Biology:Abiogenesis

Short description: Natural process by which life arises from non-living matter

Stages in the origin of life range from the well-understood, such as the habitable Earth and the abiotic synthesis of simple molecules, to the largely unknown, like the derivation of the last universal common ancestor (LUCA) with its complex molecular functionalities.

In biology, abiogenesis (from Greek ἀ- a- 'not' + βῐ́ος bios 'life' + γένεσις genesis 'origin') or the origin of life is the natural process by which life has arisen from non-living matter, such as simple organic compounds. The prevailing scientific hypothesis is that the transition from non-living to living entities on Earth was not a single event, but a process of increasing complexity involving the formation of a habitable planet, the prebiotic synthesis of organic molecules, molecular self-replication, self-assembly, autocatalysis, and the emergence of cell membranes. Many proposals have been made for different stages of the process, but the transition from non-life to life has never been observed experimentally.

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. It primarily uses tools from biology and chemistry, with more recent approaches attempting a synthesis of many sciences. Life functions through the specialized chemistry of carbon and water, and builds largely upon four key families of chemicals: lipids for cell membranes, carbohydrates such as sugars, amino acids for protein metabolism, and nucleic acid DNA and RNA for the mechanisms of heredity. Any successful theory of abiogenesis must explain the origins and interactions of these classes of molecules. 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, although other self-replicating molecules may have preceded RNA.

The classic 1952 Miller–Urey experiment demonstrated that most amino acids, the chemical constituents of proteins, can be synthesized from inorganic compounds under conditions intended to replicate those of the early Earth. External sources of energy may have triggered these reactions, including lightning, radiation, atmospheric entries of micro-meteorites and implosion of bubbles in sea and ocean waves. 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.

While the last universal common ancestor (LUCA) is thought to have been quite different from the origin of life, investigations into LUCA can guide research into early universal characteristics. A genomics approach has sought to characterise LUCA of modern organisms by identifying the genes shared by Archaea and Bacteria, members of the two major branches of life (where the Eukaryotes belong to the archaean branch in the two-domain system). 355 genes appear to be common to all life; their nature implies that the LUCA was anaerobic with the Wood–Ljungdahl pathway, deriving energy by chemiosmosis, and maintaining its hereditary material with DNA, the genetic code, and ribosomes. Although the LUCA lived over 4 billion years ago (4 Gya), researchers do not believe it was the first form of life. Earlier cells might have had a leaky membrane and been powered by a naturally occurring proton gradient near a deep-sea white smoker hydrothermal vent.

Earth remains the only place in the universe known to harbor life. Geochemical and fossil evidence from the Earth informs most studies of abiogenesis. The Earth was formed at 4.54 Gya, and the earliest evidence of life on Earth dates from at least 3.8 Gya from Western Australia. Fossil micro-organisms appear to have lived within hydrothermal vent precipitates dated 3.77 to 4.28 Gya from Quebec, soon after ocean formation 4.4 Gya during the Hadean.

Overview

Further information: Astronomy:Astrobiology

NASA's 2015 strategy for astrobiology aimed to solve the puzzle of the origin of life – how a fully functioning living system could emerge from non-living components – through research on the prebiotic origin of life's chemicals, both in space and on planets, as well as the functioning of early biomolecules to catalyse reactions and support inheritance.

Life consists of reproduction with (heritable) variations. NASA defines life as "a self-sustaining chemical system capable of Darwinian [i.e., biological] evolution." Such a system is complex; the last universal common ancestor (LUCA), presumably a single-celled organism which lived some 4 billion years ago, already had hundreds of genes encoded in the DNA genetic code that is universal today. That in turn implies a suite of cellular machinery including messenger RNA, transfer RNA, and ribosomes to translate the code into proteins. Those proteins included enzymes to operate its anaerobic respiration via the Wood–Ljungdahl metabolic pathway, and a DNA polymerase to replicate its genetic material.

The challenge for abiogenesis (origin of life) researchers is to explain how such a complex and tightly interlinked system could develop by evolutionary steps, as at first sight all its parts are necessary to enable it to function. For example, a cell, whether the LUCA or in a modern organism, copies its DNA with the DNA polymerase enzyme, which is in turn produced by translating the DNA polymerase gene in the DNA. Neither the enzyme nor the DNA can be produced without the other. The evolutionary process could have involved molecular self-replication, self-assembly such as of cell membranes, and autocatalysis. Nonetheless, the transition of non-life to life has never been observed experimentally.

The precursors to the development of a living cell like the LUCA are clear enough, if disputed in their details: a habitable world is formed with a supply of minerals and liquid water. Prebiotic synthesis creates a range of simple organic compounds, which are assembled into polymers such as proteins and RNA. The process after the LUCA, too, is readily understood: biological evolution caused the development of a wide range of species with varied forms and biochemical capabilities. The derivation of living things such as the LUCA from simple components, however, is far from understood.

Although Earth remains the only place where life is known, the science of astrobiology seeks evidence of life on other planets. The 2015 NASA strategy on the origin of life aimed to solve the puzzle by identifying interactions, intermediary structures and functions, energy sources, and environmental factors that contributed to the diversity, selection, and replication of evolvable macromolecular systems, and mapping the chemical landscape of potential primordial informational polymers. The advent of polymers that could replicate, store genetic information, and exhibit properties subject to selection was, it suggested, most likely a critical step in the emergence of prebiotic chemical evolution. Those polymers derived, in turn, from simple organic compounds such as nucleobases, amino acids, and sugars that could have been formed by reactions in the environment. A successful theory of the origin of life must explain how all these chemicals came into being.

Pre-1960s conceptual history

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.

Spontaneous generation

One ancient view of the origin of life, from Aristotle until the 19th century, is of spontaneous generation. This theory held that "lower" animals were generated by decaying organic substances, and that life arose by chance. This was questioned from the 17th century, in works like Thomas Browne's Pseudodoxia Epidemica. In 1665, Robert Hooke published the first drawings of a microorganism. In 1676, Antonie van Leeuwenhoek drew and described microorganisms, probably protozoa and bacteria. 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. In 1668 Francesco Redi showed that no maggots appeared in meat when flies were prevented from laying eggs. By the middle of the 19th century, spontaneous generation was considered disproven.

Panspermia

Another ancient idea dating back to Anaxagoras in the 5th century BC is panspermia, the idea that life exists throughout the universe, distributed by meteoroids, asteroids, comets and planetoids. It does not attempt to explain how life originated in itself, but shifts the origin of life on Earth 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 more limited set of locations (potentially even a single location), and then spread about the galaxy to other star systems via cometary or meteorite impact.

"A warm little pond": primordial soup

The idea that life originated from non-living matter in slow stages appeared in Herbert Spencer's 1864–1867 book Principles of Biology, and in William Turner Thiselton-Dyer's 1879 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, 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." Darwin 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."

Alexander Oparin in 1924 and J. B. S. Haldane in 1929 proposed that the first molecules constituting the earliest cells slowly self-organized from a primordial soup, and this theory is called the Oparin–Haldane hypothesis. Haldane suggested that the Earth's prebiotic oceans consisted of a "hot dilute soup" in which organic compounds could have formed. J. D. Bernal showed that such mechanisms could form most of the necessary molecules for life from inorganic precursors. In 1967, he suggested three "stages": the origin of biological monomers; the origin of biological polymers; and the evolution from molecules to cells.

Miller–Urey experiment

In 1952, Stanley Miller and Harold Urey carried out a chemical experiment to demonstrate how organic molecules could have formed spontaneously from inorganic precursors under prebiotic conditions like those posited by the Oparin–Haldane hypothesis. It used a highly reducing (lacking oxygen) mixture of gases—methane, ammonia, and hydrogen, as well as water vapor—to form simple organic monomers such as amino acids. Bernal said of 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." However, current scientific consensus describes the primitive atmosphere as weakly reducing or neutral, diminishing the amount and variety of amino acids that could be produced. The addition of iron and carbonate minerals, present in early oceans, however, produces a diverse array of amino acids. Later work has focused on two other potential reducing environments: outer space and deep-sea hydrothermal vents.

Producing a habitable Earth

Evolutionary history

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 accreted and began orbiting in disks of gas and dust. Gravitational accretion of material at the hot and dense centers of these protoplantary disks formed stars by the fusion of hydrogen. Early stars were massive and short-lived, producing all the heavier elements through stellar nucleosynthesis. Element formation through stellar nucleosynthesis proceeds to its most stable element Iron-56. Heavier elements were formed during supernovae at the end of a stars lifecycle. 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 twice the mass of the sun. 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. 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. 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 age of the Earth is 4.54 Gya as found by radiometric dating of calcium-aluminium-rich inclusions in carbonaceous chrondrite meteorites, the oldest material in the Solar System. The Hadean Earth (from its formation until 4 Gya) 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. Soon after initial accretion of Earth at 4.48 Ga, its collision with Theia, a hypothesised impactor, is thought to have created the ejected debris that would eventually form the Moon. This impact would have removed the Earth's primary atmosphere, leaving behind clouds of viscous silicates and carbon dioxide. This unstable atmosphere was short-lived and condensed shortly after to form the bulk silicate Earth, leaving behind an atmosphere largely consisting of water vapor, nitrogen, and carbon dioxide, with smaller amounts of carbon monoxide, hydrogen, and sulfur compounds. The solution of carbon dioxide in water is thought to have made the seas slightly acidic, with a pH of about 5.5.

Condensation to form liquid oceans is theorised to have occurred as early as the Moon-forming impact. The solution of carbon dioxide in water is thought to have made the seas slightly acidic, with a pH of about 5.5. This scenario has found support from the dating of 4.404 Gya zircon crystals with high δ¹⁸O values from metamorphosed quartzite of Mount Narryer in Western Australia. The Hadean atmosphere has been characterized as a "gigantic, productive outdoor chemical laboratory," similar to volcanic gases today which still support some abiotic chemistry. Despite the likely increased volcanism from early plate tectonics, the Earth may have been a predominantly water world between 4.4 and 4.3 Gya. It is debated whether or not crust was exposed above this ocean due to uncertainties of what early plate tectonics looked like. For early life to have developed, it is generally thought that a land setting is required, so this question is essential to determining when in Earth's history life evolved. The post-Moon-forming impact Earth likely existed with little if any continental crust, a turbulent atmosphere, and a hydrosphere subject to intense ultraviolet light from a T Tauri stage Sun, from cosmic radiation, and from continued asteroid and comet impacts. Despite all this, niche environments likely existed conducive to life on Earth in the Late-Hadean to Early-Archaean.

The Late Heavy Bombardment hypothesis posits that a period of intense impact occurred at ~3.9 Ga during the Hadean. A cataclysmic impact event would have had the potential to sterilise all life on Earth by volatilising liquid oceans and blocking the Sun needed for photosynthesising primary producers, pushing back the earliest possible emergence of life to after Late Heavy Bombardment. Recent research questions both the intensity of the Late Heavy Bombardment as well as its potential for sterilisation. Uncertainties as to whether Late Heavy Bombardment was one giant impact or a period of greater impact rates greatly changed the implication of its destructive power. The 3.9 Ga date arises from dating of Apollo return mission samples collected mostly near the Imbrium Basin, biasing the age of recorded impacts. Impact modelling of the lunar surface reveals that rather than a cataclysmic event at 3.9 Ga, multiple small-scale, short-lived periods of bombardment likely occurred. Terrestrial data backs this idea by showing multiple periods of ejecta in the rock record both before and after the 3.9 Ga marker, suggesting that the early Earth was subject to continuous impacts that would not have had as great an impact on extinction as previously thought. If the Late Heavy Bombardment didn't take place, this allows for the emergence of life to have taken place far before 3.9 Ga.

If life evolved in the ocean at depths of more than ten meters, it would have been shielded both from late impacts and the then high levels of ultraviolet radiation from the sun. Geothermically heated oceanic crust could have yielded far more organic compounds through deep hydrothermal vents than the Miller–Urey experiments indicated. The available energy is maximized at 100–150 °C, the temperatures at which hyperthermophilic bacteria and thermoacidophilic archaea live.

Earliest evidence of life

The exact timing at which life emerged on Earth is unknown. Minimum age estimates are based on evidence from the geologic rock record. The earliest physical evidence of life so far found consists of microbialites in the Nuvvuagittuq Greenstone Belt of Northern Quebec, in banded iron formation rocks at least 3.77 and possibly as old as 4.32 Gya. The micro-organisms lived within hydrothermal vent precipitates, soon after the 4.4 Gya formation of oceans during the Hadean. The microbes resembled modern hydrothermal vent bacteria, supporting the view that abiogenesis began in such an environment.

Biogenic graphite has been found in 3.7 Gya metasedimentary rocks from southwestern Greenland and in microbial mat fossils from 3.49 Gya cherts in the Pilbara region of Western Australia. 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. 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. 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. Carbon isotope ratios on graphite inclusions from the Jack Hills zircons suggest that life could have existed on Earth from 4.1 Gya.

The Pilbara region of Western Australia contains the Dresser Formation with rocks 3.48 Gya, including layered structures called stromatolites. Their modern counterparts are created by photosynthetic micro-organisms including cyanobacteria. These lie within undeformed hydrothermal-sedimentary strata; their texture indicates a biogenic origin. Parts of the Dresser formation preserve hot springs on land, but other regions seem to have been shallow seas. A molecular clock analysis suggests the LUCA emerged prior to the Late Heavy Bombardment (3.9 Gya).

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  Stromatolites in the Siyeh Formation, Glacier National Park, dated 3.5 Gya, placing them among the earliest life-forms

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  Modern stromatolites in Shark Bay, created by photosynthetic cyanobacteria

Producing molecules: prebiotic synthesis

Further information: Physics:Nucleosynthesis

All chemical elements except for hydrogen and helium derive from stellar nucleosynthesis. The basic chemical ingredients of life – the carbon-hydrogen molecule (CH), the carbon-hydrogen positive ion (CH+) and the carbon ion (C+) – were produced by ultraviolet light from stars. Complex molecules, including organic molecules, form naturally both in space and on planets. Organic molecules on the early Earth could have had either terrestrial origins, with organic molecule synthesis driven by impact shocks or by other energy sources, such as ultraviolet light, redox coupling, or electrical discharges; or extraterrestrial origins (pseudo-panspermia), with organic molecules formed in interstellar dust clouds raining down on to the planet.

Observed extraterrestrial organic molecules

An organic compound is a chemical whose molecules contain carbon. 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. Purine and pyrimidine nucleobases including guanine, adenine, cytosine, uracil, and thymine have been found in meteorites. These could have provided the materials for DNA and RNA to form on the early Earth. The amino acid glycine was found in material ejected from comet Wild 2; it had earlier been detected in meteorites. 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. 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.

PAH world hypothesis

The Cat's Paw Nebula is inside the Milky Way Galaxy, 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

Polycyclic aromatic hydrocarbons (PAH) are the most common and abundant polyatomic molecules in the observable universe, and are a major store of carbon. They seem to have formed shortly after the Big Bang, and are associated with new stars and exoplanets. They are a likely constituent of Earth's primordial sea. PAHs have been detected in nebulae, and in the interstellar medium, in comets, and in meteorites.

The PAH world hypothesis posits PAHs as precursors to the RNA world. A star, HH 46-IR, resembling the sun early in its life, is surrounded by a disk of material which contains molecules including cyanide compounds, hydrocarbons, and carbon monoxide. PAHs in the interstellar medium can be transformed through hydrogenation, oxygenation, and hydroxylation to more complex organic compounds used in living cells.

Nucleobases and Nucleotides

Further information: Biology:Nucleobase and Biology:Nucleotide

The majority of organic compounds introduced on Earth by interstellar dust particles have helped to form complex molecules, thanks to their peculiar surface-catalytic activities. Studies of the ¹²C/¹³C isotopic ratios of organic compounds in the Murchison meteorite suggest that the RNA component uracil and related molecules, including xanthine, were formed extraterrestrially. NASA studies of meteorites suggest that all four DNA nucleobases (adenine, guanine and related organic molecules) have been formed in outer space. The cosmic dust permeating the universe contains complex organics ("amorphous organic solids with a mixed aromatic–aliphatic structure") that could be created rapidly by stars. Glycolaldehyde, a sugar molecule and RNA precursor, has been detected in regions of space including around protostars and on meteorites.

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. The spontaneous formation of complex polymers from abiotically generated monomers under the conditions posited by the "soup" theory is not straightforward. 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. Biology uses essentially 20 amino acids for its coded protein enzymes, representing a very small subset of the structurally possible products. Since life tends to use whatever is available, an explanation is needed for why the set used is so small.

Sugars

The Breslow catalytic cycle for formaldehyde dimerization and C2-C6 sugar formation

Alexander Butlerov showed in 1861 that the formose reaction created sugars including tetroses, pentoses, and hexoses when formaldehyde is heated under basic conditions with divalent metal ions like calcium. R. Breslow proposed that the reaction was autocatalytic in 1959.

Nucleobases

Nucleobases, such as guanine and adenine, can be synthesized from simple carbon and nitrogen sources, such as hydrogen cyanide (HCN) and ammonia. 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 be concentrated by the evaporation of water. HCN is poisonous only to aerobic organisms (eukaryotes and aerobic bacteria), which did not yet exist. It can play roles in other chemical processes such as the synthesis of the amino acid glycine.

DNA and RNA components including uracil, cytosine and thymine can be synthesized 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. All four RNA-bases may be synthesized from formamide in high-energy density events like extraterrestrial impacts.

Other pathways for synthesizing bases from inorganic materials have been reported. Freezing temperatures are advantageous for the synthesis of purines, due to the concentrating effect for key precursors such as hydrogen cyanide. However, while adenine and guanine require freezing conditions for synthesis, cytosine and uracil may require boiling temperatures. Seven amino acids and eleven types of nucleobases formed in ice when ammonia and cyanide were left in a freezer for 25 years. S-triazines (alternative nucleobases), pyrimidines including cytosine and uracil, and adenine can be synthesized by subjecting a urea solution 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, which crowds impurities in microscopic pockets of liquid within the ice, causing the molecules to collide more often.

Producing suitable vesicles

The three main structures composed of phospholipids form spontaneously by self-assembly in solution: the liposome (a closed bilayer), the micelle and the bilayer.

The lipid world theory postulates that the first self-replicating object was lipid-like. 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. These bodies may expand by insertion of additional lipids, and may spontaneously split into two offspring of similar size and composition. The main idea is that the molecular composition of the lipid bodies is a preliminary to information storage, and that evolution led to the appearance of polymers like RNA that store information. Studies on vesicles from amphiphiles that might have existed in the prebiotic world have so far been limited to systems of one or two types of amphiphiles.

A lipid bilayer membrane could be composed of a huge number of combinations of arrangements of amphiphiles. The best of these would have favored 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 natural selection.

A protocell is a self-organized, self-ordered, spherical collection of lipids proposed as a stepping-stone to the origin of life. The theory of classical irreversible thermodynamics treats self-assembly under a generalized chemical potential within the framework of dissipative systems.

A central question in evolution is how simple protocells first arose and differed in reproductive contribution to the following generation, thus driving the evolution of life. A functional protocell has (as of 2014) not yet been achieved in a laboratory setting. 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. Irene Chen and Jack W. Szostak suggest that elementary protocells can give rise to cellular behaviors including primitive forms of differential reproduction, competition, and energy storage. Competition for membrane molecules would favor 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 and the exchange of small molecules, while retaining large biomolecules inside. Such a membrane is needed for a cell to create its own electrochemical gradient to store energy by pumping ions across the membrane. Fatty acid vesicles in conditions relevant to alkaline hydrothermal vents can be stabilized by isoprenoids which are synthesized by the formose reaction, the advantages and disadvantages of isoprenoids incorporated within the lipid bilayer in different microenvironments might have led to the divergence of the membranes of archaea and bacteria.

Producing biology

Energy and entropy

Further information: Physics:Entropy

Life requires a loss of entropy, or disorder, when molecules organize themselves into living matter. The emergence of life and increased complexity does not contradict the second law of thermodynamics, which states that overall entropy never decreases, since a living organism creates order in some places (e.g. its living body) at the expense of an increase of entropy elsewhere (e.g. heat and waste production).

Multiple sources of energy were available for chemical reactions on the early Earth. Heat from geothermal processes is a standard energy source for chemistry. Other examples include sunlight, lightning, atmospheric entries of micro-meteorites, and implosion of bubbles in sea and ocean waves. This has been confirmed by experiments and simulations. Unfavorable reactions can be driven by highly favorable ones, as in the case of iron-sulfur chemistry. For example, this was probably important for carbon fixation. 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, can drive the production of small amounts of amino acids and other biomolecules.

Chemiosmosis

Further information: Biology:Chemiosmosis

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

In 1961, Peter Mitchell proposed chemiosmosis as a cell's primary system of energy conversion. The mechanism, now ubiquitous in living cells, powers energy conversion in micro-organisms and in the mitochondria of eukaryotes, making it a likely candidate for early life. Mitochondria produce adenosine triphosphate (ATP), the energy currency of the cell used to drive cellular processes such as chemical syntheses. The mechanism of ATP synthesis involves a closed membrane in which the ATP synthase enzyme is embedded. The energy required to release strongly bound ATP has its origin in protons that move across the membrane. In modern cells, those proton movements are caused by the pumping of ions across the membrane, maintaining an electrochemical gradient. In the first organisms, the gradient could have been provided by the difference in chemical composition between the flow from a hydrothermal vent and the surrounding seawater, or perhaps meteoric quinones that were conducive to the development of chemiosmotic energy across lipid membranes if at a terrestrial origin.

Chemiosmotic coupling in the membranes of a mitochondrion

The RNA world

The RNA world hypothesis describes an early Earth with self-replicating and catalytic RNA but no DNA or proteins. Many researchers concur that an RNA world must have preceded the DNA-based life that now dominates. However, RNA-based life may not have been the first to exist. Another model echoes Darwin's "warm little pond" with cycles of wetting and drying.

RNA is central to the translation process. Small RNAs can catalyze all the chemical groups and information transfers required for life. RNA both expresses and maintains genetic information in modern organisms; and the chemical components of RNA are easily synthesized under the conditions that approximated the early Earth, which were very different from those that prevail today. The structure of the ribosome 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.

The concept of the RNA world was proposed in 1962 by Alexander Rich, and the term was coined by Walter Gilbert in 1986. There were initial 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.

The RNA world hypothesis proposes that undirected polymerisation led to the emergence of ribozymes, and in turn to an RNA replicase.

RNA replicase can function as both code and catalyst for further RNA replication, i.e. it can be autocatalytic. 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 experimental conditions. If such conditions were present on early Earth, then natural selection would favor the proliferation of such autocatalytic sets, to which further functionalities could be added. Self-assembly of RNA may occur spontaneously in hydrothermal vents. A preliminary form of tRNA could have assembled into such a replicator molecule.

Possible precursors to protein synthesis include the synthesis of short peptide cofactors or the self-catalysing 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 has argued that "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."

Phylogeny and LUCA

Further information: Biology:Last universal common ancestor

Starting with the work of Carl Woese from 1977, genomics studies have placed the last universal common ancestor (LUCA) of all modern life-forms between Bacteria and a clade formed by Archaea and Eukaryota in the phylogenetic tree of life. It lived over 4 Gya. A minority of studies have placed the LUCA in Bacteria, proposing that Archaea and Eukaryota are evolutionarily derived from within Eubacteria; Thomas Cavalier-Smith suggested in 2006 that the phenotypically diverse bacterial phylum Chloroflexota contained the LUCA.

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  Phylogenetic tree showing the last universal common ancestor (LUCA) at the root. The major clades are the Bacteria on one hand, and the Archaea and Eukaryota on the other.

In 2016, a set of 355 genes likely present in the LUCA was identified. A total of 6.1 million prokaryotic genes from Bacteria and Archaea were sequenced, identifying 355 protein clusters from among 286,514 protein clusters that were probably common to the LUCA. The results suggest that the LUCA was anaerobic with a Wood–Ljungdahl (reductive Acetyl-CoA) pathway, nitrogen- and carbon-fixing, thermophilic. Its cofactors suggest dependence upon an environment rich in hydrogen, carbon dioxide, iron, and transition metals. Its genetic material was probably DNA, requiring the 4-nucleotide genetic code, messenger RNA, transfer RNA, and ribosomes to translate the code into proteins such as enzymes. LUCA likely inhabited an anaerobic hydrothermal vent setting in a geochemically active environment. It was evidently already a complex organism, and must have had precursors; it was not the first living thing. The physiology of LUCA has been in dispute.

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  LUCA systems and environment included the Wood–Ljungdahl pathway.

Leslie Orgel argued that early translation machinery for the genetic code would be susceptible to error catastrophe. Geoffrey Hoffmann however showed that such machinery can be stable in function against "Orgel's paradox". Metabolic reactions that have also been inferred in LUCA are the incomplete reverse Krebs cycle, gluconeogenesis, the pentose phosphate pathway, glycolysis, reductive amination, and transamination.

Suitable geological environments

Further information: Biology:Alternative abiogenesis scenarios

A variety of geologic and environmental settings have been proposed for an origin of life. These theories are often in competition with one another as there are many differing views of prebiotic compound availability, geophysical setting, and early life characteristics. The first organism on Earth likely looked different from LUCA. Between the first appearance of life and where all modern phylogenies began branching, an unknown amount of time passed. Within this time, unknown gene transfer, extinctions, and evolutions may have occurred, creating adaptations for a more diverse amount of environmental niches. One notable shifts is the one from an RNA-based to an RNA-DNA-protein world. There is more known about LUCA than the first organisms due to genomic reconstructions based on modern phylogenies.

The most popular hypotheses for settings in which an origin of life are possible are deep sea hydrothermal vents and surface bodies of water. Surface waters can be broken down into hot springs, moderate temperature lakes and ponds, and cold settings.

Deep sea hydrothermal vents

Hot fluids

Further information: Earth:Hydrothermal vent

The earliest known life forms are putative fossilized microorganisms, found in white smoker hydrothermal vent precipitates. They may have lived as early as 4.28 Gya (billion years ago), relatively soon after the formation of the oceans 4.41 Gya, not long after the formation of the Earth 4.54 Gya.

Early micro-fossils may have come from a hot world of gases such as methane, ammonia, carbon dioxide, and hydrogen sulfide, toxic to much current life. Analysis of the tree of life places thermophilic and hyperthermophilic bacteria and archaea closest to the root, suggesting that life may have evolved in a hot environment. The deep sea or alkaline hydrothermal vent theory posits that life began 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 (molecular hydrogen) react with electron acceptors (carbon dioxide); see iron–sulfur world theory. These are exothermic reactions.

Chemiosmotic gradient

Early cell powered by external proton gradient near a deep-sea hydrothermal vent. As long as the membrane (or passive ion channels within it) is permeable to protons, the mechanism can function without ion pumps.

Russell demonstrated that alkaline vents created an abiogenic proton motive force chemiosmotic gradient, ideal for abiogenesis. 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. 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).

The surfaces of mineral particles inside deep-ocean 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 acids out of the dissolved CO₂ in the water, if driven by an applied voltage or by reaction with H₂ or H₂S.

The research reported by Martin in 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 the LUCA "may have depended heavily on the geothermal energy of the vent to survive". Pores at deep sea hydrothermal vents are suggested to have been occupied by membrane-bound compartments which promoted biochemical reactions. Metabolic intermediates in the Krebs cycle, gluconeogenesis, amino acid bio-synthetic pathways, glycolysis, the pentose phosphate pathway, and including sugars like ribose, and lipid precursors can occur non-enzymatically at conditions relevant to deep-sea alkaline hydrothermal vents.

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 life evolved in the ocean at depths of more than ten meters, it would have been shielded both from impacts and the then high levels of ultraviolet radiation from the sun. The available energy in hydrothermal vents is maximized at 100–150 °C, the temperatures at which hyperthermophilic bacteria and thermoacidophilic archaea live. Arguments against a hydrothermal origin of life state that hyperthermophily was a result of convergent evolution in bacteria and archaea, and that a mesophilic environment would have been more likely. This hypothesis, suggested in 1999 by Galtier, was proposed one year before the discovery of the Lost City Hydrothermal Field, where white-smoker hydrothermal vents average ~45-90 °C. Moderate temperatures and alkaline seawater at Lost City are now the favoured hydrothermal vent setting in contrast to acidic, high temperature (~350 °C) black-smokers.

Arguments against a vent setting

Production of prebiotic organic compounds at hydrothermal vents is estimated to be 1x10⁸ kg yr⁻¹. While a large amount of key prebiotic compounds, such as methane, are found at vents, they are in far lower concentrations than estimates of a Miller-Urey Experiment environment. In the case of methane, the production rate at vents is around 2-4 orders of magnitude lower than predicted amounts in a Miller-Urey Experiment surface atmosphere.

Other arguments against an oceanic vent setting for the origin of life include the inability to concentrate prebiotic materials due to strong dilution from seawater. This open-system cycles compounds through minerals that make up vents, leaving little residence time to accumulate. All modern cells rely on phosphates and potassium for nucleotide backbone and protein formation respectively, making it likely that the first life forms also shared these functions. These elements were not available in high quantities in the Archaean oceans as both primarily come from the weathering of continental rocks on land, far from vent settings. Submarine hydrothermal vents are not conducive to condensation reactions needed for polymerisation to form macromolecules. Further, these polymers were encapsulated in vesicles after condensation, which would not happen in saltwater because of the high concentrations of ions.

Surface bodies of water

Surface bodies of water provide environments able to dry out and be rewetted. Continued wet-dry cycles allow the concentration of prebiotic compounds and condensation reactions to polymerise macromolecules. Moreover, lake and ponds on land allow for detrital input from the weathering of continental rocks which contain apatite, the most common source of phosphates needed for nucleotide backbones. The amount of exposed continental crust in the Hadean is unknown, but models of early ocean depths and rates of ocean island and continental crust growth make it plausible that there was exposed land. Another line of evidence for a surface start to life is the requirement for UV for organism function. UV is necessary for the formation of the U+C nucleotide base pair by partial hydrolysis and nucleobase loss. Simultaneously, UV can be harmful and sterilising to life, especially for simple early lifeforms with little ability to repair radiation damage. Radiation levels from a young Sun were likely greater, and, with no ozone layer, harmful shortwave UV rays would reach the surface of Earth. For life to begin, a shielded environment with influx from UV-exposed sources is necessary to both benefit and protect from UV. Shielding under ice, liquid water, mineral surfaces (e.g. clay) or regolith is possible in a range of surface water settings. While deep sea vents may have input from raining down of surface exposed materials, the likelihood of concentration is lessened by the ocean's open system.

Hot springs

Most branching phylogenies are thermophilic or hyperthermophilic, making it possible that the Last universal common ancestor (LUCA) and preceding lifeforms were similarly thermophilic. Hot springs are formed from the heating of groundwater by geothermal activity. This intersection allows for influxes of material from deep penetrating waters and from surface runoff that transports eroded continental sediments. Interconnected groundwater systems create a mechanism for distribution of life to wider area.

Mulkidjanian and co-authors argue that marine environments did not provide the ionic balance and composition universally found in cells, or the ions required by essential proteins and ribozymes, especially with respect to high K⁺/Na⁺ ratio, Mn²⁺, Zn²⁺ and phosphate concentrations. They argue that the only environments that mimic the needed conditions on Earth are hot springs similar to ones at Kamchatka. Mineral deposits in these environments under an anoxic atmosphere would have suitable pH (while current pools in an oxygenated atmosphere would not), contain precipitates of photocatalytic sulfide minerals that absorb harmful ultraviolet radiation, have wet-dry cycles that concentrate substrate solutions to concentrations amenable to spontaneous formation of biopolymers created both by chemical reactions in the hydrothermal environment, and by exposure to UV light during transport from vents to adjacent pools that would promote the formation of biomolecules. The hypothesized pre-biotic environments are similar to hydrothermal vents, with additional components that help explain peculiarities of the LUCA.

A phylogenomic and geochemical analysis of proteins plausibly traced to the LUCA shows that the ionic composition of its intracellular fluid is identical to that of hot springs. The LUCA likely was dependent upon synthesized organic matter for its growth. Experiments show that RNA-like polymers can be synthesized in wet-dry cycling and UV light exposure. These polymers were encapsulated in vesicles after condensation. Potential sources of organics at hot springs might have been transport by interplanetary dust particles, extraterrestrial projectiles, or atmospheric or geochemical synthesis. Hot springs could have been abundant in volcanic landmasses during the Hadean.

Temperate surface bodies of water

A mesophilic start in surface bodies of waters hypothesis has evolved from Darwin's concept of a 'warm little pond' and the Oparin-Haldane hypothesis. Freshwater bodies under temperate climates can accumulate prebiotic materials while providing suitable environmental conditions conducive to simple life forms. The climate during the Archaean is still a highly debated topic, as there is uncertainty about what continents, oceans, and the atmosphere looked like then. Atmospheric reconstructions of the Archaean from geochemical proxies and models state that sufficient greenhouse gases were present to maintain surface temperatures between 0-40 °C. Under this assumption, there is a greater abundance of moderate temperature niches in which life could begin.

Strong lines of evidence for mesophily from biomolecular studies include Galtier's G+C nucleotide thermometer. G+C are more abundant in thermophiles due to the added stability of an additional hydrogen bond not present between A+T nucleotides. rRNA sequencing on a diverse range of modern lifeforms show that LUCA's reconstructed G+C content was likely representative of moderate temperatures.

Although most modern phylogenies are thermophilic or hyperthermophilic, it is possible that their widespread diversity today is a product of convergent evolution and horizontal gene transfer rather than an inherited trait from LUCA. The reverse gyrase topoisomerase is found exclusively in thermophiles and hyperthermophiles as it allows for coiling of DNA. The reverse gyrase enzyme requires ATP to function, both of which are complex biomolecules. If an origin of life is hypothesised to involve a simple organism that had not yet evolved a membrane, let alone ATP, this would make the existence of reverse gyrase improbable. Moreover, phylogenetic studies show that reverse gyrase had an archaeal origin, and that it was transferred to bacteria by horizontal gene transfer. This implies that reverse gyrase was not present in the LUCA.

Icy surface bodies of water

Cold-start origin of life theories stem from the idea there may have been cold enough regions on the early Earth that large ice cover could be found. Stellar evolution models predict that the Sun's luminosity was ~25% weaker than it is today. Fuelner states that although this significant decrease in solar energy would have formed an icy planet, there is strong evidence for liquid water to be present, possibly driven by a greenhouse effect. This would create an early Earth with both liquid oceans and icy poles.

Ice melts that form from ice sheets or glaciers melts create freshwater pools, another niche capable of experiencing wet-dry cycles. While these pools that exist on the surface would be exposed to intense UV radiation, bodies of water within and under ice are sufficiently shielded while remaining connected to UV exposed areas through ice cracks. Suggestions of impact melting of ice allow freshwater paired with meteoritic input, a popular vessel for prebiotic components. Near-seawater levels of sodium chloride are found to destabilize fatty acid membrane self-assembly, making freshwater settings appealing for early membranous life.

Icy environments would trade the faster reaction rates that occur in warm environments for increased stability and accumulation of larger polymers. Experiments simulating Europa-like conditions of ~20 °C have synthesised amino acids and adenine, showing that Miller-Urey type syntheses can still occur at cold temperatures. In an RNA world, the ribozyme would have had even more functions than in a later DNA-RNA-protein-world. For RNA to function, it must be able to fold, a process that is hindered by temperatures above 30 °C. While RNA folding in psychrophilic organisms is slower, the process is more successful as hydrolysis is also slower. Shorter nucleotides would not suffer from higher temperatures.

Homochirality

Many biomolecules, such as L-glutamic acid, are asymmetric, and occur in living systems in only one of the two possible forms, in the case of amino acids the left-handed form. Prebiotic chemistry would produce both forms, creating a puzzle for abiogenesis researchers.

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, 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, and spontaneous symmetry breaking.

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.

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. Amino acids from meteorites show a left-handed bias, whereas sugars show a predominantly right-handed bias, as found in living organisms, suggesting an abiogenic origin of these compounds.

In 2010, an experiment by Robert Root-Bernstein shows that "two D-RNA-oligonucleotides having inverse base sequences (D-CGUA and D-AUGC) and their corresponding L-RNA-oligonucleotides (L-CGUA and L-AUGC) were synthesized and their affinity determined for Gly and eleven pairs of L- and D-amino acids". This suggests that homochirality, including codon directionality, might have "emerged as a function of the origin of the genetic code".

See also

• Autopoiesis
• Formamide-based prebiotic chemistry
• Proto-metabolism
• GADV-protein world hypothesis
• Genetic recombination
• Shadow biosphere

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External links

• Making headway with the mysteries of life's origins – Adam Mann (PNAS; 14 April 2021)
• Exploring Life's Origins a virtual exhibit at the Museum of Science (Boston)
• How life began on Earth – Marcia Malory (Earth Facts; 2015)
• The Origins of Life – Richard Dawkins et al. (BBC Radio; 2004)
• Life in the Universe – Essay by Stephen Hawking (1996)