Related papers: A framework for parsing heritable information
Spectral densities encode the relevant information characterising the system-environment interaction in an open-quantum system problem. Such information is key to determining the system's dynamics. In this work, we leverage the potential of…
As a living information and communications system, the genome encodes patterns in single nucleotide polymorphisms (SNPs) reflecting human adaption that optimizes population survival in differing environments. This paper mathematically…
Scientists investigate the dynamics of complex systems with quantitative models, employing them to synthesize knowledge, to explain observations, and to forecast future system behavior. Complete specification of systems is impossible, so…
A model of sensory information processing is presented. The model assumes that learning of internal (hidden) generative models, which can predict the future and evaluate the precision of that prediction, is of central importance for…
Rhythmic and sequential segmentation of the embryonic body plan is a vital developmental patterning process in all vertebrate species. However, a theoretical framework capturing the emergence of dynamic patterns of gene expression from the…
Life can be viewed as a localized chemical system that sits on, or in the basin of attraction of, a metastable dynamical attractor state that remains out of equilibrium with the environment. Such a view of life allows that new living states…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
"Epigenetic Tracking" is a model of systems of biological cells, able to generate arbitrary 2 or 3-dimensional cellular shapes of any kind and complexity (in terms of number of cells, number of colours, etc.) starting from a single cell. If…
Biological organisms adapt to changes by processing informations from different sources, most notably from their ancestors and from their environment. We review an approach to quantify these informations by analyzing mathematical models of…
Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need…
The iterated learning model simulates the transmission of language from generation to generation in order to explore how the constraints imposed by language transmission facilitate the emergence of language structure. Despite each modelled…
Distributed systems, such as biological and artificial neural networks, process information via complex interactions engaging multiple subsystems, resulting in high-order patterns with distinct properties across scales. Investigating how…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
A complex system comprises multiple interacting entities whose interdependencies form a unified whole, exhibiting emergent behaviours not present in individual components. Examples include the human brain, living cells, soft matter, Earth's…
Evolutionary success depends on the capacity to adapt: organisms must respond to environmental challenges through both genetic innovation and lifetime learning. The gene-centric paradigm attributes evolutionary causality exclusively to…
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…
The constituents of a complex system exchange information to function properly. Their signalling dynamics often leads to the appearance of emergent phenomena, such as phase transitions and collective behaviors. While information exchange…
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…
A complex network is a condensed representation of the relational topological framework of a complex system. A main reason for the existence of such networks is the transmission of items through the entities of these complex systems. Here,…
Distributed sensor networks are commonly operated through coincidence logic: if detector reports overlap within a prescribed time window, an event is declared. While effective for clean, high-significance signals, this approach becomes…