Abiogenesis Explained

Jelle Kastelein
January 30, 2010

Contents 3.3.6 The origins of RNA . . . . . 33

3.3.7 Exogenesis . . . . . . . . . . 39
1 Introduction 1 3.3.8 Multiple genesis . . . . . . . 41
1.1 Spontaneous generation . . . . . . . 2 3.3.9 Early evolution . . . . . . . . 41
1.1.1 Life as a continuum . . . . . 2 3.3.10 Conclusions . . . . . . . . . . 44
1.1.2 Modern abiogenesis . . . . . 2

2 Fossil evidence of ancient life: con- 1 Introduction

straining time scales 3
2.1 Microbial fossils . . . . . . . . . . . . 3 We often hear the question how evolution explains
2.2 Fossil isotopes . . . . . . . . . . . . . 4 the origins of life. The short answer: it doesn’t.
2.3 Fossil biomolecules: (a)biosignature That is the subject of abiogenesis theory (also re-
molecules . . . . . . . . . . . . . . . 5 ferred to as origin(s) of life science). Abiogene-
2.4 Primitive aspects of modern cells . . 6 sis is basically a hybrid biochemical/geochemical
explanation for the origin of life from non-living
3 Bottom Up: Emergence and abiogen- materials. Evolution is what comes after the first
esis experiments 11 self-replicating system is produced, that is capable
3.1 Emergence . . . . . . . . . . . . . . . 11 of undergoing change. There is, of course, some
3.2 The spontaneous generation of sim- overlap, when discussing the origins of such self-
ple organic molecules . . . . . . . . . 11 replicating systems. Here, I’ll discuss some ba-
3.2.1 The Urey-Miller experiment sic observations, ideas and experiments that come
and primordial soup . . . . . 11 from abiogenesis studies. Interestingly, some of
3.2.2 Extremophiles . . . . . . . . 13 these methods are also applicable to identifying
3.2.3 Monomers from hydrother- signs of life on other planets (e.g.: future Mars mis-
mal vents . . . . . . . . . . . 14 sions), but I won’t go into that in much detail here,
3.2.4 Monomers from the Deep except where it is relevant to abiogenesis. I’ll start
Hot Biosphere . . . . . . . . 19 with some basic concepts, after which I will mention
3.2.5 Monomers from Space . . . . 19 some fossil observations of signs of life in the early
3.2.6 The radioactive beach . . . . 20 Earth to give an idea of the top-down approach
3.2.7 Chirality . . . . . . . . . . . 20 to studying life through geology and paleaontology,
3.2.8 Conclusions on monomers . . 21 and then move on to a bottom up approach which
3.3 The generation of polymers from is more akin to biochemistry, in which scientists try
monomers and the origins of self- to recreate the conditions of the early Earth in the
replication . . . . . . . . . . . . . . . 21 lab, with some successes and some open questions
3.3.1 The construction of macro- which I’ll try to point out. I won’t move far beyond
molecules . . . . . . . . . . . 22 the first self replicating systems, as that is where
3.3.2 The clay world . . . . . . . . 23 evolution starts, but I’ll briefly mention a few key
3.3.3 The origins of cell membranes 24 events that lead to the evolution of increasingly
3.3.4 Self replicating systems . . . 28 complex lifeforms. The details of these, however,
3.3.5 The origins of metabolism . . 29 are topics that should (and have been) addressed

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in other threads. I should note that my knowl-
edge is about 3 years out of date, and that I am
merely an interested layman, so new evidence may
well have been uncovered recently that I am not
aware of. This is a very active and rapidly growing
field of research. I have based this summary pri-
marily on a great 2005 introductory video lecture
series by The Teaching Company, by Robert M.
Hazen (http://www.teach12.com/). I have tried to
update this information here and there, but there
may well be some outdated information remaining.

1.1 Spontaneous generation Figure 1: Pasteur’s experiment (image from

Louis Pasteur proved that spontaneous generation http://www.angelfire.com/).
of life, which before this time had been considered
an established fact, was impossible, and that life
forming was instead the result of biogenesis (life perspective), one has to assume that life ultimately
arising from other life). Before Pasteur’s time, for came from non-life. In the end, life is chemistry,
instance, mice were thought to spontaneously ap- and its laws - on the molecular scale - do not dif-
pear from stacks of hay. Similarly, micro-organisms fer in any known significant fundamental way from
growing in colonies on a substance were thought to the normal laws of chemistry. Yet life is obviously
be born from that substance itself, or from a “life quite distinct from non living matter. Abiogene-
force” in the air. To disprove this idea, Pasteur sis, then, is not only about the transition from life
performed several experiments. He boiled a broth to non-life, but also about exploring the boundary
which he placed in vessels that were connected to between the two.
the outside air through a long, bent tube that would
not allow dust particles to pass, as well as some 1.1.1 Life as a continuum
that were completely closed off, and some that were One of the key questions in this topic is of course
completely open to the air. In addition, he did the question what life really is. There are many
the same for an unboiled broth. The experimen- conflicting definitions (almost no two people will
tal setup of the first (boiled) experiment is shown have the same definition), but most biologists today
in figure 1. Nothing grew in the closed or filtered now agree on three key properties. This is used as a
vessels holding the broth that was sterilized, but working definition. First of all, life must be able to
something did grow in the vessels holding the broth grow. Second, it must be able to reproduce. Third,
that was uncooked, independent of whether or not it must be able to undergo reproductive variability
the broth was closed to the outside air or not (he (in other words, it must be able to evolve). Under
had thereby also discovered anaerobic metabolism). this definition (or perhaps in spite of it), there is
The conclusion was that life did not come from the thought to be no sharp boundary between life and
broth or from the life force in the air, as had previ- non-life. Rather, the transition from life to non-life
ously been suggested, but from other lifeforms car- should be seen as a continuum. In that sense, the
ried on spores. Strangely enough, abiogenesis (or first self replicating systems are “somewhat alive”,
origins of life) theory is now trying to establish how but not quite as alive as the first bacterium, or us. I
primordial life once came from non living materi- would ask that you keep this in mind while reading
als. Of course, we all know that Earth worms are the rest of this summary.
not born from the Earth, but from other life forms,
particularly Earth worms. But at some point, when
1.1.2 Modern abiogenesis
upholding a scientific naturalist perspective (which
cannot comment on the existence or non-existence Charles Darwin wrote in a letter to Hooker, in
of God, and thus does not deal with the religious 1871, that life began in a “warm little pond, with

2
all sorts of ammonia and phosphoric salts, lights,
heat, electricity, etc. present, that a protein com-
pound was chemically formed ready to undergo still
more complex changes, at the present day such mat-
ter would be instantly devoured or absorbed, which
would not have been the case before living creatures
were formed.”. According to Darwin, then, it is the
present day life which prevents spontaneous gen-
eration from occurring today. The modern defini-
tion of abiogenesis is quite similar to that suggested
by Darwin. Unlike the old definition of abiogen-
esis, which was, as noted, disproved by Pasteur,
and which dealt with the spontaneous generation of
complex organisms, the modern theory is concerned
with the origins of life from primordial chemicals
under conditions thought to have been prevalent on Figure 2: The hadean era (image from
the early Earth. In the rest of this summary, I will http://www.newsback.com/).
discuss only this modern interpretation of abiogen-
esis. There is currently no broadly encompassing
at which time the composition of the atmosphere
theory, or standard model, if you will, of the origins
was very different from that of today. There is
of life. However, one can find a number of common
some controversy as to the exact contents of this
threads in these models, and all build on discoveries
early atmosphere, which we will discuss later on.
of fossil evidence, and chemical experiments carried
Here I’ll discuss some of the evidence we have con-
out in laboratories. I will start by outlining some
cerning time scales. I’m not going to go into fossil
of the fossil evidence coming from the “top down”
dating here - this is not supposed to become a full
approach to the studies of the origins of life, before
textbook, but a concise summary. Look into ra-
moving on to the “bottom up” approach that stud-
diometric, and particularly isochron dating if you
ies abiogenesis through experimental observations,
want more info on this subject.
in attempts to reconstruct early life, using plausible
early Earth conditions.
2.1 Microbial fossils
2 Fossil evidence of ancient One of the main problems with finding some of the
oldest forms of life is that it will have been engulfed,
life: constraining time that is, eaten and digested by subsequent genera-
scales tions of organisms. This is of course true for any
organism in the chain of evolution, but it is particu-
The Earth is thought to be roughly 4.6 billion years larly problematic in the case of microbial organisms
old. At first, its surface was red hot, both because - and life is thought to start out as extremely tiny,
the crust had not yet settled, and because it was cell-like self-replicating systems, much like a highly
continuously being battered by fragments of the oversimplified bacterium. Since most of the really
then forming solar system. These fragments would, ancient life was both extremely tiny and soft bod-
on impact, vaporize oceans and throw most of the ied, finding fossil evidence of the (near) first kinds
recently formed atmosphere into outer space, so of life is not an easy task. It is rare for soft tis-
that no life could survive. The oceans are thought sue to fossilize, and even when it does, microbes
to have formed approximately 200 million years af- are hard to spot. The data are sometimes highly
ter the formation of the Earth, when the surface ambiguous. Some of the fossil evidence that is not
temperature was approximately 100C. The Earth so ambiguous, and widely accepted as uncontrover-
remained most likely uninhabitable until the end of sial comes in the form of stromatolites (see figure 3;
the Hadean eon, roughly 4.1-3.8 billion years ago, more info on wikipedia), which are spherical dome-

3
like structures that are thought to be composed
of mineralized corpses of ancient microbes. These
structures have been dated at about 2.5-2.7 billion
years old, and there are some other examples of
widely accepted fossil evidence that are considered
reliable that go as far back as about 3 billion years.
There are older known fossils still, but the evidence
is often controversial in those cases, arising from
such questions as whether or not the fossils in ques-
tion are actually fossils, and not just natural min-
eral formations that happen to look like microbes,
or whether the rocks were accurately dated. The
oldest controversial fossils were dated at around 3-
3.8 billion years. Schopf’s fossils, for instance, are
about 3.465 billion years old, but it is uncertain
if what is seen in the minerals is actually micro-
bial in origin. Some images of what he found can
be seen in figure 4. Note that uncertainty does not
necessarily imply falsehood. If these oldest findings
should turn out to be confirmed, this would mean
that life formed almost as soon as it was possible for Figure 3: Stromatolites (image from
it to do so, which would have major implications for http://paleontology.edwardtbabinski.us/).
our search for possible extraterrestrial life. A final
interesting set of microbial fossils have been found
near hydrothermal vents at the bottom of the ocean tends to accumulate in organisms so that the ratio
that are about 3.5 billion years old. I will return to of C 12 to C 13 is shifted. If there is a 1% excess
hydrothermal vents later on. in C 12 from the norm, we say that this constitutes
a deviation of -10 per mil. For instance, modern
photosynthetic life has a per mil of -20 to -30, cor-
2.2 Fossil isotopes
responding to a 2 to 3% excess. Stromatolites are
There are other ways of detecting signs of life on typically in the -25.0 to -25.9 range. Photosynthetic
the early Earth. Fossil isotopes are specific isotopes life has a relatively reliable source of energy, so it
that are accumulated into unnatural concentrations is typically less efficient at storing carbon than life
by living organisms. For instance, carbon has a relying on less stable energy resources. Such non-
number of different isotopes with equivalent chem- photosynthetic life can typically be found in the -50
ical properties. The isotopes that differ from the range. In addition, there is a buildup of C 12 in or-
most common one contain one or more extra neu- ganisms higher up in the food chain. So a plant
trons in the nucleus of the atom. For instance, car- contains a higher excess of C 12 than its surround-
bon, which typically has 6 protons and 6 neutrons, ings, a herbivore contains a larger excess than that
denoted by C 12 , can also be found in isotopes with plants it eats, and a carnivore that eats the herbi-
7 or 8 neutrons, denoted C 13 and C 14 respectively. vore contains a higher excess than the herbivore.
We can measure the ratio between different isotopes So, in this way, isotopes can tell us something not
very accurately using a mass-spectrometer (I’m not only about whether some mineral was at some point
going to go into the details of how this works here, processed by living organisms (which shows up as
but you can look it up if you want to - a simple the excess deviation from the norm), but it also
schematic is given in figure 5). The natural ratio of gives us some basic information about the lifestyle
concentrations between C 12 and C 13 is about 99:1. of those organisms (which shows up as the size of
Because C 13 isotopes are heavier than their C 12 the excess). The oldest fossil isotope hint at signs
counterparts, they tend to be slightly more slug- of life comes from an island off the coast of Green-
gish in chemical interactions. Because of this, C 12 land, and gives dates of around 3.85 billion years.

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 Figure 5: A simple mass spectrometer (image from
Figure 4: Images of Schopf’s fossils (image from
http://en.wikipedia.org/).
http://www.nature.com/).

I should note that this evidence was not entirely

uncontroversial at the time I heard about it, so it and under a large variety of conditions and abun-
may have been refuted since. But there is other, dant to the extent that we can easily find traces
less controversial evidence that gives estimates in of them, they must be unique to life or non-life for
the same basic ball park figure as the more reliable biosignatures and abiosignatures respectively, and,
fossil evidence. in the case of biosignatures, they should be essen-
tial to life. For instance, hopanes (see figure 6) are
2.3 Fossil biomolecules: carbon molecules that have a molecular backbone
(a)biosignature molecules composed of several carbon rings of 6 or 5 carbon
atoms that are typically produced by the type of
A final type of fossil evidence comes in the form of synthesis found in cells, and are typically found in
more complex molecules that are typical to life on cell membranes. Their structure makes them quite
Earth today. Life uses only a tiny subset (a frac- rigid and stable, making them a good candidate
tion of a percent) of the possible carbon based com- class of molecules that is frequently considered for
pounds typically found in nature. This is due to the this type of investigation. Incidentally, work is cur-
unusual way in which these compounds are synthe- rently being done on creating a hopane-detector for
sized by the cell. So, by looking at the absence of an upcoming Mars mission by Steele et al (in the
compounds not found in life in combination with form of MASSE, Microarray Assay for Solar Sys-
the presence of those molecules that are typically tem Exploration). Some of the more convincing
found in life, we can identify strong evidence that identifications of hopanes for which non-biological
life was once present at the site of interest. We call systems were ruled out as a possible origin are given
these organic compounds biosignature molecules, by Summons, at 2.7 and 2.5 years old. The latter
and we call compounds that are never found in life sample contained traces of 2-Methylhopane, which
abiosignature molecules. Both types of signature is known to occur only in Cyanobacteria, which are
molecules must be stable over long periods of time capable of undergoing photosynthesis.

5
Figure 6: Hopane (image from
http://www.chem.qmul.ac.uk/). Figure 7: ATP (image from
http://www.dvbiology.org/).

2.4 Primitive aspects of modern

cells energy is derived from the environment and put
to use for the organism’s benefit. Metabolism-first
One final type of contribution of the top-down ap- proponents propose that the first self-reproducing
proach to abiogenesis comes from molecular phy- system of chemical interactions was a metabolic cy-
logeny. I don’t want to go into too much detail cle. Many geochemists working in the field sub-
here, but essentially it concerns the identification scribe to this idea. On the opposite side of the
of some of the most ancient cellular mechanisms. debate, the “genetics-first” viewpoint holds that
Basically, what researchers in this field do is look genetic reproduction preceded metabolism. Most
at the correspondences and differences in function- biologists tend to support this view. I’ll briefly de-
ality between the most primitive (note: primitive scribe the target feature of modern organisms that
in an evolutionary context means oldest, not nec- either viewpoint is focused on at this point in time.
essarily least complex) and most modern species of
organisms. Some mechanisms stand out as rigid
and unchanging, suggesting that they play a vital Primitive metabolism
and ancient role for life. For instance, all organisms The metabolism first point of view focuses mostly
today seem to require ATP (see figure 7), and so on one of the most fundamental metabolic path-
the genes that code for this molecule are more or ways that modern organisms employ, named the
less fixed in evolution across all organisms. Sim- citric acid cycle. This relatively simple process
ilarly, as Carl Woese noted, the genes that code forms a closed loop of reactions that halves the key
for 16S ribosomal RNA (see figure 8) are highly molecules at every turn, resulting in the release of
conserved; the correspondence between human be- energy. Interestingly, the citric acid cycle can also
ings and e-coli is about 50%. It is expected, then, run in reverse, in which case it is called the reverse
that one of the most sensible courses of action is to citric acid cycle, for obvious reasons. In this case,
look for circumstances that could have lead to the input energy is required, but the reactive loop runs
spontaneous development of such rudimentary fea- in reverse, duplicating the reactants at every turn.
tures of life. The abiogenesis community tends to In this way, the cycle can be described as a self-
be divided between two opposing viewpoints. On replicating system. I’ll describe the reverse citric
the one hand, some people promote a “metabolism- acid cycle here briefly, because some of the key re-
first” point-of-view. In this view, the most central search focuses on the molecules used in these cycles,
part of life is metabolism, the mechanism by which particularly pyruvate and oxaloacetate. A simpli-

6
 Figure 9: The citric acid cycle (image from
http://www.biologycorner.com).

use of minerals as catalysts.

Primitive genetics
As we all know, genetics deals with the macro-
Figure 8: 16S Ribozomal RNA (image from molecules (large molecules, also referred to as poly-
http://www.learner.org/). mers, which are generally built up of smaller ba-
sic molecular units, called monomers) in an organ-
ism’s cells that hold (and in some cases process)
the information for its development and function-
fied form of the cycle runs as follows, where a + in- ing, namely DNA and RNA, and possibly proteins.
dicates the addition of a certain chemical from the It may serve us well to run through the basics of
environment and a → indicates a chemical reaction proteins, DNA and RNA here, so I’ll do that briefly.
resulting in the molecule to the right of the arrow, Both DNA and RNA are made up of long chains of
starting from Acetyl-CoA: Acetyl-CoA, + CO2 → four alternating different smaller molecules called
Pyruvate, + CO2 → oxaloacetate, + H2 → Malate, nucleotides, where each nucleotide contains a dis-
+ H2 O → Famarate, + H2 → Succinate, + CoA tinct base (generally a carbon ring structure), a
→ Siccinyl-CoA, + CO2 → 2-Oxoglutarate, + H2 phosphate group, and a backbone (which links the
& CO2 → Isocitrate, + H2 O → Aconitate, + H2 O nucleotides together in a strand). The bases each
→ Citric Acid, + CoA → Acetyl-CoA & Pyruvate. line up with one (and only one) of the other bases
The (normal) citric acid cycle is shown in figure (as seen in figure 11), so that two mirror images of
9. As one can see, the last step that splits a citric two different pairs can be formed (so four base pairs
acid molecule doubles the amount of oxaloacetate, in total). Where DNA uses the bases thymine (T),
which leads to a doubling of the entire cycle, and adenine (A), glycine (G) and cytosine (C) (where
so this metabolic pathway can, in principle, be self- C can bind to G, and A to T), RNA uses uracyl
replicating. One major problem is that, in modern (U) instead of thymine (so that A binds to U). The
cells, this process requires many complex enzymes structures of the five bases and a comparison be-
(catalytic proteins) which were almost certainly not tween the structures of DNA and RNA are shown
around in a pre-biotic era. We will see later how in figure 10. Both RNA and DNA replicate by
this paradoxical situation may be resolved by the use of complementary base-pairing, where each nu-

7
 Figure 11: Base pairing and chem-
Figure 10: Comparison between DNA and RNA ical structure of DNA (image from
(image from http://en.wikipedia.org/). http://www.molecularstation.com/).

cleotide is paired up in sequence with its comple- sequence of amino acids is coded for by DNA or
mentary base (see below), producing a complemen- RNA, and this determines the protein’s form and
tary sequence. In RNA, the new sequence then (thereby) function. Proteins are the work-horses of
splits off from the old one to produce a copy. Note modern day cells. From a genetics-first abiogene-
that a copy of RNA is a complementary strand, sis point of view, the first self-replicating system
much like a cast, which can serve as a template consisted of one (or, less likely, a network) of these
for the final, actual copy. The only way in which molecules. Broadly speaking, there are 4 possibili-
RNA can replicate in one step is if the strand is ties, as outlined by Orgel:
palindromic, i.e. has the same sequence of bases 1. A self replicating peptide: This is somewhat
when read in either direction. When a sequence appealing, because amino acids, which are the
of nucleotides is its own complement in this way, basic building blocks of peptides, were (as we
we call it self-complementary. DNA has to unwind will see) likely to be readily available in the
and be split down the middle for the copy process pre-biotic environment. By contrast, the syn-
to take place (this is achieved by various proteins), thesis of nucleotides (the building blocks of
after which both strands are completed by adding DNA and RNA) has proven to be more prob-
their complementary strand to the now naked DNA lematic. We will see that Fox proposed a
half. There are a few more differences between model of this type. There are, however, two
DNA and RNA. First of all, while DNA consists basic problems with this view. First of all, pep-
of two strands (figure 10, right), RNA consists of tides would somehow need to “invent” DNA or
only a single strand (figure 10, left). Second where RNA. Second, the linking of amino acids into
DNA uses a backbone made up of a sugar called de- peptides is a messy process without the aid of
oxiribose (the D in DNA), RNA uses a slightly dif- the many proteins and other regulatory sys-
ferent sugar named ribose. Finally, the main thing tems present in modern cells.
to note about proteins is that they are made up
of sequences of molecules called amino acids. The 2. The simultaneous appearance of DNA and pro-

8
 acid cycle is central to metabolism. Before the
1980’s, people had thought that all enzymes
in a cell were catalytic proteins. But in the
early 80’s, both Altman and Cech indepen-
dently found an enzyme that consisted entirely
of RNA. This means that RNA can both con-
tain information and catalyze important reac-
tions (like self-replication). This thus resolves
the DNA/protein paradox.

RNA plays many important roles in all modern

cells. For instance, mRNA is the result of transcrib-
ing a DNA strand, and tRNA and rRNA are sub-
sequently responsible for the translation of mRNA
into amino-acid chains that we call proteins. Ad-
ditionally, RNA nucleotides play structural roles in
proteins called co-enzymes. These co-enzymes pro-
mote reactions in, among other things, the citric
acid cycle, including the production of citrate from
oxaloacytate, as well as in helping to build lipids
(which are the building blocks of cell membranes)
from other essential biomolecules. Finally, RNA
can act as chemical sensors in the form of so-called
Figure 12: Folded RNA strand (image from
riboswitches, which change shape when they come
http://www.uic.edu/).
into contact with other chemicals. This makes the
central and ancient role of RNA very plausible.
teins: Because proteins are required to unfold RNA is therefore considered the prime candidate
and copy current-day DNA, we may have to information bearing molecule. As we shall see, the
assume that they were likewise linked in the construction of its nucleotide parts has been prob-
past. For this reason, both DNA and proteins lematic. However, there are interesting hypotheses
would have to appear at the same time. This as to how this problem may be resolved. Partic-
possibility is obviously unappealing, because ularly, there may once have been close relatives of
it requires the simultaneous occurrence of two RNA that have now gone extinct, which rely on the
complicated steps of macromolecule formation. same nucleotide bases as RNA, but which use a dif-
It presents us with a paradox; in modern cells, ferent backbone. A top-down approach to studying
DNA is used as the building plan to make pro- RNA that is worth mentioning involves taking ex-
teins, but proteins are crucial in copying DNA. isting prokaryotic cells, and engineering them with
progressively fewer genes, so as to identify the min-
3. A clay world model, which we will describe in imal genetic requirements for life. John Desmond
some detail later on. Bernal called this process biopoesis.
4. A model in which a nucleic acid similar to
RNA acts as both an information carrier and Chirality
a catalyst that promotes self-replication: This A final curious feature of biomolecules is their so-
model could, according to Fox, be studied called chirality, or handedness. Most (if not all)
most easily in the laboratory. It is also the biomolecules come in mirror image pairs, that are
most likely alternative for various other rea- referred to as right-handed (abbreviated by D, for
sons. First of all, RNA, in the trinity form dextrose=right) and left-handed (L, for livo=left)
of mRNA, tRNA and rRNA, is one of the varieties. These pairs are called chirals (the differ-
most essential core molecules of ancient ge- ent instances are called enantiomers). They form
netics, in much the same way that the citric because of the tendency for carbon molecules to

9
form 4 bonds. An example of chirality can be seen
in figure 13. Most of the properties of chirals are
exactly the same. For instance, they have the exact
same composition and structure (except in a mirror
image of one another) and many of the same phys-
ical and chemical properties. However, life tends
to use only one chirality of each general group of
molecules (this is called homochirality). For in-
stance, it tends to use only right handed sugars,
and left handed amino acids. Since both chirali-
ties are equally distributed throughout nature, it
is something of a mystery why only a single chi-
rality is used. However, it has become clear that
this reliance can not be violated without cost; cells
respond differently to different chiralities Proteins
can become non-functional (because of the fact Figure 13: Chiral molecules (image from
that protein function is for a large part determined http://www.ehu.es/).
by shape) and the DNA helix (the familiar spiral
shape) a mess (because the backbone becomes de-
sible that these autotrophes evolved from surface
formed) without chiral purity. This can result in
heterotrophes, but that, as crust-dwelling microbes
anything ranging from different responses of taste
(which are often refered to as extremophiles, and
receptors to birth deformities. All of this suggests
which we will meet again later on) were better pro-
that pre-biotic synthesis was inherently asymmet-
tected from comet impacts or other natural disas-
ric, resulting in homochirality. We will later discuss
ters, their ancestral heterotrophes became extinct
some hypotheses about why this may have hap-
and the autotrophes became dominant by default.
pened. An interesting side note about chirality is
A final thing to note is that phylogeny of prokary-
that it tends to flip every few thousands of years.
otes is often complicated by their tendency for hor-
By knowing the ratio between different chirals in
izontal (or: lateral) gene transfer, in which two
current day life, fossils can therefore be dated by
individuals sometimes swap DNA. Because of this
measuring the increase in the non preferential chi-
cross linking, it is practically impossible to deter-
rality. For instance, when an organism dies, it will
mine traits of the so-called last common ancestor
have only L-amino acids. Over time, increasingly
(the lifeform from which all current life is thought
more of these flip into D-chirals until a 50/50 equi-
to be descended) purely by phylogeny.
librium is again reached, and an age estimate can
be given on the basis of the ratio of L to D amino
acids. However, chirality can also be influenced by
environmental factors, such as acidity.
I will close this part with a few more notes
from phylogenetic research. One of the key things
to note here is that microbes called prokaryotes
(bacteria and archaea are prokaryotes), which are
much simpler than eukaryotes such as ourselves,
are thought to be much older than the eukaryotes.
The archaea, which are a distinct from the bacteria,
seem to be autotrophic, rather than heterotrophic.
That is, they are capable of making their own
building blocks (their own food) and deriving their
energy from (an)organic chemical sources, rather
than from sunlight (for example, plants are het-
erotrophic, by way of photosynthesis). It is pos-

10
3 Bottom Up: Emergence and plex molecules and molecular systems. Secondly,
the ways in which these agents are interconnected
abiogenesis experiments are of great importance, both in terms of the types
of interaction, and the degree of connectivity. An
The top-down approach to identifying or constrain-
example is the way in which neurons are connected
ing the origins of life is useful for giving some time
in the brain, or, in case of abiogenesis, the ways
scale constraints, but it is inherently limited be-
in which the different chemicals in the environment
cause of the inevitably limited amount of informa-
can interact with one another. A third factor is the
tion we can deduce from it. Another, bottom-up
flow of energy through the system. There is some
approach is to try and simulate plausible condi-
critical amount of energy flow for which a system
tions of the early Earth or solar system, and try to
gives rise to emergent behavior. Too low a flow,
synthesize primitive biochemical compounds. This
and nothing happens. Too high, and the emergent
field is known as pre-biotic chemistry. Of course,
behavior is quickly reduced to rubble by the energy
we cannot say with absolute certainty that what we
influx. Finally, the way this energy cycles through
find is exactly how things went down on the early
the system is important in both the type of flow,
Earth, but as long as we use a plausible range of
and the rapidity of it. I will return to these points
conditions, these experiments, if successful, make
at the end of the next paragraph. Overall, these
the case that life can indeed form spontaneously
properties of or precursors to emergence will be ev-
from non-life, and that it does so under circum-
ident in the subsequent paragraphs.
stances that are known to occur out in the natural
world. I’ll start with a very brief description of the
basic notion of emergence, on which most of this 3.2 The spontaneous generation of
work is based in the end, and will then move on to simple organic molecules
increasingly complex experimental results, and the
underlying hypotheses of the experiments. We now know that simple organic molecules, duped
monomers, such as amino acids (which are the
building blocks of proteins), lipids (the building
3.1 Emergence blocks of cell membranes), sugars and bases (the
most integral parts of the building blocks of the nu-
Emergence (a term coined by G. H. Lewes) is a cleotides that make up DNA and RNA) can form
field of study that basically addresses the question spontaneously under a variety of circumstances.
of how nontrivial patterns arise from the interac- Cocktails of such molecules tend to be referred to as
tion between simple agents. One can think of the the pre-biotic or primordial soup, a term that was
interaction between sand grains and water that cre- coined by Oparin. I’ll discuss the most prominent
ates different characteristic patterns of bumps and of these hypotheses here. The story is very com-
ripples on a beach, the interaction between neu- plex and involves a number of models, all of which
rons from which consciousness emerges, or a com- are capable of producing monomers, and some even
plex chemical pathway that gives rise to emergent produce polymers, which are generally made up of
patterns in the resulting environment. As far as I strands of many monomers (but we’ll get to that in
can tell, emergence and chaos theory (particularly the next section). But this first part of the story
the field of synchrony, pioneered by Art Winfree) turns out to have one very simple answer: it is
seem to be intimately connected, and may well be easy to spontaneously synthesize most of the ba-
two sides of the same coin. Scientists have identi- sic building blocks of life under a huge diversity of
fied a number of key factors in an emergent system. circumstances.
The density of the agents, that is, how concentrated
they are in a given environment, is the first. There
3.2.1 The Urey-Miller experiment and pri-
are critical densities that, when crossed, give rad-
mordial soup
ically different behavior from lower or higher den-
sities. In abiogenesis, this translates into the no- The most famous experiment that demonstrated
tion that there is some minimal concentration of the the spontaneous generation of monomers was the
bioparticles present for the formation of more com- Urey-Miller experiment, which I’ll describe here.

11
 spheric gasses (simulating the atmosphere itself) as
described by Urey, and adding series of electrical
sparks as an energy source to generate a chem-
ical reaction (basically simulating lightning). In
essence, the energy blasts electrons away from the
chemical compounds, making them more reactive.
It should be noted that subsequent experiments
have also explored other energy sources, such as
UV radiation, as well as other atmospheric condi-
tions, with similar results. The water vapor, mixed
with the chemical compounds resulting from the
gas, was then condensed through a series of tubes
leading back in to the “ocean”. The basic setup of
the experiment is shown in figure 14. After only a
few days, Miller found that his mixture had syn-
thesized about half a dozen amino acids, among
other things. The experiment was confirmed inde-
pendently a number of times, and was also repeated
with variations thrown into the mix, using, for in-
stance, a different mixture of atmospheric gasses,
a different energy source, or an addition of pow-
Figure 14: Urey-Miller experiment setup (image dered minerals (representing soil). Almost every
from http://www.uic.edu/). kind of monomer used in current-day life has been
synthesized in this way, with three notable excep-
tions: ribose (a sugar), and the nucleotide bases
Since this experiments, some concerns have been adenine and guanine. It is interesting to note that
raised with regard to the validity of the un- the Urey-Miller experiment gives a similar distri-
derlying assumptions regarding the early atmo- bution of monomers to that employed by life today
sphere, but subsequent experiments have shown - though it should be noted that the experiment
that monomers also arise under a large variety of also produced many other molecules that have no
different circumstances. I’ll close this paragraph role in current-day life. What basically happens
with the main questions that challenge the Urey- in the Urey-Miller type experiments is that, un-
Miller results. Miller, for his PhD thesis, simulated der the influence of energy, the atmospheric gasses
the early atmosphere of the Earth as conceived by form a highly reactive mixture of chemicals like hy-
Urey, his adviser. Urey postulated that the early drogen cyanide (HCN) and formaldehyde (CH2 O),
Earth would have an atmosphere that is radically which easily bind to other molecules in the environ-
different from today’s. Today’s atmosphere con- ment. For instance, amino acids are made when
sists mostly of Oxygen (O2) and Nitrogen (N2), but HCN , CH2 O and N H3 undergo what is known
the high dose of oxygen is mainly due to the process as Strecker synthesis. John Or found that when
of photosynthesis carried out by plants. Urey hy- a solution of HCN was heated, adenine was pro-
pothesized that the early atmosphere would have duced. Similarly, in a rich solution of CH2 O, sug-
been highly reducing, which basically means that ars, including ribose, were spontaneously produced.
it prevented oxidation by the removal of free oxy- The problem was that Miller’s concentrations of
gen from the air. In particular, Urey hypothesized HCN and CH2 O were typically too low to pro-
that the early atmosphere was composed mainly duce the reactions. Essentially, adenine is produced
of hydrogen (H2 ), Methane (CH4 ) and ammonia when 5 HCN molecules combine, and in Miller’s
(N H3 ). Miller set up a simple and elegant experi- solution the largest chains of such molecules were
ment in which he heated up water, resembling the length four HCN chains. It turns out, though, that
Earth’s oceans, passing the water vapor through there is a solution to this problem. Orgel proposed
a series of tubes into a vat containing the atmo- that, when water freezes that contains a solution of

12
molecules, the thing that freezes most rapidly is the are easily broken down. This has to do with the
pure water. The solution therefore tends to become polarized nature of water; an H-bridge, which is re-
more concentrated during the freezing process, and sponsible for such bonds, is formed because water
this can then give rise to interesting chemical in- molecules are not radially symmetric. The result is
teractions. This is an example of emergence where that one side of the molecule has a slight positive
the energy flow has an essential role to play. These charge, while the other side has a slight negative
reactions are slowed down, however, because of the charge. The molecules can line up head-to-tail and
decrease in temperature. When Miller heard of form weak bonds between the positive and nega-
this, he decided to freeze his solution to -20C to see tive ends, which is, in a nutshell, what also leads
what happened. Apparently he forgot about it, be- to water surface tension. Also, the Miller exper-
cause it remained in his freezer for about 20 years, iment produces many chemical components that
making it one of the longest lasting experiments would cross-react with the amino acids or break
in the history of chemistry. After finally retriev- up any forming peptide chains. Hydrolization is
ing the sample, it was found that large amounts a problem that needs to be solved, which plays a
of adenine had indeed been generated. The impor- major role in many abiogenesis hypotheses, and it
tance of this is that it suggests that, although the again shows to importance of energy for emergent
ancient sea may in itself have been too diluted to behavior. Subsequent experiments have gone some
account for all monomer occurrences, as the Earth way in addressing these concerns, and I will discuss
went through subsequent periods of freezing and them further below.
heating, the monomers that function as the basis
of organic chemistry could have formed quite easily. 3.2.2 Extremophiles
There are four basic problems with the Urey
Miller experiment. First of all, there are some se- It was once assumed that most life on Earth con-
rious doubts about the composition of the simu- centrates at or near the surface of the crust that
lated atmosphere used by Urey. More recent stud- coats our planet, under circumstances that we find
ies from geochemistry suggest that the atmosphere the most familiar. However, this turns out to be an
was a less reactive atmosphere of mostly N2 and erroneous assumption. For one thing, the discovery
CO2 , lacking in CH4 and N H3 . Secondly, although of life in the deep ocean near submerged volcanic
monomers were formed, almost none of the poly- systems known as hydrothermal vents suggests that
mers (like RNA and proteins) were found, and these life can exist under much more versatile conditions
polymers really form the basis of functionality in than previously assumed. Secondly, following the
modern living cells. Third, according to Brooks discovery of life near these vents, discoveries have
and Shaw (1973), there is no evidence in the geolog- been made in recent decades (most of which since
ical record that any primordial soup existed; that the early ’90’s) that suggest that nearly half the
is, if it had, we should expect to find sedimentation Earth’s biomass (the combined mass of all living
that confirms this, but we have never seen anything organisms on the planet) may be found in subter-
of the sort. Finally, these polymer macromolecules ranean microbes (particularly archaea, which are
tend to break down under Miller’s conditions, both thought to have been around at least as long as,
because of hydrolysis and when subjected to high and possibly longer than bacteria) that live deep
doses of energy, like the electricity or ultraviolet within the crust, at depths of up to at least five
radiation used in these experiments. Hydrolysis kilometers. They can be found inside deposits of
means that, when immersed in water at room tem- granite, basalt, and other minerals that we gener-
perature and pressure, peptide bonds, which hold ally consider very inhospitable. Furthermore, living
together chains of monomers in many kinds of poly- microbes have been found under the intense heat of
mers, tend to break down, as they are not as strong volcanic areas, or under a mile of Antarctic ice. Ba-
as covalent bonds (bonds that are formed by shar- sically they are found almost anywhere wherever
ing of one or more electrons). When peptide bonds there is water present. These organisms live un-
are forged in the process known as condensation der circumstances of extreme pressures and high
polymerization, they release water, and inversely, temperatures, lacking in any significant amount of
when in the presence of lots of water, these bonds sunlight, circumstances under which most surface

13
 oceans. However, as we’ve seen there are some po-
tential problems with a theory of this kind. An-
other hypothesis came along with the discovery
of (by today many) isolated complex self-sufficient
ecosystems around hydrothermal vents at the bot-
tom of the Atlantic and pacific oceans (sometimes
referred to as “black smokers” when they emit
clouds of black material), which are almost com-
pletely cut off from the sun as a prime source of
energy and exist under crushing deep sea pres-
sures (500-2000 atmospheres) at hot temperatures
(200-300C). Hydrothermal vents are deep-ocean
cracks in the Earth’s surface from which mixtures of
heated gasses are emitted. Vent structures consist
Figure 15: A hydrothermal vent. Note the of microcaverns that are coated by thin, membrane-
tube worms at the left of the image (image from like metal sulfide walls. An image can be seen in
http://web.uvic.ca/). figure 15. The current-day ecosystems surrounding
these vents contain microbial organisms, as well as
species of crabs, shrimp and tube worms. It turns
life would be unable to survive, and they are there- out that the microbes are the primary energy pro-
fore generally called “extremophiles”. They tend ducers in these systems, reminiscent of the role of
to have an extremely slow metabolism and may be plants in more familiar ecology. These organisms
inactive for thousands of years. Cell division may exploit the mineral instability that results from
only occur once every millennium, and for the re- the hot water and gasses emanating from the deep
mainder of the time, these organisms seem to just sea vents, mixing with the cold water surrounding
sit and wait. This is particularly true for the crust- them, and flowing over sulfur-rich surface minerals
dwelling and ice-dwelling microbes (but less so for in the process. It has since been proposed, by Hoff-
those near vent-systems). There appears to be little man, Baross and Corliss, that hydrothermal vents
or no predation in these systems, and so the main may well be the best place for the formation of early
source of competition is competition for resources. life. The deep ocean would have found more shel-
Extremophiles have been an important factor in ter from comet impacts that the early Earth was
the proposal of several different alternatives to the subjected to during the Hadean eon, and the fos-
Urey-Miller source of monomers. Although they sil evidence mentioned earlier, and the observation
are generally referred to as competing hypotheses, that current day ecosystems thrive near these vents
we can view these as many simultaneously (or suc- provide strong support for this hypothesis.
cessively) productive sources of basic organic mat- There appeared to be some potential problems
ter. I will discuss some of the more prominent of here that needed to be addressed that Miller, as a
these in the next few paragraphs. One of the fun- defender of an opposing view, was obviously keen to
damental characteristics of these environments is point out. First of all, as was the case in the Urey-
that their extreme conditions can give rise to unex- Miller experiment, the heat from the vents was
pected chemical reactions, yet another example of thought to break down any macromolecules that
emergence. are formed. But, as we will see in a later paragraph,
this assumption turns out to be likely to be false
3.2.3 Monomers from hydrothermal vents (or rather, incomplete and therefore inaccurate).
Second, modern day hydrothermal vent ecologies
The idea that the sun is the prime source of en- are dependent on oxygen, which ultimately comes
ergy that ultimately feeds life on Earth is true from photosynthetic (plant) life. The early Earth
for most of the life that currently exists on Earth. would have been lacking in free oxygen. In other
Miller’s experiments are therefore based on the idea words, there would have to be a way for a rudi-
that life originated at or near the surface of the mentary metabolism to evolve that did not require

14
large amounts of oxygen. So, the hydrothermal sulfur world, and in the PAH hypothesis for the
vents theories have their problems, but they opened origins or RNA. Therefore, I’ll mention a number
the door for alternative hypotheses from the thus of preliminary experiments on origins of monomers
far unrivaled primordial soup idea. We will return here. Many (though not all) of these experiments
to these issues when we look at the emergence of incorporate minerals as key ingredients. First,
polymers and self-replicating systems. Hydrother- Hazen, Morowitz, Yoder and Cody performed sev-
mal vent discoveries also kick started the search eral experiments under high pressure, incorporat-
for other extremophile organisms, as we mentioned ing a realistic mixture of powdered minerals, atmo-
above. spheric gasses, and water. The initial motivation
for this came from the observation that the dielec-
tric constant of water, which is a measure of po-
Monomers from minerals
larity that influences the ease with which peptide
Up until now, we have focused mostly on the role
bonds can form, decreases dramatically under high
of the ocean water and the atmosphere, and have
pressures and at high temperatures, from about 80
largely ignored the role of minerals in the Earth’s
to 20. Recall that, at normal pressures and tem-
soil. Obviously, minerals and rocks may have
peratures, water acts as a(n unusually potent) nat-
played an important role. First of all, as a source
ural organic solvent which can easily break peptide
of protection, overhanging rocks can shield forming
bonds, and that this has to do with the polarized
organic molecules in a tidal pool from the UV ra-
nature of water. By decreasing the dielectric con-
diation of the sun. Second, they can protect tidal
stant, then, it may be possible for peptide bonds
pools from incoming waves, and, as water evap-
to form. Hazen et al. decided to concentrate on
orates, allow such a pool to become condensed,
the reverse citric acid cycle described earlier, par-
resulting in a less dilute soup of organic compo-
ticularly on pyruvate. Recall that pyruvate plays a
nents, which is more likely to undergo reactions and
major role in this metabolic cycle. It also plays a
polymerize. Similarly, organic molecules can accu-
fundamental role in multiple other processes, such
mulate in small pockets in, for instance, volcanic
as the splitting of glucose into 2-pyruvate (a pro-
rock, which keep them condensed as water evap-
cess known as glycolysis). Pyruvate is essential for
orates from them, as well as protected from UV
life as we know it, but it does not work in wa-
light. Additionally, many of the most common rock
ter at room temperature without a catalyst such
faces contain multiple cracks and pores roughly the
as an enzyme, and it tends to break down. To
size of a cell. Such pores and cracks result in an
test their hypothesis, they subjected a mixture of
enormous surface area on which many simultaneous
pyruvate and water to intense pressure and high
natural “experiments” for self-organization can oc-
temperatures similar to those found at hydrother-
cur. Finally, it makes sense that water, Earth, and
mal vents. The result was that pyruvate did in-
atmosphere, as the Earth’s key ingredients, played
deed react, in a big way. In fact, their experi-
a cooperative role in the formation of life. This
ment resulted in so many different chemicals (tens
section will outline several theories of monomer
of thousands) that it was impossible to analyze
(and some possible polymer) production that re-
in full; a hopelessly diverse mixture referred to as
volve around minerals, rocks, clays and crystals. As
“humpane”. What they found was that many al-
we will see, minerals have a number of important
cohols, sugars, and various larger molecules that
properties that allow them to function as catalysts,
resemble those found in biochemistry were synthe-
sources of energy, sources of protection, and as scaf-
sized (showing both ring and branching structures),
folding for the construction of larger molecules that
and that polymerization had occurred in a variety
are not stable enough to form spontaneously.
of molecules, some of which incorporated dozens of
carbon atoms. However, this abundance also posed
Hydrothermal vents revisited the question of where to go next; with such a large
Hydrothermal vents remain one of the prime candi- variety of ways, it is almost impossible to predict
dates for the place of the origins of life, and we will which roads are the most promising. There are
encounter it several more times, most notably in a few potential problems with these experiments,
Günter Wächtershäuser’s metabolism-based iron- which can be summarized as follows. First of all,

15
the concentration of pyruvate used was unrealisti- even more surprising is their discovery that this
cally high, and the end products too diluted for also lead to the rapid link chains of amino acid
continuous chemical interactions. So, for this the- formation. This contradicts the common knowl-
ory to work, a way must be found by which both edge that these chains are destroyed by high tem-
the reactants and the end products can accumu- peratures (another example of emergence). Under
late (and stay accumulated) closely together. Sec- these conditions, peptide chains are much less solu-
ond, similar to Miller’s predicament, the reactions ble and therefore more stable. If these form rapidly
resulted in a large number of products, many of near vents and then float out in clumps, into the
which play little or no role in life. The problem is cooler sea water, they separate out as a much more
then how we can explain how particular products stable second-phase product. This is quite signif-
may have been selected, and others excluded in the icant, because it gives a partial possible solution
formation of life. Third, many organic molecules to the macro-molecule construction problem. Car-
were still missing, and so other ways would have to bon fixation reactions, in which more carbon atoms
be found to account for these. are incorporated into an organic molecule to form
But several more experiments have since been larger molecules, is common and happens rapidly in
conducted. One of these experiments, by Jay Bran- hydrothermal experiments. Two of the most com-
des, featured a mixture of water, nitrogen, and iron mon pathways can be described as follows. The
rich minerals (commonly found near vents), result- first is promoted by many common minerals that
ing in ammonia (N H3 ; recall that miller assumed incorporate iron, zinc and/or copper. These min-
this to be present in the atmosphere; an assump- erals promote the so-called Fisher-Troph synthe-
tion that later turned out to be false). Ammonia sis, which is a carbon fixation reaction which re-
is an essential ingredient for amino acids. This sults in chain-like molecules. These results have
result suggests that hydrothermal vents may be been confirmed by studies at real current-day hy-
principle sources of ammonia. A follow up exper- drothermal vents, and the resulting products are
iment combined ammonia, pyruvate, and several similar to those found in petroleum. The second
common powdered minerals, resulting in (among pathway is driven by cobalt and nickel sulfurs, and
other things) large quantities of the amino acid promotes a so called CO-insertion reaction, a car-
alanine. This directly contradicts Miller’s criti- bon fixation reaction in which carbon monoxide is
cism that vent-type conditions would destroy com- inserted. If one repeats these reactions and mixes
pounds like amino acids. Additionally, Brandes re- the results, many complicated molecules can easily
vealed in a later study (on the amino acid lucene) be synthesized reliably. Finally, minerals often dis-
that at least some (and possibly all) amino acids solve at high temperatures and pressures, resulting
are much more stable in the presence of the min- in chemical reactants that can act as both cata-
eral pyritite (iron sulfur), which is often found near lysts and reactants. For instance, sulfur, can dis-
vents. As we will see, the minerals used in these solve and react with water and CO2 to give rise to
experiments are likely to be very important in un- thiols and thiolesters, which are catalysts for addi-
derstanding the origins of life. Similarly, studies tional biochemical pathways (we will discuss these
on bone fossils have revealed that certain miner- later in the thioester world hypothesis). Similarly,
als can prevent (to some extent) the rapid break- iron, water and CO2 can form so-called iron com-
down of protein structures, because of strong bond- plexes, structures which can act both as catalysts
ing between the minerals and the proteins. This and reactants (see the iron-sulfur world).
protects and preserves them, and this can work
for amino acids as well. The possible “soft tis-
sue” recently discovered in fossil T-Rex bones by
Mary H. Schweitzer may have been preserved in Hydrothermal vents run across tens of thousands
this way. In a later experiment, Kono Lemke and of miles across the ocean floors, comprising bil-
David Ross showed that, when glycine and water lions of square miles. Given the (minimum) win-
were cooked under vent-like conditions (without the dow for life’s emergence of approximately 150 mil-
addition of minerals), glycine declined much more lion years, organic compounds could be produced
slowly than under normal conditions. What was in vast quantities.

16
Günter Wächtershäuser’s hypothesis energy. This process can be mimicked by organic
Günter Wächtershäuser (a close friend of Karl Pop- compounds accumulating on unstable mineral sur-
per) has suggested a hypothesis on the origins of faces. These surfaces release energy when they in-
life, using the catalytic properties of various miner- teract with other compounds, and thereby provide
als, such as iron (Fe), nickel (Ni) and sulfur (S). a stable source of energy which is much like the
These minerals are all found in abundance near kind used by cells today. In fact, many of the key
hydrothermal vents. As we have seen, minerals proteins which catalyze modern metabolism have,
may form an energy rich surface that can catalyze at their core, a cluster of Fe or Ni atoms. Finally,
many reactions for the synthesis and assembly of Wächtershäuser argues for a metabolism-first point
monomers (and, as we will see, polymers) that may of view. In this view, the elements of life arose not
otherwise be infeasible. Wächtershäuser’s hypoth- in the form of self-reproducing genetic material, but
esis is unusually detailed, and has been designed as a self-replicating metabolic cycle of chemical re-
to be rigorously testable and falsifiable. He has actions. In other words, an early atmosphere, con-
produced more than a hundred pages of specific sisting of mainly H2 (hydrogen) and CO2 (carbon
chemical reactions that could lead to the first cycli- dioxide), under the influence of energy released by
cal metabolic system. The core of the hypothesis minerals, ultimately lead to the chemical elements
is that metabolism can proceed without catalysts that drive life. In his view, life was both inevitable,
such as proteins, which are essential to metabolism and would have arisen rapidly on the early Earth.
in modern life, when the necessary organic compo- We will return to Wächtershäuser’s model when ex-
nents are in the presence of certain minerals (such amining the origins of self-replication. His model
as Fe, Ni, and S). He makes a number of core as- has been duped “the iron-sulfur world”.
sumptions based on his observations. First, it is as-
sumed that basic random pre-biotic synthesis as in
Crystals
the Miller experiment did not play an essential role.
Gustav Arrhenius has been one of the first peo-
Wächtershäuser bases this assumption on a number
ple to suggest that certain crystal minerals may
of observations. First of all, the organic soup that
have played a major role in the synthesis of organic
would result from the Urey-Miller process would be
components. He was primarily interested in the
far too dilute for the most interesting processes to
common double-layer hydroxides, which may con-
take place. Second, the Urey Miller experiment
tain many different elements, such as Fe, Mg (mag-
catalyzed a large number of “molecular species”
nesium), Cr (chromium), Ca (calcium), Al (alu-
(group of molecules with similar properties) that
minum), Ni, etc., in many compositions, but always
could have played no conceivable role in life’s ori-
in a two layer structure with a space in between lay-
gins. In this view, the Urey-Miller experiment is
ers (see figure 16). These spaces can be occupied
largely irrelevant to the origins of life. Second, it
by small molecules like CO2 and H2 O. The organic
is proposed that life is not heterotrophic (that is,
molecules become concentrated between the layers,
gathering molecules from the environment as food),
and it has been shown that they have a tendency
but rather autotrophic (making its own molecules).
to form larger molecules that may not otherwise
Since the organic soup was probably much too di-
emerge from a primordial soup. By changing the
luted, he argues, it was an unreliable food source,
composition of these crystal structures, they can be
and so life must have been capable of producing its
fine-tuned to perform various specific tasks. For in-
own necessary building blocks. Third, it is assumed
stance, Arrhenius et al. managed to spontaneously
that energy did not come from UV radiation from
synthesize sugar phosphates, which both form the
the sun, or electricity, but rather from chemical in-
backbones of RNA and DNA, and are a key ingre-
teractions. It is argued that photosynthesis, which
dient for ATP, one of the most important molecules
is the modern process by which plants capture the
used in cell metabolism.
energy from sunlight, is far too complex to have
been a prime source of food. Additionally, UV radi-
ation and electricity are far too disruptive for most Zeolites
interesting chemicals to be stable. Finally, most life Joseph Smith proposes that a diverse class of min-
today uses chemical energy as a primary source of erals called Zeolites may have played an important

17
 Figure 17: Zeolite lattice structure (image from
http://www.healthclinic.net.au/).

role in the origins of biochemical elements. Zeo-

lites have a lattice-like framework of small pores
made up of silicon (Si), aluminum, and oxygen
atoms (a typical structure is shown in figure 17).
These canals are just the right size for a vari-
ety of simple organic molecules such as H2 O or
CO2 to enter, while larger molecules are excluded.
These molecules can then react inside the pores,
and form larger organic components. Furthermore,
Figure 16: Double layer structure of 2,4-D in [Li- under the influence of specific minerals, the larger
Al-Cl] LDH, with small biomolecules in between molecules that land on the zeolite surface can be
(image from http://www.rsc.org/). split into smaller equal size fragments (a trick com-
monly used in petroleum refinement), which can
then be used in the construction of new, larger
molecules. Zeolites are common in volcanic envi-
ronments. Smith suggests that the canals inside
these minerals may even have functioned as the
first cell walls. So far, however, no experiments
have been conducted to confirm this hypothesis.

Molten rock
Friedmann Freund et al. proposed that molten ig-
neous rock may serve as yet another prime source

18
of organic components. Molten rock is over 1000C, Russian researchers) that the Earth’s mantle may
and it inevitably contains mineral impurities, con- be a primary source for biocarbons, which form
taining, for example, traces of H2 0, N and CO2 . one of the most important groups of biomolecules.
As the rocks cool, different minerals will begin to These biocarbons, he claimed, could be the primary
crystalize in sequence at different temperatures. As source of the Earth’s petroleum deposits. He based
they cool, the impurities in the minerals tend to ac- this view mainly on the presence of helium (He)
cumulate on the outside of the crystal lattice, con- in petroleum. Helium is a very light gas which
centrated at defects in the crystal structure. These could not have come from the Earth’s atmosphere,
defects form elongated latices that allow the now and so the source of petroleum, Gold argued, must
condensed compounds to bond with each other in have come from a subterranean source, rather than
a similarly elongated, chain like structure. Such having come from surface microbes that had been
a chain like structure is frequently seen in organic buried and decomposed. The mixture of helium,
compounds, where different, smaller molecules are minerals and hydrocarbons would permeate up-
connected by a carbon backbone. The compounds ward as it is lighter than the surrounding rock,
are, of course, locked inside the surrounding rock, and the hydrocarbons within it would then be pro-
but Freund suggests that erosion eventually re- cessed by ancient subterranean microbial lifeforms.
leases these elements. In principle, every mineral This then produces the biofilm that we observe in
has the potential to drive a similar process, and petroleum that lead us to conclude that petroleum
given the enormous amounts of rock on Earth, sim- is organic in origin. Under Gold’s controversial hy-
ilarly enormous amounts of organic components pothesis, these hydrocarbons constitute a better,
could be released. This mechanism could rival the continually replenished food source than the pri-
Urey-Miller process in productivity (for instance, mordial soup, or a puddle of condensed organic
100
natural perito was found to contain 1000000 parts materials, which are, at least in principle, much
carbon, much of which was part of a carbon back- more easily exhaustible, and could therefore lead
bone). One problem with the hypothesis is that to extinction. Similar to the deep ocean vent hy-
the destructiveness of these high temperatures may potheses, the basic monomeric compounds would
still be a significant problem for the formation of be formed under the intense pressure and heat
polymer chains. Furthermore, although observa- found in the Earth’s deep crust, and Gold proposes
tions suggest that many crystallized molten rock that this was where the first proto-life may have
does indeed contain many organic molecules, it is formed. This explanation is lacking in detail, but
difficult to test, since contamination is a very likely many of the details can be borrowed from alter-
problem to occur. Almost every rock face on Earth native hypotheses, such as the hydrothermal vents
is covered in microbial life, or at least in the remains hypotheses and the various roles played by mineral
of it, and is therefore contaminated with organic surfaces as described above. It is also consistent
molecules. with the observation that hydrothermal vent en-
From this we can conclude that rocks and min- vironments may promote reactions that result in
erals are likely to play a key role in life’s origins. products commonly found in petroleum, and that
They act as catalysts for certain chemical reactions monomers may have been present in abundance
that would otherwise be unlikely to occur, they pro- during the formation of the solar system, which
vide energy to power the process, and as we will will be described below. Future discovery of mi-
see, they can provide templates for the formation crobial life below the surface of another planet in
of polymer chains. our solar system would also significantly increase
the credibility of this theory.
3.2.4 Monomers from the Deep Hot Bio-
sphere 3.2.5 Monomers from Space
One of the most surprising sources of monomers
It has been suggested by Thomas Gold that life (and possibly even some polymers) comes from
may have first arisen deep within the Earth’s core. space. It has been known for some time now that
Gold had previously suggested (and before him space, particularly the huge nebulae which are the

19
birth places of star systems, contain large amounts important building block for organic molecules like
of carbon (C), hydrogen (H), nitrogen (N) and oxy- phospholipids. Additionally, radioactive actinides
gen (O). There is also evidence from spectral anal- could have driven the formation of organo-metalic
ysis in radio astronomy that these giant clouds complexes, which could have played an important
of space dust contain large quantities of organic role as catalysts for early life. Adam’s hypothe-
molecules. Over 140 different organic components sis is confirmed by computer models from the field
have been identified in these clouds, some consist- of astrobiology, which show that these radioactive
ing of chains of at least 12 carbon atoms (and var- materials could show the necessary self-sustaining
ious other elements). This may be somewhat sur- nuclear reaction. Under this model, amino acids,
prising, since outer space is bone-chillingly cold. sugars and phosphates can all be simultaneously
The explanation for this process is that, as frozen produced.
mineral dust particles that are covered in ice travel
through these clouds, they tend to pick up atoms 3.2.7 Chirality
and molecules. These hitchhikers are then sub-
jected to UV radiation, which makes them more The first person to offer an explanation of life’s
reactive, and they then react with other atoms or chirality was Louis Pasteur. Pasteur noticed that
molecules on the particle surface to form increas- polarized light can be created by passing normal
ingly larger molecular structures. Complex dia- light through certain crystals. This means that
grams have been constructed that depict the effi- such crystals filter out light with different polari-
ciency at which particles would pick up molecules, ties, while allowing light with another polarity to
which show that there will be a gradual buildup of pass through the structure unaffected. Potentially,
increasingly larger molecules. As mentioned, neb- this can cause the selective breakdown of D-amino
ulae are the places in which star and planet forma- acids or L-sugars. In deep space, rapidly rotating
tion takes place. Stars and planets essentially form stars can also emit polarized light. Another par-
out of the gas in these nebula. During the for- tial explanation from physics comes from the weak
mation of the so-called proto-planetary disc, which nuclear force. Most forces in nature are symmet-
eventually condenses to form the various planetary ric, but the weak nuclear force is asymetric. Beta-
and asteroid bodies in a star system, there would be decay (the emission of electrons) is driven by the
a steady influx of organic particles. As a result, the weak nuclear force, and the end product of this de-
amount of organic molecules in that disc is more cay is polarized. This too may select for molecules
condensed than in the surrounding nebula. This of a particular handedness. The problem with this
condensation increases the rate of synthesis even explanation, though, is that the bias is less than
more, resulting in even more complex biomolecular 1%, and so the effect is likely to be trivial. Sim-
structures, and so organic compounds are thought ilarly, favored chirals may be slightly more stable
to be a significant component of planet formation. than their mirror image, but this effect is likewise
very minute. There is frequently a preference for
bonds between two molecules of the same chiral-
3.2.6 The radioactive beach ity over those of differing chirality, because they
A final source of monomers that I will discuss tend to fit better together. This also happened in
here is the radioactive beach hypothesis, coinded Pasteur’s experiments. So, each molecule might be
by Zachary Adam. Adam claims that the close seen as a micro-environment that selects for others
proximity of the moon to the early Earth could of the same chirality. In this case, it is possible
have concentrated grains of heavier radioactive el- that polymers have to maintain chiral purity in or-
ements, such as uranium, at the high tidal mark der to form. However, synthesis experiments seem
on beaches. According to this hypothesis, these ra- to contradict this.
dioactive materials may have provided the energy
source necessary to have driven the formation of or- Chiral selection on crystals
ganic molecules, from acetonitrile in the water. In The solution may come in the form of certain com-
addition, radioactive monazite can release soluble mon chiral mineral surfaces (such as in quartz),
phosphate into the beach sand. Phosphate is an which do show a strong preference for similar chiral-

20
ity. The crystals on which biomolecules form may surfaces.
themselves form to be chiral, purely by chance (the Looking slightly ahead, this gives a plausible sce-
formation of a seed crystal is called nucleation). nario for the formation of chiral polymers; as chiral
Local chiral environments like this are found ev- monomers line up on chiral surfaces, they undergo
erywhere on Earth. Most minerals are not chiral polymerization, resulting in homochiral polymers
(though many of the more common minerals are), (in this case, proteins). This also has significant
but even non-chiral crystals often feature patterns commercial applications, for instance, in medicine.
of chiral surface structures. Every grain of sand Recent work (in 2003) has pointed to the amino
could potentially provide a chiral surface. Again, acid serine as being a possible instigator of ho-
the chirality of mineral surfaces tends to be 50/50 mochirality in amino acids. Serine forms very
between the enantiomeres, so we have to look not strong bonds with other amino acids of the same
at the global scale, but at the local scale. Molecules chirality, resulting in an eight-molecule homochiral
that are synthesized (seeded) on such local chi- cluster. Other amino acids can form weak bonds
ral template surfaces will themselves turn out to with amino acids of the opposite chirality. It is not
be chiral. Once a simple self-replicating system clear how left handed serine in particular became
has been established on one of these crystal sur- dominant, but the results do suggest a way for ho-
faces or subsurfaces (in ways we will discuss later), mochirality to be maintained, once formed.
rapid growth can ensue in which all other molecules
are consumed as food, and the chirality of the
molecules in the self-replicating system will quickly 3.2.8 Conclusions on monomers
come to dominate the local environment. There
may then at some point have been multiple differ- As we have seen, there is an abundance of potential
ent competing chiral systems, one of which came to sources of monomers, which constitute the build-
dominate over the course of time by natural selec- ing blocks of life. No single source may have been
tion in competition for resources. dominant, but it is safe to say that monomers were
The process of looking for an environment that easily manufactured and present in abundance on
is able to separate different molecules of differing the early Earth. But this is only the first step. The
chiralities is referred to as “resolving a racemate”. main problem at this point is how and why certain
Hazen et al. carried out such an experiment on specific monomers are selected, organized and as-
chiral selection using a racemic (=50/50) mixture sembled, rather than how monomers can come into
of a specific amino acid (called aspartic acid). In existence. This will be the topic of the next section.
their experiment, they used the common mineral
calcite (CaCO3 ), which is also found in seashells.
Calcite has the desirable property that, aside from 3.3 The generation of polymers from
having different faces with corresponding differing monomers and the origins of self-
chirality, it also has cleavage faces (along which replication
the crystal breaks more easily), which have no pre-
ferred chirality. These cleavage faces should exhibit The next question to tackle is the leap that needs to
no selection preference, and thus serve as a base- be made from relatively simple monomers to poly-
line. A baseline is important here, because of the mers. In this section we will address research on
inevitability of contamination. By comparing the the question how things like the genetic code, the
ratio between differing chiral biomolecules on each cell membrane, proteins, and even systems of inter-
chiral crystal face to this baseline, excesses can be acting biomolecules that form metabolic cycles may
measured that should be independent of the con- have arisen. I will start with the formation of some
tamination that was not washed away during ster- general theories for the origins of polymers, then
ilization. Using a double blind test, they found a move to cell membranes, and then move on to pro-
difference of a few percent, with increased L-chiral teins, and subsequently to the origins of metabolic
domination of amino acids on the L-chiral crystal cycles and the genetic code. But first, I’ll men-
surfaces, R-chiral preference shown for the R-chiral tion some more general characteristics of macro-
surfaces, and no preference at all for the non-chiral molecules and problems that need to be solved.

21
3.3.1 The construction of macromolecules coming together purely by chance is simply too re-
mote. The only logical answer to this is that life
To start with, the main problem that we need to must have concentrated on some kind of surface,
address is how macromolecules are assembled. As as is a typical solution for many chemistry issues
we’ve seen, polymerization can be difficult under a where diluteness is a problem. This could be the
variety of circumstances, particularly when in the surface of a crystal or a mineral, for instance, in
presence of water or too high an influx of energy. a tidal pool where cycles of evaporation and flood-
As we will see, emergent behavior in these often ing can continually replenish and concentrate the
complex systems can give rise to unexpected re- chemicals in question, at the ocean floor (near hy-
sults. Second, we need to address the question of drothermal vents), on a particle in space, or per-
why these molecules are selected as a subset of the haps at the boundary between the ocean surface
possible polymers that could exist. At some point, and the air. In essence, any contact point between
there may have been many macromolecular vari- two distinct materials could do the trick. Finally, it
eties that currently play no role whatsoever in any may be possible for carbon to assemble its own pri-
living system. We have seen some hints of possible vate surface from the environment, which can then
explanations, for example, when discussing zeolite also be used as a template. We will see this later
crystals and chirality. It is worth investigating why on when we discuss the PAH world and RNA, for
life today uses only a handful of building blocks, example.
resulting in only a handful of basic types of chemi-
cal reactions, almost all of which are carbon-based.
Impact macromolecules
Another feature of polymers that is worth noting
One of the more exotic possible origins of macro-
in this context is their modularity. Most poly-
molecules comes from research on comet, aster-
mers (or systems thereof) are members of a small
oid and meteor impacts. At first glance, it would
number of major families (proteins or nucleic acids,
seem likely that an impact of this sort would break
and lipid cell membranes). All of these are mod-
up any complex macromolecules that could have
ular in design; they can be broken up into smaller
formed. This seemingly sensible assumption was
molecules that are by themselves monomers, like
tested by Jennifer Blank, who conducted several
amino acids (in proteins), sugars (which are com-
high velocity impact experiments. Blank shot
posed of ring structures or chains with a carbon
stainless steel capsules containing various organic
to hydrogen to oxygen ratio of 1:2:1, and are typi-
components (five different amino acids and wa-
cally locked up in polymers of millions of molecules
ter) through various rocks and minerals at approx-
like cellulose or starch), lipids (fats and oils used
imately 4000 miles per hour. This creates approxi-
in membranes, or energy storage and for various
mately 200000 atmospheres of pressure and creates
other tasks) an nucleotides (in DNA and RNA). A
temperatures up to 1000C (note the irony in her
possible explanation for this modularity is that it
last name). Blank discovered that pairs of amino
is simply more economical to do so. By using the
acids form peptide bonds in every single run at the
same building blocks for many tasks, components
expense of some other, smaller molecules (which
can be re-used and recycled, and synthesis of one
evaporated). In other words, although the number
type of building block can underlay many different
of organic components is reduced, their diversity
processes. In the same way that the cost of building
increases as the result of such impacts.
a house with individually designed bricks would be
immensely high, so too could the use of many differ-
ent complex types of reactions and building blocks Polyphosphates
be costly for life. In other words, life that makes us Another mechanism that may have driven polymer-
of such economic modular design may simply have ization may be found in the properties of polyphos-
outcompeted other possible early life by means of phates, which are formed by polymerization of
being more efficient. A general observation that we monophosphate ions (PO4-3). Several mechanisms
made in the last section is that the early oceans are have been suggested that could drive this polymer-
thought to have been simply too dilute. This im- ization process. Polyphosphates can cause poly-
plies that the probability of just the right molecules merization of amino acids into peptides, and are

22
key precursors in the synthesis of compounds like come more strongly bound to their scaffolding. In
ATP, which we discussed earlier. One problem with other words, it is not immediately clear how they
this theory is that calcium reacts with soluble phos- can become “unstuck” from the clays they reside
phates to form the insoluble apatite. This means on. A solution to this problem is to incorporate
that we are required to find a plausible mechanism tiny bits of clay within the first cell membranes as
to keep calcium ions away from the phosphates. As they form. We will read about cell membrane for-
we will see later on, lipid vesicles may be one such mation below. Jack Szostak tested this hypotheti-
mechanism. One interesting idea about the origins cal possibility by mixing together finely powdered
of phosphorus is that it nay have been introduced clays, RNA nucleotides (which were made hyperre-
on Earth by meteorites. active by addition of a catalytic molecular group),
and lipids. He found that the clay absorbs the nu-
3.3.2 The clay world cleotides, and is enclosed by forming vesicles. The
result are protobionts containing the catalytic clay
Although some of the polymers may have formed with small RNA strands.
as the result of impact events, there are other, less
disruptive ways in which they can spontaneously
assemble. In particular, mineral surfaces may have The Clay life hypothesis
played a major role, acting as catalysts, attrac- The clay hypothesis was taken a giant step fur-
tors and scaffolds in the construction of complex ther by Graham Cairns-Smith, who proposed the
molecules. We saw examples of this for monomer so-called “clay life theory”. This is where things
formation earlier. Here I will explore how a sim- turn a little odd. He suggested that fine grained
ilar principle can apply to polymerization. One (silicate) clay crystals may have been the first self-
such hypotheses, which places particular empha- replicating systems, not by virtue of RNA, but all
sis on the scaffolding principle, stems from the use by themselves. In this theory, there is no initial role
of clays. Clays are nutrient rich, and they have for biomolecules, and the first lifeforms were not
a very regular, layered atomic structure, made up carbon-based. Evolution, then, started indepen-
of two types of layers (one tetrahedral, which can dent of organic molecules. Cairns-Smith’s reason
incorporate minerals such as Si and O, and one behind this hypothesis is dependent on several ob-
octahedral, which can incorporate, among others, servations. Incidentally, Richard Dawkins supports
Mg, Al, or Fe. These layers are stacked in different this controversial view. Cairns-Smith is particu-
vertical sequences of two (tetrahedral/octahedral) larly interested in the properties of kaolinite crys-
or three (tetrahedral/octahedral/tetrahedral) lay- tals, illustrated in figure 18. First of all, it seems
ers, with spaces in between. Billions of such layers nearly impossible to build macromolecules without
may be stacked on top of one another in alternat- minerals. Clays functioned as essential scaffold-
ing ways, and clays are found everywhere on Earth, ing on which the complex molecules can be built,
resulting in an enormous overall surface area. The much like the scaffolds that hold up an arc before
layers are quite strong, but the space between them the top stone is placed. This scaffolding was later
are quite weak, which is basically what makes clay lost when it became expendable, as more efficient
slippery. Foreign molecules may accumulate be- replication systems like RNA and DNA took hold.
tween these layers and react to form increasingly Recall that we can see possible remnants of the im-
larger molecules. What is more, clays are often portance that minerals might have played in the
electrically charged, which allows them to attract, current-day role of clumps of minerals in enzymes.
and bond with, such molecules. These clays may Second, clay crystal layers have a varying internal
also catalyze reactions. Daily and seasonal cycles of structure that distantly resembles that of an infor-
heating and cooling may drive this process. As we mation carrying structure, much like, for instance,
will see later, clays may form scaffolds for RNA and RNA. Specifically, there are three possibilities for
proteins, and has even proposed to have been the the “alphabet” of clay minerals (much like the four
first form of self-replicating system (the so-called letter alphabets of RNA and DNA). First of all,
clay life hypothesis). One problem for the clay the- the composition and orientation of the layers plays
ory is that, as polymers become longer, they be- a key role. Recall that layers of clay can alternate

23
in (two or three) layered structures with spaces in
between. Two layer and three layer structures may
alternate. Each layer also has a specific orientation
which can fall along one of three equally distant
angles. Secondly, there may be variation within
layers, called twinning, in which a single layer con-
tains mixed surface patches in all three orienta-
tions. Third, clays can have a quite complicated
chemical composition. Although the crystal struc-
ture itself is very regular, the incorporated minerals
(e.g.: Fe, Mg, Al) may differ in sequence. Subse-
quent sediment can build new layers on top of the
old ones that have the same orientation, chemical
composition and surface defects. Thus, one can
say that a layer of clay can grow in this way. When
layers flakes off, and is redeposited elsewhere by
wind or water currents, this process may repeat
itself, establishing new clay “colonies”. As Cairns-
Smith points out, this looks a lot like a primitive
form of reproduction. Additionally, the more sta-
ble configurations will tend to win out over time,
Figure 18: Kaolinite crystal growth (image from
which leads us to conclude that clays can evolve.
http://originoflife.net/).
This theory makes a number of predictions. First
of all, the crystal structures must be reproduced ac-
curately enough for the term reproduction to have crystals did not achieve the copying accuracy nec-
any meaning. Furthermore, they must be able to essary for faithful transfer of information to the
compete for resources as they grow, and dissolve next generation. Of course, we do not know at
others in the process. More stable, rapidly repro- this point whether this is true for all types of clays
ducing (as the result of an abundance of certain and crystals. Should this particularly odd hypoth-
types of chemical resources) patterns should be fa- esis still turn out to be correct, then the question
vored over unstable ones or ones with lower repro- remains how we finally arrived at modern, carbon-
ductive rates, and eventually come to dominate. In based life. At some point, clays must have passed
principle, at least, these predictions are testable, on their structure to organic materials, by the pro-
but it is not known how we can synthesize clays cess we described earlier, in which the clay works
or sequence their structure as we do with DNA. as a template. The resulting RNA, DNA or protein
Furthermore, much about clays remains unknown. structure would have similar genetic information as
We don’t know how they work at the atomic scale, the clay that was their “launch stage”. Of course,
we have a limited amount of knowledge about their there is no guarantee that information is still usable
surface properties, their structure is complex and after this change in medium from clay to nucleic
very variable, and very fine grained, which makes acid.
it hard to determine which bindings occur. The hy-
pothesis that crystals can act as reproducing sys-
3.3.3 The origins of cell membranes
tems with transferable information was tested in
2007, by Kahr et al., using potassium hydrogen ph- Before we start, it is handy to give a bit of terminol-
thalate crystals. The crystals were examined for ogy at this point. The formation of cell membranes
imperfections, and then cleaved and used as seeds deals with so-called vesicles. Vesicles, or liposomes
to grow new crystals. The imperfections were in- (see figure 20), are small “sacks” containing various
deed reproduced by the clay “offspring”, but with substances surrounded by a lipid bilayer (=double
many additional imperfections. Because of these fat-based) membrane. Similar, but single layered
additional imperfections, Kahr concluded that the structures are called micelles. In modern cells, li-

24
 and transportation of specific molecules, but we
will not consider them at this point - it is as-
sumed that these regulatory structures appeared
much later in the evolution of life). Lipids are
not fond of water. They are hydrophobic, mean-
ing that they have a tendency to turn away from
water when possible. So, a way must be found to
make lipids compatible with cellular life. The an-
swer to this problem comes from the addition of a
phosphate group (a phosphate atom surrounded by
four hydrogen atoms). Phosphate molecules are hy-
drophillic, meaning that they like water, and tend
to face towards it when possible. A molecule that
has both a hydrophobic end and a hydrophillic end
is called an amphiphite. So, amphiphites have a
love/hate relationship with water. The molecule
that is the result of adding a phosphate group
Figure 19: Fatty acid and phospholipid molecules to a pair of hydrocarbon chains is called a phos-
(image from http://exploringorigins.org/). pholipid (see figure 19), and it is these types of
molecules that make up the membranes of modern
cells. When amphiphillic molecules are immersed
in water, they show a tendency to automatically ar-
posomes are used to transport of store various sub- range themselves to a state of lower energy. They
stances. When referring more generally to a col- line up end to end with the hydrophobic ends fac-
lection of abiotically synthesized compounds that ing each other, and the hydrophillic ends facing out
somehow self-organize, we may also refer to them toward the surrounding water. When multiple such
as protobionts. Protobionts are thought to have pairings of amphiphites find each other, they line
formed spontaneously as precursors to modern cells up side by side so that the inward facing hydropho-
(although a protobiont is by itself not considered bic ends are even more well-shielded from the wa-
alive). Coacervates (figure 21) are also protobionts; ter. When enough amphiphites are lined up in this
they are collections of macromolecules that assem- way they eventually tend to form a closed sphere,
ble spontaneously when shaken in water. Finally, which is the state of lowest energy. This sphere, in
protobionts may consist of molecules that represent the case of phospholipids, is called a lipid bilayer
proteins, so called proteinoids, in which case they (see figure 20), for obvious reasons. It was dis-
are referred to as microspheres. We will return to covered by Alec Bangham, who noticed that when
microspheres in the next section. lipids from egg-yoke were immersed in water, they
Recall that one of the most prolific problems spontaneously arrange themselves in this manner
faced in the construction of polymers is that they to form spherical vesicles. This lipid bilayer is used
tend to break down when immersed in water. But by all known cells. Figure 22 contrasts the lipid
here we have a paradox; almost all pre-biotic syn- bilayer with a single layered spheroid called a mi-
thesis processes eventually wind up in the ocean, celle. Subsequent pre-biotic soup experiments on
surrounded by water. And this makes sense, as vesicles (by Luigi Luisi, among others) reveal that
modern cells too contain and are most often sur- vesicles form quite easily. They show some inter-
rounded by water. At some point, then, life had to esting characteristics. Vesicles can grow by the in-
form a protective membrane to protect itself. The corporation of additional lipids. But perhaps more
cell membrane in today’s cells is comprised mainly surprising, they are auto catalytic. That is, vesicles
of two opposing layers of lipids (of course, that’s an trigger the formation of other vesicles. Moreover,
oversimplification; modern membranes are vastly under the right conditions (the right acidity levels,
more complex, with many complicated structures and the right concentration of lipids), vesicles can
in between that regulate cellular communication divide into two new vesicles, which can then grow

25
Figure 20: Liposomes and the lipid bilayer struc-
ture (image from http://porpax.bio.miami.edu/).

and divide again. This process looks surprisingly

similar to cell division in modern prokaryotes - al- Figure 21: Coacervates (image from
though it must be noted that it is obviously much http://www.daviddarling.info/).
simpler, and that vesicles are not typically consid-
ered alive by any standard. This leads us to the
so-called “lipid world” hypothesis.

The lipid world

The different large-scale scenarios for the forma-
tion of life on Earth are typically referred to as
“worlds”. The lipid world, then, hypothesize that
lipids played a central role in the formation of life on
Earth. This scenario goes as follows. Lipids are cre-
ated in abundance both on the Earth and in space.
They end up in the pre-biotic soup where they self
organize into vesicles. In the process, they capture
primitive molecules (and possibly mineral particles
like clays), which are typically thought of as infor-
mation baring molecules, such as RNA. If this RNA
is capable of self replication, they can undergo si-
multaneous replication, leading, eventually, to the
first forms of cellular life. This hypothesis was
untested as of 2005, but progress is being made in
this field to create the first synthetic life. One prob-
lem with lipid membranes is that the lipids are not
well represented in the Urey-Miller experiments. Figure 22: The difference between single lay-
A potential great source of lipids, however comes, ered micelles and bilayered vesicles (image from
again, from space. Deamer and Bangham were the http://exploringorigins.org/).
first to propose such “self-organizing space lipids”.
For vesicles to form, the lipids must have the right
size and shape. For instance, if the lipids are larger

26
than those found in current-day membranes, the
concentration of vesicles is generally lower. To test
the space lipid hypothesis, Deamer et al. examined
carbon rich meteorites, particularly a so-called car-
bonacious chondrite (see figure 23, a sample from
the Murchison meteorite) in 1989. This examina-
tion revealed many biomolecules (about 3.5% of
the total mass), including lipids. The experiment
was set up as follows. The meteorite was broken
down in a way to mimic weathering on the early
Earth. The rock was ground down in a mixture
of water, alcohol and chloroform, which was cho-
sen because it does not affect minerals, but does
dissolve a variety of biomolecules. Water and alco-
hol dissolve various amine acids and sugars, while
chloroform dissolves various lipids. The resulting
mixture was then centrifuged. This separates the
denser materials from those less dense such that the Figure 23: Carbonacious chondrites in
most massive particles sink to the bottom, while the Murchison meteorite (image from
the lighter elements remain at the top, resulting http://www.panspermia.org/).
in a mineral/chloroform/water layering. It was
found that the chloroform dissolved approximately
0.1% of the mass in the minerals, which indicates a pyruvate can eventually lead to the formation of
high concentration of lipids (which was confirmed lipids.
by chromatography). The solution of chloroform The lipid world comprises one of the best un-
was then re-concentrated and the resulting concen- derstood steps in the formation of life, but there
trate placed in water. Vesicles were found to form were still some problems with the initial hypoth-
readily. The test was repeated with multiple sam- esis. First of all, since modern cells use proteins
ples. These results were confirmed by simulations to bring in food and export waste out of the cell,
of space dust formation by Allamandera, who found it is not clear how these primitive cells, having no
in his results several so called PAHs (carbon ring proteins, would accomplish such a task. Second, bi-
structures which we will encounter again later when layer formation is impeded by magnesium and cal-
we discuss the origins of RNA, see figure 27), but cium atoms, which are inevitably found in ocean
also possible amphiphiles. When placed in water, water. Either the formation would have to take
these amphiphiles again formed vesicles. From this place in fresh water, or there would need to be an al-
it can again be concluded that it is quite likely that ternative pathway for the self organization of lipids.
our star system was likely to be rich in essential A possible solution to this second problem comes
materials for life formation even before the Earth from Christopher Dobson et al., who proposed (in
was formed. Additionally, the high pressure exper- 2000) that lipids can organize in the atmosphere as
iments on pyruvate conducted by Hazen et al. had ocean spray. Dobson noted that lipids can organize
also formed several potential lipid structures. Since in another way from the spherical vesicles. They
pyruvate is a core molecule used in metabolism, tend to accumulate on the surface, with the hy-
this naturally leads to the idea that the formation drophillic phosphate group facing towards the wa-
of metabolism and the formation of lipids may be ter, and the hydrophobic carbon chain tails facing
intimately connected. Specifically, pyruvate may towards the atmosphere. Waves can spray a mist
provide a primitive metabolic pathway for the for- of particles into the atmosphere. Each microscopic
mation of lipids. By immersing the oily residue drop of water may contain lipids that will then form
found during their experiment, it was found that a single-layered sphere (a micelle) with the phos-
vesicles did indeed form. This leads us to the con- phates facing the water, enveloping the drop and
clusion that a simple reaction between water and any substances in it. The small droplets are quite

27
stable, and can drift in the atmosphere’s currents larger molecules. The largest of these molecules (ei-
for some time, or even months or years, reaching ther a DNA, RNA or protein strand, or the largest
as high as the upper atmosphere where UV radia- molecule in a metabolic cycle) should be able to
tion is more intense, thereby promoting additional split in two, thereby replicating the cycle. This
chemical reactions inside the droplet. Together, allows for growth. Second, a plausible pre-biotic
these aerosol vesicles constitute a vast number of environment must be identified, which must sup-
micro experiments. When an airborne vesicle lands ply all the necessary raw materials and energy, in a
on the lipid covered surface, it will automatically reasonably stable flow. The molecules that are part
form the secondary layer of the membrane, result- of the cycle must be stable enough to survive in this
ing in a bilayer enclosure. In this way, trillions environment to partake in the next, duplicated cy-
of cell-like structures could have been present in cle, to keep it going. In general, chemical energy is
the early oceans, which could be viewed as precur- a preferred source over UV or electrical energy, be-
sors of populations of cells. If this process occurred cause it is much more stable. Finally, an unbroken
near a beach, where the tidal waves may have con- biochemical history must connect the Earth’s past
centrated organic molecules (much like driftwood), to its present. There must be a continuum along
this would increase the likelihood that the vesi- this path, and ancient “fossil” chemical pathways
cles would contain many organic compounds. Since should be consistent with the model. Working from
coastal waters are also generally warmer, evapo- these premises, we will now look at some of the
ration may have further concentrated the organic most important models currently in circulation.
soup. Vesicles composed mostly of water would
tend to burst easily, but the presence of proteins
or other amphiphyllic compounds (such as PAHs) Autocatalysts
can increase the stability of the structure. If such The basis of all the models of self-replicating sys-
compounds would increase the vesicle’s integrity, tems is that they (the systems as a whole) must
then that vesicle would have a competitive advan- be self-sustaining, that is, self-catalyzing. Self-
tage over others under natural selection. When a replication occurs when a molecule copies itself
vesicle would burst (one possible primordial ana- while consuming other, smaller molecules as food.
log of reproduction), it would release the generated The simplest such systems consist of one molecule,
compounds into the environment, further increas- while more complex ones consist of a network of
ing the availability of products that had accumu- interacting component molecules. If the system
lated within. Given time, this increases the chances only contains a single molecule, then that molecule
of the appearance of the first self-reproducing cel- must, by itself, be autocatalytic. It then acts as
lular life form. its own template to synthesize exact copies of it-
self. In order for such a single-step system to work,
3.3.4 Self replicating systems it must be self-complementary. That is, it must
be equal to its own template. For instance, DNA
We are now ready to look at some of the mod- is made up of complementary strands, but these
els of self replicating systems. We already saw strands are not necessarily self-complementary. Re-
that a basic form of self-replication occurs in sim- call that we mentioned earlier that, in order for
ple vesicles. However, although this is an interest- an RNA strand to be able to self replicate with-
ing result, most people would be hard-pressed to out any intermediate steps, it must be palindromic.
call the vesicles by themselves living organisms. In This combination of properties is rare, but not
the subsequent paragraphs, we will discuss several non-existent. Dawkins writes about Julius Rebek
propositions for the origins of self-replicating sys- Jr.’s findings, in which he and his colleagues com-
tems. Most of these theories are divided into two bined amino adenosine and pentafluorophenyl es-
camps; the metabolism-first view, and the genetics- ter with amino adenosine triacid ester (AATE),
first view. Although both approaches start out which is an autocatalyst. Rebek et al. managed
from a different viewpoint, they generally aim to to synthesize self-complementary, self-replicating
adhere to three basic rules. First of all, there is molecules consisting of adenine, naptaline, and im-
a cycle of progression from smaller to increasingly mite. The experiment demonstrated the possibility

28
that autocatalysts could compete within a popula- netic reproduction could take hold. By contrast,
tion of molecules in which hereditary information genetics first viewpoints maintain that life, to re-
was maintained from one generation to the next; a ally be classified as such, relies on an ability to pass
primitive form of natural selection. Unfortunately, information to offspring. Genetic material, they ar-
this molecule is an unlikely organic precursor. Ad- gue, is the most likely way to copy this complexity
ditionally, Reza Ghadiri has managed to synthesize from one generation to the next. And this view has
self-replicating peptides (amino acid chains that are a certain appeal for reasons of continuity; We know
generally smaller than proteins). In 1996, Ghadiri that this is the way current life does it. Metabolism
reported a peptide consisting of 32 amino acids that without genetics, the argument goes, is just a se-
managed to self-replicate. There was one small ries of chemical reactions without a direction or
catch: these peptides had to have two distinct spe- control. By contrast, metabolism-first proponents
cialized reactive fragments of 15 and 17 amino acids argue that life builds in small steps. Metabolic
respectively. chemistry is far simpler than genetic chemistry.
It requires only a relatively small number of rela-
Cross-catalysts and autocatalytic net- tively simple molecules for self-replicating behavior
works to emerge, as is seen in the reverse citric acid cy-
Autocatalysis in single component systems is quite cle, which is the basis of metabolism, as well as the
rare. There is only a small handful of molecules starting point for life’s biochemistry in all currently
that have these properties. Complementarity living cells. But of course, in order for a metabolism
to other molecules, by contrast, is much more first view to be taken seriously, these small build-
common. Autocatalytic molecules also typically ing steps must be specified and tested under real-
require a steady inflow of specialized chemicals. istic environmental circumstances. We will discuss
In addition, a self replicating system consisting genetics first views in a later section, but at this
of only one component is unlikely or unable to point it would be prudent to point out the para-
exhibit change from one generation to the next, doxical situation we seem to be facing; which came
and thereby evolution is inhibited. One solution first? Or, perhaps, did the two arise simultane-
to the first and last problems in particular can ously? Although a recent trend has been to explore
be found by means of cross-catalytic networks. this latter option, it is easier to imagine that these
Cross-catalysis is exhibited in a system of two (or mechanisms came about in separate events. One of
more) molecules that can catalyze the formation of the main problems for any autocatalytic metabolic
their counterparts. For instance, in a system where system is that there must be a way to avoid the
molecules AA and BB are present which are made many side reactions that may occur, which could
up of fragments A and B respectively, and where disrupt the cycle. A model by Fernando and Rowe
AA catalyzes the formation of BB from many suggests that the encapsulation of the cycle within
B’s, and BB catalyzes the formation of AA from vesicles may be one way of avoiding this problem. A
many A’s, this system as a whole can self-replicate second problem that needs to be addressed is how
by cross-catalysis. Similarly, more ellaborate metabolism may lead to the formation of nucleic
systems may exist. We will see examples of this in acids (RNA and DNA).
Kauffman’s hypothesis on metabolic networks, as
well as Eigen’s hypothesis of hypercycles in which
genetic material is thought to play a central role. Autocatalytic networks
Stuart Kauffman noted that autocatalytic networks
are the most likely form of proto-life. Such net-
3.3.5 The origins of metabolism
works could possibly be vast, and have the po-
I will now begin describing the metabolism-first tential to evolve by means of an increase in effi-
perspective. Metabolism-first views are based on ciency through the incorporation of more interact-
the observation that life inevitably requires a sta- ing agent molecules in the cycle. This generally
ble source of matter and energy to grow, survive, leads to a number of nested cycles in which vari-
and eventually reproduce. It is argued, then, that ability is nearly inevitable. According to Kauffman,
such a reliable source had to be available before ge- such a network would most likely come in the form

29
of metabolic cycles, without the need for a genetic
mechanism. Such a system would meet the mini-
mum requirements for life: reproduction, growth,
and evolvability. The problem with Kauffman’s ac-
counts is that they are purely hypothetical and very
sketchy. No specific cycle is given, although Kauff-
man does mention a number of requirements. First
of all, the system requires a reliable source of en-
ergy, preferentially in the form of chemical energy,
which is more stable than other sources. Second,
the system requires a reliable feedstock of organic
molecules, preferentially common and small ones,
like H2 O, CO2 and N H3 . Third, metabolism re-
quires that, unlike in the process of burning, energy
is harnessed for the building of new organic com-
ponent molecules, rather than dissipated.

Origins of Proteins
Proteins are the current day workhorses of cells,
and theories on proteins are therefore generally
grouped with metabolism-first views. There are
various hypotheses on the origins of proteins. Re-
turning briefly to the clay world, Leslie Orgel pro- Figure 24: A proteinoid microsphere (image from
posed that proteins may have first formed on clays. http://www.daviddarling.info/).
When amino acids accumulate on clays, they poly-
merize to form small protein-like structures as they
condense when water evaporates. These protein behavior. Furthermore, since proteins play a cen-
structures may be several dozen amino acids long. tral role in biology, this seems to form a viewpoint
Orgel also noted that different minerals select dif- consistent with biological continuity. However, Fox
ferent molecules from the solution to polymer- has been the subject of skepticism. He has been
ize. He called this process “polymerization on the known to make various far reaching claims, stat-
rocks”. ing that the proteinoids were alive, that they solve
the problems of life’s origins, and even that they
possess a rudimentary consciousness. This sug-
The proteinoid world
gests that Fox may have lost his objectivity while
Sydney Fox proposed what he called the proteinoid
studying these otherwise quite interesting struc-
world, in which proteins play a central role. Fox
tures. There is a more fundamental problem with
dried and baked amino acids on rock surfaces, us-
a protein-first point of view, and indeed, it would
ing environmental conditions plausible for volcanic
seem, with any metabolism first viewpoint. The
areas near tidal zones. These amino acids polymer-
inevitable question, of course, is, provided pro-
ized and formed protein-like structures which he
teinoids came before DNA and RNA, how could
called proteinoids. Fox observed that proteinoids
they “invent” genetic materials?
can sometimes act as catalysts. They also some-
times organize into microspheres (see figure 24),
with a bilayer structure. It should be noted that The thioester world
it is unlikely that these are the precursors to mod- Christian de Duve proposed a metabolic world
ern cell membranes, since modern membranes are called the thioester world. De Duve points out
composed of mostly lipids. The microspheres some- that, although his model is metabolism-first, he
times appear to grow and divide. Thus, this is a takes a neutral stance as to whether this means that
self-reproducing metabolic model, with interesting metabolism preceded genetics as the first life. Ac-

30
cording to his view, proto-metabolism came first, But Wächtershäuser argues that the true simplicity
but life only arose with the inclusion of genetics of his model lies in the reliance on small building
within a cell. De Duve works from a plausible pre- blocks that must have been present in the environ-
biotic volcanic environment, where there are many ment in large quantities, using only a handful of
mineralized and chemical components, specifically such building blocks, and a small number of distinct
thioesters such as Acetyl-CoA. Thioesters are so kinds of chemical reactions in the process. Such a
classified on the basis of a carbon-sulfur thioester system, he argues, does not need to rely on chance
bond, which holds energy. Thioesters are crucial in resources in any given environment, but rather it
metabolism today. They supply chemical energy, makes its own food. One of the interesting char-
and form bonds with amino acids which make them acteristics, then, is that under Wächtershäuser’s
more reactive, so that they can spontaneously as- model, there is little or no role for the pre-biotic
semble into short protein-like strands called mul- soup. The source of energy in the iron-sulfur world
timers (which are smaller than polymers). De model is chemical in origin; it comes from miner-
Duve hypothesized that thioesters played a cru- als that are out of chemical equilibrium with their
cial double role, both in providing a replacement given environment, specifically pyrrhotite, which is
for, and in the formation of ATP, which we men- a volcanic mineral with a one to one ratio of iron
tioned earlier as a crucial primordial factor in mod- and sulfur. This mineral is often found around hy-
ern metabolism. According to this hypothesis, an drothermal vents. It is unstable with respect to the
autocatalytic cycle may have emerged. De Duve’s surrounding sea water, and tends to transform into
hypothesis is well aligned with Miller’s results, and more stable minerals, in the process of which it re-
displays a clear continuity with modern biology. leases chemical energy. When pyrrhotite (FeS) re-
However, the details for this hypothesis are cur- acts with hydrogen sulfite (H2 S), it results in pyri-
rently lacking. No specific molecular interactions tite (F eS2 , which has instead a one to two ratio
are provided, and De Duve cannot give a concise of iron to sulfur), plus hydrogen (H2 ) and energy
answer as to which monomers triggered the synthe- release. But this is not the end of the reaction, be-
sis of an RNA like molecule, and how they did so. cause when H2 encounters CO2 , then, catalyzed by
The chemical reactions with thioesters that synthe- the energy released by the aforementioned reaction,
size the monomers remained unspecified as of 2005. this results in a formic acid molecule (HCOOH).
Note that here, the energy is not lost to the envi-
ronment, but is used to catalyze new reactions, and
The iron-sulfur world, bubbles and flat life this cascading of reactions is the point of the iron-
I have briefly mentioned Gunther Wächtershäuser’s sulfur model. The entire model is much to elabo-
model before. It is one of the most detailed rate to discuss here in detail, but the key point to
hypotheses in origins of life theories, and has take away from it is that the reactions proposed by
been designed specifically to be rigorously testable. Wächtershäuser form a self-consistent network. So
His model, which uses a metabolism-first ap- far, several steps in Wächtershäuser’s model have
proach, is referred to as the iron-sulfur world. been confirmed in the lab. The first step, which we
Wächtershäuser’s model assumes that life is au- described above, was confirmed by Wächtershäuser
totrophic. Chemical synthesis proceeds in small himself. Wolfgang Heinen and Annemarie Lauw-
steps, by adding a few atoms at a time, using up ers subsequently explored the model by immersing
small molecules such as H2 O and CO2 in the pro- FeS and H2 S in water with a CO2 atmosphere.
cess. Contrast this with the Urey-Miller approach, This produced a variety of interesting organic com-
in which life is heterotrophic, that is, in this view, pounds, such as acetate, amino acids, pyruvate, as
life “eats” other, larger molecules already present well as others. However, a cascade of reactions does
in the environment, rather than synthesizing them not necessarily lead to the duplication of materi-
from the ground up. This seems to be simpler; it als that is required for self-replication. For this, a
is easier to just eat the available materials than to closed metabolic cycle is required. Wächtershäuser
rebuild them yourself, and thus autotrophic cells is ultimately trying to accomplish this by synthesiz-
have to be more complex than heterotrophic ones ing the reverse citric acid cycle. This cycle, then, is
to allow for synthesis, or so the argument goes. at the heart of the iron-sulfur world model. Re-

31
call that the closely related (normal) citric acid this claim is not easy to test, as H2 S is very toxic,
cycle is the core metabolism of every living cell, and chemicals formed in the reactions may be even
and this thus fits well with biochemical continuity. more so. Hazen et al. have however performed ex-
During this cycle, larger organic molecules made of periments with citric acid in water under vent-type
carbon, hydrogen and oxygen are broken up into conditions (2000 atmospheres, 200C). They found
increasingly smaller fragments, while releasing en- indications that there may be not one, but rather
ergy. Recall also that the cycle can run in re- two distinct pathways of cyclic reactions. The first,
verse. In this case, increasingly larger molecules are which corresponds to the normal reverse citric acid
built at the cost of smaller ones (using energy or a cycle, is duped the alpha pathway. The alpha
catalyst). In current-day autotrophic life, this is pathway hits an unfortunate dead end, because ox-
how practically all essential biomolecules are built. aloacetate breaks down in water and can thus not
The aforementioned experiments have shown that be used in further reactions. However, there was
at least one of the key ingredients that drive the also indication of some second, unknown pathway,
cycle (pyruvate) can be spontaneously synthesized called the beta-pathway, that is similar to the citric
under Wächtershäuser’s model. However, in mod- acid cycle, rather than the reverse citric acid cycle.
ern cells, the reverse acid cycle depends heavily on It is speculated that this poorly understood beta
the use of complex enzymes to catalyze reactions pathway may once have been part of a now-extinct
that would otherwise not occur. And, perhaps as primordial metabolic cycle. Although it is still not
a consequence of this, no one has (as of 2005) re- well understood, it appears that at least some parts
produced the crucial step in the reverse citric acid of the beta pathway can be reversed under the in-
cycle from pyruvate to (stable) oxaloacetate (be- fluence of NiS, which would have been present at
cause oxaloacetate always breaks down in water). vents, thereby establishing an alternative reverse
So the question is then how this cycle got going cycle. Finally, one should note that the experi-
without the use of such catalysts. Wächtershäuser ments thus far were conducted using water, rather
proposes that iron sulfites can promote reactions in than hydrogen sulfite, as Wächtershäuser proposed.
much the same way that modern enzymes do. He It is important to note that the iron-sulfur world
draws on the observation that many modern en- remains experimentally unsupported. Orgel, who
zymes have iron, nickel or sulfur groups at their we will encounter in the next section, believes that
core that look exactly like small bits of sulfite there is reason to suspect that this may remain
minerals. Such non-enzymatic reactions would be so. An experiment performed by Wächtershäuser
less efficient than modern cell metabolism that re- and Huber in 1998, yielded only a relatively small
lies on catalytic proteins, but since there was no percentage (0.412.4%) of dipeptides, and an even
competition at the time, even such a less efficient smaller amount (0.003%) of tripeptides. Under the
system could have flourished and dominated over circumstances of the experiment, hydrolysis of the
other reactions by their self-replicating character- dipeptides occurred rapidly, and the criticism has
istic. Wächtershäuser notes that in many chemi- been made that the experimental setup was lack-
cal reactions, among which many of those found in ing in organic molecules that could cause cross re-
the citric acid cycle, H2 O can be substitutes for actions and break the chain.
by H2 S. H2 S is more reactive than water, and so Using the iron sulfur model, three different sce-
reactions using H2 S may be more efficient. The for- narios have been proposed for the origins of life.
mation of pyrittite near hydrothermal vents gives The first and simplest is that lipid vesicles en-
a clear indication that H2 S can be found here. As veloped the first self-replicating metabolic cycle.
there would be less H2 S available, once the sul- The second scenario, proposed by Russell and Hall,
fite version of the cycle was established, it would is that iron-sulfite bubbles may have acted as the
only be a matter of time before the H2 O variant first cell membrane. Such bubbles form sponta-
would be introduced, which, having a more reli- neously at hydrothermal vents because the less
able “food source”, would then come to dominate. acidic water emerging from the vents comes into
Wächtershäuser’s arguments, then, make the pre- contact with the more acidic ocean water. These
diction that the presence of H2 S leads to faster re- bubbles, it is proposed, can act as membranes that
actions and more available energy. Unfortunately, enclose the metabolic chemicals. The energy, in

32
this scenario, comes from the contrast in acidity development of life. Under this model, then, the
between the inside of the bubbles and their ex- last common ancestor was located and developed
ternal environments. The third scenario, which inside the microcaverns of a hydrothermal vent sys-
was proposed by Wächtershäuser himself, comes in tem, rather than free-floating in the ocean. Life
the form of “flat life”. In this scenario, the first was only able to move outside of the vent system
self-replicating metabolic cycle appeared as a thin once the first cell membranes formed. Interestingly,
layer of reactants growing on a sulfite rich mineral cell membranes in archaea and bacteria, as well as
surface, such as that found around hydrothermal eukaryotes, are quite distinct, in that completely
vents. As this cycle self-replicated, it would grow to different lipids are used in its formation. All other
spread outward laterally as a thin coating. Pieces of features of life seem to be similar in other aspects
this coating could then break off and attach to other of physiology.
rocks, where they would behave as cloned colonies
of the original - the analog of reproduction. During 3.3.6 The origins of RNA
this process, variations could arise due to the dif-
ference between the minerals and the environment, The main alternative to the metabolism first point-
leading to several competing “species” of flat life. of-view is the genetics first point-of-view, the idea
This primordial form of “life” may be much more that life started with self replicating and autocat-
resistant to high temperatures, and may therefore alytic genetic molecules, such as RNA, rather than
exist even today deep within the Earth’s crust, be- with a metabolic cycle. Such a viewpoint has obvi-
yond the reach of more efficient modern life. This is ous appeal to biologists, who correctly observe that
off course hard to detect, and the claim is therefore genetics is at the heart of modern life. Looking back
commonly dismissed by biologists, who more com- at the clay world, one possible source for the origins
monly hold the genetics-first point of view, which of RNA may be polymerization on clay surfaces.
will be discussed next. James Ferris noted that certain clays (specifically:
One of the latest versions of this hypothesis was montmorillonite, see figure 25) can act as scaffolds
suggested by Martin and Russell, in 2002. Accord- for RNA. They activate the bonding between nu-
ing to them, cellular life may have formed inside the cleotides when using a solution of so-called “ac-
microcaverns of deep sea hydrothermal vents. This tivated” nucleotides and imidazole (activated nu-
would solve several problems for the hypothesis. cleotides contain an extra molecular group that in-
First of all, it would provide a means of concentrat- creases their reactivity). Without these clay miner-
ing newly formed molecules, which would increase als, nothing happened in Ferris’ experiments even
the chances of polymerization. Secondly, the flow after weeks of waiting, but when the clays are in-
of hydrothermal water through the vent structure cluded, the nucleotides link up to strands of length
would provide a constant source of building blocks, 10 within hours, and within weeks, strands of 50
as well as energy and catalysts. Third, the temper- nucleotides were formed (recall also Szostak’s ex-
ature declines rapidly when moving away from a periments, mentioned in the clay world discussion).
vent, and this establishes an optimal zone for differ- Although these strands are random in nature, it
ent reactions at different distances from the vents. is not hard to imagine that such random linking,
For instance, monomers could form relatively close given enough opportunity and time, could eventu-
to the vents, with polymerization occurring in the ally lead to spontaneously self-replicating strands,
cooler, more distant soil. Fourth, lipid membranes and more. However, one major problem for any
can form after all other cell functions have been de- RNA-first view is that nucleotides, which are the
veloped, and then enclose this working metabolism. basic building blocks of RNA, seem to be extraor-
Finally, the model allows for a large number of sub- dinarily difficult to synthesize. A potential solution
sequent steps in the development of early life to oc- to this problem comes in the PAH world hypothe-
cur in a single structure, including monomer syn- sis, which will be described below.
thesis, protein and peptide synthesis, the synthesis
of RNA, and finally even the development of DNA. Hypercycles
The development of a lipid bilayer membrane may In the early 1970s, Manfred Eigen et al. tried to
not have happened until quite a late stage in the investigate the transition from a chaotic primor-

33
Figure 25: Calcium montmorillonite struc-
ture, here adsorbing Uranyl(VI) (image from
http://www.rsc.org/).

dial soup to a self-catalytic macro-molecular self-

reproducing cycle, duped a hypercycle. In a hyper-
cycle, an information system like RNA produces
an enzyme which helps in the catalysis of another
information bearing molecule, which in turn pro- Figure 26: Nucleic acid polymeriza-
duces another enzyme, and so on, until the last tion on a mineral surface (image from
enzyme aids in the production of the first infor- http://exploringorigins.org/).
mation bearing molecule. From a mathematical
point-of-view (see also http://pespmc1.vub.ac.be/)
hypercycles can create quasi-species capable of un- The RNA world
dergoing evolution by natural selection. A boost The RNA world hypothesis is quite possibly the
to this theory came from the discovery that RNA most influential model of life’s origins at the present
can sometimes form itself into ribozymes, RNA en- time. It was originally proposed by Leslie Orgel.
zymes capable of catalyzing their own metabolic The RNA-world hypothesis works from the obser-
reactions. However, these reactions seem to be vation that without RNA, there are no proteins,
limited mostly to self-excisions, in which an RNA and without proteins, there is no metabolism (in
molecule becomes smaller after each replication. modern cell life). Recall that a genetics-first sys-
Some much rarer reactions can add small additions tem needs a stable molecule that is stable, self-
to the RNA, but these are incapable of coding for replicating, and self replicating, and that there were
any useful protein. In addition, the hypothesis also four notable possibilities for the first information
suffers from the aforementioned problem that they bearing molecules: self-replicating peptides (such
require the existence of complex biochemicals such as those in Fox’s proteinoid world), DNA (requir-
as nucleotides, which are not synthesized under the ing the simultaneous emergence of proteins and
Urey-Miller type conditions that this research took DNA), a clay world model (like that of Graham
as its premise. Hypercycles currently only exist Cairns-Smith), or a nucleic acid like RNA. The
in the form of computer simulations (see, for in- RNA world, as the name suggests, takes the last
stance, http://walter.deback.net/, which simulates of these to be the most likely candidate hypothesis.
parasitism in a hypercycle driven RNA world). Underlying it are three basic assumptions:

34
 1. RNA (or a molecule like it - see below) pre- from the hazardous environment it would find it-
ceded DNA as an information storage system. self in. Such “proto-cells” would grow as a result
of the buildup of internal pressure by the replicat-
2. Ancient RNA replicated in the same way as ing RNA. If we assume that the protocells are in
modern RNA, by the matching of base pairs. close contact with other vesicles (possibly also con-
3. Ancient RNA played a catalytic role similar to taining their own RNA strands) with less internal
that of modern proteins. pressure, this would promote lipid exchange be-
tween the membranes, resulting in growth of one
In addition, for reasons discussed below, it is com- cell at the cost of its neighbors. This results in
monly assumed that the most likely environment a competition for space, in which protocells with
for this first RNA was within a lipid membrane (like more RNA would outcompete those with less RNA,
a vesicle), and that metabolism emerged later as a thus selecting for an increase in strand complex-
means to make replication more efficient, leading to ity. Interestingly enough, this hypothesis has been
natural selection by a competitive advantage. The tested by Szostak, who placed vesicles in a sucrose
support for this model comes mainly in the form solution. The vesicles in such a solution do in-
of the top-down evidence on the importance and deed grow by absorbing lipids from the membranes
central role of RNA in modern life, and the po- of neighboring cells. This does not happen when
tential double role of RNA as both an information the cells are placed in an environment of pure wa-
bearer and a catalyst, as discussed in section A, and ter, but it does happen in the presence of (mod-
in the previous two paragraphs. Additionally at ern) RNA as well. A consequence of this is that
least most of the component molecules of RNA can RNA does not have to make its own lipids or guide
be synthesized readily by Urey-Miller type experi- a metabolism right away, and that self-replication
ments, as well as under a variety of other plausible can, at first, happen without metabolism, so that
early-Earth conditions. the first mechanism of selection would depend on
Jack Szostak, who is currently researching the the efficiency of self-replication. Related to this
possibility of synthesizing artificial organic life, story is the work on evolving viral strains (of the
managed to engineer an evolving replicase RNA QB virus) by Sol Spiegelman. In the QB virus, QB-
molecule in the lab that can replicate parts of RNA replicase replicates QB-RNA, but it does so rather
up to 14 basepairs long. This RNA functions as sloppily. By imposing strong artificial selection for
both a code and a catalyst, and can serve as a rapidity of self replication by repeatedly moving the
copying template. He has also shown that certain complete viral strands into a new medium after an
catalytic RNAs can join smaller RNA sequences to- increasingly short time span allowed for copying,
gether, which, under the right circumstances, could Spiegelman was able to increase the copying time
lead to self-replication. Other functionalities could of the virus. After 74 trials, with average replica-
be added to such a self replicating molecule by mu- tion times decreasing at every trial, the total length
tations, such as copying errors, which could pro- of the virus was one sixth the original length, and
vide the raw material for natural selection to act replicated at 15 times the original rate. Spiegelman
on, thus opening the door to competition and evo- performed similar molecular evolution experiments
lution. The RNA world also makes use of (and for heat, acidity and a variety of other selection
is thus compatible with) the potential of vesicle pressures, which we will not discuss here. In addi-
or microsphere formation as possible enclosures in tion, one way in which these protocells could repli-
which RNA can replicate in a protected environ- cate provides an interesting insight into the prob-
ment. One possible mechanism of replication is lem of nutrient richness as well. As vesicles run
based on the self replication of RNA within a vesi- through tiny pores in mineral surfaces, they are
cle. No known geochemical environment could have squeezed and stretched out, and they can possibly
supported an isolated, naked RNA strand, which divide in this way, after which the new cell copies
would rapidly “starve” by a lack of nutrients in can grow. Recall that some such pores were found
that environment or simply break down. Vesicles to have a size similar to that of modern day cells.
pose a possible solution to this problem, because This growth and division process happens much
the RNA could, in this way, find some protection faster in the presence of fine clay minerals. Dur-

35
ing this process, some of these clay particles may in one single sweep, let alone bind the nucleotides
end up inside the vesicles. This clay can then help together. The circumstances which favor the pro-
assemble the RNA strands (as we have seen previ- duction of ribose are detrimental to the production
ously), so that these protocells would contain clay- of bases, and vice versa. By contrast, most of the
bound RNA strands. The polymerization process elements necessary to establish a metabolic cycle
is illustrated in figure 26. As mentioned, Szostak is such as the citric acid cycle are easy to synthe-
currently trying to engineer artificial life in much size. The question, then, is how to define a tran-
the same way as described here. If this can be sition stage between simple chemicals and the pro-
done, it would of course boost the credibility of the duction of self replicating RNA. The PAH-world
RNA world hypothesis. But, it should be noted hypothesis provides one possible answer. Further-
that engineered life did not arise spontaneously and more, recent experiments suggest that the original
is therefore only considered weak evidence for the size estimates for an RNA molecule capable of self-
purposes of abiogenesis. As of 2008, no one has yet replication were severely underestimated.
been able to synthesize a protocell in this manner Another way to look at this problem is reject
(nor under more plausible more conditions). the so called “naked gene” view, and adopt a
In spite of all this, there are some problems with metabolism first view, in which core metabolism
an RNA-first view of origins. First of all, RNA is established first, followed by a simple informa-
is a complex chemical element, and it relies on ex- tion carrier that is more stable than RNA, followed
act sequences of nucleotides which are much harder by the more efficient RNA, which eventually came
to synthesize than the simple chemicals needed for to dominate (until the appearance of the yet more
a metabolic system. Furthermore, RNA is sev- efficient DNA). The metabolic world would have
eral steps removed from the core metabolic cy- provided a more stable environment in which the
cle in modern cells. This is not a huge problem RNA could form. Oparin’s 1924 suggestion that
if we assume that life at first proceeded without self-replicating vesicles may have provided shelter
metabolism, but the onion-layering around the cur- from the elements is one of the first such proposals.
rent day core metabolism does seem to suggest As we’ve seen, the iron-sulfur world, the thioester
that complexity was built around it, rather than world, hypercycles, and Kauffman’s autocatalytic
the other way around. Second, it is not entirely sets are others. So, even in a metabolism-first sce-
clear where the RNA in question came from. RNA nario, the RNA-world remains a critical stage in the
is hard to build, and no one has yet identified an origins of life, albeit a relatively late one, which
experimentally tested and plausible mechanism to came after the metabolic world, but before the
link individual nucleotides end to end in an RNA DNA/protein world. Filling this gap, that is, un-
strand. If you recall Szostak and Ferris’ clay-based derstanding how we move from a metabolic world
experiments, in which the polymerization of RNA to an RNA world, remains one of the biggest open
was accomplished by using clay crystals as a tem- questions in origins of life research. One of the most
plate, you’ll note that these experiment relied on essential steps is to solve the construction problem
so-called activated nucleotides, which have an ex- that RNA faces, which is part of the so-called pre-
tra reactive chemical group attached to them which RNA world. We will discuss some possible, though
acts as a catalyst. The question remains, therefore, highly speculative solutions in the next sections.
how these strands are synthesized. As we will see,
a possible answer comes from the PAH world sce-
nario for the pre-RNA world. This hypothesis also The pre-RNA world: Nucleotides and alter-
gives a possible answer to the another objection natives to RNA
that is frequently raised: Although their compo- The synthesis of nucleotides, particularly uracyl
nents have been synthesized in several experiments, and cytosine, has proven to be problematic. At
nucleotides, in their entirety have not yet been syn- 100C, cytosine has a half life of only 19 days (al-
thesized from scratch, despite several decades of though this half life is 17000 years in ice). Further-
effort. The main problem is that there is no sin- more, the generally accepted way in which ribose is
gle known plausible mechanism to build the neces- synthesized, called the formose reaction, yields nu-
sary ribose backbone, bases and phosphate groups merous sugars, while displaying no selectivity, as

36
Larralde et al. note, from which they conclude
that ribose and other sugars are too unstable to
have functioned as the first nucleotide backbones.
The linkage between ribose and phosphoric acid in
RNA (an ester linkage) is known to be prone to hy-
drolysis, a problem we encountered numerous times
before. For much the same reasons, Miller has re-
marked that RNA itself is an unlikely candidate for
the first genetic information carrying molecule, be-
cause of its instability and the problems with syn-
thesizing nucleotides. Instead, Miller suggests that
this first molecule may have been a precursor to
modern RNA, which has the following properties:
1. It must be a long polymer (like RNA), with
information carried as a sequence of similar
molecules (much like RNA nucleotides).
2. This information is carried by the same nu- Figure 27: PAH structures (image from
cleotide bases as used by modern RNA and http://www.daviddarling.info/).
DNA, namely adenine (A), cytosine (C),
glycine (G) and thymine (T) or, more likely,
uracyl (U). plausible early Earth conditions. Both TNA and
GNA have no obvious way of emerging through self-
3. Replication occurred by the same sort of base
organization. A final example, GNA, for Glycerol
pairing mechanism as is used in the replication
Nucleic Acid, were synthesized by Ueda et al. in
of RNA today.
1971, which uses repeating glycerol units (contain-
Taken together, one can imagine this precursor of ing only three carbon atoms) linked by phosphodi-
RNA pairing up during self-replications with nu- ester bonds. This base pairing is much more stable
cleotides as found in a real RNA strand, once con- than that of RNA or DNA, and a high tempera-
ditions became favorable, giving rise to the first ture is required to melt a double strand of GNA.
true RNA. The most logical course of study, from It is also the simplest of the known nucleic acids,
this point of view, is to explore different backbone thereby making it a strong competitor for the RNA
structures that can bind to the RNA bases A, C, precursor role. Although all of this remains specu-
G and U. Several interesting candidates have been lative, the pursuit of alternative genetic molecules
found this way. to RNA and DNA turns out to have commercial
Albert Eschenmoser has theorized about more applications. New P/G/TNA-like molecules have
than a dozen backbone structures, resulting in at been synthesized to interact with RNA and DNA
least seven new stable polymers. One such molecule without interfering with normal cell functioning.
is called TNA, for Threose Nucleic Acid. Threose is As recently as January 2009, Tracey Lincoln et
a simple sugar that is formed by the simple fusion of al. have managed to synthesize (artificially) the
two carbon based molecules. TNA has not yet been first RNA strand that can self replicate indefinitely.
synthesized experimentally, however, and most of http://www.scienceblog.com/
Eschenmoser’s backbones are no more stable than
RNA under pre-biotic conditions. Another notable
polymer, duped PNA, for Peptide Nucleic Acid, The pre-RNA world: The PAH world
was synthesized by Peter Nielsen, using an amino Another potential solution to the nucleotide prob-
acid backbone. PNA is appealing for this reason, lem comes from Simon Nicholas Platts, who has
because we know that amino acids would have been duped his model the PAH world. Unlike the pre-
present in abundance on the early Earth. How- viously mentioned attempts, Platts has based his
ever, PNA ha also not yet been synthesized under model on a logical model of self-assembly. As you

37
might imagine, it relies heavily on PAH molecules
(see figure 27), Polycyclic Aromatic Hydrocarbons,
which we encountered several times before. Recall
that Allamandera found experimentally that PAHs
are likely to be abundant in space, a hypothesis that
is confirmed by the identification of multiple PAH-
rich meteorites (specifically, Mars meteorites). Fur-
thermore, in January 2004, it was reported by Witt
et al. that spectral signatures of anthracene and
pyrene had been found in the light emitted from the
Red Rectangle nebula. Recall also that vesicles are
more stable in the presence of PAHs. So far, there
is no strong experimental evidence for this hypoth-
esis, but its logic is plausible. The story goes as
follows. PAHs are molecules that consist of multi-
ple cyclic carbon molecules locked in a flat, regular
grid (see, for instance, http://www.tightrope.it/). Figure 28: A stack of PAHs bonding to nucleotide
They are thought to have been abundant in the bases(image from http://tauceti.sfsu.edu/).
pre-biotic soup. PAHs are not usually easily sol-
uble in water, but can, when exposed to sunlight,
be chemically modified, so that their usual outward
facing H atoms are lost, and can subsequently be
replaced by OH groups. When this happens, their is relevant, because the hypothesis is that a stack
solubility is much increased. As noted in the sec- of PAH-base pairs, being more stable than a sim-
tion on lipid vesicles, the resulting molecules are ple stack of bases, can sit in place long enough
amphiphilic molecules, that is, they have but a hy- for other small molecules (possibly formaldehyde
drophobic part (the carbon rings) and a hydrophilic or amino acids) to bind to the other side of the
part (the OH groups at the edges of the molecules). bases to form a backbone, linking them together in
Because of this, they will self organize (for reasons a complete strand that is a true information bear-
similar to those that apply to pairs of phospho- ing molecule. Finally, when the stacks float into a
lipids) in a stack when placed in water (see figure different environment (i.e. a different temperature
28), so that the inner rings are shielded from the or acidity), the strand could break away from the
water, while the hydrophilic outer edges face the PAH stack and free float as a stable molecule. Po-
surrounding water. These edges are chemically re- tentially, such a molecule could fold back on itself
active, and can bind to small, flat molecules like and link up base pairs, which could allow it to act
nucleotide bases, by means of a pair of OH bonds. as a catalyst, and at some point, such a molecule
As the stack of PAHs is not very stable, the PAH might have also been able to self replicate. As you
“plates” may swivel relative to each other. When might imagine, this model is highly speculative, but
this happens, any molecules that have bonded to it is considered a geochemically plausible, and con-
the stack that aren’t flat are broken off, while flat ceptually simple path from the primordial soup up
molecules can remain attached. This means that to a genetic world. The model makes many testable
there is a natural selection for nucleotide bases as predictions. First of all, PAHs must of course stack
the binding chemicals of choice. Furthermore, the in water, as expected. Furthermore, the PAHs in a
bases themselves are amphiphilic, and will stack single stack must be of about equal size and shape.
on top of each other in a similar way. When a Their edges must attract certain type of molecules,
stack of bases is lined up next to a stack of PAHs, and the (flat) bases must be preferentially selected.
they will react, and the result will be a stacking of All of this can, in principle, be experimentally ver-
PAH-base pairs. Interestingly, the space between ified. George Cody has pointed out that there is a
the PAHs in a stack is 0.34nm, which is equal to large volume of literature on PAH self-organization
the distance between bases in RNA and DNA. This into stacks of discs from coal research.

38
3.3.7 Exogenesis methanol, ammonia and carbon monoxide was sub-
jected to UV radiation, thereby providing plausible
A final set of hypothetical origins that I want to environmental conditions to simulate those found
mention briefly are somewhat less commonly ac- in outer space. The experiment yielded large quan-
cepted than the hypotheses mentioned above, al- tities of biomolecules, which self organized into pro-
though not all of them are mutually exclusive. tobiont bubbles when immersed in water, of sizes
Specifically, I want to discuss exogenesis. Exoge- measuring between 10 and 40 micrometers, which
nesis is the hypothesis that primitive life may have is a size similar to that of red blood cells. These
originated elsewhere in (or even outside of) the so- bubbles seem to resemble cell membranes such as
lar system, on a nearby planet or in space. A closely those found on Earth life. In addition, they fluo-
related concept, called panspermia, holds that the resced when exposed to UV light. This means that
seeds of life may be present all over the universe. the more energetic UV light was absorbed and then
Panspermia, however, is much less widely accepted re-emitted as lower energy, visible light. This was
as a realistic hypothesis, and there is no evidence considered a possible way of providing the hypo-
to either support or falsify it. I will concentrate thetical primitive cell with energy, that could have
here on life in our solar system. One of the reasons been a precursor to primitive photosynthesis. Fur-
why this prospect of extraterrestrial origins may be thermore, it also acts as a sunscreen, by diffusing
appealing to some is because of the short window damage that would otherwise result from the UV
for life’s emergence; the most recent estimates from exposure. This is also relevant for early Earth life,
fossil research place the emergence of life at some- since the early Earth would lack an ozone layer,
where between 3.8 and 4 billion years ago, almost which currently blocks out the most harmful UV
immediately after the Earth became habitable. As radiation. The ozone layer only emerged after pho-
noted in before, organic compounds are relatively tosynthetic life began to produce oxygen approxi-
common in space. This is especially true in the mately 2.2 billion years ago. Of course, this type of
outer solar system, where volatile compounds are explanation does not give us an actual explanation
not rapidly evaporated by sunlight. The Cassini- for life’s origins (merely moving the origins loca-
Huygens space probe has confirmed the existence of tion and conditions), but rather a broader set of
water and organic compounds in our solar system. tentative conditions that may be worth looking at.
Comets are encrusted by a layer of dark material Under this scenario, life could really have formed
that is thought to be composed of a tar-like sub- anywhere in the universe, only to be subsequently
stance, composed of organic material that formed dispersed, even to other star systems across the
from simple carbon molecules after exposure to ul- galaxy, by comet and meteor impacts We may have
traviolet radiation. Comet material raining down to wait for samples to be gathered from comets and
on the early Earth could have spread significant other planets (like Mars, see below) before we can
amounts of organic materials on its surface, and it make any more specific claims.
is speculated that even very simple life may have
formed in space and may have been brought down
to our planet in the same way. Although there is Life on Mars
only some very circumstantial evidence for this type One possible exogenesis scenario is that life orig-
of hypothesis, it extends the range of potential con- inally originated on Mars, but was subsequently
ditions under which life may have formed tremen- transported to Earth when parts of the Martian
dously, from the early Earth’s plausible conditions, crust was thrown into space by a comet or asteroid
to practically all conditions found in the known impact. Mars is much smaller than the Earth, and
universe. Our current knowledge on extremophilic therefore cooled faster than our planet did, allow-
species suggests that life may be much more ro- ing life to form more rapidly there, by a factor of
bust and versatile than once thought. A recent hundreds of millions of years (which is significant
discovery of a bacterial ecosystem that derives its compared to the 150 million year window that is
energy from radioactivity provides further support considered the likely norm for Earth). It continued
for the hypothesis. Jason Dworkin performed a re- to cool rapidly after the supposed impact events,
cent experiment in which a frozen mixture of water, having now lost its atmosphere due to suffering

39
 from low volcanism, and it has by now become
an inhospitable place for life. Nevertheless, NASA
has been searching for signs of pre-biotic life on
Mars. Mars meteorites have been found on Earth,
and recent studies of meteorites found in Antarc-
tica support the exogenesis idea. Allan Hills, who
investigated a Mars meteorite, found large quanti-
ties of PAHs, which commonly form when cells are
exposed to temperatures above boiling point. This
points to presence of significant amounts of carbon
on Mars. He also discovered microscopic globules
of carbonate minerals, as are found in Earth cave
walls. On Earth, these are often deposited by liquid
water passing through cracks and fissures, which
suggests that liquid water may have been present
on Mars. This is also reminiscent of minerals de-
Figure 29: Mars meteorite ALH84001 sample (im- posited by microbes on Earth. Hills also found
age from http://tycho.bgsu.edu/). quantities of sulfite (in the form of pyritite) and
ironoxide (in magnetite). These were ordered in an
unusually pure and linearly ordered arrangement
(see figure 30), which is only known from magneto-
tactic microbes, bacteria that use the Earth’s mag-
netic field to orient themselves, to distinguish up
from down (incidentally, when one places magne-
totactic bacteria from the southern hemisphere in
northern hemisphere soil, they will inadvertently
bury themselves alive). Finally, Hills found vari-
ous microscopic “sausage shaped objects” (see fig-
ure 29), that are somewhat reminiscent of known
types of microbes, only far smaller. However, critics
of Hills have since pointed out that none of his finds
are conclusive. PAHs are common in the cosmos,
and are synthesized by natural processes on both
Mars and in interstellar dust. Additionally, the me-
teorites are very likely to have been polluted while
sitting on the antarctic ice. In addition, carbon-
ate globules can form by other processes, such as
when minerals react with CO2 . There is some evi-
dence that the globules formed above boiling point
(though this is debatable), and so it may be un-
likely that they could have formed by water running
through cracks in the mineral, but even so, the ev-
Figure 30: Above: modern magnetotactic bacte- idence is not very strong. Thirdly, magnetites are
ria showing chain of magnetite crystals. Below: common in meteorites, and although their arrange-
chains of magnetite crystals in the Martian mete- ment is quite unusual, magnetotactic microbes re-
orite. Each chrystal is about one-millionth of an quire a sufficiently strong field to use magnetites
inch in diameter. Image - NASA AMES (image for orientation purposes. Mars’ magnetic field is
from http://www.abc.net.au/). much weaker than that of the Earth. Fourth, the
“Mars fossils” were much smaller than any known
microbe, consisting of no more than a few hundred

40
biomolecules. There are alternative known pro- acquiring the ability to fix nitrogen. Fi-
cesses that could have produced similar structures. nally phosphate was incorporated into the
Finally, research has subsequently revealed that all evolving system which allowed the synthe-
known meteorites reveal signs of life. But this life sis of nucleotides and phospholipids. If
is terrestrial in origin; contamination is nearly in- biosynthesis recapitulates biopoesis, then
evitable. Future Mars missions will have to reveal the synthesis of amino acids preceded
more about possible life once living (and perhaps the synthesis of the purine and pyrim-
still) on or within the Martian crust. It is of course idine bases. Furthermore the polymer-
possible that, if such life was found, it could have ization of the amino acid thioesters into
been transported from Earth to Mars, rather than polypeptides preceded the directed poly-
the other way around. However, this is much less merization of amino acid esters by polynu-
likely. First of all, Mars has a weaker gravitational cleotides.
field (Mars is about 1/10th the Earth’s mass). Sec-
ond, the Earth is closer to the sun, which means Another reason why we may not be able to dis-
that the gravitational pull would tend to draw par- cern other primordial life comes from horizontal
ticles from Mars towards the Earth, but not the gene transfer between bacteria. As mentioned ear-
other way around. If a Mars rover did find life, then lier, bacteria frequently exchange genetic material,
the possibility remains that this is due to contam- making it nearly impossible to determine a straight
ination. The only true confirmation of extrater- path through the evolutionary tree. Many distinct
restrial life, then, would come from the discovery organisms may in this way have contributed to
of a so-called “second genesis”; the discovery that what we now think of as the Last Universal Com-
life emerged on another, distant planet that is al- mon Ancestor (LUCA) of modern life. Lynn Mar-
most certainly independent from the formation of gulis’ endosymbiosis theory also suggests that mul-
life on Earth. A main sign of such life is to look for tiple bacteria and archaea may have entered into
the presence of liquid water, and more importantly, a symbiotic relationship to for the first eukaryotic
an oxygen rich atmosphere. Alternatively, second cell. Such symbiosis is promoted by horizontal gene
genesis could be found on a more nearby planet transfer, and this thus makes the relation likely to
if the lifeforms found differed significantly from all be even more complicated.
life currently found on Earth.
3.3.9 Early evolution
3.3.8 Multiple genesis
As we have already seen, the earliest form of evo-
Not all scientists are convinced that life on Earth lution would act on many simple organic molecules
emerged only once. Different forms of life may have on the early earth to sort them out, by means of
emerged nearly simultaneously (in terms of geolog- attracting and concentrating them near a partic-
ical time scales). These other forms of life may ei- ular mineral. Some molecules are inherently un-
ther have gone extinct (perhaps having left distinc- stable or unusually reactive, and would have been
tive fossils by their differing chemical composition, sorted out early. Others would have been too eas-
for instance, using arsenic instead of phosphorus). ily soluble. Their presence in the primordial soup
Alternatively they may currently live as undiscov- would be too dilute, and eventually they would
ered extremophiles, or be so similar to other life on be removed from organic use for lack of reliabil-
Earth that they have simply escaped our attention. ity. Some molecules would bind permanently to
For example, Hartman notes that: surfaces of minerals that did not help them repro-
duce and take over, or would clump together into
The first organisms were self-replicating tar-like masses that would have been unable to re-
iron-rich clays which fixed carbon dioxide act with anything else in order to for a self repli-
into oxalic and other dicarboxylic acids. cating system, and would thus also have been no
This system of replicating clays and their use for life. All of this selection may have been
metabolic phenotype then evolved into amplified by cyclical processes on earth (hot/cold,
the sulfide rich region of the hotspring dry/wet, light/dark), such as UV fragmentation

41
of unstable elements over the course of days and
seasons, the ocean tides, or the pulsation of hy-
drothermal water around deep sea vents. This
pulsation would have delivered new chemicals into
the system, which would then be absorbed by cer-
tain reactive minerals or eventually detached from
their surfaces. This process would serve to con-
centrate a subset of molecular species. Over time,
this lead to a refinement of the available subset
of chemicals in any given environment, each dis-
tinct environment having its own unique inhibiting
and promoting factors. This finally lead to a sta-
ble state of equilibrium, until self-replication could
eventually emerge. After the first replicating sys-
tem came into existence, evolution would take over.
When part of a self-replicating cycle, even unstable
chemicals could persist and increase in number if
they could make copies of themselves more rapidly
than they were being broken down. Self-replicating
systems would initially thrive in competition with Figure 31: The Genetic code (image from
their non-reproducing neighboring chemicals, and http://plato.stanford.edu/).
eventually multiple replicants might meet, result-
ing in more serious competition. Eventually, vari-
ation in these complex cycles of replication would
that tRNA is used to translate (mRNA from) DNA
emerge, providing the raw material for natural se-
into proteins, so that the tRNA determines the ge-
lection to build on. Organic evolution would begin
netic alphabet by mapping from triplets to specific
here. There would have been competition for re-
amino acids. This mapping may be arbitrary, or
sources and space, leading to an increase in com-
it may simply be the most efficient way of transla-
plexity driven by a selection pressure towards in-
tion due to chemical or physical restrictions. This
creased efficiency and stability, eventually leading
suggests that a possible intermediate stage between
to the formation of the earliest life. The transition
the RNA and DNA worlds where the genetic code
would have been fuzzy, but eventually prokaryotic
consisted of only two bases, C and G, and four cor-
life would have emerged, much like the bacteria and
responding amino acids. Later, this code may have
archaea that still exist today.
become more complex as new nucleotides A and
T/U were added. Since this more complex code can
result in more complex and more efficient proteins,
The early evolution of DNA
selection would favor this more complex code.
It is commonly believed that DNA evolved from
RNA. A system of proteins and DNA is more ef- In a recent article (see also figures 32 and 33, and
ficient than one of just RNA. An interesting ob- http://www.sciencedaily.com/) Bokov and Stein-
servation for a possible transitional stage between berg seem to have tackled the origins of the ribo-
RNA and DNA worlds comes from our genetic code some. This presents another milestone in our un-
itself (see figure 31). The most primitive and eas- derstanding of the origins of modern life and early
iest to synthesize amino acids, glycine (GG*), as evolution.
well as alanine (GC*), proline (CC*) and arginine This is as far as I will take this document. The
(CG*), are all coded for by bases guanine and cyto- evolution of DNA and proteins is a subject that
sine. Interestingly, both these amino acids and the one can write a book about, and it takes us beyond
bases that code for them are synthesized in Urey- the origins of life and into evolution. If you want
Miller type experiments. These amino acids can to learn more about this subject, a good website
self organize to form functional proteins. Recall to check out is http://www.evolutionofdna.com/. I

42
 Figure 33: The aggrandizement of the 23S rRNA
structure during its evolution. ae, the proto-
ribosome with 0 (a), 8 (b), 20 (c), 50 (d) and all 59
Figure 32: The location of the identified elements (e) elements added. The proto-ribosome is red, el-
in the E. coli 23S rRNA secondary structure (a) and ements forming the proto-ribosome foundation are
the network of D1 and D2 dependencies between them blue, the protuberances are yellow, and 16S rRNA
(b). Each element has the same colour in a and b. is purple. The complete list of the elements form-
The roman numerals indicate secondary-structure do- ing structures ae is given in Supplementary figure
mains. PTC stands for the symmetrical arrangement
f, The top view of the 23S rRNA structure shown
in domain V containing the peptidyl-transferase centre
in e. g, The positions of the parts of 23S rRNA
(the proto-ribosome). a, The two halves of the proto-
ribosome are blue and red. Red asterisks indicate the shown in ae in the context of the whole ribosome.
four elements that form two non-local pseudoknots 2739 The structures of the 50S and 30S subunits are con-
and 3340. b, An arrow connecting two elements Q → toured by the blue and red line, respectively. 13 are
P indicates that the position of P depends on the pres- the L7/L12, central and L1 protuberances, respec-
ence of Q. Black and coloured arrows represent D1 and tively; 4 is the exit channel; 59 are the structures
D2 dependencies, respectively. Red arrows Q → P rep- shown in ae, respectively; 10 is the part of 50S sub-
resent A-minor interactions formed by a double helix unit that does not include 23S rRNA. This part is
of element Q and a nucleotide stack of element P. Two formed by ribosomal proteins and 5S rRNA.
violet arrows originate from the dissection of two non-
local pseudoknots (see Supplementary Notes 1). The
numbers of levels are shown on the left. The detailed
description of all elements and of all D2 dependencies
is given in Supplementary Data 1 and 2.

43
will conclude this section by simply listing a num- 2: The origin of biological polymers.
ber of key events in subsequent early evolution:
3: The evolution from molecules to cell.
1. The rise of prokaryotes and archaea. Bernal suggests that evolution by natural selection
may have occurred as early as between stages 1 and
2. The evolution of cyanobacteria, capable of un-
2. A rough outline of the general patterns that seem
dergoing photosynthesis, eventually resulting
to emerge of the primordial soup of hypotheses that
in the development of the current atmospheric
we’ve discussed can be given in the following way:
composition of the earth.
First of all, as we have seen, monomers can be syn-
3. The evolution of eukaryotes by means of en- thesized in a number of ways, including the primor-
dosymbiosis. dial soup, deep sea vents, the deep crust, in mud
puddles, or even in outer space. Secondly, it seems
4. The evolution of multi-celled life, over a billion clear that the cell membrane forms by self organiz-
years ago (which is frequently illustrated using ing sets of phospholipids of an appropriate length
a current day organism called volvox, and its into lipid bilayers. Third, several different hypothe-
close relatives) and sexual reproduction. ses exist for the origins of the first self-replicating
molecular system, be it an RNA precursor (or RNA
5. From there, the very basic outline is: Flat itself), or a self-replicating metabolic cycle. An in-
worms → hemivertebrata → vertebrata → teresting development in late 2009 was published in
fish → amphibians → mammal-like reptiles → PNAS. Vasasa, Szathmrya and Santosa conducted
mammals → simians → hominids → human a study in which they tested whether the stability
beings. of auto-catalytic sets is sufficient for such networks
to have undergone evolution. If there is too much
3.3.10 Conclusions variance in how a network of molecules reproduces
itself, then any effects of natural selection would be
There is currently no single, broadly accepted sci-
overwritten by the sheer rate of mutation. As with
entific theory on the origins of life, but much head-
Kahr’s results on clay crystal reproduction, their
way has already been made in the last few decades.
results suggest that such networks lack the required
The models that exist can be broadly subdivided
stability. What this means is that, although auto-
into three distinct categories:
catalytic sets may still have played a vital role in
1. Life began autotrophic, starting with the origins of life, they would not by themselves
metabolism, and only later incorporating have been capable of evolving, and would thus not
genetic molecules into the mix. be considered truly alive by the criteria that abio-
genesis researchers generally agree upon. But the
2. Life began with genetics, possibly autotrophic, metabolic and genetic accounts are not necessarily
or possibly heterotrophic. Metabolism devel- mutually exclusive. Either way, at some time, RNA
oped as the genetic material slowly became en- is thought to have dominated the globe. For in-
riched. stance, selection pressures favoring replication and
metabolic efficiency may have first resulted in the
3. Life began as cooperation between genetic ma-
development of ribozomes, and with them, the for-
terial and a metabolic system. Although this
mation of small proteins. Eventually, this may
may seem like a stretch, focus of research seems
have resulted in the first ribosome, which would
to be shifting towards this point of view, al-
have lead to more protein synthesis. Proteins are
though no detailed hypothesis exists (as far as
more efficient catalysts than ribozymes, and there-
I’m aware).
fore become the dominant polymer molecules, leav-
The three stages that have to be solved to come ing RNA to their modern use as mostly carriers of
up with a complete theory of the origins of life are genetic information.
summed up by Desmond Bernal: Much remains to be discovered in abiogenesis
research, and undoubtedly, many new discoveries
1: The origin of biological monomers. will be made. I’m sure some new ones have

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been made that I myself am not aware of, as my
knowledge is somewhat out of date. At any rate,
I am optimistic about the future of this field of
research.

This document Jelle

c Kastelein, 2009.

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