2017
Evolutionary interplay between structure, energy and epistasis in the coat protein of the φX174 phage family
R.A.F. Redondo, H.P. de Vladar, T. W lodarski, J.P. Bollback
arXiv:1320724 [q-bio.PE] 5 Aug 2015
J. R. Soc. Interface 14: 20160139. Volume 14, Issue 126, 2017
Viral capsids are structurally constrained by interactions amongst the amino acids of the constituting proteins. Therefore, epistasis is expected to evolve amongst sites engaged in physical interactions, and to in uence their substitution rates. In order to study the distribution of structural epistasis, we modeled in silico the capsid of 18 species of the φX174 family, including the wild type. φX174 is amongst the simplest organisms, making it suitable for experimental evolution and in silico modeling. We found nearly 40 variable amino acid sites in the main capsid protein across the 18 species. To study how epistasis evolved in this group, we reconstructed the ancestral sequences using a Bayesian phylogenetic framework. The ancestral states include 8 variable amino acids, for a total of 256 possible haplotypes. The dN=dS ratio is low, suggesting strong purifying selection, consistent with the idea that the structure is constrained by some form of stabilizing selection. For each haplotype in the ancestral node and for the extant species we estimated in silico the distribution of free energies and of epistasis. We found that free energy has not signicantly increased but epistasis has. We decomposed epistasis up to fth order and found that high-order epistasis can sometimes compensate pairwise interactions, often making the free energy seem additive. By synthesizing some of the ancestral haplotypes of the capsid gene, we measured their tness experimentally, and found that the predicted deviations in the coat protein free energy do not signicantly aecttness, which is consistent with the stabilizing selection hypothesis.
Grand Views of Evolution
Harold P. de Vladar, Mauro Santos, Eörs Szathmáry
Trends in Ecology & Evolution 2017
Despite major advances in evolutionary theories, some aspects of evolution remain neglected: whether evolution: would come to a halt without abiotic change; is unbounded and open-ended; or is progressive and something beyond fitness is maximized. Here, we discuss some models of ecology and evolution and argue that ecological change, resulting in Red Queen dynamics, facilitates (but does not ensure) innovation. We distinguish three forms of open-endedness. In weak open-endedness, novel phenotypes can occur indefinitely. Strong open-endedness requires the continual appearance of evolutionary novelties and/or innovations. Ultimate open-endedness entails an indefinite increase in complexity, which requires unlimited heredity. Open-ended innovation needs exaptations that generate novel niches. This can result in new traits and new rules as the dynamics unfolds, suggesting that evolution is not fully algorithmic.
Cognitive architecture with evolutionary dynamics solves insight problem
Anna Fedor, István Zachar, András Szilágyi, Michael Öllinger, Harold P. de Vladar, Eörs Szathmáry
Front. Psychol. 8:427 2017
In this paper, we show that a neurally implemented a cognitive architecture with evolutionary dynamics can solve the four-tree problem. Our model, called Darwinian Neurodynamics, assumes that the unconscious mechanism of problem solving during insight tasks is a Darwinian process. It is based on the evolution of patterns that represent candidate solutions to a problem, and are stored and reproduced by a population of attractor networks. In our first experiment, we used human data as a benchmark and showed that the model behaves comparably to humans: it shows an improvement in performance if it is pretrained and primed appropriately, just like human participants in Kershaw et al.'s 2013 experiment. In the second experiment, we further investigated the effects of pretraining and priming in a two-by-two design and found a beginner's luck type of effect: solution rate was highest in the condition that was primed, but not pretrained with patterns relevant for the task. In the third experiment, we showed that deficits in computational capacity and learning abilities decreased the performance of the model, as expected. We conclude that Darwinian Neurodynamics is a promising model of human problem solving that deserves further investigation.
Cognitive cultural dynamics
Harold P. de Vladar
Proceeding GECCO '17 Proceedings of the Genetic and Evolutionary Computation Conference Companion Pages 1165-1171 Berlin, Germany — July 15 - 19, 2017
Based on previous results on language games here I study cultural dynamics extended in spatial environments. The underlying model makes assumptions regarding cognitive aspects of the individuals based on the Neuronal Replicator hypothesis. Although I assume a simple and minimal version of cultures, this model allows exploring the effects of idiosyncratic as well as externally environmentally imposed preferences on cultural traits. I also study the case of dispersal of individuals and find that this factor is key for the rapid spread of cultural traits.
Reaction-Diffusion Models for Glioma Tumor Growth
Miguel Martín-Landrove
arXiv:1707.09409v1 [physics.med-ph]
Mathematical modelling of tumor growth is one of the most useful and inexpensive approaches to determine and predict the stage, size and progression of tumors in realistic geometries. Moreover, these models has been used to get an insight into cancer growth and invasion and in the analysis of tumor size and geometry for applications in cancer treatment and surgical planning. The present revision attempts to present a general perspective of the use of models based on reaction-diffusion equations not only for the description of tumor growth in gliomas, addressing for processes such as tumor heterogeneity, hypoxia, dormancy and necrosis, but also its potential use as a tool in designing optimized and patient specific therapies.
Dental Information Along Curved Slices
C. González, Ma.I. Pérez, M. Lentini, D. Ríos, G. Albrecht, M. Paluszny
Computing Conference 2017, 18-20 July 2017, London, UK
Within the family of ruled surfaces, the developable curved slices have a special property: they may be flattened without deformation. In this paper we introduce a technique to visualize information encoded in a 3D tomographic volume along such a curved slice. This property is deemed useful in clinical diagnosis, especially for inspection purposes, and mainly because allows for flat measurements which correspond precisely to the 3D measurement along the surface. The paper focuses on human maxillofacial tomographic data and the curved slices run along the full jaw or a number of dental pieces.
