Related papers: Mathematic principles underlying genetic structure…
The present paper is devoted to foundations of p-adic modelling in genomics. Considering nucleotides, codons, DNA and RNA sequences, amino acids, and proteins as information systems, we have formulated the corresponding p-adic formalisms…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
It is often stated that there are no laws in biology, where everything is contingent and could have been otherwise, being solely the result of historical accidents. Furthermore, the customary introduction of fundamental biological entities…
Theory and empirical science should be in constant dialogue, but often find it hard to understand one another. Here we describe a graduate-level university course we developed to improve matters. The course was designed to help…
The poly-tRNA model was recently presented for the origin and evolution of genetic coding. This model has led to a rather precise description of what might have occurred at the beginning of protein synthesis in the first life form. Here, we…
The sequence of nucleotide bases occurring in an organism's DNA is often regarded as a codescript for its construction. However, information in a DNA sequence can only be regarded as a codescript relative to an operational biochemical…
This paper discusses the benefits of describing the world as information, especially in the study of the evolution of life and cognition. Traditional studies encounter problems because it is difficult to describe life and cognition in terms…
Social norms and conventions are commonly accepted and adopted behaviors and practices within a social group that guide interactions -- e.g., how to spell a word or how to greet people -- and are central to a group's culture and identity.…
Mathematical modelling allows us to concisely describe fundamental principles in biology. Analysis of models can help to both explain known phenomena, and predict the existence of new, unseen behaviours. Model analysis is often a complex…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance…
Complexity in biology is often described using a multi-map architecture, where the genotype, representing the encoded information, is mapped to the functional level, known as the phenotype, which is then connected to a latent phenotype we…
In this article, the notion of a mathematical model in science is attempted to be enlightened from several points of view. In particular, it is shown that mathematical models are introduced differently and used differently in different…
Despite the obvious advantage of simple life forms capable of fast replication, different levels of cognitive complexity have been achieved by living systems in terms of their potential to cope with environmental uncertainty. Against the…
Mathematical research is often motivated by the desire to reach a beautiful result or to prove it in an elegant way. Mathematician's work is thus strongly influenced by his aesthetic judgments. However, the criteria these judgments are…
We define the concept of dependence among multiple variables using maximum entropy techniques and introduce a graphical notation to denote the dependencies. Direct inference of information theoretic quantities from data uncovers…
Mathematical models are increasingly a part of microbiological research. Here, we share our perspective on how modeling advances the discipline by: (i) enforcing logical consistency, (ii) enabling quantitative prediction, (iii) extracting…
By linking conceptual theories with observed data, generative models can support reasoning in complex situations. They have come to play a central role both within and beyond statistics, providing the basis for power analysis in molecular…
The structure of the genetic code is discussed in formal terms. A rectangular table of the code ("the code matrix"), whose properties reveal its arithmetical content tagged with the information symbols in several notations. New parameters…
Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regulatory code, the sequence rules by which non-coding regions regulate genes. In this perspective,…