Search Rutherford Discovery Fellowship awards 2010–2017

Public Summary: The astral sciences in the Indian subcontinent---that is, mathematics, astronomy, and related disciplines---have been flourishing for over two and a half millennia, and this culture of inquiry has produced insights and techniques that are central to many of our scientific practices today, such as the base ten decimal place value system and trigonometry. Indeed, many of their technical procedures, such as infinite series expansions for various mathematical relations predated those that were developed with the advent of the Calculus, but notably in contrasting intellectual circumstances with distinctly different epistemic priorities. However, while many histories of science have centered on the so-called `western miracle' in their analysis of the ignition and flourishing of modern science, they have done so at the expense of other non-European traditions. Yet these traditions can provide some powerful contrasts and cross-cultural comparisons for our attempts to delineate and illuminate the scope of scientific activity more broadly. This comprehensive and far reaching research programme aims to rectify this disparity by bringing more prominently into the mainstream key perspectives, features, and themes of this important, yet understudied, tradition of scientific inquiry.
Accounting for India's past in social sciences has always been influenced to some extent by `Indian Exceptionalism', that is, the conviction that India can be accounted for only on its own special terms, and this sentiment has pervaded modern traditions of social and historical studies with some notable consequences. This is particularly pertinent in approaching its scientific tradition, as science is frequently championed as universalistic and transcendent of culture. However, the Indian tradition emblematises how intellectual demands, context, and ambient social circumstances can distinctly shape the goals and priorities of an active scientific culture of inquiry, with ramifications for how we shape our efforts to document this tradition, as well as approach other important scientific contexts in Eurasia. By a comprehensive survey of Sanskrit scientific primary source material, careful textual analyses of key hitherto unexamined works and artifacts, and contextual synthesising studies in light of these analyses, this research program will contribute to developing our understanding of the features and themes of the astral sciences in India, and its connections more broadly in the history of science.

Public Summary: We intend to synthesize novel nanostructured materials and build devices for solar cells and LEDs. Nanostructured materials such as quantum dots, semiconductor nanocrystals, metal clusters and ammonium metal halide perovskites have been the focus of intense research over the last five years for their unique light absorbing properties and their ability to be deposited by solution rather than vacuum processes. Recent reports have indicated the feasibility, for the first time, of using solution-deposited nanomaterials in commercial solar cells, replacing traditional semiconductors such as polycrystalline silicon and newer thin films materials like lead telluride or conductive polymers. This should allow cheaper, greener nanomaterials to be used for energy generation instead of toxic, rare or energy intensive minerals traditionally used in these applications. Furthermore, there remain many fundemental questions about how light harvesting, charge generation and charge transport occur in different target classes of nanomaterials. Using the unique spectroscopic, electronic and materials characterization techniques available at VUW, I believe we can measure many of these processes and develop models for understanding how these materials, and devices based on them, work. This should enable us to develop novel nanostructured materials aimed at improving the efficiency of optoelectronic devices such as solar cells and LEDs. As a new faculty member at VUW, I am hoping to use this fellowship to improve the understanding of how materials function at the nanoscale, as well as develop novel device architectures. In doing so, I hope to be able to make major discoveries in a fast moving and high impact field. I believe this research program will eventually help mark New Zealand as a great place to do world-class technology research and a leader in the global research community.

Public Summary: Evolutionary analysis of large molecular sequence data is widely employed throughout modern biology, medicine, and pharmacology. Thanks to next generation sequencing technologies, thousands of whole genome sequences are constantly produced at low cost. Today's computational methods and technologies are barely prepared to analyze the big omics data and answer basic biological questions in a statistically sound way. As a result many big data sets are analyzed with simple and inappropriate models, or using approximations that may produce inaccurate inferences. The roots of the problem lie in our lack of understanding of fundamental mathematical principles that form the grounds for evolutionary analysis of omics data. Many recent breakthroughs in computational biology were made possible due to mathematical advances. Previously unimagined fields of applied mathematics such as mathematical oncology are currently being developed to help clinicians make diagnostic and treatment decisions based on quantitatively justified verifiable grounds. More and more healthcare institutions are hiring mathematicians and computer scientists to deal with the problems arising in these areas. The pressing need to develop effective computational methods that can accurately analyze big omics data under appropriately complex evolutionary models constantly requires new algorithmic ideas as well as solutions of standing computational challenges. The ever-accelerating pace at which genomic, transcriptomic, and proteomic data is produced in the modern world makes it impractical to rerun all analyses every time new data arrives or existing data is refined. The need to rerun the same analysis over and over again with slightly different data is a fundamental reason why inaccurate and often unreliable heuristics are favored over statistically sound methods. This motivates research on so-called 'online' computational biology algorithms capable of integrating new data as it appears. In this research program we will develop mathematical, statistical, and computational machinery for evolutionary analysis of omics data, with a specific focus of enabling such online algorithms. We will apply methods from modern branches of computational geometry, data science, and computer science to enhance statistical and computational performance of evolutionary approaches used in infectious disease and cancer research, ecology, and pharmacology. Specifically, we will develop efficient online methods and algorithms for several classes of inference problems that arise in evolutionary biology. The possibility and potential of such methods is already clear to the computational biology society, so there will be no lack of support from the community. In return, we will implement our methods in openly distributed software packages useful for the wide community of evolutionary scientists.

Public Summary: Ocean acidification is caused by the increased absorption of human-derived atmospheric CO2 by the oceans and is a major global threat to marine life. Ocean acidification results in elevated seawater CO2 concentrations and reduced pH, which negatively impacts the growth and internal chemistry of many marine species. Coralline algae are calcifying red seaweed, which are ecologically important organisms that create and bind together rocky reefs throughout New Zealand and globally. They also act as a nursery for species important to New Zealand fisheries, such as sea urchins and abalone. Because of their highly soluble calcium carbonate skeletons, there is a prevailing view that coralline algae will be among the species most at risk from ocean acidification. Here I challenge this idea, as certain species or populations could have greater tolerance to ocean acidification. It is unknown why some coralline algae are more affected by ocean acidification than others. My aim is to investigate whether tolerance to ocean acidification is due to physiological or environmental factors. I hypothesize that certain species have the physiological machinery to cope with ocean acidification by elevating pH within their skeleton while they grow. I also hypothesize that populations and species which have evolved in more variable pH environments will have greater tolerance to ocean acidification. My research will use state-of-the-art geochemical techniques, in-depth physiological assessments, and multi-generational laboratory experiments to determine exactly how physiological and environmental controls impart tolerance to ocean acidification in multiple coralline algal species. Coralline algae can encounter large daily shifts in pH when they co-exist with fleshy macroalgae. New Zealand kelp forests are a common habitat for coralline algae, but are also amongst the most variable pH environments known to science. Macroalgal photosynthesis during the day can drive pH far above ambient levels due to CO2 uptake, while respiration of CO2 at night can reduce pH below levels commonly expected to occur by the end of the 21st century due to ocean acidification. It is well known that marine organisms from environments with greater variability in temperature often have enhanced thermal tolerance. However, we do not know whether similar frequent exposure to low pH at night increases tolerance to ocean acidification in organisms from kelp forest habitats. I hypothesize that pH and other changing conditions within these habitats will either exacerbate or ameliorate the impacts of ocean acidification. This project will also determine if any tolerance to ocean acidification is maintained after successive generations in constant conditions. This will establish if tolerance is due to local adaptation, acclimation, or both. These findings will greatly enhance understanding of how climate change will impact coralline algae, and hence future rocky reefs. It will also enable us to understand if kelp forest habitats will protected resident organisms from ocean acidification, or harbour more tolerant populations. The outcomes of this research programme will aid in planning for shallow reef systems in the years to come.

Public Summary: The development of next-generation sequencing technologies over the past decade has revolutionised genetic testing of high-risk cancer patients in a diagnostic setting. These technologies now offer increasingly affordable and more powerful approaches for obtaining detailed genetic information. In genomic medicine, this information is used to direct clinical care of patients and their families and has significant implications for disease prevention. While genomic technologies offer great potential to transform clinical care, they also present future challenges for patients and their doctors. Deciding who should receive genetic testing, and interpreting the test results, are two major dilemmas for health care professionals. This proposal aims to address these issues by building on the experience gathered from two decades of testing for mutations in high-risk breast and ovarian cancer families. The importance of identifying individuals in these families with clinically relevant mutations in genes, such as BRCA1 and BRCA2, has led to large international research initiatives that augment current diagnostic practices. The new knowledge and expertise derived from this proposal will facilitate the development of genomic-based protocols to evaluate genetic changes responsible for other inherited diseases. Routine diagnostic BRCA1 and BRCA2 gene screening for deleterious mutations is typically performed for individuals from suspected high-risk breast-ovarian cancer families to identify the genetic cause for their disease. However, for most women with breast and ovarian cancer, the genetic changes contributing to their disease remain poorly understood. Furthermore, most people within our population at high-risk of inherited breast/ovarian cancer remain unidentified. High-throughput genomic technologies are being adopted by diagnostic laboratories worldwide, enabling mutation screening of BRCA1 and BRCA2, and other cancer related genes in a greater number of people. Determining the clinical meaning of newly discovered genetic changes will be a central challenge facing the future of genomic medicine worldwide. In 2013, Dr Walker initiated The New Zealand Familial Breast Cancer Study (NZFBCS) to address these issues in collaboration with large international consortia. Dr Walker will use this important initiative to build a world-class training environment for the next-generation of researchers working at the frontiers of genomic medicine. Through the NZFBCS, we will collect, expertly curate and disseminate genetic test results, thus providing transformative health care information to patients and their doctors. My laboratory will also pioneer new technologies for evaluating the clinical significance of genetic changes and assess their utility in a diagnostic setting. By exploiting collaborative links with huge international studies, I will be uniquely positioned to discover new genes that are associated with breast cancer risk utilising tens of thousands of patient samples. Medical genomics is an exciting and important research area that is developing at a rapid pace. Through established connections with genomic resources and cancer experts, nationally and internationally, my research team will revolutionise the utility of genomic technologies in a diagnostic setting. Furthermore, we expect to identify clinically significant genetic changes and are well positioned to guide the translation of these markers into medical care, providing life-saving information to patients and their families.

Public Summary: Cosmology is the ultimate 'big picture' science, aiming to study how the Universe began and how it evolved over time. Previously a theoretical subject, in the current era of ever-improving instruments we are starting to have the observational tools to put strong constraints on cosmological models. One key question is how the Universe evolved from its initial disordered state after the Big Bang into the highly ordered structure that we see around us today. Both observations and computational simulations support the idea that small over-dense regions gradually accumulated matter from their surroundings via gravitational attraction; some of the resulting, massive structures also collided in more violent merger events. The culmination of this process (to date) is the emergence of galaxy clusters – the largest gravitationally bound structures in the Universe. Their distribution in space, time and mass is uniquely sensitive to the cosmological parameters determining the evolution of structure in the Universe. In spite of their special status for tracing structure formation, use of clusters for cosmology is currently limited by our incomplete understanding of the physical processes that shape them. Galaxy clusters are made up of dark matter (~90%), hot intracluster gas (~10%), and galaxies (<1%). They can be observed in different ways – all of the mass via gravitational lensing; the hot gas via X-ray emission and via its interaction (the Sunyaev-Zel'dovich, SZ, effect) with the leftover radiation from the Big Bang; and the galaxies directly. The difficulty in each case is in translating the observable quantity seen on the sky to the physical quantities of interest for cosmological analyses, in particular mass. The SZ effect, visible in the radio waveband, is a particularly promising method for observing clusters since simulations predict a very tight correlation between the observable signal and mass. However, current models for translating the SZ observable to mass are over-simplistic and do not account for the disturbed structure of clusters undergoing merger events, leading to unquantifiable biases when cluster surveys are used as cosmological probes. My research aims to further our understanding of galaxy clusters with the goal of realising their potential as cosmological probes. I will use the current generation of radio telescopes to identify and observe merging clusters, and explore robust methods to model their SZ signal. In conjunction with gravitational lensing data and numerical simulations, I will investigate how to accurately translate their SZ signal into mass constraints. An exciting new era in galaxy cluster science is approaching, with instruments such as the Square Kilometre Array (SKA) radio telescope, scheduled to begin early science in 2020, as well as the eROSITA (2017) and Athena (2028) X-ray satellites, the LSST (2023) ground-based optical telescope and Euclid (2020) near-infrared satellite. Orders of magnitude more clusters will be detected, at unprecedented resolution. I will use simulations to prepare analysis techniques for SZ data arriving from the SKA, and explore synergies with the complementary instruments at other wavebands, ensuring optimal information recovery from these next-generation instruments.

Public Summary: Health education is frequently collapsed or confused with health promotion. In education settings, this results in work that tends to focus narrowly on physical activity and nutrition. Short-term behavioural interventions in schools are common, albeit regularly both unsuccessful and unstainable. Youth perspectives are almost entirely absent, as are sophisticated sociological analyses of how health knowledge is developed and applied. Understanding how contemporary youth cultures, location, ethnicity, sexuality and gender influence youth health decision-making is crucial, as is the role of schools as the official (but by no means only) arbitrators of health knowledge. This is becoming more urgent with the advent of new technologies, which allow both greater access to information and greater potential for monitoring individual and population-based health data within increasingly complex social and emotional environments. Youth from low socioeconomic communities have the least access to resources that sustain good health and yet also study health education in New Zealand (NZ) schools in unprecedented numbers. NZ is unique internationally in offering health education as a formal senior school subject for national qualifications (NCEA). This subject is chosen in years 11-13 (15-18 years of age) by disproportionate numbers of low SES youth, some who attend schools with dedicated health science academies (focused on health-related studies and careers). A new approach is needed in order to understand the complexities of youth health issues in education and how health knowledge is developed and applied by NZ youth. My research programme extends current research in four significant ways. First, it includes in-depth long-term analyses of how low SES youth develop forms of ‘health capital’ (aptitudes, skills and knowledge for health). I am re-defining this term from its previous economistic roots and using it sociologically to understand youth health from a strengths-based and contextualised perspective. In so doing, I take an entirely novel approach to the field by combining the disciplines of health sociology, health literacy, salutogenesis (wellbeing), positive psychology, physical education, and critical education to better understand the potential for diverse youth to enhance health-related decisions. Second, my research programme is transdisciplinary, engaging across disciplinary boundaries with respect to major issues of public health, non-communicable diseases, and school and community based health education. Third, my work is theoretically novel. I draw on the social theories of post-structuralist scholars such as Bourdieu, Foucault and Deleuze, combining these with feminist social geography, and post-colonial theory to create nuanced and complex analyses of youth health within particular social and geographical contexts. This approach allows for health issues to be interrogated in new ways, particularly with respect to the limits of interventionist public health initiatives. The aim is to move the field on from current narrow definitions of health (and short term interventions) toward more holistic, located and youth-centred approaches to health problems. Fourth, my work is highly innovative methodologically, combining both quantitative and qualitative analyses, with the latter including critical ethnographic methods with youth participatory, digital and visual (photo) methods so as to elucidate young people’s perspectives and experiences in new ways.

Public Summary: There are no longer any ecosystems on Earth that are untouched by human influence. Global environmental changes threaten biodiversity, but their effects on the networks of interactions connecting all living organisms are largely unknown. The structure of these networks can affect ecosystem stability, but it is not clear whether this structure arises through traits of the species within the network, or through environmental forces (such as habitat structures or available resources) that affect how species interact with one another. Furthermore, it remains opaque how traits of species, and their arrangement within the network, may affect the functions that species perform in ecosystems, e.g., pollination of crops and wild plants, or dispersal of seeds during forest regeneration. Using analyses of global datasets, combined with a field study in the unique Franz Josef chronosequence, we will: 1) determine whether network structure is driven by key species and their traits or by environmental forces, or both; 2) incorporate traits of species into network analyses to provide a direct link between network structure and ecosystem functioning; 3) examine how ecological networks break down under the stress of a changing environment; and 4) determine the elements of network structure that provide stability during this decay.

Public Summary: This research program aims to improve the understanding of stem cell regulation, which is vital to unlocking the full potential of stem cells as therapeutics and to understand their involvement in cancer. To achieve this, we will investigate signals acting on stem cells in culture, as poor control over cultured stem cells is the main barrier limiting their use in therapy and tissue engineering. Before use in patients, stem cells must be multiplied and often need to be differentiated, to ensure sufficient number of cells and to avoid tumour formation. In our bodies, the environment around cells is vastly different to that in a cell culture dish. Cellular behaviour is tightly regulated through many coupled factors, including signalling molecules and mechanical properties of the surrounding tissue. By studying cells in the laboratory, it is possible to separate the effects so that we can understand their individual and synergistic contributions to certain cellular behaviours. However, it is technically challenging to investigate these effects. This proposal will develop novel substrates that can investigate specific signals called growth factors, which are important to stem cell differentiation, and their synergy with cell adhesion. The growth factors will be encapsulated in such a way that cells have to pull on the substrate with a certain force to release them. This mimics the behaviour in our tissues, where cells have to release these potent molecules by degrading their surroundings. These novel substrates will be produced using self-assembly of block copolymers, which can form amazing nanoscale patterns spontaneously. This occurs as the polymer has two very different components, which would normally not mix. By linking these components covalently, a phase separation on the nanoscale occurs. By mixing the active molecules in the polymer solution and allowing the formation of a self-assembled thin film, they become encapsulated in molecular vessels. These vessels will be equipped with ‘lids’ that adhering cells can pull on to release the growth factors. As growth factors have been shown to act close to cell adhesion points, this mode of presentation is expected to reveal synergistic effects between cell adhesion force and growth factor signalling.

Public Summary: Destructive mega-thrust earthquakes, such as the 2011 Tohoku-oki earthquake in Japan, occur at subduction zones where one tectonic plate slides under the other. At the Hikurangi subduction zone beneath the North Island of New Zealand, the Pacific Plate thrusts downward and westward at a speed of ~4 cm per year. Two decades of geodetic monitoring has revealed that the large portion of the Hikurangi plate interface (i.e., the fault between the two tectonic plates) is currently locked, implying that stress is building up for the next large mega-thrust earthquake. However, there is a dramatic variation in the degree of locking, with the locked portion extending much deeper in the southern North Island than further to the northeast, potentially marking a limit on the growth of mega-thrust earthquakes. Observed ~100-km wide ‘slow slip’ events, that is, earthquake-free slip episodes that can involve displacements on the mega-thrust of more than 40 cm, are also shallower towards the northeast. Similar spatial variability in mega-thrust slip behaviour has been observed at many other Pacific-Rim subduction zones including Japan, Alaska, Sumatra, Costa Rica, Peru, Chile, and Cascadia (North America). Yet, the mechanism controlling the variability in fault slip behaviour at Hikurangi, as well as at other subduction zones, is not well understood. Using a state-of-the-art seismic imaging technique and long-term deformation models, combined with existing and new seismic datasets and research expertise, this project will shed light on the underlying mechanism of complex mega-thrust slip behaviour at subduction plate boundaries. This work will develop a better understanding of physical processes responsible for the spectrum of observed fault slip in a region where the degree of plate locking changes abruptly. In particular, the project will: (i) image the fine-scale 3D structure and velocity anomalies near the Hikurangi subduction interface in unprecedented detail using the advanced full-wavefield inversion of seismic waveforms recorded from earthquakes; (ii) map out details of the structure and geometry of the Hikurangi mega-thrust region using improved earthquake locations; (iii) investigate the roles of softer rocks and fluids, likely confined near the plate interface, on observed variability in mega-thrust slip behaviour; (iv) develop dynamic models of earthquake-cycle deformation with the parameters constrained by the inferred physical and mechanical properties, in order to reproduce time-dependent geodetic observations; and (v) examine the importance of observed ‘slow slip’ events in relation to the generation of nearby large mega-thrust earthquakes. Given the coverage of existing and proposed seismometer networks, well-recorded earthquakes, and the shallowness (12-25 km depth) of the subduction interface beneath the network, the Hikurangi region offers a unique opportunity for seismic imaging of the detailed material properties in the plate-locking ‘transition zone’. Well-resolved structural and material properties combined with physics-based models of earthquake-cycle deformation will provide critical insights needed to answer the globally significant question: what controls the spatial variation of mega-thrust slip behaviour and the spatial extent of large subduction earthquakes.