Related papers: Near-ideal selection for the Standard Genetic Code
In this work we propose a physical model of organismal evolution, where phenotype, organism life expectancy, is directly related to genotype i.e. the stability of its proteins which can be determined exactly in the model. Simulating the…
Researchers puzzle over questions as to how rare species survive extinction, and why a significant proportion of microbial taxa are dormant. Computational simulation modeling by a genetic algorithm provides some answers. First, a…
The genesis of the stand genetic code is considered as a result of a fusion of two AU- and GC-codes distributed in two dominant and two recessive domains. The fusion of these codes is described with simple empirical rules. This formal…
The hyperclimbing hypothesis is a hypothetical explanation for adaptation in genetic algorithms with uniform crossover (UGAs). Hyperclimbing is an intuitive, general-purpose, non-local search heuristic applicable to discrete product spaces…
A system-level genetic code is a hypothetical genetic code that exclusively or preferentially codes systems of interacting coadapted parts. System-level genetic codes differ from part-level genetic codes in which each discrete part is coded…
The post-genomic era has brought opportunities to bridge traditionally separate fields of early history of life and brought new insight into origin and evolution of biodiversity. According to distributions of codons in genome sequences, I…
The universal genetic code presents a fundamental paradox in molecular biology. Recent advances in synthetic biology have demonstrated that the code is remarkably flexible--organisms can survive with 61 codons instead of 64, natural…
A quantitative theory on the construction and the evolution of the genetic code is proposed. Through introducing the concept of mutational deterioration (MD) and developing a theoretical formalism on MD minimization we have proved: 1, the…
The standard genetic code is well known to be optimized for minimizing the phenotypic effects of single nucleotide substitutions, a property that was likely selected for during the emergence of a universal code. Given the fitness advantage…
We recently reported that the simple genetic algorithm (SGA) is capable of performing a remarkable form of sublinear computation which has a straightforward connection with the general problem of interacting attributes in data-mining. In…
The continuity of life and its evolution, we proposed, emerge from an interactive group process manifested in networks of interaction. We term this process \textit{survival-of-the-fitted}. Here, we reason that survival of the fitted results…
In this work we develop a microscopic physical model of early evolution, where phenotype,organism life expectancy, is directly related to genotype, the stability of its proteins in their native conformations which can be determined exactly…
Why is the genetic code the way it is? The most successful theory states that the codon assignments minimise the effects of errors arising in primordial living systems. Here a transversion is reported that leaves invariant degeneracy in the…
It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but…
The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. Some argue that the specific form of the code with its twenty amino-acids might be a 'frozen accident' because of the overwhelming effects of any…
Genetic Programming yields interpretable programs, but small syntactic mutations can induce large, unpredictable behavioral shifts, degrading locality and sample efficiency. We frame this as an operator-design problem: learn a continuous…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
Feature selection is an intractable problem, therefore practical algorithms often trade off the solution accuracy against the computation time. In this paper, we propose a novel multi-stage feature selection framework utilizing multiple…
We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…