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The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are…
Anthropogenic changes of the biota and human hyper-dominance are modulating the evolution of life on our planet. Humankind has spread worldwide supported by cultural and technological knowledge, and has already modified uncountable…
Evolutionary Computation is a group of biologically inspired algorithms used to solve complex optimisation problems. It can be split into Evolutionary Algorithms, which take inspiration from genetic inheritance, and Swarm Intelligence…
We demonstrate with a thought experiment that fitness-based population dynamical approaches to evolution are not able to make quantitative, falsifiable predictions about the long-term behavior of evolutionary systems. A key characteristic…
The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that do not contain any gene or gene copy. Some of these newly expressed genes…
Human communication systems, such as language, evolve culturally; their components undergo reproduction and variation. However, a role for selection in cultural evolutionary dynamics is less clear. Often neutral evolution (also known as…
The modeling of time series is becoming increasingly critical in a wide variety of applications. Overall, data evolves by following different patterns, which are generally caused by different user behaviors. Given a time series, we define…
Naturally evolving proteins gradually accumulate mutations while continuing to fold to thermodynamically stable native structures. This process of neutral protein evolution is an important mode of genetic change, and forms the basis for the…
Life forms exhibit such a degree of exquisite organization that it seems impossible that they could have developed out of a process of trial and error, as intimated by the theory of Darwinian evolution. In this general public paper I…
The evolutionary origins of ageing and age-associated diseases continue to pose a fundamental question in biology. This study is concerned with a recently proposed framework, which conceptualises development and ageing as a continuous…
Social networks exhibit strikingly systematic patterns across a wide range of human contexts. While genetic variation accounts for a significant portion of the variation in many complex social behaviors, the heritability of egocentric…
Theoretical analysis proves that human survivability is dominated by an unusual physical, rather than biological, mechanism, which yields an exact law. The law agrees with all experimental data, but, contrary to existing theories, it is the…
Evolution by Natural Selection is a process by which progeny inherit some properties from their progenitors with small variation. These properties are subject to Natural Selection and are called adaptive traits and carriers of the latter…
This paper outlines the implications of neural-level accounts of insight, and models of the conceptual interactions that underlie creativity, for a theory of cultural evolution. Since elements of human culture exhibit cumulative, adaptive,…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
If evolution can be connected to the principle of least action, and if it is depicted in evolution space versus time then it corresponds to the direction of ultimate causation. As an organism evolves and follows a path of proximate…
Whether or not biodiversity dynamics tend toward stable equilibria remains an unsolved question in ecology and evolution with important implications for our understanding of diversity and its conservation. Phylo/population genetic models…
Ecology and evolution are inseparable. Motivated by some recent experiments, we have developed models of evolutionary ecology from the perspective of dynamic networks. In these models, in addition to the intra-node dynamics, which…
Why is the genetic code the way it is? The most successful theory states that the codon assignments minimise the effects of errors arising in primordial living systems. Here a transversion is reported that leaves invariant degeneracy in the…
In quantum theory it is possible to explain time, and dynamics, in terms of entanglement. This is the timeless approach to time, which assumes that the universe is in a stationary state, where two non-interacting subsystems, the clock and…