Category: Papers

Dynamical Criticality in Gene Regulatory Networks

A well-known hypothesis, with far-reaching implications, is that biological evolution should preferentially lead to states that are dynamically critical. In previous papers, we showed that a well-known model of genetic regulatory networks, namely, that of random Boolean networks, allows one to study in depth the relationship between the dynamical regime of a living being’s gene network and its response to permanent perturbations. In this paper, we analyze a huge set of new experimental data on single gene knockouts in S. cerevisiae, laying down a statistical framework to determine its dynamical regime. We find that the S. cerevisiae network appears to be slightly ordered, but close to the critical region. Since our analysis relies on dichotomizing continuous data, we carefully consider the issue of an optimal threshold choice.


Dynamical Criticality in Gene Regulatory Networks
Marco Villani, Luca La Rocca, Stuart Alan Kauffman, and Roberto Serra

Volume 2018, Article ID 5980636, 14 pages


Social style and resilience of macaques’ networks, a theoretical investigation

Group-living animals rely on efficient transmission of information for optimal exploitation of their habitat. How efficient and resilient a network is depend on its structure, which is a consequence of the social interactions of the individuals that comprise the network. In macaques, network structure differs according to dominance style. Networks of intolerant species are more modular, more centralized, and less connected than those of tolerant ones. Given these structural differences, networks of intolerant species are potentially more vulnerable to fragmentation and decreased information transmission when central individuals disappear. Here we studied network resilience and efficiency in artificial societies of macaques. The networks were produced with an individual-based model that has been shown to reproduce the structural features of networks of tolerant and intolerant macaques. To study network resilience, we deleted either central individuals or individuals at random and studied the effects of these deletions on network cohesiveness and efficiency. The deletion of central individuals had more negative effects than random deletions from the networks of both tolerant and intolerant artificial societies. Central individuals thus appeared to aid in the maintenance of network cohesiveness and efficiency. Further, the networks of both intolerant and tolerant societies appeared to be robust to the loss of individuals, as network fragmentation was never observed. Our results suggest that despite differences in network structure, networks of tolerant and intolerant macaques may be equally resilient.


Social style and resilience of macaques’ networks, a theoretical investigation
Ivan Puga-Gonzalez, Sebastian Sosa, Cedric Sueur



Cross-boundary Behavioural Reprogrammability Reveals Evidence of Pervasive Turing-Universality

New paper sheds light on the pervasiveness of Turing universality by showing a series of behavioural boundary crossing results, including emulations (for all initial conditions) of Wolfram class 2 Elementary Cellular Automata (ECA) by Class 1 ECA, emulations of Classes 1, 2 and 3 ECA by Class 2 and 3 ECA, and of Classes 1, 2 and 3 by Class 3 ECA, along with results of even greater emulability for general CA (neighbourhood r = 3/2), including Class 1 CA emulating Classes 2 and 3, and Classes 3 and 4 emulating all other classes (1, 2, 3 and 4). The emulations occur with only a linear overhead and can be considered computationally efficient. The paper also introduces a concept of emulation networks, deriving a topologically-based measure of complexity based upon out- and in-degree connectivity establishing bridges to fundamental ideas of complexity, universality, causality and dynamical systems.


The Adaptive Behavior of a Soccer Team: An Entropy-Based Analysis

To optimize its performance, a competitive team, such as a soccer team, must maintain a delicate balance between organization and disorganization. On the one hand, the team should maintain organized patterns of behavior to maximize the cooperation between its members. On the other hand, the team’s behavior should be disordered enough to mislead its opponent and to maintain enough degrees of freedom. In this paper, we have analyzed this dynamic in the context of soccer games and examined whether it is correlated with the team’s performance. We measured the organization associated with the behavior of a soccer team through the Tsallis entropy of ball passes between the players. Analyzing data taken from the English Premier League (2015/2016), we show that the team’s position at the end of the season is correlated with the team’s entropy as measured with a super-additive entropy index. Moreover, the entropy score of a team significantly contributes to the prediction of the team’s position at the end of the season beyond the prediction gained by the team’s position at the end of the previous season.


Neuman, Y.; Israeli, N.; Vilenchik, D.; Cohen, Y.

The Adaptive Behavior of a Soccer Team: An Entropy-Based Analysis.

Entropy 2018, 20, 758.


Modeling Collective Rule at Ancient Teotihuacan as a Complex Adaptive System: Communal Ritual Makes Social Hierarchy More Effective

Experts remain divided about the nature of the sociopolitical system of ancient Teotihuacan, which was one of the earliest and largest urban civilizations of the Americas. Excavations hoping to find compelling evidence of powerful rulers, such as a royal tomb, keep coming away empty-handed. But the alternative possibility of collective rule still remains poorly understood as well. Previously we used a computational model of this city’s hypothetical sociopolitical network to show that in principle collective rule based on communal ritual could be an effective strategy of ensuring widespread social coordination, as long as we assume that the network’s structure could be transformed via social learning and local leaders were not strongly subdivided. Here we extended this model to investigate whether increased social hierarchy could mitigate the negative effects of such strong divisions. We found a special synergy between social hierarchy and communal ritual: only their combination improved the extent of social coordination, whereas the introduction of centralization and top-down influence by themselves had no effect. This finding is consistent with portrayals of the Teotihuacan elite as religious specialists serving the public good, in particular by synchronizing the city’s ritual calendar with the rhythms of the stars.


Modeling Collective Rule at Ancient Teotihuacan as a Complex Adaptive System: Communal Ritual Makes Social Hierarchy More Effective
Tom Froese & Linda R. Manzanilla

Cognitive Systems Research