Related papers: Zipf's law, unbounded complexity and open-ended ev…
The concept of evolutionary development of structures constituted a \emph{real} revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of…
We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone…
Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, due to the essentially infinite complexity of protein sequence space. We describe how evolvability can be an object…
This study introduces a novel theoretical framework, the Stacked Autoencoder Evolution Hypothesis, which proposes that biological evolutionary systems operate through multi-layered self-encoding and decoding processes, analogous to stacked…
Recently several authors have proposed stochastic evolutionary models for the growth of complex networks that give rise to power-law distributions. These models are based on the notion of preferential attachment leading to the ``rich get…
Biological information processing manifests a huge variety in its complexity and capability among different organisms, which presumably stems from the evolutionary optimization under limited computational resources. Starting from the…
We propose a novel evolutionary algorithm on bit vectors which derives from the principles of information theory. The information-theoretic evolutionary algorithm (it-EA) iteratively updates a search distribution with two parameters, the…
"Standard" information theory says nothing about the semantic content of information. Nevertheless, applications such as evolutionary theory demand consideration of precisely this aspect of information, a need that has motivated a largely…
Zipf's law is just one out of many universal laws proposed to describe statistical regularities in language. Here we review and critically discuss how these laws can be statistically interpreted, fitted, and tested (falsified). The modern…
The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…
To analyze the evolutionary emergence of structural complexity in physical processes we introduce a general, but tractable, model of objects that interact to produce new objects. Since the objects--\emph{$epsilon$-machines}--have well…
Bayesian design can be used for efficient data collection over time when the process can be described by the solution to an ordinary differential equation (ODE). Typically, Bayesian designs in such settings are obtained by maximising the…
Economists model knowledge use and acquisition as a cause-and-effect calculus associating observations made by a decision-maker about their world with possible underlying causes. Knowledge models are well-established for static contexts,…
Complex systems, from the human brain to the global economy, are made of multiple elements that interact in such ways that the behaviour of the `whole' often seems to be more than what is readily explainable in terms of the `sum of the…
The word "complexity" is most often used as a meta--linguistic expression referring to certain intuitive characteristics of a natural system and/or its scientific description. These characteristics may include: sheer amount of data that…
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…
Living systems can be understood as organized entities that capture, transform, and reproduce information. Classical gene-centered models explain adaptation through frequency changes driven by differential fitness, yet they often overlook…
Self-Other Reorganization (SOR) is a theory of how interacting entities or individuals, each of which can be described as an autocatalytic network, collectively exhibit cumulative, adaptive, open-ended change, or evolution. Zachar et al.'s…
Macroevolutionary dynamics often display sudden, explosive surges, where systems remain relatively stable for extended periods before experiencing dramatic acceleration that frequently exceeds traditional exponential growth. This pattern is…
We suggest a natural approach that leads to a modification of classical quasispecies models and incorporates the possibility of population extinction in addition to growth. The resulting modified models are called open. Their essential…