During the past two decades, philosophers of biology have increasingly turned their attention to mechanisms of biological phenomena. Through analyses of mechanistic proposals advanced by biologists, the goal of these philosophers is to understand what a mechanism is and how mechanisms explain. These analyses have generally focused on mechanistic proposals for phenomenon that occur at the cellular or sub-cellular level, such as synapse firing, protein synthesis, or metabolic pathway operation. Little is said about the mechanisms of the macromolecular reactions that (...) underpin these phenomena. These reactions comprise a diverse family of reaction types, and include protein folding, macromolecular complex formation, receptor-ligand interactions, and enzyme catalysis. In this paper, I develop an account of mechanism that focuses exclusively on macromolecular reactions. I begin by reviewing how mechanism is understood in enzymology, and how mechanistic concepts of enzymology apply to macromolecular reactions in general. We will see that the mechanism of a macromolecular reaction is most accurately described as a progression of reaction intermediates, where the evolution of intermediates, from one to the next, is characterized by an energetic coupling between chemistry and protein dynamics. I then make the case that this description necessitates a grounding in a process ontology. To describe the mechanism by which a macromolecular reaction occurs is to describe a process. (shrink)

While the British Empire conventionally is recognized as a source of research subjects and objects in anthropology, and a site where anthropological expertise might inform public administration, the settler-colonial affiliations and experiences of many leading physical anthropologists could also directly shape theories of human variation, both physical and cultural. Antipodean anthropologists like Grafton Elliot Smith were pre-adapted to diffusionist models that explained cultural achievement in terms of the migration, contact and mixing of peoples. Trained in comparative methods, these fractious cosmopolitans (...) also favoured a dynamic human biology, often emphasizing the heterogeneity and environmental plasticity of body form and function, and viewing fixed, static racial typologies and hierarchies sceptically. By following leading representatives of empire anatomy and physical anthropology, such as Elliot Smith and Frederic Wood Jones, around the globe, it is possible to recover the colonial entanglements and biases of interwar British anthropology, moving beyond a simple inventory of imperial sources, and crediting human biology and social anthropology not just as colonial sciences but as the sciences of itinerant colonials. (shrink)

Enzymes are protein catalysts of extraordinary efficiency, capable of bringing about rate enhancements of their biochemical reactions that can approach factors of 1020. Theories of enzyme catalysis, which seek to explain the means by which enzymes effect catalytic transformation of the substrate molecules on which they work, have evolved over the past century from the “lock-and-key” model proposed by Emil Fischer in 1894 to models that explicitly rely on transition state theory to the most recent theories that strive to provide (...) accounts that stress the essential role of protein dynamics. In this paper, I attempt to construct a metaphysical framework within which these new models of enzyme catalysis can be developed. This framework is constructed from key doctrines of process thought, which gives ontologic priority to becoming over being, as well as tenets of a process philosophy of chemistry, which stresses environmentally responsive molecular transformation. Enzyme catalysis can now be seen not as enzyme acting on its substrate, but rather as enzyme and substrate entering into a relation which allows them to traverse the reaction coordinate as an ontologic unity. (shrink)

Background: The American Medical Association, the British Medical Association and the Canadian Medical Association have guidelines that specifically discourage physicians from self-prescribing or prescribing to family members, but only the BMA addresses informal prescription requests between colleagues. Objective: To examine the practices of paediatric providers regarding self-prescribing, curbsiding colleagues, and prescribing and refusing to prescribe to friends and family. Methods: 1086 paediatricians listed from the American Academy of Paediatrics 2007 web-based directory were surveyed. Results: 44% of eligible survey respondents returned (...) usable surveys. Almost half of respondents had prescribed for themselves. An equal number had informally requested a prescription from a colleague. Three-quarters stated they had been asked to prescribe a prescription drug for a first-degree or second-degree relative, and 51% had been asked by their spouse. Eighty-six per cent stated that they had refused to write a prescription on at least one occasion for a friend or family member. The following reasons “strongly influenced” their decision to refuse a prescription request: outside of provider’s expertise ; patient’s need for his or her own physician ; not medically indicated ; need for a physical examination. Conclusion: These data confirm that most physicians have engaged in self-prescribing or curbside requests for prescriptions. It can be argued that curbsiding is more morally problematic than self-prescribing because it implicates a third party, and should be discouraged regardless of whether the requester is a colleague, family member or friend. (shrink)

Human suffering is a complex phenomenon that can manifest physically or psychologically. As the negative valence of affective phenomena, with the positive being pleasure or happiness, human suffering could easily be interpreted as something to avoid. Sartre explored existential aspects of human suffering in Being and Nothingness. Examining each occurrence of the word suffering in that work provides a basis for understanding the roles Sartre assigned to it within the human experience and consequently provides a more nuanced appreciation of this (...) complex phenomenon. An electronic copy of Being and Nothingness was searched for all occurrences of the word suffering (N = 50), tabularized using the Key Word In Context (KWIC) approach at the sentence level, resulting in 40 sentences for thematic analysis. That analysis resulted in 5 themes, showing the complexity of suffering in Sartre’s major philosophical work and suggesting that suffering is quintessentially human, unavoidable, and potentially liberating. (shrink)

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

A total of 1918 loci, detected by the hybridization of 938 expressed sequence tag unigenes from 26 Triticeae cDNA libraries, were mapped to wheat homoeologous group 4 chromosomes using a set of deletion, ditelosomic, and nulli-tetrasomic lines. The 1918 EST loci were not distributed uniformly among the three group 4 chromosomes; 41, 28, and 31% mapped to chromosomes 4A, 4B, and 4D, respectively. This pattern is in contrast to the cumulative results of EST mapping in all homoeologous groups, as reported (...) elsewhere, that found the highest proportion of loci mapped to the B genome. Sixty-five percent of these 1918 loci mapped to the long arms of homoeologous group 4 chromosomes, while 35% mapped to the short arms. The distal regions of chromosome arms showed higher numbers of loci than the proximal regions, with the exception of 4DL. This study confirmed the complex structure of chromosome 4A that contains two reciprocal translocations and two inversions, previously identified. An additional inversion in the centromeric region of 4A was revealed. A consensus map for homoeologous group 4 was developed from 119 ESTs unique to group 4. Forty-nine percent of these ESTs were found to be homoologous to sequences on rice chromosome 3, 12% had matches with sequences on other rice chromosomes, and 39% had no matches with rice sequences at all. Limited homology was found between wheat ESTs on homoeologous group 4 and the Arabidopsis genome. Forty-two percent of the homoeologous group 4 ESTs could be classified into functional categories on the basis of blastX searches against all protein databases. (shrink)

How do technologies that are too complex for any one individual to produce arise and persist in human populations? Contra prevailing views focusing on social learning, Osiurak and Reynaud argue that the primary driver for cumulative technological culture is our ability for technical reasoning. Whilst sympathetic to their overall position, we argue that two specific aspects of their account are implausible: first, that technical reasoning is unique to humans; and second, that technical reasoning is a necessary condition for the production (...) of cumulative technological culture. We then present our own view, which keeps technical reasoning at the forefront but jettisons these conditions. This produces an account of cumulative technological culture that maintains an important role for technical reasoning, whilst being more evolutionarily plausible. (shrink)

One of Aristotle's logic treatises, this text is published in the Oxford Classical Text series.

Nurses’ experiences in, and the overall effectiveness of, widely used alternative‐to‐discipline programs to manage nurses’ substance‐use problems have not been adequately scrutinized. We uncovered the conflicted official and experiential ways of knowing one such alternative‐to‐discipline program in a Canadian province. We explicated this conflict through an institutional ethnography analysis. Ethnographic data from interviews with 12 nurses who were enrolled in an alternative‐to‐discipline treatment program and three program administrators, as well as institutional texts, were analyzed to explore how institutional practices and (...) power relations co‐ordinated and managed nurses’ experiences. Analysis revealed the acritical acceptance of a standardized program not based on current norms of practice. Potential and actual conflicts of interest, power imbalances, and prevailing corporate interests were rife. Nurses were not afforded the same rights to quality ethical health care as other citizens. ‘Expert’ physicians’ knowledge was privileged while nurses’ knowledge was subordinated. Conclusions were that regulatory bodies cannot rely on the taken‐for‐granted standardized treatment model in widespread use. Individualized treatment alternatives reflecting current, scientific evidence must be offered to nurses, and nurses’ knowledge, expertise, and experiences need to be included in decision‐making processes in these programs. (shrink)

Until recently, Albert Einstein's complaints in his later years about the intelligibility of Quantum Mechanics often led philosophers and physicists to dismiss him as, essentially, an old fool in his dotage. Happily, this kind of thing is now coming to an end as philosophers and mathematicians of the caliber of Karl Popper and Roger Penrose conspicuously point out the continuing conceptual difficulties of quantum theory [cf. Penrose's searching discussion in The Emperor's New Mind, chapter 6, "Quantum magic and quantum mystery," (...) Oxford 1990]. The Paradox of Schrödinger's Cat is sometimes now even presented, not as a wonderful exciting implication of the theory, but for what it originally was: a reductio ad absurdum argument against the "new" quantum mechanics of Heisenberg and Bohr. Schrödinger shared the misgivings of Einstein and others. (shrink)

This paper describes a cross-cultural research project on the relation between how people conceptualize nature and how they act in it. Mental models of nature differ dramatically among and within populations living in the same area and engaged in more or less the same activities. This has novel implications for environmental decision making and management, including dealing with commons problems. Our research also offers a distinct perspective on models of culture, and a unified approach to the study of culture and (...) cognition. We argue that cultural transmission and formation does not consist primarily in shared rules or norms, but in complex distributions of causally-connected representations across minds in interaction with the environment. The cultural stability and diversity of these representations often derives from rich, biologically-prepared mental mechanisms that limit variation to readily transmissible psychological forms. This framework addresses a series of methodological issues, such as the limitations of conceiving culture to be a well-defined system or bounded entity, an independent variable, or an internalized component of minds. (shrink)

Patients have received experimental pharmaceuticals outside of clinical trials for decades. There are no industry-wide best practices, and many companies that have granted compassionate use, or ‘preapproval’, access to their investigational products have done so without fanfare and without divulging the process or grounds on which decisions were made. The number of compassionate use requests has increased over time. Driving the demand are new treatments for serious unmet medical needs; patient advocacy groups pressing for access to emerging treatments; internet platforms (...) enabling broad awareness of compelling cases or novel drugs and a lack of trust among some that the pharmaceutical industry and/or the FDA have patients’ best interests in mind. High-profile cases in the media have highlighted the gap between patient expectations for compassionate use and company utilisation of fair processes to adjudicate requests. With many pharmaceutical manufacturers, patient groups, healthcare providers and policy analysts unhappy with the inequities of the status quo, fairer and more ethical management of compassionate use requests was needed. This paper reports on a novel collaboration between a pharmaceutical company and an academic medical ethics department that led to the formation of the Compassionate Use Advisory Committee. Comprising medical experts, bioethicists and patient representatives, CompAC established an ethical framework for the allocation of a scarce investigational oncology agent to single patients requesting non-trial access. This is the first account of how the committee was formed and how it built an ethical framework and put it into practice. (shrink)

This is a general account of the Cappadocian Christian Father Gregory of Nyssa (c. 335 - c. 395 CE) as a philosopher. The article is divided into a discussion of his life and his views on God, the world, humanity, history, knowledge, and virtue. A common thread, which would later be systematized in the Palamite essence-energies distinction, is traced in all these topics. Of particular interest to philosophers are comparisons with John Locke and Immanuel Kant.

Veissière et al. must sacrifice explanatory realism and precision in order to develop a unified formal model. Drawing on examples from cognitive archeology, we argue that this makes it difficult for them to derive the kinds of testable predictions that would allow them to resolve debates over the nature of human social cognition and cultural acquisition.

The concept of Health in All Policies aims to improve the health outcomes associated with policies in an attempt to mitigate health disparities and provide optimal environments for healthier living. This multidisciplinary framework seeks to improve health through effective assessment and reformation of policy for organizations of any level and stature. The importance of integrating health in policy assessment and decision making is a key concept in the growing field of Health Impact Assessment.The World Health Organization defines Health Impact Assessment (...) as “a combination of procedures, methods, and tools by which a policy, program, or project may be judged as to its potential effects on the health of a population, and the distribution of those effects within the population.” HIA provides a mechanism for collaboration between various sectors and disciplines bridging the gap between research, policymaking, and implementation of policies, programs, and projects affecting health outcomes. In the United States, while some HIA efforts have focused on proposed public policies, HIA has been used primarily to analyze the health effects of proposed development projects and plans related to community design and transportation. (shrink)