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 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.

Two arguments are critiqued here. The first is that hominin mothers “parked” their offspring; the evidence does not support that position. The second is that motherese developed to control the behavior of nonambulatory infants. However, Falk's case is stronger if we apply it to children who are already walking and more likely to be influenced by verbal information.

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)

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)

A basic problem of daily life is determining who owns what. One way that people may solve this problem is by relying on a ‘first possession’ heuristic, according to which the first person who possesses an object is its owner, even if others subsequently possess the object. We investigated preschoolers’ use of this heuristic in five experiments. In Experiments 1 and 2, 3- and 4-year-olds inferred that an object was owned by the character who possessed it first, even though another (...) character subsequently possessed it. Two-year-olds also showed this bias, but only when the object was placed between the characters when children were asked about ownership. Experiment 3 ruled out the possibility that children’s bias to select the first possessor results from a tendency to select the character first associated with the object. Experiment 4 showed that 3- and 4-year-olds have difficulty disregarding the first possession heuristic, even when provided with evidence that the character who first possessed an object is not its owner. But Experiment 5 found that children can disregard the heuristic in at least some situations. These five experiments suggest that the first possession heuristic guides children’s ownership inferences. The findings provide the first evidence that preschoolers can infer who owns what, when not explicitly told, and when not reasoning about objects with which they are personally acquainted. (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)

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)

Self-, collective, and participative efficacy are strong predictors of sustainability action. Yet, few studies have investigated the dynamics and variability of efficacy beliefs. In this transdisciplinary study, we tested such factors in the context of a peer-to-peer coaching program for sustainability volunteers, embedded in a structured-educational context. Over weekends, 2 qualified coaches trained 36 German bottom-up, student-led sustainability initiatives. These coaches instructed students in team building, envisioning, project planning, and on-campus sustainability practice. While 317 participants completed our pre-questionnaire, N = (...) 165 completed both the pre- and post-questionnaire. As hypothesized, after having participated in the coaching weekend, action skills, collaboration skills, group identification, and self-, collective, and participative efficacy all increased. The latter of these increased, to our knowledge, for the first time in environmental psychology research. Group identification and having a vision emerged as important efficacy predictors, and participative efficacy beliefs in turn predicted volunteering. Moreover, we took initial steps in investigating the interaction of psychological and structural factors from a multilevel perspective. Our analyses revealed that efficacy beliefs on the individual level were higher when the university had a green office and when the student initiative was at a small university. We conclude by proposing an empowerment model for sustainability volunteers and by discussing the practical implications of our findings. (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)

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)

Three experiments investigated response times for remember and know responses in recognition memory. RTs to remember responses were faster than RTs to know responses, regardless of whether the remember–know decision was preceded by an old/new decision or was made without a preceding old/new decision . The finding of faster RTs for R responses was also found when remember–know decisions were made retrospectively. These findings are inconsistent with dual-process models of recognition memory, which predict that recollection is slower and more effortful (...) than familiarity. Word frequency did not influence RTs, but remember responses were faster for words than for nonwords. We argue that the difference in RTs to remember and know responses reflects the time taken to make old/new decisions on the basis of the type of information activated at test. (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.

Supporting families of people with developmental disabilities from culturally diverse backgrounds is receiving increased attention in the era of globalisation. However, there is little information about how disability policy and cultural values work together to support families. This article examined how disability policy and Chinese cultural values influence family care of children and young people with developmental disabilities. By comparing qualitative interview data from Chinese families in Taipei (15) and Sydney (10), we analysed how their expression of cultural values in (...) family care differs by policy context, relative to ethics of care claims for recognition, rights and redistribution. We found that positive expressions of Chinese culture in family care fade if policies do not complement them. Policies can alleviate potential tension with cultural values in three ways: reinforcing family capacity to care; ensuring the rights of both family caregivers and people with disabilities; and extending care choices for families. These approaches resonate with ethics of care principles. We argue that culturally responsive disability policy for families means working with cultural values to achieve ethics of care. This implies that incorporating principles of ethics of care could inform cultural responsiveness in disability policy development. (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)

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)

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)

Interest is growing in the relocalization of staple crops, including wheat, in western Washington (WWA), a nontraditional wheat-growing area. Commercial bakers are potentially important food chain intermediaries in the case of relocalized wheat production. We conducted a mail survey of commercial bakers in WWA to assess their interest in sourcing wheat/flour from WWA, identify the characteristics of bakeries most likely to purchase wheat/flour from WWA, understand the factors important to bakers in purchasing regionally produced wheat/flour, and identify perceived barriers to (...) making such purchases. Sixty-one percent of survey respondents were interested in purchasing WWA wheat/flour. Bakers who used retail strategies to market their products were more likely to be interested in WWA wheat/flour compared to those not using retail methods. Bakers’ current purchases of Washington wheat/flour were not related to their interest in purchasing WWA flour. The most important factors bakers would consider in purchasing regionally produced wheat/flour were consistency of flour quality, quality of flour, and reliability of supply. Cost was the most frequently mentioned barrier to the purchase of regionally produced wheat/flour. Our results are relevant for other areas attempting to reconnect grain producers, commercial bakers, and consumers in mutually beneficial ways. (shrink)

Criticism of sex differences in mathematical ability and sex roles in sociobiology and the pernicious influence of these ideas on education.

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.

It’s an honour to have so many major contributors to the literature respond to our article and we thank them for their thoughtful responses. There are clear shared themes across these commentaries,...