H00102--00A, Front mat Genesis
Page 38
formed deep in the crust. Samples are widely available commercially, but the
outcrops occur on the San Carlos Indian reservation, so access and collect-
ing 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 chem-
272
GENESIS
ists discount Freund’s findings as experimental artifacts resulting from sur-
face contamination. See, for example, Keppler et al. (2003) and M. Wilson
(2003).
p. 127
no single dominant source: A few authors imply that it re-
mains a mystery which of several sources of organic molecules—Miller-type
surface synthesis, hydrothermal processes, impacts, or deep-space synthe-
sis—was dominant. Orgel (1998a, p. 491), for example, states: “Three popu-
lar hypotheses attempt to explain the origin of prebiotic molecules: synthesis
in a reducing atmosphere, input in meteorites and synthesis on metal sul-
fides in deep-sea vents. It is not possible to decide which is correct.” Simi-
larly, 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 contin-
ues, “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 character-
NOTES
273
istics 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 CH in some of his experiments were
4
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 tech-
niques of textual comparison have long been employed for shorter manu-
scripts, 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 proposi-
tion 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).
274
GENESIS
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 me-
teorite 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 mat-
ter 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 car-
bonaceous 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 con-
densation of oceans, it follows that surface films would have been present at
air-water interfaces. . . . This material would thereby be concentrated for
NOTES
275
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 Con-
ference 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 sa-
linity 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). Regard-
ing Lerman’s contributions, James Ferris writes: “Unfortunately a head in-
jury 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 pro-
posal 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: Me-
tabolism Recapitulates Biogenesis. See also Lasaga et al. (1971), who estimated
276
GENESIS
that a primordial oil slick on the Archean ocean could have achieved a thick-
ness of 1 to 10 meters.
p. 157
British biophysicist John Desmond Bernal: 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 stud-
ied 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-in-
duced polymerization of RNA, principally by the common clay montmoril-
lonite 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 min-
eral 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-con-
densation of nucleotides to form the phosphodiester bond in aqueous solu-
tion. 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 imi-
dazole activating group that was introduced first by other workers and popu-
larized by Lohrmann and Orgel.” [James Ferris to RMH, 22 August 2004]
p. 158
Leslie Orgel: Experiments on polypeptide formation are de-
scribed in Ferris et al. (1996), Hill et al. (1998), and Liu and Orgel (1998).
p. 158
“polymerization on the rocks”: Orgel (1998b). See also
Acevedo and Orgel (1986).
p. 158
One possible answer: Chen et al. (2004). Subsequent work by
Szostak’s group reveals that a wide variety of powdered minerals promotes
similar vesicle formation.
p. 159
Gustaf Arrhenius: Arrhenius and co-workers’ studies of
d
ouble-layer hydroxides appear in Arrhenius et al. (1993), Gedulin and
Arrhenius (1994), and Pitsch et al. (1995).
p. 160
Joseph Smith: Smith’s mineralogical proposal on “Biochemical
evolution” appeared in J. V. Smith (1998), Parsons et al. (1998), and J. V.
Smith et al. (1999).
p. 160
A. G. (Graham) Cairns-Smith: The clay-life hypothesis first
NOTES
277
appeared in “The structure of the primitive gene and the prospect of gener-
ating life” (manuscript dated October 1964). The first publication was
Cairns-Smith (1968); see also Cairns-Smith (1977). Important book-length
elaborations include Genetic Takeover and the Mineral Origins of Life (Cairns-Smith 1982) and Clay Minerals and the Origin of Life (Cairns-Smith and
Hartman 1986). Popular accounts of these ideas include Seven Clues to the
Origin of Life (Cairns-Smith 1985a) and a Scientific American article, “Clays and the origin of life” (Cairns-Smith 1985b).
p. 160
“I believe . . . ”: Cairns-Smith (1985b, p. 900).
p. 160
“Evolution did not . . . ”: Cairns-Smith (1985a, p. 107).
p. 161
“The answer”: Cairns-Smith (1985b, pp. 91-92).
p. 161
“I’m an organic chemist . . .”: A. G. Cairns-Smith seminar, “Clay
Minerals and the Origin of Life,” Carnegie Institution, June 16, 2003.
p. 162
clay minerals commonly display: Varieties of clay defects are
illustrated in Cairns-Smith (1988, 2001).
p. 162
“In two-dimensional . . . ”: Cairns-Smith (1985b, p. 96).
p. 163
particularly stable sequences: Cairns-Smith writes: “The word
stable sounds like thermodynamically most stable whereas in fact any infor-
mational structure has to be at least a little bit unstable. Like any genetic
information it would owe its prevalence to indirect effects that favour its
own survival and/or propagation—e.g., suppose that a particular defect ar-
rangement catalyses (a little bit) the production of di- or tri-carboxylic ac-
ids, which in turn assist clay synthesis by transporting aluminum.” [A.
Graham Cairns-Smith to RMH, 31 August 2004]
p. 164
In 1988: Cairns-Smith (1988).
p. 164
“The first step . . .”: Cairns-Smith (1988, p. 244).
p. 164
“Can the material . . .”: [A. Graham Cairns-Smith to RMH, 18
December 2003]
13
LEFT AND RIGHT
p. 167
“Assemblage on corresponding . . .”: Goldschmidt (1952,