Studies in Aetiology and Historical Methodology in Herodotus

This dissertation interrogates existing scholarly paradigms regarding aetiology in the Histories of Herodotus in order to open up new avenues to approach a complex and varied topic. Since aetiology has mostly been treated as the study of cause and effect in the Histories, this work expands the purview of aetiology to include Herodotus’ explanations of origins more generally. The overarching goal in examining the methodological principles of Herodotean aetiology is to show the extent to which they resonate across the Histories according to their initial development in the proem, especially in those places that seem to deviate from the work’s driving force (i.e. the Persian Wars). Though the focus is on correlating the principles espoused in the proem with their deployment in Herodotus’ ethnographies and other seemingly divergent portions of his work, the dissertation also demonstrates the influence of these principles on some of the more “historical” aspects of the Histories where the struggle between Greeks and barbarians is concerned. The upshot is to make a novel case not only for the programmatic significance of the proem, but also for the cohesion of Herodotean methodology from cover to cover, a perennial concern for scholars of Greek history and historiography.

Chapter One illustrates how the proem to the Histories (1.1.0-1.5.3) prefigures Herodotus’ engagement with aetiological discussions throughout the Histories. Chapter Two indicates how the reading of the proem laid out in Chapter One allows for Herodotus’ deployment of aetiology in the Egyptian logos (especially where the pharaoh Psammetichus’ investigation of the origins of Egyptian language, nature, and custom are concerned) to be viewed within the methodological continuum of the Histories at large. Chapter Three connects Herodotus’ programmatic interest in the origins of erga (i.e. “works” or “achievements” manifested as monuments and deeds of abstract and concrete sorts) with the patterns addressed in Chapters One and Two. Chapter Four examines aetiological narratives in the Scythian logos and argues through them that this logos is as integral to the Histories as the analogous Egyptian logos studied in Chapter Two. Chapter Five demonstrates how the aetiologies associated with the Greeks’ collaboration with the Persians (i.e. medism) in the lead-up to the battle of Thermopylae recapitulate programmatic patterns isolated in previous chapters and thereby extend the methodological continuum of the Histories beyond the “ethnographic” logoi to some of the most representative “historical” logoi of Herodotus’ work. Chapter Six concludes the dissertation and makes one final case for methodological cohesion by showing the inextricability of the end of the Histories from its beginning.

Plato's Cretan Colony: Theology and Religion in the Political Philosophy of the Laws

The Laws is generally regarded as Plato’s attempt to engage with the practical realities of political life, as opposed to the more idealistic, or utopian, vision of the Republic. Yet modern scholars have often felt disquieted at the central role of religion in the Laws’ second-best city and regime. There are essentially the two dominant interpretations on offer today: either religion supports a repressive theocracy, which controls every aspect of the citizens’ lives to such an extent that even philosophy itself is discouraged, or religion is an example of the kind of noble lie, which the philosopher must deceive the citizens into believing—viz., that a god, not a man, is the author of the regime’s laws. I argue that neither of these interpretations do justice to the dialogue’s intricately dramatic structure, and therefore to Plato’s treatment of civil religion. What I propose is a third position in which Plato both takes seriously the social and political utility of religion, and views theology as a legitimate, and even necessary, subject of philosophical inquiry without going so far as to advocate theocracy as the second best form of regime.

I conclude that a proper focus on the dialogue form, combined with a careful historical analysis of Plato’s use of social and political institutions, reveals an innovative yet traditional form of civil religion, purified of the harmful influence of the poets, based on the authority of the oracle at Delphi, and grounded on a philosophical conception of god as the eternal source of order, wisdom, and all that is good. Through a union of traditional Delphic theology and Platonic natural theology, Plato gives the city of the Laws a common cult acceptable to philosopher and non-philosopher alike, and thus, not only bridges the gap between religion and philosophy, but also creates a sense of community, political identity, and social harmony—the prerequisites for political order and stability. The political theology of the Laws, therefore, provides a rational defense of the rule of law (νόμος) re-conceived as the application of divine Reason (νοῦς) to human affairs.

Chaucer and the Disconsolations of Philosophy: Boethius, Agency, and Literary Form in Late Medieval Literature

This study argues that Chaucer's poetry belongs to a far-reaching conversation about the forms of consolation (philosophical, theological, and poetic) that are available to human persons. Chaucer's entry point to this conversation was Boethius's Consolation of Philosophy, a sixth-century dialogue that tried to show how the Stoic ideals of autonomy and self-possession are not simply normative for human beings but remain within the grasp of every individual. Drawing on biblical commentary, consolation literature, and political theory, this study contends that Chaucer's interrogation of the moral and intellectual ideals of the Consolation took the form of philosophical disconsolations: scenes of profound poetic rupture in which a character, sometimes even Chaucer himself, turns to philosophy for solace and yet fails to be consoled. Indeed, philosophy itself becomes a source of despair. In staging these disconsolations, I contend that Chaucer asks his readers to consider the moral dimensions of the aspirations internal to ancient philosophy and the assumptions about the self that must be true if its insights are to console and instruct. For Chaucer, the self must be seen as a gift that flowers through reciprocity (both human and divine) and not as an object to be disciplined and regulated.

Chapter one focuses on the Consolation of Philosophy. I argue that recent attempts to characterize Chaucer's relationship to this text as skeptical fail to engage the Consolation on its own terms. The allegory of Lady Philosophy's revelation to a disconsolate Boethius enables philosophy to become both an agent and an object of inquiry. I argue that Boethius's initial skepticism about the pretentions of philosophy is in part what Philosophy's therapies are meant to respond to. The pressures that Chaucer's poetry exerts on the ideals of autonomy and self-possession sharpen one of the major absences of the Consolation: viz., the unanswered question of whether Philosophy's therapies have actually consoled Boethius. Chapter two considers one of the Consolation's fascinating and paradoxical afterlives: Robert Holcot's Postilla super librum sapientiae (1340-43). I argue that Holcot's Stoic conception of wisdom, a conception he explicitly links with Boethius's Consolation, relies on a model of agency that is strikingly similar to the powers of self-knowledge that Philosophy argues Boethius to posses. Chapter three examines Chaucer's fullest exploration of the Boethian model of selfhood and his ultimate rejection of it in Troilus and Criseyde. The poem, which Chaucer called his "tragedy," belonged to a genre of classical writing he knew of only from Philosophy's brief mention of it in the Consolation. Chaucer appropriates the genre to explore and recover mourning as a meaningful act. In Chapter four, I turn to Dante and the House of Fame to consider Chaucer's self-reflections about his ambitions as a poet and the demands of truth-telling.

Not published, not indexed: issues in generating and finding hospice and palliative care literature.

INTRODUCTION: Accessing new knowledge as the evidence base for hospice and palliative care grows has specific challenges for the discipline. This study aimed to describe conversion rates of palliative and hospice care conference abstracts to journal articles and to highlight that some palliative care literature may not be retrievable because it is not indexed on bibliographic databases. METHODS: Substudy A tracked the journal publication of conference abstracts selected for inclusion in a gray literature database on www.caresearch.com.au . Abstracts were included in the gray literature database following handsearching of proceedings of over 100 Australian conferences likely to have some hospice or palliative care content that were held between 1980 and 1999. Substudy B looked at indexing from first publication until 2001 of three international hospice and palliative care journals in four widely available bibliographic databases through systematic tracing of all original papers in the journals. RESULTS: Substudy A showed that for the 1338 abstracts identified only 15.9% were published (compared to an average in health of 45%). Published abstracts were found in 78 different journals. Multiauthor abstracts and oral presentations had higher rates of conversion. Substudy B demonstrated lag time between first publication and bibliographic indexing. Even after listing, idiosyncratic noninclusions were identified. DISCUSSION: There are limitations to retrieval of all possible literature through electronic searching of bibliographic databases. Encouraging publication in indexed journals of studies presented at conferences, promoting selection of palliative care journals for database indexing, and searching more than one bibliographic database will improve the accessibility of existing and new knowledge in hospice and palliative care.

Finite size effects in the presence of a chemical potential: A study in the classical nonlinear O(2) sigma model

In the presence of a chemical potential, the physics of level crossings leads to singularities at zero temperature, even when the spatial volume is finite. These singularities are smoothed out at a finite temperature but leave behind nontrivial finite size effects which must be understood in order to extract thermodynamic quantities using Monte Carlo methods, particularly close to critical points. We illustrate some of these issues using the classical nonlinear O(2) sigma model with a coupling β and chemical potential μ on a 2+1-dimensional Euclidean lattice. In the conventional formulation this model suffers from a sign problem at nonzero chemical potential and hence cannot be studied with the Wolff cluster algorithm. However, when formulated in terms of the worldline of particles, the sign problem is absent, and the model can be studied efficiently with the "worm algorithm." Using this method we study the finite size effects that arise due to the chemical potential and develop an effective quantum mechanical approach to capture the effects. As a side result we obtain energy levels of up to four particles as a function of the box size and uncover a part of the phase diagram in the (β,μ) plane. © 2010 The American Physical Society.

Consistency of financial interest disclosures in the biomedical literature: the case of coronary stents.

BACKGROUND: Disclosure of authors' financial interests has been proposed as a strategy for protecting the integrity of the biomedical literature. We examined whether authors' financial interests were disclosed consistently in articles on coronary stents published in 2006. METHODOLOGY/PRINCIPAL FINDINGS: We searched PubMed for English-language articles published in 2006 that provided evidence or guidance regarding the use of coronary artery stents. We recorded article characteristics, including information about authors' financial disclosures. The main outcome measures were the prevalence, nature, and consistency of financial disclosures. There were 746 articles, 2985 authors, and 135 journals in the database. Eighty-three percent of the articles did not contain disclosure statements for any author (including declarations of no interests). Only 6% of authors had an article with a disclosure statement. In comparisons between articles by the same author, the types of disagreement were as follows: no disclosure statements vs declarations of no interests (64%); specific disclosures vs no disclosure statements (34%); and specific disclosures vs declarations of no interests (2%). Among the 75 authors who disclosed at least 1 relationship with an organization, there were 2 cases (3%) in which the organization was disclosed in every article the author wrote. CONCLUSIONS/SIGNIFICANCE: In the rare instances when financial interests were disclosed, they were not disclosed consistently, suggesting that there are problems with transparency in an area of the literature that has important implications for patient care. Our findings suggest that the inconsistencies we observed are due to both the policies of journals and the behavior of some authors.

Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.

BACKGROUND: The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. METHODOLOGY/PRINCIPAL FINDINGS: We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. CONCLUSIONS/SIGNIFICANCE: The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics.

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.

BACKGROUND: In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required. DEVELOPMENT AND TESTING OF THE ONTOLOGY: Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar. RESULTS AND SIGNIFICANCE: Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.