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Proc. Natl. Acad. Sci. USA Vol. 96, pp. 3479-3485, March 1999 Colloquium Paper This paper was presented at the National Academy of Sciences colloquium "Geology, Mineralogy, and Human Welfare, " held November 8-9, 1998 at the Arnold and Mabel Beckman Center in Irvine, CA. ~ ;, . . .. . . ~ ., Biochemical evolution III: Polymerization on organophilic silica-rich surfaces, crystal chemical modeling, formation of first cells, and geological clues (biological evolution/silica/feldspar/zeolite/first cell walls) JOSEPH V. SMITH*T, FREDERICK P. ARNOLD, JR.l, IAN PARSONS§, AND MARTIN R. LEE§ *Department of Geophysical Sciences and Center for Advanced Radiation Sources, 5734 South Ellis Avenue, The University of Chicago, Chicago, IL 60637; "Advanced Research Systems, 5640 South Ellis Avenue, The University of Chicago, Chicago, IL 60637; and Department of Geology and Geophysics, University of Edinburgh, Edinburgh EH9 3JW, United Kingdom ABSTRACT Catalysis at organophilic silica-rich surfaces of zeolites and feldspars might generate replicating biopoly- mers from simple chemicals supplied by meteorites, volcanic gases, and other geological sources. Crystal-chemical mod- eling yielded packings for amino acids neatly encapsulated in 10-ring channels of the molecular sieve silicalite-ZSM-5- (mutirzaiteJ. Calculation of binding and activation energies for catalytic assembly into polymers is progressing for a chemical composition with one catalytic Al-OH site per 25 neutral Si tetrahedral sites. Internal channel intersections and external terminations provide special stereochemical features suitable for complex organic species. Polymer migration along nano/ micrometer channels of ancient weathered feldspars, plus exploitation of phosphorus and various transition metals in entrapped apatite and other microminerals, might have gen- erated complexes of replicating catalytic biomolecules, leading to primitive cellular organisms. The first cell wall might have been an internal mineral surface, from which the cell devel- oped a protective biological cap emerging into a nutrient-rich "soup." Ultimately, the biological cap might have expanded into a complete cell wall, allowing mobility and colonization of energy-rich challenging environments. Electron microscopy of honeycomb channels inside weathered feldspars of the Shap granite (northwest England) has revealed modern bacteria, perhaps indicative of Archean ones. All known early rocks were metamorphosed too highly during geologic time to permit simple survival of large-pore zeolites, honeycombed feldspar, and encapsulated species. Possible microscopic clues to the proposed mineral adsorbents/catalysts are discussed for planning of systematic study of black cherts from weakly metamorphosed Archaean sediments. Introduction and Summary of Biochemical Evolution: Part I. Darwin/Oparin/Haldane/Watson/Crick biological evolu- tion provides a plausible framework for integrating the patchy paleontological record with the complex biochemical zoo of the present Earth (literature review: ref. 1~. But how could the first replicating and energy-supplying molecules have been assembled from simpler materials that were undoubtedly available on the early protocontinents? Bernal preferred "life" to begin by catalytic assembly on the surface of a mineral, but all pre-1998 attempts using clays and other minerals to assem- ble an integrated scheme of physicochemical processes had significant weaknesses. Catalysis of organic compounds dis- persed in aqueous "soup" requires a mechanism for concen- trating the organic species next to each other on a catalytic substrate. Biochemically significant polymers, such as polypep PNAS is available online at www.pnas.org. tides and RNAs, must be protected from photochemical destruction by solar radiation and must not be overly heated. A stable cell wall is needed to protect the first primitive organ~sm. Part I (1) pointed out that certain inorganic materials have internal surfaces that are both organophilic and catalytic, allowing efficient capture of organic species for catalytic assembly into polymers in a protective environment. These physicochemical features are related to the state of the art for zeolite catalysts in the chemical industry, the observed prop- erties of zeolite, feldspar (2), and silica minerals, and a plausible framework for the accretion and early history of the Earth's crust and atmosphere (1~. Various materials from the zeolite, feldspar, and silica mineral groups were listed as having surfaces with the capacity to adsorb organic species preferentially over water molecules and catalyze them into polymers. We focus here on mutinaite, a zeolite mineral recently discovered in Antarctica, which is the natural analog of the ZSM-5/silicalite series of synthetic microporous mate- rials (Note: Microporous does not imply that the pores are of micrometer size; indeed the pores in zeolites are generally less than a nanometer across). This type of molecular sieve is based on a tetrahedral framework containing a three-dimensional channel system spanned by rings of 10 oxygen atoms (Fig. 1 Upper Left and Upper Right`). The silica-rich end-member of the ZSM-5 series, silicalite, is very organophilic, and Al-substituted synthetic relatives catalyze organic reactions at Al-OH re- gions. Silicalite provides a useful basis for modeling adsorp- tion/catalytic processes that would apply in principle, but not in detail, to other materials in paper I (1~. Nonexperts in computer modeling of crystal structures might note the conventions in Fig. 1 Upper Left and Upper Right. Three-dimensional imaging must be idealized and trun- cated. Fig. 1 Upper Left displays 10 oxygen atoms as spheres half the conventional atomic radius of 1.4 A. All other atoms are shown merely by the intersection of spokes. Each tetrahe- drally coordinated (T) atom lies at the intersection of four yellow spokes and each O atom at the intersection of two maroon spokes. Fig. 1 Upper Right shows all the O atoms as half-size spheres, and the Si and Al types, respectively, of T atoms as yellow and pink spheres joined by thin grey spokes. Only four 10-rings are shown lying in the wall of the channel, and you, the reader, must imagine the channel extending up and down to the surface of the crystal where some adjustment of chemical bonding is needed. Fig. 1 Upper Right is deliber- ately tilted slightly with respect to Fig. 1 Upper Left. The lTo whom reprint requests should be addressed. e-mail: smith@geol. uchicago.edu. 3479
3480 Colloquium Paper: Smith et al. Proc. Natl. Acad. Sci. USA 96 (1999J FIG. 1. Computer graphics of part of the atomic framework of silicalite/ZSM-5 with amino acids encapsulated in energetically favored positions. (Upper Left) Tetrahedral framework of silicalite/ZSM-5 showing a 10-ring channel down the y-axis. Most of the figure consists of spokes linking atom positions. One 10-ring of O atoms is shown by spheres displayed at half the formal atomic radii. See text for explanation: oxygen atoms, maroon spheres and intersection of maroon spokes; tetrahedral (T) atoms, intersection of yellow spokes. Only four 10-rings are shown, whereas a perfect crystal would have an infinite number defining the channel. Also shown are the tilted five-rings. Ten-ring channels present in the plane of the paper are difficult to see without rotation on the video display. (Upper Right) Four glycine molecules in the zwitterion configuration encapsulated in silicalite/ZSM-5. Glycine consists of a central C atom bonded to two H. one carboxyl COO-, and one amine NH3+. The cluster of three molecules near the middle of the near-vertical channel has been optimized to interact mutually by way of hydrogen bonding and to be suspended by van der Waals bonding from the O atoms of the 10-ring channel. The fourth molecule is oriented along a horizontal 10-ring channel. All the framework O atoms are represented by half-size maroon spheres. The tetrahedrally coordinated atoms are represented by small spheres differentiated by color: So, yellow, Al, pink. The glycine molecule is represented by a stick model with conventional color code: O. red; C, grey; N. blue; H. white. The orientation of the channel system is rotated slightly from that in UpperLeft. (LowerLeft) Three glycine molecules within a 10-ring channel of silicalite, viewed down the y- axis. Coloring as in Upper Left; silicalite/ZSM-5 framework shown as tetrahedra (Si, Al) and balls (O); glycine shown as tubes. Note the alignment of the amino acids parallel to the channel and restricted lateral positions within the channel. (Lower Right) Two of the glycine molecules from Lower Left, viewed along the z-axis. Note the 'head-to-tail' alignment of the carboxylate group of an amino acid with the amino group of the next amino acid. Once again, the positional constraints on the amino acids in the channel, as well as their parallel alignment with the channel, are emphasized. conventions for amino acids are given in the Fig. 1 Upper Right legend. Introduction to New Unpublished Studies. This third part integrates the current state of research on biochemical evolu
Colloquium Paper: Smith et al. tion that will be presented at the Colloquium on Geology, Mineralogy, and Human Welfare. tThe second part on weath- ered honeycombed feldspars and associated bacteria in a modern granite was under preparation as this third part was being completed and will be published (57) in the regular part of the Proceedings before this paper. Its key contents are given briefly in this paper and are illustrated in Fig. 3.] We begin with crystal-chemical modeling of amino acids inside 10-ring chan- nels of the chosen zeolite, silicalite (Figs. 1 Upper Right, Lower Left, and Lower Right and 2 Upper and Lower). The channel walls are electrically neutral except for arbitrary replacement of 4% of the silicon-oxygen tetrahedra by aluminum-oxygen- hydroxyl catalytic centers. This 1 in 25 replacement yields nice graphics and has no particular scientific significance. More- over, this ratio can be varied to increase or decrease the spacing of catalytic centers along the 10-ring channels and to vary the electrical forces on adsorbed molecules and the repeat dis- tances of the polymers generated by catalytic condensation. We end with new ideas for generating primitive protocells inside the honeycombed weathered surfaces of feldspars tPart II (57~. Fig. 3 shows scanning-electron micrographs of the crystallographically controlled channels in feldspars from the Shap granite, northwest England, together with associated modern bacteria, as models for speculation on the develop- ment of the first primitive cells. Now to details. Preliminary Simulations of Encapsulation of Amino Acids in Silicalite/ZSM-5 and Catalytic Generation of Biopolymers. The crystal-chemical reviews in refs. 1 and 2 are updated by papers in the following areas: · crystal chemistry of high-silica materials: Fourier Transform- Raman studies of single-component and binary adsorption in silicalite-1 (3~; vapor adsorption in thin silicalite-1 films studied by spectroscopic ellipsometry (4~; adsorption/de- sorption of n-alkanes on silicalite crystals (5~; adsorption equilibria of C1 to C4 alkanes, CO2, and SF6 on silicalite (6~; adsorption of linear and branched alkanes in zeolite sili- calite-1 (7~; combined quantum mechanical/molecular me- chanics ab Ratio modeling, demonstrating that the most stable Br0nsted sites occur in high-silica zeolites (8~; simu- lation of adsorption and diffusion of hydrocarbons in sili- calite, demonstrating that a linear hydrocarbon moves more freely than a branched one, whose CH group becomes locked at a channel intersection (9~; adsorption isotherms of linear alkanes in ferrierite-smaller ones, C1-C5, fill the entire pore system, whereas C6 and C7 fit only in a 10-ring channel unless forced into an eight-ring channel by pressure (10, 11~; nuclear magnetic resonance of ~H in water ad- sorbed on silicalite (12~; heterogeneity of Br0nsted acid sites in Al-substituted faujasites (13~; nuclear magnetic resonance of 170 in silica, albite glasses, and stilbite (14, 15~; simulation of alkane adsorption in aluminophosphate-5, and calorim- etry of alkane absorption in high-silica zeolites (16, 17~; hydrophobic properties of all-silica beta zeolite (18~; struc- tural location of sorbed p-nitroaniline in silicalite/MFI molecular sieves from x-ray powder diffraction and 29Si Magic Angle Spinning-NMR (19~; nature, structure, and composition of hydrocarbon species obtained by oligomer- ization of ethylene on acidic H-ZSM-5 molecular sieve (20~: su~face chemistry of various minerals: coordination models for simple surfaces of oxide and silicate minerals (214; the role of intragranular microtextures and microstructures in chemical and mechanical weathering, direct comparisons of experimentally and naturally weathered alkali feldspars (22~; synthesis: RNA-catalyzed nucleotide synthesis of a pyrimi- dine (23~; conversion of amino acids into peptides at 373 K and pH 7-10 on (Ni, Fe)S surfaces (24), synthesis of glycylglycine dipeptide in the presence of kaolin clay and zeolites of Linde Type A, faujasite, and beta types (25~; Proc. Natl. A cad. Sc~. USA 96 (1999) 3481 thermodynamic calculation of amino acid synthesis in hot water and application to hydrothermal vents (black smok ers) on ocean floor (26~; polymerization of various amino acids on hydroxylamine and illite mica, with increasing adsorption affinity of oligomers longer than 7-mer (27-29~.] Figs. 1 Upper Right, Lower Left, and Lower Right and 2 Upper and Lower illustrate the current state of chemical modeling of amino acids encapsulated in a silicalite containing one Al substitution for 25 tetrahedral Si. Simulations were carried out using the Sorption module within the MSI/Cerius 2 program system (issued by Pharmacopeia, Princeton, NJ). The Consis- tent Valence Force Field was used for all atoms. Figs. 1 Lower Left and Lower Right and 2 Upper illustrate the results of packing simulations based on Monte Carlo tech- niques for glycine and histidine molecules encapsulated within the 10-ring channels of silicalite. It is possible at low pressure to pack 28 glycine molecules per unit cell or eight histidine. Fig. 1 Lower Left, and its rotated version in Fig. 1 Lower Right, demonstrate how the restriction of lateral motion by the channel system, coupled with charge effects at the amino and carboxyl ends of the amino acids, assists in orienting them correctly for the production of polypeptides. It can also be seen from these illustrations that one of the chief difficulties of the standard model for the formation of life, that of achieving sufficient concentration of reactants while excluding or min- imizing environmental degradation, is overcome. Not only are the growing biopolymers protected from outside interference and concentrated in the channels, but the limited degrees of freedom in molecular movements assist in orienting them optimally for polymerization. Simple molecular mechanics simulations within the SPAR- TAN computer package (Wavefunction, Irvine, CA) of various model complexes are shown in Fig. 2 Upper and Lower. Fig. 2 Upper (stereoview) illustrates an adenine hydrogen bound to the hydroxyl site of the 10-ring channel, with the carboxyl end of a glycine residue bound to the amino group of the adenine. This complex is correctly oriented for protonation of the hydroxyl group of the amino acid, followed by the elimination of water and the formation of an amide bond between the base and the amino acid. Such a reaction would be facilitated by a second metal site in the region, and provides one possibility for a precursor to the autocatalytic biopolymers of the 'pre-RNA' world. Electrostatic potential calculations on the system, using the PM3 semiempirical Hamiltonian within the MOPAC mo- lecular orbital package, indicate that this orientation is favor- able for the proposed reaction. Fig. 2 Lower illustrates one possibility of the bonding of an amino acid to the hydroxyl site of a zeolite-type material. It is obvious that the nitrogen functionalities of the histidine ring could form hydrogen bonds. Furthermore, it is also possible to bind the hydroxyl group of the carboxyl functionality to the acid site within the zeolite framework, then dehydrate and form a covalent bond between the surface and the amino acid. This process is analogous to the functionalized glass or plastic beads used in commercial DNA or protein synthesis, where the polymer chain grows away from the supported terminus. Reaction with hydronium ion, presuming mildly acidic media, would enable cleavage of the chain and would release the peptide into solution. In passing, it should also be noted that the amino terminus of the amino acid, which is facing away from the viewer, is oriented along the axis of the channel and hence, in analogy to Fig. 1 Lower Right, is oriented optimally for further reaction. Speculations on Biochemical Evolution Currently Under Evaluation. These illustrative results give confidence for spec- ulations that a microporous aluminum-substituted silica ma- terial with mainly hydrophobic channels and widely spaced Al-OH catalytic centers might act as a sausage machine for production of biopolymers that became assembled into pro
3482 Colloquium Paper: Smith et al. Proc. Natl. Acad. Sci. USA 96 (1999J FIG. 2. Computer graphics of part of the atomic framework of silicalite/ZSM-5 with amino acids encapsulated in energetically favored positions. (suppers) Stereopair of 10-ring channel of silicalite, showing a hydrogen-bound adenine-glycine complex itself hydrogen-bound to an acid site of the framework. Some framework atoms removed for clarity. This stereopair illustrates the ability of the zeolitic material both to accommodate large Copolymer precursors and to provide sites at which reactions may occur. (Some students initially have difficulty viewing stereopairs. If you have this problem, try putting a bright spot at the red atoms at the extreme top right and bottom left. Your brain should then be able to make your eyes swivel to achieve stereo with the left eye seeing the left dot. This contrasts with the cross-eye technique used in some biological modeling.) iLower) Histidine and water molecules in silicalite. Histidine was chosen for modeling because its imidazole ring can switch electronic states readily to catalyze
Colloquium Paper: Smith et al. tocells in protected honeycombs in weathered feldspars. Var- ious new matters are being evaluated currently from the viewpoint of physical and chemical processes and are modeled in detail for later publication: - First, channel intersections may prove important for stere- ochemical control of larger functional groups, especially at the end of a biopolymer. The intersection of an internal channel with the outer surface should be even more impor- tant and indeed might be considered as an anchor for a polymer that projects outwards into a 'soup.' · Second, after outward migration from an internal channel, the first biopolymers would begin to coil up like a snake and in certain places, such as a tapered tube in a honeycombed feldspar approximately 5 to 100 nanometers across, would begin to interact closely with the aluminosilicate surface. · Third, various biopolymers of different types might begin to interact and begin the evolution toward a protobacterium. · Particularly important would be the first generations of persistent energy-generating species containing phosphorus and electron-transferable transition metals. Very important is that K-rich feldspars from granites contain micrometer inclusions of the calcium phosphate-hydroxide/halide mineral apatite and transition-metal oxides, including ilmen- ite, spinet, and hematite, which might well be the primary reservoirs of these key elements. - At some stage, a protocell lining inside an aluminosilicate tube might develop a bilipid lining that would extend into a cap, ultimately allowing detachment from the silicate and free motion through a soup. Again, one might imagine a sausage machine popping off a free cell as the remaining protocell reconstituted itself ready for generation of the next free cell. Schematic graphics are being envisaged along with ideas for chemical bonding schemes. - All these processes would involve subtle effects related to diurnal and annual temperature cycles and wet/dry cycling driven both by solar radiation and lunar tides that would change the spatial distribution of chemical forces across mineral surfaces. Ideas are not developed enough so far to warrant further description here. Mineralogical Observations and Speculations: Electron Microscopy of Honeycombed Weathered Feldspars Bacteria and Protocells. Turning now to mineralogical information, Fig. 3 contains four scanning-electron micrographs of the crystal- lographically controlled honeycomb weathering on a modern surface of a K-feldspar from the Shap granite (30~. Particularly important are the micrometer-scale sausage shapes inter- preted as electron scattering from bacteria, somewhat shrunken from interaction with the electron beam. Many have no particular orientation with respect to the feldspar, but the bacterium in Lower Right is interpreted as sitting neatly in a crevice. The near correspondence between the segmentation of the proposed bacterium and the spacing of the feldspar honeycomb is intriguing. Perhaps it may ultimately be possible to quantify the original chemical linkages between the inor- ganic substrate and the unshrunken bacterium and to use them for modeling the above ideas. Coupling the catalytic production of polymers at the nano- meter scale with bacteria at the micrometer scale is plausible in the geologic context, but requires many flights of imagina- tion and a lot of faith. On the present Earth, volcanic glass transforms to zeolites in continental basins and ocean floors; the zeolites become metamorphosed to feldspars; and the whole mineralogical assemblage becomes converted over geo Proc. Natl. Acad. Sci. USA 96 (1999J 3483 logic time into granitic metamorphic rocks. Hence, we are comfortable in proposing that zeolites and feldspars would have coexisted on the early Earth, for which only the resultant granitic metamorphic rocks have been seen so far. Hence we can suggest for discussion purposes that a zeolite/silica/ altered feldspar sausage machine fed a range of biological polymers into feldspar honeycombs. As discussed above, in- termingling of polymers, generation of P-bearing energy- transporting species from apatite, and hydrogen-bond cou- pling between organic species and silica-rich walls, would have generated primitive protocells. To conclude the evolution into the first organisms, a cap between the dangerous outer regime of 'soup' and the inner protected world might have expanded to completely enclose the protocell so that it could swim into the future. Part IV, under preparation, will show graphics illustrating the scientific factors underlying these flights of fancy about cell formation. Conclusion. We conclude with matters of specific geological import. From the humanistic viewpoint, it would be extremely significant if the early forms of life had left behind some physicochemical evidence of their existence. The current carbon-isotope evidence of bulk samples is indicative of some kind of early biological evolution, but has no particular import for the atomic-level ideas presented above. A review of the geological evidence indicates that at least most and perhaps all of the early Archean rocks have been metamorphosed to a high enough level that all volcanic rocks have recrystallized. There can be little doubt that volcanoes would have been pumping out ash containing crystals of K-feldspar and silica minerals. By analogy with modern conditions, much of the ash would have been converted into zeolite beds, and there might well have been zoned beds of zeolite minerals interacting with salty lakes sloshed by tides and impacts. Some K-feldspar and zeolite crystals would have been exposed to an acidic rain, and honeycombed and grooved faces should have occurred (1, 2~. Primitive molecules would certainly have been available dis- persed in 'soups', as envisaged by many writers (1~. Here are some ideas for testing whether minerals produced by metamorphic recrystallization of earlier igneous origin might have retained some specific signature indicative of subtle biological processes involving feldspar, zeolite and silica min- erals: . - Ancient cherts (silica-hydroxyl-rich aggregates) range in color at least from black to brown, red, and orange-yellow. At least some of the color variation must result from transition metals, especially Fe and Mn, at different redox states. Might some carbonaceous species have survived in the black cherts? If so, would careful analysis reveal organic breakdown products specific to primary biocatalytic precur- sors? · Because early organisms would have needed P and various transition metals, would their absence or low abundance in the metamorphosed siliceous rocks be indicative of early biological scavenging by organisms that escaped into the 'soup'? - Particularly challenging, because of the possibility of com- plete failure, would be a hunt for x-ray diffraction evidence of surviving Si-rich molecular sieves. Silicalite and other large-pore zeolites have strong low-angle diffractions that would stand out in low-background patterns obtained with synchrotron x-rays, even at a concentration below 1%. Since the review in ref. 1, the following geological/biological publications have been added: the making and breaking of bonds, as well as to provide several potential sites for binding and reactivity. The histidine molecules are shown by a ball-and-stick arrangement and are colored as in Upper. The water molecules are represented by a bent bicolor rod with two white ends representing H, and the red center represents 0. The framework is represented by tetrahedra whose shared vertices are at O positions. A further reason for choosing histidine is its prevalence as a metal-binding site in modern proteins, undoubtedly an important function in the prebiotic world.
3484 Colloquium Paper: Smith et al. Proc. Natl. Acad. Sci. USA 96 (1999J - ~ . :~;:, = ~ ~ FIG. 3. Four scanning-electron micrographs of weathered feldspar from the Shap granite. (~Upper Left) Resin cast of honeycomb texture. The cast is somewhat flexible, so that some of the etched dislocations appear to be curved, although they were almost straight in the original feldspar, which has been dissolved away in HF. (~Upper Rights A near-planar surface close to bar601 with a trace of etched dislocations running horizontally and vertically across the image with ellipsoidal bacteria, some in strings like sausages hanging in a U.K. butcher's shop. (rower Left) More deeply weathered surface showing occasional traces of etched dislocations, with sausage-shaped bacteria. (Lower Right) Detail of honeycomb on the 001 surface of a feldspar honeycomb. The holes are etch pits formed on paired outcrops of dislocations that formed on exsolution lamellae. The bacterium, although perhaps partly shrunken by the instrument vacuum, is segmented on a scale remarkably similar to the spacing of the etch pits. Details of the feldspar weathering are given in Part II (57~. · stardust and meteorites: Photochemical evolution of inter- stellar/precometary organic material (31~; silica-rich micro- meter objects in a carbonaceous chondrite (32~; · planetary impact processes: Survival of amino acid in large comet impacts (33~; · early geologic events on Earth: Nitrogen fixation by volcanic lightning (34~; redox state of upper-mantle peridotites under the ancient cratons, and possible equilibrium of diamonds with methane-nitrogen-rich fluids (35~; new revised Pb-ages of Greenland gneisses at 3.65-3.70 instead of earlier 3.85 gigayear-before-present (36~; interpretation of geologic ev- idence in favor of plate-tectonic processes in the Archean era (374; interpretation of Archean magmatism and defor- mation in nonplate tectonics terms (38~; details of Precam- brian elastic sedimentation that partly match and partly differ from recent processes (39~; evidence from mature quartz arenites in various Archean shields of stable conti- nental crust containing quartz-rich granitoid rocks (40~; microbiological evidence for Fe(III) reduction to Fe(II) on early Earth, and support for earlier idea that Fe(III) was a more likely electron acceptor than S in microbial metabo- lism (41), birth of the Earth's atmosphere, and the behavior and fate of its major elements (42~; · bacteria, cell walls, various matters: Text on bacterial bio- geochemistry, with final chapter on origins and evolution of biogeochemical cycles/prebiotic Earth and mineral cycles/ theoretical perspectives on the origins of life (Oparin- Haldane theory, Cairns-Smith ideas on clays and life, pyrite, and the origins of life, "thioester world") (43~; intracellular bacteria in protozoa (44~; plant cell wall proteins (45); gene molecular sequences of Archea and details of thermophiles and cold-dwelling types (46~; hydrogen consumption by methanogens on the early Earth (47); genome sequences from a dozen bacteria and a yeast fit with a three-kingdom world (48); 'Eukaryotes are suggested to have arisen through symbiotic association of an anaerobic strictly hydrogen- dependent strictly autotrophic archaebacterium (the host) with a eubacterium (the symbiont) that was able to respire, but generated molecular hydrogen as a waste product of anaerobic heterotrophic metabolism,' (49~; bacteria in sed- iments (50~; · chert: The following papers about the siliceous nodules known as chert and about related siliceous materials should be useful in thinking about how to characterize ancient chert: Evidence of volcanic origin of chert in the Permo- Triassic Sydney Basin (51~; growth of chalcedony by assem- bly of short linear polymers with silica monomers (52~; growth fault control of ~3.5 Gybp Early Archaean cherts, barite mounds, and chert-barite veins, North Pole Dome, Eastern Pilbara, Western Australia, carbonaceous aggre
Colloquium Paper: Smith et al. gates in grey chert (53, 54~; transformation of black to white chert (55~; classic Rhynie chert locality with evidence for a low-energy lacustrine environment with periodic desiccation on exposed mud flats (56~. To conclude: From the viewpoint of geology, mineralogy, and human welfare, it is quite obvious that major questions on biochemical evolution remain unanswered, but might become accessible to quantitative study with the new analytical tools developed over the past few decades. Surface biogeochemistry is a subject whose time has come. F.P.A. thanks Advanced Research Systems for computer facilities. I.P. and M.R.L. thank the U.K. National Environment Research Council for a grant. J.V.S. thanks many scientists at UOP for allowing him to participate in their pioneering work on organophilic silicic molecular sieves and wishes to acknowledge the pioneering indepen dent parallel studies by scientists from Mobil Corporation on the ZSM-5 zeolite series. 1. Smith, J. V. (1998) Proc. Natl. Acad. Sci. USA 95, 3370-3375. 2. Smith, J. V. (1998) Proc. Natl. Acad. Sci. USA 95, 3366-3369. 3. Ashtekar, S., Hastings, J. J. & Gladden, L. G. (1998) J. Chem. Soc. Faraday Trans. 94, 1157-1161. 4. Bjorklund, R. B., Hedlund, J., Sterte, J. & Arwin, H. (1998) J. Phys. Chem. B 102, 2245-2250. 5. Millot, B., Methivier, A. & Jobic, H. (1998) J. Phys. Chem. B 102, 35. 3210-3215. 36. 6. Sun, M. S., Shah, D. B., Xu, H. H. & Talu, O. (1998) J. Phys. 37. Chem. B 102, 1466-1473. 38. 7 Vlugt, T. J. H., Zhu, W., Kapteijn, F., Moulijn, J. A., Smit, B. & 39. Krishna, R. ~ 1998) J. Am. Chem. Soc. 120, 5599 -5600. 8. Braendle, M. & Sauer, J. (1998) J. Am. Chem. Soc. 120, 1556 1570. 9. Smit, B., Loyens, L. D. J. C. & Verbist, G. L. M. M. (1997) J. Chem. Soc. Faraday Trans. 106, 93-104. 10. van Well, W. J. M., Cottin, X., de Haan, J. W., Smit, B., Nivarathy, G., Lercher, J. A., van Hooff, J. H. C. & van Santen, R. A. (1998) J. Phys. Chem. B 102, 3945-3951. 11. van Well, W. J. M., Cottin, X., Smit, B., van Hooff, J. H. C. & van Santen, R. A. (1998) J. Phys. Chem. B 102, 3952-3958. 12. Turov, V. V., Brei, V. V., Khomenko, K. N. & Leboda, R. (1998) Microporous Mesoporous Mater. 23, 189-196. 13. Maekawa, H., Saito, T. & Yokokawa, T. (1998) J. Phys. Chem. B 102, 7523-7529. Sierka, M., Eichler, U., Datka, J. & Sauer, J. (1998) J. Phys. Chem. B 102, 6397-6404. 15. Xu, Z. & Stebbins, J. F. (1998) Geochim. Cosmochim. Acta 62, 1803-1809. 16. Maris, T., Vlugt, T. J. H. & Smit, B. (1998) J. Phys. Chem. B 102, 7183-7189. 17. Savitz, S., Siperstein, F., Gorte, R. J. & Myers, A. L. (1998) J. Phys. Chem. B 102, 6865-6872. 18. Stelzer, J., Paulus, M., Hunger, M. & Weitkamp, J. (1998) Microporous Mesoporous Mater. 22, 1-8. 19. Mentzen, B. F. & Lefebvre, F. (1998) J. Chim. Phys. Biol. 95, 1052-1067. 20. Stepanov, A. G., Luzgin, M. V., Romannikov, V. N., Sidelnikov, V. N. & Paukshtis, E. A. (1998) J. Catal. 178, 466-477. 21. Koretsky, C. M., Sverjensky, D. A. & Sahai, N. (1998)Am. J. Sci. 298, 349-438. Proc. Natl. Acad. Sci. USA 96 (1999J 3485 22. Lee, M. R., Hodson, M. E. & Parsons, I. (1998) Geochim. Cosmochim. Acta 62, 2771-2788. 23. Unrau, P. J. & Bartel, D. P. (1998) Nature (London) 260, 260-263. 24. Huber, C. & Wachtershauser, G. (1998) Science 281, 670-672. 25. Zamaraev, K. I., Salganik, R. I., Romannikov, V. N., Vlasov, V. A. & Khramtsov, V. V. (1995) Doklady Chem. (Transl. of Dokl. Akad. Nauk.) 340, 56-58. 26. Amend, J. P. & Shock, E. L. (1998) Science 281, 1659-1662. 27. Orgel, L. E. (1998) Origins Life Evol. Biosphere 28, 227-234. 28. Hill, A. R. Jr., Bohler, C & Orgel, L. E. (1998) Origins Life Evol. Biosphere 28, 235-242. 29. Liu, R. & Orgel, L. E. (1998) Origins Life Evol. Biosphere 28, 245-257. 30. Lee, M. R. & Parsons, I. (1998) J. Sediment. Res. Sect. A 68, 198-211. 31. Allamandola, L. J., Bernstein, M. P. & Sandford, S. A. (1997) in Astronomical and Biochemical Origins and the Search for Life in the Universe, eds. Cosmovici, C. B., Bowyer, S. & Wertheimer, D. (Editrice Composipori, Milan). 32. Nazarov, M. A., Kurat, G. & Brandstatter, F. (1998) A~Ieteorites Planet. Sci. 33, A115. 33. Pierazzo, E. & Chyba, C. F. (1998) Meteorites Planet. Sci. 33, A122-123. 34. Navarro-Gonzalez, R., Molina, M. J. & Molina, L. T. (1998) Geophys. Res. Lett. 25, 3123-3126. Simakov, S. K. (1998) Geochim. Cosmochim. Acta 62, 1811-1820. Kamber, B. S. & Moorbath, S. (1998) Chem. Geol. 150, 19-41. de Wit, M. J. (1998) Precambrian Res. 91, 181-226. Hamilton, W. B. (1998) Precambrian Res. 91, 143-179. Eriksson, P. G., Condie, K. C., Tirsgaard, H., Mueller, W. U., Altermann, W., Miall, A. D., Aspler, L. B., Catuneanu, O. & Chiarenzelli, J. R. (1998~. Sediment. Geol. 120, 5-53. 40. Donaldson, J. A. & de kemp, E. A. (1998) Sediment. Geol. 120, 153-176. 41. Vargas, M., Kashefi, K., Blunt-Harris, E. L. & Lovley, D. R. (1998) Nature (London) 395, 65-67. 42. Javoy, M. (1998) Chem. Geol. 147,1 1-25. 43. Fenchel, T., King, G. & Blackburn, H. (1998) Bacterial Biogeo chemistry: The Ecophysiology of Mineral Cycling (Academic, Lon don). 44. Gortz, H. & Brigge, T. (1998) Naturwissenschaften 85, 359-368. 45. Cassab, G. I. (1998)Annu. Rev. Plant Physiol. Plant Mol. Biol. 49, 281-309. 46. DeLong, E. (1998) Science 280, 542-543. 47. Kral, T. A., Brink, K. M., Miller, S. L. & McKay, C. B. (1998) Origins Life Evol. Biosphere 28, 311-319. 48. Doolittle, R. F. (1998) Nature (London) 392, 339-342. 49. Martin, W. & Muller, M. (1998) Nature (London) 392, 37-41. 50. Nealson, K. H. (1997) Annul Rev. Earth Planet. Sci. 25, 403-443. 51. Dutta, P. K. (1998) Sediment. Geol. 117, 123-132. 52. Heaney, P. J. (1993) Contrib. Mineral. Petrol. 115, 66-74. 53. Nijman, W., de Bruijne, K. H. & Valkering, M. E. (1998) Precambrian Res. 88, 25-52. 54. Sugitani, K. (1992) Precambrian Res. 57, 21-47. 55. Shanmugam, G. & JB Higgins, J. B. (1988)Am. Assoc. Pet. Geol. Bull. 72, 523-525. 56. Trewin, N. H. & Rice, C. M. (1992) Scott. J. Geol. 28, 37-47. 57. Parsons, I., Lee, M. R. & Smith, J. V. (1998) Proc. Natl. Acad. Sc~. USA 95, 15173-15176.
