Biology:Abiogenesis

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Short description: Natural process by which life arises from non-living matter
The earliest known life forms are putative fossilized microorganisms, found in hydrothermal vent precipitates, that may have lived as early as 4.28 Gya (billion years ago), relatively soon after the formation of the oceans 4.41 Gya, and not long after the formation of the Earth 4.54 Gya.[1][2]

In biology, abiogenesis or the origin of life[3][4][5] is the natural process by which life has arisen from non-living matter, such as simple organic compounds.[6][4][7][8] While the details of this process are still unknown, the prevailing scientific hypothesis is that the transition from non-living to living entities was not a single event, but an evolutionary process of increasing complexity that involved molecular self-replication, self-assembly, autocatalysis, and the emergence of cell membranes.[9][10][11] Although the occurrence of abiogenesis is uncontroversial among scientists, its possible mechanisms are poorly understood. There are several principles and hypotheses for how abiogenesis could have occurred.[12]

The study of abiogenesis aims to determine how pre-life chemical reactions gave rise to life under conditions strikingly different from those on Earth today.[13] It primarily uses tools from biology, chemistry, and geophysics,[14] with more recent approaches attempting a synthesis of all three:[15] more specifically, astrobiology, biochemistry, biophysics, geochemistry, molecular biology, oceanography and paleontology. Life functions through the specialized chemistry of carbon and water, and builds largely upon four key families of chemicals: lipids (cell membranes), carbohydrates (sugars, cellulose), amino acids (protein metabolism), and nucleic acids (DNA and RNA). Any successful theory of abiogenesis must explain the origins and interactions of these classes of molecules.[16] Many approaches to abiogenesis investigate how self-replicating molecules, or their components, came into existence. Researchers generally think that current life descends from an RNA world,[17] although other self-replicating molecules may have preceded RNA.[18][19]

The classic 1952 Miller–Urey experiment and similar research demonstrated that most amino acids, the 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 may have triggered these reactions, 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.[20]

Earth remains the only place in the universe known to harbour life,[21][22] and fossil evidence from the Earth informs most studies of abiogenesis. The age of the Earth is 4.54 Gy (billion years);[23][24][25] the earliest undisputed evidence of life on Earth dates from at least 3.5 Gya (Gy ago),[26][27][28] and possibly as early as the Eoarchean Era (3.6–4.0 Gya). In 2017, possible evidence of early life on land was found in 3.48 Gyo (Gy old) geyserite and other related mineral deposits (often found around hot springs and geysers) uncovered in the Pilbara Craton of Western Australia.[29][30][31][32] Other discoveries suggest that life may have appeared on Earth even earlier. (As of 2017), microfossils (fossilised microorganisms) within hydrothermal-vent precipitates dated 3.77 to 4.28 Gya in rocks in Quebec may harbour the oldest record of life on Earth, soon after ocean formation 4.4 Gya during the Hadean Eon.[1][2][33][34][35]

The NASA strategy on abiogenesis attempts to identify interactions, intermediary structures and functions, energy sources, and environmental factors that contributed to the diversity, selection, and replication of evolvable macromolecular systems,[36] and to map the chemical landscape of potential primordial informational polymers. The advent of polymers that could replicate, store genetic information, and exhibit properties subject to selection likely was a critical step in the emergence of prebiotic chemical evolution.[36]

Definition of life

As many as 123 definitions of life have been compiled.[37] The definition of life is somewhat disagreed upon by biology textbooks. James Gould writes that "most dictionaries define life as the property that distinguishes the living from the dead, and define dead as being deprived of life. These singularly circular and unsatisfactory definitions give us no clue to what we have in common with protozoans and plants."[38] Neil Campbell and Jane Reece state that "the phenomenon we call life defies a simple, one-sentence definition."[39] Books on the origin of life do not agree either. John Casti gives a single-sentence definition: "an entity is considered to be 'alive' if it has the capacity to carry out three basic functional activities: metabolism, self-repair, and replication".[40] In contrast, Dirk Schulze-Makuch and Louis Irwin devote the entire first chapter of their book to discussing the definition of life.[41] NASA defines life as "a self-sustaining chemical system capable of Darwinian evolution."[42][43][44]

Early universe and Earth

Short description: Universe events since the Big Bang 13.8 billion years ago

Early universe with first stars

Soon after the Big Bang, which occurred roughly 14 Gya, the only chemical elements present in the universe were hydrogen, helium, and lithium, the three lightest atoms in the periodic table. These elements gradually came together to form stars. These early stars were massive and short-lived, producing all the heavier elements through stellar nucleosynthesis. Carbon, currently the fourth most abundant chemical element in the universe (after hydrogen, helium and oxygen), was formed mainly in white dwarf stars, particularly those bigger than two solar masses.[45][46]

As these stars reached the end of their lifecycles, they ejected these heavier elements, among them carbon and oxygen, throughout the universe. These heavier elements allowed for the formation of new objects, including rocky planets and other bodies.[47]

According to the nebular hypothesis, the formation and evolution of the Solar System began 4.6 Gya with the gravitational collapse of a small part of a giant molecular cloud.[48] Most of the collapsing mass collected in the center, forming the Sun, while the rest flattened into a protoplanetary disk out of which the planets, moons, asteroids, and other small Solar System bodies formed.

Emergence of Earth

The Hadean Earth was at first inhospitable to any living organisms. During its formation, the Earth lost a significant part of its initial mass, and consequentially lacked the gravity to hold molecular hydrogen and the bulk of the original inert gases.[49] The atmosphere consisted largely of water vapor, nitrogen, and carbon dioxide, with smaller amounts of carbon monoxide, hydrogen, and sulfur compounds.[50] The solution of carbon dioxide in water is thought to have made the seas slightly acidic, giving them a pH of about 5.5.[51] The Hadean atmosphere has been characterized as a "gigantic, productive outdoor chemical laboratory,"[52] similar to volcanic gases today which still support some abiotic chemistry.[52]

Oceans may have appeared as soon as 200 My (million years) after the Earth formed, in a hot, 100 C, reducing environment, as the pH of 5.8 rose rapidly towards neutral.[53] This scenario has found support from the dating of 4.404 Gya zircon crystals from metamorphosed quartzite of Mount Narryer in Western Australia, which provide evidence that oceans and continental crust existed within 150 Ma (million years) of Earth's formation.[54] Despite the likely increased volcanism and existence of many smaller tectonic "platelets," it has been suggested that between 4.4 and 4.3 Gya, 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, from cosmic radiation, and from continued bolide (asteroid and comet) impacts.[55] 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 hypothesis for the Late Heavy Bombardment posits that the Hadean environment between 4.28[1][2] and 3.8 Gya would have been highly hazardous to modern life. Following the Nice model, changes in the orbits of the giant planets may have bombarded the Earth with asteroids and comets that pockmarked the Moon and inner planets.[56] Frequent collisions with objects up to 500 km in diameter would sterilize the planet's surface and vaporize the oceans within a few months of impact. Hot steam and rock vapor formed high altitude clouds that would completely cover the planet,[52] making photosynthesis unviable. Rains would slowly have drawn down the height of the clouds, returning the oceans to their original depth only 3,000 y after the impact event.[57] Impacts before 3.5 Gya would have brought quantities of organic material comparable to those produced by terrestrial sources.[58][59] The periods between such devastating events give time windows for the possible origin of life in early environments. If the deep marine hydrothermal setting was the site for the origin of life, then abiogenesis could have happened as early as 4.0-4.2 Gya. If the site was at the surface of the Earth, abiogenesis could have occurred only between 3.7 and 4.0 Gya.[60] However, new lunar surveys and samples have led scientists, including an architect of the Nice model, to deemphasize the Late Heavy Bombardment.[61]

If life evolved deeper than ten meters, it would have been shielded from both late impacts and high levels of UV radiation from the T Tauri stage Sun. Simulations of geothermically heated oceanic crust yield far more organic compounds than those found in the Miller–Urey experiments. 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."[62] Shock found that the available energy is maximized at 100–150 °C, precisely the temperatures at which the hyperthermophilic bacteria and thermoacidophilic archaea have been found living. These organisms are placed at the base of the phylogenetic tree of life, closest to the last Universal Common Ancestor (LUCA).[63]

Earliest evidence of life: palaeontology

Precambrian stromatolites in the Siyeh Formation, Glacier National Park. A 2002 study suggested a date of 3.5 Gya (3.5 billion year old), placing them among the earliest life-forms.
Main page: Biology:Earliest known life forms

The earliest known life on Earth existed more than 3.5 Gya (billion years ago),[26][27][28] 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 at least 3.77 and possibly 4.28 Gya.[1][64] This finding suggested life developed very soon after oceans formed. The structure of the microbes was similar to bacteria found near hydrothermal vents in the modern era, supporting the view that abiogenesis began near hydrothermal vents.[34][1]

Stromatolites in Shark Bay.

Biogenic graphite has been found in 3.7 Gyo metasedimentary rocks from southwestern Greenland [65] and in microbial mat fossils from 3.49 Gyo Western Australian sandstone.[66][67] Evidence of early life in rocks from Akilia Island, near the Isua supracrustal belt in southwestern Greenland, dating to 3.7 Gya, have shown biogenic carbon isotopes.[68][69] In other parts of the Isua supracrustal belt, graphite inclusions trapped within garnet crystals are connected to the other elements of life: oxygen, nitrogen, and possibly phosphorus in the form of phosphate, providing further evidence for life 3.7 Gya.[70] At Strelley Pool, in the Pilbara region of Western Australia, compelling evidence of early life was found in pyrite-bearing sandstone in a fossilized beach, with rounded tubular cells that oxidized sulfur by photosynthesis in the absence of oxygen.[71][72][73] Work on zircons from Western Australia in 2015 suggested that life likely existed on Earth at least 4.1 Gya.[74][75][76]

In 2019 Raphael Baumgartner and colleagues investigated rocks in the Pilbara region of Western Australia. The Dresser Formation is the oldest, with rocks 3.48 billion years old; it appears to contain layered structures called stromatolites.[77] These stromatolites lie within undeformed hydrothermal-sedimentary strata, and have textural features indicative of biogenic origins. In 2017 Tara Djokic and her team showed that parts of the Dresser formation preserve hot springs on land, but other regions seem to have been shallow seas.[78]

Biology, the product of abiogenesis

Biochemical life processes

Fermentation

Albert Lehninger stated around 1970 that fermentation, including glycolysis, was a suitable primitive energy source for the origin of life, arguing that "Since living organisms probably first arose in an atmosphere lacking oxygen, anaerobic fermentation is the simplest and most primitive type of biological mechanism for obtaining energy from nutrient molecules."[79]

Chemiosmosis

Chemiosmotic coupling mitochondrion

Instead of fermentation, Peter Mitchell proposed chemiosmosis, ubiquitous in life, as the first system of energy conversion.[80][81]

ATP synthase
ATP synthase uses the chemiosmotic proton gradient to power ATP synthesis through oxidative phosphorylation.

The mechanism of ATP synthesis involves a closed membrane in which the ATP synthase is embedded. The ATP is synthesized by the F1 subunit of ATP synthase by the binding change mechanism discovered by Paul Boyer. The energy required to release formed strongly-bound ATP has its origin in protons that move across the membrane. These protons have been set across the membrane during respiration or photosynthesis.

The RNA world

Main page: Biology:RNA world

The RNA world hypothesis describes an early Earth with self-replicating and catalytic RNA but no DNA or proteins.[82] It is widely accepted that current life on Earth descends from an RNA world,[17][83][84] although RNA-based life may not have been the first to exist.[18][19]

RNA is central to the translation process; that small RNAs can catalyze all of the chemical groups and information transfers required for life;[19][85] that RNA both expresses and maintains genetic information in modern organisms; and that the chemical components of RNA are easily synthesized under the conditions that approximated the early Earth. The structure of the ribozyme has been called the "smoking gun", with a central core of RNA and no amino acid side chains within 18 Å of the active site that catalyzes peptide bond formation.[18][86]

The concept of the RNA world was first proposed in 1962 by Alexander Rich,[87] and the term was coined by Walter Gilbert in 1986.[19][88] There were initial difficulties in the explanation of the abiotic synthesis of the nucleotides cytosine and uracil.[89] 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.[90][91]

RNA replicase can function as both code and catalyst for further RNA replication. Jack Szostak has shown that certain catalytic RNAs can join smaller RNA sequences together, creating the potential for self-replication. 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.[92][93][18] If such conditions were present on early Earth, then Darwinian natural selection would favor the proliferation of such autocatalytic sets, to which further functionalities could be added.[94][95][96]

Stan Palasek suggested that self-assembly of ribonucleic acid (RNA) molecules can occur spontaneously due to physical factors in hydrothermal vents.[97] Virus self-assembly within host cells has implications for the study of the origin of life,[98] as it lends further credence to the hypothesis that life could have started as self-assembling organic molecules.[99][100] In 2021, it was reported that a preliminary form of tRNA could have been such a replicator molecule.[101][102]

Phylogeny and LUCA

A cladogram placing other extreme hyperthermophiles alongside the LUCA at the base of the phylogenetic tree of life

Starting with the work of Carl Woese, molecular studies have placed the last universal common ancestor (LUCA) between Bacteria and a clade formed by Archaea and Eukaryota in the phylogenetic tree of life.[103][104] A minority of studies have placed the LUCA in Bacteria, proposing that archaea and eukaryotes are evolutionarily derived from within eubacteria.[105] Thomas Cavalier-Smith hypothesizes that the phenotypically diverse phylum Chloroflexi contained the LUCA.[106]

In 2005, Peter Ward proposed that abiotically synthesized RNA became enclosed within a capsule and then created RNA ribozyme replicates. This then bifurcated between Dominion Ribosa (RNA life), Domain Viorea (Viruses), and Dominion Terroa (Cellular life), which contains the LUCA of earlier phylogenic trees.[107]

In 2016, a set of 355 genes likely present in the Last Universal Common Ancestor (LUCA) of all organisms living on Earth was identified.[108] A total of 6.1 million prokaryotic genes from Bacteria and Archaea were sequenced, identifying 355 protein clusters from amongst 286,514 protein clusters that were probably common to LUCA. The result suggest that the LUCA was anaerobic with a Wood–Ljungdahl pathway, nitrogen- and carbon-fixing, thermophilic. Its cofactors suggest dependence upon an environment rich in hydrogen, carbon dioxide, iron, and transition metals. Its genetic code required nucleoside modifications and methylation. LUCA likely inhabited an anaerobic hydrothermal vent setting in a geochemically active environment.[109][110]

Conceptual history until the 1960s

The Miller–Urey experiment was a synthesis of small organic molecules in a mixture of simple gases in a thermal gradient created by heating (right) and cooling (left) the mixture at the same time, with electrical discharges.

An ancient view, from Aristotle and ancient Greek philosophy until the 19th century, is of Spontaneous generation.[111] It held that "lower" animals were generated by decaying organic substances, life arising by chance.[112][113] This was questioned from the 17th century, in works like Thomas Browne's Pseudodoxia Epidemica.[114][115] In 1665, Robert Hooke published the first drawings of a microorganism. In 1676, Antonie van Leeuwenhoek drew and described microorganisms, probably protozoa and bacteria.[116] Van Leeuwenhoek disagreed with spontaneous generation, and by the 1680s convinced himself, using experiments ranging from sealed and open meat incubation and the close study of insect reproduction, that the theory was incorrect.[117] In 1668 Francesco Redi showed that no maggots appeared in meat when flies were prevented from laying eggs.[118] By the middle of the 19th century, spontaneous generation was considered disproven.[119][120]

Panspermia is the hypothesis[121] that life exists throughout the universe, distributed by meteoroids, asteroids, comets[122] and planetoids.[123] It does not attempt to explain how life originated, but shifts the origin to another heavenly body. The advantage 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 or meteorite impact.[124]

Several plausible primordial soup hypotheses have been proposed for the origin of life, based on the framework laid out by Alexander Oparin (in 1924) and John Haldane (in 1929), that the first molecules constituting the earliest cells slowly self-organised.[125] Haldane suggested that the Earth's prebiotic oceans would have formed a "hot dilute soup" in which organic compounds could have formed.[113][126]

John Bernal showed that such mechanisms could form most of the necessary molecules for life from inorganic precursors.[127] In 1967, he suggested three "stages": the origin of biological monomers; the origin of biological polymers; and the evolution from molecules to cells.[128][129][130]

In 1952, Stanley Miller and Harold Urey performed the Miller–Urey experiment, demonstrating how organic molecules could have spontaneously formed from inorganic precursors under conditions like those posited by the Oparin-Haldane hypothesis. It used a highly reducing mixture of gases—methane, ammonia, and hydrogen, as well as water vapor—to form simple organic monomers such as amino acids.[131][132]

Primordial origin of biological molecules: chemistry

The chemical processes on the pre-biotic early Earth are called chemical evolution. The elements, except for hydrogen and helium, ultimately derive from stellar nucleosynthesis. In 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 largely the result of ultraviolet light from stars, rather than other forms of radiation from supernovae and young stars, as thought earlier.[133] Complex molecules, including organic molecules, form naturally both in space and on planets.[134] 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.[135][136] (See pseudo-panspermia)

Observed extraterrestrial organic molecules

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.[137] Carbon is abundant in the Sun, stars, comets, and in the atmospheres of most planets.[138] 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.[134][139][140][141] 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.[142] According to the computer studies, this same process may also occur around other stars that acquire planets.[142]

Amino acids

In 2009, the amino acid glycine was found in material ejected from comet Wild 2; it had earlier been detected in meteorites.[143] Comets are encrusted with dark material, thought to be a tar-like organic substance formed from simple carbon compounds under ionizing radiation. A rain of material from comets could have brought such complex organic molecules to Earth.[144][145][146][52] 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.[52]

PAH world hypothesis

Main page: Biology:PAH world hypothesis

Polycyclic aromatic hydrocarbons (PAH) are the most common and abundant of the known polyatomic molecules in the observable universe,[147][148][149][150] and are a likely constituent of the primordial sea.[147][148][149][150] In 2010, PAHs were detected in nebulae.[151] Polycyclic aromatic hydrocarbons are found in the interstellar medium, in comets, and in meteorites.[138]

The Cat's Paw Nebula lies inside the Milky Way Galaxy and is located in the constellation Scorpius.
Green areas show regions where radiation from hot stars collided with large molecules and small dust grains called "polycyclic aromatic hydrocarbons" (PAHs), causing them to fluoresce.
(Spitzer space telescope, 2018)

Other sources of complex molecules could include extraterrestrial stellar or interstellar origin. In 2004, a team detected traces of PAHs in a nebula.[152] In 2010, another team detected PAHs and fullerenes in nebulae.[151] The use of PAHs has been proposed as a precursor to the RNA world in the PAH world hypothesis.[153] The Spitzer Space Telescope has detected a star, HH 46-IR, forming by a process similar to that by which the Sun formed. In the disk of material surrounding the star, there are molecules including cyanide compounds, hydrocarbons, and carbon monoxide. In 2012, it was shown that PAHs, subjected to interstellar medium conditions, can be 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."[154][155] As a result of these transformations, the PAHs lose their spectroscopic signature, which could explain why they are not seen in "interstellar ice grains, particularly the outer regions of cold, dense clouds or the upper molecular layers of protoplanetary disks."[154][155]

More than 20% of the carbon in the universe may be associated with PAHs.[138][156] PAHs seem to have formed shortly after the Big Bang, are widespread throughout the universe,[147][148][149][150] and are associated with new stars and exoplanets.[138]

Nucleobases

Observations suggest that the majority of organic compounds introduced on Earth by interstellar dust particles are principal agents in the formation of complex molecules, thanks to their peculiar surface-catalytic activities.[157][158] 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.[159][160] In 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.[157][161][162] The cosmic dust permeating the universe contains complex organics ("amorphous organic solids with a mixed aromaticaliphatic structure") that could be created naturally, and rapidly, by stars.[163][164][165] 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."[163]

The sugar glycolaldehyde

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 Hollis.[166] 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.[167][168][169] Glycolaldehyde is needed to form RNA, similar in function to DNA. These findings suggest that complex organic molecules may form in stellar systems prior to the formation of planets, arriving on young planets early in their formation.[170][171] 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.[166]

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.[172][173] Polyphosphates are formed by polymerization of ordinary monophosphate ions PO43-. Several mechanisms of organic molecule synthesis have been investigated. 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.[174] Based on computer model studies, the complex organic molecules necessary for life may have formed in the protoplanetary disk of dust grains surrounding the Sun and other stars before the formation of the Earth.[142][175]

The accumulation and concentration of organic molecules on a planetary surface is also considered an essential early step for the origin of life.[36] Identifying and understanding the mechanisms that led to the production of prebiotic molecules in various environments is critical for establishing the inventory of ingredients from which life originated on Earth, assuming that the abiotic production of molecules ultimately influenced the selection of molecules from which life emerged.[36]

In 2019, sugar molecules, including ribose, were detected in meteorites, suggesting that chemical processes on asteroids can produce some essential bio-ingredients, supporting the notion of an RNA world prior to a DNA-based origin of life on Earth, and possibly panspermia.[176][171]

Laboratory synthesis

As early as the 1860s, experiments demonstrated that biologically relevant molecules can be produced from interaction of simple carbon sources with abundant inorganic catalysts.

Fox proteinoids

Main page: Biology:Proteinoid

In trying to uncover the intermediate stages of abiogenesis mentioned by Bernal, Sidney Fox in the 1950s and 1960s studied the spontaneous formation of peptide structures under plausibly early Earth conditions. In one of his experiments, he allowed amino acids to dry out as if puddled in a warm, dry spot in prebiotic conditions: In an experiment 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 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 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. He found that, as they dried, the amino acids formed long, often cross-linked, thread-like, submicroscopic polypeptides.[177]

Sugars

Experiments with the formose reaction by Butlerov showed that tetroses, pentoses, and hexoses are produced when formaldehyde is heated under basic conditions with divalent metal ions like calcium. The reaction was scrutinized and subsequently proposed to be autocatalytic by Breslow in 1959.

Nucleobases

Similar experiments demonstrate that nucleobases like guanine and adenine could be synthesized from simple carbon and nitrogen sources like hydrogen cyanide (HCN) and ammonia.[178] Formamide produces all four ribonucleotides when warmed with terrestrial minerals. Formamide is ubiquitous in the Universe, produced by the reaction of water and HCN. It can easily become concentrated through the evaporation of water.[90][91] HCN is poisonous only to 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.[52]

In 2015, NASA scientists formed DNA and RNA components including uracil, cytosine and thymine in the laboratory under outer space conditions, using starting chemicals such as pyrimidine found in meteorites. Pyrimidine may have been formed in red giant stars or in interstellar dust and gas clouds.[179] All four RNA-bases may be synthesized from formamide in high-energy density events like extraterrestrial impacts.[180]

Effects with temperatures around the freezing point of water

Other pathways for synthesizing bases from inorganic materials were also reported.[181] 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.[182] Research by Miller and colleagues suggested that while adenine and guanine require freezing conditions for synthesis, cytosine and uracil may require boiling temperatures.[183] 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.[184][185] 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).[186] 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.[187]

Use of less-reducing gas in Miller–Urey experiment

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[188][189] (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.[188] Other scientific research has focused on two other potential reducing environments: outer space and deep-sea thermal vents.[190][191][192]

Synthesis based on hydrogen cyanide

A research project completed in 2015 by John 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,[193][194] while not producing a wide range of other compounds.[195] The researchers used the term "cyanosulfidic" to describe this network of reactions.[194]

Issues during laboratory synthesis

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.[196] Biology uses essentially 20 amino acids for its coded protein enzymes, representing a very small subset of the structurally possible set. Most models of the origin of life suggest organisms developed from environmentally available organic compounds.[197] The fundamental roles that peptides play in biology makes it likely that peptides were key players in the origin of life.[198]

Autocatalysis

Main page: Chemistry: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 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.[199]

It has been proposed that life initially arose as autocatalytic chemical networks.[200] British ethologist Richard Dawkins wrote about autocatalysis as a potential explanation for the origin of life in his 2004 book The Ancestor's Tale.[201] In his book, Dawkins cites experiments performed by Julius Rebek 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.[202][203]

Pertinent geological environments

Darwin's little pond

An early concept, that life originated from non-living matter in slow stages, appeared in Herbert Spencer's 1864–1867 book Principles of Biology. In 1879 William Turner Thiselton-Dyer referred to this in a paper "On spontaneous generation and evolution". On 1 February 1871 Charles Darwin wrote about these publications to Joseph Hooker, and set out his own speculation,[204][205][206] suggesting 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.

A study in 2017 proposed a mathematical model that supports Darwin's concept. They suggest that interplanetary dust particles and meteorites had transported organic molecules like nucleotides to these ponds. For these biopolymers to form in the pools, there would have been wet-dry cycles for polymerization. Ben Pearce and his coauthors theorize that RNA polymers might have appeared prior to 4.17 Gya.[207][208]

Volcanic hot springs and hydrothermal vents, shallow or deep

Early micro-fossils may have come from a hot world of gases such as methane, ammonia, carbon dioxide and hydrogen sulphide, toxic to much current life.[209] Analysis of the conventional threefold tree of life places thermophilic and hyperthermophilic bacteria and archaea closest to the root, suggesting that life may have evolved in a hot environment.[210]

Deep sea hydrothermal vents

Deep-sea hydrothermal vent or black smoker

The deep sea or alkaline hydrothermal vent theory posits that life began at submarine hydrothermal vents.[211][212] Martin and 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,...[213]

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 (molecular hydrogen) react with electron acceptors (carbon dioxide); see Iron–sulfur world theory. These are exothermic reactions.[211][lower-alpha 1]

Russell demonstrated that alkaline vents created an abiogenic proton motive force chemiosmotic gradient,[213] 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 Günter Wächtershäuser.[214] 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).

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 hydrocarbonate and calcium ions has the most optimal range.[215][216] This case is similar to the origin of life in hydrothermal vents, but with hydrocarbonate and calcium ions in hot water. The research with spectral analyses was performed in Rupite, Bulgaria, with hot mineral water with calcium and hydrocarbonate ions, Anoxybacillus rupiences sp., bacteria, archaea and cyanobacteria [217][218] Mineral water with pH of 9–11 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.[219] 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.[220] 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.[221]

The surfaces of mineral particles inside hydrothermal vents have catalytic properties similar to those of enzymes and can create simple organic molecules, such as methanol (CH3OH) and formic, acetic and Pyruvic acid out of the dissolved CO2 in the water, if driven by an applied voltage or by reaction with H2 or H2S.[222][223]

The research reported by Martin in 2016 supports the thesis that life arose at hydrothermal vents,[224][225] that spontaneous chemistry in the Earth's crust driven by rock–water interactions at disequilibrium thermodynamically underpinned life's origin[226][227] and that the founding lineages of the archaea and bacteria were H2-dependent autotrophs that used CO2 as their terminal acceptor in energy metabolism.[228] Martin suggests, based upon this evidence that LUCA "may have depended heavily on the geothermal energy of the vent to survive".[229]

Fluctuating hydrothermal pools on volcanic islands or proto-continents

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.[211] 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, polyesters[230] and depsipeptides,[231] 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.[232][233]

Colín-García et al. (2016) discuss the advantages and disadvantages of hydrothermal vents as primitive environments.[211] 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.[211]

Volcanic ash in the ocean

Geoffrey W. Hoffmann has 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 primary oceans of Earth.[234] 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.

Gold's deep-hot biosphere

In the 1970s, Thomas Gold proposed the theory that life first developed not on the surface of the Earth, but several kilometers below the surface. It is claimed that the discovery of microbial life below the surface of another body in our Solar System would lend significant credence to this theory.[235]

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.[236] According to computer models,[237] 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.[238]

Thermodynamics, self-organization, and information: Physics

Thermodynamics principles: Energy and entropy

In antiquity it was commonly thought, for instance by Empedocles and Aristotle, that the life of the individuals of some species, and more generally, life itself, could start with high temperature, i.e. implicitly by thermal cycling.[239]

Life requires a loss of entropy, or disorder, when molecules organize themselves into living matter. Thus, the second law of thermodynamics needs to be considered in abiogenesis and in biology.[240] The emergence of life and increased complexity does not contradict this law: First, a living organism creates order in some places (e.g. its living body or dwelling) at the expense of an increase of entropy elsewhere (e.g. heat and waste production). Second, the Second Law of thermodynamics actually predicts an increase in complexity[241] and in correlations between a system and its surrounding, when undergoing interaction[242] - with memory and genetic adaptation being examples of such correlations between a living organism and its environment.

Obtaining free energy

Bernal said on the Miller–Urey experiment 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.[243]

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.[52] In fact, lightning is a plausible energy source for the origin of life, given that just in the tropics lightning strikes about 100 million times a year.[244]

Computer simulations also suggest that cavitation in primordial water reservoirs such as breaking sea waves, streams and oceans can potentially lead to the synthesis of biogenic compounds.[245]

Unfavorable reactions can also be driven by highly favorable 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).[lower-alpha 2] Carbon fixation by reaction of CO2 with H2S via iron-sulfur chemistry is favorable, and occurs at neutral pH and 100 °C. Iron-sulfur surfaces, which are abundant near hydrothermal vents, are also capable of producing small amounts of amino acids and other biological metabolites.[52]

Self-organization

Dissipative structuring

This theory postulates that the hallmark of the origin and evolution of life is the microscopic dissipative structuring under UVC light of organic pigments and their proliferation over the entire Earth surface.[246][247][248] Present day life augments the entropy production of Earth in its solar environment by dissipating ultraviolet and visible photons into heat through organic pigments in water. This heat then catalyzes a host of secondary dissipative processes such as the water cycle, ocean and wind currents, hurricanes, etc.[249]

Self-organization by dissipative structures

Ilya Prigogine circa 1977

The 19th-century physicist Ludwig Boltzmann first recognized that the struggle for existence of living organisms was neither over raw material nor energy, but instead had to do with entropy production derived from the conversion of the solar spectrum into heat by these systems.[250] Boltzmann thus realized that living systems, like all irreversible processes, were dependent on the dissipation of a generalized chemical potential for their existence. In his book "What is Life", the 20th-century physicist Erwin Schrödinger[251] emphasized the importance of Boltzmann's deep insight into the irreversible thermodynamic nature of living systems, suggesting that this was the physics and chemistry behind the origin and evolution of life.

However, irreversible processes, and much less living systems, could not be conveniently analyzed under this perspective until Lars Onsager,[252] and later Ilya Prigogine,[253] developed an elegant mathematical formalism for treating the "self-organization" of material under a generalized chemical potential. This formalism became known as Classical Irreversible Thermodynamics and Prigogine was awarded the Nobel Prize in Chemistry in 1977 for his work on Dissipative systems. His analysis showed that if a system were left to evolve under an imposed external potential, material could spontaneously organize (lower its entropy) forming dissipative structures which would increase the dissipation of the externally imposed potential (augment global entropy production). Non-equilibrium thermodynamics has since been applied by Karo Michaelian and others to the analysis of living systems, from the biochemical production of ATP[254] to optimizing bacterial metabolic pathways[255] to complete ecosystems.[256][257][258][259][260][261]

Encapsulation: morphology

Encapsulation without a membrane

Membraneless polyester droplets

Researchers Tony Jia and Kuhan Chandru[262] have proposed that membraneless polyesters droplets could have been significant in the Origins of Life.[263] Given the "messy" nature of prebiotic chemistry,[264][265] the spontaneous generation of these combinatorial droplets may have played a role in early cellularization before the innovation of lipid vesicles. Protein function within and RNA function in the presence of certain polyester droplets was shown to be preserved within the droplets. Additionally, the droplets have scaffolding ability, by allowing lipids to assemble around them that may have prevented leakage of genetic materials.

Proteinoid microspheres

Fox observed in the 1960s that the proteinoids that he had synthesized could form cell-like structures that have been named "proteinoid microspheres".[177]

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 Pittendrigh stated in 1967 that "laboratories will be creating a living cell within ten years," a remark that reflected the typical contemporary naivety about the complexity of cell structures.[266]

Lipid world

Main page: Biology:Gard model

The lipid world theory postulates that the first self-replicating object was lipid-like.[267][268] 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.[269] 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,[270][271] 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.[272]

Protocells

Main page: Biology: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.[269] 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. A functional protocell has (as of 2014) not yet been achieved in a laboratory setting.[273][274][275]

Self-assembled vesicles are essential components of primitive cells.[269] 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.[276] Irene Chen and Szostak suggest that elementary protocells can give rise to cellular behaviours including primitive forms of differential reproduction, competition, and energy storage.[274] 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.[274] 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.[277] Encapsulation enables increased solubility of the contained cargo within the capsule and storage of energy in an electrochemical gradient.

Lipid vesicles formation in fresh water

Bruce Damer and David Deamer argue 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.[278]

Vesicles consisting of mixtures of RNA-like biochemicals

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.[279][280] 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.[281][282]

Metal-sulfide precipitates

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,..."[213]

Origin of metabolism: physiology

Different forms of life with variable origin processes may have appeared quasi-simultaneously in the early Earth.[283] 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.[284]

Metabolism-like reactions could have occurred naturally in early oceans, before the first organisms evolved.[20][285] 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.[285]

Clay hypothesis

Montmorillonite, an abundant clay, is a catalyst for the polymerization of RNA and for the formation of membranes from lipids.[286] A model for the origin of life using clay was forwarded by Alexander Cairns-Smith in 1985 and explored as a plausible mechanism by several scientists.[287] 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 Ferris' studies have also confirmed that montmorillonite clay minerals catalyze the formation of RNA in aqueous solution, by joining nucleotides to form longer chains.[288]

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 behavior 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."[289]

Iron–sulfur world

In the 1980s, Günter Wächtershäuser, encouraged and supported by Karl Popper,[290][291][292] postulated his iron–sulfur world, a theory of the evolution of pre-biotic chemical pathways as the starting point in the evolution of life. It systematically traces today's biochemistry to primordial reactions which 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 (simulated lightning, 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, and such systems may have evolved into autocatalytic sets constituting self-replicating, metabolically active entities predating the life forms known today.[20][285] 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.[293]

Several models reject the self-replication of a "naked-gene", postulating instead the emergence of a primitive metabolism providing 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.[214] Concordantly, geochemists Szostak and Adamala demonstrated non enzymatic RNA replication in primitive protocells is only possibly in presence of weak cation chelator like citric acid, providing further evidence for central role of citric acid in primordial metabolism.[294]

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).[295][296] Physicist Jeremy England has proposed that life was inevitable from general thermodynamic considerations:

... 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.[297][298]

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 that decade. Kauffman's work has been criticized for ignoring the role of energy in driving biochemical reactions in cells.[299]

Orgel summarized his analysis 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."[300]

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, harbors mixed nickel-iron-sulfur clusters in its reaction centers and catalyzes the formation of acetyl-CoA (similar to acetyl-thiol) in a single step. There are increasing concerns, however, that prebiotic thiolated and thioester compounds are thermodynamically and kinetically unfavorable to accumulate in presumed prebiotic conditions (i.e. hydrothermal vents).[301] It has also been proposed that cysteine and homocysteine may have reacted with nitriles resulting from the Stecker reaction, readily forming catalytic thiol-rich poplypeptides.[302]

Zinc-world hypothesis

The zinc world (Zn-world) hypothesis of Mulkidjanian [303] is an extension of Wächtershäuser's pyrite hypothesis. Wächtershäuser based his theory of the initial chemical processes leading to informational molecules (RNA, peptides) on a regular mesh of electric charges at the surface of pyrite that may have facilitated the primeval polymerization by attracting reactants and arranging them appropriately relative to each other.[304] The Zn-world theory specifies and differentiates further.[303][305] 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 kilometers 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. from UV light. 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; hence 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 body fluids such as blood and lymph to seawater;[306] 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 [PO4]3−. 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 vapor-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.[307][308]

Other abiogenesis scenarios

A scenario is a set of related concepts pertinent to the origin of life, such as the Iron-Sulfur world. Some other scenarios, possibly overlapping, may equally account for abiogenesis.

Chemical pathways described by computer

In September 2020, chemists described, for the first time, possible chemical pathways from nonliving prebiotic chemicals to complex biochemicals that could give rise to living organisms, based on a new computer program named AllChemy.[309][310]

The hypercycle

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.[311] 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.

Protein amyloid

A new origin-of-life theory based on self-replicating beta-sheet structures has been put forward by Maury in 2009.[312][313] The theory suggest that self-replicating and self-assembling catalytic amyloids were the first informational polymers in a primitive pre-RNA world. The main arguments for the amyloid hypothesis is based on the structural stability, autocatalytic and catalytic properties, and evolvability of beta-sheet based informational systems. Such systems are also error correcting[314] and chiroselective.[315]

Fluctuating salinity: dilute and dry-down

Theories of abiogenesis seldom address the caveat raised by Harold Blum:[316] if the key informational elements of life – proto-nucleic acid chains – spontaneously form duplex structures, then there is no way to dissociate them.

Somewhere in this cycle work must be done, which means that free energy must be expended. If the parts assemble themselves on a template spontaneously, work has to be done to take the replica off; or, if the replica comes off the template of its own accord, work must be done to put the parts on in the first place.

The Oparin–Haldane conjecture addresses the formation, but not the dissociation, of nucleic acid polymers and duplexes. However, nucleic acids are unusual because, in the absence of counterions (low salt) to neutralize the high charges on opposing phosphate groups, the nucleic acid duplex dissociates into single chains.[317] Early tides, driven by a close moon, could have generated rapid cycles of dilution (high tide, low salt) and concentration (dry-down at low tide, high salt) that exclusively promoted the replication of nucleic acids[317] through a process dubbed tidal chain reaction (TCR).[318] This theory has been criticized on the grounds that early tides may not have been so rapid,[319] although regression from current values requires an Earth–Moon juxtaposition at around two Ga, for which there is no evidence, and early tides may have been approximately every seven hours.[320] Another critique is that only 2–3% of the Earth's crust may have been exposed above the sea until late in terrestrial evolution.[321]

The TCR (tidal chain reaction) theory has mechanistic advantages over thermal association/dissociation at deep-sea vents because TCR requires that chain assembly (template-driven polymerization) takes place during the dry-down phase, when precursors are most concentrated, whereas thermal cycling needs polymerization to take place during the cold phase, when the rate of chain assembly is lowest and precursors are likely to be more dilute.

First protein that condenses substrates during thermal cycling: thermosynthesis

Convection cells in fluid placed in a gravity field are selforganizing and enable thermal cycling of the suspended contents in the fluid such as protocells containing protoenzymes that work on thermal cycling.

The thermosynthesis hypothesis considers chemiosmosis 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.[322][323] The thermosynthesis hypothesis does not even invoke a pathway: ATP synthase's binding change mechanism resembles a physical adsorption process that yields free energy. The result would be convection which would bring a continual supply of reactants to the protoenzyme.[324] The described first protein may be simple in the sense that it requires only a short sequence of conserved amino acid residues, a sequent sufficient for the appropriate catalytic cleft.[325]

Pre-RNA world: The ribose issue and its bypass

It is possible that a different type of nucleic acid, such as peptide nucleic acid, threose nucleic acid or glycol nucleic acid, was the first to emerge as a self-reproducing molecule, only later replaced by RNA.[326][327] Larralde et al., say that

the generally accepted prebiotic synthesis of ribose, the formose reaction, yields numerous sugars without any selectivity.[328]

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.[329]

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.[330] 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.[331] 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.[332]

Viral origin

Recent evidence for a "virus first" hypothesis, which may support theories of the RNA world, has been suggested.[333][334] One of the difficulties for the study of the origins of viruses is their high rate of mutation; this is particularly the case in RNA retroviruses like HIV.[335] 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.[333] 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."[336] 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.[333][337]

A computational model (2015) has shown that virus capsids may have originated in the RNA world and that they served as a means of horizontal transfer between replicator communities since these communities could not survive if the number of gene parasites increased, with certain genes being responsible for the formation of these structures and those that favored the survival of self-replicating communities.[338] The displacement of these ancestral genes between cellular organisms could favor the appearance of new viruses during evolution.[339] Viruses retain a replication module inherited from the prebiotic stage since it is absent in cells.[339] So this is evidence that viruses could originate from the RNA world and could also emerge several times in evolution through genetic escape in cells.[339]

RNA-DNA world

In the latter half of 2020, evidence, based on a plausibly prebiotic simple compound named diamidophosphate (DAP), supporting the notion of a RNA-DNA mixture coevolution, has been presented.[340][341][342][343] The mixture of RNA-DNA sequences, called chimeras, have weak affinity and form weaker duplex structures.[344] This property is advantageous in an abiotic scenario and these chimeras have been shown to replicate RNA and DNA – overcoming the "template-product" inhibition problem, where a pure RNA or pure DNA strand is unable to replicate non-enzymatically because it binds too strongly to its partners.[345] This behavior of chimeric RNA-DNA sequences could lead to an abiotic cross-catalytic amplification of RNA and DNA—a key step toward the simultaneous emergence of RNA and DNA.

Key issues

Protein vs. nucleic acid as the precursor to protein synthesis

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.[346]

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 ["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.[347]

Emergence of the genetic code

Error in translation catastrophe

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".[348][349][350]

Homochirality

Main page: Biology:Homochirality

Homochirality is the geometric uniformity of materials composed of chiral (non mirror-symmetric) units. Living organisms use molecules that have the same chirality (handedness): with almost no exceptions,[351] 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 (racemic) mixture of both forms. 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, statistical fluctuations during racemic synthesis,[352] and spontaneous symmetry breaking.[353][354][355] Once established, chirality would be selected for.[356] A small bias (enantiomeric excess) in the population can be amplified into a large one by asymmetric autocatalysis, such as in the Soai reaction.[357] 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.[358] Homochirality may have started in outer space, as on the Murchison meteorite the amino acid L-alanine is more than twice as frequent as its D form, and L-glutamic acid is more than three times as abundant as its D counterpart.[359][360] 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.[361]

Experiments

J. Craig Venter

Both Eigen and Sol Spiegelman demonstrated that evolution, including replication, variation, and natural selection, can occur in populations of molecules as well as in organisms.[52] Following on from chemical evolution came the initiation of biological evolution, which led to the first cells.[52] No one has yet synthesized a "protocell" using simple 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.[362] However, some researchers, notably Steen Rasmussen and Szostak, have argued that a "top-down approach" is more feasible, starting with simple forms of current life. 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.[363] Craig Venter and colleagues engineered existing prokaryotic cells with progressively fewer genes, attempting to discern the minimal requirements for life.[364][365][366]

In 2018, researchers at McMaster University developed a Planet Simulator to help study abiogenesis.[367][368][369][370] It consists of a climate chamber to study how the building blocks of life were assembled and how these transitioned into self-replicating RNA.[367]

See also


References

Explanatory footnotes

  1. The reactions are:
    Reaction 1: Fayalite + water → magnetite + aqueous silica + hydrogen
    3Fe2SiO4 + 2H2O → 2Fe3O4 + 3SiO2 + 2H2
    Reaction 2: Forsterite + aqueous silica → serpentine
    3Mg2SiO4 + SiO2 + 4H2O → 2Mg3Si2O5(OH)4
    Reaction 3: Forsterite + water → serpentine + brucite
    2Mg2SiO4 + 3H2O → Mg3Si2O5(OH)4 + Mg(OH)2
    Reaction 3 describes the hydration of olivine with water only to yield serpentine and Mg(OH)2 (brucite). Serpentine is stable at high pH in the presence of brucite like calcium silicate hydrate, (C-S-H) phases formed along with portlandite (Ca(OH)2) in hardened Portland cement paste after the hydration of belite (Ca2SiO4), the artificial calcium equivalent of forsterite. Analogy of reaction 3 with belite hydration in ordinary Portland cement: Belite + water → C-S-H phase + portlandite
    2 Ca2SiO4 + 4 H2O → 3 CaO · 2 SiO2 · 3 H2O + Ca(OH)2
  2. The reactions are:
    FeS + H2S → FeS2 + 2H+ + 2e
    FeS + H2S + CO2 → FeS2 + HCOOH

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