In silico transitions to multicellularity

The emergence of multicellularity and developmental programs are among the major problems of evolutionary biology. Traditionally, research in this area has been based on the combination of data analysis and experimental work on one hand and theoretical approximations on the other. A third possibility is provided by computer simulation models, which allow to both simulate reality and explore alternative possibilities. These in silico models offer a powerful window to the possible and the actual by means of modeling how virtual cells and groups of cells can evolve complex interactions beyond a set of isolated entities. Here we present several examples of such models, each one illustrating the potential for artificial modeling of the transition to multicellularity.Comment: 21 pages, 10 figures. Book chapter of Evolutionary transitions to multicellular life (Springer

The Complexity of Fairness through Equilibrium

Competitive equilibrium with equal incomes (CEEI) is a well known fair allocation mechanism; however, for indivisible resources a CEEI may not exist. It was shown in [Budish '11] that in the case of indivisible resources there is always an allocation, called A-CEEI, that is approximately fair, approximately truthful, and approximately efficient, for some favorable approximation parameters. This approximation is used in practice to assign students to classes. In this paper we show that finding the A-CEEI allocation guaranteed to exist by Budish's theorem is PPAD-complete. We further show that finding an approximate equilibrium with better approximation guarantees is even harder: NP-complete.Comment: Appeared in EC 201

Fundamental Principles of Neural Organization of Cognition

The manuscript advances a hypothesis that there are few fundamental principles of neural organization of cognition, which explain several wide areas of the cognitive functioning. We summarize the fundamental principles, experimental, theoretical, and modeling evidence for these principles, relate them to hypothetical neural mechanisms, and made a number of predictions. We consider cognitive functioning including concepts, emotions, drives-instincts, learning, “higher” cognitive functions of language, interaction of language and cognition, role of emotions in this interaction, the beautiful, sublime, and music. Among mechanisms of behavior we concentrate on internal actions in the brain, learning and decision making. A number of predictions are made, some of which have been previously formulated and experimentally confirmed, and a number of new predictions are made that can be experimentally tested. Is it possible to explain a significant part of workings of the mind from a few basic principles, similar to how Newton explained motions of planets? This manuscript summarizes a part of contemporary knowledge toward this goal

Tagging time in prolog : the temporality effect project

This article combines a brief introduction into a particular philosophical theory of "time" with a demonstration of how this theory has been implemented in a Literary Studies oriented Humanities Computing project. The aim of the project was to create a model of text-based time cognition and design customized markup and text analysis tools that help to understand ‘‘how time works’’: more precisely, how narratively organised and communicated information motivates readers to generate the mental image of a chronologically organized world. The approach presented is based on the unitary model of time originally proposed by McTaggart, who distinguished between two perspectives onto time, the so-called A- and B-series. The first step towards a functional Humanities Computing implementation of this theoretical approach was the development of TempusMarker—a software tool providing automatic and semi-automatic markup routines for the tagging of temporal expressions in natural language texts. In the second step we discuss the principals underlying TempusParser—an analytical tool that can reconstruct temporal order in events by way of an algorithm-driven process of analysis and recombination of textual segments during which the "time stamp" of each segment as indicated by the temporal tags is interpreted