Phenex: ontological annotation of phenotypic diversity.

BACKGROUND: Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge. METHODOLOGY/PRINCIPAL FINDINGS: Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices. CONCLUSIONS/SIGNIFICANCE: Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

Disturbance, response, and persistence in self-organized forested communities: Analysis of robustness and resilience in five communities in Southern Indiana

We develop an analytic framework for the analysis of robustness in social-ecological systems (SESs) over time. We argue that social robustness is affected by the disturbances that communities face and the way they respond to them. Using Ostrom's ontological framework for SESs, we classify the major factors influencing the disturbances and responses faced by five Indiana intentional communities over a 15-year time frame. Our empirical results indicate that operational and collective-choice rules, leadership and entrepreneurship, monitoring and sanctioning, economic values, number of users, and norms/social capital are key variables that need to be at the core of future theoretical work on robustness of self-organized systems. © 2010 by the author(s).

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.

Revising Justice: Punitory Thought and Action in the Work of Atwood, Jordan, and Oates

*Designated as an exemplary master's project for 2015-16*

The Enlightening Supernatural: Ghost Stories in the Late Eighteenth-Century Germany

This dissertation explores the place of ghosts in late eighteenth-century German texts, where they appear with surprising frequency despite widespread disbelief in their ontological reality. These ghosts could simply be lingering remnants of superstition in an age where they no longer belong, but my project argues that they play a central role in the Enlightenment and its ideal of progress. The key texts analyzed in this context include three versions of the story of the Weiße Frau, as well as works by Immanuel Kant, Karl Philipp Moritz, Friedrich Schiller, and Johann Wolfgang von Goethe. In various ways, these texts demonstrate how the presentation of a ghost creates new possibilities in philosophy and aesthetics, as well as opportunities for critique. For some, the ghostly encounter produces an “Enlightening” suspense, disrupting the normal conditions of one’s understanding and creating a demand for resolution that propels one towards the future. Some recognized a dangerous manipulative potential in such suspense, and they used ghost stories to critique Enlightenment thought or imagine alternative aesthetic models. In all of these works, the ghost does not function simply as a relic of the past that needs to be left behind; it features prominently as a means of considering the present and imagining the future.

The relationship between the Enlightenment and superstitious beliefs has either been oversimplified as a basic opposition, or complicated by the recognition that the commitment to reason works as a new form of superstition. Prior scholarship has recognized the German ghost story as a primarily nineteenth-century phenomenon. This dissertation uncovers the roots of the German ghost story in unlikely texts from the eighteenth century and suggests that the relationship between ghostly apparitions and the Enlightenment was more complementary than oppositional. Ghosts do not only represent the persistence of the past, they also disrupt the normal conditions of the present in a way that enables progress towards new possibilities in aesthetics and thought.

Police is Dead: On the Birth of Economism

Police is Dead is an historiographic analysis whose objective is to change the terms by which contemporary humanist scholarship assesses the phenomenon currently termed neoliberalism. It proceeds by building an archeology of legal thought in the United States that spans the nineteenth and twentieth centuries. My approach assumes that the decline of certain paradigms of political consciousness set historical conditions that enable the emergence of what is to follow. The particular historical form of political consciousness I seek to reintroduce to the present is what I call “police:” a counter-liberal way of understanding social relations that I claim has particular visibility within a legal archive, but that has been largely ignored by humanist theory on account of two tendencies: first, an over-valuation of liberalism as Western history’s master signifier; and second, inconsistent and selective attention to law as a cultural artifact. The first part of my dissertation reconstructs an anatomy of police through close studies of court opinions, legal treatises, and legal scholarship. I focus in particular on juridical descriptions of intimate relationality—which police configured as a public phenomenon—and slave society apologetics, which projected the notion of community as an affective and embodied structure. The second part of this dissertation demonstrates that the dissolution of police was critical to emergence of a paradigm I call economism: an originally progressive economic framework for understanding social relations that I argue developed at the nexus of law and economics at the turn of the twentieth century. Economism is a way of understanding sociality that collapses ontological distinctions between formally distinct political subjects—i.e., the state, the individual, the collective—by reducing them to the perspective of economic force. Insofar as it was taken up and reoriented by neoliberal theory, this paradigm has become a hegemonic form of political consciousness. This project concludes by encouraging a disarticulation of economism—insofar as it is a form of knowledge—from neoliberalism as its contemporary doctrinal manifestation. I suggest that this is one way progressive scholarship can think about moving forward in the development of economic knowledge, rather than desiring to move backwards to a time before the rise of neoliberalism. Disciplinarily, I aim to show that understanding the legal historiography informing our present moment is crucial to this task.