Dimensionality hyper-reduction and machine learning for dynamical systems with varying parameters

Thesis (Ph.D.)--University of Washington, 2016-08

Stochastic Modeling of Reversible Biochemical Reaction-Diffusion Systems and High-Resolution Shock-Capturing Methods for Fluid Interfaces

Thesis (Ph.D.)--University of Washington, 2016-08

Conservation narratives in Peru: envisioning biodiversity in sustainable development

In the mega-diverse country Peru, a resource intensive development model collides with the interest of conserving biodiversity. Peruvian biodiversity experts have developed different lines of argumentation as to how to integrate conservation into the sustainable development of their country. Applying grounded theory, I define five groups of conservation narratives based on the analysis of 72 qualitative interviews with experts working in areas of biodiversity conservation. I have labeled them: biodiversity protectionists, biodiversity traditionalists, biodiversity localists, biodiversity pragmatists, and biodiversity capitalists. These groups are each discussed in connection with what they have to say about biodiversity in relation to human life, valuation and knowledge systems, participation and leadership, substitutability of natural capital, and its predominant political strategy. In a second step, a comparative analysis of the dominant and diverging political perspectives is made. I argue that by deconstructing underlying premises and ideologies, common ground and possible opportunities for collaboration can be identified. Moreover, although the presented results can serve as a discussion scaffold to organize conservation debates in Peru, this example demonstrates how the terms biodiversity and sustainability are operationalized in conservation narratives.

Stakeholder-led science: engaging resource managers to identify science needs for long-term management of floodplain conservation lands

Floodplains pose challenges to managers of conservation lands because of constantly changing interactions with their rivers. Although scientific knowledge and understanding of the dynamics and drivers of river-floodplain systems can provide guidance to floodplain managers, the scientific process often occurs in isolation from management. Further, communication barriers between scientists and managers can be obstacles to appropriate application of scientific knowledge. With the coproduction of science in mind, our objectives were the following: (1) to document management priorities of floodplain conservation lands, and (2) identify science needs required to better manage the identified management priorities under nonstationary conditions, i.e., climate change, through stakeholder queries and interactions. We conducted an online survey with 80 resource managers of floodplain conservation lands along the Upper and Middle Mississippi River and Lower Missouri River, USA, to evaluate management priority, management intensity, and available scientific information for management objectives and conservation targets. Management objectives with the least information available relative to priority included controlling invasive species, maintaining respectful relationships with neighbors, and managing native, nongame species. Conservation targets with the least information available to manage relative to management priority included pollinators, marsh birds, reptiles, and shore birds. A follow-up workshop and survey focused on clarifying science needs to achieve management objectives under nonstationary conditions. Managers agreed that metrics of inundation, including depth and extent of inundation, and frequency, duration, and timing of inundation would be the most useful metrics for management of floodplain conservation lands with multiple objectives. This assessment provides guidance for developing relevant and accessible science products to inform management of highly dynamic floodplain environments. Although the problems facing managers of these lands are complex, products focused on a small suite of inundation metrics were determined to be the most useful to guide the decision making process.

Ancient clam gardens, traditional management portfolios, and the resilience of coupled human-ocean systems

Indigenous communities have actively managed their environments for millennia using a diversity of resource use and conservation strategies. Clam gardens, ancient rock-walled intertidal beach terraces, represent one example of an early mariculture technology that may have been used to improve food security and confer resilience to coupled human-ocean systems. We surveyed a coastal landscape for evidence of past resource use and management to gain insight into ancient resource stewardship practices on the central coast of British Columbia, Canada. We found that clam gardens are embedded within a diverse portfolio of resource use and management strategies and were likely one component of a larger, complex resource management system. We compared clam diversity, density, recruitment, and biomass in three clam gardens and three unmodified nonwalled beaches. Evidence suggests that butter clams (Saxidomus gigantea) had 1.96 times the biomass and 2.44 times the density in clam gardens relative to unmodified beaches. This was due to a reduction in beach slope and thus an increase in the optimal tidal range where clams grow and survive best. The most pronounced differences in butter clam density between nonwalled beaches and clam gardens were found at high tidal elevations at the top of the beach. Finally, clam recruits (0.5-2 mm in length) tended to be greater in clam gardens compared to nonwalled beaches and may be attributed to the addition of shell hash by ancient people, which remains on the landscape today. As part of a broader social-ecological system, clam garden sites were among several modifications made by humans that collectively may have conferred resilience to past communities by providing reliable and diverse access to food resources.

Evaluating the conservation of graffiti based on cultural significance.

Purpose – Graffiti, both ancient and contemporary, could be argued to be significant and therefore worthy of protection. Attaching value is, however, subjective with no specific method being solely utilised for evaluating these items. The purpose of this paper to help those who are attempting to evaluate the merit of graffiti to do so, by determining “cultural significance”, which is a widely adopted concept for attaching value to the historic built environment. The current Scottish system utilised to assess “cultural significance” is the Scottish Historic Environment Policy (SHEP) which shares many common features with other determinants of cultural significance in different countries. The SHEP document, as with other systems, could however be criticised for being insufficiently sensitive to enable the evaluation of historic graffiti due, in part, to the subjective nature of determination of aesthetic value. Design/methodology/approach – A review of literature is followed by consideration of case studies taken from a variety of historical and geographical contexts. The majority of examples of graffiti included in this paper have been selected for their relative high profile, previous academic study, and breadth of geographic spread. This selection will hopefully enable a relatively comprehensive, rational assessment to be undertaken. That being said, one example has been integrated to reflect commonly occurring graffiti that is typical to all of the built environment. Findings – The determination of aesthetic value is particularly problematic for the evaluator and the use of additional art‐based mechanisms such as “significant form”, “self expression” and “meaning” may aid this process. Regrettably, these determinants are also in themselves subjective, enhancing complexity of evaluation. Almost all graffiti could be said to have artistic merit, using the aforementioned determinants. However, whether it is “good” art is an all together different question. The evaluation of “good” art and graffiti would have traditionally been evaluated by experts. Today, determination of graffiti should be evaluated and value attached by broader society, community groups, and experts alike. Originality/value – This research will assist those responsible for historic building conservation with the evaluation of whether graffiti is worthy of conservation.

Pattern formation with a conservation law

Pattern formation in systems with a conserved quantity is considered by studying the appropriate amplitude equations. The conservation law leads to a large-scale neutral mode that must be included in the asymptotic analysis for pattern formation near onset. Near a stationary bifurcation, the usual Ginzburg--Landau equation for the amplitude of the pattern is then coupled to an equation for the large-scale mode. These amplitude equations show that for certain parameters all roll-type solutions are unstable. This new instability differs from the Eckhaus instability in that it is amplitude-driven and is supercritical. Beyond the stability boundary, there exist stable stationary solutions in the form of strongly modulated patterns. The envelope of these modulations is calculated in terms of Jacobi elliptic functions and, away from the onset of modulation, is closely approximated by a sech profile. Numerical simulations indicate that as the modulation becomes more pronounced, the envelope broadens. A number of applications are considered, including convection with fixed-flux boundaries and convection in a magnetic field, resulting in new instabilities for these systems.

Rapid assessment of the fish biodiversity of the Mburo-Nakivali wetland systems and Opeta-Bisina wetland systems, Uganda

There are 46 different fish species in the Lake Kyoga basin with some of them endemic. The Nile Perch (Lates niloticus) was introduced into the main Lake Kyoga, Nakuwa and Bisina in the late 1950s to increase the fish production. The Nile Perch profileration in lakes Kyoga and Nakuwa led to the almost complete elimination of many native fish species such as Orechromis esculentus and variabilis, Mormyrus kanumme, Schilbe mystus and several Haplochromines species. Lakes Mburo, Kachera, Nakivali and Kijjanebalora are part of the complex system of lakes separated from Lake Victoria by extended swamps known as the Koki lakes, some of the satellite lakes in the Lake Victoria basin. The fisheries of these lakes are important as they contribute to government efforts of increasing food security, poverty reduction and conservation of natural resource base. These lakes are important biodiversity areas because some of these lakes have been found to contain the native tilapiine Oreochromis esculentus (Ngege), absent or threatened with extinction in the main Lakes Victoria and Kyoga. It’s also important to note that this species is only unique to the Victoria and Kyoga lake basins (Graham, 1929, Worthington, 1929). The values of some of these lake fisheries are however, threatened by human activities such as over exploitation, introduction of exotics especially water hyacinth that is already present in River Rwizi and habitat degradation among others.

Conservation of aquatic biodiversity

Uganda is rich in aquatic resources. Up to 17 % of the country's surface area is covered by Aquatic systems comprising five major lakes; Victoria, Albert, Kyoga, Edward, George, about 160 minor lakes, an extensive river and stream system, dams and ponds. These aquatic systems are associated with extensive swamps

Carbon losses in terrestrial hydrological pathways in sugarcane cropping systems of Australia

Climate change and carbon (C) sequestration are a major focus of research in the twenty-first century. Globally, soils store about 300 times the amount of C that is released per annum through the burning of fossil fuels (Schulze and Freibauer 2005). Land clearing and introduction of agricultural systems have led to rapid declines in soil C reserves. The recent introduction of conservation agricultural practices has not led to a reversing of the decline in soil C content, although it has minimized the rate of decline (Baker et al. 2007; Hulugalle and Scott 2008). Lal (2003) estimated the quantum of C pools in the atmosphere, terrestrial ecosystems, and oceans and reported a “missing C” component in the world C budget. Though not proven yet, this could be linked to C losses through runoff and soil erosion (Lal 2005) and a lack of C accounting in inland water bodies (Cole et al. 2007). Land management practices to minimize the microbial respiration and soil organic C (SOC) decline such as minimum tillage or no tillage were extensively studied in the past, and the soil erosion and runoff studies monitoring those management systems focused on other nutrients such as nitrogen (N) and phosphorus (P).

Pricing recreation use of national parks for an efficient nature conservation : an application to the portuguese case

Current institutions, research, and legislation have not yet been sufficient to achieve the conservation level of Nature as required by the society. One of the reasons that explains this relative failure is the lack of incentives to motivate local individual and Nature users in general, to adopt behaviour compliant with Nature sustainable uses. Economists believe that, from the welfare point of view, pricing is the more efficient way to make economic actors to take more environmental friendly decisions. In this paper we will discuss how efficient can be the act of pricing the recreation use of a specific natural area, in terms of maximising welfare. The main conservation issues for pricing recreation use, as well as the conditions under which pricing will be an efficient and fair instrument for the natural area will be outlined. We will conclude two things. Firstly that, from the rational utilitarian economic behaviour point of view, economic efficiency can only be achieved if the natural area has positive and known recreation marginal costs under the relevant range of the marshallian demand recreation curve and if price system management is not costly. Secondly, in order to guarantee equity for the different type of visitors when charging the fee, it is necessary to discuss differential price systems. We shall see that even if marginal recreation costs exist but are unknown, pricing recreation is still an equity instrument and a useful one from the conservation perspective, as we shall demonstrate through an empirical application to the Portuguese National Park. An individual Travel Cost Method Approach will be used to estimate the recreation price that will be set equal to the visitor’s marginal willingness to pay for a day of visit in the national park. Although not efficient, under certain conditions this can be considered a fair pricing practice, because some of the negative recreation externalities will be internalised. We shall discuss the conditions that guarantee equity on charging for the Portuguese case.

Does Landscape Context Affect Habitat Value? The Importance of Seascape Ecology in Back-reef Systems

Seascape ecology provides a useful framework from which to understand the processes governing spatial variability in ecological patterns. Seascape context, or the composition and pattern of habitat surrounding a focal patch, has the potential to impact resource availability, predator-prey interactions, and connectivity with other habitats. For my dissertation research, I combined a variety of approaches to examine how habitat quality for fishes is influenced by a diverse range of seascape factors in sub-tropical, back-reef ecosystems. In the first part of my dissertation, I examined how seascape context can affect reef fish communities on an experimental array of artificial reefs created in various seascape contexts in Abaco, Bahamas. I found that the amount of seagrass at large spatial scales was an important predictor of community assembly on these reefs. Additionally, seascape context had differing effects on various aspects of habitat quality for the most common reef species, White grunt Haemulon plumierii. The amount of seagrass at large spatial scales had positive effects on fish abundance and secondary production, but not on metrics of condition and growth. The second part of my dissertation focused on how foraging conditions for fish varied across a linear seascape gradient in the Loxahatchee River estuary in Florida, USA. Gray snapper, Lutjanus griseus, traded food quality for quantity along this estuarine gradient, maintaining similar growth rates and condition among sites. Additional work focused on identifying major energy flow pathways to two consumers in oyster-reef food webs in the Loxahatchee. Algal and microphytobenthos resource pools supported most of the production to these consumers, and body size for one of the consumers mediated food web linkages with surrounding mangrove habitats. All of these studies examined a different facet of the importance of seascape context in governing ecological processes occurring in focal habitats and underscore the role of connectivity among habitats in back-reef systems. The results suggest that management approaches consider the surrounding seascape when prioritizing areas for conservation or attempting to understand the impacts of seascape change on focal habitat patches. For this reason, spatially-based management approaches are recommended to most effectively manage back-reef systems.

The role of agriculture and food consumption in tropical conservation

A growing human population, shifting human dietary habits, and climate change are negatively affecting global ecosystems on a massive scale. Expanding agricultural areas to feed a growing population drives extensive habitat loss, and climate change compounds stresses on both food security and ecosystems. Understanding the negative effects of human diet and climate change on agricultural and natural ecosystems provides a context within which potential technological and behavioral solutions can be proposed to help maximize conservation. The purpose of this research was to (1) examine the potential effects of climate change on the suitability of areas for commercial banana plantations in Latin America in the 2050s and how shifts in growing areas could affect protected areas; (2) test the ability of small unmanned aerial vehicles (UAVs) to map productivity of banana plantations as a potential tool for increasing yields and decreasing future plantation expansions; (3) project the effects on biodiversity of increasing rates of animal product consumption in developing megadiverse countries; and (4) estimate the capacity of global pasture biomass production and Fischer-Tropsch hydrocarbon synthesis (IGCC-FT) processing to meet electricity, gasoline and diesel needs. The results indicate that (1) the overall extent of areas suitable for conventional banana cultivation is predicted to decrease by 19% by 2050 because of a hotter and drier climate, but all current banana exporting countries are predicted to maintain some suitable areas with no effects on protected areas; (2) Spatial patterns of NDVI and ENDVI were significantly positively correlated with several metrics of fruit yield and quality, indicating that UAV systems can be used in banana plantations to map spatial patterns of fruit yield; (3) Livestock production is the single largest driver of habitat loss, and both livestock and feedstock production are increasing in developing biodiverse tropical countries. Reducing global animal product consumption should therefore be at the forefront of strategies aimed at reducing biodiversity loss; (4) Removing livestock from global pasture lands and instead utilizing the biomass production could produce enough energy to meet 100% of the electricity, gasoline, and diesel needs of over 40 countries with extensive grassland ecosystems, primarily in tropical developing countries.^

When the virtual influences reality. The conservation project of the toledo gate in ciudad real (Spain)

The Toledo Gate of Ciudad Real, Spain, constructed between the late 13th and early 14th centuries, is the last remaining portion of a once complete medieval city wall. It represents the long history of the city and constitutes its main heritage symbol, dividing the historic city centre from the later 19th and 20th century expansions. In October 2012, the Town Hall and the Montemadrid Foundation started the conservation works to preserve this important monument. The preliminary phase of this project included an in-depth series of scientific studies which were carried out by a multidisciplinary team focusing on archival research, historic investigations, archaeological excavations as well as material composition analysis and main treatment application tests. As a result of these studies a series of virtual 3D models were created to inform, discuss and study the monument. A first digital model permitted visualization of the gate in the 19th century and how the main entrance to the city was integrated as a fundamental part of the city walls. This virtual reconstruction also became an important part of the campaign to raise awareness among the citizens towards a monument that had remained in the shadows for the last century, isolated in a roundabout after the systematic demolition of the city walls in the late 19th century. Over the last three years and as a result of these archaeological and historic investigations and subsequent virtual models, surprisingly new and interesting data were brought to light thus permitting the establishment and corroboration of a new and updated hypothesis of the Toledo Gate that goes beyond the previous ideas. As a result of these studies a new architectural typology with construction techniques of has been suggested. This paper describes how the results of this continuous and interdisciplinary documentation process have benefitted from a computer graphic reconstruction of the gate. It highlights how virtual reconstruction can be a powerful tool for conservation decision making and awareness raising. Furthermore, the interesting results of the final reconstruction hypothesis convinced the technical team responsible for the conservation to alter some aspects of the final project physical interventions in order to focus on some of the features and conclusions discovered through the virtual model study.