In previous research, we have argued that private companies should be more open with their scientific research findings. However, our research assumed, somewhat naively perhaps, that public institutions were quite open. Recent findings have suggested otherwise, and in this paper we explore the dilemma faced by industry, universities, and society in attempting to balance the needs of openness (to rapidly advance the body of knowledge), with secrecy (to protect the economic returns to a new innovation).

Background: SNOMED CT is a large terminology system designed to represent all aspects of healthcare. Its current form and content result from decades of bottom-up evolution. Due to SNOMED CT’s formal descriptions, it can be considered an ontology. The Basic Formal Ontology (BFO) is a foundational ontology that proposes a small set of disjoint, hierarchically ordered classes, supported by relations and axioms. In contrast, as a typical top-down endeavor, BFO was designed as a foundational framework for domain ontologies in the (...) natural sciences and related disciplines. Whereas it is mostly assumed that domain ontologies should be created as extensions of foundational ontologies, a post-hoc harmonization of consolidated domain ontologies in use, such as SNOMED CT, is known to be challenging. Methods: We explored the feasibility of harmonizing SNOMED CT with BFO, with a focus on the SNOMED CT Clinical Finding hierarchy. With more than 100,000 classes, it accounts for about one third of SNOMED CT’s content. In particular, we represented typical SNOMED CT finding/disorder concepts using description logics under BFO. Three representational patterns were created and the logical entailments analyzed. Results: Under a first scrutiny, the clinical intuition that diseases, disorders, signs and symptoms form a homogeneous ontological upper-level class appeared incompatible with BFO’s upper-level distinction into continuants and occurrents. The Clinical finding class seemed to be an umbrella for all kinds of entities of clinical interest, such as material entities, processes, states, dispositions, and qualities. This suggests the conclusion that Clinical finding would not be a suitable upper-level class from an BFO perspective. On closer inspection of the taxonomic links within this hierarchy and the implicit meaning derived thereof, it became clear that Clinical finding classes do not characterize the entity (e.g. a fracture, allergy, tumor, pain, hemorrhage, seizure, fever) in a literal sense but rather the condition of a patient having that fracture, allergy, pain etc. This gives sense to the current characteristic of the Clinical Finding hierarchy, in which complex classes are modeled as subclasses of their constituents. Most of these taxonomic links are inferred, as the consequence of the ‘role group’ design pattern, which is ubiquitous in SNOMED CT and has often been subject of controversy regarding its semantics. Conclusion: Our analyses resulted in the proposal of (i) equating SNOMED CT’s ‘role group’ property with the reflexive and transitive BFO relation ‘has occurrent part’; and (ii) reinterpreting Clinical Findings as Clinical Occurrents, i.e. temporally extended entities in an organism, having one or more occurrents as temporal parts that occur in continuants. This re-interpretation was corroborated by a manual analysis of classes under Clinical Finding, as well as the identification of similar modeling patterns in other ontologies. As a result, SNOMED CT does not require any content redesign to establish compatibility with BFO, apart from this re-interpretation, and a suggested re-labeling. Regarding the feasibility of harmonizing terminologies with principled foundational ontologies post-hoc, our results provide support to the assumption that this does not necessarily require major redesign efforts, but rather a careful analysis of the implicit assumptions of terminology curators and users. (shrink)

UNDERSTANDING SCIENTIFIC REASONING develops critical reasoning skills and guides students in the improvement of their scientific and technological literacy. The authors teach students how to understand and critically evaluate the scientific information they encounter in both textbooks and the popular media. With its focus on scientific pedagogy, UNDERSTANDING SCIENTIFIC REASONING helps students learn how to examine scientific reports with a reasonable degree of sophistication. The book also explains how to reason through case studies using the same informal logic skills employed (...) by scientists and to analyze a complex series of propositions and hypotheses using sound scientific reasoning. (shrink)

The genes involved in methionine biosynthesis are scattered throughout the Escherichia coli chromosome and are controlled in a similar but not coordinated manner. The product of the metJ gene and S‐adenosylmethionine are involved in the repression of this ‘regulon’.

Recent studies have yielded new insights into the critical importance of adequate vitamin D3 intake and metabolism. Investigations of the actions of 1,25‐dihydroxyvitamin D3 (calcitriol) on novel target tissues has revealed that this hormone has functions other than its recognized action in regulating blood calcium and phosphate levels. Reports have characterized calcitriol receptors and activities in organs and tissues as diverse as pancreas, skeletal and heart muscle, blood cells, brain, skin, pituitary, parathyroid, kidney, bone and intestine. These studies suggest functions (...) for calcitriol as varied as the regulation of insulin and prolactin secretion, muscle contractility, immune cell metabolism, melanin synthesis and differentiation of blood cells. This information may ultimately help us to understand the etiologies of several kinds of organ dysfunction and lead to the development of tissue‐specific agents for new therapies. (shrink)

Advanced Cell Technology's Ethics Advisory Board has been called window dressing for a corporate marketing plan. But the scientists and managers have paid attention, and the lawyers have gone along.

Although interactions of proteins with glycosaminoglycans (GAGs), such as heparin and heparan sulphate, are of great biological importance, structural requirements for protein‐GAG binding have not been well‐characterised. Ionic interactions are important in promoting protein‐GAG binding. Polyelectrolyte theory suggests that much of the free energy of binding comes from entropically favourable release of cations from GAG chains. Despite their identical charges, arginine residues bind more tightly to GAGs than lysine residues. The spacing of these residues may determine protein‐GAG affinity and specificity. (...) Consensus sequences such as XBBBXXBX, XBBXBX and a critical 20 Å spacing of basic residues are found in some protein sites that bind GAG. A new consensus sequence TXXBXXTBXXXTBB is described, where turns bring basic interacting amino acid residues into proximity. Clearly, protein‐GAG interactions play a prominent role in cell‐cell interaction and cell growth. Pathogens including virus particles might target GAG‐binding sites in envelope proteins leading to infection. BioEssays 20:156–167, 1998. © 1998 John Wiley & Sons, Inc. (shrink)

In the management and business ethics literatures, stakeholder engagement has been demonstrated to lead to more ethical management practices. However, there may be limits on the extent to which stakeholder engagement can, as currently conceptualized, resolve some of the more difficult ethical challenges faced by managers. In this paper we argue that stakeholder engagement, when seen as a way of reducing five types of knowledge problems—risk, ambiguity, complexity, equivocality, and a priori irreducible uncertainty—can aid managers in resolving such ethical challenges. (...) Using a practical illustration of the ethical challenges surrounding the development and application of genetic modification technologies, we demonstrate how stakeholder engagement enables managers to better address these knowledge problems, thereby to manage more ethically. In this way, we suggest that stakeholder engagement has an even more crucial role to play in business ethics research and practice. (shrink)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) testing, and (4) data (...) exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

For almost 30 years the ion channel that initiates the ON visual pathway in vertebrate vision has remained elusive. Recent findings now indicate that the pathway, which begins with unbinding of glutamate from the metabotropic glutamate receptor 6 (mGluR6), ends with the opening of the transient receptor potential (TRP)M1 cation channel. As a component of the mGluR6 signal transduction pathway, mutations in TRPM1 would be expected to cause congenital stationary night blindness (CSNB), and several such mutations have already been identified (...) in CSNB families. Furthermore, expression of TRPM1 in both the retina and skin raises the possibility that a genetic link exists between certain types of visual and skin disorders. (shrink)

Magicians use misdirection to prevent you from realizing the methods used to create a magical effect, thereby allowing you to experience an apparently impossible event. Magicians have acquired much knowledge about misdirection, and have suggested several taxonomies of misdirection. These describe many of the fundamental principles in misdirection, focusing on how misdirection is achieved by magicians. In this article we review the strengths and weaknesses of past taxonomies, and argue that a more natural way of making sense of misdirection is (...) to focus on the perceptual and cognitive mechanisms involved. Our psychologically-based taxonomy has three basic categories, corresponding to the types of psychological mechanisms affected: perception, memory, and reasoning. Each of these categories is then divided into subcategories based on the mechanisms that control these effects. This new taxonomy can help organize magicians' knowledge of misdirection in a meaningful way, and facilitate the dialog between magicians and scientists. (shrink)