Society by Numbers : Studies on Model-Based Explanations in the Social Sciences

The aim of this dissertation is to provide conceptual tools for the social scientist for clarifying, evaluating and comparing explanations of social phenomena based on formal mathematical models. The focus is on relatively simple theoretical models and simulations, not statistical models. These studies apply a theory of explanation according to which explanation is about tracing objective relations of dependence, knowledge of which enables answers to contrastive why and how-questions. This theory is developed further by delineating criteria for evaluating competing explanations and by applying the theory to social scientific modelling practices and to the key concepts of equilibrium and mechanism. The dissertation is comprised of an introductory essay and six published original research articles. The main theses about model-based explanations in the social sciences argued for in the articles are the following. 1) The concept of explanatory power, often used to argue for the superiority of one explanation over another, compasses five dimensions which are partially independent and involve some systematic trade-offs. 2) All equilibrium explanations do not causally explain the obtaining of the end equilibrium state with the multiple possible initial states. Instead, they often constitutively explain the macro property of the system with the micro properties of the parts (together with their organization). 3) There is an important ambivalence in the concept mechanism used in many model-based explanations and this difference corresponds to a difference between two alternative research heuristics. 4) Whether unrealistic assumptions in a model (such as a rational choice model) are detrimental to an explanation provided by the model depends on whether the representation of the explanatory dependency in the model is itself dependent on the particular unrealistic assumptions. Thus evaluating whether a literally false assumption in a model is problematic requires specifying exactly what is supposed to be explained and by what. 5) The question of whether an explanatory relationship depends on particular false assumptions can be explored with the process of derivational robustness analysis and the importance of robustness analysis accounts for some of the puzzling features of the tradition of model-building in economics. 6) The fact that economists have been relatively reluctant to use true agent-based simulations to formulate explanations can partially be explained by the specific ideal of scientific understanding implicit in the practise of orthodox economics.

Modelling discard ogives from Irish demersal fisheries

Annual discard ogives were estimated using generalized additive models (GAMs) for four demersal fish species: whiting, haddock, megrim, and plaice. The analysis was based on data collected on board commercial vessels and at Irish fishing ports from 1995 to 2003. For all species the most important factors influencing annual discard ogives were fleet (combination of gear, fishing ground, and targeted species), mean length of the catch and year, and, for megrim, also minimum landing size. The length at which fish are discarded has increased since 2000 for haddock, whiting, and plaice. In contrast, discarded length has decreased for megrim, accompanying a reduction in minimum landing size in 2000.

Modelling Leaf Production and Crop Development in Maize (Zea mays L.) After Tassel Initiation Under Diverse Conditions of Temperature and Photoperiod

Prediction of the initiation, appearance and emergence of leaves is critically important to the success of simulation models of crop canopy development and some aspects of crop ontogeny. Data on leaf number and crop ontogeny were collected on five cultivars of maize differing widely in maturity and genetic background grown under natural and extended photoperiods, and planted on seven sowing dates from October 1993 to March 1994 at Gatton, South-east Queensland. The same temperature coefficients were established for crop ontogeny before silking, and the rates of leaf initiation, leaf tip appearance and full leaf expansion, the base, optimum and maximum temperatures for each being 8, 34 and 40 degrees C. After silking, the base temperature for ontogeny was 0 degrees C, but the optimum and maximum temperatures remained unchanged. The rates of leaf initiation, appearance of leaf tips and full leaf expansion varied in a relatively narrow range across sowing times and photoperiod treatments, with average values of 0.040 leaves (degrees Cd)-1, 0.021 leaves (degrees Cd)-1, and 0.019 leaves (degrees Cd)-1, respectively. The relationships developed in this study provided satisfactory predictions of leaf number and crop ontogeny (tassel initiation to silking, emergence to silking and silking to physiological maturity) when assessed using independent data from Gatton (South eastern Queensland), Katherine and Douglas Daly (Northern Territory), Walkamin (North Queensland) and Kununurra (Western Australia).

Short-term responses of leaf growth rate to water deficit scale up to whole-plant and crop levels: An integrated modelling approach in maize.

Physiological and genetic studies of leaf growth often focus on short-term responses, leaving a gap to whole-plant models that predict biomass accumulation, transpiration and yield at crop scale. To bridge this gap, we developed a model that combines an existing model of leaf 6 expansion in response to short-term environmental variations with a model coordinating the development of all leaves of a plant. The latter was based on: (1) rates of leaf initiation, appearance and end of elongation measured in field experiments; and (2) the hypothesis of an independence of the growth between leaves. The resulting whole-plant leaf model was integrated into the generic crop model APSIM which provided dynamic feedback of environmental conditions to the leaf model and allowed simulation of crop growth at canopy level. The model was tested in 12 field situations with contrasting temperature, evaporative demand and soil water status. In observed and simulated data, high evaporative demand reduced leaf area at the whole-plant level, and short water deficits affected only leaves developing during the stress, either visible or still hidden in the whorl. The model adequately simulated whole-plant profiles of leaf area with a single set of parameters that applied to the same hybrid in all experiments. It was also suitable to predict biomass accumulation and yield of a similar hybrid grown in different conditions. This model extends to field conditions existing knowledge of the environmental controls of leaf elongation, and can be used to simulate how their genetic controls flow through to yield.

Inter-lamellar shear resistance confers compressive stiffness in the intervertebral disc: An image-based modelling study on the bovine caudal disc

The intervertebral disc withstands large compressive loads (up to nine times bodyweight in humans) while providing flexibility to the spinal column. At a microstructural level, the outer sheath of the disc (the annulus fibrosus) comprises 12–20 annular layers of alternately crisscrossed collagen fibres embedded in a soft ground matrix. The centre of the disc (the nucleus pulposus) consists of a hydrated gel rich in proteoglycans. The disc is the largest avascular structure in the body and is of much interest biomechanically due to the high societal burden of disc degeneration and back pain. Although the disc has been well characterized at the whole joint scale, it is not clear how the disc tissue microstructure confers its overall mechanical properties. In particular, there have been conflicting reports regarding the level of attachment between adjacent lamellae in the annulus, and the importance of these interfaces to the overall integrity of the disc is unknown. We used a polarized light micrograph of the bovine tail disc in transverse cross-section to develop an image-based finite element model incorporating sliding and separation between layers of the annulus, and subjected the model to axial compressive loading. Validation experiments were also performed on four bovine caudal discs. Interlamellar shear resistance had a strong effect on disc compressive stiffness, with a 40% drop in stiffness when the interface shear resistance was changed from fully bonded to freely sliding. By contrast, interlamellar cohesion had no appreciable effect on overall disc mechanics. We conclude that shear resistance between lamellae confers disc mechanical resistance to compression, and degradation of the interlamellar interface structure may be a precursor to macroscopic disc degeneration.

Modelling the impact of traffic incidents on travel time reliability

Traffic incidents are recognised as one of the key sources of non-recurrent congestion that often leads to reduction in travel time reliability (TTR), a key metric of roadway performance. A method is proposed here to quantify the impacts of traffic incidents on TTR on freeways. The method uses historical data to establish recurrent speed profiles and identifies non-recurrent congestion based on their negative impacts on speeds. The locations and times of incidents are used to identify incidents among non-recurrent congestion events. Buffer time is employed to measure TTR. Extra buffer time is defined as the extra delay caused by traffic incidents. This reliability measure indicates how much extra travel time is required by travellers to arrive at their destination on time with 95% certainty in the case of an incident, over and above the travel time that would have been required under recurrent conditions. An extra buffer time index (EBTI) is defined as the ratio of extra buffer time to recurrent travel time, with zero being the best case (no delay). A Tobit model is used to identify and quantify factors that affect EBTI using a selected freeway segment in the Southeast Queensland, Australia network. Both fixed and random parameter Tobit specifications are tested. The estimation results reveal that models with random parameters offer a superior statistical fit for all types of incidents, suggesting the presence of unobserved heterogeneity across segments. What factors influence EBTI depends on the type of incident. In addition, changes in TTR as a result of traffic incidents are related to the characteristics of the incidents (multiple vehicles involved, incident duration, major incidents, etc.) and traffic characteristics.

Modelling the potential spread of Solenopsis invicta Buren (Hymenoptera: Formicidae) (red imported fire ant) in Australia

Quantifying the potential spread and density of an invading organism enables decision-makers to determine the most appropriate response to incursions. We present two linked models that estimate the spread of Solenopsis invicta Buren (red imported fire ant) in Australia based on limited data gathered after its discovery in Brisbane in 2001. A stochastic cellular automaton determines spread within a location (100 km by 100 km) and this is coupled with a model that simulates human-mediated movement of S. invicta to new locations. In the absence of any control measures, the models predict that S. invicta could cover 763 000–4 066 000 km2 by the year 2035 and be found at 200 separate locations around Australia by 2017–2027, depending on the rate of spread. These estimated rates of expansion (assuming no control efforts were in place) are higher than those experienced in the USA in the 1940s during the early invasion phases in that country. Active control efforts and quarantine controls in the USA (including a concerted eradication attempt in the 1960s) may have slowed spread. Further, milder winters, the presence of the polygynous social form, increased trade and human mobility in Australia in 2000s compared with the USA in 1940s could contribute to faster range expansion.

Fluctuation phenomena in electrochemistry part II. Modelling the noise sources

A discussion of the modelling of the primary and secondary noise sources introduced in the formalism of fluctuation phenomena in a previous report is presented. It is illustrated that the generalisation of the modelling of noise sources in mass transport as given by Tyagai is limited in its applicability. A general procedure for the same is discussed in detail.

Modelling climatic risks of aflatoxin contamination in maize

Aflatoxins are highly carcinogenic mycotoxins produced by two fungi, Aspergillus flavus and A. parasiticus, under specific moisture and temperature conditions before harvest and/or during storage of a wide range of crops including maize. Modelling of interactions between host plant and environment during the season can enable quantification of preharvest aflatoxin risk and its potential management. A model was developed to quantify climatic risks of aflatoxin contamination in maize using principles previously used for peanuts. The model outputs an aflatoxin risk index in response to seasonal temperature and soil moisture during the maize grain filling period using the APSIM's maize module. The model performed well in simulating climatic risk of aflatoxin contamination in maize as indicated by a significant R2 (P ≤ 0.01) between aflatoxin risk index and the measured aflatoxin B1 in crop samples, which was 0.69 for a range of rainfed Australian locations and 0.62 when irrigated locations were also included in the analysis. The model was further applied to determine probabilities of exceeding a given aflatoxin risk in four non-irrigated maize growing locations of Queensland using 106 years of historical climatic data. Locations with both dry and hot climates had a much higher probability of higher aflatoxin risk compared with locations having either dry or hot conditions alone. Scenario analysis suggested that under non-irrigated conditions the risk of aflatoxin contamination could be minimised by adjusting sowing time or selecting an appropriate hybrid to better match the grain filling period to coincide with lower temperature and water stress conditions.

Architectural modelling of maize under water stress

Two field experiments using maize (Pioneer 31H50) and three watering regimes [(i) irrigated for the whole crop cycle, until anthesis, (ii) not at all (experiment 1) and (iii) fully irrigated and rain grown for the whole crop cycle (experiment 2)] were conducted at Gatton, Australia, during the 2003-04 season. Data on crop ontogeny, leaf, sheath and internode lengths and leaf width, and senescence were collected at 1- to 3-day intervals. A glasshouse experiment during 2003 quantified the responses of leaf shape and leaf presentation to various levels of water stress. Data from experiment 1 were used to modify and parameterise an architectural model of maize (ADEL-Maize) to incorporate the impact of water stress on maize canopy characteristics. The modified model produced accurate fitted values for experiment 1 for final leaf area and plant height, but values during development for leaf area were lower than observed data. Crop duration was reasonably well fitted and differences between the fully irrigated and rain-grown crops were accurately predicted. Final representations of maize crop canopies were realistic. Possible explanations for low values of leaf area are provided. The model requires further development using data from the glasshouse study and before being validated using data from experiment 2 and other independent data. It will then be used to extend functionality in architectural models of maize. With further research and development, the model should be particularly useful in examining the response of maize production to water stress including improved prediction of total biomass and grain yield. This will facilitate improved simulation of plant growth and development processes allowing investigation of genotype by environment interactions under conditions of suboptimal water supply.

Crystallographic and modelling studies on Mycobacterium tuberculosis RuvA: Additional role of RuvB-binding domain and inter species variability

RuvA, along with RuvB, is involved in branch migration of heteroduplex DNA in homologous recombination. The structures of three new crystal forms of RuvA from Mycobacterium tuberculosis (MtRuvA) have been determined. The RuvB-binding domain is cleaved off in one of them. Detailed models of the complexes of octameric RuvA from different species with the Holliday junction have also been constructed. A thorough examination of the structures presented here and those reported earlier brings to light the hitherto unappreciated role of the RuvB-binding domain in determining inter-domain orientation and oligomerization. These structures also permit an exploration of the interspecies variability of structural features such as oligomerization and the conformation of the loop that carries the acidic pin, in terms of amino acid substitutions. These models emphasize the additional role of the RuvB-binding domain in Holliday junction binding. This role along with its role in oligomerization could have important biological implications.

Thermal requirements, field mortality and population phenology modelling of Paropsis atomaria Olivier, an emergent pest in subtropical hardwood plantations

Paropsis atomaria is a recently emerged pest of eucalypt plantations in subtropical Australia. Its broad host range of at least 20 eucalypt species and wide geographical distribution provides it the potential to become a serious forestry pest both within Australia and, if accidentally introduced, overseas. Although populations of P. atomaria are genetically similar throughout its range, population dynamics differ between regions. Here, we determine temperature-dependent developmental requirements using beetles sourced from temperate and subtropical zones by calculating lower temperature thresholds, temperature-induced mortality, and day-degree requirements. We combine these data with field mortality estimates of immature life stages to produce a cohort-based model, ParopSys, using DYMEX™ that accurately predicts the timing, duration, and relative abundance of life stages in the field and number of generations in a spring–autumn (September–May) field season. Voltinism was identified as a seasonally plastic trait dependent upon environmental conditions, with two generations observed and predicted in the Australian Capital Territory, and up to four in Queensland. Lower temperature thresholds for development ranged between 4 and 9 °C, and overall development rates did not differ according to beetle origin. Total immature development time (egg–adult) was approximately 769.2 ± S.E. 127.8 DD above a lower temperature threshold of 6.4 ± S.E. 2.6 °C. ParopSys provides a basic tool enabling forest managers to use the number of generations and seasonal fluctuations in abundance of damaging life stages to estimate the pest risk of P. atomaria prior to plantation establishment, and predict the occurrence and duration of damaging life stages in the field. Additionally, by using local climatic data the pest potential of P. atomaria can be estimated to predict the risk of it establishing if accidentally introduced overseas. Improvements to ParopSys’ capability and complexity can be made as more biological data become available.

Graze to grain - measuring and modelling the effects of grazed pasture leys on soil nitrogen and sorghum yield on a Vertosol soil in the Australian subtropics

Highly productive sown pasture systems can result in high growth rates of beef cattle and lead to increases in soil nitrogen and the production of subsequent crops. The nitrogen dynamics and growth of grain sorghum following grazed annual legume leys or a grass pasture were investigated in a no-till system in the South Burnett district of Queensland. Two years of the tropical legumes Macrotyloma daltonii and Vigna trilobata (both self regenerating annual legumes) and Lablab purpureus (a resown annual legume) resulted in soil nitrate N (0-0.9 m depth), at sorghum sowing, ranging from 35 to 86 kg/ha compared with 4 kg/ha after pure grass pastures. Average grain sorghum production in the 4 cropping seasons following the grazed legume leys ranged from 2651 to 4012 kg/ha. Following the grass pasture, grain sorghum production in the first and second year was < 1900 kg/ha and by the third year grain yield was comparable to the legume systems. Simulation studies utilising the farming systems model APSIM indicated that the soil N and water dynamics following 2-year ley phases could be closely represented over 4 years and the prediction of sorghum growth during this time was reasonable. In simulated unfertilised sorghum crops grown from 1954 to 2004, grain yield did not exceed 1500 kg/ha in 50% of seasons following a grass pasture, while following 2-year legume leys, grain exceeded 3000 kg/ha in 80% of seasons. It was concluded that mixed farming systems that utilise short term legume-based pastures for beef production in rotation with crop production enterprises can be highly productive.

Multifaceted Modelling of Complex Business Enterprises

We formalise and present a new generic multifaceted complex system approach for modelling complex business enterprises. Our method has a strong focus on integrating the various data types available in an enterprise which represent the diverse perspectives of various stakeholders. We explain the challenges faced and define a novel approach to converting diverse data types into usable Bayesian probability forms. The data types that can be integrated include historic data, survey data, and management planning data, expert knowledge and incomplete data. The structural complexities of the complex system modelling process, based on various decision contexts, are also explained along with a solution. This new application of complex system models as a management tool for decision making is demonstrated using a railway transport case study. The case study demonstrates how the new approach can be utilised to develop a customised decision support model for a specific enterprise. Various decision scenarios are also provided to illustrate the versatility of the decision model at different phases of enterprise operations such as planning and control.

Modelling environmental effects on phenology and canopy development of diverse sorghum genotypes

The ability to predict phenology and canopy development is critical in crop models used for simulating likely consequences of alternative crop management and cultivar choice strategies. Here we quantify and contrast the temperature and photoperiod responses for phenology and canopy development of a diverse range of elite Indian and Australian sorghum genotypes (hybrid and landrace). Detailed field experiments were undertaken in Australia and India using a range of genotypes, sowing dates, and photoperiod extension treatments. Measurements of timing of developmental stages and leaf appearance were taken. The generality of photo-thermal approaches to modelling phenological and canopy development was tested. Environmental and genotypic effects on rate of progression from emergence to floral initiation (E-FI) were explained well using a multiplicative model, which combined the intrinsic development rate (Ropt), with responses to temperature and photoperiod. Differences in Ropt and extent of the photoperiod response explained most genotypic effects. Average leaf initiation rate (LIR), leaf appearance rate and duration of the phase from anthesis to physiological maturity differed among genotypes. The association of total leaf number (TLN) with photoperiod found for all genotypes could not be fully explained by effects on development and LIRs. While a putative effect of photoperiod on LIR would explain the observations, other possible confounding factors, such as air-soil temperature differential and the nature of model structure were considered and discussed. This study found a generally robust predictive capacity of photo-thermal development models across diverse ranges of both genotypes and environments. Hence, they remain the most appropriate models for simulation analysis of genotype-by-management scenarios in environments varying broadly in temperature and photoperiod.