As health systems around the world turn towards highly distributed, specialized and cooperative structures to increase quality and safety of care as well as efficiency and efficacy of delivery processes, there is a growing need for supporting communication and collaboration of all parties involved with advanced ICT solutions. The Electronic Health Record (EHR) provides the information platform which is maturing towards the eHealth core application. To meet the requirements for sustainable, semantically interoperable, and trustworthy EHR solutions, different standards and different (...) national strategies have been established. The workshop summarizes the requirements for such advanced EHR systems and their underlying architecture, presents different strategies and solutions advocated by corresponding protagonists, discusses pros and cons as well as harmonization and migration strategies for those approaches. It particularly highlights a turn towards ontology-driven architectures. (shrink)

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)

Some New Mechanists have proposed that claims of compositional relations are justified by combining the results of top-down and bottom-up interlevel interventions. But what do scientists do when they can perform, say, a cellular intervention, but not a subcellular detection? In such cases, paired interlevel interventions are unavailable. We propose that scientists use abduction and we illustrate its use through a case study of the ionic theory of resting and action potentials.

Sometimes neuroscientists discover distinct realizations for a single psychological property. In considering such cases, some philosophers have maintained that scientists will abandon the single multiply realized psychological property in favor of one or more uniquely realized psychological properties. In this paper, we build on the Dimensioned theory of realization and a companion theory of multiple realization to argue that this is not the case. Whether scientists postulate unique realizations or multiple realizations is not determined by the neuroscience alone, but by (...) the psychological theory under examination. Thus, one might say that, in the splitting or non-splitting of properties, psychology enjoys a kind of autonomy from neuroscience. (shrink)

I argue for three conclusions. First, responsibility skeptics are committed to the position that the criminal justice system should adopt a universal nonresponsibility excuse. Second, a universal nonresponsibility excuse would diminish some of our most deeply held values, further dehumanize criminals, exacerbate mass incarceration, and cause an even greater number of innocent people (nonwrongdoers) to be punished. Third, while Saul Smilansky's ‘illusionist’ response to responsibility skeptics – that even if responsibility skepticism is correct, society should maintain a responsibility‐realist/retributivist criminal justice (...) system – is generally compelling, it would not work if a majority of society were to convert, theoretically and psychologically, to responsibility skepticism. In this (highly improbable) scenario, and only in this (highly improbable) scenario, the criminal justice system would need to be reformed in such a way that it aligned with the majority's responsibility‐skeptical beliefs and attitudes. (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)

Experimental results on the Ellsberg paradox typically reveal behavior that is commonly interpreted as ambiguity aversion. The experiments reported in the current paper find the objective probabilities for drawing a red ball that make subjects indifferent between various risky and uncertain Ellsberg bets. They allow us to examine the predictive power of alternative principles of choice under uncertainty, including the objective maximin and Hurwicz criteria, the sure-thing principle, and the principle of insufficient reason. Contrary to our expectations, the principle of (...) insufficient reason performed substantially better than rival theories in our experiment, with ambiguity aversion appearing only as a secondary phenomenon. (shrink)

Language theorists have recently come to have an increasing appreciation for the fact that context contributes heavily in determining our interpretation of what is said. Indeed, it now seems clear that no complete understanding of a natural language is possible without some account of the way in which context affects our interpretation of discourse. In this paper, I will attempt to explore one facet of the language – context relationship, namely, the relation between conditionals and context. The first part of (...) the paper develops an account of truth for conditionals which allows them to depend on momentary features of the context in which they are uttered. In the second half of the paper, comparisons with other recent theories of the conditional will be considered. Particular attention will be given to the problem of whether the conditional really violates classical inferences such as Hypothetical Syllogism and Contraposition as has often been claimed in recent years. (shrink)

I argue for two propositions. First, contrary to the common wisdom, we may justly punish individuals who are not morally responsible for their crimes. Psychopaths – individuals who lack the capacity to feel sympathy – help to prove this point. Scholars are increasingly arguing that psychopaths are not morally responsible for their behavior because they suffer from a neurological disorder that makes it impossible for them to understand, and therefore be motivated by, moral reasons. These same scholars then infer from (...) this conclusion that they must also lack criminal responsibility and therefore that our continuing to punish psychopaths for their crimes is unjust. My response is that this inference is entirely fallacious. -/- Criminal responsibility turns out to be quite distinct from moral responsibility. The two kinds of responsibility require very different conditions to be satisfied. In particular, criminal responsibility, unlike moral responsibility, does not require an agent be able to grasp and follow moral reasons; it requires only that the individual be able to grasp and follow criminal laws. Once this point is recognized, it becomes much easier to accept my thesis: while the subset of psychopaths who commit crimes are not morally responsible for their criminal behavior because they cannot understand moral reasons, they are still criminally responsible because they can understand what the consequences will be if they get caught. For this reason, even though I concede that psychopaths are not morally responsible for the crimes that they commit, our practice of punishing them for these crimes is still just. -/- Second, I argue that psychopathy is a mental illness and should be recognized as such. One reason that it should be recognized as a mental illness is simply because it is; it satisfies the main criteria for inclusion in the DSM-IV, the “bible” of mental disorders. The other reason is more practical than conceptual. It starts with two facts: the U.S. Supreme Court has decided that the preventive detention of any individual who is not a criminal suspect is not constitutional unless the individual is not only dangerous but also mentally ill; and psychopathy is not currently considered to be a mental illness. So, as things now stand, we cannot preventively commit dangerous psychopaths – that is, psychopaths who have clearly indicated that they will be committing serious crimes. Instead, we must wait for them to commit the crimes before we can lock them up. Unfortunately, this incarceration always comes too late for the victims. It would therefore be better if we could lock them up before they actually inflict any harm. Once again, then, I propose that the legal and psychological communities classify psychopathy as a mental illness. (shrink)

I explicate the conditions required for criminal responsibility, provide an overview of criminal defenses, distinguish criminal responsibility from both tort liability and moral responsibility, and explicate the current state of the insanity defense.

In this Article, I will argue that a person may be deserving of criminal punishment even in certain situations where she is not necessarily morally responsible for her criminal act. What these situations share in common are two things: the psychological factors that motivate the individual’s behavior are environmentally determined and her crime is serious, making her less eligible for sympathy and therefore less likely to be acquitted. -/- To get to this conclusion, I will proceed in four steps. In (...) Part II, I will offer the first two of these steps. First, I will argue that our foundational assumption that moral responsibility is necessary for just blame and punishment is not self-evident and is actually rather difficult to explain and justify. Second, I will offer an explanation and justification that appeals to our moral psychology. Specifically, I will argue that we subscribe to this assumption ultimately because we sympathize with agents who lack responsibility for their actions. -/- Third, in Part IV, I aim to show that even if moral responsibility is not conceptually — only “emotionally” — necessary for just blame and punishment, the traditionally recognized criminal excuses are not at risk because, contrary to popular wisdom, they do not really rely on this assumption to begin with. Instead, they stand less for the metaphysical proposition that we should refrain from blaming and punishing the non-responsible and more for the normative/ethical proposition that we should refrain from blaming and punishing those whom we cannot reasonably expect to have acted better. I will further argue that the latter proposition does not necessarily reduce to the former. -/- Fourth, once I have defended my account of the excuses, I will question in Parts V and VI the increasingly popular notion that we should add certain conditions or circumstances to the list of recognized excuses. I will focus on one in particular — the psychological theory of “situationism” — and will argue that, despite its initial plausibility, it should be kept off the list. While situationism arguably does negate moral responsibility, it does not negate criminal responsibility. -/- Of course, this is a controversial point. Criminal responsibility is almost universally thought to require moral responsibility. But in a previous article, "Dangerous Psychopaths: Criminally Responsible But Not Morally Responsible, Subject to Criminal Punishment And to Preventive Detention," 48 San Diego L. Rev. 1299, I used personality psychology to drive a wedge between the two. In this article, I will use the opposite end of the psychological spectrum — social psychology — to drive the same important wedge. (shrink)

I argue that Descartes' Second Causal Proof of God in the Third Meditation evidences, and commits him to, the belief that time is "strongly discontinuous" -- that is, that there is actually a gap between each consecutive moment of time. Much of my article attempts to reconcile this interpretation, the "received view," with Descartes' statements about time, space, and matter in his other writings, including his correspondence with various philosophers.

Analytic philosophers of religion typically take God to be ‘the personal omniGod’ – a person who is omnipotent, omniscient and omnibenevolent, and who creates and sustains all else that exists. Analytic philosophers also tend to assume that the personal omniGod is the God of ‘classical’ theism. Arguably, this is a mistake. To be consistent, a classical theist or her supporter must deny that God is literally a person. They need not, however, deny the aptness of using personal language, or of (...) thinking of God as a person or personal at the level of religious psychology. (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)

This Article falls into three general parts. The first part starts with an important question: is the insanity defense constitutionally required? The United States Supreme Court will finally try to answer this question next term in the case of Kahler v. Kansas. -/- I say “finally” because the Court refused to answer this question in 2012 when it denied certiorari to an appeal brought by John Joseph Delling, a severely mentally ill defendant who was sentenced to life in prison three (...) years earlier for two murders. Delling never had the opportunity to plead the insanity defense because his home state, Idaho, had abolished it in 1982. -/- By depriving Delling of the right to plead insanity, Idaho violated Delling’s Fourteenth Amendment right to due process and his Eighth Amendment right against “cruel and unusual” punishment. Naturally, the same is true for many other mentally ill and disabled defendants who have been prosecuted in Idaho and in the other three states that have abolished the insanity defense: Kansas, Montana, and Utah. -/- The second general part of this Article notes an insight that I stumbled upon in the course of researching the first part: the insanity defense and the mistake of law defense both require ignorance of the law, what I refer to as “normative ignorance.” Indeed, normative ignorance is what makes both of these defenses exculpatory in the first place. -/- Given this critical connection, there is a way for Idaho, Kansas, Montana, and Utah to resume compliance with the Constitution. Instead of reinstating the insanity defense per se, which might be politically unpopular, they should just broaden their mistake of law defense to include normative ignorance caused by cognitive incapacity that is itself caused by mental illness or disability. -/- Still, this Article is not merely directed at these four western states. It is directed at the other forty-six states as well. Because they already have an insanity defense, they need not incorporate it into their mistake of law defense. But in the third general part, I will argue that they should still expand their mistake of law defense to cover defendants who either lack a reasonable opportunity to learn the law or reasonably but mistakenly infer from widely accepted norms or ethics that their conduct is lawful. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

There is something puzzling about statistical evidence. One place this manifests is in the law, where courts are reluctant to base affirmative verdicts on evidence that is purely statistical, in spite of the fact that it is perfectly capable of meeting the standards of proof enshrined in legal doctrine. After surveying some proposed explanations for this, I shall outline a new approach – one that makes use of a notion of normalcy that is distinct from the idea of statistical frequency. (...) The puzzle is not, however, merely a legal one. Our unwillingness to base beliefs on statistical evidence is by no means limited to the courtroom, and is at odds with almost every general principle that epistemologists have proposed as to how we ought to manage our beliefs. (shrink)

This invited entry offers a brief overview of criminal responsibility. -/- The first part starts with a question: is Clyde criminally responsible for killing his girlfriend Bonnie? The answer: it depends. Particular circumstances determine whether Clyde is guilty of murder, guilty of manslaughter, not guilty because he has a good excuse, or not guilty because he has a good justification. -/- The second part addresses the complicated relationship between criminal responsibility and moral responsibility. Until recently, both concepts were considered to (...) be more or less interchangeable. But there is a growing movement, which I refer to as "responsibility skepticism," which maintains that moral responsibility is either physically or metaphysically impossible. If the responsibility skeptics are right (that moral responsibility is impossible), then what are the implications for criminal responsibility and just criminal punishment? Should we abandon these as well? Or can they survive without moral responsibility? I try to answer these questions. -/- The third part addresses social causation. The criminal justice system tends to be "dispositionalist"; it tends, that is, to assume that criminal responsibility resides entirely within the defendant. Dispositionalism, however, overlooks the fact that who we are and what we do are significantly determined by environmental influences. I then try to show that this "situationist" alternative to dispositionalism should not radically alter our approach to criminal punishment. -/- The final part briefly discusses the difficulty in evaluating criminal responsibility when the defendant is both an offender and a victim - especially when the defendant is an offender *because* of his victimization. (shrink)

Maintaining systems of military plans is critical for military effectiveness, but is also challenging. Plans will become obsolete as the world diverges from the assumptions on which they rest. If too many ad hoc changes are made to intermeshed plans, the ensemble may no longer lead to well-synchronized and coordinated operations, resulting in the system of plans becoming itself incoherent. We describe in what follows an Adaptive Planning process that we are developing on behalf of the Air Force Research Laboratory (...) (Rome) with the goal of addressing problems of these sorts through cyclical collaborative plan review and maintenance. The interactions of world state, blue force status and associated plans are too complex for manual adaptive processes, and computer-aided plan review and maintenance is thus indispensable. We argue that appropriate semantic technology can 1) provide richer representation of plan-related data and semantics, 2) allow for flexible, non-disruptive, agile, scalable, and coordinated changes in plans, and 3) support more intelligent analytical querying of plan-related data. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

Peter Baumann uses the Monty Hall game to demonstrate that probabilities cannot be meaningfully applied to individual games. Baumann draws from this first conclusion a second: in a single game, it is not necessarily rational to switch from the door that I have initially chosen to the door that Monty Hall did not open. After challenging Baumann's particular arguments for these conclusions, I argue that there is a deeper problem with his position: it rests on the false assumption that what (...) justifies the switching strategy is its leading me to win a greater percentage of the time. In fact, what justifies the switching strategy is not any statistical result over the long run but rather the "causal structure" intrinsic to each individual game itself. Finally, I argue that an argument by Hilary Putnam will not help to save Baumann's second conclusion above. (shrink)

Gregory Kavka's 'Toxin Puzzle' suggests that I cannot intend to perform a counter-preferential action A even if I have a strong self-interested reason to form this intention. The 'Rationalist Solution,' however, suggests that I can form this intention. For even though it is counter-preferential, A-ing is actually rational given that the intention behind it is rational. Two arguments are offered for this proposition that the rationality of the intention to A transfers to A-ing itself: the 'Self-Promise Argument' and David Gauthier's (...) 'Rational Self-Interest Argument.' But both arguments – and therefore the Rationalist Solution – fail. The Self-Promise Argument fails because my intention to A does not constitute a promise to myself that I am obligated to honor. And Gauthier's Rational Self-Interest Argument fails to rule out the possibility of rational irrationality. (shrink)

Over the last 25 years, there has been a concerted effort to settle questions about multiple realization by bringing detailed scientific evidence to bear. Ken Aizawa and Carl Gillett have pursued this scientific approach to multiple realization with a precise theory and applications. This paper reviews the application of the Dimensioned approach to human color vision, addressing objections that have appeared in the literature.

In this paper we show that being blameworthy for not blaming and being blameworthy for victim blaming are structurally similar. Each involve the two traditional contours of moral responsibility: a knowledge condition and a control condition. But interestingly, in these cases knowledge and control are importantly interrelated. Being in a relationship with another person affords us varying degrees of knowledge about them. This knowledge in turn affords agents in relationships varying degrees of influence over one another. Cases where an agent (...) is especially blameworthy for failing to blame a friend, a close colleague, or a spouse highlight this. The interdependence of these two conditions in interpersonal relationships sheds (partial) light on why victim blaming is morally wrong. We argue that victim blamers suffer from a kind of moral myopia by only focusing on what the victim could do, in virtue of their being in a relationship of some sort with their abuser, to avoid abuse. We focus specifically on cases where such moral myopia is fueled by misogynistic and hierarchical gender schema and scripts. (shrink)

Prof. Cohen and I answer six questions: (1) Why do we lock people up? (2) How can involuntary civil commitment be reconciled with people's constitutional right to liberty? (3) Why don't we treat homicide as a public health threat? (4) What is the difference between legal and medical approaches to mental illness? (5) Why is mental illness required for involuntary commitment? (6) Where are we in our efforts to understand the causes of mental illness?

Consider the reaction of Trayvon Martin’s family to the jury verdict. They were devastated that George Zimmerman, the defendant, was found not guilty of manslaughter or murder. Whatever the merits of this outcome, what does the Martin family’s emotional reaction mean? What does it say about criminal punishment – especially the reasons why we punish? Why did the Martin family want to see George Zimmerman go to jail? And why were – and are – they so upset that he didn’t? (...) -/- This Article will argue for three points. First, what fuels this kind of outrage is vengeance: the desire to see defendants like George Zimmerman be forced to “pay” for the harms that they needlessly and culpably inflict on others. While this point may seem obvious, it isn’t. Most people repudiate revenge and therefore the notion that it plays any role in the criminal justice system. -/- Second, this attitude toward revenge is misguided and needs to change. We need to recognize that vengeance not only does but should play a significant role in motivating criminal punishment. Our vengeful reactions to harmful crimes are not ugly or shameful; on the contrary, they manifest a deep valuation of victims and a bitter denunciation of individuals who actively renounce this valuation through their criminal behavior. -/- Third, these two points have significant implications for the two main theories of criminal punishment: “retributivism,” which says that criminals should be punished in order to give them their “just deserts,” and “consequentialism,” which says that criminals should be punished in order to bring about such good consequences as deterrence, incapacitation, and rehabilitation. Traditionally, these two theories have been at war with one another. But I will show how recognizing revenge as a motivation and justification for punishment can help to end this war and bring these two theories together. (shrink)

Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...) consensus via a formal structured process by a panel of experts for revision of the RDC/TMD. Results: The recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for pain diagnoses and valid criteria for the most common pain-related TMDs and for one intra-articular disorder. The Axis II protocol retains selected RDC/TMD screening instruments augmented with new instruments to better assess the interactions between pain and psychosocial functioning. A comprehensive classification system is also presented. Conclusion: The recommended evidence-based DC/TMD protocol is appropriate for use in both the clinical and research settings. Simple Axis I and II screening tests augmented by validated Axis I and Axis II instruments allow for identification of simple to complex TMD patients. (shrink)

This paper draws on Maurice Merleau-Ponty’s philosophy to sketch a phenomenological interpretation of the enactivist notion of sensorimotor understanding. I begin by situating Noë’s enactive theory of vision in relation to Husserlian phenomenology. I then raise three related objections to Noë’s treatment of sensorimotor understanding in terms of practical knowledge of possibilities for action. Finally, I appeal to Phenomenology of Perception to show how two of its major operative concepts – the ‘body schema’ and ‘sedimentation’ – can help to plug (...) the gaps in Noë’s account. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of (...) making computers understand medical natural language. (shrink)

I argue that the three strongest arguments against metaphysical libertarianism—the randomness objection, the constitutive luck objection, and the physicalist objection—are actually unsuccessful and therefore that metaphysical libertarianism is more plausible than the common philosophical wisdom allows. My more positive thesis, what I will refer to as “Agent Exceptionalism,” is that, when making decisions and performing actions, human beings can indeed satisfy the four conditions of metaphysical libertarianism: the control condition, the rationality condition, the ultimacy condition, and the physicalism condition.

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

For over a century now, American scholars (among others) have been debating the merits of “bad Samaritan” laws — laws punishing people for failing to attempt easy and safe rescues. Unfortunately, the opponents of bad Samaritan laws have mostly prevailed. In the United States, the “no-duty-to-rescue” rule dominates. Only four states have passed bad Samaritan laws, and these laws impose only the most minimal punishment — either sub-$500 fines or short-term imprisonment. -/- This Article argues that every state should criminalize (...) bad Samaritanism. There are three main reasons. First, criminalization is required by the supreme value that we place on protecting human life, a value that motivates laws against both homicide and manslaughter. Second, criminalization is recommended by the “proportionality principle” — i.e., the principle that a law’s level of punishment should be directly proportional to the moral severity of the offense. Third, criminalization would yield a number of significant benefits, including helping to minimize needless deaths and injuries and providing society with an institutional outlet for its outrage against bad Samaritans. -/- Still, many objections have been leveled against bad Samaritan laws. This Article will argue that while some of these objections — for example, the objections involving foundational criminal law principles such as the actus-reus requirement, the harm principle, and causation — are all easily refuted, five other objections are not. These five objections involve pragmatic considerations such as the difficulties with obtaining evidence against bad Samaritans and psychological considerations such as people’s understandable reasons for not wanting to “get involved.” This Article will then put these five objections into reflective equilibrium with the moral arguments for bad Samaritan laws and conclude that while bad Samaritanism should indeed be criminalized, the punishment that convicted bad Samaritans receive should be mild — certainly milder than the level of punishment recommended by the “proportionality principle.” The corollary of this conclusion is that the criminal law should sometimes abandon the proportionality principle. (shrink)

It is generally thought that ought implies can. If this maxim is correct, then my inability to do otherwise entails that I cannot be blamed for failing to do otherwise. In this article, however, I use Harry Frankfurt’s famous argument against the "Principle of Alternative Possibilities" (PAP) to show that the maxim is actually false, that I can be blamed for failing to do otherwise even in situations where I could not have done otherwise. In these situations, I do not (...) act otherwise not because I cannot act otherwise but because I choose not to act otherwise.None. (shrink)

In this article, I weigh in on the debate between "Humeans" and "New Humeans" concerning David Hume's stance on the existence of causal connections in "the objects." According to New Humeans, Hume believes in causal connections; according to Humeans, he does not. -/- My argument against New Humeans is that it is too difficult to reconcile Hume's repeated claims that causal connections are inconceivable with any belief that they these inconceivable somethings still exist. Specifically, Hume either assumes or does not (...) assume that causal connections do or must exist. If he does not, then the New Hume is false. If he does, then it is only reasonable to expect him to do one of two things: (1) provide explicit and unambiguous statements to the effect that he still believes that causal connections do or must exist despite his belief that we cannot even conceive of them and/or (2) provide textual evidence that he subscribes to a reason for believing that causal connections do or must exist in the objects despite his belief that we cannot even conceive of them. I then argue that Hume never satisfies either (1) or (2). -/- My ultimate conclusion is not that the New Hume is false. On the contrary, in section IX, I will argue that the New Hume is still a viable possibility if we attribute a certain other position to Hume – what I will refer to as "Newtonian Empiricism." But I will also argue that this rather plausible interpretation of Hume is equally consistent with Hume's being an agnostic about causal connections and Hume's being a Humean about causal connections. Therefore while we have no good reason to subscribe to the New Hume (rather than Hume's being an agnostic or a Humean), we cannot conclusively rule out this interpretation. (shrink)

Lockheed Martin Corp. has funded research to generate a framework and methodology for developing semantic reasoning applications to support the discipline oflntelligence Analysis. This chapter outlines that framework, discusses how it may be used to advance the information sharing and integrated analytic needs of the Intelligence Community, and suggests a system I software architecture for such applications.

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Disclosure of true but reputation-damaging information is generally legal. But threats to disclose true but reputation-damaging information unless payment is made are generally criminal. Many scholars think that this situation is paradoxical because it seems to involve illegality mysteriously arising out of legality, a criminal act mysteriously arising out of an independently legal threat to disclose conjoined with an independently legal demand for money. -/- But this formulation is not quite right. The real paradox raised by the different legal statuses (...) of blackmail threats to disclose and disclosure itself involves a contradiction between our strong intuition that blackmail threats should be criminal and some equally strong arguments, all of which depend on the fact that disclosure is legal, that blackmail threats should be legal. So an adequate solution to the real Blackmail Paradox requires us either to drop the intuition or to refute the pro-legalization arguments. -/- This Article will adopt the latter approach. It will explain why the six main arguments for legalizing blackmail threats all fail. In the course of refuting one of these arguments, it will also offer a novel positive justification for criminalizing blackmail threats: they should be criminal for the same reason that menacing, harassment, and stalking are criminal--namely, because they involve the reasonable likelihood, and usually the intent, of putting the victim into a state of especially great fear and anxiety. -/- Of course, one might object that disclosure itself is likely to have the same effect, if not malicious purpose. Yet, again, it is still legal. But this point shows only that we as a society value freedom of speech more than we value freedom from infliction of emotional injury. It does not show that we do not value freedom from infliction of emotional injury sufficiently to protect it when competing moral or institutional interests such as freedom of speech are not at stake. (shrink)

My article concerns constitutional interpretation and substantive due process, issues that played a central role in Obergefell v. Hodges (2015), one of the two same-sex marriage cases. (The other same-sex marriage case was United States v. Windsor (2013).) -/- The late Justice Scalia consistently maintained that the Court “invented” substantive due process and continues to apply this legal “fiction” not because the Constitution supports it but simply because the justices like it. Two theories underlay his cynical conclusion. First is the (...) theory of “Constitutional Textualism”—or just plain “Textualism”—which says that the meaning of the Constitution lies entirely within the “four corners” of the document. Second is the theory of “Originalism,” which says that this meaning was fixed at the time of ratification. (Likewise, the meanings of the amendments were fixed at the time of their ratification.) -/- While Justice Scalia helped to inspire a Textualist/Originalist (and anti-substantive-due-process) movement, his Originalism has received far more attention than his Textualism. Since Judge Robert Bork first introduced Originalism to the general public during his Supreme Court nomination hearings in 1987, this theory has ignited passions on all sides and effectively re-framed the entire debate about how to interpret the Constitution. Constitutional scholars, left and right, now define themselves as either for or against Originalism. Meanwhile, Textualism has merely retreated into the background. -/- Part of the reason for this disparate treatment is that many who reject Originalism still consider themselves to be Textualists. They agree with Justice Scalia (and Judge Bork) that the text is all-important. They disagree, however, that its meaning was fixed for eternity at ratification. Instead, they maintain that either the meaning of the text or applications of this meaning to new cases can change as society changes. -/- In this Article, I bring Textualism out of Originalism’s shadow and into broad daylight. I argue that once we dig just a little deeper into the proposition that all of the meaning in the Constitution inheres in its words, we find that this theory simply cannot work. In order to interpret the nation’s foundational document, we must resort to assumptions that it does not explicitly state. (Indeed, even Textualism itself is a theory that the Constitution does not explicitly endorse.) And the notion that “extra-textual” assumptions necessarily inform our interpretations of the Constitution poses a direct and insurmountable threat to Textualism. -/- The Constitution actually requires each judge, when faced with a case concerning the right to privacy, not merely to consider the text but also to anticipate and evaluate the moral, social, and political consequences of both possible decisions before choosing between them. While this position may initially sound counterintuitive, it turns out to be a much more realistic theory of constitutional interpretation than Textualism (and Originalism). -/- I ultimately conclude that, contrary to Justice Scalia, the Constitution most certainly does protect a right to privacy. For what it’s worth, the Obergefell majority agree with me (and oppose Justice Scalia). I aim to show exactly why they are correct. (shrink)

The euthanasia literature typically discusses the difference between “active” and “passive” means of ending a patient’s life. Physician-assisted suicide differs from both active and passive forms of euthanasia insofar as the physician does not administer the means of suicide to the patient. Instead, she merely prescribes and dispenses them to the patient and lets the patient “do the rest” – if and when the patient chooses. One supposed advantage of this process is that it maximizes the patient’s autonomy with respect (...) to both her decision to die and the dying process itself. Still, despite this supposed advantage, Oregon is the only state to have legalized physician-assisted suicide. After summarizing the most important Supreme Court opinions on euthanasia (namely, Cruzan v. Director, Missouri Dep’t of Health; Vacco v. Quill; Washington v. Glucksberg; and Gonzales v. Oregon), this paper argues that while there are no strong ethical reasons against legalizing physician-assisted suicide, there are some very strong policy reasons for keeping it criminal in the other forty-nine states. (shrink)

Ontological principles are needed in order to bridge the gap between medical and biological information in a robust and computable fashion. This is essential in order to draw inferences across the levels of granularity which span medicine and biology, an example of which include the understanding of the roles of tumor markers in the development and progress of carcinoma. Such information integration is also important for the integration of genomics information with the information contained in the electronic patient records in (...) such a way that real time conclusions can be drawn. In this paper we describe a large multi-granular datasource built by using ontological principles and focusing on the case of colon carcinoma. (shrink)

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (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. (shrink)

Suppose you are at the gym trying to see some naked beauties by peeping through a hole in the wall. A policeman happens by, he asks you what you are doing, and you honestly tell him. He then arrests you for voyeurism. Are you guilty? We don’t know yet because there is one more fact to be considered: while you honestly thought that a locker room was on the other side of the wall, it was actually a squash court. Are (...) you guilty now? -/- Probably. You might argue that your scopophiliac ambition was impossible to satisfy given that you were peeping into a squash court, not a locker room. But this “Impossibility Defense” would fail because most jurisdictions follow the very influential Model Penal Code (MPC), which says that what is important about attempt is not the likelihood of success but rather what was going on in your head. You tried to peer into a locker room with the intention of seeing some nudity; that is enough for culpability. The fact that you were mistaken about the location does not exonerate you. -/- But now suppose that the particular jurisdiction you are in does not criminalize voyeurism. While most people think that voyeurism is just plain wrong, if not disgusting, the legislature just never got around to drafting a statute against it. Are you guilty now? The answer is no. But you might just be out of luck and convicted anyway. -/- The reason for this strange conclusion is that most jurisdictions have followed the Model Penal Code in yet another respect: along with the MPC’s “subjectivist” emphasis on what is in your head, they have followed the MPC’s lead in abolishing the Impossibility Defense entirely. As a result, people who believe that they are breaking laws when they really are not may still be subject to arrest, prosecution, and conviction respectively by police, prosecutors, and judges/juries merely if all three parties regard your conduct — especially your trying to violate a law that you mistakenly believed in — as morally reprehensible. The best, if not only, defense against this charge is the Impossibility Defense, but — again — most jurisdictions have decided to make this defense unavailable to defendants. -/- Depriving eligible defendants of the Impossibility Defense is unjust. It violates one of the most basic principles of criminal justice: the legality principle. The legality principle says that there cannot be just punishment without a crime, and there should not be a crime without an explicit law designating it as such. So you cannot be charged with, and convicted of, attempted voyeurism if voyeurism, reprehensible as it may be, was not explicitly prohibited at the time that you made the attempt. -/- If we believe in the legality principle, then we must restore the Impossibility Defense. Without the latter, too many defendants are being — and will continue to be — punished for attempts to perform acts that were not themselves illegal but which various parties in the criminal justice system (except the legislature) thought should be illegal based on their extralegal, moral prejudices. -/- In addition to the MPC, the principal obstacle to resurrecting the Impossibility Defense is a good deal of conceptual confusion that permeates relevant cases and scholarship. Too many courts and academics have conflated “factual impossibility” with “legal impossibility” and have fallaciously inferred “hybrid impossibility” from “hybrid mistakes” (that is, legal mistakes that derive from factual mistakes). One of the principal goals of this Article, then, is to clear up all of this confusion. I will explicate in the simplest possible terms (a) the difference between factual impossibility and legal impossibility, (b) why only legal impossibility qualifies as exculpatory, and (c) why hybrid impossibility simply does not exist. (shrink)

When a widely reused ontology appears in a new version which is not compatible with older versions, the ontologies reusing it need to be updated accordingly. Ontobull has been developed to automatically update ontologies with new term IRI(s) and associated metadata to take account of such version changes. To use the Ontobull web interface a user is required to (i) upload one or more ontology OWL source files; (ii) input an ontology term IRI mapping; and (where needed) (iii) provide update (...) settings for ontology headers and XML namespace IDs. Using this information, the backend Ontobull Java program automatically updates the OWL ontology files with desired term IRIs and ontology metadata. The Ontobull subprogram BFOConvert supports the conversion of an ontology that imports a previous version of BFO. A use case is provided to demonstrate the features of Ontobull and BFOConvert. (shrink)

There are a number of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications represent classes of entities which exist at various anatomical levels of granularity. We argue that in order to apply such representations to the Electronic Health Records one needs sound ontologies which take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal theory for addressing these issues in a (...) way that the ontologies can be used to support inferences relating to entities which exist at different anatomical levels of granularity. Our case study is the colon carcinoma, one of the most common carcinomas prevalent within the European population. (shrink)