Related papers: Local stability and evolution of the genetic code

Degeneracy of the genetic code is a biological way to minimize effects of the undesirable mutation changes. Degeneration has a natural description on the 5-adic space of 64 codons $\mathcal{C}_5 (64) = \{n_0 + n_1 5 + n_2 5^2 : n_i = 1, 2,…

Evolution depends on the possibility of successfully exploring fitness landscapes via mutation and recombination. With these search procedures, exploration is difficult in "rugged" fitness landscapes, where small mutations can drastically…

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…

Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and…

Assessing the stability of code generation from large language models (LLMs) is essential for judging their reliability in real-world development. We extend prior "structural-entropy concepts" to the program domain by pairing entropy with…

With a simple model, we study the evolution of random networks under attack and reconstruction. We introduce a new quality, invulnerability I(s), to describe the stability of the system. We find that the network can evolve to a stationary…

Cotranslational folding depends on the folding speed and stability of the nascent protein. It remains difficult, however, to predict which proteins cotranslationally fold. Here, we simulate evolution of model proteins to investigate how…

Biological functions are generated as a result of developmental dynamics that form phenotypes governed by genotypes. The dynamical system for development is shaped through genetic evolution following natural selection based on the fitness…

Spaces with locally varying scale of measurement, like multidimensional structures with differently scaled dimensions, are pretty common in statistics and machine learning. Nevertheless, it is still understood as an open question how to…

We use fitness graphs, or directed cube graphs, for analyzing evolutionary reversibility. The main application is antimicrobial drug resistance. Reversible drug resistance has been observed both clinically and experimentally. If drug…

A mutator is an allele that increases the mutation rate throughout the genome by disrupting some aspect of DNA replication or repair. Mutators that increase the mutation rate by the order of 100 fold have been observed to spontaneously…

We introduce and analyze a general model of a population evolving over a network of selectively neutral genotypes. We show that the population's limit distribution on the neutral network is solely determined by the network topology and…

We determine stability and attractor properties of random Boolean genetic network models with canalyzing rules for a variety of architectures. For all power law, exponential, and flat in-degree distributions, we find that the networks are…

Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…

In the near future, all the human genes will be identified. But understanding the functions coded in the genes is a much harder problem. For example, by using block entropy, one has that the DNA code is closer to a random code then written…

We return to the geometry optimization problem of Lennard-Jones clusters to analyze the performance dependence of "cut and splice" genetic algorithms (GAs) on the employed population size. We generally find that admixing twinning mutation…

The idea of the evolution of the genetic code from the CG to the CGUA alphabet has been developed further. The assumption of the originally triplet structure of the genetic code has been substantiated. The hypothesis of the emergence of…

Mutational robustness quantifies the effect of random mutations on fitness. When mutational robustness is high, most mutations do not change fitness or have only a minor effect on it. From the point of view of fitness landscapes, robust…

We show that our recently published Arithmetic Model of the genetic code based on Godel Encoding is robust against symmetry transformations, specially Rumer s one U > G, A > C, and constitutes a link between the degeneracy structure and the…

We derive an analytic expression for site-specific stationary distributions of amino acids from the Structurally Constrained Neutral (SCN) model of protein evolution with conservation of folding stability. The stationary distributions that…