Polynucleotide evolution, hypercycles and the origin of the genetic code

Experiments on polynucleotide replication are described within the frame of a kinetic theory of molecular evolution. Four principles of early evolution are discussed and illustrated by means of a model for the origin of translation.     

Exobiology revisited

The term “Exobiology” was introduced about 25 years ago, at a time when intensive discussions were under way concerning plans for the biological exploration of Mars. The search for life on Mars was to be a critical test of the concept of chemical evolution- not an end in itself. After the Viking mission, when it became apparent that prospects were dim for the discovery of extraterrestrial life within our solar system, many people concluded that this new field of endeavor would soon expire. Quite the contrary, over the past decade, the field has broadened considerably into a multidisciplinary approach to understanding the circumstances that led to the origin of life and the interplay between the evolution of this planet and its biota.     

Life as a set of matter transformation cycles: ecological attributes of life.

An approach to searching for extraterrestrial life on the base of "autotroph" concept of the origin of life is presented in the paper. According to this concept the origin of life took place in three stages. The first stage was developed inside the global geochemical cycle in which the turnover of different chemical transformations was implemented by solar radiation and/or heat energy of bowels of the Earth. At the second stage, after the autocatalytic systems have emerged these systems evolved as a result of "natural selection" by autocatalysis parameters up to emergence of special inheritance systems that drastically improved the autocatalysis parameters. The best in terms of autocatalysis parameters were the autocatalysis systems based on phase-separated particles where complex structures can form not only on the basis of covalent interactions. Such autocatalysis systems can emerge only in liquid in a certain range of temperatures and pressures. At this stage the geochemical cycle complicated involving new substances. At the third stage the evolution involved improvement of inheritance systems resulting in formation of the modern type of genetic apparatus. This concept formed the basis to consider approaches to experimental modeling of major aspects of the origin of life and to outlining some general features of life that can extend the sensitive horizon of searching for extraterrestrial life.     

On the levels of enzymatic substrate specificity: implications for the early evolution of metabolic pathways.

The most frequently invoked explanation for the origin of metabolic pathways is the retrograde evolution hypothesis. In contrast, according to the so-called "patchwork" theory, metabolism evolved by the recruitment of relatively inefficient small enzymes of broad specificity that could react with a wide range of chemically related substrates. In this paper it is argued that both sequence comparisons and experimental results on enzyme substrate specificity support the patchwork assembly theory. The available evidence supports previous suggestions that gene duplication events followed by a gradual neoDarwinian accumulation of mutations and other minute genetic changes lead to the narrowing and modification of enzyme function in at least some primordial metabolic pathways.     

A review of recent results on cosmic gamma-ray bursts

The results obtained on cosmic gamma-ray bursts over the last several years are reviewed and compared with the older “historical” results. Fine time resolution measurements of burster light curves continue to reveal structure at the millisecond and sub-millisecond level, suggesting a compact object origin. Similarly, the evolution of the low energy X-ray spectra of bursts towards shapes consistent with 1–2 keV blackbodies may be interpreted in terms of a neutron star origin, as can the continuing detection of absorption and emission features. The statistical evidence, however, argues strongly for an isotropic distribution which has been completely sampled. To reconcile this with galactic neutron stars requires the assumption that they are Population II objects. Counterpart searches have evolved to the point where they may be carried out within days of an event, and a soft X-ray source has now been detected in the error box of one recent burst.     

代谢起源进化的分子模拟研究

新陈代谢为生命提供了物质和能量基础,与生命起源和进化密切相关.然而,由于缺乏化石证据,代谢的起源及其影响生物进化的分子机制等重要问题尚待解决.近年来,网络扩张算法等分子模拟方法的出现为解决这些问题提供了新途径.本文综述了近年来代谢起源进化的分子模拟研究,以期为相关领域学科发展提供新思路.     

Evolution of anticodons

Anticodons are trinucleotides in transfer RNA (tRNA) molecules. The latter carry amino acids for insertion into the polypeptide sequences of proteins during the translation of messenger RNA (mRNA) molecules. Messenger RNA molecules are transcribed from genes. Evolution of tRNA molecules has resulted in a set of anticodons for the 20 amino acids that are used in protein synthesis. This set of anticodons is slightly different in mitochondrial codes from the set that is used in the nuclear “universal” code. Theories for the evolution of the code include frozen accident, doublet expansion, repeating triplets and coevolutionary distribution. The number of codons has always been fixed at 64 by mathematical rules, but because an anticodon may pair with more than one codon, the number of anticodons is only 54 in the universal code, is smaller in mitochondrial codes, and was probably even smaller in archetypal primitive codes. Evidence of anticodon evolution can be seen by comparing mitochondrial codes with the universal code. Codes used by very primitive organisms that are now extinct might have specified fewer amino acids than are now used.     

On initial steps of chemical prebiotic evolution: Triggering autocatalytic reaction of oligomerization

Searching for extraterrestrial life attracts more and more attention. However this searching hardly can be effective without sufficiently universal concept of life origin, which incidentally tackles a problem of origin of life on the Earth. A concept of initial stages of life origin is stated in the paper. The concept eliminates key difficulties in the problem of life origin, and allows experimental verification of it. According to the concept the predecessor of living beings has to be sufficiently simple to provide non-zero probability of self-assembling during short (in geological or cosmic scale) time. In addition the predecessor has to be capable of autocatalysis, and further complication (evolution). A possible scenario of initial stage of life origin, which can be realized both on other planets, and inside experimental facility is considered. In the scope of the scenario a theoretical model of multivariate oligomeric autocatalyst is presented. Results of computer simulation of two versions of oligomeric autocatalytic reactions are presented. It is shown that the contribution of monomer activation reaction is essential, and in some cases autocatalysis in polymerizing reaction can be achieved without catalyzing proper monomer binding reaction.     

Direct interaction between amino acids and nucleotides as a possible physicochemical basis for the origin of the genetic code.

A study of the association of homocodonic amino acids and selected heterocodonic amino acids with selected nucleotides in aqueous solution was undertaken to examine a possible physical basis for the origin of codon assignments. These interactions were studied using 1H nuclear magnetic resonance spectroscopy (NMR). Association constants for the various interactions were determined by fitting the changes in the chemical shifts of the anomeric and ring protons of the nucleoside moieties as a function of amino acid concentration to an isotherm which described the binding interaction. The strongest association of all homocodonic amino acids were with their respective anticodonic nucleotide sequences. The strength of association was seen to increase with increase in the chain length of the anticodonic nucleotide. The association of these amino acids with different phosphate esters of nucleotides suggests that a definite isomeric structure is required for association with a specified amino acid; the 5'-mononucleotides and (3'-5')-linked dinucleotides are the favored geometries for strong associations. Use of heterocodonic amino acids and nonprotein amino acids supports these findings. We conclude that there is at least a physicochemical, anticodonic contribution to the origin of the genetic code.     

Type I supernovae origin: “Dualistic” hypothesis

Stars that explode as Type I Supernovae (SNI) are white dwarfs with masses practically equal to the Chandrasekhar limit M_ch. These white dwarfs forme either as a result of gas overflow onto a degenerate component in a binary system or due to the evolution of nuclei of the stars whose mass, on the main sequence, was 3 to 7 M_o. The masses of their nuclei are quite close to M_ch. It is convenient to consider three types of stellar evolution 1) “hyperbolic”: masses of nuclei formed as a result of evolution are > M_ch; such evolution ends in a Type II Supernova (SNII) outburst; 2) “parabolic” - masses of nuclei ≈ M_ch, with the evolution ending in an SNI outburst; 3) “elliptical” with nuclei masses < M_ch. The latter type of evolution leads to the formation of planetary nebulae and white dwarfs. A new hypothesis is suggested that explains more frequent occurrence of SNI in irregular galaxies by flashes of star formation.     

集成化过程工程环境及其体系结构

现代化的企事业是一个极其复杂的集成化的人机系统,其内部运作需要基于计算机的应用系统的支持.因此本文讨论了一个以过程工程为核心的,将过程工程和软件工程融合为一体的集成化过程工程环境IPEE,提出了以过程模型为中心的IPEE的总体结构,并设计了分布式的过程运作环境的体系结构.     

Crushing strength of porous ice-mineral bodies-relevance for comets

In laboratory investigations with fluffy, highly porous ice and ice-dust bodies a new mechanism could be identified which strengthens the porous bodies. The process takes place under isothermal conditions and leads to the formation of ice bridges between the ice (dust) particles. It is driven solely by the dependence of the partial pressure of water vapour on the curvature of the particles. This mechanism is generally called “sintering”. A theory for the crushing strength of a porous ice and ice-dust agglomerate is developed which describes the experimental results on isothermal changes is strength due to sintering quantitatively well. The relevance for the evolution of comets is discussed.     

The influence of gravity on the structure and functions of plant material

Growth process generate plant form and relate to most physiological functions. The Earth's gravity force affects plant growth in both obvious and subtle ways. It is a major environmental influence on morphology and physiology of plants. Gravity is less important as an agent for plant stress than as an environmental signal to guide growth. The plant's bioaccelerometers are remarkably sensitive, especially in hypogravity. Simulation (clinostat) studies and experiments in satellite laboratories are needed to understand the sensing, transduction, and response characteristics of g related mechanisms. By examining how plants alter growth processes to accomplish developmental or physiological “objectives” we may find it pragmatically desirable to ask ourselves how we might design a plant to achieve such responses to environmental influences. Examples of this design engineering approach for gravity related effects are described as an aid to experimentation.     

Survival of microorganisms in space protected by meteorite material: results of the experiment 'EXOBIOLOGIE' of the PERSEUS mission.

During the early evolution of life on Earth, before the formation of a protective ozone layer in the atmosphere, high intensities of solar UV radiation of short wavelengths could reach the surface of the Earth. Today the full spectrum of solar UV radiation is only experienced in space, where other important space parameters influence survival and genetic stability additionally, like vacuum, cosmic radiation, temperature extremes, microgravity. To reach a better understanding of the processes leading to the origin, evolution and distribution of life we have performed space experiments with microorganisms. The ability of resistant life forms like bacterial spores to survive high doses of extraterrestrial solar UV alone or in combination with other space parameters, e.g. vacuum, was investigated. Extraterrestrial solar UV was found to have a thousand times higher biological effectiveness than UV radiation filtered by stratospheric ozone concentrations found today on Earth. The protective effects of anorganic substances like artificial or real meteorites were determined on the MIR station. In the experiment EXOBIOLOGIE of the French PERSEUS mission (1999) it was found that very thin layers of anorganic material did not protect spores against the deleterious effects of energy-rich UV radiation in space to the expected amount, but that layers of UV radiation inactivated spores serve as a UV-shield by themselves, so that a hypothetical interplanetary transfer of life by the transport of microorganisms inside rocks through the solar system cannot be excluded, but requires the shielding of a substantial mass of anorganic substances.     

High-velocity impact experiments needed to improve our understanding of the asteroids

The lifetime of almost all the asteroids against catastrophic impact events is less than the age of the solar system, implying that the asteroids can be considered as outcomes of catastrophic collisions. Therefore to understand their physical properties (structure, shape, rotation, regolith development) and their family memberships (since families are generated by the escape of breakup fragments), a systematic knowledge of the outcomes of catastrophic impacts under a variety of conditions seems needed. In particular, interesting fields to be explored by laboratory experiments are: the dependence of the critical energy densities associated with various degrees of fragmentation on the target's size and composition; the velocity distribution of the fragments and the inelasticity of the process in different cases; the shape of the fragments and its possible correlation with other quantities; the way a dust- or regolith-covered target affects the collisional outcomes; the angular momentum partitioning and the rotation of the fragments. On this latter problem very few experimental results are presently available; on the other hand, the rotation of small asteroids presents several intriguing “anomalies”.

A significant progress of our understanding of asteroid collisional evolution and related phenomena can be provided by new laboratory experiments of collisional breakup. The targets should have spherical and/or irregular shape (up to axial ratios of the order of 2), and should be made of (possibly different) geological materials. The interesting projectile velocities are of the order of the relative velocities commonly found among asteroids, i.e., in the range 1 to 10 Kms⁻¹. In order to get catastrophic collisions, the ratio of the projectile kinetic energy to the target mass (≡E/M) has to be chosen within a “critical” range (for basalt targets, from 10⁶ to 10⁸ erg/g). In some particular cases, this kind of experiments has been already performed in past (Gault and Wedekind [10]; Fujiwara et al. [7]; Fujiwara and Tsukamoto [9]); however the generalization of the results to a wide range of experimental conditions is lacking, and many problems of outstanding importance to model asteroid evolution are still completely open.     

Collection of cometary dust

Rendezvous Missions to Comets lead to low velocities at the nucleus of the comet. The resulting impact velocity of the cometary dust on a target will range between 10 and 400 m/s. The dust particle which impacts on a target can be collected for a subsequent in-situ analysis.

The collection efficiency of a target depends in addition to obvious geometrical conditions upon the surface of the target. The surface characteristics can be divided into two groups:

• “dirty” surfaces, covered with silicate or hydrocarbon compounds (for example vacuum grease),

• “clean” surfaces, like gold (with additional sputtering).

This paper deals with the experimental and theoretical investigation of the collection efficiency of “clean” targets. Laboratory experiments are described which were conducted at the Technische Universität München, Lehrstuhl für Raumfahrttechnik, and the Max-Planck-Institut für Kernphysik, Heidelberg. In both experiments an electromagnetic accelerator is used to accelerate different types of dust in vacuum to velocities between 10 and 400 m/s.

The target is then examined under the microscope and a secondary ion mass spectrometer (which is a model of the laboratory carried on board of the spacecraft for “in situ” analysis). The adhesion of the dust grains at the target is evaluated experimentally in an ultracentrifuge.     

面向装备RUL预测的平行仿真技术

装备平行仿真是系统建模与仿真领域的新兴仿真技术,已经成为研究热点。在装备维修保障领域中,分析了装备剩余寿命（RUL）预测存在的突出问题,即模型参数固定、不具备自适应演化能力,成为阻碍实现装备剩余寿命自适应预测的首要因素。结合装备平行仿真理论,在建模分析的基础上提出了面向装备剩余寿命预测的平行仿真框架,该框架以Wiener状态空间模型为基础仿真模型,在动态注入的装备退化观测数据驱动下,利用期望最大化（EM）算法在线更新模型参数,并利用卡尔曼滤波（KF）算法实现仿真输出数据与观测数据的同化（DA）,从而实现仿真模型动态演化,使得仿真输出不断逼近装备真实退化状态,为准确预测剩余寿命提供高逼真度仿真模型和数据输出。以某轴承性能退化数据为数据驱动源,对该框架进行了验证,仿真结果表明平行仿真方法能准确仿真装备性能退化过程,在提高预测精度的基础上实现了装备剩余寿命的自适应预测,有力证明了平行仿真方法的可行性和有效性。      

Life on Mars? II. Physical restrictions.

The primary physical factors important to life's evolution on a planet include its temperature, pressure and radiation regimes. Temperature and pressure regulate the presence and duration of liquid water on the surface of Mars. The prolonged presence of liquid water is essential for the evolution and sustained presence of life on a planet. It has been postulated that Mars has always been a cold dry planet; it has also been postulated that early mars possessed a dense atmosphere of CO2 (> or = 1 bar) and sufficient water to cut large channels across its surface. The degree to which either of these postulates is true correlates with the suitability of Mars for life's evolution. Although radiation can destroy living systems, the high fluxes of UV radiation on the martian surface do not necessarily stop the origin and early evolution of life. The probability for life to have arisen and evolved to a significant degree on Mars, based on the postulated ranges of early martian physical factors, is almost solely related to the probability of liquid water existing on the planet for at least hundreds of millions to billions of years.     

A theoretical review of SS 433

The “twin jet model” for SS 433 is briefly described, and its likely superiorority to other models demonstrated. It is then used as a framework within which the implications of the main observational results are discussed. Many theoretical questions about SS 433 are raised, but only few are answered.