Origins of Life and Evolution of Biospheres最新文献

Primeval populations replicating at high error rates required a mechanism to overcome the accumulation of mutations and information deterioration. Known strategies to overcome mutation pressures include RNA processivity, epistasis, selection, and quasispecies. We investigated the mechanism by which small molecular ribozyme populations can survive under high error rates by propagating several lineages under different mutagen concentrations. We found that every population that evolved without mutagen went extinct, while those subjected to mutagenic evolution survived. To understand how they survived, we characterized the evolved genotypic diversity, the formation of genotype-genotype interaction networks, the fitness of the most common mutants for each enzymatic step, and changes in population size along the course of evolution. We found that the elevated mutation rate was necessary for the populations to survive in the novel environment, in which all the steps of the metabolism worked to promote the survival of even less catalytically efficient ligases. Besides, an increase in population size and the mutational coupling of genotypes in close-knit networks, which helped maintain or recover lost genotypes making their disappearance transient, prevented Muller's ratchet and extinction.

After pre concentration of monomers, polymerization is the second most important step for molecular evolution. The formation of peptides is an important issue for prebiotic chemistry and consequently for the origin of life. In this work, goethite was synthesized by two different routes, named goethite-I and goethite-II. Although both samples are goethite, Far-FT-IR spectroscopy and EPR spectroscopy showed differences between them, and these differences had an effect on the polymerization of glycine and alanine. For the amino acid polymerization, three protocols were used, that resembled prebiotic Earth conditions: a) amino acid plus goethite were mixed and heated at 90 °C for 10 days in solid state, b) a wet impregnation of the amino acid in the goethite, with subsequent heating at 90 °C for 10 days in solid state, and c) 10 wet/dry cycles each one for 24 h at 90 °C. Experiments with glycine plus goethite-II, using protocols B and C, produced only Gly-Gly. In addition, for the C protocol the amount of Gly-Gly synthesized was 3 times higher than the amount of Ala-Ala. Goethite-I presented a decrease in the EPR signal, when it was submitted to the protocols with and without amino acids. It is probable the decrease in the intensity of the EPR signal was due to a decrease in the imperfections of the mineral. For all protocols the mixture of alanine plus goethite-I or goethite-II produced c(Ala-Ala). However, for wet/dry cycles, protocol C presented higher yields (p < 0.05). In addition, Ala-Ala was produced using protocols A and C. The c(Ala-Ala) formation fitted a zero-order kinetic equation model. The surface areas of goethite-I and goethite-II were 35 m² g^-1 and 37 m² g^-1, respectively. Thermal analysis indicated that the mineral changes the thermal behavior of the amino acids. The main reactions for the thermal decomposition of glycine were deamination and dehydration and for alanine was deamination.

A statistical analysis of the variation in contents with the size of the current known smallest genomes, N. deltocephalinicola, C. ruddii, N. equitans, and M. genitalium, enabled the indication of a minimal set of codons capable of naturally building a modern-type free-living unicellular organism in an early stage of evolution. Using a linear regression model, the potential codon distribution in the minimal natural cell was predicted and compared to the composition of the smallest synthetic, JCVI-Syn3.0. The distribution of the molecular weight of potentially coded amino acids was also calculated. The main differences in the features of the minimal natural cell and H. Sapiens genome were analyzed. In this regard, the content percentage of respective amino acids and their polarization charge properties were reported and compared. The fractions of occurring nucleotides were calculated, too. Then, the estimated numbers of codons in a minimal natural cell were related to the expected numbers for random distribution. Shown increase, or decrease in the contents, relative to the calculated random filling was related to the evolutionary preferences, varying with the subsequent eras of the evolution of genetic code.

A primordial environment that hosted complex pre- or proto-biochemical activity would have been subject to random fluctuations. A relevant question is then: What might be the optimum variance of such fluctuations, such that net progress could be made towards a living system? Since lipid-based membrane encapsulation was undoubtedly a key step in chemical evolution, we used a peptide-micelle system in simulated experiments where simple micelles and peptide-stabilized micelles compete for the same amphiphilic lipid substrate. As cyclic thermal driver and energy source we used a thermochemical redox oscillator, to which the micelle reactions are coupled thermally through the activation energies. The long-time series averages taken for increasing values of the fluctuation variance show two distinct minima for simple micelles, but are smoothly increasing for complex micelles. This result suggests that the fluctuation variance is an important parameter in developing and perpetuating complexity. We hypothesize that such an environment may be self-selecting for a complex, evolving chemical system to outcompete simple or parasitic molecular structures.

How life arose on the primitive Earth is one of the biggest questions in science. Biomolecular emergence scenarios have proliferated in the literature but accounting for the ubiquity of oxidized (+ 5) phosphate (PO₄^3-) in extant biochemistries has been challenging due to the dearth of phosphate and molecular oxygen on the primordial Earth. A compelling body of work suggests that exogenous schreibersite ((Fe,Ni)₃P) was delivered to Earth via meteorite impacts during the Heavy Bombardment (ca. 4.1-3.8 Gya) and there converted to reduced P oxyanions (e.g., phosphite (HPO₃^2-) and hypophosphite (H₂PO₂^-)) and phosphonates. Inspired by this idea, we review the relevant literature to deduce a plausible reduced phospholipid analog of modern phosphatidylcholines that could have emerged in a primordial hydrothermal setting. A shallow alkaline lacustrine basin underlain by active hydrothermal fissures and meteoritic schreibersite-, clay-, and metal-enriched sediments is envisioned. The water column is laden with known and putative primordial hydrothermal reagents. Small system dimensions and thermal- and UV-driven evaporation further concentrate chemical precursors. We hypothesize that a reduced phospholipid arises from Fischer-Tropsch-type (FTT) production of a C8 alkanoic acid, which condenses with an organophosphinate (derived from schreibersite corrosion to hypophosphite with subsequent methylation/oxidation), to yield a reduced protophospholipid. This then condenses with an α-amino nitrile (derived from Strecker-type reactions) to form the polar head. Preliminary modeling results indicate that reduced phospholipids do not aggregate rapidly; however, single layer micelles are stable up to aggregates with approximately 100 molecules.

Earth is one of the inner planets of the Solar System, but - unlike the others - it has an oxidising atmosphere, relatively stable temperature, and a constant geomagnetic field (GMF). The GMF does not only protect life on Earth against the solar wind and cosmic rays, but it also shields the atmosphere itself, thus creating relatively stable environmental conditions. What is more, the GMF could have influenced the origins of life: organisms from archaea to plants and animals may have been using the GMF as a source of spatial information since the very beginning. Although the GMF is constant, it does undergo various changes, some of which, e.g. a reversal of the poles, weaken the field significantly or even lead to its short-term disappearance. This may result in considerable climatic changes and an increased frequency of mutations caused by the solar wind and cosmic radiation. This review analyses data on the influence of the GMF on different aspects of life and it also presents current knowledge in the area. In conclusion, the GMF has a positive impact on living organisms, whereas a diminishing or disappearing GMF negatively affects living organisms. The influence of the GMF may also be an important factor determining both survival of terrestrial organisms outside Earth and the emergence of life on other planets.

The RNA world hypothesis relies on the double-helix complementarity principle for both replication and catalytic activity of RNA. However, the de novo appearance of the complementarity rules, without previous evolution steps, is doubtful. Another major problem of the RNA world is its isolated nature, making it almost impossible to accommodate the genetic code and transform it into modern biochemistry. These and many other unanswered questions of the RNA world led to suggestions that some simpler molecules must have preceded RNA. Most of these alternative hypotheses proposed the double-helical polymers with different backbones but used the same complementarity principle. The current paper describes a fundamentally different idea: the de novo appearance of a nucleic acid polymer without any preexisting rules or requirements. This approach, coined as the quadruplex world hypothesis, is based on (i) the ability of guanines to form stable G-tetrads that facilitate polymerization; and (ii) the unique property of polyguanines to fold into a monomolecular tetrahelix with a strictly defined building pattern and tertiary structure. The tetrahelix is capable of high-affinity intermolecular interactions and catalytic activities. The quadruplex world hypothesis has the potential to address almost all the shortcomings of the RNA world.

The origin of genetic systems is the central problem in the study of the origin of life for which various explanatory hypotheses have been presented. One model suggests that both ancestral transfer ribonucleic acid (tRNA) molecules and primitive ribosomes were originally involved in RNA replication (Campbell 1991). According to this model the early tRNA molecules catalyzed their own self-loading with a trinucleotide complementary to their anticodon triplet, while the primordial ribosome (protoribosome) catalyzed the transfer of these terminal trinucleotides from one tRNA to another tRNA harboring the growing RNA polymer at the 3´-end.Here we present the notion that the anticodon-codon-like pairs presumably located in the acceptor stem of primordial tRNAs (Rodin et al. 1996) (thus being and remaining, after the code and translation origins, the major contributor to the RNA operational code (Schimmel et al. 1993)) might have originally been used for RNA replication rather than translation; these anticodon and acceptor stem triplets would have been involved in accurately loading the 3'-end of tRNAs with a trinucleotide complementary to their anticodon triplet, thus allowing the accurate repair of tRNAs for their use by the protoribosome during RNA replication.We propose that tRNAs could have catalyzed their own trinucleotide self-loading by forming catalytic tRNA dimers which would have had polymerase activity. Therefore, the loading mechanism and its evolution may have been a basic step in the emergence of new genetic mechanisms such as genetic translation. The evolutionary implications of this proposed loading mechanism are also discussed.

The abiotic synthesis of histidine under experimental prebiotic conditions has proven to be chemically promising and plausible. Within this context, the present results suggest that histidine amino acid may function as a simple prebiotic catalyst able to enhance amino acid polymerization. This work describes an experimental and computational approach to the self-assembly and stabilization of DL-histidine on mineral surfaces using antigorite ((Mg, Fe)₃Si₂O₅(OH)₄), pyrite (FeS₂), and aragonite (CaCO₃) as representative minerals of prebiotic scenarios, such as meteorites, and subaerial and submarine hydrothermal systems. Experimental results were obtained through polarized-light microscopy, IR spectroscopy (ATR-FTIR), and differential scanning calorimetry (DSC). Molecular dynamics was performed through computational simulations with the MM + method in HyperChem software. IR spectra suggest the presence of peptide bonds in the antigorite-histidine and aragonite-histidine assemblages with the presence of amide I and amide II vibration bands. The FTIR second derivative inspection supports this observation. Moreover, DSC data shows histidine stabilization in the presence of antigorite and aragonite by changes in histidine thermodynamic properties, particularly an increase in histidine decomposition temperature (272ºC in antigorite and 275ºC in aragonite). Results from molecular dynamics are consistent with DSC data, suggesting an antigorite-histidine closer interaction with decreased molecular distances (cca. 5.5 Å) between the amino acid and the crystal surface. On the whole, the experimental and computational outcomes support the role of mineral surfaces in prebiotic chemical evolution as enhancers of organic stability.

We apply a novel definition of biological systems to a series of reproducible observations on a blockchain-based distributed virtual machine (dVM). We find that such blockchain-based systems display a number of bioanalogous properties, such as response to the environment, growth and change, replication, and homeostasis, that fit some definitions of life. We further present a conceptual model for a simple self-sustaining, self-organizing, self-regulating distributed 'organism' as an operationally closed system that would fulfill all basic definitions and criteria for life, and describe developing technologies, particularly artificial neural network (ANN) based artificial intelligence (AI), that would enable it in the near future. Notably, such systems would have a number of specific advantages over biological life, such as the ability to pass acquired traits to offspring, significantly improved speed, accuracy, and redundancy of their genetic carrier, and potentially unlimited lifespans. Public blockchain-based dVMs provide an uncontained environment for the development of artificial general intelligence (AGI) with the capability to evolve by self-direction.