Related papers: Two evolutionary lineages: Machiavellian and Bohri…
Evolving genomes increase a number of their genes by gene duplications. To escape degradation in a functionless pseudogene, any gene duplicate needs to be guarded by negative (purifying) selection from otherwise inevitable fixation of…
The most common assumption in evolutionary game theory is that players should adopt a strategy that warrants the highest payoff. However, recent studies indicate that the spatial selection for cooperation is enhanced if an appropriate…
The conceptual landscape of convection has two simple gateways: optimal function and random form. Optimal convection adjusts toward a univariate ideal called neutrality. Convection form involves elements (parcels, bubbles, drafts) whose…
In a population of size N, adaptive evolution is 2N times faster under Mendelian inheritance than the rate implied by Victorian theories of heredity and evolution.
Languages and genes are both transmitted from generation to generation, with opportunity for differential reproduction and survivorship of forms. Here we apply a rigorous inference framework, drawn from population genetics, to distinguish…
We live in a world brimming with uncertainty, where we constantly have to make a lot of decisions under incomplete information. We are firm believers that our subjective belief cannot be computed by rigorous mathematical formula; instead…
We assume that the natural intelligence (human, particularly) is equivalent to a large inferring structure, which took shape in the last 400/500 million years. Then two hypotheses, about this structure and its development, are put forward…
Biological networks such as gene regulatory networks possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated…
It is important to be clear as to whether a theory such as evolutionary archaeology pertains to biological evolution, in which acquired change is obliterated at the end of each generation, or cultural change, in which acquired change is…
These lectures contain a brief description of evolutionary models inspired by the statistical mechanics of disordered systems. After an introduction describing the Darwinian paradigm of evolving populations, the deterministic quasispecies…
We study in detail a recently proposed simple discrete model for evolution on smooth landscapes. An asymptotic solution of this model for long times is constructed. We find that the dynamics of the population are governed by correlation…
The evolution of cooperation often depends upon population structure, yet nearly all models of cooperation implicitly assume that this structure remains static. This is a simplifying assumption, because most organisms possess genetic traits…
Evolution gave rise to creatures that are arguably more sophisticated than the greatest human-designed systems. This feat has inspired computer scientists since the advent of computing and led to optimization tools that can evolve complex…
Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here…
When a neural network can learn multiple distinct algorithms to solve a task, how does it "choose" between them during training? To approach this question, we take inspiration from ecology: when multiple species coexist, they eventually…
Weak purifying selection, acting on many linked mutations, may play a major role in shaping patterns of molecular evolution in natural populations. Yet efforts to infer these effects from DNA sequence data are limited by our incomplete…
The relationship between intelligence and evolution is bidirectional: while evolution can help evolve intelligences, the degree of intelligence itself can impact evolution (Baldwin, 1896). In the field of Evolutionary Computation, the…
Darwinian evolution of the biological brain is documented through multiple lines of evidence, although the modes of evolutionary changes remain unclear. Drawing inspiration from the evolved neural systems (e.g., visual cortex), deep…
Population expansions trigger many biomedical and ecological transitions, from tumor growth to invasions of non-native species. Although population spreading often selects for more invasive phenotypes, we show that this outcome is far from…
The common understanding of protein evolution has been that neutral or slightly deleterious mutations are fixed by random drift, and evolutionary rate is determined primarily by the proportion of neutral mutations. However, recent studies…