The Science of Existence – Life Begins

Life Begins

“The intimate relationship between the vital phenomena with chemistry and its laws makes the idea of spontaneous generation conceivable.” ~ English naturalist Charles Darwin

Life originating depends upon a confluence: contained (cellular) and controlled energetic reactions (metabolism), coupled with a scripted code for reproduction (replication). The only way such processes could be initiated and sustained would be if Nature favored their occurrence. Otherwise, the odds of life ever emerging are exceedingly long indeed.

“Life cannot be explained by our current laws of physics.” ~ American astrobiologist Sara Imari Walker

Origin on Earth

The parameters surrounding the origin of life on Earth are known. The geological conditions have been discerned, the requisite chemistry understood, the timing apprehended. Yet life’s onset retains mystery to its researchers. The origin of life on Earth bristles with puzzle and paradox.

What is not yet known is exactly how and where the ingredients that spawned life came together with the spark that started life’s engine and kept it running, though the best possible spots for origination have been identified. The enigma that lingers lies in life’s spontaneous generation: the force of coherence that led life to coalesce.

(Nature commonly exhibits self-organization and hidden order within apparent disorder. Chaotically tumultuous fluids spontaneously create stripes of coherent flow alternating with turbulent regions. Liquids self-organize into crystalline structures: a phenomenon known as disordered hyperuniformity. Photons in laser light self-organize into fractal patterns. Viewed as particles in a system (instead of linearly), prime numbers exhibit an ordered structure.)

What is known is that life on Earth began as soon as environmental conditions permitted. The mathematical probability of elements randomly assembling into a metabolizing, self-replicating life is negligible. Yet it repeatedly happened, with nary a chance that it was happenstance.

“All biological molecules used by living organisms are themselves synthesized by living organisms. The most important aspect of life’s emergence was the process by which inheritable improvements were selected from a population of variants. This required molecules or molecular assemblies that can reproduce under certain kinetic constraints and resulted in the development of a specific kind of stability (known as dynamic kinetic stability) that is associated with the dynamics of reproduction.” ~ French molecular biologist Robert Pascal


Continual bombardment by gigantic comets and asteroids abated 4.1 BYA. In the relative calm, life got its start; so marked the onset of the Archean eon.

Whether life initiated under even more hostile conditions remains an open question for lack of evidence. At most, 100 million years passed from the abating of constant bombardment to life emerging on Earth.

The cosmic assault seeded life on Earth. Meteorites commonly contain water, amino acids, and nucleobases, as well as chemicals that are rare or even nonexistent on Earth.

There have been numerous hypotheses as to where life arose. For a long time, the presumption was that life began on the surface, in primordial pools brimming with organic precursors. Hydrothermal environments on land existed early in Earth’s history.

One hoary hypothesis is that lightning literally brought the spark of life; or, less dramatically, radiation. This notion was promoted by Russian biochemist Alexander Oparin in his influential book The Origin of Life (1936).

Simplifying assumptions scientists made led to thinking that life mechanistically came from a chemical brew. After the 2nd World War, Western biology moved away from thinking of cells in physicochemical (physical chemistry) terms, and toward a reductionist molecular biology approach, entranced by the nascent field of genetics. From this came a life origination hypothesis termed RNA world.

The steamy surface schema for life’s origination is less likely than those scenarios that put life’s start deep in the ocean or beneath it, near hydrothermal vents, which provide a constant source of both energy and warmth to catalyze reactions, relatively safe from bombardment. There, prebiotic evolution could have been sustained over long periods without disruption or loss of the chemical reducing power necessary for nonbiological synthesis of organic compounds. While temperatures and pressures would have been extreme, life exists there today.

It is certain that life began under inhospitable conditions, at least on the surface. Early Earth had a highly volatile atmosphere, without molecular oxygen, but with toxic gases from erupting volcanoes, methane-rich air, incredible electrical storms, and unscreened ultraviolet rays from the Sun. Acid rain was common.

By 3.5 BYA, Earth’s seas were cool, with temperatures not unlike recent times. Areas of the deep oceans were heated by hydrothermal pipes that vented mantle heat.

The Moon orbited much closer to the Earth than it does now, raising huge tides.

Volcanoes spew pumice. As it is 90% porous, pumice floats. Pumice readily absorbs a variety of chemical compounds. In the unlikely event that life was born on the surface, its cradle may have been pumice.

 Cool Life

Whereas most scenarios of the environment in which life got its start are heated, it is conceivable that life was first cradled in ice. Nooks and crevices within ice could have provided a cozy, safe place for originating lively organic molecules. As ice forms, pure water crystallizes, while salts and other bits of debris accumulate in watery pockets. These impurities lower the water’s freezing point. Little pockets may remain unfrozen within an otherwise solid chunk.

RNA construction reactions can proceed under icy conditions, albeit slower than at ambient conditions. Reaction time is an insignificant factor compared to the environmental stability required for sustaining the necessary reactions.

“Ice, a simple medium likely to have been widespread on the early Earth, can provide a propitious environment for RNA self-replication and evolution. Ice not only promotes the activity of an RNA polymerase ribozyme but also protects it from hydrolytic degradation, enabling the synthesis of exceptionally long replication products.” ~ English molecular biologist Philipp Holliger et al

 Pond Spawn

“If you think the origin of life required fixed nitrogen, as many people do, then it’s tough to have the origin of life happen in the ocean. It’s much easier to have that happen in a pond.” ~Indian astrophysicist Sukrit Ranjan

With its tight binding, nitrogen provides an ideal chemical infrastructure for molecular architecture – but only in the right form, as nitrogenous oxides (NOx).

There are 2 ways that nitrogen may have got fixed to support abiogenesis. Nitrogen could have reacted with carbon dioxide bubbling out of hydrothermal vents in the deep ocean; otherwise, lightning.

“Lightning is like a really intense bomb going off. It produces enough energy that it breaks that triple bond in atmospheric nitrogen gas, creating nitrogenous oxides that can then rain down into water bodies.” ~ Sukrit Ranjan

Lightning crackling through the early atmosphere may have produced sufficient nitrogenous oxides to fuel abiogenesis in any body of water. The critical factor is getting NOx reacting with life-forming molecules.

Shallow ponds provide an ideal environment for prebiotic reactions. The shallower the pond, the less dilution of NOx, thereby giving life a better chance to take hold. By contrast, NOx falling from the sky into the ocean are more likely to be broken down by ultraviolet light near the surface or react with dissolved iron sloughed off from benthic oceanic rocks.


Life likely began with extremophiles: single-celled organisms living under harsh conditions but in a somewhat stable environment. There are several forms of extremophiles extant today, each varying by tolerance to extreme conditions.

Extremophile-first augers for life beginning among rocks, sheltered deep underground, where planetary impacts had little to no effect. Life originating under Earth’s surface or near deep-sea fumarolic vents would have meant that the earliest metabolisms were hydrogen and sulfur-based, and non-photoactive.

Hyperthermophilic microbes like it hot. The ribosomal RNA sequences in today’s heat-loving extremophiles place them among the most ancient ancestral lineages.

Even now, an estimated 2/3rds of the microbes on Earth lurk in a subterranean world, down many kilometers deep; far from sunlight, frigid temperatures, and lethal radiation on the surface. Subsea gribblies traverse the vent system that belches steaming water and dissolved minerals into the surrounding ocean.

The winds that sweep over the seas affect deep ocean currents. At life’s onset, the skies above may have had a long reach, touching life below, particularly life’s prospects for spreading.

Bacteria play an integral role in liberating energy from rocks. Under mid-ocean ridges, the mere presence of bacteria coaxes surrounding minerals, such as quartz, to release hydrogen gas, which the microbes feast on.


“The chemistry of life is distinguished by being both highly ordered and far from thermodynamic equilibrium.” ~ Dutch physicochemist Rogier Braakman & American physicochemist Eric Smith

The ingredients of life were prescribed by chemistry, both by abundance and ability to well serve essential needs. It is likely that life everywhere in cosmos relies upon the same chemical players. Life is bound to be carbon based, as its flexibility is unparalleled, and its existence ubiquitous: the 4th most common element in the universe.

“Life as we know it depends absolutely on solution chemistry in a highly unusual solvent (water), a complex range of chemicals based on a few simple small atoms, and relatively small values of free energy.” ~ Andrew Clarke

Water is essential to life. Its unique properties ensure its necessity. Further, its constituents – hydrogen and oxygen – are readily reactive.

Conversely, the steadiness of nitrogen makes it ideal for structural stability. While carbon is the epitome of freewheeling, nitrogen provides a sturdy infrastructure.


Phosphorylation attaches a phosphoryl group to a molecule. A phosphoryl group is a randy radical of phosphorous and oxygen (P+O32–). Phosphorylation and its counterpart, dephosphorylation, are instrumental in numerous biological reactions essential to living.

“A phosphorylation chemistry could have given rise, all in the same place, to oligonucleotides, oligopeptides, and the cell-like structures to enclose them. That in turn would have allowed other chemistries that were not possible before, potentially leading to the first simple, cell-based living entities.” ~ Indian organic chemist Ramanarayanan Krishnamurthy

(Oligonucleotides are short strands of nucleotides, the chemical core ingredient for genetics. Oligopeptides are short chains of amino acids, which, when congregated coherently, comprise proteins.)

A phosphorylating agent is necessary to getting crucial biological reactions going. Diamidophosphate (DAP) was likely the compound which helped chemically kickstart life.

“With DAP and water, these 3 important classes of pre-biological molecules could come together and be transformed, creating the opportunity for them to interact together. It reminds me of the Fairy Godmother in Cinderella, who waves a wand and ‘poof,’ ‘poof,’ ‘poof,’ everything simple is transformed into something more complex and interesting.” ~ Ramanarayanan Krishnamurthy

Numerous phosphorus-nitrogen compounds have been found in interstellar gas and dust. DAP is a simple radical, and so is likely to have been tucked into early Earth minerals.


Functionally, there are 2 requirements for life: 1) elements requiring modest energy to cohere reactive substrates that can energetically perpetuate for metabolism, and 2) readily reproducible compounds for replication.

As the organic building blocks of life are readily built in space, it seems inevitable life would revolve around nucleobases and amino acids, as they demonstrate flexible complexity at a low energy cost.

The crust under the ocean is a rich reservoir of all possible ingredients for life, including rare earth elements. There exists the most extensive, concentrated library of chemical possibilities.

Hydrogen, a randy reductant, is a rich potential energy source. Hydrogen-consuming bacteria are known, though now largely confined to deep-sea hydrothermal vents where H2 is still readily available.

Thermal vents on the ocean floor and subsea are places where life originating would have been most amenable. The structural similarity between the minerals precipitated at hydrothermal vents and the most ancient enzymes shows that only a petite push of coherence would be sufficient for life to take hold.

Geologic recycling of the Earth’s crust leave scant evidence of atmospheric conditions during the first 650 million years of the planet’s history, particularly regarding which form of carbon predominated early on: CO (carbon monoxide), CO2 (carbon dioxide), or CH4 (methane). By 4.1 bya, when life originated on Earth, CO2 was the predominant atmospheric gas.

Whereas reactions in carbon dioxide are low-yield and of limited variety, reactions in methane yield abundant diverse organic compounds. This difference in energy potential was a significant factor in where early life formed.

The presumed requisite conditions for the emergence of life include water and a sufficiently stable environment. Those conditions would have been largely met near Earth’s surface by aerosols, volcanic and interplanetary dust particles, and organic films; and at depth by hydrothermal minerals, chemical precipitates, and vesicular structures of mineral and organic compounds.

Likewise, the necessary energy sources for organic compound production were available via sunlight on the surface, or in the ocean or underneath it by chemical disequilibria between hydrothermal fluids and seawater.

The reducing power of oceanic, dissolved iron was available in both environments. Iron plays a significant role in cellular respiration.


The story of life is suffused with sugar, which readily provides energy release in reactions. Structurally, ribose, a simple monosaccharide, forms part of the backbone of DNA & RNA molecules.

Ribose rides on meteorites. The most elemental sugars of life, with 2 to 3 carbon units, drift through space in gaseous molecular clouds.

Sugars are superbly flexible compounds, capable of myriad configurations. The critical requirements for the sugars of life were ease of construction and stability.


“Whenever a new planetary system is made, these kinds of things should go on. This potential to make organics and then dump them on the surfaces of any planet is probably a universal process.” ~ American astrophysicist Scott Sandford

Abiogenesis is the study of how organic life arises from inorganic matter.

For life to begin and sustain, 3 means have to arise: 1) self-contained cells (containment); 2) usable energy to produce proteins (metabolism); and 3) replication (reproduction). Any decent hypothesis of life’s origin must account for all these facets.

The requirements for life’s emergence seem to present a chicken-or-egg problem of which came first: metabolism or replication. While scientific consensus has yet to comfortably square that circle, the answer is fairly certain.

Inorganic energy provided the impetus to put together the organic building blocks that resulted in biosynthesis and nucleobase production. The complexity of both are equivalent, and both are needed.

Sequence is not the issue. The trickiest aspect is not of molecular combinations. Instead, it is the synchrony required for all the ingredients to functionally cohere; for metabolic energy to consistently be applied within a cell where and how required to sustain life, and for RNA to become the basis for reliable memory in protein production.

To simply say that “life happens,” or that energetic pathways are dictated by economy, misses the big picture as well as the myriad of details.

“No matter how minute an organism may be, or how elementary it may appear at first glance, it is nevertheless infinitely more complex than a simple solution of organic substances.” ~ Alexander Oparin

Aside from the biochemical substrates and processes, there must be a natural force of coherence that begets life. Finding favor in physics and chemistry is, by itself, inadequate.

“The underlying problem is complexity. Although we have no idea of the minimal complexity of a living organism, it is likely to be very high. It could be that some sort of complexifying principle operates in Nature, serving to drive a chaotic mix of chemicals on a fast track to a primitive microbe.” ~ Paul Davies

Above all, the macromolecules that make for the principle players in cellular life must stably self-assemble yet have the ready flexibility for different conformations to act as information storage. (A misstatement by abbreviation is made here. Matter may store information, but matter cannot use information. Information is purely conceptual, and so immaterial. As the show called Nature is made of matter, essential concepts such as information are portrayed materially – whence brains and accoutrements which comprise an ‘intelligence’ physiology. Do not confuse appearance with actuality–the very mistake matterist scientists blithely make. Information implies mentation – a mind at work.) And all this must be achievable with a mere modicum of energy. These requirements highlight how even the simplest life itself possesses an inherent sophistication that places it well beyond random chance.

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“Just as many people have been speaking prose all their lives without realizing it, many organic chemists of the 19th and the first half of the 20th century were prebiotic chemists without realizing it.” ~ English chemist Leslie Orgel

Modern organic chemistry began with German chemist Friedrich Wöhler accidentally synthesizing urea in 1828. Russian chemist Alexander Butlerov discovered the formose reaction in 1861, forming sugars from formaldehyde. This remains a cornerstone of prebiotic chemistry. These and other early experiments into synthesizing biochemicals were oriented toward practical applications, without interest in the origin of life.

The first to have such an interest was American chemist Stanley Miller, who in 1953 reduced amino acids from a brew of heated CH4, NH3, H2O, and H2 subjected to an electrical discharge. In selecting his prebiotic compounds, Miller aimed to recreate the chemical conditions of early Earth.

Miller’s assumptions were mistaken, as were many of the surmises that followed in his wake. Miller began what became a continuing quest by would-be Dr. Frankensteins to create life in a flask.

“Since we know very little about the availability of starting materials on the primitive Earth or about the physical conditions at the site where life began, it is often difficult to decide whether or not a synthesis is plausibly prebiotic. Not surprisingly, claims of the type “my synthesis is more prebiotic than yours” are common.” ~ Leslie Orgel

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From the 1960s, the idea of abiogenesis via spontaneously assembling proteins was gradually displaced by hypotheses emphasizing replication: life’s onset via RNA. This notion first developed when life was presumed to emerge from primordial pools, with RNA emerging by dint of fortuitous biochemical combination. Though the focus shifted, the axiom of life beginning via chemical elixir remained.

Another story of life’s origin starts with fool’s gold in the hydrothermal deep, arguing metabolism-first. There are similar scenarios with slightly different emphases.

Then there is the possibility that life on Earth came from outer space: a concept called panspermia. Demonstrating the natural force of coherence, organic molecules readily form where chemistry instructs they should not. One panspermia scenario has life on Mars coming here.

RNA World

“RNA is the Swiss army knife of molecules – it can have so many different functions.” ~ American microbiologist Michael McManus

An early, formulaic school of thought to life’s start was a gene-first, RNA origination, with ribozymes as the 1st actors on the stage. A ribozyme is an RNA-based enzyme.

The RNA-world hypothesis was first propounded by American biochemist Walter Gilbert in 1986, though the concept of RNA as the primordial molecule of life had been kicked around at least since 1962, by American biologist Alexander Rich. This scenario still has many researchers who are interested in discerning how RNA was able to self-assemble into a functional form and self-replicate.

“The idea that RNA was “invented” by a simpler genetic system is now a popular one, but no convincing precursor system has been described. The idea that some simpler genetic system preceded RNA opens Pandora’s box. There is very little to constrain the type of molecule involved or the environment in which it first functioned. There are numerous double-stranded structures with backbones very different from that of RNA but held together by base pairing.” ~ Leslie Orgel

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Catalysts function by lowering the energy necessary for chemical reactions, and thus increase the frequency of such reactions. Nucleobases, the basic building blocks for genetic storage (DNA and RNA), assemble spontaneously given the ingredients and proper setting.

In early RNA-world envisionings, a primordial soup that was half-sugar, half-base mixture was catalyzed with phosphate by ultraviolet light. The results of similar combinations were nucleotides of different types which zipped together to form RNA molecules. These RNA molecules, by their stable chemical structures, carried information that afforded replication. Thus, RNA acted as both a catalyst and template for self-replication.

“We are still too far removed from a comprehensive knowledge of the living organism to even dream of attempting their chemical synthesis.” ~ Alexander Oparin

Construction of usable RNA is not simple. Researchers have had difficulty reproducing the lead actor.

“Basically, we took half a base, added that to half a sugar, added the other piece of base, and so on. The key turned out to be the order that the ingredients are added and the way you put them together – like making a soufflé.” ~ English biochemist John Sutherland

The chemistry on early Earth was different than today. Meteorites seeded the planet with soluble, reactive phosphorus that could be incorporated into prebiotic molecules. In its current form on the planet, phosphorus is relatively insoluble and nonreactive.

 Viral Analogy

RNA viruses may seem something of a model for the RNA-world scenario, but the analogy is inapt, because a virus can’t replicate itself; the very thing that the RNA-world scenario aims to explain.

Retroviruses pack a tiny genome encoded in RNA. A retrovirus hijacks a host cell for replication, copying its RNA into the cell’s DNA using a reverse transcriptase enzyme. The host then duplicates, with the retrovirus genetic instructions intact.

A virus works from DNA for copying itself but bundles itself up for inheritance using RNA to transmit the hereditary data. Thus, today’s viruses are much too sophisticated, and yet not sufficiently self-sustaining, to aid in understanding how RNA replication arose.

A less obvious disadvantage to RNA life becomes apparent by comparing RNA to DNA. DNA is a richer storage medium. A retrovirus is about as complex as an RNA-encoded entity can be.


“The earliest forms of life may have arisen from a different set of nucleobases than those found in modern life.” ~ Korean American chemist Seohyun Kim

RNA encoding produces proteins, which are the workhorse molecules of life. RNA represents the language of life.

Given decent thermal conditions, organic molecules naturally form. There is a physicochemical affinity: the physics of chemistry favor the coherence of compounds that form some of the basic building blocks of life.

RNA and its cognate proteins extend the harmony. The density profiles of different nucleobases in transcribing RNA closely resemble the profiles of amino-acid affinity for these same nucleobases in the proteins they code for.

The genetic code, as embodied in RNA, is an evolutionary consequence of the direct binding propensities of amino acids for appropriate nucleobases. Nucleobases and their resultant products – amino acids – are affine. There is a molecular conformity that runs between the amino acids that comprise proteins and the nucleobases that make up RNA.


“Making RNA requires both purine and pyrimidine nucleotides to be simultaneously available.” ~ English organic chemist Matthew Powner

RNA and DNA are composed of 2 classes of organic compounds: purines and pyrimidines. Both can be assembled on the same sugar scaffold (aldehyde) to form the ribonucleotides used to construct RNA. Aldehyde is a simple sugar thought to have been present on early Earth.

“Nucleobase construction on a preformed sugar moiety would provide the simplest strategy for divergent monomer synthesis.” ~ English organic chemist Shaun Stairs

For RNA to form, both purines and pyrimidines must be present. This requires simultaneous synthesis of these 2 different compound classes.

A single chemical precursor – an 8-oxo-purine – may have been able to divergently generate both purine and pyrimidine ribonucleotides.

“8-oxo-purine ribonucleotides may have played a key role in primordial nucleic acids.” ~ Shaun Stairs

There is a stumbling block to this possibility. The resultant purine compounds have an oxygen atom bound to a carbon atom in the base, rather than a hydrogen atom as in the RNA purines today. There seems no simple way to exchange the wayward oxygen atom for hydrogen.

Once formed, purine and pyrimidine nucleotides bind to one another through specific molecular interactions that provide a mechanism which may copy and transfer information at the molecular level, given a guiding force of coherence for this process.

The unconventional oxygenated purines created via a single precursor might have been unable to form RNA analogs with the properties needed to spark life. This leave the precursor question unanswered, and as well how RNA evolved into its genic role.


RNA is far less stable than DNA: lasting, on average, only 2 minutes before degrading. But that is exactly why RNA still plays the key role in catalyzing biochemical reactions, leaving more stable DNA to heavy-lifting heredity. Unlike DNA, RNA can adopt many different molecular configurations which are readily rendered interactive.

An outstanding issue in the origination of RNA is how it became compartmentalized: packed tight enough to stay together and evolve into its functional role as an organic memory store. Various polymers are capable of compacting RNA. Which actor played that part in RNA’s meaningful origination is unknown.

Once RNA is concentrated, its reaction rate ratchets up. RNA compacted into cellular form is 70 times more reactive than when unpackaged.

RNA nominally comes coiled, while DNA naturally forms a much more complex double helix. That is not the entire gospel of RNA vis-à-vis DNA.

RNA can also be folded onto itself to form complex secondary shapes that afford a variety of functions. Some viruses employ double-stranded RNA.

RNA does not approach the structural versatility of DNA. That DNA macromolecules can take a vast variety of shapes is a major factor in its sophistication for information storage.

For all that, swarms of RNAs mixing through interconnection could have led to successful cooperative ventures that sustained nascent life. Mixtures of RNA fragments do tend to self-assemble into self-replicating ribozymes, spontaneously forming cooperative catalytic cycles and networks. While the structural differences of DNA & RNA are considerable, there are only 2 tiny chemical discrepancies between the two.

1st, remove a single oxygen atom from ribonucleic acid (RNA) to render deoxyribonucleic acid (DNA). Reactive free-radical intermediaries found in hydrothermal vents present a ready catalyst for this transition.

The RNA to DNA transition requires a single enzyme: reverse transcriptase; the very enzyme that today’s retroviruses pack in their tiny toolkit (HIV is exemplary).

While the chemical transition from RNA to DNA is easy enough, the structural transform is not so simple. As Watson and Crick observed in 1953, a double-helix structure from ribose sugar instead of deoxyribose would have been “probably impossible, as the extra oxygen atom would make too close a van der Waals contact.”

The 2nd chemical difference comes in adding a methyl group (CH3) to RNA uracil to get DNA’s thymine. Methyl groups are reactive free-radical splinters of methane gas and are plentiful in hydrothermal vents. Methylation plays a significant role in epigenetics: regulating employment of DNA codes.

The relative simplicity and efficiency of RNA versus DNA suggests that RNA preceded DNA, but nothing substantiates this supposition.

A lot of questions lack answers in the RNA-world scenario, including the origination of metabolism.

RNA itself evolved from a humble start via self-assembly of organic compounds. The earliest ribozymes were structurally simple; a step away from peptides.

Varieties arose, but with similar structures. Complexity evolved later.

The structural dynamics of RNA are understood. But in considering replication, the large issues loom, still unanswered by scientific inquiry: how did RNA take on the role of first working biological memory, and by that rememberability for heredity?

It is a large leap from a variety of RNA able to store information to actually acting as a script for protein production. No doubt a coherent force enabled this operational.

Pyrite Life

The iron-sulfur world experiments are aimed at long reaction cascades and catalytic feedback (metabolism) from the start. The maxim of the iron-sulfur world theory should therefore be “order out of order out of order.” ~ Günter Wächtershäuser

German organic chemist Günter Wächtershäuser developed the iron-sulfur world theory in the late 1980s, arguing that metabolism arose as a prerequisite to replication. Wächtershäuser and others contend that organic compounds emerged on the surface of pyrite in seafloor hydrothermal vents.

Pyrite is a mineral comprising iron and sulfur (FeS2), called fool’s gold because prospectors sometimes mistook its glimmer for gold. Pyrite is both hoary and ubiquitous. The mineral is found everywhere, even in the oldest sedimentary rocks. The chimneys of hydrothermal vents largely consist of pyrite.

While its location may appear fortuitous, Wächtershäuser’s construction was not only for geochemical reasons. On the bottom line is energy.

Pyrite is synthesized from hydrogen sulfide (H2S) and an iron salt (FeS) – abundant ingredients on primordial Earth.

H2S + FeS → FeS2 + H2 + energy

Besides releasing chemical energy from which autotrophic life may have originated, hydrogen released in the production of pyrite provides the reducing power needed to synthesize organic compounds from carbon dioxide (CO2).

Wächtershäuser developed a compelling story, but the devils in the details resulted in numerous objections by others in the field: complaints about unanswered questions concerning critical facets that are fundamental biochemical mechanisms.

Foremost, Wächtershäuser’s model requires a bootstrap technique to get from fool’s gold to life. That bootstrap is some chemical scaffolding acting as a protocell; a concept advanced by Scottish organic chemist Graham Cairns-Smith. Given a plausible scenario for a protocell, Wächtershäuser’s pyrite-pulled chemoautotrophic model appears redeemed.


“The origin of the cell is perhaps the most obscure point in the whole study of the evolution of organisms.” ~ Alexander Oparin

Some form of containment – a protocell – is essential to any scenario explaining life’s onset.

Cairns-Smith recognized that organic compounds were much too complex to be synthesized under prebiotic conditions. His proposed solution involved a 2-step to life: a literal scaffold of chemical reactions that afforded a more complex set of reactions that begat the origin of life’s molecules. Once life was on its way, like a building constructed, the scaffold that acted as the original cellular container was removed from the scene, not leaving a trace.

To Cairn-Smith and other scientists inclined to metabolism-first, the scaffold 2-step solves the complexity problem.

Hydrothermal vents may have fostered mineral cells: the necessary encapsulation for relatively stable RNA to emerge. There are other possibilities.

van der Waals interaction, an intermolecular force, can assist binding macromolecules into membranes which lead to protocells. Water droplets are a simple example of such vesicles.

Fatty acids spontaneously form double-layered spheres, much like the double-layered membrane of living cells. These protocells incorporate additional fatty acids, and spontaneously divide.

The chemistry of RNA replication works in fatty acid vesicles only if citrate is present. Otherwise, the high concentration of magnesium required for RNA copying destroys such protocells by causing fatty acid precipitation: forcing the fatty acids into a lumpy, useless mass.

Citrate is found in many modern organisms, but its abundance 4 bya is unknown. Similar molecules may have worked as well.

In 2016, physicists discovered that energetically active, chemical-laden droplets may grow through internal reactions and spontaneously divide as shape instabilities trigger division into 2 smaller daughters. Waste products may be discarded during division.

“Chemically active droplets can exhibit cycles of growth and division that resemble the proliferation of living cells.” ~ American physicist David Zwicker et al

The study was theoretical, but illustrative. With the right metabolism in place, protocell reproduction looks plausible.


Most bacteria have cell walls, but many can switch to a wall-free existence. This is termed an L-form structure, in reference to the chirality involved.

The most striking change associated with the L-form state is the way bacteria replicate. Instead of precise cell division, a bacterium simply bulges on one side and pinches off a daughter cell: a process termed blebbing.

Bacteria accomplish L-form by relying on fatty acids to hold their cells together, allowing them a shape fluidity they would lack with a cell wall.


In some ways, self-organized cellular containment seems the simplest facet in life’s origination, as numerous mechanisms exist, each with their own plausibility, and a naturally occurring combination of techniques readily conceivable. As L-form bacteria demonstrate, a protocell using fatty acids may have sufficed.

The importance of selectively permeable membranes to cellular life cannot be understated. Despite seeming simplicity as a container, the cell membrane acts as both protection and conduit; a functional wile considering the antithetical natures of its twin purposes.

Biomolecular Evolution

“All living organisms have a metabolism, a set of life-sustaining chemical transformations that provide the energy and matter needed for the functions of the cell. These metabolic transformations occurred very early in life. Organisms probably replaced chemical reactions already going on in the planet and internalized them into cells through development of enzymatic activities.” ~ Argentinian biochemist Gustavo Caetano-Anollés

Using an extensive genomic database of life, Turkish geneticist Ibrahim Koç and Argentinian biochemist Gustavo Caetano-Anollés studied the genetic evolution of molecular functions for all realms of life.

“The best way to understand an organism is through its functions. You can take an entire genome that represents an organism and visualize it through the collection of functionalities of its genes. The study of these ‘functionomes’ tells us what genes do, instead of focusing on their names and locations.” ~ Gustavo Caetano-Anollés

Koç and Caetano-Anollés figured that the genes for the most ancient functions would be shared by all organisms and exist in relatively large numbers compared to later-evolved functionality. They found metabolism and cell cohesion (binding) to be positively primordial.

“It is logical that these two functions started very early, because molecules first needed to generate energy through metabolism and had to interact with other molecules through binding.” ~ Gustavo Caetano-Anollés

The next major advance involved functions that made macromolecule production possible, which is likely when RNA entered the picture. This coincided with the trend toward specialization. The first biomolecules were multi-purpose, becoming functionally tailored through evolution.

“Ancient molecules served multiple functions and showed broad specificity. These molecular functions diversified into more specific and efficient counterparts during evolution, leading to the extraordinarily diverse and specific functions that exist in the modern biological world. That ancient enzymes were generalist multi-tasking proteins has been borne out thanks to protein resurrection experiments that use phylogenetic reconstruction to design ancestral sequences and synthesize the corresponding proteins.” ~ Ibrahim Koç & Gustavo Caetano-Anollés

Water World

“Life takes advantage of unbalanced states on the planet, which may have been the case billions of years ago at the alkaline hydrothermal vents.” ~ American geochemist Michael Russell

Derivative scenarios emerged after Wächtershäuser’s work, relying upon similar chemistry and events. One shift was the venue. Scalding hot acidic vents – “black smokers” – were originally considered the place where pyrite life emerged, owing to the highly energetic environment.

“There is a lot of CO2 dissolved in the water, which could provide the carbon that the chemistry of living organisms is based on. And there is plenty of energy, because the water is hot and turbulent. These vents also have the chemical properties that encourage molecules to recombine into those usually associated with living organisms.” ~ English chemist Nora de Leeuw

More recent work has focused on hydrogen-saturated alkaline water meeting acidic, relatively CO2-rich oceanic water at gentler, cooler underwater vents than black smokers.

In an inorganically-formed protocell pocket, this meeting – of CO2 from the ocean and H2 & CH4 from a vent – would create a proton gradient and ion pump, providing the energy for biochemical synthesis.

“Life lives off proton gradients and the transfer of electrons.” ~ American geochemist Laurie Barge

Naturally-occurring minerals in vents that would have provided a suitable substrate include pyrite (FeS2), greigite (Fe3S4), and fougèrite (Fe2+4 Fe3+2(OH)12[CO3]·3H2O).

The rare metal molybdenum, which is found in enzymes, is considered instrumental, as it transfers 2 electrons at a time rather than the usual 1; particularly useful in driving key chemical reactions.

Through erosion, rocks in deep-sea thermal vents contain labyrinths of tiny, thin-walled pores which could have acted as protocell containment, producing a proton gradient and easy electron transfer, with a concentration of organic ingredients from which complex proteins and RNA could emerge.

A cell membrane may have evolved via a simple protein that employs the influx of protons to pump sodium ions out of the protocell before largely sealing up, thus facilitating the requisite self-contained environment while sustaining limited permeability.

The earliest Ediacaran animals evolved in the deep ocean, which had a more stable environment than shallow waters. It seems likely that this scenario also applied to the origin of life. Extremophile archaea illustrate the possibility of life emerging in this watery world.

“Their biochemistry seems to emerge seamlessly from the conditions in vents.” ~ English biochemist Nick Lane



“Archaea weren’t even discovered until 1977, and were thought to be rare and unimportant, but we are beginning to realize that they not only are abundant, but they have roles that have not fully been appreciated.” ~ American oceanographer Andrew Thurber

Archaea are among the earliest life. Archaea are found most everywhere: in the seas and soil, the marshlands and the swamp known as the human colon. The methane of marsh gas, and of ruminant and human flatulence, are atmospheric contributions from resident methanogens, archaea all.

The archaea in oceanic plankton make them one of the most abundant organisms, comprising 20% of the Earth’s biomass. As planetary movers and shakers, at least by numbers, archaea have long played important roles in the carbon and nitrogen cycles of the biosphere.

Both bacteria and archaea reproduce asexually, by binary fission, fragmentation, or budding; but, unlike bacteria and some eukaryotes, no known archaea produce spores. Spores are offspring that can ride out hard times.

Many archaea are extremophiles, with exotic chemical processes within their single cell that fend off disruption by the habitat. When the going gets too tough, archaea form tough protective shells, stop their life processes, and wait it out for better days. An archaean itself becomes like a spore. Of all life, archaea are the ultimate survivors.


“The basic building blocks of life can be assembled anywhere in the solar system and perhaps beyond. The catch is that these building blocks need the right conditions in order for life to flourish.” ~ English geologist Zita Martins

2,500 years ago, Greek philosopher and cosmologist Anaxagoras proposed panspermia (Greek for “all seeds”): life delivered to Earth from space. The notion persisted for a very long time despite scant evidence for it.

As it turns out, microbes riding in comets or meteorites could have seeded the solar system with life. Conversely, terrestrial microorganisms from Earth could have been launched into space via bolide impacts that ejected rocks as far away as Saturn.

“The flux of organic matter to Earth via comets and asteroids during periods of heavy bombardment may have been as high as 10 trillion kilograms per year, delivering up to several orders of magnitude greater mass of organics than what likely pre-existed on the planet.” ~ American chemist Nir Goldman

Organic material makes its way through the cosmos on a regular basis. DNA can withstand the rigors of space. As life originates whenever and wherever it can, panspermia is entirely possible.

“An influx of dust has acted as a continuous rainfall of little reaction vessels containing both the water and organics needed for the eventual origin of life on Earth. Continuous, co-delivery of water and organics intimately intermixed.” ~ American cosmochemist Hope Ishii

 Life from Mars

“The evidence seems to be building that we are actually all Martians; that life started on Mars and came to Earth on a rock.” ~ American chemist Steven Benner

In the early 20th century, American astronomer Percival Lowell, seeing what he termed “non-natural features” on Mars, speculated that Martians had an advanced civilization, replete with crop irrigation via canals drawing water from the planet’s poles.

The molecules that combine to create genetic material may have needed more than whatever primordial prebiotic soup might have been cooked up on Earth 4 BYA.

Adding energy to organic compounds does not generate RNA. It merely makes tar. Rendering RNA requires atoms to be coaxed into shape by templating atoms on the surfaces of crystalline minerals.

The most effective minerals for patterning RNA would have dissolved in the oceans of early Earth, at a time when the planet was probably enveloped by ocean. Mars still has extensive, deep reservoirs of water, little of which stays on the surface for long.

Further, while water is essential to life as we know it, it is also corrosive to biopolymers such as RNA. The long strands needed for information storage can’t form in water.

The best RNA templating minerals are boron and molybdenum. Both are water-soluble.

Oxygenating boron births a borate (BO3). Add oxygen to molybdenum to make a molybdate (MoO4 2 and variations).

Borate minerals prevent the organic building blocks of life from devolving into tar. Molybdate can bond to the carbohydrates that borate stabilizes and catalyze a rearrangement into ribose: the R in RNA.

Besides an uncongenial aquatic surface, for lack of free atmospheric oxygen, both borate and molybdate would have been practically nonexistent on early Earth at the time life arose. In contrast, 4 BYA, the atmosphere of Mars had much more oxygen than Earth.

“The early history of Mars seems to have been very similar to that of Earth, especially with respect to the ancient hydrosphere.” ~ American geomicrobiologist Nora Noffke

Life may have evolved on Mars. From around 4.5–3.5 BYA, Mars was habitable, at least by hardy microorganisms. Even now, Earth methanogens could survive there.

While organic compounds were produced on Mars, there is no extant evidence that life ever emerged. Exploration of Mars has been slight; we know little.

The scenario of life coming to Earth from Mars seems a simple 2-step. A meteorite knocked a Martian rock with stowaway microbes aboard into space. The Martian transport becomes a meteorite that splashes down on Earth.

It is possible that a violent impact could eject material without generating so much heat that it would destroy a microbial passenger, especially if the traveler were shielded in the interior, not on the surface; likewise, in entering Earth’s atmosphere. Life nestled inside a meteorite would have a better chance of surviving the searing heat in coming down.

If Martian microbes hitched a ride on a dust particle, blistering heat may have been avoided by a gentle deceleration. But then there is the issue of travel time.

Most earthbound bits spend a long time in space. One Martian meteorite traveled for 15 million years before landing on Earth. But 1 out of 10 million objects make the journey from Mars to Earth in less than a year. This would minimize exposure to ionizing interplanetary radiation.

That said, some microbes that exist now are highly resistant to radiation, as well as being able to handle the jostle involved in projectile space travel.

As with heat, the best place to not be radiated would be inside a sizable rock. Such comfortable snuggling would also help preserve a habitat.

But then, suspended animation is possible. And pebbles are more likely to make a quick trip than boulders.

The timing of life traveling from Mars to Earth would have to have been fortuitous. Mars had a relatively oxygen-rich atmosphere 4 BYA, but its magnetic field disappeared around that time, allowing the solar wind to strip the atmosphere away.


While life from Mars is literally far-fetched, abiogenesis anywhere is itself a fantastic story. All scenarios of life’s emergence are stories of staggering complexity with intricately layered plotlines and distinct dependencies.

For one, the cellular containment issue in the pyrite-life scenario (scaffolding) also affects the plausibility of the RNA-world hypothesis, which relies heavily on catalytic peptides for protocells to form.

Like different sides of the same coin, protein-like enzymes play an analogous role in gene-first models to the ribozymes that play a central role in several metabolism-before-replication scenarios.

Data at the Dawn of Life

“Life may be characterized by its distinctive and active use of information, thus providing a roadmap to identify rigorous criteria for the emergence of life. This is in sharp contrast to a century of thought in which the transition to life has been cast as a problem of chemistry, with the goal of identifying a plausible reaction pathway from chemical mixtures to a living entity.” ~ Paul Davies

Just as physics has its information adherents, so too those interested in the origin of life. However insubstantial, it is a refreshing perspective in emphasizing functional processes over reactions.

“Functionality is not a local property of a molecule. For example, the functionality of expressed RNA and protein sequences is clearly context-dependent— only an exceedingly small subset of these molecules is causally efficacious (i.e. meaningful) in the larger biochemical network of a cell. The most important features of biological information (i.e. functionality) are decisively nonlocal, subject to informational control and feedback, so that the dynamical rules will generally change with time in a manner that is both a function of the current state and the history of the organism.” ~ American astrobiologist Sarah Imari Walker & Paul Davies

Characterizing life as an intelligent information processor sidesteps mechanics and focuses solely on the overarching issue of how life cohered. In this, the emphasis is decidedly mind over matter.

“The key distinction between the origin of life and other ’emergent’ transitions is the onset of distributed information control, enabling context-dependent causation, where an abstract and non-physical systemic entity (algorithmic information) effectively becomes a causal agent capable of manipulating its material substrate.” ~ Sarah Imari Walker & Paul Davies

Life Rising

“The species we see today are but the smallest part of what blind destiny has produced.” ~ French mathematician and philosopher Pierre Louis Maupertuis

The transition from RNA to DNA fortified life, affording survival and reproduction under exceedingly harsh conditions. DNA likely evolved independently many times by the wiliest mavens of genetic manipulation: viruses.

“RNA viruses invented DNA to protect their genomes.” ~ French molecular biologist Patrick Forterre

Archaea and bacteria are primitive DNA replicators which may have evolved under somewhat similar circumstances. They share the same DNA coding. Many details of their protein syntheses are the same. But the mechanisms of DNA replication differ greatly between archaea and bacteria. Further, viruses and plasmids have their own unique DNA replication systems.

Some viruses employ DNA; others RNA. While DNA is the universal coding schema of known life, replication systems are strikingly diverse.

“The modern-type system for double-stranded DNA replication likely evolved independently in the bacterial and archaeal/eukaryotic lineages.” ~ Russian biologist Eugene Koonin

DNA replication is not the only distinction between archaea and bacteria: their cell membranes and walls are quite distinct. These fundamental differences indicate independent origination.

Microbes Everywhere

“There is a commonality of colonisation of the subsurface of the planet.” ~ Canadian biochemist Barbara Sherwood Lollar

19 distinct microbes have been found that are distributed throughout the world, tucked deep within Earth’s crust.

“It is easy to understand how birds and fish might be similar oceans apart. But it challenges the imagination to think of nearly identical microbes 16,000 kilometers apart in the cracks of hard rock.” ~ American biogeologist Matthew Schrenk

Selfsame microorganisms live in a subterranean South African gold deposit and in frozen methane pockets beneath the Indonesian sea floor.


Evidence indicates that radically distinct species originated on Earth at different times in widely dispersed places. Yet they all share the same genetic schema; a most intriguing riddle of life’s rising.

Common Ancestor

“Universal common ancestry is a central pillar of modern evolutionary theory. A universal common ancestor is at least 102,860 times more probable than having multiple ancestors.”  ~ American biochemist Douglas Theobald

In the 1740s, Pierre Maupertuis made the first known suggestion that all of life had a common ancestor.

The common ancestor hypothesis necessitates one of 3 scenarios: 1) a prodigal life originated in 1 place, from which it spread to every location throughout the world; 2) the same life originated in multiple places; or 3) somehow life homogenized.

The notion of prodigal life (1) is logistically improbable, though conceivable. A population can widely diffuse geographically over hundreds of millions of years. Viruses, which form a worldwide community, are exemplary. But the differences between archaea and bacteria are not accounted for in this scenario.

Duplicative origination (2) is also conceivable but implies that life naturally coheres to a singular form; hence, the ready duplication of the same life. This contradicts Nature’s proclivity for diversity: a fact prodigiously proven. More specifically, duplicative origination is belied by there being 2 quite different cell types – archaea and bacteria – in the most primordial life.

That leaves 1 possibility. American microbiologist Carl Woese proposed in 1998 that there was no universal common ancestor, but that homogenization occurred among ancient communities of cellular organisms via genetic transfer.

“The ancestor cannot have been a particular organism, a single organismal lineage. It was communal, a loosely knit, diverse conglomeration of primitive cells that evolved as a unit.” ~ Carl Woese

Archaea and bacteria originated independently, but both ended up with DNA as their genetic coding regime.

“The very essence of the virus is its fundamental entanglement with the genetic and metabolic machinery of the host.” ~ American molecular biologist Joshua Lederberg

Only 1 agent had the means for worldwide DNA delivery: viruses. Comprising a worldwide community, viruses either invented DNA or appreciated the innovation and then infected other archaic life with it. Viruses’ ability to travel light and work their way into suitable hosts shows sufficient cleverness to bring off such a coup.

“Viruses are the creative front of biology, where things get figured out, and they always have been.” ~ American virologist Luis Villarreal

Both archaea and bacteria sought to rid themselves of RNA viruses early on. Archaea migrated to warm biomes and then even took to extreme environments. Bacteria designed a thicker murein cell wall that likely blocked many ancient viral families. These developments spurred viral genic innovation: the more robust DNA, which it then spread.

“Viruses have contributed enormously to the communication between cells, and to the appearance of multicellular organisms on Earth.” ~ French virologist Felix Rey

As a regular work practice, viruses insert genes into their hosts. 8% of the human genome has a viral origin.

Eukaryotic intercellular communication and organ development come courtesy of genetic information provided by viruses. Animals would have never evolved beyond blobs of cells without viral innovations. In putting all organisms on the same genetic program, viruses painted a facile picture of life having a universal common ancestor.

It was self-interest that drove viruses to unify life to a standard genetic organization. Modified genetic coding systems have independently evolved at least 34 times. Viruses have not figured out how to infect organisms with these peculiar regimes. It may be that these alternate genetic systems arose to evade viruses. Having a standard genic schema gives viruses an edge in maintaining the lifestyle to which they have become accustomed.

“Viruses are embedded in the fabric of life.” ~ Gustavo Caetano-Anollés