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Register a new userAn Illustrated Introduction to the Basic Biological Principles
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Simon Fu
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Both external environmental selection and internal lower-level evolution are essential for an integral picture of evolution. This paper proposes that the division of internal evolution into DNA/RNA pattern formation (genotype) and protein functional action (phenotype) resolves a universal conflict between fitness and evolvability. Specifically, this paper explains how this universal conflict drove the emergence of genotype-phenotype division, why this labor division is responsible for the extraordinary complexity of life, and how the specific ways of genotype-phenotype mapping in the labor division determine the paths and forms of evolution and development.
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The search for meaningful structure in biological data has relied on cutting-edge advances in computational technology and data science methods. However, challenges arise as we push the limits of scale and complexity in biological problems. Innovation in massively parallel, classical computing hardware and algorithms continues to address many of these challenges, but there is a need to simultaneously consider new paradigms to circumvent current barriers to processing speed. Accordingly, we articulate a view towards quantum computation and quantum information science, where algorithms have demonstrated potential polynomial and exponential computational speedups in certain applications, such as machine learning. The maturation of the field of quantum computing, in hardware and algorithm development, also coincides with the growth of several collaborative efforts to address questions across length and time scales, and scientific disciplines. We use this coincidence to explore the potential for quantum computing to aid in one such endeavor: the merging of insights from genetics, genomics, neuroimaging and behavioral phenotyping. By examining joint opportunities for computational innovation across fields, we highlight the need for a common language between biological data analysis and quantum computing. Ultimately, we consider current and future prospects for the employment of quantum computing algorithms in the biological sciences.
Despite numerous mass extinctions in the Phanerozoic eon, the overall trend in biodiversity evolution was not blocked and the life has never been wiped out. Almost all possible catastrophic events (large igneous province, asteroid impact, climate change, regression and transgression, anoxia, acidification, sudden release of methane clathrate, multi-cause etc.) have been proposed to explain the mass extinctions. However, we should, above all, clarify at what timescale and at what possible levels should we explain the mass extinction? Even though the mass extinctions occurred at short-timescale and at the species level, we reveal that their cause should be explained in a broader context at tectonic timescale and at both the molecular level and the species level. The main result in this paper is that the Phanerozoic biodiversity evolution has been explained by reconstructing the Sepkoski curve based on climatic, eustatic and genomic data. Consequently, we point out that the P-Tr extinction was caused by the tectonically originated climate instability. We also clarify that the overall trend of biodiversification originated from the underlying genome size evolution, and that the fluctuation of biodiversity originated from the interactions among the earths spheres. The evolution at molecular level had played a significant role for the survival of life from environmental disasters.
This is an expository introduction to simplicial sets and simplicial homotopy theory with particular focus on relating the combinatorial aspects of the theory to their geometric/topological origins. It is intended to be accessible to students familiar with just the fundamentals of algebraic topology.
Exploiting recent developments in information theory, we propose, illustrate, and validate a principled information-theoretic algorithm for module discovery and resulting measure of network modularity. This measure is an order parameter (a dimensionless number between 0 and 1). Comparison is made to other approaches to module-discovery and to quantifying network modularity using Monte Carlo generated Erdos-like modular networks. Finally, the Network Information Bottleneck (NIB) algorithm is applied to a number of real world networks, including the social network of coauthors at the APS March Meeting 2004.
Graph theoretical analyses of nervous systems usually omit the aspect of connection polarity, due to data insufficiency. The chemical synapse network of Caenorhabditis elegans is a well-reconstructed directed network, but the signs of its connections are yet to be elucidated. Here, we present the gene expression-based sign prediction of the ionotropic chemical synapse connectome of C. elegans (3,638 connections and 20,589 synapses total), incorporating available presynaptic neurotransmitter and postsynaptic receptor gene expression data for three major neurotransmitter systems. We made predictions for more than two-thirds of these chemical synapses and observed an excitatory-inhibitory (E:I) ratio close to 4:1 which was found similar to that observed in many real-world networks. Our open source tool (http://EleganSign.linkgroup.hu) is simple but efficient in predicting polarities by integrating neuronal connectome and gene expression data.
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