VictorJuiz/thesis huggingface dataset:
Predation in the Cambrian

Although predation has been suggested repeatedly as a force shaping the diversification of animals during the Cambrian period, studies of the evolutionary dynamics of predation are lacking from this time period. Radiodonta, the largest Cambrian nektonic animals, and repaired injuries on trilobites, a diverse and disparate group of prey animals, provide study systems to assess predation dynamics at this time. Radiodont fossils were first discovered over 100 years ago, but are now known worldwide from early Palaeozoic deposits which preserve soft-bodied material. Intense research on radiodonts from the Chengjiang biota (China) and Burgess Shale (Canada) since 2009 recently greatly improved our knowledge of the group, outdating previous interpretations of USA specimens, which are needed for large-scale analyses. Anecdotal reports of repaired injuries on trilobites are common in the literature, but quantitative studies on the role of morphology, behaviour, or geography have not been conducted.
I restudied radiodonts from the USA, placed them into an up to date taxonomic and taphonomic context, and revealed that these deposits hold a much higher diversity and disparity than previously reported. Findings include the first and last appearances of a number of families worldwide, and eight taxa not known from any other deposit. I used this new data to undertake the most comprehensive phylogenetic analysis and the first diversity and disparity analyses of Radiodonta, which showed two phases of evolution in the group, and that the ancestral radiodont was likely not a raptorial predator. I also performed the first quantitative measurements of predation pressure on trilobites, showing that morphology, geography, and behaviour, effect on the location and frequency of repaired injuries. These results suggest that predation pressure was a complex and changeable ecological influencing the early evolution of animals.

Advisor: Holland, P
Daley, A
V.S. Naipaul, Caribbean writing, and Caribbean thought in the postcolonial era 1960-1995

This thesis examines the position of V.S. Naipaul within the intellectual history of the postcolonial Caribbean. First, it argues that throughout his career Naipaul’s work has been shaped by the influence, and discursive provocation, of other Caribbean intellectuals. Secondly, it argues that the writings of these other Caribbean intellectuals emerged as part of a dialogue with the oeuvre of V.S. Naipaul. Reading Naipaul in dialogue with his Caribbean intertexts not only provides a new lens for understanding Naipaul’s work, but also provides new insights into the work of writers such as C.L.R. James, George Lamming, Kamau Brathwaite, Sylvia Wynter, Maryse Condé, and David Scott.
The (roughly) three decades following constitutional independence in the major Anglophone Caribbean territories were a time of political upheaval and literary innovation, in which the state of the region was being described, and the futures of its communities imagined, across a range of written forms and using different scholarly methodologies. Within this intellectual culture, stylistic, generic, and formal choices were invested with great polemical significance. This thesis is structured in three chapters, examining the significance of Naipaul’s work within three formal traditions: the novel and theories of the novel, historical writing and historiographical theory, and travel writing.
Across these three forms, I trace a developing preoccupation with the social history of colonialism in the Caribbean and its impact on the intellectual and imaginative horizons of postcolonial Caribbean thinkers. Further, I show how in this period Caribbean writers tried to articulate the specificity of Caribbean colonial experience in contrast to the colonial experiences of other parts of the world (especially Africa). Throughout, I aim to show that attention to the literary history of the Caribbean, to the evolution of stylistic and formal thought and innovation, is essential to understanding the broader intellectual history of the region.
Study of the dynamics of gene expression by mathematical modelling and systems approaches

Transcription by RNA Polymerase II (RNA PolII) is a fundamental process at the heart of gene expression, defining the phenotypes of cells. Transcription of genes does not exist in isolation, but occurs through a complex environment of DNA wrapped around chromatin, with many factors affecting the surrounding environment and association with the polymerase. The process of transcription is more complex than perhaps originally thought, with a number of factors affecting individual steps of the process of reading the DNA template. Rather than thinking of a gene as simply being on or off, the expression of a gene is regulated and fine-tuned by the modifications to the chromatin landscape, cross-talk between the chromatin and the elongation complex, pervasive non-coding transcription and the association of factors with the polymerase. By developing mathematical models of the transcription and RNA processing networks, we determine the effects of these factors on establishing the dynamics of native gene expression. Constructing best-fit models and identifying key parameters which dictate the changes to quantitative data upon genetic intervention, we identify a feedback mechanism to accommodate for changes in the rates of transcript production and polymerase stalling as a predictor of the processivity of individual genes. A number of factors are shown to control the speed and processivity of polymerase in Saccharomyces cerevisiae and HeLa cells, establishing a network of cooperative and antagonistic interactions with the RNA PolII complex. This work suggests that the dynamics of transcription are gene-specific, with the chromatin landscape and the polymerase-associating factors unique to each locus in the mammalian genome.

Advisor: Angel, A
Mellor, J
The role of Anglo-Saxon great hall complexes in Kingdom formation, in comparison and in context, AD500-750

The aim of this thesis is to explain why the early Anglo-Saxon great hall complexes were built, why and how they developed over time and why they were abandoned.
This is accomplished through two complementary studies. First, Part I of the thesis (Chapters 2-3) presents a broad comparative study of all known great hall complexes, exploring their characteristics, functions and development over time. Then, Part II (Chapters 4-8) explores the regional context of great hall complexes in the Upper Thames Valley, analysing the development of socio-economic power in the burials and settlements of the Upper Thames Valley and exploring the role of great hall complexes in this development. Chapters 8-9 bring together the conclusions from Part I and II of the thesis, building a comprehensive chronological narrative of the emergence, development and obsolescence of great hall complexes.
In the course of these two studies, this thesis finds substantial and wide-ranging evidence for a chronological development of great hall complexes, paralleling and contributing to the development of a new elite ideology and the consolidation of the newly formed Anglo-Saxon kingdoms.
The great hall complexes appear to have emerged out of the appropriation and monumentalisation of the public assembly, but as the Anglo-Saxon kings became increasingly powerful, the great hall complexes appear to have become increasingly exclusionary, shifting from public assemblies to private royal residences. At the same time, the great hall complexes appear to have become increasingly diverse, fracturing into a range of different high status sites. The combination of these two processes – the shift from public assemblies to private residences and the development of more complex settlement hierarchies – appears to have precipitated the separation of the elite from the wider populace, consolidating the new power structures of the Anglo-Saxon kingdoms and rendering the great hall complexes obsolete.

Advisor: Hamerow, H
Getting ‘the feel’: craft learning as perceptual transformation

Becoming a wooden boat builder requires ‘getting the feel’ for the tools and materials of the trade by learning to perceive these objects in terms of their practical purposes in the workshop. In this project, I explore such learning from a sensory-ethnographic perspective, journaling how my own perceptual experience transforms over six months of work building boats. To supplement this first-person method, I carry out participant observations and long-form interviews with boat builders, paying particular attention to the ways in which newcomers to the workshop are guided through the learning process. I interpret the rich accounts of learning that result through concepts from philosophy, exploring how the perception that I record can be seen to demonstrate a fundamental mode of human understanding. Using Heidegger’s idea of ‘being-in-the-world’, I show how learning entails a constant re-alignment of understanding through which individuals continually rediscover their human capacity for meaning-making. By investigating the link between perception and understanding in the craft workshop, I contribute to theoretical debates over the nature of human cognition while also illuminating the complex and often-overlooked cognitive processes that underpin practical work.

My findings show how ‘getting the feel’ entails learning to perceive practical objects in new ways, recognising aspects of tools and materials that are invisible to the unaccustomed viewer. In some cases, ‘the feel’ involves specific combinations of objects appearing together in terms of work that they perform, rather than separately as discrete entities. In other cases, it entails tools and materials appearing to transform, splitting apart or combining in perception as their defining practices demand. Throughout the investigation, I show how understanding varies between the three workshops, and how each contains its own mechanisms for introducing the newcomer to situated ways of seeing and feeling. Despite their differences, however, the workshops share three main modes of learning: self-motivated exploration, expert guidance, and participation in a community designed to reproduce the skills and understanding it requires of its future members. By continually participating in each of these three modes, boat builders accumulate expertise as they move between settings and progress within them, ‘getting the feel’ for gradually-shifting constellations of materials, people, and practices.

Keywords: carpentry
learning
education
phenomenology
craft
Heidegger
perception
boats
Advisor: Relly, S
Oancea, A
Know what? New lenses on productive knowledge shed light on long run development, structural change, job switching and the transition to the green economy

Tracing back to Adam Smith, scholars have emphasised the importance of knowledge and its profound implications for prosperity. However, measuring and analysing something as intangible and multifaceted as the knowledge collectively held and used within society has, not surprisingly, proved challenging.
This thesis advances quantitative empirical approaches for analysing productive knowledge within socio-economic systems and applies these methodologies to shed new light on (i) long run regional development and structural change (ii) labour market segregation and job switching, and (iii) the transition to the green economy.
This thesis shows that across a range of different contexts, from US regional development in the 19th century to modern-day labour markets, what places and people know matters. Measuring the type of knowledge concentrated in US states sheds new light on structural change, the decline of rust-belt states, and the reversal of patterns in income convergence. Similarly, measuring the type of knowledge held by individual workers in different occupations provides new insights on the division of labour, job transitions and future career prospects. Moreover, measuring the type of knowledge embedded within countries turns out to be particularly informative of a nation’s likelihood of success in the green economy – and its potential for green diversification in the future.
This thesis also reveals distinct segregation in societal knowledge across places and people. Such divisions could matter more than we realise. For example, the segregation of productive knowledge across US states could play a role in undermining the nation’s capacity for inclusive growth. The segregation of skills and productive capabilities across the US labour force could exacerbate the distributional consequences of labour market shocks. And moreover, the segregation across nations’ capacities to both participate and benefit from the transition to the green economy could slow or even create barriers to progressing one of the most important socio-economic transitions of our time. While this thesis has advanced new ways to identify these divisions in knowledge, further work is required to better understand their implications -- and what can be done.
Finally, this thesis suggests that future improvements in what places and people know will need to become less incremental and more transformational, if we are to successfully address the ‘twin challenges’ of poverty alleviation and climate change in the 21st century. Learning how to both navigate and drive the process of transformational change in productive capabilities could be the type of knowledge that matters more than anything else.

Keywords: structural change
green economy
economic complexity
job transitions
knowledge
Advisor: Farmer, J
Hepburn, C
Does not compute: social dissonance in England's computing education policy

The new computing component of England’s National Curriculum was promoted as an effective and egalitarian way to provide young people with the skills, knowledge, and ways of thinking necessary to participate in an increasingly digitalised world, both as citizens and as potential tech entrepreneurs or computer scientists. What policymakers did not adequately account for was how state schools would interpret this new policy, the impact it might realistically have on young people’s relationship with modern digital technologies, and whether there might be a mismatch between the pro-technology narratives represented in this curriculum and the everyday beliefs and experiences of teachers and young families.
England is at an important turning point as it haltingly transitions from its manufacturing roots to a digitalised knowledge society, with a growing nostalgia for its former position as an imperialistic power of world-leading technological advancement. Through this study I will unveil the power relationships and shared socio-cultural knowledge behind the computing education policy’s creation and its implementation. I will do this by answering the following research questions: 1) How are teachers translating the computing education policy into practice and why? 2) In what ways are the computing education policy influencing students' understanding of and disposition towards digital technology and why? and 3) What does the computing education policy – and teachers’ and students’ response to it – say about the incongruity between public policy around digital technology and people’s real-world experiences and understandings of it?
Using teacher interviews, student writing and drawings, student interviews, extensive classroom observations, and policy analysis, this ethnographic case study of four primary school classrooms in the South of England will examine how the addition of computing to England’s National Curriculum came to pass and why it is not meeting its stated goals, before discussing what this means about past assumptions and future possibilities for young people’s engagement with and understanding of modern digital technologies in formal education settings. My study contributes a unique perspective of a single education policy as it passes through three different stages in its development and implementation, encountering and being shaped by the beliefs and values of several groups along the way. The results of this study inform our understanding of how power relationships function to define a policy’s purpose and value across different settings, demonstrating how the power to define equates to the power to shape reality.

Keywords: digital skills
Michel Foucault
computing education
educational policy
primary school
England
Advisor: Eynon, R
Winters, N
Applications of electronic structure theory in electron microscopy

Furthering the integration of theoretical and computational electronic structure methods with electron microscopy techniques is the overarch- ing theme of this thesis. In this work, theoretical and computational tools are developed and applied to several specific experimental problems in electron microscopy.
Hartree-Fock theory is combined with methods for calculating damped dispersion and short-range correlation energies and used to calculate the blue shift in the 1s2 → 1s2p(1P) excitation energy as a function of the density of confined helium atoms under extreme pressures. This is then compared to existing electron energy loss spectroscopy measurements on these systems. We find that, though the trends vary widely between different experiments, our theoretical predictions do not match very closely with any of them. We conclude that this is due either to the difficulty of the experimental technique or physical effects that are not accounted for in our model or the interpretation of the data.
A general approach for obtaining projected electrostatic potentials from pseudopotential plane wave (PPW) density functional theory (DFT) is presented in detail. Projected potentials are the crucial physical quantity of interest in the simulation of (scanning) transmission electron microscopy ((S)TEM) images, and the incorporation of more accurate electronic structure theory into the calculation of these potentials improves the accuracy of (S)TEM simulations. A novel solution to the problems arising in handling the singularities due to nuclei in the projected potentials is also presented and shown to improve the precision of image simulations while simultaneously reducing the complexity of obtaining projected potentials from DFT for the user. Through its implementation in CASTEP, a PPW code, this method of obtaining projected potentials is then used to demonstrate the sensitivity of the experimental technique of (S)TEM ptychography to the electronic structure of monolayer hexagonal boron nitride.

Advisor: Nellist, P
Yates, J
Nicholls, R
Understanding drug resistance through computational models of the genotype-phenotype mapping

The emergence of drug resistance is ultimately driven by Darwinian evolution. These evolutionary dynamics are inherently two-tiered, with mutational processes at the genetic scale inducing variation in cellular phenotypes that are subject to natural selection. If we are to predict or reverse evolution, as we must to determine effective treatments for drug-resistant infections and cancers, then we must first understand the relationship between genetic and phenotypic change. This relationship, known as the genotype-phenotype (GP) mapping, is governed by a complex cascade of potentially stochastic molecular interactions that integrate genetic, epigenetic and environmental factors to determine cellular phenotype. In this thesis, we introduce abstract models of the GP-mapping to explore how its structure influences the evolution of drug resistance, and determines the efficacy of novel therapeutic strategies such as drug holidays or adaptive therapy. We begin by providing a comprehensive review of previous abstract modelling of the GP-mapping (Chapter 2). In Chapter 3, we demonstrate, by means of a fitness landscape model for the GP-mapping, that through careful selection of drug sequences evolution can be steered′sucht
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highlydrugresistantpopa̲tiondoes¬emer≥.InChapter4,we∫roduceanovelmodelfortheGP-mapπngwhere∈phe¬ypesaredeterminedbythes→ch∗icsiμlationofbistab≤chemicalreaction≠tworks(CRNs).Throughthismodelweexploretheevolutionarydynamicsofecologicalbet-hedging', a common driver of drug resistance wherein phenotypes are determined stochastically, demonstrating that the structure of the GP-mapping can slow the evolutionary loss of this trait, preserving the survival mechanism when harsh environments occur very infrequently. Thus, the capacity to steer the evolutionary loss of bet-hedging through drug holidays is dependent on the structure of the GP-map. In Chapter 5, the CRN model is extended to account for epigenetic inheritance and the potential for phenotypic memory in bet-hedging. Critically, we find that genetics, epigenetics and the GP-mapping interact non-additively to determine organismal fitness, indicating that evolution likely cannot be predicted without accounting for each of these biological processes. Finally, in Chapter 6, we explore how properties of the GP-mapping are manifested at the population scale and suggest experimental approaches to identify bet-hedging and phenotypic plasticity from population measurements. The implications of our results for the treatment of drug-resistant diseases are explored throughout.

Keywords: Evolution
Mathematical Modelling
Bet-hedging
Genotype-Phenotype mapping
Drug Resistance
Advisor: Jeavons, P
Anderson, A
Multicellular group formation in algae

The evolution of multicellular organisms from single cells has puzzled scientists for centuries. Separating this problem into smaller steps has been illuminating. The first step is multicellular group formation and the second is group transformation into an obligate multicellular entity where cells are fixed in a multicellular lifestyle and cannot reverse back to being single cells. Relatedness among cells is known to be fundamental in this major transition to an obligate lifestyle, but the role of ecology has not been addressed to such an extent. For instance, in the ecological literature, predation is known to induce defensive group formation in freshwater algae, and this has been mainly investigated as a means of harvesting algae. However, the role of algal predation in the context of multicellularity and social evolution has not been investigated as much. I use the freshwater algae Chlorella sorokiniana, Chlorella vulgaris, and Scenedesmus obliquus exposed to the predators Ochromonas, Tetrahymena thermophila, and Daphnia magna, to address why and how algae form multicellular groups. Answering why algae form groups helps us illuminate the costs and benefits involved in this cooperative behaviour. Answering how these algae form groups helps us understand whether these algae are likely to make a transition to obligate multicellularity, since we know that all obligate multicellular organisms have evolved via cells remaining stuck to their parent cell after division, not by cell aggregation. We found that these three algal species form multicellular groups in response to the three different predators, and in three predator-prey combinations this multicellular group formation was induced just by predator cues. These multicellular groups formed via aggregation of single cells and by cells remaining attached to the parent cell after division. Also, multicellular groups could form between different algal species. This group formation is costly under conditions of limited resources in C. sorokiniana, and provides a benefit in terms of avoiding ingestion by small predators, such as Ochromonos danica, but not by the larger predator D. magna. The benefit of multicellular group formation in the latter case may be that cells in multicellular groups are better able than single cells to kill their predator once they are ingested. Finally, this group formation is reversible. These results indicate that our system has not made a major transition to obligate multicellularity, but has made the first step of facultative multicellular group formation. This facultative feature of our system has therefore been ideal in allowing us to reveal the costs and benefits of multicellular group formation.

Keywords: group formation
ecology
algae
multicellularity
Daphnia
aggregates
predators
clumps
social evolution
Advisor: West, S