The Signature Fingerprint of the First Life on Earth
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I have been researching the biocosmological basis of the origin of life on Earth since the 1970s. This approach has recently become supported by several new discoveries, which are coming ever closer to resolving this founding enigma in surprising ways which are challenging to our deepest ideas of who and what we are and where we came from.
Fig 1: Biocosmological thesis: Cosmic super-force breaks symmetry, resulting in the twisted form of the forces of nature we find in the standard model of physics (b), in which matter is electromagnetically polarized, so that the up and down quarks acting under the strong (color) and weak nuclear forces result in positively charged nuclei with negatively charged orbital electrons (c). Stellar nucleosynthesis (d) then results in over 100 nuclei with distinct orbital dynamics, forming the table of the elements (e), which has graduated periodic properties resulting from non-linear orbital charge interactions. Under the diverse variation of non-equilibrium planetary conditions driven by gravitation and energizing stellar radiation, this leads interactively to the fractal structure of matter, in which far from equilibrium conditions lead to molecular complexes exemplified by ATP, molecular genetic replication, the ribosome whose function is to translate RNA messages into proteins, and ultimately to organelles illustrated by the membrane, cells, tissues and organisms. This casts life as an interactive cosmological phase transition to increasing fractal complexity that is a potentially inevitable consequence of the symmetry-breaking at the cosmological origin - paradise on the cosmic equator in space-time - as fundamental as the big bang and eventual fate of the universe as a whole. Catalytic replication in one form or another is an interactive consequence of the quantum properties of molecules under far-from-equilibrium conditions, which constitute a form of fractal spatial quantum computation. The nature of life as we know it looks to be an optimal interactive catastrophe of the elements (e) combining the most strongly covalent first row elements, the most outstanding ionic elements and key transition elements in a catalytic chain reaction.
Way back in the early days of this discovery process, several scientists had found that discharging energy, such as sparks or radiation into mixes of simple HNCO precursors could form a variety of more complex organic molecules, including amino acids, the porphyrin ring that surrounds the iron and magnesium atoms in hemoglobin and chlorophyll and some of the bases that make up RNA, the little sister of the DNA that stores our genetic information. To test the idea, I made microcells – membranous structures the same size as mushroom spores from such mixtures, showing how cellular membranes could arise spontaneously.
More recently, we have all discovered that key molecules such as HCN, H2CO, NH3 and H2O which readily polymerize to these diverse prebiotics are ubiquitous, filling the gas clouds of the galaxy such as the great Orion nebula and prominent enough cosmologically to be detected also in other distant galaxies. These molecules, in interaction can chain react to form many of the amino acids and nucleic acid bases and sugars that we find central to living systems. The amino acid glycine, for example, has also been detected directly in interstellar gas clouds.
At the same time we have discovered that the stars in the galaxies are strewn with billions of planets, some of which lie in the 'goldilocks zone' where the surface temperature permits liquid water and hence the conditions of life as we know it to exist.
Researchers quickly discovered that comets and asteroids have brought loads of such organic molecules to the surface of the early Earth, along with much of the water forming the oceans. Some of these remnants of the early solar system, in the form of carbonaceous meteorites or 'chondrites' also have a complex variety of organic molecules including amino acids and RNA bases.
A bewildering array of organics have been found in the Murchison meteorite, including a number of amino-acids, all of the RNA bases A, U, G, and C and a slew of other molecules with prebiotic significance. The Tagish Lake meteorite, was found to have a significant excess of the L-forms of the amino-acids aspartic and glutamic acid as well as a slight excess of L-alanine, implying that cosmic processes can favour the left-handed amino-acids essential to life and the genetic code. The carbon isotope ratios of these attest to an extra-terrestrial origin.
The picture that emerges is of an early Earth that is first subjected to massive bombardment, including the formation of the moon, heated both by relentless huge impacts and massive volcanism to form a hot rocky planet that is then showered with lighter molecules to the point that, by the time of about 150 million years in we can find geological evidence of a liquid ocean. Given the amount of water in the oceans, we can see that there would have likewise been massive deposits of organics with an atmosphere composed principally of CO2 with negligible oxygen and most of the nitrogen still locked in surface molecules due to redeposition from the atmosphere. Under these turbulent conditions, lightning strikes would have continued to catalyse the return of molecular nitrogen to the surface until the CO2 levels began to fall due to ocean fixation, leaving the organic HCNO species relatively abundant on the surface.
Fig 3: Extra-terrestrial evidence for prebiotic molecules. Top-left: Two comets Wild-2 and Churyumov-Gerasimenko have both shown evidence of organics with HCN, NH3 and H2S on the latter and evidence of several amino acids in the former. Top-right: The bewildering slew of organics detected in the Murchison meteroite with surface texture below. Bottom: Tagish Lake meteorite with excesses of L-amino acids, particularly glutamic and aspartic acids, which are known to crystallize into chiral forms.
But the path from simple amino acids and nucleic acid bases to replicating RNAs and proteins held together in a cell membrane was a huge challenge, which still hasn't been accomplished in the laboratory to date. There is a core reason for this. The key polymers such as nucleic acids and polypeptides have to be thermodynamically unstable molecules, requiring external energy input to sustain their existence, or they would all polymerize irreversibly to become a massive clunk of inert gunk – the ultimate death of life. Consequently it is very difficult to find and perpetuate conditions, which will cause the simple precursors to complexify into just the right combination of molecules to kick-start and sustain a self-replicating system.
Life today is informationally based on coded DNA, which is translated into proteins using RNA messages which the ribosome manufactures into proteins, but it has become increasingly obvious that RNA has the ability to both replicate using complementary bases in a double helix as DNA does, and to form catalytic enzymes called ribozymes by folding into reactive complexes as proteins do. Moreover it looks like all life today began from RNA. Retroviruses like HIV reverse the logic by using reverse transcriptase to make a DNA sequence from RNA and the ribosome and other essential key structures maintaining coded enzymes are still centrally based on catalytic RNAs. RNA also has a plausible cosmological basis. Each unit of RNA consists of a nitrogenous base, a sugar and a phosphate. The four bases A, U, G and C are all putative polymers of HCN. Adenine for example is (HCN)5 and can be made industrially from HCN. Sugars including ribose are natural products of primal carbohydrates such as H2CO and phosphate is a mineral acid salt, whose dehydration energy drives all biological processes in the form of the 'one-unit RNA' adenosine triphosphate - ATP. Other pivotal energy cofactors such as the electron carrier nicotinamide-adenine-dinucleptide - NAD are modified RNAs. But this doesnŐt mean you can just mix simple prebiotic ingredients and end up with RNA or even the right sugars and bases in any meaningful yield.
Nevertheless there have been significant strides in discovering counter-intuitive pathways for complexification, which show for example how two of the nucleotide units of RNA can self-synthesize in good yields from simple reactants in a counter-intuitive "one pot" process thought impossible by scientists who had tried to build the bases and sugars separately and then bond the completed units together.
Fig 4: Left: Three key nucleotide co-enzymes still essential to life today, ATP, NAD and SAM. Centre: tRNA illustrates the capacity of RNAs to form folded catalytic structures, which can function as ribozymes as well as being capable of genetic replication. Thus we donŐt need DNA and coded proteins but only RNA to kick-start life. Right: One-pot synthesis of the RNA unit cyclic CMP (green), compared with the classical unsuccessful approach (blue).
But as we have seen, a rich bunch of organics dropped on the early Earth isn't going to instantly form a living system because life is an energetically unstable process that survives only when sustained by a free energy source, such as photosynthesis.
What is needed is the equivalent of an origin of life lab that can maintain such a far-from-equilibrium environment for hundreds of millions of years at a stretch, including a rich array of chemical potentials, generating a natural far-from-equilibrium energy interface for maintaining such a free-energy process that can provide the Garden of Eden for replicating life to become established.
Two key pieces of research have now come together to (a) show both how such a life lab comes into existence and has continued to exist for billons of years on Earth, based on chemical processes that occur all over the galaxy, and (b) to find the actual living fingerprint of LUCA, the last universal common ancestor of all extant life on Earth and reveal its metabolism and mode of existence.
The first piece of the puzzle comes from so-called "Lost City" vents that line the mid-ocean ridges, particularly where they are spreading rather slowly. These are not the ultra-hot volcanic black smokers, or even the gentler white-smokers, but even milder processes, a little like the chemical gardens some of us will have made in children's chemical experiments using similar silicate minerals and other salts.
Fig 5: Lost City vents (a) have pores which are capable of concentrating RNAs 1000 fold (b), are spontaneously generated by crustal olivine (c), reacting with sea water, producing H2 which reacts with dissolved CO2 to produce organics, also generating an H+ and redox gradients identical with those in living cells. Olivine occurs on a galactic footing also detected raining in a star in the Orion nebula (d) with spectral signature (e), and has also been found on Mars, the Moon and the asteroid Itokawa (f).
The early Earth's atmosphere was rich in CO2 with little oxygen and a lot of nitrogen. The higher levels of CO2 caused the ocean to become acid, like coca cola. Contrasting this, much of the Earth's crust was olivine, a transparent greenish solid-solution mineral form of magnesium-iron silicate. Olivine is ubiquitous in the universe as a basic lighter crustal basalt rock. You find it on Earth, the Moon, Mars, asteroids in meteorites and has even been detected falling into infant stars.
The extraordinary thing about olivine is that it undergoes a paradoxical reaction to form fizzy columns of carbonate and silicate minerals in which alkaline fluids welling up from the basalt meet the acidic ocean to form a free-energy interface. This "chemical garden" reaction goes like this:
3Mg3Fe(SiO4)2 + 7H2O → 3Mg3Si2O5 + Fe3O4 + H2
It is thus generating reducing hydrogen, which in interaction with oceanic CO2, due to the energy interface produced can lead to all the forms of CHO molecules, from hydrocarbons to carbohydrates. The fact that these processes are still ongoing 3 billion years later and the fact that they would have been much more active on the volcanic early Earth with rapid exposure of olivine to the acidified CO2-rich oceans demonstrates the central ongoing importance of these processes to biogenesis.
In a ground-breaking project to identify genes that can illuminate the biology of LUCA, the last common ancestor of all life, a team searched among sequenced proteins in prokaryotic genomes, for the library of those that are both present in at least two higher taxa of each of bacteria and archaea, and have bacterial and archaeal monophyly, falling cleanly in each case into a generic evolutionary group. Genes meeting both criteria are unlikely to have undergone lateral gene transfer and thus were likely to be present in LUCA. By focusing on phylogeny rather than universal gene presence, which tends to reveal only genes for central genetic processes such as translation, they identified genes involved in LUCA's physiology - the ways that cells access carbon, energy and nutrients from the environment for growth.
The presence of the thermophile-specific enzyme reverse gyrase implies that LUCA was a thermophile. An ATP synthase subunit suggests LUCA was able to harness ion gradients for energy. LUCA also appears to have had a gene for a protein that could swap sodium and hydrogen ions across this gradient. These are key ionic processes defining all living cells. Cells conserve energy via membrane ion gradients using rotary ATP synthases or via substrate-level phosphorylation. LUCA's genes encompass both.
Significantly, the genes for membrane lipid biosynthesis and cell wall formation are not shared between archaea and bacteria, suggesting that LUCA had not become a fully independent cell but was environmentally dependent on the nurturing non-equilibrium environment of the Lost City vents.
Fig 6: (a) Emergence of LUCA to form archaea and bacteria appears to have preceded the genes for membrane lipid synthesis and cell wall formation since these are not shared by the two groups, implying that LUCA arose in an environment such as Lost City where cellular isolation was not necessary, as an external source of ion and redox gradients was ongoing. (b) The central pathways discovered to have a genetic basis in LUCA include mutual Na+-H+ transporters, H+ dependent ATP synthase, diverse FeS centres including those utilizing Ni-FeS in CO-methylating acetyl-CoA synthase, and Mo-FeS to fix nitrogen and radical SAM (S-adenosyl-methionine) to facilitate methyl-group transfers. The system used the Wood-Ljungdahl (WL) pathway, which uses H2 as an electron donor and CO2 as electron acceptor common to archaeal methanogens and acetogenic clostridia today. (c) A similar ion-gradient cycle is used by archaeal Halobacteria coupling a form of rhodopsin to drive an H+ ion gradient used by the rotary engine ATP-synthase to produce cellular phosphate energy. Bacteriorhodopsin is a heptahelical membrane protein homologous with the rhodopsin in our eyes and with diverse G-linked neurotransmitter receptors in our brains. (d) LUCA involved a transition from an RNA-based metabolism based on the ability of RNAs to acts as replicating catalysts, to the genetic code and then to DNA based transcription and protein translation over a period. Traces of this are still evident in rRNA being essential to protein translation, viral RNA polymerases and reverse transcriptase, which makes DNA from RNA and shares an evolutionary relationship with the telomerase essential to maintain our chromosomes. LUCA's gene list reveals only 9 nucleotide biosynthesis and 5 amino acid biosynthesis proteins suggesting that LUCA might not yet have evolved such genes prior to the bacterial-archaeal split. (e) mRNA SECIS element essential for editing the genetic code to incorporate seleno-cysteine into proteins evolved in LUCA, as selenophosphate synthase is in the LUCA gene library and SECIS elements are common to all domains of life.
The only energy pathway enzymes present were those of a particular anaerobic Wood-Ljungdahl (WL) pathway, which uses H2 as an electron donor and CO2 as electron acceptor. LUCA's WL enzymes are replete with FeS and NiFeS centres, indicating transition-metal requirements, also requiring organic, metallic and nucleotide cofactors. This is consistent with a long-standing idea that transition element catalysis, particularly FeS centres involved in electron transfer, and lower-energy sulphur bonds have been essential to primal metabolic processes. The molybdenum-iron proteins indicate active nitrogen fixation, despite being one of the most inscrutable of all prokaryote enzymes. This implicates the FeS-Mo centre of nitrogenase, as well as the FeS-Ni centre of a key methylating enzyme CO-methylating acetyl-CoA synthase as having a primordial catalytic geochemical status.
Analysis of the trees constructed from the 355 protein families places bacterial clostridia and archaeal methanogens as the earliest-diverging organisms - both of which are anaerobic, H2-dependent and use the WL pathway. The implication is that LUCA was very much dependent on abiotic sources of H2 to provide it with energy, consistent with a metabolism associated with Lost City vents.
LUCA's genes for RNA nucleoside modification indicate that it performed chemical modification of tRNA and rRNA involved in protein translation using methyl groups. This picture indicates the antiquity and functional significance of methylated bases in the evolution of the ribosome and the genetic code. Notably selenophosphate synthase is included in the LUCA list implicating primal dependence on selenium-catalysed transformations which are unique in requiring a special SECIS motif in the messenger RNA to override the stop codon of the genetic code to include selenocysteine in a seleno-protein
LUCA's gene list reveals only nine nucleotide biosynthesis and five amino acid biosynthesis proteins. The paucity of enzymes for essential amino acid, nucleoside and cofactor biosyntheses suggests that LUCA might not yet have evolved the genes in question prior to the bacterial-archaeal split, with the pathway products for LUCA being still provided by primordial geochemistry.
It has also been proposed, on the basis of the highly-conserved commonality of transcription and translation proteins to all life, but the apparently independent emergence of distinct DNA replication enzymes in archaea/eucaryotes and bacteria, that LUCA had a mixed RNA-DNA metabolism based on reverse transcriptase, pinpointing it to the latter phases of the RNA era.
It has also been proposed, on the basis of the highly-conserved commonality of transcription and translation proteins to all life, but the apparently independent emergence of distinct DNA replication enzymes in archaea/eucaryotes and bacteria, that
had a mixed RNA-DNA metabolism based on reverse transcriptase, pinpointing it to the latter phases of the RNA era.
Fig 7: Left: Evolutionary tree of ribosomal rRNA shows thermophilic species close to the root, consistent with a hot origin for life. Inset: Eukaryotes, comprising higher organisms and their single celled relatives, arose from a symbiotic fusion of an archea with a proteobacterium, resulting in the respiring mitochondria that provide most of our energy. Right: Four species close to the root. The red Pyrococcus furiosus, an extreme thermophile that lives at 100oC and has a metabolism involving 11 metals listed below including tungsten, nickel, molybdenum and vanadium. Purple Clostridium difficile. Green two methanogens.
Models of the Hadean atmosphere around 3.8 billion years ago, suggest abiotic nitrogen fixation was active in the early high CO2 atmosphere but had declined by 2.2 billion years ago as the CO2 levels fell resulting in nitrogen getting trapped as atmospheric N2. The rapid growth of metabolic gene diversity in the Archaean 3.4-3.0 billion years ago puts LUCA into the zone between 3.8 and 3.4 bya. This indicates that the supply of prebiotic HCN and O-containing molecules was sufficient to support biogenesis, driven by the ongoing energy interface of Lost City vents for some 400 million years until life had become established, but that the Archaean nitrogen crisis, as CO2 levels fell, had set in before LUCA had diverged into the archaea and bacteria.
The late heavy bombardment of Earth by comets and asteroids approximately 4-3.8 billion years ago probably resulted in Earth being periodically heated to the point that the oceans boiled, meaning that only hyperthermophiles survived. When we look at the metabolism of LUCA, we are thus looking at the dominant and most successful kind of metabolism on the planet before the bacteria and archaea diverged.
This picture is broadly consistent with the thermophilic organisms close to the root of the ribosomal RNA evolutionary tree and with other studies based on searching for genes common to all branches of life, which indicate that LUCA had an advanced metabolic network, rich in nucleotide metabolism enzymes, had primordial pathways for the biosynthesis of membrane glycerol ether and lipids, crucial elements of translation, including aminoacyl-tRNA synthases and a primordial ribosome with protein synthesis capabilities. However, it lacked transcription from DNA to RNA, processes for extracellular communication, and enzymes for deoxyribonucleotide synthesis, and in advanced evolutionary stages stored genetic information in RNA (not DNA) molecules, as there is no evidence LUCA possessed ribonucleotide reductases, which create the deoxy-versions of ribonucleotides, the building blocks of DNA.
Fig 8: Evolution of gene diversity underwent a massive expansion around 3.4 billion years ago, forming the majority of metabolic genes found today, thus placing LUCA's radiation at this point in time. Fig 9: Above: Stromatolites from Shark Bay Australia, Below: Putative stromatolites from Isua, Greenland dating to 3.7 billion years.
The geological evidence is likewise consistent with a very early origin for life as soon as there is evidence of a liquid ocean. Apatite grains in the Isua formation of Greenland dating from 3.85 billion years ago have carbon 12 to 13 ratios consistent with the grains originating from living matter. Although indications from zircon crystals suggest a solid crust 4.2 billion years ago, no intact rocks have been discovered older than 3.96 billion years. The moon and Earth was heavily bombarded with meteors up to 3.8 billion years ago, suggesting that life evolved on earth as soon as environmental conditions allowed. The discovery of disordered graphite inclusions of zircons from Western Australia, with a high 12C content, consistent with abiogenic origin, that formed 4.1 billion years, suggests life was prevalent enough before then to become included in the geological record. This date is highly significant, since the oldest direct evidence for the presence of surface waters are slightly younger ca. ~3.8 billion years old.
Fig 9: Above: Stromatolites from Shark Bay Australia,
Below: Putative stromatolites from Isua, Greenland dating to 3.7 billion years.
The oldest fossil evidence for cellular life has been discovered on a 3.43-billion-year-old beach in western Australia. Its grains of sand provided a home for cells that lived on sulphur in a largely oxygen-free world. The origins of the first fossil life forms including the stromatolites, likewise lie at the limits of the geological record, at around 3.5 - 3.7 billion years old.