. (2012).
27.Carey (2011), pp. 217–19.
28.Nelson et al. (2012), Mattick (2012).
29.Lumey et al. (2009), Heijmans et al. (2008).
30.Daxinger and Whitelaw (2012).
31.Francis (2011).
32.Rechavi et al. (2011).
33.Heard and Martienssen (2014), Yu et al. (2013).
34.Cortijo et al. (2014), Bond and Baulcombe (2014, 2015).
35.Heard and Martienssen (2014).
36.For a recent presentation of these two views, see Laland et al. (2014).
37.Gayon (2006).
38.For a fascinating exploration of Lamarck’s ideas in their historical context, and the importance of his thinking for the acceptance of the idea of evolution, see Mayr (1972).
39.Gayon (1998).
40.See, for example, http://www.technologyreview.com/news/411880/a-comeback-for-lamarckian-evolution.
41.Li and Xie (2011).
42.Crick (1958), p. 144.
43.Hartl et al. (2011), Morange (2005b).
44.Anonymous (1997).
45.Crick to Temin, 3 August 1970. http://profiles.nlm.nih.gov/ps/access/SCBBMG.pdf. See also Strasser (2006).
46.Marahiel (2009).
47.Shen et al. (2015).
48.Mosini (2013).
49.Morange (2005b).
Chapter 14
1.Gibson et al. (2010).
2.For Venter’s account of this work, see Venter (2013). The existence of the code was announced here: http://www.jcvi.org/cms/press/press-releases/full-text/article/first-self-replicating-synthetic-bacterial-cell-constructed-by-j-craig-venter-institute-researcher/. For a clear explanation of the code, and details of how it was cracked, see https://genomevolution.org/wiki/index.php/Mycoplasma_mycoides_JCVI-syn1.0_Decoded.
3.New York Times, 18 November 2013.
4.For an excellent overview of all aspects of biotechnology, which covers the subject in far more detail than space allows here, see Rutherford (2013).
5.Readers of a certain age may recall the satirical 1983 hit song by Orchestral Manoeuvres in the Dark entitled ‘Genetic engineering’ (http://www.youtube.com/watch?v=OddgsPyCJmU). According to the Oxford English Dictionary, ‘biotechnology’ was first used in 1921, by the US Department of Agriculture.
6.Lazaris et al. (2002); The Guardian, 14 January 2012; Rutherford (2013).
7.Source: USDA Economic Research Service. http://www.ers.usda.gov/data-products/adoption-of-genetically-engineered-crops-in-the-us.aspx.
8.Relyea (2012), Annett et al. (2014).
9.Moran and Jarvik (2010), Boto (2014).
10.Remigi et al. (2014).
11.Kim et al. (2014).
12.Goldman et al. (2013). In the 1980s, a series of sequences were introduced into E. coli bacteria that encoded simple Venus-like icons as part of an art project called Microvenus (Davis, 1996).
13.Church et al. (2012); The New Yorker, 24 November 2014.
14.Farzadfard and Lu (2014).
15.Schneider’s web site is delightfully retro: http://users.fred.net/tds/leftdna/.
16.Marvin et al. (1961), van Dam and Levitt (2000).
17.Wang et al. (1979), Morange (2007b).
18.Morange (2007b).
19.Rich (2004). Bizarro is the name of Superman’s alter ego, a fractured mirror image for whom all of Superman’s moral code is reversed.
20.New York Times, 29 June 1999; Rich and Zhang (2003).
21.Du et al. (2013).
22.Rich et al. (1961).
23.Safaee et al. (2013).
24.Pinheiro et al. (2012).
25.Joyce (2012a, b).
26.Wolfe-Simon et al. (2011). The article was accompanied by a series of critical comments and an explanation from the editor of Science, Bruce Alberts.
27.Reaves et al. (2012), Erb et al. (2012).
28.Cleland and Copley (2005), Wolfe-Simon et al. (2009). The title of the Wolfe-Simon et al. article is ‘Did nature also choose arsenic?’, thereby inadvertently extending to scientific articles Betteridge’s law of headlines, which states that ‘Any headline which ends in a question mark can be answered by the word no.’
29.Davies et al. (2009), Toomey (2013).
30.Davis and Chin (2013). For a description of other approaches, see Johnson et al. (2010).
31.Switzer et al. (1989), Piccirilli et al. (1990).
32.Yang et al. (2011).
33.For example, the drug acyclovir – O’Brien and Campoli-Richards (1989).
34.Malyshev et al. (2014).
35.Jackson et al. (1972).
36.Berg et al. (1974).
37.Berg et al. (1975), Berg (2008). See also Morange (1998), Rasmussen (2014), Rutherford (2013) and above all Wright (1994). Some researchers had already begun to circumvent the voluntary moratorium, such was the pressure to make use of these new techniques (Comfort, 2014; Rasmussen, 2014).
38.Watanabe et al. (2014).
39.The Guardian, 11 June 2014. For an online discussion of this experiment, with useful points on both sides, see http://whyevolutionistrue.wordpress.com/2014/06/12/mad-scientists-or-is-there-any-justification-for-trying-to-recreate-a-deadly-virus/.
40.http://news.sciencemag.org/biology/2014/10/researchers-rail-against-moratorium-risky-virus-experiments.
41.Friedmann and Roblin (1972).
42.Mavilio (2012).
43.‘Gene therapy’s big comeback’, Forbes Magazine, 14 April 2014.
44.Jinek et al. (2012). This publication was followed weeks later by a similar announcement from a group based in France, Lithuania and the US (Gasiunas et al., 2012).
45.Cong et al. (2013), Mali et al. (2013).
46.New York Times, 4 March 2014. For a more technical summary, see Hsu et al. (2014).
47.The Independent, 7 November 2013.
48.Sheridan (2014), http://www.technologyreview.com/view/526726/broad-institute-gets-patent-on-revolutionary-gene-editing-method.
49.O’Connell et al. (2014).
50.Esvelt et al. (2014).
51.Oye et al. (2014).
52.Mandel et al. (2015), Rover et al. (2015).
53.Berg (2008), pp. 290–1.
Chapter 15
1.Miller (1953), Bada and Lazcano (2000).
2.Elsila et al. (2009). In 2008, after Miller’s death, researchers examined vials left over from a similar experiment he had carried out in the 1950s. Using modern techniques, they discovered that the levels of amino acids produced by the experiment were even higher than those originally reported (Johnson et al., 2008).
3.Lane and Martin (2012), Martin et al. (2014). See also Koonin and Martin (2005), Fellermann and Solé (2007).
4.Baaske et al. (2007).
5.For a summary of molecular evidence supporting this view, see Di Giulio (2013a).
6.Crick (1981), pp. 15–16. Nature mischievously asked the Bishop of Birmingham to review the book; the Bishop countered Crick’s directed panspermia hypothesis by outlining the evidence for a purely terrestrial origin of life, while inevitably leaving the door open for ‘divine providence’, for which there is arguably even less evidence than for space aliens (Montefiore, 1982).
7.See shCherbak and Makukov (2013) for a suggestion that the genetic code contains an intelligent signature.
8.Gilbert (1986).
9.Joyce (2002), Paul and Joyce (2004), Robertson and Joyce (2012).
10.Pross (2012), p. 63.
11.A handful of scientists are not convinced there was such a thing as the RNA world. See, for example, Caetano-Anollés and Seufferheld (2013).
12.Hotchkiss (1995). This brilliant insight had little consequence.
13.Powner et al. (2009). However, as Adam Rutherford points out, John Sutherland’s research on the spontaneous synthesis of RNA bases found that the yield of uracil was increased in the presence of ultraviolet radiation, hinting that the synthesis of early RNA may have taken place close to the surface (Rutherford, 2013, p. 96).
14.Lincoln and Joyce (2009).
15.Yarus (2010), p. 97.
16.Noller (2012).
17.Yarus (2010), p. 179.
18.There is a massive literature on this topic. What follows is based mainly on Koonin and Novozhilov (2009), Yarus (2010) and Rutherford (2013).
19.See, for example, Woese (1965).
20.Polyanski et al. (2013).
21.Crick (1968).
22.Freeland and Hurst (1998), Freeland et al. (2000).
23.Yarus et al. (2005).
24.Koonin and Novozhilov (2009), p. 108. See the special issue of Journal of Molecular Evolution in 2013, which contained four papers, each outlining a different explanation (Di Giulio, 2013b).
25.Behura and Severson (2013).
26.Cannarozzi et al. (2010).
27.Bernardi (2000).
28.Eyre-Walker and Hurst (2001).
29.Romiguier et al. (2010), Katzman et al. (2011).
30.Stergachis et al. (2013).
31.http://www.washington.edu/news/2013/12/12/scientists-discover-double-meaning-in-genetic-code/.
32.For example, Birnbaum et al. (2012) and Lin et al. (2011).
33.People were also annoyed by the use of the neologism ‘duon’ to describe the codons that have both coding and transcription factor binding functions (I predict this coinage will not have a long life). For examples of spontaneous and more considered responses, see https://twitter.com/edyong209/status/411283930294534144 and http://pasteursquadrant.wordpress.com/2013/12/14/on-duons-and-cargo-cult-science/.
34.Itzkovitz et al. (2010).
35.Mignone et al. (2002).
36.Yáñez-Cuna et al. (2013).
37.Maraia and Iben (2014).
38.Apter and Wolpert (1965). For a discussion of the role of metaphor in science in general, with a particular emphasis on chemistry, see Brown (2003).
39.For example, Fabris (2009), Gatlin (1966, 1968, 1972), Holzmüller (1984), Lean (2014), Longo et al. (2012), Schneider et al. (1986), Spetner (1968), Yockey (1992).
40.Maynard Smith and Szathmáry (1997).
41.Maynard Smith (1999, 2000a, b). Other contributors to the debates include: Bergstrom and Rosvall (2011a, b), Collier (2008), GarcÌa-Sancho (2007) Godfrey-Smith (2000a, b, 2007, 2011), Griffiths (2001), Kjosavik (2014), Kogge (2012), Levy (2011), Maclaurin (2011), Sarkar (1996a, b, 2000, 2013), Shea (2011), Stegmann (2004, 2005, 2009, 2012, 2013, 2014a, b), Šustar (2007). I am grateful to Ulrich Stegmann for his comments on this section on the philosophy of genetic information; however, grumpy philosophers and others should address their criticisms to me, not him.
42.Maynard Smith (2000a), p. 190. This point was first made by Kimura (1961).
43.Maynard Smith (2000a), p. 190.
44.For example, Jablonka (2002).
45.Maynard Smith (2000a), p. 193.
46.Griffiths (2001), Stegmann (2014b).
47.For a critique of the idea of the gene as a program, see Planer (2014).
48.Sarkar (1996a), p. 107.
49.Sarkar (2000).
50.Godfrey-Smith (2011), p. 180.
51.Sarkar (1996b), p. 863.
52.Dudai et al. (1976).
53.http://flybase.org/reports/FBgn0000479.html.
54.For example, Sarkar (1996a), Keller (1995, 2000, 2002)
55.Crick (1958), p. 144, pp. 138–9.
56.For example, Oyama (2000). For a clear introduction to this view, and to other aspects of philosophy and genetics, see Griffiths and Stotz (2013).
57.For example, Commoner (1968), de Lorenzo (2014), Noble (2013), Shapiro (2009).
58.Walker (2007).
59.Crabbe et al. (1999).
60.Wahlsten et al. (2006).
61.Rietveld et al. (2014).
62.Maynard Smith (2000a, b).
63.Noble (2002), Newman (2003).
64.For example, Cosentino and Bates (2012).
65.Cobb (2011). For the fate of the British branch of cybernetics, see Pickering (2010). Medina (2011) provides a fascinating exploration of how in the early 1970s applied cybernetics was used in the doomed attempt to peacefully transform the Chilean economy under the socialist President, Salvador Allende.
Conclusion
1.Pickstone (2001).
2.Gilbert (1991).
3.Wood et al. (2014).
LIST OF ILLUSTRATIONS
&nbs
p; 1Erwin Schrödinger, President Hyde and Prime Minster De Valera, Dublin 1943 © Ewald Collection/American Institute of Physics/Science Photo Library
2Norbert Wiener © Emilio Segre Visual Archives/American Institute of Physics/Science Photo Library
3Oswald Avery © The Oswald T. Avery Collection/US National Library of Medicine /Courtesy of Maclyn McCarty
4Claude Shannon © Alfred Eisenstaedt/Getty Images
5Harriett Ephrussi-Taylor, Boris Ephrussi and Leo Szilárd, courtesy of Cold Spring Harbor Laboratory Archives
6Alfred Mirsky with Masson Gulland, courtesy of Cold Spring Harbor Laboratory Archives
7André Boivin with Joshua Lederberg, courtesy of Cold Spring Harbor Laboratory Archives
8Salvador Luria with Max Delbrück © The Salvador E. Luria Papers/US National Library of Medicine/Courtesy of Daniel D. Luria
9Leo Szilárd with Al Hershey, courtesy of Cold Spring Harbor Laboratory Archives
10Team photo of Al Hershey’s laboratory, courtesy of Cold Spring Harbor Laboratory Archives
11Rosalind Franklin © The Rosalind Franklin Papers /US National Library of Medicine /Courtesy of Vittorio Luzzati
12Maurice Wilkins © Keystone/Getty Images
13James D. Watson, courtesy of Cold Spring Harbor Laboratory Archives
14Watson and Crick © A. Barrington Brown/Science Photo Library
15Letter by George Gamow © Courtesy estate of George Gamow. Original item held in the Ava Helen and Linus Pauling Papers, Oregon State University Libraries and George Gamow Papers, collection MS0252, Special Collections Research Center, The George Washington University, Washington, DC
16George Gamow © Emilio Segre Visual Archives/American Institute of Physics/Science Photo Library
17Crick, Rich, Orgel and Watson. Image courtesy of Alexander Rich
18Heinrich Matthaei with Marshall Nirenberg © National Library of Medicine/Science Photo Library
19Crick, Benzer and Jacob attending Moscow Biochemistry Congress, 1961, courtesy of Cold Spring Harbor Laboratory Archives
20Crick’s annotated programme © Francis Crick Papers/Wellcome Library, London
21François Jacob with his wife, Lise, on the beach, courtesy of Cold Spring Harbor Laboratory Archives
22Jacques Monod with Sydney Brenner, courtesy of Cold Spring Harbor Laboratory Archives.
23François Jacob with Jacques Monod © AFP/Getty Images
24Francis Crick speaking in 1963, courtesy of Cold Spring Harbor Laboratory Archives