Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community (...) critique and to describe a number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (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)

In a quantum universe with a strong arrow of time, it is standard to postulate that the initial wave function started in a particular macrostate---the special low-entropy macrostate selected by the Past Hypothesis. Moreover, there is an additional postulate about statistical mechanical probabilities according to which the initial wave function is a ''typical'' choice in the macrostate. Together, they support a probabilistic version of the Second Law of Thermodynamics: typical initial wave functions will increase in entropy. Hence, there are two (...) sources of randomness in such a universe: the quantum-mechanical probabilities of the Born rule and the statistical mechanical probabilities of the Statistical Postulate. I propose a new way to understand time's arrow in a quantum universe. It is based on what I call the Thermodynamic Theories of Quantum Mechanics. According to this perspective, there is a natural choice for the initial quantum state of the universe, which is given by not a wave function but by a density matrix. The density matrix plays a microscopic role: it appears in the fundamental dynamical equations of those theories. The density matrix also plays a macroscopic / thermodynamic role: it is exactly the projection operator onto the Past Hypothesis subspace. Thus, given an initial subspace, we obtain a unique choice of the initial density matrix. I call this property "the conditional uniqueness" of the initial quantum state. The conditional uniqueness provides a new and general strategy to eliminate statistical mechanical probabilities in the fundamental physical theories, by which we can reduce the two sources of randomness to only the quantum mechanical one. I also explore the idea of an absolutely unique initial quantum state, in a way that might realize Penrose's idea of a strongly deterministic universe. (shrink)

This paper has three main objectives: (a) Discuss the formal analogy between some important symmetry-invariance arguments used in physics, probability and statistics. Specifically, we will focus on Noether’s theorem in physics, the maximum entropy principle in probability theory, and de Finetti-type theorems in Bayesian statistics; (b) Discuss the epistemological and ontological implications of these theorems, as they are interpreted in physics and statistics. Specifically, we will focus on the positivist (in physics) or subjective (in statistics) interpretations (...) vs. objective interpretations that are suggested by symmetry and invariance arguments; (c) Introduce the cognitive constructivism epistemological framework as a solution that overcomes the realism-subjectivism dilemma and its pitfalls. The work of the physicist and philosopher Max Born will be particularly important in our discussion. (shrink)

The ontological models framework distinguishes ψ-ontic from ψ-epistemic wave- functions. It is, in general, quite straightforward to categorize the wave-function of a certain quantum theory. Nevertheless, there has been a debate about the ontological status of the wave-function in the statistical interpretation of quantum mechanics: is it ψ-epistemic and incomplete or ψ-ontic and complete? I will argue that the wave- function in this interpretation is best regarded as ψ-ontic and incomplete.

In this paper, I reconstruct the development and the complex character of Zilsel’s conception of scientific laws. This concept functions as a fil rouge for understanding Zilsel’s philosophy throughout different times (here, the focus is on his Viennese writings and how they pave the way to the more renown American ones) and across his many fields of work (from physics to politics). A good decade before Heisenberg’s uncertainty principle was going to mark the outbreak of indeterminism in quantum physics, Edgar (...) Zilsel started to develop a complex logical-philosophical theory in which statistical and causal laws were given an indeterministic foundation (Zilsel 1916). However, in developing his thoughts on the emergence of regularities from disorder, Zilsel arrives at a profound ambiguity with respect to the ontological or the epistemic nature of laws and order in the world: Whether this order is to be conceived of as an empirical finding or as the product of reason – this would have to remain unclear. This tension between rationalism and empiricism, as well as a tension between a realist and an anti-realist conception of lawfulness, can be identified in both Zilsel’s Viennese and American writings: a tension which touches the core of the “application problem” that would keep haunting Zilsel until his premature death. (shrink)

ABSTRACT. Two arguments have recently been advanced that Maxwell-Boltzmann particles are indistinguishable just like Bose-Einstein and Fermi-Dirac particles. Bringing modal metaphysics to bear on these arguments shows that ontological indistinguishability for classical (MB) particles does not follow. The first argument, resting on symmetry in the occupation representation for all three cases, fails since peculiar correlations exist in the quantum (BE and FD) context as harbingers of ontic indistinguishability, while the indistinguishability of classical particles remains purely epistemic. The second argument, deriving (...) from the classical limits of quantum statistical partition functions, embodies a conceptual confusion. After clarifying the doctrine of haecceitism, a third argument is considered that attempts to deflate metaphysical concerns altogether by showing that the phase-space and distribution-space representations of MB-statistics have contrary haecceitistic import. Careful analysis shows this argument to fail as well, leaving de re modality unproblematically grounding particle identity in the classical context while genuine puzzlement about the underlying ontology remains for quantum statistics. (shrink)

There is a common misconception across the lntelligence Community (IC) to the effect that information trapped within multiple heterogeneous data silos can be semantically integrated by the sorts of meaning-blind statistical methods employed in much of artificial intelligence (Al) and natural language processlng (NLP). This leads to the misconception that incoming data can be analysed coherently by relying exclusively on the use of statistical algorithms and thus without any shared framework for classifying what the data are about. Unfortunately, such approaches (...) do not yield sustainable results where we are dealing with widely distributed, highly heterogeneous and often changing bodies of data. We argue here that the needed integration requires the use of what we call an lntegrating Semantic Framework (ISF), which provldes a consistent set of categories and relationships that can be reused over and over again to tag successive bodies of data in ways which foster more coherent representation and reasoning. (shrink)

The pantheist ontology of Baruch Spinoza (b.1632 – d.1677) is an attempt to deny the accountability of political evil. -/- Spinoza’s instinct for statist control and his distrust of the common man are displayed in Theological-Political Treatise (published 1670). His masterwork, Ethics (published posthumously in 1677), is a bold attempt (in the guise of ontology) to classify minds and bodies as attributes of the State. -/- In Ethics, Spinoza ‘outlaws’ any vantage point from which we can address or (...) protest the kind of ‘perfect power’ -- and its attendant evils -- that constitute the essence and existence of the State. (shrink)

The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We use statistical methods (...) and formal ontological principles as a first step towards finding answers to this question. (shrink)

In this paper epistemological, ontological and sociological questions concerning the statistical significance of sharp hypotheses in scientific research are investigated within the framework provided by Cognitive Constructivism and the FBST (Full Bayesian Significance Test). The constructivist framework is contrasted with the traditional epistemological settings for orthodox Bayesian and frequentist statistics provided by Decision Theory and Falsificationism.

The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in (...) publicly available databases. Such annotation enables several objectives, including searching, browsing and cross-database data integration. A key benefit conferred by realismbased ontology is that suitably annotated research results are able to be aggregated and compared in a fashion that is based on the underlying reality that the science is studying. This has the potential of increasing the power of statistical analysis and meta-analysis in data-driven science. This aspect has been fruitfully exploited in the investigation of the functions of genes in molecular biology. Cognitive neuroscience uses functional neuroimaging to investigate the brain correlates of areas of mental functioning such as memory, planning and emotion. The use of functional neuroimaging to study affective phenomena such as the emotions is called ‘affective neuroscience’. BrainMap is the largest curated database of coordinates and metadata for studies in cognitive neuroscience, including affective neuroscience (Laird et al., 2005). BrainMap data is already classified and indexed using a terminology for classification, called the ‘Cognitive Paradigm Ontology’ (CogPO), that has been developed to facilitate searching and browsing. However, CogPO has been developed specifically for the BrainMap database, and the data are thus far not annotated to a realism-based ontology which would allow the discovery of interrelationships between research results across different databases on the basis of what the research is about. In this contribution, we describe ongoing work that aims to annotate affective neuroscience data, starting with the BrainMap database, using the Emotion Ontology. We describe our objectives and technical approach to the annotation, and mention some of the challenges. (shrink)

The conspicuous similarities between interpretive strategies in classical statistical mechanics and in quantum mechanics may be grounded on their employment of common implementations of probability. The objective probabilities which represent the underlying stochasticity of these theories can be naturally associated with three of their common formal features: initial conditions, dynamics, and observables. Various well-known interpretations of the two theories line up with particular choices among these three ways of implementing probability. This perspective has significant application to debates on primitive (...) class='Hi'>ontology and to the quantum measurement problem. (shrink)

The main goal of this article is to use the epistemological framework of a specific version of Cognitive Constructivism to address Piaget’s central problem of knowledge construction, namely, the re-equilibration of cognitive structures. The distinctive objective character of this constructivist framework is supported by formal inference methods of Bayesian statistics, and is based on Heinz von Foerster’s fundamental metaphor of objects as tokens for eigen-solutions. This epistemological perspective is illustrated using some episodes in the history of chemistry concerning the (...) definition or identification of chemical elements. Some of von Foerster’s epistemological imperatives provide general guidelines of development and argumentation. (shrink)

A version of the growing block theory of time is developed based on the choice of both consciousness and mathematics as fundamental substances, while dismissing the reality/semantics distinction usually assumed by works on time theory. The well-analyzable growing block structure of mathematical ontology revealed by mathematical logic, is used as a model for a possible deeper working of conscious time. Physical reality is explained as emerging from a combination of both substances, with a proposed specific version of the Consciousness (...) Causes Collapse interpretation. This leads to new solutions to old problems, including the epistemic problem and issues with Relativity. (shrink)

Scientists use models to understand the natural world, and it is important not to conflate model and nature. As an illustration, we distinguish three different kinds of populations in studies of ecology and evolution: theoretical, laboratory, and natural populations, exemplified by the work of R.A. Fisher, Thomas Park, and David Lack, respectively. Biologists are rightly concerned with all three types of populations. We examine the interplay between these different kinds of populations, and their pertinent models, in three examples: the notion (...) of “effective” population size, the work of Thomas Park on /Tribolium/ populations, and model-based clustering algorithms such as /Structure/. Finally, we discuss ways to move safely between three distinct population types while avoiding confusing models and reality. (shrink)

Functional reductionism characterises inter-theoretic reduction as the recovery of the upper-level behaviour described by the reduced theory in terms of the lower-level reducing theory. For instance, finding a statistical mechanical realiser that plays the functional role of thermodynamic entropy allows for establishing a reductive link between thermodynamics and statistical mechanics. This view constitutes a unique approach to reduction that enjoys a number of positive features, but has received limited attention in the philosophy of science. -/- This paper aims to clarify (...) the meaning of functional reductionism in science, with a focus on physics, to define both its place with respect to other approaches to reduction and its connection to ontology. To do so, we develop and explore two alternative frameworks for functional reduction, called Syntactic Functional Reductionism and Semantic Functional Reductionism. They represent two different possible stances on the view that expand and improve the basic functional reductionist approach along different lines, and make clear how the approach works in practice. The former elaborates on David Lewis’ account, is connected with the syntactic view of theories, is committed to a logical characterisation of functional roles, and is embedded within Nagelian reductionism. The latter adopts a semantic view of theories, spells out functional roles mainly in terms of mathematical roles within the models of theories, and is expressed in terms of the related structuralist approach to reduction. The development of these frameworks has the final goal of advancing functional reductionism, to make it a fully-fledged alternative account for reduction in science. (shrink)

The importance of corporate social responsibility is shaping investment decisions and entrepreneurial actions in diverse perspectives. The rapid growth of SMEs has tremendous impacts on the environment. Nonetheless, the economic emergence plan of Cameroon has prompted government support of SMEs through diverse projects. This saw economic growth increased to 3.8% and unemployment dropped to 4.3% caused by the expansion of private sector investments. The dilemma that necessitated this study is the response strategy of SMEs operators towards environmental sustainability. This study, (...) thus seeks to examine the effects of entrepreneurial intentions and actions on environmental sustainability. The research is a conclusive case study design supported by the philosophical underpins of objectivism ontology and positivism epistemology. Data was sourced from four hundred (400) SMEs operators purposively sampled from the Centre and Littoral regions of Cameroon using structured questionnaire. Data was analysed using the Structural Equation Modelling technique with the aid of statistical packages including: SPSS 24 and AMOS 23. The study revealed that entrepreneurial action has weak positive statistical significant impacts on environmental sustainability; whereas entrepreneurial intention has strong positive statistical significant effects on environmental sustainability. Entrepreneurial intention comprised of self-efficacy and perceived control whereas, entrepreneurial actions involved entrepreneurial alertness and uncertainty. This study concludes that entrepreneurs in Cameroon have sustainable intentions to protect the environment but; the current actions taken are inadequate. This research recommends that entrepreneurs should enhance efforts toward attaining the state of genuine sustainability. (shrink)

Two of the most difficult problems in the foundations of physics are (1) what gives rise to the arrow of time and (2) what the ontology of quantum mechanics is. I propose a unified 'Humean' solution to the two problems. Humeanism allows us to incorporate the Past Hypothesis and the Statistical Postulate into the best system, which we then use to simplify the quantum state of the universe. This enables us to confer the nomological status to the quantum state (...) in a way that adds no significant complexity to the best system and solves the ''supervenient-kind problem'' facing the original version of the Past Hypothesis. We call the resultant theory the Humean unification. It provides a unified explanation of time asymmetry and quantum entanglement. On this theory, what gives rise to time's arrow is also responsible for quantum phenomena. The new theory has a separable mosaic, a best system that is simple and non-vague, less tension between quantum mechanics and special relativity, and a higher degree of theoretical and dynamical unity. The Humean unification leads to new insights that can be useful to Humeans and non-Humeans alike. (shrink)

In a quantum universe with a strong arrow of time, we postulate a low-entropy boundary condition to account for the temporal asymmetry. In this paper, I show that the Past Hypothesis also contains enough information to simplify the quantum ontology and define a unique initial condition in such a world. First, I introduce Density Matrix Realism, the thesis that the quantum universe is described by a fundamental density matrix that represents something objective. This stands in sharp contrast to Wave (...) Function Realism, the thesis that the quantum universe is described by a wave function that represents something objective. Second, I suggest that the Past Hypothesis is sufficient to determine a unique and simple density matrix. This is achieved by what I call the Initial Projection Hypothesis: the initial density matrix of the universe is the normalized projection onto the special low-dimensional Hilbert space. Third, because the initial quantum state is unique and simple, we have a strong case for the \emph{Nomological Thesis}: the initial quantum state of the universe is on a par with laws of nature. This new package of ideas has several interesting implications, including on the harmony between statistical mechanics and quantum mechanics, the dynamic unity of the universe and the subsystems, and the alleged conflict between Humean supervenience and quantum entanglement. (shrink)

This article explores the metaphor of Science as provider of sharp images of our environment, using the epistemological framework of Objective Cognitive Constructivism. These sharp images are conveyed by precise scientific hypotheses that, in turn, are encoded by mathematical equations. Furthermore, this article describes how such knowledge is pro-duced by a cyclic and recursive development, perfection and reinforcement process, leading to the emergence of eigen-solutions characterized by the four essential properties of precision, stability, separability and composability. Finally, this article discusses (...) the role played by ontology and metaphysics in the scientific production process, and in which sense the resulting knowledge can be considered objective. (shrink)

The main objective of this dissertation is to philosophically assess how the use of informational concepts in the field of classical thermostatistical physics has historically evolved from the late 1940s to the present day. I will first analyze in depth the main notions that form the conceptual basis on which 'informational physics' historically unfolded, encompassing (i) different entropy, probability and information notions, (ii) their multiple interpretative variations, and (iii) the formal, numerical and semantic-interpretative relationships among them. In the following, I (...) will assess the history of informational thermophysics during the second half of the twentieth century. Firstly, I analyse the intellectual factors that gave rise to this current in the late forties (i.e., popularization of Shannon's theory, interest in a naturalized epistemology of science, etc.), then study its consolidation in the Brillouinian and Jaynesian programs, and finally claim how Carnap (1977) and his disciples tried to criticize this tendency within the scientific community. Then, I evaluate how informational physics became a predominant intellectual current in the scientific community in the nineties, made possible by the convergence of Jaynesianism and Brillouinism in proposals such as that of Tribus and McIrvine (1971) or Bekenstein (1973) and the application of algorithmic information theory into the thermophysical domain. As a sign of its radicality at this historical stage, I explore the main proposals to include information as part of our physical reality, such as Wheeler’s (1990), Stonier’s (1990) or Landauer’s (1991), detailing the main philosophical arguments (e.g., Timpson, 2013; Lombardi et al. 2016a) against those inflationary attitudes towards information. Following this historical assessment, I systematically analyze whether the descriptive exploitation of informational concepts has historically contributed to providing us with knowledge of thermophysical reality via (i) explaining thermal processes such as equilibrium approximation, (ii) advantageously predicting thermal phenomena, or (iii) enabling understanding of thermal property such as thermodynamic entropy. I argue that these epistemic shortcomings would make it impossible to draw ontological conclusions in a justified way about the physical nature of information. In conclusion, I will argue that the historical exploitation of informational concepts has not contributed significantly to the epistemic progress of thermophysics. This would lead to characterize informational proposals as 'degenerate science' (à la Lakatos 1978a) regarding classical thermostatistical physics or as theoretically underdeveloped regarding the study of the cognitive dynamics of scientists in this physical domain. (shrink)

Zero and One is Circumference and Diameter (Literally and Figuratively) (Abstract and Concrete) (Unity and Duality) (Unity and Duplicity).

Epistemic reasons are mental states. They are not propositions or non-mental facts. The discussion proceeds as follows. Section 1 introduces the topic. Section 2 gives two concrete examples of how our topic directly affects the internalism/externalism debate in normative epistemology. Section 3 responds to an argument against the view that reasons are mental states. Section 4 presents two problems for the view that reasons are propositions. Section 5 presents two problems for the view that reasons are non-mental facts. Section 6 (...) argues that reasons are mental states. Section 7 responds to objections. (shrink)

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of (...) certain organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

Statistical mechanics is a strange theory. Its aims are debated, its methods are contested, its main claims have never been fully proven, and their very truth is challenged, yet at the same time, it enjoys huge empirical success and gives us the feeling that we understand important phenomena. What is this weird theory, exactly? Statistical mechanics is the name of the ongoing attempt to apply mechanics, together with some auxiliary hypotheses, to explain and predict certain phenomena, above all those described (...) by thermodynamics. This paper shows what parts of this objective can be achieved with mechanics by itself. It thus clarifies what roles remain for the auxiliary assumptions that are needed to achieve the rest of the desiderata. Those auxiliary hypotheses are described in another paper in this journal, Foundations of statistical mechanics: The auxiliary hypotheses. (shrink)

Because climate change can be seen as the blind spot of contemporary philosophy of technology, while the destructive side effects of technological progress are no longer deniable, this article reflects on the role of technologies in the constitution of the (post)Anthropocene world. Our first hypothesis is that humanity is not the primary agent involved in world-production, but concrete technologies. Our second hypothesis is that technological inventions at an ontic level have an ontological impact and constitutes world. As we object to (...) classical philosophers of technology like Ihde and Heidegger, we will sketch the progressive contribution of our conceptuality to understand the role of technology in the Anthropocene world. Our third hypothesis is that technology has emancipatory potential and in this respect, can inaugurate a post-Anthropocene World. We consider these three hypotheses to develop a philosophical account of the ontology of technology beyond an abstract and deterministic understanding. This concept enables us to philosophically reflect on the role of technology in the Anthropocene World in general, and its contribution to the transition to the post-Anthropocene World in particular. (shrink)

This thesis develops a detailed account of the emergence of for all practical purposes continuous, quasi-classical world histories from the discontinuous, stochastic micro dynamics of Minimal Bohmian Mechanics (MBM). MBM is a non-relativistic quantum theory. It results from excising the guiding equation from standard Bohmian Mechanics (BM) and reinterpreting the quantum equilibrium hypothesis as a stochastic guidance law for the random actualization of configurations of Bohmian particles. On MBM, there are no continuous trajectories linking up individual configurations. Instead, individual configurations (...) are actualized independently of each other, carving out the decoherence-induced branching structure of the universal wave function. Yet, by contrast to the Everett interpretation, branches of the universal wave function are not actualized in parallel, i.e. all at the same time. Rather, world branches, on MBM, are actualized sequentially. -/- For an introduction to MBM, the transition from BM to MBM is described, and their empirical equivalence is established. I present the conditions under which MBM can be classified as a primitive ontology (PO) theory, regarded as crucial for the acceptance of a theory as Bohmian by many proponents of BM. While rendering MBM compatible with the PO approach, it must not fall prey to the problem of communication, arising from the two-space reading of BM. -/- The issue of temporal solipsism, identified by Bell as a serious problem for his “Everett (?) theory” – the historic predecessor of MBM – is discussed. I argue that Barbour’s time capsule approach does not provide a satisfactory solution. In particular, his adopting a more than minimal psychophysical parallelism between brain processes and experience of macroscopic change is argued to be reasonable in light of our current best neuroscience, yet problematic for theories relying solely on time capsules, understood as highly structured, individual, internally static configurations. As a solution, I introduce worlds, and world histories, as key concepts in providing a link between MBM’s micro dynamics and macroscopic phenomena. Worlds, other than time capsules, are coarse-grained regions in phase- or configuration space, defined as sets of possible micro states satisfying a relation of sufficient similarity from a macroscopic perspective, with respect to a given micro state. Hence, worlds may overlap. -/- I argue that worlds thus construed are a reasonable option for replacing the disjoint macro regions of phase space, resulting from the usual way of partitioning phase space in the standard framework of Boltzmannian statistical mechanics. This move solves the issue of discontinuous change of macro variables upon the micro state crossing the boundary between different macro regions. -/- I adapt this move for MBM’s discontinuous micro dynamics in configuration space. Issues revolving around the microscopic-macroscopic distinction, particle identity, impenetrability and haecceity in light of the desideratum of particle number conservation, etc., are discussed. I provide a detailed explanation of how overlapping worlds in MBM form world histories, thereby linking up macroscopically distinct worlds. Thus, the problem of temporal solipsism is resolved in a way that is compatible with a more than minimal psychophysical parallelism. (shrink)

We provide a methodology for the creation of ontological partitions in biomedicine and we test the methodology via an application to the phenomenon of blood pressure. An ontology of blood pressure must do justice to the complex networks of intersecting pathways in the organism by which blood pressure is regulated. To this end it must deal not only with the anatomical structures and physiological processes involved in such regulation but also with the relations between these at different levels of (...) granularity. For this purpose our ontology offers a variety of distinct partitions � of substances, processes and functions � and integrates these together within a single framework via transitive networks of part-whole and dependence relations among the entities in each of these categories. The paper concludes with a comparison of this methodology with the approaches of GOTM, KEGG, DIP and BIND and provides an outline of how the methodology is currently being applied in the field of biomedical database integration. (shrink)

Racial constructionists, anti-naturalists, and anti-realists have challenged users of the biological race concept to provide and defend, from the perspective of biology, biological philosophy, and ethics, a biologically informed concept of race. In this paper, an ontoepistemology of biology is developed. What it is, by this, to be "biological real" and "biologically meaningful" and to represent a "biological natural division" is explained. Early 18th century race concepts are discussed in detail and are shown to be both sensible and not greatly (...) dissimilar to modern concepts. A general biological race concept (GBRC) is developed. It is explained what the GBRC does and does not entail and how this concept unifies the plethora of specific ones, past and present. Other race concepts as developed in the philosophical literature are discussed in relation to the GBRC. The sense in which races are both real and natural is explained. Racial essentialism of the relational sort is shown to be coherent. Next, the GBRC is discussed in relation to anthropological discourse. Traditional human racial classifications are defended from common criticisms: historical incoherence, arbitrariness, cluster discordance, etc. Whether or not these traditional human races could qualify as taxa subspecies – or even species – is considered. It is argued that they could qualify as taxa subspecies by liberal readings of conventional standards. Further, it is pointed out that some species concepts potentially allow certain human populations to be designated as species. It is explained why, by conventional population genetic and statistical standards, genetic differences between major human racial groups are at least moderate. Behavioral genetic differences associated with human races are discussed in general and in specific. The matter of race differences in cognitive ability is briefly considered. Finally, the race concept is defended from various criticisms. First, logical and empirical critiques are dissected. These include: biological scientific, sociological, ontological, onto-epistemological, semantic, and teleological arguments. None are found to have any merit. Second, moral-based arguments are investigated in context to a general ethical frame and are counter-critiqued. Racial inequality, racial nepotism, and the “Racial Worldview" are discussed. What is dubbed the Anti-Racial Worldview is rejected on both empirical and moral grounds. Finally, an area of future investigation – the politics of the destruction of the race concept – is pointed to. (shrink)

It is argued that the many-worlds interpretation is by far the best interpretation of quantum mechanics. The key points of this view are viewing the wave functions of worlds in three dimensions and understanding probability through self-locating uncertainty.

In this paper I propose an interpretation of classical statistical mechanics that centers on taking seriously the idea that probability measures represent complete states of statistical mechanical systems. I show how this leads naturally to the idea that the stochasticity of statistical mechanics is associated directly with the observables of the theory rather than with the microstates (as traditional accounts would have it). The usual assumption that microstates are representationally significant in the theory is therefore dispensable, a consequence which suggests (...) interesting possibilities for developing non-equilibrium statistical mechanics and investigating inter-theoretic answers to the foundational questions of statistical mechanics. (shrink)

Is it possible that the most famous critic of quantum mechanics actually invented most of its fundamentally important concepts? -/- In his 1905 Brownian motion paper, Einstein quantized matter, proving the existence of atoms. His light quantum hypothesis showed that energy itself comes in particles (photons). He showed energy and matter are interchangeable, E = mc2. In 1905 Einstein was first to see nonlocality and instantaneous action-at-a-distance. In 1907 he saw quantum “jumps” between energy levels in matter, six years before (...) Bohr postulated them in his atomic model. Einstein saw wave-particle duality and the “collapse” of the wave in 1909. And in 1916 his transition probabilities for emission and absorption processes introduced ontological chance when matter and radiation interact, making quantum mechanics statistical. He discovered the indistinguishability and odd quantum statistics of elementary particles in 1925 and in 1935 speculated about the nonseparability of interacting identical particles. -/- It took physicists over twenty years to accept Einstein’s light-quantum. He explained the relation of particles to waves fifteen years before Heisenberg matrices and Schrödinger wave functions. He saw indeterminism ten years before the uncertainty principle. And he saw nonlocality as early as 1905, presenting it formally in 1927, but was ignored. In the 1935 Einstein-Podolsky-Rosen paper, he explored nonseparability, which was dubbed “entanglement” by Schrödinger. The EPR paper has gone from being irrelevant to Einstein’s most cited work and the basis for today’s “second revolution in quantum mechanics.” -/- In a radical revision of the history of quantum physics, Bob Doyle develops Einstein’s idea of objective reality to resolve several of today’s most puzzling quantum mysteries, including the two-slit experiment, quantum entanglement, and microscopic irreversibility. (shrink)

Abstract: We propose a dichotomy between object-entities and meaning-entities. The former are entities such as molecules, cells, organisms, organizations, numbers, shapes, and so forth. The latter are entities such as concepts, propositions, and theories belonging to the realm of logic. Frege distinguished analogously between a ‘realm of reference’ and a ‘realm of sense’, which he presented in some passages as mutually exclusive. This however contradicts his assumption elsewhere that every entity is a referent (even Fregean senses can be referred to (...) by means of suitably constructed expressions). We apply the meaning/object dichotomy to mathematical and fictional entities, and develop a view of mathematical and other abstract objects as the results of certain types of demarcation – as for example the North Sea is the result of demarcations built into naval charts. Such demarcations reflect demarcatory acts, which presuppose complex cognitive and social structures enabling the creation of maps, of theories (of mathematics, of natural science), and of novels. (shrink)

The concept of fields available in physics will be considered for application to unravel the mysteries of form, structure and function of human consciousness and mind. The sameness of functions of human consciousness and mind in language acquisition and communication and also acquiring knowledge of various kinds and its will be discussed. In the light of this the limitations of concepts of pure physics and modern physics probes will be discussed. -/- The information and ideas available in the Upanishads in (...) the form of Brahmajnaana will be applied to understand the physical nature of human consciousness and mind and their functions. This information and translation into modern and cognitive scientific terms would be correlated with brainwaves concept of modern physiology. The physiochemical, physical and chemical natures of experiences, purport, meanings, ideas, thoughts and expressions will be presented based on Upanishadic insight thus acquired. The advantage of this alternative probe, method and model to understand the functions of human consciousness and mind will be demonstrated. -/- This model of human consciousness and mental functions is also correlated to brain wave EEG frequency changes. -/- . (shrink)

What are words? What makes two token words tokens of the same word-type? Are words abstract entities, or are they (merely) collections of tokens? The ontology of words tries to provide answers to these, and related questions. This article provides an overview of some of the most prominent views proposed in the literature, with a particular focus on the debate between type-realist, nominalist, and eliminativist ontologies of words.

Charlotte Witt's finely crafted book offers an original and powerful account of social role normativity––the normativity of norms associated with social ro.

The ontology of Local Quantum Physics, Rudolf Haag’s framework for relativistic quantum theory, is reviewed and discussed. It is one of spatiotemporally localized events and unlocalized causal intermediaries, including the elementary particles, which come progressively into existence in accordance with a fundamental arrow of time. Haag’s conception of quantum theory is distinguished from others in which events are also central, especially those of Niels Bohr and John Wheeler, with which it has been compared.

Scientism denies change and creation in science, and humanism denies change and creation in humanity. They leave no room for freedom, equality and fraternity. This book is written as the deconstruction of both scientism and humanism.

What is the ontology of collective action? I have in mind three connected questions. 1. Do the truth conditions of action sentences about groups require there to be group agents over and above individual agents? 2. Is there a difference, in this connection, between action sentences about informal groups that use plural noun phrases, such as ‘We pushed the car’ and ‘The women left the party early’, and action sentences about formal or institutional groups that use singular noun phrases, (...) such as ‘The United States declared war on Japan on December 8th, 1941’ and ‘The Supreme Court ruled that segregation is unconstitutional in 1954 in Brown vs. Board of Education’? 3. Under what conditions does it make sense to speak of a group doing something together, and what, if anything, is a collective action? In this paper, I argue that a) understanding action sentences about groups does not commit us to the existence of group agents per se, but only to the existence of individual agents; b) there is no difference in this regard between sentences which attribute actions to informal groups on the one hand and institutional groups on the other; c) collective action can be both intentional and unintentional; d) any random group of agents each of whom does something is also a group which does something together; e) while there is a sense in which groups per se perform no primitive collective actions, and therefore no actions at all, f) there is a sensible extension of talk of actions to groups, though it should be treated strictly speaking, like talk of group agents, as a façon de parler, for g) the only agents per se are individuals and the only actions are theirs. -/-. (shrink)

In intelligence, the ontological problem is related to the nature and characteristics of entities that threaten and are threatened. Developing a threat ontology requires a taxonomy. An ontology for threat analysis and action must be able to shape ontological distinctions between potential and viable threats. This provides a better understanding of how threats (ie intentions, capabilities, and opportunities) can exist and can be changed over time. Escalating threats from a state of potency to a state of viability could (...) be avoided by using appropriate threat mitigation techniques. DOI: 10.13140/RG.2.2.25163.54569 . (shrink)

The starting point of this article is the observation that the emergence of the Anthropocene rehabilitates the need for philosophical reflections on the ontology of technology. In particular, if technological innovations on an ontic level of beings in the world are created, but these innovations at the same time _create_ the Anthropocene World at an ontological level, this raises the question how World creation has to be understood. We first identify four problems with the traditional concept of creation: the (...) anthropocentric, ontic and outcome orientation of traditional concepts of creation, as well as its orientation of material fabrication. We subsequently develop a progressive concept of World creation with four characteristics that move beyond the traditional conceptuality: (1) a materialistic concept of creation that accounts for (2) the ontogenetic process and (3) the ontic and ontological nature of creation, and (4) is conceptualized as semantic creation of the World in which we live and act. (shrink)

We propose an ontological theory that is powerful enough to describe both complex spatio-temporal processes (occurrents) and the enduring entities (continuants) that participate in such processes. For this purpose we distinguish between meta-ontology and token ontologies. Token ontologies fall into two major categories: ontologies of type SPAN and ontologies of type SNAP. These represent two complementary perspectives on reality and result in distinct though compatible systems of categories. The meta-ontological level then describes the relationships between the different token ontologies. (...) In a SNAP (snapshot) ontology we have enduring entities such as substances, qualities, roles, functions as these exist to be inventoried at a given moment of time. In a SPAN ontology we have perduring entities such as processes and their parts and aggregates. We argue that both kinds of ontological theory are required, together with the metaontology which joins them together, in order to give a non-reductionistic account of both static and dynamic aspects of the geospatial world. (shrink)

In this paper we propose an Ontology of Commercial Exchange (OCE) based on Basic Formal Ontology. OCE is designed for re-use in the Industrial Ontologies Foundry (IOF) and in other ontologies addressing different aspects of human social behavior involving purchasing, selling, marketing, and so forth. We first evaluate some of the design patterns used in the Financial Industry Business Ontology (FIBO) and Product Types Ontology (PTO). We then propose terms and definitions that we believe will improve (...) the representation of contractual obligations, sales processes, and their associated documents. A commercial exchange, for instance, involves mutual agreement to reciprocate actions, such as transferring money, performing a service, or transferring goods. (shrink)

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our (...) best conceptualisation of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles. (shrink)

One famous scene in The Wolf of Wall Street (2013) is the dialogue between the young Jordan Belfort (Leonardo DiCaprio) and the expert trader Mark Hanna (Matthew McConaughey). Hanna is complaining that the stock market is unpredictable; it’s “fugazi … it’s fairy dust. It doesn’t exist. It’s never landed. It is not matter. It’s not on the element chart. It’s not real”. But the fact that something is unpredictable and non-physical does not imply that it does not exist. On the (...) other hand, its unpredictability, non-physicality, and the fact that the stock market trend is largely determined by investors’ beliefs, do make its nature difficult to grasp. -/- This special issue of Rivista di Estetica aims to explore the financial sector from an ontological point of view. While the ontology of money has been extensively studied, few scholars have focused on the stock market and, more generally, on those entities belonging to the investment landscape. Matters are made more complicated by the fact that the financial sector is characterized by an ever-increasing use of digital technology, including software elements that trade in the market themselves. We believe that a careful study of this phenomenon may help us better to understand the role of artificial agents in the social world. (shrink)

This chapter focuses on the methodological challenges and practical implications of the experimental ontology of music. It offers an overview of the existing research, primarily focusing on how people judge whether two musical performances are of one and the same or two distinct musical works, followed by a discussion of the current methodological debates in this field and, finally, an exploration of its potential legal implications.

Statistical mechanics is often taken to be the paradigm of a successful inter-theoretic reduction, which explains the high-level phenomena (primarily those described by thermodynamics) by using the fundamental theories of physics together with some auxiliary hypotheses. In my view, the scope of statistical mechanics is wider since it is the type-identity physicalist account of all the special sciences. But in this chapter, I focus on the more traditional and less controversial domain of this theory, namely, that of explaining the thermodynamic (...) phenomena.What are the fundamental theories that are taken to explain the thermodynamic phenomena? The lively research into the foundations of classical statistical mechanics suggests that using classical mechanics to explain the thermodynamic phenomena is fruitful. Strictly speaking, in contemporary physics, classical mechanics is considered to be false. Since classical mechanics preserves certain explanatory and predictive aspects of the true fundamental theories, it can be successfully applied in certain cases. In other circumstances, classical mechanics has to be replaced by quantum mechanics. In this chapter I ask the following two questions: I) How does quantum statistical mechanics differ from classical statistical mechanics? How are the well-known differences between the two fundamental theories reflected in the statistical mechanical account of high-level phenomena? II) How does quantum statistical mechanics differ from quantum mechanics simpliciter? To make our main points I need to only consider non-relativistic quantum mechanics. Most of the ideas described and addressed in this chapter hold irrespective of the choice of a (so-called) interpretation of quantum mechanics, and so I will mention interpretations only when the differences between them are important to the matter discussed. (shrink)

The paper points out that the modern formulation of Bohm’s quantum theory known as Bohmian mechanics is committed only to particles’ positions and a law of motion. We explain how this view can avoid the open questions that the traditional view faces according to which Bohm’s theory is committed to a wave-function that is a physical entity over and above the particles, although it is defined on configuration space instead of three-dimensional space. We then enquire into the status of the (...) law of motion, elaborating on how the main philosophical options to ground a law of motion, namely Humeanism and dispositionalism, can be applied to Bohmian mechanics. In conclusion, we sketch out how these options apply to primitive ontology approaches to quantum mechanics in general. (shrink)