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)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

Kimberlé Crenshaw arrived at her famous phrase “intersectionality” by carefully thinking through speeches and writings given to us by early Black feminists, such as like Sojourner Truth and Anna J. Cooper. In this paper, I expand on this groundbreaking work in two somewhat surprising ways. First, I bring the ideas of these early Black feminists together with important, related proposals from W.E.B. Du Bois, Karl Marx, Hannah Arendt, and Simone de Beauvoir. Second, I relate these works to central ideas (...) in Kant’s practical philosophy in an effort to develop a Kantian theory of intersectionality. In addition to grasping the distinctive, destructive directions of oppressive forces aimed at women, the poor, and minorities, I seek to understand better the new, violently destructive elements found in European modernity, as evidenced both in European colonialization as well as the Holocaust. -/- This book is published under the OA CC-BY 4.0 license. (shrink)

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)

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)

In the world of philosophy of science, the dominant theory of confirmation is Bayesian. In the wider philosophical world, the idea of inference to the best explanation exerts a considerable influence. Here we place the two worlds in collision, using Bayesian confirmation theory to argue that explanatoriness is evidentially irrelevant.

This paper examines how a person’s life may be shaped by living with a sense of the mystery of reality. What virtues, if any, are encouraged by such a sense? The first section rehearses a radical ”doctrine of mystery’, according to which reality as it anyway is, independently of human perspectives, is ineffable. It is then argued that a sense of mystery may provide ”measure’ for human lives. For it is possible for a life to be ”consonant’ with this sense (...) -- through exercising humility, for example -- and even to emulate mystery. A further section corrects a misunderstanding about the connection between a sense of mystery and the virtues it invites, while a final section considers the relationship between living with mystery and religious faith. (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)

This chapter describes the potential far‐reaching consequences of contemplative higher education for the fields of science and medicine.

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)

It is true now that man lives in a world of conflict. Conflict is an ever-present process in human relations. Conflict situations indeed appear frequently in daily, public and private life. Conflict may occur within and among families, groups, communities or nations; and they may be fuelled by ethnic, racial, religious, or economic differences, or may arise from differences in ideologies, values and beliefs. Conflict may be on a small or large scale. Conflict charge the people with tensions, threats, fears, (...) anxieties and uncertainties. What makes a society ideal is the extent to which the conflicting interests and needs in a society are constructively managed so that violence does not threaten its continued existence. Since it is obvious that conflicts in any given society is inevitable, management and resolution of conflict is the very essence of talking about conflict. This is what this work is set to achieve and to offer suggestions on how to manage and resolve conflict thereby reducing its negative and destructive effects. This work showed the church has the potential to contribute to the management and resolution of conflicts in Nigeria. (shrink)

For many years there has been a debate about the role of the parietal lobe in the generation of behavior. Does it generate movement plans (intention) or choose objects in the environment for further processing? To answer this, we focus on the lateral intraparietal area (LIP), an area that has been shown to play independent roles in target selection for saccades and the generation of visual attention. Based on results from a variety of tasks, we propose that LIP acts as (...) a priority map in which objects are represented by activity proportional to their behavioral priority. We present evidence to show that the priority map combines bottom-up inputs like a rapid visual response with an array of top-down signals like a saccade plan. The spatial location representing the peak of the map is used by the oculomotor system to target saccades and by the visual system to guide visual attention. (shrink)

W.E.B. Du Bois’s socialism has provoked debate for decades. His democratic theory and critique of political economy supports democratic socialism. In this article, I offer a philosophical reconstruction of the normative foundation of his democratic socialism in three steps. First, I argue that his philosophy of the modern democratic state supports the people’s advance of the principle of free and equal citizenship or civic equality. Next, I present his critique of the modern American welfare state, which asserts the fair value (...) of political liberty and democratic control over productive activities. Finally, I introduce the method of the excluded groups from Darkwater as an ideal procedure for guiding democratic deliberation in a profoundly nonideal public sphere. The method foregrounds the voices of excluded groups to correct asymmetrical relations of practical power and to infuse democratic reason with practical intelligence, namely, new content and values that can lead to the development of a democratic socialist state. (shrink)

In this paper I borrow from Maria Lugones’ work on playful “world-traveling” and W.E.B. Du Bois’ notion of “double consciousness” to make the case that humor can facilitate an openness and cooperative attitude among an otherwise closed, even adversarial audience. I focus on what I call “subversive” humor, that which is employed by or on behalf of those who have been continually marginalized. When effectively used, such humor can foster the inclination and even desire to listen to others and, if (...) only for brief moments, adopt their point of view. To be able to see oneself as others see you can also be a desirable capacity, because along with such multidimensional seeing comes an epistemic advantage lacking in those who have no need nor desire to see as others do, especially if the vision of the others happens to be from below where one perceives that the promises of our explicit ideals are constantly being implicitly broken. Such humor is aesthetic, pleasurable in and of itself, and not amenable to scientific dissection. But it is also a skill that can be honed into a powerful tool of persuasion in circumstances where straightforward arguments are less effective. It can raise consciousness about the lived experiences of those suffering under systemic oppression and foster world travelling. Subversive humor encourages audiences, especially those who contribute to what Jean Harvey calls “civilized oppression”, to playfully travel across worlds and “tarry along” with the perspectives of the marginalized. (shrink)

In her book Specifications Grading, Linda B. Nilson advocates for a grading regimen she claims will save faculty time, increase student motivation, and improve the quality and rigor of student work. If she is right, there is a strong case for many faculty to adopt some version of the system she recommends. In this paper, we argue that she is mostly right and recommend that faculty move away from traditional grading. We begin by rehearsing the central features of specifications grading (...) and providing two examples of how to implement it in philosophy classes. In light of the examples, we argue that specifications grading fulfills two of Nilson’s central desiderata but not the third. Since specifications grading generates two benefits that when combined increase student learning, without adding or increasing burdens, we conclude that student learning increases when courses are revised to include aspects of specifications grading. (shrink)

Nothing was more important for W. E. B. Du Bois than to promote the upward mobility of African Americans. This essay revisits his “The Conversation of Races” to demonstrate its general philosophical importance. Ultimately, Du Bois’s three motivations for giving the address reveal his view of the nature of philosophical inquiry: to critique earlier phenotypic conceptions of race, to show the essentiality of history, and to promote a reflexive practice. Commentators have been unduly invested in the hermeneutic readings and as (...) a result have misunderstood it as a philosophical text. Du Bois did more than introduce the concept of race into the purview of philosophy, he provided a method for philosophical inquiry into a concept that is notoriously difficult to approach with precision. My goal here is to show why no introduction to philosophy and no discussion about the nature of philosophical inquiry is complete without consideration of “Conservation.” Certainly, it is a text about race, but it is also an important philosophical text in general. (shrink)

This essay presents the normative foundation of W.E.B. Du Bois’s constructivist theory of justice in three steps. First, I show that for Du Bois the public sphere in Anglo-European modern states consists of a dialectical interplay between reasonable persons and illiberal rogues. Second, under these nonideal circumstances, the ideal of autonomy grounds reasonable persons’ deliberative openness, an attitude of public moral regard for others which is necessary for constructing the terms of political rule. Though deliberative openness is the essential vehicle (...) of construction, reasonable persons only have a pragmatic political obligation to forge ties of deliberative reciprocity with likeminded persons whom they trust will listen and not harm them. Finally, I present Du Bois’s defense of black suffragists’ support of the 19th Amendment to illustrate pragmatic political obligation in action. I sketch successful democratic engagement that reconstitutes a nonideal public sphere. (shrink)

A review of David E. Cooper's book, "Animals and Misanthropy", which argues that reflection on awful treatment of animals justifies a negative critical judgment on human life and culture.

In this tour-de-force, Elvira Basevich examines this paradox by tracing the development of W.E.B. Du Bois's life and thought and the relevance of his legacy to our troubled age. She adroitly analyzes the main concepts that inform Du Bois’s critique of American democracy, such as the color line and double consciousness, before examining how these concepts might inform our understanding of contemporary struggles, from Black Lives Matter to the campaign for reparations for slavery. She stresses the continuity in Du Bois’s (...) thought, from his early writings to his later embrace of self-segregation and Pan-Africanism, while not shying away from assessing the challenging implications of his later work.This wonderful book vindicates the power of Du Bois’s thought to help transform a stubbornly unjust world. It is essential reading for racial justice activists as well as students of African American philosophy and political thought. (shrink)

Precision Medicine is driven by the idea that the rapidly increasing range of relatively cheap and efficient self-tracking devices make it feasible to collect multiple kinds of phenotypic data. Advocates of N = 1 research emphasize the countless opportunities personal data provide for optimizing individual health. At the same time, using biomarker data for lifestyle interventions has shown to entail complex challenges. In this paper, we argue that researchers in the field of precision medicine need to address the performative dimension (...) of collecting data. We propose the fun-house mirror as a metaphor for the use of personal health data; each health data source yields a particular type of image that can be regarded as a ‘data mirror’ that is by definition specific and skewed. This requires competence on the part of individuals to adequately interpret the images thus provided. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

Freud proposes that in unconscious processing, logical connections are also (heavily) based upon phonological similarities. Repressed concerns, for example, would also be expressed by way of phonologic ambiguity. In order to investigate a possible unconscious influence of phonological similarity, 31 participants were submitted to a tachistoscopic subliminal priming experiment, with prime and target presented at 1ms. In the experimental condition, the prime and one of the 2 targets were phonological reversed forms of each other, though graphemically dissimilar (e.g., “nice” and (...) “sign”); in the control condition the targets were pseudo-randomly attributed to primes to which they don’t belong. The experimental task was to “blindly” pick the choice most similar to the prime. ERPs were measured with a focus on the N320, which is known to react selectively to phonological mismatch in supraliminal visual word presentations. The N320 amplitude-effects at the electrodes on the midline and at the left of the brain significantly predicted the participants’ net behavioral choices more than half a second later, while their subjective experience is one of arbitrariness. Moreover, the social desirability score (SDS) significantly correlates with both the behavioral and the N320 brain responses of the participants. It is proposed that in participants with low SDS the phonological target induces an expected reduction of N320 and this increases their probability to pick this target. In contrast, high defensive participants have a perplexed brain reaction upon the phonological target, with a negatively peaking N320 as compared to control and this leads them to avoid this target more often. Social desirability, which is understood as reflecting defensiveness, might also manifest itself as a defense against the (energy-consuming) ambiguity of language. The specificity of this study is that all of this is happening totally out of awareness and at the level of very elementary linguistic distinctions. (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)

Functional diversity holds the promise of understanding ecosystems in ways unattainable by taxonomic diversity studies. Underlying this promise is the intuition that investigating the diversity of what organisms actually do—i.e. their functional traits—within ecosystems will generate more reliable insights into the ways these ecosystems behave, compared to considering only species diversity. But this promise also rests on several conceptual and methodological—i.e. epistemic—assumptions that cut across various theories and domains of ecology. These assumptions should be clearly addressed, notably for the sake (...) of an effective comparison and integration across domains, and for assessing whether or not to use functional diversity approaches for developing ecological management strategies. The objective of this contribution is to identify and critically analyze the most salient of these assumptions. To this aim, we provide an “epistemic roadmap” that pinpoints these assumptions along a set of historical, conceptual, empirical, theoretical, and normative dimensions. (shrink)

Metaphors for describing the introduction, impacts, and management of non-native species are numerous and often quite outspoken. Policy-makers have adopted increasingly disputed metaphorical terms from scientific discourse. We performed a critical analysis of the use of strong metaphors in reporting scientific findings to policy-makers. Our analysis shows that perceptions of harm, invasiveness or nativeness are dynamic and inevitably display multiple narratives in science, policy or management. Improving our awareness of multiple expert and stakeholder narratives that exist in the context of (...) non-native species management, as well as metaphorical alternatives, is critical. (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)

Psychopathy refers to a range of complex behaviors and personality traits, including callousness and antisocial behavior, typically studied in criminal populations. Recent studies have used self-reports to examine psychopathic traits among noncriminal samples. The goal of the current study was to examine the underlying factor structure of the Self-Report of Psychopathy Scale–Short Form (SRP-SF) across complementary samples and examine the impact of gender on factor structure. We examined the structure of the SRP-SF among 2,554 young adults from three undergraduate samples (...) and a high-risk young adult sample. Using confirmatory factor analysis, a four-correlated factor model and a four-bifactor model showed good fit to the data. Evidence of weak invariance was found for both models across gender. These findings highlight that the SRP-SF is a useful measure of low-level psychopathic traits in noncriminal samples, although the underlying factor structure may not fully translate across men and women. (shrink)

As schools publicly modernize in response to societal changes, additional teaching and learning methods are developed, observed, and used since learners have different learning styles that make it easier for them to grasp and retain the material. During the COVID-19 pandemic, teachers require different media to keep the classroom involved while presenting the lesson materials online, one of which is video tutorials. The purpose of this study was to analyze the extent of contextual effects of video tutorials used in general (...) chemistry, determine the relationship between video tutorial effectiveness and the respondents' academic performance, and analyze the significant difference between the four indicators of contextual effects of video tutorials and the respondents' profile. A descriptive-correlational quantitative research design was used in this study. The participants in this study were 144 Grade 12 STEM students from a private school in Sultan Kudarat, Philippines, who took their general chemistry course during the pandemic. The respondents were given a survey questionnaire created with Google Forms. The students agreed with all the assertions and rated them as effective in terms of their perceptions of general chemistry, implying that video tutorials are useful in teaching the subject. With p-values of .023, .046, and .010, respectively, the findings revealed a significant relationship between the overall mean of students' perceptions of the subject of General Chemistry, the concept and application of chemical knowledge and understanding, and their influence on students' academic performance. In terms of their perception, ideas, and application of chemical knowledge and comprehension, the results demonstrated that there is no statistically significant difference between the general mean of male and female students' responses. This basically means that by using video lectures, STEM students of all genders appreciate and understand General Chemistry as a subject. -/- . (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)

In this essay I suggest that we view design principles in systems biology as minimal models, for a design principle usually exhibits universal behaviors that are common to a whole range of heterogeneous (living and nonliving) systems with different underlying mechanisms. A well-known design principle in systems biology, integral feedback control, is discussed, showing that it satisfies all the conditions for a model to be a minimal model. This approach has significant philosophical implications: it not only accounts for how design (...) principles explain, but also helps clarify one dispute over design principles, e.g., whether design principles provide mechanistic explanations or a distinct kind of explanations called design explanations. (shrink)

In this essay I propose that what design principles in systems biology and systems neuroscience do is to present abstract characterizations of mechanisms, and thereby facilitate mechanistic explanation. To show this, one design principle in systems neuroscience, i.e., the multilayer perceptron, is examined. However, Braillard (2010) contends that design principles provide a sort of non-mechanistic explanation due to two related reasons: they are very general and describe non-causal dependence relationships. In response to this, I argue that, on the one hand, (...) all mechanisms are more or less general (or abstract), and on the other, many (if not all) design principles are causal systems. (shrink)

Contrary to the dominant arguments put forth by Black feminist scholars, this essay argues that W.E.B. Du Bois’ pioneering role in establishing the principles of Black sociology, ethnological arguments and long-range development of Pan-Africanism as an ideological rival to colonial imperialism/Westernism suggests that the masculine roots informing his approach to the Black intellectual endeavor is a positive and humanistic rather than a restrictive marker of his thought. If Du Bois’ masculinization of Black agency and intellectual endeavors were simply indicative of (...) mimesis – his internalization of the very sexism against which he fought anchored to a view of freedom for Black people which materialized as a struggle among men over the control of the bodies of Black women – then there should be textual evidence demonstrating that he (like some of his Black female peers) supported the relegation of Black women to domesticity or was in favor of US imperialism against darker races abroad. But rather than an imitative aspiration towards Black nationalist patriarchy and the subordination of Black women to men’s will, the logical consequence of Du Bois’ masculinist (ethnological) thinking as it relates to the Black intellectual endeavor and the problem of race in America materialized as the formulation of Black sociology to study Black men and women as agents of history who were endowed with unique insights stemming from their experiences of marginalization, his articulation of an anti-colonial and egalitarian Black manhood, and his laying an intellectual basis for Pan-Africanism to emerge as an anti-colonial ideology. (shrink)

This essay conducts a diachronic examination of the thought of W.E.B. Du Bois. In so doing, it reveals a corpus that is marked by a tradition of thinking rarely acknowledged by scholars today: Black nationalism. Du Bois’s early focus on the relationship between racism and imperialism and ideological conflicts with Booker T. Washington and Marcus Garvey laid the basis for his intellectual maturation around the concept of self-determination. After synthesizing the insights of his former ideological rivals, this essay will show (...) that Du Bois affected a revolution in Black nationalist (and human) thought by making the common humanity and autonomy of African/African-descended peoples (and all colonized people) thinkable through the ideology of Pan-Africanism: a truly universal idea of freedom which was antagonistic to Westernism (Liberal Capitalist and Marxist thought). (shrink)

Blame is multifarious. It can be passionate or dispassionate. It can be expressed or kept private. We blame both the living and the dead. And we blame ourselves as well as others. What’s more, we blame ourselves, not only for our moral failings, but also for our non-moral failings: for our aesthetic bad taste, gustatory self-indulgence, or poor athletic performance. And we blame ourselves both for things over which we exerted agential control (e.g., our voluntary acts) and for things over (...) which we lacked such control (e.g., our desires, beliefs, and intentions). I argue that, despite this manifest diversity in our blaming practices, it’s possible to provide comprehensive account of blame. Indeed, I propose a set of necessary and sufficient conditions that aims to specify blame’s extension in terms of its constitution as opposed to its function. And I argue that this proposal has a number of advantages beyond accounting for blame in all its disparate forms. For one, it can account for the fact that one’s having had control over whether one was to φ is a necessary condition for one’s being fittingly blamed for having φ-ed. For another, it can account for why, unlike fitting shame, fitting blame is always deserved, which in turn explains why there is something morally problematic about ridding oneself of one’s fitting self-blame (e.g., one’s fitting guilt). (shrink)

Can new technology enhance purpose-driven, democratic dialogue in groups, governments, and societies? Online Deliberation: Design, Research, and Practice is the first book that attempts to sample the full range of work on online deliberation, forging new connections between academic research, technology designers, and practitioners. Since some of the most exciting innovations have occurred outside of traditional institutions, and those involved have often worked in relative isolation from each other, work in this growing field has often failed to reflect the full (...) set of perspectives on online deliberation. This volume is aimed at those working at the crossroads of information/communication technology and social science, and documents early findings in, and perspectives on, this new field by many of its pioneers. -/- CONTENTS: -/- Introduction: The Blossoming Field of Online Deliberation (Todd Davies, pp. 1-19) -/- Part I - Prospects for Online Civic Engagement -/- Chapter 1: Virtual Public Consultation: Prospects for Internet Deliberative Democracy (James S. Fishkin, pp. 23-35) -/- Chapter 2: Citizens Deliberating Online: Theory and Some Evidence (Vincent Price, pp. 37-58) -/- Chapter 3: Can Online Deliberation Improve Politics? Scientific Foundations for Success (Arthur Lupia, pp. 59-69) -/- Chapter 4: Deliberative Democracy, Online Discussion, and Project PICOLA (Public Informed Citizen Online Assembly) (Robert Cavalier with Miso Kim and Zachary Sam Zaiss, pp. 71-79) -/- Part II - Online Dialogue in the Wild -/- Chapter 5: Friends, Foes, and Fringe: Norms and Structure in Political Discussion Networks (John Kelly, Danyel Fisher, and Marc Smith, pp. 83-93) -/- Chapter 6: Searching the Net for Differences of Opinion (Warren Sack, John Kelly, and Michael Dale, pp. 95-104) -/- Chapter 7: Happy Accidents: Deliberation and Online Exposure to Opposing Views (Azi Lev-On and Bernard Manin, pp. 105-122) -/- Chapter 8: Rethinking Local Conversations on the Web (Sameer Ahuja, Manuel Pérez-Quiñones, and Andrea Kavanaugh, pp. 123-129) -/- Part III - Online Public Consultation -/- Chapter 9: Deliberation in E-Rulemaking? The Problem of Mass Participation (David Schlosberg, Steve Zavestoski, and Stuart Shulman, pp. 133-148) -/- Chapter 10: Turning GOLD into EPG: Lessons from Low-Tech Democratic Experimentalism for Electronic Rulemaking and Other Ventures in Cyberdemocracy (Peter M. Shane, pp. 149-162) -/- Chapter 11: Baudrillard and the Virtual Cow: Simulation Games and Citizen Participation (Hélène Michel and Dominique Kreziak, pp. 163-166) -/- Chapter 12: Using Web-Based Group Support Systems to Enhance Procedural Fairness in Administrative Decision Making in South Africa (Hossana Twinomurinzi and Jackie Phahlamohlaka, pp. 167-169) -/- Chapter 13: Citizen Participation Is Critical: An Example from Sweden (Tomas Ohlin, pp. 171-173) -/- Part IV - Online Deliberation in Organizations -/- Chapter 14: Online Deliberation in the Government of Canada: Organizing the Back Office (Elisabeth Richard, pp. 177-191) -/- Chapter 15: Political Action and Organization Building: An Internet-Based Engagement Model (Mark Cooper, pp. 193-202) -/- Chapter 16: Wiki Collaboration Within Political Parties: Benefits and Challenges (Kate Raynes-Goldie and David Fono, pp. 203-205) -/- Chapter 17: Debian’s Democracy (Gunnar Ristroph, pp. 207-211) -/- Chapter 18: Software Support for Face-to-Face Parliamentary Procedure (Dana Dahlstrom and Bayle Shanks, pp. 213-220) -/- Part V - Online Facilitation -/- Chapter 19: Deliberation on the Net: Lessons from a Field Experiment (June Woong Rhee and Eun-mee Kim, pp. 223-232) -/- Chapter 20: The Role of the Moderator: Problems and Possibilities for Government-Run Online Discussion Forums (Scott Wright, pp. 233-242) -/- Chapter 21: Silencing the Clatter: Removing Anonymity from a Corporate Online Community (Gilly Leshed, pp. 243-251) -/- Chapter 22: Facilitation and Inclusive Deliberation (Matthias Trénel, pp. 253-257) -/- Chapter 23: Rethinking the ‘Informed’ Participant: Precautions and Recommendations for the Design of Online Deliberation (Kevin S. Ramsey and Matthew W. Wilson, pp. 259-267) -/- Chapter 24: PerlNomic: Rule Making and Enforcement in Digital Shared Spaces (Mark E. Phair and Adam Bliss, pp. 269-271) -/- Part VI - Design of Deliberation Tools -/- Chapter 25: An Online Environment for Democratic Deliberation: Motivations, Principles, and Design (Todd Davies, Brendan O’Connor, Alex Cochran, Jonathan J. Effrat, Andrew Parker, Benjamin Newman, and Aaron Tam, pp. 275-292) -/- Chapter 26: Online Civic Deliberation with E-Liberate (Douglas Schuler, pp. 293-302) -/- Chapter 27: Parliament: A Module for Parliamentary Procedure Software (Bayle Shanks and Dana Dahlstrom, pp. 303-307) -/- Chapter 28: Decision Structure: A New Approach to Three Problems in Deliberation (Raymond J. Pingree, pp. 309-316) -/- Chapter 29: Design Requirements of Argument Mapping Software for Teaching Deliberation (Matthew W. Easterday, Jordan S. Kanarek, and Maralee Harrell, pp. 317-323) -/- Chapter 30: Email-Embedded Voting with eVote/Clerk (Marilyn Davis, pp. 325-327) -/- Epilogue: Understanding Diversity in the Field of Online Deliberation (Seeta Peña Gangadharan, pp. 329-358). -/- For individual chapter downloads, go to odbook.stanford.edu. (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)

The author supported Barack Obama for president, and he agrees with Obama on most issues. However, he opposes the federal funding of human embryonic stem cell (hESC) research. Besides involving the destruction of human life, hESC research can (1) result in the exploitation of women, and (2) cause human reproduction to become a means to an end, i.e., human embryos will become commodities to be bought and sold. Recent scientific developments show the growing potential of induced pluripotent stem (iPS) cells (...) and the diminishing promise of their embryonic counterparts. When President Obama lifted restrictions on hESC research on March 9, 2009, he missed an opportunity to show moral leadership on a politically controversial issue. (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)

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)

In this chapter, I consider the largely overlooked influence of E. W. von Tschirnhaus' treatise on method, the Medicina mentis, on Wolff's early philosophical project (in both its conception and execution). As I argue, part of Tschirnhaus' importance for Wolff lies in the use he makes of principles gained from experience as a foundation for the scientific enterprise in the context of his broader philosophical rationalism. I will show that this lesson from Tschirnhaus runs through Wolff's earliest philosophical discussions, and (...) indeed continues to inform his major texts in logic and mathematics just before the publication of the German Metaphysics. In the end, my discussion has the effect of revealing Tschirnhaus to be an exceptionally important influence on Wolff's development, perhaps even as important (or so I suggest) as Leibniz. (shrink)

What makes it the case that an utterance constitutes an illocutionary act of a given kind? This is the central question of speech-act theory. Answers to it—i.e., theories of speech acts—have proliferated. Our main goal in this chapter is to clarify the logical space into which these different theories fit. -/- We begin, in Section 1, by dividing theories of speech acts into five families, each distinguished from the others by its account of the key ingredients in illocutionary acts. Are (...) speech acts fundamentally a matter of convention or intention? Or should we instead think of them in terms of the psychological states they express, in terms of the effects that it is their function to produce, or in terms of the norms that govern them? In Section 2, we take up the highly influential idea that speech acts can be understood in terms of their effects on a conversation’s context or “score”. Part of why this idea has been so useful is that it allows speech-act theorists from the five families to engage at a level of abstraction that elides their foundational disagreements. In Section 3, we investigate some of the motivations for the traditional distinction between propositional content and illocutionary force, and some of the ways in which this distinction has been undermined by recent work. In Section 4, we survey some of the ways in which speech-act theory has been applied to issues outside semantics and pragmatics, narrowly construed. (shrink)

Perceptual experience is often said to be transparent; that is, when we have a perceptual experience we seem to be aware of properties of the objects around us, and never seem to be aware of properties of the experience itself. This is a introspective fact. It is also often said that we can infer a metaphysical fact from this introspective fact, e.g. a fact about the nature of perceptual experience. A transparency theory fills in the details for these two facts, (...) and bridges the gap between them. We have three aims: to scrutinize Michael Tye’s transparency theory :137–151, 2002; Consciousness revisited: materialism without phenomenal concepts, MIT Press, Cambridge, 2009; Philos Stud 170:39–57, 2014a), introduce a new transparency theory, and advance a meta-theoretical hypothesis about the interest, and import, of transparency theories. (shrink)

When William James published Pragmatism, he gave it a subtitle: A New Name for Some Old Ways of Thinking. In this article, I argue that pragmatism is an epistemological method for articulating success in, and between, a plurality of practices, and that this articulation helped James develop radical empiricism. I contend that this pluralistic philosophical methodology is evident in James’s approach to philosophy of religion, and that this method is also exemplified in the work of one of James’s most famous (...) students, W.E.B. Du Bois, specifically in the closing chapter of The Souls of Black Folk, “Of the Sorrow Songs.” I argue that “Sorrow Songs” can be read as an epistemological text, and that once one identifies the epistemic standards of pragmatism and radical empiricism in the text, it’s possible to identify an implicit case for moderate fideism in “Sorrow Songs.” I contend that this case illuminates the pluralistic philosophical methodology James worked throughout his career to develop, and that the James-Du Bois approach to philosophy may even help locate the epistemic value of other religious practices, beyond the singing of hymns, and identify terrain mainstream philosophy has long neglected. (shrink)

It seems that we can be directly accountable for our reasons-responsive attitudes—e.g., our beliefs, desires, and intentions. Yet, we rarely, if ever, have volitional control over such attitudes, volitional control being the sort of control that we exert over our intentional actions. This presents a trilemma: (Horn 1) deny that we can be directly accountable for our reasons-responsive attitudes, (Horn 2) deny that φ’s being under our control is necessary for our being directly accountable for φ-ing, or (Horn 3) deny (...) that the relevant sort of control is volitional control. This paper argues that we should take Horn 3. (shrink)

The authors included in this anthology of historical texts on aesthetics and philosophy of art, address the big questions. They attempt to place art within experience generally or within the life of a community; or they attempt to understand the nature of the aesthetic and its role within experience. Topics include mimesis, the relation between art and truth, the metaphysics of beauty, the function of art, and the ontology of art. All of the extracts included were written prior to the (...) middle of this century. The only aspect of this anthology which suggests that it was published recently is the inclusion of three Chinese pieces and one Indian piece. (shrink)

It is widely held that counterfactuals, unlike attitude ascriptions, preserve the referential transparency of their constituents, i.e., that counterfactuals validate the substitution of identicals when their constituents do. The only putative counterexamples in the literature come from counterpossibles, i.e., counterfactuals with impossible antecedents. Advocates of counterpossibilism, i.e., the view that counterpossibles are not all vacuous, argue that counterpossibles can generate referential opacity. But in order to explain why most substitution inferences into counterfactuals seem valid, counterpossibilists also often maintain that counterfactuals (...) with possible antecedents are transparency‐preserving. I argue that if counterpossibles can generate opacity, then so can ordinary counterfactuals with possible antecedents. Utilizing an analogy between counterfactuals and attitude ascriptions, I provide a counterpossibilist‐friendly explanation for the apparent validity of substitution inferences into counterfactuals. I conclude by suggesting that the debate over counterpossibles is closely tied to questions concerning the extent to which counterfactuals are more like attitude ascriptions and epistemic operators than previously recognized. (shrink)

Harmonia Spoleczna -- Social Harmony. In this book, I set out to prove that once we correctly identify human nature and organize our world according to the principle of cooperation, we can arrive at a world of social harmony. The current disharmony in the world, which can be observed especially in the field of politics and economics, is largely related to the erroneous modern Western philosophical assertions identifying the human being with an individual moved by desires and the will to (...) power, and the phenomenon of life with an endless conflict. An additional influence is provided by the flawed postmodernist conceptions of culture and family. These errors have enormous implications with regard to how we picture the world in which we live. I want to show that cooperation is an integral part of human nature, and that the society organized according to the requirements of nature is a truly happy society. Principles of happy society and of good governance are introduced. (shrink)