astrobiology, homochirality, and origins of life int. j. astrobio. 3, 209 (2004), 4, 75 (2005),...
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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
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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
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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
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From From exoplanets toexoplanets toextremophilesextremophiles
Radial vel.Radial vel.TransitsTransitsDirectDirect
microlensingmicrolensing
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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
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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
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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
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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
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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
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Racemic mixtureRacemic mixture(from lecture of(from lecture ofAntoine Weiss)Antoine Weiss)
RacemizationRacemizationdating methoddating method
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Origins of HomochiralityOrigins of Homochirality
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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!
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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
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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
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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
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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
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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
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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
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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
*
*
*
*
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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:
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(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
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1D reduced model 1D reduced model (reaction-diffusion equation)(reaction-diffusion equation)
Propagation into racemic environmentPropagation into racemic environment
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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]]
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Piecewise linear increasePiecewise linear increase
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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
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Initial e.e. not related to final e.e.Initial e.e. not related to final e.e.
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3-D and effects of turbulence3-D and effects of turbulence
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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
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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
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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, …