Nivens: So tell me Mary. What exactly do you do for NASA? Sefton: My speciality is exobiology. Nivens: Exobiology? Sefton: It’s a study of what alien life

Nivens: So tell me Mary. What exactly do you do for NASA?Sefton: My speciality is exobiology.Nivens: Exobiology?Sefton: It’s a study of what alien life forms might be like.Nivens: You actually makea living at that? Seems like it would be mostly guesswork.Sefton: Well, we had a little joke in school. That ours is the only science that didn't have a subject matter.

Life, the Universe, and the "Scientific Method"

Robert HeinleinThe Puppet MastersHollywood Pictures (1994)

© Steven Benner, 2009

Science without a subject matter?

Galileo’s big question: Does the Earth circle the sun?Scientists often study what they do not observe

His adversaries had the stronger argumentIf the Earth circled the sun, then we would feel its motionWe do not feel its motionTherefore, Earth does not circle the sun

What Galileo actually did:Rolled balls down inclined planes. These experiments suggested that the air, Earth, and people move together, making it impossible for us to sense our motion relative to the others. The connection is hard to understand, but it exists.

We need a theory of life as a universalAnd we already have several candidates

Cell theory Evolution theory Gene theory

Jerry Donohue

NN

NR

H O

HH

NN

N

N

O

N

HH

HH

NN

OR

H O

NN

N

N

N

H

HH

HH

oo

o

o

What is our equivalent of Galileo?Four indirect ways to understand life as a universal

O

CHH

H C NHO

C C

O

HHH

Paleogenetics

A path to the simplest first life

C C C N

Eucarya

interstellar organics

Life as a universal

HO

CNH2H

backwardsin time tosimplerlife

forwards from chemistry

Archaea Bacteria

infer ancestral life forms; resurrect for laboratory study

PrebioticChemistry

Synthetic biologyBaross, Benner et al. (2007) Natl. Res. Councl.Limits toLife

Ricardo et al. (2004) Science 303, 196

Benner et al. (2007) Adv. Enzymol. Mol. Biol. Protein Evol. 75, 1-132

Benner (2004) Acc. Chem. Res. 37, 784-797

N

N

OR

RN

N N

NNN

O

RH

H

H

H

H

N N

N

RN

H H

N N

N NO

O

R

H

N

NR

RO

N N

N NO

N

R

H H

H

H

H

HH

N

OR

RN

N N

N NN

O

R

H

H

H

H

H

Construct life in the lab

Search cosmos

discover alien life

independent genesis?

"Constructive belief" in scienceWe need not believe what we say we believe

Viking 1976 mission to MarsThree "life detection experiments"(a) Release dioxide (CO2) when fed(b) Release dioxygen (O2) when watered(c) Fix carbon from atmospheric CO2 & CO

The tests constructively applied a metabolism theory of life.(a) You metabolize food to release CO2

(b) Terran plants release O2 when watered(c) Terran organisms at bottom of food chain fix carbon

© Jake Fuller from the bookLife, the Universe and the Scientific Method

These 1976 experiments did not apply a cell theory of life, or an evolutionary theory of life, or a gene theory of life.

Anthropology to decide what is believed

Metabolism tests positive for Mars lifeCO2 and O2 were released; carbon was fixedThen a gas chromatograph-mass spec came on line

GC-MS result: No organic molecules containing reduced carbon (compounds with a C-H bond) were found, even though these fall to Mars daily from outer space.

Conclusion: Life is absent from the surface of MarsConstructively, the Viking 1976 scientists had a "reduced carbon" theory of life as a universal

Non-life explanations for signs of Martian life were easily developed …

H

H

O

H

H

O

H

H

O

H

HO HH

H

O

H O

ultravioletlight

recombineradicals

dihydrogen escapes

into space

hydrogen peroxide remains in soil

two hydroxyl radicals

two hydrogen atoms

This stuff bubbles O2, especially with iron

This is water

UV light comes to surface because Martian air lacks ozone

This tells us something about "the" scientific method.

...as soon as the community decided that such explanations were needed.

Science as actually practiced. For two decades, “settled science” held that Mars surface is highly oxidizingResults mean what the culture needs them to mean.

Oxidants (HO and H2O2) used to explain away signs of Martian life

oxidantCO2

Dry H2O2O2

(a)(b)

H2O, Fe+++

CO + CO2

UV light organics(c)

O

COHH

O

COHC

H

HO H

O

COHC

H3C

H OH

O

COHC

H3C

H2N H

O

COHC

H3C

H NH2

O

COHC

H3C

HO H

O

COHC

H

H2N H

L-lactic acidD-lactic acid

L-alanineD-alanine

glycineglycolic acid

formic acid

© Jake Fuller from the bookLife, the Universe and the Scientific Method

Community was despondent about the chances of finding alien life on MarsUntil 1996

In 1996, something happened to change the culture and what it believed was “settled science”

What happened in 1996 to make the community no longer despondent about the chances of finding alien life on Mars?

David McKay applied the cell theory of life as a universal © Jake Fuller

Life, the Universe and the Scientific Method

Allan Hills 84001rock from Mars

Microstructures in Allan Hills 84001

What did I forget to put on the picture?Microscopy 101.

Scale bar1 micrometer

Some in the community:The “cells” are “too small” to be “life”.Universal theory of life that presumes a volume for a presumed set of needed contents.

Size of a typical bacterial cell

Too small for what? The ribosome.

Ribosome, the machine in terran life that makes proteins.The structures fit only four ribosomes across.Protein theory of life

1 micrometer

oo

o

o

Does life universally need proteins?What “scientific method” would we use to decide?

O

CHH

H C NHO

C C

O

HHH

Paleogenetics


C C C N

Eucarya


Life as a universal

HO

CNH2H



Archaea Bacteria


PrebioticChemistry





N

N

OR

RN

N N

NNN

O

RH

H

H

H

H

N N

N

RN

H H

N N

N NO

O

R

H

N

NR

RO

N N

N NO

N

R

H H

H

H

H

HH

N

OR

RN

N N

N NN

O

R

H

H

H

H

H


Search cosmos

discover alien life


xx x x x xxx x x x xx

>3000 B.C.

Proto-Germanic

MiddleEnglish

Old English

Old HighGerman

Gothicsnaiws

snow

snaw

sneoChurchSlavonic

snegu

Old Irish

Proto-Indoeuropean

Old Norse

Greekφιν

.Old Fr

Latin

OldPrussian

snechte

œsn rnoif

, nix nivus

α

*snigw -h

xx

Slavic Germanic Romance Celtic

Reconstruction says something about the Proto-Indoeuropeans. They lived in a cold climate. They had no gold or silver. But they had dogs (*kwón-), horses (*ékwo-), sheep (*H3éwi-), ox (*gwów-), pigs (*suH-), grain (*yewo), vehicles (*wogho-) with wheels (*kwekwlo-); They could count to 100 (*kmtóm)

Using parsimony to go back in timeWe can infer ancient forms from descendent forms

Paleogenetics:Resurrect ancient proteins via biotechnology. Apply "the experimental method" to them.Benner, S. A. in Experimental Paleogenetics, D. A. Liberles, ed. Academic Press, pp. 3-19 (2007)

Resurrecting ancient proteins (1989)

10 20 . | . |ox KETAAAKFERQHMDSSTSAA || ||||||||||||||| |sheep KESAAAKFERQHMDSSTSSAcamel SETAAEKFERQHMDSYSSSSAncestor KERAAAKFERQHMDSSTSSA

closer homologs

more distant homologs

present

past

both reconstructions require one mutation

SerThr

Ser?

position 3

Thr?

Thr Ser

Thr

Thr Ser Thr

add outgroup; best reconstruction clear

orThrposition 1

Lys

Lys Lys

1 reconstruction no mutation

Gaucher, E. A., Thomson, J. M., Burgan, M. F., Benner, S. A. (2003) Inferring paleoenvironments based on resurrected ancestral proteins.

Nature 425, 285-288

Inference from paleogenetics. The farther back in time, the smaller the role for proteins vs. RNA

• Elongation factor (EF) helps RNA present amino acids to ribosomes • EF homologous in all terran life• Sequences of 2 billion year old ancestral EF inferred from descendent sequences• Ancient EF resurrected

Elongation Factor

0

0.2

0.4

0.6

0.8

1

20 30 40 50 60 70 80 90 100

E. coli

oC

Relative amount [

3H] GDP

Incorporation

Elongation factors maximally active at the temperature host lives: E. coli 37 °C

Eric Gaucher

0

0.2

0.4

0.6

0.8

1

20 30 40 50 60 70 80 90 100

E. coli

Thermus

oC

Relative amount [

3H] GDP

Incorporation

Elongation factors maximally active at the temperature host lives: Thermus 65 °C

Eric Gaucher

0

0.2

0.4

0.6

0.8

1

20 30 40 50 60 70 80 90 100

E. coli

Thermus

PSA

oC

Relative amount [

3H] GDP

Incorporation

Ancestral elongation factor most active at 65°C

Eric Gaucher

0

0.2

0.4

0.6

0.8

1

20 30 40 50 60 70 80 90 100

E. coli

Thermus

PSA

MLSA

oC

Relative amount [

3H] GDP

Incorporation

This inference is robust

Gaucher et al. (2003) Inferring paleoenvironments during the origins of bacteria based on resurrected ancestral proteins. Nature 425, 285-288

Temperature history of bacterial EF

α proteobacteriamitochondria

proteobacteria

39.1°

57.7° 53.7°

44.1°51.0°

66.2° 73.3°

Thermotoga

firmicutes

60.8°53.7°

chloroplastsactinobacteria

cyanobacteria

chlamydiae

Eric A. Gaucher

48.4°

Gaucher, E. A. et al. (2008) Paleotemperature trend for Precambrian life inferred from resurrected proteins. Nature 451, 704.

Not a lot of snow

Paleogenetics suggest bigger role for RNA in ancient world; not just EFs

OCH

CH CHCH

HO OH

CH2O ON

C

CN

CHN

CH

NCH2N

PO

P

O O OO

OP

O O

Adenosine triphosphate (ATP)phosphate transfer

OOP

O O

OP

O O

Pyrophosphate works just as well in phosphate transfer as ATP

OCH

CH CHCH

HO OH

CH

CH NHCH2

O

CH2CH2CO CON

C

CN

CHN

CH

NCH2N

PO

P

O O OO

HO

CH3

CH3

O

NH CH2

CH2 SH

Coenzyme A(vitamin = pantothenic acid)carbon-carbon bond formation

CH

CH NHCH2

O

CH2 CCOprote in

OP

O O

HO

CH3

CH3

O

NH CH2

CH2 SH

Truncated form of Coenzyme A(vitamin = pantothenic acid)carbon-carbon bond formation in fat synthesis

RNA in cofactors throughout life in forms for which RNA is not uniquely adapted.Molecular "Panda’s Thumb"

ATP

Coenzyme A

Paleogenetics suggests an “RNA World”

An ancestral form of life on Earth that used RNAas its only encoded biopolymer. Life with only RNA.

Rich, A. (1962) On the problems of evolution and biochemical information transfer. Horizons in Biochemistry, Kasha, M. and Pullman, B. editors, N.Y., Acad. Press, 103White III, H.B. (1976) Coenzymes as fossils of an earlier metabolic state. J. Mol. Evol. 7, 101Visser C.M., Kellogg R.M. (1978) Biotin. Its place in evolution. J. Mol. Evol. 11, 171Usher, D. A., McHale, A. H. (1976) Hydrolytic stability of helical RNA. Selective advantage for the natural 3',5'-bond. Proc. Nat. Acad. Sci. 73, 1149

+

Proteins are not necessary for life if one has RNA

Benner, S. A., Ellington, A. D., Tauer, A. (1989) Modern metabolism as a palimpsest of the RNA world. Proc. Nat. Acad. Sci. 86, 7054-7058

Enough “standard of proof” for meWe worked backwards in time to model the RNA World as a rich biosystem without proteins.

• The RNA world had a rich metabolism based on RNA cofactors• DNA was invented in the RNA world before proteins• B12 and possibly chlorophyll emerged in the RNA world• The RNA world invented terpenes• Many of these hypotheses were tested

Tauer, A., Benner, S.A. (1997) A B12-dependent ribonucleotide reductase from the Archaea Thermoplasma acidophila. Proc. Natl. Acad. Sci. 94, 53-58

PaleogeneticsEucarya

Box of uncertainty

backward in time

Archaea Bacteria

Infer metabolism

of ancient life


Others came to a constructive belief in an "RNA world" only after the structure of the ribosome was solved• RNA part of the ribosome is the part that makes proteins• Ergo: RNA came before proteins• Double ergo: Life is possible without proteins

Courtesy Ada Yonath

70% of the non-solvent volume of E. coli cell (scale bar, 1 micrometer) used to make proteins.Therefore …

Life based on RNA alone without proteins can be much smallerSize Limits of Very Small Microorganisms: Proceedings of a Workshop, Steering Group on Astrobiology. National Research Council, pp. 126-135

Triple ergo. The Allan Hills structures are not too small to be life. A Galileo-like argument. In fact, the most abundant life in the cosmos may be RNA life.

oo

o

o

It would help if we had evidence that RNA could have arisen prebiotically

O

CHH

H C NHO

C C

O

HHH

Paleogenetics


C C C N

Eucarya


Life as a universal

HO

CNH2H



Archaea Bacteria


PrebioticChemistry





N

N

OR

RN

N N

NNN

O

RH

H

H

H

H

N N

N

RN

H H

N N

N NO

O

R

H

N

NR

RO

N N

N NO

N

R

H H

H

H

H

HH

N

OR

RN

N N

N NN

O

R

H

H

H

H

H


Search cosmos

Look for alien life

A thought: Life might be different

CN NH2

CN NH2

NC

H2NNH

N N

N NH

N

NH2

hν15% 7%HCN

The Oró:Orgel prebiotic synthesis of adenine

The bases in RNA are easy

Jerry Donohue

NN

NR

H O

HH

NN

N

N

O

N

HH

HH

NN

OR

H O

NN

N

N

N

H

HH

HH

OO

OO

P

O O

H

P

O

P

O O

O

NN

NN

N ON

NN OOO N

O

N

OOP

O

N

O

N

O

O

N

OPO

N

XXX

N

N

O OO N

ON

O

O

O

N

OOOP

N

O O

O

NN

N ON

N

HH

HH

H

H

P

O

HH

H

H

H H

H

O

NN

N N

O

N

OO

X

OO

P

O O

H

H

O

O

R

R

-

base pairs

charged phosphate backboneT/U

G

T/U

G

sugar as scaffold

C

AC

- - -

----

Larralde, Robertson, Miller (1995) Proc. Natl. Acad. Sci. USA 92, 8158

But ribose (the R in RNA) is hard

"stability considerations preclude the use of ribose and other sugars as prebiotic reagents …. It follows that ribose and other sugars were not components of the first genetic material…"

Formose process (1867)Ca(OH)2 + HCHO + heat -> sweet stuff (carbohydrates, some ribose) But the ribose is not stable.

OHC

HC CH

HC

OHHO

OH

CH2HO

People had hopes

What organic molecules do if given energy, versusWhat organic molecules do if given energy + Darwinian evolution

Energy without Darwin = tar Energy + Darwin = life

tar

The paradox at life’s origin

Stanley Miller

Tar formation intrinsic to ribose and other molecules with C=O carbonyl groups

The nucleophile is the species that brings the two electrons needed to form a new chemical bond.The electrophile is the species that does not.

nucleophile

electrophile

O

C CR

OH H

R'

C

O

R'""R

O

C CR

OH

R'C

O

R'""R

H

H

H

aldol addition

O

CHR'

C

R

O

H

O

C CR

OH H

R'

H

enolizationH

© Jake Fuller, from Life, the Universe and the Scientific Method

The meaning of the C=O carbonyl group

HOOH

H H

HO H

O

H H

HOOH

H H

HO H

OH

H

HOOH

H H

OH

OH

H H

HO

H H

HO H

O

H OH

OH

H H

HOO

H H

HO H H

HO CH2

HOOH

H H

HO CH2

O

H H

OH

OH

HO

H H

HO H

OH

OH

OH

H H

HO

H H

HO H

OH

O

OH

H HH2C

OH

HOOH

H H

HO CH2

OH

H

OH

HO

H H

HO CH2

O

H OH

OH

HOO

H H

HO CH2

CH2

H

OH

OH

H HHO

OH

HO

H H

HO CH2

OH

OH

OH

OH

H H

no enolization; retroaldol gives 2 x C3

no enolization;no elimination,retroaldol gives C2 + C3

HO

H H

HO H

OH

OH

OH

HH2C

OH

HO

H H

HO CH2

O

HO CH2

OH

OH

H H

OH

no enolizationno retroaldolisolated

HO

H H

HO CH2

HO

O

OH

OH

H HCH2

OH

continued chain growth and termination; retroaldol -> 2 x C4

HO

H H

HO H

OH

O

H OHH2C

OH

OH

H H

HO

H H

HO H

OH

HO

O

HH2C

OH

CH2

OH

no enolization; retroaldol to C3 + C4

C4

C5

HCHO, primary C nucleophile HCHO, secondary C nucleophile

HCHO, secondary C nucleophile

no interesting retroaldolonly one enol


HCHO, primary C nucleophile

only one enol

HCHO, secondary C nucleophile HCHO, primary

C nucleophile



HO

H H

HO H

OH

OH

OHH2C

OH

OH

H H

C7

C6

HO

H H

HO CH2

HO

OH

OH

OH

HCH2

OH

HCHO, secondary C nucleophile HCHO, secondary

C nucleophile



HO

H H

HO H

OH

O

HO CH2H2C

OH

OH

H H

OH

no enolization; retroaldol -> C2 + bC6

HO

H H

HO H

OH

CH2

OH2C

OH

OH

H H

C8

HO

OH

HO

H H

HO CH2

HO

O

OH

H OHCH2

OH

HO

H H

HO CH2

HO

CH2

OH

O

HCH2

OH

HO

OH

OH

H H

no enolization; retroaldol -> C3 + bC5

continued chain growth and termination; retroaldol -> 3 + C5

2 + 4

3 + 3

retroaldol to C3 + C4retroaldol to C2 + C5



O

H

HO

H OH

H H

HO OH

H H

OH

H

C2,3 HOH

OH

H

OHHO

O

H H H H

FormosePathway



HOH

O

H H enolization

aldol at primary C

aldol at secondary C

retroaldol

crowded bond (retroaldols)

O

H

HO

HOH2C OH

H H

dead end sugar, no enolization, no retroaldol (other than giving HCHO)

The Butlerov formose process has many C=O’s

Progress curve of sugar formation in formose reaction at 40 C

0

2000000

4000000

6000000

8000000

100 110 125 130 135 145 150 160

Time (min)

Absolute Intensity

4

5

6

7

8

9

Carbohydrates are made, then destroyed

• At high pH in presence of HCHO, enolization is irreversible• HCHO, when present, is the dominant electrophile• HCHO adds to the less hindered center of an enediol• Retroaldol reactions that extrude HCHO are slow• Cyclic hemiacetal formation slows enolization

Ricardo, et al. (2006) J. Org. Chem. 71, 9503

Very little C5 ribose is formed, and it does not last

Consider the minerals present on early Earth with boron.

A borate moderated ribose synthesis?

Alonso RicardoMatt CarriganHyo-Joong KimMyung-Jung KimHeshan Illangkoon

Tourmaline concentrates boron in igneous rocks

Peridotite. MgFe silicate weathers to give alkali

Colemanite, semi-soluble calcium borate

+

Borate binds to 1,2-di-OH compoundsCyclic ribose has a 1,2-diol and lacks C=O

Borate guides the formation of ribose (C5) from C2 + C3. Complex to the 1,2-diol of glyceraldehyde forces C3 unit to be the electrophile.

Mendicino, J. F. (1960) Effect of borate on alkali-catalyzed isomerization of sugars. J. Am. Chem. Soc. 82 4975-4979Prieur. B. E. (2001) Étude de l’activité prébiotique potentielle de l’acide borique. C. R. Acad. Sci. Paris, Chimie / Chemistry 4, 667–670Ricardo, A., Carrigan, M. A., Olcott, A. N., Benner, S. A. (2004) Borate minerals stabilize ribose. Science 303, 19

O

C CH

OH H

H

C

O

HO

C

H

HC

O

HH H

H

O

C CH

OH

H

C

O

HO

C

H

HC

O

HH

H

H

H

OHC

HC CH

CH

CH2 O

O O

HO

ribose-borate

No C=O reactivity

HO

HC

HC CH

CH

CH2 O

O O

HO

B

O O

H

HH

glycolaldehyde

glyceraldehyde

Is there a prebiotic cycle that might fix HCHO in the presence of borate?

HCHO + HCHO -> glycolaldehyde is slow. Need cycles to fix HCHO. Borate inhibits these cycles.

O

CHC

HO

H H

C C

O-HO

H H

O

CHH

COH

CH O

CH

H

O

C CO-HO

H Hglycolaldehyde

OHC

HC CH

CH

CH2 OH

O O

HO

ribose

Ca(OH)2

Ca++

Ca(OH)2

enolize

3 + 21 + 1 2 + 1

C OH

C OH

CH

H

OH

HO

CHHC OH

C O

CH

H

OH

C OHH

H

HC O

C OH

CH O

C OHH

H

H

H

H

Breslow autocatalytic cycle

B-

OO

B-O

O

O

CHH

2 of these

borate inhibits this

borate stabilizes this

_

_

3 + 1

Immediately, we encounter a new problem

Cycle net2 HCHO ->glycolaldehyde

Yes. A “prebiotic metabolic cycle” fed by formaldehyde and controlled by borate Compound in red are prebiotic

Net:5 HCHO ->Pentose (C5H10O5)

OHC

CC

O

HH

OH

H

H

HC

CC

OH

OH

OH

HH H

CC

O

HOH

H

H

CC

OH

HOH

H

CC

H

HO

O

HOC

CC

HOH H

HO

H

H

HOC

CC

CC

HH

HO H

OH

O

OH

HHH

HOC

CC

COH

HH

HOH

O

HH

HOC

CC

COH

HH

HO H

OH

H

HOC

CC

CO

HH

HO H

C

H

OHHO

HH

pentuloses, borate stabilizes

xylose

HOC

CC

OH

HH

O

HH

Erythrulose

Dihydroxyacetone

HCHO

HCHO

HCHO

xylulose

H

CC

H

HO

O

HOC

CC

HOH H

HO

H

H H

CC

H

HO

O

HOC

CC

HOH H

HO

H

HH

CC

H

HO

O

HOC

CC

HOH H

HO

H

H

lyxose arabinoseribose

pentoses. borate stabilizes

HOC

CC

CO

HH

HO H

C

H

OHHO

HH

HOC

CC

CC

HH

HO H

OH

O

OH

HHH

ribulose

threo

erythro

HOC

CC

OH

HH HH

HO H

Glycerol

Glycolaldehyde

enolization enolization

enolization aldol additionborate influences diastereoselectivity

aldol addition

aldol addition

H2O2Fe++

branched pentoses

retroaldol fragmentationslowed by borate complexation

cannot enolize

equilibrate in borate

enolization

Glyceraldehyde

C3

C4 C5

C3C2

C5 linear pentoses

Hyo-Joong Kim

ribose xylose

arabinosexylulose

erythro branched pentoseribulose

Glycolaldehyde + glyceraldehyde Borate, pH 10.5, 65 °C, 1 hour

Not tar

Where might a pre-metabolic pathway occur?Borates in alkaline evaporates in deserts?

Tourmaline weathers to water soluble borates

Olivine. MgFe silicate weathers to give alkali

Example today: Death Valley California. Alkaline borates from the Sierra Nevada’s igneous rocks.

So maybe RNA was available on early Earth, Darwinian evolution started with RNA only, and the RNA structure supporting Darwinianism is a character of life universally

oo

o

o

If we’re so smart, can we synthesize life?Synthesis as a demonstration of understanding

O

CHH

H C NHO

C C

O

HHH

Paleogenetics

We have the pieces of RNA

C C C N

Eucarya


Life as a universal

HO

CNH2H

Earth life maybe was different


Archaea Bacteria


PrebioticChemistry





N

N

OR

RN

N N

NNN

O

RH

H

H

H

H

N N

N

RN

H H

N N

N NO

O

R

H

N

NR

RO

N N

N NO

N

R

H H

H

H

H

HH

N

OR

RN

N N

N NN

O

R

H

H

H

H

H


Search cosmos

Look for alien life

A thought: life might be different

Watson-Crick base pair follows two rules of complementarity(a) Large pairs with small (purine vs. pyrimidine)(b) Hydrogen bond donor (N-H) pairs with hydrogen bond acceptor (O: or N:).

CHC

HCN

C

N:

CC

NC

N

CN

CHN

:O RH

N

R

H C

O:H

NH

C

HCN

C

H

N

CC

:NC

N

CN

CHN

N RH

O:

R

H

H

HN

HO:

CH3

aminoadenine

thymine

guaninecytosine

pyADA

puDADpuADD

pyDAA

Acceptor

Donor

Donor

Donor

Acceptor

Donor

Acceptor

Donor

Acceptor

Donor

Acceptor

Acceptor

.. ..

C GT

"A"

A theory that enables synthesis defines understanding and its language

Note: No quantum mechanics or number crunching in the language of this “theory of life”. Just ball-and-stick chemistry. Can the core of life possibly be so simple?

The structures that Jerry Donohue explained to Jim Watson

If it is so simple, then we should be able to synthesize artificial genetic systems…

An artificial, synthetic genetic system with 12 letters, not just the four of standard DNA.

…just by moving hydrogen bonds around

CC

HCN

C

N:

CC

NC

N

CN

CHN

N RH

O:

R

H

C

H:O

H

N

HCC

C H

N:

NC

NC

N

CN

CHHC

:O RH

N

R

H

H

H

:O

N

H

CC

NC

C

N

NC

:NC

N

CN

CHHC

:O RH

N

R

H

C

O:H

NH

C

NC

C

H

N

NC

:NC

N

CN

CHHC

HR

N

O:

R

H

H:O

H

H

N

N

R

R

R

pyAAD

puDDA

Acceptor

Acceptor

Donor

Donor

Donor

Acceptor

pyDDA

puAAD

pyADD

puDAA

Acceptor

Acceptor

Donor

Donor

Acceptor

Acceptor

Acceptor

Donor

Acceptor

Acceptor

Donor

Donor

Donor

Donor

Acceptor

Donor

Acceptor

DonorpyDAD

puADA

standard template

standard template

synthetic template

standard synthetic syntheticsynthetic standardstandardprimer

no kids

no kids

no kids

standardkids

standardkids

synthetic kids

Yes, we can. Here is a PCR amplification of a six letter synthetic genetic system

Zunyi Yang

CC

HCN

C

N

CC

:NC

N

CN

CHN

N RH

O:

R

H

H

H

O

CH3

pyADA

puDAD

Donor

Acceptor

Donor

Acceptor

Donor

Acceptor

CHC

HCN

C

N:

CC

NC

N

CN

CHN

:O RH

N

R

H

O:H

NH

H

puADD

pyDAA

Acceptor

Donor

Donor

Donor

Acceptor

Acceptor

..

HCC

HCC

C

N

NC

:NC

N

CN

CHHC

:O RH

N

R

O:H

NH

H

O2N

pyDDA

puAAD

Acceptor

Acceptor

Donor

Donor

Donor

Acceptor

NN

N

R O

HH

NN

N

N

O

N

RH

HH

Donor

Acceptor

Acceptor

N

NO2N

R O

NN

NN

O

N

R

HH

Acceptor

Acceptor

Donor

HH

H

deprotonated dZ pairs with dG protonated dC pairs with dP

Donor

Donor

Acceptor

Acceptor

Donor

Donor

p H d e p e n d e n c e w i t h T a q

0

1 0

2 0

3 0

4 0

5 0

6 0

p H

Retention of Z:P pair

p H 7 . 5

p H 7 . 8

p H 8 . 0

p H 8 . 5

Every now and then, an error

Replication with imperfections, where those imperfections are themselves replicatable, just like natural RNA.

A

G

T

Ctransversion

transversionA standard base is replaced by a non-standard base, vice versa

CC

HCN

C

N

CC

:NC

N

CN

CHN

N RH

O:

R

H

H

H

O

CH3

pyADA

puDAD

Donor

Acceptor

Donor

Acceptor

Donor

Acceptor

CHC

HCN

C

N:

CC

NC

N

CN

CHN

:O RH

N

R

H

O:H

NH

H

puADD

pyDAA

Acceptor

Donor

Donor

Donor

Acceptor

Acceptor

..

HCC

HCC

C

N

NC

:NC

N

CN

CHHC

:O RH

N

R

O:H

NH

H

O2N

pyDDA

puAAD

Acceptor

Acceptor

Donor

Donor

Donor

Acceptor

A synthetic chemical system capable of Darwinian evolution with 6-letter "RNA"

Is this synthetic life?It still relies on proteins.It is not self-sustaining.

Life: A self-sustaining chemical system capable of Darwinian evolution

This is not self-sustaining

Life: A self-sustaining chemical system capable of Darwinian evolution

The differences between this and a 6-letter RNA system capable of assisted Darwinian evolution in a test tube are more than obvious.

oo

o

o

O

CHH

H C NHO

C C

O

HHH

Paleogenetics


C C C N

Eucarya


Life as a universal

HO

CNH2H



Archaea Bacteria


PrebioticChemistry





N

N

OR

RN

N N

NNN

O

RH

H

H

H

H

N N

N

RN

H H

N N

N NO

O

R

H

N

NR

RO

N N

N NO

N

R

H H

H

H

H

HH

N

OR

RN

N N

N NN

O

R

H

H

H

H

H


Search cosmos

discover alien life


A general theory of life as a universal? No, but we are constraining the black box.

Documents

Nivens: So tell me Mary. What exactly do you do for NASA? Sefton: My speciality is exobiology. Nivens: Exobiology? Sefton: It’s a study of what alien life