The Nature and Origin of Life - Sonoma State University · 1 The Nature and Origin of Life Instructor: Carl B. Pilcher OLLI at SSU/Oakmont Life in the Universe: The Science of Astrobiology

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The Nature and Origin of Life

Instructor: Carl B. Pilcher

OLLI at SSU/Oakmont

Life in the Universe: The Science of Astrobiology

Week 2—January 21, 2016

Outline•  DiversityofLife•  An2quityofLife•  EarlyLifeandtheLastUniversalCommonAncestor(LUCA)

•  Originoflife•  Canwedefinelife?•  Doesithavetobecarbonandwater?•  Detec2ngalienlife

TheDiversityofLife

Temperature (°C)

47 27 37

Normal

Medical Emergency

Death

Human Physiological Limits

Normal 7.4

7.3

7.5

Blood pH

Acidosis

Alkalosis

SlidecourtesyofT.Hoehler

0

2

4

6

8

10

12

14

-30 10 50 90 130

1

1

1

Temperature (°C)

pH

You Are Here

(salinity, pressure, radiation, dessication…)

Range of Documented

Biological Activity

SlidecourtesyofT.Hoehler

OctopusSpring,YellowstoneNa2onalPark

RioTinto,SpainpH~2

Gypsumendolith

Photocredit:NikoFinke

GuerreroNegro,BajaCaliforniaSur,Mexico

“LostCity”pH10-11T~50-90CCarbonatechimneys

BlackSmokerspH3-5T~350CMetalsulfide

chimneys

SubmarineHydrothermalVents

Tardigrades:Extremotolerantmul2cellularanimals

Life on Earth as we thought about it 30 years ago

Five Kingdoms Fungi Animals Plants

Protists

Monera (Bacteria)

Cow Mushroom Tomato

Amoeba, Ciliates, Giardia

E. coli, Bacillus, bacteria in general

Euka

ryot

es

Prokaryotes

The Universal"Tree of Life"(adapted from Pace;"Science 276, 734, 1997)"

Bacteria

Archaea

Eucarya

Youarehere

Most Energy

(chocolate!)

Least Energy

(celery!)

Worst Oxidant

Best Oxidant

MetabolicDiversity

Reductants

TheAn2quityofLife

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Life on Earth 3.5 billion years ago Stromatolites: Ancient and modern

LifeisoldLife3.43billionyearsago(Allwoodetal.,Nature441:714-718,8June2006)

OctopusSpringrun-offchannel

Narrow, 2-5µm Cylindrical Cells APEX CHERT Microfossils (~3,465 Ma)

Medium, 3-6µm Discoidal Cells Broad, 6-9µm Cylindrical Cells

SlidecourtesyJ.WilliamSchopf

Clement Conditions in the Hadean (>3.9 BY)? Mark Harrison (UCLA), Steve Mojzsis (U. Colorado) and coworkers John Valley (U. Wisc.), Aaron Cavosie (U. Puerto Rico) and coworkers

EarlyLifeandtheLastUniversalCommonAncestor(LUCA)

The Universal"Tree of Life"(adapted from Pace;"Science 276, 734, 1997)"

Bacteria

Archaea

Eucarya

Twopossibleearlymetabolisms

4H2+CO2CH4+2H2Omethanogenesis

H2+S0 H2Ssulfurrespira2on

Thesetwometabolismsarerelatedbiochemically:bothinvolvebreakingbondsbetweensulfuratoms

Wastheancestorofalllifeacommunityofmethanogensandsulfur-u6lizingmicrobesthatlivedathigh

temperature?

AllLifeonEarthSharesManyCommonCharacteris2cs

•  Gene2cinforma2onencodedinDNAmadeupofapar2cular5-carbonsugar(ribose),phosphategroups,andfourpar2cularnucleo2des(the“lehers”inourgene2calphabet)

•  Biochemicalreac2onscatalyzedbyproteinsmadeupoftwentyspecificlej-handedaminoacids

•  Cellmembranesmadeofphospholipidbilayers•  EnergycarryingmoleculeisATP(adenosine

triphosphate)producedviatheproton-mo2veforce

•  Gene2cinforma2onistranscribed(copied)intoRNAandtranslatedintoproteinsbytheribosome

•  Energyisstoredincarbohydratesmadeupofasmallnumberof6-carbonright-handedsugars

These must all have been characteristics of LUCA

LUCA LastUniversalCommonAncestor

HorizontalGeneTransfer

•  HorizontalgenetransfermayhavebeenmuchmoreprevalentearlyinthehistoryoflifeonEarthwhencellsweremuchlessdeveloped(e.g.,“leaky”membranes)thantheyarenow.

•  Thismeansthat“ver2cal”inheritance/evolu2onimpliedbythetreestructuremaybeanoversimplifica2on.

LUCA

TheLastUniversalCommonAncestor(LUCA)

•  LUCAwasnotadiscreteorganism.

•  Itwasacommunityofprimi2vecellsrapidlyexchanginggene2cinforma2on.

•  ItdidnotexhibitDarwinianevolu2on(dominanceofver2calgenetransfer)

•  Over2me,LUCArefinedintoincreasinglycomplexcelltypesthatledtotheancestorsofthreedomainsoflife.

LUCAisveryfarremovedfromtheoriginoflife!

TheOriginofLife

SomeChallengesfortheOriginofLife•  Manybiochemicalmolecules(polymers)areformedbyremovingawatermoleculefromapairofsmallermolecules(monomers)

•  Butitisverydifficulttodothisabio2callyinthepresenceoflotsandlotsofwater,e.g.,anearlyocean.

•  Ifyoutakeamixtureoforganicmolecules(the“rawingredientsoflife”)andaddenergy(e.g.,heat),youdon’tgetlife,yougettar!

•  Akeypropertyoflifeisthatthemoleculesinourcellsarecapableofreproducingthemselves,aprocesscalled“autocatalysis.”Itisverychallengingtoproduceautocataly2csystems(wecan’treallydoitinthelaboratory).

LifeasanEmergentPhenomenoninaComplexSystem

1.  Acomplexsystemhasmanyinterac2ngpar2clesor“agents.”

2.  Whenenergyflowsthroughthesystemofpar2cles,newpahernsorbehaviorsemergethatarenotmanifestbytheindividualagents.

3.  Emergentphenomena,bydefini2on,cannotbepredictedevenwithperfectknowledgeabouttheindividualpar2clesinacomplexsystem.

4.Forexample,perfectknowledgeofanindividualsandgrainwouldnotallowyoutopredictthepahernsofsanddunesinthedesert(createdbywindenergy).

Severalwaystothinkaboutandinves2gatetheoriginoflife

•  Lifeisanemergentpropertyofacomplexprebio2cchemicalsystemindisequilibrium.1.  Onecanstudytheprebio2ccomponentsofthesystemtotryto

understandhowcomplexityleadstotheproper2esoflivingsystems,e.g.,autocatalysis(self-reproduc2on),encapsula2on.{BoCom-up}

2.  Onecanstudylivingsystemsandahempttoinferwhatweretheproper2esoftheveryfirstlivingsystems.{Top-down}

•  Onecanconductbohom-uportop-downinves2ga2onsfromthreedifferentperspec2ves:1.  Lifebeganwithmetabolism;gene2cmoleculeswereincorporated

later.2.  Lifebeganwithself-replica2nggene2c(informa2onal)molecules;

metabolismwasincorporatedlater.3.  Lifebeganasacoopera2vechemicalphenomenonarisingbetween

metabolismandgene2cs.

AFamousBohom-upExperiment:Miller-UreySynthesis(1953)

Miller-UreySynthesis•  Originalexperimentsusedsimulatedatmosphereof

hydrogen(H2),methane(CH4),ammonia(NH3),andH2O•  Thiscomposi2onisnowthoughttobemuchmore

reducedthanEarth’searlyatmosphere,whichwaslikelycomposedofcarbondioxide(CO2),nitrogen(N2),andtracesofreducedgases.

•  Similarexperimentswithmorerealis2cmodelatmospheresalsoproduceaminoacidsandotherbiologicallyrelevantmolecules,butinsmalleramounts.

•  H2OandCO2canreacttoformformaldehyde(CH2O),whichcaninturnpolymerizetoformcarbohydrates

•  Conclusion:itisnotdifficulttoformprebio6cmoleculesunderchemicalcondi6onsthoughtrealis6cforearlyEarth

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Rawmaterialsoflifefromspace?

Jason P. Dworkin et al. PNAS 2001;98:815-819

SpontaneousVesicleForma2on

Laboratorysimula2onsofinterstellaricesJ.P.Dworkinetal.,

2001

Muchisonmeteorite

organicextractD.W.Deamer,1999

Phase Fluorescence

PhospholipidBilayer

Membranes(moderncells)

Iron-Sulfur(FeS)Catalysts•  SomeoftheearliestproteinsthatenablelifetousesimplemoleculeslikeH2andN2andtotransferelectrons(e.g.,inmetabolism)containFe-Sclustersattheircataly2ccenters(e.g.,Fe2S2)

•  ThestructureoftheseclustersisverysimilartothestructureofFe-Smineralssuchasgreigite(Fe3S4)

•  Fe-Sminerals,includingpyrite(FeS2),areknowntobeexcellentcatalystsandwerepresentontheearlyEarth

•  Wereprebiologicalchemicalnetworks,catalyzedbyFe-Sminerals,theprecursorsofbiologybasedonthesamechemistry?

DidLifeBeginataHydrothermalVent?

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Russell & Martin (2004)

Russell & Martin (2004)

TheProton-mo2veForce

Lodishetal.,MolecularCellBiology3rdEd.,Sci.Amer.Books,1995

Ordidlifebeginina2depool?

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ClayMinerals

ThePossibleRoleofClayMinerals

•  Claysarecommonmineralsformedbytheac2on(weathering)ofwateronigneousandmetamorphicrocks.

•  Theyarehighlylayeredwithastrongsurfaceelectrosta2ccharge.

•  Duetoitslayeredstructure,agramofclaycanhaveasurfaceareaofseveralsquarefeet!

•  Asaresult,clayreadilyadsorbsorganicmolecules.•  Whenmoleculesadsorbinproximityonaclaysurface,they

readilyreact,forexample,bypolymerizing.•  Claysmaythushaveplayedanimportantcataly2crolein

crea2ngproto-biopolymers,byconcentra2ngreactantsonclaysurfacesandpromo2ngchemicalreac2ons.

TheRNAWorld•  Inmodernlife,DNAstoresgene2cinforma2onandproteinscatalyze

biochemicalreac2ons.•  Butproteinsynthesisrequiresthegene2cinforma2onofDNA,andDNA

synthesisrequiresproteinsascatalysts.•  Thisleadstoa“chickenandegg”problem:Whichcamefirst?•  RNAcanbothstoregene2cinforma2onandcatalyzebiochemical

reac2ons.It’saverysimilarmoleculetoDNA,butmuchmorechemicallyreac2ve.–  Thecataly2cac2vityoftheribosome,theproteinfactoryinalllivingcells,is

duetoanRNAcatalyst(a“ribozyme”)•  Aleading“informa2onfirst”theoryoftheoriginoflifepositsthatthe

DNA-proteinworldwasprecededbyanRNAworldinwhichRNAperformedthefunc2onsofbothoftheotherbiopolymers.

•  TheproblemwiththistheoryisthatthesynthesisofRNAfromsimplemoleculesinaprebio2cworldisverydifficult.AnRNAworldwasprobablyprecededbyasimplerlivingworldthat“invented”RNA,leavinguss2llwithalargegaptoexplainbetweentheabio2candlivingworlds.

Canwedefinelife?

CampbellEssen6alBiologywithPhysiology

EricJ.Simon,JeanL.Dickey,JaneBReece

Manydefini2onsoflifearelistsofproper2es.Here’sonesuchlistfrommydaughter’sbiologytextbook:

•  Proper2esofLife–  Order–  Regula2on(internalenvironment)–  Growthanddevelopment–  Energyprocessing–  Responsetotheenvironment–  Reproduc2on–  Evolu2on

•  Bythisdefini2on,isonerabbitalive?Isamule?–  Onerabbitcan’treproduce,norcananynumberofmules.

•  Whataboutaforestfire?–  Itregulatesitsinternalenvironment,growsanddevelops,processesenergy,respondstotheenvironment,andreproduces.

ANASAcommiheecameupwithadefini2onthatahemptedtoavoidthesedifficul2es:

“Lifeisaself-sustainingchemicalsystemcapableofDarwinianevolu6on.”

NotethatDarwinianevolu2oninvolves

–  Amoleculargene2csystem–  Imperfectreplica2on–  Thereplica2onof“mistakes”–  Differen2alfitnessbetweenreplicates

G.F.Joyce,1994

Wouldpre-LUCAlifesa2sfythisdefini2on?

•  ClelandandChybaarguethatwecannotdefinelifebecausewedon’thaveanunderlyingtheoryofbiology.

•  Theylikenourignorancetothatofsomeonetryingtodefine“water”priortothedevelopmentofmodernchemistryinthe19thCentury.

•  Onecoulddescribewater’sproper2es(liquid,quenchesthirst,putsoutfires,freezes,boils,etc.)

•  Butnotun2lthedevelopmentofatomicandmoleculartheorycouldwesaythatwaterisH2Oandexplainthedetailsofthestructurethataccountsforitsproper2es.

•  Soasa2sfactorydefini2onoflifemayhavetoawaitanunderlyingtheoryofbiology.

C.E.ClelandandC.F.Chyba,OriginsofLifeandEvolu6onoftheBiosphere32:387-393,2002

Doeslifehavetobebasedoncarbonandwater?

No,but…

WaterandCarbon•  Waterismadefromthefirst(hydrogen)andthird(oxygen)mostabundantelementsintheuniverse.

•  Wateriseverywhere!–  Andweknowit’sanexcellentsolventforlife.

•  Carbonistheonlyelementthatformscomplex,long-chainmoleculesinwater.

•  Earth’scarbon-basedlifeisextremelyspecific!•  Onecaneasilyimaginecarbon-basedlifeinwaterthatisverydifferentfromlifeonEarth.

•  Socarbonandwaterareagoodstar2ngpoint,butweshouldnotexcludeothercombina2onsfromourconsidera2on.

Detec2ngAlienLife

Slide courtesy C. McKay

Abiotic distributions are smooth Biotic distributions are spiked

McKay 2004 PLoS Biol 2(9)1260-12623

McKay 2004 PLoS Biol 2(9)1260-12623

alien!

Abiotic distributions are smooth Biotic distributions are spiked

exploringorigins.org

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Questions?

QUESTIONS?