Origin of life



Research into the origin of life 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 gravity 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: abiogenesis
Main article: Abiogenesis

Research into the origin of life is the modern incarnation of the ancient concept of abiogenesis. Abiogenesis, in its most general sense, is the generation of life from non-living matter. The term is primarily used in the context of biology and the origin of life. Abiogenesis was long considered to be a very common occurrence until the Law of Biogenesis (omne vivum ex ovo or "all life from an egg") became firmly established in modern biology as a result of the work of Louis Pasteur.

Charles Darwin in a letter to J.D. Hooker of February 1 1871, made the suggestion that life may have begun in a "warm little pond, with all sorts of ammonia and phosphoric salts, lights, heat, electricity, etc. present, that a protein compound was chemically formed ready to undergo still more complex changes, at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed." Thus, it is the presence of life itself, operating in an oxygen rich atmosphere, itself a product of life, which prevents "spontaneous generation" from occurring on Earth today.

This modern definition of abiogenesis is concerned with the formation of the simplest forms of life from primordial chemicals, in an environment regarded as similar to that at the time shortly after the formation of the Earth. This is significantly different from the concept of Aristotelian abiogenesis, which postulated the formation of complex organisms. This article reviews different hypotheses for modern abiogenetic processes that are currently under debate.

More recently, the study of the origin of life was revived by the Russian biochemist, Aleksandr Ivanovich Oparin, in his 1936 book by the name "The Origin of Life on Earth". Rejecting the panspermia theory that life was seeded from outer space, Oparin criticised Pasteur's disproof of spontaneous abiogenisis by demonstrating 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. Oparin argued that a "primeval soup" of organic molecules could be created in an oxygen-less atmosphere, through the limitless energy of sunlight. These he suggested combine in more complex fashion until they are dissolved into a coacervate droplet. These, he suggested, "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 Oparins ideas as a starting point.

Current models of the origin of life
There is no truly "standard" model of the origin of life, however most currently accepted models build in one way or another upon a number of discoveries concerning 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 Urey-Miller experiment by Stanley L. Miller and Harold C. Urey in 1953.
 * 2) Phospholipids (of an appropriate length) can spontaneously form lipid bilayers, one of the two basic components of a 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 (see Origin of organic molecules) 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 formed are methane (CH4), ammonia (NH3), water (H2O), hydrogen sulfide (H2S), carbon dioxide (CO2), and phosphate (PO43-). As of 2004, no one has yet synthesized a "protocell" using basic components which has 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 Jack Szostak at Harvard. 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 involved 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, in coining the term Biopoesis for this process 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.

Origin of organic molecules: Miller, Eigen and Wächtershäuser's theories
The "Miller experiments" (including the original Miller&#8211;Urey experiment of 1953, by Harold Urey and his graduate student Stanley Miller) are performed under simulated conditions resembling those thought at the time to have existed shortly after Earth first accreted from the primordial solar nebula. The experiment used a highly reduced mixture of gases (methane, ammonia and hydrogen). However, it should be noted that 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; however, 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. Further, according to Brooks and Shaw (1973), there is no evidence in the geological record that any soup existed.


 * "If there ever was a primitive soup, then we would expect to find at least somewhere on this planet either massive sediments containing enormous amounts of the various nitrogenous organic compounds, acids, purines, pyrimidines, and the like; or in much metamorphosed sediments we should find vast amounts of nitrogenous cokes. In fact no such materials have been found anywhere on earth."

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.

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 aids catalyse 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.

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 (e. g. 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&#8211;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 has been 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: 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.
 * 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.

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. However, there are many different hypotheses regarding the path that might have been taken. 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
Main article: RNA world hypothesis

The RNA world hypothesis, for example, suggests that relatively short RNA molecules could have spontaneously formed that were capable of catalyzing their own continuing replication. Although the spontaneous formation of RNA has been suggested to be extremely improbable, there are various theories of possible methods of formation. Early cell membranes could have formed spontaneously from proteinoids, protein-like molecules that are produced when amino acid solutions are heated. Other possibilities include systems of chemical reactions taking place within clay substrates or on the surface of pyrite rocks. At this time however, these 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 determine what may have actually happened in reality. At this time however, no prebiotically plausible experiment has confirmed this assumption. Further, recent experiments suggest that the original estimates of the size of an RNA molecule capable of self-replication were most probably vast underestimates. Worse, RNA itself does not appear to be a prebiotically plausible molecule; therefore, 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).

"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 proposed by Günter Wächtershäuser, could form spontaneously remains unsupported. Further, 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."

The 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. They are not a likely precursor to the modern cell membrane, though, 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.

Clay theory of the origin of life
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 complex organic molecules arising 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".

Cairns-Smith is a staunch critic of other models of chemical evolution (see Genetic Takeover: And the Mineral Origins of Life ISBN 0-52123-312-7). However, he admits, that like many models of the origin of life, his own also has its shortcomings (Horgan 1991). It is truly, "life from a rock".

"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 has life first developing 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 around the same time or earlier than bacteria, 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 (note that exogenesis is related to, but is 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 cometary material on the early Earth could have brought significant quantities of complex organic molecules, and that it is possible that primitive life itself may have formed in space was brought to the surface along with it. A related hypothesis holds that life may have formed first on early Mars, and been transported to Earth when crustal material was blasted off of Mars by asteroid and comet impacts to later fall to Earth's surface. Both of these hypotheses are even more difficult to find evidence for, and may have to wait for samples to be taken from comets and Mars for study, and neither of them actually answers the question of how life first originated, merely shifting it to another planet/comet. However, this hypothesis extends tremendously the array of conditions under which life may have formed, from early Earth plausible conditions to literally any conditions possible in the universe.

Relevant fields

 * Astrobiology is a field that may shed light on the nature of life in general, instead of just life as we know it on Earth, and may give clues as to how life originates.
 * Complex systems