The complex co-evolutionary systems approach (CCeSA) provides a well-suited framework for analysing agricultural systems, serving as a bridge between biophysical and socioeconomic sciences, allowing for the explanation of phenomena, and for the use of metaphors for thinking and action. By studying agricultural systems as self-generated, hierarchical, complex co-evolutionary farming systems (CCeFSs), one can investigate the interconnections between the elements that constitute CCeFSs, along with the relationships between CCeFSs and other systems, as a fundamental step to understanding sustainability as an emergent property of the system. CCeFSs are defined as human activity systems emerging from the purposes, gestalt, mental models, history and weltanschauung of the farm manager, and from his dynamic co-evolution with the environment while managing the resources at his hand to achieve his own multiple, conflicting, dynamic, semi-structured and constrained purposes. A sustainable CCeFS is described as one that exhibits both enough fitness to achieve its multiple, dynamic, constrained, semi-structured, and often incommensurable and conflicting purposes while performing above threshold values for failure, and enough flexibility to dynamically co-evolve with its changing biophysical and socioeconomic environment for a given future period. Fitness and flexibility are essential features of sustainable CCeFSs because they describe the systems' dynamic capacity to explore and exploit its dynamic phase space while co-evolving with it. This implies that a sustainable CCeFS is conceived as a set of dynamic, co-evolutionary processes, contrasting with the standard view of sustainability as an equilibrium or steady state. Achieving sustainable CCeFSs is a semi-structured, constrained, multi-objective, and dynamic optimisation management problem with an intractable search phase space, that can be solved within the CCeSA with the help of a multi-objective co-evolutionary optimisation tool. Carnico-ICSPEA2, a Co-Evolutionary Navigator (CoEvoNav) used as a CCeSA's tool for harnessing the complexity of the CCeFS of interest and its environment towards sustainability, is introduced. The software was designed by its end-user - the farm manager and author of this thesis - as an aid for the analysis and optimisation of the "San Francisco" ranch, a beef cattle enterprise running on temperate pastures and fodder crops in the central plateau of Mexico. By combining a non-linear simulator and a multi-objective evolutionary algorithm with a deterministic and stochastic framework, the CoEvoNav imitates the co-evolutionary pattern of the CCeFS of interest. As such, the software was used by the farm manager to "navigate" through his CCeFS's co-evolutionary phase space towards achieving sustainability at farm level. The ultimate goal was to enhance the farm manager's decision-making process and co-evolutionary skills, through an increased understanding of his system, the co-evolutionary process between his mental models, the CCeFS, and the CoEvoNav, and the continuous discovery of new, improved sets of heuristics. An overview of the methodological, theoretical and philosophical framework of the thesis is introduced. Also, a survey of the Mexican economy, its agricultural sector, and a statistical review of the Mexican beef industry are presented. Concepts such as modern agriculture, the reductionist approach to agricultural research, models, the system's environment, sustainability, conventional and sustainable agriculture, complexity, evolution, simulators, and multi-objective optimization tools are extensively reviewed. Issues concerning the impossibility of predicting the long-term, detailed future behaviour of CCeFSs, along with the use of simulators as decision support tools in the quest for sustainable CCeFSs, are discussed. The rationale behind the simulator used for this study, along with that of the multi-objective evolutionary tools used as the makeup of Carnico-ICSPEA2, are explained. A description of the "San Francisco" ranch, its key on-farm sustainability indicators in the form of objective functions, constraints, and decision variables, and the semi-structured, multi-objective, dynamic, constrained management problem posed by the farm manager's planned introduction of a herd of bulls for fattening as a way to increase the fitness of his CCeFS via a better management of the system's feed surpluses and the acquisition of a new pick-up truck are described as a case study. The tested scenario and the experimental design for the simulations are presented as well. Results from using the CoEvoNav as the farm manager's extended phenotype to solve his multi-objective optimisation problem are described, along with the implications for the management and sustainability of the CCeFS. Finally, the approach and tools developed are evaluated, and the progress made in relation to methodological, theoretical, philosophical and conceptual notions is reviewed along with some future topics for research.

Made available in DSpace on 2016-06-02T19:05:22Z (GMT). No. of bitstreams: 1 DissAFT.pdf: 987671 bytes, checksum: a50597a438e0122d6e69ee6481e7d4a3 (MD5) Previous issue date: 2006-09-13 / This work focuses on the problem of automatic generation of fuzzy systems through evolutionary computation, specifically using the approach of co-evolution. Coevolution is based on the idea of modular modeling of the problem subcomponents. In this work the subcomponents are represented by different species, which have a collaborative relation among them. The fuzzy system to be created has the objective of pattern classification. Basically, the evolutionary scheme is composed by four different species, which have a hierarchical collaboration both in the generation of the species and in the fitness determination of the individuals of these species. These species are organized in levels, where the contribution in the species generation happens from the lowest to highest levels and the contribution in the fitness determination happens from the highest to lowest levels. The results obtained indicate that the studied approach is very promising and, through its use, one can generate efficient classification systems, that present a performance similar to other approaches found in the literature. / Este trabalho enfoca o problema de geração automática de sistemas nebulosos por meio da computação evolutiva, mais especificamente por meio da abordagem de coevolução. A co-evolução baseia-se na idéia de modelagem modular de subcomponentes do problema. Neste trabalho esses subcomponentes são representados por espécies diferentes, que têm uma relação colaborativa entre si. Essa relação força uma evolução co-adaptada entre as populações das espécies. O sistema nebuloso a ser gerado tem como objetivo a classificação de padrões. Basicamente, o esquema evolutivo é formado por quatro espécies diferentes, que têm uma colaboração hierárquica, tanto na geração das espécies, quanto na determinação da aptidão dos indivíduos dessas espécies. Essas espécies são organizadas em níveis, onde a colaboração na geração das espécies se dá dos níveis mais baixos para os mais altos, e a colaboração na determinação das aptidões se dá dos níveis mais altos para os mais baixos. Os resultados obtidos indicam que a abordagem estudada é bastante promissora e pode-se obter, por meio dela, sistemas de classificação eficientes que apresentam desempenho semelhante ao de outras abordagens encontradas na literatura.

Située au carrefour de la didactique des langues et cultures et des sciences de l’éducation, la présente thèse porte sur l’appropriation, par les enseignants du cycle primaire au Bénin, de l’Initiative Francophone pour la Formation à Distance des Maîtres (IFADEM) en tant que dispositif de formation continue, en enseignement-apprentissage du FLES. L’objectif consiste à apporter des pistes pour améliorer l’appropriation du dispositif. A partir d’un modèle théorique d’appropriation, mis en place au regard d’une approche théorique transdisciplinaire et des spécificités du contexte d’étude, doublé d’une démarche de triangulation articulant enquêtes par questionnaires, par entretiens semi-directifs, d’auto-confrontation et par observations de pratiques effectives (situantes), nous nous sommes attachés à identifier les « indicateurs » d’appropriation ainsi que les « effets » du dispositif de formation sur les « pratiques pédagogiques effectives » des enseignants. Les théories holistiques de l’apprentissage des langues et spécifiquement l’éducation bilingue, le translanguaging et les théories sur l’enseignement-apprentissage de l’oral, ont constitué un socle pour l’analyse et la compréhension de la situation de recherche. La stabilité de nos analyses, offerte par le choix d’une méthodologie par triangulation, confirme que le parcours d’appropriation est déterminé par des relations d’interdépendance entre des facteurs situationnels (contextualisation), relationnels (relation avec les pairs) et individuels (self-system, réflexivité, recul épistémologique). Elle nous permet également d’aboutir aux conclusions suivantes : les enseignants bénéficiaires de la formation IFADEM font usage de la formation de façon instrumentale, et notamment des tâches qui leurs sont proposées pour améliorer l’enseignement oral du et en français afin de faire face au plurilinguisme. Ils sont exposés à plusieurs variations d’échelle, sources de contraintes et de tensions dans leurs activités pédagogiques, et ces dernières constituent un frein à l’appropriation du dispositif. L’analyse du processus d’appropriation au regard de l’émergentisme et des systèmes complexes d’activité permet d’aboutir au fait que les tensions générées par le déploiement du dispositif IFADEM font partie intégrante du processus de transformation de ce dernier. C’est l’absence de feed-back soutenu et institutionnalisé qui constitue une entrave à l’appropriation du dispositif. Afin de réagir positivement à ces écarts et de garantir l’appropriation du dispositif, le recours à la médiation ainsi qu’à une approche par tâches constituerait une voie intermédiaire. Elle permettrait notamment au dispositif de formation IFADEM, de s’inscrire dans une démarche co-évolutive, essentielle à l’équilibre des systèmes. C’est en tenant compte de l’ensemble de ces analyses et ajustements que cette recherche aboutit à l’élaboration d’un modèle d’appropriation. / This PhD thesis, situated at the crossroads of two domains – language and culture learning and teaching and learning sciences – deals with the way Beninese primary school teachers appropriated the IFADEM programme - « Initiative Francophone pour la Formation à Distance des Maîtres » (Francophone Initiative for Distance Education of Teachers), as a lifelong education environment in the teaching and learning of « French as Foreign/Second Language Learning ». Our purpose is to suggest new avenues aimed at improving the appropriation of this education environment. Our approach is based on a theoretical model of appropriation informed by a transdisciplinary theoretical stance and by the specifics of the context under study, but also on a triangulation method mixing questionnaire surveys, semi-directive interviews, self-confrontation interviews and observations of actual practises (situating). We try to identify the « indicators » of appropriation as well as the « effects » of the education environment on the « actual pedagogical practises » of teachers. Holistic theories of language learning – and more specifically bilingual education, translanguaging and the theories on oral skills development have given a foundation to the analysis and the comprehension of the research situation. The stability of our analyses, made possible by the choice of a triangulation methodology, confirms that the appropriation paths are determined by interdependency relations between factors of situational (contextualisation), relational (relationships with peers) and individual (self-system, reflexivity, epistemological distancing) natures. It also allows us to reach the following conclusions : the teachers who benefitted from the IFADEM training use it instrumentally and more specifically use the tasks they were proposed to improve the teaching of oral skills in and of French, in order to tackle the question of plurilingualism. These teachers are faced with several scale variations which engender constraints and tensions in their pedagogical activities, thus hindering the appropriation of the education environment. The analysis of the appropriation process in the light of emergentism and of complex systems of activity leads to the conclusion that the tensions generated by the implementation of the IFADEM progamm are part and parcel of its process of transformation. The absence of institutionalised and sustained feedback is the real hindrance to the appropriation of the education environment. In order to reduce these discrepancies in a positive way and to guarantee appropriation, turning to mediation and a task-based approach would constitute a middle way. In particular, it would allow the IFADEM environment to come within the scope of a co-evolutive approach, which is essential to the balance of systems. Taking into account all these analyses and adjustments helps this research to reach the elaboration of a model of appropriation.

Does the active membrane transporter, Na+,K+-ATPase dimerize? If it does, whatis the functional benefit? Does it increase or decrease the turnover rate? Theseare still unanswered questions and current research topics. Previous studies havedemonstrated dimerizations in closely related proteins of the P-type ATPase family.For the Na+, K+-ATPase a first indication of dimerization has been shown viaFluorescence lifetime imaging microscopy (FLIM) or Fluorescence resonance energytransfer - Fluorescence correlation spectroscopy (FRET-FCS) experiments. Theprecise dimer structure, dimerization process, and its ultimate functional effecthowever, remain to be found. This master thesis approaches those questions froma co-evolutionary standpoint. It predicts a possible dimer structure by starting with amultiple sequence alignment, direct coupling analysis, and structural contact filteringalgorithm. This model would strengthen the dimerization model of a decreasedturnover rate due to a competitive behavior of two Na+, K+-ATPases for its energysource ATP. / Dimeriserar den aktiva membrantransporten Na+,K+-ATPas? Om den gör det,vad är den funktionella nyttan? Ökar eller minskar det omsättningshastigheten?Dessa är obesvarade frågor och rådande forskningsämnen. Tidigare studier hardemonstrerat dimeriseringar i nära relaterade proteiner av P-typ ATPas-familjen.För Na+, K+-ATPas har en första indikation av dimerisering visats via ”Flourescencelifetime imaging microscopy (FLIM)” eller ”Flourescence resonance energy transfer- Flourescence correlation spectroscopy (FRET-FCS)”. Den precisa dimerstrukturen,dimeriseringsprocessen och dess slutgiltiga funktionella effekt emellertid, återståratt ses. Detta examensarbete på masternivå närmar sig dessa frågor från ettsamevolutionärt perspektiv. Det förutser en möjlig dimerstruktur genom att utgåfrån en flersekvenslinjering, direkt kopplingsanalys och en strukturell kontaktfiltreringsalgoritm. Denna modell skulle stärka dimeriseringsmodellen av minskadomsättningshastighet till följd av tävlingsbeteende mellan två Na+,K+-ATPaser fördess energikälla ATP.

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Mounting concerns about drug-resistant pathogenic bacteria have rekindled the interest in bacteriophages (bacterial viruses). As bacteria’s natural predators, bacteriophages offer a critical advantage over antibiotics, namely that they can be highly specific. This means that phage therapeutics can be designed to destroy only the infectious agent(s), without causing any harm to our microbiota. However, the potential secondary effects on the balance of microbiota through bacteriophage-induced genome evolution remains as one of the critical apprehensions regarding phage therapy. There exists a significant gap in knowledge regarding the direct and indirect effect of phage therapeutics on the microbiota. The aim of this thesis was to: (1) establish an in vivo model for investigation of the evolutionary dynamics and co-evolution of therapeutic phage and its corresponding host bacterium in the gut; (2) determine if phage therapy can affect the composition of the gut microbiota, (3) observe the differences of phage-resistant bacteria mutants evolved in vivo in comparison to those evolved in vitro. We used germ-free mice colonized with a consortium of eight known bacteria, known as the altered Schaedler flora (ASF). The colonizing strain of choice (mock infection) was a non-pathogenic strain E. coli K-12 (JM83) known to co-colonize the ASF model, which was challenged in vivo with T7 phage (strictly lytic). We compared the composition of the gut microbiota with that of mice not subject to phage therapy. Furthermore, the resistant mutants evolved in vivo and in vitro were characterized in terms of growth fitness and motility. / Thesis / Master of Applied Science (MASc) / Bacteriophages are viruses that infect bacteria. After their discovery in 1917, bacteriophages were a primary cure against infectious disease for 25 years, before being completely overshadowed by antibiotics. With the rise of antibiotic resistance, bacteriophages are being explored again for their antibacterial activity. One of the critical apprehensions regarding bacteriophage therapy is the possible perturbations to our microbiota. We set out to explore this concern using a simplified microbiome model, namely germ-free mice inoculated with only 8 bacteria plus a mock infection challenged with bacteriophage. We monitored this model for 9 weeks and isolated a collection of phage-resistant bacterial mutants from the mouse gut that developed post phage challenge, maintaining the community of mock infection inside the gut. A single dose of lytic phage challenge effectively decreased the mock infection without causing any extreme long-term perturbations to the gut microbiota.

Text in Afrikaans / During the last few decades the need existed for a new framework to give direction to development and ecological thought in respect of the sustaining of nature in order to place development and ecological thought within the limits of nature. However, development thought and the debate relating to nature are to some extent still treated in theory and practice as two separate entities. One of the current challenges for sustainable development is to reconcile the development and ecological branches of this debate. The thesis firstly explains the origin and characteristics of sustainable development. Secondly, the crisis in nature is discussed, followed by a discussion of the most important ecological views relating to sustainable development. Then issues in development thought that relates to sustainable development is discussed, as well as the changing emphasis in development thought that stimulated the growth of sustainable development. The mainstream development view, as the other main branch of sustainable development thinking, is then discussed. In conclusion, some issues relating to the operationalisation of sustainable development is discussed. / Development Studies / D. Litt. et Phil. (Ontwikkelingstudies)

Les logiciels sont en constante évolution, nécessitant une maintenance et un développement continus. Ils subissent des changements tout au long de leur vie, que ce soit pendant l'ajout de nouvelles fonctionnalités ou la correction de bogues. Lorsque les logiciels évoluent, leurs architectures ont tendance à se dégrader et deviennent moins adaptables aux nouvelles spécifications des utilisateurs. En effet, les architectures de ces logiciels deviennent plus complexes et plus difficiles à maintenir à cause des nombreuses dépendances entre les artefacts. Par conséquent, les développeurs doivent comprendre les dépendances entre les artefacts des logiciels pour prendre des mesures proactives qui facilitent les futurs changements et ralentissent la dégradation des architectures des logiciels. D'une part, le maintien d'un logiciel sans la compréhension des les dépendances entre ses artefacts peut conduire à l'introduction de défauts. D'autre part, lorsque les développeurs manquent de connaissances sur l'impact de leurs activités de maintenance, ils peuvent introduire des défauts de conception, qui ont un impact négatif sur l'évolution du logiciel. Ainsi, les développeurs ont besoin de mécanismes pour comprendre comment le changement d'un artefact impacte le reste du logiciel. Dans cette thèse, nous proposons trois contributions principales : La spécification de deux nouveaux patrons de changement et leurs utilisations pour fournir aux développeurs des informations utiles concernant les dépendances de co-changement. La spécification de la relation entre les patrons d'évolutions des artefacts et les fautes. La découverte de la relation entre les dépendances des anti-patrons et la prédisposition des différentes composantes d'un logiciel aux fautes. / Program maintenance accounts for the largest part of the costs of any program. During maintenance activities, developers implement changes (sometimes simultaneously) on artefacts to fix bugs and to implement new requirements. Thus, developers need knowledge to identify hidden dependencies among programs artefacts and detect correlated artefacts. As programs evolved, their designs become more complex over time and harder to change. In the absence of the necessary knowledge on artefacts dependencies, developers could introduce design defects and faults that causes development and maintenance costs to rise. Therefore, developers must understand the dependencies among program artefacts and take proactive steps to facilitate future changes and minimize fault proneness. On the one hand, maintaining a program without understanding the different dependencies between their artefacts may lead to the introduction of faults. On the other hand, when developers lack knowledge about the impact of their maintenance activities, they may introduce design defects, which have a negative impact on program evolution. Thus, developers need mechanisms to understand how a change to an artefact will impact the rest of the programs artefacts and tools to detect design defects impact. In this thesis, we propose three principal contributions. The first contribution is two novel change patterns to model new co-change and change propagation scenarios. We introduce the Asynchrony change pattern, corresponding to macro co-changes, i.e., of files that co-change within a large time interval (change periods), and the Dephase change pattern, corresponding to dephase macro co-changes, i.e., macro co-changes that always happen with the same shifts in time. We present our approach, named Macocha, and we show that such new change patterns provide interesting information to developers. The second contribution is proposing a novel approach to analyse the evolution of different classes in object-oriented programs and to link different evolution behaviour to faults. In particular, we define an evolution model for each class to study the evolution and the co-evolution dependencies among classes and to relate such dependencies with fault-proneness. The third contribution concerns design defect dependencies impact. We propose a study to mine the link between design defect dependencies, such as co-change dependencies and static relationships, and fault proneness. We found that the negative impact of design defects propagate through their dependencies. The three contributions are evaluated on open-source programs.

The effect of a free-living stage in host-parasite coevolution: a skink mite phylogenetic study in New Zealand. During the last decade, phylogenetic trees have even been used to compare ecologically related taxa such as parasites and their hosts, and are used to determine their level of coevolution or reciprocal adaptation in time. Diverse coevolutionary events have been detected for this ecological association, where generally the parasite has been regarded as one that feeds exclusively on the host and is likely to cospeciate with it. A different coevolutionary pattern might occur when the parasite has a free-living stage in its life cycle, in which the parasite may have the opportunity to abandon its host and successfully colonise a new species (host-switching) making cospeciation less likely. Many New Zealand skinks are infested with a parasitic mite, Odontacarus sp. (Prostigmata: Leeuwenhoekiidae), which becomes free-living as an adult. The genetic variation of these mites found on four hosts was analyzed for host- parasite coevolutionary events. The hosts were the McCann’s skink and the common skink in coastal Birdling Flat, Canterbury, plus these species and the Grand and Otago skinks in Macraes Flat, Central Otago, South Island, New Zealand. The genetic variation of fast evolving nuclear Internal Transcribed Spacers 2 and mitochondrial Cytochrome c Oxidase I in Odontacarus mites found on these hosts was determined by PCR and DNA sequencing and phylogenetic trees were built using the computer programs PAUP*4 and MrBayes 3. The results show that mite haplotypes only had a significant geographical division and no host-related differences. In Birdling Flat, the COI haplotypes were represented in two groups that infested both regional hosts and had 5.7 % divergence. The same individual mites belonged to a single ITS 2 haplotype, thus indicating a historical geographical division between two populations that now interbreed successfully. The Macraes Flat mites were divided into two COI haplotypes with 2.4% divergence and internal nodes, which showed greater genetic variability than the Birdling Flat populations. The Macraes Flat mites formed two ITS 2 haplotypes with 6% divergence. This greater geographical structure of the Otago mites is probably due to the older age of the mainland area compared to the recently exposed coastal locality of Birdling Flat. The COI haplotypes from the two different regions had a mean distance of 15.5%, with an earlier divergence time than that known for the hosts. For both genes, the haplotypes from different regions had 100% bootstrap support and the parasite showed no host specificity. Mites of the different COI and ITS haplotypes were found on most of the host species that were sampled in Canterbury and Otago. The results of this study suggest that a free-living stage in a parasite’s life cycle can favour coevolutionary events such as inertia (failure to speciate) and host-switching, probably as a result of resource-tracking of the parasite. NB: Electronic files contained on CD to accompany print copy are not included with this version of the thesis.

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