User:Drewbie/Macromolecules/Origins

Abiogenesis
In the physical sciences, abiogenesis, the question of the origin of life, is the study of how life on Earth might have evolved from non-life sometime between 3.9 and 3.5 billion years ago. This topic also includes theories and ideas regarding possible extra-planetary or extra-terrestrial origin of life hypotheses, thought to have possibly occurred over the last 13.7 billion years in the evolution of the known universe since the big bang.

Origin of life studies is a limited field of research despite its profound impact on biology and human understanding of the natural world. Progress in this field is generally slow and sporadic, though it still draws the attention of many due to the eminence of the question being investigated. A few facts give insight into the conditions in which life may have emerged, but the mechanisms by which non-life became life are still elusive.

For the observed evolution of life on earth, see the timeline of life.

History of the concept
In a letter to Joseph Dalton Hooker of February 1 1871, Charles Darwin made the suggestion that the original spark of life may have begun in a "warm little pond, with all sorts of ammonia and phosphoric salts, lights, heat, electricity, etc. present, [so] that a protein compound was chemically formed ready to undergo still more complex changes". He went on to explain that "at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed." In other words, the presence of life itself prevents the spontaneous generation of simple organic compounds from occurring on Earth today – a circumstance which makes the search for the origin of life dependent on the sterile conditions of the laboratory.

An experimental approach to the question was beyond the scope of laboratory science in Darwin's day, and no real progress was made until 1936 when Aleksandr Ivanovich Oparin demonstrated that it was the presence of atmospheric oxygen and other more sophisticated life-forms that prevented the chain of events that would lead to the evolution of life. In his The Origin of Life on Earth, Oparin argued that a "primeval soup" of organic molecules could be created in an oxygen-less atmosphere through the action of sunlight. These would combine in ever-more complex fashion until they dissolved into a coacervate droplet. These droplets would "grow" by fusion with other droplets, and "reproduce" through fission into daughter droplets, and so have a primitive metabolism in which those factors which promote "cell integrity" survive, those that don't become extinct. All modern theories of the origin of life take Oparin's ideas as a starting point.

Current models
There is no truly "standard" model of the origin of life. But most currently accepted models build in one way or another upon a number of discoveries about the origin of molecular and cellular components for life, which are listed in a rough order of postulated emergence:


 * 1) Plausible pre-biotic conditions result in the creation of certain basic small molecules (monomers) of life, such as amino acids. This was demonstrated in the Miller-Urey experiment by Stanley L. Miller and Harold C. Urey in 1953.
 * 2) Phospholipids (of an appropriate length) can spontaneously form lipid bilayers, a basic component of the cell membrane.
 * 3) The polymerization of nucleotides into random RNA molecules might have resulted in self-replicating ribozymes (RNA world hypothesis).
 * 4) Selection pressures for catalytic efficiency and diversity result in ribozymes which catalyse peptidyl transfer (hence formation of small proteins), since oligopeptides complex with RNA to form better catalysts. Thus the first ribosome is born, and protein synthesis becomes more prevalent.
 * 5) Proteins outcompete ribozymes in catalytic ability, and therefore become the dominant biopolymer. Nucleic acids are restricted to predominantly genomic use.

The origin of the basic biomolecules, while not settled, is less controversial than the significance and order of steps 2 and 3. The basic inorganic chemicals from which life was thought to have formed are methane (CH4), ammonia (NH3), water (H2O), hydrogen sulfide (H2S), carbon dioxide (CO2), and phosphate (PO43-).

As of 2006, no one has yet synthesized a "protocell" using basic components which would have the necessary properties of life (the so-called "bottom-up-approach"). Without such a proof-of-principle, explanations have tended to be short on specifics. However, some researchers are working in this field, notably Steen Rasmussen at Los Alamos National Laboratory and Jack Szostak at Harvard University. Others have argued that a "top-down approach" is more feasible. One such approach, attempted by Craig Venter and others at The Institute for Genomic Research, involves engineering existing prokaryotic cells with progressively fewer genes, attempting to discern at which point the most minimal requirements for life were reached. The biologist John Desmond Bernal, coined the term Biopoesis for this process, and suggested that there were a number of clearly defined "stages" that could be recognised in explaining the origin of life.

Stage 1: The origin of biological monomers Stage 2: The origin of biological polymers Stage 3: The evolution from molecules to cell

Bernal suggested that Darwinian evolution may have commenced early, some time between Stage 1 and 2.

Miller's experiments
Experiments were performed by Stanley Miller starting in 1953, under simulated conditions resembling those then thought to have existed shortly after Earth first accreted from the primordial solar nebula. The experiments are called the "Miller experiments". The original experiment in 1953 was done by Miller as a graduate student and his professor Harold Urey. The experiment used a highly reduced mixture of gases (methane, ammonia and hydrogen). However, the composition of the prebiotic atmosphere of Earth is currently controversial. Other less reducing gases produce a lower yield and variety. It was once thought that appreciable amounts of molecular oxygen were present in the prebiotic atmosphere, which would have essentially prevented the formation of organic molecules; however, the current scientific consensus is that such was not the case.

The experiment showed that some of the basic organic monomers (such as amino acids) that form the polymeric building blocks of modern life can be formed spontaneously. Simple organic molecules are of course a long way from a fully functional self-replicating life form. But in an environment with no pre-existing life these molecules may have accumulated and provided a rich environment for chemical evolution ("soup theory"). On the other hand, the spontaneous formation of complex polymers from abiotically generated monomers under these conditions is not at all a straightforward process. Besides the necessary basic organic monomers, also compounds that would have prohibited the formation of polymers were formed in high concentration during the experiments.

Other sources of complex molecules have been postulated, including sources of extra-terrestrial stellar or interstellar origin. For example, from spectral analyses, organic molecules are known to be present in comets and meteorites. In 2004, a team detected traces of polycyclic aromatic hydrocarbons (PAH's) in a nebula, the most complex molecule, to that date, found in space. The use of PAH's has also been proposed as a precursor to the RNA world in the PAH world hypothesis.

It can be argued that the most crucial challenge unanswered by this theory is how the relatively simple organic building blocks polymerise and form more complex structures, interacting in consistent ways to form a protocell. For example, in an aqueous environment hydrolysis of oligomers/polymers into their constituent monomers would be favored over the condensation of individual monomers into polymers. Also, the Miller experiment produces many substances that would undergo cross-reactions with the amino acids or terminate the peptide chain.

Eigen's hypothesis
In the early 1970s a major attack on the problem of the origin of life was organised by a team of scientists gathered around Manfred Eigen of the Max Planck Institute. They tried to examine the transient stages between the molecular chaos in a prebiotic soup and the transient stages of a self replicating hypercycle, between the molecular chaos in a prebiotic soup and simple macromolecular self-reproducing systems.

In a hypercycle, the information storing system (possibly RNA) produces an enzyme, which catalyzes the formation of another information system, in sequence until the product of the last aids in the formation of the first information system. Mathematically treated, hypercycles could create quasispecies, which through natural selection entered into a form of Darwinian evolution. A boost to hypercycle theory was the discovery that RNA, in certain circumstances forms itself into ribozymes, a form of RNA enzyme.

Wächtershäuser's hypothesis
Another possible answer to this polymerization conundrum was provided in 1980s by Günter Wächtershäuser, in his iron-sulfur world theory. In this theory, he postulated the evolution of (bio)chemical pathways as fundamentals of the evolution of life. Moreover, he presented a consistent system of tracing today's biochemistry back to ancestral reactions that provide alternative pathways to the synthesis of organic building blocks from simple gaseous compounds.

In contrast to the classical Miller experiments, which depend on external sources of energy (such as simulated lightning or UV irradiation), "Wächtershäuser systems" come with a built-in source of energy, sulfides of iron and other minerals (e.g. pyrite). The energy released from redox reactions of these metal sulfides is not only available for the synthesis of organic molecules, but also for the formation of oligomers and polymers. It is therefore hypothesized that such systems may be able to evolve into autocatalytic sets of self-replicating, metabolically active entities that would predate the life forms known today.

The experiment as performed, produced a relatively small yield of dipeptides (0.4% to 12.4%) and a smaller yield of tripeptides (0.003%) and the authors note that: "under these same conditions dipeptides hydrolysed rapidly." Another criticism of the result is that the experiment did not include any organomolecules that would most likely cross-react or chain-terminate (Huber and Wächtershäuser, 1998).

The latest modification of the iron-sulfur-hypothesis was provided by William Martin and Michael Russell in 2002. According to their scenario, the first cellular life forms may have evolved inside so-called black smokers at seafloor spreading zones in the deep sea. These structures consist of microscale caverns that are coated by thin membraneous metal sulfide walls. Therefore, these structures would solve several critical points of the "pure" Wächtershäuser systems at once:


 * 1) The micro-caverns provide a means of concentrating newly synthesised molecules, thereby increasing the chance of forming oligomers;
 * 2) The steep temperature gradients inside a black smoker allow for establishing "optimum zones" of partial reactions in different regions of the black smoker (e.g. monomer synthesis in the hotter, oligomerisation in the colder parts);
 * 3) The flow of hydrothermal water through the structure provides a constant source of building blocks and energy (freshly precipitated metal sulfides);
 * 4) The model allows for a succession of different steps of cellular evolution (prebiotic chemistry, monomer and oligomer synthesis, peptide and protein synthesis, RNA world, ribonucleoprotein assembly and DNA world) in a single structure, facilitating exchange between all developmental stages;
 * 5) Synthesis of lipids as a means of "closing" the cells against the environment is not necessary, until basically all cellular functions are developed.

This model locates the "last universal common ancestor" (LUCA) inside a black smoker, rather than assuming the existence of a free-living form of LUCA. The last evolutionary step would be the synthesis of a lipid membrane that finally allows the organisms to leave the microcavern system of the black smokers and start their independent lives. This postulated late acquisition of lipids is consistent with the presence of completely different types of membrane lipids in archaebacteria and eubacteria (plus eukaryotes) with highly similar cellular physiology of all life forms in most other aspects.

Another unsolved issue in chemical evolution is the origin of homochirality, i.e. all monomers having the same "handedness" (amino acids being left handed, and nucleic acid sugars being right handed). Homochirality is essential for the formation of functional ribozymes (and probably proteins too). The origin of homochirality might simply be explained by an initial asymmetry by chance followed by common descent. Work performed in 2003 by scientists at Purdue identified the amino acid serine as being a probable root cause of organic molecules' homochirality. Serine forms particularly strong bonds with amino acids of the same chirality, resulting in a cluster of eight molecules that must be all right-handed or left-handed. This property stands in contrast with other amino acids which are able to form weak bonds with amino acids of opposite chirality. Although the mystery of why left-handed serine became dominant is still unsolved, this result suggests an answer to the question of chiral transmission: how organic molecules of one chirality maintain dominance once asymmetry is established.

From organic molecules to protocells
The question "How do simple organic molecules form a protocell?" is largely unanswered but there are many hypotheses. Some of these postulate the early appearance of nucleic acids ("genes-first") whereas others postulate the evolution of biochemical reactions and pathways first ("metabolism-first"). Recently, trends are emerging to create hybrid models that combine aspects of both.

"Genes first" models: the RNA world
The RNA world hypothesis suggests that relatively short RNA molecules could have spontaneously formed that were capable of catalyzing their own continuing replication. It is difficult to gauge the probability of this formation. A number of theories of modes of formation have been put forward. Early cell membranes could have formed spontaneously from proteinoids, protein-like molecules that are produced when amino acid solutions are heated - when present at the correct concentration in aqueous solution, these form microspheres which are observed to behave similarly to membrane-enclosed compartments. Other possibilities include systems of chemical reactions taking place within clay substrates or on the surface of pyrite rocks. Factors supportive of an important role for RNA in early life include its ability to replicate (see Spiegelman Monster); its ability to act both to store information and catalyse chemical reactions (as a ribozyme); its many important roles as an intermediate in the expression and maintenance of the genetic information (in the form of DNA) in modern organisms; and the ease of chemical synthesis of at least the components of the molecule under conditions approximating the early Earth.

A number of problems with the RNA world hypothesis remain, particularly the instability of RNA when exposed to ultraviolet light, the difficulty of activating and ligating nucleotides and the lack of available phosphate in solution required to constitute the backbone, and the instability of the base cytosine (which is prone to hydrolysis). Recent experiments also suggest that the original estimates of the size of an RNA molecule capable of self-replication were most probably vast underestimates. More-modern forms of the RNA World theory propose that a simpler molecule was capable of self-replication (that other "World" then evolved over time to produce the RNA World). At this time however, the various hypotheses have incomplete evidence supporting them. Many of them can be simulated and tested in the lab, but a lack of undisturbed sedimentary rock from that early in Earth's history leaves few opportunities to test this hypothesis robustly.

"Metabolism first" models: iron-sulfur world and others
Several models reject the idea of the self-replication of a "naked-gene" and postulate the emergence of a primitive metabolism which could provide an environment for the later emergence of RNA replication.

One of the earliest incarnations of this idea was put forward in 1924 with Alexander Oparin's notion of primitive self-replicating vesicles which predated the discovery of the structure of DNA. More recent variants in the 1980s and 1990s include Günter Wächtershäuser's iron-sulfur world theory and models introduced by Christian de Duve based on the chemistry of thioesters. More abstract and theoretical arguments for the plausibility of the emergence of metabolism without the presence of genes include a mathematical model introduced by Freeman Dyson in the early 1980s and Stuart Kauffman's notion of collectively autocatalytic sets, discussed later in that decade.

However, the idea that a closed metabolic cycle, such as the reductive citric acid cycle, could form spontaneously (proposed by Günter Wächtershäuser) remains unsupported. According to Leslie Orgel, a leader in origin-of-life studies for the past several decades, there is reason to believe the assertion will remain so. In an article entitled "Self-Organizing Biochemical Cycles" (PNAS, vol. 97, no. 23, November 7, 2000, p12503-12507), Orgel summarizes his analysis of the proposal by stating, "There is at present no reason to expect that multistep cycles such as the reductive citric acid cycle will self-organize on the surface of FeS/FeS2 or some other mineral." It is possible that another type of metabolic pathway was used at the beginning of life. For example, instead of the reductive citric acid cycle, the "open" acetyl-CoA pathway (another one of the four recognised ways of carbon dioxide fixation in nature today) would be even more compatible with the idea of self-organisation on a metal sulfide surface. The key enzyme of this pathway, carbon monoxide dehydrogenase/acetyl-CoA synthase harbours mixed nickel-iron-sulfur clusters in its reaction centers and catalyses the formation of acetyl-CoA (which may be regarded as a modern form of acetyl-thiol) in a single step.

Bubble Theory
Waves breaking on the shore create a delicate foam composed of bubbles. Winds sweeping across the ocean have a tendency to drive things to shore, much like driftwood collecting on the beach. It is possible that organic molecules were concentrated on the shorelines in much the same way. Shallow coastal waters also tend to be warmer, further concentrating the molecules through evaporation. While bubbles comprised of mostly water burst quickly, oily bubbles happen to be much more stable, lending more time to the particular bubble to perform these crucial experiments.

The phospholipid is a good example of an oily compound believed to have been prevalent in the prebiotic seas. Because phospholipids contain a hydrophilic head on one end, and a hydrophobic tail on the other, they have the tendency to spontaneously form lipid membranes in water. A lipid monolayer bubble can only contain oil, and is therefore not conducive to harbouring water-soluble organic molecules. On the other hand, a lipid bilayer bubble can contain water, and was a likely precursor to the modern cell membrane. If a protein came along that increased the integrity of its parent bubble, then that bubble had an advantage, and was placed at the top of the natural selection waiting list. Primitive reproduction can be envisioned when the bubbles burst, releasing the results of the experiment into the surrounding medium. Once enough of the 'right stuff' was released into the medium, the development of the first prokaryotes, eukaryotes, and multicellular organisms could be achieved. This theory is expanded upon in the book, "The Cell: Evolution of the First Organism" by Joseph Panno Ph.D.

Similarly, bubbles formed entirely out of protein-like molecules, called microspheres, will form spontaneously under the right conditions. But they are not a likely precursor to the modern cell membrane, as cell membranes are composed primarily of lipid compounds rather than amino-acid compounds.

Hybrid models
A growing realization of the inadequacy of either pure "genes-first" or "metabolism-first" models is leading the trend towards models that incorporate aspects of each.

Autocatalysis
British ethologist Richard Dawkins wrote about autocatalysis as a potential explanation for the origin of life in his 2004 book The Ancestor's Tale. Autocatalysts are substances which catalyze the production of themselves, and therefore have the property of being a simple molecular replicator. In his book, Dawkins cites experiments performed by Julius Rebek and his colleagues at the Scripps Research Institute in California in which they combined amino adenosine and pentafluorophenyl ester with the autocatalyst amino adenosine triacid ester (AATE). One system from the experiment contained variants of AATE which catalysed the synthesis of themselves. This experiment demonstrated the possibility that autocatalysts could exhibit competition within a population of entities with heredity, which could be interpreted as a rudimentary form of natural selection.

Clay theory
A hypothesis for the origin of life based on clay was forwarded by Dr A. Graham Cairns-Smith of the University of Glasgow in 1985 and adopted as a plausible illustration by just a handful of other scientists (including Richard Dawkins). Clay theory postulates that complex organic molecules arose gradually on a pre-existing, non-organic replication platform -- silicate crystals in solution. Complexity in companion molecules developed as a function of selection pressures on types of clay crystal is then exapted to serve the replication of organic molecules independently of their silicate "launch stage". It is, truly, "life from a rock."

Cairns-Smith is a staunch critic of other models of chemical evolution (see Genetic Takeover: And the Mineral Origins of Life ISBN 0-521-23312-7). However, he admits, that like many models of the origin of life, his own also has its shortcomings (Horgan 1991).

Peggy Rigou of the National Institute of Agronomic Research (INRA), in Jouy-en-Josas, France reports in the February 11, 2006 edition of Science News that prions are capable of binding to clay particles and migrate off the particles when the clay becomes negatively charged. While no reference is made in the report to implications for origin-of-life theories, this research may suggest prions as a likely pathway to early reproducing molecules.

"Deep-hot biosphere" model of Gold
The discovery of nanobes (filamental structures smaller than bacteria containing DNA) in deep rocks, led to a controversial theory put forward by Thomas Gold in the 1990s that life first developed not on the surface of the Earth, but several kilometers below the surface. It is now known that microbial life is plentiful up to five kilometers below the earth's surface in the form of archaea, which are generally considered to have originated either before or around the same time as eubacteria, most of which live on the surface including the oceans. It is claimed that discovery of microbial life below the surface of another body in our solar system would lend significant credence to this theory. He also noted that a trickle of food from a deep, unreachable, source promotes survival because life arising in a puddle of organic material is likely to consume all of its food and become extinct.

"Primitive" extraterrestrial life
An alternative to Earthly abiogenesis is the hypothesis that primitive life may have originally formed extraterrestrially, either in space or on a nearby planet (Mars). (Note that exogenesis is related to, but not the same as, the notion of panspermia).

Organic compounds are relatively common in space, especially in the outer solar system where volatiles are not evaporated by solar heating. Comets are encrusted by outer layers of dark material, thought to be a tar-like substance composed of complex organic material formed from simple carbon compounds after reactions initiated mostly by irradiation by ultraviolet light. It is supposed that a rain of material from comets could have brought significant quantities of such complex organic molecules to Earth.

An alternative but related hypothesis, proposed to explain the presence of life on Earth so soon after the planet had cooled down, with apparently very little time for prebiotic evolution, is that life formed first on early Mars. Due to its smaller size Mars cooled before Earth(a difference of hundred of millions of years), allowing prebiotic processes there while Earth was still too hot. Life was then transported to the cooled Earth when crustal material was blasted off Mars by asteroid and comet impacts. Mars continued to cool faster and eventually became hostile to the continued evolution or even existence of life (it lost its atmosphere due to low volcanism), Earth is following the same fate as Mars, but at a slower rate.

Neither hypothesis actually answers the question of how life first originated, but merely shifts it to another planet or a comet. However, the advantage of an extraterrestrial origin of primitive life is that life is not required to have evolved on each planet it occurs on, but rather in a single location, and then spread about the galaxy to other star systems via cometary and/or meteorite impact. Evidence to support the plausibility of the concept is scant, but it finds support in recent study of Martian meteorites found in Antartica and in studies of extremophile microbes.[2] Additional support comes from a recent discovery of a bacterial ecosytem whose energy source is radioactivity.[3]

RNA world hypothesis
The RNA world hypothesis proposes that RNA was the first life-form on earth, later developing a cell membrane around itself and becoming the first prokaryotic cell.

Support
The RNA World hypothesis is supported by the RNA's ability to store, transmit, and duplicate genetic information, just like DNA does. RNA can also act as a ribozyme (an enzyme made of ribonucleic acid). Because it can reproduce on its own, performing the tasks of both DNA and proteins (enzymes), RNA is believed to have once been capable of independent life. Further, while nucleotides were not found in Miller-Urey's experiments, they were found by others' simulations, notably those of Joan Oro. Experiments with basic ribozymes, like the viral RNA Q-beta, have shown that simple self-replicating RNA structures can withstand even strong selective pressures (e.g., opposite-chirality chain terminators) (The Basics of Selection (London: Springer, 1997)).

The phrase "RNA World" was first used by Walter Gilbert in 1986. However, the idea of independent RNA life is older and can be found in Carl Woese's book The Genetic Code (New York: Harper and Row, 1967). Five years earlier, the molecular biologist Alexander Rich, of the Massachusetts Institute of Technology, had posited much the same idea in an article he contributed to a volume issued in honor of Nobel-laureate physiologist Albert Szent-Györgyi.

Base pairing
RNA and DNA are made of long stretches of specific nucleotides, often called "bases", attached to a sugar-phosphate backbone. The RNA world hypothesis holds that in the primordial soup / primordial sandwich there existed free-floating nucleotides. These nucleotides regularly formed bonds with one another which often broke because the change in energy was so low. However, certain sequences of base pairs have catalytic properties that lower the energy of their chain being created, causing them to stay together for longer periods of time. As each chain grew longer it attracted more matching nucleotides faster, causing chains to now form faster than they were breaking down.

These chains are proposed as the first, primitive forms of life. In an RNA world, different forms of RNA compete with each other for free nucleotides and are subject to natural selection. The most efficient molecules of RNA, the ones able to efficiently catalyze their own reproduction, survived and evolved, forming modern RNA.

Competition between RNA may have favored the emergence of cooperation between different RNA chains, opening the way for the formation of the first proto-cell. Eventually, RNA chains randomly developed with catalytic properties that help amino acids bind together (peptide-bonding). These amino acids could then assist with RNA synthesis, giving those RNA chains that could serve as ribozymes the selective advantage. Eventually DNA, lipids, carbohydrates, and all sorts of other chemicals were recruited into life. This led to the first prokaryotic cells, and eventually to life as we know it.

Nucleic acid fragility
At first glance, the RNA world hypothesis seems implausible because, in today's world, large RNA molecules are inherently fragile and can easily be broken down into their constituent nucleotides through hydrolysis. The aromatic bases comprising RNA also absorb strongly in the ultraviolet region, and would have been liable to damage and breakdown by background radiation. (Pääbo 1993, Lindahl 1993).

Carl Zimmer has been working on a controversial hypothesis that viruses were instrumental in the transition from RNA to DNA and the evolution of Bacteria, Archae, and Eukarya. He believes the last common ancestor was RNA-based and evolved RNA viruses. Some of the viruses evolved into DNA viruses to protect their genes from attack. Through the process of viral infection into hosts the three domains of life evolved. [1]

A proposed alternative to RNA in an "RNA World" is the peptide nucleic acid, PNA. PNA is more stable than RNA and appears to be more readily synthesised in prebiotic conditions, especially where the synthesis of ribose and adding phosphate groups are problematic. Threose nucleic acid (TNA) has also been proposed as a starting point, as has Glycol nucleic acid GNA.

A different alternative to the assembly of RNA is proposed in the PAH world hypothesis.

Additionally, in the past a given RNA molecule might have survived longer than it can today. Ultraviolet light can cause RNA to polymerize while at the same time breaking down other types of organic molecules that could have the potential of catalyzing the break down of RNA (ribonucleases), suggesting that RNA may have been a relatively common substance on early Earth. This aspect of the theory is still untested and is based on a constant concentration of sugar-phosphate molecules.

Implications
The RNA world hypothesis, if true, has important implications for the very definition of life. For the majority of the time following the elucidation of the structure of DNA by Watson and Crick, life was considered as being largely defined in terms of DNA and proteins: DNA and proteins seemed to be the dominant macromolecules in the living cell, with RNA serving only to aid in creating proteins from the DNA blueprint.

The RNA world hypothesis places RNA at center-stage when life originated. This has been accompanied by many studies in the last ten years demonstrating important aspects of RNA function that were not previously known, and support the idea of a critical role for RNA in the functionality of life. In 2001, the RNA world hypothesis was given a major boost with the deciphering of the 3-dimensional structure of the ribosome, which revealed the key catalytic sites of ribosomes to be composed of RNA and for the proteins to hold no major structural role, and be of peripheral functional importance. Specifically, the formation of the peptide bond, the reaction that binds amino acids together into proteins, is now known to be catalyzed by an adenine residue in the rRNA: the ribosome is a ribozyme. This finding suggests that RNA molecules were most likely capable of generating the first proteins. Other interesting discoveries demonstrating a role for RNA beyond a simple message or transfer molecule include the importance of small nuclear ribonucleoproteins (SnRNPs) in the processing of pre-mRNA and RNA editing and reverse transcription from RNA in the maintenance of telomeres in the telomerase reaction.

Difficulties
The base cytosine does not have a plausible prebiotic simulation method because it easily undergoes hydrolysis.

Prebiotic simulations making nucleotides have conditions incompatible with those for making sugars (lots of formaldehyde). So they must somehow be synthesized, then brought together. However, they do not react in water. Anhydrous reactions bind with purines, but only 8% of them bind with the correct carbon atom on the sugar bound to the correct nitrogen atom on the base. Pyrimidines, however, do not react with ribose, even anhydrously.

Then phosphate must be introduced, but in nature phosphate in solution is extremely rare because it is so readily precipitated. After being introduced, the phosphate must combine with the nucleoside and the correct hydroxyl must be phosphorylated.

For the nucleotides to form RNA, they must be activated themselves. Activated purine nucleotides form small chains on a pre-existing template of all-pyrimidine RNA. However, this does not happen in reverse because the pyrimidine nucleotides do not stack well.

Additionally, the ribose must all be the same enantiomer, because any nucleotides of the wrong chirality act as chain terminators. [1]

A.G. Cairns-Smith in 1982 criticized writers for exaggerating the implications of the Miller-Urey experiment. He argued that the experiment showed, not the possibility that nucleic acids preceded life, but its implausibility. He claimed that the process of constructing nucleic acids would require 18 distinct conditions and events that would have to occur continually over millions of years in order to build up the required quantities.

One of the leading researchers into RNA world models, wrote: "The most reasonable assumption is that life did not start with RNA .... The transition to an RNA world, like the origins of life in general, is fraught with uncertainty and is plagued by a lack of experimental data.

— Gerald Joyce, 1989

Miller-Urey experiment
The Miller-Urey experiment (or Urey-Miller experiment) was an experiment that simulated hypothetical conditions present on the early Earth and tested for the occurrence of chemical evolution (the Oparin and Haldane hypothesis stated that conditions on the primitive Earth favored chemical reactions that synthesized organic compounds from inorganic precursors; the Miller-Urey tested this hypothesis). The experiment is considered to be the classic experiment on the origin of life. It was conducted in 1953 by Stanley L. Miller and Harold C. Urey at the University of Chicago.

Experiment and interpretation
The experiment used water (H2O), methane (CH4), ammonia (NH3) and hydrogen (H2). The chemicals were all sealed inside a sterile array of glass tubes and flasks connected together in a loop, with one flask half-full of liquid water and another flask containing a pair of electrodes. The liquid water was heated to induce evaporation, sparks were fired between the electrodes to simulate lightning through the atmosphere and water vapor, and then the atmosphere was cooled again so that the water could condense and trickle back into the first flask in a continuous cycle.

At the end of one week of continuous operation, Miller and Urey observed that as much as 10-15% of the carbon within the system was now in the form of organic compounds. Two percent of the carbon had formed amino acids, including 13 of the 22 that are used to make proteins in living cells, with glycine as the most abundant. As observed in all consequent experiments, both left-handed (L) and right-handed (D) optical isomers were created in a racemic mixture.

The molecules produced were simple organic molecules, far from a complete living biochemical system, but the experiment established that the hypothetical processes could produce some building blocks of life without requiring life to synthesize them first.

Other experiments
This experiment inspired many experiments in a similar vein. In 1961, Joan Oró found that amino acids could be made from hydrogen cyanide (HCN) and ammonia in a water solution. He also found that his experiment produced a large amount of the nucleotide base adenine. Experiments conducted later showed that the other RNA and DNA bases could be obtained through simulated prebiotic chemistry with a reducing atmosphere.

There were similar (electric discharge) experiments on the origin of life prior to or contemporaneous with Miller-Urey:

An article in The New York Times, March 8, 1953, page E9, titled "Looking Back Two Billion Years" describes the work of Wollman [sic] (William) M. MacNevin at Ohio State University. (The Miller Science paper was not published until May 1953.) MacNevin was passing 100,000 volt sparks through methane and water vapor and produced "resinous solids" that were "too complex for analysis." The article describes other early earth experiments being done by MacNevin. It is not clear if he ever published any of these results in the primary scientific literature.

K. A. Wilde submitted a paper to Science on December 15, 1952 (which was prior to the Miller submission date of February 14, 1953) that was published on July 10, 1953 (Science, 1953, 118(3054), 43-44). Wilde only used voltages up to 600 V on a binary mixture of CO2 and water in a flow system. He only observed small amounts of CO2 reduction to CO and no other significant reduction products or newly formed carbon compounds.

Earth's early atmosphere
There have been a number of objections to the implications derived from these experiments. Scientists believe that Earth's original atmosphere might contain less of the reducing molecules as was thought at the time of Miller-Urey experiment:

Originally it was thought that the primitive secondary atmosphere contained mostly NH3 and CH4. However, it is likely that most of the atmospheric carbon was CO2 with perhaps some CO and the nitrogen mostly N2. The reasons for this are (a) volcanic gas has more CO2, CO and N2 than CH4 and NH3 and (b) UV radiation destroys NH3 and CH4 so that these molecules would have been short-lived. UV light photolyses H2O to H· and ·OH radicals. These then attack methane, giving eventually CO2 and releasing H2 which would be lost into space.

In practice gas mixtures containing CO, CO2, N2, etc. give much the same products as those containing CH4 and NH3 so long as there is no O2. The H atoms come mostly from water vapor. In fact, in order to generate aromatic amino acids under primitive earth conditions it is necessary to use less hydrogen-rich gaseous mixtures. Most of the natural amino acids, hydroxyacids, purines, pyrimidines, and sugars have been produced in variants of the Miller experiment.[1]

More recent results may question these conclusions. The University of Waterloo and University of Colorado conducted simulations in 2005 that indicated that the early atmosphere of Earth could have contained up to 40 percent hydrogen---implying a much more hospitable environment for the formation of prebiotic organic molecules. The escape of hydrogen from Earth's atmosphere into space may have occurred at only one percent of the rate previously believed based on revised estimates of the upper atmosphere's temperature.[2] One of the authors, Prof. Owen Toon notes: "In this new scenario, organics can be produced efficiently in the early atmosphere, leading us back to the organic-rich soup-in-the-ocean concept... I think this study makes the experiments by Miller and others relevant again." Outgassing calculations using a chondritic model for the early earth, (Washington University, September 2005) complement the Waterloo/Colorado results in re-establishing the importance of the Miller-Urey experiment.[3]

Although lightning storms are thought to have been very common in the primordial atmosphere, they are not thought to have been as common as the amount of electricity used by the Miller-Urey experiment implied. These factors suggest that much lower concentrations of biochemicals would have been produced on Earth than was originally predicted (although the time scale would be 100 million years instead of a week). Similar experiments, both with different sources of energy and with different mixtures of gases, have resulted in amino and hydroxy acids being produced; it is likely that at least some organic compounds would have been generated on the early Earth.

However, when oxygen gas is added to this mixture, no organic molecules are formed. Opponents of Miller-Urey hypothesis seized upon recent research that shows the presence of uranium in sediments dated to 3.7 Ga and indicates it was transported in solution by oxygenated water (otherwise it would have precipitated out) (Rosing & Frei 2004). These opponents argue that this presence of oxygen precludes the formation of prebiotic molecules via a Miller-Urey-like scenario, attempting to invalidate the hypothesis of abiogenesis. However, the authors of the paper are arguing that this presence of oxygen merely evidences the existence of photosynthetic organisms 3.7 Ga ago (a value about 200 Ma earlier than current values[4]), a conclusion which while pushing back the time frame in which Miller-Urey reactions and abiogenesis could potentially have occurred, would not preclude them. Though there is somewhat controversial evidence for very small (less than 0.1%) amounts of oxygen in the atmosphere almost as old as Earth's oldest rocks the authors are not in any way arguing for the existence of a strongly oxygen containing atmosphere occurring any earlier than previously thought, and they state: ". . . In fact most evidence suggests that oxygenic photosynthesis was present during time periods from which there is evidence for a non-oxygenic atmosphere".

Conditions similar to those of the Miller-Urey experiments are present in other regions of the solar system, often substituting ultraviolet light for lightning as the driving force for chemical reactions. On September 28, 1969, the Murchison meteorite that fell near Murchison, Victoria, Australia was found to contain over 90 different amino acids, nineteen of which are found in Earth life. Comets and other icy outer-solar-system bodies are thought to contain large amounts of complex carbon compounds (such as tholins) formed by these processes, in some cases so much so that the surfaces of these bodies are turned dark red or as black as asphalt. The early Earth was bombarded heavily by comets, possibly providing a large supply of complex organic molecules along with the water and other volatiles they contributed. (This could also imply an origin of life outside of Earth, which then migrated here. See: Panspermia)

Recent related studies
During recent years, studies have been made of the amino acid composition of the products of "old" areas in "old" genes, defined as those that are found to be common to organisms from several widely separated species, assumed to share only the last universal ancestor (LUA) of all extant species. These studies found that the products of these areas are enriched in those amino acids that are also most readily produced in the Miller-Urey experiment. This suggests that the original genetic code was based on a smaller number of amino acids -- only those available in prebiotic nature -- than the current one (Brooks et al. 2002).