Astrobiology, homochirality, Astrobiology, homochirality, and origins of lifeand origins of life

Int. J. Astrobio. Int. J. Astrobio. 33, 209 (2004), , 209 (2004), 44, 75 (2005),, 75 (2005),Orig. Life Evol. Biosph. Orig. Life Evol. Biosph. 3535, 225 (2005), , 225 (2005), 3535, 507 (2005), 507 (2005)

Astrobiology 7, 725 (2007)Astrobiology 7, 725 (2007)

The four corner stones of astrobiologyAstrobiology in Nordic countries

Role of NorditaOur current interests:

homochirality and origin of lifepeptide world, RNA world

Pencil CodeCommunity effortSuitable for distributed systems

2

Topics at Nordic AB meetings

Martian gulliesMartian gulliesIcelandic analoguesIcelandic analogues

Subglacial lakesSubglacial lakes

Mars simulatorMars simulatorInterstellar chem.Interstellar chem.

Ancient DNA, PNA,Ancient DNA, PNA,Early life evidenceEarly life evidence

Climate, exoplanetsClimate, exoplanets

AtmosphericAtmosphericescapeescape

GeologicalGeologicalevolutionevolution

ExtremophilesExtremophilesDeep biosphereDeep biosphere

CyanobacteriaCyanobacteriaDeep biosphereDeep biosphere

NucleotideNucleotideSynthesisSynthesisIn spaceIn space

MeteoritesMeteoritesstarduststardustRNA worldRNA world

GeochemistryGeochemistryastrochemistryastrochemistry

DeepDeepbiosphbiosph

3

Urey-Miller experiment (1953)Urey-Miller experiment (1953)

15 organic compounds15 organic compounds2% amino acids (11 different ones)2% amino acids (11 different ones)

Wait 1 weekWait 1 week Reduced gases: HReduced gases: H22, NH, NH33, CH, CH44, CO, CO

Result: NHResult: NH22-CH-CH22-COOH, etc-COOH, etc

From From exoplanets toexoplanets toextremophilesextremophiles

Radial vel.Radial vel.TransitsTransitsDirectDirect

microlensingmicrolensing

On Earth: On Earth: Life 3.8 GyrLife 3.8 Gyr

agoago

Frozen/liquid water on MarsFrozen/liquid water on Mars

Carbonic and organic carbon, CaCOCarbonic and organic carbon, CaCO3 3 versus (CHversus (CH22O) O) nn

6

Time lineTime line104 yr 106 yr 108 yr 109 yr

planetesimalsplanetesimals

Sun ignitesSun ignitesAll gas goneAll gas gone

Remaining dust Remaining dust settlessettles

First lifeFirst life

T0=1010 yr after Big Bang

7

Astrobiology: Astrobiology: the range of problemsthe range of problems

• From dust to planets– Exoplanets– Water delivery– Habitable worlds

• Archaen world– Volcanos, carbon cycle– Impacts, panspermia– Greenhouse effect

• Miller experiment– Amino acids, chemistry

• Artificial life• Origin of life

– RNA world, PNA world– homochirality

• Early life– Extremophiles– Cyanobacteria– Oxygen, methane evol.– LUCA

8

Onset of lifeOnset of life

• There is no good definition of life– replication (birth/death), evolution, metabolism– Protolife (simplistic): 2H2+CO2 (CH2O)+H2O– Ignores waste produced: CH4 , H3C-COOH, or O2

– Ignores replication machinery

• Hypothesis: primitive life is unavoidable– Several independent geneses of life on early Earth?– No serious competitors to carbon-based life

Aminoacids in proteins: left-handedAminoacids in proteins: left-handedSugars in DNA and RNA: right-handedSugars in DNA and RNA: right-handed

Louis PasteurLouis Pasteur(1822-1895)(1822-1895)

animoanimogroupgroup

carboxylcarboxylgroupgroup

chlorophyllchlorophyll

Is chirality:Is chirality:(i) prerequisite(i) prerequisite

(ii) consequence(ii) consequenceof life?of life?

26126chem.

22 6SOHCCO6SH6

10

Racemic mixtureRacemic mixture(from lecture of(from lecture ofAntoine Weiss)Antoine Weiss)

RacemizationRacemizationdating methoddating method

11

Origins of HomochiralityOrigins of Homochirality

12

Origin of life ~ origin of Origin of life ~ origin of homochiralityhomochirality

• Life requires homochirality– wrong enantiomer: stops polymerization– right and left do not cooperate

• Dead cells racemize• Also: protolife may produce chirality

– encymatic reactions keep system from equilibrium– as a result of polymerization

• But: prebiotic soup was racemic!

13

Producing enantiomeric excess (e.e.)Producing enantiomeric excess (e.e.)

• Life only develops in homochiral environment– Homochirality is then a prerequisite

• However: no mechanism produces 100% e.e.– only minute partial excess possible (electroweak)– slightly bigger for large Z, goes like Z5 Cu (II) ions

• Still need amplification mechanism– Frank (1953) model (plus extensions): nucleotides– Autocatalysis and enantiomeric cross inhibition– Plasson, Bersini, Commeyras (2004): peptides

14

Chirality selection during polymerizationChirality selection during polymerizationof the first replicating molecule?of the first replicating molecule?

RR

LL

Isotactic polymer (same chirality)

“waste” (enantiomericcross-inhibition)

dual worlddual worldRNA worldRNA worldPNA worldPNA worldlipid worldlipid world

RNARNARNARNADNADNA

proteinsproteins

Rasmussen et al (2003Rasmussen et al (2003Artif. LifeArtif. Life 99, 269-316), 269-316)

achiralachiral

chiralchiral

PolymerizationPolymerization

15

Exponential amplificationExponential amplificationrecap of Frank-type model (Frank 1953)recap of Frank-type model (Frank 1953)

auto-catalysis aloneauto-catalysis alone

LLLS

DDDSk

k

LS

DSL

D

]][[d

][d

]][[d

][d

LSkt

L

DSkt

D

C

C

kinetic equationkinetic equation

enantiomeric excess:enantiomeric excess:

const.][[D]

][-[D]

][[D]

][-[D]e.e.

00

00

L

L

L

L

][

e[L][L]

e[D][D]

0

0

SkC

t

t

exponentialexponentialgrowthgrowth

catalystcatalyst

16

Need also mutual antagonismNeed also mutual antagonism(to siphon off the bad guys)(to siphon off the bad guys)

add cross-inhibitionadd cross-inhibition

DLLD Ik

]][[]][[d

][d

]][[]][[d

][d

LDkLSkt

L

DLkDSkt

D

IC

IC

kinetic equationkinetic equation

2

2

][]][[][d

][d

][]][[][d

][d

LkLDkLkt

L

DkDLkDkt

D

I

I

unspecific antagonismunspecific antagonism

17

Prebiotic experiments: nucleotidesPrebiotic experiments: nucleotides

poly (Cpoly (CDD) ) oligo (G oligo (GDD))

Mononucleotides with wrongMononucleotides with wrongchirality terminate chain growthchirality terminate chain growth

cytosinecytosine guanineguanine

okok

poisonedpoisonedJoyc

e et

al.

(198

4)Jo

yce

et a

l. (1

984)

(HPLC)(HPLC)

template-directed polymerizationtemplate-directed polymerization~polymerase chain reaction (PCR)~polymerase chain reaction (PCR)

Serious difficulty:Serious difficulty:requires building blocksrequires building blocks

of the same chiralityof the same chirality

18

Contergan: was sold as racemic mixtureContergan: was sold as racemic mixture

causes misformationscauses misformations Cures morning sicknessCures morning sicknessduring pregnancyduring pregnancy

(abandoned in December 1961)(abandoned in December 1961)

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Steps toward realismSteps toward realism(i) Consider polymerization of nucleotides

i.e. homochirality developed during RNA world

autocatalysis requires longish polymers

(ii) Peptide world (new mechanism)no explicit autocatalysis required

appears chemically feasible

(iii) Spatially extended systemsindependent origins at different locations on Earth

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(i) Polymerization model of Sandars(i) Polymerization model of Sandars

]][[2][ 11

211

LLkLdt

d

LLL

nSn

nk

nS

Reaction for left-handed monomersReaction for left-handed monomers

Loss term for each constituentLoss term for each constituent

Orig. Life Evol. BiosphOrig. Life Evol. Biosph. . 3333, 575-587 (2003), 575-587 (2003)

]][[2][ 11

12

1

RLkRLdt

d

RLRL

nIn

nk

nI

21

3 different classes of mechanisms3 different classes of mechanisms

(i) Autocatalysis and mutual antagonism-- Frank (1953) model- Grow both, and dump pairs- Has been applied to RNA world

(ii) crystal growth with stirring- larger crystals spawn more nucelation sites

(iii) constructive autocatalysis (see below)- has been applied to peptides

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(ii) RNA versus peptide worlds(ii) RNA versus peptide worlds

• Activation D D*, L L*

• Polymerization D+D DD, L+L LL

• Epimerization DL LL, LD DD

• Depolymerization DD D+D, LL L+L

• Template-directed (PCR-like)

• Enantiomeric cross-inhibition

• Autocatalytic production of new mono-nucleotides ( but uncertain)

• RNA stability…

RNA worldRNA world peptide worldpeptide world

AP

ED

model (P

lasson et al.)A

PE

D m

odel (Plasson et al.)

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Net reactionsNet reactions

*

*

LL

DDa

a

LLLLDLLD

DDDDLDDL

LLLLLL

DDDDDD

hep

hep

hp

hp

*

*

*

*

24

Reduced APED modelReduced APED model

][][1

12][][

d

d2 LDLD

t

a one way a one way round-aboutround-about

For nearly racemic state:For nearly racemic state:

(iii) Spatially extended model(iii) Spatially extended model

Propagating front solutionsPropagating front solutions

Reaction-diffusion equationReaction-diffusion equation

Proto type: Fisher’s equationProto type: Fisher’s equation

'')1( XXXX

)( ctxfX 2c

wave speedwave speed

wwith Tuomas Multamith Tuomas Multamääki, Int. J. Astrobio. 3, 209 (2004)ki, Int. J. Astrobio. 3, 209 (2004)

Spread of the black Spread of the black deathdeath

LLRLLR

L

dt

dL

RRRLLR

R

dt

dR

222

2

222

2

)(

)(

13501350

13491349

13481348

13471347

26

1D reduced model 1D reduced model (reaction-diffusion equation)(reaction-diffusion equation)

Propagation into racemic environmentPropagation into racemic environment

27

2D model (reaction-diffusion equation)2D model (reaction-diffusion equation)

XX (X-Y)[1-(X-Y)(X-Y)[1-(X-Y)2 2 X-YX-Y]]

28

Piecewise linear increasePiecewise linear increase

29

Piecewise linear increasePiecewise linear increase

SAA

A

t

Ad

1

1

d

d

2

2

SSS 221

ASAAS

ASA 2

22

222

add/subtract:add/subtract:

LRLLR

L

dt

dL

RRLLR

R

dt

dR

)(

)(

22

2

22

2

Reduced equationsReduced equations

trrrr 212

30

Initial e.e. not related to final e.e.Initial e.e. not related to final e.e.

31

3-D and effects of turbulence3-D and effects of turbulence

32

Where could this work?Where could this work?

Braun & Libchaber (2003)Braun & Libchaber (2003)

a) hydrothermal ventsa) hydrothermal vents

b) Deep biosphereb) Deep biosphere

Michael J. RussellMichael J. Russell(2006, Am. Sci. 94, 32-39)(2006, Am. Sci. 94, 32-39)

ideas about firstideas about firstProtocellsProtocells

April 21, 2023

PencilPencilCodeCode

• Started in Sept. 2001 with Wolfgang Dobler• High order (6th order in space, 3rd order in time)• Cache & memory efficient• MPI, can run PacxMPI (across countries!)• Maintained/developed by ~40 people (SVN)• Automatic validation (over night or any time)• Max resolution so far 10243 , 4096 procs• http://pencil-code.googlecode.com

• Isotropic turbulence– MHD, passive scl, CR

• Stratified layers– Convection, radiation

• Shearing box– MRI, dust, interstellar– Self-gravity

• Sphere embedded in box– Fully convective stars– geodynamo

• Other applications– Homochirality– Spherical coordinates

34

35

36

ConclusionsConclusions• Astrobiology: need to be prepared…

• Polymerization model:– Based on measurable processes

• Reduction to accurate simplified model– Homochirality in space (earth, interstellar, etc)– Timescales 500 Myr; fossil evidence of spatially fragmented

homochirality?

• Pencil Code: just google for it– Detailed manual, …