Genesis: The Scientific Quest for Life's Origin

by Robert M. Hazen

  p. 212 Cody found evidence: Cody et al. (2001b); see also Cody (2004). They observe the reaction of 1-nonene (a 9-carbon molecule) with nickel sulfide in a formic acid solution to 10-carbon carboxylic acids. This reaction implies that a similar beta-pathway reaction of 3-carbon propene to form 4-carbon methyl acrylic acid is possible.

  p. 212 And perhaps someday: The lack of experimental verification of many chemical steps in the Iron–Sulfur World hypothesis remains a point of criticism (de Duve and Miller 1991). In particular, the relative instability of oxaloacetate, which tends to decarboxylate rapidly, poses a significant challenge to the development of a reductive citric acid cycle before enzymes (Lazcano and Miller 1996).

  p. 213 Michael Russell and Allan Hall: Russell and Hall (Russell et al. 1993, 1994; Russell and Hall 1997, 2002). An intriguing feature of the Russell and Hall model is its reliance on mineral phases with iron and/or nickel in more than one valence state: Mackinawite [(Fe,Ni)1+xS] is proposed as the principal membrane sulfide, whereas greigite (Fe3S4) and violarite (FeNi2S4) serve the role of catalysts. The structures of these minerals bear striking resemblances to the structures of Fe–Ni–S clusters at the core of key metabolic enzymes, including ferredoxins and CO dehydrogenase (Russell and Hall 2002). See also Adams (1992), Beinert et al. (1997), Rawls (2000), Doukov et al. (2002), and J. W. Peters (2002) for descriptions of a variety of metal–sulfur clusters in enzymes.

  p. 213 “flat life”: Wächtershäuser's Iron–Sulfur World hypothesis, for example, relies on two-dimensional growth across a pyrite surface. A number of other authors have speculated on the possibility of flat life, including E. Smith and Morowitz (2004). For a critique of this proposal, see de Duve and Miller (1991) and Wills and Bada (2000, p. 138).

  16

  THE RNA WORLD

  p. 215 “It is generally believed …”: Joyce (1991, p. 391).

  p. 215 classic 1968 paper: Orgel (1968, p. 381) writes, “It is argued that the evolution of the genetic apparatus must have required the abiotic formation of macromolecules capable of residue-by-residue replication. This suggests that polynucleotides were present even in the most primitive ancestors of contemporary organisms.”

  p. 216 a messy business: Fox and Harada (1958).

  p. 216 “I must confess …”: Orgel (1986, p. 127).

  p. 216 RNA ribozymes: Early work on ribozymes includes Kruger et al. (1982), Guerrier-Takada et al. (1983), Bass and Cech (1984), Zaug and Cech (1986), Been and Cech (1988), and Altman et al. (1989). Subsequent work has produced ribozymes that accomplish a wide range of catalytic function (see, e.g., Cech 1990, 1993; Noller et al. 1992).

  In fact, the theoretical papers of Woese (1967), Crick (1968), and Orgel (1968) all anticipated the discovery of ribozymes by postulating the existence of genetic molecules that act as catalysts.

  p. 217 RNA World: The term “RNA World” was proposed in a short note by Harvard chemist Walter Gilbert (1986), in the same year that Alberts (1986) and Lazcano (1986) proposed that catalytic RNA preceded DNA. Gilbert postulated the RNA World as a step in life's development when RNA molecules were sufficient “to carry out all the chemical reactions necessary for the first cellular structures.” These ideas received much subsequent elaboration, for example by Orgel (1986), Joyce et al. (1987), Joyce (1989, 1991, 1996), Biebricher et al. (1993), Lehman and Joyce (1993), and Joyce and Orgel (1993).

  p. 217 study of ribosomes: Ban et al. (2000) and Nissen et al. (2000). Nobelist Thomas Cech (2000) contributed a high-profile analysis of this work, entitled “The ribosome is a ribozyme.”

  Jack Szostak writes: “You could write a book on just the intrigue and controversy and personalities involved in determining the structure of the ribosome—arguably the most important ‘molecular fossil' of modern cells (all right, at least comparable to the citric acid cycle).” [Jack Szostak to RMH, 21 August 2004].

  p. 218 called coenzymes: Lehninger et al. (1993) provide an overview of the functions of coenzyme-A and other coenzymes that incorporate nucleotides.

  p. 218 “riboswitches”: Winkler et al. (2002, 2004) and Sudarsan et al. (2003).

  p. 218 uses rather simple molecules: e.g., Lehninger et al. (1993).

  p. 219 RNA nucleotides, by contrast: RNA nucleotides are themselves assembled from three smaller molecules: the 5-carbon sugar ribose, one of four different cyclic compounds called bases, and an orthophosphate (PO4) group. Bases have been synthesized in a variety of plausible prebiotic experiments, including S. L. Miller's (1953) original experiments and in many subsequent studies (Oró 1960, 1961a; Sanchez et al. 1967; Ferris et al. 1978; Robertson and Miller 1995; Shapiro 1995; and Hill and Orgel 2002). For an excellent overview of this progress, see S. L. Miller and Lazcano (2002, pp. 92-100).

  The synthesis of the 5-carbon sugar ribose, a relatively unstable molecule, is more difficult, though it has been produced in modest yields by the reaction of formaldehyde—the so-called formose reaction (Butlerow 1861, Reid and Orgel 1967, Cairns-Smith et al. 1972, Shapiro 1988, and Schwartz and de Graaf 1993). Interestingly, Ricardo et al. (2004) report that borate minerals may stabilize ribose preferentially, and Springsteen and Joyce (2004) find that ribose passes through lipid membranes an order of magnitude more easily than other 5-carbon sugars. These effects may have enhanced the prebiotic selection of ribose.

  Equally problematic is a reliable prebiotic source of orthophosphate (Weber 1982, Westheimer 1987, Yamagata et al. 1991, de Graaf et al. 1995, Lazcano and Miller 1996, Kornberg et al. 1999, Kornberg and Fraley 2000, and de Graaf and Schwartz 2000).

  Even more daunting is a viable mechanism to assemble the three components—base, sugar, and phosphate—into a nucleotide. Pitsch et al. (1995) reported successful synthesis of sugar phosphates, but ribose and bases are, in general, not stable under the same set of conditions (Joyce 1989, Joyce and Orgel 1993, Lahav 1999, and Zubay and Mui 2001). Wills and Bada (2000, p. 131) conclude: “It is very difficult to imagine how even the building blocks of RNA could have arisen by themselves, much less chains of RNA constructed from the building blocks.”

  p. 219 catalytic RNA sequences: Even if individual nucleotides could be synthesized in abundance, there is no known way to induce them to polymerize in a realistic prebiotic environment. A number of experiments have demonstrated the spontaneous formation of nucleotide–nucleotide bonds, for example, in the presence of clay minerals (Ferris et al. 1988, 1996; Ferris and Ertem 1992, 1993; and Ertem and Ferris 1996, 1997), but these nucleotides were “activated”—chemically altered to enhance their reactivity.

  p. 219 Biologists seem reasonably confident: An extensive half-century of literature, commencing with the work of George Gamow (1954), considers the origin of the DNA-Protein world and the genetic code. This topic postdates the chemical origin of life and thus is beyond the scope of this book. For reviews, see de Duve (1995a, Chapter 6), Lahav (1999, Chapter 17), Maynard-Smith and Szathmáry (1999, Chapter 4), and Wills and Bada (2000, Chapter 7). Hayes (2004) provides a concise survey of the origin of the genetic code.

  p. 219 intractable gap: Leslie Orgel (2003, p. 213) states, “I believe that it is very unlikely that RNA did arise prebiotically on the primitive Earth.” S. L. Miller (1997, p. 167) echoes that belief: “RNA is an unlikely candidate.”

  17

  THE PRE-RNA WORLD

  p. 221 “I've been waiting …”: [Simon Nicholas Platts to RMH, 27 May 2004]

  p. 221 “Identifying the first …”: S. L. Miller (1997, p. 167).

  p. 221 Albert Eschenmoser: Eschenmoser's first studies (Eschenmoser 1991, 1993, 1994, 1999; Bolli et al. 1997) focused on 6-carbon (or hexose) sugars, which assemble into polymers called pyranosyls (he called these alternative nucleic acids p-RNAs). In 2000, his group reported the surprising synthesis of TNA nucleic acid with the 4-carbon sugar threose (Schöning et al. 2000). Leslie Orgel (2000, p. 1307) writes: “The existence of a molecule that is significantly ‘simpler' than RNA, that resembles RNA more closely than do peptide nucleic acids … is encour
aging to those who believe that RNA was preceded by one or more simpler genetic materials.” For useful overviews, see Eschenmoser (1999, 2004).

  Regarding this work, Jack Szostak writes: “Eschenmoser [is] one of the world's pre-eminent organic chemists, who should have shared the Nobel Prize with Woodward for conformational analysis and B12 synthesis—who in his retirement has taken on the task of synthesizing systematically all the reasonable alternatives to RNA in order to answer the question of why nature chose the nucleic acids that are used today in all cellular life.” [Jack Szostak to RMH, 21 August 2004]

  p. 222 “peptide nucleic acid”: The concept of PNAs was introduced by Nielsen et al. (1991), Egholm et al. (1992), and Nielsen (1993), and elaborated on by many other researchers (Wittung et al. 1994, Diederichsen 1996, Diederichsen and Schmitt 1998, Nielsen 1999, and Orgel 2003). Stanley Miller (1997, p. 169) comments, “PNA has demonstrated that nucleic acids with backbones other than sugar phosphates need to be considered.”

  The original PNA used a nonbiological amino acid called aminoethyl glycine—a nonchiral molecule. Subsequent studies found that PNA cannot form a DNA-like double strand if the peptide backbone is constructed from homochiral biological amino acids (known as amino acids). Rather, the backbone must consist either of so-called amino acids or of strictly alternating D and L amino acids (Diederichsen 1996, Diederichsen and Schmitt 1998, and Orgel 2003).

  p. 222 plausible genetic molecules: Steven Benner takes the chemical range of RNA-like molecules even further as he imagines the possibilities of alternate biochemistries (Switzer et al. 1989, Piccirilli et al. 1990, Bain et al. 1992, and Hutter and Benner 2003). He has developed an Artificially Expanded Genetic Information System (AEGIS) with eight new base pairs and a variety of new genetic polymers, some of which might be stable in nonaqueous liquids, such as ammonia, and thus serve as models for alien biochemistries (Benner and Hutter 2002). Miller and co-workers also explored the possibility of alternative bases (Kolb et al. 1994).

  p. 222 The PAH World: [This section is based in part on extensive notes provided by Simon Nicholas Platts to RMH, 10 August 2004]

  p. 223 Max Bernstein: Bernstein's seminar on November 19, 2001, was entitled “Interstellar Inception of Meteoritic Organics and Implications for the Origin of Life.” The seminar is archived at www.origins.rpi.edu. The talk on ultraviolet irradiation of PAHs was based on research described in Bernstein et al. (1999b). Becker et al. (1997) present analytical evidence for PAHs delivered from space.

  p. 223 September 2003 conference: The Seventh Trieste Conference on Chemical Evolution and the Origin of Life was held at the International Centre for Theoretical Physics, Trieste, Italy.

  p. 224 “On the return flight”: Nick Platts' airline ticket is dated September 30, 2003.

  p. 224 PAHs would have been abundant: Desiraju and Gavezzotti (1989) present a useful review of PAH structures. An unfortunate confusion in nomenclature arises, because many chemists refer to PAHs as “polynuclear aromatics,” or PNAs—the same abbreviation origin-of-life workers use for peptide nucleic acids.

  p. 224 “functionalized”: Bernstein et al. (1999b, 2003)

  p. 229 discotic organization: Discotic self-organization was first described by Chandrasekhar et al. (1977). For reviews, see Chandrasekhar (1993), Kumar (2002, 2003), Chandrasekhar and Balagurusamy (2002), and Friedlein et al. (2003).

  p. 230 “I think it's worth pursuing …”: [Jack Szostak to RMH, 3 June 2004]

  p. 230 “An experimental demonstration …”: [Leslie Orgel to RMH, 4 June 2004]

  p. 230 “I thought it was interesting …”: [Gerald Joyce to RMH, 7 June 2004]

  p. 230 “For now it is fascinating …”: [Andrew H. Knoll to RMH, 7 June 2004]

  p. 230 “Thank you for submitting …”: [Editors of Nature to Simon Nicholas Platts, 10 June 2004]. We later learned that, owing to an unusual glut of submissions, they never considered the scientific merits of the piece.

  p. 231 HBC for a thousand dollars: The Norwegian chemical company Chiron AS offers 10 milligrams of hexabenzocoronene for $1,078 including shipping. Other possible gratis sources included Prof. Klaus Muellen at the Max Planck Institute for Polymer Research in Mainz, Germany, and Prof. Shigeru Ohshima and Dr. Minoru Takekawa at Toho University in Chiba, Japan.

  p. 231 informal talk: The Carnegie talk was part of an irregular series by the Geobiology Discussion Group. The NASA video seminar was part of the Forum for Astrobiology Research.

  p. 231 thesis defense: The thesis incorporated a range of projects related to origins chemistry, though the PAH World idea formed the centerpiece.

  p. 232 Dave had also published: Deamer (1997, p. 249). Deamer envisioned individual functionalized PAHs incorporated sideways into membranes, where they could absorb near-ultraviolet and blue wavelengths and effectively act as photoelectric power sources.

  18

  THE EMERGENCE OF COMPETITION

  p. 233 “It is evident …”: Sagan (1961, p. 177).

  p. 233 Origin of Species: Darwin (1859).

  p. 233 continue unabated: Scientists who trivialize these public concerns regarding the validity of scientific accounts of life's origin and evolution do so at their peril. The theory of evolution, by which random molecular changes led through a chance process to the human species, can be seen as raising perplexing philosophical questions about the origin and meaning of human existence (see, e.g., National Academy of Sciences 1998, Gould 1999, K. R. Miller 1999, Fry 2000, Ruse 2000, Pennock 2002, Witham 2002, and Forrest and Gross 2004).

  p. 235 Competition among self-replicating cycles: See, for example, Ycas (1955) and de Duve (2005).

  p. 236 Here's what Spiegelman: Mills et al. (1967). Note that the rapid evolution of this system involved a cycling imposed by the experimenters. Recall that cycling is one of four factors that may promote emergent behaviors (see Chapter 1).

  p. 237 “Our ultimate goal …”: Zimmer (2004, p. 37).

  p. 237 yeast chromosomes: Murray and Szostak (1983).

  p. 237 “Even then …”: [Jack Szostak to RMH, 21 August 2004] He continues: “We tried to build an artificial chromosome in yeast by putting together all the pieces known at the time—centromeres, origins of replication, telomeres, genes. But the construct we made didn't behave like a normal chromosome, which led to the discovery that simple length was important…. I'm still following this principle. We think we understand ‘life'—if we're right, we should be able to build a cell that acts like it's alive.”

  p. 237 first series of ribozyme experiments: Doudna and Szostak (1989), Doudna et al. (1991), Bartel and Szostak (1992), and Green and Szostak (1991).

  Szostak writes: “[Jennifer Doudna] was actually the first person in my lab other than myself to start working with ribozymes…. The other students involved in that work were David Bartel and Rachel Green—also both remarkable success stories.” [Jack Szostak to RMH, 21 August 2004]

  p. 237 Szostak's objective: Ellington and Szostak (1990, 1992), Bartel and Szostak (1993), Szostak and Ellington (1993), Sassanfar and Szostak (1993), and C. Wilson and Szostak (1995). Early work is described in Joyce (1992). For a review, see Lorsch and Szostak (1996).

  Recent experiments by Szostak's group focus on the evolution of an alternative TNA molecule—the simpler analog of RNA that incorporates the 4-carbon sugar threose. Szostak writes: “By doing in vitro evolutionary experiments with TNA sequences (something we're just now able to start) we can see if it's possible to evolve TNA molecules with specific binding or catalytic properties. If the answer is yes, then one could at least imagine TNA based life-forms.” [Jack Szostak to RMH, 21 August 2004]

  p. 238 David Bartel: Szostak et al. (2001).

  p. 238 Synthetic Life: See, for example, Szostak et al. (2001), Gibbs (2004), and Rasmussen et al. (2004). Szostak writes, “What we're doing is really no different from what you or any other pre-biotic chemist is trying to do. We define possible reactions, see what works and what doesn't, and hope it all points to a plausib
le pathway. Our experiments happen to involve polymers and large aggregates of small molecules, instead of small molecule reactions, but the principle of testing by experiment is the same.” [Jack Szostak to RMH, 21 August 2004]

  p. 239 Martin Hanczyc and Shelley Fujikawa: Hanczyc et al. (2003).

  p. 239 encapsulated RNA strands: David Deamer has demonstrated another simple mechanism for incorporating RNA into vesicles. When he dried a solution with lipid vesicles and RNA strands, the vesicles collapsed into thin layers of molecules with RNA interleaved. When water was added, the vesicles reformed with RNA trapped inside (Shew and Deamer 1983). See also Deamer (1997, pp. 254-255).

  Swiss biochemist Pier Luigi Luisi demonstrated that lipid vesicles could “replicate” if larger vesicles were forced through a fine mesh (Luisi and Varela 1989, Luisi 2004).

  p. 239 To test their ideas: Chen et al. (2004, p. 1476) conclude, “Darwinian evolution at the organismal level might therefore have emerged earlier than previously thought—at the level of a one-gene cell.”

  When asked if this model represents a metabolism-first or genetics-first origin, Szostak replied: “I don't think it's metabolism first, at least in the way that's normally thought of, but it's also more than the simplest genetics-first models since there is both the spatial and informational aspect to the system…. Of course, if there is a way of having [RNA nucleotides] generated inside the vesicle by some network of metabolic reactions, that would be great. In fact, if the network of metabolic reactions works by the uptake of small membrane permeable molecules … and generates larger impermeable molecules, then the same osmotic effects would operate and drive vesicle growth, potentially providing a selection for better metabolic networks.” [Jack Szostak to RMH, 7 September 2004]

  p. 239 “If we can get …”: Jack Szostak, as quoted in Howard Hughes Medical Institute News, September 2, 2004.