Abiogenesis

"Origin of life" redirects here. For non-scientific views on the origins of life, see Creation myth.

Precambrian stromatolites in the Siyeh Formation, Glacier National Park. In 2002, a paper in the scientific journal Nature suggested that these 3.5 Ga (billion years) old geological formations contain fossilized cyanobacteria microbes. This suggests they are evidence of one of the earliest life forms on Earth.

Abiogenesis (British English: /ˌeɪˌbaɪoʊˈdʒɛnɪsɪs, -ˌbaɪə-, -ˌbiːoʊ-, -ˌbiːə-/), biopoiesis, or informally, the origin of life, is the natural process by which life arises from non-living matter, such as simple organic compounds. Abiogenesis is studied through a combination of paleontology, laboratory experiments and extrapolation from the characteristics of modern organisms, and aims to determine how pre-life chemical reactions gave rise to life on Earth.

The study of abiogenesis can be geophysical, chemical, or biological, with more recent approaches attempting a synthesis of all three. Life itself is dependent upon the specialized chemistry of carbon and water and is largely based upon five different families of chemicals. Lipids are fatty molecules comprising large chemical chains of hydrocarbons and play an important role in the structure of living cell membranes, actively and passively determining the transport of other molecules into and out of cells. Carbohydrates are sugars, and as monomer units can be assembled into polymers called polysaccharides, such as Cellulose, the rigid chemical of most plant cell walls. Nitrogenous bases are organic molecules in which the amine group of nitrogen combined with two hydrogen atoms, play an important part. Chlorophyll is based upon a porphyrin ring derived from amine monomer units, and is important in the capture of the energy needed for life. Nucleic acid monomers are made from a carbohydrate monosaccharide a nitrogenous base and one or more high energy phosphate groups. When joined together they form either the unit of inheritance, the gene, made from DNA or RNA, which translates the genetic information into protein structures. The monomer unit of a protein is always one of 20 amino acids, comprising an amine group, a hydrocarbon and a carboxylic acid. Through a condensation reaction, in which the carboxylic acid of one amino acid is linked to the amine of another with removal of a water molecule, a peptide bond is formed. Polymers of amino acids are termed proteins and these molecules provide many catalytic metabolic functions for living processes. Any successful theory of abiogenesis must explain the origins and interactions of these five classes of molecules.

Many approaches to abiogenesis investigate how self-replicating molecules, or their components, came into existence. It is generally thought that current life on Earth is descended from an RNA world, although RNA-based life may not have been the first life to have existed. The classic Miller–Urey experiment and similar research demonstrated that most amino acids, the basic chemical constituents of the proteins used in all living organisms, can be synthesized from inorganic compounds under conditions intended to replicate those of the early Earth. Various external sources of energy that may have triggered these reactions have been proposed, including lightning and radiation. Other approaches ("metabolism-first" hypotheses) focus on understanding how catalysis in chemical systems on the early Earth might have provided the precursor molecules necessary for self-replication. Complex organic molecules have been found in the Solar System and in interstellar space, and these molecules may have provided starting material for the development of life on Earth.

The panspermia hypothesis alternatively suggests that microscopic life was distributed to the early Earth by meteoroids, asteroids and other small Solar System bodies and that life may exist throughout the Universe. It is speculated that the biochemistry of life may have begun shortly after the Big Bang, 13.8 billion years ago, during a habitable epoch when the age of the universe was only 10 to 17 million years. The panspermia hypothesis therefore answers questions of where, not how, life came to be; it only postulates that life may have originated in a locale outside the Earth.

Nonetheless, Earth remains the only place in the Universe known to harbour life, and fossil evidence from the Earth informs most studies of abiogenesis. The age of the Earth is about 4.54 billion years; the earliest undisputed evidence of life on Earth dates from at least 3.5 billion years ago, and possibly as early as the Eoarchean Era, after geological crust started to solidify following the molten Hadean Eon. In recent years, there have been a number of discoveries that have pushed the estimated start of abiogenesis further in time. Currently, microfossils within rocks dated from 3.77 to 4.28 billion years old found in Quebec, Canada are the oldest record of life on earth, suggesting a rapid origin of life after ocean formation 4.4 billion years ago. According to Stephen Blair Hedges, "If life arose relatively quickly on Earth … then it could be common in the universe."

Early geophysical conditions on Earth

Main article: Timeline of the evolutionary history of life

The Hadean Earth is thought to have had a secondary atmosphere, formed through degassing of the rocks that accumulated from planetesimal impactors. At first, it was thought that the Earth's atmosphere consisted of hydrogen compounds—methane, ammonia and water vapour—and that life began under such reducing conditions, which are conducive to the formation of organic molecules. During its formation, the Earth lost a significant part of its initial mass, with a nucleus of the heavier rocky elements of the protoplanetary disk remaining. According to later models, suggested by study of ancient minerals, the atmosphere in the late Hadean period consisted largely of water vapour, nitrogen and carbon dioxide, with smaller amounts of carbon monoxide, hydrogen, and sulfur compounds. As Earth lacked the gravity to hold any molecular hydrogen, this component of the atmosphere would have been rapidly lost during the Hadean period, along with the bulk of the original inert gases. The solution of carbon dioxide in water is thought to have made the seas slightly acidic, giving it a pH of about 5.5. The atmosphere at the time has been characterized as a "gigantic, productive outdoor chemical laboratory." It may have been similar to the mixture of gases released today by volcanoes, which still support some abiotic chemistry.

Oceans may have appeared first in the Hadean Eon, as soon as two hundred million years (200 Ma) after the Earth was formed, in a hot 100 °C (212 °F) reducing environment, and the pH of about 5.8 rose rapidly towards neutral. This has been supported by the dating of 4.404 Ga-old zircon crystals from metamorphosed quartzite of Mount Narryer in the Western Australia Jack Hills of the Pilbara, which are evidence that oceans and continental crust existed within 150 Ma of Earth's formation. Despite the likely increased volcanism and existence of many smaller tectonic "platelets," it has been suggested that between 4.4 and 4.3 Ga (billion year), the Earth was a water world, with little if any continental crust, an extremely turbulent atmosphere and a hydrosphere subject to intense ultraviolet (UV) light, from a T Tauri stage Sun, cosmic radiation and continued bolide impacts.

The Hadean environment would have been highly hazardous to modern life. Frequent collisions with large objects, up to 500 kilometres (310 mi) in diameter, would have been sufficient to sterilize the planet and vaporize the ocean within a few months of impact, with hot steam mixed with rock vapour becoming high altitude clouds that would completely cover the planet. After a few months, the height of these clouds would have begun to decrease but the cloud base would still have been elevated for about the next thousand years. After that, it would have begun to rain at low altitude. For another two thousand years, rains would slowly have drawn down the height of the clouds, returning the oceans to their original depth only 3,000 years after the impact event.

Earliest biological evidence for life on Earth

For branching of Bacteria phyla, see Bacterial phyla.

Main article: Earliest known life forms

The most commonly accepted location of the root of the tree of life is between a monophyletic domain Bacteria and a clade formed by Archaea and Eukaryota of what is referred to as the "traditional tree of life" based on several molecular studies starting with C. Woese. A very small minority of studies have concluded differently, namely that the root is in the Domain Bacteria, either in the phylum Firmicutes or that the phylum Chloroflexi is basal to a clade with Archaea+Eukaryotes and the rest of Bacteria as proposed by Thomas Cavalier-Smith. More recently Peter Ward has established an alternative view which is rooted in abiotic RNA synthesis which becomes enclosed within a capsule and then creates RNA ribosyme replicates. It is proposed that this then bifurcates between Dominion Ribosa (hypothetical Domain Ribosa or RNA life), and after the loss of ribozymes RNA viruses as Domain Viorea, and Dominion Terroa, which after creating a large cell within a lipid wall, creating DNA the 20 based amino acids and the triplet code, is established as the last universal common ancestor or LUCA, of earlier phylogenic trees.

The earliest life on Earth existed more than 3.5 billion years ago, during the Eoarchean Era when sufficient crust had solidified following the molten Hadean Eon. The earliest physical evidence so far found consists of microfossils in the Nuvvuagittuq Greenstone Belt of Northern Quebec, in "banded iron formation" rocks 3.8 billion years old. This finding suggested that there was almost instant development of life after oceans were formed. The structure of the microbes was noted to be similar to bacteria found near hydrothermal vents in the modern era, and provided support for the hypothesis that abiogenesis began near hydrothermal vents.

Also noteworthy is biogenic graphite in 3.7 billion-year-old metasedimentary rocks from southwestern Greenland and microbial mat fossils found in 3.48 billion-year-old sandstone from Western Australia. Evidence of early life in rocks from Akilia Island, near the Isua supracrustal belt in southwestern Greenland, dating to 3.7 billion years ago have shown biogenic carbon isotopes. At Strelley Pool, in the Pilbarra region of Western Australia, compelling evidence of early life was been found in pyrite-bearing sandstone in a fossilized beach, that showed rounded tubular cells that oxidized sulfur by photosynthesis in the absence of oxygen. Further research on zircons from Western Australia in 2015 suggested evidence that life likely existed on Earth at least 4.1 billion years ago.

Traditionally it was thought that during the period between 3.8 and 4.1 Ga, changes in the orbits of the giant planets may have caused a heavy bombardment by asteroids and comets that pockmarked the Moon and the other inner planets (Mercury, Mars, and presumably Earth and Venus). This would likely have repeatedly sterilized the planet, had life appeared before that time. Geologically, the Hadean Earth would have been far more active than at any other time in its history. Studies of meteorites suggests that radioactive isotopes such as aluminium-26 with a half-life of 7.17×10⁵ years, and potassium-40 with a half-life of 1.250×10⁹ years, isotopes mainly produced in supernovae, were much more common. Internal heating as a result of gravitational sorting between the core and the mantle would have caused a great deal of mantle convection, with the probable result of many more smaller and more active tectonic plates than now exist.

The time periods between such devastating environmental events give time windows for the possible origin of life in the early environments. If the deep marine hydrothermal setting was the site for the origin of life, then abiogenesis could have happened as early as 4.0 to 4.2 Ga. If the site was at the surface of the Earth, abiogenesis could only have occurred between 3.7 and 4.0 Ga.

In 2016, a set of 355 genes likely present in the Last Universal Common Ancestor (LUCA) of all organisms living on Earth was identified. A total of 6.1 million prokaryotic protein coding genes from various phylogenic trees were sequenced, identifying 355 protein clusters from amongst 286,514 protein clusters that were probably common to LUCA. The results "depict LUCA as anaerobic, CO₂-fixing, H₂-dependent with a Wood–Ljungdahl pathway, N₂-fixing and thermophilic. LUCA’s biochemistry was replete with FeS clusters and radical reaction mechanisms. Its cofactors reveal dependence upon transition metals, flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, corrins and selenium. Its genetic code required nucleoside modifications and S-adenosylmethionine-dependent methylations." The results depict methanogenic clostria as a basal clade in the 355 phylogenies examined, and suggest that LUCA inhabited an anaerobic hydrothermal vent setting in a geochemically active environment rich in H₂, CO₂ and iron. M.D. Brazier has shown that the tiny fossils discovered came from a hot poisonous world of the toxic gases methane, ammonia, carbon dioxide and hydrogen sulphide. An analysis of the conventional three fold tree of life shows thermophilic and hyperthermophilic bacteria and archaea are closest to the root, suggesting that life may have evolved in a hot environment.

Conceptual history

Spontaneous generation

Main article: Spontaneous generation

Belief in spontaneous generation of certain forms of life from non-living matter goes back to Aristotle and ancient Greek philosophy and continued to have support in Western scholarship until the 19th century. This belief was paired with a belief in heterogenesis, i.e., that one form of life derived from a different form (e.g., bees from flowers). Classical notions of spontaneous generation held that certain complex, living organisms are generated by decaying organic substances. According to Aristotle, it was a readily observable truth that aphids arise from the dew that falls on plants, flies from putrid matter, mice from dirty hay, crocodiles from rotting logs at the bottom of bodies of water, and so on. In the 17th century, people began to question such assumptions. In 1646, Sir Thomas Browne published his Pseudodoxia Epidemica (subtitled Enquiries into Very many Received Tenets, and commonly Presumed Truths), which was an attack on false beliefs and "vulgar errors." His contemporary, Alexander Ross, erroneously refuted him, stating: "To question this [Ed.: i.e., spontaneous generation], is to question Reason, Sense, and Experience: If he doubts of this, let him go to Ægypt, and there he will finde the fields swarming with mice begot of the mud of Nylus, to the great calamity of the Inhabitants."

In 1665, Robert Hooke published the first drawings of a microorganism. Hooke was followed in 1676 by Antonie van Leeuwenhoek, who drew and described microorganisms that are now thought to have been protozoa and bacteria. Many felt the existence of microorganisms was evidence in support of spontaneous generation, since microorganisms seemed too simplistic for sexual reproduction, and asexual reproduction through cell division had not yet been observed. Van Leeuwenhoek took issue with the ideas common at the time that fleas and lice could spontaneously result from putrefaction, and that frogs could likewise arise from slime. Using a broad range of experiments ranging from sealed and open meat incubation and the close study of insect reproduction he became, by the 1680s, convinced that spontaneous generation was incorrect.

The first experimental evidence against spontaneous generation came in 1668 when Francesco Redi showed that no maggots appeared in meat when flies were prevented from laying eggs. It was gradually shown that, at least in the case of all the higher and readily visible organisms, the previous sentiment regarding spontaneous generation was false. The alternative seemed to be biogenesis: that every living thing came from a pre-existing living thing (omne vivum ex ovo, Latin for "every living thing from an egg").

In 1768, Lazzaro Spallanzani demonstrated that microbes were present in the air, and could be killed by boiling. In 1861, Louis Pasteur performed a series of experiments that demonstrated that organisms such as bacteria and fungi do not spontaneously appear in sterile, nutrient-rich media, but could only appear by invasion from without.

The belief that self-ordering by spontaneous generation was impossible begged for an alternative. By the middle of the 19th century, the theory of biogenesis had accumulated so much evidential support, due to the work of Pasteur and others, that the alternative theory of spontaneous generation had been effectively disproven. John Desmond Bernal, a pioneer in X-ray crystallography, suggested that earlier theories such as spontaneous generation were based upon an explanation that life was continuously created as a result of chance events.

Etymology

Main article: Biogenesis

The term biogenesis is usually credited to either Henry Charlton Bastian or to Thomas Henry Huxley. Bastian used the term around 1869 in an unpublished exchange with John Tyndall to mean "life-origination or commencement". In 1870, Huxley, as new president of the British Association for the Advancement of Science, delivered an address entitled Biogenesis and Abiogenesis. In it he introduced the term biogenesis (with an opposite meaning to Bastian's) as well as abiogenesis:

And thus the hypothesis that living matter always arises by the agency of pre-existing living matter, took definite shape; and had, henceforward, a right to be considered and a claim to be refuted, in each particular case, before the production of living matter in any other way could be admitted by careful reasoners. It will be necessary for me to refer to this hypothesis so frequently, that, to save circumlocution, I shall call it the hypothesis of Biogenesis; and I shall term the contrary doctrine–that living matter may be produced by not living matter–the hypothesis of Abiogenesis.

Subsequently, in the preface to Bastian's 1871 book, The Modes of Origin of Lowest Organisms, Bastian referred to the possible confusion with Huxley's usage and explicitly renounced his own meaning:

A word of explanation seems necessary with regard to the introduction of the new term Archebiosis. I had originally, in unpublished writings, adopted the word Biogenesis to express the same meaning—viz., life-origination or commencement. But in the mean time the word Biogenesis has been made use of, quite independently, by a distinguished biologist [Huxley], who wished to make it bear a totally different meaning. He also introduced the word Abiogenesis. I have been informed, however, on the best authority, that neither of these words can—with any regard to the language from which they are derived—be supposed to bear the meanings which have of late been publicly assigned to them. Wishing to avoid all needless confusion, I therefore renounced the use of the word Biogenesis, and being, for the reason just given, unable to adopt the other term, I was compelled to introduce a new word, in order to designate the process by which living matter is supposed to come into being, independently of pre-existing living matter.

Louis Pasteur and Charles Darwin

Charles Darwin in 1879

Louis Pasteur remarked, about a finding of his in 1864 which he considered definitive, "Never will the doctrine of spontaneous generation recover from the mortal blow struck by this simple experiment." One alternative was that life's origins on Earth had come from somewhere else in the Universe. Periodically resurrected (see Panspermia, above) Bernal said that this approach "is equivalent in the last resort to asserting the operation of metaphysical, spiritual entities... it turns on the argument of creation by design by a creator or demiurge." Such a theory, Bernal said, was unscientific. A theory popular around the same time was that life was the result of an inner "life force", which in the late 19th century was championed by Henri Bergson.

The idea of evolution by natural selection proposed by Charles Darwin put an end to these metaphysical theologies. In a letter to Joseph Dalton Hooker on 1 February 1871, Darwin discussed the suggestion that the original spark of life may have begun in a "warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, &c., present, that a proteine 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." He had written to Hooker in 1863 stating that, "It is mere rubbish, thinking at present of the origin of life; one might as well think of the origin of matter." In On the Origin of Species, he had referred to life having been "created", by which he "really meant 'appeared' by some wholly unknown process", but had soon regretted using the Old Testament term "creation".

"Primordial soup" hypothesis

Main article: Primordial soup

Further information: Miller–Urey experiment

File:Aleksandr Oparin and Andrei Kursanov in enzymology laboratory 1938.jpg

Alexander Oparin (right) in his laboratory, 1938

No new notable research or theory on the subject appeared until 1924, when Alexander Oparin reasoned that atmospheric oxygen prevents the synthesis of certain organic compounds that are necessary building blocks for the evolution of life. In his book The Origin of Life, Oparin proposed that the "spontaneous generation of life" that had been attacked by Louis Pasteur did in fact occur once, but was now impossible because the conditions found on the early Earth had changed, and preexisting organisms would immediately consume any spontaneously generated organism. Oparin argued that a "primeval soup" of organic molecules could be created in an oxygenless atmosphere through the action of sunlight. These would combine in ever more complex ways until they formed coacervate droplets. These droplets would "grow" by fusion with other droplets, and "reproduce" through fission into daughter droplets, and so have a primitive metabolism in which factors that promote "cell integrity" survive, and those that do not become extinct. Many modern theories of the origin of life still take Oparin's ideas as a starting point.

Robert Shapiro has summarized the "primordial soup" theory of Oparin and J. B. S. Haldane in its "mature form" as follows:

1. The early Earth had a chemically reducing atmosphere.
2. This atmosphere, exposed to energy in various forms, produced simple organic compounds ("monomers").
3. These compounds accumulated in a "soup" that may have concentrated at various locations (shorelines, oceanic vents etc.).
4. By further transformation, more complex organic polymers - and ultimately life - developed in the soup.

About this time, Haldane suggested that the Earth's prebiotic oceans (quite different from their modern counterparts) would have formed a "hot dilute soup" in which organic compounds could have formed. Bernal called this idea biopoiesis or biopoesis, the process of living matter evolving from self-replicating but non-living molecules, and proposed that biopoiesis passes through a number of intermediate stages.

One of the most important pieces of experimental support for the "soup" theory came in 1952. Stanley L. Miller and Harold C. Urey performed an experiment that demonstrated how organic molecules could have spontaneously formed from inorganic precursors under conditions like those posited by the Oparin-Haldane hypothesis. The now-famous Miller–Urey experiment used a highly reducing mixture of gases - methane, ammonia, and hydrogen, as well as water vapour - to form basic organic monomers such as amino acids. The mixture of gases was cycled through an apparatus that delivered electrical sparks to the mixture. After one week, it was found that about 10% to 15% of the carbon in the system was then in the form of a racemic mixture of organic compounds, including amino acids, which are the building blocks of proteins. This provided direct experimental support for the second point of the "soup" theory, and it is around the remaining two points of the theory that much of the debate now centres.

Bernal showed that based upon this and subsequent work there is no difficulty in principle in forming most of the molecules we recognize as the basic molecules of life from their inorganic precursors. The underlying hypothesis held by Oparin, Haldane, Bernal, Miller and Urey, for instance, was that multiple conditions on the primeval Earth favoured chemical reactions that synthesized the same set of complex organic compounds from such simple precursors. A 2011 reanalysis of the saved vials containing the original extracts that resulted from the Miller and Urey experiments, using current and more advanced analytical equipment and technology, has uncovered more biochemicals than originally discovered in the 1950s. One of the more important findings was 23 amino acids, far more than the five originally found. However, Bernal said that "it is not enough to explain the formation of such molecules, what is necessary, is a physical-chemical explanation of the origins of these molecules that suggests the presence of suitable sources and sinks for free energy."

Proteinoid microspheres

Main article: Proteinoid

In trying to uncover the intermediate stages of abiogenesis mentioned by Bernal, Sidney W. Fox in the 1950s and 1960s studied the spontaneous formation of peptide structures under conditions that might plausibly have existed early in Earth's history. He demonstrated that amino acids could spontaneously form small chains called peptides. In one of his experiments, he allowed amino acids to dry out as if puddled in a warm, dry spot in prebiotic conditions. He found that, as they dried, the amino acids formed long, often cross-linked, thread-like, submicroscopic polypeptide molecules now named "proteinoid microspheres."

In another experiment using a similar method to set suitable conditions for life to form, Fox collected volcanic material from a cinder cone in Hawaii. He discovered that the temperature was over 100 °C (212 °F) just 4 inches (100 mm) beneath the surface of the cinder cone, and suggested that this might have been the environment in which life was created—molecules could have formed and then been washed through the loose volcanic ash and into the sea. He placed lumps of lava over amino acids derived from methane, ammonia and water, sterilized all materials, and baked the lava over the amino acids for a few hours in a glass oven. A brown, sticky substance formed over the surface and when the lava was drenched in sterilized water a thick, brown liquid leached out. It turned out that the amino acids had combined to form proteinoids, and the proteinoids had combined to form small globules that Fox called "microspheres." His proteinoids were not cells, although they formed clumps and chains reminiscent of cyanobacteria, but they contained no functional nucleic acids or any encoded information. Based upon such experiments, Colin S. Pittendrigh stated in December 1967 that "laboratories will be creating a living cell within ten years," a remark that reflected the typical contemporary levels of innocence of the complexity of cell structures.

Current models

There is no single, generally accepted model for the origin of life. Scientists have proposed several plausible theories, which share some common elements. While differing in the details, these theories are based on the framework laid out by Alexander Oparin (in 1924) and by J. B. S. Haldane (in 1925), who postulated the molecular or chemical evolution theory of life. According to them, the first molecules constituting the earliest cells "were synthesized under natural conditions by a slow process of molecular evolution, and these molecules then organized into the first molecular system with properties with biological order". Oparin and Haldane suggested that the atmosphere of the early Earth may have been chemically reducing in nature, composed primarily of methane (CH₄), ammonia (NH₃), water (H₂O), hydrogen sulfide (H₂S), carbon dioxide (CO₂) or carbon monoxide (CO), and phosphate (PO₄³⁻), with molecular oxygen (O₂) and ozone (O₃) either rare or absent. According to later models, the atmosphere in the late Hadean period consisted largely of nitrogen (N₂) and carbon dioxide, with smaller amounts of carbon monoxide, hydrogen (H₂), and sulfur compounds; while it did lack molecular oxygen and ozone, it was not as chemically reducing as Oparin and Haldane supposed. In the atmosphere proposed by Oparin and Haldane, electrical activity can produce certain basic small molecules (monomers) of life, such as amino acids. The Miller–Urey experiment reported in 1953 demonstrated this.

Bernal coined the term biopoiesis in 1949 to refer to the origin of life. In 1967, he suggested that it occurred in three "stages":

1. the origin of biological monomers
2. the origin of biological polymers
3. the evolution from molecules to cells

Bernal suggested that evolution commenced between stages 1 and 2. Bernal regarded the third stage - discovering methods by which biological reactions were incorporated behind a cell's boundary - as the most difficult. Modern work on the way that cell membranes self-assemble, and the work on micropores in various substrates may be a halfway house towards the development of independent free-living cells.

The chemical processes that took place on the early Earth are called chemical evolution. Both Manfred Eigen and Sol Spiegelman demonstrated that evolution, including replication, variation, and natural selection, can occur in populations of molecules as well as in organisms. Spiegelman took advantage of natural selection to synthesize the Spiegelman Monster, which had a genome with just 218 nucleotide bases, having deconstructively evolved from a 4500-base bacterial RNA. Eigen built on Spiegelman's work and produced a similar system further degraded to just 48 or 54 nucleotides - the minimum required for the binding of the replication enzyme.

Following on from chemical evolution came the initiation of biological evolution, which led to the first cells. No one has yet synthesized a "protocell" using basic components with the necessary properties of life (the so-called "bottom-up-approach"). Without such a proof-of-principle, explanations have tended to focus on chemosynthesis. However, some researchers work in this field, notably Steen Rasmussen and Jack W. Szostak. Others have argued that a "top-down approach" is more feasible. One such approach, successfully attempted by Craig Venter and others at J. Craig Venter Institute, involves engineering existing prokaryotic cells with progressively fewer genes, attempting to discern at which point the most minimal requirements for life are reached.

Chemical origin of organic molecules

The elements, except for hydrogen, ultimately derive from stellar nucleosynthesis.On the 12th of October 2016, astronomers reported that the very basic chemical ingredients of life—the carbon-hydrogen molecule (CH, or methylidyne radical), the carbon-hydrogen positive ion (CH+) and the carbon ion (C+)—are the result, in large part, of ultraviolet light from stars, rather than in other ways, such as the result of turbulent events related to supernovae and young stars, as thought earlier. Complex molecules, including organic molecules, form naturally both in space and on planets. There are two possible sources of organic molecules on the early Earth:

1. Terrestrial origins – organic molecule synthesis driven by impact shocks or by other energy sources (such as UV light, redox coupling, or electrical discharges) (e.g., Miller's experiments)
2. Extraterrestrial origins – formation of organic molecules in interstellar dust clouds, which rain down on planets. (See pseudo-panspermia)

A cladogram demonstrating extreme hyperthermophiles at the base of the phylogenetic tree of life.

Based on recent computer model studies, the complex organic molecules necessary for life may have formed in the protoplanetary disk of dust grains surrounding the Sun before the formation of the Earth. According to the computer studies, this same process may also occur around other stars that acquire planets. (Also see Extraterrestrial organic molecules).

Estimates of the production of organics from these sources suggest that the Late Heavy Bombardment before 3.5 Ga within the early atmosphere made available quantities of organics comparable to those produced by terrestrial sources.

It has been estimated that the Late Heavy Bombardment may also have effectively sterilized the Earth's surface to a depth of tens of metres. If life evolved deeper than this, it would have also been shielded from the early high levels of ultraviolet radiation from the T Tauri stage of the Sun's evolution. Simulations of geothermically heated oceanic crust yield far more organics than those found in the Miller-Urey experiments (see below). In the deep hydrothermal vents, Everett Shock has found "there is an enormous thermodynamic drive to form organic compounds, as seawater and hydrothermal fluids, which are far from equilibrium, mix and move towards a more stable state." Shock has found that the available energy is maximized at around 100 – 150 degrees Celsius, precisely the temperatures at which the hyperthermophilic bacteria and thermoacidophilic archaea have been found, at the base of the phylogenetic tree of life closest to the Last Universal Common Ancestor (LUCA).

Chemical synthesis

While features of self-organization and self-replication are often considered the hallmark of living systems, there are many instances of abiotic molecules exhibiting such characteristics under proper conditions. Stan Palasek suggested based on a theoretical model that self-assembly of ribonucleic acid (RNA) molecules can occur spontaneously due to physical factors in hydrothermal vents. Virus self-assembly within host cells has implications for the study of the origin of life, as it lends further credence to the hypothesis that life could have started as self-assembling organic molecules.

Multiple sources of energy were available for chemical reactions on the early Earth. For example, heat (such as from geothermal processes) is a standard energy source for chemistry. Other examples include sunlight and electrical discharges (lightning), among others. Unfavourable reactions can also be driven by highly favourable ones, as in the case of iron-sulfur chemistry. For example, this was probably important for carbon fixation (the conversion of carbon from its inorganic form to an organic one). Carbon fixation via iron-sulfur chemistry is highly favourable, and occurs at neutral pH and 100 °C (212 °F). Iron-sulfur surfaces, which are abundant near hydrothermal vents, are also capable of producing small amounts of amino acids and other biological metabolites.

Formamide produces all four ribonucleotides and other biological molecules when warmed in the presence of various terrestrial minerals. Formamide is ubiquitous in the Universe, produced by the reaction of water and hydrogen cyanide (HCN). It has several advantages as a biotic precursor, including the ability to easily become concentrated through the evaporation of water. Although HCN is poisonous, it only affects aerobic organisms (eukaryotes and aerobic bacteria), which did not yet exist. It can play roles in other chemical processes as well, such as the synthesis of the amino acid glycine.

In 1961, it was shown that the nucleic acid purine base adenine can be formed by heating aqueous ammonium cyanide solutions. Other pathways for synthesizing bases from inorganic materials were also reported. Leslie E. Orgel and colleagues have shown that freezing temperatures are advantageous for the synthesis of purines, due to the concentrating effect for key precursors such as hydrogen cyanide. Research by Stanley L. Miller and colleagues suggested that while adenine and guanine require freezing conditions for synthesis, cytosine and uracil may require boiling temperatures. Research by the Miller group notes the formation of seven different amino acids and 11 types of nucleobases in ice when ammonia and cyanide were left in a freezer from 1972 to 1997. Other work demonstrated the formation of s-triazines (alternative nucleobases), pyrimidines (including cytosine and uracil), and adenine from urea solutions subjected to freeze-thaw cycles under a reductive atmosphere (with spark discharges as an energy source). The explanation given for the unusual speed of these reactions at such a low temperature is eutectic freezing. As an ice crystal forms, it stays pure: only molecules of water join the growing crystal, while impurities like salt or cyanide are excluded. These impurities become crowded in microscopic pockets of liquid within the ice, and this crowding causes the molecules to collide more often. Mechanistic exploration using quantum chemical methods provide a more detailed understanding of some of the chemical processes involved in chemical evolution, and a partial answer to the fundamental question of molecular biogenesis.

At the time of the Miller–Urey experiment, scientific consensus was that the early Earth had a reducing atmosphere with compounds relatively rich in hydrogen and poor in oxygen (e.g., CH₄ and NH₃ as opposed to CO₂ and nitrogen dioxide (NO₂)). However, current scientific consensus describes the primitive atmosphere as either weakly reducing or neutral (see also Oxygen Catastrophe). Such an atmosphere would diminish both the amount and variety of amino acids that could be produced, although studies that include iron and carbonate minerals (thought present in early oceans) in the experimental conditions have again produced a diverse array of amino acids. Other scientific research has focused on two other potential reducing environments: outer space and deep-sea thermal vents.

The spontaneous formation of complex polymers from abiotically generated monomers under the conditions posited by the "soup" theory is not at all a straightforward process. Besides the necessary basic organic monomers, compounds that would have prohibited the formation of polymers were also formed in high concentration during the Miller–Urey and Joan Oró experiments. The Miller–Urey experiment, for example, produces many substances that would react with the amino acids or terminate their coupling into peptide chains.

A research project completed in March 2015 by John D. Sutherland and others found that a network of reactions beginning with hydrogen cyanide and hydrogen sulfide, in streams of water irradiated by UV light, could produce the chemical components of proteins and lipids, as well as those of RNA, while not producing a wide range of other compounds. The researchers used the term "cyanosulfidic" to describe this network of reactions.

Autocatalysis

Main article: Autocatalysis

Autocatalysts are substances that catalyze the production of themselves and therefore are "molecular replicators." The simplest self-replicating chemical systems are autocatalytic, and typically contain three components: a product molecule and two precursor molecules. The product molecule joins together the precursor molecules, which in turn produce more product molecules from more precursor molecules. The product molecule catalyzes the reaction by providing a complementary template that binds to the precursors, thus bringing them together. Such systems have been demonstrated both in biological macromolecules and in small organic molecules. Systems that do not proceed by template mechanisms, such as the self-reproduction of micelles and vesicles, have also been observed.

It has been proposed that life initially arose as autocatalytic chemical networks. British ethologist Richard Dawkins wrote about autocatalysis as a potential explanation for the origin of life in his 2004 book The Ancestor's Tale. In his book, Dawkins cites experiments performed by Julius Rebek, Jr. and his colleagues in which they combined amino adenosine and pentafluorophenyl esters with the autocatalyst amino adenosine triacid ester (AATE). One product was a variant of AATE, which catalyzed 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.

In the early 1970s, Manfred Eigen and Peter Schuster examined the transient stages between the molecular chaos and a self-replicating hypercycle in a prebiotic soup. 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 of ribozymes capable of catalyzing their own chemical reactions. The hypercycle theory requires the existence of complex biochemicals, such as nucleotides, which do not form under the conditions proposed by the Miller–Urey experiment.

Geoffrey W. Hoffmann has shown that an early error-prone translation machinery can be stable against an error catastrophe of the type that had been envisaged as problematical for the origin of life, and was known as "Orgel's paradox".

Hoffmann has furthermore argued that a complex nucleation event as the origin of life involving both polypeptides and nucleic acid is compatible with the time and space available in the primitive oceans of Earth Hoffmann suggests that volcanic ash may provide the many random shapes needed in the postulated complex nucleation event. This aspect of the theory can be tested experimentally.

Homochirality

Main article: Homochirality

Homochirality refers to the geometric property of some materials that are composed of chiral units. Chiral refers to nonsuperimposable 3D forms that are mirror images of one another, as are left and right hands. Living organisms use molecules that have the same chirality ("handedness"): with almost no exceptions, amino acids are left-handed while nucleotides and sugars are right-handed. Chiral molecules can be synthesized, but in the absence of a chiral source or a chiral catalyst, they are formed in a 50/50 mixture of both enantiomers (called a racemic mixture). Known mechanisms for the production of non-racemic mixtures from racemic starting materials include: asymmetric physical laws, such as the electroweak interaction; asymmetric environments, such as those caused by circularly polarized light, quartz crystals, or the Earth's rotation; and statistical fluctuations during racemic synthesis.

Once established, chirality would be selected for. A small bias (enantiomeric excess) in the population can be amplified into a large one by asymmetric autocatalysis, such as in the Soai reaction. In asymmetric autocatalysis, the catalyst is a chiral molecule, which means that a chiral molecule is catalyzing its own production. An initial enantiomeric excess, such as can be produced by polarized light, then allows the more abundant enantiomer to outcompete the other.

Clark has suggested that homochirality may have started in outer space, as the studies of the amino acids on the Murchison meteorite showed that L-alanine is more than twice as frequent as its D form, and L-glutamic acid was more than three times prevalent than its D counterpart. Various chiral crystal surfaces can also act as sites for possible concentration and assembly of chiral monomer units into macromolecules. Compounds found on meteorites suggest that the chirality of life derives from abiogenic synthesis, since amino acids from meteorites show a left-handed bias, whereas sugars show a predominantly right-handed bias, the same as found in living organisms.

Self-enclosement, reproduction, duplication and the RNA world

Protocells

Main article: Protocell

The three main structures phospholipids form spontaneously in solution: the liposome (a closed bilayer), the micelle and the bilayer.

A protocell is a self-organized, self-ordered, spherical collection of lipids proposed as a stepping-stone to the origin of life. A central question in evolution is how simple protocells first arose and differed in reproductive contribution to the following generation driving the evolution of life. Although a functional protocell has not yet been achieved in a laboratory setting, there are scientists who think the goal is well within reach.

Self-assembled vesicles are essential components of primitive cells. The second law of thermodynamics requires that the Universe move in a direction in which entropy increases, yet life is distinguished by its great degree of organization. Therefore, a boundary is needed to separate life processes from non-living matter. Researchers Irene A. Chen and Jack W. Szostak amongst others, suggest that simple physicochemical properties of elementary protocells can give rise to essential cellular behaviours, including primitive forms of differential reproduction competition and energy storage. Such cooperative interactions between the membrane and its encapsulated contents could greatly simplify the transition from simple replicating molecules to true cells. Furthermore, competition for membrane molecules would favour stabilized membranes, suggesting a selective advantage for the evolution of cross-linked fatty acids and even the phospholipids of today. Such micro-encapsulation would allow for metabolism within the membrane, the exchange of small molecules but the prevention of passage of large substances across it. The main advantages of encapsulation include the increased solubility of the contained cargo within the capsule and the storage of energy in the form of a electrochemical gradient.

A 2012 study led by Armen Y. Mulkidjanian of Germany's University of Osnabrück, suggests that inland pools of condensed and cooled geothermal vapour have the ideal characteristics for the origin of life. Scientists confirmed in 2002 that by adding a montmorillonite clay to a solution of fatty acid micelles (lipid spheres), the clay sped up the rate of vesicles formation 100-fold.

Another protocell model is the Jeewanu. First synthesized in 1963 from simple minerals and basic organics while exposed to sunlight, it is still reported to have some metabolic capabilities, the presence of semipermeable membrane, amino acids, phospholipids, carbohydrates and RNA-like molecules. However, the nature and properties of the Jeewanu remains to be clarified.

Electrostatic interactions induced by short, positively charged, hydrophobic peptides containing 7 amino acids in length or fewer, can attach RNA to a vesicle membrane, the basic cell membrane.

RNA world

Main article: RNA world

Molecular structure of the ribosome 30S subunit from Thermus thermophilus. Proteins are shown in blue and the single RNA chain in orange.

The RNA world hypothesis describes an early Earth with self-replicating and catalytic RNA but no DNA or proteins. It is generally accepted that current life on Earth descends from an RNA world, although RNA-based life may not have been the first life to exist. This conclusion is drawn from many independent lines of evidence, such as the observations that RNA is central to the translation process and that small RNAs can catalyze all of the chemical groups and information transfers required for life. The structure of the ribosome has been called the "smoking gun," as it showed that the ribosome is a ribozyme, with a central core of RNA and no amino acid side chains within 18 angstroms of the active site where peptide bond formation is catalyzed. The concept of the RNA world was first proposed in 1962 by Alexander Rich, and the term was coined by Walter Gilbert in 1986.

Possible precursors for the evolution of protein synthesis include a mechanism to synthesize short peptide cofactors or form a mechanism for the duplication of RNA. It is likely that the ancestral ribosome was composed entirely of RNA, although some roles have since been taken over by proteins. Major remaining questions on this topic include identifying the selective force for the evolution of the ribosome and determining how the genetic code arose.

Eugene Koonin said, "Despite considerable experimental and theoretical effort, no compelling scenarios currently exist for the origin of replication and translation, the key processes that together comprise the core of biological systems and the apparent pre-requisite of biological evolution. The RNA World concept might offer the best chance for the resolution of this conundrum but so far cannot adequately account for the emergence of an efficient RNA replicase or the translation system. The MWO [Ed.: "many worlds in one"] version of the cosmological model of eternal inflation could suggest a way out of this conundrum because, in an infinite multiverse with a finite number of distinct macroscopic histories (each repeated an infinite number of times), emergence of even highly complex systems by chance is not just possible but inevitable."

Viral origins and the RNA World

Recent evidence for a "virus first" hypothesis, which may support theories of the RNA world have been suggested in new research. One of the difficulties for the study of viral origins and evolution is their high rate of mutation; this is particularly the case in RNA retroviruses like HIV. A 2015 study compared protein fold structures across different branches of the tree of life, where researchers can reconstruct the evolutionary histories of the folds and of the organisms whose genomes code for those folds. They argue that protein folds are better markers of ancient events as their three-dimensional structures can be maintained even as the sequences that code for those begin to change. Thus, the viral protein repertoire retain traces of ancient evolutionary history that can be recovered using advanced bioinformatics approaches. Those researchers think that "the prolonged pressure of genome and particle size reduction eventually reduced virocells into modern viruses (identified by the complete loss of cellular makeup), meanwhile other coexisting cellular lineages diversified into modern cells. The data suggest that viruses originated from ancient cells that co-existed with the ancestors of modern cells. These ancient cells likely contained segmented RNA genomes.

RNA synthesis and replication

The RNA world hypothesis has spurred scientists to determine if RNA molecules could have spontaneously formed able to catalyze their own replication. Evidence suggests that the chemical conditions, including the presence of boron, molybdenum and oxygen needed for the initial production of RNA molecules, may have been better on the planet Mars than on the planet Earth. If so, life-suitable molecules originating on Mars, may have later migrated to Earth via meteor ejections.

A number of hypotheses of formation of RNA have been put forward. As of 1994, there were difficulties in the explanation of the abiotic synthesis of the nucleotides cytosine and uracil. Subsequent research has shown possible routes of synthesis; for example, formamide produces all four ribonucleotides and other biological molecules when warmed in the presence of various terrestrial minerals. Early cell membranes could have formed spontaneously from proteinoids, which are protein-like molecules produced when amino acid solutions are heated while in the correct concentration of aqueous solution. These are seen to form micro-spheres which are observed to behave similarly to membrane-enclosed compartments. Other possible means of producing more complicated organic molecules include chemical reactions that take place on clay substrates or on the surface of the mineral pyrite.

Factors supportive of an important role for RNA in early life include its ability to act both to store information and to catalyze chemical reactions (as a ribozyme); its many important roles as an intermediate in the expression of 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 RNA molecule under the conditions that approximated the early Earth. Relatively short RNA molecules have been artificially produced in labs, which are capable of replication. Such replicase RNA, which functions as both code and catalyst provides its own template upon which copying can occur. Jack W. Szostak has shown that certain catalytic RNAs can join smaller RNA sequences together, creating the potential for self-replication. If these conditions were present, Darwinian natural selection would favour the proliferation of such autocatalytic sets, to which further functionalities could be added. Such autocatalytic systems of RNA capable of self-sustained replication have been identified. The RNA replication systems, which include two ribozymes that catalyze each other's synthesis, showed a doubling time of the product of about one hour, and were subject to natural selection under the conditions that existed in the experiment. In evolutionary competition experiments, this led to the emergence of new systems which replicated more efficiently. This was the first demonstration of evolutionary adaptation occurring in a molecular genetic system.

Depending on the specific definition used, life can be considered to have emerged when RNA chains began to express the basic conditions necessary for natural selection to operate as conceived by Darwin: heritability, variation of type, and differential reproductive output. The fitness of an RNA replicator (its per capita rate of increase) would likely be a function of its adaptive capacities that are intrinsic (in the sense that they were determined by the nucleotide sequence) and the availability of its resources. The three primary adaptive capacities may have been (1) the capacity to replicate with moderate fidelity, giving rise to both heritability while allowing variation of type, (2) the capacity to avoid decay, and (3) the capacity to acquire and process resources. These capacities would have been determined initially by the folded configurations of the RNA replicators that, in turn, would be encoded in their individual nucleotide sequences. Relative reproductive success, competition, between different replicators would have depended on the relative values of their adaptive capacities.

Pre-RNA world

It is possible that a different type of nucleic acid, such as PNA, TNA or GNA, was the first to emerge as a self-reproducing molecule, only later replaced by RNA. Larralde et al., say that "the generally accepted prebiotic synthesis of ribose, the formose reaction, yields numerous sugars without any selectivity." and they conclude that their "results suggest that the backbone of the first genetic material could not have contained ribose or other sugars because of their instability." The ester linkage of ribose and phosphoric acid in RNA is known to be prone to hydrolysis.

Pyrimidine ribonucleosides and their respective nucleotides have been prebiotically synthesized by a sequence of reactions which by-pass the free sugars, and are assembled in a stepwise fashion by using nitrogenous or oxygenous chemistries. Sutherland has demonstrated high yielding routes to cytidine and uridine ribonucleotides built from small 2 and 3 carbon fragments such as glycolaldehyde, glyceraldehyde or glyceraldehyde-3-phosphate, cyanamide and cyanoacetylene. One of the steps in this sequence allows the isolation of enantiopure ribose aminooxazoline if the enantiomeric excess of glyceraldehyde is 60% or greater. This can be viewed as a prebiotic purification step, where the said compound spontaneously crystallized out from a mixture of the other pentose aminooxazolines. Ribose aminooxazoline can then react with cyanoacetylene in a mild and highly efficient manner to give the alpha cytidine ribonucleotide. Photoanomerization with UV light allows for inversion about the 1' anomeric centre to give the correct beta stereochemistry. In 2009 they showed that the same simple building blocks allow access, via phosphate controlled nucleobase elaboration, to 2',3'-cyclic pyrimidine nucleotides directly, which are known to be able to polymerize into RNA. This paper also highlights the possibility for the photo-sanitization of the pyrimidine-2',3'-cyclic phosphates.

Origin of biological metabolism

Metabolism-like reactions could have occurred naturally in early oceans, before the first organisms evolved. Metabolism may predate the origin of life and life may have evolved from the chemical conditions that prevailed in the world's earliest oceans. Reconstructions in laboratories show that some of these reactions can produce RNA, and some others resemble two essential reaction cascades of metabolism: glycolysis and the pentose phosphate pathway, that provide essential precursors for nucleic acids, amino acids and lipids. A study at the University of Düsseldorf created phylogenic trees based upon 6 million genes from bacteria and archaea, and identified 355 protein families that were probably present in LUCA. They were based upon an anaeobic metabolism fixing carbon dioxide and nitrogen. It suggests that LUCA evolved in an environment rich in hydrogen, carbon dioxide and iron. Following are some observed discoveries and related hypotheses.

Iron–sulfur world

Main article: Iron–sulfur world theory

In the 1980s, Günter Wächtershäuser, encouraged and supported by Karl R. Popper, postulated in his iron–sulfur world, a theory of the evolution of pre-biotic chemical pathways as the starting point in the evolution of life. It presents 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 ultraviolet irradiation), "Wächtershäuser systems" come with a built-in source of energy, sulfides of iron (iron pyrite) and other minerals . The energy released from redox reactions of these metal sulfides is available for the synthesis of organic molecules. It is therefore hypothesized that such systems may be able to evolve into autocatalytic sets of self-replicating, metabolically active entities that predate the life forms known today. Experiments with such sulfides in an aqueous environment at 100 °C produced a relatively small yield of dipeptides (0.4% to 12.4%) and a smaller yield of tripeptides (0.10%) although under the same conditions, dipeptides were quickly broken down.

Several models reject the idea of the self-replication of a "naked-gene" but postulate the emergence of a primitive metabolism which could provide a safe environment for the later emergence of RNA replication. The centrality of the Krebs cycle (citric acid cycle) to energy production in aerobic organisms, and in drawing in carbon dioxide and hydrogen ions in biosynthesis of complex organic chemicals, suggests that it was one of the first parts of the metabolism to evolve. Somewhat in agreement with these notions, geochemist Michael Russell has proposed that "the purpose of life is to hydrogenate carbon dioxide" (as part of a "metabolism-first," rather than a "genetics-first," scenario). Physicist Jeremy England of MIT has proposed that thermodynamically, life was bound to eventually arrive, as based on established physics, he mathematically indicates "...that when a group of atoms is driven by an external source of energy (like the sun or chemical fuel) and surrounded by a heat bath (like the ocean or atmosphere), it will often gradually restructure itself in order to dissipate increasingly more energy. This could mean that under certain conditions, matter inexorably acquires the key physical attribute associated with life."

One of the earliest incarnations of this idea was put forward in 1924 with Oparin's notion of primitive self-replicating vesicles which predated the discovery of the structure of DNA. Variants in the 1980s and 1990s include 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.

Orgel summarized 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 five recognized ways of carbon dioxide fixation in nature today) would be compatible with the idea of self-organization 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 centres and catalyzes the formation of acetyl-CoA (which may be regarded as a modern form of acetyl-thiol) in a single step. There are increasing concerns, however, that prebiotic thiolated (i.e.Thioacetic acid) and Thioester compounds are thermodynamically and kinetically unfavourable to accumulate in presumed prebiotic conditions (i.e. Hydrothermal vents).

Zn-world hypothesis

The Zn-world (zinc world) theory of Armen Y. Mulkidjanian is an extension of Wächtershäuser's pyrite hypothesis. Wächtershäuser based his theory of the initial chemical processes leading to informational molecules (i.e., RNA, peptides) on a regular mesh of electric charges at the surface of pyrite that may have made the primeval polymerization thermodynamically more favourable by attracting reactants and arranging them appropriately relative to each other. The Zn-world theory specifies and differentiates further. Hydrothermal fluids rich in H₂S interacting with cold primordial ocean (or Darwin's "warm little pond") water leads to the precipitation of metal sulfide particles. Oceanic vent systems and other hydrothermal systems have a zonal structure reflected in ancient volcanogenic massive sulfide deposits (VMS) of hydrothermal origin. They reach many kilometres in diameter and date back to the Archean Eon. Most abundant are pyrite (FeS₂), chalcopyrite (CuFeS₂), and sphalerite (ZnS), with additions of galena (PbS) and alabandite (MnS). ZnS and MnS have a unique ability to store radiation energy, e.g. provided by UV light. Since during the relevant time window of the origins of replicating molecules the primordial atmospheric pressure was high enough (>100 bar, about 100 atmospheres) to precipitate near the Earth's surface and UV irradiation was 10 to 100 times more intense than now, the unique photosynthetic properties mediated by ZnS provided just the right energy conditions to energize the synthesis of informational and metabolic molecules and the selection of photostable nucleobases.

The Zn-world theory has been further filled out with experimental and theoretical evidence for the ionic constitution of the interior of the first proto-cells before archaea, bacteria and proto-eukaryotes evolved. Archibald Macallum noted the resemblance of organism fluids such as blood, and lymph to seawater; however, the inorganic composition of all cells differ from that of modern seawater, which led Mulkidjanian and colleagues to reconstruct the "hatcheries" of the first cells combining geochemical analysis with phylogenomic scrutiny of the inorganic ion requirements of universal components of modern cells. The authors conclude that ubiquitous, and by inference primordial, proteins and functional systems show affinity to and functional requirement for K⁺, Zn²⁺, Mn²⁺, and phosphate. Geochemical reconstruction shows that the ionic composition conducive to the origin of cells could not have existed in what we today call marine settings but is compatible with emissions of vapour-dominated zones of what we today call inland geothermal systems. Under the oxygen depleted, CO₂-dominated primordial atmosphere, the chemistry of water condensates and exhalations near geothermal fields would resemble the internal milieu of modern cells. Therefore, the precellular stages of evolution may have taken place in shallow "Darwin ponds" lined with porous silicate minerals mixed with metal sulfides and enriched in K⁺, Zn²⁺, and phosphorus compounds.

Deep sea vent hypothesis

Deep-sea hydrothermal vent or 'black smoker'

The deep sea vent, or alkaline hydrothermal vent, theory for the origin of life on Earth posits that life may have begun at submarine hydrothermal vents, William Martin and Michael Russell have suggested "that life evolved in structured iron monosulphide precipitates in a seepage site hydrothermal mound at a redox, pH and temperature gradient between sulphide-rich hydrothermal fluid and iron(II)-containing waters of the Hadean ocean floor. The naturally arising, three-dimensional compartmentation observed within fossilized seepage-site metal sulphide precipitates indicates that these inorganic compartments were the precursors of cell walls and membranes found in free-living prokaryotes. The known capability of FeS and NiS to catalyze the synthesis of the acetyl-methylsulphide from carbon monoxide and methylsulphide, constituents of hydrothermal fluid, indicates that pre-biotic syntheses occurred at the inner surfaces of these metal-sulphide-walled compartments,..." These form where hydrogen-rich fluids emerge from below the sea floor, as a result of serpentinization of ultra-mafic olivine with seawater and a pH interface with carbon dioxide-rich ocean water. The vents form a sustained chemical energy source derived from redox reactions, in which electron donors, such as molecular hydrogen, react with electron acceptors, such as carbon dioxide (see Iron–sulfur world theory). These are highly exothermic reactions.

Michael Russell demonstrated that alkaline vents created an abiogenic proton motive force (PMF) chemiosmotic gradient, in which conditions are ideal for an abiogenic hatchery for life. Their microscopic compartments "provide a natural means of concentrating organic molecules," composed of iron-sulfur minerals such as mackinawite, endowed these mineral cells with the catalytic properties envisaged by Wächtershäuser. This movement of ions across the membrane depends on a combination of two factors:

1. Diffusion force caused by concentration gradient—all particles including ions tend to diffuse from higher concentration to lower.
2. Electrostatic force caused by electrical potential gradient—cations like protons H⁺ tend to diffuse down the electrical potential, anions in the opposite direction.

These two gradients taken together can be expressed as an electrochemical gradient, providing energy for abiogenic synthesis. The proton motive force can be described as the measure of the potential energy stored as a combination of proton and voltage gradients across a membrane (differences in proton concentration and electrical potential).

White smokers emitting liquid carbon dioxide (CO₂) at the Champagne vent, Marianas Trench Marine National Monument

Jack W. Szostak suggested that geothermal activity provides greater opportunities for the origination of life in open lakes where there is a buildup of minerals. In 2010, based on spectral analysis of sea and hot mineral water, Ignat Ignatov and Oleg Mosin demonstrated that life may have predominantly originated in hot mineral water. The hot mineral water that contains bicarbonate and calcium ions has the most optimal range. This case is similar to the origin of life in hydrothermal vents, but with bicarbonate and calcium ions in hot water. This water has a pH of 9–11 and is possible to have the reactions in seawater. According to Melvin Calvin, certain reactions of condensation-dehydration of amino acids and nucleotides in individual blocks of peptides and nucleic acids can take place in the primary hydrosphere with pH 9-11 at a later evolutionary stage. Some of these compounds like hydrocyanic acid (HCN) have been proven in the experiments of Miller. This is the environment in which the stromatolites have been created. David Ward of Montana State University described the formation of stromatolites in hot mineral water at the Yellowstone National Park. Stromatolites survive in hot mineral water and in proximity to areas with volcanic activity. Processes have evolved in the sea near geysers of hot mineral water. In 2011, Tadashi Sugawara from the University of Tokyo created a protocell in hot water.

Experimental research and computer modelling suggest that the surfaces of mineral particles inside hydrothermal vents have catalytic properties similar to those of enzymes and are able to create simple organic molecules, such as methanol (CH₃OH) and formic, acetic and pyruvic acid out of the dissolved CO₂ in the water.

The research reported above by William F. Martin in July 2016 supports the thesis that life arose at hydrothermal vents, that spontaneous chemistry in the Earth’s crust driven by rock–water interactions at disequilibrium thermodynamically underpinned life’s origin and that the founding lineages of the archaea and bacteria were H2-dependent autotrophs that used CO2 as their terminal acceptor in energy metabolism. Martin suggests, based upon this evidence that LUCA "may have depended heavily on the geothermal energy of the vent to survive".

Thermosynthesis

Today's bioenergetic process of fermentation is carried out by either the aforementioned citric acid cycle or the Acetyl-CoA pathway, both of which have been connected to the primordial Iron–sulfur world. In a different approach, the thermosynthesis hypothesis considers the bioenergetic process of chemiosmosis, which plays an essential role in cellular respiration and photosynthesis, more basal than fermentation: the ATP synthase enzyme, which sustains chemiosmosis, is proposed as the currently extant enzyme most closely related to the first metabolic process.

First, life needed an energy source to bring about the condensation reaction that yielded the peptide bonds of proteins and the phosphodiester bonds of RNA. In a generalization and thermal variation of the binding change mechanism of today's ATP synthase, the "first protein" would have bound substrates (peptides, phosphate, nucleosides, RNA 'monomers') and condensed them to a reaction product that remained bound until after a temperature change it was released by thermal unfolding.

The energy source under the thermosynthesis hypothesis was thermal cycling, the result of suspension of protocells in a convection current, as is plausible in a volcanic hot spring; the convection accounts for the self-organization and dissipative structure required in any origin of life model. The still ubiquitous role of thermal cycling in germination and cell division is considered a relic of primordial thermosynthesis.

By phosphorylating cell membrane lipids, this "first protein" gave a selective advantage to the lipid protocell that contained the protein. This protein also synthesized a library of many proteins, of which only a minute fraction had thermosynthesis capabilities. As proposed by Dyson, it propagated functionally: it made daughters with similar capabilities, but it did not copy itself. Functioning daughters consisted of different amino acid sequences.

Whereas the Iron–sulfur world identifies a circular pathway as the most simple, the thermosynthesis hypothesis does not even invoke a pathway: ATP synthase's binding change mechanism resembles a physical adsorption process that yields free energy, rather than a regular enzyme's mechanism, which decreases the free energy. It has been claimed that the emergence of cyclic systems of protein catalysts is implausible.

Other models

Clay hypothesis

Montmorillonite, an abundant clay, is a catalyst for the polymerization of RNA and for the formation of membranes from lipids. A model for the origin of life using clay was forwarded by Alexander Graham Cairns-Smith in 1985 and explored as a plausible mechanism by several scientists. The clay hypothesis postulates that complex organic molecules arose gradually on pre-existing, non-organic replication surfaces of silicate crystals in solution.

At the Rensselaer Polytechnic Institute, James P. Ferris' studies have also confirmed that clay minerals of montmorillonite catalyze the formation of RNA in aqueous solution, by joining nucleotides to form longer chains.

In 2007, Bart Kahr from the University of Washington and colleagues reported their experiments that tested the idea that crystals can act as a source of transferable information, using crystals of potassium hydrogen phthalate. "Mother" crystals with imperfections were cleaved and used as seeds to grow "daughter" crystals from solution. They then examined the distribution of imperfections in the new crystals and found that the imperfections in the mother crystals were reproduced in the daughters, but the daughter crystals also had many additional imperfections. For gene-like behaviour to be observed, the quantity of inheritance of these imperfections should have exceeded that of the mutations in the successive generations, but it did not. Thus Kahr concluded that the crystals "were not faithful enough to store and transfer information from one generation to the next."

Gold's "deep-hot biosphere" model

In the 1970s, Thomas Gold proposed the theory that life first developed not on the surface of the Earth, but several kilometres below the surface. 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. Thomas Gold also asserted that a trickle of food from a deep, unreachable, source is needed for survival because life arising in a puddle of organic material is likely to consume all of its food and become extinct. Gold's theory is that the flow of such food is due to out-gassing of primordial methane from the Earth's mantle; more conventional explanations of the food supply of deep microbes (away from sedimentary carbon compounds) is that the organisms subsist on hydrogen released by an interaction between water and (reduced) iron compounds in rocks.

Panspermia

Main article: Panspermia

Panspermia is the hypothesis that life exists throughout the Universe, distributed by meteoroids, asteroids, comets, planetoids, and, also, by spacecraft in the form of unintended contamination by microorganisms.

Panspermia hypothesis does not attempt to explain how life first originated, but merely shifts it to another planet or a comet. The advantage of an extraterrestrial origin of primitive life is that life is not required to have formed 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 hypothesis is scant, but it finds support in studies of Martian meteorites found in Antarctica and in studies of extremophile microbes' survival in outer space tests. (See also: List of microorganisms tested in outer space.)

Extraterrestrial organic molecules

See also: List of interstellar and circumstellar molecules and Panspermia § Pseudo-panspermia

Methane is one of the simplest organic compounds

An organic compound is any member of a large class of gaseous, liquid, or solid chemicals whose molecules contain carbon. Carbon is the fourth most abundant element in the Universe by mass after hydrogen, helium, and oxygen. Carbon is abundant in the Sun, stars, comets, and in the atmospheres of most planets. Organic compounds are relatively common in space, formed by "factories of complex molecular synthesis" which occur in molecular clouds and circumstellar envelopes, and chemically evolve after reactions are initiated mostly by ionizing radiation. Based on computer model studies, the complex organic molecules necessary for life may have formed on dust grains in the protoplanetary disk surrounding the Sun before the formation of the Earth. According to the computer studies, this same process may also occur around other stars that acquire planets.

Observations suggest that the majority of organic compounds introduced on Earth by interstellar dust particles are considered principal agents in the formation of complex molecules, thanks to their peculiar surface-catalytic activities. Studies reported in 2008, based on ¹²C/¹³C isotopic ratios of organic compounds found in the Murchison meteorite, suggested that the RNA component uracil and related molecules, including xanthine, were formed extraterrestrially. On 8 August 2011, a report based on NASA studies of meteorites found on Earth was published suggesting DNA components (adenine, guanine and related organic molecules) were made in outer space. Scientists also found that the cosmic dust permeating the Universe contains complex organics ("amorphous organic solids with a mixed aromatic–aliphatic structure") that could be created naturally, and rapidly, by stars. Sun Kwok of The University of Hong Kong suggested that these compounds may have been related to the development of life on Earth said that "If this is the case, life on Earth may have had an easier time getting started as these organics can serve as basic ingredients for life."

Formation of glycolaldehyde in stardust

Glycolaldehyde, the first example of an interstellar sugar molecule, was detected in the star-forming region near the centre of our galaxy. It was discovered in 2000 by Jes Jørgensen and Jan M. Hollis. In 2012, Jørgensen's team reported the detection of glycolaldehyde in a distant star system. The molecule was found around the protostellar binary IRAS 16293-2422 400 light years from Earth. Glycolaldehyde is needed to form RNA, which is similar in function to DNA. These findings suggest that complex organic molecules may form in stellar systems prior to the formation of planets, eventually arriving on young planets early in their formation. Because sugars are associated with both metabolism and the genetic code, two of the most basic aspects of life, it is thought the discovery of extraterrestrial sugar increases the likelihood that life may exist elsewhere in our galaxy.

NASA announced in 2009 that scientists had identified another fundamental chemical building block of life in a comet for the first time, glycine, an amino acid, which was detected in material ejected from comet Wild 2 in 2004 and grabbed by NASA's Stardust probe. Glycine has been detected in meteorites before. Carl Pilcher, who leads the NASA Astrobiology Institute commented that "The discovery of glycine in a comet supports the idea that the fundamental building blocks of life are prevalent in space, and strengthens the argument that life in the Universe may be common rather than rare." Comets are encrusted with 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 ionizing radiation. It is possible that a rain of material from comets could have brought significant quantities of such complex organic molecules to Earth. Amino acids which were formed extraterrestrially may also have arrived on Earth via comets. It is estimated that during the Late Heavy Bombardment, meteorites may have delivered up to five million tons of organic prebiotic elements to Earth per year.

An illustration of typical polycyclic aromatic hydrocarbons. Clockwise from top left: benz(e)acephenanthrylene, pyrene and dibenz(ah)anthracene.

Polycyclic aromatic hydrocarbons (PAH) are the most common and abundant of the known polyatomic molecules in the observable universe, and are considered a likely constituent of the primordial sea. In 2010, PAHs, along with fullerenes (or "buckyballs"), have been detected in nebulae. In March 2015, NASA scientists reported that, for the first time, complex DNA and RNA organic compounds of life, including uracil, cytosine and thymine, have been formed in the laboratory under outer space conditions, using starting chemicals, such as pyrimidine, found in meteorites. Pyrimidine, like PAHs, the most carbon-rich chemical found in the Universe, may have been formed in red giant stars or in interstellar dust and gas clouds. A group of Czech scientists reported that all four RNA-bases may be synthesized from formamide in the course of high-energy density events like extraterrestrial impacts.

Lipid world

Main article: Gard model

The lipid world theory postulates that the first self-replicating object was lipid-like. It is known that phospholipids form lipid bilayers in water while under agitation—the same structure as in cell membranes. These molecules were not present on early Earth, but other amphiphilic long-chain molecules also form membranes. Furthermore, these bodies may expand (by insertion of additional lipids), and under excessive expansion may undergo spontaneous splitting which preserves the same size and composition of lipids in the two progenies. The main idea in this theory is that the molecular composition of the lipid bodies is the preliminary way for information storage, and evolution led to the appearance of polymer entities such as RNA or DNA that may store information favourably. Studies on vesicles from potentially prebiotic amphiphiles have so far been limited to systems containing one or two types of amphiphiles. This in contrast to the output of simulated prebiotic chemical reactions, which typically produce very heterogeneous mixtures of compounds. Within the hypothesis of a lipid bilayer membrane composed of a mixture of various distinct amphiphilic compounds there is the opportunity of a huge number of theoretically possible combinations in the arrangements of these amphiphiles in the membrane. Among all these potential combinations, a specific local arrangement of the membrane would have favoured the constitution of a hypercycle, actually a positive feedback composed of two mutual catalysts represented by a membrane site and a specific compound trapped in the vesicle. Such site/compound pairs are transmissible to the daughter vesicles leading to the emergence of distinct lineages of vesicles which would have allowed Darwinian natural selection.

Polyphosphates

A problem in most scenarios of abiogenesis is that the thermodynamic equilibrium of amino acid versus peptides is in the direction of separate amino acids. What has been missing is some force that drives polymerization. The resolution of this problem may well be in the properties of polyphosphates. Polyphosphates are formed by polymerization of ordinary monophosphate ions PO₄⁻³. Several mechanisms for such polymerization have been suggested. Polyphosphates cause polymerization of amino acids into peptides. They are also logical precursors in the synthesis of such key biochemical compounds as adenosine triphosphate (ATP). A key issue seems to be that calcium reacts with soluble phosphate to form insoluble calcium phosphate (apatite), so some plausible mechanism must be found to keep calcium ions from causing precipitation of phosphate. There has been much work on this topic over the years, but an interesting new idea is that meteorites may have introduced reactive phosphorus species on the early Earth.

PAH world hypothesis

Main article: PAH world hypothesis

Polycyclic aromatic hydrocarbons (PAH) are known to be abundant in the Universe, including in the interstellar medium, in comets, and in meteorites, and are some of the most complex molecules so far found in space.

Other sources of complex molecules have been postulated, including extraterrestrial 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 PAHs in a nebula. In 2010, another team also detected PAHs, along with fullerenes, in nebulae. The use of PAHs has also been proposed as a precursor to the RNA world in the PAH world hypothesis. The Spitzer Space Telescope has detected a star, HH 46-IR, which is forming by a process similar to that by which the Sun formed. In the disk of material surrounding the star, there is a very large range of molecules, including cyanide compounds, hydrocarbons, and carbon monoxide. In September 2012, NASA scientists reported that PAHs, subjected to interstellar medium conditions, are transformed, through hydrogenation, oxygenation and hydroxylation, to more complex organics—"a step along the path toward amino acids and nucleotides, the raw materials of proteins and DNA, respectively." Further, as a result of these transformations, the PAHs lose their spectroscopic signature which could be one of the reasons "for the lack of PAH detection in interstellar ice grains, particularly the outer regions of cold, dense clouds or the upper molecular layers of protoplanetary disks."

NASA maintains a database for tracking PAHs in the Universe. More than 20% of the carbon in the Universe may be associated with PAHs, possible starting materials for the formation of life. PAHs seem to have been formed shortly after the Big Bang, are widespread throughout the Universe, and are associated with new stars and exoplanets.

Radioactive beach hypothesis

Zachary Adam claims that tidal processes that occurred during a time when the Moon was much closer may have concentrated grains of uranium and other radioactive elements at the high-water mark on primordial beaches, where they may have been responsible for generating life's building blocks. According to computer models, a deposit of such radioactive materials could show the same self-sustaining nuclear reaction as that found in the Oklo uranium ore seam in Gabon. Such radioactive beach sand might have provided sufficient energy to generate organic molecules, such as amino acids and sugars from acetonitrile in water. Radioactive monazite material also has released soluble phosphate into the regions between sand-grains, making it biologically "accessible." Thus amino acids, sugars, and soluble phosphates might have been produced simultaneously, according to Adam. Radioactive actinides, left behind in some concentration by the reaction, might have formed part of organometallic complexes. These complexes could have been important early catalysts to living processes.

John Parnell has suggested that such a process could provide part of the "crucible of life" in the early stages of any early wet rocky planet, so long as the planet is large enough to have generated a system of plate tectonics which brings radioactive minerals to the surface. As the early Earth is thought to have had many smaller plates, it might have provided a suitable environment for such processes.

Multiple genesis

Different forms of life with variable origin processes may have appeared quasi-simultaneously in the early history of Earth. The other forms may be extinct (having left distinctive fossils through their different biochemistry—e.g., hypothetical types of biochemistry). It has been proposed that:

The first organisms were self-replicating iron-rich clays which fixed carbon dioxide into oxalic and other dicarboxylic acids. This system of replicating clays and their metabolic phenotype then evolved into the sulfide rich region of the hotspring acquiring the ability to fix nitrogen. Finally phosphate was incorporated into the evolving system which allowed the synthesis of nucleotides and phospholipids. If biosynthesis recapitulates biopoiesis, then the synthesis of amino acids preceded the synthesis of the purine and pyrimidine bases. Furthermore the polymerization of the amino acid thioesters into polypeptides preceded the directed polymerization of amino acid esters by polynucleotides.

Fluctuating hydrothermal pools on volcanic islands or proto-continents

Armid Mulkidjanian and co-authors think that the marine environments did not provide the ionic balance and composition universally found in cells, as well as of ions required by essential proteins and ribozymes found in virtually all living organisms, especially with respect to K⁺/Na⁺ ratio, Mn²⁺, Zn²⁺ and phosphate concentrations. The only known environments that mimic the needed conditions on Earth are found in terrestrial hydrothermal pools fed by steam vents. Additionally, mineral deposits in these environments under an anoxic atmosphere would have suitable pH (as opposed to current pools in an oxygenated atmosphere), contain precipitates of sulfide minerals that block harmful UV radiation, have wetting/drying cycles that concentrate substrate solutions to concentrations amenable to spontaneous formation of polymers of nucleic acids, and a continual supply of abiotically generated organic molecules, both by chemical reactions in the hydrothermal environment, as well as by exposure to UV light during transport from vents to adjacent pools. Their hypothesized pre-biotic environments are similar to the deep-oceanic vent environments most commonly hypothesized, but add additional components that help explain peculiarities found in reconstructions of the Last Universal Common Ancestor (LUCA) of all living organisms.

Bruce Damer and David Deamer have come to the conclusion that cell membranes cannot be formed in salty seawater, and must therefore have originated in freshwater. Before the continents formed, the only dry land on Earth would be volcanic islands, where rainwater would form ponds where lipids could form the first stages towards cell membranes. These predecessors of true cells are assumed to have behaved more like a superorganism rather than individual structures, where the porous membranes would house molecules which would leak out and enter other protocells. Only when true cells had evolved would they gradually adapt to saltier environments and enter the ocean.

Colín-García et al. (2016) discuss the advantages and disadvantages of hydrothermal vents as primitive environments. They mention the exergonic reactions in such systems could have been a source of free energy that promoted chemical reactions, additional to their high mineralogical diversity which implies the induction of important chemical gradients, thus favoring the interaction between electron donors and acceptors. Colín-García et al. (2016) also summarize a set of experiments proposed to test the role of hydrothermal vents in prebiotic synthesis.

Information theory

A theory that speaks to the origin of life on Earth and other rocky planets posits life as an information system in which information content grows because of selection. Life must start with minimum possible information, or minimum possible departure from thermodynamic equilibrium, and it requires thermodynamically free energy accessible by means of its information content. The most benign circumstances, minimum entropy variations with abundant free energy, suggest the pore space in the first few kilometres of the surface. Free energy is derived from the condensed products of the chemical reactions taking place in the cooling nebula.

See also

3

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External links

• "Exploring Life's Origins: A Virtual Exhibit". Exploring Life's Origins: A Virtual Exhibit. Arlington County, VA: National Science Foundation. Retrieved 2 July 2015.
• "The Geochemical Origins of Life by Michael J. Russell & Allan J. Hall". Glasgow, Scotland: University of Glasgow. 13 December 2008. Retrieved 2 July 2015.
• Malory, Marcia. "How life began on Earth". Earth Facts. Retrieved 2 July 2015.