The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

What minimal role—if any—must consciousness of morally significant information play in an account of moral worth? According to one popular view, a right action is morally worthy only if the agent is conscious (in some sense) of the facts that make it right. I argue against this consciousness condition and close cousins of it. As I show, consciousness of such facts requires much more sophistication than writers typically suggest—this condition would bar from moral worth most ordinary, intuitively morally worthy agents. (...) Moreover, I show that the attraction to this flavor of consciousness condition rests on mistaken assumptions about what is required for a right act to be non-accidentally right and attributable to the agent. Drawing some lessons from the discussion, I defend a Value-Secured Reliability Theory of Moral Worth and show how a minimal yet indispensable role for consciousness falls out from it. On this independently plausible theory, an action can be morally worthy even when the agent is unaware of the right-making features of her action. (shrink)

In this paper, I explore a possible convergence between two great twentieth century thinkers, Nishida Kitarō of Japan and Martin Heidegger of Germany. The focus is on the quasi-religious language they employ in discussing the grounding of human existence in terms of an encompassing Wherein for our being. Heidegger speaks of “the sacred” and “the passing of the last god” that mark an empty clearing wherein all metaphysical absolutes or gods have withdrawn but are simultaneously indicative of an opening wherein (...) beings are given. Nishida speaks of “the religious” dimension in the depths of one's being, that he calls “place,” and that somehow envelops the world through its kenotic self-negation. In both we find reference to a kind of originary space—the open or place—associated with quasireligious themes. I also point to their distinct approaches to metaphysical language in their attempts to give voice to that abysmal thought. (shrink)

The representational theory of phenomenal experience is often stated in terms of a supervenience thesis: Byrne recently characterises it as the thesis that “there can be no difference in phenomenal character without a difference in content”, while according to Tye, “[a]t a minimum, the thesis is one of supervenience: necessarily, experiences that are alike in their representational contents are alike in their phenomenal character.” Consequently, much of the debate over whether representationalism is true centres on purported counter-examples – that is (...) to say, purported failures of supervenience. The refutation of putative counter-examples has been, it seems to me, by and large successful. But there is a certain class of these for which the representationalist response has been something less than completely convincing. These are the cross-modality cases. I will explain what I mean, and then argue that the response in question is not only unconvincing but actually undermines the representationalist position. (shrink)

This paper explores the question of whether the United Nations should engage in preventive military actions. Correlatively, it asks whether UN preventive military actions could satisfy just war principles. Rather than from the standpoint of the individual nation state, the ethics of preventive war is discussed from the standpoint of the UN. For the sake of brevity, only the legitimate authority, just cause, last resort, and proportionality principles are considered. Since there has been disagreement about the specific content of these (...) principles, a third question also is explored: How should they be formulated? Moreover, these questions are addressed in the context of a particular issue: the goals of the non-proliferation and the abolition of weapons of mass destruction. (shrink)

In Social Imaginaries, vol. 1, nr. 1 (Spring 2015) due out in May 2015.

This paper investigates the meaning of the neo-Confucian concept of 'li'. From early on, it has the sense of a pattern designating how things are and ought to be. But it takes on the appearance of something transcendent to the world only at a certain point in history, when it becomes juxtaposed to 'qi'. Zhu Xi has been criticized for this 'li-qi' dichotomization and the transcendentalization of 'li'. The paper re-examines this putative dualism and transcendentalism, looking into both Zhu's discussions (...) and pre- and post-Zhu discussions of 'li', and concludes it to be an inter-connective threading immanent to the world. (shrink)

I examine the role of the imagination (Einbildung) for Martin Heidegger after his Kant-reading of 1929. In 1929 he broadens the imagination to the openness of Dasein. But after 1930 Heidegger either disparages it as a representational faculty belonging to modernity; or further develops and clarifies its ontological broadening as the clearing or poiesis. If the hylo-morphic duality implied by Kantian imagination requires a prior unity, that underlying power unfolding beings in aletheic formations (poiesis) of being (the happening of being, (...) the opening of the world) would have to ultimately be in excess to any spontaneous power of subjectivity. (shrink)

This paper discusses the idea of "pure experience" within the context of the Buddhist tradition and in connection with the notions of emptiness and dependent origination via a reading of Dale Wright's reading of 'Huangbo' in his 'Philosophical Meditations on Zen Buddhism'. The purpose is to appropriate Wright's text in order to engender a response to Steven Katz's contextualist-constructivist thesis that there are no "pure" (i.e., unmediated) experiences. In light of the Mahayana claim that everything is empty of substance, i.e., (...) originates dependently through conditions, contingencies, and contexts, what does the "purity" of the Enlightenment experience mean for Chan/Zen Buddhism? (shrink)

: Two major philosophers of the twentieth century, the German existential phenomenologist Martin Heidegger and the seminal Japanese Kyoto School philosopher Nishida Kitarō are examined here in an attempt to discern to what extent their ideas may converge. Both are viewed as expressing, each through the lens of his own tradition, a world in transition with the rise of modernity in the West and its subsequent globalization. The popularity of Heidegger's thought among Japanese philosophers, despite its own admitted limitation to (...) the Western "history of being," is connected to Nishida's opening of a uniquely Japanese path in its confrontation with Western philosophy. The focus is primarily on their later works (the post-Kehre Heidegger and the works of Nishida that have been designated "Nishida philosophy"), in which each in his own way attempts to overcome the subject-object dichotomy inherited from the tradition of Western metaphysics by looking to a deeper structure from out of which both subjectivity and objectivity are derived and which embraces both. For Heidegger, the answer lies in being as the opening of unconcealment, from out of which beings emerge, and for Nishida, it is the place of nothingness within which beings are co-determined in their oppositions and relations. Concepts such as Nishida's "discontinuous continuity," "absolutely self-contradictory identity" (between one and many, whole and part, world and things), the mutual interdependence of individuals, and the self-determination of the world through the co-relative self-determination of individuals, and Heidegger's "simultaneity" (zugleich) and "within one another" (ineinander) (of unconcealment and concealment, presencing and absencing), and their "between" (Zwischen) and "jointure" (Fuge) are examined. Through a discussion of these ideas, the suggestion is made of a possible "transition" (Übergang) of both Western and Eastern thinking, in their mutual encounter, both in relation to each other and each in relation to its own past history, leading to both a self-discovery in the other and to a simultaneous self-reconstitution. (shrink)

Imaginative resistance (IR) is rejecting a claim that is true within a fictional world. Accounts that describe IR hold that readers exit a fiction at points of resistance. But if resistance entails exiting a fiction, then learning morality from fiction doesn’t occur. But moral learning from fiction does occur; some such cases are instances of accepting a norm one first denied. I amend current solutions to IR with poetic license. The more poetic license granted a work, the more flexible one (...) is regarding perceived falsehoods. Instead of exiting the fiction, one has the chance to stay engaged and possibly learn norms she previously denied. (shrink)

Automated reasoning about uncertain knowledge has many applications. One difficulty when developing such systems is the lack of a completely satisfactory integration of logic and probability. We address this problem directly. Expressive languages like higher-order logic are ideally suited for representing and reasoning about structured knowledge. Uncertain knowledge can be modeled by using graded probabilities rather than binary truth-values. The main technical problem studied in this paper is the following: Given a set of sentences, each having some probability of being (...) true, what probability should be ascribed to other (query) sentences? A natural wish-list, among others, is that the probability distribution (i) is consistent with the knowledge base, (ii) allows for a consistent inference procedure and in particular (iii) reduces to deductive logic in the limit of probabilities being 0 and 1, (iv) allows (Bayesian) inductive reasoning and (v) learning in the limit and in particular (vi) allows confirmation of universally quantified hypotheses/sentences. We translate this wish-list into technical requirements for a prior probability and show that probabilities satisfying all our criteria exist. We also give explicit constructions and several general characterizations of probabilities that satisfy some or all of the criteria and various (counter) examples. We also derive necessary and sufficient conditions for extending beliefs about finitely many sentences to suitable probabilities over all sentences, and in particular least dogmatic or least biased ones. We conclude with a brief outlook on how the developed theory might be used and approximated in autonomous reasoning agents. Our theory is a step towards a globally consistent and empirically satisfactory unification of probability and logic. (shrink)

The following essay, “The Unsolved Issue of Consciousness” (Torinokosaretaru ishiki no mondai 取残されたる意識の問題), by Nishida Kitarō 西田幾多郎 from 1927 is significant in regard to the development of what has come to be called “Nishida philosophy” (Nishida tetsugaku 西田哲学). In what follows, in addition to providing some commentary on the important points of his essay, I would like to show its relevance or significance not only for those who would like to study Nishida’s thought but also for philosophy in general, especially (...) in the contemporary setting. It was first published in 1927 by Iwanami Publishers in a collection of essays by different authors, Philosophical Essays in Commemoration of the Sixtieth Birthday of Dr. .. (shrink)

Loneliness in medicine is a serious problem not just for patients, for whom illness is intrinsically isolating, but also for physicians in the contemporary condition of medicine. We explore this problem by investigating the ideal physician-patient relationship, whose analogy with friendship has held enduring normative appeal. Drawing from Talbot Brewer and Nir Ben-Moshe, we argue that this appeal lies in a dynamic form of companionship incompatible with static models of friendship-like physician-patient relationships: a mutual refinement of embodied virtue that draws (...) both persons together. The ideal physician-patient relationship has a dialectical character that fosters each member's improvement of phenomenologically recognizing and embodying moral virtues. A key component of this dynamic is a commitment to the common goal of the patient's health, realized through joint interactivities and conversations over time. The physician's presence to the patient's suffering—understood best as an alienating phenomenological condition for the patient—orients and discloses possibilities for virtuous caregiving by structuring the meanings of the goals, conversations, and joint narrative constitutive of their relationship. Presence to suffering, paradoxically, is perhaps an important prerequisite for this dynamic partnership. These activities dialectically build an interpretive horizon of understanding through which moral goods and character refinement—in and for the other—may become revealed for both persons in their shared being-in-the-world. This analysis of suffering, mood, and revealing of (possible) moral goods has implications for addressing the modern problem of loneliness for patients and physicians, who are increasingly inhibited from building flourishing relationships with each other. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

ArgumentIn the United States, scientific knowledge is brought before the courts by way of testimony – the testimony of scientific experts. We argue that this expertise is best understoodfirstas related to the quality of the underlying scienceand thenin terms of who delivers it. Bloodstain pattern analysis (BPA), a contemporary forensic science, serves as the vaulting point for our exploration of objectivity as a metric for the quality of a science in judicial contexts. We argue that BPA fails to meet the (...) minimal standard set by Helen Longino’s social-procedural account of objectivity (1990, 2002). In light of some pressing issues for social-procedural accounts, we offer an infrastructural account of objectivity. This account offers what amounts to a friendly amendment to Longino’s account and adds to the ways in which we might analyze social-procedural objectivity. Finally, we address an issue that is pressing in the legal context: given that scientific knowledge is delivered by individuals, not communities, at least in U.S. courts, we (may) need a way to evaluate individual scientific and epistemic agents. We suggest a means for making this evaluation that is derived from our infrastructural account of objectivity. (shrink)

Discerning the decisionmaking of Kim Jong-Un and the North Korean regime on issues of peaceful engagement and warlike actions endures as a mighty challenge for U.S. intelligence analysts and policymakers. In this report, we seek to inform analysis of Democratic People’s Republic of Korea (DPRK) leadership decisionmaking. To do so, we use three discussion papers that were written to facilitate discussion of an interagency working group. The three papers are assembled here in a single report. The first discussion paper describes (...) decisionmaking among different authoritarian regimes, including North Korea, and the opening up of those economies to outside engagement. The second paper outlines two different scenarios that might occur when conventional deterrence on the Korean Peninsula breaks down and the resulting decisions that North Korea’s leadership could face. The third paper assesses DPRK decisionmaking about nuclear weapon use. The report concludes with some observations, drawn from the issues covered in these three discussion papers, about DPRK decisionmaking and stability on the Korean Peninsula. (shrink)

Reasoning about analogical arguments is known to be subject to a variety of cognitive biases, and a lack of clarity about which factors can be considered strengths or weaknesses of an analogical argument. This can make it difficult both to design empirical experiments to study how people reason about analogical arguments, and to develop scalable tutoring tools for teaching how to reason and analyze analogical arguments. To address these concerns, we describe WG-A (Warrant Game — Analogy), a framework for people (...) to analyze analogical arguments based on Bartha’s (2010) Articulation Model of analogical argumentation. We carry out two experiments designed to probe WG-A’s effectiveness in improving participants’ ability to reason about analogical arguments and argumentation in general, and argue that WG-A is a promising approach, though it is in need of further development. (shrink)

This paper details how ghost hunting, as a set of learning activities, can be used to enhance critical thinking and philosophy of science classes. We describe in some detail our own work with ghost hunting, and reflect on both intended and unintended consequences of this pedagogical choice. This choice was partly motivated by students’ lack of familiarity with science and philosophic questions about it. We offer reflections on our three different implementations of the ghost hunting activities. In addition, we discuss (...) the practical nuances of implementing these activities, as well the relation of ghost hunting to our course content, including informal fallacies and some models for scientific inference. We conclude that employing ghost hunting along-side traditional activities and content of critical thinking and philosophy of science offers a number of benefits, including being fun, increasing student attendance, enhancing student learning, and providing a platform for campus wide dialogues about philosophy. (shrink)

There has been a recent explosion of undergraduate philosophy conferences across the United States. In this paper, we explore undergraduate conferences along three lines. First, we argue that, as a well-designed learning activity, undergraduate conferences can serve to increase gender parity in philosophical spaces—a widely accepted and important goal for our discipline. Second, we argue that this increase in parity is due, at least in part, to the proper design of undergraduate conferences as High-Impact Practices. Our empirical work on our (...) own undergraduate conference demonstrates that properly designing the conference as a High-Impact learning activity does, as expected, benefit underserved student populations, including women. Additionally, the study also revealed unexpected opportunities to intervene on student learning. Third, we argue, also in line with our data, that undergraduate conferences occupy a previously taxonomically unrecognized grouping among recognized High-Impact Practices. (shrink)

Nanotechnology, as with many technologies before it, places a strain on existing legislation and poses a challenge to all administrative agencies tasked with regulating technology-based products. It is easy to see how statutory schemes become outdated, as our ability to understand and affect the world progresses. In this article, we address the regulatory problems that nanotechnology posses for the Food and Drug Administration’s (FDA) classification structure for ‘‘drugs’’ and ‘‘devices.’’ The last major modification to these terms was in 1976, with (...) the enactment of the Medical Device Amendments. There are serious practical differences for a classification as a drug or device in terms of time to market and research. Drugs are classified, primarily, as acting by ‘‘chemical action.’’ We lay out some legal, philosophic, and scientific tools that serve to provide a useful, as well as legally and scientifically faithful, distinction between drugs and devices for the purpose of regulatory classification. These issues we raise are worth the consideration of anyone who is interested in the regulation of nano-products or other novel technologies. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

Results: We analyzed 1,402 surveys and 15 in-depth interviews. Many (32%) CL participants reported greater difficulty refilling medications and a minority (14%) reported greater difficulty accessing HIV care during the pandemic. Most (99%) Opt4Mamas participants reported no difficulty refilling medications or accessing HIV/pregnancy care. Among the CL participants, older women were less likely (aOR = 0.95, 95% CI: 0.92–0.98) and women with more children were more likely (aOR = 1.13, 95% CI: 1.00–1.28) to report difficulty refilling medications. Only 2% of (...) CL participants reported greater difficulty managing FP and most (95%) reported no change in likelihood of using FP or desire to get pregnant. Qualitative analysis revealed three major themes: (1) adverse organizational/economic implications of the pandemic, (2) increased importance of pregnancy prevention during the pandemic, and (3) fear of contracting COVID-19. (shrink)

The current assessment of behaviors in the inventories to diagnose autism spectrum disorders (ASD) focus on observation and discrete categorizations. Behaviors require movements, yet measurements of physical movements are seldom included. Their inclusion however, could provide an objective characterization of behavior to help unveil interactions between the peripheral and the central nervous systems. Such interactions are critical for the development and maintenance of spontaneous autonomy, self-regulation and voluntary control. At present, current approaches cannot deal with the heterogeneous, dynamic and stochastic (...) nature of development. Accordingly, they leave no avenues for real-time or longitudinal assessments of change in a coping system continuously adapting and developing compensatory mechanisms. We offer a new unifying statistical framework to reveal re-afferent kinesthetic features of the individual with ASD. The new methodology is based on the non-stationary stochastic patterns of minute fluctuations (micro-movements) inherent to our natural actions. Such patterns of behavioral variability provide re-entrant sensory feedback contributing to the autonomous regulation and coordination of the motor output. From an early age, this feedback supports centrally driven volitional control and fluid, flexible transitions between intentional and spontaneous behaviors. We show that in ASD there is a disruption in the maturation of this form of proprioception. Despite this disturbance, each individual has unique adaptive compensatory capabilities that we can unveil and exploit to evoke faster and more accurate decisions. Measuring the kinesthetic re-afference in tandem with stimuli variations we can detect changes in their micro-movements indicative of a more predictive and reliable kinesthetic percept. Our methods address the heterogeneity of ASD with a personalized approach grounded in the inherent sensory-motor abilities that the individual has already developed. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory (...) of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the “bottom up” approach) and (4) how to infer the nature of the last universal common ancestor (the “top down” approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin.We also describe another family of paths motivated by a” circularity” approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question. (shrink)

In this paper, I contest increasingly common "realist" interpretations of Hegel's theory of "the concept" (der Begriff), offering instead a "isomorphic" conception of the relation of concepts and the world. The isomorphism recommended, however, is metaphysically deflationary, for I show how Hegel's conception of conceptual form creates a conceptually internal standard for the adequacy of concepts. No "sideways-on" theory of the concept-world relationship is envisioned. This standard of conceptual adequacy is also "graduated" in that it allows for a lack of (...) fit between concept and world. The possibility for a "maximally isomorphic" fit between concept and world obtains through the teleological realization of concepts, which marks especially the "artificial" world of human culture (law, art, religion, etc.). Some of the most seemingly exaggerated claims Hegel makes about the concept, I contend, can be understood when we consider the significance Hegel ascribes to human making, which is provided for in his conceptual theory. But my framework provides an interpretive key for the way Hegel sees concepts imperfectly realized in the natural world as well. (shrink)

Clade selection is unpopular with philosophers who otherwise accept multilevel selection theory. Clades cannot reproduce, and reproduction is widely thought necessary for evolution by natural selection, especially of complex adaptations. Using microbial evolutionary processes as heuristics, I argue contrariwise, that (1) clade growth (proliferation of contained species) substitutes for clade reproduction in the evolution of complex adaptation, (2) clade-level properties favoring persistence – species richness, dispersal, divergence, and possibly intraclade cooperation – are not collapsible into species-level traits, (3) such properties (...) can be maintained by selection on clades, and (4) clade selection extends the explanatory power of the theory of evolution. (shrink)

Experiences of embodied remembering are familiar and diverse. We settle bodily into familiar chairs or find our way easily round familiar rooms. We inhabit our own kitchens or cars or workspaces effectively and comfortably, and feel disrupted when our habitual and accustomed objects or technologies change or break or are not available. Hearing a particular song can viscerally bring back either one conversation long ago, or just the urge to dance. Some people explicitly use their bodies to record, store, or (...) cue memories. Others can move skilfully, without stopping to think, in complex and changing environments thanks to the cumulative expertise accrued in their history of fighting fires, or dancing, or playing hockey. The forms of memory involved in these cases may be distinct, operating at different timescales and levels, and by way of different mechanisms and media, but they often cooperate in the many contexts of our practices of remembering. (shrink)

In his recent article, “God and Horrendous Suffering,” John W. Loftus argues that what he calls horrendous suffering is incompatible with traditional theism. The extent of horrendous suffering in the world, he says, “means that either God does not care enough to eliminate it, or God is not smart enough to eliminate it, or God is not powerful enough to eliminate it.” For Loftus, however, the problem is not simply evil, but horrendous suffering, a particularly acute form of evil (...) which renders theism completely untenable. Here I will argue in reply, first, that because horrendous suffering is itself a form of evil, it cannot be easily reconciled with naturalism, since naturalism actually precludes the existence of evil. Then I will argue that horrendous suffering is not only compatible with theism, but is best explained in the context of Christian theism in particular. Finally I will suggest that because God’s work of creation is not yet complete, we have good reason for maintaining hope even in the face of horrendous evils. (shrink)

The method of reflective equilibrium (MRE) is a method of justification popularized by John Rawls and further developed by Norman Daniels, Michael DePaul, Folke Tersman, and Catherine Z. Elgin, among others. The basic idea is that epistemic agents have justified beliefs if they have succeeded in forming their beliefs into a harmonious system of beliefs which they reflectively judge to be the most plausible. Despite the common reference to MRE as a method, its mechanisms or rules are typically expressed (...) in a metaphorical or simplified manner and are therefore criticized as too vague. Recent efforts to counter this criticism have been directed towards the attempt to provide formal explications of MRE. This paper aims to supplement these efforts by providing an informal working definition of MRE. This approach challenges the view that MRE can adequately be characterized only in the negative as a set of anti-essentialisms. I argue that epistemic agents follow MRE iff they follow four interconnected rules, which are concerned with a minimalistic form of foundationalism, a minimalistic form of fallibilism, a moderate form of holism, and a minimalistic form of rationality. In the critical spirit of MRE, the corresponding working definition is, of course, provisional and revisable. In general, the aim is to contribute to a reflective equilibrium (RE) concerning MRE. If it is successful, this working definition provides a better grasp of the most basic elements of the method and thereby enhances our understanding of it. (shrink)

The fructose 6-phosphate (Fru-6P) saturation curve for phosphofructokinase (PFK) from E. coli is sigmoidal in the presence of saturating MgATP levels, while the corresponding curve for B. stearothermophilus PFK is essentially hyperbolic. Sigmoidality can be due to apparent cooperativity arising from the kinetic mechanism of an enzyme. We have determined the kinetic mechanism of B. stearothermophilus PFK (BsPFK). BsPFK was found to obey a non rapid-equilibrium random mechanism similar to the one E. coli PFK (EcPFK) follows. Substrate inhibition by MgATP (...) was observed. We propose that substrates bind to BsPFK through two alternative pathways, one of which is slower. The substrate inhibition arises in part from reaction flux through the slower pathway. Although EcPFK and BsPFK obey similar kinetic mechanisms, they are inhibited differently by MgATP: EcPFK is profoundly inhibited, BsPFK only weakly. The structural basis for this difference could be closure of the active site via a conformational transition that occurs in EcPFK, but not BsPFK. To investigate the importance of this transition for MgATP inhibition of EcPFK, we have constructed a chimeric enzyme (ChiPFK) that contains the "rigid" ATP-binding domain of BsPFK grafted onto the remainder of the EcPFK subunit. Our results indicate that ChiPFK is locked in an "open" structure resembling the activated form of EcPFK. It is insensitive to heterotropic regulation. Nevertheless, ChiPFK exhibits residual cooperativity. Possible explanations for the cooperativity are discussed. The 6F loop is proposed to be important in PFK allosteric behavior. Residues along the loop are largely conserved between BsPFK and EcPFK, except for 161, which is a glutamate in BsPFK, and a glutamine in EcPFK. Using site-directed mutagenesis, Glu 161 of BsPFK has been changed to glutamine and alanine. Similarly, Gin 161 of EcPFK has been changed to glutamate, arginine and alanine. Of the five mutants, one, QA161, was particularly interesting. Though activated normally by GDP, it was completely insensitive to PEP inhibition. This indicates that the hydrogen-bonding ability of residue 161 is critical for PEP inhibition of EcPFK, and that GDP activation and PEP inhibition follow different structural pathways. (shrink)

The articles included in this issue represent some of the most recent thinking in the area of critical thinking in higher education. While the emphasis is on work being done in the Australasian region, there are also papers from the USA and UK that demonstrate the international interest in advancing research in the area. -/- ‘Critical thinking’ in the guise of the study of logic and rhetoric has, of course, been around since the days of the ancient Greeks and the (...) early beginnings of universities. In a narrower sense, critical thinking has been central to higher education as a desirable attribute of graduates since at least the beginning of the twentieth century. The work of John Dewey, and others, emphasised the importance of ‘good habits of thinking’ as early as 1916. In 1945, the Harvard Committee placed emphasis on the importance of ‘thinking effectively’ as one of three desirable educational abilities in their General education in a free society. This was later endorsed in 1961 by the US-based Educational Policies Commission: ‘The purpose which runs through and strengthens all other educational purposes … is the development of the ability to think’ (Kennedy, Fisher, & Ennis, 1991, pp. 11–12). -/- In recent times, universities have made a point of emphasising the importance of critical thinking as a ‘generic skill’ that is central to most, if not all, subjects. There is not a university today (in Australia at least) that does not proudly proclaim that their graduates will – as a result of a degree program in their institution – learn to think critically. Further, there is rarely a subject taught that does not offer the opportunity to acquire skills in critical thinking. However, where is the evidence that we teach critical thinking in higher education? Disturbingly, despite our best intentions, it appears we may be teaching very little of it. (shrink)

En temps normal, les contrefactuels sont conçus comme produisant des énoncés portant sur des états de choses, mais des états de choses se trouvant dans des mondes simplement possibles ou alternes. Analysés ainsi, il s’avère que presque tous les contrefactuels sont incohérents. Tout contrefactuel analysé de la sorte exige qu’il y ait un monde métaphysiquement (et pas épistémiquement seulement) possible w où les lois sont les mêmes qu’ici, et où la quasi-totalité des faits sont les mêmes qu’ici. (Les différences factuelles (...) sont liées à l’antécédent et au conséquent du contrefactuel.) Mais comme je vais le montrer, cette exigence implique de manière typique la postulation de mondes dont on peut démontrer la nécessaire non-existence au moyen de déductions assez élémentaires. De plus, l’analyse des contrefactuels en termes de mondes possibles est coupable de circularité cachée. Analysés ainsi, les contrefactuels ne peuvent effectivement être compris qu’en termes de lois de la nature (les lois qui s’appliquent ici sont présupposées dans le monde hypothétique — excepté dans le cas atypique où le contrefactuel est également un contre-nomique). Mais il y a un argument répandu voulant que le concept de loi ne puisse pas être défini lui-même, sinon dans les termes de la notion de contrefactuel (une loi est, entre autres, quelque chose qui vient à l’appui des contrefactuels). Je donnerai une analyse purement épistémique des contrefactuels, déclarant que ce sont des propositions pseudo-probabilistes. Je déclarerai également que le type de probabilité en question peut être défini intégralement en termes de ce qui a été le cas (non pas de ce qui aurait été le cas, ni même de ce qui doit être le cas en un sens nomique.) Mon analyse n’est donc coupable d’aucune sorte de circularité. (shrink)

The evolution of life on Earth has produced an organism that is beginning to model and understand its own evolution and the possible future evolution of life in the universe. These models and associated evidence show that evolution on Earth has a trajectory. The scale over which living processes are organized cooperatively has increased progressively, as has its evolvability. Recent theoretical advances raise the possibility that this trajectory is itself part of a wider developmental process. According to these theories, the (...) developmental process has been shaped by a yet larger evolutionary dynamic that involves the reproduction of universes. This evolutionary dynamic has tuned the key parameters of the universe to increase the likelihood that life will emerge and produce outcomes that are successful in the larger process (e.g. a key outcome may be to produce life and intelligence that intentionally reproduces the universe and tunes the parameters of ‘offspring’ universes). Theory suggests that when life emerges on a planet, it moves along this trajectory of its own accord. However, at a particular point evolution will continue to advance only if organisms emerge that decide to advance the developmental process intentionally. The organisms must be prepared to make this commitment even though the ultimate nature and destination of the process is uncertain, and may forever remain unknown. Organisms that complete this transition to intentional evolution will drive the further development of life and intelligence in the universe. Humanity’s increasing understanding of the evolution of life in the universe is rapidly bringing it to the threshold of this major evolutionary transition. (shrink)

In Plato’s Statesman, the Eleatic Stranger applies a specialized method of inquiry—the “method of collection and division”, or “method of division”—in order to discover the nature of statecraft. This paper articulates some consequences of the fact that the method is both a tool for identifying natural kinds—that is, a tool for carving the world by its joints (Phaedrus 265b-d)—and social kinds—that is, the kinds depending on human beings for their existence and explanation. A central goal of the paper is to (...) illuminate the extent to which this use of the method of division allows us to identify Plato as an early historical forerunner of racialism, which is an ideology according to which humanity divides into races differentiated by heritable physiological, cultural, and intellectual traits, as a way of vindicating oppressive and exploitative social, political, and economic systems. -/- I defend an interpretation of the Stranger’s claim, much discussed in the literature, that the division of humankind into Greek and barbarian is unnatural (Politicus 262c-263a). I argue that, in the Stranger’s view, this division reflects subjective illusion and prejudice, rather than the fundamental, and teleological, structure of human social organization, which concerns how human beings rationally cooperate to self-produce as a species. Nonetheless, the Stranger’s alternative theory of the natural structure of human society, I suggest, is proto-racial in another way. Through a brief consideration of the Stranger’s affirmative and complex division of kinds in the city, I argue that he re-introduces naturalistic foundations for unjust human hierarchies through his alternative theory of natural kinds and human social teleology. (shrink)

It is commonly agreed that so-called echo chambers and epistemic bubbles, associated with social media, are detrimental to liberal democracies. Drawing on John Rawls’s political liberalism, we offer a novel explanation of why social media platforms amplifying echo chambers and epistemic bubbles are likely contributing to the violation of the democratic norms connected to the ideal of public reason. These norms are clarified with reference to the method of (full) reflective equilibrium, which we argue should be cultivated as a (...) civic virtue in the context of political justification. The paper demonstrates how epistemic bubbles and echo chambers are likely to be detrimental to the disposition to follow the method of reflective equilibrium in the political context. Based on this diagnosis the paper highlights the need for interventions that help cultivate reflective equilibrium as a civic virtue and the need for corresponding interdisciplinary research. (shrink)

While more species are being identified as cultural on a regular basis, stark differences between human and animal cultures remain. Humans are more richly cultural, with group-specific practices and social norms guiding almost every element of our lives. Furthermore, human culture is seen as cumulative, cooperative, and normative, in contrast to animal cultures. One hypothesis to explain these differences is grounded in the observation that human children across cultures appear to spontaneously over-imitate silly or causally irrelevant behaviors that they observe. (...) The few studies on over-imitation in other species are largely taken as evidence that spontaneous over-imitation is not present in other species. This leads to the over-imitation hypothesis – that the differences between human culture and animal cultures can be traced to the human unique tendency to over-imitate. In this paper, we analyze the current state of the literature on animal over-imitation and challenge the adequacy of the over-imitation hypothesis for the differences between humans and animal cultures. To make this argument, we first argue that the function of human over-imitation is norm-learning and that over-imitation, like skill-learning, should be subject to selective social learning effects. Then we review the empirical evidence against animal over-imitation and argue that these studies do not take into account the relevant variables given the normative and selective nature of over-imitation. We then analyze positive empirical evidence of over-imitation in great apes and canids from the experimental literature and conclude that the current body of evidence suggests that some canids and primates may have the capacity for over-imitation. This paper offers a methodological suggestion for how to study animal over-imitation, and a theoretical suggestion that over-imitation might be much more widely found among species. The larger implication for claims about human uniqueness suggests that if we do find widespread evidence of over-imitation across species, many of the current theories of human uniqueness that focus on human hyper-cooperation or social norms may have only identified a difference of degree, not of kind, between humans and other animals. (shrink)

In the discipline of international relations there are contending general theories or theoretical perspectives. Realism, also known as political realism, is a view of international politics that stresses its competitive and conflictual side. It is usually contrasted with idealism or liberalism, which tends to emphasize cooperation. Realists consider the principal actors in the international arena to be states, which are concerned with their own security, act in pursuit of their own national interests, and struggle for power. The negative side of (...) the realists’ emphasis on power and selfinterest is often their skepticism regarding the relevance of ethical norms to relations among states. National politics is the realm of authority and law, whereas international politics, they sometimes claim, is a sphere without justice, characterized by active or potential conflict among states. Not all realists, however, deny the presence of ethics in international relations. The article presents a comprehensive picture of political realism. -/- Korab-Karpowicz, W. Julian, "Political Realism in International Relations", The Stanford Encyclopedia of Philosophy (Summer 2018 Edition), Edward N. Zalta (ed.). (shrink)

This paper questions the idea that theism can function as an explanatory hypothesis to account for the nature and origins of the cosmos. Invoking God cannot dissolve the mystery of existence, and the characteristic religious response here is one of awe and humility. I then address David E. Cooper’s challenge of showing how a ”doctrine of mystery’ can have any discursible content. It is argued that certain aspects of our human experience afford us glimpses of the divine nature -- (...) intimations of the transcendent, which shine through from the ineffable source of our being to the human world we inhabit. (shrink)

Tractatus Politico-Philosophicus (Political-Philosophical Treatise) aims to establish the principles of good governance and of a happy society, and to open up new directions for the future development of humankind. W. Julian Korab-Karpowicz demonstrates the necessity of, and provides a guide for, the redirection of humanity. He argues that this paradigm shift must involve changing the character of social life and politics from competitive to cooperative, encouraging moral and intellectual virtues, providing foundations for happy societies, promoting peace among countries and building (...) a strong international community. (shrink)

Is logic normative for reasoning? In the wake of work by Gilbert Harman and John MacFarlane, this question has been reduced to: are there any adequate bridge principles which link logical facts to normative constraints on reasoning? Hitherto, defenders of the normativity of logic have exclusively focussed on identifying adequate validity bridge principles: principles linking validity facts—facts of the form 'gamma entails phi'—to normative constraints on reasoning. This paper argues for two claims. First, for the time being at least, (...) Harman’s challenge cannot be surmounted by articulating validity bridge principles. Second, Harman’s challenge can be met by articulating invalidity bridge principles: principles linking invalidity facts of the form 'gamma does not entail phi' to normative constraints on reasoning. In doing so, I provide a novel defence of the normativity of logic. (shrink)

According to John Martin Fischer and Anthony Brueckner’s unique version of the deprivation approach to accounting for death’s badness, it is rational for us to have asymmetric attitudes toward prenatal and posthumous nonexistence. In previous work, I have defended this approach against a criticism raised by Jens Johansson by attempting to show that Johansson’s criticism relies on an example that is incoherent. Recently, Duncan Purves has argued that my defense reveals an incoherence not only in Johansson’s example but also (...) in Fischer and Brueckner’s approach itself. Here I argue that by paying special attention to a certain feature of Fischer and Brueckner’s approach, we can dispense of not only Johansson’s criticism but also of Purves’s objection to Fischer and Brueckner’s approach. (shrink)

The foundations of research ethics are riven with fault lines emanating from a fear that if research is too closely connected to weighty social purposes an imperative to advance the common good through research will justify abrogating the rights and welfare of study participants. The result is an impoverished conception of the nature of research, an incomplete focus on actors who bear important moral responsibilities, and a system of ethics and oversight highly attuned to the dangers of research but largely (...) silent about threats of ineffective, inefficient, and inequitable medical practices and health systems. -/- In For the Common Good: Philosophical Foundations of Research Ethics, Alex John London defends a conception of the common good that grounds a moral imperative with two requirements. The first is to promote research that generates the information necessary to enable key social institutions to effectively, efficiently, and equitably safeguard the basic interests of individuals. The second is to ensure that research is organized as a voluntary scheme of social cooperation that respects its various contributors' moral claims to be treated as free and equal. Connecting research to the goals of a just social order grounds a framework for assessing and managing research risk that reconciles these requirements and justifies key oversight practices in non-paternalistic terms. Reconceiving research ethics as resolving coordination problems and providing credible assurance that these requirements are being met expands the issues and actors that fall within the purview of the field and provides the foundation for a more unified and coherent approach to domestic and international research. -/- This is an open access title available under the terms of a CC BY-NC-ND 4.0 license. It is free to read at Oxford Scholarship Online and offered as a free PDF download from OUP and selected open access locations. (shrink)

A review of "Intellectual virtues: an essay in regulative epistemology" by Robert Roberts and Jay Wood.

Death can be bad for an individual who has died, according to the “deprivation approach,” by depriving that individual of goods. One worry for this account of death’s badness is the Lucretian symmetry argument: since we do not regret having been born later than we could have been born, and since posthumous nonexistence is the mirror image of prenatal nonexistence, we should not regret dying earlier than we could have died. Anthony Brueckner and John Martin Fischer have developed a (...) response to the Lucretian challenge by arguing that it is rational to have asymmetric attitudes toward posthumous and prenatal nonexistence. Recently, Jens Johansson has criticized the Brueckner/Fischer position, claiming that it is irrelevant whether it is actually rational to care about future pleasures but not past pleasures. What matters, according to Johansson, is whether it would be rational for us to care about past pleasures had we come into existence earlier. In this paper, I add to the conversation between Johansson and Brueckner/Fischer by suggesting a way to defend the latter side’s position in a way that has not yet been suggested. I do this by considering a suggestion of Johansson’s for interpreting the Brueckner/Fischer position and by arguing that Johansson’s worry for the position I consider is actually incoherent. (shrink)

In this article I argue that it is underdetermined what Spinoza is arguing for when he says in Proposition 72 of Part IV of the Ethics that (translated) "A free man never acts deceitfully, but always in good faith." In "Spinoza, Lying, and Acting in Good Faith," John Bauer has argued that Spinoza lays down an absolute moral prohibition never to lie.