Related papers: System-Level Genetic Codes: An Explanation for Bio…
Emergent behavior in complex systems arises from nonlinear interactions among components, yet the intricate nature of self-organization often obscures the underlying causal relationships, long regarded as the "holy grail" of complexity…
Understanding how genes interact and relate to each other is a fundamental question in biology. However, current practices for describing these relationships, such as drawing diagrams or graphs in a somewhat arbitrary manner, limit our…
The origin of diversification and coexistence of genes and species have been traditionally studied in isolated biological levels. Ecological and evolutionary views have focused on the mechanisms that enable or constrain species coexistence,…
How to represent the genetic code? Despite the fact that it is extensively known, the DNA mapping into proteins remains as one of the relevant discoveries of genetics. However, modern genomic signal processing usually requires converting…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
Proteins are responsible for the most diverse set of functions in biology. The ability to extract information from protein sequences and to predict the effects of mutations is extremely valuable in many domains of biology and medicine.…
How does the genome encode the form of the organism? What is the nature of this genomic code? Inspired by recent work in machine learning and neuroscience, we propose that the genome encodes a generative model of the organism. In this…
Background The theoretical requirements for a genetic code were well defined and modeled by George Gamow and Francis Crick in the 50-es. Their models failed. However the valid Genetic Code, provided by Nirenberg and Matthaei in 1961,…
The standard genetic code is known to be much more efficient in minimizing adverse effects of misreading errors and one-point mutations in comparison with a random code having the same structure, i.e. the same number of codons coding for…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
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…
The digital transformation of automation places new demands on data acquisition and processing in industrial processes. Logical relationships between acquired data and cyclic process sequences must be correctly interpreted and evaluated. To…
We present a theoretical as well as experimental investigation of a population of self-replicating segments of code subject to random mutation and survival of the fittest. Under the assumption that such a system constitutes a minimal system…
The correlations between the sequence of monomers in a polymer and its three-dimensional structure is a grand challenge in polymer science and biology. The properties and functions of macromolecules depend on their 3D shape that has…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
The evolution processes of complex systems carry key information in the systems' functional properties. Applying machine learning algorithms, we demonstrate that the historical formation process of various networked complex systems can be…
Having a model and being able to implement open-ended evolutionary systems is important for advancing our understanding of open-endedness. Complex systems science and newest generation high-level programming languages provide intriguing…
Complex Systems were identified and studied in different fields, such as physics, biology, and economics. These systems exhibit exciting properties such as self-organization, robust order, and emergence. In recent years, software systems…
Complex systems, such as life and languages, are governed by principles of evolution. The analogy and comparison between biology and linguistics\cite{alphafold2, RoseTTAFold, lang_virus, cell language, faculty1, language of gene, Protein…
A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…