abiogenesis primer

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Abiogenesis Explained

Jelle Kastelein

January 30, 2010

Contents

1 Introduction 1

1.1 Spontaneous generation . . . . . . . 2

1.1.1 Life as a continuum . . . . . 21.1.2 Modern abiogenesis . . . . . 2

2 Fossil evidence of ancient life: con-

straining time scales 3

2.1 Microbial fossils . . . . . . . . . . . . 32.2 Fossil isotopes . . . . . . . . . . . . . 42.3 Fossil biomolecules: (a)biosignature

molecules . . . . . . . . . . . . . . . 52.4 Primitive aspects of modern cells . . 6

3 Bottom Up: Emergence and abiogen-

esis experiments 113.1 Emergence . . . . . . . . . . . . . . . 113.2 The spontaneous generation of sim-

ple organic molecules . . . . . . . . . 113.2.1 The Urey-Miller experiment

and primordial soup . . . . . 113.2.2 Extremophiles . . . . . . . . 133.2.3 Monomers from hydrother-

mal vents . . . . . . . . . . . 143.2.4 Monomers from the Deep

Hot Biosphere . . . . . . . . 193.2.5 Monomers from Space . . . . 193.2.6 The radioactive beach . . . . 20

3.2.7 Chirality . . . . . . . . . . . 203.2.8 Conclusions on monomers . . 21

3.3 The generation of polymers frommonomers and the origins of self-replication . . . . . . . . . . . . . . . 213.3.1 The construction of macro-

molecules . . . . . . . . . . . 223.3.2 The clay world . . . . . . . . 233.3.3 The origins of cell membranes 243.3.4 Self replicating systems . . . 283.3.5 The origins of metabolism . . 29

3.3.6 The origins of RNA . . . . . 333.3.7 Exogenesis . . . . . . . . . . 393.3.8 Multiple genesis . . . . . . . 413.3.9 Early evolution . . . . . . . . 413.3.10 Conclusions . . . . . . . . . . 44

1 Introduction

We often hear the question how evolution explainsthe origins of life. The short answer: it doesnt.That is the subject of abiogenesis theory (also re-ferred to as origin(s) of life science). Abiogene-sis is basically a hybrid biochemical/geochemicalexplanation for the origin of life from non-livingmaterials. Evolution is what comes after the first

self-replicating system is produced, that is capableof undergoing change. There is, of course, someoverlap, when discussing the origins of such self-replicating systems. Here, Ill discuss some ba-sic observations, ideas and experiments that comefrom abiogenesis studies. Interestingly, some ofthese methods are also applicable to identifyingsigns of life on other planets (e.g.: future Mars mis-sions), but I wont go into that in much detail here,except where it is relevant to abiogenesis. Ill startwith some basic concepts, after which I will mentionsome fossil observations of signs of life in the earlyEarth to give an idea of the top-down approachto studying life through geology and paleaontology,and then move on to a bottom up approach whichis more akin to biochemistry, in which scientists tryto recreate the conditions of the early Earth in thelab, with some successes and some open questionswhich Ill try to point out. I wont move far beyondthe first self replicating systems, as that is whereevolution starts, but Ill briefly mention a few keyevents that lead to the evolution of increasinglycomplex lifeforms. The details of these, however,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 ammerely an interested layman, so new evidence maywell have been uncovered recently that I am notaware of. This is a very active and rapidly growingfield of research. I have based this summary pri-marily on a great 2005 introductory video lectureseries by The Teaching Company, by Robert M.Hazen (http://www.teach12.com/). I have tried toupdate this information here and there, but theremay well be some outdated information remaining.

1.1 Spontaneous generation

Louis Pasteur proved that spontaneous generationof life, which before this time had been consideredan established fact, was impossible, and that lifeforming was instead the result of biogenesis (lifearising from other life). Before Pasteurs time, forinstance, mice were thought to spontaneously ap-pear from stacks of hay. Similarly, micro-organismsgrowing in colonies on a substance were thought tobe born from that substance itself, or from a lifeforce in the air. To disprove this idea, Pasteurperformed several experiments. He boiled a brothwhich he placed in vessels that were connected to

the outside air through a long, bent tube that wouldnot allow dust particles to pass, as well as somethat were completely closed off, and some that werecompletely open to the air. In addition, he didthe same for an unboiled broth. The experimen-tal setup of the first (boiled) experiment is shownin figure 1. Nothing grew in the closed or filteredvessels holding the broth that was sterilized, butsomething did grow in the vessels holding the broththat was uncooked, independent of whether or notthe broth was closed to the outside air or not (hehad thereby also discovered anaerobic metabolism).The conclusion was that life did not come from thebroth or from the life force in the air, as had previ-ously been suggested, but from other lifeforms car-ried on spores. Strangely enough, abiogenesis (ororigins of life) theory is now trying to establish howprimordial life once came from non living materi-als. Of course, we all know that Earth worms arenot born from the Earth, but from other life forms,particularly Earth worms. But at some point, whenupholding a scientific naturalist perspective (whichcannot comment on the existence or non-existenceof God, and thus does not deal with the religious

Figure 1: Pasteurs experiment (image from

http://www.angelfire.com/).

perspective), one has to assume that life ultimatelycame from non-life. In the end, life is chemistry,and its laws - on the molecular scale - do not dif-fer in any known significant fundamental way fromthe normal laws of chemistry. Yet life is obviouslyquite distinct from non living matter. Abiogene-sis, then, is not only about the transition from lifeto non-life, but also about exploring the boundarybetween the two.

1.1.1 Life as a continuum

One of the key questions in this topic is of coursethe question what life really is. There are manyconflicting definitions (almost no two people willhave the same definition), but most biologists todaynow agree on three key properties. This is used as aworking definition. First of all, life must be able togrow. Second, it must be able to reproduce. Third,it must be able to undergo reproductive variability(in other words, it must be able to evolve). Underthis definition (or perhaps in spite of it), there is

thought to be no sharp boundary between life andnon-life. Rather, the transition from life to non-lifeshould be seen as a continuum. In that sense, thefirst self replicating systems are somewhat alive,but not quite as alive as the first bacterium, or us. Iwould ask that you keep this in mind while readingthe rest of this summary.

1.1.2 Modern abiogenesis

Charles Darwin wrote in a letter to Hooker, in1871, that life began in a warm little pond, with

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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 thepresent day life which prevents spontaneous gen-eration from occurring today. The modern defini-tion of abiogenesis is quite similar to that suggestedby Darwin. Unlike the old definition of abiogen-esis, which was, as noted, disproved by Pasteur,and which dealt with the spontaneous generation ofcomplex organisms, the modern theory is concerned

with the origins of life from primordial chemicalsunder conditions thought to have been prevalent onthe early Earth. In the rest of this summary, I willdiscuss only this modern interpretation of abiogen-esis. There is currently no broadly encompassingtheory, or standard model, if you will, of the originsof life. However, one can find a number of commonthreads in these models, and all build on discoveriesof fossil evidence, and chemical experiments carriedout in laboratories. I will start by outlining someof the fossil evidence coming from the top downapproach to the studies of the origins of life, before

moving on to the bottom up approach that stud-ies abiogenesis through experimental observations,in attempts to reconstruct early life, using plausibleearly Earth conditions.

2 Fossil evidence of ancientlife: constraining timescales

The Earth is thought to be roughly 4.6 billion yearsold. At first, its surface was red hot, both becausethe crust had not yet settled, and because it wascontinuously being battered by fragments of thethen forming solar system. These fragments would,on impact, vaporize oceans and throw most of therecently formed atmosphere into outer space, sothat no life could survive. The oceans are thoughtto have formed approximately 200 million years af-ter the formation of the Earth, when the surfacetemperature was approximately 100C. The Earthremained most likely uninhabitable until the end ofthe Hadean eon, roughly 4.1-3.8 billion years ago,

Figure 2: The hadean era (image fromhttp://www.newsback.com/).

at which time the composition of the atmospherewas very different from that of today. There issome controversy as to the exact contents of thisearly atmosphere, which we will discuss later on.Here Ill discuss some of the evidence we have con-cerning time scales. Im not going to go into fossildating here - this is not supposed to become a fulltextbook, but a concise summary. Look into ra-diometric, and particularly isochron dating if youwant more info on this subject.

2.1 Microbial fossils

One of the main problems with finding some of theoldest forms of life is that it will have been engulfed,that is, eaten and digested by subsequent genera-tions of organisms. This is of course true for anyorganism in the chain of evolution, but it is particu-larly problematic in the case of microbial organisms- and life is thought to start out as extremely tiny,cell-like self-replicating systems, much like a highlyoversimplified bacterium. Since most of the reallyancient life was both extremely tiny and soft bod-ied, finding fossil evidence of the (near) first kindsof life is not an easy task. It is rare for soft tis-sue to fossilize, and even when it does, microbesare hard to spot. The data are sometimes highlyambiguous. Some of the fossil evidence that is notso ambiguous, and widely accepted as uncontrover-sial comes in the form of stromatolites (see figure 3;more info on wikipedia), which are spherical dome-

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like structures that are thought to be composed

of mineralized corpses of ancient microbes. Thesestructures have been dated at about 2.5-2.7 billionyears old, and there are some other examples ofwidely accepted fossil evidence that are consideredreliable that go as far back as about 3 billion years.There are older known fossils still, but the evidenceis often controversial in those cases, arising fromsuch 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. Theoldest controversial fossils were dated at around 3-3.8 billion years. Schopfs fossils, for instance, are

about 3.465 billion years old, but it is uncertainif what is seen in the minerals is actually micro-bial in origin. Some images of what he found canbe seen in figure 4. Note that uncertainty does notnecessarily imply falsehood. If these oldest findingsshould turn out to be confirmed, this would meanthat life formed almost as soon as it was possible forit to do so, which would have major implications forour search for possible extraterrestrial life. A finalinteresting set of microbial fossils have been foundnear hydrothermal vents at the bottom of the oceanthat are about 3.5 billion years old. I will return to

hydrothermal vents later on.

2.2 Fossil isotopes

There are other ways of detecting signs of life onthe early Earth. Fossil isotopes are specific isotopesthat are accumulated into unnatural concentrationsby living organisms. For instance, carbon has anumber of different isotopes with equivalent chem-ical properties. The isotopes that differ from themost common one contain one or more extra neu-trons in the nucleus of the atom. For instance, car-bon, which typically has 6 protons and 6 neutrons,denoted by C12, can also be found in isotopes with7 or 8 neutrons, denoted C13 and C14 respectively.We can measure the ratio between different isotopesvery accurately using a mass-spectrometer (Im notgoing to go into the details of how this works here,but you can look it up if you want to - a simpleschematic is given in figure 5). The natural ratio ofconcentrations between C12 and C13 is about 99:1.Because C13 isotopes are heavier than their C12

counterparts, they tend to be slightly more slug-gish in chemical interactions. Because of this, C12

Figure 3: Stromatolites (image fromhttp://paleontology.edwardtbabinski.us/).

tends to accumulate in organisms so that the ratioof C12 to C13 is shifted. If there is a 1% excess

in C12

from the norm, we say that this constitutesa deviation of -10 per mil. For instance, modernphotosynthetic life has a per mil of -20 to -30, cor-responding to a 2 to 3% excess. Stromatolites aretypically in the -25.0 to -25.9 range. Photosyntheticlife has a relatively reliable source of energy, so itis typically less efficient at storing carbon than liferelying on less stable energy resources. Such non-photosynthetic life can typically be found in the -50range. In addition, there is a buildup ofC12 in or-ganisms higher up in the food chain. So a plantcontains a higher excess ofC12 than its surround-ings, a herbivore contains a larger excess than thatplants it eats, and a carnivore that eats the herbi-vore contains a higher excess than the herbivore.So, in this way, isotopes can tell us something notonly about whether some mineral was at some pointprocessed by living organisms (which shows up asthe excess deviation from the norm), but it alsogives us some basic information about the lifestyleof those organisms (which shows up as the size ofthe excess). The oldest fossil isotope hint at signsof life comes from an island off the coast of Green-land, and gives dates of around 3.85 billion years.

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Figure 4: Images of Schopfs fossils (image fromhttp://www.nature.com/).

I should note that this evidence was not entirelyuncontroversial at the time I heard about it, so itmay have been refuted since. But there is other,less controversial evidence that gives estimates inthe same basic ball park figure as the more reliablefossil evidence.

2.3 Fossil biomolecules:(a)biosignature molecules

A final type of fossil evidence comes in the form ofmore complex molecules that are typical to life onEarth today. Life uses only a tiny subset (a frac-tion of a percent) of the possible carbon based com-pounds typically found in nature. This is due to theunusual way in which these compounds are synthe-sized by the cell. So, by looking at the absence ofcompounds not found in life in combination withthe presence of those molecules that are typicallyfound in life, we can identify strong evidence thatlife was once present at the site of interest. We callthese organic compounds biosignature molecules,and we call compounds that are never found in lifeabiosignature molecules. Both types of signaturemolecules must be stable over long periods of time

Figure 5: A simple mass spectrometer (image fromhttp://en.wikipedia.org/).

and under a large variety of conditions and abun-dant to the extent that we can easily find tracesof them, they must be unique to life or non-life forbiosignatures and abiosignatures respectively, and,in the case of biosignatures, they should be essen-tial to life. For instance, hopanes (see figure 6) arecarbon molecules that have a molecular backbonecomposed of several carbon rings of 6 or 5 carbonatoms that are typically produced by the type ofsynthesis found in cells, and are typically found incell membranes. Their structure makes them quiterigid and stable, making them a good candidateclass of molecules that is frequently considered forthis type of investigation. Incidentally, work is cur-rently being done on creating a hopane-detector foran upcoming Mars mission by Steele et al (in theform of MASSE, Microarray Assay for Solar Sys-tem Exploration). Some of the more convincingidentifications of hopanes for which non-biologicalsystems were ruled out as a possible origin are givenby Summons, at 2.7 and 2.5 years old. The lattersample contained traces of 2-Methylhopane, whichis known to occur only in Cyanobacteria, which arecapable of undergoing photosynthesis.

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Figure 6: Hopane (image fromhttp://www.chem.qmul.ac.uk/).

2.4 Primitive aspects of moderncells

One final type of contribution of the top-down ap-proach to abiogenesis comes from molecular phy-logeny. I dont want to go into too much detailhere, but essentially it concerns the identification

of some of the most ancient cellular mechanisms.Basically, what researchers in this field do is lookat the correspondences and differences in function-ality between the most primitive (note: primitivein an evolutionary context means oldest, not nec-essarily least complex) and most modern species oforganisms. Some mechanisms stand out as rigidand unchanging, suggesting that they play a vitaland ancient role for life. For instance, all organismstoday seem to require ATP (see figure 7), and sothe genes that code for this molecule are more orless fixed in evolution across all organisms. Sim-ilarly, as Carl Woese noted, the genes that codefor 16S ribosomal RNA (see figure 8) are highlyconserved; the correspondence between human be-ings and e-coli is about 50%. It is expected, then,that one of the most sensible courses of action is tolook for circumstances that could have lead to thespontaneous development of such rudimentary fea-tures of life. The abiogenesis community tends tobe divided between two opposing viewpoints. Onthe one hand, some people promote a metabolism-first point-of-view. In this view, the most centralpart of life is metabolism, the mechanism by which

Figure 7: ATP (image fromhttp://www.dvbiology.org/ ).

energy is derived from the environment and putto use for the organisms benefit. Metabolism-firstproponents propose that the first self-reproducingsystem of chemical interactions was a metabolic cy-cle. Many geochemists working in the field sub-scribe to this idea. On the opposite side of the

debate, the genetics-first viewpoint holds thatgenetic reproduction preceded metabolism. Mostbiologists tend to support this view. Ill briefly de-scribe the target feature of modern organisms thateither viewpoint is focused on at this point in time.

Primitive metabolism

The metabolism first point of view focuses mostlyon one of the most fundamental metabolic path-ways that modern organisms employ, named thecitric acid cycle. This relatively simple processforms a closed loop of reactions that halves the keymolecules at every turn, resulting in the release ofenergy. Interestingly, the citric acid cycle can alsorun in reverse, in which case it is called the reversecitric acid cycle, for obvious reasons. In this case,input energy is required, but the reactive loop runsin reverse, duplicating the reactants at every turn.In this way, the cycle can be described as a self-replicating system. Ill describe the reverse citricacid cycle here briefly, because some of the key re-search focuses on the molecules used in these cycles,particularly pyruvate and oxaloacetate. A simpli-

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Figure 8: 16S Ribozomal RNA (image from

http://www.learner.org/).

fied form of the cycle runs as follows, where a + in-dicates the addition of a certain chemical from theenvironment and a indicates a chemical reactionresulting in the molecule to the right of the arrow,starting from Acetyl-CoA: Acetyl-CoA, + CO2 Pyruvate, + CO2 oxaloacetate, + H2Malate,+ H2O Famarate, + H2 Succinate, + CoA Siccinyl-CoA, + CO2 2-Oxoglutarate, + H2& CO2 Isocitrate, + H2O Aconitate, + H2O Citric Acid, + CoA Acetyl-CoA & Pyruvate.The (normal) citric acid cycle is shown in figure9. As one can see, the last step that splits a citricacid molecule doubles the amount of oxaloacetate,which leads to a doubling of the entire cycle, andso this metabolic pathway can, in principle, be self-replicating. One major problem is that, in moderncells, this process requires many complex enzymes(catalytic proteins) which were almost certainly notaround in a pre-biotic era. We will see later howthis paradoxical situation may be resolved by the

Figure 9: The citric acid cycle (image fromhttp://www.biologycorner.com).

use of minerals as catalysts.

Primitive genetics

As we all know, genetics deals with the macro-molecules (large molecules, also referred to as poly-

mers, which are generally built up of smaller ba-sic molecular units, called monomers) in an organ-isms cells that hold (and in some cases process)the information for its development and function-ing, namely DNA and RNA, and possibly proteins.It may serve us well to run through the basics ofproteins, DNA and RNA here, so Ill do that briefly.Both DNA and RNA are made up of long chains offour alternating different smaller molecules callednucleotides, where each nucleotide contains a dis-tinct base (generally a carbon ring structure), aphosphate group, and a backbone (which links thenucleotides together in a strand). The bases eachline up with one (and only one) of the other bases(as seen in figure 11), so that two mirror images oftwo different pairs can be formed (so four base pairsin total). Where DNA uses the bases thymine (T),adenine (A), glycine (G) and cytosine (C) (whereC can bind to G, and A to T), RNA uses uracyl(U) instead of thymine (so that A binds to U). Thestructures of the five bases and a comparison be-tween the structures of DNA and RNA are shownin figure 10. Both RNA and DNA replicate byuse of complementary base-pairing, where each nu-

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Figure 12: Folded RNA strand (image fromhttp://www.uic.edu/).

teins: Because proteins are required to unfoldand copy current-day DNA, we may have toassume that they were likewise linked in thepast. For this reason, both DNA and proteinswould have to appear at the same time. Thispossibility is obviously unappealing, becauseit requires the simultaneous occurrence of twocomplicated steps of macromolecule formation.It presents us with a paradox; in modern cells,DNA is used as the building plan to make pro-teins, but proteins are crucial in copying DNA.

3. A clay world model, which we will describe in

some detail later on.4. A model in which a nucleic acid similar to

RNA acts as both an information carrier anda catalyst that promotes self-replication: Thismodel could, according to Fox, be studiedmost easily in the laboratory. It is also themost likely alternative for various other rea-sons. First of all, RNA, in the trinity formof mRNA, tRNA and rRNA, is one of themost essential core molecules of ancient ge-netics, in much the same way that the citric

acid cycle is central to metabolism. Before the

1980s, people had thought that all enzymesin a cell were catalytic proteins. But in theearly 80s, both Altman and Cech indepen-dently found an enzyme that consisted entirelyof RNA. This means that RNA can both con-tain information and catalyze important reac-tions (like self-replication). This thus resolvesthe DNA/protein paradox.

RNA plays many important roles in all moderncells. 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 inproteins called co-enzymes. These co-enzymes pro-mote reactions in, among other things, the citricacid cycle, including the production of citrate fromoxaloacytate, as well as in helping to build lipids(which are the building blocks of cell membranes)from other essential biomolecules. Finally, RNAcan act as chemical sensors in the form of so-calledriboswitches, which change shape when they comeinto contact with other chemicals. This makes thecentral and ancient role of RNA very plausible.RNA is therefore considered the prime candidateinformation bearing molecule. As we shall see, theconstruction of its nucleotide parts has been prob-lematic. However, there are interesting hypothesesas to how this problem may be resolved. Partic-ularly, there may once have been close relatives ofRNA that have now gone extinct, which rely on thesame nucleotide bases as RNA, but which use a dif-ferent backbone. A top-down approach to studyingRNA that is worth mentioning involves taking ex-isting prokaryotic cells, and engineering them withprogressively fewer genes, so as to identify the min-imal genetic requirements for life. John Desmond

Bernal called this process biopoesis.

Chirality

A final curious feature of biomolecules is their so-called chirality, or handedness. Most (if not all)biomolecules come in mirror image pairs, that arereferred to as right-handed (abbreviated by D, fordextrose=right) and left-handed (L, for livo=left)varieties. These pairs are called chirals (the differ-ent instances are called enantiomers). They formbecause of the tendency for carbon molecules to

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form 4 bonds. An example of chirality can be seen

in figure 13. Most of the properties of chirals areexactly the same. For instance, they have the exactsame composition and structure (except in a mirrorimage of one another) and many of the same phys-ical and chemical properties. However, life tendsto use only one chirality of each general group ofmolecules (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, itis something of a mystery why only a single chi-rality is used. However, it has become clear thatthis reliance can not be violated without cost; cells

respond differently to different chiralities Proteinscan become non-functional (because of the factthat protein function is for a large part determinedby shape) and the DNA helix (the familiar spiralshape) a mess (because the backbone becomes de-formed) without chiral purity. This can result inanything ranging from different responses of tastereceptors to birth deformities. All of this suggeststhat pre-biotic synthesis was inherently asymmet-ric, resulting in homochirality. We will later discusssome hypotheses about why this may have hap-pened. An interesting side note about chirality is

that it tends to flip every few thousands of years.By knowing the ratio between different chirals incurrent day life, fossils can therefore be dated bymeasuring the increase in the non preferential chi-rality. For instance, when an organism dies, it willhave only L-amino acids. Over time, increasinglymore of these flip into D-chirals until a 50/50 equi-librium is again reached, and an age estimate canbe given on the basis of the ratio of L to D aminoacids. However, chirality can also be influenced byenvironmental factors, such as acidity.

I will close this part with a few more notesfrom phylogenetic research. One of the key thingsto note here is that microbes called prokaryotes(bacteria and archaea are prokaryotes), which aremuch 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 ownbuilding blocks (their own food) and deriving theirenergy from (an)organic chemical sources, ratherthan from sunlight (for example, plants are het-erotrophic, by way of photosynthesis). It is pos-

Figure 13: Chiral molecules (image fromhttp://www.ehu.es/).

sible that these autotrophes evolved from surfaceheterotrophes, but that, as crust-dwelling microbes(which are often refered to as extremophiles, andwhich we will meet again later on) were better pro-tected from comet impacts or other natural disas-ters, their ancestral heterotrophes became extinctand the autotrophes became dominant by default.A final thing to note is that phylogeny of prokary-

otes is often complicated by their tendency for hor-izontal (or: lateral) gene transfer, in which twoindividuals sometimes swap DNA. Because of thiscross linking, it is practically impossible to deter-mine traits of the so-called last common ancestor(the lifeform from which all current life is thoughtto be descended) purely by phylogeny.

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3 Bottom Up: Emergence and

abiogenesis experimentsThe top-down approach to identifying or constrain-ing the origins of life is useful for giving some timescale constraints, but it is inherently limited be-cause of the inevitably limited amount of informa-tion we can deduce from it. Another, bottom-upapproach is to try and simulate plausible condi-tions of the early Earth or solar system, and try tosynthesize primitive biochemical compounds. Thisfield is known as pre-biotic chemistry. Of course,we cannot say with absolute certainty that what we

find is exactly how things went down on the earlyEarth, but as long as we use a plausible range ofconditions, these experiments, if successful, makethe case that life can indeed form spontaneouslyfrom non-life, and that it does so under circum-stances that are known to occur out in the naturalworld. Ill start with a very brief description of thebasic notion of emergence, on which most of thiswork is based in the end, and will then move on toincreasingly complex experimental results, and theunderlying hypotheses of the experiments.

3.1 Emergence

Emergence (a term coined by G. H. Lewes) is afield of study that basically addresses the questionof how nontrivial patterns arise from the interac-tion between simple agents. One can think of theinteraction between sand grains and water that cre-ates different characteristic patterns of bumps andripples on a beach, the interaction between neu-rons from which consciousness emerges, or a com-plex chemical pathway that gives rise to emergentpatterns in the resulting environment. As far as Ican tell, emergence and chaos theory (particularlythe field of synchrony, pioneered by Art Winfree)seem to be intimately connected, and may well betwo sides of the same coin. Scientists have identi-fied a number of key factors in an emergent system.The density of the agents, that is, how concentratedthey are in a given environment, is the first. Thereare critical densities that, when crossed, give rad-ically different behavior from lower or higher den-sities. In abiogenesis, this translates into the no-tion that there is some minimal concentration of thebioparticles present for the formation of more com-

plex molecules and molecular systems. Secondly,

the ways in which these agents are interconnectedare of great importance, both in terms of the typesof interaction, and the degree of connectivity. Anexample is the way in which neurons are connectedin the brain, or, in case of abiogenesis, the waysin which the different chemicals in the environmentcan interact with one another. A third factor is theflow of energy through the system. There is somecritical amount of energy flow for which a systemgives rise to emergent behavior. Too low a flow,and nothing happens. Too high, and the emergentbehavior is quickly reduced to rubble by the energyinflux. Finally, the way this energy cycles through

the system is important in both the type of flow,and the rapidity of it. I will return to these pointsat the end of the next paragraph. Overall, theseproperties of or precursors to emergence will be ev-ident in the subsequent paragraphs.

3.2 The spontaneous generation ofsimple organic molecules

We now know that simple organic molecules, dupedmonomers, such as amino acids (which are thebuilding blocks of proteins), lipids (the building

blocks of cell membranes), sugars and bases (themost integral parts of the building blocks of the nu-cleotides that make up DNA and RNA) can formspontaneously under a variety of circumstances.Cocktails of such molecules tend to be referred to asthe pre-biotic or primordial soup, a term that wascoined by Oparin. Ill discuss the most prominentof these hypotheses here. The story is very com-plex and involves a number of models, all of whichare capable of producing monomers, and some evenproduce polymers, which are generally made up ofstrands of many monomers (but well get to that inthe next section). But this first part of the storyturns out to have one very simple answer: it iseasy to spontaneously synthesize most of the ba-sic building blocks of life under a huge diversity ofcircumstances.

3.2.1 The Urey-Miller experiment and pri-

mordial soup

The most famous experiment that demonstratedthe spontaneous generation of monomers was theUrey-Miller experiment, which Ill describe here.

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Figure 14: Urey-Miller experiment setup (imagefrom http://www.uic.edu/).

Since this experiments, some concerns have been

raised with regard to the validity of the un-derlying assumptions regarding the early atmo-sphere, but subsequent experiments have shownthat monomers also arise under a large variety ofdifferent circumstances. Ill close this paragraphwith the main questions that challenge the Urey-Miller results. Miller, for his PhD thesis, simulatedthe early atmosphere of the Earth as conceived byUrey, his adviser. Urey postulated that the earlyEarth would have an atmosphere that is radicallydifferent from todays. Todays atmosphere con-sists mostly of Oxygen (O2) and Nitrogen (N2), butthe high dose of oxygen is mainly due to the processof photosynthesis carried out by plants. Urey hy-pothesized that the early atmosphere would havebeen highly reducing, which basically means thatit prevented oxidation by the removal of free oxy-gen from the air. In particular, Urey hypothesizedthat the early atmosphere was composed mainlyof hydrogen (H2), Methane (CH4) and ammonia(NH3). Miller set up a simple and elegant experi-ment in which he heated up water, resembling theEarths oceans, passing the water vapor througha series of tubes into a vat containing the atmo-

spheric gasses (simulating the atmosphere itself) as

described by Urey, and adding series of electricalsparks as an energy source to generate a chem-ical reaction (basically simulating lightning). Inessence, the energy blasts electrons away from thechemical compounds, making them more reactive.It should be noted that subsequent experimentshave also explored other energy sources, such asUV radiation, as well as other atmospheric condi-tions, with similar results. The water vapor, mixedwith the chemical compounds resulting from thegas, was then condensed through a series of tubesleading back in to the ocean. The basic setup ofthe 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, amongother things. The experiment was confirmed inde-pendently a number of times, and was also repeatedwith variations thrown into the mix, using, for in-stance, a different mixture of atmospheric gasses,a different energy source, or an addition of pow-dered minerals (representing soil). Almost everykind of monomer used in current-day life has beensynthesized in this way, with three notable excep-tions: ribose (a sugar), and the nucleotide basesadenine and guanine. It is interesting to note that

the Urey-Miller experiment gives a similar distri-bution of monomers to that employed by life today- though it should be noted that the experimentalso produced many other molecules that have norole in current-day life. What basically happensin the Urey-Miller type experiments is that, un-der the influence of energy, the atmospheric gassesform a highly reactive mixture of chemicals like hy-drogen cyanide (HCN) and formaldehyde (CH2O),which easily bind to other molecules in the environ-ment. For instance, amino acids are made whenHCN, CH2O and NH3 undergo what is knownas Strecker synthesis. John Or found that whena solution of HCN was heated, adenine was pro-duced. Similarly, in a rich solution ofCH2O, sug-ars, including ribose, were spontaneously produced.The problem was that Millers concentrations ofHCN and CH2O were typically too low to pro-duce the reactions. Essentially, adenine is producedwhen 5 HCN molecules combine, and in Millerssolution the largest chains of such molecules werelength four HCN chains. It turns out, though, thatthere is a solution to this problem. Orgel proposedthat, when water freezes that contains a solution of

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molecules, the thing that freezes most rapidly is the

pure water. The solution therefore tends to becomemore concentrated during the freezing process, andthis can then give rise to interesting chemical in-teractions. This is an example of emergence wherethe energy flow has an essential role to play. Thesereactions are slowed down, however, because of thedecrease in temperature. When Miller heard ofthis, he decided to freeze his solution to -20C to seewhat happened. Apparently he forgot about it, be-cause it remained in his freezer for about 20 years,making it one of the longest lasting experimentsin the history of chemistry. After finally retriev-ing the sample, it was found that large amounts

of adenine had indeed been generated. The impor-tance of this is that it suggests that, although theancient sea may in itself have been too diluted toaccount for all monomer occurrences, as the Earthwent through subsequent periods of freezing andheating, the monomers that function as the basisof organic chemistry could have formed quite easily.

There are four basic problems with the UreyMiller experiment. First of all, there are some se-rious doubts about the composition of the simu-lated atmosphere used by Urey. More recent stud-ies from geochemistry suggest that the atmosphere

was a less reactive atmosphere of mostly N2 andCO2, lacking in CH4 and NH3. Secondly, althoughmonomers were formed, almost none of the poly-mers (like RNA and proteins) were found, and thesepolymers really form the basis of functionality inmodern living cells. Third, according to Brooksand Shaw (1973), there is no evidence in the geolog-ical record that any primordial soup existed; thatis, if it had, we should expect to find sedimentationthat confirms this, but we have never seen anythingof the sort. Finally, these polymer macromoleculestend to break down under Millers conditions, bothbecause of hydrolysis and when subjected to highdoses of energy, like the electricity or ultravioletradiation used in these experiments. Hydrolysismeans that, when immersed in water at room tem-perature and pressure, peptide bonds, which holdtogether chains of monomers in many kinds of poly-mers, tend to break down, as they are not as strongas covalent bonds (bonds that are formed by shar-ing of one or more electrons). When peptide bondsare forged in the process known as condensationpolymerization, they release water, and inversely,when in the presence of lots of water, these bonds

are easily broken down. This has to do with the

polarized nature of water; an H-bridge, which is re-sponsible for such bonds, is formed because watermolecules are not radially symmetric. The result isthat one side of the molecule has a slight positivecharge, while the other side has a slight negativecharge. The molecules can line up head-to-tail andform weak bonds between the positive and nega-tive ends, which is, in a nutshell, what also leadsto water surface tension. Also, the Miller exper-iment produces many chemical components thatwould cross-react with the amino acids or breakup any forming peptide chains. Hydrolization isa problem that needs to be solved, which plays a

major role in many abiogenesis hypotheses, and itagain shows to importance of energy for emergentbehavior. Subsequent experiments have gone someway in addressing these concerns, and I will discussthem further below.

3.2.2 Extremophiles

It was once assumed that most life on Earth con-centrates at or near the surface of the crust thatcoats our planet, under circumstances that we findthe most familiar. However, this turns out to be an

erroneous assumption. For one thing, the discoveryof life in the deep ocean near submerged volcanicsystems known as hydrothermal vents suggests thatlife can exist under much more versatile conditionsthan previously assumed. Secondly, following thediscovery of life near these vents, discoveries havebeen made in recent decades (most of which sincethe early 90s) that suggest that nearly half theEarths biomass (the combined mass of all livingorganisms on the planet) may be found in subter-ranean microbes (particularly archaea, which arethought to have been around at least as long as,and possibly longer than bacteria) that live deepwithin the crust, at depths of up to at least fivekilometers. They can be found inside deposits ofgranite, basalt, and other minerals that we gener-ally consider very inhospitable. Furthermore, livingmicrobes have been found under the intense heat ofvolcanic areas, or under a mile of Antarctic ice. Ba-sically they are found almost anywhere whereverthere is water present. These organisms live un-der circumstances of extreme pressures and hightemperatures, lacking in any significant amount ofsunlight, circumstances under which most surface

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Figure 15: A hydrothermal vent. Note thetube worms at the left of the image (image fromhttp://web.uvic.ca/).

life would be unable to survive, and they are there-fore generally called extremophiles. They tendto have an extremely slow metabolism and may beinactive for thousands of years. Cell division mayonly occur once every millennium, and for the re-mainder of the time, these organisms seem to justsit and wait. This is particularly true for the crust-

dwelling and ice-dwelling microbes (but less so forthose near vent-systems). There appears to be littleor no predation in these systems, and so the mainsource of competition is competition for resources.Extremophiles have been an important factor inthe proposal of several different alternatives to theUrey-Miller source of monomers. Although theyare generally referred to as competing hypotheses,we can view these as many simultaneously (or suc-cessively) productive sources of basic organic mat-ter. I will discuss some of the more prominent ofthese in the next few paragraphs. One of the fun-damental characteristics of these environments isthat their extreme conditions can give rise to unex-pected chemical reactions, yet another example ofemergence.

3.2.3 Monomers from hydrothermal vents

The idea that the sun is the prime source of en-ergy that ultimately feeds life on Earth is truefor most of the life that currently exists on Earth.Millers experiments are therefore based on the ideathat life originated at or near the surface of the

oceans. However, as weve seen there are some po-

tential problems with a theory of this kind. An-other hypothesis came along with the discoveryof (by today many) isolated complex self-sufficientecosystems around hydrothermal vents at the bot-tom of the Atlantic and pacific oceans (sometimesreferred to as black smokers when they emitclouds of black material), which are almost com-pletely cut off from the sun as a prime source ofenergy and exist under crushing deep sea pres-sures (500-2000 atmospheres) at hot temperatures(200-300C). Hydrothermal vents are deep-oceancracks in the Earths surface from which mixtures ofheated gasses are emitted. Vent structures consist

of microcaverns that are coated by thin, membrane-like metal sulfide walls. An image can be seen infigure 15. The current-day ecosystems surroundingthese vents contain microbial organisms, as well asspecies of crabs, shrimp and tube worms. It turnsout that the microbes are the primary energy pro-ducers in these systems, reminiscent of the role ofplants in more familiar ecology. These organismsexploit the mineral instability that results fromthe hot water and gasses emanating from the deepsea vents, mixing with the cold water surroundingthem, and flowing over sulfur-rich surface minerals

in the process. It has since been proposed, by Hoff-man, Baross and Corliss, that hydrothermal ventsmay well be the best place for the formation of earlylife. The deep ocean would have found more shel-ter from comet impacts that the early Earth wassubjected to during the Hadean eon, and the fos-sil evidence mentioned earlier, and the observationthat current day ecosystems thrive near these ventsprovide strong support for this hypothesis.

There appeared to be some potential problemshere that needed to be addressed that Miller, as adefender of an opposing view, was obviously keen topoint out. First of all, as was the case in the Urey-Miller experiment, the heat from the vents wasthought to break down any macromolecules thatare formed. But, as we will see in a later paragraph,this assumption turns out to be likely to be false(or rather, incomplete and therefore inaccurate).Second, modern day hydrothermal vent ecologiesare dependent on oxygen, which ultimately comesfrom photosynthetic (plant) life. The early Earthwould have been lacking in free oxygen. In otherwords, there would have to be a way for a rudi-mentary metabolism to evolve that did not require

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large amounts of oxygen. So, the hydrothermal

vents theories have their problems, but they openedthe door for alternative hypotheses from the thusfar unrivaled primordial soup idea. We will returnto these issues when we look at the emergence ofpolymers and self-replicating systems. Hydrother-mal vent discoveries also kick started the searchfor other extremophile organisms, as we mentionedabove.

Monomers from minerals

Up until now, we have focused mostly on the roleof the ocean water and the atmosphere, and have

largely ignored the role of minerals in the Earthssoil. Obviously, minerals and rocks may haveplayed an important role. First of all, as a sourceof protection, overhanging rocks can shield formingorganic molecules in a tidal pool from the UV ra-diation of the sun. Second, they can protect tidalpools from incoming waves, and, as water evap-orates, allow such a pool to become condensed,resulting in a less dilute soup of organic compo-nents, which is more likely to undergo reactions andpolymerize. Similarly, organic molecules can accu-mulate in small pockets in, for instance, volcanicrock, which keep them condensed as water evap-

orates from them, as well as protected from UVlight. Additionally, many of the most common rockfaces contain multiple cracks and pores roughly thesize of a cell. Such pores and cracks result in anenormous surface area on which many simultaneousnatural experiments for self-organization can oc-cur. Finally, it makes sense that water, Earth, andatmosphere, as the Earths key ingredients, playeda cooperative role in the formation of life. Thissection will outline several theories of monomer(and some possible polymer) production that re-volve around minerals, rocks, clays and crystals. As

we will see, minerals have a number of importantproperties that allow them to function as catalysts,sources of energy, sources of protection, and as scaf-folding for the construction of larger molecules thatare not stable enough to form spontaneously.

Hydrothermal vents revisited

Hydrothermal vents remain one of the prime candi-dates for the place of the origins of life, and we willencounter it several more times, most notably inGunter Wachtershausers metabolism-based iron-

sulfur world, and in the PAH hypothesis for the

origins or RNA. Therefore, Ill mention a numberof preliminary experiments on origins of monomershere. Many (though not all) of these experimentsincorporate minerals as key ingredients. First,Hazen, Morowitz, Yoder and Cody performed sev-eral experiments under high pressure, incorporat-ing a realistic mixture of powdered minerals, atmo-spheric gasses, and water. The initial motivationfor this came from the observation that the dielec-tric constant of water, which is a measure of po-larity that influences the ease with which peptidebonds can form, decreases dramatically under highpressures and at high temperatures, from about 80

to 20. Recall that, at normal pressures and tem-peratures, water acts as a(n unusually potent) nat-ural organic solvent which can easily break peptidebonds, and that this has to do with the polarizednature of water. By decreasing the dielectric con-stant, then, it may be possible for peptide bondsto form. Hazen et al. decided to concentrate onthe reverse citric acid cycle described earlier, par-ticularly on pyruvate. Recall that pyruvate plays amajor role in this metabolic cycle. It also plays afundamental role in multiple other processes, suchas the splitting of glucose into 2-pyruvate (a pro-

cess known as glycolysis). Pyruvate is essential forlife as we know it, but it does not work in wa-ter at room temperature without a catalyst suchas an enzyme, and it tends to break down. Totest their hypothesis, they subjected a mixture ofpyruvate and water to intense pressure and hightemperatures similar to those found at hydrother-mal vents. The result was that pyruvate did in-deed react, in a big way. In fact, their experi-ment resulted in so many different chemicals (tensof thousands) that it was impossible to analyzein full; a hopelessly diverse mixture referred to ashumpane. What they found was that many al-cohols, sugars, and various larger molecules thatresemble those found in biochemistry were synthe-sized (showing both ring and branching structures),and that polymerization had occurred in a varietyof molecules, some of which incorporated dozens ofcarbon atoms. However, this abundance also posedthe question of where to go next; with such a largevariety of ways, it is almost impossible to predictwhich roads are the most promising. There area few potential problems with these experiments,which can be summarized as follows. First of all,

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the concentration of pyruvate used was unrealisti-

cally high, and the end products too diluted forcontinuous chemical interactions. So, for this the-ory to work, a way must be found by which boththe reactants and the end products can accumu-late (and stay accumulated) closely together. Sec-ond, similar to Millers predicament, the reactionsresulted in a large number of products, many ofwhich play little or no role in life. The problem isthen how we can explain how particular productsmay have been selected, and others excluded in theformation of life. Third, many organic moleculeswere still missing, and so other ways would have tobe found to account for these.

But several more experiments have since beenconducted. One of these experiments, by Jay Bran-des, featured a mixture of water, nitrogen, and ironrich minerals (commonly found near vents), result-ing in ammonia (NH3; recall that miller assumedthis to be present in the atmosphere; an assump-tion that later turned out to be false). Ammoniais an essential ingredient for amino acids. Thisresult suggests that hydrothermal vents may beprinciple sources of ammonia. A follow up exper-iment combined ammonia, pyruvate, and severalcommon powdered minerals, resulting in (among

other things) large quantities of the amino acidalanine. This directly contradicts Millers criti-cism that vent-type conditions would destroy com-pounds like amino acids. Additionally, Brandes re-vealed in a later study (on the amino acid lucene)that at least some (and possibly all) amino acidsare much more stable in the presence of the min-eral pyritite (iron sulfur), which is often found nearvents. As we will see, the minerals used in theseexperiments are likely to be very important in un-derstanding the origins of life. Similarly, studieson bone fossils have revealed that certain miner-als can prevent (to some extent) the rapid break-down of protein structures, because of strong bond-ing between the minerals and the proteins. Thisprotects and preserves them, and this can workfor amino acids as well. The possible soft tis-sue recently discovered in fossil T-Rex bones byMary H. Schweitzer may have been preserved inthis way. In a later experiment, Kono Lemke andDavid Ross showed that, when glycine and waterwere cooked under vent-like conditions (without theaddition of minerals), glycine declined much moreslowly than under normal conditions. What was

even more surprising is their discovery that this

also lead to the rapid link chains of amino acidformation. This contradicts the common knowl-edge that these chains are destroyed by high tem-peratures (another example of emergence). Underthese conditions, peptide chains are much less solu-ble and therefore more stable. If these form rapidlynear vents and then float out in clumps, into thecooler sea water, they separate out as a much morestable second-phase product. This is quite signif-icant, because it gives a partial possible solutionto the macro-molecule construction problem. Car-bon fixation reactions, in which more carbon atomsare incorporated into an organic molecule to form

larger molecules, is common and happens rapidly inhydrothermal experiments. Two of the most com-mon pathways can be described as follows. Thefirst is promoted by many common minerals thatincorporate iron, zinc and/or copper. These min-erals promote the so-called Fisher-Troph synthe-sis, which is a carbon fixation reaction which re-sults in chain-like molecules. These results havebeen confirmed by studies at real current-day hy-drothermal vents, and the resulting products aresimilar to those found in petroleum. The secondpathway is driven by cobalt and nickel sulfurs, and

promotes a so called CO-insertion reaction, a car-bon fixation reaction in which carbon monoxide isinserted. If one repeats these reactions and mixesthe results, many complicated molecules can easilybe synthesized reliably. Finally, minerals often dis-solve at high temperatures and pressures, resultingin chemical reactants that can act as both cata-lysts and reactants. For instance, sulfur, can dis-solve and react with water and CO2 to give rise tothiols and thiolesters, which are catalysts for addi-tional biochemical pathways (we will discuss theselater in the thioester world hypothesis). Similarly,iron, water and CO2 can form so-called iron com-plexes, structures which can act both as catalystsand reactants (see the iron-sulfur world).

Hydrothermal vents run across tens of thousandsof miles across the ocean floors, comprising bil-lions of square miles. Given the (minimum) win-dow for lifes emergence of approximately 150 mil-lion years, organic compounds could be producedin vast quantities.

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Gunter Wachtershausers hypothesis

Gunter Wachtershauser (a close friend of Karl Pop-per) has suggested a hypothesis on the origins oflife, using the catalytic properties of various miner-als, such as iron (Fe), nickel (Ni) and sulfur (S).These minerals are all found in abundance nearhydrothermal vents. As we have seen, mineralsmay form an energy rich surface that can catalyzemany reactions for the synthesis and assembly ofmonomers (and, as we will see, polymers) that mayotherwise be infeasible. Wachtershausers hypoth-esis is unusually detailed, and has been designedto be rigorously testable and falsifiable. He hasproduced more than a hundred pages of specific

chemical reactions that could lead to the first cycli-cal metabolic system. The core of the hypothesisis that metabolism can proceed without catalystssuch as proteins, which are essential to metabolismin modern life, when the necessary organic compo-nents are in the presence of certain minerals (suchas Fe, Ni, and S). He makes a number of core as-sumptions based on his observations. First, it is as-sumed that basic random pre-biotic synthesis as inthe Miller experiment did not play an essential role.Wachtershauser bases this assumption on a numberof observations. First of all, the organic soup that

would result from the Urey-Miller process would befar too dilute for the most interesting processes totake place. Second, the Urey Miller experimentcatalyzed a large number of molecular species(group of molecules with similar properties) thatcould have played no conceivable role in lifes ori-gins. In this view, the Urey-Miller experiment islargely irrelevant to the origins of life. Second, itis proposed that life is not heterotrophic (that is,gathering molecules from the environment as food),but rather autotrophic (making its own molecules).Since the organic soup was probably much too di-luted, he argues, it was an unreliable food source,and so life must have been capable of producing itsown necessary building blocks. Third, it is assumedthat energy did not come from UV radiation fromthe sun, or electricity, but rather from chemical in-teractions. It is argued that photosynthesis, whichis the modern process by which plants capture theenergy from sunlight, is far too complex to havebeen a prime source of food. Additionally, UV radi-ation and electricity are far too disruptive for mostinteresting chemicals to be stable. Finally, most lifetoday uses chemical energy as a primary source of

energy. This process can be mimicked by organic

compounds accumulating on unstable mineral sur-faces. These surfaces release energy when they in-teract with other compounds, and thereby providea stable source of energy which is much like thekind used by cells today. In fact, many of the keyproteins which catalyze modern metabolism have,at their core, a cluster of Fe or Ni atoms. Finally,Wachtershauser argues for a metabolism-first pointof view. In this view, the elements of life arose notin the form of self-reproducing genetic material, butas a self-replicating metabolic cycle of chemical re-actions. In other words, an early atmosphere, con-sisting of mainly H2 (hydrogen) and CO2 (carbon

dioxide), under the influence of energy released byminerals, ultimately lead to the chemical elementsthat drive life. In his view, life was both inevitable,and would have arisen rapidly on the early Earth.We will return to Wachtershausers model when ex-amining the origins of self-replication. His modelhas been duped the iron-sulfur world.

Crystals

Gustav Arrhenius has been one of the first peo-ple to suggest that certain crystal minerals mayhave played a major role in the synthesis of organic

components. He was primarily interested in thecommon double-layer hydroxides, which may con-tain many different elements, such as Fe, Mg (mag-nesium), Cr (chromium), Ca (calcium), Al (alu-minum), Ni, etc., in many compositions, but alwaysin a two layer structure with a space in between lay-ers (see figure 16). These spaces can be occupiedby small molecules like CO2 and H2O. The organicmolecules become concentrated between the layers,and it has been shown that they have a tendencyto form larger molecules that may not otherwiseemerge from a primordial soup. By changing the

composition of these crystal structures, they can befine-tuned to perform various specific tasks. For in-stance, Arrhenius et al. managed to spontaneouslysynthesize sugar phosphates, which both form thebackbones of RNA and DNA, and are a key ingre-dient for ATP, one of the most important moleculesused in cell metabolism.

Zeolites

Joseph Smith proposes that a diverse class of min-erals called Zeolites may have played an important

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Figure 16: Double layer structure of 2,4-D in [Li-Al-Cl] LDH, with small biomolecules in between(image from http://www.rsc.org/).

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

role in the origins of biochemical elements. Zeo-lites have a lattice-like framework of small poresmade up of silicon (Si), aluminum, and oxygenatoms (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 H2O orCO2 to enter, while larger molecules are excluded.These molecules can then react inside the pores,and form larger organic components. Furthermore,under the influence of specific minerals, the largermolecules that land on the zeolite surface can besplit into smaller equal size fragments (a trick com-

monly used in petroleum refinement), which canthen be used in the construction of new, largermolecules. Zeolites are common in volcanic envi-ronments. Smith suggests that the canals insidethese minerals may even have functioned as thefirst cell walls. So far, however, no experimentshave 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

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of organic components. Molten rock is over 1000C,

and it inevitably contains mineral impurities, con-taining, for example, traces of H20, N and CO2.As the rocks cool, different minerals will begin tocrystalize in sequence at different temperatures. Asthey cool, the impurities in the minerals tend to ac-cumulate on the outside of the crystal lattice, con-centrated at defects in the crystal structure. Thesedefects form elongated latices that allow the nowcondensed compounds to bond with each other ina similarly elongated, chain like structure. Sucha chain like structure is frequently seen in organiccompounds, where different, smaller molecules areconnected by a carbon backbone. The compounds

are, of course, locked inside the surrounding rock,but Freund suggests that erosion eventually re-leases these elements. In principle, every mineralhas the potential to drive a similar process, andgiven the enormous amounts of rock on Earth, sim-ilarly enormous amounts of organic componentscould be released. This mechanism could rival theUrey-Miller process in productivity (for instance,natural perito was found to contain 100

1000000parts

carbon, much of which was part of a carbon back-bone). One problem with the hypothesis is thatthe destructiveness of these high temperatures may

still be a significant problem for the formation ofpolymer chains. Furthermore, although observa-tions suggest that many crystallized molten rockdoes indeed contain many organic molecules, it isdifficult to test, since contamination is a very likelyproblem to occur. Almost every rock face on Earthis covered in microbial life, or at least in the remainsof it, and is therefore contaminated with organicmolecules.

From this we can conclude that rocks and min-erals are likely to play a key role in lifes origins.They act as catalysts for certain chemical reactionsthat would otherwise be unlikely to occur, they pro-vide energy to power the process, and as we willsee, they can provide templates for the formationof polymer chains.

3.2.4 Monomers from the Deep Hot Bio-

sphere

It has been suggested by Thomas Gold that lifemay have first arisen deep within the Earths core.Gold had previously suggested (and before him

Russian researchers) that the Earths mantle may

be a primary source for biocarbons, which formone of the most important groups of biomolecules.These biocarbons, he claimed, could be the primarysource of the Earths petroleum deposits. He basedthis view mainly on the presence of helium (He)in petroleum. Helium is a very light gas whichcould not have come from the Earths atmosphere,and so the source of petroleum, Gold argued, musthave come from a subterranean source, rather thanhaving come from surface microbes that had beenburied and decomposed. The mixture of helium,minerals and hydrocarbons would permeate up-ward as it is lighter than the surrounding rock,

and the hydrocarbons within it would then be pro-cessed by ancient subterranean microbial lifeforms.This then produces the biofilm that we observe inpetroleum that lead us to conclude that petroleumis organic in origin. Under Golds controversial hy-pothesis, these hydrocarbons constitute a better,continually replenished food source than the pri-mordial soup, or a puddle of condensed organicmaterials, which are, at least in principle, muchmore easily exhaustible, and could therefore leadto extinction. Similar to the deep ocean vent hy-potheses, the basic monomeric compounds would

be formed under the intense pressure and heatfound in the Earths deep crust, and Gold proposesthat this was where the first proto-life may haveformed. This explanation is lacking in detail, butmany of the details can be borrowed from alter-native hypotheses, such as the hydrothermal ventshypotheses and the various roles played by mineralsurfaces as described above. It is also consistentwith the observation that hydrothermal vent en-vironments may promote reactions that result inproducts commonly found in petroleum, and thatmonomers may have been present in abundanceduring the formation of the solar system, whichwill be described below. Future discovery of mi-crobial life below the surface of another planet inour solar system would also significantly increasethe credibility of this theory.

3.2.5 Monomers from Space

One of the most surprising sources of monomers(and possibly even some polymers) comes fromspace. It has been known for some time now thatspace, particularly the huge nebulae which are the

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birth places of star systems, contain large amounts

of carbon (C), hydrogen (H), nitrogen (N) and oxy-gen (O). There is also evidence from spectral anal-ysis in radio astronomy that these giant cloudsof space dust contain large quantities of organicmolecules. Over 140 different organic componentshave been identified in these clouds, some consist-ing of chains of at least 12 carbon atoms (and var-ious other elements). This may be somewhat sur-prising, since outer space is bone-chillingly cold.The explanation for this process is that, as frozenmineral dust particles that are covered in ice travelthrough these clouds, they tend to pick up atomsand molecules. These hitchhikers are then sub-

jected to UV radiation, which makes them morereactive, and they then react with other atoms ormolecules on the particle surface to form increas-ingly larger molecular structures. Complex dia-grams have been constructed that depict the effi-ciency at which particles would pick up molecules,which show that there will be a gradual buildup ofincreasingly larger molecules. As mentioned, neb-ulae are the places in which star and planet forma-tion takes place. Stars and planets essentially formout of the gas in these nebula. During the for-mation of the so-called proto-planetary disc, which

eventually condenses to form the various planetaryand asteroid bodies in a star system, there would bea steady influx of organic particles. As a result, theamount of organic molecules in that disc is morecondensed than in the surrounding nebula. Thiscondensation increases the rate of synthesis evenmore, resulting in even more complex biomolecularstructures, and so organic compounds are thoughtto be a significant component of planet formation.

3.2.6 The radioactive beach

A final source of monomers that I will discusshere is the radioactive beach hypothesis, coindedby Zachary Adam. Adam claims that the closeproximity of the moon to the early Earth couldhave concentrated grains of heavier radioactive el-ements, such as uranium, at the high tidal markon beaches. According to this hypothesis, these ra-dioactive materials may have provided the energysource necessary to have driven the formation of or-ganic molecules, from acetonitrile in the water. Inaddition, radioactive monazite can release solublephosphate into the beach sand. Phosphate is an

important building block for organic molecules like

phospholipids. Additionally, radioactive actinidescould have driven the formation of organo-metaliccomplexes, which could have played an importantrole as catalysts for early life. Adams hypothe-sis is confirmed by computer models from the fieldof astrobiology, which show that these radioactivematerials could show the necessary self-sustainingnuclear reaction. Under this model, amino acids,sugars and phosphates can all be simultaneouslyproduced.

3.2.7 Chirality

The first person to offer an explanation of lifeschirality was Louis Pasteur. Pasteur noticed thatpolarized light can be created by passing normallight through certain crystals. This means thatsuch crystals filter out light with different polari-ties, while allowing light with another polarity topass through the structure unaffected. Potentially,this can cause the selective breakdown of D-aminoacids or L-sugars. In deep space, rapidly rotatingstars can also emit polarized light. Another par-tial explanation from physics comes from the weaknuclear force. Most forces in nature are symmet-

ric, but the weak nuclear force is asymetric. Beta-decay (the emission of electrons) is driven by theweak nuclear force, and the end product of this de-cay is polarized. This too may select for moleculesof a particular handedness. The problem with thisexplanation, though, is that the bias is less than1%, and so the effect is likely to be trivial. Sim-ilarly, favored chirals may be slightly more stablethan their mirror image, but this effect is likewisevery minute. There is frequently a preference forbonds between two molecules of the same chiral-ity over those of differing chirality, because theytend to fit better together. This also happened in

Pasteurs experiments. So, each molecule might beseen as a micro-environment that selects for othersof the same chirality. In this case, it is possiblethat polymers have to maintain chiral purity in or-der to form. However, synthesis experiments seemto contradict this.

Chiral selection on crystals

The solution may come in the form of certain com-mon chiral mineral surfaces (such as in quartz),which do show a strong preference for similar chiral-

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ity. The crystals on which biomolecules form may

themselves form to be chiral, purely by chance (theformation of a seed crystal is called nucleation).Local chiral environments like this are found ev-erywhere on Earth. Most minerals are not chiral(though many of the more common minerals are),but even non-chiral crystals often feature patternsof chiral surface structures. Every grain of sandcould potentially provide a chiral surface. Again,the chirality of mineral surfaces tends to be 50/50between the enantiomeres, so we have to look notat the global scale, but at the local scale. Moleculesthat are synthesized (seeded) on such local chi-ral template surfaces will themselves turn out to

be chiral. Once a simple self-replicating systemhas been established on one of these crystal sur-faces or subsurfaces (in ways we will discuss later),rapid growth can ensue in which all other moleculesare consumed as food, and the chirality of themolecules in the self-replicating system will quicklycome to dominate the local environment. Theremay then at some point have been multiple differ-ent competing chiral systems, one of which came todominate over the course of time by natural selec-tion in competition for resources.

The process of looking for an environment that

is able to separate different molecules of differingchiralities is referred to as resolving a racemate.Hazen et al. carried out such an experiment onchiral selection using a racemic (=50/50) mixtureof a specific amino acid (called aspartic acid). Intheir experiment, they used the common mineralcalcite (CaCO3), which is also found in seashells.Calcite has the desirable property that, aside fromhaving different faces with corresponding differingchirality, it also has cleavage faces (along whichthe crystal breaks more easily), which have no pre-ferred chirality. These cleavage faces should exhibitno selection preference, and thus serve as a base-line. A baseline is important here, because of theinevitability of contamination. By comparing theratio between differing chiral biomolecules on eachchiral crystal face to this baseline, excesses can bemeasured that should be independent of the con-tamination that was not washed away during ster-ilization. Using a double blind test, they found adifference of a few percent, with increased L-chiraldomination of amino acids on the L-chiral crystalsurfaces, R-chiral preference shown for the R-chiralsurfaces, and no preference at all for the non-chiral

surfaces.

Looking slightly ahead, this gives a plausible sce-nario for the formation of chiral polymers; as chiralmonomers line up on chiral surfaces, they undergopolymerization, resulting in homochiral polymers(in this case, proteins). This also has significantcommercial applications, for instance, in medicine.

Recent work (in 2003) has pointed to the aminoacid serine as being a possible instigator of ho-mochirality in amino acids. Serine forms verystrong bonds with other amino acids of the samechirality, resulting in an eight-molecule homochiralcluster. Other amino acids can form weak bondswith amino acids of the opposite chirality. It is notclear how left handed serine in particular becamedominant, but the results do suggest a way for ho-mochirality to be maintained, once formed.

3.2.8 Conclusions on monomers

As we have seen, there is an abundance of potentialsources of monomers, which constitute the build-ing blocks of life. No single source may have beendominant, but it is safe to say that monomers wereeasily manufactured and present in abundance on

the early Earth. But this is only the first step. Themain problem at this point is how and why certainspecific monomers are selected, organized and as-sembled, rather than how monomers can come intoexistence. This will be the topic of the next section.

3.3 The generation of polymers frommonomers and the origins of self-replication

The next question to tackle is the leap that needs tobe made from relatively simple monomers to poly-mers. In this section we will address research onthe question how things like the genetic code, thecell membrane, proteins, and even systems of inter-acting biomolecules that form metabolic cycles mayhave arisen. I will start with the formation of somegeneral theories for the origins of polymers, thenmove to cell membranes, and then move on to pro-teins, and subsequently to the origins of metaboliccycles and the genetic code. But first, Ill men-tion some more general characteristics of macro-molecules and problems that need to be solved.

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3.3.1 The construction of macromolecules

To start with, the main problem that we need toaddress is how macromolecules are assembled. Asweve seen, polymerization can be difficult under avariety of circumstances, particularly when in thepresence of water or too high an influx of energy.As we will see, emergent behavior in these oftencomplex systems can give rise to unexpected re-sults. Second, we need to address the question ofwhy these molecules are selected as a subset of thepossible polymers that could exist. At some point,there may have been many macromolecular vari-eties that currently play no role whatsoever in any

living system. We have seen some hints of possibleexplanations, for example, when discussing zeolitecrystals and chirality. It is worth investigating whylife today uses only a handful of building blocks,resulting in only a handful of basic types of chemi-cal reactions, almost all of which are carbon-based.Another feature of polymers that is worth notingin this context is their modularity. Most poly-mers (or systems thereof) are members of a smallnumber of major families (proteins or nucleic acids,and lipid cell membranes). All of these are mod-ular in design; they can be broken up into smaller

molecules that are by themselves monomers, likeamino acids (in proteins), sugars (which are com-posed of ring structures or chains with a carbonto hydrogen to oxygen ratio of 1:2:1, and are typi-cally locked up in polymers of millions of moleculeslike cellulose or starch), lipids (fats and oils usedin membranes, or energy storage and for variousother tasks) an nucleotides (in DNA and RNA). Apossible explanation for this modularity is that itis simply more economical to do so. By using thesame building blocks for many tasks, componentscan be re-used and recycled, and synthesis of onetype of building block can underlay many differentprocesses. In the same way that the cost of buildinga house with individually designed bricks would beimmensely high, so too could the use of many differ-ent complex types of reactions and building blocksbe costly for life. In other words, life that makes usof such economic modular design may simply haveoutcompeted other possible early life by means ofbeing more efficient. A general observation that wemade in the last section is that the early oceans arethought to have been simply too dilute. This im-plies that the probability of just the right molecules

coming together purely by chance is simply too re-

mote. The only logical answer to this is that lifemust have concentrated on some kind of surface,as is a typical solution for many chemistry issueswhere diluteness is a problem. This could be thesurface of a crystal or a mineral, for instance, ina tidal pool where cycles of evaporation and flood-ing can continually replenish and concentrate thechemicals in question, at the ocean floor (near hy-drothermal vents), on a particle in space, or per-haps at the boundary between the ocean surfaceand the air. In essence, any contact point betweentwo distinct materials could do the trick. Finally, itmay be possible for carbon to assemble its own pri-

vate surface from the environment, which can thenalso be used as a template. We will see this lateron when we discuss the PAH world and RNA, forexample.

Impact macromolecules

One of the more exotic possible origins of macro-molecules comes from research on comet, aster-oid and meteor impacts. At first glance, it wouldseem likely that an impact of this sort would breakup any complex macromolecules that could haveformed. This seemingly sensible assumption was

tested by Jennifer Blank, who conducted severalhigh velocity impact experiments. Blank shotstainless steel capsules containing various organiccomponents (five different amino acids and wa-ter) through various rocks and minerals at approx-imately 4000 miles per hour. This creates approxi-mately 200000 atmospheres of pressure and createstemperatures up to 1000C (note the irony in herlast name). Blank discovered that pairs of aminoacids form peptide bonds in every single run at theexpense of some other, smaller molecules (whichevaporated). In other words, although the number

of organic components is reduced, their diversityincreases as the result of such impacts.

Polyphosphates

Another mechanism that may have driven polymer-ization may be found in the properties of polyphos-phates, which are formed by polymerization ofmonophosphate ions (PO4-3). Several mechanismshave been suggested that could drive this polymer-ization process. Polyphosphates can cause poly-merization of amino acids into peptides, and are

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key precursors in the synthesis of compounds like

ATP, which we discussed earlier. One problem withthis theory is that calcium reacts with soluble phos-phates to form the insoluble apatite. This meansthat we are required to find a plausible mechanismto keep calcium ions away from the phosphates. Aswe will see later on, lipid vesicles may be one suchmechanism. One interesting idea about the originsof phosphorus is that it nay have been introducedon Earth by meteorites.

3.3.2 The clay world

Although some of the polymers may have formed

as the result of impact events, there are other, lessdisruptive ways in which they can spontaneouslyassemble. In particular, mineral surfaces may haveplayed a major role, acting as catalysts, attrac-tors and scaffolds in the construction of complexmolecules. We saw examples of this for monomerformation earlier. Here I will explore how a sim-ilar principle can apply to polymerization. Onesuch hypotheses, which places particular empha-sis on the scaffolding principle, stems from the useof clays. Clays are nutrient rich, and they havea very regular, layered atomic structure, made up

of two types of layers (one tetrahedral, which canincorporate minerals such as Si and O, and oneoctahedral, which can incorporate, among others,Mg, Al, or Fe. These layers are stacked in differentvertical sequences of two (tetrahedral/octahedral)or three (tetrahedral/octahedral/tetrahedral) lay-ers, with spaces in between. Billions of such layersmay be stacked on top of one another in alternat-ing ways, and clays are found everywhere on Earth,resulting in an enormous overall surface area. Thelayers are quite strong, but the space between themare quite weak, which is basically what makes clayslippery. Foreign molecules may accumulate be-tween these layers and react to form increasinglylarger molecules. What is more, clays are oftenelectrically charged, which allows them to attract,and bond with, such molecules. These clays mayalso catalyze reactions. Daily and seasonal cycles ofheating and cooling may drive this process. As wewill see later, clays may form scaffolds for RNA andproteins, and has even proposed to have been thefirst form of self-replicating system (the so-calledclay life hypothesis). One problem for the clay the-ory is that, as polymers become longer, they be-

come more strongly bound to their scaffolding. In

other words, it is not immediately clear how theycan become unstuck from the clays they resideon. A solution to this problem is to incorporatetiny bits of clay within the first cell membranes asthey form. We will read about cell membrane for-mation below. Jack Szostak tested this hypotheti-cal possibility by mixing together finely powderedclays, RNA nucleotides (which were made hyperre-active by addition of a catalytic molecular group),and lipids. He found that the clay absorbs the nu-cleotides, and is enclosed by forming vesicles. Theresult are protobionts containing the catalytic claywith small RNA strands.

The Clay life hypothesis

The clay hypothesis was taken a giant step fur-ther by Graham Cairns-Smith, who proposed theso-called clay life theory. This is where thingsturn a little odd. He suggested that fine grained(silicate) clay crystals may have been the first self-replicating systems, not by virtue of RNA, but allby themselves. In this theory, there is no initial rolefor biomolecules, and the first lifeforms were notcarbon-based. Evolution, then, started indepen-

dent of organic molecules. Cairns-Smiths reasonbehind this hypothesis is dependent on several ob-servations. Incidentally, Richard Dawkins supportsthis controversial view. Cairns-Smith is particu-larly interested in the properties of kaolinite crys-tals, illustrated in figure 18. First of all, it seemsnearly impossible to build macromolecules withoutminerals. Clays functioned as essential scaffold-ing on which the complex molecules can be built,much like the scaffolds that hold up an arc beforethe top stone is placed. This scaffolding was laterlost when it became expendable, as more efficientreplication systems like RNA and DNA took hold.Recall that we can see possible remnants of the im-portance that minerals might have played in thecurrent-day role of clumps of minerals in enzymes.Second, clay crystal layers have a varying internalstructure that distantly resembles that of an infor-mation carrying structure, much like, for instance,RNA. Specifically, there are three possibilities forthe alphabet of clay minerals (much like the fourletter alphabets of RNA and DNA). First of all,the composition and orientation of the layers playsa key role. Recall that layers of clay can alternate

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in (two or three) layered structures with spaces in

between. Two layer and three layer structures mayalternate. Each layer also has a specific orientationwhich can fall along one of three equally distantangles. Secondly, there may be variation withinlayers, called twinning, in which a single layer con-tains mixed surface patches in all three orienta-tions. Third, clays can have a quite complicatedchemical 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 theold ones that have the same orientation, chemicalcomposition and surface defects. Thus, one can

say that a layer of clay can grow in this way. Whenlayers flakes off, and is redeposited elsewhere bywind or water currents, this process may repeatitself, establishing new clay colonies. As Cairns-Smith points out, this looks a lot like a primitiveform of reproduction. Additionally, the more sta-ble configurations will tend to win out over time,which leads us to conclude that clays can evolve.This theory makes a number of predictions. Firstof all, the crystal structures must be reproduced ac-curately

abiogenesis primer

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