Felipe Xavier Costa, Jordan C. Rozum, Austin M. Marcus, and Luis M. Rocha

Entropy 2023, 25(2), 374

Biomolecular network dynamics are thought to operate near the critical boundary between ordered and disordered regimes, where large perturbations to a small set of elements neither die out nor spread on average. A biomolecular automaton (e.g., gene, protein) typically has high regulatory redundancy, where small subsets of regulators determine activation via collective canalization. Previous work has shown that effective connectivity, a measure of collective canalization, leads to improved dynamical regime prediction for homogeneous automata networks. We expand this by (i) studying random Boolean networks (RBNs) with heterogeneous in-degree distributions, (ii) considering additional experimentally validated automata network models of biomolecular processes, and (iii) considering new measures of heterogeneity in automata network logic. We found that effective connectivity improves dynamical regime prediction in the models considered; in RBNs, combining effective connectivity with bias entropy further improves the prediction. Our work yields a new understanding of criticality in biomolecular networks that accounts for collective canalization, redundancy, and heterogeneity in the connectivity and logic of their automata models. The strong link we demonstrate between criticality and regulatory redundancy provides a means to modulate the dynamical regime of biochemical networks.

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Venverloo T, Duarte F, Benson T, Leoni P, Hoogendoorn S, Ratti C (2023) Tracking stolen bikes in Amsterdam. PLoS ONE 18(2): e0279906.

Crime has major influences in urban life, from migration and mobility patterns, to housing prices and neighborhood liveability. However, urban crime studies still largely rely on static data reported by the various institutions and organizations dedicated to urban safety. In this paper, we demonstrate how the use of digital technologies enables the fine-grained analysis of specific crimes over time and space. This paper leverages the rise of ubiquitous sensing to investigate the issue of bike theft in Amsterdam—a city with a dominant cycling culture, where reportedly more than 80,000 bikes are stolen every year. We use active location tracking to unveil where stolen bikes travel to and what their temporal patterns are. This is the first study using tracking technologies to focus on two critical aspects of contemporary cities: active mobility and urban crime.

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Richard Creath 

Theory in Biosciences volume 142, pages61–66 (2023)

There is an old attempt to divide the sciences into sciences of laws and the historical sciences. More recently, John Beatty has drawn the distinction so that biology is a historical science and urged that there are no genuinely biological laws. This paper shows that there are indeed biological laws, specifically statistical ones, notably in evolutionary theory. Moreover, all or almost all other areas of biology involve laws as well. Even history involves laws. Finally, the paper shows that this pervasiveness of laws is compatible with the most basic commitments of those who, like Beatty, would claim that biology is only historical.

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Tomas Veloz, Francis Heylighen, and Olaf Witkowski

Entropy 2023, 25(2), 286

Understanding the underlying structure of evolutionary processes is one the most important issues of scientific enquiry of this century. In the twentieth century, scientific thinking witnessed the overwhelming power of the evolutionary paradigm. It not only solidified the foundations of diverse areas, such as cell-biology, ecology, and economics, but also fostered the development of novel mathematical and computational tools to model and simulate how evolutionary processes take place.
In addition to the application of the evolutionary paradigm and the discovery of the evolutionary features for processes of diverse nature, there is another interesting aspect which touches upon the emergence of novel evolutionary processes. Namely, the emergence of an evolutionary process requires a complex transition between a prior form where no evolutionary process is undergoing and a posterior form where the evolutionary process has been triggered.
Theoretical methods to describe the emergence of evolutionary processes require the consideration of complex systemic notions, such as self-organization, resilience, contextuality, among others. Therefore, complexity and evolution became intertwined notions: evolution not only leads to but also depends on the development of increasingly complex forms and functions.
In this Special Issue, we put together eight articles, mostly of interdisciplinary nature, that explore from recent advances in the modeling of complex systems, as well as of the increasing modeling power and growth of databases associated to evolutionary processes.

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Francis Heylighen 

Foundations of Science volume 28, pages 85–107 (2023)

Quantum phenomena are notoriously difficult to grasp. The present paper first reviews the most important quantum concepts in a non-technical manner: superposition, uncertainty, collapse of the wave function, entanglement and non-locality. It then tries to clarify these concepts by examining their analogues in complex, self-organizing systems. These include bifurcations, attractors, emergent constraints, order parameters and non-local correlations. They are illustrated with concrete examples that include Rayleigh–Bénard convection, social self-organization and Gestalt perception of ambiguous figures. In both cases, quantum and self-organizing, the core process appears to be a symmetry breaking that irreversibly and unpredictably “collapses” an ambiguous state into one of a number of initially equivalent “eigenstates” or “attractors”. Some speculations are proposed about the non-linear amplification of quantum fluctuations of the vacuum being ultimately responsible for such symmetry breaking.

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