Genesis: The Scientific Quest for Life's Origin

by Robert M. Hazen

  p. 118 Such reactions occur rapidly: These experiments are detailed in Cody et al. (2004).

  p. 118 Fischer–Tropsch (F–T) synthesis: A number of researchers have studied F–T synthesis under hydrothermal conditions (McCollom and Simoneit 1999, McCollom and Seewald 2001, Foustoukos and Seyfried 2004).

  p. 118 Recent intriguing analyses: Sherwood-Lollar et al. (1993, 2002).

  p. 119 thiols and thioesters: The possible role of these sulfur-containing compounds in life's origins has been detailed by de Duve (1995a, 1995b).

  9

  PRODUCTIVE ENVIRONMENTS

  p. 121 “The limits of life …”: Nealson (1997b, p. 23677). Nealson notes that the quote appeared “again in slightly different form in 1998 in a Caltech lecture, and in the final form in Nealson and Conrad (1999).”

  p. 121 immense tenuous clouds: Ehrenfreund and Charnley (2000) enumerate several types of interstellar structures where organic synthesis occurs. The density of these structures ranges from about one atom per cubic centimeter in “interstellar clouds” to a million atoms per cubic centimeter in “dense molecular clouds.” Louis Allamandola writes: “A volume roughly the size of a large auditorium is home to only one tenth-micronsized dust grain. It is the dust which absorbs background starlight, making dark interstellar molecular clouds dark. Thus their sizes are enormous, often measured in thousands of light-years.” He notes that in these clouds, PAHs, which are produced primarily during earlier star-formation processes, are more abundant than all other interstellar molecules combined. [Louis Allamandola to RMH, 16 July 2004]

  p. 122 more than 140 different compounds: Infrared spectroscopy of molecular clouds is reviewed by Pendleton and Chiar (1997) and Rawls (2002). An up-to-date list of all identified interstellar molecular species is available at: http://www-691.gsfc.nasa.gov/cosmic.ice.lab/interstellar.htm.

  p. 122 Allamandola and co-workers' experiments: See, for example, Bernstein et al. (2002). A lively, accessible, and richly illustrated account of this research appears in Scientific American (Bernstein et al. 1999a). Similar experiments have been performed by a research team based at the Leiden Observatory in The Netherlands (Muñoz Caro et al. 2002).

  James Ferris writes: “[Allamandola] spent a good part of his career working in Mayo Greenberg's lab in Leiden before going to Ames. Greenberg developed this apparatus and approach and Allamandola adopted the design after going to Ames.” [James Ferris to RMH, 22 August 2004]

  p. 123 Evidence from space: Reviews of the rich variety of organic molecules recovered from meteorites include Cronin and Chang (1993), Glavin et al. (1999), Becker et al. (1999), Ehrenfreund and Charnley (2000), and Cody et al. (2001a). Cometary organic molecules, though less well documented, are described by Chyba et al. (1990) and Ehrenfreund and Charnley (2000). Kwok (2004) also emphasizes the important role of “proto-planetary nebulae”—the envelopes of gas and dust around newly forming stars—in the production of organic molecules. See also Oró (1961b), Urey (1966), Kvenvolden et al. (1970), Cronin and Pizzarello (1983), Anders (1989), Cronin (1989), Delsemme (1991), Engel and Macko (1997), Irvine (1998), and Pizzarello and Cronin (2000).

  p. 123 seeded abundantly: Allamandola argues that interstellar ice particles could have provided much more than simple organic building blocks. “These could well have been a source of prebiotic/biogenic molecules which played a specific role in the origin of life. Going even further, I am beginning to think we should also consider the possibility that the chemistry in these ices might be even more advanced, perhaps being a fountainhead of life” [Louis Allamandola to RMH, 16 July 2004]

  p. 123 “that's garbage …”: Stanley Miller as quoted by Radetsky (1992, p. 80).

  p. 123 “Even if cosmic debris …”: Jeffrey Bada as quoted by Radetsky (1998, p. 37). More recently Bada (2004, p. 7) has softened his objections and points to a combination of sources: “It is now generally assumed that the inventory of organic compounds on the early Earth would have been derived from a combination of both direct Earth-based syntheses and inputs from space.”

  p. 123 It's hard to imagine: In the mid-1990s, when NASA scientists subjected carbon-rich meteorite fragments to realistic impact velocities of 3 miles per second, about 99.9 percent of the amino acids were obliterated (Peterson et al. 1997). They concluded that impact velocities of the Murchison and other amino-acid-bearing meteorites must have been significantly less, perhaps owing to aerobraking, thus preserving more of the delicate organic molecules.

  p. 123 impacts don't destroy all: Other shock experiments to induce organic synthesis have been reported by C. P. McKay and Borucki (1997), who used a high-energy infrared YAG laser to shock-heat a gaseous sample to temperatures greater than 10,000°C. These experiments simulate the effects of an impact on the atmosphere.

  p. 123 giant experimental gas gun: See Blank et al. (2001).

  p. 124 idea of Friedemann Freund: Freund et al. (1980, 1999, 2001).

  p. 124 “Maybe,” he remarked: Friedemann Freund to Wesley Huntress, undated note ca. 2000 attached to a copy of Freund et al. (1999).

  p. 125 “I am a hundred percent sure …”: [Anne M. Hofmeister to RMH, 21 November 2002]

  p. 125 synthetic magnesium oxide: Crystal growth of MgO is described by Freund et al. (1999), who also document the identity of extracted carboxylic acids. Freund's studies on MgO properties include Kathrein and Freund (1983), Kötz et al. (1983), and Freund et al. (1983).

  p. 126 gem-quality olivine: Freund's olivine samples come from the classic San Carlos, New Mexico, locality, which is an active gem-producing area. The gemmy green olivine crystals (also known as peridot), as much as an inch across, comprise up to 50 percent of the basaltic rock, which was formed deep in the crust. Samples are widely available commercially, but the outcrops occur on the San Carlos Indian reservation, so access and collecting is restricted.

  p. 126 100 parts per million carbon: Keppler et al. (2003) disagree with this claim for San Carlos olivine. Their experiments on olivine growth under carbon-saturated conditions produced crystals with no more than 0.5 part per million carbon.

  p. 126 “I ran a sample …”: [George R. Rossman to Anne M. Hofmeister, 20 December 2002] Many mineralogists and solid-state chemists discount Freund's findings as experimental artifacts resulting from surface contamination. See, for example, Keppler et al. (2003) and M. Wilson (2003).

  p. 127 no single dominant source: A few authors imply that it remains a mystery which of several sources of organic molecules—Miller-type surface synthesis, hydrothermal processes, impacts, or deep-space synthesis—was dominant. Orgel (1998a, p. 491), for example, states: “Three popular hypotheses attempt to explain the origin of prebiotic molecules: synthesis in a reducing atmosphere, input in meteorites and synthesis on metal sulfides in deep-sea vents. It is not possible to decide which is correct.” Similarly, Miller and his colleagues have at times discounted both hydrothermal zones and extraterrestrial sources as trivial (S. L. Miller and Bada 1988; Stanley Miller and Jeffrey Bada as quoted in Radetsky 1992, 1998). Other more ecumenical estimations of multiple organic sources include Chyba and Sagan (1992) and Lahav (1999).

  INTERLUDE—MYTHOS VERSUS LOGOS

  p. 129 “People of the past …”: Armstrong (2000, p. xiii). She continues, “Myth looked back to the origins of life, to the foundations of culture, and to the deepest levels of the human mind. Myth was not concerned with practical matters, but with meaning.” By contrast, “Logos was the rational, pragmatic, and scientific thought.” Armstrong argues, “People of Europe and America [have] achieved such astonishing success in science and technology that they began to think that logos was the only means to truth and began to discount mythos as false and superstitious.”

  p. 129 “Whoa, …”: [Margaret H. Hazen to RMH, 30 May 2004]

  10

  THE MACROMOLECULES OF LIFE

  p. 133 “To purify …”: Lehninger et al. (1993, p. 5).

  p. 133 One of the transforming discoveries: Lehninger et al. (1993). The
extraordinary Web site http://biocyc.org/ECOO157/new-image?object=Compounds tabulates all known small organic molecules from the microbe Escherichia coli.

  p. 134 “I can no longer …”: Friedrich Wöhler to his teacher Jacob Berzelius, February 28, 1828. This discovery (Wöhler 1828) was made in the same year that Wöhler isolated and named the element beryllium.

  p. 134 Four key types of molecules: For an overview of the characteristics of sugars, amino acids, carbohydrates, and nucleic acids, see Lehninger et al. (1993).

  p. 135 Sugars are the basic building blocks: Estimates of Earth's total biomass place cellulose, the abundant glucose polymer that forms leaves, stems, trunks, and other plant support structures, at the top of the list (Lehninger et al. 1993, pp. 298 et seq).

  p. 135 For every useful molecule: Of the several proposed prebiotic mechanisms for biomolecular synthesis, Miller's original spark experiments produce perhaps the highest percentage of useful molecules. Fully 6 percent of the carbon atoms introduced as CH4 in some of his experiments were incorporated into amino acids, for example (S. L. Miller and Urey 1959a). For this reason alone, Miller and his supporters often argue that electric discharge in a reducing atmosphere is the most likely origin scenario.

  p. 136 life is even choosier: See, for example, Bonner (1995). The problem of chiral selection is discussed in more detail in Chapter 13.

  p. 136 molecular phylogeny: See, for example, Pace (1997), Pennisi (1998), and Sogin et al. (1999).

  p. 137 The Canterbury Tales: Barbrook et al. (1998). Similar techniques of textual comparison have long been employed for shorter manuscripts, but this study used the same computer algorithms as applied to genomic data.

  p. 138 Carl Woese: The original proposal for three domains of life, including the Archaea, appears in Woese and Fox (1977). See also Woese (1978, 1987, 2000, 2002). A biographical sketch of Carl Woese, including an overview of his work, is provided by Morell (1997).

  p. 139 thrive at elevated temperature: Perspectives on the proposition that the last common ancestor was an extremophile are provided, for example, by Gogarten-Boekels et al. (1995), Forterre (1996), and Reysenbach et al. (1999).

  Bruce Runnegar writes, “There is a last common ancestor and it was a highly derived organism. It tells us very little about Earth's earliest cells in the same way that living birds do not reveal the attributes of dinosaurs.” [B. Runnegar to RMH, 4 March 2005]

  p. 141 swap sections of DNA: Gogarten et al. (1999), Doolittle (2000), and Woese (2002).

  p. 141 “last common ancestor”: See, for example, Woese (1998) and Ellington (1999). An important conclusion of recent studies is that, because of gene transfer, there is no single last common cellular ancestor. Woese (1998, p. 6854) writes: “The universal ancestor is not a discrete entity. It is, rather, a diverse community of cells that survives as a biological unit. The universal ancestor has a physical history but not a genealogical one.”

  p. 141 all cells employ RNA: Woese (2002).

  p. 141 simple metabolic strategy: Woese (1998, p. 6855) states that the biochemical repertoire of the universal ancestor included “a complete tricarboxylic acid cycle, polysaccharide metabolism, both sulfur oxidation and reduction, and nitrogen fixation.” Pace (1997, p. 734) comments that “the earliest life was based on inorganic nutrition.”

  p. 142 primordial “oil slick”: Lasaga et al. (1971). See also Morowitz (1992).

  11

  ISOLATION

  p. 143 “The self-assembly process …”: Deamer (2003, p. 21).

  p. 143 Lipid molecules: For an accessible overview of lipid molecules and their spontaneous organization into bilayers, see Tanford (1978) and Segré et al. (2001).

  p. 144 Alec Bangham: See, for example, Bangham et al. (1965). Some researchers initially called these structures “banghasomes.” [Harold Morowitz to RMH, 10 August 2004]

  p. 144 Luisi and co-workers: Luisi (1989, 2004), Luisi and Varela (1989), Luisi et al. (1994), Bachmann et al. (1992), and Szostak et al. (2001). See also Segré et al. (2001).

  p. 145 counted as classics: Pasteur (1848), Miller (1953), and Bernstein et al. (1999b).

  p. 146 Deamer returned: Deamer and Pashley (1989). For additional information, see Zimmer (1993) and Deamer and Fleischaker (1994).

  p. 146 Murchison meteorite: For a description of the Murchison meteorite and related research, see Grady (2000, pp. 350-352).

  p. 147 Their straightforward procedure: The eclectic mix of organic molecules in Murchison included some species, like amino acids, that were soluble in water; some, like lipids, that were soluble in chloroform or other organic solvents; and a complex tarry residue, called by the generic name “kerogen,” which is difficult to analyze. Recent studies by Cody et al. (2001a) suggest that this residue consists of a complexly linked mass of rings, chains, and other smaller groups of atoms. It is not evident that such insoluble matter could have played much of a role in prebiotic chemistry.

  p. 148 breakthrough moment: The discovery paper by Deamer and Pashley (1989) was entitled “Amphiphilic components of the Murchison carbonaceous chondrite: Surface properties and membrane formation.” In this article they state, “If amphiphilic substances derived from meteoric infall and chemical evolution were available on the prebiotic earth following condensation of oceans, it follows that surface films would have been present at air-water interfaces…. This material would thereby be concentrated for self-assembly into boundary structures with barrier properties relevant to function as early membranes.”(p. 37) This paper was especially noteworthy because it followed by a year the publication of a theoretical paper by Morowitz et al. (1988) that proposed such an origin scenario.

  p. 148 NASA Ames team: Dworkin et al. (2001).

  p. 149 a colorful photograph: The Washington Post (Kathy Sawyer, “IN SPACE; CLUES TO THE SEEDS OF LIFE,” January 30, 2001, p. A1).

  p. 149 astrobiology meetings: The First Astrobiology Science Conference was held April 3–5, 2000, at the NASA Ames Research Center, Moffett Field, California. Deamer's lecture was entitled “Self-assembled Vesicles of Monocarboxylic Acids and Alcohols: A Model Membrane System for Early Cellular Life” (Apel et al. 2000).

  p. 151 we had made bilayer membranes: These results were reported at the 221st Annual Meeting of the American Chemical Society, held in San Diego, California, April 1-5, 2001.

  p. 151 Recent work: Knauth (1998) provides estimates of higher salinity in the Archean ocean. Salt inhibition of amphiphile self-organization is reported in Monnard et al. (2002).

  p. 152 atmospheric aerosols: Dobson et al. (2000). See also Ellison et al. (1999), Tuck (2002), and Donaldson et al. (2004). These studies, which present theoretical analyses of aerosol dynamics and atmospheric residence times, build on earlier speculative comments regarding the possible roles of aerosols by Woese (1978) and Lerman (1986, 1994a, 1994b, 1996). Regarding Lerman's contributions, James Ferris writes: “Unfortunately a head injury in an automobile accident had a major effect on his life and he was unable to get a full paper written on this proposal. He discussed this proposal at meetings and it was well known in the origins of life community.” [James Ferris to RMH, 22 August 2004].

  12

  MINERALS TO THE RESCUE

  p. 155 “But I happen to know …”: Updike (1986, pp. 328-329).

  p. 155 The first living entity: Portions of this chapter were adapted from Hazen (2001).

  p. 156 Mineralogist Joseph V. Smith: J. V. Smith (1998), Parsons et al. (1998), and J. V. Smith et al. (1999). Other authors, including Cairns-Smith et al. (1992), have also proposed that porous minerals might have provided a measure of protection for proto-life.

  p. 157 a primitive slick: The oil-slick hypothesis was championed by Morowitz (1992) in his influential book The Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis. See also Lasaga et al. (1971), who estimated that a primordial oil slick on the Archean ocean could have achieved a thickness of 1 to 10 meters.

  p. 157 British biophysicist John Desmond Ber
nal: Bernal (1949, 1951). The Swiss-born geochemist Victor Goldschmidt also suggested that minerals played a role in life's origin, but his thoughts, presented as a lecture in 1945 and published posthumously (Goldschmidt 1952), had little impact on the origins community (Lahav 1999, p. 250).

  p. 157 In a 1978 study: Lahav et al. (1978). See also Lahav and Chang (1976) and Lahav (1994).

  p. 157 NASA-sponsored teams: Among the chemists who have studied roles of clays and other fine-grained minerals in prebiotic processes, two NASA Specialized Center of Research and Training (NSCORT) groups at Scripps Institution of Oceanography (La Jolla, California) and Rensselaer Polytechnic Institute (Troy, New York) have made notable contributions.

  p. 157 James Ferris: Reports by Ferris and colleagues on mineral-induced polymerization of RNA, principally by the common clay montmorillonite and the phosphate hydroxyapatite, include Ferris (1993, 1999), Holm et al. (1993), Ferris and Ertem (1992, 1993), Ferris et al. (1996), and Ertem and Ferris (1996, 1997). Images of organic molecules on ideally smooth mineral surfaces have been published, for example, by Sowerby et al. (1996) and Uchihashi et al. (1999).

  p. 157 “activated” RNA: Ferris writes: “My experiments work only if activated nucleotides are reacted. The thermodynamics is against self-condensation of nucleotides to form the phosphodiester bond in aqueous solution. That's why nature uses ATP in place of AMP to form RNA. By the way, ATP and ADP do not work in the clay catalyzed reaction so we use the imidazole activating group that was introduced first by other workers and popularized by Lohrmann and Orgel.” [James Ferris to RMH, 22 August 2004]

  p. 158 Leslie Orgel: Experiments on polypeptide formation are described in Ferris et al. (1996), Hill et al. (1998), and Liu and Orgel (1998).