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In evolutionary biology, abiogenesis, or informally the origin of life (OoL),^[3][4][5][a] 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-replicatingmolecules, 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]

Miller–Urey experiment Synthesis of small organic molecules in a mixture of simple gases that is placed in a thermal gradient by heating (left) and cooling (right) the mixture at the same time, a mixture that is also subject to electrical discharges

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. Scientists have proposed various external sources of energy that 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]

The alternative panspermia hypothesis^[21] speculates that microscopic life arose outside Earth by unknown mechanisms, and spread to the early Earth on space dust^[22] and meteoroids.^[23] It is known that complex organic molecules occur in the Solar System and in interstellar space, and these molecules may have provided starting material for the development of life on Earth.^{[24][25][26][27]}

Earth remains the only place in the universe known to harbour life,^[28][29] and fossil evidence from the Earth informs most studies of abiogenesis. The age of the Earth is 4.54 Gy (Giga or billion year);^[30][31][32] the earliest undisputed evidence of life on Earth dates from at least 3.5 Gya (Gy ago),^[33][34][35] and possibly as early as the Eoarchean Era (3.6-4.0 Gya). In 2017 scientists found possible evidence of early life on land 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.^{[36][37][38][39]} However, a number of discoveries suggest that life may have appeared on Earth even earlier. As of 2017^[update], 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, suggesting life started soon after ocean formation 4.4 Gya during the HadeanEon.^{[1][2][40][41][42]}

The NASA strategy on abiogenesis states that it is necessary to identify interactions, intermediary structures and functions, energy sources, and environmental factors that contributed to the diversity, selection, and replication of evolvable macromolecular systems.^[43] Emphasis must continue 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.^[43]

Thermodynamics, self-organization, and information: Physics[edit]

Thermodynamics principles: Energy and entropy[edit]

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.^[44]

Similarly, it was realized early on that life requires a loss of entropy, or disorder, when molecules organize themselves into living matter. This Second Law of thermodynamics needs to be considered when self-organization of matter to higher complexity happens. Because living organisms are machines,^[45] the Second Law applies to life as well.

Obtaining free energy[edit]

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.^[46]

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.^[47] 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.^[48]

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.^[49]

Unfavourable reactions can also be driven by highly favourable ones, as in the case of iron-sulfur chemistry. For example, this was probably important for carbon fixation (the conversion of carbon from its inorganic form to an organic one).^[b] Carbon fixation via iron-sulfur chemistry is highly favourable, and occurs at neutral pH and 100C. Iron-sulfur surfaces, which are abundant near hydrothermal vents, are also capable of producing small amounts of amino acids and other biological metabolites.^[47]

Self-organization[edit]

The discipline of synergetics studies self-organization in physical systems. In his book Synergetics^[50]Hermann Haken has pointed out that different physical systems can be treated in a similar way. He gives as examples of self-organization several types of lasers, instabilities in fluid dynamics, including convection, and chemical and biochemical oscillations. In his preface he mentions the origin of life, but only in general terms:

The spontaneous formation of well organized structures out of germs or even out of chaos is one of the most fascinating phenomena and most challenging problems scientists are confronted with. Such phenomena are an experience of our daily life when we observe the growth of plants and animals. Thinking of much larger time scales, scientists are led into the problems of evolution, and, ultimately, of the origin of living matter. When we try to explain or understand in some sense these extremely complex biological phenomena it is a natural question, whether processes of self-organization may be found in much simpler systems of the unanimated world.

In recent years it has become more and more evident that there exists numerous examples in physical and chemical systems where well organized spatial, temporal, or spatio-temporal structures arise out of chaotic states. Furthermore, as in living organisms, the functioning of these systems can be maintained only by a flux of energy (and matter) through them. In contrast to man-made machines, which are devised to exhibit special structures and functionings, these structures develop spontaneously—they are selforganizing. ...^[51]

Multiple dissipative structures[edit]

This theory postulates that the hallmark of the origin and evolution of life is the microscopic dissipative structuring of organic pigments and their proliferation over the entire Earth surface.^[52] Present day life augments the entropy production of Earth in its solar environment by dissipating ultraviolet and visiblephotons 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.^[53][54]

Selforganization by dissipative structures[edit]

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.^[55] 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^[56] 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,^[57] and later Ilya Prigogine,^[58] 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 contributions to non-equilibrium thermodynamics, particularly the theory of dissipative structures". The analysis by Prigogine showed that if a system were left to evolve under an imposed external potential, material could spontaneously organize (lower its entropy) forming what he called "dissipative structures" which would increase the dissipation of the externally imposed potential (augment the global entropy production). Non-equilibrium thermodynamics has since been successfully applied to the analysis of living systems, from the biochemical production of ATP^[59] to optimizing bacterial metabolic pathways^[60] to complete ecosystems.^[61][62][63]

Current life, the result of abiogenesis: biology[edit]

Definition of life[edit]

When discussing the origin of life, a definition of life obviously is helpful. This definition turns out not to be easy. Different biology textbooks define life differently. James Gould:

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. ^[64]

whereas according to Neil Campbell and Jane Reece

The phenomenon we call life defies a simple, one-sentence definition.^[65]

This difference can also be found in books on the origin of life. John Casti gives a single sentence:

By more or general consensus nowadays, an entity is considered to be "alive" if it has the capacity to carry out three basic functional activities: metabolism, self-repair, and replication. ^[66]

Dirk Schulze-Makuch and Louis Irwin spend in contrast the whole first chapter of their book on this subject.^[67]

Fermentation[edit]

Overall diagram of the chemical reactions of metabolism, in which the citric acid cycle can be recognized as the circle just below the middle of the figure

Albert Lehninger has stated around 1970 that fermentation, including glycolysis, is a suitable primitive energy source for the origin of life.^[68]

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.

Fermentation involves glycolysis, which, rather inefficiently, transduces the chemical energy of sugar into the chemical energy of ATP.

Chemiosmosis[edit]

Oxidative phosphorylation

Chemiosmotic coupling mitochondrion

As Fermentation had around 1970 been elucidated, whereas the mechanism of oxidative phosphorylation had not and some controversies still existed, fermentation may have looked too complex for investigators of the origin of life at that time. Peter Mitchell's Chemiosmosis is now however generally accepted as correct.

Even Peter Mitchell himself assumed that fermentation preceded chemiosmosis. Chemiosmosis is however ubiquitous in life. A model for the origin of life has been presented in terms of chemiosmosis. ^[69][70]

Both respiration by mitochondria and photosynthesis in chloroplasts make use of chemiosmosis to generate most of their ATP.

Today the energy source of all life can be linked to photosynthesis, and one speaks of primary production by sunlight. The oxygen used for oxidizing reducing compounds by organisms at hydrothermal vents at the bottom of the ocean is the result of photosynthesis at the Oceans' surface.

ATP synthase[edit]

The mechanism of ATP synthesis is complex and 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.

RNA world[edit]

The RNA world hypothesis describes an early Earth with self-replicating and catalytic RNA but no DNA or proteins.^[72] It is widely accepted that current life on Earth descends from an RNA world,^[17][73][74]although RNA-based life may not have been the first life to exist.^[18][19] This conclusion is drawn from many independent lines of evidence, such as the observations that RNA is central to the translation process and that small RNAs can catalyze all of the chemical groups and information transfers required for life.^[19][75] The structure of the ribosome has been called the "smoking gun," as it showed that the ribosome is a ribozyme, with a central core of RNA and no amino acid side chains within 18 angstroms of the active site where peptide bond formation is catalyzed.^[18][76]

The concept of the RNA world was first proposed in 1962 by Alexander Rich,^[77] and the term was coined by Walter Gilbert in 1986.^[19][78] In March 2020, astronomer Tomonori Totani presented a statistical approach for explaining how an initial active RNA molecule might have been produced randomly in the universe sometime since the Big Bang.^[79][80]

Phylogeny and LUCA[edit]

The most commonly accepted location of the root of the tree of life is between a monophyletic domain Bacteria and a clade formed by Archaea and Eukaryota of what is referred to as the "traditional tree of life" based on several molecular studies starting with Carl Woese.^[81][82]

A very small minority of studies have concluded differently, namely that the root is in the domain Bacteria, either in the phylum Firmicutes^[83] or that the phylum Chloroflexi is basal to a clade with Archaea+Eukaryotes and the rest of Bacteria as proposed by Thomas Cavalier-Smith.^[84] More recently, Peter Ward has proposed an alternative view which is rooted in abiotic RNA synthesis which becomes enclosed within a capsule and then creates RNA ribozyme replicates. It is proposed that this then bifurcates between Dominion Ribosa (RNA life), and after the loss of ribozymes RNA viruses as Domain Viorea, and Dominion Terroa^{[clarification needed]}, which after creating a large cell within a lipid wall, creating DNA the 20 based amino acids and the triplet code, is established as the last universal common ancestor or LUCA, of earlier phylogenic trees.^[85]

In 2016, a set of 355 genes likely present in the Last Universal Common Ancestor (LUCA) of all organismsliving on Earth was identified.^[86] A total of 6.1 million prokaryotic protein coding genes from various phylogenic trees were sequenced, identifying 355 protein clusters from amongst 286,514 protein clusters that were probably common to LUCA. The results

. . . depict LUCA as anaerobic, CO₂-fixing, H₂-dependent with a Wood–Ljungdahl pathway, N₂-fixing and thermophilic. LUCA's biochemistry was replete with FeS clusters and radical reaction mechanisms. Its cofactors reveal dependence upon transition metals, flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, corrins and selenium. Its genetic code required nucleoside modifications and S-adenosylmethionine-dependent methylations."

The results depict methanogenicclostridia as a basal clade in the 355 phylogenies examined, and suggest that LUCA inhabited an anaerobic hydrothermal vent setting in a geochemically active environment rich in H₂, CO₂ and iron.^[87]

A study at the University of Düsseldorf created phylogenic trees based upon 6 million genes from bacteria and archaea, and identified 355 protein families that were probably present in the LUCA. They were based upon an anaerobic metabolism fixing carbon dioxide and nitrogen. It suggests that the LUCA evolved in an environment rich in hydrogen, carbon dioxide and iron.^[88]

Key issues in abiogenesis[edit]

What came first: protein or nucleic acids?[edit]

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.^[89]

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.^[90]

Emergence of the genetic code[edit]

See: Genetic code.

Error in translation catastrophe[edit]

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".^[91][92][93]

Homochirality[edit]

Homochirality refers to a geometric uniformity of some materials composed of chiral units. Chiral refers to nonsuperimposable 3D forms that are mirror images of one another, as are left and right hands. Living organisms use molecules that have the same chirality ("handedness"): with almost no exceptions,^[94] amino acids are left-handed while nucleotides and sugars are right-handed. Chiral molecules can be synthesized, but in the absence of a chiral source or a chiral catalyst, they are formed in a 50/50 mixture of both enantiomers (called a racemic mixture). Known mechanisms for the production of non-racemic mixtures from racemic starting materials include: asymmetric physical laws, such as the electroweak interaction; asymmetric environments, such as those caused by circularly polarized light, quartz crystals, or the Earth's rotation, statistical fluctuations during racemic synthesis,^[95] and spontaneous symmetry breaking.^[96][97][98]

Once established, chirality would be selected for.^[99] A small bias (enantiomeric excess) in the population can be amplified into a large one by asymmetric autocatalysis, such as in the Soai reaction.^[100] 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.^[101]

Clark has suggested that homochirality may have started in outer space, as the studies of the amino acids on the Murchison meteorite showed that L-alanine is more than twice as frequent as its D form, and L-glutamic acid was more than three times prevalent than its D counterpart. Various chiral crystal surfaces can also act as sites for possible concentration and assembly of chiral monomer units into macromolecules.^[102][103] 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.^[104]

Early universe and Earth: astronomy and geology[edit]

Early universe with first stars[edit]