Related papers: On Modelling Life
Life is a discrete, stochastic phenomena : for a biological organism, the time of the two most important events of its life (reproduction and death) is random and these events change the number of individuals of the species by single units.…
A full accounting of biological robustness remains elusive; both in terms of the mechanisms by which robustness is achieved and the forces that have caused robustness to grow over evolutionary time. Although its importance to topics such as…
Ecologists are interested in understanding and predicting how ecological communities change through time. While it might seem natural to measure this through changes in species' abundances, computational limitations mean transitions between…
A fundamental question in the conjunction of information theory, biophysics, bioinformatics and thermodynamics relates to the principles and processes that guide the development of natural intelligence in natural environments where…
The evolution of microbial and viral organisms often generates clonal interference, a mode of competition between genetic clades within a population. In this paper, we show that interference strongly constrains the genetic and phenotypic…
We propose a model to characterize how a diffusing population adapts under a time periodic selection, while its environment undergoes shifts and size changes, leading to significant differences with classical results on fixed domains. After…
In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated…
We analyze the fate of dynamical systems that consist of two kind of processes. The first type is supposed to perform a certain function by processing information at a required high accuracy, which is, however, limited to less than 100…
G. Edelman, O. Sporns, and G. Tononi have introduced the neural complexity of a family of random variables, defining it as a specific average of mutual information over subfamilies. We show that their choice of weights satisfies two natural…
We review models of biological evolution in which the population frequency changes deterministically with time. If the population is self-replicating, although the equations for simple prototypes can be linearised, nonlinear equations arise…
Comparison-based algorithms are algorithms for which the execution of each operation is solely based on the outcome of a series of comparisons between elements. Comparison-based computations can be naturally represented via the following…
This article presents a naturalist approach to cognition understood as a network of info-computational, autopoietic processes in living systems. It provides a conceptual framework for the unified view of cognition as evolved from the…
Microbial ecosystems exhibit a surprising amount of functionally relevant diversity at all levels of taxonomic resolution, presenting a significant challenge for most modeling frameworks. A long-standing hope of theoretical ecology is that…
Evolutionary complexity is here measured by the number of trials/evaluations needed for evolving a logical gate in a non-linear medium. Behavioural complexity of the gates evolved is characterised in terms of cellular automata behaviour. We…
An agent-based computer simulation of death by inheritable mutations in a changing environment shows a maximal population, or avoids extinction, at so intermediate mutation rate of the individuals. Thus death seems needed to al for…
We review a collection of models of random simplicial complexes together with some of the most exciting phenomena related to them. We do not attempt to cover all existing models, but try to focus on those for which many important results…
We propose a stochastic model for evolution. Births and deaths of species occur with constant probabilities. Each new species is associated with a fitness sampled from the uniform distribution on [0,1]. Every time there is a death event…
The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the corresponding growth rates. By…
Diversity is a fundamental feature of ecosystems, even when the concept of ecosystem is extended to sociology or economics. Diversity can be intended as the count of different items, animals, or, more generally, interactions. There are two…
Proteins are essential components of living systems, capable of performing a huge variety of tasks at the molecular level, such as recognition, signalling, copy, transport, ... The protein sequences realizing a given function may largely…