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Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
The role of historical contingency in the origin of life is one of the great unknowns in modern science. Only one example of life exists--one that proceeded from a single self-replicating organism (or a set of replicating hyper-cycles) to…
We study the evolution of cooperation in the prisoner's dilemma game, whereby a coevolutionary rule is introduced that molds the random topology of the interaction network in two ways. First, existing links are deleted whenever a player…
The evolution and long-term sustenance of cooperation has consistently piqued scholarly interest across the disciplines of evolutionary biology and social sciences. Previous theoretical and experimental studies on collective risk social…
We explore the evolution of cooperation in the framework of the evolutionary game theory using the prisoner's dilemma as metaphor of the problem. We present a minimal model taking into account the growing process of the systems and…
A simple, heuristic formula with parallels to the Drake Equation is introduced to help focus discussion on open questions for the origins of life in a planetary context. This approach indicates a number of areas where quantitative progress…
Emergence of new protein structures has proved difficult to trace in nature and engineer in the laboratory. However, one aspect of structure evolution has proved immensely helpful for determining the three-dimensional structure of proteins…
Cooperative behavior, the costly provision of benefits to others, is common across all domains of life. This review article discusses cooperative behavior in the microbial world, mediated by the exchange of extracellular products called…
The present view of biological phenomena is based on a biochemical paradigm that development of living organisms is defined by information stored in a molecular form as some genetic code. However, new discoveries indicate that biological…
A group of non-cooperating agents can succumb to the \emph{tragedy-of-the-commons} if all of them seek to maximize the same resource channel to improve their viability. In nature, however, groups often avoid such collapses by…
How evolution favors cooperation is a fundamental issue in social and economic systems. In the business world, actively selecting a suitable project is usually helpful for a businessman to be in an advantageous position. By incorporating…
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.…
Numerous living systems are hierarchically organised, whereby replicating components are grouped into reproducing collectives -- e.g., organelles are grouped into cells, and cells are grouped into multicellular organisms. In such systems,…
Cooperation is prevalent in nature, not only in the context of social interactions within the animal kingdom, but also on the cellular level. In cancer for example, tumour cells can cooperate by producing growth factors. The evolution of…
Molecular evolution is the process of simulating the natural evolution of molecules in chemical space to explore potential molecular structures and properties. The relationships between similar molecules are often described through…
Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics…
Feature interaction selection is a fundamental problem in commercial recommender systems. Most approaches equally enumerate all features and interactions by the same pre-defined operation under expert guidance. Their recommendation is…
Recent years have witnessed the detection of an increasing number of complex organic molecules in interstellar space, some of them being of prebiotic interest. Disentangling the origin of interstellar prebiotic chemistry and its connection…
A system-level genetic code is a hypothetical genetic code that exclusively or preferentially codes systems of interacting coadapted parts. System-level genetic codes differ from part-level genetic codes in which each discrete part is coded…
Systems with simultaneous cooperation and competition among the elements are ubiquitous. In spite of their practical importance, knowledge on the evolution mechanism of this class of complex system is still very limit. In this work, by…