Evolutionary synthesis of stochastic gene network models using feature-based search spaces

A feature-based fitness function is applied in a genetic programming system to synthesize stochastic gene regulatory network models whose behaviour is defined by a time course of protein expression levels. Typically, when targeting time series data, the fitness function is based on a sum-of-errors involving the values of the fluctuating signal. While this approach is successful in many instances, its performance can deteriorate in the presence of noise. This thesis explores a fitness measure determined from a set of statistical features characterizing the time series' sequence of values, rather than the actual values themselves. Through a series of experiments involving symbolic regression with added noise and gene regulatory network models based on the stochastic 'if-calculus, it is shown to successfully target oscillating and non-oscillating signals. This practical and versatile fitness function offers an alternate approach, worthy of consideration for use in algorithms that evaluate noisy or stochastic behaviour.

Evolutionary Origin and Maintenance of Sociality in the Small Carpenter Bees

Many arthropods exhibit behaviours precursory to social life, including adult longevity, parental care, nest loyalty and mutual tolerance, yet there are few examples of social behaviour in this phylum. The small carpenter bees, genus Ceratina, provide important insights into the early stages of sociality. I described the biology and social behaviour of five facultatively social species which exhibit all of the preadaptations for successful group living, yet present ecological and behavioural characteristics that seemingly disfavour frequent colony formation. These species are socially polymorphic with both / solitary and social nests collected in sympatry. Social colonies consist of two adult females, one contributing both foraging and reproductive effort and the second which remains at the nest as a passive guard. Cooperative nesting provides no overt reproductive benefits over solitary nesting, although brood survival tends to be greater in social colonies. Three main theories explain cooperation among conspecifics: mutual benefit, kin selection and manipulation. Lifetime reproductive success calculations revealed that mutual benefit does not explain social behaviour in this group as social colonies have lower per capita life time reproductive success than solitary nests. Genetic pedigrees constructed from allozyme data indicate that kin selection might contribute to the maintenance of social nesting -, as social colonies consist of full sisters and thus some indirect fitness benefits are inherently bestowed on subordinate females as a result of remaining to help their dominant sister. These data suggest that the origin of sociality in ceratinines has principal costs and the great ecological success of highly eusociallineages occurred well after social origins. Ecological constraints such as resource limitation, unfavourable weather conditions and parasite pressure have long been considered some of the most important selective pressures for the evolution of sociality. I assessed the fitness consequences of these three ecological factors for reproductive success of solitary and social colonies and found that nest sites were not limiting, and the frequency of social nesting was consistent across brood rearing seasons. Local weather varied between seasons but was not correlated with reproductive success. Severe parasitism resulted in low reproductive success and total nest failure in solitary nests. Social colonies had higher reproductive success and were never extirpated by parasites. I suggest that social nesting represents a form of bet-hedging. The high frequency of solitary nests suggests that this is the optimal strategy when parasite pressure is low. However, social colonies have a selective advantage over solitary nesting females during periods of extreme parasite pressure. Finally, the small carpenter bees are recorded from all continents except Antarctica. I constructed the first molecular phylogeny of ceratinine bees based on four gene regions of selected species covering representatives from all continents and ecological regions. Maximum parsimony and Bayesian Inference tree topology and fossil dating support an African origin followed by an Old World invasion and New World radiation. All known Old World ceratinines form social colonies while New World species are largely solitary; thus geography and phylogenetic inertia are likely predictors of social evolution in this genus. This integrative approach not only describes the behaviour of several previously unknown or little-known Ceratina species, bu~ highlights the fact that this is an important, though previously unrecognized, model for studying evolutionary transitions from solitary to social behaviour.

Ethics, tourists and the environmental practices of the North American cruise ship industry: a comparison study of the ethical standards of Alaskan and Caribbean cruise ship tourists

Please consult the paper edition of this thesis to read. It is available on the 5th Floor of the Library at Call Number: Z 9999 R43 S54 2005

Plant rhizosphere specificity and variability in the insect and plant adhesins, Madl and Mad2, within the genus Metarhizium suggest plant adaptation as an evolutionary force

Metarhizium is a soil-inhabiting fungus currently used as a biological control agent against various insect species, and research efforts are typically focused on its ability to kill insects. In section 1, we tested the hypothesis that species of Metarhizium are not randomly distributed in soils but show plant rhizosphere-specific associations. Results indicated an association of three Metarhizium species (Metarhizium robertsii, M. brunneum and M. guizhouense) with the rhizosphere of certain types of plant species. M. robertsii was the only species that was found associated with grass roots, suggesting a possible exclusion of M. brunneum and M. guizhouense, which was supported by in vitro experiments with grass root exudate. M. guizhouense and M. brunneum only associated with wildflower rhizosphere when co-occurring with M. robertsii. With the exception of these co-occurrences, M. guizhouense was found to associate exclusively with the rhizosphere of tree species, while M. brunneum was found to associate exclusively with the rhizosphere of shrubs and trees. These associations demonstrate that different species of Metarhizium associate with specific plant types. In section 2, we explored the variation in the insect adhesin, Madl, and the plant adhesin, Mad2, in fourteen isolates of Metarhizium representing seven different species. Analysis of the transcriptional elements within the Mad2 promoter region revealed variable STRE, PDS, degenerative TATA box, and TATA box-like regions. Phylogenetic analysis of 5' EF-Ia, which is used for species identification, as well as Madl and Mad2 sequences demonstrated that the Mad2 phylogeny is more congruent with 5' EF-1a than Madl. This suggests Mad2 has diverged among Metarhizium lineages, contributing to clade- and species-specific variation. While other abiotic and biotic factors cannot be excluded in contributing to divergence, it appears that plant associations have been the driving factor causing divergence among Metarhizium species.

Variability in the Insect and Plant Adhesins, Mad1 and Mad2, within the Fungal Genus Metarhizium Suggest Plant Adaptation as an Evolutionary Force

Several species of the insect pathogenic fungus Metarhizium are associated with certain plant types and genome analyses suggested a bifunctional lifestyle; as an insect pathogen and as a plant symbiont. Here we wanted to explore whether there was more variation in genes devoted to plant association (Mad2) or to insect association (Mad1) overall in the genus Metarhizium. Greater divergence within the genus Metarhizium in one of these genes may provide evidence for whether host insect or plant is a driving force in adaptation and evolution in the genus Metarhizium. We compared differences in variation in the insect adhesin gene, Mad1, which enables attachment to insect cuticle, and the plant adhesin gene, Mad2, which enables attachment to plants. Overall variation for the Mad1 promoter region (7.1%), Mad1 open reading frame (6.7%), and Mad2 open reading frame (7.4%) were similar, while it was higher in the Mad2 promoter region (9.9%). Analysis of the transcriptional elements within the Mad2 promoter region revealed variable STRE, PDS, degenerative TATA box, and TATA box-like regions, while this level of variation was not found for Mad1. Sequences were also phylogenetically compared to EF-1a, which is used for species identification, in 14 isolates representing 7 different species in the genus Metarhizium. Phylogenetic analysis demonstrated that the Mad2 phylogeny is more congruent with 59 EF-1a than Mad1. This would suggest that Mad2 has diverged among Metarhizium lineages, contributing to clade- and species-specific variation, while it appears that Mad1 has been largely conserved. While other abiotic and biotic factors cannot be excluded in contributing to divergence, these results suggest that plant relationships, rather than insect host, have been a major driving factor in the divergence of the genus Metarhizium.

Predicting Physical, Verbal, Social, Racial, and Sexual Bullying with Individual and Environmental Factors from an Evolutionary Ecological Framework

Evidence exists for subtypes of bullying, but there is a lack of studies simultaneously investigating the factors that influence each subtype. The purpose of my thesis was to investigate how individual and environmental factors independently and interactively predict physical, verbal, social, racial, and sexual bullying using an evolutionary ecological framework. Adolescents (N = 225, M = 14.05, SD = 1.54) completed self-reports on demographics, HEXACO personality, Rothbart’s temperament, parenting, friendship quality, school connectedness, and socio-economic status. Subtypes were predicted by low Honesty-Humility in addition to other personality and demographic factors with the exception of physical bullying, which was predicted by environmental factors. Results suggest adolescents adaptively and selectively use bullying to exploit victims and obtain resources, although the subtype used may depend on individual factors bullies possess within Bronfenbrenner’s microsystem, instead of the meso- and exo- systems. Anti-bullying efforts should target these factors and reinforce alternative strategies to obtain resources.

The Perceptions of Kinesiologists of Ethics and Professionalism as Established by the College of Kinesiologists of Ontario

As of April 1, 2013 kinesiology became a regulated health profession in Ontario. With its own governing body, the College of Kinesiologists of Ontario (CKO), there are new ethical and professional standards to which kinesiologists must adhere. The purpose of this study is to investigate kinesiologists’ thoughts and perceptions regarding the CKO’s Practice Standards, Guidelines and Code of Ethics, and their level of ethical knowledge and training. Eleven semi-structured interviews were carried out with kinesiologists. Interview data was analyzed through the development of general themes. Findings revealed that kinesiologists are confident of their ethical decision making skills but are in need of more ethical and professional education and training in order to become respected healthcare professionals in the healthcare community and in the eyes of the public. Furthermore, there were key areas identified in need of improvement regarding the quality of the Practice Standards, Guidelines and Code of Ethics. Additional findings, implications and recommendations for future research were also discussed.

Variability in the Insect and Plant Adhesins, Mad1 and Mad2, within the Fungal Genus Metarhizium Suggest Plant Adaptation as an Evolutionary Force

Several species of the insect pathogenic fungus Metarhizium are associated with certain plant types and genome analyses suggested a bifunctional lifestyle; as an insect pathogen and as a plant symbiont. Here we wanted to explore whether there was more variation in genes devoted to plant association (Mad2) or to insect association (Mad1) overall in the genus Metarhizium. Greater divergence within the genus Metarhizium in one of these genes may provide evidence for whether host insect or plant is a driving force in adaptation and evolution in the genus Metarhizium. We compared differences in variation in the insect adhesin gene, Mad1, which enables attachment to insect cuticle, and the plant adhesin gene, Mad2, which enables attachment to plants. Overall variation for the Mad1 promoter region (7.1%), Mad1 open reading frame (6.7%), and Mad2 open reading frame (7.4%) were similar, while it was higher in the Mad2 promoter region (9.9%). Analysis of the transcriptional elements within the Mad2 promoter region revealed variable STRE, PDS, degenerative TATA box, and TATA box-like regions, while this level of variation was not found for Mad1. Sequences were also phylogenetically compared to EF-1a, which is used for species identification, in 14 isolates representing 7 different species in the genus Metarhizium. Phylogenetic analysis demonstrated that the Mad2 phylogeny is more congruent with 59 EF-1a than Mad1. This would suggest that Mad2 has diverged among Metarhizium lineages, contributing to clade- and species-specific variation, while it appears that Mad1 has been largely conserved. While other abiotic and biotic factors cannot be excluded in contributing to divergence, these results suggest that plant relationships, rather than insect host, have been a major driving factor in the divergence of the genus Metarhizium.

Psychopathy and the Ability to Detect Cheaters: An Evolutionary Perspective

This research examined psychopathy as an evolutionary adaptation that involves cheating and deception. I theorized that this strategy should be associated with certain abilities. This research examined the association between psychopathic traits and the ability to detect cheaters, altruism, deception, and psychopathic traits. Results indicated that psychopathic traits were not significantly associated with the ability to detect cheaters or altruism. Results indicated that high Factor 1 psychopathy scores, and low Factor 2 psychopathy scores, were indicative of higher ratings of deception when viewing deceptive videos. Conversely, when viewing truthful videos, Factor 1 was a significant predictor of higher ratings of deception. Finally, our results indicated that total psychopathy scores were associated the ability to identify psychopathic traits in others. Taken together the results provide mixed support for the evolutionary perspective of psychopathy.

Christian Education and the Ethics of Authenticity

A qualitative study was undertaken to explore the concept of authenticity in Christian education. The study was situated in the context of Christian schools in Ontario. Some of these schools have experienced declining enrolment and all of these schools face the challenge of being distinctive in a secular culture. To investigate the potential of the concept of authenticity for reclaiming the vision of Christian education, interviews were conducted with 3 experienced principals of Christian schools. Data analysis yielded an emergent conceptual framework of authenticity consisting of 5 concepts: authorship, relatedness, reflection, autonomy, and excellence. Authenticity was found to be a useful tool for school analysis of both the deep structures and the surface structures within Christian schools. To offset unauthentic tendencies that can arise within these schools, this study calls for an intentional use of the lens of authenticity to expose these tendencies and revitalize core expectations. Through the narratives shared by the Christian school principals, the study also develops a picture of the role of authentic Christian education in the development of the authentic Christian person.

The Axiomatic Approach to Population Ethics

This paper examines several families of population principles in the light of a set of axioms. In addition to the critical-level utilitarian, number-sensitive critical-level utilitarian and number-dampened families and their generalized counterparts, we consider the restricted number-dampened family (suggested by Hurka) and introduce two new families : the restricted critical-level and restricted number-dependent critical-level families. Subsets of the restricted families have nonnegative critical levels and avoid both the repugnant and sadistic conclusions but fail to satisfy an important independence condition. We defend the critical-level principles with positive critical levels.

Population Ethics and the Value of Life

Public policies often involve choices of alternatives in which the size and the composition of the population may vary. Examples are the allocation of resources to prenatal care and the design of aid packages to developing countries. In order to assess the corresponding feasible choices on normative grounds, criteria for social evaluation that are capable of performing variable-population comparisons are required. We review several important axioms for welfarist population principles and discuss the link between individual well-being and the desirability of adding a new person to a given society.

Population Ethics

This paper reviews the welfarist approach to population ethics. We provide an overview of the critical-level utilitarian population principles and their generalized counterparts, examine important properties of these principles and discuss their relationships to other variable-population social-evaluation rules. We illustrate the difficulties arising in population ethics by means of an impossibility result and present characterizations of the critical-level generalized-utilitarian principles and of three of their sub-classes.

Examining discourses on the ethics and public understanding of cognitive enhancement with methylphenidate

L’émergence de l’utilisation du méthylphénidate (MPH; Ritalin) par des étudiants universitaires afin d’améliorer leur concentration et leurs performances universitaires suscite l’intérêt du public et soulève d’importants débats éthiques auprès des spécialistes. Les différentes perspectives sur l’amélioration des performances cognitives représentent une dimension importante des défis sociaux et éthiques autour d’un tel phénomène et méritent d’être élucidées. Ce mémoire vise à examiner les discours présents dans les reportages internationaux de presse populaire, les discours en bioéthique et en en santé publique sur le thème de l’utilisation non médicale du méthylphénidate. Cette recherche a permis d’identifier et d’analyser des « lacunes » dans les perspectives éthiques, sociales et scientifiques de l’utilisation non médicale du méthylphénidate pour accroître la performance cognitive d’individus en santé. Une analyse systématique du contenu des discours sur l’utilisation non médicale du méthylphénidate pour accroître la performance cognitive a identifié des paradigmes divergents employés pour décrire l’utilisation non médicale du méthylphénidate et discuter ses conséquences éthiques. Les paradigmes « choix de mode de vie », « abus de médicament » et « amélioration de la cognition » sont présents dans les discours de la presse populaire, de la bioéthique et de la santé publique respectivement. Parmi les principales différences entre ces paradigmes, on retrouve : la description de l’utilisation non médicale d’agents neuropharmacologiques pour l’amélioration des performances, les risques et bénéfices qui y sont associés, la discussion d’enjeux éthiques et sociaux et des stratégies de prévention et les défis associés à l’augmentation de la prévalence de ce phénomène. La divergence de ces paradigmes reflète le pluralisme des perceptions de l’utilisation non médicale d’agents neuropharmacologiques Nos résultats suggèrent la nécessité de débats autour de l’amélioration neuropharmacologique afin de poursuivre l’identification des enjeux et de développer des approches de santé publique cohérentes.

Ethics and Social Responsibility in the Life Sciences

Social Sciences and Humanities Research CouncilHomerton College, Cambridge, U.K.