2 The raw materials of life: synthesis and the importance of handedness

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Figure 13.2 Left- and right-handed enantiomers of the amino acid

alanine. The left-handed type is referred to as levorotary or l-alanine;

the right-handed is dextrorotary, or d-alanine.



of each other. A molecule that is not superimposable on its mirror image is chiral. When a molecule with a definite sense of

handedness reacts chemically with one that is symmetric (or

otherwise does not have a particular handedness), the left- and

right-handed amino acids have similar properties. Likewise, the

chemical properties of an interaction between two left-handed

molecules or two right-handed molecules are the same. However, neither of these interactions is the same as when a left- and

right-handed molecule are interacting with each other. Hence,

the handedness of biological molecules such as amino acids or

nucleotides plays a role in their functionality.

Earthly life has the remarkable property that virtually all

proteins are constructed only from left-handed amino acids,

whereas the nucleic acids RNA and DNA utilize only righthanded sugars in their structures. Terrestrial organisms cannot

utilize right-handed proteins (with a few exceptions) or lefthanded sugars in their biochemical processes; they would starve

to death if such wrong-handed materials were the sole food

source. Yet, abiotically produced amino acids such as those

in meteorites and the Miller–Urey experiments are a roughly

equal mixture of left-handed (l) and right-handed (d) molecules

(there is one meteorite in which there is a modest excess of

left-handed amino acids). Furthermore, chemical production of

polymers such as proteins or nucleotides does not prefer a particular handedness when the starting molecules are a mixture of

l- and d-enantiomers.

In the remainder of this chapter, we use the term chirality to

indicate a strong sense of handedness (left or right) in a particular

molecular species. Racemic means that comparable amounts of

left- and right-handed, non-superimposable, molecules with a

given chemical formula are present, and nonchiral means that

the molecule can be superimposed on its mirror image. Chirality

is a property; enantiomers are the left- and right-handed versions

of a molecule that exhibits chirality.

An important consequence of chirality in biological molecules

is that a nonbiological mix of l- and d-type amino acids occurring in meteorites, or in a flask after irradiation (Miller–Urey

synthesis), represents more of a problem than a solution to life’s

origin. How could a particular handedness be selected by prebiological, or primitive-biological, chemistry? We return to this

issue later in the chapter because it stands as one of the major

challenges to theories of life’s origin in which RNA plays an

early, primary role.



13.3 Two approaches to life’s origin

From here, the road to take is far from certain. The synthesis

of amino acids is a far cry from the construction of complex,



self-replicating molecules that carry enough information to construct proteins from amino acids. Two approaches to the origin

of life from the soup of organics are usually called “metabolism

first” and “genetics first” (Figure 13.3). In metabolism first, one

argues that certain structures could form spontaneously, capable

of isolating parts of the chemical soup from the environment.

These vesicles, if the right chemicals were present, could have

become little factories of increasing chemical complexity, eventually growing and splitting in two but still lacking a reliable (or

any) genetic code for reproducing the chemical activity within

them. The other approach focuses on the genetic code, in particular RNA, which might have been synthesized in the environment of the chemical soup, and once synthesized, multiplied

and co-opted vesicles to form cells. Neither approach yet tells a

convincing story, but both have led to some tantalizing suggestions as to how life could have arisen from complex, energetic

chemical systems.



13.4 The vesicle approach and autocatalysis

We consider first the vesicles. One of the crucial properties of

certain biochemical substances is their ability to enable or speed

up reactions, without themselves being expended. This chemical

effect is called catalysis; some biological catalysts are called

enzymes. Catalysis is a common feature in many nonbiological

chemical systems, and is essential in biology. A special kind of

catalysis is autocatalysis, in which a product of a reaction acts

as a catalyst in its own production.

Autocatalysis is a process that can lead to complex behavior. Beginning with two chemical substances that tend to react

with each other, and supplying enough such reactants to maintain vigorous chemical reactions, progressively more complex

molecules can be built up in the soup, including molecules that

catalyze certain reactions. The key is a continuous supply of

reactants, and a source of energy, that is, the system must be

maintained far from equilibrium.

Even more significant is that complicated autocatalytic systems, as simulated in computers, have the capacity to increase

their level of organization over time. If several sets of autocatalytic cycles are in operation in the same environment, they have

the possibility of producing complex chemical species that can

couple the sets together and create further organization and complexity. These self-organizing chemical systems increase their

network of reaction steps and become more organized so long

as energy is available to hold them far from equilibrium.

Scientists have argued that perhaps such autocatalytic sets

brought organic chemical systems from the simplest starting

components – amino acids and nucleic acid bases, for example –

to increasing levels of complexity until primitive proteins and

other structures were produced. To do this, the chemical system must have been held far from equilibrium, which means

isolating the system from the surrounding environment and

enabling energy and reactants to be pumped in and products

to be removed. This is where vesicles play a role. In a watery

(aqueous) medium, certain simple molecules spontaneously

form bilayer membranes that partition off an “inside” from

an “outside.” Biological materials such as egg white will do

this. Simpler organic molecules called lipids, which need not be



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153



soup ingredients:

small carbon-based molecules



Genetics first



Metabolism first



Nucleic acid

monomers form.



Simple catalysts

form and expand the

inventory of

molecules



Monomers

combine.



Polymers

catalyze

formation of Networks of reactions

monomers. arise: cyclic reaction

sequences provide a

pathway to lower

energy levels for

high-energy electrons

produced in primordial

environment.



Simple informationcarrying polymers

Polymers direct assembly

of identical polymers.



Selection leads to increased

catalytic versatility; metabolism

continuse to evolve into its present

(fainter indicates expired/

form.

extinct cycles)



Simple

nucleotide

B=nucleic

acid base

–



O

H



OH



O

O



B

O



O



B

HO



O



Selection promotes efficlency and

acquisition of additional functions. Over

time, DNA takes over information storage

function, proteins take over catalytic and

structural functions.



Figure 13.3 Two different conceptual models for the origin of life, “genetics first” (left) and “metabolism first” (right). In each case, one begins

with small organic molecules synthesized abiotically on the Earth or even in parent bodies of meteorites. With genetics first, an information

carrying molecule arises spontaneously and eventually controls chemical reactions in primitive cells. With metabolism first, undirected networks

of chemical reactions – autocatalytic cycles – evolve to progressively higher complexity until they develop information-carrying molecules that

eventually control the production of catalysts. Adapted from a figure by Trefil et al. (2009), with notional nucleotide from Englehart and Hud

(2010).



produced biologically, will do likewise. So, in the early Earth’s

oceans, it may have been that small environments, microns or

less in size, were partitioned off spontaneously by simple organic

molecules.

Within the interior of a vesicle, the environment was partially

isolated from the outside. It then would be possible to create a

small system, out of equilibrium, within which complex chemical reactions, perhaps autocatalytic sets, could have occurred.



To do so, we must specify two essential ingredients, namely,

energy and a pathway for introducing reactants and removing

products.

The spontaneously formed vesicles would not themselves be

a source of energy, except for the heat given off by chemical

reactions inside them. This heat, though, represents increase of

entropy and is not available to do work inside the vesicle. Likewise, heating from the outside is possible but would merely tend



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(a) RNA



(b) DNA



O−

O



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P



O−



G

O



CH2



O−



O

O



P



G

CH2



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O−



O OH



O



O



H



P



O



C

O



P



CH2



O



O−



C

O



O



CH2



O−



O OH



O



O



H



P



O



U

O



P



CH2



O



O−



T

O



O



CH2



O−



O OH



O



O



H



P



O



A

O



P

O−



O



CH2



A

O



O



OH OH



CH2



O−

OH



O



H



Figure 13.4 (a) Primary structure of the RNA molecule. Nucleotides are labeled within circles by the first letter of their name (for example, G

for guanine). Other letters are elements (O for oxygen, P for phosphorus, etc.). Carbon atoms occupy the unlabeled vertices, in accordance with

common chemical convention. The straight lines show single and double bonds, which reflect the number of electrons shared. (b) Structure of a

DNA molecule. The differences between RNA and DNA are highlighted on the two structures.



to equalize the inside and outside temperatures – not a promising

start for bringing our environment away from equilibrium. One

novel suggestion that has been made recently is that certain simple organic molecules, attachable to the vesicle, may have had

the capacity for capturing light energy from the Sun and using it

to ionize parts of the vesicle membrane. Although speculative,

such molecules would transduce energy from the Sun and make

it available as chemical energy (via the ions formed from the

membrane) inside the vesicle.

What about the transfer of reactants and products? This also

appears to be possible through a particular set of complex

organic molecules that could have acted as channels, filtering

some substances through and excluding others. Some preliminary experiments have suggested the possibility that such an

attribute might be developed on the vesicles through molecules

available in the organic soup of the early ocean.

Although still hypothetical, we have conjectured a vesicle

machine that can be charged up, transfer molecules in and out,

and serve as an isolated environment for autocatalytic reactions –

all of this using molecules plausibly available in the prebiotic environment. The purpose of the machine is simply to

make molecules of higher and higher complexity. Whether such

molecules eventually would move toward proteins and enzymes

is completely unclear. The principle, though, is simple: hold it

away from equilibrium and let it get more complex!



13.5 The RNA world: a second option

Although vesicles appear to be a natural and compelling structure for evolving complicated chemical factories, they lack a

detailed, formalized set of instructions for producing molecules



of the complexity of proteins, and for reliably reproducing themselves. A vesicle that has split off from another, and floated off

to a slightly different environment in the early ocean, might well

become host to completely different chemical cycles, which fail

to sustain autocatalytic sets. Living forms are able to continue

their chemical processes from one generation to the next. They

also exhibit the ability to self-regulate their internal processes in

the face of environmental changes that would completely alter

or shut down nonbiological chemical cycles – a capability called

homeostasis.



13.5.1 The promise: RNA as replicator and catalyst

The genetics-first school holds that the formation of life had as

its essential step the formation of RNA from abiotic chemical

processes. The RNA would then function as a primitive form of

life unto itself, existing perhaps in the early ocean and quickly

co-opting protective structures such as lipid-like vesicles. The

proponents of this view prefer RNA over DNA because it plays

various central roles in all cells today. Not only does it synthesize

proteins, but it also primes DNA for replication. In modern

cells, DNA is required to produce and regulate RNA, but this

may be a later refinement in the evolution of life. In fact, the

modification of an RNA molecule to make a single strand of

DNA is a relatively minor chemical step (Figure 13.4). There is

little argument among biologists that RNA came before DNA.

What made the notion of an RNA world so attractive was

the discovery by T. Cech, S. Altman, and colleagues that RNA

molecules can act as catalysts, participating in and speeding up

the production of nucleic acid sequences and other biological

molecules. Although biologically occurring RNA molecules

are rather weak catalysts, these abilities can be enhanced and



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ARCHEAN EON: MECHANISMS



expanded in the laboratory, by splicing and reproduction of

selected sequences on the RNA chain of nucleotides. The resulting modified RNA structures are sufficiently impressive catalysts that it is possible to imagine early RNA as biological catalyst in place of the present-day proteins that function as enzymes.

Thus, RNA could have been both the reproductive and the catalytic molecule of the very early stages of life on Earth, acting

in autocatalytic cycles to sustain a primitive biology.



13.5.2 The problem: invention of RNA

Most serious is how to put the jigsaw-puzzle RNA together in

the first place. To understand whether RNA could have been

synthesized in the absence of pre-existing biological molecules,

it is convenient to consider the three fundamental chemical parts

of an RNA molecule: (i) the nucleic acid bases A, G, C, and U;

(ii) a phosphate group that contains the element phosphorus

and serves as the connector of each of the bases; (iii) the sugar

ribose that functions as the binder or backbone of the molecule,

so that each nucleic acid base is bound to a sugar and these

in turn are attached to each other by the phosphate groups. (As

noted in Chapter 12, each unit composed of a ribose, a phosphate

group, and a nucleic acid base is called a nucelotide; the polymer

composed of a string of nucelotides is an RNA molecule.)

The production of nucleic acid bases by nonbiological means

appears to be understood at least in the case of adenine (A),

cytosine (C), and uracil (U); there does not seem to be any fundamental hurdle in eventually making guanine (G). Somewhat

more difficult is the understanding of how a phosphate group

would tend to attach to the right position of a ribose molecule

to provide the necessary chemical activity; the same challenge

is present in attaching the nucleic acid bases to the ribose. However, one might imagine a random assortment of nucleotide-type

molecules, those of which that happened to be configured like

an RNA nucleotide possessing a chemical advantage.

The real problem lies in the synthesis and preservation of

ribose, with the right chirality. Carbohydrates possessing the

formula Cn H2n On , where n represents a number 1, 2, 3, . . . ,

including the sugar ribose, are readily manufactured by reacting

formaldehyde (nCH2 O) with itself. A catalyst is required to

initiate the reaction, but this is not a problem. The problem is

that ribose is not particularly preferred over other sugars nor

is it stable. Hence, an autocatalytic cycle designed to produce

large amounts of carbohydrates from formaldehyde will not

preferentially make ribose nor preserve it.

One novel suggestion that has been made is that clay minerals may have been involved to concentrate ribose. Clay minerals

have ordered surfaces that could form templates, forcing organic

molecules that bind to their surfaces to form certain structures.

Although no synthesis of RNA has occurred this way, the suggestion is in the right direction: force molecules away from

randomly defined patterns to a subset of structures that might

allow ribose to form preferentially. This suggestion is also geologically consistent because, with the formation of an ocean

in the Hadean era, the environment would have become suitable for formation of clays. One then faces the question of how

ribose molecules were maintained against chemical processes

that tend to decompose them quickly into a nondescript assemblage of polymeric mixtures. A group led by A. Ricardo at the

University of Florida found that the mineral borate tends to



155



stabilize ribose against such decomposition. Hence, particularly

on the Earth, where borate-containing minerals should have been

common in the crust, repositories of ribose for production of

RNA may have been available as raw material for long periods

of time.

Yet there are still more difficulties. The ribose produced must

have the correct handedness or chirality; on Earth, d-sugars

are exclusively involved in living processes. Production of a

mixture of d- and l-sugars produces nucelotides that do not

fit together properly, producing a very open, weak structure

that cannot survive to replicate, catalyze, or synthesize other

biological molecules. In fact, the synthesis of the RNA molecule

itself is interrupted by mixing nucleotides of different chirality;

only in a controlled laboratory experiment or theoretical model

can such an assemblage be realized (Figure 13.5).

To create a properly functioning RNA molecule out of a batch

of heterochiral l- and d-sugars is a daunting challenge. Two

approaches have been pursued. The first is to consider precursor

molecules with function similar to RNA but which are much

easier to synthesize. The second approach is to understand how

prebiological or very primitive biological processes could have

selected a particular chirality and allowed its dominance, and

hence permitted RNA. In a sense, these two approaches are

linked; some precursor chemistry must have operated out of a

heterochiral soup prior to the concentration of the d-sugars.

Considering the first approach, it is possible to imagine substituting another sugar for ribose in making RNA, and in particular

a sugar that is symmetric and hence nonchiralic. Possible sugars suggested by University of California biologist G. Joyce

include glycerol; others have suggested additional candidates

such as glucose. Candidates proposed are generally ones that

could have been fairly easily synthesized on the early Earth

by nonbiological processes, and as sugars, they are capable of

binding a nucleic acid base and a phosphate group. However,

the properties of the resulting pseudo nucleic acids can be very

different. Some have much more flexible structures than RNA,

leading to a much greater chance of break up and hence replication or catalysis failure in a fluctuating environment. Others are

too stable, and may not catalyze. Finally, many of these substitutes allow not only complimentary pairing (A with U, G with

C, as in Chapter 12) but also other pairings (A with C, A with

A, G with U, etc.). Under such conditions, the genetic template

that sustains a particular kind of chemistry and set of structures

is quickly lost after just one generation.

Other possibilities have been conceptualized. For example,

amino acids are found readily in meteorites and synthesized

under early Earth conditions; could they substitute for sugars

as the RNA foundation? Indeed, one can synthesize a backbone

composed of glycine (an amino acid) attached to a nitrogen

and hydrocarbon unit. This then can attach to a nucleic acid

base and a phosphate group to form a nucleotide. The resulting

structure is a peptide nucleic acid, or PNA. PNAs have been

synthesized and shown both to be sturdy and to produce pairing

of complementary nucleic acid bases (i.e., A with U, G with C).

They could therefore serve as a replicator molecule. However,

three open questions remain. Can PNA function as a catalyst?

Can one actually induce the polymerization of the amino acid

with the nucleic acid bases to make PNA in a plausible prebiotic

setting? Is PNA subject to the same chiral restrictions that RNA

is? (Recall that many amino acids exhibit chirality.)



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(a)



(b)



Figure 13.5 The disaster of heterochirality (mixing l- and d-sugars in nucleotides): (a) a normal DNA molecule built of nucleotides of a single

chirality; (b) a DNA molecule built with just one nucleotide of the opposite chirality (i.e., all d-ribose except for one nucleotide with l-ribose). The

one-defect DNA is forced into a much looser structure. The strain in the chemical bonds created by trying to force l- and d-nucleotides together

causes bond breakages elsewhere in the structure. The result is a much more open, loose DNA molecule, which is very fragile and thus cannot

carry out its templating and replicating functions before falling apart. A similar problem faces the synthesis of RNA from a heterochiralic soup of

nucleotides. Photographs reproduced from Avetisov et al. (1991) by permission of American Institute of Physics.



The second approach is to understand how the dominance of

d-sugars and l-amino acids took place on the early Earth from an

initially heterochiralic soup. One would first look to some innate

preference for one or the other handedness in the environment

or the nature of the molecules. The environment itself yields

small effects, which tend to select out one or the other sense of

handedness, but some means to amplify the selection must be

found. Interestingly, at the subatomic physics level, there is a

very small preference for right-handed sugars and left-handed

amino acids, the current state on Earth. Such a preference is so

small, however, that it cannot by itself lead to the distillation of

l-amino acids and d-sugars from a heterochiralic soup. Recent

analysis of the Murchison meteorite indicates a significant overabundance of some l-amino acids relative to d-amino acids,

but the origin of this imbalance and its possible connection to

prebiotic chemistry have not yet been explored.

If there is an answer to the development of preferred handedness at the dawn of life, it might well lie in the propensity of

complex physical systems to self-organize, as discussed at the

very beginning of this chapter. Mathematical models of autocatalytic systems in which polymer production takes place in

a racemic environment show that, under certain conditions, the

system can exhibit a transition in which the symmetric treatment

of d- and l-molecules is broken, and the system rapidly evolves

toward a single kind of chirality. No simple physical preference is at work here; instead it is the intrinsic chaotic nature of

a complicated physical system, held far from thermodynamic

equilibrium, that leads to such a self-organizing property. Certainly an autocatalytic system, enclosed in a special environment

that allows energy flow and reactants (nutrient) in and products

(waste) out, is a candidate to exhibit such behavior. It is in the

necessity to invoke such a behavior to make chirally sensitive

molecules such as RNA that we might find the combination of

the vesicle world and the RNA world to be a requirement for the

formation of life.



13.6 The essentials of a cell and the

unification of the two approaches

What are the essentials of a cell? Operationally, they are:

1. a dynamic membrane that exhibits fluid-like, flexible motion

2. a set of embedded, membrane proteins that capture energybearing molecules (metabolites) from the environment, and

transport them into the cell

3. a set of enzymes that break down the metabolites and use

the breakdown products to construct more membrane, more

enzymes, and more genetic material (RNA/ DNA)

4. a genetic string, RNA coded by DNA, which encodes for the

set of enzymes

5. a genetic program, DNA primed by RNA, consisting of the

set of triggering relations between the various genes. The

program will cause the cell to grow, duplicate the geneticstring DNA, and eventually divide when it has gotten large

enough, resulting in two cells that will continue to metabolize, grow, and divide.

The chemical vesicle factories embody in a primitive way

properties (1) through (3); the RNA world covers (4) and (5).

Neither model yields all five properties. It may be that if the

origin of life occurred as a natural chemical process on Earth,

the first step was the formation of the autocatalytic vesicles,

which were short-lived and formed over and over again in different varieties over millions of years – chemical experiments

that failed repeatedly. However, at some point a vesicle system

exhibited the property of producing polymers of a dominantly

single chirality, either sugars or amino acids, and within this

system the production of an RNA, a PNA, or other nucleic

acid structure (ONA) was enabled. ONA varieties with catalytic

capability became coupled into the autocatalytic networks of



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chemical synthesis of

organic compounds



prebiotic

world



157



primordial

chemical diversity



autocatalytic reaction sets:

self-complexity

(in vesicles?)

decreasing



synthesis of heterochiralic

nucleotides



chemical

diversity



synthesis of non-chiralic

PNA or ONA

phase-transition/chiralic

symmetry breaking

protobiological

world



takeover of medium by

chiralic nucleotides

synthesis of chiralic RNA



first

RNA

world

(RNA as

replicator

and catalyst)



encapsulation in vesicles

(if not already achieved)

formation of chiralic amino acid sets

with RNA mediation

formation of enzymatic proteins



second

RNA world

(RNA as replicator)



b

o

t

t

l

e

n

e

c

k



first enzyme-mediated cells

formation of DNA

universal cellular ancestor



morphological

diversity

and



prokaryotic life (bacteria)



chemical uniformity



DNA

world



Figure 13.6 One possible schedule of the steps by which life formed. In the left-hand sequence, RNA appears before encapsulation in vesicles,

although as the text argues, the reverse might well have been the case. The bottleneck in the origin of a chemically uniform, morphologically

diverse biology from a chemically diverse terrestrial environment is illustrated on the right, aligned with the chemical/biological steps on the left.

Adapted from Cloud (1988).



some vesicles, and a subset of these used the energy and catalytic properties of the sets to reproduce. Such symbiosis, which

is a theme in the evolution of life, could have represented the

very primitive precursor to a biological cell. All of the ingredients, (1)–(5), of a cellular structure capable of maintaining and

reproducing itself are present in such an RNA-primed vesicle.

Although from here, the formation of DNA is not well understood either, the jump in complexity from RNA to DNA is not

considered by biochemists to be as much of a hurdle. Along the

way, in some RNA-driven vesicle, DNA may have arisen, and

the universal cellular ancestor of all Earthly life was born.

Figure 13.6 suggests two ways to look at the origin-of-life

issue. One, on the left, is to try to list the steps, in order, by

which life began; this approach is fraught with dissent because



we still do not know whether vesicles, RNA, ONA, chirality,

or other precursors came first. (For example, Nobel Laureate

C. de Duve notes that the development of energy storage in

phosphorus-bearing molecules such as adenosine triphosphate

[ATP] is yet another problem that requires the identification of

simpler precursor molecules.) The other approach is to recognize

that biology represents a self-controlled selection of a subset of

possible molecules out of an enormous range of possibilities.

DNA, for example, has four kinds of letters and about 1,000,000

base pairs (ladder rungs) per molecule. The number of possible

varieties of DNA molecules then is 41,000,000 , or 4 followed by

one million zeros. It is the role of enzymes, biological catalysts,

to suppress the random nature of chemical reactions so as to

preserve and ensure a particular suite of biological molecules



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che

mic

a



prebiotic

chemical

selection



l ev

olu

tion



self-organizing

chemical

systems

Titan



Mars



log

ica

l ev

olu



biochemical

diversity

and

morphological

simplicity



time



Europa



bio

tion



True life in the Archean, that which left stromatolites and other

faint records, consisted of the most primitive type of cells called

prokaryotes. The more complex eukaryotes were apparently not

present in the Archean, and we tackle their origin in Chapter 19

in the context of the formation of an oxygen-rich atmosphere

during the Proterozoic eon. At least in terms of structural complexity of the container of living processes, it does not seem like

such a long step from the vesicles of the theorists to the bacterial

prokaryotes of the Archean.

When did the prokaryotes form? Certainly before 3.5 billion

years ago, based on fossil evidence of photosynthesizing bacteria

in Australia, more than perhaps 3.9 billion years ago from isotopic evidence, but after the formation of the liquid water ocean,

4 billion years ago or earlier. The limiting factor may have been

the rate of large impacts: if the early Earth environment was

rendered unstable by a high frequency of such impacts, there

would be no chance for robust vesicles (or RNA) to form. Until

the timescale for forming self-sustaining vesicles is understood,

we can make no reliable judgment as to when the environment

became sufficiently stable. Sometime after the formation of the

water ocean, and perhaps sooner rather than later, life appeared

on Earth.

What drove organic chemistry toward the threshold to life?

Harold Morowitz and colleagues at George Mason University

have likened the inevitability of such a bottleneck to other disequilibrium phenomena such as flowing water runs down a hill.

While it may flow uniformly as a sheet initially, soon it carves

channels, which become gullies and eventually dendritic valleys. Indeed, the energy imbalance represented by the presence

of water at the top of a hill is corrected by a process that leads to



primordial chemical

diversity



proto-biology



13.7 The Archean situation



Comets, Pluto



life begins



at the rate needed to sustain the production and replication of

the whole system.

In this regard, it is perhaps most instructive to view the righthand sketch in Figure 13.6. The prebiotic Earth was a system

of high chemical diversity, but with an environment that tended

to select certain elements and naturally occurring molecules

as preferred in increasingly complicated autocatalytic chemical

systems. Reaction sets that straddle the barrier between biology

and chemistry were still chemically diverse, and likely limited

in size and capability to interact with the environment: morphologically (appearance-wise) simple. It is the bottleneck of

morphologically simple, protobiotic chemical systems that lies

at the crux of understanding how life began. As one kind of

reliable protobiochemistry took hold, the chemical diversity of

protobiology plummeted, but the success of the system was such

as to allow the blossoming of a great diversity of morphologies

that functionally allowed different kinds of interactions with

a changing environment. Today, biological processes have coopted most of the available carbon and oxygen in the atmosphere,

ocean, and continental surface of Earth, so that the chemistry

of these elements is largely limited to the rather uniform and

specific biochemical processes that sustain life. Most or all of

the other planetary environments in our solar system may never

have crossed this bottleneck, but how close they came is an

intriguing question (Figure 13.7).



biochemical uniformity

and

morphological diversity

Earth



Figure 13.7 Another look at the transition from chemical to

biochemical evolution. Conservative guesses as to where various

planetary bodies lie on the hourglass are indicated. The cold distant

bodies of the outer solar system – Kuiper Belt comets and Pluto – store

organic molecules relatively unaltered from interstellar processes.

Europa or Enceladus, or both, may harbor life in a subsurface water

ocean. Titan’s hydrocarbon seas might be sterile or play host to a kind

of biochemistry very different from that on Earth. Mars may have had

conditions early in its history, and in brief episodes thereafter, capable

of sustaining a primitive biota; life might eke out an existence in the

planet’s water-charged silicate crust. Only Earth, in our solar system,

has an atmosphere, ocean, and crust that play host to an extensive

biochemistry expressed in the great diversity of life-forms we see

today.



a kind of spatial ordering of channels separated by ridges. The

build up of electric charge differences between a cloud and the

ground is not relieved by a uniform flow of electrons; it occurs

within a narrow channel maintained far from equilibrium with

the surrounding air by the driven flow of the charged particles

themselves. One can mentally reduce organic chemical systems

to their essence: the charging of electrons within molecules of

those systems. The flow of electrons toward lower energy states

is not a simple, disordered process if the system is held far

from equilibrium by available sources of energy: instead, preferred paths such as particular metabolic cycles may develop.

Morowitz and colleagues offer the citric acid cycle, run in reverse

so that CO2 and water are converted to organic molecules with

the application of available energy, as a possible example of

an early, fundamental metabolic cycle. Whether they are right

about the particular metabolic cycles that were foundational,



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ARCHEAN EON: MECHANISMS



the general point – that life is an inevitable response of an

organic chemical system held far from equilibrium – would

argue that life is a common feature of the cosmos and that even



159



in exotic environments such as the hydrocarbon seas of Titan,

the complexity and specificity of life should arise from abiotic

chemistry.



Summary

The second law of thermodynamics states that entropy, a

quantity that measures (inversely) the ability of a system to

do work, increases with time in any real-world process. Life

is a consequence of, not an exception to, the second law of

thermodynamics. Given the large amount of energy available

(directly or indirectly) from the Sun to do work, and the presence of nutrients in the environment, living systems represent

a high degree of organization but at the same time generate entropy, when the surrounding environment is considered.

Therefore, the origin of life need not be seen as a miraculous

or even singular event, but rather as the outcome of the natural evolution of organic chemistry in an early planetary environment suffused with energy, organic molecules, and water.

Whether this environment was on Earth itself, or elsewhere

such as Mars, is not known. Meteorites and cometary debris

raining down on the Earth early in its history would have provided our planet with the raw materials for life, and possibly even primitive life itself. The specific steps by which life

arose from organic chemistry are not known. Examination of

biochemistry reveals that it differs from abiotic organic chemistry in its selective nature. Out of many hundreds of different

types of amino acids, only 22 are used by living processes. Life

uses, with rare exceptions, only left-handed amino acids and

right handed sugars – “chiral” molecules that are not symmetric when reflected in the sense of a mirror. These and other

examples reveal the high degree of order (low entropy) and



selectivity which characterize living systems. Prior to the

appearance of the first self-replicating molecule – be it DNA,

RNA or a simpler precursor – organic chemistry could have

become ordered through networks of reactions generating their

own catalysts – according to the laws of physics and chemistry,

but in the absence of “natural selection” that is the hallmark of

evolution as discussed in Chapter 18. Once a molecule capable of carrying the information needed to synthesize catalysts

appeared, the success of subsequent generations of chemical

systems depended on adaptation to the environment. At what

stage self-replicating, information-carrying molecules appeared

is not known, and two different models for the origin of life

have been promulgated: one in which metabolic cycles developed before molecules such as RNA and DNA, and the other

in which the sequence was reversed. Regardless, the first selfreplicating information-carrying molecule was unlikely to be

DNA; RNA was almost certainly its precursor. But RNA is sufficiently sophisticated that it may have had precursors whose

presence was not recorded in life as we know it. Vesicles –

self-folding organic structures allowing chemical networks to

be partially isolated from the environment, may have played

an important role, as did perhaps surface chemistry on mineral

templates like clays. However it began, life had a toehold on

the Earth sometime in the Archean, certainly before 3.5 billion years ago and possibly as early as 3.9 billion years before

present.



Questions

1. Imagine a planet with two well-developed biota, one able to



3. Entropy is defined mathematically as the logarithm of the



synthesize left-handed sugars and use right-handed amino

acids, the other synthesizing right-handed sugars and using

left-handed amino acids. What kinds of competition might

ensue in such a situation? Is it intrinsically unstable, i.e., will

one form of life win out?

2. If indeed RNA was the initial genetic encoder and DNA

developed later, do you think that some viruses might be

remnants of that earlier epoch? Why or why not?



number of possible states accessible to a system, multiplied by a constant (a fixed number). What is the ratio of

entropies of an abiotic system that indiscirminantly incorporates sugars of either handedness versus life that uses only

right-handed sugars?

4. The sequence of steps toward the origin of life in Figure 13.6

is notional. Construct an alternative, based on the discussion

in the text or articles you find in the literature, and contrast

it with that in the figure.



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THE HISTORICAL PLANET



General reading

Avetisov, V. A., Goldanskii, V. I., and Kuz’min, V. V. 1991. Handedness, origin of life and evolution. Physics Today 44 (7),

pp. 33–41.

Bagley, R. J. and Farmer, J. D. 1992. Spontaneous emergence of

a metabolism. In Artificial Life II (Langdon, C. G., Taylor,

C., Farmer, J. D., and Rasmussen, S. eds). Addison-Wesley,

Redwood City, California, pp. 93–140.



Levy, S. 1992. Artificial Life: A Report from the Frontier Where

Computers Meet Biology. Vintage Books, New York.

Morrison, R. T., and Boyd, R. N. 2008. Organic Chemistry, 6th edn.

Prentice Hall, New York.



References

Ehrenfreund, P. and Cami, J. 2010. Cosmic carbon chemistry: from

the interstellar medium to the early Earth. Cold Spring Harbor

Perspectives in Biology 2, a002097.

Engel, M. H. and Macko, S. A. 1997. Isotopic evidence for extraterrestrial non-racemic amino acids in the Murchison meteorite.

Nature 389, 265–7.

Engelhart, A. E. and Hud, N. V. 2010. Primitive genetic polymers.

Cold Spring Harbor Perspectives in Biology 2, a002196.

Lauterbur, P. C. 2008. The spontaneous development of biology

from chemistry. Astrobiology 8, 3–8.

Lazcano, A. 2010. Historical development of origins research. Cold

Spring Harbor Perspectives in Biology 2, a002089.

Morowitz, H. and Smith, E. 2007. Energy flow and the organization

of life. Complexity 13, 51–9.



Orgel, L. 2000. A simpler nucleic acid. Science 290, 1306–7.

Pace, N. 1996. New perspectives on the natural microbial world:

molecular microbial ecology. ASM News 62, 463–70.

Schwartz, A. W. 1995. The RNA world and its origins. Planetary

and Space Science 43, 161–5.

Ricardo, A., Carrigan, M. A., Olcutt, A. N., and Benner, S. A. 2004.

Borate minerals stabilize ribose. Science 303, 196.

Trefil, J. Morowitz, H. J., and Smith, E. 2009. The origin of life.

American Scientist 97, 206–13.

Zhu, T. F. and Szostak, J. W. 2009. Coupled growth and division

of model protocell membranes. J. American Chem. Soc. 131,

5,705–13.



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14

The first greenhouse crisis: the faint

young Sun

Introduction

from the physics of nuclear fusion, that the Sun has not really

shined with constant output over time. Indeed, when the Sun

was young, it almost certainly had a lower output than today by

a significant amount, leading to what is called the “faint early

Sun” or “faint young Sun” problem. This chapter explores the

physics of that variation and the implications for Earth’s ancient

climate.



If there is one thing we depend on, it is the assurance that the

Sun will shine day after day, year after year, constantly and

dependably. We base this sense of certainty on the collective

human experience of a constant Sun, and indeed, the concern or even terror that total solar eclipses brought on was a

strong motivation for building eclipse predictors such as, possible, Stonehenge (Chapter 2). And yet there is strong evidence

from the record of climate, from observing other stars, and



14.1 The case for an equable climate

in the Archean

hydrogen), whereas the number of atomic nuclei goes down

(four hydrogen nuclei having combined to make one helium

nucleus). As the core evolves toward a state of heavier but fewer

atomic nuclei, it compresses, forcing the density up. The compression of the core toward higher density, in turn, increases

the average temperature of the material as the energy of compression is converted into the random energy of collisions of

nuclei.

Finally, the rate of fusion is very sensitive to the temperature,

such that small increases in temperature lead to a large increase

in the rate of fusion. This is the case because fusion requires a

threshold collisional speed in order to allow protons (hydrogen

nuclei) to overcome their intrinsic repulsion and bind together

(see Chapter 3). Hence, a small increase in the mean speed of

collisions (small temperature increase) leads to a very much

larger percentage of collisions in which the hydrogen nuclei can

fuse to form helium. Therefore, over time, the Sun has gotten

more luminous. Computer models predict that, at the time of

the early Archean, 3.8 billion years ago, the Sun’s luminosity

was 75% of the present value, that is, it was 25% dimmer than

at present. By the end of the Archean eon, 2.5 billion years

ago, the Sun’s luminosity was 82% of the present-day value

(Figure 14.2).

With less sunlight streaming to Earth in the past, the surface

would have been colder than at present. The surface temperature of Earth’s oceans today, averaged over their surface and

over a year, is 288 K. A very rough guide to what the surface



There is ample evidence that the Archean Earth possessed liquid water. The existence of metamorphosed sedimentary rocks

from this period, as discussed in Chapter 11, require erosion by

liquid water and deposition in a lake or marine environment.

The presence of life itself, recorded through isotopic signatures

and fossil evidence, also implies liquid water. As discussed in

Chapter 12, we know of no living thing today that can get by

without water. Many don’t require oxygen (and are poisoned by

it), but all require liquid water.

Figure 14.1 summarizes constraints arguing for Earth’s mean

temperatures being above the melting point of water during

the Archean. In Chapter 15, we explore the case for a Martian

climate, at the time of Earth’s Archean eon, which was warmer

than at present (either continuously or episodically). In total,

the evidence on Earth and Mars points to planetary climates at

least as warm as those experienced today. Surprisingly, as we

now show, such climates impose rather strong constraints on

the nature of the Archean atmospheres of the Earth and Mars –

provided our understanding of the evolution of the Sun is correct.



14.2 The faint young Sun

Simple reasoning about the physics of hydrogen fusion indicates

that the Sun was cooler in the past than it is at present. As the

Sun converts hydrogen to helium, the mean atomic weight of

the atoms in the core goes up (helium is four times heavier than



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THE HISTORICAL PLANET

oldest known sedimentary rocks



Surface temperature (kelvin)



340

chert data



?

320



300



280

sedimentary rocks exist

melting point of pure water

260



ition



e of present compos



perature for atmospher



average surface tem

4.0



3.8



3.6



3.4



3.2



3.0



Age before present (billions of years)



Figure 14.1 Some constraints on Earth’s surface temperature during the early to mid-Archean. The line marked “average surface temperature for

atmosphere of present composition,” derived from Figure 14.2, shows what happens if today’s atmosphere is combined with the fainter Archean

sun: surface temperatures lie well below freezing. The chert data described in Chapter 6 suggest ocean surface temperatures at 3.4 billion years ago

much higher than today’s. A more robust but looser constraint is the appearance of metamorphosed sedimentary rocks in the geologic record after

3.85 billion years ago, indicating that widespread liquid water was present and hence that the global mean surface temperature was above the

melting point of water.



1



Temperature, K



300



275



freezing point of water



0.9



Ts

S/So

250



225



0.8



Te



4



3



2



1



0



Solar luminosity relative to present value



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0.7



Billions of years before present



Figure 14.2 The faint young Sun problem. Plotted as a function of

time before present are Earth’s surface temperature (Ts ), its effective

temperature (Te ), and the luminosity of the Sun relative to its present

value (solid curve). The temperature values are to be read on the

left-hand axis; the luminosity refers to the right-hand axis. The surface

temperature assumes an atmospheric composition through time

identical to the present one, just to illustrate the problem. Under this

restriction, Earth’s mean surface temperature remains below the

freezing point of water (dashed horizontal line) for the first 3 billion

years of Earth’s history. Reproduced from Kasting (1989) by

permission of Academic Press, Inc.



temperature would be for lower solar luminosities (all else kept

the same) is given by scaling the temperature to the fourth root

of the solar luminosity. (Such a scaling derives from the way

in which photons are emitted from a surface that is heated at

a given rate.) Hence, at 82% of the solar luminosity, the mean

surface temperature is 288 × (0.82)1/4 = 274 K; for 75% of the

solar luminosity, the surface temperature becomes 268 K, below

the freezing point of water.

The sensitivity, though, is actually greater than this, because

as Earth cools, the atmosphere cannot hold as much water vapor,

and this dryness leads to an even lower temperature through the

greenhouse effect, which we describe in the following sections.

Work by Pennsylvania State University atmospheric scientist

James Kasting indicates an Earth surface temperature of 255 K

at the start of the Archean. Such an Earth could not have had

a stable, liquid water ocean. What kept the oceans from being

frozen? To answer this question, we need to consider how the

atmospheric greenhouse effect works.



14.3 The greenhouse effect

It is a sunny midsummer day and you have parked your car, windows closed, in the asphalt parking lot of your favorite shopping

center for an hour of shopping. Upon leaving the building, you

notice that the outside air temperature is warm but not broiling. Once the car door opens, though, that familiar blast of heat

greets you from the hellishly torrid interior. What happened?



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