Related papers: Evolutionary models for simple biosystems
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
An autocatalytic pattern matching polymer system is studied as an abstract model for chemical ecosystem evolution. Highly ordered populations with particular sequence patterns appear spontaneously out of a vast number of possible states.…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
Co-evolution exhibited by a network system, involving the intricate interplay between the dynamics of the network itself and the subsystems connected by it, is a key concept for understanding the self-organized, flexible nature of…
As early indicated by Charles Darwin, languages behave and change very much like living species. They display high diversity, differentiate in space and time, emerge and disappear. A large body of literature has explored the role of…
Clusters appear in nature in a diversity of contexts, involving distances as long as the cosmological ones, and down to atoms and molecules and the very small nuclear size. They also appear in several other scenarios, in particular in…
Systems evolving according to the standard concept of biological or technological evolution are often described by catalytic evolution equations. We study the structure of these equations and find a deep relationship to classical…
Flocks of birds and schools of fish are familiar examples of spatial patterns formed by living organisms. In contrast to the patterns on the skins of, say, zebra and giraffe, the patterns of our interest are {\it transient} although…
At odds with a traditional view of molecular evolution that seeks a descent-with-modification relationship between functional sequences, new functions can emerge {\it de novo} with relative ease. At early times of molecular evolution,…
Hierarchy is one of the most conspicuous features of numerous natural, technological and social systems. The underlying structures are typically complex and their most relevant organizational principle is the ordering of the ties among the…
Evolution occurs in populations of reproducing individuals. The structure of a biological population affects which traits evolve. Understanding evolutionary game dynamics in structured populations is difficult. Precise results have been…
We propose a general scenario to analyze social and economic changes in modern environments. We illustrate the ideas with a model that incorporating the main trends is simple enough to extract analytical results and, at the same time,…
Links in a practical network may have different functions, which makes the original network a combination of some functional subnetworks. Here, by a model of coupled oscillators, we investigate how such functional subnetworks are evolved…
Complex change is often described as "evolutionary" in economics, policy, and technology, yet most system dynamics models remain constrained to fixed state spaces and equilibrium-seeking behavior. This paper argues that evolutionary…
We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…
Understanding how the structure of community interactions is modified by coevolution is vital for understanding system responses to change at all scales. However, in absence of a group selection process, collective community behaviours…
A class of models for large-scale evolution and mass extinctions is presented. These models incorporate environmental changes on all scales, from influences on a single species to global effects. This is a step towards a unified picture of…
A biological circuit is a neural or biochemical cascade, taking inputs and producing outputs. How have biological circuits learned to solve environmental challenges over the history of life? The answer certainly follows Dobzhansky's famous…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…