Darwin’s warm little pond revisited: from molecules to the origin of life

Origin of the RNA World in Cold Hadean Geothermal Fields Enriched in Zinc and Potassium: Abiogenesis as a Positive Fallout from the Moon-Forming Impact?

The ubiquitous, evolutionarily oldest RNAs and proteins exclusively use rather rare zinc as transition metal cofactor and potassium as alkali metal cofactor, which implies their abundance in the habitats of the first organisms. Intriguingly, lunar rocks contain a hundred times less zinc and ten times less potassium than the Earth's crust; the Moon is also depleted in other moderately volatile elements (MVEs). Current theories of impact formation of the Moon attribute this depletion to the MVEs still being in a gaseous state when the hot post-impact disk contracted and separated from the nascent Moon. The MVEs then fell out onto juvenile Earth's protocrust; zinc, as the most volatile metal, precipitated last, just after potassium. According to our calculations, the top layer of the protocrust must have contained up to 1019 kg of metallic zinc, a powerful reductant. The venting of hot geothermal fluids through this MVE-fallout layer, rich in metallic zinc and radioactive potassium, both capable of reducing carbon dioxide and dinitrogen, must have yielded a plethora of organic molecules released with the geothermal vapor. In the pools of vapor condensate, the RNA-like molecules may have emerged through a pre-Darwinian selection for low-volatile, associative, mineral-affine, radiation-resistant, nitrogen-rich, and polymerizable molecules.

Prebiotic RNA self-assembling and the origin of life: Mechanistic and molecular modeling rationale for explaining the prebiotic origin and replication of RNA

In recent years, a great interest has been focused on the prebiotic origin of nucleic acids and life on Earth. An attractive idea is that life was initially based on an autocatalytic and autoreplicative RNA (the RNA-world). RNA duplexes are right-handed helical chains with antiparallel orientation, but the rationale for these features is not yet known. An antiparallel (inverted) stacking of purine nucleosides was reported in crystallographic studies. Molecular modeling also supports the inverted orientation of nucleosides. This preferential stacking can also appear when nucleosides are included in a montmorillonite clay matrix. Free-energy values and geometrical parameters show that D-ribose chirality is preferred for the formation of right-handed RNA molecules. Thus, a "zipper" model with antiparallel and auto-intercalated nucleosides linked by phosphate groups can be proposed to form single RNA chains. Unstacking with strand separation and base pairing by H-bonding, results in shortening and inclination of ribose-phosphate chains, leading to right-handed helicity and antiparallel duplexes. Incorporation of complementary precursors on the major groove template by a self-assembly mechanism provides a prebiotic (non-enzymatic) "tetris" replication model by formation of a transient RNA tetrad and tetraplex. Original hairpin motifs appear as simple building units that form typical RNA structures such as hammerheads, cloverleaves and dumbbells. They occur today in the circular viroids and virusoids, as well as in highly branched and complex rRNA molecules.

The Possible Crystallization Process in the Origin of Bacteria, Archaea, Viruses, and Mobile Elements

We propose a hypothesis for the simultaneous emergence of bacteria, archaea, viruses, and mobile elements by sequential and concrete biochemical pathways. The emergence process can be considered analogous to crystallization, where genetic and biochemical systems stabilize as organisms evolve from their common ancestor, the LUCA, which was a non-free-living pool of single operon type genomes including double-stranded (ds) DNA at an ancient submarine alkaline vent. Each dsDNA operon was transcribed by different systems in σ, TFIIB, or TBP genomes. Double-stranded DNA operons can fuse and stabilize through the action of specific transcription systems, leading to differentiation between the Bacteria (σ genome) and Archaea (TBP genome) domains. Error catastrophe can be overcome by the parallel gain of DNA replication and DNA repair mechanisms in both genomes. Enlarged DNA enabled efficient local biochemical reactions. Both genomes independently recruited lipids to facilitate reactions by forming coacervates at the chamber of the vent. Bilayer lipid membrane formation, proto-cell formation with a permeable membrane, proto-cell division, and the evolution of membrane-associated biochemistry are presented in detail. Simultaneous crystallization of systems in non-free-living bacteria and non-free-living archaea triggered the co-crystallization of primitive viruses and mobile elements. An arms race between non-free-living cells and primitive viruses finally led to free-living cells with a cell wall and mature viruses.

A Bayesian Analysis of the Probability of the Origin of Life Per Site Conducive to Abiogenesis

The emergence of life from nonlife, or abiogenesis, remains a fundamental question in scientific inquiry. In this article, we investigate the probability of the origin of life (per conducive site) by leveraging insights from Earth's environments. If life originated endogenously on Earth, its existence is indeed endowed with informative value, although the interpretation of the attendant significance hinges critically upon prior assumptions. By adopting a Bayesian framework, for an agnostic prior, we establish a direct connection between the number of potential locations for abiogenesis on Earth and the probability of life's emergence per site. Our findings suggest that constraints on the availability of suitable environments for the origin(s) of life on Earth may offer valuable insights into the probability of abiogenesis and the frequency of life in the universe.

The bubble theory: exploring the transition from first replicators to cells and viruses in a landscape-based scenario

This study proposes a landscape-based scenario for the origin of viruses and cells, focusing on the adaptability of preexisting replicons from the RNP (ribonucleoprotein) world. The scenario postulates that life emerged in a subterranean "warm little pond" where organic matter accumulated, resulting in a prebiotic soup rich in nucleotides, amino acids, and lipids, which served as nutrients for the first self-replicating entities. Over time, the RNA world, followed by the RNP world, came into existence. Replicators/replicons, along with the nutritious soup from the pond, were washed out into the river and diluted. Lipid bubbles, enclosing organic matter, provided the last suitable environment for replicons to replicate. Two survival strategies emerged under these conditions: cell-like structures that obtained nutrients by merging with new bubbles, and virus-like entities that developed various techniques to transmit themselves to fresh bubbles. The presented hypothesis provides the possibility for the common origin of cells and viruses on rocky worlds hosting liquid water, like Earth.

Microfluidics-Based Drying-Wetting Cycles to Investigate Phase Transitions of Small Molecules Solutions

Drying-wetting cycles play a crucial role in the investigation of the origin of life as processes that both concentrate and induce the supramolecular assembly and polymerization of biomolecular building blocks, such as nucleotides and amino acids. Here, we test different microfluidic devices to study the dehydration-hydration cycles of the aqueous solutions of small molecules, and to observe, by optical microscopy, the insurgence of phase transitions driven by self-assembly, exploiting water pervaporation through polydimethylsiloxane (PDMS). As a testbed, we investigate solutions of the chromonic dye Sunset Yellow (SSY), which self-assembles into face-to-face columnar aggregates and produces nematic and columnar liquid crystal (LC) phases as a function of concentration. We show that the LC temperature-concentration phase diagram of SSY can be obtained with a fair agreement with previous reports, that droplet hydration-dehydration can be reversibly controlled and automated, and that the simultaneous incubation of samples with different final water contents, corresponding to different phases, can be implemented. These methods can be further extended to study the assembly of diverse prebiotically relevant small molecules and to characterize their phase transitions.

Phosphate in Cardiovascular Disease: From New Insights Into Molecular Mechanisms to Clinical Implications

Hyperphosphatemia is a common feature in patients with impaired kidney function and is associated with increased risk of cardiovascular disease. This phenomenon extends to the general population, whereby elevations of serum phosphate within the normal range increase risk; however, the mechanism by which this occurs is multifaceted, and many aspects are poorly understood. Less than 1% of total body phosphate is found in the circulation and extracellular space, and its regulation involves multiple organ cross talk and hormones to coordinate absorption from the small intestine and excretion by the kidneys. For phosphate to be regulated, it must be sensed. While mostly enigmatic, various phosphate sensors have been elucidated in recent years. Phosphate in the circulation can be buffered, either through regulated exchange between extracellular and cellular spaces or through chelation by circulating proteins (ie, fetuin-A) to form calciprotein particles, which in themselves serve a function for bulk mineral transport and signaling. Either through direct signaling or through mediators like hormones, calciprotein particles, or calcifying extracellular vesicles, phosphate can induce various cardiovascular disease pathologies: most notably, ectopic cardiovascular calcification but also left ventricular hypertrophy, as well as bone and kidney diseases, which then propagate phosphate dysregulation further. Therapies targeting phosphate have mostly focused on intestinal binding, of which appreciation and understanding of paracellular transport has greatly advanced the field. However, pharmacotherapies that target cardiovascular consequences of phosphate directly, such as vascular calcification, are still an area of great unmet medical need.

Information Transmission via Molecular Communication in Astrobiological Environments

The ubiquity of information transmission via molecular communication between cells is comprehensively documented on Earth; this phenomenon might even have played a vital role in the origin(s) and early evolution of life. Motivated by these considerations, a simple model for molecular communication entailing the diffusion of signaling molecules from transmitter to receiver is elucidated. The channel capacity C (maximal rate of information transmission) and an optimistic heuristic estimate of the actual information transmission rate ℐ are derived for this communication system; the two quantities, especially the latter, are demonstrated to be broadly consistent with laboratory experiments and more sophisticated theoretical models. The channel capacity exhibits a potentially weak dependence on environmental parameters, whereas the actual information transmission rate may scale with the intercellular distance d as ℐ ∝ d-4 and could vary substantially across settings. These two variables are roughly calculated for diverse astrobiological environments, ranging from Earth's upper oceans (C ∼ 3.1 × 103 bits/s; ℐ ∼ 4.7 × 10-2 bits/s) and deep sea hydrothermal vents (C ∼ 4.2 × 103 bits/s; ℐ ∼ 1.2 × 10-1 bits/s) to the hydrocarbon lakes and seas of Titan (C ∼ 3.8 × 103 bits/s; ℐ ∼ 2.6 × 10-1 bits/s).

On the potential roles of phosphorus in the early evolution of energy metabolism

Energy metabolism in extant life is centered around phosphate and the energy-dense phosphoanhydride bonds of adenosine triphosphate (ATP), a deeply conserved and ancient bioenergetic system. Yet, ATP synthesis relies on numerous complex enzymes and has an autocatalytic requirement for ATP itself. This implies the existence of evolutionarily simpler bioenergetic pathways and potentially primordial alternatives to ATP. The centrality of phosphate in modern bioenergetics, coupled with the energetic properties of phosphorylated compounds, may suggest that primordial precursors to ATP also utilized phosphate in compounds such as pyrophosphate, acetyl phosphate and polyphosphate. However, bioavailable phosphate may have been notably scarce on the early Earth, raising doubts about the roles that phosphorylated molecules might have played in the early evolution of life. A largely overlooked phosphorus redox cycle on the ancient Earth might have provided phosphorus and energy, with reduced phosphorus compounds potentially playing a key role in the early evolution of energy metabolism. Here, we speculate on the biological phosphorus compounds that may have acted as primordial energy currencies, sources of environmental energy, or sources of phosphorus for the synthesis of phosphorylated energy currencies. This review encompasses discussions on the evolutionary history of modern bioenergetics, and specifically those pathways with primordial relevance, and the geochemistry of bioavailable phosphorus on the ancient Earth. We highlight the importance of phosphorus, not only in the form of phosphate, to early biology and suggest future directions of study that may improve our understanding of the early evolution of bioenergetics.

Peptide Bonds in the Interstellar Medium: Facile Catalytic Formation from Nitriles on Water-Ice Grains

A recent suggestion that acetamide, CH₃C(O)NH₂, could be readily formed on water-ice grains by the acid induced addition of water across the C≡N bond has now been shown to be credible. Computational modeling of the reaction between R-CN (R = H, CH₃) and a cluster of 32 molecules of water and one H₃O⁺ proceeds catalytically to form first a hydroxy imine R-C(OH)═NH and second an amide R-C(O)NH₂. Quantum mechanical tunneling, computed from small-curvature estimates, plays a key role in the rates of these reactions. This work represents the first reasonable effort to show, in general, how amides can be formed from nitriles and water, which are abundant substrates, reacting on a water-ice cluster containing catalytic amounts of hydrons in the interstellar medium with consequential implications toward the origins of life.

Spark of Life: Role of Electrotrophy in the Emergence of Life

The emergence of life has been a subject of intensive research for decades. Different approaches and different environmental "cradles" have been studied, from space to the deep sea. Since the recent discovery of a natural electrical current through deep-sea hydrothermal vents, a new energy source is considered for the transition from inorganic to organic. This energy source (electron donor) is used by modern microorganisms via a new trophic type, called electrotrophy. In this review, we draw a parallel between this metabolism and a new theory for the emergence of life based on this electrical electron flow. Each step of the creation of life is revised in the new light of this prebiotic electrochemical context, going from the evaluation of similar electrical current during the Hadean, the CO₂ electroreduction into a prebiotic primordial soup, the production of proto-membranes, the energetic system inspired of the nitrate reduction, the proton gradient, and the transition to a planktonic proto-cell. Finally, this theory is compared to the two other theories in hydrothermal context to assess its relevance and overcome the limitations of each. Many critical factors that were limiting each theory can be overcome given the effect of electrochemical reactions and the environmental changes produced.

Probing the Relationship Between Declining Renal Glomerular Filtration Over the Life Span and General Biological Aging: Does the Former Provide Means to Estimate the Latter?

While a consistent, gradual decline in the renal glomerular filtration rate (GFR) is a characteristic occurrence over the human life span, the exact pathophysiology behind this event remains unresolved. Evidence to date suggests that the endogenous glucose-insulin system could be involved at some level. Diabetic-induced nephropathy, one of the most prevalent chronic renal diseases, is closely linked to a severe form of insulin resistance (IR). Nevertheless, it is less certain that the ubiquitous milder forms of IR in nondiabetics ascribed customarily to routine, poor choices in diet and exercise management can over time diminish GFR and adversely influence other renal functions to any perceptible extent.

Baseline data for cross-sectional analyses were obtained from a cohort of healthy, nondiabetic volunteers (fasting blood glucose [FBG] ≤ 125 mg/dL) involved in prior clinical studies. Slope-based rather than threshold analyses were mainly employed. These measurements were applied for the most part to correlate age, FBG levels used as an estimate of IR activity, and systolic blood pressure (SBP) to a variety of metabolic parameters during aging with a primary focus on GFR.

Considering cause and effect, FBG and SBP correlate positively with the diminishing GFR over a major part of the life span. The decline in GFR begins somewhere around the mid-20s and coincides with key temporal increases in FBG and SBP levels.

A close time-based setting suggests that IR plays a prominent role in the declining GFR that occurs over the life span. This is perhaps due in part through deleterious effects of rising levels of insulin, glucose, and SBP individually or combined that are also popular proposed causative factors for human aging in general. On the philosophical side, the latter fact suggests that the declining GFR might provide a practical way to estimate the rate of overall human biological aging.

Formation and evolution of C-C, C-O, C[double bond, length as m-dash]O and C-N bonds in chemical reactions of prebiotic interest

A series of prebiotic chemical reactions yielding the precursor building blocks of amino acids, proteins and carbohydrates, starting solely from HCN and water is studied here. We closely follow the formation and evolution of the pivotal C-C, C-O, C[double bond, length as m-dash]O, and C-N bonds, which dictate the chemistry of the molecules of life. In many cases, formation of these bonds is set in motion by proton transfers in which individual water molecules act as catalysts so that water atoms end up in the products. Our results indicate that the prebiotic formation of carbon dioxide, formaldehyde, formic acid, formaldimine, glycolaldehyde, glycine, glycolonitrile, and oxazole derivatives, among others, are best described as highly nonsynchronous concerted single step processes. Nonetheless, for all reactions involving double proton transfer, the formation and breaking of O-H bonds around a particular O atom occur in a synchronous fashion, apparently independently from other primitive processes. For the most part, the first process to initiate seems to be the double proton transfer in the reactions where they are present, then bond breaking/formation around the reactive carbon in the carbonyl group and finally rupture of the C-N bonds in the appropriate cases, which are the most reluctant to break. Remarkably, within the limitations of our non-dynamical computational model, the wide ranges of temperature and pressure in which these reactions occur, downplay the problematic determination of the exact constraints on the early Earth.

Protocells: Milestones and Recent Advances

The origin of life is still one of humankind's great mysteries. At the transition between nonliving and living matter, protocells, initially featureless aggregates of abiotic matter, gain the structure and functions necessary to fulfill the criteria of life. Research addressing protocells as a central element in this transition is diverse and increasingly interdisciplinary. The authors review current protocell concepts and research directions, address milestones, challenges and existing hypotheses in the context of conditions on the early Earth, and provide a concise overview of current protocell research methods.

Hot Spring Microbial Community Elemental Composition: Hot Spring and Soil Inputs, and the Transition from Biocumulus to Siliceous Sinter

Hydrothermal systems host microbial communities that include some of the most deeply branching members of the tree of life, and recent work has suggested that terrestrial hot springs may have provided ideal conditions for the origin of life. Hydrothermal microbial communities are a potential source for biosignatures, and the presence of terrestrial hot spring deposits in 3.48 Ga rocks as well as on the surface of Mars lends weight to a need to better understand the preservation of biosignatures in these systems. Although there are general patterns of elemental enrichment in hydrothermal water dependent on physical and geochemical conditions, the elemental composition of bulk hydrothermal microbial communities (here termed biocumulus, including cellular biomass and accumulated non-cellular material) is largely unexplored. However, recent work has suggested both bulk and spatial trace element enrichment as a potential biosignature in hot spring deposits. To elucidate the elemental composition of hot spring biocumulus samples and explore the sources of those elements, we analyzed a suite of 16 elements in hot spring water samples and corresponding biocumulus from 60 hot springs sinter samples, and rock samples from 8 hydrothermal areas across Yellowstone National Park. We combined these data with values reported in literature to assess the patterns of elemental uptake into biocumulus and retention in associated siliceous sinter. Hot spring biocumuli are of biological origin, but organic carbon comprises a minor percentage of the total mass of both thermophilic chemotrophic and phototrophic biocumulus. Instead, the majority of hot spring biocumulus is inorganic material-largely silica-and the distribution of major and trace elements mimics that of surrounding rock and soil rather than the hot spring fluids. Analyses indicate a systematic loss of biologically associated elements during diagenetic transformation of biocumulus to siliceous sinter, suggesting a potential for silica sinter to preserve a trace element biosignature.

Chance and Necessity in the Evolution of Matter to Life: A Comprehensive Hypothesis

Specialists in several branches of life sciences are trying to solve, piece by piece, the immensely complex puzzle of the origin of life. Some parts of the puzzle seem to appear with a rather high degree of clarity, while others remain totally obscure. We cannot be sure that life emerged only on our Earth, but we believe that the presence of large amounts of water in its liquid state is absolutely essential for the emergence and evolution of living matter. We can also assume that the latter exploits everywhere the same light elements, mainly C, H, O, N, S, and P, and somehow manipulates the same simple monomeric and polymeric organic compounds, such as alpha-amino acids, carbohydrates, nucleic bases, and surface-active carboxylic acids. The author contributes to the field by stating that all fundamental particles of our matter are “homochiral” and predominantly produce in an absolute asymmetric synthesis amino acids of L-configuration and carbohydrates of D-series. Another important point is that free atmospheric oxygen mainly stems from the photolysis of water molecules by cosmic irradiation and is not necessarily bound to living organisms on the planet.

The Riddle of Atmospheric Oxygen: Photosynthesis or Photolysis?

Abstract

The stoichiometry of the photosynthetic reaction requires that the quantities of the end products (organic biomaterial and free oxygen) be equal. However, the correct balance of the amounts of oxygen and organic matter that could have been produced by green plants on the land and in the ocean since the emergence of unique oxygenic photosynthetic systems (no more than 2.7 billion years ago) is virtually impossible, since the vast majority of oxygen was lost in oxidizing the initially reducing matter of the planet, and the bulk of organic carbon is scattered in sedimentary rocks. In recent decades, convincing information has been obtained in favor of the large-scale photolysis of water molecules in the upper atmosphere with the scattering of light hydrogen into space and the retention of heavier oxygen by gravity. This process has been operating continuously since the formation of the Earth. It is accompanied by huge losses of water and the oxidation of salts of ferrous iron and sulfide sulfur in the oceans and methane in the atmosphere. The main stages of the evolution of the atmosphere and surface layers of the Earth’s crust are analyzed for the first time in this work by considering the parallel processes of photosynthesis and photolysis. Large-scale photolysis of water also provides consistent explanations for the main stages in the evolution of the nearest planets of our Solar System.

Driving forces in the origins of life

What were the physico-chemical forces that drove the origins of life? We discuss four major prebiotic 'discoveries': persistent sampling of chemical reaction space; sequence-encodable foldable catalysts; assembly of functional pathways; and encapsulation and heritability. We describe how a 'proteins-first' world gives plausible mechanisms. We note the importance of hydrophobic and polar compositions of matter in these advances.

Prebiotic Organic Chemistry of Formamide and the Origin of Life in Planetary Conditions: What We Know and What Is the Future

The goal of prebiotic chemistry is the depiction of molecular evolution events preceding the emergence of life on Earth or elsewhere in the cosmos. Plausible experimental models require geochemical scenarios and robust chemistry. Today we know that the chemical and physical conditions for life to flourish on Earth were at work much earlier than thought, i.e., earlier than 4.4 billion years ago. In recent years, a geochemical model for the first five hundred million years of the history of our planet has been devised that would work as a cradle for life. Serpentinization processes in the Hadean eon affording self-assembled structures and vesicles provides the link between the catalytic properties of the inorganic environment and the impressive chemical potential of formamide to produce complete panels of organic molecules relevant in pre-genetic and pre-metabolic processes. Based on an interdisciplinary approach, we propose basic transformations connecting geochemistry to the chemistry of formamide, and we hint at the possible extension of this perspective to other worlds.

Arsenic Response of Three Altiplanic Exiguobacterium Strains With Different Tolerance Levels Against the Metalloid Species: A Proteomics Study

Exiguobacterium is a polyextremophile bacterial genus with a physiology that allows it to develop in different adverse environments. The Salar de Huasco is one of these environments due to its altitude, atmospheric pressure, solar radiation, temperature variations, pH, salinity, and the presence of toxic compounds such as arsenic. However, the physiological and/or molecular mechanisms that enable them to prosper in these environments have not yet been described. Our research group has isolated several strains of Exiguobacterium genus from different sites of Salar de Huasco, which show different resistance levels to As(III) and As(V). In this work, we compare the protein expression patterns of the three strains in response to arsenic by a proteomic approach; strains were grown in absence of the metalloid and in presence of As(III) and As(V) sublethal concentrations and the protein separation was carried out in 2D electrophoresis gels (2D-GE). In total, 999 spots were detected, between 77 and 173 of which showed significant changes for As(III) among the three strains, and between 90 and 143 for As(V), respectively, compared to the corresponding control condition. Twenty-seven of those were identified by mass spectrometry (MS). Among these identified proteins, the ArsA [ATPase from the As(III) efflux pump] was found to be up-regulated in response to both arsenic conditions in the three strains, as well as the Co-enzyme A disulfide reductase (Cdr) in the two more resistant strains. Interestingly, in this genus the gene that codifies for Cdr is found within the genic context of the ars operon. We suggest that this protein could be restoring antioxidants molecules, necessary for the As(V) reduction. Additionally, among the proteins that change their expression against As, we found several with functions relevant to stress response, e.g., Hpf, LuxS, GLpX, GlnE, and Fur. This study allowed us to shed light into the physiology necessary for these bacteria to be able to tolerate the toxicity and stress generated by the presence of arsenic in their niche.

Productivity and Community Composition of Low Biomass/High Silica Precipitation Hot Springs: A Possible Window to Earth's Early Biosphere?

Terrestrial hot springs have provided a niche space for microbial communities throughout much of Earth's history, and evidence for hydrothermal deposits on the Martian surface suggest this could have also been the case for the red planet. Prior to the evolution of photosynthesis, life in hot springs on early Earth would have been supported though chemoautotrophy. Today, hot spring geochemical and physical parameters can preclude the occurrence of oxygenic phototrophs, providing an opportunity to characterize the geochemical and microbial components. In the absence of the photo-oxidation of water, chemoautotrophy in these hot springs (and throughout Earth's history) relies on the delivery of exogenous electron acceptors and donors such as H2, H2S, and Fe2+. Thus, systems fueled by chemoautotrophy are likely energy substrate-limited and support low biomass communities compared to those where oxygenic phototrophs are prevalent. Low biomass silica-precipitating systems have implications for preservation, especially over geologic time. Here, we examine and compare the productivity and composition of low biomass chemoautotrophic versus photoautotrophic communities in silica-saturated hot springs. Our results indicate low biomass chemoautotrophic microbial communities in Yellowstone National Park are supported primarily by sulfur redox reactions and, while similar in total biomass, show higher diversity in anoxygenic phototrophic communities compared to chemoautotrophs. Our data suggest productivity in Archean terrestrial hot springs may be directly linked to redox substrate availability, and there may be high potential for geochemical and physical biosignature preservation from these communities.

Exposed Areas Above Sea Level on Earth >3.5 Gyr Ago: Implications for Prebiotic and Primitive Biotic Chemistry

How life began on Earth is still largely shrouded in mystery. One of the central ideas for various origins of life scenarios is Darwin’s “warm little pond”. In these small bodies of water, simple prebiotic compounds such as amino acids, nucleobases, and so on, were produced from reagents such as hydrogen cyanide and aldehydes/ketones. These simple prebiotic compounds underwent further reactions, producing more complex molecules. The process of chemical evolution would have produced increasingly complex molecules, eventually yielding a molecule with the properties of information storage and replication prone to random mutations, the hallmark of both the origin of life and evolution. However, there is one problematic issue with this scenario: On the Earth >3.5 Gyr ago there would have likely been no exposed continental crust above sea level. The only land areas that protruded out of the oceans would have been associated with hotspot volcanic islands, such as the Hawaiian island chain today. On these long-lived islands, in association with reduced gas-rich eruptions accompanied by intense volcanic lightning, prebiotic reagents would have been produced that accumulated in warm or cool little ponds and lakes on the volcano flanks. During seasonal wet–dry cycles, molecules with increasing complexity could have been produced. These islands would have thus been the most likely places for chemical evolution and the processes associated with the origin of life. The islands would eventually be eroded away and their chemical evolution products would have been released into the oceans where Darwinian evolution ultimately produced the biochemistry associated with all life on Earth today.

Is pre-Darwinian evolution plausible?

Background

This essay highlights critical aspects of the plausibility of pre-Darwinian evolution. It is based on a critical review of some better-known open, far-from-equilibrium system-based scenarios supposed to explain processes that took place before Darwinian evolution had emerged and that resulted in the origin of the first systems capable of Darwinian evolution. The researchers’ responses to eight crucial questions are reviewed. The majority of the researchers claim that there would have been an evolutionary continuity between chemistry and “biology”. A key question is how did this evolution begin before Darwinian evolution had begun? In other words the question is whether pre-Darwinian evolution is plausible.

Results

Strengths and weaknesses of the reviewed scenarios are presented. They are distinguished between metabolism-first, replicator-first and combined metabolism-replicator models. The metabolism-first scenarios show major issues, the worst concerns heredity and chirality. Although the replicator-first scenarios answer the heredity question they have their own problems, notably chirality. Among the reviewed combined metabolism-replicator models, one shows the fewest issues. In particular, it seems to answer the chiral question, and eventually implies Darwinian evolution from the very beginning. Its main hypothesis needs to be validated with experimental data.

Conclusion

From this critical review it is that the concept of “pre-Darwinian evolution” appears questionable, in particular because it is unlikely if not impossible that any evolution in complexity over time may work without multiplication and heritability allowing the emergence of genetically and ecologically diverse lineages on which natural selection may operate. Only Darwinian evolution could have led to such an evolution. Thus, Pre-Darwinian evolution is not plausible according to the author. Surely, the answer to the question posed in the title is a prerequisite to the understanding of the origin of Darwinian evolution.

Reviewers

This article was reviewed by Purificacion Lopez-Garcia, Anthony Poole, Doron Lancet, and Thomas Dandekar.

Systems protobiology: origin of life in lipid catalytic networks

Life is that which replicates and evolves, but there is no consensus on how life emerged. We advocate a systems protobiology view, whereby the first replicators were assemblies of spontaneously accreting, heterogeneous and mostly non-canonical amphiphiles. This view is substantiated by rigorous chemical kinetics simulations of the graded autocatalysis replication domain (GARD) model, based on the notion that the replication or reproduction of compositional information predated that of sequence information. GARD reveals the emergence of privileged non-equilibrium assemblies (composomes), which portray catalysis-based homeostatic (concentration-preserving) growth. Such a process, along with occasional assembly fission, embodies cell-like reproduction. GARD pre-RNA evolution is evidenced in the selection of different composomes within a sparse fitness landscape, in response to environmental chemical changes. These observations refute claims that GARD assemblies (or other mutually catalytic networks in the metabolism first scenario) cannot evolve. Composomes represent both a genotype and a selectable phenotype, anteceding present-day biology in which the two are mostly separated. Detailed GARD analyses show attractor-like transitions from random assemblies to self-organized composomes, with negative entropy change, thus establishing composomes as dissipative systems-hallmarks of life. We show a preliminary new version of our model, metabolic GARD (M-GARD), in which lipid covalent modifications are orchestrated by non-enzymatic lipid catalysts, themselves compositionally reproduced. M-GARD fills the gap of the lack of true metabolism in basic GARD, and is rewardingly supported by a published experimental instance of a lipid-based mutually catalytic network. Anticipating near-future far-reaching progress of molecular dynamics, M-GARD is slated to quantitatively depict elaborate protocells, with orchestrated reproduction of both lipid bilayer and lumenal content. Finally, a GARD analysis in a whole-planet context offers the potential for estimating the probability of life's emergence. The invigorated GARD scrutiny presented in this review enhances the validity of autocatalytic sets as a bona fide early evolution scenario and provides essential infrastructure for a paradigm shift towards a systems protobiology view of life's origin.

Construction of tunable peptide nucleic acid junctions

We report here the construction of 3-way and 4-way peptide nucleic acid (PNA) junctions as basic structural units for PNA nanostructuring. The incorporation of amino acid residues into PNA chains makes PNA nanostructures with more structural complexity and architectural flexibility possible, as exemplified by building 3-way PNA junctions with tunable nanopores. Given that PNA nanostructures have good thermal and enzymatic stabilities, they are expected to have broad potential applications in biosensing, drug delivery and bioengineering.

Thermal decomposition of the amino acids glycine, cysteine, aspartic acid, asparagine, glutamic acid, glutamine, arginine and histidine

Background

The pathways of thermal instability of amino acids have been unknown. New mass spectrometric data allow unequivocal quantitative identification of the decomposition products.

Results

Calorimetry, thermogravimetry and mass spectrometry were used to follow the thermal decomposition of the eight amino acids G, C, D, N, E, Q, R and H between 185 °C and 280 °C. Endothermic heats of decomposition between 72 and 151 kJ/mol are needed to form 12 to 70% volatile products. This process is neither melting nor sublimation. With exception of cysteine they emit mainly H₂O, some NH₃ and no CO₂. Cysteine produces CO₂ and little else. The reactions are described by polynomials, AA→a NH₃+b H₂O+c CO₂+d H₂S+e residue, with integer or half integer coefficients. The solid monomolecular residues are rich in peptide bonds.

Conclusions

Eight of the 20 standard amino acids decompose at well-defined, characteristic temperatures, in contrast to commonly accepted knowledge. Products of decomposition are simple. The novel quantitative results emphasize the impact of water and cyclic condensates with peptide bonds and put constraints on hypotheses of the origin, state and stability of amino acids in the range between 200 °C and 300 °C.

The minimotif synthesis hypothesis for the origin of life

Several theories for the origin of life have gained widespread acceptance, led by primordial soup, chemical evolution, metabolism first, and the RNA world. However, while new and existing theories often address a key step, there is less focus on a comprehensive abiogenic continuum leading to the last universal common ancestor. Herein, I present the "minimotif synthesis" hypothesis unifying select origin of life theories with new and revised steps. The hypothesis is based on first principles, on the concept of selection over long time scales, and on a stepwise progression toward complexity. The major steps are the thermodynamically-driven origination of extant molecular specificity emerging from primordial soup leading to the rise of peptide catalysts, and a cyclic feed-forward catalytic diversification of compound and peptides in the primordial soup. This is followed by degenerate, semi-partially conservative peptide replication to pass on catalytic knowledge to progeny protocells. At some point during this progression, the emergence of RNA and selection could drive the separation of catalytic and genetic functions, allowing peptides and proteins to permeate the catalytic space, and RNA to encode higher fidelity information transfer. Translation may have emerged from RNA template driven organization and successive ligation of activated amino acids as a predecessor to translation.

Emergent properties arising from the assembly of amphiphiles. Artificial vesicle membranes as reaction promoters and regulators

This article deals with artificial vesicles and their membranes as reaction promoters and regulators. Among the various molecular assemblies which can form in an aqueous medium from amphiphilic molecules, vesicle systems are unique. Vesicles compartmentalize the aqueous solution in which they exist, independent on whether the vesicles are biological vesicles (existing in living systems) or whether they are artificial vesicles (formed in vitro from natural or synthetic amphiphiles). After the formation of artificial vesicles, their aqueous interior (the endovesicular volume) may become - or may be made - chemically different from the external medium (the exovesicular solution), depending on how the vesicles are prepared. The existence of differences between endo- and exovesicular composition is one of the features on the basis of which biological vesicles contribute to the complex functioning of living organisms. Furthermore, artificial vesicles can be formed from mixtures of amphiphiles in such a way that the vesicle membranes become molecularly, compositionally and organizationally highly complex, similarly to the lipidic matrix of biological membranes. All the various properties of artificial vesicles as membranous compartment systems emerge from molecular assembly as these properties are not present in the individual molecules the system is composed of. One particular emergent property of vesicle membranes is their possible functioning as promoters and regulators of chemical reactions caused by the localization of reaction components, and possibly catalysts, within or on the surface of the membranes. This specific feature is reviewed and highlighted with a few selected examples which range from the promotion of decarboxylation reactions, the selective binding of DNA or RNA to suitable vesicle membranes, and the reactivation of fragmented enzymes to the regulation of the enzymatic synthesis of polymers. Such type of emergent properties of vesicle membranes may have been important for the prebiological evolution of protocells, the hypothetical compartment systems preceding the first cells in those chemical and physico-chemical processes that led to the origin of life.

Non-enzymatic ribonucleotide reduction in the prebiotic context

Model studies of prebiotic chemistry have revealed compelling routes for the formation of the building blocks of proteins and RNA, but not DNA. Today, deoxynucleotides required for the construction of DNA are produced by reduction of nucleotides catalysed by ribonucleotide reductases, which are radical enzymes. This study considers potential non-enzymatic routes via intermediate radicals for the ancient formation of deoxynucleotides. In this context, several mechanisms for ribonucleotide reduction, in a putative H2 S/HS(.) environment, are characterized using computational chemistry. A bio-inspired mechanistic cycle involving a keto intermediate and HSSH production is found to be potentially viable. An alternative pathway, proceeding through an enol intermediate is found to exhibit similar energetic requirements. Non-cyclical pathways, in which HSS(.) is generated in the final step instead of HS(.) , show a markedly increased thermodynamic driving force (ca. 70 kJ mol(-1) ) and thus warrant serious consideration in the context of the prebiotic ribonucleotide reduction.

Evolution of the first genetic cells and the universal genetic code: a hypothesis based on macromolecular coevolution of RNA and proteins

A qualitative hypothesis based on coevolution of protein and nucleic acid macromolecules was developed to explain the evolution of the first genetic cells, from the likely organic chemical-rich environment of early earth, through to the Last Universal Common Ancestor (LUCA). The evolution of the first genetic cell was divided into three phases, proto-genetic cells I, II and III, and the transition to each milestone is described, based on development of chemical cross-catalysis, bio-cross-catalysis, and the universal genetic code, respectively. Selection of macromolecular properties of both peptides and nucleic acids, in response to environmental factors, was likely to be a key aspect of early evolution. The development of hereditable nucleic acids with various key functions; translation, transcription and replication, is described. These functions are envisaged to have coevolved with protein enzymes, from simple organic precursors. Genetically heritable nucleotides may have developed after the local earth environment had cooled below 63 °C. Around this temperature G-C bases would have been preferentially utilized for nucleotide synthesis. Under these conditions RNA type nucleotides were then likely selected from a range of different types of nucleotide backbones through template-based synthesis. Initial development of the genetic coding system was simplified by the availability of proto-messenger RNA sequences that contained only G and C bases, and the need to encode only four amino acids. The step-wise addition of further amino acids to the code was predicted to parallel the growing metabolic complexity of the proto-genetic cell. On completion of this evolutionary process the proto-genetic cell is envisaged to have become the LUCA, the last common ancestor of bacteria, eukaryote and archaea domains. Key issues addressed by the model include: (a) the transition from non-hereditable random sequences of peptides and nucleic acids to specific proteins coded by hereditable nucleotide sequences, (b) the origin of homochiral amino acids and sugars, and (c) the mutation limits on the sizes of early nucleic acid genomes. The first genome was limited to a size of about 200 base pairs.

Borophosphates and silicophosphates as plausible contributors to the emergence of life

Scientific explanations for the origin of life are incomplete and may differ on some issues. Here, we argue that some prebiological steps have occurred in environments with borophosphates and/or silicophosphates in the form of hydrogels, on the basis of their chemical groups and structural properties. These could have decreased the diffusion rate of some prebiotic molecules, stabilized molecules with vicinal cis-diol groups, reduced the hydrolytic activity of water and inserted catalytic metal ions into their networks. Additionally, these hydrogels could have acted as reaction media, supplied a phosphate source for phosphorylations and produced crystals that may have permitted enantiomeric enrichment of prebiotic molecules, thus providing conditions for the emergence of protocells.

Emergence of life from multicomponent mixtures of chemicals: the case for experiments with cycling physicochemical gradients

The emergence of life from planetary multicomponent mixtures of chemicals is arguably the most complicated and least understood natural phenomenon. The fact that living cells are non-equilibrium systems suggests that life can emerge only from non-equilibrium chemical systems. From an astrobiological standpoint, non-equilibrium chemical systems arise naturally when solar irradiation strikes rotating surfaces of habitable planets: the resulting cycling physicochemical gradients persistently drive planetary chemistries toward "embryonic" living systems and an eventual emergence of life. To better understand the factors that lead to the emergence of life, I argue for cycling non-equilibrium experiments with multicomponent chemical systems designed to represent the evolving chemistry of Hadean Earth ("prebiotic soups"). Specifically, I suggest experimentation with chemical engineering simulators of Hadean Earth to observe and analyze (i) the appearances and phase separations of surface active and polymeric materials as precursors of the first "cell envelopes" (membranes) and (ii) the accumulations, commingling, and co-reactivity of chemicals from atmospheric, oceanic, and terrestrial locations.

Aqueous phase separation as a possible route to compartmentalization of biological molecules

How could the incredible complexity of modern cells evolve from something simple enough to have appeared in a primordial soup? This enduring question has sparked the interest of researchers since Darwin first considered his theory of natural selection. Organic molecules, even potentially functional molecules including peptides and nucleotides, can be produced abiotically. Amphiphiles such as surfactants and lipids display remarkable self-assembly processes including the spontaneous formation of vesicles resembling the membranes of living cells. Nonetheless, numerous questions remain. Given the presumably dilute concentrations of macromolecules in the prebiotic pools where the earliest cells are thought to have appeared, how could the necessary components become concentrated and encapsulated within a semipermeable membrane? What would drive the further structural complexity that is a hallmark of modern living systems? The interior of modern cells is subdivided into microcompartments such as the nucleoid of bacteria or the organelles of eukaryotic cells. Even within what at first appears to be a single compartment, for example, the cytoplasm or nucleus, chemical composition is often nonuniform, containing gradients, macromolecular assemblies, and/or liquid droplets. What might the internal structure of intermediate evolutionary forms have looked like? The nonideal aqueous solution chemistry of macromolecules offers an attractive possible answer to these questions. Aqueous polymer solutions will form multiple coexisting thermodynamic phases under a variety of readily accessible conditions. In this Account, we describe aqueous phase separation as a model system for biological compartmentalization in both early and modern cells, with an emphasis on systems that have been encapsulated within a lipid bilayer. We begin with an introduction to aqueous phase separation and discuss how this phenomenon can lead to microcompartmentalization and could facilitate biopolymer encapsulation by partitioning of solutes between the phases. We then describe primitive model cells based on phase separation inside lipid vesicles, which mimic several basic properties of biological cells: microcompartmentation, protein relocalization in response to stimulus, loss of symmetry, and asymmetric vesicle division. We observe these seemingly complex phenomena in the absence of genetic molecules, enzymes, or cellular machinery, and as a result these processes could provide clues to possible intermediates in the early evolution of cell-like assemblies.

Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life

This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution-leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other.

Protein ultrastructure and the nanoscience of complement activation

The complement system constitutes an important barrier to infection of the human body. Over more than four decades structural properties of the proteins of the complement system have been investigated with X-ray crystallography, electron microscopy, small-angle scattering, and atomic force microscopy. Here, we review the accumulated evidence that the nm-scaled dimensions and conformational changes of these proteins support functions of the complement system with regard to tissue distribution, molecular crowding effects, avidity binding, and conformational regulation of complement activation. In the targeting of complement activation to the surfaces of nanoparticulate material, such as engineered nanoparticles or fragments of the microbial cell wall, these processes play intimately together. This way the complement system is an excellent example where nanoscience may serve to unravel the molecular biology of the immune response.

Pumice as a remarkable substrate for the origin of life

The context for the emergence of life on Earth sometime prior to 3.5 billion years ago is almost as big a puzzle as the definition of life itself. Hitherto, the problem has largely been addressed in terms of theoretical and experimental chemistry plus evidence from extremophile habitats like modern hydrothermal vents and meteorite impact structures. Here, we argue that extensive rafts of glassy, porous, and gas-rich pumice could have had a significant role in the origin of life and provided an important habitat for the earliest communities of microorganisms. This is because pumice has four remarkable properties. First, during eruption it develops the highest surface-area-to-volume ratio known for any rock type. Second, it is the only known rock type that floats as rafts at the air-water interface and then becomes beached in the tidal zone for long periods of time. Third, it is exposed to an unusually wide variety of conditions, including dehydration. Finally, from rafting to burial, it has a remarkable ability to adsorb metals, organics, and phosphates as well as to host organic catalysts such as zeolites and titanium oxides. These remarkable properties now deserve to be rigorously explored in the laboratory and the early rock record.

On the Theory of Evolution Versus the Concept of Evolution: Three Observations

Here we address three misconceptions stated by Rice et al. in their observations of our article Paz-y-Miño and Espinosa (Evo Edu Outreach 2:655-675, 2009), published in this journal. The five authors titled their note "The Theory of Evolution is Not an Explanation for the Origin of Life." First, we argue that it is fallacious to believe that because the formulation of the theory of evolution, as conceived in the 1800s, did not include an explanation for the origin of life, nor of the universe, the concept of evolution would not allow us to hypothesize the possible beginnings of life and its connections to the cosmos. Not only Stanley Miller's experiments of 1953 led scientists to envision a continuum from the inorganic world to the origin and diversification of life, but also Darwin's own writings of 1871. Second, to dismiss the notion of Rice et al. that evolution does not provide explanations concerning the universe or the cosmos, we identify compelling scientific discussions on the topics: Zaikowski et al. (Evo Edu Outreach 1:65-73, 2008), Krauss (Evo Edu Outreach 3:193-197, 2010), Peretó et al. (Orig Life Evol Biosph 39:395-406, 2009) and Follmann and Brownson (Naturwissenschaften 96:1265-1292, 2009). Third, although we acknowledge that the term Darwinism may not be inclusive of all new discoveries in evolution, and also that creationists and Intelligent Designers hijack the term to portray evolution as ideology, we demonstrate that there is no statistical evidence suggesting that the word Darwinism interferes with public acceptance of evolution, nor does the inclusion of the origin of life or the universe within the concept of evolution. We examine the epistemological and empirical distinction between the theory of evolution and the concept of evolution and conclude that, although the distinction is important, it should not compromise scientific logic.

Stability of heterochiral hybrid membrane made of bacterial sn-G3P lipids and archaeal sn-G1P lipids

The structure of membrane lipids in Archaea is different from those of Bacteria and Eucarya in many ways including the chirality of the glycerol backbone. Until now, heterochiral membranes were believed to be unstable; thus, no cellular organism could have existed before the separation of the groups of life. In this study, we tested the formation of heterochiral hybrid membrane made of Bacterial sn-glycerol-3-phosphate-type polar lipid and Archaeal sn-glycerol-1-phosphate-type polar lipid using the fluorescence probe. The stability of the hybrid liposomes made of phosphatidylethanolamines or phosphatidylcholines or polar lipids of thermophilic Bacteria and polar lipids of Archaea were investigated. The hybrid liposomes are all stable compared with homochiral liposome made of dimyristoylphosphatidylethanolamine and dipalmitoylphosphatidylcholine. However, the stability was drastically changed with increasing carbon chain length. Accordingly, "chirality" may not be but chain length is important. From these results, we suggest that the heterochiral hybrid membrane could be used as the membrane lipid for the last universal common ancestor (Commonote) before the emergence of Archaea and Bacteria.