This is an anthology of ?fteen papers concerning various philosophical problems related to the topic of self-knowledge. All but one of the papers were previously unpublished, and all but two are descendants of presentations at a conference on self-knowledge held at the University of St Andrews in 1995. The collection.

To Aaron Pacitti and Michael Cauvel–whose journal article, “Rent-Seeking Behavior and Economic Justice: A Classroom Exercise” broadly argues that “understanding the [complexities] of rent-seeking behavior helps fill the gap between economics and politics”–the varieties of rent are wide and, therefore, can only be described in their category-specific positions. I will discuss three of these categories in more detail below, but for now, I propose that a useful working grasp of economic rent involves “the amount paid to the owner of (...) a factor of production over the cost that is to be necessarily incurred on utilizing such elements in the production process.” In math terms, ‘economic rent’ equals the agreed-upon-amount paid by the consumer (when that amount far exceeds the market value of the product) minus the cost spent by the producer to make the product (when that cost is far below the typical amount to produce the product). Originally, the concept of economic rent concerned land ownership and the production of natural goods. Two major economists, Adam Smith and David Ricardo, offered insights into the general makeup and logic of what they called, the rent of land and simply rent, respectively. (shrink)

This article offers a novel, conservative account of material constitution, one that incorporates sortal essentialism and features a theory of dominant sortals. It avoids coinciding objects, temporal parts, relativizations of identity, mereological essentialism, anti-essentialism, denials of the reality of the objects of our ordinary ontology, and other departures from the metaphysic implicit in ordinary ways of thinking. Defenses of the account against important objections are found in Burke 1997, 2003, and 2004, as well as in the often neglected six paragraphs (...) that conclude section V of this article. (shrink)

Dion is a full-bodied man. Theon is that part of him which consists of all of him except his left foot. What becomes of Dion and Theon when Dion’s left foot is amputated? Employing the doctrine of sortal essentialism, I defend a surprising answer last defended by Chrysippus: that Dion survives while the seemingly unscathed Theon perishes. For replies to critics, see my publications of 1997 and (especially) 2003.

On the most popular account of material constitution, it is common for a material object to coincide precisely with one or more other material objects, ones that are composed of just the same matter but differ from it in sort. I argue that there is nothing that could ground the alleged difference in sort and that the account must be rejected.

It is hard to see why the head and other brain-containing parts of a person are not themselves persons, or at least thinking, conscious beings. Some theorists have sought to reconcile us to the existence of thinking person-parts. Others have sought to avoid them but have relied on radical theories at odds with the metaphysic implicit in ordinary ways of thinking. This paper offers a novel, conservative solution, one on which the heads and other brain-containing parts of persons do exist (...) but are neither persons, thinkers, nor conscious beings. A much briefer statement of the solution is found in section 5 of Burke 2004. (shrink)

Dion is a full-bodied man. Theon is that part of him which consists of all of him except his left foot. What becomes of Dion and Theon when Dion’s left foot is amputated? In Burke 1994, employing the doctrine of sortal essentialism, I defended a surprising position last defended by Chrysippus: that Dion survives while the seemingly unscathed Theon perishes. This paper defends that position against objections by Stone, Carter, Olson, and others. Most notably, it offers a novel, conservative solution (...) to the many-thinkers problem, a solution that enables us to accept the existence of brain-containing person-parts while denying that those person-parts are thinking, conscious beings. (shrink)

The “staccato run,” in which a runner stops infinitely often while running from one point to another, is a prototypical “superfeat,” that is, a feat involving the completion in a finite time of an infinite sequence of distinct acts. There is no widely accepted demonstration that superfeats are impossible logically, but I argue here, contra Grunbaüm, that they are impossible dynamically. Specifically, I show that the staccato run is excluded by Newton’s three laws of motion, when those laws are supplemented (...) with a defensible philosophical judgment. (shrink)

(The downloadable document, posted 07/23/22, incorporates post-publication corrections/refinements, mainly of section II.) The article gives a novel argument to show that there is sense of 'exists' suitable for posing a substantive issue between presentists and eternalists. It then seeks to invigorate a neglected variety of presentism. There are seven doctrines, widely accepted even among presentists, that create problems for presentism. Without distinguishing existence and being, presentists can comfortably reject all seven. Doing so would dispose of the majority of presentism’s problems. (...) Further, it would enable presentists to reduce A-judgments to B-judgments, thereby insulating presentism from doubts about the intelligibility of A-theories. For reasons indicated very briefly, it might also make presentism less difficult to reconcile with special relativity, though the point is not pursued here. (shrink)

Suppose that five minutes ago, to our astonishment, a healthy, full-grown duck suddenly popped into existence on the table in front of us. Suppose further that there was no first time at which the duck existed but rather a last time, T, at which it had yet to exist. Then for each time t at which the duck has existed, there is an explanation of why the duck existed at t: there was a time t’ earlier than t but later (...) than T such that the duck existed at t’, and it was only to be expected that a healthy duck would survive the brief period from t’ to t. But would these explanations remove the mystery? Taken collectively, would they explain why the duck has existed since T rather than never having existed at all? Presumably not. But if not, this seems to discredit the style of explanation offered by Hume and Edwards for the infinite regress they hypothesize of causes and effects. (shrink)

Simple regression (regression analysis with a single explanatory variable), and multiple regression (regression models with multiple explanatory variables), typically correspond to very different biological questions. The former use regression lines to describe univariate associations. The latter describe the partial, or direct, effects of multiple variables, conditioned on one another. We suspect that the superficial similarity of simple and multiple regression leads to confusion in their interpretation. A clear understanding of these methods is essential, as they underlie a large range of (...) procedures in common use in biology. Beyond simple and multiple regression in their most basic forms, understanding the key principles of these procedures is critical to understanding, and properly applying, many methods, such as mixed models, generalised models, and causal inference using graphs (including path analysis and its extensions). A simple, but careful, look at the distinction between these two analyses is valuable in its own right, and can also be used to clarify widely-held misconceptions about collinearity (correlations among explanatory variables). There is no general sense in which collinearity is a problem. We suspect that the perception of collinearity as a hindrance to analysis stems from misconceptions about interpretation of multiple regression models, and so we pursue discussions about these misconceptions in this light. In particular, collinearity causes multiple regression coefficients to be less precisely estimated than corresponding simple regression coefficients. This should not be interpreted as a problem, as it is perfectly natural that direct effects should be harder to characterise than univariate associations. Purported solutions to the perceived problems of collinearity are detrimental to most biological analyses. (shrink)

The current rise of neurodevelopmental disorders poses a critical need to detect risk early in order to rapidly intervene. One of the tools pediatricians use to track development is the standard growth chart. The growth charts are somewhat limited in predicting possible neurodevelopmental issues. They rely on linear models and assumptions of normality for physical growth data – obscuring key statistical information about possible neurodevelopmental risk in growth data that actually has accelerated, non-linear rates-of-change and variability encompassing skewed distributions. Here, (...) we use new analytics to profile growth data from 36 newborn babies that were tracked longitudinally for 5 months. By switching to incremental (velocity-based) growth charts and combining these dynamic changes with underlying fluctuations in motor performance – as the transition from spontaneous random noise to a systematic signal – we demonstrate a method to detect very early stunting in the development of voluntary neuromotor control and to flag risk of neurodevelopmental derail. (shrink)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

This paper, while neutral on questions about the minimality of truth, argues for the non-minimality of truth-aptness.

White progressives in the U.S. are currently experiencing two profound reckonings that typically are assumed to be unrelated. On the one hand, the Dobbs verdict overturned the assumption that the right to choose with respect to abortion is too socially entrenched, juridically settled, or politically sacred to be denied. On the other hand, climatological conditions of possibility for comfortable existence are increasingly under threat in locales in which residents have come to expect to enjoy secure lives and livelihoods. This essay (...) highlights what Indigenous communities across the U.S. already know well. Namely, threats to reproductive freedom and climate crisis are neither new nor separable. Both phenomena have common colonial roots that continue to proliferate. Each is a result of the disruption and destruction of Indigenous kinship assemblages. Indeed, in aiming to remediate their current reckonings, white progressives routinely (if unthinkingly) support forms of settler state violence that perpetuate reproductive and climate injustice in Indigenous communities. We appeal to white progressives, notably including white feminists, to embrace the proposition that their reckonings cannot be properly understood, nor successfully addressed without prioritizing Indigenous futurity. We call for centering forms of Indigenous feminist praxis that facilitate robust Indigenous coalitions of anti-colonial resistance. (shrink)

We often talk and behave as if being a man required more than just being male, and being a woman required more than just being female. There are expectations that need to be met if someone wants to fully qualify as a man or a woman in their social environment, expectations regarding their behaviour as well as character. It is, however, not entirely obvious what ‘being a man’ or ‘being a woman’ actually means and in what way and to what (...) extent it defines our identity, making us who we are. Would I be a different person if I were a woman? And what would it take for me to be a woman? Could I conceivably be neither? Or both? If gender were nothing but sex, telling a man to ‘be a man’ would make little sense. We may have different ideas about what it means to be a man or woman and how we need to behave in order to secure or maintain our manhood or womanhood, but we are all likely to have some deeply ingrained understanding of what makes a man a man and a woman a woman that goes beyond mere biology. Does it, however, follow that gender can, if necessary or desired, be completely detached from sex, that I can be a woman despite having all the physical attributes of a male member of my species, or a man despite being biologically female? If so, on what grounds exactly would we decide who is what? (shrink)

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...) paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

Letter commenting on the paper Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick, "Ontology and the Future of Dental Research Informatics", Journal of the American Dental Association 141 2010;(10):1173-75 with responses by the authors of the paper.

The discipline of applied ethics already has a certain familiarity in the Anglo-Saxon world, above all through the work of Peter Singer. Applied ethics uses the tools of moral philosophy to resolve practical problems of the sort which arise, for example, in the running of hospitals. In the University at Buffalo (New York) there was organized on April 24-25 1998 the world's first conference on a new, sister discipline, the discipline of applied ontology. Applied ontologists seek to apply ontological tools (...) to solving practical problems of the sort which arise in various extra-philosophical domains, including law and government administration. (shrink)

Risk Management Strategies and Investment Behaviors are considered important factors in the investing activities of the retail investors. This study seeks to determine the relationship between Risk Management Strategies and Investment Behavior of Generation Z retail investors. The study is a correlational research and purposive sampling was used to select the respondents for this study. Cochran’s formula was utilized to determine the total sample size or total number of respondents. Spearman’s Rank-Order Correlation was employed to assess the significant relationship of (...) Risk Management Strategies and Investment Behaviors. Based on the results, it showed that risk management strategies have a significant relationship with one or more of the investment behaviors. Risk avoidance has a significant relationship with confirmation bias. Risk reduction has a significant relationship with all of the investment behaviors such as overconfidence, loss-aversion, recency bias, and confirmation bias. Risk transfer shows a significant relationship with only loss-aversion and confirmation bias. And lastly, risk acceptance also has a significant relationship with all of the investment behaviors. This study recommends exploring other types of behavioral biases under cognitive bias and emotional bias to determine their correlation with risk management strategies. Also, broadening the sample size, demographic scope, and geographic scope of the study can improve the generalizability of the study and provide a more comprehensive understanding of the relationship between investment behavior and risk management strategies. The researchers also recommend to utilize interviews and focus group discussions to gain an in-depth understanding of the underlying values and attitudes concerning investment behavior. (shrink)

The current resurgence of interest in cognition and in the nature of cognitive processing has brought with it also a renewed interest in the early work of Husserl, which contains one of the most sustained attempts to come to grips with the problems of logic from a cognitive point of view. Logic, for Husserl, is a theory of science; but it is a theory which takes seriously the idea that scientific theories are constituted by the mental acts of cognitive subjects. (...) The present essay begins with an exposition of Husserl's act-based conception of what a science is, and goes on to consider his account of the role of linguistic meanings, of the ontology of scientific objects, and of evidence and truth. The essay concentrates almost exclusively on the Logical Investigations of 1900/01. This is not only because this work, which is surely Husserl's single most important masterpiece, has been overshadowed first of all by his Ideas I and then later by the Crisis. It is also because the Investigations contain, in a peculiarly clear and pregnant form, a whole panoply of ideas on logic and cognitive theory which either simply disappeared in Husserl's own later writings or became obfuscated by an admixture of that great mystery which is 'transcendental phenomenology'. (shrink)

Ang papel ay paglalagom ng itinuturing na pinakamahalagang yugto ng buhay ni José Rizal—ang kanyang pagkakatapon sa Dapitan, sa lente ng konseptong “bagani” ng ating mga ninuno. Sa pagbanggit sa lang nauna nang pag-aaral ukol kay Rizal, ipapakitang kung papaanong ang yugto sa Dapitan ay ang katuparan ng kanyang mga layunin sa La Liga Filipina, na kanyang isinabuhay kasama ang bayan. Sa lente ng kasalukuyang pandemyang COVID 19, makikita natin na tila naranasan din ni Rizal sa kanyang pagkakatapon ang ilang (...) bagay na ating dinaranas ngayon, na tila siya isang frontliner na nasa lockdown, inilagay sa kuwarentena, nag-homeschooling, nagkaroon ng lockdown sickness at namahagi ng ayudang pangkabuhayan sa mga mamamayan ng isang natutulog na bayan upang ito ay sumiglang muli. Nawa ay maging inspirasyon sa bayan na anuman ang hamon at mga balakid, walang makapipigil sa isang Pilipino na magsilbi sa bayan gamit ang kanyang mga talento at manatiling liwanag ng katotohanan at kaalaman. (shrink)

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...) advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of data. To provide effective solutions computers need to integrate data deriving from myriad heterogeneous sources by bringing the data together within a single framework. The meeting brought together leaders in the field of what are called "top-level ontologies" to address this issue, and to establish strategies among leaders in (...) the field of biomedical ontology for the creation of interoperable biomedical ontologies which will serve the goal of useful data integration. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...) large amounts of ncRNA biological and clinical data. (shrink)

In a series of recent publications, orofacial researchers have debated the question of how ‘bruxism’ should be defined for the purposes of accurate diagnosis and reliable clinical research. Following the principles of realism-based ontology, we performed an analysis of the arguments involved. This revealed that the disagreements rested primarily on inconsistent use of terms, so that issues of ontology were thus obfuscated by shortfalls in terminology. In this paper, we demonstrate how bruxism terminology can be improved by paying attention to (...) the relationships between (1) particulars and types, and (2) continuants and occurrents. (shrink)

An ontology of geographic kinds is designed to yield a better understanding of the structure of the geographic world, and to support the development of geographic information systems that are conceptually sound. This paper first demonstrates that geographical objects and kinds are not just larger versions of the everyday objects and kinds previously studied in cognitive science. Geographic objects are not merely located in space, as are the manipulable objects of table-top space. Rather, they are tied intrinsically to space, and (...) this means that their spatial boundaries are in many cases the most salient features for categorization. The ontology presented here will accordingly be based on topology (the theory of boundary, contact and separation) and on mereology (the theory of extended wholes and parts). Geographic reality comprehends mesoscopic entities, many of which are best viewed as shadows cast onto the spatial plane by human reasoning and language. Because of this, geographic categories are much more likely to show cultural differences in category definitions than are the manipulable objects of table-top space. (shrink)

Analogical reminding in humans and machines is a great source for chance discoveries because analogical reminding can produce representational change and thereby produce insights. Here, we present a new kind of representational change associated with analogical reminding called packing. We derived the algorithm in part from human data we have on packing. Here, we explain packing and its role in analogy making, and then present a computer model of packing in a micro-domain. We conclude that packing is likely used in (...) human chance discoveries, and is needed if our machines are to make their own chance discoveries. (shrink)

The COVID-19 pandemic revealed numerous weaknesses in pandemic preparedness and response, including underfunding, inadequate surveillance, and inequitable distribution of countermeasures. To overcome these weaknesses for future pandemics, WHO released a zero draft of a pandemic treaty in February, 2023, and subsequently a revised bureau's text in May, 2023. COVID-19 made clear that pandemic prevention, preparedness, and response reflect choices and value judgements. These decisions are therefore not a purely scientific or technical exercise, but are fundamentally grounded in ethics. The latest (...) treaty draft reflects these ethical considerations by including a section entitled Guiding Principles and Approaches. Most of these principles are ethical—they establish core values that undergird the treaty. Unfortunately, the treaty draft's set of principles are numerous, overlapping, and show inadequate coherence and consistency. We propose two improvements to this section of the draft pandemic treaty. First, key guiding ethical principles should be clearer and more precise than they currently are. Second, the link between ethical principles and policy implementation should be clearly established and define boundaries on acceptable interpretation, ensuring that signatories abide by these principles. (shrink)

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

An intuitive view regarding the epistemic significance of disagreement says that when epistemic peers disagree, they should suspend judgment. This abstemious view seems to embody a kind of detachment appropriate for rational beings; moreover, it seems to promote a kind of conciliatory inclination that makes for irenic and cooperative further discussion. Like many strategies for cooperation, however, the abstemious view creates opportunities for free-riding. In this essay, the authors argue that the believer who suspends judgment in the face of peer (...) disagreement is vulnerable to a kind of manipulation on the part of more tenacious peers. The result is that the abstemious view can have the effect of encouraging dogmatism. (shrink)

E-money systems have revolutionized global business transactions through digital payment methods. This quantitative correlational study aimed to assess the awareness and acceptance of e-money among individuals in Balayan, Batangas. Employing quota and purposive sampling, 100 participants aged 21 to 70 completed a survey questionnaire. Statistical analysis revealed that consumers were aware of e-money but lacked comprehensive knowledge. They acknowledged the convenience of e-money for online shopping and expense tracking. Age significantly influenced acceptance, while gender did not exhibit a similar effect. (...) Significant differences were observed in awareness and acceptance levels. Recommendations for improving acceptance include administrator-led campaigns, business incentives, consumer education, financial institution partnerships, and integration into student curricula. The study underscores the need for targeted strategies to translate e-money knowledge into practical use. Future research should explore adoption trends over time, barriers, and the impact of regulations on e-money utilization. (shrink)

This paper argues that Kant’s concept of ‘respect’ for the moral law has roots in Adam Smith’s concept of ‘regard’ for the general rules of conduct, which was translated as Achtung in the first German translation of the Theory of Moral Sentiments. After illustrating that Kant’s technical understanding of respect appeared relatively late in his intellectual development, I argue that Kant’s concept of respect and Smith’s concept of regard share a basic similarity: they are both a single complex (...) phenomenon with two core aspects, namely an attitude and a feeling. I then suggest that the concept of regard offered Kant a way to deal a problem concerning moral motivation that he was trying to solve at the time he likely first read Smith. I conclude by drawing some implications from the account I have offered for our understanding of Kant’s relation to Smith more generally. (shrink)

Population obesity and associated morbidities pose significant public health and economic burdens in the United Kingdom, United States, and globally. As a response, public health initiatives often seek to change individuals’ unhealthy behavior, with the dual aims of improving their health and conserving health care resources. One such initiative—taxes on sugar‐sweetened beverages (SSB)—has sparked considerable ethical debate. Prominent in the debate are arguments seeking to demonstrate the supposed impermissibility of SSB taxes and similar policies on the grounds that they interfere (...) with individuals’ freedom and autonomy. Commentators have often assumed that a policy intended to restrict or change private individuals’ consumption behavior will necessarily curtail freedom and, as a corollary, will undermine individuals’ autonomy with respect to their consumption choices. Yet this assumption involves a conceptual mistake. To address the misunderstanding, it’s necessary to attend to the differences between negative liberty, freedom of options, and autonomy. Ultimately, concerns about negative liberty, freedom, and autonomy do not provide strong grounds for opposing SSB taxes. (shrink)

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two (...) fatal problems that leave us without any viable form of rule-utilitarianism. (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)

The goal of the 2010 Ontology Summit was to address the current shortage of persons with ontology expertise by developing a strategy for the education of ontologists. To achieve this goal we studied how ontologists are currently trained, the requirements identified by organizations that hire ontologists, and developments that might impact the training of ontologists in the future. We developed recommendations for the body of knowledge that should be taught and the skills that should be developed by future ontologists; these (...) recommendations are intended as guidelines for institutions and organizations that may consider establishing a program for training ontologists. Further, we recommend a number of specific actions for the community to pursue. (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)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Machine learning algorithms may radically improve our ability to diagnose and treat disease. For moral, legal, and scientific reasons, it is essential that doctors and patients be able to understand and explain the predictions of these models. Scalable, customisable, and ethical solutions can be achieved by working together with relevant stakeholders, including patients, data scientists, and policy makers.

Michael B. Gill’s A Philosophy of Beauty: Shaftesbury on Nature, Virtue, and Art focuses on Shaftesbury’s thinking about nature, religion, morality, and art. This beautifully and engagingly written book is insightful for scholars and general readers alike, and invites readers to explore the philosophical issues that arise from Shaftesbury’s philosophy. Gill not only shows how Shaftesbury’s ideas were revolutionary at the turn of the eighteenth century but also how they remain relevant today. Shaftesbury’s major work, Characteristicks of Men, Manners, (...) Opinions, Times, was one of the most influential books published during the first half of the eighteenth century. According to Gill, “[i]t played a momentous role in turning European thought away from the negative and toward the positive—in nature, religion, morality, and art” (1). Although Characteristicks serves as a major source, Gill also engages with numerous other published and unpublished writings by Shaftesbury. A Philosophy of Beauty is divided into five chapters which focus respectively on nature and God, virtue, art, painting, and writing. (shrink)