Related papers: General Mechanism of Evolution Shared by Proteins …
We propose that the distribution of DNA words in genomic sequences can be primarily characterized by a double Pareto-lognormal distribution, which explains lognormal and power-law features found across all known genomes. Such a distribution…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…
A simple spatial computer simulation model was recently introduced to study the evolution of the linguistic diversity. The model considers processes of selective geographic colonization, linguistic anomalous diffusion and mutation. In the…
Linguistic laws constitute one of the quantitative cornerstones of modern cognitive sciences and have been routinely investigated in written corpora, or in the equivalent transcription of oral corpora. This means that inferences of…
(shortened version) Religions and languages are social variables, like age, sex, wealth or political opinions, to be studied like any other organizational parameter. In fact, religiosity is one of the most important sociological aspects of…
This chapter investigates the evolutionary ecology of software, focusing on the symbiotic relationship between software and innovation. An interplay between constraints, tinkering, and frequency-dependent selection drives the complex…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…
A unified mathematical language for medicine and science will be presented. Using this language, models for DNA replication, protein synthesis, chemical reactions, neurons and a cardiac cycle of a heart have been built. Models for Turing…
With the exponential increase of the protein sequence databases over time, multiple-sequence alignment (MSA) methods, like PSI-BLAST, perform exhaustive and time-consuming database search to retrieve evolutionary information. The resulting…
Mathematical language in scientific communications and educational scenarios is important yet relatively understudied compared to natural languages. Recent works on mathematical language focus either on representing stand-alone mathematical…
The basic mechanics of evolution have been understood since Darwin. But debate continues over whether macroevolutionary phenomena are driven primary by the fitness structure of genotype space or by ecological interaction. In this paper we…
Introduction: While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and…
Human beings possess the most sophisticated computational machinery in the known universe. We can understand language of rich descriptive power, and communicate in the same environment with astonishing clarity. Two of the many contributors…
We outline a phenomenological theory of evolution and origin of life by combining the formalism of classical thermodynamics with a statistical description of learning. The maximum entropy principle constrained by the requirement for…
At the intersection of the rapidly growing biological data landscape and advancements in Natural Language Processing (NLP), protein language models (PLMs) have emerged as a transformative force in modern research. These models have achieved…
Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…
Proteins populate a manifold in the high-dimensional sequence space whose geometrical structure guides their natural evolution. Leveraging recently-developed structure prediction tools based on transformer models, we first examine the…
Modern Protein Language Models (PLMs) apply transformer-based model architectures from natural language processing to biological sequences, predicting a variety of protein functions and properties. However, protein language has key…
A growing number of experimental evidence shows that it is general for a ligand binding protein to have a potential for allosteric regulation and for further evolution. In addition, such proteins generically change their conformation upon…