Formamide and the origin of life

The complexity of life boils down to the definition: “self-sustained chemical system capable of undergoing Darwinian evolution” (Joyce, 1994) [1]. The term “self-sustained” implies a set of chemical reactions capable of harnessing energy from the environment, using it to carry out programmed anabolic and catabolic functions. We briefly present our opinion on the general validity of this definition.Running anabolic and catabolic functions entails complex chemical information whose stability, reproducibility and evolution constitute the core of what is dubbed genetics.Life as-we-know-it is made of the intimate interaction of metabolism and genetics, both built around the chemistry of the most common elements of the Universe (hydrogen, oxygen, nitrogen, carbon). Other elements like phosphorus and sulphur play important but ancillary and potentially replaceable roles.The reproducible interaction of metabolic and genetic cycles results in the hypercycles of organization and de-organization of chemical information that we consider living entities. In order to approach the problem of the origin of life it is therefore reasonable to start from the assumption that both metabolism and genetics had a common origin, shared a common chemical frame, were embedded in physical–chemical conditions favourable for the onset of both.The most abundant three-atoms organic compound in interstellar environment is hydrogen cyanide HCN, the most abundant three-atoms inorganic compound is water H₂O. The combination of the two results in the formation of formamide H₂NCOH. We have explored the chemistry of formamide in conditions compatible with the synthesis and the stability of compounds of potential pre-genetic and pre-metabolic interest. We discuss evidence showing (i) that all the compounds necessary for the build-up of nucleic acids are easily obtained abiotically, (ii) that essentially all the steps leading to the spontaneous generation of RNA are abiotically possible, (iii) that the key compounds of extant metabolic cycles are obtained in the same chemical frame, often in the same test tube.How close are these observations to a plausible scenario for the origin of life?     

Prebiological evolution and the physics of the origin of life

The basic tenet of the heterotrophic theory of the origin of life is that the maintenance and reproduction of the first living systems depended primarily on prebiotically synthesized organic molecules. It is unlikely that any single mechanism can account for the wide range of organic compounds that may have accumulated on the primitive Earth, suggesting that the prebiotic soup was formed by contributions from endogenous syntheses in reducing environments, metal sulphide-mediated synthesis in deep-sea vents, and exogenous sources such as comets, meteorites and interplanetary dust. The wide range of experimental conditions under which amino acids and nucleobases can be synthesized suggests that the abiotic syntheses of these monomers did not take place under a narrow range defined by highly selective reaction conditions, but rather under a wide variety of settings. The robustness of this type of chemistry is supported by the occurrence of most of these biochemical compounds in the Murchison meteorite. These results lend strong credence to the hypothesis that the emergence of life was the outcome of a long, but not necessarily slow, evolutionary processes. The origin of life may be best understood in terms of the dynamics and evolution of sets of chemical replicating entities. Whether such entities were enclosed within membranes is not yet clear, but given the prebiotic availability of amphiphilic compounds this may have well been the case. This scheme is not at odds with the theoretical models of self-organized emerging systems, but what is known of biology suggest that the essential traits of living systems could have not emerged in the absence of genetic material able to store, express and, upon replication, transmit to its progeny information capable of undergoing evolutionary change. How such genetic polymer first evolved is a central issue in origin-of-life studies.     

物理学中的“规范”及其历史起源

本文对物理学中的规范理论作了通俗介绍,然后讨论物理学中"规范"一词的起源.规范本来是尺子或者测度标准的意思.经典电磁学中使用"规范"一词是在外尔1928~1929年提出电磁场中量子带电粒子的规范原理之后.如果不是因为外尔曾经于1918~1919年作过失败的尝试,试图从时空中平行移动导致的尺度变化来导出电磁矢量势,那么后来人们就不会将"规范"一词用于电磁矢量势.本文也梳理薛定谔、福克和伦敦的贡献.     

"Magic melters" have geometrical origin

Recent experimental reports bring out extreme size sensitivity in the heat capacities of gallium and aluminum clusters. In the present work we report results of our extensive ab initio molecular dynamical simulations on Ga30 and Ga31, the pair which has shown rather dramatic size sensitivity. We trace the origin of this size sensitive heat capacities to the relative order in their respective ground state geometries. Such an effect of nature of the ground state on the characteristics of heat capacity is also seen in case of small gallium and sodium clusters, indicating that the observed size sensitivity is a generic feature of small clusters.     

Chromosome evolution with naked eye: palindromic context of the life origin

Based on the representation of the DNA sequence as a two-dimensional (2D) plane walk, we consider the problem of identification and comparison of functional and structural organizations of chromosomes of different organisms. According to the characteristic design of 2D walks we identify telomere sites, palindromes of various sizes and complexity, areas of ribosomal RNA, transposons, as well as diverse satellite sequences. As an interesting result of the application of the 2D walk method, a new duplicated gigantic palindrome in the X human chromosome is detected. A schematic mechanism leading to the formation of such a duplicated palindrome is proposed. Analysis of a large number of the different genomes shows that some chromosomes (or their fragments) of various species appear as imperfect gigantic palindromes, which are disintegrated by many inversions and the mutation drift on different scales. A spread occurrence of these types of sequences in the numerous chromosomes allows us to develop a new insight of some accepted points of the genome evolution in the prebiotic phase.     

Neutrinos,supernovae, and the origin of the heavy elements

Stars of～8-100 M_⊙end their lives as core-collapse supernovae(SNe). In the process they emit a powerful burst of neutrinos,produce a variety of elements, and leave behind either a neutron star or a black hole. The wide mass range for SN progenitors results in diverse neutrino signals, explosion energies, and nucleosynthesis products. A major mechanism to produce nuclei heavier than iron is rapid neutron capture, or the r process. This process may be connected to SNe in several ways. A brief review is presented on current understanding of neutrino emission, explosion, and nucleosynthesis of SNe.     

Microscopic origin of the phenomenological equilibrium "Doping limit Rule" in n-type III-V semiconductors

The highest equilibrium free-carrier doping concentration possible in a given material is limited by the "pinning energy" which shows a remarkable universal alignment in each class of semiconductors. Our first-principles total energy calculations reveal that equilibrium n-type doping is ultimately limited by the spontaneous formation of close-shell acceptor defects: the (3-)-charged cation vacancy in AlN, GaN, InP, and GaAs and the (1-)-charged DX center in AlAs, AlP, and GaP. This explains the alignment of the pinning energies and predicts the maximum equilibrium doping levels in different materials.     

Evolutionary dynamics of RNA-like replicator systems: A bioinformatic approach to the origin of life

We review computational studies on prebiotic evolution, focusing on informatic processes in RNA-like replicator systems. In particular, we consider the following processes: the maintenance of information by replicators with and without interactions, the acquisition of information by replicators having a complex genotype–phenotype map, the generation of information by replicators having a complex genotype–phenotype–interaction map, and the storage of information by replicators serving as dedicated templates. Focusing on these informatic aspects, we review studies on quasi-species, error threshold, RNA-folding genotype–phenotype map, hypercycle, multilevel selection (including spatial self-organization, classical group selection, and compartmentalization), and the origin of DNA-like replicators. In conclusion, we pose a future question for theoretical studies on the origin of life.     

Quantum gravity,the origin of time and time's arrow

The local Lorentz and diffeomorphism symmetries of Einstein's gravitational theory are spontaneously broken by a Higgs mechanism by invoking a phase transition in the early universe, at a critical temperature T_c below which the symmetry is restored. The spontaneous breakdown of the vacuum state generates an external time, and the wave function of the universe satisfies a time-dependent Schrödinger equation, which reduces to the Wheeler-deWitt equation in the classical regime for T<T_c, allowing a semiclassical WKB approximation to the wave function. The conservation of energy is spontaneously violated for T>T_c, and matter is created fractions of seconds after the big bang, generating the matter in the Universe. The time direction of the vacuum expectation value of the scalar Higgs field generates a time asymmetry, which defines the cosmological arrow of time and the direction of increasing entropy as the Lorentz symmetry is restored at low temperatures.     

Insoluble organic matter in chondrites: Archetypal melanin-like PAH-based multifunctionality at the origin of life?

An interdisciplinary review of the chemical literature that points to a unifying scenario for the origin of life, referred to as the Primordial Multifunctional organic Entity (PriME) scenario, is provided herein. In the PriME scenario it is suggested that the Insoluble Organic Matter (IOM) in carbonaceous chondrites, as well as interplanetary dust particles from meteorites and comets may have played an important role in the three most critical processes involved in the origin of life, namely 1) metabolism, via a) the provision and accumulation of molecules that are the building blocks of life, b) catalysis (e.g., by templation), and c) protection of developing life molecules against radiation by excited state deactivation; 2) compartmentalization, via adsorption of compounds on the exposed organic surfaces in fractured meteorites, and 3) replication, via deaggregation, desorption and related physical phenomena. This scenario is based on the hitherto overlooked structural and physicochemical similarities between the IOM and the dark, insoluble, multifunctional melanin polymers found in bacteria and fungi and associated with the ability of these microorganisms to survive extreme conditions, including ionizing radiation. The underlying conceptual link between these two materials is strengthened by the fact that primary precursors of bacterial and fungal melanins (collectively referred to herein as allomelanins) are hydroxylated aromatic compounds like homogentisic acid and 1,8-dihydroxynaphthalene, and that similar hydroxylated aromatic compounds, including hydroxynaphthalenes, figure prominently among possible components of the organic materials on dust grains and ices in the interstellar matter, and may be involved in the formation of IOM in meteorites. Inspired by this rationale, a vis-à-vis review of the properties of IOM from various chondrites and non-nitrogenous allomelanin pigments from bacteria and fungi is provided herein. The unrecognized similarities between these materials may pave the way for a novel scenario at the origin of life, in which IOM-related complex organic polymers delivered to the early Earth are proposed to serve as PriME and were preserved and transformed in those primitive forms of life that shared the ability to synthesize melanin polymers playing an important role in the critical processes underlying the establishment of terrestrial eukaryotes.