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The Ocean Laboratory: Exploration, Fieldwork, and Science at Sea
No full textThesis (Ph.D.)--University of Washington, 2014In framing the history of field sciences most historians emphasize terrestrial sites rather than marine ones. But, to ignore marine spaces is to omit an extensive geography to which the abstract notion of "the field" has also been applied. While the importance of laboratories as a space for scientific work has been well established by historians, and though there has been a growing body of recent scholarship on the history of field science, the link between laboratories, ships, museums, and the development of oceanography as a field science has yet to be fully explored. Tracing this history sets the history of oceanography within the larger history of science in the field and thereby offers to the history of science a contribution which bridges two subfields, the history of the development of laboratory and field sciences and the history of the exploration of the marine environment. A central theme of this project is the shifting conception of the research vessel over the period from ca. 1830 to present, as it underwent a change from the ship as instrument, to the ship as laboratory, and finally, in its most recent incarnation, to the ship as invisible technician operating within an ocean transformed into credible scientific space. Beginning with a description of expeditionary science at the turn of the nineteenth century, this dissertation charts a gradual re-centering of spaces of scientific analysis from the metropole to the field, via the marine station and finally, the research vessel. In doing so, it examines the social, political, and cultural context in which these shifts took place, and reveals an emerging scientific and political discourse equating international cooperation, and progress in marine science. These were both goals of Prince Albert Ist of Monaco; his scientific program, and the oceanographic institutions he founded, helped permanently link these dual agendas. Thus, this study sheds light on the social and cultural processes involved in the emergence of global sciences framed in terms of large-scale systems, both physical and political. Furthermore, by tracing the development of oceans as scientific spaces, this work demonstrates how the idea of a "Pacific World," with roots in nineteenth-century expeditionary science, contributed to the self-conscious geopolitical construction of this concept in the interwar period. Public proclamations about the Pacific World, along with the development of museum exhibits focused on marine science and interpreting the results of oceanographic expeditions, demonstrate the ways in which popular culture and politics interacted with the cultures of marine science. Hence, in the twentieth century, world's fairgrounds on the west coast of the United States became an important venue for popularizing large-scale science and presenting appeals for scientific internationalism in the Pacific
Lu & Velarde 1 The Effects of Predation by the Pacific North West Nudibranch Janolus fuscus (O’Donoghue) on the Bryozoan larvae of Bugula pugeti (Robertson)
No full textThe sensory organs of larvae of the bryozoan Bugula c.f. californica are very important during the short transition from the swimming phase to the brief settlement phase. These sensory organs detect environmental cues that initiate and regulate settlement within a favorable habitat. However, these organs may also allow the larvae to perceive unfavorable habitat and avoid predation. This study looked at the settlement response of the competent larvae of Bugula c.f. californica when they came in contact with traces of a predatory nudibranch, Janolus fuscus, with a known positive settlement cue (biofilm), and with traces of a non-predatory nudibranch, Archidoris montereyensis. A known number of larvae were kept in small petri dishes filled with filtered seawater at about 12 degrees Celsius with no flow inside the dishes. Prior to adding the newly released larvae, the petri dishes were divided into four groups that were smeared with the three following treatments: mucus from the predatory nudibranch, mucus from the non-predatory nudibranch, and a thin layer of biofilm. Clean (un-filmed) dishes with FSW served as the control. A second study looked at preferential settlement with the known positive- biofilm, the biofilm substratum with predatory water, and ½ biofilm substratum next to ½ predatory mucus substratum. We found that the larvae in the biofilm with FSW settled early in their planktonic period. The larvae in the dishes with predator mucus, dishes with biofilm and predator water, in dishes with a choice of biofilm or predator mucus delay their settlement- perhaps in search of optimal habitats. Furthermore, when the biofilm and predator mucus exist in the same dish, the larvae preferentially settle in the side with biofilm, which suggests that they try to avoid potential predation
The Ecology of Human Diets during the Holocene at North Creek Shelter, Utah
No full textThesis (Ph.D.)--University of Washington, 2014This research examines the ecology of human diet using archeological evidence from a specific site in western North America, North Creek Shelter (NCS) near Escalante, Utah. I use ecological measures and theory to quantify human dietary change during the early to middle Holocene and in the context of local ecosystems that supplied plant and animal food resources. Vegetation sampling techniques are used to quantify the landscape and dietary palettes that may have been available to the occupants of NCS during the Holocene. According to my sampling, the pinyon-juniper woodland and cool desert scrub vegetation types would have supplied the majority of dietary plant resources, while the other types were either devoid of, or had low cover by, dietary species. I also combine evidence from dietary plant macro- and microfossil remains with dietary faunal remains to examine this comprehensive dataset in the context of ground stone abundance and environmental change. Two periods of increased dietary species richness occurred at 9400 and 8000 14C BP, when people were focusing their subsistence on deer and Chenopodium seeds, respectively. The shift in emphasis between deer and Chenopodium was accompanied by a shift in stone tool technology. The assemblage of chipped stone tools in substratum 3e (9400 14C BP) was dominated by hunting and bone-processing implements. Ground stone tools became dominant in substratum 5t (8000 14C BP), simultaneous with a peak in Chenopodium abundance. Increasing aridity began by 9000 14C BP and had progressed significantly by 8000 14C BP, indicated by a shift in vegetation from a mixed conifer forest of cool-adapted species to a semi-arid woodland and shrub mosaic. This coincided with a broadening of the diet dependent upon an intensified use of small seeds and ground stone technology. Intensive processing of small seeds on ground stone tools was not the only such practice at NCS. Underground storage organs were also processed and possibly roasted in pits uniquely found on the living surface of substratum 5t (8000 14C BP). Although taxonomic assignments for the starch grains are difficult at this point, there are minimally two "taxa" ("centric" and "eccentric") that can be added to the tally of dietary species richness developed from macrobotanical remains (above). Adding these starch-producing plants to dietary species richness would accentuate a shift toward broader diet concurrent with a period of rapid environmental change during the middle Holocene
The association between cardiometabolic risk factors and breast cancer outcomes
No full textThesis (Ph.D.)--University of Washington, 2014Background: Prevalence of cardiometabolic risk factors contributing to metabolic syndrome is common, and numerous metabolic syndrome components are associated with increased primary breast cancer risk. However, less is known about their relation to breast cancer outcomes. In addition, adherence to chronic medications for metabolic syndrome risk factors such as diabetes is generally low and associated with adverse health outcomes. The growing population of breast cancer survivors and increasingly high prevalence of comorbidity warrants better understanding of medication adherence and clinical management. We sought to evaluate whether metabolic syndrome risk factors increase risk of second breast cancer events (SBCE) and breast cancer-specific mortality and describe whether adherence to oral diabetes medications and clinical control of diabetes vary prior to and following breast cancer treatment. Methods: We conducted a retrospective cohort study among female health plan enrollees ages ≥18 years diagnosed with stage I or II breast cancer between 1990-2008 via the Surveillance, Epidemiology, and End Results registry. Data sources included automated health plan data and medical records. We used Cox regression models to estimate the relation between metabolic syndrome components and SBCE (first of recurrence or second primary) and breast cancer-specific mortality while adjusting for potential confounders. We measured adherence and discontinuation of oral diabetes medications, biguanides (i.e., metformin) and sulfonylureas using medication possession ratios (MPR) and discontinuation rates (DR) in the year prior to incident cancer diagnosis, during treatment and the subsequent three years. We evaluated medication adherence (MPR ≥0.80), persistence (1-DR) and glycemic control (HbA1c ≤7.0%) in corresponding periods. Results: Among the 4,216 women in the cohort, 26% had ≥3 metabolic syndrome components and 13% developed SBCE during follow-up. Presence of metabolic syndrome (≥3 components) was associated with increased risk of SBCE (HR 1.50, 95% CI 1.08-2.07) and increased risk of breast cancer-specific mortality (HR 1.65, 95% CI 1.02-2.69). Among the 509 oral diabetes medication users, the proportion of adherent users declined during breast cancer treatment (75.3% versus 24.6%, P7.0%) was increased in the year following treatment (34.9% versus 51.1%, P<0.001) compared with baseline. Conclusion: Risk of SBCE and breast cancer-specific mortality may be altered by cardiometabolic risk factors contributing to metabolic syndrome. Adherence to oral medications for diabetes and glycemic control declines during and following breast cancer diagnosis. Further research in larger more diverse populations as well as other site-specific cancers and comorbidities is warranted
Auxin-induced degradation dynamics and plant development
No full textThesis (Ph.D.)--University of Washington, 2014Development requires cells to send and receive information, often in the form of small molecules or peptides. An emerging theme in biology is that information can be encoded in the dynamics of signaling, not just in the relative abundance of signaling molecules. In plants, response to the hormone auxin is a useful tool for studying the role that signal dynamics play in development. Auxin triggers degradation of an Aux/IAA repressor protein, which activates transcription of a large number of genes. Auxin facilitates Aux/IAA degradation by mediating interaction between Aux/IAAs and auxin receptors called TIR1/AFBs. Each component in the auxin signaling pathway belongs to a gene family, and different family members play distinct roles throughout development. Our work building a synthetic auxin response system in yeast revealed that Aux/IAAs exhibit a range of degradation rates. I hypothesized that these IAA degradation rates act as biological pacemakers to coordinate developmental processes. To test this, I characterized the effect of altered rates of Aux/IAA degradation on lateral root initiation. These studies demonstrate that Aux/IAA degradation dynamics determine the rate of progression through lateral root development in Arabidopsis. This work has revealed a molecular connection between the dynamics of auxin signaling and the dynamics of organogenesis, supporting the hypothesis that the Aux/IAAs act as auxin-induced pacemakers in plant development
Remains
No full textThesis (Master's)--University of Washington, 2014to write requires dedication to word selection, imagery illumination, supple flow, integrity, faith, exploration. authors are embedded in their work. there is no way to be rid of the author. the ugliness, inhumanity, splendor, stimulation is born of their flesh. motivation is an intimate festering until it is bled onto the page. writers are made vulnerable by their words. there is relief and strength and growth in such vulnerability. they do themselves a joyous violence to put the words on the page, give the page to the public. the manuscript has a life of its own. it exists beyond its creator. it reincarnates with each new reader. great works embed themselves in minds. the book communicates the pulse, the synaptic firings, the exhalations of its author across time. to read another's work it to enter into a relationship of trust. the reader is infected. what is read cannot be unread. it lives, both excised and embedded, fertile ground and bountiful fruit, harbor and harvest
DNA methylation variation in gametes and larvae of the Pacific oyster, Crassostrea gigas
No full textThesis (Master's)--University of Washington, 2014Epigenetics describes DNA modifications that change gene expression without altering the underlying nucleotide sequence. Epigenetic mechanisms such as DNA methylation can change genome function under external influences. The focus of this project is examining one epigenetic modification, DNA methylation, in oysters. DNA methylation has been well studied in vertebrates, but remains understudied in invertebrates. Furthermore, the amounts and functions of DNA methylation in organisms are extremely diverse and variable across taxa. This thesis determines patterns of DNA methylation in C. gigas to elucidate the functional role of DNA methylation. The first chapter examines the genome-wide DNA methylation profile in C. gigas male gamete cells using whole-genome bisulfite sequencing. RNA-Seq analysis was also performed on the same tissue to provide insight into the mechanisms by which DNA methylation impacts transcriptional processes. The work presented in Chapter 2 examines methylation patterns of C. gigas during early oyster developmental stages (spermatozoa and larvae). Together these data were used to test the predictions that DNA methylation is involved in gene regulatory activity and is heritable. This work also describes individual variation, parental transmission and developmental patterns of DNA methylation in oysters. Our results indicate a positive relationship between DNA methylation and gene expression, and that DNA methylation patterns are inherited in oysters
Polishing A Gem On The Surface Of The Sea
No full textPolishing a Gem on the Surface of the Sea is a hybrid work that is non-fiction, creative fiction, fiction and poetry but, for classification purposes, I label it fiction. The narrative and poetry sections focus on grief, becoming a writer, writing, personal growth, metaphysics, travel, memory, family, consciousness, identity, choice, intellect, change, and race consciousness. The writer does not advocate for any single stance but instead presents material for the reader to consider. The writer is also still contemplating the ideas presented in this work and believes that thought is malleable and subject to change as new information arises. This work will likely continue to develop over a number of years but can stand as a reflection on an individuals experience at a specific point in time
Analysis of an Aggregation-based Algebraic Multigrid Method and its Parallelization
No full textThesis (Ph.D.)--University of Washington, 2014The interests of this thesis are twofold. First, a two-grid convergence analysis based on the paper [ \textit{Algebraic analysis of aggregation-based multigrid } by A. Napov and Y. Notay, Numer. Lin. Alg. Appl. 18 (2011), pp. 539-564 ] is derived for various aggregation schemes applied to a finite element discretization of a rotated anisotropic diffusion equation. As expected, it is shown that the best aggregation scheme is one in which aggregates are aligned with the anisotropy. In practice, however, this is not what automatic aggregation procedures do. We suggest an approach for determining appropriate aggregates based on eigenvectors associated with small eigenvalues of a block splitting matrix. In the second part of the thesis several issues regarding the parallel implementation of aggregation-based multigrid methods are discussed. The coarsest grid solving stage of multigrid cycles has been a bottleneck for parallel multigrid algorithms to attain a good speedup. A comparison between a parallel linear system direct solver (MUMPS) and a few steps of preconditioned conjugate gradient (PCG) methods for solving the coarsest grid system is carried out and tested on TACC Lonestar multi-processor machine. Regarding the preconditioner of conjugate gradient iterations, a parallel sparse approximate inverse (SAI) algorithm is used to construct an approximate inverse of the original matrix in order to replace the preconditioner solving step, which is inherently sequential, by matrix-vector multiplications. The linear systems tested arise from discretization of 2D or 3D partial differential equations, which are symmetric positive definite. The results exhibit that using PCG on the coarsest grid attains better speedup and overall better performance than MUMPS when the number of processors is greater than about 100. The effects of different decompositions of the physical domain (rows/slab versus blocks/pencils) on the scaling and efficiency of aggregation-based algebraic multigrid are also studied and one sees that the blocks/pencils decomposition of the physical domain reduces the amount of communication and hence has better performance