The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (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)

Until recently, psychologists have conceptualised and studied trust in God (TIG) largely in isolation from contemporary work in theology, philosophy, history, and biblical studies that has examined the topic with increasing clarity. In this article, we first review the primary ways that psychologists have conceptualised and measured TIG. Then, we draw on conceptualizations of TIG outside the psychology of religion to provide a conceptual map for how TIG might be related to theorised predictors and outcomes. Finally, we provide a research (...) agenda for future empirical work in this area, as well as practical applications for counsellors and religious leaders. (shrink)

Causal determinism is the view that all events in the universe are predetermined and that the laws of nature causally necessitate these events. In the debates on free will, there are two different positions called incompatibilism and compatibilism. Accordingly, compatibilist accounts claim that free will and causal determinism can be compatible and coexist. On the contrary, incompatibilist accounts defend that compatibilist accounts are problematic and claim that free will cannot exist in a universe where causal determinism holds. The main approach (...) that we will consider in this work will be the incompatibilist approach of the American philosopher Peter van Inwagen, which he defends in free will debates. The arguments put forward by Peter van Inwagen as the basis of incompatibilism can be summarized as the consequence argument and the Mind argument. The consequence argument, hypothetically takes into account a world in which causally deterministic and claiming that free will doesn't exist in such a world. Peter van Inwagen's Mind argument, on the other hand, claims that agent-causation cannot be sufficient for a definite possession of free will because a person who represents oneself as an agent in every event s/he is involved in, cannot be sure whether the consequences of these events are due to chance. In both arguments, Peter van Inwagen refers to philosophical moves that affirm incompatibilism is consistent for free will debate. Therefore in my dissertation, I argue that incompatibilism is actually a sufficient step towards solving the free will and causal determinism dilemma in a theoretical sense. This work also deals with Peter van Inwagen's views on philosophy of action and philosophy of religion in general. Additionally, in order to draw the relational framework between causal determinism and free will, the concepts of 'event', 'causal powers' and 'states of affairs' are used methodologically. Instead of just having an ethical discussion of free will, I took care to stay within the boundaries of the metaphysics of free will. (shrink)

Epistemic defeat is standardly understood in either evidentialist or responsibilist terms. The seminal treatment of defeat is an evidentialist one, due to John Pollock, who famously distinguishes between undercutting and rebutting defeaters. More recently, an orthogonal distinction due to Jennifer Lackey has become widely endorsed, between so-called doxastic (or psychological) and normative defeaters. We think that neither doxastic nor normative defeaters, as Lackey understands them, exist. Both of Lackey’s categories of defeat derive from implausible assumptions about epistemic responsibility. Although Pollock’s (...) evidentialist view is superior, the evidentialism per se can be purged from it, leaving a general structure of defeat that can be incorporated in a reliabilist theory that is neither evidentialist nor responsibilist in any way. (shrink)

Experimental philosophers have gathered impressive evidence for the surprising conclusion that philosophers' intuitions are out of step with those of the folk. As a result, many argue that philosophers' intuitions are unreliable. Focusing on the Knobe Effect, a leading finding of experimental philosophy, we defend traditional philosophy against this conclusion. Our key premise relies on experiments we conducted which indicate that judgments of the folk elicited under higher quality cognitive or epistemic conditions are more likely to resemble those of the (...) philosopher. We end by showing how our experimental findings can help us better understand the Knobe Effect. (shrink)

This paper focuses on invasive therapeutic procedures, defined as procedures requiring the introduction of hands, instruments, or devices into the body via incisions or punctures of the skin or mucous membranes performed with the intent of changing the natural history of a human disease or condition for the better. Ethical and methodological concerns have been expressed about studies designed to evaluate the effects of invasive therapeutic procedures. Can such studies meet the same standards demanded of those, for example, evaluating pharmaceutical (...) agents? This paper describes a research project aimed at examining the interplay and sometimes apparent conflict between ethical standards for human research and standards for methodological rigor in trials of invasive procedures. The paper discusses how the authors plan to develop a set of consensus standards that, if met, would result in substantial and much-needed improvements in the methodological and ethical quality of such trials. (shrink)

Background: Emergentism as an ontology of consciousness leaves unanswered the question as to its mechanism. Aim: I aim to solve the Body-Mind problem by explaining how conscious organisms emerged on an evolutionary basis at various times in accordance with an accepted scientific principle, through a mechanism that cannot be understood, in principle. Proposal: The reason for this cloak of secrecy is found in a seeming contradiction in the behaviour of information with respect to the first two laws of thermodynamics. Information, (...) the microstate of particles within an isolated system’s macrostate, can, like first law energy, be neither created nor destroyed, yet the information in the system, like second law entropy, will inevitably increase. To explain information increasing without being created, Laplace’s demon is invoked, able to predict where each particle is destined. This doesn’t work for emerging events like consciousness, which are unpredictable. This can be understood in terms of the derivation of entropy, and the emergence of classical physics, from the Relativistic Transactional Interpretation of Quantum Mechanics. I propose that the increased entropy in a time-irreversible, unpredictable (emergent) isolated system requires the simultaneous deletion of information concerning the steps, or calculations, involved. Conclusion: Thus, the steps leading to consciousness are immediately destroyed and must remain a mystery. Implications include that entropy, not panpsychism, is the Universal principle generative of consciousness, that our being conscious proves that we are not predetermined, and that consciousness requires assuming an “entropy debt” that can only be repaid by living organisms, prohibiting the emergence of conscious machines. (shrink)

Background If trials of therapeutic interventions are to serve society's interests, they must be of high methodological quality and must satisfy moral commitments to human subjects. The authors set out to develop a clinical - trials compendium in which standards for the ethical treatment of human subjects are integrated with standards for research methods. Methods The authors rank-ordered the world's nations and chose the 31 with >700 active trials as of 24 July 2008. Governmental and other authoritative entities of the (...) 31 countries were searched, and 1004 English-language documents containing ethical and/or methodological standards for clinical trials were identified. The authors extracted standards from 144 of those: 50 designated as ‘core’, 39 addressing trials of invasive procedures and a 5% sample of the remainder. As the integrating framework for the standards we developed a coherent taxonomy encompassing all elements of a trial's stages. Findings Review of the 144 documents yielded nearly 15 000 discrete standards. After duplicates were removed, 5903 substantive standards remained, distributed in the taxonomy as follows: initiation, 1401 standards, 8 divisions; design, 1869 standards, 16 divisions; conduct, 1473 standards, 8 divisions; analysing and reporting results, 997 standards, four divisions; and post-trial standards, 168 standards, 5 divisions. Conclusions The overwhelming number of source documents and standards uncovered in this study was not anticipated beforehand and confirms the extraordinary complexity of the clinical trials enterprise. This taxonomy of multinational ethical and methodological standards may help trialists and overseers improve the quality of clinical trials, particularly given the globalisation of clinical research. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Our aim in this paper is to suggest that most current theories of global justice fail to adequately recognise the importance of global public goods. Broadly speaking, this failing can be attributed at least in part to the complexity of the global context, the individualistic focus of most theories of justice, and the localised nature of the theoretical foundations of most theories of global justice. We argue ? using examples (particularly that of protecting antibiotic efficacy) ? that any truly effective (...) theory of global justice must recognise the importance of global public goods. Global public goods confer significant benefits to individuals yet can only be effectively promoted and preserved through collective action and the restriction of individual choice; something which most theories of justice are structurally unequipped to sufficiently promote. (shrink)

Analysing the demands of global justice for the distribution of resources is a complex task and requires consideration of a broad range of issues. Of particular relevance is the effect that different distributions will have on global population growth and individual welfare. Since changes in the consumption and distribution of resources can have major effects on the welfare of the global population, and the rate at which it increases, it is important to establish meaningful principles to ensure a just distribution (...) of resources. In order to establish such principles we must consider the scope of any reproductive rights, and rights to other goods, such as food and health care, as well as examine the extent of duties correlating to those rights. In addition to the impact that distributions of global goods have on the welfare of current generations, it is also important to consider what duties we have, if any, to future generations. -/- The final version of this paper is available to download here: http://dx.doi.org/10.1002/9780470015902.a0024140. (shrink)

Skeptical theists are seeking for some reasonable solutions to the evidential problem of evil. One of the most fundamental responses of skeptical theism is that the concept of “gratuitous evil”, which cannot be a proof of the absence of God. Therefore, it is not the existence of God that skeptical theism suspects. Instead, skeptical theism contemplates whether the evil in the world really has a “gratuitous” basis. This paper focuses on Peter van Inwagen's “no-minimum claim”. No-minimum claim” stands in (...) opposition to the views that assume that God minimizes the evils that exist in the world in order to achieve justice. “No-minimum claim” acknowledges that these evils still have enormous amounts to people. Thus “no-minimum claim” suggests that the evils experienced in the world are incompatible with the “best of all possible worlds” views or the other explanations of classical theodicy. According to the “no minimum claim”, the reason why the amount of evil in the world still seems so high may be God’s deliberate calculations in effecting the distribution of these evils. In order to reach these calculations, it is not necessary for the amount of evil that God allowed to reflect on the world to be perfectly manifested at the minimum level. The purpose of this paper is to consider the skeptical theism approach within the framework of Peter van Inwagen's “no-minimum claim” and to limit his arguments to an alternative approach to skeptic theism. Our claim is that such view coincides with skeptical theism, but the “no- minimum claim” still has some ambiguities at the point of the limits of evil. From this, we can conclude that the “no minimum claim” has received many objections in the skeptical theism literature and these objections are justified at certain points. (shrink)

Modern humans are probably a product of social and anatomical preadaptations on the part of our Miocene australopithecine ancestors combined with the increasingly high amplitude, high frequency climate variation of the Pleistocene. The genus Homo first appeared in the early Pleistocene as ice age climates began to grip the earth. We hypothesize that this co-occurrence is causal. The human ability to adapt by cultural means is, in theory, an adaptation to highly variable environments because cultural evolution can better track rapidly (...) changing environments than can genes. High resolution ice and sediment cores published in the early 1990s showed the last ice age was characterized by high amplitude millennial and submillenial scale variation, exactly the sort of variation mathematical models suggest should favor a costly capacity for culture. More recent cores suggest that over the last several 100 thousand year glacial cycles the amount of millennial scale variation has increased rather dramatically in parallel with increases in hominin brain size and sophistication of the artifacts they made. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

Deleuze’ün Spinozacı yaşam tahayyülünde ‘ne yapmalıyız?’ sorusuna normatif, ahlaki ya da siyasi bir yanıt bulamıyoruz ama varoluşu düşünmenin içkin bir olanağını keşfediyoruz. Düşünmeye 'dışarıdan' yani dünyadan başlamak insani (kurgusal) bir dünyaya değil, içinde yaşadığımız gerçek dünyaya inanmak demektir. İçkinliğin politik anlamı düşünceyi dünyaya getirmektir.

This study was conducted to determine the effectiveness of utilizing the Dual-axis Solar Tracker in harnessing solar energy and storing it in lithium-ion batteries in terms of voltage and milliamps per hour gained. This study utilized two solar panel systems, the Static Solar Panel System and the Dual-Axis Solar Tracker and aimed to prove the significant difference generated by solar panel systems in terms of voltage and milliamps per hour. This study employed an Applied Experimental Research Design utilizing Arduino Uno, (...) light-dependent resistors, micro servos, and solar panels to create the Dual-Axis Solar Tracker. The data gathered from the electric quantities during the seven-day sun exposure were tabulated, analyzed, and computed using mean tests, standard deviation, and T-tests to find the significant difference between the two solar panels. Based on the analyses of the data, it was revealed that the Dual-Axis Solar Tracker was superior in terms of voltage and milliamps per hour generated compared to the Static Solar Panel System. Moreover, computations using the T-test found that in terms of voltage and milliamps per hour generated, there was a significant difference between the Dual-Axis Solar Tracker and the Static Solar Panel System. Based on the findings of the study, it is concluded that the utilization of the Dual-Axis Solar Tracker statistically increases the effectiveness of solar panels in harnessing energy generation. (shrink)

We model scientific theories as Bayesian networks. Nodes carry credences and function as abstract representations of propositions within the structure. Directed links carry conditional probabilities and represent connections between those propositions. Updating is Bayesian across the network as a whole. The impact of evidence at one point within a scientific theory can have a very different impact on the network than does evidence of the same strength at a different point. A Bayesian model allows us to envisage and analyze the (...) differential impact of evidence and credence change at different points within a single network and across different theoretical structures. (shrink)

Die Welt ist voller Leid. Gott ist entweder unfähig, es zu verhindern – dann ist Er nicht allmächtig –, oder Er will es nicht verhindern – dann ist Er nicht vollkommen gut. Seit Generationen wird dies als das schlagendste Argument gegen den Glauben angesehen, daß ein allmächtiges und allgütiges Wesen existiert. Natürlich haben Theisten sich die größte Mühe gegeben, eine angemessene Erwiderung vorzubringen. ... Selbst wenn nur ein einziges Individuum unnötigerweise für einen kurzen Moment eine leichte Unannehmlichkeit zu ertragen hätte, (...) wäre das Problem logisch ebenso real – obwohl es nicht so schmerzhaft wäre oder möglicherweise sogar unbemerkt bliebe. (shrink)

Die Welt ist voller Leid. Gott ist entweder unfähig, es zu verhindern – dann ist Er nicht allmächtig –, oder Er will es nicht verhindern – dann ist Er nicht vollkommen gut. Seit Generationen wird dies als das schlagendste Argument gegen den Glauben angesehen, daß ein allmächtiges und allgütiges Wesen existiert. Natürlich haben Theisten sich die größte Mühe gegeben, eine angemessene Erwiderung vorzubringen. ... Selbst wenn nur ein einziges Individuum unnötigerweise für einen kurzen Moment eine leichte Unannehmlichkeit zu ertragen hätte, (...) wäre das Problem logisch ebenso real – obwohl es nicht so schmerzhaft wäre oder möglicherweise sogar unbemerkt bliebe. (shrink)

Concordance of the poetic works of Giorgos Seferis which presents all the principal “words” of the texts in an alphabetical list, stating how often each word occurs, giving a precise location and a relevant piece of text for each occurrence. We found ca. 9500 different Greek words in 39000 different occurrences, so our concordance has 50.000 lines of text. The technical procedure required four main steps: text entry and tagging, production of the concordance, correction of the contexts, formatting for print.

In this paper, we defend Socratic studies as a research programme against several recent attacks, including at least one recently published in Polis . Critics have argued that the study of Socrates, based upon evidence mostly or entirely derived from some set of Plato's dialogues, is founded upon faulty and indefensible historical or hermeneutical technique. We begin by identifying what we believe are the foundational principles of Socratic studies, as the field has been pursued in recent years, and we then (...) show how the research programme that derives from accepting these principles is not defeated by any of the most common recent criticisms of it. Specifically, we argue that challenges to sorting Plato's dialogues by date, more general challenges to historicist interpretations of Plato's dialogues, as well as recent literary criticisms of Socratic studies all fail to undermine the research programme. We conclude with some thoughts about how and why Socratic studies has proved itself a valuable and fruitful research programme. (shrink)

This article addresses ontological negotiations in the Global South through three case studies of community-based research in Brazil and Ghana. We argue that ontological perspectives of Indigenous and other subjugated communities require an ontological pluralism that recognizes the plurality of both representational tools and ways of being in the world. Locating these two readings of ontological pluralism in the politics of the Global South, the article highlights a wider dynamic from ontological paternalism to ontological diversity to ontological decolonization. We conclude (...) by arguing that this dynamic provides important lessons for reorienting agendas in social ontology through Southern Ontologies. (shrink)

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)

The precarious rights of senior citizens, especially those who are highly educated and who are expected to counsel and guide the younger generations, has stimulated the creation internationally of advocacy associations and opinion leader groups. The strength of these groups, however, varies from country to country. In some countries, they are supported and are the focus of intense interest; in others, they are practically ignored. For this is reason we believe that the creation of a network of all these associations (...) is essential. The proposed network would act as a support for the already-existing policies of the United Nations’ High Commission for Human Rights, of independent experts, and of the Global Alliance for the Rights of Older People. All three have long ago recommended the creation of a recognized instrument for uniting presently scattered efforts. The proposed network, therefore, will seek to promote the international exchange of relevant expertise, and it will reinforce the commitments and actions that single countries are currently taking to meet these objectives. For example, informative public events can be organised to promote particular support initiatives and to provide an opportunity for new members of the network to be presented. The network will promote health for senior citizens, disease prevention, senior mobility, safe free time for seniors, alimentary education, protection against new risks and dangers, as well as equity in the services necessary for seniors to adopt new information and communication technologies. In the case of retired academic members, the network will promote equality with respect to continuing use of digital technologies (particularly email), continuing access to research libraries, and the guaranteed ability for seniors to fund their own research programs and to deliver free seminars. (shrink)

Shortages of new therapeutics to treat coronavirus disease (COVID-19) have forced clinicians, public health officials, and health systems to grapple with difficult questions about how to fairly allocate potentially life-saving treatments when there are not enough for all patients in need (1). Shortages have occurred with remdesivir, tocilizumab, monoclonal antibodies, and the oral antiviral Paxlovid (2) -/- Ensuring equitable allocation is especially important in light of the disproportionate burden experienced during the COVID-19 pandemic by disadvantaged groups, including Black, Hispanic/Latino and (...) Indigenous communities, individuals with certain disabilities, and low-income persons. However, many health systems have resorted to first-come, first-served approaches to allocation, which tend to disadvantage individuals with barriers in access to care (3). There is mounting evidence of racial, ethnic, and socioeconomic disparities in access to medications for COVID-19 (4, 5). -/- One potential method to promote equitable allocation is to use a weighted lottery, which is an allocation strategy that gives all eligible patients a chance to receive the scarce treatment while also allowing the assignment of higher or lower chances according to other ethical considerations (6). We sought to assess the feasibility of implementing a weighted lottery to allocate scarce COVID-19 medications in a large U.S. health system and to determine whether the weighted lottery promotes equitable allocation. (shrink)

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented (...) and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. -/- This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. -/- Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. -/- The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses. (shrink)

Peter Singer’s famous and influential article is criticised in three main ways that can be considered libertarian, although many non-libertarians could also accept them: 1) the relevant moral principle is more plausibly about upholding an implicit contract rather than globalising a moral intuition that had local evolutionary origins; 2) its principle of the immorality of not stopping bad things is paradoxical, as it overlooks the converse aspect that would be the positive morality of not starting bad things and also (...) thereby conceptually eliminates innocence; and 3) free markets—especially international free trade—have been cogently explained to be the real solution to the global “major evils” of “poverty” and “pollution”, while “overpopulation” does not exist in free-market frameworks; hence charity is a relatively minor alleviant to the problem of insufficiently free markets. There are also various subsidiary arguments throughout. (shrink)

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented (...) and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. -/- This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. -/- Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. -/- The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses. (shrink)

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented (...) and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense.] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics and there are many new abstractions from advances in mathematics. Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. -/- This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. -/- Sections 1 through 4 are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. -/- The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses. (shrink)

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented (...) and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. -/- This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. -/- Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. -/- The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses. (shrink)

Objective: Primary care, which is often the first level of contact for patients with various communicable diseases (CDs) and noncommunicable diseases (NCDs), might exhibit patterns of injectable drug utilization different from hospitals. We aimed to examine injection prescribing to adults with CD or NCD in primary care. -/- Methods: In this retrospective study, single-diagnosis injectable drug-containing prescription data from Family Medicine Information System comprising 32 provinces of Turkey were analysed. The prescriptions were grouped by diagnosis as “CD” (n=3848) and “NCD” (...) (n=9338). Injectable drug utilization patterns in these groups were analysed by demographics, diagnoses, and drug subgroups. -/- Results: Out of 13186 prescriptions, 70.8% were issued for NCDs. NCD prescriptions were mostly generated for women and elderly (p<0.05 for both). About 63.3% (n=2948) of injectable drugs in CD prescriptions were antibiotics and 12.6% were analgesics. Cefazolin (15.2%) was the most commonly prescribed antibiotic for acute pharyngitis and acute sinusitis, and benzathine benzylpenicillin (12.8%) was the top-choice for acute tonsillitis and rheumatic fever. In NCD prescriptions, 34.0% (n=4214) of injectable agents were analgesics and 16.9% were muscle relaxants. The most frequently encountered drug in NCD prescriptions was thiocolchicoside (16.3%), which was the top-choice in all seven common musculoskeletal diagnoses. -/- Conclusion: Muscle relaxants and analgesics were the most commonly prescribed injectable drugs for NCDs, musculoskeletal diseases in particular. Antibiotics were frequently encountered in CD prescriptions, mostly as broad-spectrum for lower respiratory tract infections (RTIs) and narrow-spectrum for upper RTIs. These findings may elucidate the issues to especially focus on regarding excessive use of injections. (shrink)

Eser, yazarın 2008 yılında tamamlamış olduğu “Kur’an’ın Tasdik Ettiği Tevrat’taki Konular” isimli doktora tezinin 2011 yılında “Tevrat’ın Kur’an’a Arzı-Kur’an’ın Tevrat’ta Tasdik Ettiği Konular” ismiyle basılmasıyla yayın hayatına kazandırılmıştır. Kur’an ve Tevrat’taki konular bu çalışmanın öncesinde ve sonrasında genellikle mukayeseli bir biçimde çalışılmıştır. Gerek Kur’an ve Tefsir alanında gerekse Dinler Tarihi alanında kıssalar, tarihi olaylar, hükümler, uygulamalar gibi pek çok açıdan Kur’an ve Tevrat’a dair özellikle mukayese içeren tezler ve eserler bulunmaktadır. Bu çalışmanın alandaki diğer eserlerden farkı Kur’an’ın Tevrat’ı tasdik edici (...) olmasının ne mânaya geldiğini izah etmesi ve Tevrat’ta yer alan hangi konuları doğrulayıcı olduğunu derli toplu bir şekilde ortaya koymasıdır. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney (...) and skin. (shrink)

• Aggregates of previously isolated cells of Hydra are capable, under suitable solvant conditions, of regeneration forming complete animals. In a first stage, ecto- and endodermal cells sort out, producing the bilayered hollow structure characteristic of Hydra tissue; thereafter, heads are formed (even if the original cell preparation contained no head cells), eventually leading to the separation of normal animals with head, body column and foot. Hydra appears to be the highest type of organism that allows for regeneration of the (...) entire structure from random cell aggregates. The system is particularly useful for studying cell interactions, tissue polarity, pattern formation, and cell differentiation. (shrink)

This chapter describes the potential far‐reaching consequences of contemplative higher education for the fields of science and medicine.

A Conspectus of A. N. Whitehead's Metaphysics .

Many ethical frameworks require artificial intelligence (AI) systems to be explainable. Explainable AI (XAI) models are frequently tested for their adequacy in user studies. Since different people may have different explanatory needs, it is important that participant samples in user studies are large enough to represent the target population to enable generalizations. However, it is unclear to what extent XAI researchers reflect on and justify their sample sizes or avoid broad generalizations across people. We analyzed XAI user studies (N = (...) 220) published between 2012 and 2022. Most studies did not offer rationales for their sample sizes. Moreover, most papers generalized their conclusions beyond their target population, and there was no evidence that broader conclusions in quantitative studies were correlated with larger samples. These methodological problems can impede evaluations of whether XAI systems implement the explainability called for in ethical frameworks. We outline principles for more inclusive XAI user studies. (shrink)

You may not know me well enough to evaluate me in terms of my moral character, but I take it you believe I can be evaluated: it sounds strange to say that I am indeterminate, neither good nor bad nor intermediate. Yet I argue that the claim that most people are indeterminate is the conclusion of a sound argument—the indeterminacy paradox—with two premises: (1) most people are fragmented (they would behave deplorably in many and admirably in many other situations); (2) (...) fragmentation entails indeterminacy. I support (1) by examining psychological experiments in which most participants behave deplorably (e.g., by maltreating “prisoners” in a simulated prison) or admirably (e.g., by intervening in a simulated theft). I support (2) by arguing that, according to certain plausible conceptions, character evaluations presuppose behavioral consistency (lack of fragmentation). Possible reactions to the paradox include: (a) denying that the experiments are relevant to character; (b) upholding conceptions according to which character evaluations do not presuppose consistency; (c) granting that most people are indeterminate and explaining why it appears otherwise. I defend (c) against (a) and (b). (shrink)

Although commonly cited as one of the philosophers responsible for the resurgence of interest in pragmatism, Wilfrid Sellars was also the son of Roy Wood Sellars, one of the most dedicated critical realists of the early 20th century. Given his father’s realism and his own ‘scientific realism,’ one might assume that the history of realism – and, despite contemporary interest, not pragmatism – would best serve as the historical background for Wilfrid Sellars’ philosophy. I argue that Wilfrid Sellars, far from (...) being the adherent to classical pragmatism assumed by some, holds more in common with critical realism - specifically, a realism that was framed in opposition to pragmatism – than one finds amongst the writings of Charles Sanders Peirce, William James, or John Dewey. I support this claim by examining Wilfrid Sellars’ adoption of his father’s criticisms of C.I. Lewis, and offer various arguments and historical considerations against thematic accounts that insist on a strong connection between Wilfrid Sellars and pragmatism. (shrink)

It is unknown to what extent medical researchers generalize study findings beyond their samples when their sample size, sample diversity, or knowledge of conditions that support external validity do not warrant it. It is also unknown to what extent medical researchers describe their results with precise quantifications or unquantified generalizations, i.e., generics, that can obscure variations between individuals. We therefore systematically reviewed all prospective studies (n = 533) published in the top four highest ranking medical journals, Lancet, New England Journal (...) of Medicine (NEJM), Journal of the American Medical Association (JAMA), and the British Medical Journal (BMJ), from January 2022 to May 2023. We additionally reviewed all NEJM Journal Watch clinical research summaries (n = 143) published during the same time. Of all research articles reporting prospective studies, 52.5% included generalizations beyond specific national study populations, with the numbers of articles with generics varying significantly between journals (JAMA = 12%; Lancet = 77%) (p < 0.001, V = 0.48). There was no evidence that articles containing broader generalizations or generics were correlated with larger or more nationally diverse samples. Moreover, only 10.2% of articles with generalizations beyond specific national populations reported external validity strengthening factors that could potentially support such extrapolations. There was no evidence that original research articles and NEJM Journal Watch summaries intended for practitioners differed in their use of broad generalizations, including generics. Finally, from the journal with the highest citation impact, articles containing broader conclusions were correlated with more citations. Since there was no evidence that studies with generalizations beyond specific national study populations or with generics were associated with larger, more nationally diverse samples, or with reports of population similarity that may permit extensions of conclusions, our findings suggest that the generalizations in many articles were insufficiently supported. Caution against overly broad generalizations in medical research is warranted. (shrink)

The aim of this paper is to outline Dorothy Emmet’s (1904-2000) account of perception in The Nature of Metaphysical Thinking (published in 1945). Emmet’s account of perception is part of a wider attempt to rehabilitate metaphysics in the face of logical positivism and verificationism (of the kind espoused most famously by A. J. Ayer). It is thus part of an attempt to stem the tide of anti-metaphysical thought that had become widespread in British philosophy by the middle of the twentieth (...) century. In pursuit of that aim, Emmet draws on the work of figures like A. N. Whitehead and Henri Bergson, rather than more mainstream analytic thinkers like Bertrand Russell or G. E. Moore, for inspiration. Indeed, Emmet’s ideas stand in contrast to the prevailing tides of British philosophy during her lifetime. This makes Emmet a figure of considerable historical interest; she does not fit neatly into the traditional narrative of the continental-analytic divide, proposed a way forward for metaphysics in one of its greatest times of crisis, and pre-empted certain movements in more contemporary philosophy of perception. By espousing her unique account of perception and drawing out its connections to her wider philosophy, I hope to put Emmet ‘on the map’, so to speak, of twentieth century British thought. (shrink)

Selective scientific realists disagree on which theoretical posits should be regarded as essential to the empirical success of a scientific theory. A satisfactory account of essentialness will show that the (approximate) truth of the selected posits adequately explains the success of the theory. Therefore, (a) the essential elements must be discernible prospectively; (b) there cannot be a priori criteria regarding which type of posit is essential; and (c) the overall success of a theory, or ‘cluster’ of propositions, not only individual (...) derivations, should be explicable. Given these desiderata, I propose a “unification criterion” for identifying essential elements. (shrink)

A fully developed sophisticated response-dependent account would fill in specifications for B (the beings) and C (the conditions), would probably replace the reference to disapproval with a reference to a more complex response, and might involve a more complex scheme.[ii] For simplicity, however, I shall focus my argument on the above simple scheme of moral wrongness, since added complexities will be irrelevant to my argument.