[Show abstract][Hide abstract] ABSTRACT: Adaptive immune responses depend on the capacity of T cells to target specific antigens. As similar antigens can be expressed by pathogens and host cells, the question naturally arises of how can T cells discriminate friends from foes. In this work, we suggest that T cells tolerate cells whose proliferation rates remain below a permitted threshold. Our proposal relies on well-established facts about T-cell dynamics during acute infections: T-cell populations are elastic (they expand and contract) and they display inertia (contraction is delayed relative to antigen removal). By modelling inertia and elasticity, we show that tolerance to slow-growing populations can emerge as a population-scale feature of T cells. This result suggests a theoretical framework to understand immune tolerance that goes beyond the self versus non-self dichotomy. It also accounts for currently unexplained observations, such as the paradoxical tolerance to slow-growing pathogens or the presence of self-reactive T cells in the organism.
Preview · Article · Jul 2015 · Royal Society Open Science
[Show abstract][Hide abstract] ABSTRACT: Dynamical systems often contain oscillatory forces or depend on periodic
potentials. Time or space periodicity is reflected in the properties of these
systems through a dependence on the parameters of their periodic terms. In this
paper we provide a general theoretical framework for dealing with these kinds
of systems, regardless of whether they are classical or quantum, stochastic or
deterministic, dissipative or nondissipative, linear or nonlinear, etc. In
particular, we are able to show that simple symmetry considerations determine,
to a large extent, how their properties depend functionally on some of the
parameters of the periodic terms. For the sake of illustration, we apply this
formalism to find the functional dependence of the expectation value of the
momentum of a Bose-Einstein condensate, described by the Gross-Pitaewskii
equation, when it is exposed to a sawtooth potential whose amplitude is
periodically modulated in time. We show that, by using this formalism, a small
set of measurements is enough to obtain the functional form for a wide range of
parameters. This can be very helpful when characterizing experimentally the
response of systems for which performing measurements is costly or difficult.
Full-text · Article · Feb 2015 · Physical Review E
[Show abstract][Hide abstract] ABSTRACT: Cooperativeness is a defining feature of human nature. Theoreticians have suggested several mechanisms to explain this ubiquitous phenomenon, including reciprocity, reputation, and punishment, but the problem is still unsolved. Here we show, through experiments conducted with groups of people playing an iterated Prisoner's Dilemma on a dynamic network, that it is reputation what really fosters cooperation. While this mechanism has already been observed in unstructured populations, we find that it acts equally when interactions are given by a network that players can reconfigure dynamically. Furthermore, our observations reveal that memory also drives the network formation process, and cooperators assort more, with longer link lifetimes, the longer the past actions record. Our analysis demonstrates, for the first time, that reputation can be very well quantified as a weighted mean of the fractions of past cooperative acts and the last action performed. This finding has potential applications in collaborative systems and e-commerce.
Full-text · Article · Jan 2015 · Scientific Reports
[Show abstract][Hide abstract] ABSTRACT: Large sets of genotypes give rise to the same phenotype, because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as the genotype mutates into another one on the same set. By linking every pair of genotypes that are mutually accessible through mutation, genotypes organize themselves into neutral networks (NNs). These networks are known to be heterogeneous and assortative, and these properties affect the evolutionary dynamics of the population. By studying the dynamics of populations on NNs with arbitrary topology, we analyse the effect of assortativity, of NN (phenotype) fitness and of network size. We find that the probability that the population leaves the network is smaller the longer the time spent on it. This progressive 'phenotypic entrapment' entails a systematic increase in the overdispersion of the process with time and an acceleration in the fixation rate of neutral mutations. We also quantify the variation of these effects with the size of the phenotype and with its fitness relative to that of neighbouring alternatives.
Preview · Article · Jan 2015 · Journal of The Royal Society Interface
[Show abstract][Hide abstract] ABSTRACT: Resource allocation is one of the most relevant problems in the area of Mechanism Design for computing systems. Devising algorithms capable of providing efficient and fair allocation is the objective of many previous research efforts. Usually, the mechanisms they propose deal with selfishness by introducing utility transfers or payments. Since using payments is undesirable in some contexts, a family of mechanisms without payments is proposed in this paper. These mechanisms extend the Linking Mechanism of Jackson and Sonnenschein introducing a generic concept of fairness with correlated preferences. We prove that these mechanisms have good incentive, fairness, and efficiency properties. To conclude, we provide an algorithm, based on the mechanisms, that could be used in practical computing environments.
[Show abstract][Hide abstract] ABSTRACT: The genotype-phenotype map is an essential object in our understanding of
organismal complexity and adaptive properties, determining at once genomic
plasticity and those constraints that may limit the ability of genomes to
attain evolutionary innovations. An exhaustive experimental characterization of
the relationship between genotypes and phenotypes is at present out of reach.
Therefore, several models mimicking that map have been proposed and
investigated, leading to the identification of a number of general features:
genotypes differ in their robustness to mutations, phenotypes are represented
by a broadly varying number of genotypes, and simple point mutations seem to
suffice to navigate the space of genotypes while maintaining a phenotype.
However, most current models address only one level of the map (sequences and
folded structures in RNA or proteins; networks of genes and their dynamical
attractors; sets of chemical reactions and their ability to undergo molecular
catalysis), such that many relevant questions cannot be addressed. Here we
introduce toyLIFE, a multi-level model for the genotype-phenotype map based on
simple genomes and interaction rules from which a complex behavior at upper
levels emerges, remarkably plastic gene regulatory networks and metabolism.
toyLIFE is a tool that permits the investigation of how different levels are
coupled, in particular how and where do mutations affect phenotype or how the
presence of certain metabolites determines the dynamics of toyLIFE gene
regulatory networks. The possibilities of this model are not exhausted by the
results presented in this contribution. It can be easily generalized to
incorporate evolution through mutations that change genome length or through
recombination, to consider gene duplication or deletion, and therefore to
explore further properties of extended genotype-phenotype maps.
[Show abstract][Hide abstract] ABSTRACT: When a population is engaged in successive prisoner's dilemmas, indirect
reciprocity through reputation fosters cooperation through the emergence of
moral and action rules. A simplified model has recently been proposed where
individuals choose between helping or not others, and are judged good or bad
for it by the rest of the population. The reputation so acquired will condition
future actions. In this model, eight strategies (referred to as 'leading
eight') enforce a high level of cooperation, generate high payoffs and are
therefore resistant to invasions by other strategies. Here we show that, by
assigning each individual one out of two labels that peers can distinguish
(e.g., political ideas, religion, skin colour...) and allowing moral and action
rules to depend on the label, intolerant behaviours can emerge within
minorities under sufficient economic stress. We analyse the sets of conditions
where this can happen and also discuss the circumstances under which tolerance
can be restored. Our results agree with empirical observations that correlate
intolerance and economic stress, and predict a correlation between the degree
of tolerance of a population and its composition and ethical stance.
[Show abstract][Hide abstract] ABSTRACT: We have carried out a comparative analysis of data collected in three experiments on Prisoner's Dilemmas on lattices available in the literature. We focus on the different ways in which the behavior of human subjects can be interpreted, in order to empirically narrow down the possibilities for behavioral rules. Among the proposed update dynamics, we find that the experiments do not provide significant evidence for non-innovative game dynamics such as imitate-the-best or pairwise comparison rules, whereas moody conditional cooperation is supported by the data from all three experiments. This conclusion questions the applicability of many theoretical models that have been proposed to understand human behavior in spatial Prisoner's Dilemmas. A rule compatible with all our experiments, moody conditional cooperation, suggests that there is no detectable influence of interaction networks on the emergence of cooperation in behavioral experiments.
[Show abstract][Hide abstract] ABSTRACT: The emergence of cooperation among unrelated human subjects is a long-standing conundrum that has been amply studied both theoretically and experimentally. Within the question, a less explored issue relates to the gender dependence of cooperation, which can be traced back to Darwin, who stated that "women are less selfish but men are more competitive". Indeed, gender has been shown to be relevant in several game theoretical paradigms of social cooperativeness, including prisoner's dilemma, snowdrift and ultimatum/dictator games, but there is no consensus as to which gender is more cooperative. We here contribute to this literature by analyzing the role of gender in a repeated Prisoners' Dilemma played by Spanish high-school students in both a square lattice and a heterogeneous network. While the experiment was conducted to shed light on the influence of networks on the emergence of cooperation, we benefit from the availability of a large dataset of more 1200 participants. We applied different standard econometric techniques to this dataset, including Ordinary Least Squares and Linear Probability models including random effects. All our analyses indicate that being male is negatively associated with the level of cooperation, this association being statistically significant at standard levels. We also obtain a gender difference in the level of cooperation when we control for the unobserved heterogeneity of individuals, which indicates that the gender gap in cooperation favoring female students is present after netting out this effect from other socio-demographics factors not controlled for in the experiment, and from gender differences in risk, social and competitive preferences.
[Show abstract][Hide abstract] ABSTRACT: A recent paper [P. J. Martínez and R. Chacón, Phys. Rev. E 87, 062114 (2013)] presents numerical simulations on a system exhibiting directed ratchet transport of a driven overdamped Brownian particle subjected to a spatially periodic, symmetric potential. The authors claim that their simulations prove the existence of a universal waveform of the external force that optimally enhances directed transport, hence confirming the validity of a previous conjecture put forth by one of them in the limit of vanishing noise intensity. With minor corrections due to noise, the conjecture holds even in the presence of noise, according to the authors. On the basis of their results the authors claim that all previous theories, which predict a different optimal force waveform, are incorrect. In this Comment we provide sufficient numerical evidence showing that there is no such universal force waveform and that the evidence obtained by the authors otherwise is due to their particular choice of parameters. Our simulations also suggest that previous theories correctly predict the shape of the optimal waveform within their validity regime, namely, when the forcing is weak. On the contrary, the aforementioned conjecture does not hold.
No preview · Article · Dec 2013 · Physical Review E
[Show abstract][Hide abstract] ABSTRACT: Ratchets are devices able to rectify an otherwise oscillatory behavior by
exploiting an asymmetry of the system. In rocking ratchets the asymmetry is
induced through a proper choice of external forces and modulations of nonlinear
symmetric potentials. The ratchet currents thus obtained in systems as
different as semiconductors, Josephson junctions, optical lattices, or
ferrofluids, show a set of universal features. A satisfactory explanation for
them has challenged theorist for decades, and so far we still lack a general
theory of this phenomenon. Here we provide such a theory by exploring
---through functional analysis--- the constraints that the simple assumption of
time-shift invariance of the ratchet current imposes on its dependence on the
external drivings. Because the derivation is based on so general a principle,
the resulting expression is valid irrespective of the details and the nature of
the physical systems to which it is applied, and of whether they are classical,
quantum, or stochastic. The theory also explains deviations observed from
universality under special conditions, and allows to make predictions of
phenomena not yet observed in any experiment or simulation.
[Show abstract][Hide abstract] ABSTRACT: Large sets of genotypes give rise to the same phenotype because phenotypic
expression is highly redundant. Accordingly, a population can accept mutations
without altering its phenotype, as long as they transform its genotype into
another one on the same set. By linking every pair of genotypes that are
mutually accessible through mutation, genotypes organize themselves into
genotype networks (GN). These networks are known to be heterogeneous and
assortative. As these features condition the probability that mutations keep
the phenotype unchanged---hence becoming blind to natural selection---it
follows that the topology of the GN will influence the evolutionary dynamics of
the population. In this letter we analyze this effect by studying the dynamics
of random walks (RW) on assortative networks with arbitrary topology. We find
that the probability that a RW leaves the network is smaller the longer the
time spent in it---i.e., the process is not Markovian. From the biological
viewpoint, this "phenotypic entrapment" entails an acceleration in the fixation
of neutral mutations, thus implying a non-uniform increase in the ticking rate
of the molecular clock with the age of branches in phylogenetic trees. We also
show that this effect is stronger the larger the fitness of the current
phenotype relative to that of neighboring phenotypes.
[Show abstract][Hide abstract] ABSTRACT: Indirect reciprocity is one of the main mechanisms to explain the emergence and sustainment of altruism in societies. The standard approach to indirect reciprocity is reputation models. These are games in which players base their decisions on their opponent's reputation gained in past interactions with other players (moral assessment). The combination of actions and moral assessment leads to a large diversity of strategies; thus determining the stability of any of them against invasions by all the others is a difficult task. We use a variant of a previously introduced reputation-based model that let us systematically analyze all these invasions and determine which ones are successful. Accordingly, we are able to identify the third-order strategies (those which, apart from the action, judge considering both the reputation of the donor and that of the recipient) that are evolutionarily stable. Our results reveal that if a strategy resists the invasion of any other one sharing its same moral assessment, it can resist the invasion of any other strategy. However, if actions are not always witnessed, cheaters (i.e., individuals with a probability of defecting regardless of the opponent's reputation) have a chance to defeat the stable strategies for some choices of the probabilities of cheating and of being witnessed. Remarkably, by analyzing this issue with adaptive dynamics we find that whether an honest population resists the invasion of cheaters is determined by a Hamilton-like rule, with the probability that the cheat is discovered playing the role of the relatedness parameter.
[Show abstract][Hide abstract] ABSTRACT: The emergence and promotion of cooperation are two of the main issues in
evolutionary game theory, as cooperation is amenable to exploitation by
defectors, which take advantage of cooperative individuals at no cost, dooming
them to extinction. It has been recently shown that the existence of purely
destructive agents (termed jokers) acting on the common enterprises (public
goods games) can induce stable limit cycles among cooperation, defection, and
destruction when infinite populations are considered. These cycles allow for
time lapses in which cooperators represent a relevant fraction of the
population, providing a mechanism for the emergence of cooperative states in
nature and human societies. Here we study analytically and through agent-based
simulations the dynamics generated by jokers in finite populations for several
selection rules. Cycles appear in all cases studied, thus showing that the
joker dynamics generically yields a robust cyclic behavior not restricted to
infinite populations. We also compute the average time in which the population
consists mostly of just one strategy and compare the results with numerical
Full-text · Article · Oct 2012 · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
[Show abstract][Hide abstract] ABSTRACT: Reciprocity or conditional cooperation is one of the most prominent mechanisms proposed to explain the emergence of cooperation in social dilemmas. Recent experimental findings on networked games suggest that conditional cooperation may also depend on the previous action of the player. We here report on experiments on iterated, multi-player Prisoner's dilemma, on groups of 2 to 5 people. We confirm the dependence on the previous step and that memory effects for earlier periods are not significant. We show that the behavior of subjects in pairwise dilemmas is qualitatively different from the cases with more players; After an initial decay, cooperation increases significantly reaching values above 80%. The strategy of the players is rather universal as far as their willingness to reciprocate cooperation is concerned, whereas there is much diversity in their initial propensity to cooperate. Our results indicate that, for cooperation to emerge and thrive, three is a crowd.
[Show abstract][Hide abstract] ABSTRACT: The size and complexity of actual networked systems hinders the access to a global knowledge of their structure. This fact pushes the problem of navigation to suboptimal solutions, one of them being the extraction of a coherent map of the topology on which navigation takes place. In this paper, we present a Markov chain based algorithm to tag networked terms according only to their topological features. The resulting tagging is used to compute similarity between terms, providing a map of the networked information. This map supports local-based navigation techniques driven by similarity. We compare the efficiency of the resulting paths according to their length compared to that of the shortest path. Additionally we claim that the path steps towards the destination are semantically coherent. To illustrate the algorithm performance we provide some results from the Simple English Wikipedia, which amounts to several thousand of pages. The simplest greedy strategy yields over an 80% of average success rate. Furthermore, the resulting content-coherent paths most often have a cost between one- and threefold compared to shortest-path lengths.
[Show abstract][Hide abstract] ABSTRACT: It is not fully understood why we cooperate with strangers on a daily basis. In an increasingly global world, where interaction networks and relationships between individuals are becoming more complex, different hypotheses have been put forward to explain the foundations of human cooperation on a large scale and to account for the true motivations that are behind this phenomenon. In this context, population structure has been suggested to foster cooperation in social dilemmas, but theoretical studies of this mechanism have yielded contradictory results so far; additionally, the issue lacks a proper experimental test in large systems. We have performed the largest experiments to date with humans playing a spatial Prisoner's Dilemma on a lattice and a scale-free network (1,229 subjects). We observed that the level of cooperation reached in both networks is the same, comparable with the level of cooperation of smaller networks or unstructured populations. We have also found that subjects respond to the cooperation that they observe in a reciprocal manner, being more likely to cooperate if, in the previous round, many of their neighbors and themselves did so, which implies that humans do not consider neighbors' payoffs when making their decisions in this dilemma but only their actions. Our results, which are in agreement with recent theoretical predictions based on this behavioral rule, suggest that population structure has little relevance as a cooperation promoter or inhibitor among humans.
Full-text · Article · Jul 2012 · Proceedings of the National Academy of Sciences
[Show abstract][Hide abstract] ABSTRACT: Recent experimental evidence [Grujić Fosco, Araujo, Cuesta, Sánchez, 2010. Social experiments in the mesoscale: humans playing a spatial Prisoner's dilemma. PLoS ONE 5, e13749] on the spatial Prisoner's Dilemma suggests that players choosing to cooperate or not on the basis of their previous action and the actions of their neighbors coexist with steady defectors and cooperators. We here study the coexistence of these three strategies in the multiplayer iterated Prisoner's Dilemma by means of the replicator dynamics. We consider groups with n=2, 3, 4 and 5 players and compute the payoffs to every type of player as the limit of a Markov chain where the transition probabilities between actions are found from the corresponding strategies. We show that for group sizes up to n=4 there exists an interior point in which the three strategies coexist, the corresponding basin of attraction decreasing with increasing number of players, whereas we have not been able to locate such a point for n=5. We analytically show that in the limit n --> ∞ no interior points can arise. We conclude by discussing the implications of this theoretical approach on the behavior observed in experiments.
Full-text · Article · May 2012 · Journal of Theoretical Biology