Stability-complexity relationships within models of natural systems

Drawing on the qualitative loop analysis models prepared by Lane for a Delaware Bay plankton community, we evaluated 12 systems that ranged from 14 to 18 entities (population, guild or nutrient). Our approach was to study models of extended trophic biotic communities and examine the stability-complexity issue not only as it exists between systems (the traditional approach) but also with respect to the entities and relationships within a given system. We found no statistically significant inverse relationship for stability and complexity between systems. Within a system, a significant inverse relationship at the entity level was observed embedded in an increasing stability positively related to increasing subsystem size. Also, within a system and from system to system, several entities were seen to vary their roles with respect to stability. These results extend the stability-complexity issue to models of relatively large biotic communities and raise issues concerning the roles, with respect to stability, played by entities within communities.     

An ecosystem organization model explaining diversity at an ecosystem level: Coevolution of primary producer and decomposer

Ecological complexity of species interactions and habitat heterogeneity creates and maintains biodiversity at a trophic level in an ecosystem. This biodiversity simultaneously serves as raw material on which selective forces for organizing ecosystems operate. As a result of this organization process, differences in structure and functioning of ecosystems (diversity at ecosystem level) are generated. Although understanding diversity at the ecosystem level has attracted great interest, recent theoretical advances toward this aim have not been fully appreciated yet. Following Higashi et al. (1993), this report presents a theoretical framework that deals with the organization process of an ecosystem as a consequence of the interactions among its biotic components and their modification of ecological traits. Specifically, the ecosystem organization process of a terrestrial ecosystem is analyzed, including primary producers and decomposers. This model sheds new insight into the differences between temperate and tropical forest ecosystems.     

Effects of eight different ligament property datasets on biomechanics of a lumbar L4-L5 finite element model

Ligaments assist trunk muscles in balancing external moments and providing spinal stability. In absence of the personalized material properties for ligaments, finite element (FE) models use dispersed data from the literature. This study aims to investigate the relative effects of eight different ligament property datasets on FE model responses. Eight L4-L5 models distinct only in ligament properties were constructed and loaded under moment (15 N m) alone or combined with a compressive follower load (FL). Range of motions (RoM) of the disc-alone model matched well in vitro data. Ligament properties significantly affected only sagittal RoMs (∼3.0–7.1° in flexion and ∼3.8–5.8° in extension at 10 N m). Sequential removal of ligaments shifted sagittal RoMs in and out of the corresponding in vitro ranges. When moment was combined with FL, center of rotation matched in vivo data for all models (3.8 ± 0.9 mm and 4.3 ± 1.8 mm posterior to the disc center in flexion and extension, respectively). Under 15 N m sagittal moments, ligament strains were often smaller or within the in vitro range in flexion whereas some posterior ligament forces approached their failure forces in some models. Ligament forces varied substantially within the models and affected the moment-sharing and internal forces on the disc and facet joints. Intradiscal pressure (IDP) had the greatest variation between models in extension. None of the datasets yielded results in agreement with all reported measurements. Results emphasized the important role of ligaments especially under larger moments and the need for their accurate representation in search for valid spinal models.     

Species richness of woody plants in the landscapes of Central Spain: the role of management disturbances,environment and non‐stationarity

Questions: How important is management disturbance on gamma species richness of woody plants at intermediate landscape scales? How is species richness related to other climatic and biotic factors in the study area? How does the assumption of spatial stationarity affect assessment of relationships among species richness and explanatory variables (e.g. management, biotic and climatic factors) across extensive study areas? Location: Central Spain (regions of Castilla y León, Madrid and Castilla‐La Mancha). Scale: Extent: 150 000 km². Grain: 25 km² (5 × 5‐km cells). Methods: Information from 21 064 plots from the 3SNFI was used to evaluate richness of tree and shrub species at intermediate landscape scales. In addition to variables well known to explain biodiversity, e.g. environmental and biotic factors, effect of management treatments was evaluated by assessing clearcutting, selection cutting, stand improvement treatments and agrosilvopastoral systems (dehesas). Results from GWR techniques were compared with those from OLS regression. Results: Patterns of gamma species richness, although strongly affected by both environmental and biotic variables, were also significantly modified by management factors. Species richness increased with percentage of selection cutting stands and improvement treatments but decreased with percentage of clearcutting stands. Reduced species richness of woody plants was associated with agrosilvopastoral practices. Species richness for trees was closely related to basal area, annual precipitation and topographic complexity; species richness for shrubs was closely related to topographic complexity and agrosilvopastoral systems. Most relationships between species richness and environmental or biotic factors were non‐stationary. Relationships between species richness and management effects tended to be stationary, with a few exceptions. Conclusions: Landscape models of biodiversity in Central Spain were more informative when they accounted for effects of management practices, at least at intermediate scales. In the context of current rural abandonment, silvicultural disturbances of intermediate intensity increased gamma species richness of woody plants. Exclusion of factors such as agrosilvopastoral systems from models could have led to spurious relationships with other spatially co‐varying factors (e.g. summer precipitation). Patterns of spatial variation in relationships, provided by GWR models, allowed formulating hypotheses about potential ecological processes underlying them, beyond generalizations resulting from global (OLS) models.     

On modeling and complexity of developing systems

We consider the general properties of developing systems, the approaches to their modeling, and the question of their complexity. The notion “complex system” is vague; somewhat more distinct is the complexity of the model describing a phenomenon. We propose to discuss two pertinent issues. (i) The complexity of basic models is minimal; in other words, complicated basic models are needless. (ii) Living systems are simpler than inanimate ones. Though developing systems are seen in abiotic as well as in biotic nature, the fundamental difference is that living beings are capable of goal-setting and purposeful development; hence they can be described with simpler basic models.     

Differences between non-specific and bio-specific, and between equilibrium and non-equilibrium, interactions in biological systems

The interaction forces between biological molecules and surfaces are much more complex than those between non-biological molecules or surfaces, such as colloidal particle surfaces. This complexity is due to a number of factors: (i) the simultaneous involvement of many different molecules and different non-covalent forces - van der Waals, electrostatic, solvation (hydration, hydrophobic), steric, entropic and 'specific', and (ii) the flexibility of biological macromolecules and fluidity of membranes. Biological interactions are better thought of as 'processes' that evolve in space and time and, under physiological conditions, involve a continuous input of energy. Such systems are, therefore, not at thermodynamic equilibrium, or even tending towards equilibrium. Recent surface forces apparatus (SFA) and atomic force microscopy (AFM) measurements on supported model membrane systems (protein-containing lipid bilayers) illustrate these effects. It is suggested that the major theoretical challenge is to establish manageable theories or models that can describe the spatial and time evolution of systems consisting of different molecules subject to certain starting conditions or energy inputs.     

Simultaneous prediction of muscle and contact forces in the knee during gait

Musculoskeletal models are currently the primary means for estimating in vivo muscle and contact forces in the knee during gait. These models typically couple a dynamic skeletal model with individual muscle models but rarely include articular contact models due to their high computational cost. This study evaluates a novel method for predicting muscle and contact forces simultaneously in the knee during gait. The method utilizes a 12 degree-of-freedom knee model (femur, tibia, and patella) combining muscle, articular contact, and dynamic skeletal models. Eight static optimization problems were formulated using two cost functions (one based on muscle activations and one based on contact forces) and four constraints sets (each composed of different combinations of inverse dynamic loads). The estimated muscle and contact forces were evaluated using in vivo tibial contact force data collected from a patient with a force-measuring knee implant. When the eight optimization problems were solved with added constraints to match the in vivo contact force measurements, root-mean-square errors in predicted contact forces were less than 10 N. Furthermore, muscle and patellar contact forces predicted by the two cost functions became more similar as more inverse dynamic loads were used as constraints. When the contact force constraints were removed, estimated medial contact forces were similar and lateral contact forces lower in magnitude compared to measured contact forces, with estimated muscle forces being sensitive and estimated patellar contact forces relatively insensitive to the choice of cost function and constraint set. These results suggest that optimization problem formulation coupled with knee model complexity can significantly affect predicted muscle and contact forces in the knee during gait. Further research using a complete lower limb model is needed to assess the importance of this finding to the muscle and contact force estimation process.     

Simplicity and complexity in MIRROR universes

The scientific simplicity principle (OCCAM's razor) has always been strongly enforced by the available modelling tools. Moreover, the concept of simplicity itself is shaped by these (classical) tools. Computer models are less subject to simplicity constraints than other models are. It may be argued that complexity is the preeminent property for biological systems to study. In this paper we discuss our MIRROR modelling methodology in which (a concept of) simplicity is reconciled with biological complexity. Simplicity resides in the simple "TODO" ("do what there is to do") of the "individuals" (molecules, cells, organisms) which inhabit the model universe. The complexity appears in the multiple (levels of) individuals and the multiple levels of observable behavior of the universe. Examples are given of the development of complex, self-regulating social structures by simple interactions of individuals, and the adaptability of TODO based entities is compared to that of evolving entities. On the basis of these examples we sketch a slightly unconventional image of the evolution of complexity in biotic systems and discuss observations on the molecular record of biotic evolution which seem to fit this image.     

Adaptive properties of living beings: proposal for a generic mechanism. (Self-programming machines III)

Living systems are capable to have appropriate responses to unpredictable environment. This kind of self-organization seems to operate as a self-programming machine, i.e. an organization able to modify itself. Until now the models of self-organization of living beings proposed are functions solutions of differential systems or transition functions of automata. These functions are fixed and these models are therefore unable to modify their organization. On the other hand, computer science propose a lot of models having the properties of adaptive systems of living beings, but all these models depend on the comparison between a goal and the results and ingenious choices of parameters by programmers, whereas there are no programmer's intention nor choice in the living systems. From two best known examples of adaptive systems of living beings, nervous system and immune system that have in common that the external signals modify the rewriting of their organization and therefore work as self-organizing machines, we devised machines with a finite set of inputs, based upon a recurrence, are able to rewrite their organization (Self-programming machines or m(sp)) whenever external conditions vary and have striking properties of adaptation. M(sp) have similar properties whatever the operation defining the recurrence maybe. These results bring us to make the following statement: adaptive properties of living systems can be explained by their ability to rewrite their organization whenever external conditions vary under the only assumption that the rewriting mechanism be a deterministic constant recurrence in a finite state set.     

Exploring the compass of potential changes induced by climate warming in plant communities

New models are required to predict the impacts of future climate change on biodiversity. A move must be made away from individual models of single species toward approaches with synergistically interacting species. The focus should be on indirect effects due to biotic interactions. Here we propose a new parsimonious approach to simulate direct and indirect effects of global warming on plant communities. The methodology consists of five steps: a) field survey of species abundances, b) quantitative assessment of species co-occurrences, c) assignment of a theorised effect of increased temperature on each species, d) creation of a community model to project community dynamics, and e) exploration of the potential range of temperature change effects on plant communities.We explored the possible climate-driven dynamics in an alpine vegetation community and gained insights into the role of biotic interactions as determinants of plant species response to climate change at local scale. The study area was the uppermost portion of Alpe delle Tre Potenze (Northern Apennines, Italy) from 1500 m up to the summit at 1940 m.Our work shows that: 1) unexpected climate-driven dynamics can emerge, 2) interactive communities with indirect effects among species can overcome direct effects induced by global warming; 3) if just one or few species react to global warming the new community configuration could be unexpected and counter-intuitive; 4) timing of species reactions to global warming is an important driver of community dynamics; 5) using simulation models with a limited amount of data in input, it is possible to explore the full range of potential changes in plant communities induced by climate warming.     

Complexity of Multi-Dimensional Spontaneous EEG Decreases during Propofol Induced General Anaesthesia

Emerging neural theories of consciousness suggest a correlation between a specific type of neural dynamical complexity and the level of consciousness: When awake and aware, causal interactions between brain regions are both integrated (all regions are to a certain extent connected) and differentiated (there is inhomogeneity and variety in the interactions). In support of this, recent work by Casali et al (2013) has shown that Lempel-Ziv complexity correlates strongly with conscious level, when computed on the EEG response to transcranial magnetic stimulation. Here we investigated complexity of spontaneous high-density EEG data during propofol-induced general anaesthesia. We consider three distinct measures: (i) Lempel-Ziv complexity, which is derived from how compressible the data are; (ii) amplitude coalition entropy, which measures the variability in the constitution of the set of active channels; and (iii) the novel synchrony coalition entropy (SCE), which measures the variability in the constitution of the set of synchronous channels. After some simulations on Kuramoto oscillator models which demonstrate that these measures capture distinct ‘flavours’ of complexity, we show that there is a robustly measurable decrease in the complexity of spontaneous EEG during general anaesthesia.     

A novel biologically and psychologically inspired fuzzy decision support system: hierarchical complementary learning

A computational intelligent system that models the human cognitive abilities may promise significant performance in problem learning because human is effective in learning and problem solving. Functionally modelling the human cognitive abilities not only avoids the details of the underlying neural mechanisms performing the tasks, but also reduces the complexity of the system. The complementary learning mechanism is responsible for human pattern recognition, i.e. human attends to positive and negative samples when making decision. Furthermore, human concept learning is organized in a hierarchical fashion. Such hierarchical organization allows the divide-and-conquer approach to the problem. Thus, integrating the functional models of hierarchical organization and complementary learning can potentially improve the performance in pattern recognition. Hierarchical complementary learning (HCL) exhibits many of the desirable features of pattern recognition. It is further supported by the experimental results that verify the rationale of the integration and that the HCL system is a promising pattern recognition tool.     

Effects of supplemental food on the social organization of Mongolian gerbils during the breeding season

Social groups occur in many rodents and vary in size and complexity under varying environments. Food availability is often limited in northern temperate regions and alters the life history and behavior of rodents. Increased food availability is hypothesized to increase the size and complexity of rodent social groups by enhancing individual survival and philopatry. We tested this hypothesis in Mongolian gerbils Meriones unguiculatus under semi-natural conditions in Inner Mongolia, China. The Mongolian gerbil is a cooperative breeder living in groups year-round. Gerbil colonies in 10 m × 10 m chambers were the experimental units, with four replicate chambers each for food supplementation and food unsupplemented controls in 2004 and six replicate chambers for each treatment in 2005. At 2-day intervals wheat grain supplemented the normal food in experimental chambers throughout the breeding season (May through August). We estimated founder mortality, cumulative recruitment, proportion of philopatric juveniles, ages at sexual maturity and social group size in each colony from May through August. Rates of change in group size were inversely related to social group size. The social organization of Mongolian gerbils did not differ in any of the measured parameters between food-supplemented and -unsupplemented chambers. Therefore, additional food does not influence the social organization of Mongolian gerbils during the breeding season.     

Cluster organization and pore structure of ion channels formed by beticolin 3, a nonpeptidic fungal toxin

Beticolin 3 (B3) belongs to a family of nonpeptidic phytotoxins produced by the fungus Cercospora beticola, which present a broad spectrum of cytotoxic effects. We report here that, at cytotoxic concentration (10 microM), B3 formed voltage-independent, weakly selective ion channels with multiple conductance levels in planar lipid bilayers. In symmetrical standard solutions, conductance values of the first levels were, respectively, 16 +/- 1 pS, 32 +/- 2 pS, and 57 +/- 2 pS (n = 4) and so on, any conductance level being roughly twice the lower one. Whether a cluster organization of elementary channels or different channel structures underlies this particular property was addressed by investigating the ionic selectivity and the pore size corresponding to the first three conductance levels. Both selectivity and pore size were found to be almost independent of the conductance level. This indicated that multiple conductance behavior resulted from a cluster organization of "B3 elementary channels." According to the estimated pore size and analyses of x-ray diffraction of B3 microcrystals, a structural model for "B3 elementary channels" is proposed. The ability to form channels is likely to be involved in the biological activity of beticolins.     

Local-scale drivers of tree survival in a temperate forest

Tree survival plays a central role in forest ecosystems. Although many factors such as tree size, abiotic and biotic neighborhoods have been proposed as being important in explaining patterns of tree survival, their contributions are still subject to debate. We used generalized linear mixed models to examine the relative importance of tree size, local abiotic conditions and the density and identity of neighbors on tree survival in an old-growth temperate forest in northeastern China at three levels (community, guild and species). Tree size and both abiotic and biotic neighborhood variables influenced tree survival under current forest conditions, but their relative importance varied dramatically within and among the community, guild and species levels. Of the variables tested, tree size was typically the most important predictor of tree survival, followed by biotic and then abiotic variables. The effect of tree size on survival varied from strongly positive for small trees (1-20 cm dbh) and medium trees (20-40 cm dbh), to slightly negative for large trees (>40 cm dbh). Among the biotic factors, we found strong evidence for negative density and frequency dependence in this temperate forest, as indicated by negative effects of both total basal area of neighbors and the frequency of conspecific neighbors. Among the abiotic factors tested, soil nutrients tended to be more important in affecting tree survival than topographic variables. Abiotic factors generally influenced survival for species with relatively high abundance, for individuals in smaller size classes and for shade-tolerant species. Our study demonstrates that the relative importance of variables driving patterns of tree survival differs greatly among size classes, species guilds and abundance classes in temperate forest, which can further understanding of forest dynamics and offer important insights into forest management.     

Habitat formation prevails over predation in influencing fouling communities

Coastal human‐made structures, such as marinas and harbors, are expanding worldwide. Species assemblages described from these artificial habitats are novel relative to natural reefs, particularly in terms of the abundance of nonindigenous species (NIS). Although these fouling assemblages are clearly distinctive, the ecosystem functioning and species interactions taking place there are little understood. For instance, large predators may influence the fouling community development either directly (feeding on sessile fauna) or indirectly (feeding on small predators associated with these assemblages). In addition, by providing refuges, habitat complexity may modify the outcome of species interactions and the extent of biotic resistance (e.g., by increasing the abundance of niche‐specific competitors and predators of NIS). Using experimental settlement panels deployed in the field for 2.5 months, we tested the influence of predation (i.e., caging experiment), artificial structural complexity (i.e., mimics of turf‐forming species), and their interactions (i.e., refuge effects) on the development of sessile and mobile fauna in two marinas. In addition, we tested the role of biotic complexity—arising from the habitat‐forming species that grew on the panels during the trial—on the richness and abundance of mobile fauna. The effect of predation and artificial habitat complexity was negligible, regardless of assemblage status (i.e., native, cryptogenic, and nonindigenous). Conversely, habitat‐forming species and associated epibionts, responsible for biotic complexity, had a significant effect on mobile invertebrates (richness, abundance, and community structure). In particular, the richness and abundance of mobile NIS were positively affected by biotic complexity, with site‐dependent relationships. Altogether, our results indicate that biotic complexity prevails over artificial habitat complexity in determining the distribution of mobile species under low predation pressure. Facilitation of native and non‐native species thus seems to act upon diversity and community development: This process deserves further consideration in models of biotic resistance to invasion in urban marine habitats.     

Computational models for wall shear stress estimation in scaffolds: a comparative study of two complete geometries

Fluid mechanical stimuli are known to upregulate cell differentiation and matrix formation. Since wall shear stress plays an important role various studies tried to estimate the scaffold fluid dynamic environment. However, because of the geometrical complexity, nearly all studies created their CFD model based on a submodel of the entire scaffold assuming that the model covers heterogeneity sufficiently. However to the authors' knowledge no study exist providing guidelines in this matter. In a previous study we demonstrated that submodels are influenced by the boundary conditions, inevitable when flow channels are chopped off. For the current study we therefore developed μCT based models of two complete scaffold geometries (one titanium and one hydroxyapatite). Imposing a 0.04 ml/min flow rate resulted in a surface area averaged wall shear stress of 1.41 mPa for titanium and 1.09 mPa for hydroxyapatite. In order to get insight in required model size we subdivided the domain in regions of different size. From our results we propose a model size between 6 and 10 times the average pore size. The wall shears stress should be calculated on a region at least one pore size away from the boundaries. These guidelines could be of use for computationally more costly simulations where it is not possible to simulate the complete scaffold domain.     

Principles of organization of polistinae (Hymenoptera,Vespidae) population

The paper describes some invariant relations of the Polistinae population structure, including resistance to abiotic and biotic factors that occurs against the background of the hierarchy of biological systems and increasing autonomy of their functioning. A decrease in the dependence on the hostile environment is shown to be due to the activity of foundresses and workers adjusting to external rhythms, developing specialized responses to predators and parasites (predictable external noise of biotic nature), and creating new information. The population organization of Polistinae wasps is considered in the framework of Anokhin’s theory of functional systems and systemogenesis. There are specific processes in the population that unite individual colonies and their reproduction; they are accompanied by the formation of an advanced feedback and functional systems. Systemic processes can be simultaneously regarded as “adaptation” (reflecting the organization of environmental elements) and as “adaptiveness” (reflecting the organization of the activity of intra-colony processes and the organization of reproduction). The organization of the colony activity and reproduction in functional systems reflects the future survival rather than the preceding phenomena and events. The behavior of individuals in a colony is determined not only by the effects of abiotic and biotic factors (via transformation of cues into behavioral programs), but also by previous adaptations (stored in the “memory” as images of still absent events). General progress, limited or partial progress, and narrow specialization in the organization of polistine colonies and populations are considered using the examples of morphofunctional, environmental, energy and information criteria. The emphasis on invariant relations makes it possible to more fully describe biological systems in terms of such general categories as isomorphism, homeostasis or self-organization, and also enables us to use more effectively the theory of general functional systems in studying social insects.