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)

Functional diversity holds the promise of understanding ecosystems in ways unattainable by taxonomic diversity studies. Underlying this promise is the intuition that investigating the diversity of what organisms actually do—i.e. their functional traits—within ecosystems will generate more reliable insights into the ways these ecosystems behave, compared to considering only species diversity. But this promise also rests on several conceptual and methodological—i.e. epistemic—assumptions that cut across various theories and domains of ecology. These assumptions should be clearly addressed, notably for the sake (...) of an effective comparison and integration across domains, and for assessing whether or not to use functional diversity approaches for developing ecological management strategies. The objective of this contribution is to identify and critically analyze the most salient of these assumptions. To this aim, we provide an “epistemic roadmap” that pinpoints these assumptions along a set of historical, conceptual, empirical, theoretical, and normative dimensions. (shrink)

The view that it is better for life to be created free of disability is pervasive in both common sense and philosophy. We cast doubt on this view by focusing on an influential line of thinking that manifests it. That thinking begins with a widely-discussed principle, Procreative Beneficence, and draws conclusions about parental choice and disability. After reconstructing two versions of this argument, we critique the first by exploring the relationship between different understandings of well-being and disability, and the second (...) by more briefly focusing on the idea of a significant reason. By placing these results against the broader historical and ongoing contexts in which the lives of those with disabilities have been deemed of inferior quality, we conclude with a call for greater humility about disability and well-being in thought and practice. (shrink)

The main objective o f this descriptive paper is to present the general notion of translation between logical systems as studied by the GTAL research group, as well as its main results, questions, problems and indagations. Logical systems here are defined in the most general sense, as sets endowed with consequence relations; translations between logical systems are characterized as maps which preserve consequence relations (that is, as continuous functions between those sets). In this sense, logics together with translations form a (...) bicomplete category of which topological spaces with topological continuous functions constitute a full subcategory. We also describe other uses of translations in providing new semantics for non-classical logics and in investigating duality between them. An important subclass of translations, the conservative translations, which strongly preserve consequence relations, is introduced and studied. Some specific new examples of translations involving modal logics, many-valued logics, para- consistent logics, intuitionistic and classical logics are also described. (shrink)

FDE, LP and K3 are closely related to each other and admit of an intuitive informational interpretation. However, all these logics are co-NP complete, and so idealized models of how an agent can think. We address this issue by shifting to signed formulae, where the signs express imprecise values associated with two bipartitions of the corresponding set of standard values. We present proof systems whose operational rules are all linear and have only two structural branching rules that express a generalized (...) Principle of Bivalence. Each of these systems leads to defining an infinite hierarchy of tractable approximations to the respective logic, in terms of the maximum number of allowed nested applications of the two branching rules. Further, each resulting hierarchy admits of an intuitive 5-valued non-deterministic semantics. (shrink)

The impressive variation amongst biological individuals generates many complexities in addressing the simple-sounding question what is a biological individual? A distinction between evolutionary and physiological individuals is useful in thinking about biological individuals, as is attention to the kinds of groups, such as superorganisms and species, that have sometimes been thought of as biological individuals. More fully understanding the conceptual space that biological individuals occupy also involves considering a range of other concepts, such as life, reproduction, and agency. There has (...) been a focus in some recent discussions by both philosophers and biologists on how evolutionary individuals are created and regulated, as well as continuing work on the evolution of individuality. (shrink)

ABSTRACT Drawing inspiration from Fred Dretske, L. S. Carrier, John A. Barker, and Robert Nozick, we develop a tracking analysis of knowing according to which a true belief constitutes knowledge if and only if it is based on reasons that are sensitive to the fact that makes it true, that is, reasons that wouldn’t obtain if the belief weren’t true. We show that our sensitivity analysis handles numerous Gettier-type cases and lottery problems, blocks pathways leading to skepticism, and validates (...) the epistemic closure thesis that correct inferences from known premises yield knowledge of the conclusions. We discuss the plausible views of Ted Warfield and Branden Fitelson regarding cases of knowledge acquired via inference from false premises, and we show how our sensitivity analysis can account for such cases. We present arguments designed to discredit putative counterexamples to sensitivity analyses recently proffered by Tristan Haze, John Williams and Neil Sinhababu, which involve true statements made by untrustworthy informants and strange clocks that sometimes display the correct time while running backwards. Finally, we show that in virtue of employing the paradox-free subjunctive conditionals codified by Relevance Logic theorists instead of the paradox-laden subjunctive conditionals codified by Robert Stalnaker and David Lewis. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

A far-reaching and influential view in evolutionary biology claims that species are cohesive units held together by gene flow. Biologists have recognized empirical problems facing this view; after sharpening the expression of the view, we present novel conceptual problems for it. At the heart of these problems is a distinction between two importantly different concepts of cohesion, what we call integrative and response cohesion. Acknowledging the distinction problematizes both the explanandum of species cohesion and the explanans of gene flow that (...) are central to the view we discuss. We conclude by tracing four broader implications for the study and conceptualization of species. (shrink)

In a recent very interesting and important challenge to tracking theories of knowledge, Williams & Sinhababu claim to have devised a counter-example to tracking theories of knowledge of a sort that escapes the defense of those theories by Adams & Clarke. In this paper we will explain why this is not true. Tracking theories are not undermined by the example of the backward clock, as interesting as the case is.

The current study is conducted to examine the following research questions: 1) What information sources on social media are associated with the general intention to try space tourism? 2) Does the automatically recommended information moderate the associations between multiple sources of information and the intention to try space tourism?

The current study is conducted to examine the following research questions: 1) How is the relationship between general coastal activities enabling close connections and mental health in the previous year conditional on the nature connectedness? 2) How is the relationship between general coastal activities enabling close connections and perceived general health in the previous year conditional on the nature connectedness?

The current study is conducted to examine the following research questions: 1) Is the relationship between the enjoyment of and connection to the coastal environment and the visitors’ mental health and perceived general health conditional on the duration of daily visits to the coast in the previous year? 2) Is the relationship between the enjoyment of and connection to the coastal environment and the visitors’ mental health and perceived general health conditional on the duration of stay visits to the coast (...) in the previous year? (shrink)

We are immersed within an odorous sea of chemical currents that we parse into individual odors with complex structures. Odors have been posited as determined by the structural relation between the molecules that compose the chemical compounds and their interactions with the receptor site. But, naturally occurring smells are parsed from gaseous odor plumes. To give a comprehensive account of the nature of odors the chemosciences must account for these large distributed entities as well. We offer a focused review of (...) what is known about the perception of odor plumes for olfactory navigation and tracking, which we then connect to what is known about the role odorants play as properties of the plume in determining odor identity with respect to odor quality. We end by motivating our central claim that more research needs to be conducted on the role that odorants play within the odor plume in determining odor identity. (shrink)

The current study is conducted to examine the following research question: What are the factors associated with the sensitivity towards the air quality rating index to reduce outdoor activities?

On November 3 and 4, 2023, Dr. Nguyen Minh Hoang (Phenikaa University), co-author of the BMF Analytics [1], gave a lecture on computational approaches using bayesvl and BMF application for social science research.

“[…] To alleviate the boredom, after catching a fish, Kingfisher would press all three buttons before swallowing the fish. Pressing the buttons has gradually become somewhat of a new technological ritual.” -/- —In “Innovation”; The Kingfisher Story Collection [1].

This letter was submitted to the Senate Standing Committee on Legal and Constitutional Affairs, Government of Canada, on 29th January, 2021, as final debate over Bill C-7 was being undertaken in the Senate regarding MAiD and the strong opposition to the legislation expressed across the Canadian disability community. It draws on our individual and joint work on eugenics, well-being, and disability.

In “Beat the (Backward) Clock,” we argued that John Williams and Neil Sinhababu’s Backward Clock Case fails to be a counterexample to Robert Nozick’s or Fred Dretske’s Theories of Knowledge. Williams’ reply to our paper, “There’s Nothing to Beat a Backward Clock: A Rejoinder to Adams, Barker and Clarke,” is a further attempt to defend their counterexample against a range of objections. In this paper, we argue that, despite the number and length of footnotes, Williams is still wrong.

The current study is conducted to examine the following research questions: -/- - What are the consequences of blockage, vandalism, and harassment activities for the cause of climate change mitigation? - What kind of environmental activism leads to the escalation of violence? - Which pathways (e.g., survival threats) do the activism lead to violence escalation? -/- The findings from this study are expected to provide insights into the effectiveness and appropriateness of strategies to raise public awareness and support and contribute (...) to the societal transitions to address climate change. (shrink)

The methodology title on BMF analytics is now in its third year of service to our research community, enabling many researchers to implement their research pursuits.

This month, the AISDL Team was glad to see its continuing effort to raise the voice for conserving wildlife appearing in Pacific Conservation Biology (published by CSIRO/the Australian Academy of Science). The article stipulates the need for weaving humane values with scientific information, leveraging the sociocultural power to harmonize humans with nature. The article articulates the coauthors’ idea of building a funding source to contribute to the nature conservation cause by investing in some listed stocks. Technically, stocks we intend to (...) invest in must possess some key features of (i) having significant growth potential, (ii) containing little environmental risk of potential moral-practical gaps in their CSR missions, and (iii) showing a certain degree of “relevance” with AISDL’s fundamentals. (shrink)

Closure is the epistemological thesis that if S knows that P and knows that P implies Q, then if S infers that Q, S knows that Q. Fred Dretske acknowledges that closure is plausible but contends that it should be rejected because it conflicts with the plausible thesis: Conclusive reasons (CR): S knows that P only if S believes P on the basis of conclusive reasons, i.e., reasons S wouldn‘t have if it weren‘t the case that P. Dretske develops an (...) analysis of knowing that centers on CR, and argues that the requirement undermines skepticism by implying the falsity of closure. We develop a Dretske-style analysis of knowing that incorporates CR, and we argue that this analysis not only accords with closure, but also implies it. In addition, we argue that the analysis accounts for the prima facie plausibility of closure-invoking skeptical arguments, and nonetheless implies that they are fallacious. If our arguments turn out to be sound, the acceptability of Dretske‘s analysis of knowing will be significantly enhanced by the fact that, despite implying closure, it undermines closure-based skepticism. (shrink)

Our latest contribution to the world’s battle against climate and biodiversity crises was an expert commentary on Vietnamese forests and the prospect of carbon credits trade. The article appeared in the Land and Climate Review on Feb. 2, 2024.

The current study is conducted to examine the following research questions: 1) How are the father’s interactions with children regarding energy saving associated with the children’s energy conservation behaviors? 2) How are the mother’s interactions with children regarding energy saving associated with the children’s energy conservation behaviors?

The current study is conducted to examine the following research questions: 1) How are coastal activities enabling close connections to nature associated with the mental health condition of the visitors in the previous year? 2) How are coastal activities that have close connections to nature associated with the perceived general health condition of the visitors in the previous year?

The current study is conducted to examine how investors’ information priorities for investment decision-making influence their fear during the crisis.

The current study is conducted to examine the following research questions: 1) How are the father’s interactions with children regarding waste recycling associated with the children’s recycling behaviors? 2) How are the mother’s interactions with children regarding waste recycling associated with the children’s recycling behaviors?

The current study has four objectives to examine whether: -/- The family’s provisions of cultural-historical knowledge of other countries, communication methods with people in different cultures, and encouragement to learn foreign languages are associated with students’ willingness to exchange historical and cultural information with other people. Students’ willingness to exchange historical and cultural information with others is associated with their awareness of cultural diversity. Students’ willingness to exchange historical and cultural information with others is associated with their awareness of global (...) interdependence. Students’ willingness to exchange historical and cultural information with others is associated with their awareness of peace protection. (shrink)

TS. Nguyễn Minh Hoàng (ngoài cùng; tay trái) và KS. Lã Việt Phương (ngoài cùng; tay phải) ở trong rừng nguyên sinh, tại điểm tập kết “thuốc lào hạnh phúc” của đồng bào Mường đi rừng.

The current study is conducted to examine the following research question: 1) Who were the people who had no access to wildfire smoke notifications during the smoke event in the summer of 2018 in the Boise Metropolitan Area in Idaho? 2) Who were the people who were not familiar with the air quality rating system?

Trong thế giới cạnh tranh thời đại số (“digital”), phương tiện kỹ thuật cung cấp nhiều thuận lợi cho việc sản xuất nội dung. Tuy thế, sự phong phú nội dung và đầu tư cho xúc tiến, tiếp thị gia tăng cũng lại khiến cho quá trình cạnh tranh tìm một chỗ đứng cho sản phẩm trở nên hết sức gian nan.Sản phẩm gần đây của nhóm nghiên cứu, chuyên khảo [1] của AISDL, ra đời sau những bài học gian (...) khó thu lượm được từ trước. Như thế, ý thức của mọi người về mức độ thách thức trong việc “chạm tới” người tiêu dùng. (shrink)

Nhân dịp khai giảng năm học 2023-24, nhóm nghiên cứu báo cáo thống kê số lần bayesvl tải về (downloads) từ The Comprehensive R Archive Network (CRAN).

The current study is conducted to examine the following research questions: 1) How are the enjoyment of and connection to the coastal environment associated with the perceived health outcomes during the previous year’s coastal visits? 2) How are the perceived health outcomes during the previous year’s coastal visits associated with visitors’ mental health and perceived general health? 3) Do the perceived health outcomes during the previous year’s coastal visits mediate the relationships between the enjoyment of and connection to the coastal (...) environment and the visitors’ mental health and perceived general health? (shrink)

Are the sculpture and the mass of gold which permanently makes it up one object or two? In this article, we argue that the monist, who answers ‘one object’, cannot accommodate the asymmetry of material constitution. To say ‘the mass of gold materially constitutes the sculpture, whereas the sculpture does not materially constitute the mass of gold’, the monist must treat ‘materially constitutes’ as an Abelardian predicate, whose denotation is sensitive to the linguistic context in which it appears. We motivate (...) this approach in terms of modal analyses of material constitution, but argue that ultimately it fails. The monist must instead accept a deflationary, symmetrical use of ‘materially constitutes’. We argue that this is a serious cost for her approach. (shrink)

Essentialism is widely regarded as a mistaken view of biological kinds, such as species. After recounting why (sections 2-3), we provide a brief survey of the chief responses to the “death of essentialism” in the philosophy of biology (section 4). We then develop one of these responses, the claim that biological kinds are homeostatic property clusters (sections 5-6) illustrating this view with several novel examples (section 7). Although this view was first expressed 20 years ago, and has received recent discussion (...) and critique, it remains underdeveloped and is often misrepresented by its critics (section 8). (shrink)

Although Paul Churchland and Jerry Fodor both subscribe to the so-called theory-theory– the theory that folk psychology (FP) is an empirical theory of behavior – they disagree strongly about FP’s fate. Churchland contends that FP is a fundamentally flawed view analogous to folk biology, and he argues that recent advances in computational neuroscience and connectionist AI point toward development of a scientifically respectable replacement theory that will give rise to a new common-sense psychology. Fodor, however, wagers that FP will be (...) largely preserved and vindicated by scientific investigations of behavior. Recent findings by developmental psychologists, I argue, will push both Churchlandians and Fodorians toward the pessimistic view that FP is a misguided theory that will never be displaced, because it is, so to speak, built into our cognitive systems. I explore the possibility of preserving optimism by rejecting the theory-theory and adopting the simulation theory, a competing view developed by Robert Gordon, Alvin Goldman, and Jane Heal. According to simulationists, common-sense interpretation of behavior is accomplished by means of pretense-like operations that deploy the cognitive system’s own reasoning capabilities in a disengaged manner. Since on this view no theory-like set of principles would be needed, the simulation theory seems to enjoy a simplicity advantage over the theory-theory. Steven Stich and Shawn Nichols, however, contend that as the cognitive system would require special mechanisms for disengaged operation, the simplicity question cannot be resolved until suitable computational models are developed. I describe a set of models I have constructed to meet this need, and I discuss the contribution such models can make to determining FP’s fate. (shrink)

In this paper we distinguish two issues that are often run together in discussions about physicalism. The first issue concerns levels. How do entities picked out by non-physical terminology, such as biological or psychological terminology, relate to physical entities? Are the former identical to, or metaphysically supervenient on, the latter? The second issue concerns physical parts and wholes. How do macroscopic physical entities relate to their microscopic parts? Are the former generally determined by the latter? We argue that views on (...) these two issues are independent of one another and should not be conflated. (shrink)

The article attempts to show how the dialog Charmides is a skillful and subtle response by Plato to the contradictions and challenges of his time and not, as one could assume, a fruitless search for a definition or a vain intellectual exercise. To do that, we’ll contextualize the dialog through a reconstruction of the historical and political conjuncture of the archaic and classical periods, using the notion of temperance (σωφροσύνη) as our guide.

About six weeks ago, our post referred to the long-winding path to a new theoretical innovation as the pursuit of “useless knowledge” in Flexner’s terms. That little creation is the freshly minted informational entropy-based definition of value, presented in a very short paper, initially regarded by its authors as a research note. (And it still is.) Well, only two and a half months since its birth, this new concept of value has had enough time to power up several of our (...) publications in different disciplinary fields. The first published paper using the new definition deals with climate change denialism. The second paper (forthcoming) discusses the problem of academic retractions amidst the growing influence of generative AI. And the third, just accepted, explains the underlying mechanism of submission mechanism employed by journal editors and peer-reviewers, and the information-value nexus associated with it. (shrink)

Every quantum state can be represented as a probability distribution over the outcomes of an informationally complete measurement. But not all probability distributions correspond to quantum states. Quantum state space may thus be thought of as a restricted subset of all potentially available probabilities. A recent publication (Fuchs and Schack, arXiv:0906.2187v1, 2009) advocates such a representation using symmetric informationally complete (SIC) measurements. Building upon this work we study how this subset—quantum-state space—might be characterized. Our leading characteristic is that the inner (...) products of the probabilities are bounded, a simple condition with nontrivial consequences. To get quantum-state space something more detailed about the extreme points is needed. No definitive characterization is reached, but we see several new interesting features over those in Fuchs and Schack (arXiv:0906.2187v1, 2009), and all in conformity with quantum theory. (shrink)

When and why does awareness of a belief's genealogy render it irrational to continue holding that belief? According to explanationism, awareness of a belief’s genealogy gives rise to an epistemic defeater when and because it reveals that the belief is not explanatorily connected to the relevant worldly facts. I argue that an influential recent version of explanationism, due to Korman and Locke, incorrectly implies that it is not rationally permissible to adopt a “sparse” ontology of worldly facts or states of (...) affairs. I then propose a new explanationist account of genealogical defeat capable of accommodating rational belief in ontological sparsity. According to my account, awareness of a belief’s genealogy gives rise to a defeater when and because it reveals that the belief is not explanatorily connected to its truthmaker. (shrink)

This is the first chapter to our edited collection of essays on the nature and ethics of blame. In this chapter we introduce the reader to contemporary discussions about blame and its relationship to other issues (e.g. free will and moral responsibility), and we situate the essays in this volume with respect to those discussions.

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)

Recent research has relied on trolley-type sacrificial moral dilemmas to study utilitarian versus nonutili- tarian modes of moral decision-making. This research has generated important insights into people’s attitudes toward instrumental harm—that is, the sacrifice of an individual to save a greater number. But this approach also has serious limitations. Most notably, it ignores the positive, altruistic core of utilitarianism, which is characterized by impartial concern for the well-being of everyone, whether near or far. Here, we develop, refine, and validate a (...) new scale—the Oxford Utilitarianism Scale—to dissociate individual differences in the ‘negative’ (permissive attitude toward instrumental harm) and ‘positive’ (impartial concern for the greater good) dimensions of utilitarian thinking as manifested in the general population. We show that these are two independent dimensions of proto-utilitarian tendencies in the lay population, each exhibiting a distinct psychological profile. Empathic concern, identification with the whole of humanity, and concern for future generations were positively associated with impartial beneficence but negatively associated with instrumental harm; and although instrumental harm was associated with subclinical psychopathy, impartial beneficence was associated with higher religiosity. Importantly, although these two dimensions were independent in the lay population, they were closely associated in a sample of moral philosophers. Acknowledging this dissociation between the instrumental harm and impartial beneficence components of utilitarian thinking in ordinary people can clarify existing debates about the nature of moral psychology and its relation to moral philosophy as well as generate fruitful avenues for further research. (shrink)

Negative facts get a bad press. One reason for this is that it is not clear what negative facts are. We provide a theory of negative facts on which they are no stranger than positive atomic facts. We show that none of the usual arguments hold water against this account. Negative facts exist in the usual sense of existence and conform to an acceptable Eleatic principle. Furthermore, there are good reasons to want them around, including their roles in causation, chance-making (...) and truth-making, and in constituting holes and edges. (shrink)

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

Today marks the 7th anniversary of the Centre for Interdisciplinary Social Research (ISR), at Phenikaa University. ISR has for seven years now the place where the co-founders of this portal have been working and producing publications. A special event occurs now as the Current Conservation magazine publishes a new writing piece by our member, Dr Minh-Hoang Nguyen.