Complex Systems Science: Dreams of Universality, Reality of Interdisciplinarity

Using a large database (~ 215 000 records) of relevant articles, we empirically study the "complex systems" field and its claims to find universal principles applying to systems in general. The study of references shared by the papers allows us to obtain a global point of view on the structure of this highly interdisciplinary field. We show that its overall coherence does not arise from a universal theory but instead from computational techniques and fruitful adaptations of the idea of self-organization to specific systems. We also find that communication between different disciplines goes through specific "trading zones", ie sub-communities that create an interface around specific tools (a DNA microchip) or concepts (a network).Comment: Journal of the American Society for Information Science and Technology (2012) 10.1002/asi.2264

Density-Dependence as a Size-Independent Regulatory Mechanism

The growth function of populations is central in biomathematics. The main dogma is the existence of density dependence mechanisms, which can be modelled with distinct functional forms that depend on the size of the population. One important class of regulatory functions is the $\theta$-logistic, which generalises the logistic equation. Using this model as a motivation, this paper introduces a simple dynamical reformulation that generalises many growth functions. The reformulation consists of two equations, one for population size, and one for the growth rate. Furthermore, the model shows that although population is density-dependent, the dynamics of the growth rate does not depend either on population size, nor on the carrying capacity. Actually, the growth equation is uncoupled from the population size equation, and the model has only two parameters, a Malthusian parameter $\rho$ and a competition coefficient $\theta$. Distinct sign combinations of these parameters reproduce not only the family of $\theta$-logistics, but also the van Bertalanffy, Gompertz and Potential Growth equations, among other possibilities. It is also shown that, except for two critical points, there is a general size-scaling relation that includes those appearing in the most important allometric theories, including the recently proposed Metabolic Theory of Ecology. With this model, several issues of general interest are discussed such as the growth of animal population, extinctions, cell growth and allometry, and the effect of environment over a population.Comment: 41 Pages, 5 figures Submitted to JT

A two-stage growth model for gilthead sea bream (Sparus aurata) based on the thermal growth coefficient

Several authors have proposed models to describe fish growth taking the influence of temperature into account, and one of the most interesting is the "thermal unit growth coefficient" (TGC). Recent research has demonstrated that TGC varies throughout the growth cycle of fish, making it necessary to establish different stanzas. In this work, the original TGC model using 1/3 as an exponent was compared with a new model considering 2/3. Likewise, two stages for the growth of gilthead sea bream under commercial conditions in marine farms were detected by means of TGC seasonal models using the continuous temperature curve. A critical value for weight around 117g was obtained, which could mark the transition between two growth dynamics. To describe the weight evolution during a complete production cycle, the two growth stages were described by two separate seasonal TGC models (1/3-TGC model and 2/3-TGC model), and with an integrated model named the Mixed-TGC model, which presents interesting properties of continuity and differentiability and could be an important tool for fish farm management.V.D. Estruch and M. Jover were partially supported by the Universitat Politecnica de Valencia, PAID 2009-2010.Mayer, P.; Estruch Fuster, VD.; Jover Cerdá, M. (2012). A two-stage growth model for gilthead sea bream (Sparus aurata) based on the thermal growth coefficient. Aquaculture. 358-359:6-13. https://doi.org/10.1016/j.aquaculture.2012.06.016S613358-35

Towards Autopoietic Computing

A key challenge in modern computing is to develop systems that address complex, dynamic problems in a scalable and efficient way, because the increasing complexity of software makes designing and maintaining efficient and flexible systems increasingly difficult. Biological systems are thought to possess robust, scalable processing paradigms that can automatically manage complex, dynamic problem spaces, possessing several properties that may be useful in computer systems. The biological properties of self-organisation, self-replication, self-management, and scalability are addressed in an interesting way by autopoiesis, a descriptive theory of the cell founded on the concept of a system's circular organisation to define its boundary with its environment. In this paper, therefore, we review the main concepts of autopoiesis and then discuss how they could be related to fundamental concepts and theories of computation. The paper is conceptual in nature and the emphasis is on the review of other people's work in this area as part of a longer-term strategy to develop a formal theory of autopoietic computing.Comment: 10 Pages, 3 figure

A holistic multi-methodology for sustainable renovation

A review of the barriers for building renovation has revealed a lack of methodologies, which can promote sustainability objectives and assist various stakeholders during the design stage of building renovation/retrofitting projects. The purpose of this paper is to develop a Holistic Multi-methodology for Sustainable Renovation, which aims to deal with complexity of renovation projects. It provides a framework through which to involve the different stakeholders in the design process to improve group learning and group decision-making, and hence make the building renovation design process more robust and efficient. Therefore, the paper discusses the essence of multifaceted barriers in building renovation regarding cultural changes and technological/physical changes. The outcome is a proposal for a multi-methodology framework, which is developed by introducing, evaluating and mixing methods from Soft Systems Methodologies (SSM) with Multiple Criteria Decision Making (MCDM). The potential of applying the proposed methodology in renovation projects is demonstrated through a case study

Stochastic Physics, Complex Systems and Biology

In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated equilibrium, spontaneous random "mutations" and "adaptations". On an evlutionary time scale it produces sustainable diversity among individuals in a homogeneous population rather than convergence as usually predicted by a deterministic dynamics. The emergent discrete states in such a system, i.e., attractors, have natural robustness against both internal and external perturbations. Phenotypic states of a biological cell, a mesoscopic nonlinear stochastic open biochemical system, could be understood through such a perspective.Comment: 10 page

Milionella subrotunda (Montague 1803), a miliolid foraminifer building large agglutinated tubes for a temporary epibenthic livestyle.

Live observations, cytological characteristics and biometrical measurements on Miliolinella subrotunda (Montagu, 1803) sampled from the northern and southern Atlantic Ocean are presented.M. subrotunda facultatively constructs a long, detritic tube lifting the test several millimeters above the sediment surface. A thickened conical base anchors the construction on the sediment surface and a long, flexible tube protrudes into the velocity profile of the bottom currents. The miliolid test is placed on top, surrounded by the uppermost part of the tube. This construction allows the organisms to feed in the particle stream above the sediment surface. In comparison to species living in and on the surface sediments,M. subrotunda apparently shows higher nutritional values in food ingested and larger amounts of reserve substances. Characteristics of the shape and structure that reduce drag on the tubes include a broadened conical base, a flexible tube, and a rounded top. From biometrical measurements it is concluded, that the tubes are constructed over a short period of their ontogeny

The Roots of Bioinformatics in Theoretical Biology

From the late 1980s onward, the term “bioinformatics” mostly has been used to refer to computational methods for comparative analysis of genome data. However, the term was originally more widely defined as the study of informatic processes in biotic systems. In this essay, I will trace this early history (from a personal point of view) and I will argue that the original meaning of the term is re-emerging