Landscape valuation through discrete choice experiments: Current practice and future research reflections

This work has been presented in: V Conference AERNA, Faro (Portugal), 30 May 2012-1 June 2012 and IV Workshop on Valuation Methods in Agro-food and Environmental Economics, Castelldefels (Barcelona, Spain), 12 July 2012-13 July 2012.

SUSTAINABILITY OF OPEN ACCESS SERVICES: Phase 3: The Collective Provision of Open Access Resources

The report ‘Sustainability of Open Access Services - Phase 3: The Collective Provision of Open Access Resources’ discusses the economic and institutional issues faced by those sustaining free infrastructure services. It also identifies strategies to coordinate the collective provision of infrastructure services. These considerations are valuable input for the phases 4 and 5 of the project ‘Sustainability of Open Access Services’. This body of work will lead to practical recommendations for funders and project planners to consider when initiating an infrastructure service. The report was written by Raym Crow and funded by SPARC. Several key messages from the report are of interest. Providing infrastructure services as a public good imposes specific requirements on the design of the sustainability model. The challenge is to get enough institutions to reveal their demand for the service and support this. Arguments for an institution to support can be altruism or reciprocity or there being sufficient benefit to the institution for supporting a service. Institutions can also work together on a service through collective action (collecting voluntary contributions) and cross subsidies (funding collected by offering exclusive benefits to contributors).

Community Turnover of Wood-Inhabiting Fungi across Hierarchical Spatial Scales

For efficient use of conservation resources it is important to determine how species diversity changes across spatial scales. In many poorly known species groups little is known about at which spatial scales the conservation efforts should be focused. Here we examined how the community turnover of wood-inhabiting fungi is realised at three hierarchical levels, and how much of community variation is explained by variation in resource composition and spatial proximity. The hierarchical study design consisted of management type (fixed factor), forest site (random factor, nested within management type) and study plots (randomly placed plots within each study site). To examine how species richness varied across the three hierarchical scales, randomized species accumulation curves and additive partitioning of species richness were applied. To analyse variation in wood-inhabiting species and dead wood composition at each scale, linear and Permanova modelling approaches were used. Wood-inhabiting fungal communities were dominated by rare and infrequent species. The similarity of fungal communities was higher within sites and within management categories than among sites or between the two management categories, and it decreased with increasing distance among the sampling plots and with decreasing similarity of dead wood resources. However, only a small part of community variation could be explained by these factors. The species present in managed forests were in a large extent a subset of those species present in natural forests. Our results suggest that in particular the protection of rare species requires a large total area. As managed forests have only little additional value complementing the diversity of natural forests, the conservation of natural forests is the key to ecologically effective conservation. As the dissimilarity of fungal communities increases with distance, the conserved natural forest sites should be broadly distributed in space, yet the individual conserved areas should be large enough to ensure local persistence.

Proteomic Analysis of the Ubiquitin Landscape in the Drosophila Embryonic Nervous System and the Adult Photoreceptor Cells

Background Ubiquitination is known to regulate physiological neuronal functions as well as to be involved in a number of neuronal diseases. Several ubiquitin proteomic approaches have been developed during the last decade but, as they have been mostly applied to non-neuronal cell culture, very little is yet known about neuronal ubiquitination pathways in vivo. Methodology/Principal Findings Using an in vivo biotinylation strategy we have isolated and identified the ubiquitinated proteome in neurons both for the developing embryonic brain and for the adult eye of Drosophila melanogaster. Bioinformatic comparison of both datasets indicates a significant difference on the ubiquitin substrates, which logically correlates with the processes that are most active at each of the developmental stages. Detection within the isolated material of two ubiquitin E3 ligases, Parkin and Ube3a, indicates their ubiquitinating activity on the studied tissues. Further identification of the proteins that do accumulate upon interference with the proteasomal degradative pathway provides an indication of the proteins that are targeted for clearance in neurons. Last, we report the proof-of-principle validation of two lysine residues required for nSyb ubiquitination. Conclusions/Significance These data cast light on the differential and common ubiquitination pathways between the embryonic and adult neurons, and hence will contribute to the understanding of the mechanisms by which neuronal function is regulated. The in vivo biotinylation methodology described here complements other approaches for ubiquitome study and offers unique advantages, and is poised to provide further insight into disease mechanisms related to the ubiquitin proteasome system.

Tailored seeding geometries for the multi-fidelity design of compression systems

Design optimisation of compressor systems is a computationally expensive problem due to the large number of variables, complicated design space and expense of the analysis tools. One approach to reduce the expense of the process and make it achievable in industrial timescales is to employ multi-fidelity techniques, which utilise more rapid tools in conjunction with the highest fidelity analyses. The complexity of the compressor design landscape is such that the starting point for these optimisations can influence the achievable results; these starting points are often existing (optimised) compressor designs, which form a limited set in terms of both quantity and diversity of the design. To facilitate the multi-fidelity optimisation procedure, a compressor synthesis code was developed which allowed the performance attributes (e.g. stage loadings, inlet conditions) to be stipulated, enabling the generation of a variety of compressors covering a range of both design topology and quality to act as seeding geometries for the optimisation procedures. Analysis of the performance of the multi-fidelity optimisation system when restricting its exploration space to topologically different areas of the design space indicated little advantage over allowing the system to search the design space itself. However, comparing results from optimisations started from seed designs with different aerodynamic qualites indicated an improved performance could be achieved by starting an optimisation from a higher quality point, and thus that the choice of starting point did affect the final outcome of the optimisations. Both investigations indicated that the performance gains through the optimisation were largely defined by the early exploration of the design space where the multi-fidelity speedup could be exploited, thus extending this region is likely to have the greatest effect on performance of the optimisation system. © 2013 by the American Institute of Aeronautics and Astronautics, Inc. All rights reserved.

Tailored seeding geometries for the multi-fidelity design of compression systems

Design optimisation of compressor systems is a computationally expensive problem due to the large number of variables, complicated design space and expense of the analysis tools. One approach to reduce the expense of the process and make it achievable in industrial timescales is to employ multi-fidelity techniques, which utilise more rapid tools in conjunction with the highest fidelity analyses. The complexity of the compressor design landscape is such that the starting point for these optimisations can influence the achievable results; these starting points are often existing (optimised) compressor designs, which form a limited set in terms of both quantity and diversity of the design. To facilitate the multi-fidelity optimisation procedure, a compressor synthesis code was developed which allowed the performance attributes (e.g. stage loadings, inlet conditions) to be stipulated, enabling the generation of a variety of compressors covering a range of both design topology and quality to act as seeding geometries for the optimisation procedures. Analysis of the performance of the multi-fidelity optimisation system when restricting its exploration space to topologically different areas of the design space indicated little advantage over allowing the system to search the design space itself. However, comparing results from optimisations started from seed designs with different aerodynamic qualites indicated an improved performance could be achieved by starting an optimisation from a higher quality point, and thus that the choice of starting point did affect the final outcome of the optimisations. Both investigations indicated that the performance gains through the optimisation were largely defined by the early exploration of the design space where the multi-fidelity speedup could be exploited, thus extending this region is likely to have the greatest effect on performance of the optimisation system. © 2012 AIAA.

Robustness and Coherence of a Three-Protein Circadian Oscillator: Landscape and Flux Perspectives

Three-protein circadian oscillations in cyanobacteria sustain for weeks. To understand how cellular oscillations function robustly in stochastic fluctuating environments, we used a stochastic model to uncover two natures of circadian oscillation: the potential landscape related to steady-state probability distribution of protein concentrations; and the corresponding flux related to speed of concentration changes which drive the oscillations. The barrier height of escaping from the oscillation attractor on the landscape provides a quantitative measure of the robustness and coherence for oscillations against intrinsic and external fluctuations. The difference between the locations of the zero total driving force and the extremal of the potential provides a possible experimental probe and quantification of the force from curl flux. These results, correlated with experiments, can help in the design of robust oscillatory networks.

Potential energy landscape and robustness of a gene regulatory network: Toggle switch

Finding a multidimensional potential landscape is the key for addressing important global issues, such as the robustness of cellular networks. We have uncovered the underlying potential energy landscape of a simple gene regulatory network: a toggle switch. This was realized by explicitly constructing the steady state probability of the gene switch in the protein concentration space in the presence of the intrinsic statistical fluctuations due to the small number of proteins in the cell. We explored the global phase space for the system. We found that the protein synthesis rate and the unbinding rate of proteins to the gene were small relative to the protein degradation rate; the gene switch is monostable with only one stable basin of attraction. When both the protein synthesis rate and the unbinding rate of proteins to the gene are large compared with the protein degradation rate, two global basins of attraction emerge for a toggle switch. These basins correspond to the biologically stable functional states. The potential energy barrier between the two basins determines the time scale of conversion from one to the other. We found as the protein synthesis rate and protein unbinding rate to the gene relative to the protein degradation rate became larger, the potential energy barrier became larger. This also corresponded to systems with less noise or the fluctuations on the protein numbers.

Quantifying robustness and dissipation cost of yeast cell cycle network: The funneled energy landscape perspectives

We study the origin of robustness of yeast cell cycle cellular network through uncovering its underlying energy landscape. This is realized from the information of the steady-state probabilities by solving a discrete set of kinetic master equations for the network. We discovered that the potential landscape of yeast cell cycle network is funneled toward the global minimum, G1 state. The ratio of the energy gap between G1 and average versus roughness of the landscape termed as robustness ratio ( RR) becomes a quantitative measure of the robustness and stability for the network. The funneled landscape is quite robust against random perturbations from the inherent wiring or connections of the network. There exists a global phase transition between the more sensitive response or less self-degradation phase leading to underlying funneled global landscape with large RR, and insensitive response or more self-degradation phase leading to shallower underlying landscape of the network with small RR. Furthermore, we show that the more robust landscape also leads to less dissipation cost of the network. Least dissipation and robust landscape might be a realization of Darwinian principle of natural selection at cellular network level. It may provide an optimal criterion for network wiring connections and design.

Funneled landscape leads to robustness of cellular networks: MAPK signal transduction

We uncover the underlying potential energy landscape for a cellular network. We find that the potential energy landscape of the mitogen-activated protein-kinase signal transduction network is funneled toward the global minimum. The funneled landscape is quite robust against random perturbations. This naturally explains robustness from a physical point of view. The ratio of slope versus roughness of the landscape becomes a quantitative measure of robustness of the network. Funneled landscape is a realization of the Darwinian principle of natural selection at the cellular network level. It provides an optimal criterion for network connections and design. Our approach is general and can be applied to other cellular networks.

A river of memory: landscape, narrative and identity in the Lee Valley, Co. Cork, Ireland

In moments of rapid social changes, as has been witnessed in Ireland in the last decade, the conditions through which people engage with their localities though memory, individually and collectively, remains an important cultural issue with key implications for questions of heritage, preservation and civic identity. In recent decades, cultural geographers have argued that landscape is more than just a view or a static text of something symbolic. The emphasis seems to be on landscape as a dynamic cultural process – an ever-evolving process being constructed and re-constructed. Hence, landscape seems to be a highly complex term that carries many different meanings. Material, form, relationships or actions have different meanings in different settings. Drawing upon recent and continuing scholarly debates in cultural landscapes and collective memory, this thesis sets out to examine the generation of collective memory and how it is employed as a cultural tool in the production of memory in the landscape. More specifically, the research considers the relationships between landscape and memory, investigating the ways in which places are produced, appropriated, experienced, sensed, acknowledged, imagined, yearned for, appropriated, re-appropriated, contested and identified with. A polyvocal-bricoleur approach aims to get below the surface of a cultural landscape, inject historical research and temporal depth into cultural landscape studies and instil a genuine sense of inclusivity of a wide variety of voices (role of monuments and rituals and voices of people) from the past and present. The polyvocal-bricoleur approach inspires a mixed method methodology approach to fieldsites through archival research, fieldwork and filmed interviews. Using a mixture of mini-vignettes of place narratives in the River Lee valley in the south of Ireland, the thesis explores a number of questions on the fluid nature of narrative in representing the story and role of the landscape in memory-making. The case studies in the Lee Valley are harnessed to investigate the role of the above questions/ themes/ debates in the act of memory making at sites ranging from an Irish War of Independence memorial to the River Lee’s hydroelectric scheme to the valley’s key religious pilgrimage site. The thesis investigates the idea that that the process of landscape extends not only across space but also across time – that the concept of historical continuity and the individual and collective human engagement and experience of this continuity are central to the processes of remembering on the landscape. In addition the thesis debates the idea that the production of landscape is conditioned by several social frames of memory – that individuals remember according to several social frames that give emphasis to different aspects of the reality of human experience. The thesis also reflects on how the process of landscape is represented by those who re-produce its narratives in various media.

Lost in Translation, book review of Urban Landscape Perspectives

In Sofia Coppola's 2003 film Lost in Translation, Bill Murray and Scarlett Johansson's characters find themselves culturally stranded and oddly mismatched as an improvised tourist couple in contemporary Tokyo. This is an urban landscape that they cannot comprehend but only temporarily experience, in a fragmented and surreptitious way that allows no possible understanding and categorizations, but offers physical inclusion, emotional participation and momentary embeddedness.

Prehistoric Pinus woodland dynamics in an upland landscape in northern Scotland: the roles of climate change and human impact

Pollen, microscopic charcoal, palaeohydrological and dendrochronological analyses are applied to a radiocarbon and tephrochronologically dated mid Holocene (ca. 8500–3000 cal B.P.) peat sequence with abundant fossil Pinus (pine) wood. The Pinus populations on peat fluctuated considerably over the period in question. Colonisation by Pinus from ca. 7900–7600 cal B.P. appears to have had no specific environmental trigger; it was probably determined by the rate of migration from particular populations. The second phase, at ca. 5000–4400 cal B.P., was facilitated by anthropogenic interference that reduced competition from other trees. The pollen record shows two Pinus declines. The first at ca. 6200–5500 cal B.P. was caused by a series of rapid and frequent climatic shifts. The second, the so-called pine decline, was very gradual (ca. 4200–3300 cal B.P.) at Loch Farlary and may not have been related to climate change as is often supposed. Low intensity but sustained grazing pressures were more important. Throughout the mid Holocene, the frequency and intensity of burning in these open Pinus–Calluna woods were probably highly sensitive to hydrological (climatic) change. Axe marks on several trees are related to the mid to late Bronze Age, i.e., long after the trees had died.

“Islands” in Holocene forests: implications for forest openness, landscape clearance and “culture-steppe” species

Human activity has undoubtedly had a major impact on Holocene forested ecosystems, with the concurrent expansion of plants and animals associated with cleared landscapes and pasture, also known as 'culture-steppe'. However, this anthropogenic perspective may have underestimated the contribution of autogenic disturbance (e.g. wind-throw, fire), or a mixture of autogenic and anthropogenic processes, within early Holocene forests. Entomologists have long argued that the north European primary forest was probably similar in structure to pasture woodland. This idea has received support from the conservation biologist Frans Vera, who has recently strongly argued that the role of large herbivores in maintaining open forests in the primeval landscapes of Europe has been seriously underestimated. This paper reviews this debate from a fossil invertebrate perspective and looks at several early Holocene insect assemblages. Although wood taxa are indeed important during this period, species typical of open areas and grassland and dung beetles, usually associated with the dung of grazing animals, are persistent presences in many early woodland faunas. We also suggest that fire and other natural disturbance agents appear to have played an important ecological role in some of these forests, maintaining open areas and creating open vegetation islands within these systems. More work, however, is required to ascertain the role of grazing animals, but we conclude that fossil insects have a significant contribution to make to this debate. This evidence has fundamental implications in terms of how the palaeoecological record is interpreted, particularly by environmental archaeologists and palaeoecologists who may be more interested in identifying human-environment interactions rather than the ecological processes which may be preserved within palaeoecological records.