Related papers: Evolution of default genetic control mechanisms
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…
With the number of sequenced genomes now over one hundred, and the availability of rough functional annotations for a substantial proportion of their genes, it has become possible to study the statistics of gene content across genomes. Here…
It has recently been suggested that the fundamental haploid-diploid cycle of eukaryotic sex exploits a rudimentary form of the Baldwin effect. Thereafter the other associated phenomena can be explained as evolution tuning the amount and…
As Evolutionary Dynamics moves from the realm of theory into application, algorithms are needed to move beyond simple models. Yet few such methods exist in the literature. Ecological and physiological factors are known to be central to…
The influence of time-dependent fitnesses on the infinite population dynamics of simple genetic algorithms (without crossover) is analyzed. Based on general arguments, a schematic phase diagram is constructed that allows one to characterize…
Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available…
Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well documented to much more tightly than traditionally assumed,…
Despite the significant advances in identifying the driver nodes and energy requiring in network control, a framework that incorporates more complicated dynamics remains challenging. Here, we consider the conformity behavior into network…
Robustness to genetic or environmental disturbances is often considered as a key property of living systems. Yet, in spite of being discussed since the 1950s, how robustness emerges from the complexity of genetic architectures and how it…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…
We propose a physical model to describe the mechanisms of two major scenarios of the genetic code evolution, the codon capture and ambiguous intermediate scenarios, in a consistent manner. We sketch the lowest dimensional version of our…
We study the Tangled Nature model of macro evolution and demonstrate that the co-evolutionary dynamics produces an increasingly correlated core of well occupied types. At the same time the entire configuration of types becomes increasing…
The development of a large non-coding fraction in eukaryotic DNA and the phenomenon of the code-bloat in the field of evolutionary computations show a striking similarity. This seems to suggest that (in the presence of mechanisms of code…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of…
Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory…
Biological functions are generated as a result of developmental dynamics that form phenotypes governed by genotypes. The dynamical system for development is shaped through genetic evolution following natural selection based on the fitness…
Here we propose a new approach to modeling gene expression based on the theory of random dynamical systems (RDS) that provides a general coupling prescription between the nodes of any given regulatory network given the dynamics of each node…
Gene expression is inherently noisy as many steps in the read-out of the genetic information are stochastic. To disentangle the effect of different sources of stochasticity in such systems, we consider various models that describe some…
We study the spread of a novel state in a network, in the presence of an exogenous control. The considered controlled evolutionary dynamics is a non-homogeneous Markov process that describes the evolution of the states of all nodes in the…