1,964 research outputs found
Optimality Properties of a Proposed Precursor to the Genetic Code
We calculate the optimality of a doublet precursor to the canonical genetic
code with respect to mitigating the effects of point mutations and compare our
results to corresponding ones for the canonical genetic code. We find that the
proposed precursor has much less optimality than that of the canonical code.
Our results render unlikely the notion that the doublet precursor was an
intermediate state in the evolution of the canonical genetic code. These
findings support the notion that code optimality reflects evolutionary
dynamics, and that if such a doublet code originally had a biochemical
significance, it arose before the emergence of translation
Characterizing Scales of Genetic Recombination and Antibiotic Resistance in Pathogenic Bacteria Using Topological Data Analysis
Pathogenic bacteria present a large disease burden on human health. Control
of these pathogens is hampered by rampant lateral gene transfer, whereby
pathogenic strains may acquire genes conferring resistance to common
antibiotics. Here we introduce tools from topological data analysis to
characterize the frequency and scale of lateral gene transfer in bacteria,
focusing on a set of pathogens of significant public health relevance. As a
case study, we examine the spread of antibiotic resistance in Staphylococcus
aureus. Finally, we consider the possible role of the human microbiome as a
reservoir for antibiotic resistance genes.Comment: 12 pages, 6 figures. To appear in AMT 2014 Special Session on
Advanced Methods of Interactive Data Mining for Personalized Medicin
Origin of symbol-using systems: speech, but not sign, without the semantic urge
Natural language—spoken and signed—is a multichannel phenomenon, involving facial and body expression, and voice and visual intonation that is often used in the service of a social urge to communicate meaning. Given that iconicity seems easier and less abstract than making arbitrary connections between sound and meaning, iconicity and gesture have often been invoked in the origin of language alongside the urge to convey meaning. To get a fresh perspective, we critically distinguish the origin of a system capable of evolution from the subsequent evolution that system becomes capable of. Human language arose on a substrate of a system already capable of Darwinian evolution; the genetically supported uniquely human ability to learn a language reflects a key contact point between Darwinian evolution and language. Though implemented in brains generated by DNA symbols coding for protein meaning, the second higher-level symbol-using system of language now operates in a world mostly decoupled from Darwinian evolutionary constraints. Examination of Darwinian evolution of vocal learning in other animals suggests that the initial fixation of a key prerequisite to language into the human genome may actually have required initially side-stepping not only iconicity, but the urge to mean itself. If sign languages came later, they would not have faced this constraint
Dissociation in a polymerization model of homochirality
A fully self-contained model of homochirality is presented that contains the
effects of both polymerization and dissociation. The dissociation fragments are
assumed to replenish the substrate from which new monomers can grow and undergo
new polymerization. The mean length of isotactic polymers is found to grow
slowly with the normalized total number of corresponding building blocks.
Alternatively, if one assumes that the dissociation fragments themselves can
polymerize further, then this corresponds to a strong source of short polymers,
and an unrealistically short average length of only 3. By contrast, without
dissociation, isotactic polymers becomes infinitely long.Comment: 16 pages, 6 figures, submitted to Orig. Life Evol. Biosp
Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment
The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes. In this paper we propose an alternative method of phylogenetic analysis using compositional statistics for all protein sequences from complete genomes. This new method is conceptually simpler than and computationally as fast as the one proposed by Qi et al. (2004b) and Chu et al. (2004). The same data sets used in Qi et al. (2004b) and Chu et al. (2004) are analyzed using the new method. Our distance-based phylogenic tree of the 109 prokaryotes and eukaryotes agrees with the biologists tree of life based on 16S rRNA comparison in a predominant majority of basic branching and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated to two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution
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