Rethinking Causation for Data-intensive Biology: Constraints,Cancellations, and Quantized Organisms

Complex organisms thwart the simple rectilinear causality paradigm of “necessary and sufficient,” with its experimental strategy of “knock down and overexpress.” This Essay organizes the eccentricities of biology into four categories that call for new mathematical approaches; recaps for the biologist the philosopher's recent refinements to the causation concept and the mathematician's computational tools that handle some but not all of the biological eccentricities; and describes overlooked insights that make causal properties of physical hierarchies such as emergence and downward causation straightforward. Reviewing and extrapolating from similar situations in physics, it is suggested that new mathematical tools for causation analysis incorporating feedback, signal cancellation, nonlinear dependencies, physical hierarchies, and fixed constraints rather than instigative changes will reveal unconventional biological behaviors. These include “eigenisms,” organisms that are limited to quantized states; trajectories that steer a system such as an evolving species toward optimal states; and medical control via distributed “sheets” rather than single control points.     

An improved approach to evaluate car sharing options

We develop an improved approach to evaluate car sharing options under uncertain environments with the combination of Fuzzy Analytic Hierarchy Process (F-AHP) and Fuzzy Technique for Order Preference by Similarity to Ideal Solution (F-TOPSIS), which consists of three steps. In the first step, we propose a SCUMN (Specific, Comprehensive, Understandable, Measurable, and Neutral) methodology to identify appropriate indicators and obtain a final list of 24 indicators according to their relevance to car sharing options. In the second step, we determine the weight of each indicator with F-AHP and conduct consistency check of the comparison matrix of selected indicators. In the third step, comparison of different options is performed with selected indicators and F-TOPSIS. A case study is provided to validate the proposed approach. Twenty-four indicators are identified to evaluate five different car sharing options and rank them according to their closeness coefficients in decreasing order. And thirty-one sensitivity analysis experiments are conducted to figure out the influence of indicators on decision making. The experimental results show that the proposed approach is capable of evaluating car sharing options with uncertainty and vagueness. F-AHP is able to determine the weight for each selected indicator and F-TOPSIS demonstrates its advantage in comparing potential options.     

Evaluation of environmentally conscious manufacturing programs using a three-hybrid multi-criteria decision analysis method

Environmental management, being an important component in strategies for achieving sustainable development of processes and products, has emerged as a proactive approach in majority of the manufacturing organizations. From the strategic perspective environmentally conscious manufacturing (ECM) programs lead to better environmental management practice. The objective of the current paper is to present an integrated and holistic framework to evaluate ECM programs. This framework combines three multi-criteria decision analysis (MCDA) methods to consider eight major environmentally conscious manufacturing indicators (ECMI) in order to identify the efficiency of each ECM program. First the interdependence relationship among the ECMIs is established using decision-making trail and evaluation laboratory (DEMATEL). Then a range of weightage (i.e. upper and lower bounds) is created for each ECMI using analytic network process (ANP) to include managerial preferences. Finally, this range of weightage for each indicator is applied to perform restricted multiplier data envelopment analysis (RMDEA). Results show that the technical efficiency of the inefficient ECM programs for integrated RMDEA, on average, is calculated as 53.2% whereas traditional input oriented DEA provides the same score as 72.3%. This clearly indicates that integrated RMDEA is better than the input oriented DEA because same level of output could be produced with lesser resources if the ECM programs perform on the frontier. Hence, the advantage of this methodology is that the managerial preferences are successfully implemented through this newly developed hybrid methodology that will help to reduce less resource consumption and lead to better environmental policy.     

Social dominance in female bighorn sheep

A group of six individually identified bighorn ewes (Ovis canadensis canadensis) in the Denver Zoo, Denver, Colorado, was studied to determine the existence of a dominance hierarchy. Using success in displacement interactions as an index to rank, a very linear, age-related hierarchy was found.     

Simulated responses to hypothetical fundamental niches

Abstract. Two graphical models of plant competition, the ‘ghost of competition past’ and the ‘hierarchical’ model are compared using a greatly simplified individual-based forest dynamics simulation. Assumed fundamental niche shapes are used to determine the basic growth responses of the species, but competition alters the realized niche. Differences in the two models, amount of niche overlap, disturbance, and removal and invasion of species are examined in simulation experiments. Without disturbance, the realized niche responses reveal abrupt boundaries between species in all cases, and thus the responses are generally platykurtic to rectangular with little overlap. In some cases overlap through the extension of abundance of weaker competitors into the area of greater resources — dominated by better competitors but still within their fundamental niche — creates skewed distributions, as have been observed and simulated in the past. When species are removed or invade, the abrupt boundaries and the lack of difference in final response shape indicate that past removals may be difficult to detect. This difficulty may be important because former species may be influencing the responses that are observed in common non-equilibrium distributions. Even when assumptions favor the illustration of a competitive hierarchy, actual distributions and dynamics do not differentiate between it and a model of the ghost of competition past.     

Movements,status, access to nectar,and spatial organisation of the tui

Abstract

Movements of tui (Prosthetnadera novaeseelandiae) breeding on Tiritiri Matangi Island were followed and related to changes in nectar access. The island has limited nectar sources and birds must move to gain access to nectar year round. All tui leave the island, although the extent and timing of movement varies for different individuals. Tui return for breeding but again the timing of the return varies for individuals. Nectar sources were typically concentrated in both time and space, and access was related to individual asymmetries such as sex, residential status and age. These same asymmetries also relate to the timing of individuals movements, and where individuals nest relative to nectar sources. At concentrated food sources, access was determined by an absolute social hierarchy. Although tui defend exclusive feeding territories, breeding territories are not exclusive and access to nectar is determined by distance to nest site. Such variability in spatial organisation is related to a continuum concept of social organisation.     

COMT Val158Met moderates the link between rank and aggression in a non‐human primate

The COMT Val¹⁵⁸Met polymorphism is one of the most widely studied genetic polymorphisms in humans implicated in aggression and the moderation of stressful life event effects. We screened a wild primate population for polymorphisms at the COMT Val¹⁵⁸Met site and phenotyped them for aggression to test whether the human polymorphism exists and is associated with variation in aggressive behavior. Subjects were all adults from 4 study groups (37 males, 40 females) of Assamese macaques (Macaca assamensis) in their natural habitat (Phu Khieo Wildlife Sanctuary, Thailand). We collected focal animal behavioral data (27 males, 36 females, 5964 focal hours) and fecal samples for non‐invasive DNA analysis. We identified the human COMT Val¹⁵⁸Met polymorphism (14 Met/Met, 41 Val/Met and 22 Val/Val). Preliminary results suggest that COMT genotype and dominance rank interact to influence aggression rates. Aggression rates increased with rank in Val/Val, but decreased in Met/Met and Val/Met individuals, with no significant main effect of COMT genotype on aggression. Further support for the interaction effect comes from time series analyses revealing that when changing from lower to higher rank position Val/Val individuals decreased, whereas Met/Met individuals increased their aggression rate. Contradicting the interpretation of earlier studies, we show that the widely studied Val¹⁵⁸Met polymorphism in COMT is not unique to humans and yields similar behavioral phenotypes in a non‐human primate. This study represents an important step towards understanding individual variation in aggression in a wild primate population and may inform human behavioral geneticists about the evolutionary roots of inter‐individual variation in aggression.