The ancient Virus World and evolution of cells
E. Koonin, T. Senkevich, V. Dolja
BackgroundRecent advances in genomics of viruses and cellular life forms have greatly stimulated interest in the origins and evolution of viruses and, for the first time, offer an opportunity for a data-driven exploration of the deepest roots of viruses. Here we briefly review the current views of virus evolution and propose a new, coherent scenario that appears to be best compatible with comparative-genomic data and is naturally linked to models of cellular evolution that, from independent considerations, seem to be the most parsimonious among the existing ones.ResultsSeveral genes coding for key proteins involved in viral replication and morphogenesis as well as the major capsid protein of icosahedral virions are shared by many groups of RNA and DNA viruses but are missing in cellular life forms. On the basis of this key observation and the data on extensive genetic exchange between diverse viruses, we propose the concept of the ancient virus world. The virus world is construed as a distinct contingent of viral genes that continuously retained its identity throughout the entire history of life. Under this concept, the principal lineages of viruses and related selfish agents emerged from the primordial pool of primitive genetic elements, the ancestors of both cellular and viral genes. Thus, notwithstanding the numerous gene exchanges and acquisitions attributed to later stages of evolution, most, if not all, modern viruses and other selfish agents are inferred to descend from elements that belonged to the primordial genetic pool. In this pool, RNA viruses would evolve first, followed by retroid elements, and DNA viruses. The Virus World concept is predicated on a model of early evolution whereby emergence of substantial genetic diversity antedates the advent of full-fledged cells, allowing for extensive gene mixing at this early stage of evolution. We outline a scenario of the origin of the main classes of viruses in conjunction with a specific model of precellular evolution under which the primordial gene pool dwelled in a network of inorganic compartments. Somewhat paradoxically, under this scenario, we surmise that selfish genetic elements ancestral to viruses evolved prior to typical cells, to become intracellular parasites once bacteria and archaea arrived at the scene. Selection against excessively aggressive parasites that would kill off the host ensembles of genetic elements would lead to early evolution of temperate virus-like agents and primitive defense mechanisms, possibly, based on the RNA interference principle. The emergence of the eukaryotic cell is construed as the second melting pot of virus evolution from which the major groups of eukaryotic viruses originated as a result of extensive recombination of genes from various bacteriophages, archaeal viruses, plasmids, and the evolving eukaryotic genomes. Again, this vision is predicated on a specific model of the emergence of eukaryotic cell under which archaeo-bacterial symbiosis was the starting point of eukaryogenesis, a scenario that appears to be best compatible with the data.ConclusionThe existence of several genes that are central to virus replication and structure, are shared by a broad variety of viruses but are missing from cellular genomes (virus hallmark genes) suggests the model of an ancient virus world, a flow of virus-specific genes that went uninterrupted from the precellular stage of life's evolution to this day. This concept is tightly linked to two key conjectures on evolution of cells: existence of a complex, precellular, compartmentalized but extensively mixing and recombining pool of genes, and origin of the eukaryotic cell by archaeo-bacterial fusion. The virus world concept and these models of major transitions in the evolution of cells provide complementary pieces of an emerging coherent picture of life's history.ReviewersW. Ford Doolittle, J. Peter Gogarten, and Arcady Mushegian.
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Biology, Medicine
Understanding the role of autoencoders for stiff dynamical systems using information theory
Vijayamanikandan Vijayarangan, Harshavardhana A. Uranakara, Francisco E. Hernández–Pérez
et al.
Using information theory, this study provides insights into how the construction of latent space of autoencoder (AE) using deep neural network (DNN) training finds a smooth (non-stiff) low-dimensional manifold in the stiff dynamical system. Our recent study (Vijayarangan et al. 2023) reported that an AE combined with neural ODE (NODE) as a surrogate reduced order model (ROM) for the integration of stiff chemically reacting systems led to a significant reduction in the temporal stiffness, and the behavior was attributed to the identification of a slow invariant manifold by the nonlinear projection using the AE. The present work offers a fundamental understanding of the mechanism of formation of a non-stiff latent space and stiffness reduction by employing concepts from information theory and better mixing. The learning mechanisms of both the encoder and the decoder are explained by plotting the evolution of mutual information and identifying two different phases. Subsequently, the density distribution is plotted for the physical and latent variables, which shows the transformation of the rare event in the physical space to a highly likely (more probable) event in the latent space provided by the nonlinear autoencoder. Finally, the nonlinear transformation leading to density redistribution is explained using concepts from information theory and probability.
Electrical engineering. Electronics. Nuclear engineering, Computer software