Some experts have argued that patients should routinely be told the specific magnitude and absolute probability of potential risks and benefits of screening tests. This position is motivated by the idea that framing risk information in ways that are less precise violates the ethical principle of respect for autonomy and its application in informed consent or shared decisionmaking. In this Perspective, we consider a number of problems with this view that have not been adequately addressed. The most important challenges stem (...) from the danger that patients will misunderstand the information or have irrational responses to it. Any initiative in this area should take such factors into account and should consider carefully how to apply the ethical principles of respect for autonomy and beneficence. (shrink)

Patients should not always receive hard data about the risks and benefits of a medical intervention. That information should always be available to patients who expressly ask for it, but it should be part of standard disclosure only sometimes, and only for some patients. And even then, we need to think about how to offer it.

While several tests and strategies are recommended for colorectal cancer (CRC) screening, studies suggest that primary care providers often recommend colonoscopy without providing information about its risks or alternatives. These observations raise concerns about the quality of informed consent for screening colonoscopy.

Accounts of the concepts of function and dysfunction have not adequately explained what factors determine the line between low‐normal function and dysfunction. I call the challenge of doing so the line‐drawing problem. Previous approaches emphasize facts involving the action of natural selection (Wakefield 1992a, 1999a, 1999b) or the statistical distribution of levels of functioning in the current population (Boorse 1977, 1997). I point out limitations of these two approaches and present a solution to the line‐drawing problem that builds on the (...) second one. (shrink)

Similarly to other accounts of disease, Christopher Boorse’s Biostatistical Theory (BST) is generally presented and considered as conceptual analysis, that is, as making claims about the meaning of currently used concepts. But conceptual analysis has been convincingly critiqued as relying on problematic assumptions about the existence, meaning, and use of concepts. Because of these problems, accounts of disease and health should be evaluated not as claims about current meaning, I argue, but instead as proposals about how to define and use (...) these terms in the future, a methodology suggested by Quine and Carnap. I begin this article by describing problems with conceptual analysis and advantages of “philosophical explication,” my favored approach. I then describe two attacks on the BST that also question the entire project of defining “disease.” Finally, I defend the BST as a philosophical explication by showing how it could define useful terms for medical science and ethics. (shrink)

"Modern History" versions of the etiological theory claim that in order for a trait X to have the proper function F, individuals with X must have been recently favored by natural selection for doing F (Godfrey-Smith 1994; Griffiths 1992, 1993). For many traits with prototypical proper functions, however, such recent selection may not have occurred: traits may have been maintained due to lack of variation or due to selection for other effects. I examine this flaw in Modern History accounts and (...) offer an alternative etiological theory, the Continuing Usefulness account, which appears to avoid such problems. (shrink)

I argue that ductal carcinoma in situ (DCIS), the tumor most commonly diagnosed by breast mammography, cannot be confidently classified as cancer, that is, as pathological. This is because there may not be dysfunction present in DCIS—as I argue based on its high prevalence and the small amount of risk it conveys—and thus DCIS may not count as a disease by dysfunction-requiring approaches, such as Boorse’s biostatistical theory and Wakefield’s harmful dysfunction account. Patients should decide about treatment for DCIS based (...) on the risks it poses and the risks and benefits of treatment, not on its disease status. (shrink)

Ethics should guide the design of electronic health records (EHR), and recognized principles of bioethics can play an important role. This approach was adopted recently by a team of informaticists designing and testing a system where patients exert granular control over who views their personal health information. While this method of building ethics in from the start of the design process has significant benefits, questions remain about how useful the application of bioethics principles can be in this process, especially when (...) principles conflict. For instance, while the ethical principle of respect for autonomy supports a robust system of granular control, the principles of beneficence and non-maleficence counsel restraint due to the danger of patients being harmed by restrictions on provider access to data. Conflict between principles has long been recognized by ethicists and has even motivated attacks on approaches that state and apply principles. In this paper we show how using ethical principles can help in the design of EHRs by first, explaining how ethical principles can and should be used generally, and then by, discuss how attention to details in specific cases can show that the tension between principles is not as bad as it initially appeared. We conclude by suggesting further ways in which the application of these (and other) principles can add value to the ongoing discussion of patient involvement in their health care. This is a new approach to linking principles to informatics design that we expect will stimulate further interest. (shrink)

With the growing focus on prevention in medicine, studies of how to describe risk have become increasing important. Recently, some researchers have argued against giving patients “comparative risk information,” such as data about whether their baseline risk of developing a particular disease is above or below average. The concern is that giving patients this information will interfere with their consideration of more relevant data, such as the specific chance of getting the disease (the “personal risk”), the risk reduction the treatment (...) provides, and any possible side effects. I explore this view and the theories of rationality that ground it, and I argue instead that comparative risk information can play a positive role in decision-making. The criticism of disclosing this sort of information to patients, I conclude, rests on a mistakenly narrow account of the goals of prevention and the nature of rational choice in medicine. (shrink)

Imagine you fly home from vacation with your one-and-a-half-year-old son who is traveling for free as a “lap child.” In the airport parking lot, you put him into his forward-facing car seat, where he sits much more contentedly than he did in the rear-facing one that was mandatory until his first birthday. After he falls asleep on the way home, you transfer him to his crib without waking him, lowering the side rail so you can lift him in more easily. (...) -/- Many parts of this idyllic parenting picture are deemed unacceptably risky according to recent child safety proposals. While these proposals all aim to improve child safety, their possible impact is unclear because there has been little discussion of the absolute risk and risk reduction involved in each. And while precise figures are lacking, rough estimates indicate that the magnitudes are quite small. I will argue that this risk and benefit data raises important questions about the proposals, including whether parents might reasonably believe that the small absolute risk reduction offered by the proposed changes does not justify the attendant burdens. This possibility—termed the “prevention paradox” in other contexts—highlights ethical and theoretical challenges in this area of public health. (shrink)

This paper delves into the nature of intellectual property rights in aesthetic creations, particularly works of visual art and literary works. The discussion focuses on copyrights interests, but there are also implications for trademark and patent rights. The argument assumes a fairly conventional definition of "property," namely, the set of legal relations between the owner and all other persons relating to the use, enjoyment and disposition of a tangible thing. The problem with such a definition as applied to aesthetic creations (...) is that no ordinary tangible thing necessarily embodies a creation which can exist in multiple copies, so the paper takes the transcendent view that the tangible thing subject to legal relations is the entire terra firma or material universe being shaped in the image, sounds or words of the aesthetic creation. Therefore, the paradigm suggested for intellectual property is a monopoly on shaping the entire physical universe, thus the Worldmaking concept. It then follows that intellectual property in an aesthetic creation enables the owner to stop plagiarists from using any part of the material world to recreate in the audience the imaginative experiences first created by the protected work. (shrink)

Although there is a growing recognition that older adults and those with extensive comorbid conditions undergo cancer screening too frequently, there is little information about patients’ perceptions regarding cessation of cancer screening. Information on older adults’ views of screening cessation would be helpful both for clinicians and for those designing interventions to reduce overscreening.

Most people do not know there are different kinds of medical studies; some are conducted on people who already have a disease or medical condition, and others are performed on healthy volunteers who want to help science find answers. No matter what sort of research you are invited to participate in, or whether you are a patient when you are asked, it’s entirely up to you whether or not to do it. This decision is important and may have many implications (...) for your health and well-being, as well as those of other patients now and in the future. Making a good decision – the right one for you – requires you to become educated about topics you may not have thought about before, some of which may be quite complicated. This chapter explains the key issues to help you make a good decision. (shrink)

Trademarks are not just property; they are aesthetic creations that pervade everyday experience. As pervasive aesthetic creations having literary, pictorial, graphic, sculptural, and musical content, trademarks deserve aesthetic analysis. So this paper discusses the origins, strength, appeal, and effectiveness of trademarks within the context of aesthetic considerations such as meaning, intention, authorship, and mode of creation. Also reviewed are morphemic and phonemic analysis of trademarks, semantic positioning, the dichotomy between creation and discovery of trademarks, and the differences between trademarks and (...) titles. The discussion is confined to "word marks" consisting of alphanumeric characters because discussing other kinds of marks (such as designs, configurations, sounds, colors, and scents) would raise issues well beyond the scope of a single article. (shrink)

Consider the following patient: a 40-year-old man who has had back pain that radiates down his left leg, on and off for 2 months. He performs his normal activities and does not have any “red flag”...

Some experts have argued that patients facing certain types of choices should not be told whether their risk is above or below average, because this information may trigger a bias (Fagerlin et al. 2007). But careful consideration shows that the comparative risk heuristic can usefully guide decisions and improve their quality or rationality. Building on an earlier paper of mine (Schwartz 2009), I will argue here that doctors and decision aids should provide comparative risk information to patients, even while further (...) research is conducted. (shrink)

“Never attribute to malice that which is adequately explained by stupidity”—so says Hanlon’s Razor. This principle is designed to curb the human tendency toward explaining other people’s behavior by moralizing it. We ask whether Hanlon’s Razor is good or bad advice. After offering a nuanced interpretation of the principle, we critically evaluate two strategies purporting to show it is good advice. Our discussion highlights important, unsettled questions about an idea that has the potential to infuse greater humility and civility into (...) discourse and debate. (shrink)

Objective: There are benefits and risks of giving patients more granular control of their personal health information in electronic health record (EHR) systems. When designing EHR systems and policies, informaticists and system developers must balance these benefits and risks. Ethical considerations should be an explicit part of this balancing. Our objective was to develop a structured ethics framework to accomplish this. -/- Methods: We reviewed existing literature on the ethical and policy issues, developed an ethics framework called a “Points to (...) Consider” (P2C) document, and convened a national expert panel to review and critique the P2C. -/- Results: We developed the P2C to aid informaticists designing an advanced query tool for an electronic health record (EHR) system in Indianapolis. The P2C consists of six questions (“Points”) that frame important ethical issues, apply accepted principles of bioethics and Fair Information Practices, comment on how questions might be answered, and address implications for patient care. -/- Discussion: The P2C is intended to clarify whatis at stake when designers try to accommodate potentially competing ethical commitments and logistical realities. The P2C was developed to guide informaticists who were designing a query tool in an existing EHR that would permit patient granular control. While consideration of ethical issues is coming to the forefront of medical informatics design and development practices, more reflection is needed to facilitate optimal collaboration between designers and ethicists. This report contributes to that discussion. (shrink)

Background: In prevalence studies of sexually transmitted infections (STIs), investigators often provide syndromic management for symptomatic participants, but may not provide specific treatment for asymptomatic individuals with positive laboratory test results due to the delays between sample collection and availability of results as well as logistical constraints in recontacting study participants. Methods: To characterize the extent of this issue, 80 prevalence studies from the World Health Organization’s Report on global sexually transmitted infection surveillance, 2018, were reviewed. Studies were classified as (...) to whether clinically relevant positive results were returned or if this was not specified. Results: More than half (56%) of the cited studies did not specify if participants were notified of clinically relevant positive STI test results. The percentages were similar for low- and middle-income country populations (57%) and high-income country populations (53%). Conclusions: The absence of documentation of the provision of test results raises the possibility that in some instances, results may not have been communicated, with potential negative effects for participants, their sexual partners, and newborns. From an ethical perspective, clinically relevant results should be returned to study participants and treating clinicians in a timely fashion to ensure appropriate management of identified infections. Study authors should document if they returned test results to study participants and report on numbers lost to follow-up. (shrink)

Conspectus of part of John R. Smythies' Analysis of Perception (1956). It presents a summary of his ideas on phenomenal space – the space of one’s imagination, dreams, psychedelic experiences, somatic sensations, visions, hynagogia, etc. – and its relation to physical space.

The thesis that follows proffers a solution to the mind-matter problem, the problem as to how mind and matter relate. The proposed solution herein is a variant of panpsychism – the theory that all (pan) has minds (psyche) – that we name pansentient monism. By defining the suffix 'psyche' of panpsychism, i.e. by analysing what 'mind' is (Chapter 1), we thereby initiate the effacement of the distinction between mind and matter, and thus advance a monism. We thereafter critically examine the (...) prevalent view, antithetical to a pansentient monism, that mind is not identical to matter but emergent therefrom (Chapter 2). This anti-emergentist critique acts also as a fortification of the Genetic Argument for panpsychism: if mind is not emergent (nor distinct) from matter, mind must always have existed with matter. But what is 'matter'? Chapter 3 investigates what we understand by 'matter', or 'the physical', and exposes it as a highly deficient concept and percept that in concreto points to its identity with that denoted by 'mind'. This also acts as a fortification of the Abstraction Argument for panpsychism, employing a new taxonomy of physicalism and a new taxonomy of the varieties of abstraction. Thus do we reach a monism that is a parsimonious psycho-physical identity theory. But here we face what can be called The Identity Problem for Panpsychism: if our panpsychism is a psycho-physical identity theory, how can it respond to the powerful objections that beset the identity theory of the twentieth century? In Chapter 4 it will be argued that, like emergentism, this psycho-neural identity theory presupposed a deficient concept of 'matter', down to which mind was reduced away, let alone identified. But to identify down phenomena to what is actually an abstraction is to commit failure of explanation. When the theory is amended accordingly, we move from a psycho-neural identity theory to a genuine psycho-physical identity theory that as such can overcome the aforementioned identity problem. Furthermore, as Chapter 5 clarifies, our pansentient monism has, in addition to parsimony, the explanatory power to resolve the problem of mental causation that afflicts both the reductive physicalism of psycho-neural identity theory and the non-reductive physicalism of emergentism, by genuinely identifying physical and mental causation. Jaegwon Kim considers the place of consciousness in a physical world and the nature of mental causation to be the two key components of the mind-matter problem. Through the critical analysis of our prosaic understanding of mind and matter in this thesis, which incorporates the thought of both classical and contemporary thinkers through a novel fusion, it is hoped that both components are addressed and redressed. That is to say that I present this pansentient monism as a plausible, parsimonious, explanatory, and thus, I think, powerful position towards this ever-perplexing mind-matter mystery. -/- [This thesis was passed in January 2019 with viva examination from Galen Strawson and Joel Krueger. (shrink)

This paper uses an extended discussion of Nietzsche’s essay “The Greek State” to uncover the political aspects of his early thinking. The paper builds on a similar discussion of another essay from the same period, “Homer on Competition,” in arguing that Nietzsche’s thinking is based on a confrontation with the work of Plato. It is argued that the key to understanding “The Greek State” is seeing it, in its entirety, as an enigmatic interpretation and re-writing of Plato’s Republic. Nietzsche interprets (...) the Republic as Plato’s accomplishment of the task of the genuine philosopher: the legislation of values and the moulding of human character. (shrink)

Dr Peter Sjöstedt-H reviews Dr Andrew R. Gallimore's book, Alien Information Theory. -/- This was published on PsyPressUK on 13 June 2019.

An exploration into the reciprocity between Nietzsche's drug use and his philosophy.

A mildly chronological overview of the philosophers who may have been inspired by the use of psychoactive chemicals, inc. Plato, de Quincey, Davy, Schopenhauer, Nietzsche, James, Bergson, Benjamin, Jünger, Paz, Marcuse, Sartre, Foucault; and a mention of the Outsight project. -/- This article was based on a talk given for the University of Exeter Philosophy Society and at the ICPR2016 conference.

This public article presents three arguments for the plausibility of panpsychism: the view that sentience is a fundamental and ubiquitous element of actuality. Thereafter is presented a brief exploration of why panpsychism has been spurned. The article was commissioned by High Existence. -/- – Introduction – 1. The Genetic Argument – 2. The Abstraction Argument – 3. The Inferential Argument – Why Panpsychism is Spurned – End Remarks.

Through Alfred North Whitehead’s metaphysics, the Philosophy of Organism, it will be argued that psychedelic experience is a vertical, lateral and temporal integration of sentience.

A Conspectus of A. N. Whitehead's Metaphysics .

Master's Dissertation -/- (Awarded Distinction from Warwick University – assessed by Professors Stephen Houlgate and Christine Battersby, 2002).

Pressure and influences on school leaders as school policy makers during COVID-19 have made the task of interpreting, translating and implementing guidance more a complex and essential operation. School leaders need to prioritise and balance ever-changing government policy advice, against limitations of school buildings, the welfare of students and staff as well as the needs of the communities their schools serve. By surveying and interviewing headteachers, senior leaders and governors, this paper identifies the inputs school leaders have had to react (...) and respond to when creating policy in the context of COVID-19. The paper addresses the nature of, and factors affecting, pressures school leaders feel in authoring policy. The considerable challenges school-based policy makers face in implementing social distancing policy are non-trivial and increase tension to what is already highly stressful work. The report draws on data collected from a randomised, stratified sample of primary and secondary school leaders from across England in early June 2020, during the time of social distancing and school closure for most students. Findings suggest quality, quantity and frequency of top-down communication have contributed to school leader stress, while horizontal communication and collaboration between school leaders and across school communities helped to support leaders during rapid change. We recommend government and the education sector address communication, collaboration and change, to harness the challenges and opportunities identified by school leaders during the COVID-19 pandemic. (shrink)

This paper is a study about Philadelphia’s comprehensive user engagement sites (CUESs) as the authors address and examine issues related to the upcoming implementation of a CUES while seeking solutions for its disputed questions and plans. Beginning with the federal drug schedules, the authors visit some of the medical and public health issues vis-à-vis safe injection facilities (SIFs). Insite, a successful Canadian SIF, has been thoroughly researched as it represents a paradigm for which a Philadelphia CUES can expand upon. Also, (...) the existing criticisms against SIFs are revisited while critically unpackaged and responded to in favor of the establishment. In the main section, the authors propose the layout and services of the upcoming CUES, much of which would be in congruent to Vancouver’s Insite. On the other hand, the CUES would be distinct from Insite, as the authors emphasize, in that it will offer an information center run by individuals in recovery and place additional emphasis on early education for young healthcare professionals by providing them a platform to work at the site. The paper will also briefly investigate the implementation of a CUES site under an ethical scope of the Harm Reduction Theory. Lastly, the authors recommend some strategic plans that the Philadelphia City government may consider employing at this crucial stage. (shrink)

Animal ethicists have recently debated the ethical questions raised by disenhancing animals to improve their welfare. Here, we focus on the particular case of breeding hens for commercial egg-laying systems to become blind, in order to benefit their welfare. Many people find breeding blind hens intuitively repellent, yet ‘welfare-only’ positions appear to be committed to endorsing this possibility if it produces welfare gains. We call this the ‘Blind Hens’ Challenge’. In this paper, we argue that there are both empirical and (...) theoretical reasons why even those adopting ‘welfare-only’ views should be concerned about breeding blind hens. But we also argue that alternative views, which (for example) claim that it is important to respect the telos or rights of an animal, do not offer a more convincing solution to questions raised by the possibility of disenhancing animals for their own benefit. (shrink)

Recent studies show that racism still exists in the American medical profession, the fact of which legitimizes the historically long-legacy of mistrust towards medical profession and health authorities among African Americans. Thus, it was suspected that the participation of black patients in end-of-life care has always been significantly low stemmed primarily from their mistrust of the medical profession. On the other hand, much research finds that there are other reasons than the mistrust which makes African Americans feel reluctant to the (...) end-of-life care, such as cultural-religious difference and genuine misunderstanding of the services. If so, two crucial questions are raised. One is how pervasive or significant the mistrust is, compared to the other factors, when they opt out of the end-of-life care. The other is if there is a remedy or solution to the seemingly broken relationship. While no studies available answer these questions, we have conducted an experiment to explore them. The research was performed at two Philadelphia hospitals of Mercy Health System, and the result shows that Black patients’ mistrust is not too great to overcome and that education can remove the epistemic obstacles as well as overcome the mistrust. (shrink)

Ebola is a deadly disease with no cure; there is no vaccine developed yet. Many died during the 2014 outbreak in West Africa, and many healthcare professionals went to the virus infected area to treat the patients while placing their lives in danger. Not every medical professional placed in the field is a fully trained specialist, and sometimes one or two under-trained doctors are in charge of the entire clinic with some nurses and operating technicians. When unexpected outbreaks of the (...) virus occur in the places, the doctor(s) would encounter medical and ethical dilemmas. Should they leave or stay? In fact, this dilemma is not confined to the Ebola pandemic but relevant to all similar cases. In this paper, three authors, a medical resident, a clinical bioethicist, and a theoretical bioethicist respond to the dilemma. (shrink)

The Deaf culture in the United States is a unique culture that is not widely understood. To members of the Deaf community in the United States, deafness is not viewed as a disease or pathology to be treated or cured; instead it is seen as a difference in human experience. Members of this community do not hide their deafness; instead they take great pride in their Deaf identity. The Deaf culture in the United States is very communitarian not individualistic. Mary (...) Beth and Dominic are a married couple in their late 20s who are genetically deaf. They are active members in the Deaf community and work as advocates for individuals who are deaf, family members of Deaf people and sign language interpreters who identify with the Deaf culture. Mary Beth and Dominic approach the fertility clinic with a request that they only want a child with the genetic gene for deafness. They would want the embryos that do not have the gene to be destroyed. This would entail creating a child who would have the gene for deafness. Medically and ethically, should the fertility clinic agree to the couple’s request? The authors argue that the couple's request should be denied and provide reasons for it from the perspectives of foundational and clinical ethics. (shrink)

As the Zika virus pandemic continues to bring worry and fear to health officials and medical scientists, Centers for Disease Control and Prevention (CDC) and World Health Organization (WHO) have recommended that residents of the Zika-infected countries, e.g., Brazil, and those who have traveled to the area should delay having babies which may involve artificial contraceptive, particularly condom. This preventive policy, however, is seemingly at odds with the Roman Catholic Church’s position on the contraceptive. As least since the promulgation of (...) Paul VI’s 1968 encyclical, Humanae Vitae, the Church has explicitly condemned artificial birth control as intrinsic evil. However, the current pontiff, Pope Francis, during his recent visit to Latin America, remarked that the use of artificial contraception may not be in contradiction to the teaching of Humanae Vitae while drawing a parallel between the current Zika Crisis and the 1960’s Belgian Congo Nun Controversy. The pope mentioned that the traditional ethical principle of the lesser of two evils may be the doctrine that justified the exceptions. The authors of this paper attempt to expand the theological rationale of the pope’s suggestion. In so doing, the authors rely on casuistical reasoning as an analytic tool that compares the Belgian Congo Nun case and the given Zika case, and suggest that the former is highly similar to, if not the same as, the latter in terms of normative moral feature. That is, in both cases the use of artificial contraception is theologically justified in reference to the criteria that the doctrine of the lesser of two evils requires. The authors wish that the paper would provide a solid theological-ethical ground based on which condom-use as the most immediate and effective preventive measure can be recommended in numerous Catholic hospitals as well as among Catholic communities in the world, particularly the most Zika-affected and largest Catholic community in the world, Brazil – 123 million present Brazilian citizens are reported to be Roman Catholic. (shrink)

The protection of rare species abounds with scientific and ethical considerations. An ethical dilemma can emerge when the life of one species is valued higher than that of another, and so we discuss the basis of ranking, protection, and valuation of plants and animals. A duty to protect rare species exists in this age of great losses to plant and animal life, but the scientific and public communities are not always in agreement regarding what species deserve protection. Using a case (...) study, we illustrate how the decision to kill beavers to protect a rare plant and rare animals found in a tidewater creek demanded an ecological ethic approach. We present the concept of a" conservation mediator" and how its use may help find a common ground between stakeholders and decision-makers in similar situations. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (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)

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)

Utilitarianism has a fairly bad reputation in military ethics, mainly because it is thought to make military expedience override all other concerns. The atomic bombing of Hiroshima and Nagasaki is a famous instance of such a skewed utilitarian calculation that “the rules of war and the rights they are designed to protect” should have stopped (Walzer 1992: 263-8). Most of its critics seem to think that utilitarianism is not bad per se, but prone to be misapplied in a self-serving way. (...) That idea, William H. Shaw argues in his careful and mostly convincing defense of utilitarian thinking about the moral issues that war occasions, is misguided, as are most of the other common objections to utilitarian thinking about the moral issues war raises. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

According to Hempel's paradox, evidence (E) that an object is a nonblack nonraven confirms the hypothesis (H) that every raven is black. According to the standard Bayesian solution, E does confirm H but only to a minute degree. This solution relies on the almost never explicitly defended assumption that the probability of H should not be affected by evidence that an object is nonblack. I argue that this assumption is implausible, and I propose a way out for Bayesians. Introduction Hempel's (...) paradox, the standard Bayesian solution, and the disputed assumption Attempts to defend the disputed assumption Attempts to refute the disputed assumption A way out for Bayesians Conclusion. (shrink)

In “Logic and Conversation,” H. P. Grice posits that in conversations, we are “always-already” implying certain things about the subjects of our words while abiding by certain rules to aid in understanding. It is my view, however, that Grice’s so-called “cooperative principle” can be analyzed under the traditional Heideggerian dichotomy of ready-to-hand and present-at-hand wherein language can be viewed as a “mere” tool that sometimes breaks. Ultimately, I contend that the likening of language to a tool allows for a more (...) robust understanding of it and conversational failures, while ontologically recategorizing language as an object of sorts. (shrink)