biochemical evolution iii: polymerization on organophilic ...mineralogy, and human welfare. [the...

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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 evolutionysilicayfeldsparyzeoliteyfirst cell walls) JOSEPH V. SMITH* ² ,FREDERICK P. ARNOLD,JR. ,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- (mutinaite). 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 nanoy 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 adsorbentsycatalysts are discussed for planning of systematic study of black cherts from weakly metamorphosed Archaean sediments. Introduction and Summary of Biochemical Evolution: Part I. DarwinyOparinyHaldaneyWatsonyCrick 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- 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 organism. 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- tionycatalytic 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 Å. 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 PNAS is available online at www.pnas.org. ² To whom reprint requests should be addressed. e-mail: smith@geo1. uchicago.edu. 3479 Downloaded by guest on June 26, 2020

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Page 1: Biochemical evolution III: Polymerization on organophilic ...Mineralogy, and Human Welfare. [The second part on weath-ered honeycombed feldspars and associated bacteria in a modern

Proc. Natl. Acad. Sci. USAVol. 96, pp. 3479–3485, March 1999Colloquium 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 organophilicsilica-rich surfaces, crystal–chemical modeling, formationof first cells, and geological clues

(biological evolutionysilicayfeldsparyzeoliteyfirst cell walls)

JOSEPH V. SMITH*†, FREDERICK P. ARNOLD, JR.‡, 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, Universityof Edinburgh, Edinburgh EH9 3JW, United Kingdom

ABSTRACT Catalysis at organophilic silica-rich surfacesof zeolites and feldspars might generate replicating biopoly-mers from simple chemicals supplied by meteorites, volcanicgases, and other geological sources. Crystal–chemical mod-eling yielded packings for amino acids neatly encapsulated in10-ring channels of the molecular sieve silicalite-ZSM-5-(mutinaite). Calculation of binding and activation energies forcatalytic assembly into polymers is progressing for a chemicalcomposition with one catalytic Al–OH site per 25 neutral Sitetrahedral sites. Internal channel intersections and externalterminations provide special stereochemical features suitablefor complex organic species. Polymer migration along nanoymicrometer channels of ancient weathered feldspars, plusexploitation of phosphorus and various transition metals inentrapped apatite and other microminerals, might have gen-erated complexes of replicating catalytic biomolecules, leadingto primitive cellular organisms. The first cell wall might havebeen 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 expandedinto a complete cell wall, allowing mobility and colonization ofenergy-rich challenging environments. Electron microscopyof honeycomb channels inside weathered feldspars of the Shapgranite (northwest England) has revealed modern bacteria,perhaps indicative of Archean ones. All known early rockswere metamorphosed too highly during geologic time topermit simple survival of large-pore zeolites, honeycombedfeldspar, and encapsulated species. Possible microscopic cluesto the proposed mineral adsorbentsycatalysts are discussedfor planning of systematic study of black cherts from weaklymetamorphosed Archaean sediments.

Introduction and Summary of Biochemical Evolution: PartI. DarwinyOparinyHaldaneyWatsonyCrick biological evolu-tion provides a plausible framework for integrating the patchypaleontological record with the complex biochemical zoo ofthe present Earth (literature review: ref. 1). But how could thefirst replicating and energy-supplying molecules have beenassembled from simpler materials that were undoubtedlyavailable on the early protocontinents? Bernal preferred ‘‘life’’to begin by catalytic assembly on the surface of a mineral, butall pre-1998 attempts using clays and other minerals to assem-ble an integrated scheme of physicochemical processes hadsignificant 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 catalyticsubstrate. Biochemically significant polymers, such as polypep-

tides and RNAs, must be protected from photochemicaldestruction by solar radiation and must not be overly heated.A stable cell wall is needed to protect the first primitiveorganism.

Part I (1) pointed out that certain inorganic materials haveinternal surfaces that are both organophilic and catalytic,allowing efficient capture of organic species for catalyticassembly into polymers in a protective environment. Thesephysicochemical features are related to the state of the art forzeolite catalysts in the chemical industry, the observed prop-erties of zeolite, feldspar (2), and silica minerals, and aplausible framework for the accretion and early history of theEarth’s crust and atmosphere (1). Various materials from thezeolite, feldspar, and silica mineral groups were listed ashaving surfaces with the capacity to adsorb organic speciespreferentially over water molecules and catalyze them intopolymers. We focus here on mutinaite, a zeolite mineralrecently discovered in Antarctica, which is the natural analogof the ZSM-5/silicalite series of synthetic microporous mate-rials (Note: Microporous does not imply that the pores are ofmicrometer size; indeed the pores in zeolites are generally lessthan a nanometer across). This type of molecular sieve is basedon a tetrahedral framework containing a three-dimensionalchannel system spanned by rings of 10 oxygen atoms (Fig. 1Upper Left and Upper Right). The silica-rich end-member of theZSM-5 series, silicalite, is very organophilic, and Al-substitutedsynthetic relatives catalyze organic reactions at Al–OH re-gions. Silicalite provides a useful basis for modeling adsorp-tionycatalytic processes that would apply in principle, but notin detail, to other materials in paper I (1).

Nonexperts in computer modeling of crystal structuresmight note the conventions in Fig. 1 Upper Left and UpperRight. Three-dimensional imaging must be idealized and trun-cated. Fig. 1 Upper Left displays 10 oxygen atoms as sphereshalf the conventional atomic radius of 1.4 Å. All other atomsare shown merely by the intersection of spokes. Each tetrahe-drally coordinated (T) atom lies at the intersection of fouryellow spokes and each O atom at the intersection of twomaroon spokes. Fig. 1 Upper Right shows all the O atoms ashalf-size spheres, and the Si and Al types, respectively, of Tatoms 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 upand down to the surface of the crystal where some adjustmentof chemical bonding is needed. Fig. 1 Upper Right is deliber-ately tilted slightly with respect to Fig. 1 Upper Left. The

PNAS is available online at www.pnas.org.†To whom reprint requests should be addressed. e-mail: [email protected].

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conventions for amino acids are given in the Fig. 1 Upper Rightlegend.

Introduction to New Unpublished Studies. This third partintegrates the current state of research on biochemical evolu-

FIG. 1. Computer graphics of part of the atomic framework of silicaliteyZSM-5 with amino acids encapsulated in energetically favored positions.(Upper Left) Tetrahedral framework of silicaliteyZSM-5 showing a 10-ring channel down the y-axis. Most of the figure consists of spokes linkingatom positions. One 10-ring of O atoms is shown by spheres displayed at half the formal atomic radii. See text for explanation: oxygen atoms, maroonspheres and intersection of maroon spokes; tetrahedral (T) atoms, intersection of yellow spokes. Only four 10-rings are shown, whereas a perfectcrystal would have an infinite number defining the channel. Also shown are the tilted five-rings. Ten-ring channels present in the plane of the paperare difficult to see without rotation on the video display. (Upper Right) Four glycine molecules in the zwitterion configuration encapsulated insilicaliteyZSM-5. Glycine consists of a central C atom bonded to two H, one carboxyl COO2, and one amine NH3

1. The cluster of three moleculesnear the middle of the near-vertical channel has been optimized to interact mutually by way of hydrogen bonding and to be suspended by van derWaals bonding from the O atoms of the 10-ring channel. The fourth molecule is oriented along a horizontal 10-ring channel. All the frameworkO atoms are represented by half-size maroon spheres. The tetrahedrally coordinated atoms are represented by small spheres differentiated by color:Si, yellow, Al, pink. The glycine molecule is represented by a stick model with conventional color code: O, red; C, grey; N, blue; H, white. Theorientation of the channel system is rotated slightly from that in Upper Left. (Lower Left) Three glycine molecules within a 10-ring channel of silicalite,viewed down the y- axis. Coloring as in Upper Left; silicaliteyZSM-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 glycinemolecules from Lower Left, viewed along the z-axis. Note the ‘head-to-tail’ alignment of the carboxylate group of an amino acid with the aminogroup of the next amino acid. Once again, the positional constraints on the amino acids in the channel, as well as their parallel alignment with thechannel, are emphasized.

3480 Colloquium Paper: Smith et al. Proc. Natl. Acad. Sci. USA 96 (1999)

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tion that will be presented at the Colloquium on Geology,Mineralogy, and Human Welfare. [The second part on weath-ered honeycombed feldspars and associated bacteria in amodern granite was under preparation as this third part wasbeing completed and will be published (57) in the regular partof the Proceedings before this paper. Its key contents are givenbriefly in this paper and are illustrated in Fig. 3.] We begin withcrystal–chemical modeling of amino acids inside 10-ring chan-nels of the chosen zeolite, silicalite (Figs. 1 Upper Right, LowerLeft, and Lower Right and 2 Upper and Lower). The channelwalls are electrically neutral except for arbitrary replacementof 4% of the silicon–oxygen tetrahedra by aluminum-oxygen-hydroxyl catalytic centers. This 1 in 25 replacement yields nicegraphics and has no particular scientific significance. More-over, this ratio can be varied to increase or decrease the spacingof catalytic centers along the 10-ring channels and to vary theelectrical forces on adsorbed molecules and the repeat dis-tances of the polymers generated by catalytic condensation.

We end with new ideas for generating primitive protocellsinside the honeycombed weathered surfaces of feldspars [PartII (57)]. Fig. 3 shows scanning-electron micrographs of thecrystallographically controlled channels in feldspars from theShap granite, northwest England, together with associatedmodern bacteria, as models for speculation on the develop-ment of the first primitive cells. Now to details.

Preliminary Simulations of Encapsulation of Amino Acidsin SilicaliteyZSM-5 and Catalytic Generation of Biopolymers.The crystal–chemical reviews in refs. 1 and 2 are updated bypapers in the following areas:

Y crystal chemistry of high-silica materials: Fourier Transform-Raman studies of single-component and binary adsorptionin silicalite-1 (3); vapor adsorption in thin silicalite-1 filmsstudied by spectroscopic ellipsometry (4); adsorptionyde-sorption of n-alkanes on silicalite crystals (5); adsorptionequilibria 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 mechanicalymolecular me-chanics ab initio modeling, demonstrating that the moststable Brønsted sites occur in high-silica zeolites (8); simu-lation of adsorption and diffusion of hydrocarbons in sili-calite, demonstrating that a linear hydrocarbon moves morefreely than a branched one, whose CH group becomeslocked at a channel intersection (9); adsorption isotherms oflinear alkanes in ferrierite— smaller ones, C1–C5, fill theentire pore system, whereas C6 and C7 fit only in a 10-ringchannel unless forced into an eight-ring channel by pressure(10, 11); nuclear magnetic resonance of 1H in water ad-sorbed on silicalite (12); heterogeneity of Brønsted acid sitesin Al-substituted faujasites (13); nuclear magnetic resonanceof 17O in silica, albite glasses, and stilbite (14, 15); simulationof 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 silicaliteyMFImolecular sieves from x-ray powder diffraction and 29SiMagic Angle Spinning–NMR (19); nature, structure, andcomposition of hydrocarbon species obtained by oligomer-ization of ethylene on acidic H-ZSM-5 molecular sieve (20):

Y surface chemistry of various minerals: coordination modelsfor simple surfaces of oxide and silicate minerals (21); therole of intragranular microtextures and microstructures inchemical and mechanical weathering, direct comparisons ofexperimentally and naturally weathered alkali feldspars(22);

Y synthesis: RNA-catalyzed nucleotide synthesis of a pyrimi-dine (23); conversion of amino acids into peptides at 373 Kand pH 7–10 on (Ni, Fe)S surfaces (24), synthesis ofglycylglycine dipeptide in the presence of kaolin clay andzeolites of Linde Type A, faujasite, and beta types (25);

thermodynamic calculation of amino acid synthesis in hotwater and application to hydrothermal vents (black smok-ers) on ocean floor (26); polymerization of various aminoacids on hydroxylamine and illite mica, with increasingadsorption affinity of oligomers longer than 7-mer (27–29).]

Figs. 1 Upper Right, Lower Left, and Lower Right and 2 Upperand Lower illustrate the current state of chemical modeling ofamino acids encapsulated in a silicalite containing one Alsubstitution for 25 tetrahedral Si. Simulations were carried outusing the Sorption module within the MSIyCerius 2 programsystem (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 theresults of packing simulations based on Monte Carlo tech-niques for glycine and histidine molecules encapsulated withinthe 10-ring channels of silicalite. It is possible at low pressureto 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 thechannel system, coupled with charge effects at the amino andcarboxyl ends of the amino acids, assists in orienting themcorrectly for the production of polypeptides. It can also be seenfrom these illustrations that one of the chief difficulties of thestandard model for the formation of life, that of achievingsufficient concentration of reactants while excluding or min-imizing environmental degradation, is overcome. Not only arethe growing biopolymers protected from outside interferenceand concentrated in the channels, but the limited degrees offreedom in molecular movements assist in orienting themoptimally for polymerization.

Simple molecular mechanics simulations within the SPAR-TAN computer package (Wavefunction, Irvine, CA) of variousmodel complexes are shown in Fig. 2 Upper and Lower. Fig. 2Upper (stereoview) illustrates an adenine hydrogen bound tothe hydroxyl site of the 10-ring channel, with the carboxyl endof a glycine residue bound to the amino group of the adenine.This complex is correctly oriented for protonation of thehydroxyl group of the amino acid, followed by the eliminationof water and the formation of an amide bond between the baseand the amino acid. Such a reaction would be facilitated by asecond metal site in the region, and provides one possibility fora precursor to the autocatalytic biopolymers of the ‘pre-RNA’world. Electrostatic potential calculations on the system, usingthe 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 anamino acid to the hydroxyl site of a zeolite-type material. It isobvious that the nitrogen functionalities of the histidine ringcould form hydrogen bonds. Furthermore, it is also possible tobind the hydroxyl group of the carboxyl functionality to theacid site within the zeolite framework, then dehydrate andform a covalent bond between the surface and the amino acid.This process is analogous to the functionalized glass or plasticbeads used in commercial DNA or protein synthesis, where thepolymer chain grows away from the supported terminus.Reaction with hydronium ion, presuming mildly acidic media,would enable cleavage of the chain and would release thepeptide into solution. In passing, it should also be noted thatthe amino terminus of the amino acid, which is facing awayfrom the viewer, is oriented along the axis of the channel andhence, in analogy to Fig. 1 Lower Right, is oriented optimallyfor further reaction.

Speculations on Biochemical Evolution Currently UnderEvaluation. These illustrative results give confidence for spec-ulations that a microporous aluminum-substituted silica ma-terial with mainly hydrophobic channels and widely spacedAl–OH catalytic centers might act as a sausage machine forproduction of biopolymers that became assembled into pro-

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FIG. 2. Computer graphics of part of the atomic framework of silicaliteyZSM-5 with amino acids encapsulated in energetically favored positions.(Upper) Stereopair of 10-ring channel of silicalite, showing a hydrogen-bound adenine–glycine complex itself hydrogen-bound to an acid site of theframework. Some framework atoms removed for clarity. This stereopair illustrates the ability of the zeolitic material both to accommodate largebiopolymer precursors and to provide sites at which reactions may occur. (Some students initially have difficulty viewing stereopairs. If you havethis 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 eyesswivel to achieve stereo with the left eye seeing the left dot. This contrasts with the cross-eye technique used in some biological modeling.) (Lower)Histidine and water molecules in silicalite. Histidine was chosen for modeling because its imidazole ring can switch electronic states readily to catalyze

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tocells in protected honeycombs in weathered feldspars. Var-ious new matters are being evaluated currently from theviewpoint of physical and chemical processes and are modeledin detail for later publication:

Y First, channel intersections may prove important for stere-ochemical control of larger functional groups, especially atthe end of a biopolymer. The intersection of an internalchannel with the outer surface should be even more impor-tant and indeed might be considered as an anchor for apolymer that projects outwards into a ‘soup.’

Y Second, after outward migration from an internal channel,the first biopolymers would begin to coil up like a snake andin certain places, such as a tapered tube in a honeycombedfeldspar approximately 5 to 100 nanometers across, wouldbegin to interact closely with the aluminosilicate surface.

Y Third, various biopolymers of different types might begin tointeract and begin the evolution toward a protobacterium.

Y Particularly important would be the first generations ofpersistent energy-generating species containing phosphorusand electron-transferable transition metals. Very importantis that K-rich feldspars from granites contain micrometerinclusions of the calcium—phosphate–hydroxideyhalidemineral apatite and transition-metal oxides, including ilmen-ite, spinel, and hematite, which might well be the primaryreservoirs of these key elements.

Y At some stage, a protocell lining inside an aluminosilicatetube might develop a bilipid lining that would extend into acap, ultimately allowing detachment from the silicate andfree motion through a soup. Again, one might imagine asausage machine popping off a free cell as the remainingprotocell reconstituted itself ready for generation of the nextfree cell. Schematic graphics are being envisaged along withideas for chemical bonding schemes.

Y All these processes would involve subtle effects related todiurnal and annual temperature cycles and wetydry cyclingdriven both by solar radiation and lunar tides that wouldchange the spatial distribution of chemical forces acrossmineral surfaces. Ideas are not developed enough so far towarrant further description here.

Mineralogical Observations and Speculations: ElectronMicroscopy of Honeycombed Weathered Feldspars—Bacteriaand Protocells. Turning now to mineralogical information, Fig.3 contains four scanning-electron micrographs of the crystal-lographically controlled honeycomb weathering on a modernsurface of a K-feldspar from the Shap granite (30). Particularlyimportant are the micrometer-scale sausage shapes inter-preted as electron scattering from bacteria, somewhatshrunken from interaction with the electron beam. Many haveno particular orientation with respect to the feldspar, but thebacterium in Lower Right is interpreted as sitting neatly in acrevice. The near correspondence between the segmentationof the proposed bacterium and the spacing of the feldsparhoneycomb is intriguing. Perhaps it may ultimately be possibleto quantify the original chemical linkages between the inor-ganic substrate and the unshrunken bacterium and to use themfor modeling the above ideas.

Coupling the catalytic production of polymers at the nano-meter scale with bacteria at the micrometer scale is plausiblein the geologic context, but requires many flights of imagina-tion and a lot of faith. On the present Earth, volcanic glasstransforms to zeolites in continental basins and ocean floors;the zeolites become metamorphosed to feldspars; and thewhole mineralogical assemblage becomes converted over geo-

logic time into granitic metamorphic rocks. Hence, we arecomfortable in proposing that zeolites and feldspars wouldhave coexisted on the early Earth, for which only the resultantgranitic metamorphic rocks have been seen so far. Hence wecan suggest for discussion purposes that a zeoliteysilicayaltered feldspar sausage machine fed a range of biologicalpolymers 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 havegenerated primitive protocells. To conclude the evolution intothe first organisms, a cap between the dangerous outer regimeof ‘soup’ and the inner protected world might have expandedto completely enclose the protocell so that it could swim intothe future. Part IV, under preparation, will show graphicsillustrating the scientific factors underlying these flights offancy about cell formation.

Conclusion. We conclude with matters of specific geologicalimport. From the humanistic viewpoint, it would be extremelysignificant if the early forms of life had left behind somephysicochemical evidence of their existence. The currentcarbon-isotope evidence of bulk samples is indicative of somekind of early biological evolution, but has no particular importfor the atomic-level ideas presented above. A review of thegeological evidence indicates that at least most and perhaps allof the early Archean rocks have been metamorphosed to a highenough level that all volcanic rocks have recrystallized. Therecan be little doubt that volcanoes would have been pumpingout ash containing crystals of K-feldspar and silica minerals.By analogy with modern conditions, much of the ash wouldhave been converted into zeolite beds, and there might wellhave been zoned beds of zeolite minerals interacting with saltylakes sloshed by tides and impacts. Some K-feldspar and zeolitecrystals would have been exposed to an acidic rain, andhoneycombed 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 producedby metamorphic recrystallization of earlier igneous originmight have retained some specific signature indicative of subtlebiological processes involving feldspar, zeolite and silica min-erals:

Y Ancient cherts (silica–hydroxyl-rich aggregates) range incolor at least from black to brown, red, and orange-yellow.At least some of the color variation must result fromtransition metals, especially Fe and Mn, at different redoxstates. Might some carbonaceous species have survived inthe black cherts? If so, would careful analysis reveal organicbreakdown products specific to primary biocatalytic precur-sors?

Y Because early organisms would have needed P and varioustransition metals, would their absence or low abundance inthe metamorphosed siliceous rocks be indicative of earlybiological scavenging by organisms that escaped into the‘soup’?

Y Particularly challenging, because of the possibility of com-plete failure, would be a hunt for x-ray diffraction evidenceof surviving Si-rich molecular sieves. Silicalite and otherlarge-pore zeolites have strong low-angle diffractions thatwould stand out in low-background patterns obtained withsynchrotron x-rays, even at a concentration below 1%.

Since the review in ref. 1, the following geologicalybiologicalpublications 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 bya ball-and-stick arrangement and are colored as in Upper. The water molecules are represented by a bent bicolor rod with two white ends representingH, and the red center represents O. The framework is represented by tetrahedra whose shared vertices are at O positions. A further reason forchoosing histidine is its prevalence as a metal-binding site in modern proteins, undoubtedly an important function in the prebiotic world.

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Y stardust and meteorites: Photochemical evolution of inter-stellaryprecometary organic material (31); silica-rich micro-meter objects in a carbonaceous chondrite (32);

Y planetary impact processes: Survival of amino acid in largecomet impacts (33);

Y early geologic events on Earth: Nitrogen fixation by volcaniclightning (34); redox state of upper-mantle peridotites underthe ancient cratons, and possible equilibrium of diamondswith methane-nitrogen-rich fluids (35); new revised Pb-agesof Greenland gneisses at 3.65–3.70 instead of earlier 3.85gigayear-before-present (36); interpretation of geologic ev-idence in favor of plate-tectonic processes in the Archeanera (37); interpretation of Archean magmatism and defor-mation in nonplate tectonics terms (38); details of Precam-brian clastic sedimentation that partly match and partlydiffer from recent processes (39); evidence from maturequartz 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) onearly Earth, and support for earlier idea that Fe(III) was amore likely electron acceptor than S in microbial metabo-lism (41), birth of the Earth’s atmosphere, and the behaviorand fate of its major elements (42);

Y bacteria, cell walls, various matters: Text on bacterial bio-geochemistry, with final chapter on origins and evolution of

biogeochemical cyclesyprebiotic Earth and mineral cyclesytheoretical 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); intracellularbacteria in protozoa (44); plant cell wall proteins (45); genemolecular sequences of Archea and details of thermophilesand cold-dwelling types (46); hydrogen consumption bymethanogens on the early Earth (47); genome sequencesfrom a dozen bacteria and a yeast fit with a three-kingdomworld (48); ‘Eukaryotes are suggested to have arisen throughsymbiotic 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 ofanaerobic heterotrophic metabolism,’ (49); bacteria in sed-iments (50);

Y chert: The following papers about the siliceous nodulesknown as chert and about related siliceous materials shouldbe useful in thinking about how to characterize ancientchert: 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-

FIG. 3. Four scanning-electron micrographs of weathered feldspar from the Shap granite. (Upper Left) Resin cast of honeycomb texture. Thecast 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 Right) A near-planar surface close to bar601 with a trace of etched dislocations running horizontallyand vertically across the image with ellipsoidal bacteria, some in strings like sausages hanging in a U.K. butcher’s shop. (Lower Left) More deeplyweathered surface showing occasional traces of etched dislocations, with sausage-shaped bacteria. (Lower Right) Detail of honeycomb on the 001surface of a feldspar honeycomb. The holes are etch pits formed on paired outcrops of dislocations that formed on exsolution lamellae. Thebacterium, 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).

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Page 7: Biochemical evolution III: Polymerization on organophilic ...Mineralogy, and Human Welfare. [The second part on weath-ered honeycombed feldspars and associated bacteria in a modern

gates in grey chert (53, 54); transformation of black to whitechert (55); classic Rhynie chert locality with evidence for alow-energy lacustrine environment with periodic desiccationon exposed mud flats (56).

To conclude: From the viewpoint of geology, mineralogy,and human welfare, it is quite obvious that major questions onbiochemical evolution remain unanswered, but might becomeaccessible to quantitative study with the new analytical toolsdeveloped over the past few decades. Surface biogeochemistryis 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 ResearchCouncil for a grant. J.V.S. thanks many scientists at UOP for allowinghim to participate in their pioneering work on organophilic silicicmolecular sieves and wishes to acknowledge the pioneering indepen-dent parallel studies by scientists from Mobil Corporation on theZSM-5 zeolite series.

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