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)

Background Intestinal transplant in infants with severe short bowel syndrome (SBS) is an emerging therapy, yet without sufficient long-term data or established guidelines, resulting in possible variation in practice. Objectives To assess current attitudes and counselling practices among physicians regarding intestinal transplant in infants with SBS, and to determine whether counselling and management vary between subspecialists or centres. Methods A national sample of practicing paediatric surgeons and neonatologists was surveyed via the American Academy of Paediatrics listserves. Results were analysed by (...) physician subspecialty and again by presence or absence of intestinal transplant at respondent's centre. Results The survey was completed by 433 respondents, consisting of 363 neonatologists and 70 paediatric surgeons. Fifty-seven respondents (13.2%) practiced at a centre that performed intestinal transplants in children. The vast majority of respondents (91% for preterm, 95% for term neonates) felt that maintaining a neonate with SBS on total parenteral nutrition for intestinal transplant was ethically optional (neither impermissible nor obligatory), and that parents should be given an informed choice whether to pursue that option. However, only 33% indicated they often/always offer intestinal transplant as a treatment option to families in this situation. Conclusions There is a marked disparity between individual physicians’ beliefs regarding the acceptability of intestinal transplant for severe SBS and their reported practice. Wide variability exists among physicians with respect to their knowledge, beliefs and practice regarding severe SBS, raising concerns about transparency and justice. Survival data prior to transplant, currently unavailable, are essential to rational decision making and informed parental permission. (shrink)

The persistent failure of public schooling in low-income communities constitutes one of our nation's most pressing civil rights and social justice issues. Many school reformers recognize that poverty, racism, and a lack of power held by these communities undermine children's education and development, but few know what to do about it. A Match on Dry Grass argues that community organizing represents a fresh and promising approach to school reform as part of a broader agenda to build power for low-income communities (...) and address the profound social inequalities that affect the education of children. Based on a comprehensive national study, the book presents rich and compelling case studies of prominent organizing efforts in Chicago, New York City, Los Angeles, Denver, San Jose, and the Mississippi Delta. The authors show how organizing groups build the participation and leadership of parents and students so they can become powerful actors in school improvement efforts. They also identify promising ways to overcome divisions and create the collaborations between educators and community residents required for deep and sustainable school reform. Identifying the key processes that create strong connections between schools and communities, Warren, Mapp, and their collaborators show how community organizing builds powerful relationships that lead to the transformational change necessary to advance educational equity and a robust democracy. (shrink)

ObjectiveMost young adults diagnosed with breast or gynecologic cancers experience adverse reproductive or sexual health outcomes due to cancer and its treatment. However, evidence-based interventions that specifically address the RSH concerns of young adult and/or LGBTQ+ survivor couples are lacking. Our goal is to develop a feasible and acceptable couple-based intervention to reduce reproductive and sexual distress experience by young adult breast and gynecologic cancer survivor couples with diverse backgrounds.MethodsWe systematically adapted an empirically supported, theoretically grounded couple-based intervention to address (...) the RSH concerns of young couples coping with breast or gynecologic cancer through integration of stakeholder perspectives. We interviewed 11 couples with a history of breast or gynecologic cancer to review and pretest intervention materials. Three of these couples were invited to review and comment on intervention modifications. Content experts in RSH and dyadic coping, clinicians, and community advisors participated throughout the adaptation process.ResultsFindings confirmed the need for an online, couple-based intervention to support young couples experiencing RSH concerns after breast or gynecologic cancer. Qualitative themes suggested intervention preferences for: A highly flexible intervention that can be tailored to couples’ specific RSH concerns; Active steps to help members of a dyad “get on the same page” in their relationship and family building plans; A specific focus on raising partners’ awareness about how cancer can affect body image and physical intimacy; and Accessible, evidence-based information about RSH for both partners. These results, along with feedback from stakeholders, informed adaptation and finalization of the intervention content and format. The resulting virtual intervention, Opening the Conversation, includes five weekly sessions offering training to couples in communication and dyadic coping skills for addressing RSH concerns.ConclusionThe systematic adaptation process yielded a theory-informed intervention for young adult couples facing breast and gynecological cancers, which will be evaluated in a randomized controlled trial. The long-term goal is to implement and disseminate Opening the Conversation broadly to reach young adult couples with diverse backgrounds who are experiencing RSH concerns in cancer survivorship. (shrink)

A recent article by Vihalemm (Foundations of Chemistry, 2003) is critical of an earlier essay. We find that there is some justification for his criticism of vagueness in defining terms. Nevertheless the main conclusions of the earlier work, when carefully restated to deflect Vihalemm’s criticisms, are unaffected by his arguments. The various dicta that are used as the bases of chemical explanations are different in character, and are used in a different way from the laws and theories in classical physics.

This study examined the efficacy of corrected feedback for improving consent recall throughout the course of an ongoing longitudinal study. Participants were randomly assigned to either a corrected feedback or a no-feedback control condition. Participants completed a consent quiz 2 weeks after consenting to the host study and at months 1, 2, and 3. The corrected feedback group received corrections to erroneous responses and the no-feedback control group did not. The feedback group displayed significantly greater recall overall and in specific (...) content areas. Results support the use of corrected feedback for improving consent recall. (shrink)

The socioeconomic and ethnic characteristics of parents are some of the most important correlates of adverse health outcomes in childhood. However, the relationships between ethnic, economic, and behavioral factors and the health outcomes responsible for this pervasive finding have not been specified in child health epidemiology. The general objective of this paper is to propose a theoretical approach to the study of maternal behaviors and child health in diverse ethnic and socioeconomic environments. The specific aims are: (a) to describe a (...) causal pathway between the utility that women obtain through work outside the home and through child care and disease hazard rates in childhood using an optimization model; (b) to specify the influence of ethnic and socioeconomic factors on model constraints; (c) to use the model as a tool to learn about how different combinations of maternal wage labor and child care time might influence child health outcomes in diverse social contexts; (d) to identify parameters that will require measurement in future research; (e) to discuss research strategies that will enable us to obtain these measurements; and (f) to discuss the implications of the model for biostatistical modeling and public health intervention. Optimization models are powerful heuristic tools for understanding how ethnic, environmental, family, and personal characteristics can place important constraints on both the quality and quantity of care that women can provide to their children. They provide a quantitative appreciation for the difficult trade-offs that most women face between working in order to purchase basic goods that children cannot do without (e.g., food, clothing, shelter, health insurance), and increasing offspring well-being through child care (e.g., training in social skills, affection, protection from environmental hazards, help with homework). (shrink)

Zonulin is a physiological modulator of intercellular tight junctions, which upregulation is involved in several diseases like celiac disease (CeD). The polyQ gliadin fragment binds to the CXCR3 chemokine receptor that activates zonulin upregulation, leading to increased intestinal permeability in humans. Here, we report a general hypothesis based on the structural connection between the polyQ sequence of the immunogenic CeD protein, gliadin, and enteric coccidian parasites proteins. Firstly, a novel interaction pathway between the parasites and the host is described based (...) on the structural similarities between polyQ gliadin fragments and the parasite proteins. Secondly, a potential connection between coccidial infections as a novel environmental trigger of CeD is hypothesized. Therefore, this report represents a promising breakthrough for coccidian research and points out the potential role of coccidian parasites as a novel trigger of CeD that might define a preventive strategy for gluten‐related disorders in general. Also see the video abstract here: https://youtu.be/oMaQasStcFI. (shrink)

The selected effects or ‘etiological’ theory of Proper function is a naturalistic and realist account of biological teleology. It is used to analyse normativity in philosophy of language, philosophy of mind, philosophy of medicine and elsewhere. The theory has been developed with a simple and intuitive view of natural selection. Traits are selected because of their positive effects on the fitness of the organisms that have them. These ‘selected effects’ are the Proper functions of the traits. Proponents argue that this (...) analysis of biological teleology has the unique advantage that the selected effect function of a trait is also a causal explanation of the trait: the trait exists because it performs this function. We show, however, that selected effect functions as currently defined explain the existence of traits only under highly restrictive assumptions about evolutionary dynamics. In many common scenarios in which traits evolve by natural selection, selected effect functions do not explain those traits. This is because definitions of selected effect function extract from any evolutionary scenario only the information that would be explanatorily relevant in the simple evolutionary scenario implicit in those definitions. When applied to more complex scenarios selected effect functions omit the key information that is explanatorily relevant in those scenarios. The assumptions required for selected effect functions to be explanatory are particularly unlikely to hold in the domain that its proponents care most about - the evolution of representation. A more adequate selected effects theory of Proper functions may be possible, but will require much greater attention to the structure of actual evolutionary explanations. (shrink)

Aristotle’s theory of spontaneous generation offers many puzzles to those who wish to understand his theory both within the context of his biology and within the context of his more general philosophy of nature. In this paper, I approach the difficult and vague elements of Aristotle’s account of spontaneous generation not as weaknesses, but as opportunities for an interesting glimpse into the thought of an early scientist struggling to reconcile evidence and theory. The paper has two goals: to give as (...) charitable and full an account as possible of what Aristotle’s theory of spontaneous generation was, and to examine some of its consequences; and to reflect on Aristotle as a scientist, and what his comments reveal about how he approached a difficult problem. In particular, I propose that the well-recognized problem of the incompatibility between Aristotle’s concept of spontaneity and his theory of spontaneous generation presents an opportunity for insight into his scientific methodology when approaching ill-understood phenomena. (shrink)

This Article explores the relationship between the legitimacy of international courts and expansive judicial lawmaking. We compare lawmaking by three regional integration courts - the Court of Justice of the European Union, the Andean Tribunal of Justice, and the ECOWAS Community Court of Justice. These courts have similar jurisdictional grants and access rules, yet each has behaved in a strikingly different way when faced with opportunities to engage in expansive judicial lawmaking. The CJEU is the most activist, but its audacious (...) legal doctrines have been assimilated as part of the court’s legitimate authority. The ATJ and ECOWAS have been more cautious, but there is little to suggest that this caution has enhanced the legitimacy of either court. The ATJ has avoided serious challenges from governments, but its rulings have had little political impact. Conversely, the ECCJ’s circumspection has not shielded it from political opposition to its adjudication of clearly-established human rights. This pattern is at odds with the oft-voiced conventional wisdom that expansive judicial lawmaking undermines judicial legitimacy. Our modest goal in this Article is to problematize that claim and to posit an alternative hypothesis - that ICs spark legitimacy challenges due to the domestic political effects of their decisions, regardless of whether those decisions are expansionist. (shrink)

The interventionist account of causation has been largely dismissed as a serious candidate for application in physics. This dismissal is related to the problematic assumption that physical causation is entirely a matter of dynamical evolution. In this article, I offer a fresh look at the interventionist account of causation and its applicability to thermodynamics. I argue that the interventionist account of causation is the account of causation that most appropriately characterizes the theoretical structure and phenomenal behavior of thermodynamics.

This book describes the adventures in Russia of Samuel Bentham, the brother of the famous law-reformer, Jeremy Bentham. Shipbuilder, technical expert and inventor, his talents were employed for several years in serving the government of Catherine II, involving him in activities both in peace and war, and in extensive travel through the Russian Empire. The Russian court, war against the Turks, commercial enterprise in Siberia, are a few of the themes illuminated by his correspondence which forms the basis for this (...) book. (shrink)

This invaluable resource is the first one-volume, in-depth, comprehensive history of modern science ever published.

Is it possible to take the enterprise of physics seriously while also holding the belief that the world contains an order beyond the reach of that physics? Is it possible to simultaneously believe in objective laws of nature and in miracles? Is it possible to search for the truths of physics while also acknowledging the limitations of that search as it is carried out by limited human knowers? As a philosopher, as a Christian, and as a participant in the physics (...) of his day, Leibniz had an interesting view that bears on all of these questions. This paper examines the status of laws of nature in Leibniz's philosophy and how the status of these laws fits into his larger philosophical picture of the limits of human knowledge and the wise and omniscient God who created the actual world. (shrink)

The manipulationist account of causation provides a conceptual analysis of cause-effect relationships in terms of hypothetical experiments. It also explains why and how experiments are used for the empirical testing of causal claims. This paper attempts to apply the manipulationist account of causation to a broader range of experiments—a range that extends beyond experiments explicitly designed for the testing of causal claims. I aim to show that the set of causal inferences afforded by an experiment is determined solely on the (...) basis of contrasting case structures that I call “experimental series”, and that the conditions that suffice for causal inference obtain quite commonly, even among “ordinary” experiments that are not explicitly designed for the testing of causal claims. (shrink)

Paul Needham has claimed in several recent papers that Dalton’s chemical atomism was not explanatory. I respond to his criticism of Dalton by arguing that explanation admits of degrees and that under a view that allows for a spectrum of explanatory value, it is possible to see ample worth in Dalton’s atomistic explanations. Furthermore, I argue that even Duhem, who rejected atomism, acknowledged the explanatory worth of Dalton’s atomism.

The current consensus view of causation in physics, as commonly held by scientists and philosophers, has several serious problems. It fails to provide an epistemology for the causal knowledge that it claims physics to possess; it is inapplicable in a prominent area of physics (classical thermodynamics); and it is difficult to reconcile with our everyday use of causal concepts and claims. In this dissertation, I use historical examples and philosophical arguments to show that the interventionist account of causation constitutes a (...) promising alternative for a “physically respectable” account of causation. The interventionist account explicates important parts of the experimental practice of physics and important aspects of the ways in which physical theory is used and applied. Moreover, the interventionist account succeeds where the consensus view of causation in physics fails. I argue that the interventionist account provides an epistemology of causal knowledge in physics that is rooted in experiment. On the interventionist view, there is a close link between experiment and the testing of causal claims. I give several examples of experiments from the early history of thermodynamics that scientists used in interventionist-type arguments. I also argue that interventionist claims made in the context of a physical theory can be epistemically justified by reference to the experimental interventions and observations that serve as evidence for the theory. I then show that the interventionist account of causation is well-suited to the patterns of reasoning that are intrinsic to thermodynamic theory. I argue that interventionist reasoning constitutes the structural foundation of thermodynamic theory, and that thermodynamic theory can provide clear answers to meaningful questions about whether or not a certain variable is a cause of another in a given context. Finally, I argue that the interventionist account offers the prospect of a unification of “physically respectable” causation and our everyday notion of causation. I conclude the dissertation by sketching an anti-foundationalist unification of causation, according to which causal reasoning occurs in the same manner in physics as it does in other branches of life and scientific research. (shrink)

Historical research on John Dalton has been dominated by an attempt to reconstruct the origins of his so-called "chemical atomic theory". I show that Dalton's theory is difficult to define in any concise manner, and that there has been no consensus as to its unique content among his contemporaries, later chemists, and modern historians. I propose an approach which, instead of attempting to work backward from Dalton's theory, works forward, by identifying the research questions that Dalton posed to himself and (...) attempting to understand how his hypotheses served as answers to these questions. I describe Dalton's scientific work as an evolving set of puzzles about natural phenomena. I show how an early interest in meteorology led Dalton to see the constitution of the atmosphere as a puzzle. In working on this great puzzle, he gradually turned his interest to specifically chemical questions. In the end, the web of puzzles that he worked on required him to create his own novel philosophy of chemistry for which he is known today. (shrink)

This volume provides a comparative philosophical investigation into a particular concept from a variety of angles—in this case, the concept of “miracle.” The text covers deeply philosophical questions around the miracle, with a multiplicity of answers. Each chapter brings its own focus to this multifaceted effort. The volume rejects the primarily western focus that typically dominates philosophy of religion and is filled with particular examples of miracle narratives, community responses, and polemical scenarios across widely varying religious contexts and historical periods. (...) Some of these examples defy religious categorization, and some papers challenge the applicability of the concept “miracle,” which is of western and monotheistic origin. By examining miracles thru a wide comparative context, this text presents a range of descriptive content and analysis, with attention to the audience, to the subjective experiences being communicated, and to the flavor of the narratives that come to surround miracles. This book appeals to students and researchers working in philosophy of religion and science, as well those in comparative religion. It represents, in written form, some of the perspectives and dialogue achieved in The Comparison Project’s 2017–2019 lecture series on miracles. The Comparison Project is an enterprise in comparing a variety of religious voices, allowing them to stand in dialogue. (shrink)

Outside Waco, Texas, on 19 April 1993, a 51-day standoff between the Federal Bureau of Investigation and David Koresh and the Branch Davidians concluded with a devastating fire. Despite the fact that FBI negotiators talked on the telephone with Koresh or his main spokesman almost every day, the negotiators were unable to bring the standoff to a peaceful end. A frustrating yet persistent aspect for the FBI negotiators was the Davidians' talk about the Bible and their religious beliefs, what agents (...) dismissively described as `Bible babble'. In this study, we analyze several exchanges between Koresh and one of the FBI agents. The analysis shows how the FBI's identifying their problem as `Bible babble' contributed to the negotiation failure. Through their talk, Koresh was positioned as a biblical expert and the FBI agent as a novice. The FBI's talk also supported Koresh's face. These two conversational patterns, we argue, legitimated God as a key party and Koresh as the person who could best speak for him. In the conclusion, we suggest how a renaming of the problem might have reshaped the FBI's moves. (shrink)

Tobacco mosaic virus has served as a model organism for pathbreaking work in plant pathology, virology, biochemistry and applied genetics for more than a century. We were intrigued by a photograph published in Phytopathology in 1934 showing that Tabasco pepper plants responded to TMV infection with localized necrotic lesions, followed by abscission of the inoculated leaves. This dramatic outcome of a biological response to infection observed by Francis O. Holmes, a virologist at the Rockefeller Institute for Medical Research, was used (...) to score plants for resistance to TMV infection. Our objective was to gain a better understanding of early to mid-twentieth century ideas of genetic resistance to viruses in crop plants. We investigated Holmes’ observation as a practical exercise in reworking an experiment, having been inspired by Pamela Smith’s innovative Making and Knowing Project. We had a great deal of difficulty replicating Holmes’ experiment, finding that biological materials and experimental customs change over time, in ways that ideas do not. Using complementary tools plus careful study and interpretation of the original text and figures, we were able to rework, yet only partially replicate, this experiment. Reading peer-reviewed manuscripts that cited Holmes’ 1934 report provided an additional level of insight into the interpretation and replication of this work in the decades that followed. From this, we touch on how experimental reworking can inform our strategies to address the reproducibility “crisis” in twenty-first century science. (shrink)

The church's response to the gay and lesbian community: a brief history -- Same-sex relations in ancient Jewish and Christian thought -- Key arguments in today's debate on same-sex relationships -- Fifty shekels for rape? Making sense of Old Testament laws -- What is ethical? Interpreting the Bible like Jesus -- The question of celibacy for gay and lesbian people -- Is it Adam's fault? Why the origin of same-sex attraction matters -- Imagining a new response to the gay and (...) lesbian community. (shrink)