Leonelli (2016) suggested a relational view of data against a representational view by emphasizing data-centric biology rather than the theory-centric tradition in the philosophy of science. This is because the first view allows for data journeys across laboratories using public database resources, whereas the second does not. This paper examines Leonelli’s strategies to defend the relational view of data. Contrary to Leonelli’s intention, it indicates that her strategies led to unnecessary misunderstandings (...) of the relationships among data, representation, and evidential values. It will be argued that evidential values of data are inevitably based on a representational feature and that it is better to reconcile both views of data as complementary rather than contrasting. (shrink)

Many philosophers are skeptical about the scientific value of the concept of biological information. However, several have recently proposed a more positive view of ascribing information as an exercise in scientific modeling. I argue for an alternative role: guiding empirical data collection for the sake of theorizing about the evolution of semantics. I clarify and expand on Bergstrom and Rosvall’s suggestion of taking a “diagnostic” approach that defines biological information operationally as a procedure for collecting empirical cases. The more (...) recent modeling-based accounts still perpetuate a theory-centric view of scientific concepts, which motivated philosophers’ misplaced skepticism in the first place. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified (...) forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

Knowledge-making practices in biology are being strongly affected by the availability of data on an unprecedented scale, the insistence on systemic approaches and growing reliance on bioinformatics and digital infrastructures. What role does theory play within data-intensive science, and what does that tell us about scientific theories in general? To answer these questions, I focus on Open Biomedical Ontologies, digital classification tools that have become crucial to sharing results across research contexts in the biological and biomedical sciences, and (...) argue that they constitute an example of classificatory theory. This form of theorizing emerges from classification practices in conjunction with experimental know-how and expresses the knowledge underpinning the analysis and interpretation of data disseminated online. (shrink)

Criticism of big data has focused on showing that more is not necessarily better, in the sense that data may lose their value when taken out of context and aggregated together. The next step is to incorporate an awareness of pitfalls for aggregation into the design of data infrastructure and institutions. A common strategy minimizes aggregation errors by increasing the precision of our conventions for identifying and classifying data. As a counterpoint, we argue that there are (...) pragmatic trade-offs between precision and ambiguity that are key to designing effective solutions for generating big data about biodiversity. We focus on the importance of theory-dependence as a source of ambiguity in taxonomic nomenclature and hence a persistent challenge for implementing a single, long-term solution to storing and accessing meaningful sets of biological specimens. We argue that ambiguity does have a positive role to play in scientific progress as a tool for efficiently symbolizing multiple aspects of taxa and mediating between conflicting hypotheses about their nature. Pursuing a deeper understanding of the trade-offs and synthesis of precision and ambiguity as virtues of scientific language and communication systems then offers a productive next step for realizing sound, big biodiversity data services. (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)

Research, innovation, and progress in the life sciences are increasingly contingent on access to large quantities of data. This is one of the key premises behind the “open science” movement and the global calls for fostering the sharing of personal data, datasets, and research results. This paper reports on the outcomes of discussions by the panel “Open science, data sharing and solidarity: who benefits?” held at the 2021 Biennial conference of the International Society for the History, Philosophy, (...) and Social Studies of Biology, and hosted by Cold Spring Harbor Laboratory. (shrink)

Near-Death Experiences (NDEs) have gripped the public imagination ever since Raymond Moody’s watershed book Life After Life brought them to widespread attention in 1975. These experiences are commonly reported to involve the sensation of leaving one’s body and watching efforts by medical per-sonnel at resuscitation or even events further afield, as well as experiences of passing through a tunnel towards a being of light and love and meeting deceased friends and relatives. Such experiences are some-times alleged to constitute evidence for (...) an afterlife, but exactly how they do so is seldom spelled out pre-cisely. The aim of this paper, then, is to carefully consider three different inferential pathways from data about NDEs to the conclusion that there is an afterlife. I shall argue that at least two of them provide moderately strong support to this conclusion. (shrink)

This theme issue has the founding ambition of landscaping Data Ethics as a new branch of ethics that studies and evaluates moral problems related to data (including generation, recording, curation, processing, dissemination, sharing, and use), algorithms (including AI, artificial agents, machine learning, and robots), and corresponding practices (including responsible innovation, programming, hacking, and professional codes), in order to formulate and support morally good solutions (e.g. right conducts or right values). Data Ethics builds on the foundation provided by (...) Computer and Information Ethics but, at the same time, it refines the approach endorsed so far in this research field, by shifting the Level of Abstraction of ethical enquiries, from being information-centric to being data-centric. This shift brings into focus the different moral dimensions of all kinds of data, even the data that never translate directly into information but can be used to support actions or generate behaviours, for example. It highlights the need for ethical analyses to concentrate on the content and nature of computational operations — the interactions among hardware, software, and data — rather than on the variety of digital technologies that enables them. And it emphasises the complexity of the ethical challenges posed by Data Science. Because of such complexity, Data Ethics should be developed from the start as a macroethics, that is, as an overall framework that avoids narrow, ad hoc approaches and addresses the ethical impact and implications of Data Science and its applications within a consistent, holistic, and inclusive framework. Only as a macroethics Data Ethics will provide the solutions that can maximise the value of Data Science for our societies, for all of us, and for our environments. (shrink)

The setting of evidential standards is a core practice of scientific assessment for policy. Persuaded by considerations of inductive risk, philosophers generally agree that the justification of evidential standards must appeal to non-epistemic values but debate whether the balance of non-epistemic reasons favours varying evidential standards versus maintaining fixed high evidential standards in assessment, as both sets of standards promote different and important political virtues of advisory institutions. In this paper, I adjudicate the evidential standards (...) debate by developing a novel argument from justice, drawing on the IPCC’s assessment of climate impacts as a case study. I argue that in assessments marked by background evidential inequality, maintaining fixed high evidential standards results in an unequal distribution of ‘epistemic power’ among stakeholders, producing a ‘powerful assessment’ for the data-rich (a high rate of findings) and a ‘weak assessment’ for the data-poor (a low rate of findings). Where such inequalities of epistemic power disadvantage those in data-poor regions with respect to fundamental interests, such as basic human rights, we have decisive reasons of justice to vary evidential standards. (shrink)

This paper addresses a relatively new mode of ecological research: data synthesis studies. Data synthesis studies involve reusing data to create a general model as well as a reusable, aggregated dataset. Using a case from movement ecology, I analyse the trade-offs and strategies involved in data synthesis. Like theoretical ecological modelling, I find that synthesis studies involve a modelling trade-off between generality, precision and realism; they deal with this trade-off by adopting a pragmatic kludging strategy. I (...) also identify an additional trade-off, the synthesis trade-off, between making data easy to synthesise for a particular project, on the one hand, and facilitating data reuse for other projects, on the other. In response to this synthesis trade-off, researchers create flexible datasets that are relatively easy to use for particular projects and can be adjusted to suit some other purposes. The flexibility compromise is also found in broader open data efforts, making it a significant element in the future of data-intensive ecology. (shrink)

Bioinformatics scientists often describe their own scientific activities as the practice of working with large amounts of data using computing devices. An essential part of their self-identification is also the development of ways to visually represent the results of this work. Some of these methods are aimed at building convenient representations of data and demonstrating patterns present in them (graphics, diagrams, graphs). Others are ways of visualizing objects that are not directly accessible to human perception (microphotography, X-ray). Both (...) the construction of visualizations and (especially) the creation of new computer visualization methods are considered in bioinformatics as significant scientific achievements. Representations of the three-dimensional structure of protein molecules play a special role in the inquiries of bioinformatics scientists. 3D-visualization of a macromolecule, on the one hand, is, like a graph, a representation of the results of computer processing of data arrays obtained by material methods – spatiotemporal coordinates of structural elements of the molecule. On the other hand, like microphotography, these 3D structures should serve as accurate representations of specific scientific objects. This leads to the parallel existence of two contradictory epistemic regimes: creative arbitrariness in making convenient, communicatively successful models, is combined with commitment to the object “as it really is”. The paradox is reinforced by the fact that the scientific study of objects in question (determining the properties of the structure, its functions, comparison with other structures) by means of computers does not require visualization at all. Its obviously high value for bioinformatics does not look justified if we take into account the prominent artificiality and artistry of the resulting images. However, the status of these images becomes clearer if we relate them to earlier notions of the role of the visual in scientific discovery. The highest estimation of visualization as the final result of scientific research was characteristic of Renaissance science. The artistic representation of ideal essential properties, instead of a strict correspondence to a particular biological object, is an epistemic virtue typical of the naturalists of the 17th and 18th centuries. Both suggested a close collaboration between the scientist and the artist; and standards for visualizing macromolecules in bioinformatics grow out of a similar collaboration (Geis’ drawings). The desire for maximum accuracy and detail inherits the regulation of “mechanical objectivity” (as Daston and Galison put it into words), for which it is also important to eliminate humans from the image production process (in bioinformatics, to transfer these functions to computer programs). Thus, 3D-visualization of protein structures bears traces of historically different value orientations, but the scientific practice of the 20th and 21st centuries, supplemented by computer technologies, allows them to be intertwined in particular disciplinary units. (shrink)

My belief that Socrates was wise, and your belief that Socrates was mortal can be said to have a common focus, insofar as both these thoughts are about Socrates. In Peter Geach’s terminology, the objects of our beliefs bear the feature of intentional identity, because our beliefs share the same putative target. But what if it turned out that Socrates never existed? Can a pair of thoughts share a common focus if the object both thoughts are about, does not actually, (...) really exist? Object-centric accounts of intentionality which explain the aboutness or directedness of thought in terms of the intentional object the thought in question is about, contend that thoughts which share a common focus do so in virtue of both thoughts simply being about the same intentional object. However, Alexander Sandgren contends that such theories face difficulties in explaining a puzzle of intentional identity put forward by Walter Edelberg, in which a pair of sentences seem to differ in truth value but are purportedly logically equivalent on the object-centric theory. If this is right, then it seems that any account which explains intentionality with reference to an intentional object is threatened by this result, whether this object be abstract, merely possible, Meinongian, or otherwise. In this paper, I argue that Edelberg’s Puzzle is analogous to Frege’s Puzzle and the same tools conventionally used to solve Frege’s Puzzle can be used to solve Edelberg’s Puzzle. I then propose a new object-centric solution to Edelberg’s Puzzle which takes into account modes of presentation and which is able to accommodate all the relevant linguistic data. (shrink)

The boundaries of social categories are frequently altered to serve normative projects, such as social reform. Griffiths and Khalidi argue that the value-driven modification of categories diminishes the epistemic value of social categories. I argue that concerns over value-modified categories stem from problematic assumptions of the value-free ideal of science. Contrary to those concerns, non-epistemic value considerations can contribute to the epistemic improvement of a scientific category. For example, the early history of the category infantile autism shows how non-epistemic value (...) considerations can contribute to delimiting and establishing infantile autism as a distinct category in mainstream psychiatry. In the case of infantile autism, non-epistemic considerations have led to a new interpretation of existing data, the expansion of research to include biology, and the creation of diagnostic criteria that further contribute to collecting relevant data. Given this case study, it can be argued that non-epistemic values can improve our knowledge of scientific categories. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data (...) visualization’, ‘statistical data analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

Despite widespread recognition of an emergent politics of data in our midst, we strikingly lack a political theory of data. We readily acknowledge the presence of data across our political lives, but we often do not know how to conceptualize the politics of all those data points—the forms of power they constitute and the kinds of political subjects they implicate. Recent work in numerous academic disciplines is evidence of the first steps toward a political theory of (...) data. This article maps some limits of this emergent literature with an eye to enriching its theoretical range. The literature on data politics, both within political theory and elsewhere, has thus far focused almost exclusively on the algorithm. This article locates a further dimension of data politics in the work of formatting technology or, more simply, formats. Formats are simultaneously conceptual and technical in the ways they define what can even count as data, and by extension who can count as data and how they can count. A focus on formats is of theoretical value because it provides a bridge between work on the conceptual contours of categories and the technology-centric literature on algorithms that tends to ignore the more conceptual dimensions of data technology. The political insight enabled by format theory is shown in the context of an extended interrogation of the politics of racialized redlining. (shrink)

The term “Complex Systems Biology” was introduced a few years ago [Kaneko, 2006] and, although not yet of widespread use, it seems particularly well suited to indicate an approach to biology which is well rooted in complex systems science. Although broad generalizations are always dangerous, it is safe to state that mainstream biology has been largely dominated by a gene-centric view in the last decades, due to the success of molecular biology. So the one gene - one trait approch, (...) which has often proved to be effective, has been extended to cover even complex traits. This simplifying view has been appropriately criticized, and the movement called systems biology has taken off. Systems biology [Noble, 2006] emphasizes the presence of several feedback loops in biological systems, which severely limit the range of validity of explanations based upon linear causal chains (e.g. gene → behaviour). Mathematical modelling is one the favourite tools of systems biologists to analyze the possible effects of competing negative and positive feedback loops which can be observed at several levels (from molecules to organelles, cells, tissues, organs, organisms, ecosystems). Systems biology is by now a well-established field, as it can be inferred by the rapid growth in number of conferences and journals devoted to it, as well as by the existence of several grants and funded projects.Systems biology is mainly focused upon the description of specific biological items, like for example specific organisms, or specific organs in a class of animals, or specific genetic-metabolic circuits. It therefore leaves open the issue of the search for general principles of biological organization, which apply to all living beings or to at least to broad classes. We know indeed that there are some principles of this kind, biological evolution being the most famous one. The theory of cellular organization also qualifies as a general principle. But the main focus of biological research has been that of studying specific cases, with some reluctance to accept (and perhaps a limited interest for) broad generalizations. This may however change, and this is indeed the challenge of complex systems biology: looking for general principles in biological systems, in the spirit of complex systems science which searches for similar features and behaviours in various kinds of systems. The hope to find such general principles appears well founded, and I will show in Section 2 that there are indeed data which provide support to this claim. Besides data, there are also general ideas and models concerning the way in which biological systems work. The strategy, in this case, is that of introducing simplified models of biological organisms or processes, and to look for their generic properties: this term, borrowed from statistical physics, is used for those properties which are shared by a wide class of systems. In order to model these properties, the most effective approach has been so far that of using ensembles of systems, where each member can be different from another one, and to look for those properties which are widespread. This approach was introduced many years ago [Kauffman, 1971] in modelling gene regulatory networks. At that time one had very few information about the way in which the expression of a given gene affects that of other genes, apart from the fact that this influence is real and can be studied in few selected cases (like e.g. the lactose metabolism in E. coli). Today, after many years of triumphs of molecular biology, much more has been discovered, however the possibility of describing a complete map of gene-gene interactions in a moderately complex organism is still out of reach. Therefore the goal of fully describing a network of interacting genes in a real organism could not be (and still cannot be) achieved. But a different approach has proven very fruitful, that of asking what are the typical properties of such a set of interacting genes. Making some plausible hypotheses and introducing some simplifying assumptions, Kauffman was able to address some important problems. In particular, he drew attention to the fact that a dynamical system of interacting genes displays selforganizing properties which explain some key aspects of life, most notably the existence of a limited number of cellular types in every multicellular organism (these numbers are of the order of a few hundreds, while the number of theoretically possible types, absent interactions, would be much much larger than the number of protons in the universe). In section 3 I will describe the ensemble based approach in the context of gene regulatory networks, and I will show that it can describe some important experimental data. Finally, in section 4 I will discuss some methodological aspects. (shrink)

As opposed to a ‘one size fits all’ approach, precision medicine uses relevant biological, medical, behavioural and environmental information about a person to further personalize their healthcare. This could mean better prediction of someone’s disease risk and more effective diagnosis and treatment if they have a condition. Big data allows for far more precision and tailoring than was ever before possible by linking together diverse datasets to reveal hitherto-unknown correlations and causal pathways. But it also raises ethical issues relating (...) to the balancing of interests, viability of anonymization, familial and group implications, as well as genetic discrimination. This article analyses these issues in light of the values of public benefit, justice, harm minimization, transparency, engagement and reflexivity and applies the deliberative balancing approach found in theEthical Framework for Big Data in Health and Research to a case study on clinical genomic data sharing. Please refer to that article for an explanation of how this framework is to be used, including a full explanation of the key values involved and the balancing approach used in the case study at the end. Our discussion is meant to be of use to those involved in the practice as well as governance and oversight of precision medicine to address ethical concerns that arise in a coherent and systematic manner. (shrink)

Background: Smart sensors have been developed as diagnostic tools for rehabilitation to cover an increasing number of geriatric patients. They promise to enable an objective assessment of complex movement patterns. -/- Objective: This research aimed to identify and analyze the conflicting ethical values associated with smart sensors in geriatric rehabilitation and provide ethical guidance on the best use of smart sensors to all stakeholders, including technology developers, health professionals, patients, and health authorities. -/- Methods: On the basis of a systematic (...) literature search of the scientific databases PubMed and ScienceDirect, we conducted a qualitative document analysis to identify evidence-based practical implications of ethical relevance. We included 33 articles in the analysis. The practical implications were extracted inductively. Finally, we carried out an ethical analysis based on the 4 principles of biomedical ethics: autonomy, beneficence, nonmaleficence, and justice. The results are reported in categories based on these 4 principles. -/- Results: We identified 8 conflicting aims for using smart sensors. Gains in autonomy come at the cost of patient privacy. Smart sensors at home increase the independence of patients but may reduce social interactions. Independent measurements performed by patients may result in lower diagnostic accuracy. Although smart sensors could provide cost-effective and high-quality diagnostics for most patients, minorities could end up with suboptimal treatment owing to their underrepresentation in training data and studies. This could lead to algorithmic biases that would not be recognized by medical professionals when treating patients. -/- Conclusions: The application of smart sensors has the potential to improve the rehabilitation of geriatric patients in several ways. It is important that patients do not have to choose between autonomy and privacy and are well informed about the insights that can be gained from the data. Smart sensors should support and not replace interactions with medical professionals. Patients and medical professionals should be educated about the correct application and the limitations of smart sensors. Smart sensors should include an adequate representation of minorities in their training data and should be covered by health insurance to guarantee fair access. (shrink)

Archaeological data are shadowy in a number of senses. Not only are they notoriously fragmentary but the conceptual and technical scaffolding on which archaeologists rely to constitute these data as evidence can be as constraining as it is enabling. A recurrent theme in internal archaeological debate is that reliance on sedimented layers of interpretative scaffolding carries the risk that “preunderstandings” configure what archaeologists recognize and record as primary data, and how they interpret it as evidence. The selective (...) and destructive nature of data capture in archeology further suggests that there may be little scope for putting “legacy” data to work in new ways. And yet archaeologists have been strikingly successful in mining old datasets for new insights. I situate these concerns in the broader context of debate about the epistemic standing of the historical sciences, and then consider three strategies by which archaeologists address the challenges posed by legacy data. The first two – secondary retrieval and recontextualization – are a matter of reconfiguring the scaffolding that underpins evidential reasoning. The third turns on redeploying old data in the context of computational models that support the experimental simulation of the cultural systems and contexts under study. (shrink)

Using as case studies two early diagrams that represent mechanisms of the cell division cycle, we aim to extend prior philosophical analyses of the roles of diagrams in scientific reasoning, and specifically their role in biological reasoning. The diagrams we discuss are, in practice, integral and indispensible elements of reasoning from experimental data about the cell division cycle to mathematical models of the cycle’s molecular mechanisms. In accordance with prior analyses, the diagrams provide functional explanations of the cell cycle (...) and facilitate the construction of mathematical models of the cell cycle. But, extending beyond those analyses, we show how diagrams facilitate the construction of mathematical models, and we argue that the diagrams permit nomological explanations of the cell cycle. We further argue that what makes diagrams integral and indispensible for explanation and model construction is their nature as locality aids: they group together information that is to be used together in a way that sentential representations do not. (shrink)

By integration with cloud computing, cybersecurity and generative AI, the insurance industry is being transformed from high efficiency, low cost, and better customer service. However, these advanced technologies can also be used by insurers to automate and streamline processes like claims handling, underwriting, and policy generation, which are majorly time consuming and error prone. In predictive analytics, fraud detection, and personalized customer experience, generative AI makes it possible for insurers to mitigate risks and, at the same time, provide more personalized (...) services to customers. With cloud platforms, data management is scalable, flexible and secure, offering real time access to data that drives value by accelerating sound decisions in the insurance value chain. Sensitive data is protected against cybersecurity threats, staying compliant with regulations and marginally reducing risk. Guidewire’s unified technology stack allows insurers to leverage the integrated nature of these technologies through end-to-end integration to improve operational resilience and customer satisfaction. It is these synergies that are the future of insurance which is why transparency, ethical practices in AI as well as proactive cybersecurity are vital. It will become an arms race for insurers to keep pace with these changes and move away from being rigid and slow to adapt; they will need to stay agile and quick, especially with the landscape changing so rapidly. (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)

With the growth of data, data-intensive approaches for sustainability are becoming widespread and have been endorsed by various stakeholders. To understand their implications, in this paper data-intensive approaches for sustainability will be explored by conducting an extensive review. The current data-intensive approaches are defined as an amalgamation of traditional data-collection methods, like surveys and data from monitoring networks, with new data-collection methods that involve new information communication technology. Based on a comprehensive review of (...) the current dataintensive approaches for sustainability, key challenges are identified: the lack of data availability, diverse indicators developed from a narrowly viewed base, diverse definitions and values, skewed global representation, and the lack of social and economic information collected, especially among the business indicators. To clarify the implications of these trends, four major research assumptions regarding dataintensive approaches are elaborated: the methodology, epistemology, normativity, and ontology. Caution is required when data-intensive approaches are masked as “objective”. Overcoming this issue requires interdisciplinary and community-based approaches that can offer ways to address the subjectivities of data-intensive approaches. The current challenges to interdisciplinarity and community-based approaches are also identified, and possible solutions are explored, so that researchers can employ them to make the best use of data-intensive approaches. (shrink)

Tracking technology has been heralded as transformative for animal ecology. In this paper I examine what changes are taking place, showing how current animal movement research is a field ripe for philosophical investigation. I focus first on how the devices alter the limitations and biases of traditional field observation, making observation of animal movement and behaviour possible in more detail, for more varied species, and under a broader variety of conditions, as well as restricting the influence of human presence and (...) observer bias. I reconstruct these as shifts in scope, objectivity, accuracy and fruitfulness. The second transformation is slightly less obvious but equally significant for animal ecology. Tracking devices generate complex data that demands both statistical and biological expertise, which has led to increasingly frequent and intensive collaborations between statisticians and biologists. Based on interviews, I examine how researchers in these interdisciplinary collaborations negotiate the collection, analysis and interpretation of movement data, integrating research interests, methodological constraints, previous field observations, and background theory. Tracking technology is therefore also shifting which disciplinary considerations are brought to bear on research into animal movement and behaviour and how this research is conducted. (shrink)

The goal of the Department of Defense Net-Centric Data Strategy is to improve data sharing throughout the DoD. Data sharing is a critical element of interoperability in the emerging system-of-systems. Achieving interoperability requires the elimination of two types of data heterogeneity: differences of syntax and differences of semantics. This paper builds a path toward semantic uniformity through application of a disciplined approach to ontology. An ontology is a consensus framework representing the types of entities within (...) a given domain and the relations between them. The construction of an ontology begins when a Community of Interest (COI) identifies its authoritative data sources (ADS), which are usually manifest in relevant doctrinal publications, glossaries, data dictionaries, and logical data models. The identified terms are then defined in relation to a common logical framework that has been designed to ensure interoperability with other ontologies created on the basis of the same strategy. As will be described, the Command and Control (C2) Ontology will include representations of a substantial number of entities within the Command and Control (C2) domain. If domain ontologies (e.g. Strike and Counterinsurgency) semantically align with the C2 Ontology, then a substantial barrier to systems interoperability is thereby crossed. (shrink)

Cattle farming is a traditional agricultural system that contributes to the rural economic, social, and cultural values of the communities. Cattle as common with other livestock, are affected by many diseases that cause mortality and economic losses. In many rural households, the use of plants and associated knowledge are popular for managing cattle diseases, especially in areas experiencing challenges with conventional veterinary medicine. Evidence on the documentation of indigenous knowledge and biological evaluation of plants used against cattle diseases remain understudied (...) and fragmented. The aim of the review is to collate and analyze the ethnoveterinary knowledge and biological evaluation of plants used against cattle diseases in South Africa. Different scientific databases were systematically explored to extract data from 37 eligible studies. A total of 310 medicinal plants from 81 families were used to treat 10 categories of cattle diseases across seven (7) provinces in South Africa. Leguminosae (Fabaceae), Compositae (Asteraceae), Asparagaceae, and Xanthorrhoeaceae were the most frequently used plant families. Common plant parts used were leaves and roots. Twenty-seven (27) combination remedies involving 2–6 plants were identified as treatment regimes against cattle diseases. Common preparation methods were infusion and decoction while the administration mode was predominantly unspecified (52%) while oral and topical contributed 26 and 22%, respectively. In terms of diseases, the most treated ones were general systems infection, reproduction disorders, and gastrointestinal problems. Currently, an estimated 21% of the 310 plants have been evaluated for diverse biological activities using relevant bioassays related to cattle diseases. Antibacterial activity remained the most studied biological activity. Evidence from the review revealed the significance of ethnoveterinary medicine against cattle diseases especially in rural areas of South Africa. Nevertheless, the use of plants for cattle diseases among other ethnic groups, particularly in the Northern Cape and Western Cape, remains understudied. (shrink)

DOI: 10.1080/00031305.2018.1564697 When the editors of Basic and Applied Social Psychology effectively banned the use of null hypothesis significance testing (NHST) from articles published in their journal, it set off a fire-storm of discussions both supporting the decision and defending the utility of NHST in scientific research. At the heart of NHST is the p-value which is the probability of obtaining an effect equal to or more extreme than the one observed in the sample data, given the null hypothesis (...) and other model assumptions. Although this is conceptually different from the probability of the null hypothesis being true, given the sample, p-values nonetheless can provide evidential information, toward making an inference about a parameter. Applying a 10,000-case simulation described in this article, the authors found that p-values’ inferential signals to either reject or not reject a null hypothesis about the mean (α = 0.05) were consistent for almost 70% of the cases with the parameter’s true location for the sampled-from population. Success increases if a hybrid decision criterion, minimum effect size plus p-value (MESP), is used. Here, rejecting the null also requires the difference of the observed statistic from the exact null to be meaningfully large or practically significant, in the researcher’s judgment and experience. The simulation compares performances of several methods: from p-value and/or effect size-based, to confidence-interval based, under various conditions of true location of the mean, test power, and comparative sizes of the meaningful distance and population variability. For any inference procedure that outputs a binary indicator, like flagging whether a p-value is significant, the output of one single experiment is not sufficient evidence for a definitive conclusion. Yet, if a tool like MESP generates a relatively reliable signal and is used knowledgeably as part of a research process, it can provide useful information. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for (...) the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

We undeniably live in an information age—as, indeed, did those who lived before us. After all, as the cultural historian Robert Darnton pointed out: ‘every age was an age of information, each in its own way’ (Darnton 2000: 1). Darnton was referring to the news media, but his insight surely also applies to the sciences. The practices of acquiring, storing, labeling, organizing, retrieving, mobilizing, and integrating data about the natural world has always been an enabling aspect of scientific work. (...) Natural history and its descendant discipline of biological taxonomy are prime examples of sciences dedicated to creating and managing systems of ordering data. In some sense, the idea of biological taxonomy as an information science is commonplace. Perhaps it is because of its self-evidence that the information science perspective on taxonomy has not been a major theme in the history and philosophy of science. The botanist Vernon Heywood once pointed out that historians of biology, in their ‘preoccupation with the development of the sciences of botany and zoology… [have] diverted attention from the role of taxonomy as an information science’ (Heywood 1985: 11). More specifically, he argued that historians had failed to appreciate how principles and practices that can be traced to Linnaeus constituted ‘a change in the nature of taxonomy from a local or limited folk communication system and later a codified folk taxonomy to a formal system of information science [that] marked a watershed in the history of biology’ (ibid.). A similar observation could be made about twentieth-century philosophy of biology, which mostly skipped over practical and epistemic questions about information management in taxonomy. The taxonomic themes that featured in the emerging philosophy of biology literature in the second half of the twentieth century were predominantly metaphysical in orientation. This is illustrated by what has become known as the ‘essentialism story’: an account about the essentialist nature of pre- Darwinian taxonomy that used to be accepted by many historians and philosophers, and which stimulated efforts to document and interpret shifts in the metaphysical understanding of species and (natural) classification (Richards 2010; Winsor 2003; Wilkins 2009). Although contemporary debates in the philosophy of taxonomy have moved on, much discussion continues to focus on conceptual and metaphysical issues surrounding the nature of species and the principles of classification. Discussions centring on whether species are individuals, classes, or kinds have sprung up as predictably as perennials. Raucous debates have arisen even with the aim of accommodating the diversity of views: is monism, pluralism, or eliminativism about the species category the best position to take? In addition to these, our disciplines continue to interrogate what is the nature of these different approaches to classification: are they representational or inferential roles of different approaches to classification (evolutionary taxonomy, phenetics, phylogenetic systematics)? While there is still much to learn from these discussions—in which we both actively participate—our aim with this topical collection has been to seek different entrypoints and address underexposed themes in the history and philosophy of taxonomy. We believe that approaching taxonomy as an information science prompts new questions and can open up new philosophical vistas worth exploring. A twenty-first century information science turn in the history and philosophy of taxonomy is already underway. In scientific practice and in daily life it is hard to escape the imaginaries of Big Data and the constant threats of being ‘flooded with data’. In the life sciences, these developments are often associated with the socalled bioinformatics crisis that can hopefully be contained by a new, interdisciplinary breed of bioinformaticians. These new concepts, narratives, and developments surrounding the centrality of data and information systems in the biological and biomedical sciences have raised important philosophical questions about their challenges and implications. But historical perspectives are just as necessary to judge what makes our information age different from those that preceded us. Indeed, as the British zoologist Charles Godfray has often pointed out, the piles of data that are being generated in contemporary systematic biology have led to a second bioinformatics crisis, the first being the one that confronted Linnaeus in the mid-18th century (Godfray 2007). Although our aim is to clear a path for new discussions of taxonomy from an information science-informed point of view, we continue where others in the history, philosophy, and sociology of science have already trod. We believe that an appreciation of biological taxonomy as an information science raises many questions about the philosophical, theoretical, material, and practical aspects of the use and revision of biological nomenclatures in different local and global communities of scientists and citizen scientists. In particular, conceiving of taxonomy as an information science directs attention to the temporalities of managing an accumulating data about classified entities that are themselves subject to revision, to the means by which revision is accomplished, and to the semantic, material, and collaborative contexts that mediate the execution of revisions. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for (...) the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

In this paper, we analyse the relation between the use of environmental data in contemporary health sciences and related conceptualisations and operationalisations of the notion of environment. We consider three case studies that exemplify a different selection of environmental data and mode of data integration in data-intensive epidemiology. We argue that the diversification of data sources, their increase in scale and scope, and the application of novel analytic tools have brought about three significant conceptual shifts. (...) First, we discuss the EXPOsOMICS project, an attempt to integrate genomic and environmental data which suggests a reframing of the boundaries between external and internal environments. Second, we explore the MEDMI platform, whose efforts to combine health, environmental and climate data instantiate a reframing and expansion of environmental exposure. Third, we illustrate how extracting epidemiological insights from extensive social data collected by the CIDACS institute yields innovative attributions of causal power to environmental factors. Identifying these shifts highlights the benefits and opportunities of new environmental data, as well as the challenges that such tools bring to understanding and fostering health. It also emphasises the constraints that data selection and accessibility pose to scientific imagination, including how researchers frame key concepts in health-related research. (shrink)

Suppose that disgust can provide evidence of moral wrongdoing. What account of disgust might make sense of this? A recent and promising theory is the social contagion view, proposed by Alexandra Plakias. After criticizing both its descriptive and normative claims, I draw two conclusions. First, we should question the wisdom of drawing so straight a line from biological poisons and pathogens to social counterparts. Second, we don’t need to explain the evidential value of disgust by appealing to what the (...) response tracks. These lessons point toward an alternative: namely, that disgust is a moral heuristic. On the heuristic view, disgust is a trigger for the subconscious use of a particular rule: I show how this view fits with a plausible hypothesis about the social function of disgust, and then apply it to Leon Kass’s famous use of repugnance to criticize cloning. (shrink)

Does a diagnosis of brain dysfunction matter for ascriptions of moral responsibility? This chapter argues that, while knowledge of brain pathology can inform judgments of moral responsibility, its evidential value is currently limited for a number of practical and theoretical reasons. These include the problem of establishing causation from correlational data, drawing inferences about individuals from group data, and the reliance of the interpretation of brain findings on well-established psychological findings. Brain disorders sometimes matter for moral responsibility, (...) however, because they change an individual’s moral psychology in a way that is beyond their control. While control over psychological changes is not an excusing factor, brain disorders can mitigate moral responsibility because they confront individuals with new psychological deficits or urges for which their previous moral education and existing external and internal moral resources have not prepared them. (shrink)

Biomarkers are widely used not only as prognostic or diagnostic indicators, or as surrogate markers of disease in clinical trials, but also to formulate theories of pathogenesis. We identify two problems in the use of biomarkers in mechanistic studies. The first problem arises in the case of multifactorial diseases, where different combinations of multiple causes result in patient heterogeneity. The second problem arises when a pathogenic mediator is difficult to measure. This is the case of the oxidative stress (OS) theory (...) of disease, where the causal components are reactive oxygen species (ROS) that have very short half-lives. In this case, it is usual to measure the traces left by the reaction of ROS with biological molecules, rather than the ROS themselves. Borrowing from the philosophical theories of signs, we look at the different facets of biomarkers and discuss their different value and meaning in multifactorial diseases and system medicine to inform their use in patient stratification in personalized medicine. (shrink)

All too often, the requirements for actionability and accountability of data infrastructures are conceptualised as incompatible and leading to a trade-off situation where increasing one will unavoidably decrease the other. Through a comparative analysis of two data infrastructures used to share genomic data about the SARS-COV-2 virus, we argue that making data actionable for knowledge development involves a commitment to ensuring that the data in question are representative of the phenomena being studied and accountable to (...) data subjects and users. This in turn presupposes that: (1) enough data are contributed by a wide and diverse set of relevant sources; (2) mechanisms of feedback and inclusion are set up to ensure that data contributors can participate data governance and interpretation, thereby helping to adequately contextualise data; and (3) accountability extends to the ways in which data infrastructures are run, financed and positioned vis-à-vis the communities they are meant to serve. Such a model of data sharing can only work on the understanding that data do not need to be easily accessible to be actionable; rather, actionability depends on the responsiveness and accountability of data infrastructures, and the efforts invested in ensuring open communication among contributors. (shrink)

"Scientific Research in the Era of Big Data" - this book was also published in French (Mimesis) in 2019 and in Portuguese in 2022 (FIOCRUZ editors).

This article defends a version of the Westermarck Effect, integrating existing clinical, biological, and philosophical dimensions to incest avoidance. By focusing on care-based attachment in primates, my formulation of the effect suggests the power of a phylogenetic argument widely accepted by primatologists but not by cultural anthropologists. Identifying postadoption incest as a phenomenon with underexplored evidential value, the article sketches an explanatory strategy for reconciling the effect with the clinical reality of incest, concluding with an explicit argument against culture-first (...) or conventionalist accounts of incest avoidance prevalent in anthropology. (shrink)

We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) perspectives within a single framework. (...) We examine how BFO-conformant domain ontologies can deal with the consistent representation of scientific data deriving from the measurement of processes of different types, and we outline on this basis the first steps of an approach to the classification of such processes within the BFO framework. (shrink)

There are two motivations commonly ascribed to historical actors for taking up statistics: to reduce complicated data to a mean value (e.g., Quetelet), and to take account of diversity (e.g., Galton). Different motivations will, it is assumed, lead to different methodological decisions in the practice of the statistical sciences. Karl Pearson and W. F. R. Weldon are generally seen as following directly in Galton’s footsteps. I argue for two related theses in light of this standard interpretation, based on a (...) reading of several sources in which Weldon, independently of Pearson, reflects on his own motivations. First, while Pearson does approach statistics from this "Galtonian" perspective, he is, consistent with his positivist philosophy of science, utilizing statistics to simplify the highly variable data of biology. Weldon, on the other hand, is brought to statistics by a rich empiricism and a desire to preserve the diversity of biological data. Secondly, we have here a counterexample to the claim that divergence in motivation will lead to a corresponding separation in methodology. Pearson and Weldon, despite embracing biometry for different reasons, settled on precisely the same set of statistical tools for the investigation of evolution. (shrink)

In this article, I will explore how the underlying research values of ‘openness’ and ‘mutual responsiveness’, which are central to open science practices, can be integrated into a new ethos of science. Firstly, I will revisit Robert Merton's early contribution to this issue, examining whether the ethos of science should be understood as a set of norms for scientists to practice ‘good’ science or as a set of research values as a functional requirement of the scientific system to produce knowledge, (...) irrespective of individual adherence to these norms. Secondly, I will analyse the recent codification of scientific practice in terms of ‘scientific integrity’, a framework that Merton did not pursue. Based on this analysis, and illustrated on the case of COVID-19 as a case in which the institution of science was challenged to deliver urgently on societal desirable outcomes, I will argue that promoting open science and its core norms of collaboration and openness requires broader governance of the institution of science in its relationship with society at large, rather than relying solely on self-governance within the scientific community through a new ethos of science. This conclusion has implications for re-evaluating research assessments, suggesting that the evaluation of the scientific system should take precedence over evaluating individual researchers, and that incentives should be provided to encourage specific research behaviour rather than solely focusing on individual research outputs. This article is followed up by Commentaries of Carl Mitcham, Alfred Nordmann, Sabina Leonelli, Lukas Fuchs, Monica Edwards-Schachter. (shrink)

In this study, I aimed to subject to philosophical analysis the scientific data from biological science researches that are conducted into the phenomenon of homosexuality in order to give philosophical interpretation to it thereby establishing the normative values of the scientific findings. From the study, I observed that much of the scientific data on homosexuality established the phenomenon as ingrained in the human biological construct. I argued that although homoeroticism is biological construct of the homosexual, parenting plays significant (...) role in the sexual identity ultimately developed by an individual. I have presented three conceptual frameworks to show how this happens. I determined that homoeroticism and homosexuality are not exactly the same thing; homoeroticism is a biological construct, while homosexuality is a social construct. I also determine that sexual orientation (which results from eros) is not necessarily the same thing as sexual identity (such as homosexuality or heterosexuality, which results from socialization processes). I argued that sexuality is a synthesis of dialectical interactions between the factors internal within and external to the homosexual’s body; but that the external is conditioned by the internal. I adopted the paradigm of existentialism as the philosophical framework for the analysis. In conclusion, I argued that if the homosexual’s sexual orientation is native biological construct of his/her body, then the homosexual has no control over his/her sexual orientation. The philosophical implication of that finding is that homoeroticism is facticity; and as facticity the homosexual cannot escape from being homosexual. Despite this, I used the Two-Way Test (TWT) to show that homosexuality is immoral act; although the homosexual is not an immoral person. However, I have demonstrated that the failed moral status of homosexuality is not enough ground to criminalize homosexuality. (shrink)

I argue that the evolutionary history of anger has substantive implications for normative ethics. In the process, I develop an evolutionary account of anger and its influence on action. First, I consider a prominent argument by Peter Singer and Joshua Greene. They conclude that evolutionary explanations of human cooperation debunk – or undercut the evidential value of – the moral intuitions supporting duty ethics (as opposed to utilitarian or consequentialist ethics). With this argument they aim to defend consequentialist theories. (...) However, their argument also threatens to debunk intuitions that support consequentialist theories. I give a novel argument that overcomes this difficulty. Specifically, I offer an evolutionary story about anger that can explain retributive, duty-oriented intuitions concerning punishment. This explanation debunks these intuitions (and not others) by showing that they were selected for their biological consequences rather than their accuracy (concerning duties to punish). I develop this explanation by raising and resolving three additional problems. First, prominent evolutionary explanations of retributive motives fail because they appeal to models that apply only to organisms with strategic insight. To mitigate this problem, I explain the existence of a retributive-like motive in rodents by appealing to an economic model of resource competition, which applies to organisms without strategic insight. Second, I show that human anger was shaped by resource competition of this kind. To do so, I develop evidential criteria to determine when psychological systems in different species share common evolutionary origins. I deploy these criteria to argue that human anger and the retributive motive in rodents derive from the same ancestral trait. Finally, the continuity of anger across human and nonhuman animals stands in tension with the idea that anger causes purposive behavior like retribution or retaliation. I argue that differences between the angry behaviors of human and nonhuman animals are differences in degree and not in kind. In the end, this evolutionary story both explains and undermines retributive intuitions, but not in the straightforward way that Singer and Greene suppose. (shrink)

Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate representation (...) of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information. (shrink)

This book is the sixth volume in the series of Collected Papers on Advancing Uncertain Combinatorics through Graphization, Hyperization, and Uncertainization: Fuzzy, Neutrosophic, Soft, Rough, and Beyond. Building upon the foundational contributions of previous volumes, this edition focuses on the exploration and development of Various New Uncertain Concepts, further enriching the study of uncertainty and complexity through innovative theoretical advancements and practical applications. The volume is meticulously organized into 15 chapters, each presenting unique perspectives and contributions to the field. From (...) theoretical explorations to real-world applications, these chapters provide a cohesive and comprehensive overview of the state of the art in uncertain combinatorics, emphasizing the versatility and power of the newly introduced concepts and methodologies. The first chapter (SuperHypertree-depth – Structural Analysis in SuperHyperGraphs) explores the concept of SuperHypertree-depth, an extension of the classical graph parameter Tree-depth and its hypergraph counterpart Hypertree-depth. By introducing hierarchical nesting within SuperHyperGraphs, where both vertices and edges can represent recursive subsets, this study investigates the mathematical properties and structural implications of these extended parameters. The findings highlight the relationships between SuperHypertree-depth and its traditional graph-theoretic equivalents, providing a deeper understanding of their applicability to hierarchical and complex systems. The second chapter (Obstructions for Hypertree-width and SuperHypertree-width) examines the role of ultrafilters as obstructions in determining Hypertree-width and extends the concept to SuperHypertree-width. Building on hypergraph theory, which abstracts traditional graph frameworks into more complex domains, the study investigates how recursive structures within SuperHyperGraphs redefine the computational and structural properties of these parameters. Ultrafilters, with their broad mathematical significance, serve as critical tools for understanding the limitations and potentials of these advanced graph metrics. The third chapter (SuperHypertree-Length and SuperHypertree-Breadth in SuperHyperGraphs) investigates the extension of the graph-theoretic parameters Tree-length and Tree-breadth to the realms of hypergraphs and SuperHyperGraphs. By leveraging the hierarchical nesting of SuperHyperGraphs, the study explores how these parameters adapt to increasingly complex and multi-level structures. Comparative analyses between these extended parameters and their classical counterparts reveal new insights into their relevance and utility in advanced graph and hypergraph theory. Plithogenic Sets, which generalize Fuzzy and Neutrosophic Sets, are extended in the fourth chapter (Extended HyperPlithogenic Sets and Generalized Plithogenic Graphs) to Extended Plithogenic Sets, HyperPlithogenic Sets, and SuperHyperPlithogenic Sets. This study further investigates their application to graph theory through the concepts of Extended Plithogenic Graphs and Generalized Extended Plithogenic Graphs. The chapter provides a concise exploration of these frameworks, offering insights into their potential for addressing uncertainty and complexity in graph structures. Soft Sets provide an effective framework for decision-making by mapping parameters to subsets of a universal set, addressing uncertainty and vagueness. The fifth chapter (Double-Framed Superhypersoft Set and Double-Framed Treesoft Set) introduces the Double-Framed SuperHypersoft Set and the Double-Framed Treesoft Set as extensions of traditional and advanced soft set frameworks, such as Hypersoft and SuperHypersoft Sets. The chapter explores their relationships with existing concepts, offering new tools to handle complex decision-making scenarios with enhanced structural flexibility. The sixth paper (HyperPlithogenic Cubic Set and SuperHyperPlithogenic Cubic Set) introduces the concepts of the HyperPlithogenic Cubic Set and SuperHyperPlithogenic Cubic Set, which extend the Plithogenic Cubic Set by integrating both interval-valued and single-valued fuzzy memberships. These sets leverage multi-attribute aggregation techniques inherent to plithogenic structures, allowing for nuanced representations of uncertainty. Additionally, related constructs such as the HyperPlithogenic Fuzzy Cubic Set, HyperPlithogenic Intuitionistic Fuzzy Cubic Set, and HyperPlithogenic Neutrosophic Cubic Set are explored, further enriching the theoretical and practical applications of this framework. The seventh chapter (L-Neutrosophic Sets and Nonstationary Neutrosophic Sets) extends the foundational concepts of fuzzy sets by integrating Neutrosophic and Plithogenic frameworks. By introducing L-Neutrosophic Sets and Nonstationary Neutrosophic Sets, the study enhances the representation of uncertainty through independent membership components: truth, indeterminacy, and falsity. These advanced constructs also incorporate multi-dimensional and contradictory attributes, providing a robust means of modeling complex decision-making and uncertain data. Plithogenic and Rough Sets, known for generalizing uncertainty modeling and classification, are extended in the eight chapter (Forest HyperPlithogenic and Forest HyperRough Sets) to Forest HyperPlithogenic Sets, Forest SuperHyperPlithogenic Sets, Forest HyperRough Sets, and Forest SuperHyperRough Sets. These frameworks incorporate hierarchical and recursive structures to advance existing set-theoretic paradigms. The chapter explores their applications in multi-level data analysis and uncertainty classification, demonstrating their adaptability to complex systems. Building on Fuzzy, Neutrosophic, and Plithogenic Sets, the tenth chapter (Symbolic HyperPlithogenic Sets) introduces Symbolic HyperPlithogenic Sets and Symbolic n-SuperHyperPlithogenic Sets. These sets incorporate symbolic components and algebraic coefficients, enabling flexible operations within a defined prevalence order. By extending symbolic representation into hyperplithogenic and superhyperplithogenic domains, the chapter opens new pathways for addressing uncertainty and hierarchical complexity in mathematical modeling. Soft Sets, designed to manage uncertainty and imprecision, have evolved through various extensions like Hypersoft Sets and SuperHypersoft Sets. The eleventh chapter (N-SuperHypersoft and Bijective SuperHypersoft Sets) introduces N-SuperHypersoft Sets, N-Treesoft Sets, Bijective SuperHypersoft Sets, and Bijective Treesoft Sets. These new constructs enhance decision-making frameworks by incorporating advanced hierarchical and bijective relationships, building on existing theories and expanding their applications. Plithogenic Sets, known for integrating multi-valued attributes and contradictions, and Rough Sets, which partition data into definable approximations, are combined in the twelfth chapter (Plithogenic Rough Sets) to form Plithogenic Rough Sets. This fusion provides a powerful framework for addressing uncertainty in dynamic and complex decision-making scenarios, offering a novel approach to uncertainty modeling. Expanding on Neutrosophic Sets, which represent truth, indeterminacy, and falsehood, this chapter introduces Plithogenic Duplets and Plithogenic Triplets. These constructs leverage the Plithogenic framework to incorporate attributes, values, and contradiction measures. The thirteenth chapter (Plithogenic Duplets and Triplets) examines their relationships with Neutrosophic Duplets and Triplets, offering new tools for multi-dimensional data representation and decision-making. Building on foundational concepts like Rough Sets and Vague Sets, the fourteenth chapter (SuperRough and SuperVague Sets) introduces SuperRough Sets and SuperVague Sets. These generalized frameworks extend uncertainty modeling by incorporating hierarchical structures. The study also demonstrates that SuperRough Sets can evolve into SuperHyperRough Sets, providing further generalizations for advanced data classification and analysis. The fifteenth chapter (Neutrosophic TreeSoft Expert and ForestSoft Sets) revisits the Neutrosophic TreeSoft Set, which combines the hierarchical structure of TreeSoft Sets with the Neutrosophic framework for uncertainty representation. Additionally, it introduces the Neutrosophic TreeSoft Expert Set, incorporating expert knowledge into the model. The chapter also explores the ForestSoft Set and its extension, the Neutrosophic ForestSoft Set, to provide multi-level, tree-structured approaches for complex data representation and analysis. (shrink)

Do epistemic intuitions tell us anything about knowledge? Stich has argued that we respond to cases according to our contingent cultural programming, and not in a manner that tends to reveal anything significant about knowledge itself. I’ve argued that a cross-culturally universal capacity for mindreading produces the intuitive sense that the subject of a case has or lacks knowledge. This paper responds to Stich’s charge that mindreading is cross-culturally varied in a way that will strip epistemic intuitions of their (...) class='Hi'>evidential value. I argue that existing work on cross-cultural variation in mindreading favors my position over Stich’s. (shrink)

A model of face representation, inspired by the biology of the visual system, is compared to experimental data on the perception of facial similarity. The face representation model uses aggregate primary visual cortex (V1) cell responses topographically linked to a grid covering the face, allowing comparison of shape and texture at corresponding points in two facial images. When a set of relatively similar faces was used as stimuli, this Linked Aggregate Code (LAC) predicted human performance in similarity judgment experiments. (...) When faces of perceivable categories were used, dimensions such as apparent sex and race emerged from the LAC model without training. The dimensional structure of the LAC similarity measure for the mixed category task displayed some psychologically plausible features but also highlighted differences between the model and the human similarity judgements. The human judgements exhibited a racial perceptual bias that was not shared by the LAC model. The results suggest that the LAC based similarity measure may offer a fertile starting point for further modelling studies of face representation in higher visual areas, including studies of the development of biases in face perception. (shrink)