Arrival of the Fittest: Solving Evolution's Greatest Puzzle (32 page)

56
. See Mayr (1982), 304.

CHAPTER TWO: THE ORIGIN OF INNOVATION

1
. See Pasteur (1864).

2
. See Horowitz (1956).

3
. Ibid.

4
. Pasteur was aware that these microbes could enter the growth medium from dust grains in the air. See Pasteur (1864).

5
. See Cropper (2001), 259.

6
. See Sleep (2010).

7
. See Sleep (2010) and Delsemme (1998).

8
. See Schopf et al. (2002), but also Brasier et al. (2006).

9
. See Mojzsis et al. (1996), but also Lepland et al. (2005).

10
. See Oparin (1952) and Haldane (1929).

11
. Darwin’s letter from February 1, 1871, to his friend J. D. Hooker is available as letter 7471 from the Darwin Correspondence Project (http://www.darwinproject.ac.uk/entry-7471).

12
. In the interest of historical accuracy, I note that the German chemist Friedrich Wöhler first showed that an organic molecule, urea, could be made from inorganic ingredients.

13
. See Miller (1953).

14
. See Miller (1998).

15
. For the reanalysis of the meteorite content, see Schmitt-Kopplin et al. (2010). The comet’s impact is documented by the Meteoritical Society at http://www.lpi.usra.edu/meteor/metbull.php?code=16875. See also Bryson (2003).

16
. See Sephton (2001) and Radetsky (1998).

17
. See Delsemme (1998).

18
. Ibid.

19
. See Deamer (1998).

20
. See Delsemme (1998).

21
. See Watson and Crick (1953).

22
. It turns out that even DNA can catalyze some chemical reactions, as Ronald Breaker demonstrated in 1994. However, thus far DNA catalysts exist only in the laboratory.

23
. It had been hypothesized that RNA might be a catalyst, partly because it can fold into elaborate spatial structures, but the proof was provided in Guerrier-Takada et al. (1983) and Kruger et al. (1982).

24
. Other roles of RNA were known as well, such as that of the transfer RNA that loads the ribosome with amino acids, but none as important as that of a catalyst.

25
. The notion of an RNA world comes from Gilbert (1986).

26
. See Cech (2000).

27
. To be precise, this molecule would actually replicate a template, not itself, so at least two molecules are needed to start the process.

28
. See Johnston et al. (2001), as well as Zaher and Unrau (2007) and Cheng and Unrau (2010).

29
. See Eigen (1971).

30
. See Szostak (2012), as well as Eigen (1971) and Kun, Santos, and Szathmary (2005). This is really just a rule of thumb. The needed accuracy depends also on other factors, such as how much worse the unfaithful copies of an RNA replicase are at replication.

31
. See Johnston et al. (2001).

32
. See Drake et al. (1998).

33
. See Kelman and O’Donnell (1995). The precursors are molecules like deoxy-ATP, whose incorporation into newly synthesized DNA requires energy, which is obtained by cleaving two phosphate residues in the precursor.

34
. This calculation is based on a replicase with 189 nucleotides, the same length as the polymerase found by Johnston et al. (2001), as well as on an average molecular weight of 340 grams per mole of a nucleotide building block. It takes into account that one replicase molecule is needed to replicate another molecule, which would decrease the doubling rate of a replicase population. The polymerization rate of one polymerization reaction per second is taken from the so-called class I ligase discussed in Ekland, Szostak, and Bartel (1995), but I note that even if this rate were orders of magnitude slower, there would still be an exponentially growing requirement for nutrients.

35
. See Szostak (2012).

36
. See Miller (1998).

37
. See also Martin et al. (2008) and Braakman and Smith (2013). One of the most prescient early views is provided, once again, by J. B. S. Haldane. See Haldane (1929).

38
. See Stryer (1995). Enzymes with especially high rates of acceleration include alkaline phosphatase and urease. Some enzymes, so-called promiscuous enzymes, can catalyze multiple reactions, but one of them is usually catalyzed with the highest efficiency. See Stryer (1995).

39
. See Wachtershauser (1992), Wachtershauser (1990), Morowitz et al. (2000), Copley, Smith, and Morowitz (2007), Bada and Lazcano (2002), Ycas (1955), and Martin et al. (2008).

40
. See Delsemme (1998).

41
. See Corliss et al. (1979).

42
. Hot springs and geysers are terrestrial hydrothermal vents.

43
. More specifically, they are
chemoautotrophic
organisms that build their bodies using inorganic molecules as energy sources, as opposed to
photoautotrophic
organisms—mostly plants—that use light energy. Organisms like us are
heterotrophic,
feeding on organic molecules that have been created by other organisms.

44
. See Martin et al. (2008)

45
. See Beatty et al. (2005)

46
. “The deep hot biosphere,” Wikipedia, http://en.wikipedia.org/wiki/Hydrothermal_vent#The_deep_hot_biosphere.

47
. See Kashefi and Lovley (2003).

48
. See Holm and Andersson (1998), as well as Martin et al. (2008).

49
. See Budin and Szostak (2010), as well as Kelley et al. (2005).

50
. See Smil (2000). These kinds of metals have served as valuable catalysts to industrial chemists for a long time. The Haber-Bosch process that sustains a third of the world’s population, for example, uses iron to create five hundred million tons of ammonium fertilizer every year. See Holm and Andersson (1998), as well as Hsu-Kim et al. (2008).

51
. The citric acid cycle is also called the tricarboxylic acid cycle or the Krebs cycle, after the German-born Nobel Prize–winning biochemist Hans Adolf Krebs. See Braakman and Smith (2013) for some variants on this theme as a possible origin of metabolism.

52
. See Morowitz et al. (2000), as well as Braakman and Smith (2013).

53
. See Stryer (1995), as well as Smith and Morowitz (2004).

54
. What I have described first is the more primitive
reductive
TCA cycle, which uses energy from reduced inorganic molecules and carbon from CO
₂
to synthesize precursors for other molecules. In contrast, the
oxidative
TCA cycle in heterotrophic organisms (like us) extracts energy from organic molecules to produce both energy—ultimately, ATP—and building blocks for biosyntheses, as well as the CO
₂
waste product that we exhale.

55
. See Hugler et al. (2007), as well as Smith and Morowitz (2004).

56
. See Zhang and Martin (2006) and Cody et al. (2000).

57
. Theoretical treatments of autocatalytic networks include those by Eigen and Schuster (1979) and Kauffman (1986). It is easy to see how the state of a metabolism can be inherited from parent to offspring, but such inheritance is unlikely to be very faithful, for example because it is subject to stochastic fluctuations in the concentrations of metabolites and catalysts among offspring from the same parent. Nucleic acids clearly provide a superior means of faithful inheritance.

58
. See Williams et al. (2011), Huang and Ferris (2006), Ferris et al. (1996), and Holm (1992).

59
. See Budin and Szostak (2010).

60
. See Deamer (1998).

61
. See Budin, Bruckner, and Szostak (2009).

62
. Curiously, Pasteur rang the death knell for spontaneous creation, but he still believed that a vital force was necessary for fermentation, which Buchner later showed to require only inanimate enzymes.

63
. The numbers I cite here are taken from well-studied cells, such as those of the bacterium
E. coli.
See Neidhardt (1996) and Feist et al. (2007). Although the chemical composition of biomass and thus its building blocks vary among organisms, some important principles hold broadly, such as that proteins, RNA, and DNA typically constitute the majority of biomass.

64
. Our human metabolism is even more complex. It has more than two thousand reactions and more than two thousand small molecules. Current knowledge about the
E. coli
network is summarized in Feist et al. (2007), and about the human network by Duarte et al. (2007). Both bodies of knowledge will undoubtedly grow in the future.

65
. More precisely, the microbes in our gut synthesize biotin.

66
. See Wolfenden and Yuan (2008). I note that sucrase, like other enzymes, does not float through a cell’s interior, but is anchored to the membrane of intestinal cells.

67
. Some reactions are catalyzed by more than one enzyme, and some enzymes catalyze more than one reaction.

68
. To be precise, sucrase is a protein that consists of two identical polypeptides. See Sim et al. (2010).

69
. This holds for metabolic enzymes. There are other enzymes, most notably protein kinases, that add phosphates to other proteins, which are large molecules.

70
. See Tanenbaum (1988), 254.

71
. To be precise, there are several related molecules that can also serve to store energy, such as GTP and deoxy CTP, but they are very similar in chemical structure to ATP, and they use the same kind of chemical bond for energy storage.

72
. There are many different kinds of lipids, and membranes vary in their lipid content among organisms, but the principle that membrane molecules are amphiphilic remains unchanged.

73
. Some organisms show minor variations from the genetic code. See Knight, Freeland, and Landweber (2001), but these variants most likely originated after the most recent common ancestor of all extant life.

74
. One of the alternatives to ATP is its close relative GTP, and one alternative to DNA is PNA (peptide nucleic acid). See Nelson, Levy, and Miller (2000). Chapter 3 of Wagner (2005b) reviews some relevant literature on the genetic code. One of the alternatives may be superior, but that’s beside the point. Even if natural selection has caused the demise of the others, the current standards tell us that we descend from a single ancestor.

CHAPTER THREE: THE UNIVERSAL LIBRARY

1
. This analogy is inspired by a famous short story of the Argentine author Jorge Luis Borges entitled “The Library of Babel” (Spanish original: “La biblioteca de Babel”), published in English translation in Borges (1962). The idea behind this short story, however, predates Borges. It has been used by many other authors, including Umberto Eco and Daniel Dennett.

2
. The BioCyc database can be found at http://biocyc.org/ and is described in Caspi et al. (2012). For the KEGG database see Ogata et al. (1999). Yet another relevant database is described in Chang et al. (2009).