Related papers: Evolutionary models for simple biosystems
A general and basic model of primordial evolution--a soup of reacting finitary and discrete processes--is employed to identify and analyze fundamental mechanisms that generate and maintain complex structures in prebiotic systems. The…
How multicellular life forms evolved out from unicellular ones constitutes a major problem in our understanding of the evolution of our biosphere. A recent set of experiments involving yeast cell populations has shown that selection for…
The dynamic instability of the living systems and the "superposition" of different forms of randomness are viewed as a component of the contingently increasing organization of life along evolution. We briefly survey how classical and…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…
We apply the theory of learning to physically renormalizable systems in an attempt to develop a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution…
Establishing the emergence of evolutionary behavior as a defining characteristic of 'life' is a major step in the Artificial life (ALife) studies. We present here an abstract formal framework for this aim based upon the notion of high-level…
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…
The networks of predator-prey interactions in ecological systems are remarkably complex, but nevertheless surprisingly stable in terms of long term persistence of the system as a whole. In order to understand the mechanism driving the…
Life occurs in concentrated `Ringer Solutions' derived from seawater that Lesser Blum studied for most of his life. As we worked together, Lesser and I realized that the questions asked of those solutions were quite different in biology…
An important feature of many complex systems, both natural and artificial, is the structure and organization of their interaction networks with interesting properties. Here we present a theory of self-organization by evolutionary adaptation…
A model of pattern formation in living systems is presented. The pattern is achieved by the sequential interaction of two signaling pathways. The coupling of the pattern to the (thick) epithelial sheet changes is given, when the Gauss…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…
A theoretical study of cell evolution is presented here. By using a toolbox containing an intracellular catalytic reaction network model and a mutation-selection process, four distinct phases of self-organization were unveiled. First, the…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
The mutual influence of dynamics and structure is a central issue in complex systems. In this paper we study by simulation slow evolution of network under the feedback of a local-majority-rule opinion process. If performance-enhancing local…
There has been a long debate on how new levels of organization have evolved. It might seem unlikely, as cooperation must prevail over competition. One well-studied example is the emergence of autocatalytic sets, which seem to be a…
Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which…
The evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Here we review patterns and processes that…
The basic mechanics of evolution have been understood since Darwin. But debate continues over whether macroevolutionary phenomena are driven primary by the fitness structure of genotype space or by ecological interaction. In this paper we…