Origin and evolution of heredity-metabolism system

The role of "theoretical physics" in the elucidation of the origin of life has been advanced by Eigen's hypercycle theory on ancient protein synthesis system and by Dyson's random drift theory on the autocatalytic formation of enzymes, although these approaches from the informational side involve many problems to be resolved. On the other hand, our C4N model calls for a stronger role of physico-chemistry in the understanding of the origin of life. Plant virus and movable genes could be the fossil vestiges of the ancient protein synthetic system, where tRNA identical to mRNA identical to gene. It is pointed out that functional differentiation of proteins closely correlates with the structure of the primitive tRNAs. Possible initial forms of the primitive tRNAs used by the earliest organisms are explicitly shown, in which the above correlation is carefully taken into account. The system of the primitive genes and the primitive enzymes in the proto-cellular membrane, say the marigranule, might simulate the earliest organism.     

Growth of a hypercycle and comparison with conventional autocatalysis

The hypercycle is a chemical model for reproduction which has been advocated for early stages of biological evolution. Its advantage is thought to lie in the high rate of growth conferred by hyperbolic kinetics. Earlier work has also indicated a saturation phase at large constituent concentrations. The present paper shows that both the saturation phase and the phase of hyperbolic growth have been introduced into the kinetics by making some of the reactions reversible. Reversibility is not essential to the operation of the hypercycle and the system with irreversible reactions grows faster. However, even the fastest hypercycle does not grow as fast as the simple auto-catalyst obtained by removing that reaction which is characteristic of the hypercycle. Also, both because the hypercycle is not a coherent system and because its growth requires reactions among separated constituents in the medium, it is more subject to decay than a simple autocatalytic particle. With greater complexity, slower growth, and more severe decay, the hypercycle is not a satisfactory alternative to conventional models of reproduction.     

面向生态文明的超循环经济:理论、模型与实例

在全球气候变化背景下,研究适应生态文明要求的新的经济运行模式——超循环经济的基本原理、结构模型、运行机理和实际应用。首先,运用系统结构分析方法梳理不同时期经济运行模式的演进过程:由"从摇篮到产品"的粗放经济,到"从摇篮到坟墓"的末端治理经济,再到"从摇篮到摇篮"的循环经济。延续这一绿色发展趋势,根据文明演化的共生理论和艾根创立的超循环理论,提出超循环经济的理论构想,并描绘"从孕育到孕育"的超循环经济的概念结构。其次,将超循环经济思想应用于林纸拓展系统(EFPS)。在分析中国造纸工业的发展现状和瓶颈及其与林业和生态环境相互关系的基础上,按照资源链、生态链和价值链(简称"三链",或3C)逐层拓展的逻辑顺序,研究EFPS超循环经济的系列结构模型。具体来说,依次建立起各层次的超循环结构模型——制浆造纸系统的资源链核心层模型、供应链系统的资源链拓展层模型、生态环境系统的生态链拓展层模型,以及社会经济系统的价值链拓展层模型。然后将各层次的结构模型综合起来,形成EFPS超循环经济的多重拓展-嵌套整体模型。该模型既能展示EFPS超循环经济系统的全貌,又包含其各层次的系统结构。因此既能为各级政府在制定国家和地区的循环经济总体发展规划时提供参考,又能为制造企业、营林组织、供应链、行业协会等各类经济主体的绿色经营决策提供支撑。最后,在上述实证研究的基础上进行理论提升。一方面提出超循环经济的5R原则:减量化、再循环、再利用、再分配和再培育。另一方面基于5R原则和3C循环链,构建5R-3C理论模型,并研究其5R-3C共生运行机理。研究表明,在超循环经济模式下,产业与生态系统可以实现互利共生的良性循环。以上研究成果的主要创新之处在于:在原理上,揭示了面向生态文明的超循环经济的概念结构、本质属性和5R原则;在机理上,创立了超循环经济的5R-3C模型及其共生运行机理;在实施上,以林纸拓展系统为例,为超循环经济理论的"落地生根"和推广应用构建了具体的多重拓展-嵌套模型。     

Hypercycles versus parasites in the origin of life: model dependence in spatial hypercycle systems

Spatial hypercycle systems can be modelled by means of cellular automata or partial differential equations. In either model, two dimensional spirals or clusters can be formed. Different models give rise to slightly different spatial structures, but the response to parasites is fundamentally different: In cellular automata the hypercycle is resistant to parasites that are fatal in a partial differential equations model. In three dimensions scroll rings correspond to the two dimensional spirals. Numerical simulations on a partial differential equations model indicate that the scroll rings are unstable: The contract by a power law and disappear. Therefore, in three dimensions clusters seem to be the best candidate for the hypercycle resistant to parasites.     

Spatial stability analysis of Eigen's quasispecies model and the less than five membered hypercycle under global population regulation

A generalization of the “constant overall organization” constraint of Eigen's quasispecies and hypercycle models, called herein “global population regulation”, is shown to lead to mathematically tractable spatial generalizations of these two models. The spatially uniform steady state of Eigen's quasispecies model is shown to be stable and globally attracting for all possible values of the mutation and replication rates. In contrast, the spatially and temporally uniform solutions to the hypercycle with fewer than five members, the only ones insensitive to stochastic perturbations, are shown to be unstable, and a lower bound to the spatial inhomogeneities is obtained. The prospect that the spatially localized hypercycle might be immune to various instabilities cited in the literature is then briefly considered. Although spatial localization makes possible a much richer dynamical repertoire than previously considered, it is also more difficult to understand how Darwinian selection of hypercycles could result in a unique genetic code.     

Origin and evolution of heredity-metabolism system

The role of theoretical physics in the elucidation of the origin of life has been advanced by Eigen's hypercycle theory on ancient protein synthesis system and by Dyson's random drift theory on the autocatalytic formation of enzymes, although these approaches from the informational side involve many problems to be resolved. On the other hand, our C4N model calls for a stronger role of physico-chemistry in the understanding of the origin of life.Plant virus and movable genes could be the fossil vestiges of the ancient protein synthetic system, where tRNAmRNAgene. It is pointed out that functional differentiation of proteins closely correlates with the structure of the primitive tRNAs. Possible initial forms of the primitive tRNAs used by the earliest organisms are explicitly shown, in which the above correlation is carefully taken into account. The system of the primitive genes and the primitive enzymes in the proto-cellular membrane, say the marigranule, might simulate the earliest organism.     

A solvable selfreproductive hypercycle model for the selection of biological molecules

Summary By introducing a modified enzyme coupling in Eigen's hypercycle equations we have produced an exactly solvable selfreproductive hypercycle model. The model shows explicitly how collections of different macromolecular information carriers may coexist, through internal couplings, in the presence of constraints. We show how the selective value concept is manifested in the model and give simple criteria for selection among competing hypercycles.     

Natural self-organization of polynucleotides and polypeptides in protobiogenesis: Appearance of a protohypercycle

Basic thermal polyamino acids or proteinoids have been reported to be catalytic for both self-instructing polymerization of amino acids and internucleotide synthesis. We show theoretically that a complex suspension of thermal proteinoids, free amino acids, nucleotides and ATP as an energy source can exhibit an evolutionary character. The suspension can produce a prototype of Eigen's hypercycle, or protohypercycle, for which translation proceeds from amino acid to nucleotide. The protohypercycle is suggested to be an evolutionary precursor of the hypercycle, in which translation is from nucleotide to amino acid. The possibility that the Fox-Nakashima microsphere containing both lysine-rich and acidic proteinoids may work as a model of a protohypercycle is considered.     

Codons and Hypercycles

Several hypotheses on the origin of codon assignments imply that the present protein synthesizing machinery was already in place when the assignments were made. These are examined by computer modeling. The results do not suggest that assignments were optimized for resistance to reading and mutation errors, nor that the assignments are random. It is improbable that the number of species of amino acids increased in the course of evolution. An originally ambiguous dictionary is likely to have been subject to error catastrophe and is improbable. A relation between amino acid properties and their codons exists, and suggests that the codon assignments were established at the time of origin of the hypercycle, i.e. a system of aminoacyl synthetases which attaches amino acids to tRNA, and before the present protein synthesizing machinery was in place. The origin of a hypercycle is only possible if the system began with components which were catalytically active even when they did not form a self-replicating system. A model of such a system is proposed.     

Bifurcations and phase transitions in spatially extended two-member hypercycles

Mounting theoretical and experimental evidence indicates that the success of molecular replicators is strongly tied to the local nature of their interactions. Local dispersal in a given spatial domain, particularly on surfaces, might strongly enhance the growth and selection of fit molecules and their resistance to parasites. In this work the spatial dynamics of a simple hypercycle model consisting of two molecular species is analysed. In order to characterize it, both mean field models and stochastic, spatially explicit approaches are considered. The mean field approach predicts the presence of a saddle-node bifurcation separating a phase involving stable hypercycles from extinction, consistently with spatially explicit models, where an absorbing first-order phase transition is shown to exist and diffusion is explicitly introduced. The saddle-node bifurcation is shown to leave a ghost in the phase plane. A metapopulation-based model is also developed in order to account for the observed phases when both diffusion and reaction are considered. The role of information and diffusion as well as the relevance of these phases and the underlying spatial structures are discussed, and their potential implications for the evolution of early replicators are outlined.     

On the dimerization of the primitive tRNAs: implications in the origin of genetic code

RNAs that catalyse their own aminoacylation have been recently selected in vitro. These findings support the notion that the primitive aminoacyl-tRNA synthetases may have been RNAs. In this paper, we propose a structural model for the first aminoacyl-tRNA synthetase consisting of an RNA complex formed between two primitive tRNA molecules through two intermolecular loop-strand interactions, and with implications in the origin of the genetic code.     

Salinity Effects on the Adsorption of Nucleic Acid Compounds on Na-Montmorillonite: a Prebiotic Chemistry Experiment

Any proposed model of Earth’s primitive environments requires a combination of geochemical variables. Many experiments are prepared in aqueous solutions and in the presence of minerals. However, most sorption experiments are performed in distilled water, and just a few in seawater analogues, mostly inconsistent with a representative primitive ocean model. Therefore, it is necessary to perform experiments that consider the composition and concentration of dissolved salts in the early ocean to understand how these variables could have affected the absorption of organic molecules into minerals. In this work, the adsorption of adenine, adenosine, and 5’AMP onto Na⁺montmorillonite was studied using a primitive ocean analog (4.0 Ga) from experimental and computational approaches. The order of sorption of the molecules was: 5’AMP?>?adenine > adenosine. Infrared spectra showed that the interaction between these molecules and montmorillonite occurs through the NH₂ group. In addition, electrostatic interaction between negatively charged montmorillonite and positively charge N1 of these molecules could occur. Results indicate that dissolved salts affect the sorption in all cases; the size and structure of each organic molecule influence the amount sorbed. Specifically, the X-ray diffraction patterns show that dissolved salts occupy the interlayer space in Na-montmorillonite and compete with organic molecules for available sites. The adsorption capacity is clearly affected by dissolved salts in thermodynamic terms as deduced by isotherm models. Indeed, molecular dynamic models suggest that salts are absorbed in the interlamellar space and can interact with oxygen atoms exposed in the edges of clay or in its surface, reducing the sorption of the organic molecules. This research shows that the sorption process could be affected by high concentration of salts, since ions and organic molecules may compete for available sites on inorganic surfaces. Salt concentration in primitive oceans may have strongly affected the sorption, and hence the concentration processes of organic molecules on minerals.     

The information capacity of hypercycles

Hypercycles are information integration systems which are thought to overcome the information crisis of prebiotic evolution by ensuring the coexistence of several short templates. For imperfect template replication, we derive a simple expression for the maximum number of distinct templates n_m that can coexist in a hypercycle and show that it is a decreasing function of the length L of the templates. In the case of high replication accuracy we find that the product n_mL tends to a constant value, limiting thus the information content of the hypercycle. Template coexistence is achieved either as a stationary equilibrium (stable fixed point) or a stable periodic orbit in which the total concentration of functional templates is nonzero. For the hypercycle system studied here we find numerical evidence that the existence of an unstable fixed point is a necessary condition for the presence of periodic orbits.     

Dynamics of DNA molecules in gel studied by fluorescence microscopy

The dynamics of individual DNA molecules in a thin gel were studied with fluorescence microscopy. Driven by an electric field, molecules hooked around isolated obstacles and became extended. By analyzing molecular images, we identified the reptation tube and primitive chain. When the field was turned off, the molecules relaxed. The relaxation time tau1 and primitive chain length at equilibrium depend on N, the size of the molecule in base pairs, consistently with reptation theory. Using five yeast chromosomal DNAs ranging in size from 245 kb to 980 kb, we found that: These results constitute a way of sizing individual DNA molecules by imaging rather than by gel electrophoresis.     

Studies on evolutionary and selective properties of hypercycles using a Monte Carlo method

Summary The most relevant properties of hypercycles were previously studied mainly from a theoretical point of view. We have developed a Monte Carlo method simulating hypercyclic organization to obtain information about the dynamics of this prebiotic organization. Nucleation, growth, and selective properties have been tested and the results obtained are in good agreement with those of the theoretical predictions. The influence of hypercyclic organization of the error threshold has also been studied. As a consequence of the emergence of a hypercycle, the value of this threshold decreases. The amount of this decrease depends on the population size. Moreover, for some interval of quality factor values, either the hypercycle organization or an error catastrophe can be produced, depending on the initial conditions. The influence of these phenomena on both the dynamic behavior and evolutionary advantages of the hypercycle, as well as their decisive roles on genome size, are discussed.Presented at the FEBS Symposium on Genome Organization and Evolution, held in Crete, Greece, September 1–5, 1986     

Rates of fixation by lightning of carbon and nitrogen in possible primitive atmospheres

A thermochemical-hydrodynamic model of the production of trace species by electrical discharges has been used to estimate the rates of fixation of C and N by lightning in the primitive atmosphere. Calculations for various possible mixtures of CH4, CO2, CO, N2, H2, and H2O reveal that the prime species produced were probably HCN and NO and that the key parameter determining the rates of fixation was the ratio of C atoms to O atoms in the atmosphere. Atmospheres with C more abundant than O have large HCN fixation rates, in excess of 10(17) molecules J-1, but small NO yields. However, when O is more abundant than C, the NO fixation rate approaches 10(17) molecules J-1 while the HCN yield is small. The implications for the evolution of life are discussed.     

Formation of bioorganic compounds in aqueous solution induced by flames

Flames of flammable gases, when blown against a surface of an aqueous solution of organic compounds, were found to induce oxidation as well as other reactions in the solution. This reaction would be regarded as a new model for formation of bioorganic molecules in the primitive hydrosphere exposed to some radical-containing atmosphere.     

Group selection of early replicators and the origin of life

A major problem of the origin of life has been that of information integration. As Eigen (1971) has shown, a mutant distribution of RNAs replicating without the aid of a replicase cannot integrate sufficient information for the functioning of a higher-level unit utilizing several types of encoded enzymes. He proposed the hypercycle model to bridge this gap in prebiology. It can be shown by a nonlinear game model, incorporating mutation of a hypercycle, that the selection properties of hypercycles make them inefficient information integrators as they cannot compete favourably with all kinds of less efficient information carriers or mutationally coupled hypercycles. The stochastic corrector model is presented as an alternative resolution of Eigen's paradox. It assumes that replicative templates are competing within replicative compartments, whose selective values depend on the internal template composition via a catalytic acid in replication and "metabolism". The dynamics of template replication are analyzed by numerical simulation of master equations. Due to the stochasticity in replication and compartment fission the best compartment types recur. An Eigen equation at the compartment level is set up and calculated. Even selfish template mutants cannot destroy the system though they make it less efficient. The genetic information of templates is evaluated at both levels, and the higher (compartment) level successfully constrains the lower (template) one. Compartmentation together with stochastic effects is sufficient to integrate information dispersed in competitive replicators. Compartment selection is considered to be group selection of replicators. Implications for the origin of life are discussed.     

An organismic critique of molecular darwinism

The molecular darwinian approach to the emergence of life treats the competition between RNA sequences for nucleotide resources as the primordial selective process in prebiotic evolution, which prescribes possible pathways for the subsequent elaboration of organizational relationships. Since success in this competition is determined by the "phenotypic" properties of RNA strands in the absence of organizational context, the genesis of biotic organization is dependent upon the establishment of co-operative, hypercyclic interactions between competing RNA sequences. The thesis of this paper is that hypercycle theory is based on unwarranted assumptions about the conditions of prebiotic evolution, and that the implications of these assumptions run counter to both empirical evidence and to the rational by which natural selection operates in evolution generally. An organismic alternative to hypercycle theory is suggested, based on the catalytic microsphere and the thermodynamics of selection.     

Study of an error-prone hypercycle formed from two kinetically distinguishable species

Asymmetry within both the amplification factor values (Ak) and cross-catalytic hypercyclic constant (Kjk) and its influence on the stability of a two-membered error-prone hypercycle has been exhaustively studied from a deterministic point of view and the bifurcation diagram as a function of the quality factor (Q) has been obtained. In the more general case, several Q critical values appear, changing their relative position in the diagram depending on the Ak and Kjk values. The order of the Q critical values affects both the general properties of the system and the stability of the hypercyclic organization. The importance of this asymmetry in the selective and evolutionary properties of the hypercycle is also discussed.