A Field Trip to the Archaean in Search of Darwin's Warm Little Pond

life

Essay A Field Trip to the Archaean in Search of Darwin’s Warm Little Pond

Bruce Damer 1,2

1 Department of Biomolecular Engineering, Baskin School of Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA; [email protected]; Tel.: +1-831-459-2158 2 DigitalSpace Research, Boulder Creek, CA 95006, USA

Academic Editor: Niles Lehman Received: 22 March 2016; Accepted: 20 May 2016; Published: 25 May 2016

Abstract: Charles Darwin’s original intuition that life began in a “warm little pond” has for the last three decades been eclipsed by a focus on marine hydrothermal vents as a venue for abiogenesis. However, thermodynamic barriers to polymerization of key molecular building blocks and the difficulty of forming stable membranous compartments in seawater suggest that Darwin’s original insight should be reconsidered. I will introduce the terrestrial origin of life hypothesis, which combines field observations and laboratory results to provide a novel and testable model in which life begins as protocells assembling in inland fresh water hydrothermal fields. Hydrothermal fields are associated with volcanic landmasses resembling Hawaii and Iceland today and could plausibly have existed on similar land masses rising out of Earth’s first oceans. I will report on a field trip to the living and ancient stromatolite fossil localities of Western Australia, which provided key insights into how life may have emerged in Archaean, fluctuating fresh water hydrothermal pools, geological evidence for which has recently been discovered. Laboratory experimentation and fieldwork are providing mounting evidence that such sites have properties that are conducive to polymerization reactions and generation of membrane-bounded protocells. I will build on the previously developed coupled phases scenario, unifying the chemical and geological frameworks and proposing that a hydrogel of stable, communally supported protocells will emerge as a candidate Woese progenote, the distant common ancestor of microbial communities so abundant in the earliest fossil record.

Keywords: origin of life; hydrothermal systems; progenote; microbial communities; stromatolites

1. Introduction Most workers investigating the origin of life conﬁne their horizons to theoretical papers, computational models or laboratory simulations that use a narrow spectrum of commercial reagents reacting in buffered aqueous solutions. The results are then related to prebiotic conditions with the assumption that laboratory or in silico results can plausibly occur in the early Earth environment. A complementary approach is to visit sites that are analogs to candidate venues for biogenesis. Such ﬁeldwork broadens our perspective by providing a more realistic assessment of the actual conditions in which physical and chemical reactions progressed toward life’s beginning approximately four billion years ago. Furthermore, geologists familiar with the most ancient, Archaean fossil sites can interpret the rock record and provide knowledgeable advice about geochemical conditions to guide model building and laboratory experiments.

Life 2016, 6, 21; doi:10.3390/life6020021 www.mdpi.com/journal/life Life 2016, 6, 21 2 of 14 Life 2016, 6, 21 2 of 14 2. A Field Trip in Deep Time to the Archaean 2. A Field Trip in Deep Time to the Archaean In July 2015, I joined a unique scientific field trip led by Malcolm Walter and Martin Van KranendonkIn Julyof the 2015, Australian I joined Centre a unique for Astrobiology scientific fieldat the trip University led by of Malcolm New South Walter Wales. and This 3000 Martinkm trek Van (Figure Kranendonk 1) by air, of thebus, Australian utility vehicle Centre and for Astrobiologyfoot traveled at through the University 3.5 Ga of(billion) New South years of Earth’sWales. history This across 3000 km Western trek (Figure Australia,1) by air,from bus, Perth utility to vehicleHamelin and Pool foot (1) traveled at Shark through Bay, 3.5northward Ga (billion) years of Earth’s history across Western Australia, from Perth to Hamelin Pool (1) at Shark Bay, through the Hamersley Range and Fortescue Group (2–4) to the Marble Bar area (5) and finally to northward through the Hamersley Range and Fortescue Group (2–4) to the Marble Bar area (5) and sites (6–8) in the remote North Pole Dome of the Pilbara Craton. During the ten-day tour, new ideas finally to sites (6–8) in the remote North Pole Dome of the Pilbara Craton. During the ten-day tour, emergednew ideasthrough emerged examination through examinationof evidence of from evidence the fromearliest the earliestknown, known, Archaean Archaean geological geological settings inhabitedsettings by inhabited microbial by life. microbial life.

FigureFigure 1. Route 1. Route taken taken fromfrom Perth, Perth, Western Western Australia Austra to Sharklia to Bay Shark near Denham,Bay near north Denham, via Paraburdoo north via Paraburdooand Tom and Price Tom into thePrice Pilbara into the region Pilbara before region departure before from departure Port Hedland. from Sites Port visited Hedland. are marked Sites visited in are markedred (1–8). in Source: red (1–8). Government Source: of WesternGovernment Australia of DepartmentWestern Australia of Mines andDepartment Petroleum. of Mines and Petroleum. 3. Living Marine Stromatolites and Inland Microbial Communities 3. LivingThe Marine journey Stromatolites began with a visitand toInland one of Microbial the best examples Communities of living stromatolites, in Hamelin Pool at Shark Bay (Figure2). These shallow water domical and mat-like structures are formed by microbial The journey began with a visit to one of the best examples of living stromatolites, in Hamelin communities under conditions of elevated salinity that prevents larger organisms from feeding on Pool theat Shark communities. Bay (Figure The organisms 2). These that shallow form stromatoliteswater domical cause and carbonate mat-like minerals structures to precipitate are formed in by microbialdistinctive communities layers, forming under structures conditions that of can elevated be preserved salinity for billions that prevents of years inlarger the fossil organisms record. from feeding on the communities. The organisms that form stromatolites cause carbonate minerals to precipitate in distinctive layers, forming structures that can be preserved for billions of years in the fossil record.

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Figure 2. (Left) Underwater view of stromatolites in Hamelin Pool, Shark Bay, Western Australia Figure 2. (Left) Underwater view of stromatolites in Hamelin Pool, Shark Bay, Western Australia (credit: (credit:Figure 2.Marisol (Left) UnderwaterJuarez Rivera). view (Center of stromatolites) Eroded sectionin Hamelin through Pool, a Sharkrecently Bay, exposed Western Shark Australia Bay Marisol Juarez Rivera). (Center) Eroded section through a recently exposed Shark Bay stromatolite, stromatolite,(credit: Marisol showing Juarez the Rivera). domical (Center shape) andEroded crude section laminations through of athese recently large, exposed lithified Sharkstructures Bay showing the domical shape and crude laminations of these large, lithiﬁed structures (width of central (widthstromatolite, of central showing stromatolites the domical is ~20 shape cm). and (Right crude) Oblique laminations view downof these onto large, silt lithifiedand sand-covered, structures stromatolites is ~20 cm). (Right) Oblique view down onto silt and sand-covered, living microbial living(width microbial of central mat stromatolites from Shark is Bay. ~20 Thecm). ragged (Right textured) Oblique edge view in downthe photo onto is silt an anderoded sand-covered, section cut mat from Shark Bay. The ragged textured edge in the photo is an eroded section cut through the throughliving microbial the microbial mat from mat, Shark which Bay. exhibits The ragged rubbery textured cohesion edge as in it the is composedphoto is an of eroded a community section cut of microbial mat, which exhibits rubbery cohesion as it is composed of a community of microorganisms. microorganisms.through the microbial These mat,contemporary which exhibits versions rubbery of the cohesion Earth’s most as it ancient is composed microbial of aecosystem community were of These contemporary versions of the Earth’s most ancient microbial ecosystem were later compared to later compared to Archaean stromatolite fossils. Center and right photos by author. Archaeanmicroorganisms. stromatolite These fossils. contemporary Center and versions right photosof the Earth’s by author. most ancient microbial ecosystem were later compared to Archaean stromatolite fossils. Center and right photos by author. The stromatolites produced by microbial communities at Shark Bay require near-continuous immersionThe stromatolites in a marine produced environment. by microbial By way communities of contrast, atterrestrial Shark BayBay microbial requirerequire near-continuousnear-continuousmats were also immersionobserved on inin the a a marine exposedmarine environment. rockenvironment. surfaces By of wayBy Gallery way of contrast, ofH illcontrast, in terrestrial the semi-desert terrestrial microbial Pilbaramicrobial mats region were mats also near were observed Marble also onBarobserved the(Figure exposed on 3). the Hydrating exposed rock surfaces rocka dry surfaces mat of Gallery (by ofsimulated Gallery Hill in rainfall)H theill in semi-desert the showed semi-desert that Pilbara the Pilbara mat region quickly region near absorbed near Marble Marble Barthe (FigurewaterBar (Figure and3). Hydratingretained 3). Hydrating it afar dry alonger dry mat mat (bythan (by simulated surrounding simulated rainfall) rainfall) mineral showed showed surfaces that that the(as the documented mat mat quickly quickly absorbedelsewhere absorbed the theby waterVerrecchia and retainedetretained al. [1]). itSignificantly, farfar longerlonger thanthan the moistened surroundingsurrounding mat mineralmineral had the surfaces same physical (as documented consistency elsewhere as the living by Verrecchiastromatolite etet al.al.mats [[1]1]). ).at Signiﬁcantly,Significantly, Hamelin Pool. thethe moistenedmoistened This microbial matmat hadhad community thethe samesame physicalphysical inhabited consistencyconsistency a rock-soil asas the margin living stromatoliteresembling a mats shorelinemats at at Hamelin Hamelinand depended Pool. Pool. This on microbialThis infrequent microbial community precipitation. community inhabited inhabited a rock-soil a marginrock-soil resembling margin aresembling shoreline anda shoreline depended and on depended infrequent on precipitation. infrequent precipitation.

Figure 3. (Left) Author photos of microbial mats growing on exposed rocks at Gallery Hill; and (FigureCenter )3. and (Left (Right) Author) hydrating photos a of mat microbial and testing mats its growin plasticity.g on exposed rocks at Gallery Hill; and Figure 3. (Left) Author photos of microbial mats growing on exposed rocks at Gallery Hill; and (Center) and (Right) hydrating a mat and testing its plasticity. (Center) and (Right) hydrating a mat and testing its plasticity. Could there have been an evolutionary link between marine stromatolites and these primitive microbialCould mats there pointing have been back an to evolutionarya common ancestor link be tweendepending marine on astromatolites more reliable and fluctuating these primitive source ofmicrobial freshCould water?mats there pointing haveIf so, been howback an toco evolutionary auld common these ancestorfresh link betweenwater depending mats marine haveon stromatolitesa moreevolved reliable to and survivefluctuating these primitiveextensive source microbialdehydrationof fresh water? mats and pointing exposureIf so, backhow to the toco auld much common these higher ancestorfresh ultraviolet water depending mats (UV) componenthave on a moreevolved reliable of Archaeanto survive ﬂuctuating sunlight? extensive source ofdehydration freshA possible water? and If answer so,exposure how was could to suggestedthe these much fresh higherby water examination ul matstraviolet have of (UV) evolvedone component of the to survivemany of Archaeanflat extensive rocks sunlight? dehydrationlittering the andsurface exposureA possibleof Gallery to answer the Hill much (Figure was higher suggested 4). ultravioletThe rock by layexamination (UV) on componenta weathered of one of surface Archaeanof the coveredmany sunlight? flat by rockswhat islittering known the as “desertsurface ofvarnish”, Gallery Hilla favorite (Figure canvas4). The rockfor Aboriginallay on a weathered artists. surfaceBeneath covered the rock by whatwas ais knownmicrobial as “desert varnish”, a favorite canvas for Aboriginal artists. Beneath the rock was a microbial

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A possible answer was suggested by examination of one of the many ﬂat rocks littering the surface of Gallery Hill (Figure4). The rock lay on a weathered surface covered by what is known as “desert varnish”,Life 2016 a favorite, 6, 21 canvas for Aboriginal artists. Beneath the rock was a microbial community4 of thriving 14 in moist sediments (center), consisting of cyanobacteria shaded from the ultraviolet component of sunlightLifecommunity 2016 but, 6, 21 able thriving to gather in moist enough sediments diffuse light(center), for consisting metabolism of (ascyanobacteria noted elsewhere shaded infrom the4 of the 14 Pilbara ultraviolet component of sunlight but able to gather enough diffuse light for metabolism (as noted by Hoshinocommunity and thriving George in [2 ]).moist On thesediments early Earth,(center), shade consisting provided of cyanobacteria by rocks and shaded minerals from would the have elsewhere in the Pilbara by Hoshino and George [2]). On the early Earth, shade provided by rocks protectedultraviolet against component ultraviolet of sunlight light andbut able retained to gath moistureer enough essential diffuse light for for life. metabolism Cracks within (as noted mineral and minerals would have protected against ultraviolet light and retained moisture essential for life. surfaceselsewhere (right) in can the alsoPilbara provide by Hoshino such protection and George for [2]). cryptoendolithic On the early Earth, microorganisms shade provided that by thrive rocks today Cracks within mineral surfaces (right) can also provide such protection for cryptoendolithic in theand Antarctic minerals high would deserts have protected [3]. against ultraviolet light and retained moisture essential for life. microorganisms that thrive today in the Antarctic high deserts [3]. Cracks within mineral surfaces (right) can also provide such protection for cryptoendolithic microorganisms that thrive today in the Antarctic high deserts [3].

Figure 4. Author photos of rock next to an impression of its earlier resting place on Gallery Hill Figure 4. Author photos of rock next to an impression of its earlier resting place on Gallery Hill (Left); (Left); microbial community in moist sediments beneath it (Center); and view of rock underside Figure 4. Author photos of rock next to an impression of its earlier resting place on Gallery Hill microbial(Right community). in moist sediments beneath it (Center); and view of rock underside (Right). (Left); microbial community in moist sediments beneath it (Center); and view of rock underside (Right). TheseThese observations observations suggested suggested an interestingan interesting comparison comparison between between two two sites sites proposed proposed for for the the origin origin of life: submarine hydrothermal vents [4–8] and hydrothermal fields on exposed land surfaces of life: submarineThese observations hydrothermal suggested vents an [ 4interesting–8] and hydrothermal comparison between ﬁelds on two exposed sites proposed land surfaces for the [9,10]. [9,10]. Assuming a source of organic compounds such as amphiphiles, amino acids, and nucleobases Assumingorigin of a sourcelife: submarine of organic hydrothermal compounds vents such [4–8] as amphiphiles, and hydrothermal amino fields acids, on exposed and nucleobases land surfaces supplied supplied by extraterrestrial infall [11–13] or geochemical synthesis [14,15], these compounds would by extraterrestrial[9,10]. Assuming infall a source [11 –of13 organic] or geochemical compounds synthesissuch as amphiphiles, [14,15], these amino compounds acids, and nucleobases would either be either be present as a dilute solution in the Archaean ocean [16] or deposited on volcanic land supplied by extraterrestrial infall [11–13] or geochemical synthesis [14,15], these compounds would presentmasses. as a diluteExposed solution rocky surfaces in the Archaean that support ocean loca [lized16] or pooling deposited from on precipitation volcanic land would masses. provide Exposed a either be present as a dilute solution in the Archaean ocean [16] or deposited on volcanic land rockyvenue surfaces for early that microbial support localizedcommunities, pooling as illustrated from precipitation by the isolated would pools provideon the ca. a3.4 venue Ga jasper for early masses. Exposed rocky surfaces that support localized pooling from precipitation would provide a microbialformation communities, at Marble Bar as illustrated(Figure 5). Fluctuating by the isolated pools filled pools by on precipitation the ca. 3.4 today Ga jasper support formation living at venue for early microbial communities, as illustrated by the isolated pools on the ca. 3.4 Ga jasper Marblemicrobial Bar (Figure mat communities5). Fluctuating (Figure pools 5, left) ﬁlled and by show precipitation evidence of today microbial support chemical living staining microbial when mat formation at Marble Bar (Figure 5). Fluctuating pools filled by precipitation today support living communitiesdehydrated (Figure (Figure5, 5, left) right). and During show the evidence Archaean, of microbialorganic compounds chemical woul stainingd accumulate when dehydrated in such microbial mat communities (Figure 5, left) and show evidence of microbial chemical staining when pools and would be concentrated during cycles of dehydration by evaporation. (Figuredehydrated5, right). (Figure During 5, right). the Archaean, During the organic Archaean, compounds organic compounds would accumulate would accumulate in such in pools such and wouldpools be and concentrated would be concentrated during cycles during of dehydration cycles of dehydration by evaporation. by evaporation.

Figure 5. Author photos of rock-crevice pool (Left) at Marble Bar concentrating moisture and organic solutes capable of supporting microbial mats (Inset). (Right) Dried pool illustrating microbial Figure 5. Author photos of rock-crevice pool (Left) at Marble Bar concentrating moisture and organic chemical staining on the rock surface. Figuresolutes 5. Author capable photos of supporting of rock-crevice microbial pool mats (Left (Inset) at Marble). (Right Bar) Dried concentrating pool illustrating moisture microbial and organic soluteschemical capable staining of supporting on the rock microbial surface. mats (Inset). (Right) Dried pool illustrating microbial chemical staining on the rock surface.

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4. Fossil Fossil Stromatolites Stromatolites Well-preserved fossilfossil stromatolitesstromatolites are are abundant abundant in in the theca. ca.2.7 2.7 Ga Ga Tumbiana Tumbiana Formation. Formation. These These are “domical”are “domical” (dome-shaped) (dome-shaped) stromatolites stromatolites (Figure 6),(Fig whichure bear6), which a clear resemblancebear a clear to cross-sectionsresemblance ofto cross-sectionsthe stromatolites of the at Hamelin stromatolites Pool (Figureat Hamelin2, center). Pool The(Figure ﬁeld 2, trip center). also touredThe field the trip oldest also rocks toured of thethe oldestPilbara rocks region, of thethe ApexPilbara chert, region, Strelley the PoolApex and cher Dressert, Strelley formations. Pool and FigureDresser6 (right formations. bottom) Figure shows 6 (righta cross-sectional bottom) shows view a through cross-sectionalca. 3.4Ga view stromatolites through ca. between 3.4 Ga stromatolites beds of black between chert at beds the “Trendall of black chertlocality” at the on the“Trendall Shaw River. locality” Morphological on the Shaw similarity River. Morphological with modern day similarity stromatolites with modern at Shark day Bay stromatolitessuggests that at these Shark structures Bay suggests are indicative that these of biogenicity structures [are17– 19indicative]. Biogenicity of biogenicity is also supported [17–19]. Biogenicityby the fact thatis also black supported chert from by thesethe fact localities that black has preservedchert from rarethese microfossils localities has [20 ].preserved Whereas rare the microfossilsstromatolites [20]. of the Whereas Strelley the Pool stromatolites Formation formedof the Strelley in a shallow Pool marineFormation environment formed in [ 21a ]shallow with at marineleast a local environment inﬂuence [21] of hydrothermal with at least activitya local influence [22], the ca. of 3.48hydrothermal Ga Dresser activity Formation, [22], whichthe ca.contains 3.48 Ga Dresserthe oldest Formation, convincing which evidence contains for lifethe onoldest Earth conv [23incing,24], was evidence deposited for life within on Earth an active [23,24], volcanic was depositedcaldera. The within presence an active of geyserite volcanic provides caldera. clearThe evidencepresence of extensive,geyserite provides fresh water clear hydrothermal evidence of extensive,systems on fresh an exposed water hydrothermal land surface, includingsystems on geyser an exposed activity land [25]. surface, Furthermore, including concentrated geyser activity boron [25].occurs Furthermore, in tourmaline-rich concentrated crusts, boron together occurs with in phosphatetourmaline-rich in hydrothermal crusts, together veins, with and phosphate clays from in hydrothermalacid-sulfate hydrothermal veins, and clays alteration. from acid-sulfate These mineral hydrothermal components alteration. are considered These mineral to be components cofactors of prebioticare considered chemical to be reactions cofactors related of prebiotic to life’s chem originical [14 reactions]. related to life’s origin [14].

Figure 6.6. (Left(Left)) Author’s Author’s photo photo of overheadof overhead view view of ca. of2.7 ca. Ga 2.7 domical Ga domical stromatolites stromatolites from the Tumbianafrom the TumbianaFormation, Formation, Fortescue Fortescue Group. (Right Group. top (Right) Cross-section top) Cross-section of a Tumbiana of a Tumbiana stromatolite stromatolite (credit: (credit: Martin VanMartin Kranendonk). Van Kranendonk). (Right bottom(Right )bottom Author’s) Author’s photo of photo cross-sectional of cross-sectional view of centimeter-scale,view of centimeter-scale, domical domicalstromatolites stromatolites in black chert in black from chert the “Trendall from the locality” “Trendall outcrop locality” of the outcropca. 3.4 Ga of Strelleythe ca. Pool3.4 Ga Formation Strelley Poolon the Formation Shaw River. on the Shaw River.

5. A A novel novel Model Model for for a a Terrestrial Terrestrial Origin Origin of of Life Life “It is often said that all the the conditions conditions for the the first ﬁrst production production of a a living living organism organism are present, which could ever have been present. But if (and oh what a big if) we co coulduld conceive in some warm little pond with all sorts of ammonia and phosphoric salts, light, he heat,at, electricity etcetera present, that a protein compound was chemically formed, ready to undergo still more complex changes changes [...]” [...]” ~Charles Darwin, Darwin, in in an an 1871 letter to Joseph Hooker [26]. [26]. The above speculation by Charles Darwin on where and how life might have begun is prescient and deeply insightful: a warm little pond in which a useful polymer forms and evolves to ever

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The above speculation by Charles Darwin on where and how life might have begun is prescient and deeply insightful: a warm little pond in which a useful polymer forms and evolves to ever increasing complexity of structure and function. By expanding Darwin’s insight with today’s knowledge of chemistry and biochemistry, it is possible to propose a novel scenario for the origin of cellular life in a small, hot, cycling pool [27]: A source of energy acts on a mixture of simple organic compounds to produce a large number of random polymers. By chance, a few rare polymers happen to form protocells defined as functional systems which are encapsulated within membranous compartments that are subject to combinatorial selection. The encapsulated polymer systems continuously cycle within a kinetic trap in which the rate of synthesis exceeds the rate of hydrolysis [28,29]. Over a large number of such cycles, populations of protocells emerge that are capable of growth and replication. Combinatorial selection of protocells that are better able to survive environmental stresses and more efficient in capturing energy and nutrients, drives the evolution of populations toward the first primitive forms of life. It is difficult to imagine how the above scenario could be applied to an origin of life at marine settings such as hydrothermal vents. First, the continuous presence of water puts thermodynamic limits on the condensation reactions that are required for polymerization of monomers. Furthermore, high concentrations of salt and divalent cations at vents or tide pools impose osmotic stresses on membranous compartments. Life today has evolved complex homeostatic mechanisms to regulate cell volume by actively pumping osmotically active ions and thereby maintain transmembrane sodium and potassium gradients as noted by Mulkidjanian et al. [10]. These concerns led to consideration of an alternative scenario that life began in fresh water hydrothermal fields subject to cycles of dehydration and hydration as outlined by Deamer and Georgiou [30]. To summarize briefly, given a process that could synthesize functional polymers, the polymers become enclosed within compartments, referred to as protocells, in order to prevent dispersion into a bulk aqueous phase. The polymers would resemble RNA and peptides, as well as possible complexes of RNA and peptides. The boundary membranes of protocellular compartments must be selectively permeable to permit access to nutrients from the surrounding environment. A single protocell containing random polymers cannot evolve biologically relevant functions in isolation. Instead, a combinatorial process is necessary to generate large populations of protocells, test the functional fitness of encapsulated systems of polymers, and permit these polymers to be expressed in later cycles of the population. The transition to life is a continuum, along which the synthesis of functional polymers moves beyond physical self-assembly and comes under the control of an autonomous set of molecular processes driven by instructions, itself subject to replication, mutation and propagation through generations of protocells.

6. Linking Chemical Reactions to the Physical Properties of Hydrothermal Pools Hydrothermal pools may contain mixtures of organic solutes, some of which are potential monomers, and others capable of forming membranous vesicles. During the evaporation that drives the dehydration phase of a cycle, layers of lipid membranes form ﬁlms on mineral surfaces at the pool edge as the water level ﬂuctuates. Amphiphilic molecules assemble into multilamellar structures in which monomers are captured between the lipid bilayers [31]. Figure7, bottom inset shows the multilamellar character of one such amphiphile, in this case anhydrous phosphatidylcholine. The concentrated monomers (shown in red) are organized within a two-dimensional reaction space, and reduced water activity drives condensation reactions in which water becomes a leaving group, resulting in synthesis of ester bonds and peptide bonds, the primary links of biopolymers today. Assuming that amino acids and nucleotides are among the potential reactants [32], the synthesis of peptide bonds and phosphodiesters will occur and this has recently been demonstrated in laboratory simulations [33–37]. By chance, some of the polymers will have functions that are relevant to selection as components of protocells. Life 2016, 6, 21 7 of 14 Life 2016, 6, 21 7 of 14

FigureFigure 7. 7.Protocells Protocells cycling cycling between between three three coupled coupled phases. phases. Hydrated Hydrated phase phase ( Top(Top),), inset: inset: protocells protocells containingcontaining DNA DNA growing growing out out of a of dried a dried mixture mixture of DNA of andDNA phospholipid, and phospholipid, hydrated hydrated by water, by stained water, withstained acridine withorange. acridine Gel orange. phase Gel (Center phase), inset:(Center hydrogel), inset: ofhydrogel lipid with of approximatelylipid with approximately 50% water 50% by Bottom weightwater showingby weight lipid showing vesicles lipid fusing vesicles into lamellae. fusing Dehydratedinto lamellae. phase Dehydrated ( ),phase inset: ( freezeBottom fracture), inset: image of anhydrous lipid lamellae of phosphatidylcholine. Micrographs credit: David Deamer. freeze fracture image of anhydrous lipid lamellae of phosphatidylcholine. Micrographs credit: David Deamer. Short term dehydration and rehydration of the pool through periodic ﬂuctuations in hydrothermal water supply,Short term rainfall dehydration events, and and dew fromrehydration day-night of cycles the orpool through through changing periodic humidity fluctuations cause the in outerhydrothermal layers of the water dried supply, lamellae rainfa to dispersell events, large and numbers dew from of protocells day-night into cycles the bulk or solution.through changing Some of thesehumidity protocells cause will the containouter la randomyers of the sets dried of polymers lamellae (Figure to disperse7, top-inset large numbers shows DNA of protocells encapsulation). into the Thebulk protocells solution. are Some then subjectof these to prot selectiveocells processing will contain in whichrandom the sets aqueous of polymers environment (Figure disrupts 7, top-inset some protocellsshows DNA while encapsulation). encapsulated functionalThe protocells polymers are then stabilize subject their to membranousselective processing compartments in which and the therebyaqueous increase environment their robustness disrupts some [38]. protocells Stabilized wh protocellsile encapsulated would persist functional and returnpolymers to depositstabilize theirtheir surviving membranous cargos compartments of polymers and back thereby into the increase lamellae their as robustness protocells dry[38]. down Stabilized and undergoprotocells fusion.would Inpersist this mannerand return the to polymers deposit aretheir “coupled” surviving betweencargos of phases polymers and back cycled into within the lamellae a kinetic as trap,protocells permitting dry generationsdown and ofundergo polymers fusion. to be re-synthesized,In this manner tested the polymers and, as Darwin are “coupled” intuited, becomebetween increasinglyphases and complex.cycled within a kinetic trap, permitting generations of polymers to be re-synthesized, testedThe and, kinetic as Darwin trap provides intuited, scaffoldingbecome increasingly for the stepwise complex. emergence of encapsulated systems of functionalThe kinetic polymers trap provides described scaffolding earlier in for the thecoupled stepwise phases emergencescenario of proposed encapsulated by Damer systems and of Deamerfunctional [27 ].polymers Functions described emerge earlier as selective in the pressures coupled phases present scenario hurdles proposed for populations by Damer of and protocells Deamer undergoing[27]. Functions chemical emerge evolution. as selective The hurdles pressures can bepresent surmounted hurdles by thefor stepwisepopulations accumulation of protocells of functionsundergoing such chemical as membrane evolution. stabilization; The hurdles osmotic can be equilibration surmounted and by transportthe stepwise by transmembrane accumulation of pores;functions primitive such as metabolism membrane utilizing stabilization; nutrients osmotic and equilibration energy sources and available transport in by the transmembrane environment; feedbackpores; primitive controls; metabolism and catalytic utilizing cycles enablingnutrients replicationand energy of sources polymers. available For Darwinian in the environment; selection tofeedback begin to controls; operate, and simple catalytic self-assembly cycles enabling must be replication supplemented of polymers. and ultimately For Darwinian replaced selection by active to processesbegin to encodedoperate, simple in informational self-assembly polymers. must be The supplemented RNA-World and hypothesis ultimately [39 ,replaced40] suggests by active that transferprocesses of proto-genomicencoded in informational sequence information polymers. couldThe RNA-World be ﬁrst expressed hypothesis by simple [39,40] oligonucleotide suggests that templatingtransfer of [ 41proto-genomic] then later through sequence the information combinatorial could selection be first of expressed a pool of functional by simple ribozymesoligonucleotide [42] sometemplating of which [41] are then capable later ofthrough RNA-catalyzed the combinatorial template-driven selection synthesis of a pool ofof otherfunctional RNA ribozymes sequences by[42] activesome ribozymesof which are [43 capable,44]. These of RNA-catalyzed laboratory tests temp of RNAlate-driven World conceptssynthesis require of other cycling, RNA sequences interaction by active ribozymes [43,44]. These laboratory tests of RNA World concepts require cycling, interaction

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and combinatorial selection of large numbers of polymers encapsulated in glassware. A natural kinetic trap of the kind described above may have supported some version of these powerful laboratory demonstrations of molecular evolution and brought an RNA World, or perhaps more likely, an RNA-Protein World, into existence.

Life 2016, 6, 21 8 of 14 7. A Gel Phase as Candidate Progenote It is a common observation that terrestrial microbial life in the form of mats is metabolically and combinatorial selection of large numbers of polymers encapsulated in glassware. A natural most active in a moist, gradually dehydrating state following a short term hydration event such as kinetic trap of the kind described above may have supported some version of these powerful rain fall [1]. This property suggests a link with an earlier form which can only occur in fluctuating laboratory demonstrations of molecular evolution and brought an RNA World, or perhaps more pools: a hydrogel that emerges naturally when sufficiently large populations of stable protocells likely, an RNA-Protein World, into existence. crowd together next to mineral surfaces as the pool water level drops. Figure 7, center-inset 7.illustrates A Gel Phase lipid as Candidatevesicles (~50% Progenote water by weight), which aggregate and form such a “gel phase” during dehydration. In a hydrothermal pool such gel structures would contain concentrated organic solutesIt is aand common mineral observation grains along that terrestrialwith systems microbial of randomly life in the synthesized form of mats functional is metabolically and inert mostpolymers. active in A a self-assembled moist, gradually gel dehydrating aggregate can state act following as a scaffold a short for the term emergence hydration of event key suchbiological as rainfunctions fall [1]. as This suggested property by suggests Tevors and a link Pollack with an[45], earlier and possesses form which properties can only suggesting occur in fluctuating evolutionary pools:continuity a hydrogel [46] thatwith emerges later microbial naturally communities. when sufficiently A gel largeaggregate populations also represents of stable the protocells first example crowd of togetherniche construction next to mineral described surfaces by as Odling-Smee the pool water [47] level in which drops. a Figuremicro-environment7, center-inset is illustrates modified lipid for the vesiclesbenefit (~50% of its watermembers by weight),in a primordi whichal aggregateexample of and endosymbiosis form such a “gel[48–50]. phase” during dehydration. In a hydrothermalA gradient poolof selective such gel pressures structures would would be containrequired concentrated to give rise organicto adaptations solutes that and mineralenable the grainstransition along withfromsystems a non-living of randomly gel phase synthesized to a primitive functional microbial and inert population. polymers. AExamples self-assembled of such gelselective aggregate pressures can act as are a scaffoldexposure for to the environmental emergence of gradients key biological such functions as pH, temperature, as suggested nutrient by Tevors and andsalt Pollack concentrations. [45], and possesses Stromatolite properties fossils suggesting observed evolutionary today were continuitypresumably [46 ]produced with later by microbial complex communities.microbial communities A gel aggregate with alsoa number represents of finely the firsttuned example adaptations of niche (Figure construction 8, right). described These include by Odling-Smeemat formation [47] inusing which an aexcreted micro-environment polymeric su isbstance, modified specialization for the benefit of ofcommunity its members members in a primordialcarrying exampleout photosynthesis, of endosymbiosis chemosynthesis [48–50]. and other metabolic functions, cementation of mineral sediments,A gradient and of tolerance selective for pressures fluctuating would hydration be required and salinity to give [51,52]. rise to It adaptations follows that thatthe microbial enable thepopulations transition fromforming a non-living stromatolites gel phase able to to tolerate a primitive Archaean microbial marine population. shorelines Examples had advanced of such far selectivealong the pressures evolutionary are exposure gradient. to environmental gradients such as pH, temperature, nutrient and salt concentrations.A predecessor Stromatolite would therefore fossils possess observed a todaysubset wereof these presumably adaptations. produced The microbial by complex mats microbialobserved communities at Gallery withHill (Figure a number 8, ofcenter) finely are tuned suggestive adaptations of intermediate (Figure8, right). form These between include an matearlier formationancestor using and ana marine excreted stromatolite. polymeric substance, However, specialization it should be ofnoted community that microbial members communities carrying out as photosynthesis,represented by chemosynthesis living examples and today other as metabolic well as in functions, the earliest cementation fossil record of mineral arose long sediments, after LUCA, and tolerancethe last foruniversal fluctuating common hydration ancestor. and The salinity path [ 51from,52]. an It early follows form that of the life microbial to autonomous populations cellular formingstructures stromatolites defined as able LUCA to is tolerate not expected Archaean to be marine tree-like, shorelines but will hadmore advanced likely resemble far along the shrub the evolutionarymetaphor of gradient. Doolittle [53].

Figure 8. Desert microbial mats (Center); suggestive of an intermediate form between marine Figure 8. Desert microbial mats (Center); suggestive of an intermediate form between marine stromatolites (Right); and an ancestral form of all microbial communities (Left). stromatolites (Right); and an ancestral form of all microbial communities (Left).

A predecessor would therefore possess a subset of these adaptations. The microbial mats observed at Gallery Hill (Figure8, center) are suggestive of intermediate form between an earlier ancestor and a marine stromatolite. However, it should be noted that microbial communities as represented by living examples today as well as in the earliest fossil record arose long after LUCA, the last universal common Life 2016, 6, 21 9 of 14 ancestor. The path from an early form of life to autonomous cellular structures deﬁned as LUCA is not expected to be tree-like, but will more likely resemble the shrub metaphor of Doolittle [53]. A gel phase (Figure8, left) can retain moisture and concentrate nutrients, providing for the emergence, testing and sharing of polymer functions such as membrane stabilization and pores required for solute transport in and out of protocells. With nutrient solute transport come opportunities to support primitive metabolic processes within protocells. A gel is also an ideal venue for protocell competition [54,55]. Furthermore, a gel would tend to retain the components of disrupted protocells, thereby selecting for surviving protocells that can absorb these in a primitive form of heterotrophy. A gel would also help to maintain a collective transmembrane solute balance, thereby protecting all its member protocells against osmotic stress. Lastly, a gel would be subject to group selection in which a metabolic product or functional innovation from one protocell would diffuse throughout the gel, beneﬁting the entire population suggesting an early pattern resembling horizontal gene transfer, central to microbial evolution today. I propose that the protocell gel phase is a candidate progenote as described by Woese and Fox [56,57], in which its member protocells are engaged in the collective process of evolving the relationship between genotype and phenotype. As individual protocells gradually accumulate and internalize proto-genomic functions, they will develop more autonomous phenotypic expression. A new evolutionary phase of the progenote will arise when member protocells can enzymatically replicate encapsulated genomic and functional polymers and pass them on to daughter cells without depending on dehydration synthesis. The resulting speciation and specialization of increasingly independent protocells will lead to communities becoming robust to steeper gradients of environmental pressures. Some individual protocells will eventually become advanced enough to survive and reproduce independent of their source community, passing an important milestone on the continuum to life. Wider distribution and direct competition between free-living cells will drive this early life along the long winding road to LUCA.

8. The Adaptive Radiation of the Progenote A protocell gel progenote possesses one more property that supports its central role in the origin of life: mobility. As soon as the components cycling in a hydrothermal “origin pool” (Figure9, upper) reach a steady state incorporating a kinetic trap, they will give rise to a robust, growing and adaptable progenote. This has the potential to be distributed (Figure9, center left) as a raft, transported by gravity downstream in its hydrated phase, or as a film detached by wind from mineral surfaces and dispersed in the dry phase. Distribution is essential because the initial sustaining ‘Goldilocks’ conditions at the origin pool may not persist. When they arrive at new aqueous venues dispersed throughout the geological context of an Archaean volcanic island (Figure9, lower), progenote aggregates will continue to undergo adaptive radiation by responding to environmental pressures and accumulating innovations through individual and group selection. Innovations will be continuously mixed and shared by combining functions from different gel aggregates. The lower figure insets illustrate some informed guesses as to the effect of various geological venues in the downhill journey of the progenote as it evolves toward the living microbial communities which ultimately build the stromatolites so abundant in the earliest fossil record. This unified view of chemical and geological contexts completes a high level treatment of the terrestrial origin of life hypothesis, offered as a model to the astrobiology community. Life 2016, 6, 21 10 of 14 Life 2016, 6, 21 10 of 14

Figure 9. Overview of the unified chemical (Upper) and geological (Lower) contexts and their Figure 9. Overview of the uniﬁed chemical (Upper) and geological (Lower) contexts and their interface interface through protocell gel progenote distribution (Center) comprises the model of the terrestrial through protocell gel progenote distribution (Center) comprises the model of the terrestrial origin of origin of life hypothesis. life hypothesis. 9. Summary of Novel Features and Testable Predictions of the Model The novel features of the model are summarized below, each carrying predictions that can be subject to testing by experimentalists:

Life 2016, 6, 21 11 of 14

9. Summary of Novel Features and Testable Predictions of the Model The novel features of the model are summarized below, each carrying predictions that can be subject to testing by experimentalists:

i A kinetic trap cycling polymers through coupled phases of hydration and dehydration will produce large numbers of random molecular systems synthesized between dehydrated lipid lamellae (Figure9, upper left), which become encapsulated within large numbers of lipid compartments (protocells). ii Combinatorial selection of encapsulated functional polymers will be observed within this kinetic trap. The initial selection criterion will be the ability of encapsulated polymers to enhance the stability of their membranous compartments, which will be tested in the hydrous phase (Figure9, upper right). iii During dehydration, stable protocells will crowd together with concentrated solutes forming a third, gel phase (Figure9, center) which provides a protective environment. Interaction of protocells within the gel will enable early forms of metabolism, competition, and sharing of functions and products across the gel. iv These three phases will provide continuous resources and subject molecular systems to a variety of selective pressures, driving the system to surmount hurdles to achieve stepwise molecular evolution of new functions. v Pure self assembly and random synthesis will enable the initial stages of the model, but eventually, active functions expressed through sets of robust, heritable proto-genomic instructions will enable Darwinian evolution to take hold. vi Degradation rates of synthesized polymers will set upper bounds on the permitted dwell time within each phase suggesting the necessity of reliable, repetitive fluid refilling typical of hydrothermal fields. Expressing a pattern emerging later as the life cycle, degraded polymers and other inert byproducts must be periodically reused or expelled and functional systems continually re-synthesized through proto-genomic blueprints drawing from solute sources (Figure9, upper right). vii A candidate protocell gel progenote capable of growth and evolutionary adaptation will emerge and become robust to distribution to a variety of watery venues in a plausible Archaean volcanic landscape. Extensive laboratory growth, testing, and analysis of such progenotes will provide insight to possible pathways to the first microbial communities and viable free-living cells.

10. Conclusions A field trip in Western Australia to venues ranging from living marine stromatolites to inland Archaean stromatolite fossil localities tested the coupled phases scenario for an origin of life. A novel terrestrial origin of life hypothesis was developed through the unification of chemical and geological settings. The model is centered upon the insight into a protocell gel progenote, a candidate common ancestor of microbial communities. It seems inescapable that very soon after the first robust protocells emerged, they became communal. Primitive protocells floating free in the Archaean environment would be unlikely to survive, while selection would favor the protective, nutritional and collaborative advantages of a protocell gel progenote. This progenote is a model for an amphibious, communal aggregate of protocells that preceded LUCA, a much more highly evolved population of cells able to independently support their own metabolism and reproduction. The progenote described here represents a common pool, or roots from which the earliest inhabitants of the tree of life emerged.

Acknowledgments: I would like to acknowledge the assistance of David Deamer, Malcolm Walter, Martin Van Kranendonk, and Tara Djokic who provided key subject matter expertise in support of this work. Ryan Norkus is also gratefully acknowledged for his production of graphics for this article. Resources: A website has been established to support collaboration, testable hypotheses and research results on the terrestrial origin of life hypothesis at: http://origins.biota.org. Life 2016, 6, 21 12 of 14

Conﬂicts of Interest: The author declares no conﬂict of interest.

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