Related papers: Why don't the modules dominate - Investigating the…
A central biological question is how natural organisms are so evolvable (capable of quickly adapting to new environments). A key driver of evolvability is the widespread modularity of biological networks--their organization as functional,…
We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of…
We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of…
Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show…
Discrete gene regulatory networks (GRNs) play a vital role in the study of robustness and modularity. A common method of evaluating the robustness of GRNs is to measure their ability to regulate a set of perturbed gene activation patterns…
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…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
The dynamics of adaptation is difficult to predict because it is highly stochastic even in large populations. The uncertainty emerges from number fluctuations, called genetic drift, arising in the small number of particularly fit…
Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous…
The mechanisms by which modularity emerges in complex networks are not well understood but recent reports have suggested that modularity may arise from evolutionary selection. We show that finding the modularity of a network is analogous to…
In this paper, we inspect well-known population genetics and social dynamics models. In these models, interacting individuals, while participating in a self-organizing process, give rise to the emergence of complex behaviors and patterns.…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Existing theoretical models of evolution focus on the relative fitness advantages of different mutants in a population while the dynamic behavior of the population size is mostly left unconsidered. We here present a generic stochastic model…
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…
It has long been believed that the brain is highly modular both in terms of structure and function, although recent evidence has led some to question the extent of both types of modularity. We used artificial neural networks to test the…
The question as to why most higher organisms reproduce sexually has remained open despite extensive research, and has been called "the queen of problems in evolutionary biology". Theories dating back to Weismann have suggested that the key…
Evolution and learning are two of the fundamental mechanisms by which life adapts in order to survive and to transcend limitations. These biological phenomena inspired successful computational methods such as evolutionary algorithms and…
This paper investigates how often the popular configurations of Differential Evolution generate solutions outside the feasible domain. Following previous publications in the field, we argue that what the algorithm does with such solutions…
Modularity has been widely studied as a mechanism to improve the capabilities of neural networks through various techniques such as hand-crafted modular architectures and automatic approaches. While these methods have sometimes shown…
These notes introduce probabilistic landscape models defined on high-dimensional discrete sequence spaces. The models are motivated primarily by fitness landscapes in evolutionary biology, but links to statistical physics and computer…