Related papers: Information processing in living systems
By considering the energy cost of messages carried by proteins as proportional to their information content we found experimental proof that proteins from all living organisms tend to have their estimated semantic content of information per…
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…
The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of being alive. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic…
Can we use the flow of information to understand type systems? I present two familiar type systems in pursuit of an `Information Aware' style, using information effects to reveal data flow and help in implementing them. I also calculate a…
Escherichia coli has long been used as a model organism due to the extensive experimental characterization of its pathways and molecular components. Take chemotaxis as an example, which allows bacteria to sense and swim in response to…
A central task in analyzing complex dynamics is to determine the loci of information storage and the communication topology of information flows within a system. Over the last decade and a half, diagnostics for the latter have come to be…
Consider a tree network T, where each edge acts as an independent copy of a given channel M, and information is propagated from the root. For which T and M does the configuration obtained at level n of T typically contain significant…
Motivated by the fact that entities in a social network or biological system often interact by exchanging information, we propose an efficient info-clustering algorithm that can group entities into communities using a parametric max-flow…
Stochastic networks represent very important subject of research because they have been found in almost all branches of modern science, including also sociology and economy. We provide a information theory point of view, mostly based on its…
Many biological regulatory systems process signals out of steady state and respond with a physiological delay. A simple model of regulation which respects these features shows how the ability of a delayed output to transmit information is…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
We consider possible designs and experimental realiza-tions in synthesized rather than naturally occurring bio-chemical systems of a selection of basic bio-inspired information processing steps. These include feed-forward loops, which have…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
The concept of autonomy is fundamental for understanding biological organization and the evolutionary transitions of living systems. Understanding how a system constitutes itself as an individual, cohesive, self-organized entity is a…
Given the stochastic nature of gene expression, genetically identical cells exposed to the same environmental inputs will produce different outputs. This heterogeneity has been hypothesized to have consequences for how cells are able to…
We present a study of information flow that takes into account the observation that an item relevant to one person is more likely to be of interest to individuals in the same social circle than those outside of it. This is due to the fact…
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…
Information theory is a branch of probability and statistics involving the analysis of communications. Information theory enables us to analyze and quantify the information content of predictions made in the context of plant disease…
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…
A celebrated and controversial hypothesis conjectures that some biological systems --parts, aspects, or groups of them-- may extract important functional benefits from operating at the edge of instability, halfway between order and…