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)

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.

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)

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)

"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)

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.

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)

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)

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.

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)

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”...

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)

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.

“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)

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)

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)

This book is a translation of W.V. Quine's Kant Lectures, given as a series at Stanford University in 1980. It provide a short and useful summary of Quine's philosophy. There are four lectures altogether: I. Prolegomena: Mind and its Place in Nature; II. Endolegomena: From Ostension to Quantification; III. Endolegomena loipa: The forked animal; and IV. Epilegomena: What's It all About? The Kant Lectures have been published to date only in Italian and German translation. The present book is filled out (...) with the translator's critical Introduction, "The esoteric Quine?" a bibliography based on Quine's sources, and an Index for the volume. (shrink)

Martine Nida-Rümelin (1996) argues that color science indicates behaviorally undetectable spectrum inversion is possible and raises this possibility as an objection to functionalist accounts of visual states of color. I show that her argument does not rest solely on color science, but also on a philosophically controversial assumption, namely, that visual states of color supervene on physiological states. However, this assumption, on the part of philosophers or vision scientists, has the effect of simply ruling out certain versions of functionalism. While (...) Nida-Rümelin is quite right to search for empirical tests for claims about the nature of visual states, philosophical issues remain pivotal in determining the correctness of these claims. (shrink)

I argue that phenomenal externalism is preferable to phenomenal internalism on the basis of externalism's explanatory power with respect to qualitative character. I argue that external qualities, namely, external physical properties that are qualitative independent of consciousness, are necessary to explain qualitative character, and that phenomenal externalism is best understood as accepting external qualities while phenomenal internalism is best understood as rejecting them. I build support for the claim that external qualities are necessary to explain qualitative character on the basis (...) of a model of color perception as a certain sort of information filter by which perceivers gain access to external qualities. (shrink)

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

With the success of cognitive science's interdisciplinary approach to studying the mind, many theorists have taken up the strategy of appealing to science to address long standing disputes about metaphysics and the mind. In a recent case in point, philosophers and psychologists, including Robert Kane, Daniel C. Dennett, and Daniel M. Wegner, are exploring how science can be brought to bear on the debate about the problem of free will. I attempt to clarify the current debate by considering how empirical (...) research can be useful. I argue that empirical findings don't apply to one basic dimension of the problem, namely the dispute between compatibilism and incompatibilism. However, I show that empirical research can provide constraints in connection with another fundamental dimension, namely the dispute between libertarianism, which claims that indeterminacy is, in certain contexts, sufficient for freedom, and hard determinism and compatibilism, which deny this. I argue that the source of the most powerful constraint is psychological research into the accuracy of introspection. (shrink)

I propose a strategy for a metaphysical reduction of perceived color, that is, an identification of perceived color with properties characterizable in non-qualitative terms. According to this strategy, a description of visual experience of color, which incorporates a description of the appearance of color, is a reference-fixing description. This strategy both takes color appearance seriously in its primary epistemic role and avoids rendering color as metaphysically mysterious. I’ll also argue that given this strategy, a plausible account of perceived color claims (...) that colors are physical properties of physical objects. (shrink)

There has been some recent optimism that addressing the question of how we distinguish sensory modalities will help us consider whether there are limits on a scientific understanding of perceptual states. For example, Block has suggested that the way we distinguish sensory modalities indicates that perceptual states have qualia which at least resist scientific characterization. At another extreme, Keeley argues that our common-sense way of distinguishing the senses in terms of qualitative properties is misguided, and offers a scientific eliminativism about (...) common-sense modalities which avoids appeal to qualitative properties altogether. I’ll argue contrary to Keeley that qualitative properties are necessary for distinguishing senses, and contrary to Block that our common-sense distinction doesn’t indicate that perceptual states have qualia. A non-qualitative characterization of perceptual states isn’t needed to avoid the potential limit on scientific understanding imposed by qualia. (shrink)

The current study is a pilot trial to examine the effects of a nonelective, classroom-based, teacher-implemented, mindfulness meditation intervention on standard clinical measures of mental health and affect in middle school children. A total of 101 healthy sixth-grade students (55 boys, 46 girls) were randomized to either an Asian history course with daily mindfulness meditation practice (intervention group) or an African history course with a matched experiential activity (active control group). Self-reported measures included the Youth Self Report (YSR), a modified (...) Spielberger State-Trait Anxiety Inventory, and the Cognitive and Affective Mindfulness Measure –Revised. Both groups decreased significantly on clinical syndrome subscales and affect but did not differ in the extent of their improvements. Meditators were significantly less likely to develop suicidal ideation or thoughts of self-harm than controls. These results suggest that mindfulness training may yield both unique and non-specific benefits that are shared by other novel activities. (shrink)

This chapter examines the spectrum inversion hypothesis as an argument against certain kinds of account of what it’s like to be conscious of color. The hypothesis aims to provide a counterexample to accounts of what it’s like to be conscious of color in non-qualitative terms, as well as to accounts of what it’s like to be conscious of color in terms of the representational content of conscious visual states (which, according to some philosophers, is in turn given an account in (...) non-qualitative terms). I explain the hypothesis’s reasoning in sections 1 and 2. I then take up background issues: since the counterexample provided by the hypothesis is typically given as a possibility rather than an actuality, I briefly discuss the kind of possibility involved in section 3, and the methodologies used to evaluate the plausibility of possibilities in section 4. In section 5, I describe some general considerations that are commonly used against the spectrum inversion hypothesis. I take up attempts to support the hypothesis with findings from color science in section 6. I end with comments skeptical of both the motivation for the spectrum inversion hypothesis and the methodology used to support it. (shrink)

This thesis is a study of the notion of time in modern physics, consisting of two parts. Part I takes seriously the doctrine that modern physics should be treated as the primary guide to the nature of time. To this end, it offers an analysis of the various conceptions of time that emerge in the context of various physical theories and, furthermore, an analysis of the relation between these conceptions of time and the more orthodox philosophical views on the nature (...) of time. In Part II I explore the interpretation of nonrelativistic quantum mechanics in light of the suggestion that an overly Newtonian conception of time might be contributing to some of the difficulties that we face in interpreting the quantum mechanical formalism. In particular, I argue in favour of introducing backwards-in-time causal influences as part of an alternative conception of time that is consistent with the picture of reality that arises in the context of the quantum formalism. Moreover, I demonstrate that this conception of time can already be found in a particular formulation of classical mechanics. One might see that one of the central themes of Part II originates from a failure to heed properly the doctrine of Part I: study into the nature of time should be guided by modern physics and thus we should be careful not to insert a preconceived Newtonian conception of time unwittingly into our interpretation of the quantum mechanical formalism. Thus, whereas Part I is intended as a demonstration of methodology with respect to the study of time, Part II in a sense explores a confusion that can be seen as arising in the absence of this methodology. (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)

Color subjectivists claim that, despite appearances to the contrary, the world external to the mind is colorless. However, in giving an account of color perception, subjectivists about the nature of perceived color must address the nature of perceived spatial location as well. The argument here will be that subjectivists’ problems with coordinating the metaphysics of perceived color and perceived location render color perception implausibly mysterious. Consequently, some version of color realism, the view that colors are (physical, dispositional, functional, sui generis, (...) or some other) properties of physical objects, is correct. (shrink)

"The Location Problem for Color Subjectivism" response to commentators.

In Ruling Passions, Simon Blackburn contends that we should reject sensibility theory because it serves to support a conservative complacency. Blackburn's strategy is attractive in that it seeks to win this metaethical dispute – which ultimately stems from a deep disagreement over antireductionism – on the basis of an uncontroversial normative consideration. Therefore, Blackburn seems to offer an easy solution to an apparently intractable debate. We will show, however, that Blackburn's argument against sensibility theory does not succeed; it is no (...) more supportive of conservative complacency than Blackburn's noncognitivism. A victory for noncognitivism cannot be so easily won. (shrink)

Martine Nida-Rümelin (1996) argues that color science indicates behaviorally undetectable spectrum inversion is possible and raises this possibility as an objection to functionalist accounts of visual states of color. I show that her argument does not rest solely on color science, but also on a philosophically controversial assumption, namely, that visual states of color supervene on physiological states. However, this assumption, on the part of philosophers or vision scientists, has the effect of simply ruling out certain versions of functionalism. While (...) Nida-Rümelin is quite right to search for empirical tests for claims about the nature of visual states, philosophical issues remain pivotal in determining the correctness of these claims. (shrink)

We initially characterize what we’ll call existence problems as problems where there is evidence that a putative entity exists and this evidence is not easily dismissed; however, the evidence is not adequate to justify the claim that the entity exists, and in particular the entity hasn’t been detected. The putative entity is elusive. We then offer a strategy for determining whether an existence problem is philosophical or scientific. According to this strategy (1) existence problems are characterized in terms of causal (...) roles, and (2) these problems are categorized as scientific or philosophical on the basis of the epistemic context of putative realizers. We argue that the first step of the strategy is necessary to avoid begging the question with regard to categorization of existence problems, and the second step categorizes existence problems on the basis of a distinction between two ways in which an entity can be elusive. This distinction between kinds of elusiveness takes as background a standard account of inference to the best explanation. Applying this strategy, we argue that the existence of a multiverse is a scientific problem. (shrink)

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.

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.

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

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