Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in the (...) form of a list of terms and definitions designed to provide a consistent starting point for the representation of both disease and diagnosis in information systems in the future. (shrink)

This study takes as its starting point the problems religious educators experience in communicating the message of the Bible. After analysing the causes of the problems, an alternative approach is presented which is designed to help assure a future for the Bible. The first cause which is discussed is biblical fundamentalism. We present the literal meaning of the Bible as a developmental stage of every human person. Problems arise when people refuse to grow beyond this stage or when, not having (...) had the opportunity of learning about alternative approaches, they reject the Bible together with the fundamentalist approach. The second cause of the problems in teaching the Bible today is called ‘scientific’ fundamentalism. With this we refer to a specific way of using the historical-critical method which accepts nothing but its own methodology as a hermeneutic approach and ends up with a fundamentalist reading of its own research results. The third cause of the problem is the widespread moralising use of the biblical message. This approach tends to reduce the biblical message to its ethical dimension and to reduce the ethical dimension to moralising. In a fourth section, we present the opportunities and dangers presented by the digitalisation of the biblical text. While we acknowledge the inherent dangers and recognise the problem of the first three mentioned problems all find their way into the digital presentation of the Bible, we nevertheless recognise the great opportunities which the new media provide in making the approach to the Bible more dynamic and interactive. In the second part, we present an alternative model. We propose an understanding of the Bible and its genesis as witness to the ongoing dialogue between God and human persons in community. With the writing of the last word of the Bible and the closing of the canon, revelation has not come to its end. Reading the Bible does not excuse us from having to enter into a personal relationship with God. The Bible itself leaves much room for creative interpretation and invites critical dialogue. As a criterion for the reading of the Bible, we propose the question whether a reading opens up a future for all or whether it helps some gain advantages at the cost of others. We are convinced that the Bible will have a future, if its reading and interpretation enables people to participate in building the future that is according to God’s design. (shrink)

The purpose of this book is to provide you with tools to become a better reader of nonfiction, argumentative texts.

The book investigates theories dating from the 13th to the 18th century on the moral indifference of human action with a view to substantiating the hypothesis of a heterogeneous genealogy of the specifically modern concept of 'aesthetics'. Aesthetic discourse on art did not develop of its own self and in its own right but was essentially based on genuinely moral-theological concepts (or concepts evolving in the context of moral theology) relating to the eventuality of human action being adiaphoric in origin. (...) Both in methodological terms and in conjunction with its subject, this study proposes an aetiology, rather than a pre-history, of aesthetic thinking. (shrink)

After a short introduction into the history of the building of the Physics Institute of the University of Breslau, the development under Otto Lummer is sketched: influenced by the newly founded Technische Hochschule, the building as well as the faculty, were enlarged. The collection of instruments for instruction and research was built up and the cooperation with industry and with guests from abroad strengthened. Young scientists were promoted, making Lummer’s institute into one of the leading ones in optics at that (...) time. (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)

The 1994 Letter Ordinatio sacerdotalis of Pope John Paul II focuses mainly on the argument from Scripture. It states that women cannot be ordained priests in the Roman Catholic Church because Jesus consciously and in harmony with God’s will only chose men to be his apostles. In this article we confront the arguments and presuppositions of this way of reason with the results of historical-critical exegesis. We arrive at the conclusion that the letter’s identification of the apostles with the Twelve (...) takes as historical the theology of apostleship found in Luke and neglects Paul’s views on apostleship as well as thee evidence of women’s involvement in ministry in the Pauline churches. In a second part this study pursues the question why, according to Ordinatio sacerdotalis, the Twelve had to be men. While the letter does not take any explicit stand on this issue, we come to the conclusion that it implicitly presupposes a theological difference between men and women. (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)

Wie finden Medien Eingang in die Theorie der Rhetorik? Und wie findet Rhetorik Eingang in die Praxis der Medien? Der vorliegende Band erschließt die Beziehung zwischen der Rhetorik und den Medien sowohl historisch und systematisch als auch in aktuellen Fallstudien. Im ersten Teil wird dargelegt, wie die mediale Grundstruktur der Rhetorik reflektiert wurde – in die Bedeutung von Medien für das überzeugende Handeln von der Antike und Spätantike über Mittelalter, Renaissance, Barock sowie Aufklärung und Moderne bis zu gegenwärtigen Theorien. Im (...) systematischen Teil wird erörtert, wie das Verhältnis von Rhetorik und Medien in Bezug auf unterschiedliche Medienträger wie Bild, Rede, Musik, Architektur, Werbung, Websites etc. spezifiziert werden kann. Die Fallstudien stellen an konkreten Beispielen vor, wie sich die Mediengestaltung von heute der Rhetorik bedienen kann. Der Band liefert so einen umfassenden Einblick und ist somit für jeden Medienschaffenden eine wichtige Grundlage. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

When developing the Ontology of Biomedical Investigations (OBI), the process of adding classes with similar patterns of logical definition is time consuming, error prone, and requires an editor to...

Gersonides' Afterlife is the first full-scale treatment of the reception of one of the greatest scientific minds of medieval Judaism: Gersonides (1288-1344). An outstanding representative of the Hebrew Jewish culture that then flourished in southern France, Gersonides wrote on mathematics, logic, astronomy, astrology, physical science, metaphysics and theology, and commented on almost the entire bible. His strong-minded attempt to integrate these different areas of study into a unitary system of thought was deeply rooted in the Aristotelian tradition and yet innovative (...) in many respects, and thus elicited diverse and often impassionate reactions. For the first time, the twenty-one papers collected here describe Gersonides' impact in all fields of his activity and the reactions from his contemporaries up to present-day religious Zionism. (shrink)

Gersonides' Afterlife is the first full-scale treatment of the reception of one of the greatest scientific minds of medieval Judaism: Gersonides (1288-1344). An outstanding representative of the Hebrew Jewish culture that then flourished in southern France, Gersonides wrote on mathematics, logic, astronomy, astrology, physical science, metaphysics and theology, and commented on almost the entire bible. His strong-minded attempt to integrate these different areas of study into a unitary system of thought was deeply rooted in the Aristotelian tradition and yet innovative (...) in many respects, and thus elicited diverse and often impassionate reactions. For the first time, the twenty-one papers collected here describe Gersonides' impact in all fields of his activity and the reactions from his contemporaries up to present-day religious Zionism. (shrink)

This guide accompanies the following article(s): ‘Full Disclosure of the “Raw Data” of Research on Humans: Citizens’ Rights, Product Manufacturer’s Obligations and the Quality of the Scientific Database.’Philosophy Compass 6/2 (2011): 90–99. doi: 10.1111/j.1747‐9991.2010.00376.x Author’s Introduction Securing consent (and informed consent) from patients and research study participants is a key concern in patient care and research on humans. Yet, the legal doctrines of consent and informed consent differ in their applications. In patient care, the judicial doctrines of consent and informed (...) consent are disclosure doctrines based on the obligation of physicians to inform their patients of the following types of information: the nature of the procedure the physician is recommending in the patent’s care (P), the alternatives to the physician‐recommendation (A), and the risks of procedure and its alternatives (R). In addition, the physician must provide truthful answers to the patient’s questions (Q) to the best of the physician’s abilities. In research on humans, the onus of disclosure by study sponsors and principal investigators is much greater than in patient care precisely because the purpose of research is not patient care. The purpose of research is the identification and development of new generalizable knowledge. Thus, participation in a research study or trial may not benefit the study volunteer at all. In addition, the participant may carry a heavy risk burden in relationship to any testing of a newly designed drug or device as part of their experiences in the research study. Presently, despite the risks borne by the research study participant, the raw data collected from volunteers in research trials are treated by courts as if they were the private property of the study sponsor rather than generally owed to the public as would be expected by an effort like research participation aimed at contributing to the development of generalizable knowledge. This paper reviews the obligations that study sponsors owe to their study participants based on the very definition of research as a systematic activity whose purpose is to develop generalizable knowledge to help all humans. Author Recommends Court cases Canterbury v. Spence, United States Court of Appeals, District of Columbia Circuit 464 F.2d 772 (1972). (Federal appellate decision heard in the District of Columbia, USA) Reibl v. Hughes, 2 S.C.R. 880 (1980). (Supreme Court of Canada) Rogers v. Whitaker, 175 C.L. R. 479 (1992). (High Court of Australia) Sidaway v. Board of Governors of the Bethlem Royal Hospital and the Maudsley Hospital and Others. 1 A.C. 871 (1985) (House of Lords) Canterbury v. Spence is the landmark Federal informed consent case in the United States heard in the District of Columbia. In this case, Judge Spottswood Robinson articulated the reasonable person standard of informed consent. This standard was subsequently adopted by the Supreme Court of Canada (Reibl v. Hughes, 2 S.C.R. 880 (1980)) and the High Court of Australia (Rogers v. Whitaker, 175 C.L. R. 479 (1992)). The House of Lords rejected the reasonable person standard in England in Sidaway v. Board of Governors of the Bethlem Royal Hospital and the Maudsley Hospital and Others. 1 A.C. 871 (1985). Book Mazur, Dennis J. The Science and Ethics of Research on Humans. Baltimore, MD: Johns Hopkins University Press, 2007. This book is a detailed guide for the review of scientific and ethical aspects of research on humans contained in the research study protocols and research informed consent forms which need to be submitted by study sponsors and principal investigators to institutional review boards (IRBs) for IRB review before a research study can receive approval to be conducted within a human study population in those institutions over which the IRB has authority. It also presents basic definitions in the area of research on humans and basic approaches to help conduct a deep review of the underlying scientific and ethical issues that are present within a research study protocol and its accompanying research informed consent form. Report National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research. The Belmont Report: Ethical Guidelines for the Protection of Human Subjects of Research. Washington, DC: DHEW Publications, 1978 (78‐0012). This U.S. National Commission in the Belmont Report argued for the necessity of a reasonable volunteer standard in research on humans in the United States. Arguing that the professional standard and the reasonable person standard of consent and informed consent were insufficient to base a disclosure standard in research on humans, this National Commission developed the reasonable volunteer standard where a study participant is to be approached in research informed consent with that information that a reasonable volunteer would want to know. Online Materials Belmont Report: Syllabus Topics for Lecture and Discussion Week I: Introduction and Overview Readings: Rogers v. Whitaker, 175 C.L.R. 479 (1992). (High Court of Australia) Sidaway v. Board of Governors of the Bethlem Royal Hospital and the Maudsley Hospital and Others. 1 A.C. 871 (1985) (House of Lords) Week II: The Different Standards of Consent and Informed Consent Readings: Canterbury v. Spence, 464 F.2d 772 (1972). (Federal appellate opinion heard in the District of Columbia) Sidaway v. Board of Governors of the Bethlem Royal Hospital and the Maudsley Hospital and Others. 1 A.C. 871 (1985) (House of Lords) Week III: Definition of Research Reading: Mazur, Dennis J. The Science and Ethics of Research on Humans. Baltimore, MD: Johns Hopkins University Press, 2007. (Especially Chapters 2 and 3) Week IV: How to Review a Research Study Protocol and Research Informed Consent Form Reading: Mazur, Dennis J. The Science and Ethics of Research on Humans. Baltimore, MD: Johns Hopkins University Press, 2007. (Especially Chapters 4–6, 10, and 12–14) Week V: Obligations in Research of Humans Versus Patient Care Reading: National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research. The Belmont Report: Ethical Guidelines for the Protection of Human Subjects of Research. Washington, DC: DHEW Publications, 1978 (78‐0012). Focus Questions • How do the judicial doctrines of consent in England and Australia compare to the judicial doctrines of informed consent in the United States and Canada? • How does a professional standard of disclosure differ from a reasonable person standard of disclosure? • What is the definition of research? • How is a research study (study proposal and research informed consent form) reviewed from scientific and ethical bases for considerations of approval by an IRB? • How do the obligations of a study sponsor, a principal investigator, and a research team conducting a research trial on human study participants differ from the obligations of a physician caring for a patient? • Should all raw data of research derived from humans be made available to the public for use in developing generalizable knowledge to help others, or should raw data be considered the private property of the study sponsors (for example, prescription drug manufacturers), who fund the research trials? Seminar/project Idea Draw a timeline of the development of the basic concepts of consent and informed consent in patient care and in patient research. On this timeline, first place the dates of the key court cases in England, the United States, Canada, and Australia on consent and informed consent. Then place the date of the development of the Belmont Report. Why do differences exist between these four countries in terms of the legal requirements of informedness of a patient (in medical care) and a study participant (in medical research)? What roles if any do the concepts of self‐determination and self‐decision have in consent and informed consent in patient care and in informed consent in research on humans among the four countries of interest? What are the realities of research on human participants that require a new standard of informed consent, the reasonable volunteer standard, to be developed beyond the two standards in patient care, the professional standard, and the reasonable person standard? Counterpoint Arguments The following are counterpoint arguments that need to be appreciated to more fully understand the concepts that impact the thesis that ‘raw data’ should be open to the public to allow the opportunity of checking of the results of its associated scientific paper and for further analysis. De‐Identified (Anonymized) Raw Data A current approach to identifying (anonymizinig) raw data is based on the Health Insurance Portability and Accountability Act (HIPAA) of 1996 (P.L.104‐191). HIPAA was enacted by the U.S. Congress in 1996 to keep a person’s medical information private. In a research study, a person’s private medical information can become research data. HIPAA’s Privacy Rule allows a covered entity to de‐identify data by removing all 18 elements that could be used to identify the individual or the individual’s relatives, employers, or household members; these elements are enumerated in the Privacy Rule. The covered entity must also have no actual knowledge that the remaining information could be used alone or in combination with other information to identify the individual who is the subject of the information. Under this method, the identifiers that must be removed are the following: 1 Names. 2 All geographic subdivisions smaller than a state, including street address, city, county, precinct, ZIP Code, and their equivalent geographical codes, except for the initial three digits of a ZIP Code if, according to the current publicly available data from the Bureau of the Census: 2a. The geographic unit formed by combining all ZIP Codes with the same three initial digits contains more than 20,000 people. 2b. The initial three digits of a ZIP Code for all such geographic units containing 20,000 or fewer people are changed to 000. 3 All elements of dates (except year) for dates directly related to an individual, including birth date, admission date, discharge date, and date of death, and all ages over 89 and all elements of dates (including year) indicative of such age, except that such ages and elements may be aggregated into a single category of age 90 or older. 4 Telephone numbers. 5 Facsimile numbers. 6 Electronic mail addresses. 7 Social security numbers. 8 Medical record numbers. 9 Health plan beneficiary numbers. 10 Account numbers. 11 Certificate/license numbers. 12 Vehicle identifiers and serial numbers, including license plate numbers. 13 Device identifiers and serial numbers. 14 Web universal resource locators (URLs). 15 Internet protocol (IP) address numbers. 16 Biometric identifiers, including fingerprints and voiceprints. 17 Full‐face photographic images and any comparable images. 18 Any other unique identifying number, characteristic, or code, unless otherwise permitted by the Privacy Rule for re‐identification. Even though ‘raw data’ can be de‐identified (anonymized) so that there is no way to trace back the data to the study participant from which it was drawn, there are still questions whether the ‘de‐identified raw data’ can be given to other researchers or made public without the original study participant’s approval. It may be the case that this approval could be done at the start of any research study where the individual considering study participation would be counseled on what the process of de‐identification consists of and would be asked whether the participant would allow use of the data by other researchers or made available to the public in a de‐identified state. However, there may be questions of the study participants as to whether the data are truly de‐identified and untraceable back to the study participant since the participant would not be able to see the process actually being carried out in detail in all relevant circumstances. Using Raw Data in Context Simply being in possession of raw data is never enough to build on that data from a research perspective. Researchers need to understand the context of the scientific research study in which the data were collected. This research context includes (but is not limited to): (i) the scientific hypothesis of the research study, (ii) the inclusion and exclusion criteria selected by the research designers of the study to determine which study participants were included and which were excluded from the study, (iii) the methods used to collect the data and possibilities of errors in the data collection processes, and (iv) answers to questions regarding whether any data were excluded from the study data and why these data were excluded. Ownership Rights Over Data There are ownership rights over data. Ownership rights include court decision making related to the question which parties are to be considered as the owners of the data. Possible owners here include (but are not limited to) (i) the study sponsor whose only role was to fund that study, (ii) the principal investigator(s) who developed the scientific hypothesis, and (iii) individual study participants through special contracts made by individual participants who negotiate such contracts with study sponsors and principal investigators to share in the ownership of data. Examples of such data are participant sources of unique gene lines or unique cell lines to be used in future research. Objections to Data Sharing Finally, individual researchers may simply object to sharing data. A researcher’s arguments here may be simply stating that he or she has a right to fully analyze the data since the collection of the data was the researchers’ idea in the first place. These researchers may argue that they have the right to mine the data as fully as they can before deciding to make the data open to the public for others to analyze. Works Cited 1 Kaiser, J. ‘Making Clinical Data Widely Available.’Science 322.5899 (10 Oct. 2008): 217–8. 2 de Lusignan, S., J.F. Metsemakers, P. Houwink, V. Gunnarsdottir, and J. van der Lei. ‘Routinely Collected General Practice Data: Goldmines for Research? A Report of the European Federation for Medical Informatics Primary Care Informatics Working Group (EFMI PCIWG) from MIE2006, Maastricht, The Netherlands.’Informatics in Primary Care 14.3 (2006): 203–9. 3 Sim, I. ‘Human Studies Database Project’, CTSA Data Repositories Symposium (17 Oct. 2008). 23 Nov. 2010. 4 Sim, I., C.G. Chute, H. Lehmann, R. Nagarajan, M. Nahm, and R.H. Scheuermann. ‘Keeping Raw Data in Context.’Science 323.5915 (6 Feb. 2009): 713. 5 U.S. Department of Health and Human Services, National Institutes of Health, HIPAA Privacy Rule, Information for Researchers. 13 Nov. 2010. 6 Wilczynski, N.L., R.B. Haynes, and Hedges Team. ‘EMBASE Search Strategies for Identifying Methodologically Sound Diagnostic Studies for Use by Clinicians and Researchers.’BMC Medicine 29.3 (March 2005): 7. (shrink)

I argue that the distinctions Robert Batterman (2004) presents between ‘epistemically fundamental’ versus ‘ontologically fundamental’ theoretical approaches can be subsumed by methodologically fundamental procedures. I characterize precisely what is meant by a methodologically fundamental procedure, which involves, among other things, the use of multilinear graded algebras in a theory’s formalism. For example, one such class of algebras I discuss are the Clifford (or Geometric) algebras. Aside from their being touted by many as a “unified mathematical language for physics,” (Hestenes (1984, (...) 1986) Lasenby, et. al. (2000)) Finkelstein (2001, 2004) and others have demonstrated that the techniques of multilinear algebraic ‘expansion and contraction’ exhibit a robust regularizablilty. That is to say, such regularization has been demonstrated to remove singularities, which would otherwise appear in standard field-theoretic, mathematical characterizations of a physical theory. I claim that the existence of such methodologically fundamental procedures calls into question one of Batterman’s central points, that “our explanatory physical practice demands that we appeal essentially to (infinite) idealizations” (2003, 7) exhibited, for example, by singularities in the case of modeling critical phenomena, like fluid droplet formation. By way of counterexample, in the field of computational fluid dynamics (CFD), I discuss the work of Mann & Rockwood (2003) and Gerik Scheuermann, (2002). In the concluding section, I sketch a methodologically fundamental procedure potentially applicable to more general classes of critical phenomena appearing in fluid dynamics. (shrink)

The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical (...) presentation including signs and symptoms. (shrink)

This guide accompanies the following article(s): ‘Full Disclosure of the “Raw Data” of Research on Humans: Citizens’ Rights, Product Manufacturer’s Obligations and the Quality of the Scientific Database.’Philosophy Compass 6/2 (2011): 90–99. doi: 10.1111/j.1747‐9991.2010.00376.x Author’s Introduction Securing consent (and informed consent) from patients and research study participants is a key concern in patient care and research on humans. Yet, the legal doctrines of consent and informed consent differ in their applications. In patient care, the judicial doctrines of consent and informed (...) consent are disclosure doctrines based on the obligation of physicians to inform their patients of the following types of information: the nature of the procedure the physician is recommending in the patent’s care (P), the alternatives to the physician‐recommendation (A), and the risks of procedure and its alternatives (R). In addition, the physician must provide truthful answers to the patient’s questions (Q) to the best of the physician’s abilities. In research on humans, the onus of disclosure by study sponsors and principal investigators is much greater than in patient care precisely because the purpose of research is not patient care. The purpose of research is the identification and development of new generalizable knowledge. Thus, participation in a research study or trial may not benefit the study volunteer at all. In addition, the participant may carry a heavy risk burden in relationship to any testing of a newly designed drug or device as part of their experiences in the research study. Presently, despite the risks borne by the research study participant, the raw data collected from volunteers in research trials are treated by courts as if they were the private property of the study sponsor rather than generally owed to the public as would be expected by an effort like research participation aimed at contributing to the development of generalizable knowledge. This paper reviews the obligations that study sponsors owe to their study participants based on the very definition of research as a systematic activity whose purpose is to develop generalizable knowledge to help all humans. Author Recommends Court cases Canterbury v. Spence, United States Court of Appeals, District of Columbia Circuit 464 F.2d 772 (1972). (Federal appellate decision heard in the District of Columbia, USA) Reibl v. Hughes, 2 S.C.R. 880 (1980). (Supreme Court of Canada) Rogers v. Whitaker, 175 C.L. R. 479 (1992). (High Court of Australia) Sidaway v. Board of Governors of the Bethlem Royal Hospital and the Maudsley Hospital and Others. 1 A.C. 871 (1985) (House of Lords) Canterbury v. Spence is the landmark Federal informed consent case in the United States heard in the District of Columbia. In this case, Judge Spottswood Robinson articulated the reasonable person standard of informed consent. This standard was subsequently adopted by the Supreme Court of Canada (Reibl v. Hughes, 2 S.C.R. 880 (1980)) and the High Court of Australia (Rogers v. Whitaker, 175 C.L. R. 479 (1992)). The House of Lords rejected the reasonable person standard in England in Sidaway v. Board of Governors of the Bethlem Royal Hospital and the Maudsley Hospital and Others. 1 A.C. 871 (1985). Book Mazur, Dennis J. The Science and Ethics of Research on Humans. Baltimore, MD: Johns Hopkins University Press, 2007. This book is a detailed guide for the review of scientific and ethical aspects of research on humans contained in the research study protocols and research informed consent forms which need to be submitted by study sponsors and principal investigators to institutional review boards (IRBs) for IRB review before a research study can receive approval to be conducted within a human study population in those institutions over which the IRB has authority. It also presents basic definitions in the area of research on humans and basic approaches to help conduct a deep review of the underlying scientific and ethical issues that are present within a research study protocol and its accompanying research informed consent form. Report National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research. The Belmont Report: Ethical Guidelines for the Protection of Human Subjects of Research. Washington, DC: DHEW Publications, 1978 (78‐0012). This U.S. National Commission in the Belmont Report argued for the necessity of a reasonable volunteer standard in research on humans in the United States. Arguing that the professional standard and the reasonable person standard of consent and informed consent were insufficient to base a disclosure standard in research on humans, this National Commission developed the reasonable volunteer standard where a study participant is to be approached in research informed consent with that information that a reasonable volunteer would want to know. Online Materials Belmont Report: Syllabus Topics for Lecture and Discussion Week I: Introduction and Overview Readings: Rogers v. Whitaker, 175 C.L.R. 479 (1992). (High Court of Australia) Sidaway v. Board of Governors of the Bethlem Royal Hospital and the Maudsley Hospital and Others. 1 A.C. 871 (1985) (House of Lords) Week II: The Different Standards of Consent and Informed Consent Readings: Canterbury v. Spence, 464 F.2d 772 (1972). (Federal appellate opinion heard in the District of Columbia) Sidaway v. Board of Governors of the Bethlem Royal Hospital and the Maudsley Hospital and Others. 1 A.C. 871 (1985) (House of Lords) Week III: Definition of Research Reading: Mazur, Dennis J. The Science and Ethics of Research on Humans. Baltimore, MD: Johns Hopkins University Press, 2007. (Especially Chapters 2 and 3) Week IV: How to Review a Research Study Protocol and Research Informed Consent Form Reading: Mazur, Dennis J. The Science and Ethics of Research on Humans. Baltimore, MD: Johns Hopkins University Press, 2007. (Especially Chapters 4–6, 10, and 12–14) Week V: Obligations in Research of Humans Versus Patient Care Reading: National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research. The Belmont Report: Ethical Guidelines for the Protection of Human Subjects of Research. Washington, DC: DHEW Publications, 1978 (78‐0012). Focus Questions • How do the judicial doctrines of consent in England and Australia compare to the judicial doctrines of informed consent in the United States and Canada? • How does a professional standard of disclosure differ from a reasonable person standard of disclosure? • What is the definition of research? • How is a research study (study proposal and research informed consent form) reviewed from scientific and ethical bases for considerations of approval by an IRB? • How do the obligations of a study sponsor, a principal investigator, and a research team conducting a research trial on human study participants differ from the obligations of a physician caring for a patient? • Should all raw data of research derived from humans be made available to the public for use in developing generalizable knowledge to help others, or should raw data be considered the private property of the study sponsors (for example, prescription drug manufacturers), who fund the research trials? Seminar/project Idea Draw a timeline of the development of the basic concepts of consent and informed consent in patient care and in patient research. On this timeline, first place the dates of the key court cases in England, the United States, Canada, and Australia on consent and informed consent. Then place the date of the development of the Belmont Report. Why do differences exist between these four countries in terms of the legal requirements of informedness of a patient (in medical care) and a study participant (in medical research)? What roles if any do the concepts of self‐determination and self‐decision have in consent and informed consent in patient care and in informed consent in research on humans among the four countries of interest? What are the realities of research on human participants that require a new standard of informed consent, the reasonable volunteer standard, to be developed beyond the two standards in patient care, the professional standard, and the reasonable person standard? Counterpoint Arguments The following are counterpoint arguments that need to be appreciated to more fully understand the concepts that impact the thesis that ‘raw data’ should be open to the public to allow the opportunity of checking of the results of its associated scientific paper and for further analysis. De‐Identified (Anonymized) Raw Data A current approach to identifying (anonymizinig) raw data is based on the Health Insurance Portability and Accountability Act (HIPAA) of 1996 (P.L.104‐191). HIPAA was enacted by the U.S. Congress in 1996 to keep a person’s medical information private. In a research study, a person’s private medical information can become research data. HIPAA’s Privacy Rule allows a covered entity to de‐identify data by removing all 18 elements that could be used to identify the individual or the individual’s relatives, employers, or household members; these elements are enumerated in the Privacy Rule. The covered entity must also have no actual knowledge that the remaining information could be used alone or in combination with other information to identify the individual who is the subject of the information. Under this method, the identifiers that must be removed are the following: 1 Names. 2 All geographic subdivisions smaller than a state, including street address, city, county, precinct, ZIP Code, and their equivalent geographical codes, except for the initial three digits of a ZIP Code if, according to the current publicly available data from the Bureau of the Census: 2a. The geographic unit formed by combining all ZIP Codes with the same three initial digits contains more than 20,000 people. 2b. The initial three digits of a ZIP Code for all such geographic units containing 20,000 or fewer people are changed to 000. 3 All elements of dates (except year) for dates directly related to an individual, including birth date, admission date, discharge date, and date of death, and all ages over 89 and all elements of dates (including year) indicative of such age, except that such ages and elements may be aggregated into a single category of age 90 or older. 4 Telephone numbers. 5 Facsimile numbers. 6 Electronic mail addresses. 7 Social security numbers. 8 Medical record numbers. 9 Health plan beneficiary numbers. 10 Account numbers. 11 Certificate/license numbers. 12 Vehicle identifiers and serial numbers, including license plate numbers. 13 Device identifiers and serial numbers. 14 Web universal resource locators (URLs). 15 Internet protocol (IP) address numbers. 16 Biometric identifiers, including fingerprints and voiceprints. 17 Full‐face photographic images and any comparable images. 18 Any other unique identifying number, characteristic, or code, unless otherwise permitted by the Privacy Rule for re‐identification. Even though ‘raw data’ can be de‐identified (anonymized) so that there is no way to trace back the data to the study participant from which it was drawn, there are still questions whether the ‘de‐identified raw data’ can be given to other researchers or made public without the original study participant’s approval. It may be the case that this approval could be done at the start of any research study where the individual considering study participation would be counseled on what the process of de‐identification consists of and would be asked whether the participant would allow use of the data by other researchers or made available to the public in a de‐identified state. However, there may be questions of the study participants as to whether the data are truly de‐identified and untraceable back to the study participant since the participant would not be able to see the process actually being carried out in detail in all relevant circumstances. Using Raw Data in Context Simply being in possession of raw data is never enough to build on that data from a research perspective. Researchers need to understand the context of the scientific research study in which the data were collected. This research context includes (but is not limited to): (i) the scientific hypothesis of the research study, (ii) the inclusion and exclusion criteria selected by the research designers of the study to determine which study participants were included and which were excluded from the study, (iii) the methods used to collect the data and possibilities of errors in the data collection processes, and (iv) answers to questions regarding whether any data were excluded from the study data and why these data were excluded. Ownership Rights Over Data There are ownership rights over data. Ownership rights include court decision making related to the question which parties are to be considered as the owners of the data. Possible owners here include (but are not limited to) (i) the study sponsor whose only role was to fund that study, (ii) the principal investigator(s) who developed the scientific hypothesis, and (iii) individual study participants through special contracts made by individual participants who negotiate such contracts with study sponsors and principal investigators to share in the ownership of data. Examples of such data are participant sources of unique gene lines or unique cell lines to be used in future research. Objections to Data Sharing Finally, individual researchers may simply object to sharing data. A researcher’s arguments here may be simply stating that he or she has a right to fully analyze the data since the collection of the data was the researchers’ idea in the first place. These researchers may argue that they have the right to mine the data as fully as they can before deciding to make the data open to the public for others to analyze. Works Cited 1 Kaiser, J. ‘Making Clinical Data Widely Available.’Science 322.5899 (10 Oct. 2008): 217–8. 2 de Lusignan, S., J.F. Metsemakers, P. Houwink, V. Gunnarsdottir, and J. van der Lei. ‘Routinely Collected General Practice Data: Goldmines for Research? A Report of the European Federation for Medical Informatics Primary Care Informatics Working Group (EFMI PCIWG) from MIE2006, Maastricht, The Netherlands.’Informatics in Primary Care 14.3 (2006): 203–9. 3 Sim, I. ‘Human Studies Database Project’, CTSA Data Repositories Symposium (17 Oct. 2008). 23 Nov. 2010. 4 Sim, I., C.G. Chute, H. Lehmann, R. Nagarajan, M. Nahm, and R.H. Scheuermann. ‘Keeping Raw Data in Context.’Science 323.5915 (6 Feb. 2009): 713. 5 U.S. Department of Health and Human Services, National Institutes of Health, HIPAA Privacy Rule, Information for Researchers. 13 Nov. 2010. 6 Wilczynski, N.L., R.B. Haynes, and Hedges Team. ‘EMBASE Search Strategies for Identifying Methodologically Sound Diagnostic Studies for Use by Clinicians and Researchers.’BMC Medicine 29.3 (March 2005): 7. (shrink)

What is to be learned from the chaotic downfall of the Weimar Republic and the erosion of European liberal statehood in the interwar period vis-a-vis the ongoing European crisis? This book analyses and explains the recurrent emergence of crises in European societies. It asks how previous crises can inform our understanding of the present crisis. The particular perspective advanced is that these crises not only are economic and social crises, but must also be understood as crises of public power, order (...) and authority. In other words, it argues that substantial challenges to the functional and normative setup of democracy and the rule of law were central to the emergence and the unfolding of these crises. The book draws on and adds to the rich ’crises literature’ developed within the critical theory tradition to outline a conceptual framework for understanding what societal crises are. The central idea is that societal crises represent a discrepancy between the unfolding of social processes and the institutional frameworks that have been established to normatively stabilize such processes. The crises at issue emerged in periods characterized by strong social, economic and technological transformations as well as situations of political upheaval. As such, the crises represented moments where the existing functional and normative grid of society, as embodied in notions of public order and authority, were severely challenged and in many instances undermined. Seen in this perspective, the book reconstructs how crises unfolded, how they were experienced, and what kind of responses the specific crises in question provoked. -/- Table of Contents -/- Introduction: European Crises of Public Power: From Weimar until Today, Poul F. Kjaer & Niklas Olsen / Part I: Semantics, Notions and Narratives of Societal Crisis / 1. What Time Frame Makes Sense for Thinking About Crises?, David Runciman / 2. The Stakes of Crises, Janet Roitman / Part II: Weimar and the Interwar Period: Ideologies of Anti-Modernism and Liberalism / 3. The Crisis of Modernity – Modernity as Crisis: Towards a Typology of Crisis Discourses in Interwar East Central Europe and Beyond, Balázs Trencsényi / 4. European Legitimacy Crisis – Weimar and Today: Rational and Theocratic Authority in the Schmitt-Strauss Exchange, John P. McCormick / 5. Crisis and the Consumer: Reconstructions of Liberalism in Twentieth Century Political Thought , Niklas Olsen / Part III: The Causes of Crises: From Corporatism to Governance / 6. The Constitutionalization of Labour Law and the Crisis of National Democracy , Chris Thornhill / 7. The Crisis in Labour Law: From Weimar to Austerity Ruth Dukes / 8. From the Crisis of Corporatism to the Crisis of Governance, Poul F. Kjaer / Part IV: The Euro and the Crisis of Law and Democracy / 9. What is left of the European Economic Constitution II? From Pyrrhic Victory to Cannae Defeat Christian Joerges / 10. Reflections on Europe’s “Rule of Law Crisis”, Jan-Werner Müller. 11. Democracy under Siege: The Decay of Constitutionalisation and the Crisis of Public Law and Public Opinion, Hauke Brunkhorst/ Part V: The Consequences of Crises and the Future of Europe / 12. Crises and Extra-Legality: From Above and From Below, William E. Scheuermann / 13. “We could all go Down the Road of Lebanon” – Crisis Thinking on the Anti-Muslim Far Right, Mikkel Thorup / 14. Conclusions and Perspectives: The Re-Constitution of Europe, Poul F. Kjaer & Niklas Olsen Index . (shrink)

Though some influentially critical objections have been raised during the ‘classical’ pre-computational simulation philosophy of science tradition, suggesting a more nuanced methodological category for experiments, it safe to say such critical objections have greatly proliferated in philosophical studies dedicated to the role played by computational simulations in science. For instance, Eric Winsberg suggests that computer simulations are methodologically unique in the development of a theory’s models suggesting new epistemic notions of application. This is also echoed in Jeffrey Ramsey’s notions of (...) “transformation reduction,”—i.e., a notion of reduction of a more highly constructive variety. Computer simulations create a broadly continuous arena spanned by normative and descriptive aspects of theory-articulation, as entailed by the notion of transformation reductions occupying a continuous region demarcated by Ernest Nagel’s logical-explanatory “domain-combining reduction” on the one hand, and Thomas Nickels’ heuristic “domain-preserving reduction,” on the other. I extend Winsberg’s and Ramsey’s points here, by arguing that in the field of computational fluid dynamics as well as in other branches of applied physics, the computer plays a constitutively experimental role—supplanting in many cases the more traditional experimental methods such as flow-visualization, etc. In this case, however CFD algorithms act as substitutes, not supplements when it comes to experimental practices. I bring up the constructive example involving the Clifford-Algebraic algorithms for modeling singular phenomena in CFD by Gerik Scheuermann and Steven Mann & Alyn Rockwood who demonstrate that their algorithms offer greater descriptive and explanatory scope than the standard Navier-Stokes approaches. The mathematical distinction between Navier-Stokes-based and Clifford-Algebraic based CFD has essentially to do with the regularization features exhibited to a far greater extent by the latter, than the former. Hence, CACFD indicate that the utilization of computational techniques can be based on principled reasons, as opposed to merely practical. CACFD hence exhibit a new generative role in the field of fluid mechanics, by offering categories of experimental evidence that are optimally descriptive and explanatory—i.e., pace Batterman can be both ontologically and epistemically fundamental. (shrink)