Complex networks of interacting stochastic tipping elements: cooperativity of phase separation in the large-system limit

Tipping elements in the Earth System receive increased scientific attention over the recent years due to their nonlinear behavior and the risks of abrupt state changes. While being stable over a large range of parameters, a tipping element undergoes a drastic shift in its state upon an additional small parameter change when close to its tipping point. Recently, the focus of research broadened towards emergent behavior in networks of tipping elements, like global tipping cascades triggered by local perturbations. Here, we analyze the response to the perturbation of a single node in a system that initially resides in an unstable equilibrium. The evolution is described in terms of coupled nonlinear equations for the cumulants of the distribution of the elements. We show that drift terms acting on individual elements and offsets in the coupling strength are sub-dominant in the limit of large networks, and we derive an analytical prediction for the evolution of the expectation (i.e., the first cumulant). It behaves like a single aggregated tipping element characterized by a dimensionless parameter that accounts for the network size, its overall connectivity, and the average coupling strength. The resulting predictions are in excellent agreement with numerical data for Erd\"os-R\'enyi, Barab\'asi-Albert and Watts-Strogatz networks of different size and with different coupling parameters

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Thermodynamic patterns of life: emergent phenomena in reaction networks

Reaction networks are an important tool for the analysis of complex chemical reaction systems. They help us understand systems ranging from specific metabolisms to planetary atmospheres. This thesis develops methods for the analysis of living systems by using reaction networks with a focus on the inclusion of thermodynamic properties. New methods for more realistic artificial chemistries are developed using thermodynamic constraints. A model of evolvable artificial ecosystems is created to understand the effect of evolution and life on the flow of matter and energy through the system. To investigate general thermodynamic properties of large-scale reaction networks, artificial reaction networks are created with a simple scheme for deriving thermodynamically consistent reaction rates. Linear and nonlinear networks using four different complex network models are simulated to their non-equilibrium steady state for various boundary fluxes. Increasing the flow through nonlinear networks shows to increases the number of cycles and leads to a narrower distribution of chemical potentials. In the context of finding signs of life by detecting chemical disequilibrium, a photochemical model of the modern atmosphere and a model of the Archean atmosphere are compared. Calculating the reaction pathways that are most relevant for explaining their reaction network's steady state with a new method allows for the detection of topological differences between the two models. Pathways of the modern Earth atmosphere are simpler (less reactions) and contain fewer cycles than their Archean counterparts. To model the influence of life on reaction pathways, an artificial ecosystem model is developed. Evolution of the reaction networks entails an evolution of reaction pathways towards simplicity, thus indicating that the presence of pronounced, relatively simple pathways in real systems is a consequence of an evolutionary mechanism

A complex systems approach to education in Switzerland

The insights gained from the study of complex systems in biological, social, and engineered systems enables us not only to observe and understand, but also to actively design systems which will be capable of successfully coping with complex and dynamically changing situations. The methods and mindset required for this approach have been applied to educational systems with their diverse levels of scale and complexity. Based on the general case made by Yaneer Bar-Yam, this paper applies the complex systems approach to the educational system in Switzerland. It confirms that the complex systems approach is valid. Indeed, many recommendations made for the general case have already been implemented in the Swiss education system. To address existing problems and difficulties, further steps are recommended. This paper contributes to the further establishment complex systems approach by shedding light on an area which concerns us all, which is a frequent topic of discussion and dispute among politicians and the public, where billions of dollars have been spent without achieving the desired results, and where it is difficult to directly derive consequences from actions taken. The analysis of the education system's different levels, their complexity and scale will clarify how such a dynamic system should be approached, and how it can be guided towards the desired performance

Épistémologie de la biologie synthétique et pluralisme du concept de « vivant »

Selon la théorie cellulaire, issue des travaux de M. J. Schleiden, T. Schwann et R. Virchow au 19e siècle, le plus petit niveau d’organisation comprenant toutes les caractéristiques nécessaires et essentielles au vivant serait la cellule. Cette affirmation est aujourd’hui remise en question par les scientifiques et philosophes, d’une part à la suite de l’analyse d’entités biologiques ambiguës aux frontières (inférieures et supérieures) de la « cellule vivante », et d’autre part de l’avènement des récents enjeux en lien avec la création et la recherche de nouvelles entités vivantes. Un pluralisme épistémologique du concept de « vivant » a ainsi émergé, duquel aucune définition claire et unanime n’est encore acceptée. L’objectif général de cette thèse est de trouver des pistes de solution au problème du pluralisme épistémologique du concept de « vivant » ainsi qu’aux enjeux pratiques reliés à ce concept en biologie. Pour ce faire, je propose l’idée que les enjeux pratiques peuvent contribuer à résoudre le pluralisme conceptuel du « vivant », en particulier que la biologie synthétique est à même de nous offrir une définition du vivant permettant de dépasser l’actuel pluralisme de ce concept. Plus spécifiquement, en ce qui a trait à la question du pluralisme, j’expose dans cette thèse un pluralisme « biologique » et « philosophique ». Du côté « biologique », je démontre la flexibilité d’application ainsi que le pluralisme du concept de « vivant » grâce à l’exposition de cas ambigus d’entités biologiques issues de divers niveaux hiérarchiques de complexité du vivant. Ce faisant, je défends une position symbiotique et holistique d’organisation du vivant (permettant d’inclure et d’articuler ces divers niveaux hiérarchiques). Du côté « philosophique », je démontre le pluralisme du concept de « vivant » à la suite d’une analyse que je qualifierai de disciplinaire, ontologique, linguistique et épistémologique. Ce faisant, je défends une position gradualiste et opérationnelle du concept de « vivant ». En ce qui concerne les enjeux pratiques, j’explore principalement la discipline de la biologie synthétique, qui s’est donné l’objectif de construire de nouvelles entités biologiques vivantes et ainsi le fort potentiel de contribuer au développement de nouvelles connaissances sur le vivant. Ce faisant, je prends ainsi la position que la biologie synthétique peut apporter des pistes de solution pragmatiques (par la construction d’entités vivantes fonctionnelles) au pluralisme épistémologique du concept de « vivant ». Finalement, après une analyse de théories de la connaissance associées à ces enjeux, de définitions stipulatives, ainsi que de concepts du vivant issus de la biologie synthétique, je développe mon propre modèle du « vivant» (que je qualifie de biosynthétique), qui se veut « pragmatique » (en accord avec la pratique des biologistes synthétiques), « progressiste » (s’adaptant à de futures découvertes dans le domaine), « holistique » (s’appliquant à l’ensemble des niveaux d’organisation du vivant) ainsi que « minimaliste et universelle» (correspondant aux caractéristiques essentielles de base retrouvées au sein de toutes les entités vivantes). Cette thèse présentera ainsi « pourquoi » et « comment » la biologie synthétique peut répondre à la question de la définition du vivant.According to the cell theory, resulting from the works of M. J. Schleiden, T. Schwann and R. Virchow in the 19th century, the smallest level of organization including all the necessary and essential characteristics to the living would be the cell. This assertion is now challenged by scientists and philosophers, on the one hand following the analysis of ambiguous biological entities at the boundaries (lower and upper) of the "living cell", and on the other hand the advent of recent issues related to the creation and search for new living entities. An epistemological pluralism of the "living" concept has thus emerged, from which no clear and unanimous definition is yet accepted. The general objective of this thesis is to find possible solutions to the problem of epistemological pluralism of the "living" concept and to the practical issues related to this concept in biology. To do this, I propose the idea that practical issues can contribute to solving the conceptual pluralism of the concept "living", in particular that synthetic biology is able to offer us a definition of the living allowing to overcome the current pluralism of this concept. More specifically, regarding the question of pluralism, I expose in this thesis a "biological" and "philosophical" pluralism. On the "biological" side, I demonstrate the flexibility of application as well as the pluralism of the concept "living" following the description of ambiguous cases of biological entities coming from various hierarchical levels of complexity of life. In doing so, I defend a symbiotic and holistic view of organization of the living (allowing to include and articulate these various hierarchical levels). On the "philosophical" side, I demonstrate the pluralism of the "living" concept following an analysis that I will describe as disciplinary, ontological, linguistic and epistemological. In doing so, I defend a gradualist and operational position of the concept "living". Regarding practical issues, I am mainly exploring the discipline of synthetic biology, which has set itself the goal of building new living biological entities and thus the potential to contribute to the development of new knowledge about life. In doing so, I take the position that synthetic biology can provide pragmatic solutions (through the construction of functional living entities) to the pluralism of the concept "living". Finally, after an analysis of the relevant theories of knowledge associated with these issues, of stipulative definitions, as well as of living concepts stemming from synthetic biology, I develop my own model of the "living" (that I call biosynthetic), which is "pragmatic" (in agreement with the practice of synthetic biologists), "progressive" (adapting to future discoveries in the field), "holistic" (applying to all levels of organization of the living) as well as "minimalist and universal" (corresponding essential characteristics found within all living entities). This thesis will present “why” and “how” synthetic biology can provide an answer to the question “what is life ?”

Une histoire de la chimie atmosphérique globale: Enjeux disciplinaires et d'expertise de la Couche d'ozone et du Changement climatique

Until now, the history of environmental sciences has not extensively documented the input of atmospheric chemists, who formalize the chemical reactions that take place in the atmosphere. This PhD dissertation focuses on chemistry of the global atmosphere. Atmospheric chemistry has been in the heart of the expertise on the anthropogenic destruction of the ozone layer from 1970 on. Since the end of the 1980s, atmospheric chemists have also taken part in the writing of the IPCC reports. They have also contributed to the more holistic works on the “Earth system”. Combining different approaches for studying sciences and techniques, this PhD dissertation writes a "social" history of the academic field on chemistry of the global atmosphere since the 1920s. Our narrative is mainly focused on the evolution of the scientific practices of chemistry of the global atmosphere, on social and disciplinary changes, and on the new types of expertise that have emerged within the field. The author mainly concentrates on three "moments": the first two decades of the Coldwar; the “environmental(ist) turn” of atmospheric sciences in the 1970s and 80s; the climate change governance.L’histoire des sciences de l’environnement a, jusqu’à présent, peu documenté l’apport des chimistes de l’atmosphère, qui formalisent les réactions chimiques se produisant au sein de l’atmosphère. Cette thèse porte spécifiquement sur la chimie atmosphérique globale. La chimie de l’atmosphère a été au centre de l’expertise sur la destruction anthropique de la couche d’ozone à partir de 1970. Les chimistes de l’atmosphère ont également participé à l’élaboration des rapports du GIEC (Groupe d’experts intergouvernemental sur l'évolution du climat) à partir de la fin des années 1980, ainsi qu’à des travaux au sein de la science dite « du système Terre ». En combinant différentes approches de l’étude des sciences et des techniques, ce mémoire de thèse fait une histoire "sociale" du champ d’étude sur la chimie atmosphérique globale depuis les années 1920. Le cœur du récit porte sur l’évolution des pratiques scientifiques de la chimie atmosphérique globale, les reconfigurations disciplinaires et sociales, et l’apparition de nouvelles formes d’expertise et de figures d’expert propres à ce champ d’étude. L’auteur examine dans le détail trois "moments": les deux premières décennies de la Guerre froide ; le "tournant environnemental(iste)" des sciences de l’atmosphère dans les années 1970- 80 ; la gouvernance du changement climatique