Thesis (Ph.D.) - University of St Andrews, March 2008.

Thesis (D. Min.)--Gordon-Conwell Theological Seminary, South Hamilton, MA, 2003. / Vita. Includes bibliographical references (leaves 110-115).

Benthic foraminifera inhabiting the mudflats of the Eden Estuary, NE Scotland, exhibited a single annual peak in abundance at both high (270 individuals 10 cm⁻²) and low shore (210 individuals 10 cm⁻²) intertidal sampling stations during June 2000. The increased total abundance coincided with reproduction in the two dominant foraminiferal species Elphidium williamsoni (May) and Haynesina germanica (June) at both sites. Benthic diatom biomass, measured as chlorophyll c, peaked at the high intertidal site during March and April 2001 (36 and 37 mg m cm⁻², respectively) and at the low intertidal site in June2000 (45 mg m cm⁻²). The high intertidal foraminiferal populations appeared to display a lagged response to increases in chlorophyll c. Multivariate statistics suggest that abiotic factors control the abundance of foraminifera at the high intertidal site. At the low intertidal site, total foraminiferal abundance demonstrated an almost immediate response to increased chlorophyll c and multivariate statistics suggested biotic factors are more important in controlling foraminiferal species abundance here. Ingestion rates of ¹³C-Iabelled benthic diatoms over a five-day experimental period were high (e.g. enrichment values for Elphidium were recorded as 687 ± 121 % after 1 day) in intertidal benthic foraminifera. Laboratory observations of E. williamsoni demonstrated rapid asexual reproduction (within 3 days) and growth rates of up to 14 µm day⁻¹ were estimated. Three benthic foraminiferal species E. williamsoni, H germanica and E. oceanensis ingest motile benthic diatoms as a food resource on the intertidal mudflats of the Eden Estuary. Novel application of natural abundance stable isotope (δ¹³C and δ¹⁵N) techniques demonstrated the trophic position of intertidal benthic foraminifera, confirming that they largely ingest and assimilate organic matter derived from benthic diatoms. Foraminifera have largely been overlooked in meiofaunal studies, but play a significant role in the rapid transfer of autotrophic carbon to higher trophic levels within benthic marine food webs.

Contexte : La structure du sommeil évolue grandement dans les premières années de vie. Les réveils nocturnes occasionnels chez les enfants d'âge préscolaire font partie d’un processus normal de développement et de maturation du sommeil. Ils sont cependant considérés comme anormalement fréquents lorsqu’ils surviennent une nuit sur deux ou plus. La littérature suggère que les réveils nocturnes fréquents sont associés de manière transversale à des difficultés comportementales du jeune enfant. Or, l’évolution des réveils nocturnes dans la petite enfance, les facteurs associés à leurs trajectoires et les liens longitudinaux avec le comportement sont peu connus. Objectifs : Modéliser l’évolution des réveils nocturnes entre l’âge de 2 et 5-6 ans et explorer leurs liens avec des facteurs précoces familiaux et de l’enfant. Analyser les associations entre les trajectoires de réveils nocturnes et le comportement de l’enfant avant l’entrée à l’école. Population et méthode : Nos analyses ont porté sur les données de l’étude EDEN. Il s’agit d’une cohorte mère enfant, qui a recruté 2 002 femmes enceintes entre 2003 et 2006 dans les maternités de Nancy et Poitiers. Les réveils nocturnes et le comportement ont été mesurés par des questionnaires parentaux à l’âge de 2, 3 et 5-6 ans. La méthode du « group-based trajectory modeling » nous a permis de modéliser l’évolution des réveils nocturnes et de difficultés d’attention, et ainsi d’identifier des trajectoires, décrivant différentes histoires développementales entre l’âge de 2 et 5-6 ans. Les analyses statistiques pour mesurer les associations entre les trajectoires de réveils nocturnes, les facteurs précoces et le comportement de l’enfant, ont été faites par régressions logistiques, ajustées sur les facteurs de confusion potentiels. Résultats : Deux trajectoires distinctes de réveils nocturnes ont été identifiées chez les enfants entre 2 et 5-6 ans. L’une, nommée “réveils nocturnes rares”, représentait 77% des enfants. Ce groupe suivait une trajectoire linéaire proche de zéro et légèrement décroissante avec le temps. La seconde trajectoire, nommée « réveils nocturnes communs », représentait 23% des enfants. Elle était plus haute que la première trajectoire à chaque point de suivi, et présentait un pic à l’âge de 3 ans. Les facteurs de risque d’appartenir à la trajectoire de « réveils nocturnes communs » étaient essentiellement environnementaux : l’exposition au tabagisme passif, un mode de garde collectif et le temps passé devant la télévision. Les enfants appartenant à la trajectoire de réveils nocturnes communs présentent un risque accru de présenter des symptômes émotionnels, des problèmes de conduite et des problèmes d'hyperactivité/inattention à l’âge de 5-6 ans. Aucune association n'a été trouvée avec le comportement pro-social ou avec les problèmes de relations avec les pairs. Trois trajectoires d’inattention/hyperactivité ont été identifiées, une trajectoire basse, intermédiaire et une haute, toutes trois stables au cours du temps. Le risque d’appartenir à une trajectoire haute d’inattention/hyperactivité, par rapport à une trajectoire basse, était quatre fois plus important pour les enfants avec une trajectoire de « réveils nocturnes communs » comparativement à ceux avec trajectoire de « réveils nocturnes rares ». Conclusion : Les réveils nocturnes et les troubles d’inattention/hyperactivité persistent dans la petite enfance. Une trajectoire de réveils nocturnes communs durant cette période est un facteur de risque de plusieurs troubles du comportement : symptôme émotionnel, troubles de conduites et inattention/hyperactivité. Ces derniers co-évoluent avec les troubles du sommeil. Nos résultats soulignent l’importance d’identifier et de prendre en charge les difficultés de sommeil dès le plus jeune âge, surtout en présence de difficultés de comportement. / Context: The structure of sleep evolves greatly in the first years of life. Occasional nightwaking is thus normal in young children, but waking-up every other night or more is considered adversely frequent. The scientific literature suggests that frequent night-waking is associated with concomitant behavioral difficulties in children. Yet, little is known about the evolution of night-waking in preschool years and its longitudinal association with behavior. Objectives: To model the evolution of night-waking between the age of 2 and 5-6 years and explore the association with family and child related factors. To analyze the associations between night-waking trajectories and behavior before school entry. Population and methods: Analyses were based on the French birth-cohort study EDEN, which recruited 2 002 pregnant women between 2003 and 2006 in the maternity of Poitiers and Nancy. Information regarding night-waking and behavior were assessed using parental questionnaires at the ages of 2, 3 and 5-6 years. The « group based trajectory modeling » method allowed us to model the evolution of night-waking and of inattention/hyperactivity, describing different developmental trends between the age of 2 and 5-6 years. The associations between night-waking trajectories, family and child related factors and behavior, were analyzed using logistic regressions, adjusted on potential confounding factors. Results: Two distinct night-waking trajectories were identified in children between the age of 2 and 5-6 years. One, named « rare night-waking », represented 77% of the children. This group followed a linear trajectory, which was close to zero and slightly declining with time. The second trajectory, named « common night-waking », represented 23% of the children. It was higher than the first trajectory at each time-point, and a peak was observed at age 3. Risk factors for belonging to the « common night-waking » trajectory were life-style related factors: exposures to second hand smoking, collective care arrangement, and time spent in front of the television. Children belonging to the common night-waking trajectory had higher risk of having emotional symptoms, conduct problems and inattention/hyperactivity at age 5-6. No associations were found with prosocial behavior nor peer-relationship problems. Three trajectories of inattention/hyperactivity were identified, a low, an intermediate and a high one, all stable in time. The risk of belonging to a high inattention/hyperactivity trajectory, compared to a low one, were four time more important for children with a « common night-waking » trajectory. Conclusion: Night-waking and inattention/hyperactivity persist in preschool years. A common night-waking trajectory during this period is a risk factor of diverse behavioral difficulties: emotional symptoms, conduct problems and inattention/hyperactivity. The latter co-evolves with night-waking. Our results highlight the importance of identifying sleep problems in early years, especially in the presence of behavioral difficulties.

Located on the central Oregon coast, the Umpqua Eden site (35D083) yielded an artifact assemblage which is one of the five largest assemblages from the Oregon coast. The first aspect of the site that I looked at is the people who lived at the site, the ancestors of the Confederated Tribes of the Coos, Lower Umpqua and Siuslaw. In turn, I consulted with Patty Whereat, the Cultural Resources Director for the tribes, which resulted in a more holistic view of the site. Additionally, I attempted to uncover possible women's and men's activity areas of the Umpqua Eden site. A wealth of information on the native peoples of the Oregon coast was discovered, revealing that the sexual division of labor was not extremely rigid before Euro-American contact and the social category of "female" was expanded to more than two genders with consideration given to the two-spirited individual. I also attempted to engender the archaeological record by looking at the processes involved in the manufacture of smoking pipes and the cultivation of tobacco. During the ethnographic period, women were not smoking pipes; however, they were probably cultivating the tobacco and possibly gathering the clay for smoking pipes. I suggest that there was an agricultural element to the hunter-gatherer native populations of the central Oregon coast and challenge Western assumptions of individualism in precontact groups of the Oregon coast. I also provide a comparative analysis of clay, schist and steatite pipes of the Oregon coast. The smoking pipes are all straight and tubular (9% are shouldered) and the Umpqua Eden site pipes have the most artistic motifs. My analysis shows that the sandstone pipe dates to approximately 2,000 years ago and the clay smoking pipe may have replaced the sandstone pipe. Schist and steatite pipes were also used by the people of the Oregon coast and may have possibly been traded into the site from southern groups. Microscopic analysis of the pipes provided evidence that people were firing their clay pipes in a low temperature reducing atmosphere and using sand temper. In addition, I found a wide range of pipes being used on the Oregon coast given its relatively small geographic location. All of the this archaeological inquiry has helped in understanding the Umpqua Eden site and helped to give us a clearer picture of pre-contact Lower Umpqua life. / Graduation date: 2000

Intertidal cohesive sediment systems are found throughout the world in areas of low hydrodynamic energy. These systems are ecologically and economically important but are under pressure from global warming, sea level rise and other anthropogenic influences. To protect and conserve these systems it is important to understand the sediment dynamics, especially the erosional properties of the sediment. The study of sediment erosion and transport is complex, encompassing biological, chemical and physical properties of the ecosystem. This thesis contributes towards this area of research, firstly in regard to the methods used to measure sediment erosion on exposed and submerged sediments and secondly with respect to assessing influences upon sediment stability through changes in the ecosystem, comprising of both the sediment environment and the macrofaunal community. Chapter 3: In partnership with Sediment Service a thorough re-evaluation of the Cohesive Strength Meter (CSM), a commercially available device used to measure surface sediment strength, was performed. New components, deployment method and calibration protocol were devised and tested. The new design was not effective, but the deployment and calibration have improved the ease of use and interpretation CSM data. Chapter 4: The study of intertidal sediment stability was conducted during the submerged period of the tidal cycle. Protocols and methods were devised or modified to sample submerged sediments with the aim to determine how sediment properties are affected by submersion and the resulting effect on sediment stability. Sediment stability increased with submersion. The existence of a fine layer of sediment on the surface, similar to the fluff layer found in submerged sediments, is given as a suggested explanation as it may be removed by the incoming tide. However, no other changes in sediment properties were detected. This may be due to flaws in the methods used in detecting fine scale changes in the sediment surface. In situ and laboratory experiments revealed contrasting effects of submersion on sediment stability with disturbance from the sampling and movement of sediment from the field to the laboratory given as an explanation for this. Chapter 5: The influence of the ecosystem engineering polychaete Arenicola marina on sediment properties was examined with an exclusion experiment. A. marina was excluded from five 20m² plots on an intertidal mudflat on the German island of Sylt. A holistic approach was used to measure the ecosystem, including a range of biotic and abiotic sediment properties as well as the macrofauna community. It was hypothesised that A. marina’s exclusion would alter the macrofaunal community and increase sediment stability. However, there was no consistent change in the macrofauna community or sediment environment with the exclusion of A. marina and subsequently no change in sediment stability. Chapter 6: The impact of bait digging for A. marina was examined with six 5m² plots dug up and A. marina removed, the plots were then monitored over a three month period. Bait digging disturbance was expected to have an impact upon the sediment environment and macrofauna community, resulting in a reduction in both sediment stability and microphytobenthic abundance. However, bait digging had minimal impact on the macrofauna community and caused no change in the sediment environment, despite the removal of a large proportion of the A. marina population. No change was recorded in the sediment stability or biomass of the microphytobenthos, indicating that with the exception of removing A. marina, bait digging of this nature was not detrimental to the sediment ecosystem. However, the consequences of larger, longer term digging operations can not be determined from this work and further studies are suggested. The study of intertidal sediment stability was progressed with advances made in methods and protocols. The work highlighted the importance of studying sediment stability as an ecosystem function through a holistic ecosystem approach rather than isolating individual variables.

In this thesis I investigate the role of spatial structure, cell-cell interactions and horizontal gene transfer on the genetic composition of growing microbial colonies. In the first part I study how the roughness of the growing layer of the colony depends on the shape of colony-forming cells. To study its impact I develop an off-lattice Eden-like model in which cells are represented as spherocylinders with a variable aspect ratio. I show that the roughness of the expansion front is not significantly affected by the shape of cells and that the dynamic scaling of growing front belongs to the KPZ universality class. Roughness is an important and easy to measure feature which affects the probability of fixation of genetic lineages in the colony. Another feature contributing to the genetic composition of a microbial community is horizontal gene transfer, which is investigated in the second part of this thesis. I develop an agent-based computational model of bacterial cells which grow, divide, and interact mechanically. I focus on plasmid conjugation, in which donors transfer a plasmid (a small, circular DNA molecule) to plasmid-free recipients. I show that bacteria in the expanding colony segregate into sectors of donors and acceptors. Donor sectors grow at the expense of acceptor sectors and that effect can be effectively described by coalescing random walkers that perform biased random walk on the colony expansion front. I use numerical and analytical methods to show that the plasmid eventually spreads to the whole colony given enough time, and I also show that this time is unrealistically long for experimentally determined conjugation rates and therefore real colonies are expected to have both acceptor and donor sectors. Furthermore, my simulations show that segregative plasmid loss at the moment of cell division can counteract the effect of conjugation and can lead to fixation of plasmid free cells. I also show that changes in nutrient concentration and the resultant change in roughness of the expansion front affect the rate of plasmid spread into population. Quantitative and qualitative results obtained in this section may serve as a tool to extract plasmid invasion rates from experimental data. In the last part of this thesis I investigate how the physical factors, such as finite strength of conjugative junctions, affect the conjugation process. I develop a computational model of plasmid transfer in which conjugative junctions are explicitly modelled as short, spring-like tubes that connect conjugating cells. My results show that factors such as junction creation rate and its strength can significantly affect the conjugation performance. I study different situations corresponding to different experimental scenarios (well-mixed colony on a filter paper, colliding colonies) and show that shear forces acting between cells can significantly lower the rate of plasmid transfer. My results can explain why conjugation occurs very rarely in some of these scenarios investigates in laboratory assays.

Best known if not equally understood for having a madman proclaim the demise of God, Friedrich Nietzsche’s thought has served as a fecund resource for disparate groups advancing diverse agendas. This paper critically examines the phenomenon of invoking Nietzsche as the final word. This paper argues that, far from being a conversation-stopper, Nietzsche can be understood as enhancing dialogue, across disciplines and between groups such as philosophers and theologians more prone to militant rhetoric than fruitful dialogue. In order to validate this claim it will be necessary to examine in detail the two aspects of Nietzsche’s thought most often invoked as conversation stoppers: the madman’s proclamation of the death of God; and Nietzsche’s devastating critique of Christian morality. Ultimately, this thesis will conclude that when properly understood Nietzsche serves as a unique interpreter locating himself between modernity and postmodernity, as well as between philosophy and religious thought.

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Diss.--Philosophische Fakultät--Bonn--Rheinische Friedrich-Wilhelms-Universität, 2000. / Bibliogr. p. 398-431. Index.