Related papers: Complex versus Complicated Systems Biology, Univer…
"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…
We consider the links between consistent and approximate descriptions of the quantum-classical systems, i.e. systems are composed of two interacting subsystems, one of which behaves almost classically while the other requires a quantum…
If a concept is not well defined, there are grounds for its abuse. This is particularly true of complexity, an inherently interdisciplinary concept that has penetrated very different fields of intellectual activity from physics to…
Disordered systems theory provides powerful tools to analyze the generic behaviors of highdimensional systems, such as species-rich ecological communities or neural networks. By assuming randomness in their interactions, universality…
The organism is a fundamental concept in biology. However there is no universally accepted, formal, and yet broadly applicable definition of what an organism is. Here we introduce a candidate definition. We adopt the view that the…
Here we introduce a new design framework for synthetic biology that exploits the advantages of Bayesian model selection. We will argue that the difference between inference and design is that in the former we try to reconstruct the system…
Systems biology seeks to create math models of biological systems to reduce inherent biological complexity and provide predictions for applications such as therapeutic development. However, it remains a challenge to determine which math…
In an attempt to explain the uniqueness of the coding mechanism of living cells as contrasted with multi-species structure of ecosystems we examine two models of individuals with some replicative properties. In the first model the system…
Aging is a fundamental aspect of living systems that undergo a progressive deterioration of physiological function with age and an increase of vulnerability to disease and death. Living systems, known as complex systems, require complexity…
Mathematical models are increasingly a part of microbiological research. Here, we share our perspective on how modeling advances the discipline by: (i) enforcing logical consistency, (ii) enabling quantitative prediction, (iii) extracting…
A model of an organism as an autonomous intelligent system has been proposed. This model was used to analyze learning of an organism in various environmental conditions. Processes of learning were divided into two types: strong and weak…
We present several philosophical ideas emerging from the studies of complex systems. We make a brief introduction to the basic concepts of complex systems, for then defining "abstraction levels". These are useful for representing…
This short text summarizes the work in biology proposed in our book, Perspectives on Organisms, where we analyse the unity proper to organisms by looking at it from different viewpoints. We discuss the theoretical roles of biological time,…
Complex systems are characterized by many interacting units that give rise to emergent behavior. A particularly advantageous way to study these systems is through the analysis of the networks that encode the interactions among the system's…
This chapter does not deal with specific tools and techniques for managing complex systems, but proposes some basic concepts that help us to think and speak about complexity. We review classical thinking and its intrinsic drawbacks when…
We describe a design principle for adaptive systems under which adaptation is driven by particular challenges that the environment poses, as opposed to average or otherwise aggregated measures of performance over many challenges. We trace…
We consider the basic features of complex dynamical and control systems. Special attention is paid to the problems of synthesis of dynamical models of complex systems, construction of efficient control models, and to the development of…
In abstract terms, ecosystem ecology is about determining when two ecosystems, superficially different, are alike in some deeper way. An external observer can choose any ecosystem property as being important. In contrast, two ecosystems are…
We present an approach of using AI to model and simulate biology and life. Why is it important? Because at the core of medicine, pharmacy, public health, longevity, agriculture and food security, environmental protection, and clean energy,…
Context dependence is central to the description of complexity. Keying on the pairwise definition of "set complexity" we use an information theory approach to formulate general measures of systems complexity. We examine the properties of…