Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species

Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn –algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata. Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an internal re-structuring of major submodules of the genome and Interactome networks related to cell cycling and cell growth. Contrary to the commonly held view of `standard’ Darwinist models of evolution, the evolution of organisms and species occurs through coupled multi-molecular transformations induced not only by the environment but actually realized through internal re-organizations of genome and interactome networks. The biological, evolutionary processes involve certain epigenetic transformations that are responsible for phenotypic expression of the genome and Interactome transformations initiated at the quantum-molecular level. It can thus be said that only quantum genetics can provide correct explanations of evolutionary processes that are initiated at the quantum--multi-molecular levels and propagate to the higher levels of organismal and species evolution.

Biological evolution should be therefore regarded as a multi-scale process which is initiated by underlying quantum (coupled) multi-molecular transformations of the genomic and interactomic networks, followed by specific phenotypic transformations at the level of organism and the variable biogroupoids associated with the evolution of species which are essential to the survival of the species. The theoretical framework introduced in this article also paves the way to a Quantitative Biology approach to biological evolution at the quantum-molecular, as well as at the organismal and species levels. This is quite a substantial modification of the 'established’ modern Darwinist, and also of several so-called `molecular evolution’ theories

Adaptive evolution of molecular phenotypes

Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a quantitative trait under time-dependent selection, which arises from environmental changes or through fitness interactions with other co-evolving phenotypes. We analyze a model of trait evolution under mutations and genetic drift in a single-peak fitness seascape. The fitness peak performs a constrained random walk in the trait amplitude, which determines the time-dependent trait optimum in a given population. We derive analytical expressions for the distribution of the time-dependent trait divergence between populations and of the trait diversity within populations. Based on this solution, we develop a method to infer adaptive evolution of quantitative traits. Specifically, we show that the ratio of the average trait divergence and the diversity is a universal function of evolutionary time, which predicts the stabilizing strength and the driving rate of the fitness seascape. From an information-theoretic point of view, this function measures the macro-evolutionary entropy in a population ensemble, which determines the predictability of the evolutionary process. Our solution also quantifies two key characteristics of adapting populations: the cumulative fitness flux, which measures the total amount of adaptation, and the adaptive load, which is the fitness cost due to a population's lag behind the fitness peak.Comment: Figures are not optimally displayed in Firefo

Molecular Evolution in Time Dependent Environments

The quasispecies theory is studied for dynamic replication landscapes. A meaningful asymptotic quasispecies is defined for periodic time dependencies. The quasispecies' composition is constantly changing over the oscillation period. The error threshold moves towards the position of the time averaged landscape for high oscillation frequencies and follows the landscape closely for low oscillation frequencies.Comment: 5 pages, 3 figures, Latex, uses Springer documentclass llncs.cl

Molecular Evolution in Collapsing Prestellar Cores

We have investigated the evolution and distribution of molecules in collapsing prestellar cores via numerical chemical models, adopting the Larson-Penston solution and its delayed analogues to study collapse. Molecular abundances and distributions in a collapsing core are determined by the balance among the dynamical, chemical and adsorption time scales. When the central density n_H of a prestellar core with the Larson-Penston flow rises to 3 10^6 cm^{-3}, the CCS and CO column densities are calculated to show central holes of radius 7000 AU and 4000 AU, respectively, while the column density of N2H+ is centrally peaked. These predictions are consistent with observations of L1544. If the dynamical time scale of the core is larger than that of the Larson-Penston solution owing to magnetic fields, rotation, or turbulence, the column densities of CO and CCS are smaller, and their holes are larger than in the Larson-Penston core with the same central gas density. On the other hand, N2H+ and NH3 are more abundant in the more slowly collapsing core. Therefore, molecular distributions can probe the collapse time scale of prestellar cores. Deuterium fractionation has also been studied via numerical calculations. The deuterium fraction in molecules increases as a core evolves and molecular depletion onto grains proceeds. When the central density of the core is n_H=3 10^6 cm^{-3}, the ratio DCO+/HCO+ at the center is in the range 0.06-0.27, depending on the collapse time scale and adsorption energy; this range is in reasonable agreement with the observed value in L1544.Comment: 21 pages, 17 figure

The evolution of Giant Molecular Filaments

In recent years there has been a growing interest in studying giant molecular filaments (GMFs), which are extremely elongated (> 100pc in length) giant molecular clouds (GMCs). They are often seen as inter-arm features in external spiral galaxies, but have been tentatively associated with spiral arms when viewed in the Milky Way. In this paper, we study the time evolution of GMFs in a high-resolution section of a spiral galaxy simulation, and their link with spiral arm GMCs and star formation, over a period of 11Myrs. The GMFs generally survive the inter-arm passage, although they are subject to a number of processes (e.g. star formation, stellar feedback and differential rotation) which can break the giant filamentary structure into smaller sections. The GMFs are not gravitationally bound clouds as a whole, but are, to some extent, confined by external pressure. Once they reach the spiral arms, the GMFs tend to evolve into more substructured spiral arm GMCs, suggesting that GMFs may be precursors to arm GMCs. Here, they become incorporated into the more complex and almost continuum molecular medium that makes up the gaseous spiral arm. Instead of retaining a clear filamentary shape, their shapes are distorted both by their climb up the spiral potential and their interaction with the gas within the spiral arm. The GMFs do tend to become aligned with the spiral arms just before they enter them (when they reach the minimum of the spiral potential), which could account for the observations of GMFs in the Milky Way.Comment: 15 pages, 11 figures, MNRAS accepte

Galaxy chemical evolution models: The role of molecular gas formation

In our classical grid of multiphase chemical evolution models, star formation in the disc occurs in two steps: first, molecular gas forms, and then stars are created by cloud-cloud collisions or interactions of massive stars with the surrounding molecular clouds. The formation of both molecular clouds and stars are treated through the use of free parameters we refer to as efficiencies. In this work, we modify the formation of molecular clouds based on several new prescriptions existing in the literature, and we compare the results obtained for a chemical evolution model of theMilkyWay Galaxy regarding the evolution of the Solar region, the radial structure of the Galactic disc and the ratio between the diffuse and molecular components, H I /H 2 . Our results show that the six prescriptions we have tested reproduce fairly consistent most of the observed trends, differing mostly in their predictions for the (poorly constrained) outskirts of the Milky Way and the evolution in time of its radial structure. Among them, the model proposed by Ascasibar et al. (in preparation), where the conversion of diffuse gas into molecular clouds depends on the local stellar and gas densities as well as on the gas metallicity, seems to provide the best overall match to the observed data

Molecular evolution research Annual report

Amino acid syntheses by heating formaldehyde and ammonia mixtures in molecular evolution researc