Simulation modelling of ecological hierarchies in constructive dynamical systems

Organized complexity is a characteristic feature of ecological systems with heterogeneous components interacting at several spatio-temporal scales. The hierarchy theory is a powerful epistemological framework to describe such systems by decomposing them vertically into levels and horizontally into holons. It was at first developed in a temporal and functional perspective and then, in the context of landscape ecology, extended to a spatial and structural approach. So far, most ecological applications of this theory were restricted to observational purposes, using multi-scale analysis to describe hierarchies. In spite of an increasing attention to dynamics of hierarchically structured ecological systems, current simulation models are still very limited in their representation of self-organization in complex adaptive systems. An ontological conceptualization of the hierarchy theory is outlined, focusing on key concepts, such as levels of organization and the compound and component faces of the holons. Various existing formalisms are currently used in simulation modelling, such as system dynamics, discrete event and agent based paradigms. Their ability to express the hierarchical organization of dynamical ecological systems is discussed. It turns out that a multi-modelling approach linking all these formalisms and oriented toward the specification of a constructive dynamical system would be able to express the dynamical structure of the hierarchy (creation, destruction and change of holons) and the functional and structural links between levels of organization.     

Levels of organization in biology: on the nature and nomenclature of ecology's fourth level

Viewing the universe as being composed of hierarchically arranged systems is widely accepted as a useful model of reality. In ecology, three levels of organization are generally recognized: organisms, populations, and communities (biocoenoses). For half a century increasing numbers of ecologists have concluded that recognition of a fourth level would facilitate increased understanding of ecological phenomena. Sometimes the word "ecosystem" is used for this level, but this is arguably inappropriate. Since 1986, I and others have argued that the term "landscape" would be a suitable term for a level of organization defined as an ecological system containing more than one community type. However, "landscape" and "landscape level" continue to be used extensively by ecologists in the popular sense of a large expanse of space. I therefore now propose that the term "ecoscape" be used instead for this fourth level of organization. A clearly defined fourth level for ecology would focus attention on the emergent properties of this level, and maintain the spatial and temporal scale-free nature inherent in this hierarchy of organizational levels for living entities.     

On the thermodynamics of multilevel evolution

Biodiversity is hierarchically structured both phylogenetically and functionally. Phylogenetic hierarchy is understood as a product of branching organic evolution as described by Darwin. Ecosystem biologists understand some aspects of functional hierarchy, such as food web architecture, as a product of evolutionary ecology; but functional hierarchy extends to much lower scales of organization than those studied by ecologists. We argue that the more general use of the term “evolution” employed by physicists and applied to non-living systems connects directly to the narrow biological meaning. Physical evolution is best understood as a thermodynamic phenomenon, and this perspective comfortably includes all of biological evolution. We suggest four dynamical factors that build on each other in a hierarchical fashion and set the stage for the Darwinian evolution of biological systems: (1) the entropic erosion of structure; (2) the construction of dissipative systems; (3) the reproduction of growing systems and (4) the historical memory accrued to populations of reproductive agents by the acquisition of hereditary mechanisms. A particular level of evolution can underpin the emergence of higher levels, but evolutionary processes persist at each level in the hierarchy. We also argue that particular evolutionary processes can occur at any level of the hierarchy where they are not obstructed by material constraints. This theoretical framework provides an extensive basis for understanding natural selection as a multilevel process. The extensive literature on thermodynamics in turn provides an important advantage to this perspective on the evolution of higher levels of organization, such as the evolution of altruism that can accompany the emergence of social organization.     

Evaluating Environmental Performance of Pulp and Paper Manufacturing Using the Analytic Hierarchy Process and Life-Cycle Assessment

This article addresses the need for a structured and compre-hensive methodology for assessing the environmental perfor-mance of manufacturing processes. The analytic hierarchy pro-cess (AHP) is used as the basic framework for analyzing environmental impacts and improvement options following a streamlined life-cycle assessment (LCA) approach that is fo-cused on the manufacturing operation. The multicriteria de-cision analysis approach of the AHP is consistent with the LCA concept because the environmental factors can be hierarchi-cally structured into impacts and improvement options. Its po-tential as a valuation tool for impact and improvement assess-ment addresses both qualitative and quantitative issues in environmental decision making.
Through application to a pulp and paper manufacturing case study, the viability of the AHP for evaluating environmen-tal impacts and prioritizing process improvement options rela-tive to these impacts is demonstrated. AHP was used to pro-vide a quantitative tool for the design of a set of weighting factors for impact and improvement analyses.     

Can community composition be predicted from pairwise species interactions?

Plant communities are often structured by interactions among species, such as competition or facilitation. If competition is an important factor that controls the presence and absence of species within intact communities, then a competitive hierarchy, a ranked order from competitive dominant to competitive subordinate, should predict the composition of intact communities. We tested whether a competitive hierarchy derived from pairwise comparisons accurately predicts species abundances within a constructed polyculture community consisting of seven species common to old-field plant communities. We first conducted a pot experiment in field conditions wherein we grew the species in all possible combinations, then created a competitive hierarchy derived from both competitive effect and competitive response for each species. Concurrently, at the same site in native field soil, we constructed polycultures consisting of the same seven species and calculated an abundance hierarchy based on foliar cover, biomass, and an index of species performance. The competitive hierarchy was not concordant with the abundance hierarchy, indicating that simple pairwise comparisons may not account for other factors that influence the abundance of species within relatively complex communities.     

Diversity concept in ecology

Hierarchy of systems organization is used as a framework in advancing methodological guidelines for posing correct questions related to ecological diversity.Diversity if defined in general terms as a property of a set of elements dependent on and determines: by the epistemological perspective. Ontological diversity, because it is indefinite, is regarded as unmeasurable.Ecological diversity — be it species, spatial, reproductive or trophic, is a particular case of diversity of matter and must be precisely defined on the studied level of system organization.Diversity measurements combining more than one level of organization are information-void, for data become irretrievable as a result of such a treatment.Hypotheses explaining diversity sources are briefly surveyed. An integrated model interrelating them is constructed as a result of some basic views on the structure of matter coupled with the empirical knowledge of involved factors. The model reflects hierarchies of systems, their dynamics, and the complexities of factors affecting diversity. The model's properties suggest that it is conceptually related to an imaginary model of organization of ecological systems. Parameters recognized as invariant components of this complexity are: habitat differentiation, ecological specialization of species, ambiental changes, and integration of this system.Finally, it is shown that the peculiar shape of the species abundances curve is a necessary consequence of stratification of the system structure, which is an intrinsic attribute of hierarchical organization.     

A computational model for the primate neocortex based on its functional architecture

Experimental evidence has shown that the primate neocortex consists in the main of a set of cortical regions which form a perception hierarchy, an action hierarchy and connections between them. By using a computer science analysis, we develop a computational architecture for the brain in which each cortical region is represented by a computational module with processing and storage abilities. Modules are interconnected according to the connectivity of the corresponding cortical regions. We develop computational principles for designing such a hierarchical and parallel computing system. We demonstrate this approach by proposing a causal functioning model of the brain. We report on results obtained with an implementation of this model. We conclude with a brief discussion of some consequences and predictions of our work.     

Competing Models of Stability in Complex, Evolving Systems: Kauffman vs. Simon

I criticize Herbert Simon's argument for the claim that complex natural systems must constitute decomposable, mereological or functional hierarchies. The argument depends on certain assumptions about the requirements for the successful evolution of complex systems, most importantly, the existence of stable, intermediate stages in evolution. Simon offers an abstract model of any process that succeeds in meeting these requirements. This model necessarily involves construction through a decomposable hierarchy, and thus suggests that any complex, natural, i.e., evolved, system is constituted by a decomposable hierarchy. I argue that Stuart Kauffman's recent models of genetic regulatory networks succeed in specifying processes that could meet Simon's requirements for evolvability without requiring construction through a decomposable hierarchy. Since Kauffman's models are at least as plausible as Simon's model, Simon's argument that complex natural systems must constitute decomposable, mereological or functional hierarchies does not succeed.     

The case for primate V3

The visual system in primates is represented by a remarkably large expanse of the cerebral cortex. While more precise investigative studies that can be performed in non-human primates contribute towards understanding the organization of the human brain, there are several issues of visual cortex organization in monkey species that remain unresolved. In all, more than 20 areas comprise the primate visual cortex, yet there is little agreement as to the exact number, size and visual field representation of all but three. A case in point is the third visual area, V3. It is found relatively early in the visual system hierarchy, yet over the last 40 years its organization and even its very existence have been a matter of debate among prominent neuroscientists. In this review, we discuss a large body of recent work that provides straightforward evidence for the existence of V3. In light of this, we then re-examine results from several seminal reports and provide parsimonious re-interpretations in favour of V3. We conclude with analysis of human and monkey functional magnetic resonance imaging literature to make the case that a complete V3 is an organizational feature of all primate species and may play a greater role in the dorsal stream of visual processing.     

Levels of organization of living systems: Cooperons

All creatures living on Earth are traditionally discussed in the context of structuralmorphological approach, in frame of which there are considered various systems (for instance, organisms and ecosystems) that have different sizes and organization and use different resources for their existence. These characteristics are sometimes added by some particular functional and ecological characteristics, but usually with respect to the structural ones. We believe that such traditional approach, although illustrating, but distracts from the circumstance that any living systems is to be considered an integrated structural-functional complex, the maintenance of existence of this system being impossible without the processes occurring constantly in it and aimed at preserving this complex. This leads us to the concept of cooperons—the self-preserved dynamic structures existing only as a result of various specifically organized cooperative processes (their intensities can vary depending on circumstances). From our point of view, all living systems are cooperons of different hierarchy levels. Some other systems, specifically the symbiotic ones, also are cooperons. In frame of this concept, it is possible to discuss functioning of living systems of different types of organization in a new context closer to physiologists, both for the case of “norm” and for the situation when the cooperative interrelations of parts of the system are impaired (for instance, in systemic diseases).     

Expert System for Modeling and Simulating the Action of Electric and Electromagnetic Fields on Biological Membranes

The biological effects and applications in the developing technology involving electric and electromagnetic fields are as promising as they are diverse. Their effects, leading to remission in certain patients, can be obtained through electroporation, electrochemotherapy, electrotherapy, electroimmunotherapy, and gene electrotherapy. The main therapeutic uses of electromagnetic fields (EMF) are the introduction of chemical or organic substances into opportunely opened cells (electro-chimiotherapy) and the stimulation of specific elements of the immune system (electro-immunotherapy). Their benefits can be modeled by the use of expert systems, constructed to mimic human reasoning. As well as testing new therapies, such systems can analyze and synthesize existing data, and provide a new pedagogical device, and can be implemented on the Internet network. These techniques can be performed conjointly with other therapies like X-ray therapy, neutrotherapy and, in certain conditions, will optimize their effects. Some mathematical models, representing the electromagnetic field's action on cellular membranes, have been elaborated by means of the SADT method (a structured hierarchy modular method) and implanted into the expert system SEI4. This expert system simulates the immune system's behavior when facing electromagnetic fields, in the face of immunodeficient illness such as some cancers or AIDS.     

Problems of biochemical organization]

Biological organization has been defined as a unity of structure, function and regulation. Biological organization of hierarchical multilevel biological systems is represented by a hierarchy of functioning controllable structures. The hierarchy of levels of material organization predetermines the existence of a hierarchy of regulatory mechanisms. Biochemical organization involves the levels of material organization corresponding to biomacromolecules, supramolecular complexes and cellular organelles. The levels of biomacromolecules and supramolecular structures effectuating elementary functions and controlled by basic regulatory mechanisms occupy key positions in biological systems. These levels play the role of standard functional blocks; their combination leads to hierarchically higher structural levels (cell, tissue, organ, systems of organs, organism) performing more complex functions and controlled by hierarchically more important regulatory mechanisms. The peculiarities of regulation of biological systems that are due to the existence of a hierarchy of regulatory mechanisms are discussed.     

Reflection in the electrical activity of the brain of the activities of the mechanisms regulating the functional state

On the basis of analysis of the results of author's studies and literature data, theoretical notions are developed, according to which spatial-temporal organization of cortical biopotentials is a result of activity of nonspecific different level systems subtly regulating current alertness in conformity with needs of the actual and forthcoming activities. In the hierarchy of regulating systems, in conditions of alertness, nonspecific thalamic and midbrain system is leading. Activity of these regulation levels provides in alertness for formation and destruction of functional neuronal ensembles which realize elementary informational transformations. The role is emphasized of asynchronous processes in the central nervous system activity.     

Units and passages: A view for evolutionary biology and ecology

Many authors, including paleobiologists, cladists and so on, adopt a nested hierarchical viewpoint to examine the relationships among different levels of biological organization. Furthermore, species are often considered to be unique entities in functioning evolutionary processes and one of the individuals forming a nested hierarchy.I have attempted to show that such a hierarchical view is inadequate in evolutionary biology. We should define units depending on what we are trying to explain. Units that play an important role in evolution and ecology do not necessarily form a nested hierarchy. Also the relationships among genealogies at different levels are not simply nested. I have attempted to distinguish the different characteristics of passages when they are used for different purposes of explanation. In my analysis, species and monophyletic taxa cannot be uniquely defined as single units that function in ecological and evolutionary processes.The view discussed in this paper may provide a more general basis for testing competing theories in evolution, and provide new insights for future empirical studies.     

Hawaii as a Model System for Human Ecodynamics

The human ecodynamics approach in archaeology privileges landscape as a core concept, asserting that there can be no environment or ecosystem detached from humans and their behavior. Drawing on recent research of a multidisciplinary biocomplexity project, I explore in this article the Hawaiian archipelago as a model system for studying human ecodynamics. Natural patterns of biogeochemical and climate gradients constrained the development of intensive agroecosystems over 1,000 years. An early phase of exponential population growth was linked with agricultural intensification of terraced irrigation systems, primarily on the older islands. After C.E. 1400, expansion of population onto the leeward slopes of the young islands of Maui and Hawai'i was accompanied by intensification of dryland agricultural field systems. These changes were in turn linked to significant transformations of social and political formations, including restructuring of the system of land tenure and descent group organization, and the imposition of a system of surplus extraction organized around a ritual hierarchy of temples.     

Hierarchy measure for complex networks

Nature, technology and society are full of complexity arising from the intricate web of the interactions among the units of the related systems (e.g., proteins, computers, people). Consequently, one of the most successful recent approaches to capturing the fundamental features of the structure and dynamics of complex systems has been the investigation of the networks associated with the above units (nodes) together with their relations (edges). Most complex systems have an inherently hierarchical organization and, correspondingly, the networks behind them also exhibit hierarchical features. Indeed, several papers have been devoted to describing this essential aspect of networks, however, without resulting in a widely accepted, converging concept concerning the quantitative characterization of the level of their hierarchy. Here we develop an approach and propose a quantity (measure) which is simple enough to be widely applicable, reveals a number of universal features of the organization of real-world networks and, as we demonstrate, is capable of capturing the essential features of the structure and the degree of hierarchy in a complex network. The measure we introduce is based on a generalization of the m-reach centrality, which we first extend to directed/partially directed graphs. Then, we define the global reaching centrality (GRC), which is the difference between the maximum and the average value of the generalized reach centralities over the network. We investigate the behavior of the GRC considering both a synthetic model with an adjustable level of hierarchy and real networks. Results for real networks show that our hierarchy measure is related to the controllability of the given system. We also propose a visualization procedure for large complex networks that can be used to obtain an overall qualitative picture about the nature of their hierarchical structure.     

Periodic orbits: a new language for neuronal dynamics.

A new nonlinear dynamical analysis is applied to complex behavior from neuronal systems. The conceptual foundation of this analysis is the abstraction of observed neuronal activities into a dynamical landscape characterized by a hierarchy of "unstable periodic orbits" (UPOs). UPOs are rigorously identified in data sets representative of three different levels of organization in mammalian brain. An analysis based on UPOs affords a novel alternative method of decoding, predicting, and controlling these neuronal systems.     

Distributing and searching concept hierarchies: an adaptive DHT-based system

Concept hierarchies greatly help in the organization and reuse of information and are widely used in a variety of information systems applications. In this paper, we describe a method for efficiently storing and querying data organized into concept hierarchies and dispersed over a DHT. In our method, peers individually decide on the level of indexing according to the granularity of the incoming queries. Roll-up and drill-down operations are performed on a per-node basis in order to minimize the required bandwidth for answering queries on variable aggregation levels. We motivate our approach by applying it on a large-scale Grid system: Specifically, we apply our fully decentralized scheme that creates, queries and updates large volumes of hierarchical data on-line and replace the traditional centralized and strictly indexed information systems. Our extensive experimental results support this argument on many diverse configurations: Our system proves very efficient in skewed workloads, both over single and multiple hierarchy levels at the same time. It adapts to sudden changes in popularity and effectively stores and updates large amounts of data at very low cost.