NOTES
PROLOGUE: WORLD ENOUGH, AND TIME
1.The assumption that these processes proceeded through most of the earth’s history at the same rate as today is a principle of geology known as uniformitarianism.
2.See Zimmer (2001), 60.
3.See Burchfield (1974). A relevant passage can be found in chapter 10, page 338, of the sixth edition of Darwin’s central opus, On the Origin of Species by Means of Natural Selection. See Darwin (1872). Darwin published six English-language editions of this book in his lifetime, each different from the one before. In these endnotes I cite page numbers from the sixth edition, as reprinted by A. L. Burt (New York), but usually the first edition, i.e., Darwin (1859), is cited.
4.See Burchfield (1990), 164. This often-quoted anecdote obscures the true reason for Kelvin’s error (which is unimportant for my point here). It was his assumption that thermal conductivity is uniform throughout the earth’s interior, as discussed in England, Molnar, and Richter (2007).
5.See Sibley (2001).
6.See Schwab (2012), 188, as well as Tucker (2000).
7.See Goldsmith (2006).
8.Human nails and birds’ claws are composed of proteins from different keratin subfamilies, known as α-keratins and β-keratins respectively. See Greenwold and Sawyer (2011) for the origin of β-keratins.
9.See Kappe et al. (2010).
10.See Shimeld et al. (2005) and Feuda et al. (2012). Vertebrates themselves originated in the Cambrian explosion more than five hundred million years ago, but some of their proteins may be much older.
11.This number has been estimated as being no greater than 1090. See “Observable universe,” Wikipedia, http://en.wikipedia.org/wiki/Observable_universe, for a more conservative, smaller estimate.
12.A year has 365 days, and if the universe is on the order of 2 × 1010 years old, winning a jackpot every day adds up to only 7.3 × 1012 jackpots, a ridiculously small number compared to what is needed.
CHAPTER ONE: WHAT DARWIN DIDN’T KNOW
1.A thorough and well-sourced account of the history of biology through the mid-twentieth century is Mayr (1982). I will cite extensively from it.
2.See Mayr (1982), 362.
3.Ibid., 390.
4.Ibid., 351.
5.Ibid., 363.
6.Ibid., 259.
7.See Whitehead (1978), 39.
8.This essentialist concept of a species is also sometimes called the typological species concept. See Futuyma (1998), 448.
9.Successful hybridization that creates new species is not uncommon, especially in plants. See Futuyma (1998). Because bacteria do not reproduce sexually like we do, the concept of a biological species does not apply to them. Nonetheless, they frequently exchange genetic material through a process known as lateral gene transfer, and are thus even more plastic than species of higher organisms. See Bushman (2002).
10.See Mayr (1982), 304.
11.I note that Eupodophis itself was only discovered recently. See Houssaye et al. (2011).
12.See Gilbert (2003). Darwin himself made contributions to this area through his extensive studies on barnacles (Cirripedia).
13.See Mayr (1982), 439.
14.Aside from his contemporary Alfred Russel Wallace, who proposed a similar theory at about the same time, Darwin is peerless in his radical application of the concept of natural selection, and in the body of evidence he accumulated for its importance. The concept of natural selection existed long before Darwin’s theory, but selection was then usually thought to help eliminate degenerate forms, not to help gradually improve existing forms. See Mayr (1982), 488–500.
15.See Darwin (1872), chapter 1, page 12.
16.See Mayr (1982), 710.
17.Mendel’s laws are summarized in biology textbooks, such as Griffiths et al. (2004). In some Mendelian traits, the offspring of two pure-breeding parents can be intermediate between the parents. The particulate nature of genes can then still be revealed in the second generation, where some individuals display the parental phenotype.
18.Mendel (1866).
19.See Kottler (1979), Corcos and Monaghan (1985), Mayr (1982), 728, as well as Schwartz (1999), chapter 7.
20.See Johannsen (1913). The term pangene comes from the word pangenesis, the ancient notion that all parts of a body, including eyes, hair, and nails, contribute to inheritance. According to pangenesis, brown-eyed parents, for example, tend to have brown-eyed children because eyes contribute to whatever material a man and woman exchange in procreating. Darwin also believed in pangenesis. See Mayr (1982), 693. We now know pangenesis to be wrong. Not all parts of our body, but only reproductive cells such as oocytes, contribute inherited material to the next generation.
21.See Mayr (1982), 783.
22.This statement is usually attributed to de Vries, and I follow this tradition. It is the closing statement in de Vries (1905), 825. However, de Vries does not claim to be the originator of this statement, but attributes it to Arthur Harris without further reference. Harris makes this statement in a little-noted article, where he declares it a quote but does not provide the source. See Harris (1904). The statement has resurfaced periodically in the literature, for example in the title of research papers like that by Fontana and Buss (1994).
23.Johannsen himself was very careful not to ascribe any physical reality to genes. See Johannsen (1913), 143–46.
24.The opposite of such discrete inheritance is also called blending inheritance.
25.Darwin knew about discrete inheritance but did not think it was very important. See Mayr (1982), 543.
26.Macromutations may be more frequent in plants than in animals. See Theissen (2006).
27.See Goldschmidt (1940), 391. In the eyes of mutationists, such mutations were much more important to evolution than selection. See Mayr (1982), 540–50.
28.The story of the peppered moth is one of the oldest and most-cited instances of “evolution in action” that have been observed within a human life span. See Kettlewell (1973), as well as Cook et al. (2012). Haldane showed how even such rapid genetic change does not require very strong selection. See Haldane (1924).
29.This assessment comes from human diseases, an especially well studied class of traits. About 1 percent of humans are affected by Mendelian diseases that are caused by mutations in single genes, whereas a much larger percentage of the total population is affected by diseases associated with mutations of weak effects in multiple genes, such as hypertension or diabetes. See Benfey and Protopapas (2005).
30.There are exceptions that prove the rule, such as the phenomenon of polyploidization, where the entire genetic material of an organism becomes duplicated, which can result in major phenotypic change. Many crop plants are polyploids.
31.See Huxley (1942).
32.This quote is itself a simplification from the original in Einstein (1934).
33.See Mayr (1982), 400.
34.See Morgan (1932), 177. Curiously, Morgan was an embryologist before he became a geneticist. For a broader discussion see Gilbert (2003).
35.Population genetics and quantitative genetics have gradually become more sophisticated, and allowed that genes contribute in complex nonlinear ways to a phenotype. They also study multivariate phenotypes, phenotypes that cannot be written as single scalar quantities but are represented as vectors. But even these representations cannot encapsulate the true complexity of phenotypes such as the fold of a protein, which is best represented through the atomic coordinates and molecular motions of its amino acids. The formation of this phenotype is completely determined by its genotype, the amino acid chain, yet it is so complex that we still cannot compute it from information in the genotype.
36.The term enzyme itself had been coined already in 1877 by the German physiologist Wilhelm Kühne.
37.See Stryer (1995).
38.See Desmond and Moore (1994). The fifth edition is the first to use the phrase “su
rvival of the fittest,” which had been coined by the philosopher Herbert Spencer.
39.See Mayr (1982), chapter 19.
40.See Avery, MacLeod, and McCarty (1944).
41.See Watson and Crick (1953).
42.For which Max Perutz and John Kendrew would share the 1962 Nobel Prize in Chemistry.
43.See Benfey and Protopapas (2005). The very earliest techniques to study genetic variation did not yet read DNA directly, but used alternative measures to measure genetic variation, such as the mobility of different variants of a protein in an electric field. See, for example, Lewontin and Hubby (1966).
44.See Kreitman (1983) and Oqueta et al. (2010).
45.See Eng, Luczak, and Wall (2007). Such individuals metabolize alcohol more efficiently into acetaldehyde, which causes the undesired side effects.
46.The notion of a “paradigm shift” leading to incompatible worldviews was immortalized by the historian Thomas Kuhn. See Kuhn (1962).
47.See Nikaido et al. (2011).
48.One of several differences between the English alphabet and the molecular alphabet of DNA is that they contain different numbers of letters and each letter thus carries different amounts of information.
49.The first draft sequence from both the publicly and the privately funded projects was based on DNA not from just one individual but from multiple individuals. In the privately funded project, some of that DNA came from the project leader himself. See Venter (2003).
50.The diseases he refers to are so-called complex diseases like diabetes, caused by mutations in multiple genes (and influenced by environmental factors such as diet), as opposed to Mendelian diseases, which are caused by mutations in single genes.
51.Other molecular interactions, such as those between proteins and DNA that help regulate genes, are also important in signaling, as chapter 5 will point out.
52.Such mathematical descriptions of biochemical systems existed for many decades, since biologists first described enzymes and the rates at which they can catalyze chemical reactions. See Fell (1997). However, in the last decade of the twentieth century, molecular biology embraced such descriptions as essential to understanding biochemical systems in a newly fashionable branch of biology called systems biology.
53.See Sedaghat, Sherman, and Quon (2002) for a mathematical model of insulin signaling, and Draznin (2006) for some hypotheses of the mechanisms behind insulin resistance. Sanghera and Blackett (2012) discuss some of the genetic complexities of type 2 diabetes.
54.As many scientists after Darwin have forcefully argued. See, for example, Dawkins (1997).
55.To my knowledge, the term genotype-phenotype map was coined by the Spanish developmental biologist Pere Alberch, who studied macroscopic phenotypes that were too complex to draw this map in molecular detail. See Alberch (1991). However, the idea behind such maps can be found in the work of many others, such as Sewall Wright, one of the founders of the modern synthesis, or the embryologist Conrad Hal Waddington. See Waddington (1959).
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.or
g/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).
Arrival of the Fittest: Solving Evolution's Greatest Puzzle Page 23