VictorJuiz/thesis huggingface dataset:
The anatomy of unbelief: a critical assessment of the cognitive science of (non)religion


A number of scholars of (non)religion and secularity have argued in recent years for the need to get beyond the neat binaries and the negative identities signalled by atheism and agnosticism (e.g., Taves, Asprem and Ihm 2018). However, these binaries are deeply ingrained in the landscape of ideas that have shaped the way we do scholarship.
In this thesis, I critically investigate the approach called cognitive science of religion (CSR), which Justin Barrett and Emily Burdett describe as "the scientific approach to the study of religion that combines methods and theory from cognitive, developmental and evolutionary psychology with the sorts of questions that animate anthropologists and historians of religion" developed to further the understanding of "the reasons for initial acquisition, recurrence, and continued transmission of religious concepts and behaviour" (2011: 252). My main focus is the way CSR defines and studies nonreligion. This work consists of the two moves: the deconstructive and the reconstructive. In the deconstructive part, I challenge the "C" (cognition) and the "R" (religion and nonreligion) models employed by this field. In the reconstructive part, I propose a biocultural approach that replaces the computational paradigm with 4E cognition theories, and the belief/ unbelief binary with material religion and secularisms.
One of the "umbrella" problems I focus on in this thesis is the issue of disembodiment that I have discovered to be central to the majority of the CSR approaches to nonreligion. Therefore, the word "anatomy" in the title of this thesis is meant to highlight the theoretical and methodological concern of my approach, which is focused on materialising the field of CSR. My focus on the "anatomy of unbelief" aims to challenge the current CSR approach by bringing the body and the culture back into the scientific study of nonreligion.

Keywords: embodied cognition
biocultural
nonreligion
material secularisms
CSR
cognitive science of religion
material religion
Advisor: McGrath, A
Leonora Carrington and Goliarda Sapienza: anarchic bodies

This thesis brings together two little-know figures in the history of 20th-century literature: Leonora Carrington (1917-2011) and Goliarda Sapienza (1924-1996). Building on recent academic and public interest in both women, this research offers a new perspective by reading their literary work outside of its immediate cultural context.
Despite their differences, Carrington and Sapienza encounter many of the same cultural phenomena, and they share a sense of embodied, individual resistance to institutional power. Restraint enters the works of both authors via the Catholic church, psychiatric treatment, gender norms, and the rigidity of written language. In addition to closely analysing these themes through the comparison of several key texts, this thesis has a broader scope of considering the roles of autobiography, embodiment, and gender in the expression of identity.
Both Carrington and Sapienza, I find, evoke a sense of limitlessness in their depiction of personal identity. This resistance to restraint is carried over into the methodological approach of this comparison, bringing Carrington away from her Surrealist label, and bringing Sapienza toward it, and therefore casting their work in a new light.

Keywords: embodiment
Goliarda Sapienza
surrealism
gender
Leonora Carrington
autobiography
Advisor: Marcus, L
Stellardi, G
Reynolds, M
Disability's cost and coasts in Mombasa, Kenya

This project tracks the intimate and social dimensions of disability in Mombasa to explore the impasses people with disabilities face, and how they navigate and transform constraints for and before survival. It details socio-historical conditions that figure disability as a cost showing how people with disabilities face impasses within four ethnographic sites: Africa’s largest disability school, constructed and managed by a cement company; a rehabilitation and education center for neurodevelopmental disabilities frequented by a Muslim minority of Indian descent; a “sheltered workshop” offering disability employment, housing, welfare, and activism; and itinerant sites an litigious insurgency group uses to lay claim on the sheltered workshop. Against these costs I highlights patterns of coasting, which are non-negative practices of living precipitated by, but irreducible to, these impasses. Coasting gestures to the ways people with disabilities work within, around, and at the limits of an impasse, movements made without wholly relying on power or resistance to what blocks the continuity of life. Four coasting patterns are detailed across the life course: drifting within institutional captivity, by which disabled children wander off from scenes of initiation and build other forms of life; brooding as a prospective orientation for parents charting paths around uncertainties; oblique mobility by which disability activists cunningly mobilize within development, state, and market discourses to open pathways and solidarities outside them; and insurgent motility which enables recurring aggressions against, and ingressions into, institutions that have disposed elderly people with disabilities and rendered them jobless and homeless.

Keywords: mobility studies
liminality
Africa
disability
(new) kinship
ritual studies
Advisor: Cousins, T
Pratten, D
Functional adaptation in Toll-like receptors of wild and domesticated animals

Animals sense their pathogens through detection of conserved pathogen-associated molecules by pattern-recognition receptors (PRRs). The best characterised family of PRRs is the Toll-like receptors. TLR subfamilies retain specificity for particular agonist classes over great evolutionary distances. This does not, however, mean that TLRs are evolutionarily static. TLRs, along with other pathogen-facing immune genes, frequently undergo directional selection to maintain leverage in the perpetual arms race between hosts and pathogens.
In this thesis, I argue that TLRs are critical determinants of disease susceptibility and resistance, and are therefore under strong selective pressures. To support this, I provide evidence of adaptive evolution operating over multiple nested timescales. For instance, I show that, even in the few thousand years since the domestication of chickens, TLRs have undergone adaptation, likely to better deal with higher pathogen loads in denser, commercialised populations. At the other extreme (hundreds of millions of years), I document the repurposing of the CpG-DNA-recognising TLR21 between fishes and birds, arguing that this compensated for the loss of the unrelated CpG-recognising TLR9 in the birds and reptiles.
To contextualise and reinforce my bioinformatic findings, I provide evidence from laboratory experiments to confirm changes in TLR function. For instance, I demon- strate that two positively selected sites in Gentoo penguin TLR5 are sufficient to change the responsiveness of the receptor to its agonist, flagellin. Furthermore, I demonstrate that the ancestor to the Eudyptes (crested) penguins had a cryptic pseu- dogene for TLR15 that was then overtly pseudogenised several independent times in the genus. Functional evidence was crucial in both of these conclusions, and neither could have been deduced from bioinformatic methods alone.
Taken together, this body of work provides several lines of evidence that TLRs are key targets for natural selection across multiple evolutionary scales, and that functional evidence plays an important role in interpreting bioinformatic predictions. In addition to contributing to the fundamental understanding of how hosts cope with changing pathogen landscapes, this work provides important information for conservation and sustainable food production.

Keywords: adaptive evolution
comparative immunology
Toll-like receptors
host-pathogen interactions
Advisor: Smith, A
Frantz, L
The role of cyclic nucleotide signalling in L. mexicana flagellar motility

Cyclic AMP (cAMP) is a ubiquitous conserved second messenger involved in diverse biological function across the Eukaryotic kingdom. Here we explore components of the divergent cAMP signalling pathway, including divergent protein kinase A (PKA), in the early diverging protozoan Leishmania mexicana, with an aim to understand how cAMP contributes to its canonical motile flagellum. While cAMP may transduce external signals, it is ultimately the regulation of dynein activity that determines the waveform. Therefore, we assessed the contribution of all 10 axonemal dyneins to gain a deeper understanding how each one contributes to L. mexicana waveforms. To tackle these aims, we used CRISPR-Cas9 gene deletion and endogenous fluorescent tagging combined with microscopy techniques to localise our proteins of interest and assess their contributions to flagellar wave shape and direction. We found that 24 of 35 putative cyclic nucleotide signalling components were present in the flagellum, notably in either the distal, proximal or entire axoneme. We identified cAMP at the flagellar tip serves as the main regulator of parasite swim speed. Sequence analysis, homology modelling and predicted cAMP docking suggested that only CARP1, firmly embedded in the flagellar cytoskeleton, binds cAMP via classical binding mechanisms. △CARP1 flagella demonstrated reduced beat frequencies and a higher propensity for ciliary beating. Moreover, we described the pairing preferences of PKAR1 with PKAC1/ PKAC2 in the flagellar cytoskeleton, and PKAR3 with PKAC3 to the cell body. Loss-of-function phenotypes showing distinct effects on motility with loss of PKAC1 being the most severe. Lastly, we found that the double headed axonemal dyneins were indispensable for cell displacement, however the single headed dyneins contributed more specifically to either beat frequency or amplitude. Ultimately, the findings of this thesis have systematically pinpointed the contributing components of the divergent cAMP signalling pathway to flagellar motility. What remains, is to unpick the mechanistic details of how CARP1 is interacting within its local axoneme environment to affect wave shape and direction of travel.

Keywords: second messenger signalling
flagellar motility regulation
Advisor: Gluenz, E
Fodor, E
Using local and indigenous ecological knowledge to examine local-scale perceptions, effects of, and resilience and adaptation to, climate change on human/landscape interactions on the Pacific coast of North America

The aims of this research were to investigate the perceptions and impacts of climate change on the ecological and cultural aspects of landscape through understanding local and Indigenous knowledge. Key cultural and ecological species were chosen for study by bridging Traditional Ecological Knowledge (TEK) and western scientific knowledge in a constructive, equitable, and practical way. These Cultural Keystone Indicator Species (CKIS) provide a novel and cross-culturally meaningful analytical framework for investigating the socio-ecological effects of environmental change.
In 2013 and 2014 I interviewed 96 resource users in 11 Indigenous communities in Northern British Columbia and Southeast Alaska. TEK data was collected on weather and landscape changes, resilience and adaptation techniques, and changes in biodiversity. I also reviewed the scientific and ethnoecological literature, and meteorological data. Three CKIS groups were chosen for monitoring: five species of salmon, five species of berries, and Sitka black-tailed deer, all key species highly impacted by weather changes.
The findings from the research show that these communities are observing and adapting to significant environmental changes, including more rain, warmer temperatures, and less snow, which have been accelerating over the last 15–20 years. These weather changes are impacting the terrain (e.g. isostatic rebound, erosion), the distribution and availability of marine and terrestrial resources, and people’s confidence and ease in moving about their territory and ability to harvest and preserve resources. This research suggests that delineating CKIS is an efficient way of understanding the impacts of climate change, envisioning potential adaptation opportunities, and creating resilient social-ecological ecosystems.

Keywords: Pacific Northwest coast
local knowledge
adaptation
climate change
ethnoecology
Advisor: Thornton, T
The politics of social assistance in emerging market economies: on the interplay of electoral and contentious politics

This dissertation contributes to the literature on the politics of social assistance in Emerging Market Economies. It builds upon existing theoretical frameworks across several academic fields and offers empirical evidence on the influence of politics in the expansion and distribution of social assistance programs. Paper 1 provides a novel contribution to existing political explanations of social assistance expansion by theorizing and testing how electoral competition and contentious politics mediate each other’s effect on social assistance spending on a global scale. The analysis finds this election-contention-nexus to influence social assistance spending in Middle-income countries in particular. Paper 2 offers a longitudinal analysis of the influence of the interaction of protests and electoral competition on social assistance in Turkey to uncover how the election-contention-nexus plays out at the national level. In addition, due to the available micro-data, it assesses the targeting of programs to characterize who receives benefits as a response to political factors. The results suggest that this co-occurrence can lead to higher levels of coverage of social assistance benefits among the poor in Turkey. Paper 3 introduces a framework to examine differences in the distributional logic used by governments across different social assistance types to provide a systematic understanding of political distribution of benefits that goes beyond aggregate spending or single flagship programs. The results suggest that the main benefit types that are used for political purposes in Turkey are meager cash and in-kind benefits that I classify as poverty mitigating social assistance. Further, the type of challenging party is found to have differential effects on the distribution of social assistance programs. Lastly, Paper 4 examines the role of federal politics in India to explain stark differences in unmet demand for the world’s largest public works program. It finds that state-level party strategy and party alignment across levels of government are important factors that can explain unmet demand in the program. Further, it highlights that one benefit can be utilized by many political actors across levels of governments for different purposes. Surprisingly, district-level economic or political dynamics are not found to influence rationing rates of the public works program.

Keywords: social assistance
political economy
protests
India
social protection
Turkey
social policy
emerging markets welfare
politics of policy reform
social movements
quantitative methods
Advisor: Ebbinghaus, B
Yörük, E
Structural and functional studies with native mass spectrometry — insights into membranes and glycoproteins

The membrane is a boundary between extracellular and intracellular environments or separates intracellular spaces. It also plays a vital and irreplaceable role in hosting membrane protein and is a matrix or media to exchange material and information in and out of the cell. Hence understanding the protein structure, tracing the signalling and investigating active ligands are essential. This thesis studies the structure details of glycoproteins, molecular events of rhodopsin in disc membrane, and the endogenous ligands of voltage-dependent potassium ion channel beta subunits. Native mass spectrometry (native MS) monitors the photoactivation and regeneration of rhodopsin in membrane in Chapter 3. The retinal isomerisation and hydrolysis process are slower than in the detergent environment. It is also discovered that the membrane component, N-ret-PE is a source of cis-retinal for rhodopsin regeneration. This pathway is independent of other cells and does not require conversion between retinal and retinol, which may improve the efficiency of vision persistence. Later in Chapter 4, the phototransduction of rhodopsin in membrane is further studied with native MS. The GDP release from the transducin is directly observed on transducin when it couples with rhodopsin. Hence the activated Gtα-PDE6 hydrolyses and releases cGMP. This detection of photoactivation and transduction in the membrane can be used for rhodopsin-targeting compounds. These provide insights into the regulation of rhodopsin-base active ligands for rhodopsin signalling. Apart from the static observation of protein structure, employment of native MS reveals occupancy of N- and O-glycans, LacNAcs, GlcNAc branches on N-glycans and linkage of glycans applied in transferrin, fetuin, epoetin and alpha 1-acid glycoprotein in Chapter 5. In Chapter 6, native MS detects cofactor and active ligands that monitor Kvβ2, both aldo-keto reductase and potassium ion channel beta subunit. An endogenous inhibitory ligand is likely to be an inhibitor of Kvβ2, maintaining an increasing redox state in the ratio of NADPH/NADP+. The finding of a small ligand may result in a possible drug prototype for sleep rhythm. This thesis shows that the new application of native MS providing detailed information in structural, functional and metabolomic biology studies. Together these studies by the means of native MS advance the understanding in protein structure and functions.

Keywords: glycoproteins
native mass spectrometry
rhodopsin
disc membrane
Advisor: Robinson, C
Investigating the role of serine-ADP-ribosylation in human cells

ADP-ribosylation (ADPr) is a widespread post-translational modification that controls many cellular processes, in particular DNA repair. Poly(ADP-ribose) polymerase 1 (PARP1) is the main ADPr enzyme that performs about 85-90% of DNA damage-induced ADPr. In response to DNA damage, PARP1 rapidly binds to DNA ends at the sites of DNA damage and modifies itself, histones and other proteins, thus promoting and regulating DNA repair. However, despite the critical role of PARP1 in DNA repair, for over 50 years the amino acid specificity of PARP1 remained controversial. Recently, our group and others discovered that PARP1 in complex with HPF1 predominantly performs ADPr at serine residues, both in response to exogenous DNA damage and under physiological conditions, and ARH3 is the hydrolase responsible for its timely reversal.
Here, we assessed the abundance of serine-ADPr in human cells, and performed the validation of several serine-ADPr substrates, including histones. Our results established serine as the primary site of ADPr in DNA damage signalling and described serine-ADPr as an additional component of histone code.
Then, we investigated the relationship between the levels of physiological serine-ADPr and cell sensitivity to PARP inhibitors, which are currently approved or in clinical trials against various types of cancer. We demonstrated that serine-ADPr, in particular on PARP1 serines 499, 507 and 519, counteracts PARP inhibitor-induced DNA damage and cell death, contributing to PARP inhibitor resistance.
Furthermore, we discovered a synthetic lethal interaction between ARH3 and the main poly-ADPr hydrolase PARG. We showed that simultaneous suppression of the two hydrolases results in excessive accumulation of poly-ADPr on serine residues, which disrupts histone modification and transcription states, and eventually leads to PARP-dependent cell death.
Overall, our findings provide novel insights into the role of serine-ADPr in human cells and highlight serine-ADPr regulators HPF1 and ARH3 as novel biomarkers for cancer cell sensitivity to PARP and PARG inhibitors. Fundamentally, our results allow us to suggest the existence of minimum and maximum thresholds for serine-ADPr, crossing of which would be detrimental to cellular homeostasis.

Advisor: Ahel, I
The development of partially coherent X-ray beam ptychography and adaptable optics for the study of nanomaterials

Advances in synchrotron and X-ray free electron laser (XFEL) sources have led to ptychography emerging as a powerful tool in X-ray microscopy. Ptychography uses overlapping diffraction patterns scanned across a sample and computational techniques to reconstruct the complex probe and sample transmission functions with spatial resolutions beyond the image forming optics. Ptychography's ability to reconstruct the complex probe has seen it widely adopted as a metrology technique, particularly as focal sizes approach ever smaller length regimes. However, most sources do not yet produce completely coherent beams, which had previously restricted ptychography to specialised, high-coherence beamlines. Including a multi-modal probe in the reconstruction algorithm developed in the presented study has alleviated this requirement, making it more widely accessible. As sources have evolved, so has the need for high-quality X-ray optics for focussing. Aberrations introduced during fabrication degrade the performance of X-ray optics and their ability to achieve diffraction limited focusing. Corrective optics are a new method that can counteract these errors by introducing controlled wavefront modifications before the optic, which cancels out the distortions.
This thesis consolidates a range of work centred on improving the understanding of partially coherent ptychography. This includes successfully implementing partially coherent ptychography as an imaging and X-ray optic metrology technique developed for the B16 Test beamline at Diamond Light Source. And then its subsequent development into an at-wavelength metrology technique for characterising fabrication aberrations of X-ray optics. A new class of dynamic corrective optics is demonstrated and characterised using the aforementioned ptychography technique. The results will apply to a wide variety of high numerical aperture X-ray optics aiming to achieve diffraction limited focusing. Finally, some typical applications of partially coherent and regular ptychography are presented as case studies of nanomaterials. Gold nanoparticles are used to validate the imaging capabilities of the partially coherent ptychography technique and discuss how other decoherence effects can be accounted for, such as fly-scan ptychography. The processing steps of a typical ptychotomography experiment studying silica diatoms are presented, and the associated coherent properties are examined.

Keywords: optics
ptychography
imaging
partially coherent
CDI
X-ray
Advisor: Korsunsky, A
Laundy, D
Sawhney, K