Research on the human microbiome has gen- erated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units—the metagenome, core microbiome, and entero- type—have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statisti- cal methods, coupled with a translational imperative, are the primary drivers of this new ontology. By reducing (...) the dimensionality of variation in the human microbiome, these new units render it more tractable and easier to interpret, and hence serve an important heuristic role. Nonetheless, there are several reasons to be cautious about these new categories prematurely ‘‘hardening’’ into natural units: a lack of constraints on what can be sequenced metagenomically, freedom of choice in taxonomic level in defining a ‘‘core microbiome,’’ typological framing of some of the concepts, and possible reification of statistical constructs. Finally, lessons from the Human Genome Project have led to a translational imperative: a drive to derive results from the exploration of microbiome variation that can help to articulate the emerging paradigm of per- sonalized genomic medicine (PGM). There is a tension between the typologizing inherent in much of this research and the personal in PGM. (shrink)

A consumer health information system must be able to comprehend both expert and non-expert medical vocabulary and to map between the two. We describe an ongoing project to create a new lexical database called Medical WordNet (MWN), consisting of medically relevant terms used by and intelligible to non-expert subjects and supplemented by a corpus of natural-language sentences that is designed to provide medically validated contexts for MWN terms. The corpus derives primarily from online health information sources targeted to consumers, (...) and involves two sub-corpora, called Medical FactNet (MFN) and Medical BeliefNet (MBN), respectively. The former consists of statements accredited as true on the basis of a rigorous process of validation, the latter of statements which non-experts believe to be true. We summarize the MWN / MFN / MBN project, and describe some of its applications. (shrink)

I argue that the human sciences (i.e. humanities, social- and behavioural sciences) should not try to imitate the methodology of the natural sciences. The human sciences study meaningful phenomena whose nature is decisively different from the merely physical phenomena studied by the natural sciences, and whose study therefore require different methods; meaningful phenomena do not obviously obey natural laws while the merely physical necessarily does. This is not to say that the human sciences do not study an objective (...) reality about which we cannot have genuine knowledge. The notion of objective reality is discussed, and it is suggested that social constructions can be understood as objectively real entities. (shrink)

Biomedical terminologies are focused on what is general, Electronic Health Records (EHRs) on what is particular, and it is commonly assumed that the step from the one to the other is unproblematic. We argue that this is not so, and that, if the EHR of the future is to fulfill its promise, then the foundations of both EHR architectures and biomedical terminologies need to be reconceived. We accordingly describe a new framework for the treatment of both generals and particulars (...) in biomedical information systems that is designed: 1) to provide new opportunities for the sharing and management of data within and between healthcare institutions, 2) to facilitate interoperability among different terminology and record systems, and thereby 3) to allow new kinds of reasoning with biomedical data. (shrink)

It is an ongoing controversy whether natural selection is a cause of population change, or a mere statistical description of how individual births and deaths accumulate. In this paper I restate the problem in terms of the reference class problem, and propose how the structure of stable equilibrium can provide a solution in continuity with biological practice. Insofar natural selection can be understood as a tendency towards equilibrium, key statisticalist criticisms are avoided. Further, in a modification of the Newtonian-force analogy, (...) it can be suggested that a better metaphor for natural selection is that of an emergent force, similar in nature to entropic forces: with magnitude and direction, but lacking a spatiotemporal origin or point of application. (shrink)

The two principal models of design in methodological circles in architecture—analysis/synthesis and conjecture/analysis—have their roots in philosophy of science, in different conceptions of scientific method. This paper explores the philosophical origins of these models and the reasons for rejecting analysis/synthesis in favour of conjecture/analysis, the latter being derived from Karl Popper’s view of scientific method. I discuss a fundamental problem with Popper’s view, however, and indicate a framework for conjecture/analysis to avoid this problem.

The widespread mistrust of metaphysics-the main obstacle to the unification of physics and philosophy-is based on the myth that metaphysical claims cannot be falsified or verified, because they are supposedly true independently of empirical knowledge. This is not true of metaphysical naturalism, whose approach is to critically reflect on the theories and findings of all the empirical disciplines and abstract from them a theory about such general features of reality that no single empirical discipline can be the authority on. (...) Causation is such a feature, since its instances include anything from planetary motions to particle interactions, chemical reactions, biological functions, and closing a door. Consequently, a general account of causation is beyond any particular empirical discipline. Metaphysical naturalism takes a meta-perspective on the results of the empirical sciences and attempts to figure out how it fits together in a coherent whole, e.g. by offering a general account of causation. General accounts of this kind are falsifiable in so far as the theories are falsifiable from which they are generalizations. The paper also discusses some fundamental metaphysical principles implicitly assumed by the sciences generally, and why they imply that unification is methodologically virtuous. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of (...) biological reality through both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

We present the details of a methodology for quality assurance in large medical terminologies and describe three algorithms that can help terminology developers and users to identify potential mistakes. The methodology is based in part on linguistic criteria and in part on logical and ontological principles governing sound classifications. We conclude by outlining the results of applying the methodology in the form of a taxonomy different types of errors and potential errors detected in SNOMED-CT.

It is now increasingly accepted that many existing biological and medical ontologies can be improved by adopting tools and methods that bring a greater degree of logical and ontological rigor. In this chapter we will focus on the merits of a logically sound approach to ontologies from a methodological point of view. As we shall see, one crucial feature of a logically sound approach is that we have clear and functional definitions of the relational expressions such as ‘is a’ (...) and ‘part of ’. (shrink)

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

World food production is facing exorbitant challenges like climate change, use of resources, population growth, and dietary changes. These, in turn, raise major ethical and political questions, such as how to uphold the right to adequate nutrition, or the right to enact a gastronomic culture and to preserve the conditions to do so. Proposals for utopic solutions vary from vertical farming and lab meat to diets filled with the most fanciful insects and seaweeds. Common to all proposals is a (...) polarized understanding of food and diets, famously captured by Warren Belasco in the contraposition between technological fixes and anthropological fixes. According to the first, technology will deliver clean, just, pleasurable, affordable food; future generations will not need to adjust much of their dietary cultures. According to the second, future generations should dramatically change their dietary habits (what they eat and how they eat it) to achieve a sustainable diet. The two fixes found remarkably distinct perspectives over dietary politics and the ethics of food production and consumption. In this paper we argue that such polarized thinking rests on a misrepresentation of the ontological status of food, which in turn affects the underlying ethical and political issues. Food is a socially constructed object that draws in specific ways on habits, norms, traditions, geographical, and climatic conditions. Although this thesis seems somewhat obvious, its consequences on the ethical and political perspectives on the future of food have not been derived properly. After introducing the issue at stake (¤1), we point out the polarities that characterize food utopias (¤2) and their ontological faults (¤3). We hence suggest that a socio-ontological analysis of food can better deliver the principles for a foundation of food utopias (¤4). (shrink)

Much of the ontology made in the analytic tradition of philosophy nowadays is founded on some of Quine’s proposals. His naturalism and the binding between existence and quantification are respectively two of his very influential metaphilosophical and methodological theses. Nevertheless, many of his specific claims are quite controversial and contemporaneously have few followers. Some of them are: (a) his rejection of higher-order logic; (b) his resistance in accepting the intensionality of ontological commitments; (c) his rejection of first-order modal logic; (...) and (d) his rejection of the distinction between analytic and synthetic statements. I intend to argue that these controversial negative claims are just interconnected consequences of those much more accepted and apparently less harmful metaphilosophical and methodological theses, and that the glue linking all these consequences to its causes is the notion of extensionality. (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)

Foundational ontologies, central constructs in ontological investigations and engineering alike, are based on ontological categories. Firstly proposed by Aristotle as the very ur- elements from which the whole of reality can be derived, they are not easy to identify, let alone partition and/or hierarchize; in particular, the question of their number poses serious challenges. The late medieval philosopher Dietrich of Freiberg wrote around 1286 a tutorial that can help us today with this exceedingly difficult task. In this paper, I (...) discuss ontological categories and their importance for foundational ontologies from both the contemporary perspective and the original Aristotelian viewpoint, I provide the translation from the Latin into English of Dietrich's De origine II with an introductory elaboration, and I extract a foundational ontology–that is in fact a single-category one–from this text rooted in Dietrich's specification of types of subjecthood and his conception of intentionality as causal operation. (shrink)

Political science is divided between methodological individualists, who seek to explain political phenomena by reference to individuals and their interactions, and holists (or nonreductionists), who consider some higher-level social entities or properties such as states, institutions, or cultures ontologically or causally significant. We propose a reconciliation between these two perspectives, building on related work in philosophy. After laying out a taxonomy of different variants of each view, we observe that (i) although political phenomena result from underlying individual attitudes and (...) behavior, individual-level descriptions do not always capture all explanatorily salient properties, and (ii) nonreductionistic explanations are mandated when social regularities are robust to changes in their individual-level realization. We characterize the dividing line between phenomena requiring nonreductionistic explanation and phenomena permitting individualistic explanation and give examples from the study of ethnic conflicts, social-network theory, and international-relations theory. (shrink)

This paper aims to suggest a new approach to Plato’s theory of being in Republic V and Sophist based on the notion of difference and the being of a copy. To understand Plato’s ontology in these two dialogues we are going to suggest a theory we call Pollachos Esti; a name we took from Aristotle’s pollachos legetai both to remind the similarities of the two structures and to reach a consistent view of Plato’s ontology. Based on this (...) theory, when Plato says that something both is and is not, he is applying difference on being which is interpreted here as saying, borrowing Aristotle’s terminology, 'is is (esti) in different senses'. I hope this paper can show how Pollachos Esti can bring forth not only a new approach to Plato’s ontology in Sophist and Republic but also a different approach to being in general. -/- Keywords Plato; being; difference; image; pollachos esti; pollachos legetai 1. Being, Not-Being and Difference The three dialogues where the notion of "difference" attaches to the notion of being, namely Parmenides II, Sophist and Timaeus,and specifically the first two we try to discuss here. In these dialogues, Plato is going to achieve a new and revolutionary understanding of being which is not anymore based on the notion of "same" as it was before in Greek ontology. It was his discovery, I think, that the notion of being in the Greek ontology is attached to the notion of the "same" and it is because of this attachment that there have always been many problems understanding being especially after Parmenides. That being has always been relying on the "same" can be found out from the way most of the Presocratics understood it. It was based on such a relationship between being and "same" that a later Ionian, Heraclitus of Ephesus, rejected Being by rejecting its sameness: unable to be the same, being cannot be being anymore but becoming. Heraclitus’ criticism of his predecessors’ understanding of being was due to his discovery that what they call being is not the same but different in every moment. The relation of being and sameness reaches to its highest point in Parmenides. What Plato does in using the "difference" is nothing but the establishment of a creative relation between being and "difference". In this new relation, although he is in agreement with Heraclitus that being is not the same but different, he does not do it by use of becoming. He disagrees, on the other hand, with Parmenides that such a relation between being and difference leads to not being. At Parmenides 142b5-6 it is said that if One is, it is not possible for it to be without partaking (μετέχειν) of being (οὐσίας), which leads to the distinction of being and one: -/- So there would be also the being of the one (ἡ οὐσία του̑ ἑνὸς) which is not the same (ταὐτὸν) as the one. Otherwise, it wouldn’t be its being, nor the one would partake of it. (142b7-c1) -/- The fact that what is (ἔστι) signifies (σημαῖνον) is other (ἀλλο) than what One signifies (c4-5), is being taken as a reason for their distinction. The conclusion is that when we say 'one is', we speak of two different things, one partaking of the other (c5-7). Having repeated these arguments of the otherness of being and one at 143a-b, Parmenides says that the cause of this otherness can be neither Being nor One but "difference": -/- So if being is something different (ἕτερον) and one something different (ἕτερον), it is not by being one that the one is different from being nor by its being being that being is other than one, but they are different from each other (ἕτερα ἀλλήλων) by difference (τῷ ἑτερῳ) and otherness (ἄλλῳ). (143b3-6) -/- The fifth hypothesis, 'one is not' (160b5ff.) is also linked with the notion of difference. When we say about two things, largeness and smallness, that they are not, it is clear that we are talking about not being of different (ἕτερον) things (160c2-4). When it is said that something is not, besides the fact that there must be knowledge of that thing, we can say that it entails also its difference: 'difference in kind pertains to it in addition to knowledge' (160d8). Parmenides explains the reason as such: -/- For someone doesn’t speak of the difference in kind of the others when he says that the one is different from the others, but of that thing’s own difference in kind. (160e1-2) -/- Although the theory of being as "difference" is not fulfilled yet, an exact look at what occurs in Sophist can make us sure that this was the launching step for "difference" to get its deserved role in Plato’s ontology. The notion of the "difference" is not yet well-functioned in Parmenides because we can see that being is still attached to the same: -/- For that which is the same is being (ὄν γὰρ ἐστι τὸ ταὐτόν) (162d2-3). -/- The notion of difference in Sophist is the key element based on which a new understanding of being is presented and the problem of not being is somehow resolved. The friends of Forms, the Stranger says, are those who distinguish between being and becoming (248a7-8) and believe that we deal with the latter with our body and through perception while with the former, the real being (ὄντως οὐσίαν) with our soul and through reasoning (a10-11). Being is then bound with the "same" by adding: -/- You say that being always stays the same and in the same state (ἣν ἀεὶ κατὰ ταὐτὰ ὡσαύτως ἔχειν) but becoming varies from one time to another (δὲ ἄλλοτε ἄλλως). (248a12-13) -/- That the theory of the relation of being and capacity (247d8f., 248c4-5) matches more with becoming than with being (248c7-9) must be rejected because being is also the subject of knowledge which is kind of doing something (248d-e). It does, however, confirm that 'both that which changes and also change have to be admitted as existing things (ὄντα) (249b2-3). I believe that this is what Socrates would incline to do at Theaetetus 180e-181a, that is, putting a fight between two parties of Parmenidean being and Heraclitean becoming and then escaping. The solution is that becoming is itself a kind of being and we ought to accept what changes as being. This is what must be done by a philosopher, namely, to refuse both the claim that 'everything is at rest' and that 'being changes in every way' and beg, like a child, for both and say being (τὸὄν) is both the unchanging and that which changes (249c10-d4). This kind of begging for both is obviously under the attack of contradiction (249e-250b). For both and each of rest and change similarly are (250a11-12) but it cannot be said either that both of them change or both of them rest, being must be considered as a third thing both of the rest and change associate with (250b7-10). The conclusion is that 'being is not both change and rest but different (ἕτερον) from them instead' (c3-4). The notion of difference helps Plato to take being departed from both rest and change because it was their sophisticated relation with being that made the opposition of being and becoming. Plato is now trying to separate being from rest and, thus, from "same" by "difference". Such a crucial change is great enough to need a 'fearless' decision (256d5-6). The possibility of being of not being is resulted (d11-12) comes as the answer to the question 'so it’s clear that change is not being and also is being (ἡ κίνησις ὄντως οὐκ ὄν ἐστι καὶ ὄν) since it partakes in being?' (d8-9). It is then by the notion of difference that becoming is considered as that which both is and is not. This coincidence of being and not being about change is apparently similar to Socrates’ paradoxical statement at Republic 477a about what both is and is not. -/- Introduction The Republic 476-477 has always been a matter of controversy mainly about two interwoven points. The first problem is the meaning of being here; that whether what he has in mind is a veridical, existential or propositional sense of being. The second problem is his distinction between the objects of knowledge and opinion which seems to lead, some believe, to the Two Worlds (TW) theory. The crucial point in Republic is that what is considered between knowledge (ἐπιστήμης) and ignorance (α͗γνοιας), namely opinion, must have a different object that leads Socrates to draw the distinction of knowledge and opinion between their objects. The problem of understanding being in the fifth book of the Republic is that when it is said that the Form of F is F but a particular participating in F, both is and is not F, it sounds too bizarre and unacceptable. It cannot be imaginable how a thing can be existent and non-existent at the same time. At the first sight, the only solution seems to be the degrees of existence which is called by Annas (1981, 197) a 'childish fallacy' and a 'silly argument'. Kirwan (1974, 118) thinks that Republic V does not attribute 'any doctrine about existence' to Plato and Kahn (1966, 250) claims that the most fundamental value of einai when used alone (without predicate) is not "to exist" but "to be so", "to be the case" or "to be true". The problems of understanding being in Republic and Sophist besides the difficulties of the existential reading led scholars to the other senses of being, mostly related to the well-known Aristotelian distinctions between different senses of being. In the predicative reading, Annas, for example, refers this difference to the qualified and unqualified application. Whereas the Form of F is unqualifiedly F, a particular instance of F can be F only qualifiedly (1981, 221). Vlastos’ well-known substitution of 'degrees of reality' for 'degrees of being/existence' must be categorized as a predicative reading. Kahn thinks that the basic sense of being for Plato is 'something like propositional structure, involving both predication and truth claims, together with existence for the subject of predication' (2013, 96). Believing that the complete-incomplete distinction terminology is misleading about Plato, he thinks that semantic functions are only second-order uses of the verb and it is the predicative or incomplete function which is fundamental. Suggesting a veridical reading, Fine (2003, 70 ff) thinks that while both existential and predicative readings separate the objects of knowledge and belief, it is only her reading which does not force such separation of the objects and thus does not imply TW. Stokes (1998, 266) thinks that though Fine is right saying that Plato does not endorse TW in book V, she is wrong in rejecting existential in favor of the veridical reading. The reception of existential reading can be seen more obviously in Calvert who thinks, in agreement with Runciman, that 'it would be safer to say that Plato’s gradational ontology is probably not entirely free from degrees of existence' (1970, 46). At Sophist 254d-e Plato singles out five most important kinds (or Forms!?) in which the same (ταὐτὸν) and difference (θάτερον) are regarded besides being, rest and change. They are, therefore, neither the same nor the difference but share in both (b3). Being (τὸ ὄν) cannot be the same also because if they 'do not signify distinct things' both change and rest will have the same label when we say they are (255b11-c1). We have then four distinct kinds, being, change, rest and same, none of them is the other. The case of difference is more complicated. When the stranger wants to assess the relation of being and difference, he can say simply neither that they are distinct nor that they are not. He has to make an important distinction inside being to get able to draw the relation of being and difference: -/- But I think you'll admit that some of the things that are (τῶν ὄντων) are said (λέγεσθαι) by themselves (αὐτὰ καθ’ αὑτά) but some [are said] always referring to (πρὸς) other things (ἄλλα) (255b12-13) -/- The difference is always said referring to other things (τὸδέγ’ ἕτερον ἀεὶ πρὸς ἕτερον) (255d1). It pervades all kinds because each of them should be different from the others and is so due to the difference and not its own nature (253e3f.) After asserting that change is different from being and therefore both is and is not (256d), the difference is described as what makes all the other kinds not be, by making each different from being. Given that all of them are by being, this association of being and difference is the cause of their being and not-being at the same time, the issue that its version at RepublicV made all those controversies we discussed above: -/- So in the case of change and all the kinds, not being necessarily is (Ἔστιν ἄρα ἐξ ἀναγκης τὸ μὴ ὄν). Τhat’s because as applied to all of them, the nature of the difference (ἡ θατέρον φύσις) makes each of them not be by making it different from being. And we’re going to be right if we say that all of them are not in the same way. And conversely [we’re also going to be right if we say] that they are because they partake in being. (Sophist 256d11-e3) -/- Plato’s new construction of five distinct kinds and the role he gives to thedifference among them is aimed to resolve the old problem of understanding being which has always been annoying from the time of Heraclitus and Parmenides. Both the ontological status of becoming and that of not being were, in Plato’s mind, based on the absolute domination of the notion of the Same over being. Now, not only becoming is understandable as being but also not being which is not the contrary of being anymore but only different (ἕτερον) (257b3-4). Though I agree partly with Frede that the account of not being which is needed for false statements is more complicated than just saying, as Cropsey (1995, 101) says, that Plato is substituting 'X is not Y' with 'X is different from Y', I totally disagree with him that when we say X is not beautiful, Plato could not have thought that it is not a matter of its being different from beautiful because 'it would be different from beauty even if it were beautiful by participation in beauty' (1992, 411). Conversely, as we will discuss, it is exactly the relation of the beautiful thing, X, and the beautiful itself, in which X shares that is to be solved by the notion of not being as difference. Though it is beautiful because of sharing in beauty, X is not beautiful because it is different from beautiful itself. What the difference is to do is to show how something can both be and not be the same thing. The difference is what makes one thing both be and not be a certain other thing. This equips the difference with the ability to explain a certain thing’s not-being when it is. Thanks to the notion of difference, it is now possible to explain not only not being but also the simultaneous being and not being of a thing: 'What we call "not-beautiful" is the thing that ἕτερόν ἐστιν from nothing other than του̑ καλου̑ φύσεως' (257d10-11). The result is that not beautiful happens to be (συμβέβηκεν εἶναι) one single thing among kinds of beings (τι τῶν ὄντων τινὸς ἑνὸς γένους) and at the same time set over against one of the beings (πρός τι τῶν ὄντων αὖ πάλιν ἀντιτεθὲν) (257e2-4) and thus be something that happens to be not beautiful (εἶναί τις συμβαίνει τὸ μὴ καλόν); a being set over against being (ὄντος δὴ πρὸς ὄν ἀντίθεσις) (e6-7). Neither the beautiful is more a being (μα̑λλον ... ἐστι τῶν ὄντων) nor not beautiful less (e9-10) and thus both the contraries similarly are (ὁμοίως εἶναι) (258a1). This conclusion, it is emphasized again (a7-9), owes to θατέρου φύσις now turned out as being. Therefore, each of the many things that are of the nature of the difference and set over each other in being (τῆς τοῦ ὄντος πρὸς ἄλληλα ἀντικειμένων ἀντίθεσις) is being as being itself is being (αὐτοῦ τοῦὄν τοςοὐσία ἐστιν) and not less. They are different from, and not the contrary of, each other (a11-b3). This is exactly τὸμὴὄν, the subject of the inquiry (b6-7). Hence, not being has its own nature (b10) and is one εἶδοςamong the many things that are (b9-c3). Such far departing from Parmenides’ ontological principle is done on the basis of the nature of the difference. It was the discovery of such a notion that made the stranger brave enough to say that not being is each part of the nature of the difference that is set over against being (258d7-e3, cf. 260b7-8). That the relation of being and difference is difference is the key element of the new ontology. The difference is, only because of its sharing in being, but it is not that which it shares in but different from it (259a6-8). Not being is exactly based on this difference: ἕτερον δὲ τοῦ ὄντος ὄν ἔστι σαφέστατα ἐξ ἀνάγκης εἶναι μὴ ὄν (a8-b1). 2. Difference and the Being of a Copy We discussed above that the sense of being of particulars in Republic V made so many debates that whether being is there used in an existential sense or not. Particulars in Republic are regarded as images in the allegories of Line and Cave. The being of an image/copy makes, thus, the same problem. Plato’s analogy of original -copy for the relation of Forms and their particulars in Republic has obviously a different attitude to being. The main question is that what is the ontological status of a copy in respect of its original? Are there two kinds of being, 'real being' versus 'being' as Ketchum says (1980, 140) or only one kind? What is the difference of being in an original and its copy? Is it a matter of degrees of being or reality as some commentators have suggested? Is it a matter of being relational? By reducing the ontological issue to an epistemological one, Vlastos’ suggestion of degrees of reality in an article with the same name does neither, I think, pay attention to the problem nor resolve it. He agrees that Plato never speaks of "degrees" or "grades" of reality (1998, 219). What allows him to entitle it as such are some of Plato’s words in Republic as well as Plato’s words in some other dialogues (1998, 219). When Plato states that the Forms only can completely, purely or perfectly be real he means, Vlastos says, they are cognitively reliable (1998, 229); an obvious reduction of the issue to an epistemological one. He thinks that when in Republic we are being said that a particular’s being F is less pure than its Form, it is because it is not exclusively F, but it is and is not F and this being adulterated by contrary characters is the reason of our confused and uncertain understanding of it (1998, 222). Ketchum rightly criticizes Vlastos’ doctrine in its disparting from ontology thinking that 'to understand Plato’s talk of being as talk of reality is to obscure the close relation that exists between "being" and the verb "to be"' (1980, 213). He thinks, therefore, that οὐσία must be understοοd as being rather than reality, τὸὄν as "that which is" and not "that which is real" and … (ibid). His conclusion is that degrees of reality cannot interpret Plato correctly and we must accept degrees of being. Allen believes that a 'purely epistemic' reading of the passage in Republic is patently at odds with Plato’s text (1961, 325). He thinks that not only degrees of reality but also degrees of reality must be maintained (1998, 67). What Cooper suggests gets close to this paper’s solution: -/- Plato does not I think wish to suggest that existence is a matter of degree in the way in which being pleasant or painful is a matter of degree. Rather there are different grades of ontological status. (1986, 241) -/- A more ontological solution for the problem of understanding the being of a copy and its relation with the being of its original is suggested by the theory of copy as a relational entity. Based on this interpretation, 'the very being of a reflection is relational, wholly dependent upon what is other than itself: the original…' (Allen, 1998, 62). As relational entities, particulars have no independent ontological status; they are purely relational entities which derive their whole character and existence from Forms (ibid, 67). Although these relational entities are and have a kind of existence, we must also say that 'they do not have existence in the way that Forms, things which are fully real, do' (ibid). Allen (1961, 331) extends his theory to Phaedo where it is said that particulars are deficient (74d5-7, 75a2-3, 75b4-8), 'wish' to be like (74d10) or desire to be of its nature (75a2); an extension that, like F.C. white (1977, 200), I cannot admit. He correctly states that Plato did not start out with a doctrine of particulars as images and semblances but come to such a view after Phaedo, or perhaps after Republic V (1977, 202). Though we may not agree with him about Republic V, if we have to consider its last pages also, we must agree with him that not only the ontology of Phaedo but also that of Republic II-V (except the last pages of the latter book) are somehow different from (but at the same time appealing to) the ontology of original-copy which should exclusively assign to Sophist, Timaeus and RepublicVI-VII besides the last pages of book V. The answer to the problem of Plato’s sense of being in RepublicV can be reached only if we read Republic V based on and as following Sophist. We can find out his meaning of that which both is and is not only by the ontological status he assigns to a copy in Sophist. The kind of being of a copy in Sophist reveals as Plato’s key for the lock of the problem of not being. Let’s see how the ontological status of a copy is the critical point of Plato’s ontology. In the earlier pages of Sophist, we are still in the same situation about not being. To think that that which is not is is called a rash assumption (237a3-4) and Parmenides’ principle of the impossibility of being of not being is still at work (a8-9). At 237c1-4, the problem of "not being" is noticed in a new way which shows some kinds of a more realistic position to the problem of not being. Nevertheless, not being is still unthinkable, unsayable, unutterable and unformulable in speech (238c10). Soon after mentioning that it is difficult even to refuse not being (238d), the solution to the problem appears: the being of a copy (εἴδωλον) (239d). A copy is, says Theaetetus, something that is made referring to a true thing (πρὸς τἀληθινὸν) but still is 'another such thing (ἕτεροντοιου̑τον)' (240a8). Nevertheless, this 'another such thing' cannot be another such real or true thing. In answer to the question of the Stranger that if this 'another such thing' is the true thing (240a9), Theaetetus answers: οὐδαμῶς ἀληθινόν γε, ἀλλ’ ἐοικὸςμὲν (240b2). A copy’s being 'another such thing' does not mean another true thing but only a resemblance of it. Not only is not a copy another true thing besides the original, but it is the opposite of the true thing (b5) because only its original is the thing genuinely and being a copy is being the thing only untruly. The word ἐοικὸς is opposed to ὄντως ὄν in the next line (240b7): 'So you are saying that that which is like (ἐοικὸς) is not really that which is (οὐκ ὄντως [οὐκ] ὄν)'. But still a copy 'is in a way (ἔστι γε μήν πως)' (b9). While it is not really what it is its resemblance, it has its own being and reality because it really is a likeness (εἰκων ὄντως) (b11). The Stranger asks: -/- So it is not really what is (οὐκ ὄν ἄρα [οὐκ] ὄντως ἐστὶν) but it really is what we call a likeness (ὄντως ἣν λέγομεν εἰκόνα)? (b12-13) -/- This is Plato’s innovative ontological solution to the problem of not being. Theaetetus’ answer confirms this: 'Maybe that which is not is woven together with that which is' (c1-2). Therefore, a copy neither is what really is nor is not-being but only is what in a way is. Thanks to the ontological status of a copy, the third status intermediate between being and not being is brought forth. The essence of an image, in Kohnke’s words, does not consist 'solely in the negation of what is genuine and has real being' because otherwise 'it would be an ὄντως οὐκ ὄν,essentially and really a not being' (1957, 37). The characteristics of a copy can be summed up as folows: i) A copy is a copy by referring to a true thing (πρὸς τἀληθινὸν). ii) A copy is different from that of which it is a copy (ἕτερον). iii) A copy is not itself a true thing (ἀληθινόν) as that of which it is a copy but only that which is like it (ἐοικὸς). iv) It is not really that which really is (ὄντως ὄν) but only really a likeness (εἰκων ὄντως). The conclusion is that: v) A copy in a way (πως) is that means it both is and in not, the product of interweaving being with not being. This leads to the refutation of father Parmenides’ principle, accepting that 'that which is not somehow is (τό τε μὴ ὄν ὡς ἔστι)' and 'that which is, somehow is not (τό ὄν ὡς οὐκ ἔστι) (241d5-7). Besides copies and likenesses (εἰκόνων), we have also imitations (μιμημάτων) and appearances (φαντασμάτων) as the subjects of this new kind of being and thus false belief (241e3). In Timaeus, the world of becoming which cannot correctly be called and thus we have to call it "what is such" (τὸ τοιου̑τον) (49e5) or "what is altogether such" (τὸ διἀ παντὸς τοιου̑τον) (e6-7), consists solely of imitations (μιμημάτα) (50c5) which are identifiable only by the things that they are their imitations. The word τοιου̑τον which had been used to determine the situation of a copy in respect of its original, now becomes the definition of the world of becoming in which everything is an image of another thing, a Being, that stays always the same and is different and separated from its image. Cherniss, in my view rightly, draws attention to the very important point about the ontological status of an image that can at the same time be considered a criticism of the relational theory. What we are being said in Timaeus, he thinks,cannot be explained by saying that an image is not self-related and making its being relational. What is crucial about an image is that it 'stands for something, refers to something, means something and this meaning the image has not independently as its own but only in reference to something else apart from it' (1998, 296). This function finds its best explanation in the theory we are to suggest in the following. 3. πολλαχῶς ἔστι The best way to understand the ontological status of an image in Plato is to see first how his most clever pupil, Aristotle, resolved the same problem that Plato brought his theory of image for its sake. Aristotle’s theory of pollachos legetai is a brilliant and, at the same time, deviated version of Plato’s theory that is able, however, to help us read Plato in a better way. We discuss Aristotle’s theory to reach to a full understanding of Plato’s theory because it is, firstly, constructed in Aristotle in a more clear way and, secondly, it can also be taken as an evidence that our reading of Plato is legitimate. The phrase τὸ ὄν πολλαχῶς λέγεται, a so much repeated phrase in Aristotle’s works, is his resolution for some of the ontological problems of his predecessors all treating being as if it has only one sense. Aristotle is right in his criticism of the philosophical tradition specially Heraclitus, Parmenides and Plato since all did presuppose only one sense for being and his theory is, thus, a creative and revolutionary solution for many problems that all the past philosophers were stuck in. But it is at the same time somehow a borrowed theory. As we will discuss, both the structure of the doctrine and the problems it tries to resolve are the same as Plato’s doctrine (and even is comparable in its phraseology) though it is in Aristotle, as can be expected, a more clear and better structured doctrine. 1) Associated with the theory of pros hen and the theory of substance, the theory of several senses of being provides a structure which, I insist, is the best guide to understand Plato’s theory of Being in Sophist, Timeaus and Republic. a) Although the theory of pollachos legetai is not necessarily based on the theory of pros hen, they become tightly interdependent about being: -/- Being is said in many ways/senses (τὸ δὲ ὄν λέγεται μὲν πολλαχῶς) but by reference to one (πρὸς ἕν) [way/sense] and one kind of nature (μίαν τινὰ φύσιν). (Metaphysics 1003a33-34) -/- The doctrine of pros hen which is Aristotle’s initiative third alternative besides the homonymous and synonymous application of words, is primarily a linguistic theory that tries to provide a new theory to explain the different implementations of the same word. The pros hen implementation of being is to provide an alternative for the theory of the synonymous (in Plato: homonymous) implementation of being which says being is said in one sense (kath hen) (1060b 32-33). That both the pros hen and the kath hen implementation of a word has one thing (hen) as what is common, makes them in opposition to the homonymous implementation which does not consider anything in common. Whereas both pros hen and kath hen assume a common nature, with which all the implementations of the word have some kind of relation, their difference is that while kath hen takes all the implementations of the word as the same with the common nature, pros hen makes them different. Substance is called πρῶτον ὄν because it is said to be primarily: -/- For as is (τὸ ἔστιν) is predicated of all things, not however in the same way (οὐχ ὁμοίως) but of one sort of thing primarily and of others in a secondary way. So too τὸτί ἐστιν belongs simply (ἁπλῶς) to substance but in a limited sense (πῶς) to the others [other categories] (1030a21-23). -/- The word ἁπλῶς standing against κατὰ συμβεβηκός tries to make substance different from the accidents. When we are being said that τὸ ὄν πολλαχῶς λέγεται, it means that only the substance that is simply (ἁπλῶς) the ἕν, the common nature, τὸὄν. When we use the word 'being' about a substance, the being is said differently from when we use 'being' about an accident. The distinction between the substance and the other categories is a distinction between what simply is said to be and what only with reference to (pros) the substance is said to be. The doctrine of pros hen, changing kath hen to pros hen in respect of to on, makes a distinction that wants to show that while there is a kind of implementing the word being that is simply being, there is another kind which is called being only by reference to that which is simply being. In the doctrine of pros hen it is not so that all the things that are said to be are only by reference to a common one thing, but that while one thing is called being because it is that thing itself, the other things are called so without being that thing itself but only by referring to it. At the very beginning of book Γ, it is said that: -/- Being is said in many senses but all refer to one arche. Some things are said to be because they are substances, others because they are affections of substances, others because they are a process towards substances or destructions or privations or qualities of substances … (1003b5-9, cf. 1028a18-20) -/- Substance is what really is said to be and all other things that are said to be are said only in favor of it. This difference of substance from all other senses of being is what is, I believe, primarily aimed in Aristotle’s interrelated theories of pollachos legetai,pros hen and the theory of substance. b) The difference of the implementation of being in the case of substance and the accidents goes so deep that while substance is considered as the real being, the accidents are almost not being. An accident is a mere name (Metaphysics 1026b13-14) and is obviously akin to not being (b21). Aristotle adds that Plato was 'in a sense not wrong' saying that sophists deal with not being (τὸ μὴ ὄν) because the arguments of sophists are, above all, about the accidental (1026b13-16). At the beginning of book , he says about quality and quantity (which look to be more of a being than other accidents) that they are not existent (οὐδ̕ ὄντα ὡς εἰπεῖν) in an unqualified sense (ἁπλῶς) (1069a21-22). The two above-mentioned points, Aristotle’s (a) interwoven theories of pollachos legetai, pros hen and the theory of substance and (b) taking accidents almost as not being, comparedwith substance, brings forth a structure that I shall call Pollachos Legetai (with capital first letters). What is of the highest importance in this structure for me is the difference of substance from accidents and the kind of relation which is settled between them. There is a substance that without any qualification is said to be and the accidents that are said to be only by reference (pros) to it. Adding Aristotle’s point about accidents that they are nearly not being to this relation and difference, we can obviously see how much this structure is close to Plato’s original-copy ontology. We spoke of the relation of being and difference in Plato’s model and the way Plato construes the being of a copy. A copy is a copy only by referring to (pros) a model; it is different from (ἕτερον) that of which it is a copy; it is not itself a true thing as its model and not really that which is (ὄντως ὄν) but only is in a way (πῶς). If we behold the difference of substance and accident in the context of the theory of pollachos legetai and pros hen, we can observe its fundamental similarity with Plato’s original-copy theory in its structure. Allen draws attention to the fact that the relation between Forms and particulars in Plato’s original-copy model is 'something intermediate between univocity and full equivocity' (1998, 70, n. 24) and the same as what Aristotle calls it pros hen (ibid). What made us compare the two structures was not, of course, the complete similarity of two structures (we have to agree with many possible differences of the two theories) but exactly the specific relation between an original and its copy on the one hand, and a substance and its accident on the other hand. As substance and accident do not share a common character and the substance -accident model hints that they stand in a certain relation, there is no common character between the original and copy in Plato’s model as well. Furthermore, their similarity is not confined to their structure only; they are also aimed to solve the same problem. The central point of the theory is that all the predecessors took being in one sense and this was their weakness point. Besides the mentioned above passages about the relation of pollachos legetai and presocratics’, as well as Plato’s, ontology, the relation of the theory with the problem of not being is clear in several passages. In Metaphysics, it is said: 'Being is then said in many senses… It is for this reason that we say even of not being that it is not being' (1003b5-10). Discussing the accidental sense of being, Aristotle points that it is in the accidental way that we say, for example, that not-white is because that of which it is an accident is (1017a18-19, cf. 1069a22-24). We mentioned that he thought Plato was right saying that sophistic deals with not being because sophistic deals with accidental, which is somehow not being (1026b14-16). Plato turned sophistic not-being to what both is and is not and Aristotle to what accidentally is said to be. What helps Aristotle to resolve the problem of not being is his distinction between ἁπλῶς and κατὰ σθμβεβηκός. Aristotle’s "qua" (ᾕ) which is directly linked with his distinction between καθ’ αὑτο λέγεται and κατὰ συμβεβηκός λέγεται, is used to resolve the old problem of coming to be out of not being (Physics 191b4-10). He strictly asserts that his predecessors could not solve the problem because they failed to observe the distinction of "qua itself" from "qua another thing" (b10-13). He then continues: -/- We ourselves are in agreement with them in holding that nothing can be said simply (ἁπλως) to come from not being (μὴὄντος). But nevertheless we maintain that a thing may come to be from not being in an accidental way (κατὰ συμβεβηκός). For from privation which ὅ ἐστι καθ’ αὑτο μὴ ὄν, nothing can become. (Phy. 191b13-16, cf. b19-25) . (shrink)

Both Franz Brentano and Edmund Husserl addressed sound while trying to explain the inner consciousness of time and gave to it the status of a supporting example. Although their inquiries were not aimed at clarifying in detail the nature of the auditory experience or sounds themselves, they made some interesting observations that can contribute to the current philosophical discussion on sounds. On the other hand, in analytic philosophy, while inquiring the nature of sounds, their location, auditory experience or the audible (...) qualities and so on, the representatives of that trend of thought have remained silent about the depiction of sound and the auditory phenomena in the phenomenological tradition. The paper’s intention is to relate both endeavours, yet the perspective carried out is that of analytic philosophy and, thus, I pay special attention to conceptual analysis as a methodological framework. In this sense, I first explain what sound ontology is in the context of analytic philosophy and the views that it encompasses— namely, the Property View (PV), the Wave View (WV) and the Event View (EV)—. Secondly, I address the problems it entails, emphasising that of sound individuation. In a third section, I propose the possibly controversial conjunction of a “Brentano-Husserl Analysis of the Consciousness of Time” (for short “Brentano-Husserl analysis”) and outline the commonalities of both authors, without ignoring its discrepancies. My main focus is Husserl’s 1905 Vorlesungen zur Phänomenologie des Inneren Zeitbewusstseins. While addressing the Brentano-Husserl analysis, I elaborate on the problem of temporal and spatial extension (Raumlichkeit and Zeitlichkeit, respectively) of both consciousness and sound. Such comparison is a key one, since after these two developments, one can notice some theoretical movements concerning the shift of attention from sounds to the unity of consciousness, and how they mirror each other. After examining the controversial claims concerning the temporal and spatial extension of both consciousness and sound, I argue in the concluding paragraphs that while considering the accounts of sound ontology, the Brentano-Husserl analysis would probably endorse a Property View and that this could have interesting consequences for the issue of Sound Individuation. (shrink)

I begin by “deconstructing” the title and explaining that Feyerabend does not really use the word “ontology”, though he does call his position sometimes (and the “sometimes” is important) ontological realism. I explain that he talks about his position as indifferently a “general methodology” or a “general cosmology”, and that he seems to be be hostile to the very enterprise of ontology, conceived of as “school philosophy”. I then go on to say that there is perhaps a (...) concept of a different type of ontology, that I call a “diachronic ontology” that perhaps he would have accepted,and that is very different from ontology as ordinarily thought, which I claim to be synchronic ontology (having no room for the dialogue with Being, but just supposing that Being is already and always there without our contribution). I discuss Althusser and Graham Harman as exemplifying synchronic ontology, giving a reading of Harman’s recent book THE THIRD TABLE. I then discuss Feyerabend’s ideas as showing a different way, that of a diachronic ontology, in which there is no stable framework or fixed path. I end with Andrew Pickering whose essay NEW ONTOLOGIES makes a similar distinction to mine, expressing it in the imagistic terms of a De Kooningian (diachronic) versus a Mondrianesque (synchronic) approach. (shrink)

In conceptual modeling (CM) as a subdiscipline of software engineering, current proposed ontologies (categorical analysis of entities) are typically established through whole adoption of philosophical theories (e.g. Bunge’s). In this paper, we pursue an interdisciplinary research approach to develop a diagrammatic-based ontological foundation for CM using philosophical ontology as a secondary source. It is an endeavor to escape an offshore procurement of ontology from philosophy and implant it in CM. In such an effort, the CM diagrammatic language (...) plays an important role in contrast to dogmatic philosophical languages’ obsession with abstract entities. Specifically, this paper is about developing a descriptive (in contrast to formal) ontology that a modeler accepts as a supplementary account of reality when using thinging machines (TMs; i.e. a reality that uncovers the ontology of things that TM modeling discusses or “talks about,” akin to the ontology of natural language). Although existence is a well-established notion, we defend subsistence (Stoic term) as a supplementary mode of reality (e.g. reflection of event). The aim here is aligned toward developing CM notions and processes that are firm enough. Classical analysis of being per se (e.g. identity, substance, classes, objects) is de-emphasized in this work; nevertheless, philosophical concepts form an acknowledged authority to compare to. As a case study, such a methodology is applied to the notion of information that provides a common-sense understanding of the world. This application would enhance understanding of the TM methodology and clarify some of the issues that shed light on the question of the nature of information as an important concept in software engineering. Information is defined as about events; that is, it is about existing things. It is viewed as having a subsisting nature that exists only through being “carried on” by other things. The results seem to indicate a promising approach to define information and understand its nature. (shrink)

The Elementary Process Theory (EPT) is a collection of seven elementary process-physical principles that describe the individual processes by which interactions have to take place for repulsive gravity to exist. One of the two main problems of the EPT is that there is no proof that the four fundamental interactions (gravitational, electromagnetic, strong, and weak) as we know them can take place in the elementary processes described by the EPT. This paper sets forth the method by which it can be (...) proven that the EPT agrees with the knowledge that derives from the successful predictions of a modern interaction theory T. This determines a fundamentally new research program in theoretical physics. (shrink)

Applied technological developments are represented by (1) genetic engineering as management tools of biological evolution and (2) socio-economic engineering as management tools of civilizational and socio-cultural development. This binary structure logically follows from the postulated three-module organization of the sustainable evolutionary strategy of the sentient human being. Naturphilosophy once again acquires the status of the basis of the theory of evolution in an explicit way. There is a system of metaphysical postulates and ontological categories derived from the anthropic (...) principle of participation. For modern neoliberal political democracy, bio-power and biopolitics look like the most effective technology for stabilizing the scenarios and trends of the global evolutionary process that are optimal within this ideological system. Conclusions.Transbipolitics in our understanding is a political problematic related to the rationalization of the global evolutionary process. In the coming decades transbipolitics will become the carrier element of the global process of evolution of the noosphere with the consequent complication and increase of cohesion between the individual socio-cultural types that are part of the system of modern globalizing civilization. (shrink)

Social ontology focuses on questions about the reality of human categories. The typical examples are gender and race. Common questions about them are: Do they exist? What is their nature? Do they exist in the best possible way? Meanwhile, the philosophy of psychiatry has been discussing the reality of psychopathology, what is the best way to classify mental disorders, and whether it is possible to define them without normative vocabulary. I think there is something not only strange but inadequate (...) about these discussions being held apart. Particularly, I hold that by being held separately these discussions are philosophically incomplete. In this paper, I argue that these debates are parallel in crucial aspects, but more importantly that they can benefit from each other if they start a dialogue. I suggest some paths we can take to start fruitful discussions and offer examples of the kind of outcomes we can expect. However, my main contribution is to sketch a common framework to map current discussions, make comparisons between them, and, more importantly, guide new research. (shrink)

In this paper recognition is taken to be a question of social ontology, regarding the very constitution of the social space of interaction. I concentrate on the question of whether certain aspects of the theory of recognition can be translated into the terms of a socio-ontological paradigm: to do so, I make reference to some conceptual tools derived from John Searle's social ontology and Robert Brandom's normative pragmatics. My strategy consists in showing that recognitive phenomena cannot be (...) isolated at the level of human interaction, and are, rather, in part proper to animal interaction as well. Furthermore, it is argued that recognitive powers are constitutive powers more basic than deontic ones and play a role much broader than the one they in fact assume in Searle and in Brandom. (shrink)

In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous sources. In this position paper, we present a set of (...) principles learned from the successful Open Biomedical Ontologies (OBO) Foundry initiative to guide the design and development of the Industrial Ontologies Foundry (IOF), which is a counterpart to the OBO Foundry initiative for the manufacturing industry. We also illustrate the potential utility of these principles by sketching the conceptual design of a framework for sustainable IOF development. (shrink)

The ontological turn (OT) is a loose cluster of theoretical approaches within cultural anthropology that advocates a synthetic, overarching way forward for ethnographically oriented cultural anthropology. We argue that in order to contribute substantively to ethnobiology the OT needs to distance itself from a long-standing tradition of thinking within ethnography that assumes some kind of fundamental divide between the natural and the social sciences. This distancing seems especially unlikely in light of the meta-anthropological nature of the OT as primarily (...) a perspective on ethnographic methodology. Instead, we advocate for naturalistic theoretical alternatives for thinking about human sociality, where philosophical innovation develops in concert with ongoing empirical work across the biological, cognitive, and social sciences. We illustrate this perspective by drawing on two naturalistic accounts likely to prove more fruitful for ethnobiological practice, namely, trans-genera models of sociality and progenerative views of kinship. (shrink)

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through (...) which semantic similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results. (shrink)

Meta-ontology (in van Inwagen's sense) concerns the methodology of ontology, and a controversial meta-ontological issue is to what extent ontology can rely on linguistic analysis while establishing the furniture of the world. This paper discusses an argument advanced by some ontologists (I call them unifiers) against supporters of or coincident entities (I call them multipliers) and its meta-ontological import. Multipliers resort to Leibniz's Law to establish that spatiotemporally coincident entities a and b are distinct, by pointing (...) at a predicate F () made true by a and false by b . Unifiers try to put multipliers in front of a dilemma: in attempting to introduce metaphysical differences on the basis of semantic distinctions, multipliers either (a) rest on a fallacy of verbalism, entailed by a trade-off between a de dicto and a de re reading of modal claims, or (b) beg the question against unifiers by having to assume the distinction between a and b beforehand. I shall rise a tu quoque, showing that unifiers couldn't even distinguish material objects (or events) from the spatiotemporal regions they occupy unless they also resorted to linguistic distinctions. Their methodological aim to emancipate themselves from linguistic analysis in ontological businesses is therefore problematic. (shrink)

In this article, we analyse how researchers use the categories of race and ethnicity with reference to genetics and genomics. We show that there is still considerable conceptual “messiness” (despite the wide-ranging and popular debate on the subject) when it comes to the use of ethnoracial categories in genetics and genomics that among other things makes it difficult to properly compare and interpret research using ethnoracial categories, as well as draw conclusions from them. Finally, we briefly reconstruct some of (...) the biases of reductionism to which geneticists (as well as other researchers referring to genetic methods and explanations) are particularly exposed to, and we analyse the problem in the context of the biologization of ethnoracial categories. Our work constitutes a novel, in-depth contribution to the debate about reporting race and ethnicity in biomedical and health research. First, we reconstruct the theoretical background assumptions about racial ontology which researchers implicitly presume in their studies with the aid of a sample of recent papers published in medical journals about COVID-19. Secondly, we use the typology of the biases of reductionism to the problem of biologization of ethnoracial categories with reference to genetics and genomics. (shrink)

The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the (...) kinds of entities which are fundamental to an ontology of colon carcinoma. We here describe the problems we uncovered concerning classification, synonymy, relations and definitions, and we draw conclusions for the work needed to establish the NCIT as a reference ontology for the cancer domain in the future. (shrink)

When reusing existing ontologies for publishing a dataset in RDF (or developing a new ontology), preference may be given to those providing extensive subcategorization for important classes (denoted as focus classes). The subcategories may consist not only of named classes but also of compound class expressions. We define the notion of focused categorization power of a given ontology, with respect to a focus class and a concept expression language, as the (estimated) weighted count of the categories that can (...) be built from the ontology’s signature, conform to the language, and are subsumed by the focus class. For the sake of tractable initial experiments we then formulate a restricted concept expression language based on existential restrictions, and heuristically map it to syntactic patterns over ontology axioms (so-called FCE patterns). The characteristics of the chosen concept expression language and associated FCE patterns are investigated using three different empirical sources derived from ontology collections: first, the concept expression pattern frequency in class definitions; second, the occurrence of FCE patterns in the Tbox of ontologies; and last, for class expressions generated from the Tbox of ontologies (through the FCE patterns); their ‘meaningfulness’ was assessed by different groups of users, yielding a ‘quality ordering’ of the concept expression patterns. The complementary analyses are then compared and summarized. To allow for further experimentation, a web-based prototype was also implemented, which covers the whole process of ontology reuse from keyword-based ontology search through the FCP computation to the selection of ontologies and their enrichment with new concepts built from compound expressions. (shrink)

The purpose of this paper is to analyze the theoretical commitments of autopoietic enactivism in relation to Errol E Harris’s dialectical holism in the interest of establishing a common metaphysical ground. This will be undertaken in three stages. First, it is argued that Harris’s reasoning provides a means of developing enactivist ontology beyond discussions limited to cognitive science and into domains of metaphysics that have traditionally been avoided by phenomenologists. Here, I maintain enactivist commitments are consistent with Harris’s reasoning (...) from certain synthetic a priori first principles, to his derivation of a teleological anthropic principle, which asserts the necessity of consciousness within the cosmos. Second, it is proposed that Steven Rosen’s long-standing proposal for a topology of phenomenology may provide a common logical foundation for both Harris and enactivists regarding anthropic reasoning. Third, it is argued that a pragmatic approach to process ontology is the most rigorous way of responding to the realism/anti-realism concerns that inevitably follow. If successful, this work will update Harris’s arguments with contemporary scientific and philosophical terminology and extend enactivism from philosophy of mind, into a general phenomenological ontology. (shrink)

Knowledge is correct and reliable when its foundation is correct, but humans never have the correct beliefs and methodology. Thus, knowledge is unreliable and the foundation of knowledge needs to be reconstructed. A pure rationalist only believes in logic. Thus, all matter and experience must be propositions derived from logic. The logically necessary consequence of this belief is truth; logically possible consequences are phenomena, and logically impossible consequence are fallacies and evils. This paper introduces belief and its logical (...) consequences, such as discovering first knowledge, both logically and illogically, establishing logical methodology, deducing truths purely through logic, and discovering unprovable truths by imitating the Universe. Logic and illogic are undeniable beliefs, and the reality of the Universe is the ultimate cause of everything. (shrink)

Because an unmeasured quantum system consists of information — neither tangible existence nor its complete absence — no property can be assigned a definite value, only a range of likely values should it be measured. The instantaneous transition from information to matter upon measurement establishes a gradient between being and not-being. A quantum system enters a determinate state in a particular moment until this moment is past, at which point the system resumes its default state as an evolving superposition (...) of potential values of properties, neither strictly being nor not-being. Like a “self-organized” chemical system that derives energy from breaking down environmental gradients, a quantum system derives information from breaking down the ontological gradient. An organism is a body in the context of energy and a mind in the context of information. (shrink)

This is a long critical discussion of Frank Wilderson's Afropessimism, focusing primarily on Wilderson's claim that Blackness is equivalent to Slaveness. The article draws out some strengths of the book, but argues that the book's central arguments often rest on shaky methodological, metaphysical, epistemic, and political grounds. Along the way, we consider some complications endemic to the project of evaluating a text so clearly geared towards Black audiences from the perspective of a non-Black reader.

It has recently become popular to suggest that questions of ontology ought be settled by determining, first, which fundamental things exist, and second, which derivative things depend on, or are grounded by, those fundamental things. This methodology typically leads to a hierarchical view of ontology according to which there are chains of entities, each dependent on the next, all the way down to a fundamental base. In this paper we defend an alternative ontological picture according to which (...) there is no ontological hierarchy. Such a picture appears counterintuitive (at least to many), in part because in the absence of a hierarchical structure to our world, there would be no structure apt to back metaphysical explanations. There are two reasons to suppose this is so. First, there would be no structure apt to back metaphysical explanations because there would be a fatal mismatch between the formal features of metaphysical explanation, on the one hand, and the structure of the world, on the other hand. Second, in the absence of an ontological hierarchy there would be no structure apt to back metaphysical explanations because the only connections that would obtain between relevant facts are mere correlational connections. But mere correlations are not the right kinds of relations to back metaphysical explanations: explanation requires something more. This paper aims to show that neither of these is a good reason to prefer a hierarchical view of ontology. (shrink)

The book is a collection of papers and aims to unify the questions of syntax and semantics of language, which are included in logic, philosophy and ontology of language. The leading motif of the presented selection of works is the differentiation between linguistic tokens (material, concrete objects) and linguistic types (ideal, abstract objects) following two philosophical trends: nominalism (concretism) and Platonizing version of realism. The opening article under the title “The Dual Ontological Nature of Language Signs and the Problem (...) of Their Mutual Relations” provides a broad introduction into the problem area connected with this differentiation, while the logic-formal characteristics of the distinction are framed in the work entitled “On the Type-Token Relationships” (Chapter 1). The basic part of the book deals with issues relating to syntax (Chapters 2-4) and semantics of language (Chapters 5-6), as well as pertaining to syntactic-semantic pragmatic questions (Chapters 7-13). Throughout the book, language, categorial language, is characterized syntactically as generated by classical categorial grammar (Chapter 2) and formalized on two opposing levels: as language of expression-tokens (level of tokens) and language of expression-types (level of types). The author’s considerations contained in Chapters 2 and 4 lead to the important philosophical conclusion that in formal-logical syntactic studies on language the assumption that expression-types constitute the primary language layer while expression-tokens make the secondary one, can be neglected; thus, this speaks in favour of the opposing standpoint—the concretistic one—in the ontology of language syntax. In the works “Meaning and Interpretations”, Parts I and II (Chapters 5 and 6), it is underlined, however, that such semantic concepts as: meaning, denotation and interpretation are defined on the types level, yet their formal definitions require making use of notions of the tokens level. The semantic notions introduced in the above-mentioned articles are also used in the following works of the present selection, under the titles: “Three Principles of Compositionality” and “On Metaknowledge and Truth” (Chapters 7 and 8). They formalize two principles of compositionality that are well known in the literature on the subject, deriving from Frege, i.e. those of meaning and of denotation; they are related to the syntactic principle of compositionality which was introduced by the author. All the three principles are, at the same time, three conditions of homomorphism of categorial language algebra into three kinds of non-standard models of language (one syntactic and two semantic ones: intensional and extensional), which allows introducing three definitions of truthfulness into these models. The next two works in the collection, entitled: “On Language Adequacy” and “What is the Sense in Logic and Philosophy of Language” (Chapters 9 and 10) concern adequacy of categorial language syntax along with its dual semantics: intensional and extensional, and categorial compatibility of any of its syntactic categories with two corresponding semantic categories: intensional and extensional, based on the compatibility the syntactic category of each language expression with the ontological category assigned to its denotatum. The well-known problem of categorial compatibility for first-order quantifiers finds its solution in the paper “Categories of First-Order Quantifiers” (Chapter 11). In the work “Logic and Ontology of Language” (Chapter 12), being in a sense a summary of the considerations presented in the preceding chapters of the book, language is treated as an ontological being, characterized in compliance with the logical conception of language proposed by Ajdukiewicz. Application—like throughout the book—of tools of classical logic and set theory has resulted in emergence of a general formal logical theory of syntax, semantics and pragmatics of language, which takes into account duality in the understanding of linguistic expressions as tokens (concretes) and types (abstract objects). In terms that take into account a functional approach to language itself, there comes out an ontological neutrality of logic with respect to existential assumptions relating to the ontological nature of linguistic expressions and their extra-linguistic ontological counterparts. The issues connected with applying logic while explaining the manner of using linguistic tokens and linguistic types to determine notions of language communication are raised and illustrated in the last chapter of the work, bearing the title “A Logical Conceptualization of Knowledge on the Notion of Language Communication”. (shrink)

It is discerned what light can bring the recent historical reconstructions of maxwellian optics and electromagnetism unification on the following philosophical/methodological questions. I. Why should one believe that Nature is ultimately simple and that unified theories are more likely to be true? II. What does it mean to say that a theory is unified? III. Why theory unification should be an epistemic virtue? To answer the questions posed genesis and development of Maxwellian electrodynamics are elucidated. It is enunciated that the (...) Maxwellian Revolution is a far more complicated phenomenon than it may be seen in the light of Kuhnian and Lakatosian epistemological models. Correspondingly it is maintained that maxwellian electrodynamics was elaborated in the course of the old pre-maxwellian programmes’ reconciliation: the electrodynamics of Ampére-Weber, the wave theory of Young-Fresnel and Faraday’s programme. To compare the different theoretical schemes springing from the different language games James Maxwell had constructed a peculiar neutral language. Initially it had encompassed the incompressible fluid models; eventually – the vortices ones. The three programmes’ encounter engendered the construction of the hybrid theory at first with an irregular set of theoretical schemes. However, step by step, on revealing and gradual eliminating the contradictions between the programmes involved, the hybrid set is “put into order” (Maxwell’s term). A hierarchy of theoretical schemes starting from ingenious crossbreeds (the displacement current) and up to usual hybrids is set up. After the displacement current construction the interpenetration of the pre-maxwellian programmes begins that marks the commencement of theoretical schemes of optics, electricity and magnetism real unification. Maxwell’s programme surpassed that of Ampére-Weber because it did absorb the ideas of the Ampére-Weber programme, as well as the presuppositions of the programmes of Young-Fresnel and Faraday properly co-ordinating them with each other. But the opposite statement is not true. The Ampére-Weber programme did not assimilate the propositions of the Maxwellian programme. Maxwell’s victory over his rivals became possible because the gist of Maxwell’s unification strategy was formed by Kantian epistemology looked in the light of William Whewell and such representatives of Scottish Enlightenment as Thomas Reid and Sir William Hamilton. Maxwell did put forward as basic synthetic principles the ideas that radically differed from that of Ampére-Weber approach by their open, flexible and contra-ontological, genuinly epistemological, Kantian character. For Maxwell, ether was not the ultimate building block of physical reality, from which all the charges and fields should be constructed. “Action at a distance”, “incompressible fluid”, “molecular vortices”, etc. were contrived analogies for Maxwell, capable only to direct the researcher at the “right” mathematical relations. Key words: J.C. Maxwell, unification of optics and electromagnetism, I. Kant, T. Reid, W. Hamilton . (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages (...) for all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

Spinoza’s conatus doctrine, the main proposition of which claims, “[e]ach thing, to the extent it is in itself, strives [conatur] to persevere in its being” (E3p6), has been the subject of growing interest. This is understandable, for Spinoza’s psychology and ethics are based on this doctrine. In my paper I shall examine the way Spinoza argues for E3p6 in its demonstration which runs as follows: "For singular things are modes by which God’s attributes are expressed in a certain and determinate (...) way (by 1p25c), i.e. (by 1p34), things that express, in a certain and determinate way, God’s power, by which God is and acts. And no thing has anything in itself by which it can be destroyed, or which takes its existence away (by p4). On the contrary, it is opposed to everything which can take its existence away (by p5). Therefore, to the extent it can, and is in itself, it strives to persevere in its being." This argument has been severely criticized for being defective in many ways. E3p6d contains four items, E1p25c, 1p34, 3p4, and 3p5. Most often, only the two last mentioned are regarded as doing any real work in the demonstration. However, I shall argue that having a proper grasp of Spinoza’s concept of power enables us see that the demonstration’s beginning, built on E1p25c and 1p34, brings forth a certain dynamic framework in which finite things are centers of causal power, capable of producing effects in virtue of their essences. My examination of this framework shows the beginning of the demonstration to be irreplaceable: in the end, conatus is one form of power, and E1p25c and 1p34 not only bring the notion of power into play, but also inform us on how finite things’ power should be understood in the monistic system. So, I disagree with such commentators as Jonathan Bennett, Edwin Curley, Daniel Garber, Michael Della Rocca, and Richard Manning, who see Spinoza as trying to derive the conatus doctrine from E3p4 and 3p5 alone; and I agree with Alexandre Matheron, Henry Allison, and Martin Lin, who stress the importance of E1p25c and 1p34. -/- However, this still leaves us the task of reconstructing the whole derivation and showing how its various ingredients fit together. If E1p25c and 1p34 are so important, could E3p6 not be derived from them alone, as Martin Lin has argued? In other words, why are E3p4 and 3p5 needed at all? To answer these questions I shall provide an interpretation of E3p6d that explains how the argument is supposed to work. E1p25c and 1p34 say that finite things are, in essence, dynamic causers, which, in case of opposition, truly resist opposing factors with their power and do not simply cease their causal activities whenever facing obstacles; in other words, they strive against any opposition. However, this is not enough to guarantee that they could not act self-destructively or restrain their own power, which would make them incapable of self-preservation. But this would go against E3p4, “No thing can be destroyed except through an external cause,” and Spinoza uses it to claim, “no thing has anything in itself by which it can be destroyed, or which takes its existence away.” So all this allows Spinoza to hold that finite things are consistent causers, that is, entities endowed with power and, insofar they cause effects solely in virtue of their essence, they never use their power self-destructively. The significance and role of the final item in the demonstration, E3p5 (“Things are of a contrary nature, i.e., cannot be in the same subject, insofar as one can destroy the other”), still needs to be determined. Indeed, considering its content and the way it is used in the demonstration, it seems to be a surprisingly decisive ingredient in the argument. Namely, what “each thing, to the extent it is in itself,” that is, insofar as any thing is considered disregarding everything external to it, strives to preserve, is its being (esse), not simply its present state. This together with E3p5’s view of subjecthood – which I shall explicate in my paper – suggests that we should rethink what kind of “being” or “existence” is meant in E3p6. Indeed, for Spinoza, each subject has a definable essence from which, as far as the subject in question is in itself, certain properties or effects necessarily follow; consequently a subject’s full being involves not only instantiating a certain essence, but also those properties inferable from the essence-expressing definition. Thus, E3p5 is meant to bring forward that things are not merely non-self-destroyers but subjects from whose definitions properties follow; and as Spinoza thinks to have shown (by E1p25c and 1p34) that finite modifications are entities endowed with power, any subject has true power to produce the properties or effects derivable from its definition, which, Spinoza claims, implies opposing everything harmful. In other words, things exercise power as their definition states, i.e. according to their definitions, and thus bringing in the idea of things as expressers of power enables Spinoza to convert logical oppositions (of E3p5) into real ones (of E3p6). To summarize, Spinoza reasons that each true finite thing is, in itself, an expresser of power (E1p25c, 1p34) that never acts self-destructively (E3p4) but instead strives to drive itself through opponents to produce effects as they follow from the definition of the thing in question (E1p25c, 1p34, and 3p5). Therefore, “each thing, to the extent it is in itself, strives to persevere in its being.” The demonstration of E3p6 has its roots deep in Spinoza’s ontology, and since its concept of power is supposed to provide the metaphysical grounding for real opposition, the importance of E1p25c and 1p34 should not be underestimated just because Spinoza – as often happens – puts his point exceedingly briefly. Moreover, the derivation is basically valid and contains no superfluous elements. Finally, all this tells us something decisive about the meaning of Spinoza’s doctrine: according to it, things are active causers whose “power to exist and act” has conatus character in temporality, amounting not only to striving to prolong the duration of one’s actualization but also to striving to be as active or autonomous as possible, that is, to attain a state determined by the striving subject’s essence alone. (shrink)

In this condensed survey, I look to recent perspectives on evolution suggesting that cultural change likely alters the genome. Since theories of development are nested within assumptions about evolution (evo-devo), I next review some oft-cited developmental theories and other psychological theories of the 20th century to see if any match the emerging perspectives in evolutionary theory. I seek theories based neither in nature (genetics) nor nurture (the environment) but in the creative play of human communication responding to necessity. This survey (...) finally looks to more recent work to do with the appearance of independent self-consciousness in the individual following empathic group awareness. The result of such self-created group awareness and symbolic communication is seen to be cultural consciousness, unique to humanity, from which individual consciousness and personhood derive. I conclude by noting the general implications for these approaches in our schools, politics, and in ultimate ontological questions. (shrink)

This work aims to make tense logic a more robust tool for ontologists, philosophers, knowledge engineers and programmers by outlining a fusion of tense logic and ontology of time. In order to make tense logic better understandable, the central formal primitives of standard tense logic are derived as theorems from an informal and intuitive ontology of time. In order to make formulation of temporal propositions easier, temporal operators that were introduced by Georg Henrik von Wright are developed, (...) and mapped to the ontology of time. (shrink)

In this paper, I argue that Nietzsche’s published works contain a substantial, although implicit, argument for the will to power as ontology—a critical and descriptive, rather than positive and explanatory, theory of reality. Further, I suggest this ontology is entirely consistent with a naturalist methodology. The will to power ontology follows directly from Nietzsche’s naturalist rejection of three metaphysical presuppositions: substance, efficient causality, and final causality. I show that a number of interpretations, including those of (...) Clark, Schacht, Reginster, and Richardson, are inconsistent with Nietzsche’s naturalism, because they presuppose efficient or final causality. In contrast, I argue that the will to power is not an explanatory theory, but a description of the basic, necessary character of reality, designed to critically reveal and minimize metaphysical presuppositions—to reject false explanations of reality and human behavior. It avoids substance-metaphysics by describing reality as will, a causal process without discrete efficient causes or agents. It eliminates efficient causality by describing events as maximal manifestations of power, rather than as agent-actualized potentialities. Finally, it opposes teleology by describing life as tending toward the activity of resistance as such, rather than toward explanatory end-states, such as the accumulation of power or overcoming of resistances. (shrink)

Every metaphysic, according to Reiner Schürmann, involves the positing of a first principle for thinking and doing whereby the world becomes intelligible and masterable. What happens when such rules or norms no longer have the power they previously had? According to Cornelius Castoriadis, the world makes sense through institutions of imaginary significations. What happens when we discover that these significations and institutions truly are imaginary, without ground? Both thinkers begin their ontologies by acknowledging a radical finitude that threatens to destroy (...) meaning or order. For Schürmann it is the ontological anarchy revealed between epochs when principles governing modes of thinking and doing are foundering but new principles to take their place have not yet emerged. For Castoriadis it is chaos that names the indeterminationdetermination that governs the unfolding of the socio-historical with contingency and unpredictability. And yet for both thinkers their respective ontologies have political or ethical implications. On the basis of the anarchy of being, Schürmann unfolds an anarchic praxis or ethos of “living without why.” And on the basis of his notion of being as chaos, Castoriadis develops his political praxis of autonomy. The challenge for both is this move from ontology to practical philosophy, how to bridge theory and practice. The key for both seems to be a certain ontologically derived sense of freedom. In this paper, I analyze and compare their respective thoughts, and pursue the question of how anarchy or chaos and the implied sense of an ontological freedom might be made viable and sensible for human praxis, how radical finitude in the face of ontological groundlessness might nevertheless serve to situate a viable political praxis. (shrink)

Noam Chomsky’s well-known claim that linguistics is a “branch of cognitive psychology” has generated a great deal of dissent—not from linguists or psychologists, but from philosophers. Jerrold Katz, Scott Soames, Michael Devitt, and Kim Sterelny have presented a number of arguments, intended to show that this Chomskian hypothesis is incorrect. On both sides of this debate, two distinct issues are often conflated: (1) the ontological status of language and (2) the relation between psychology and linguistics. The ontological issue (...) is, I will argue, not the relevant issue in the debate. Even if this Chomskian position on the ontology of language is false, linguistics may still be a subfield of psychology if the relevant methods in linguistic theory construction are psychological. Two options are open to the philosopher who denies Chomskian conceptualism: linguistic nominalism or linguistic platonism. The former position holds that syntactic, semantic, and phonological properties are primarily properties, not of mental representations, but rather of public languagesentence tokens; The latter position holds that the linguistic properties are properties of public language sentence types. I will argue that both of these positions are compatible with Chomsky’s claim that linguistics is a branch of psychology, and the arguments that have been given for nominalism and platonism do not establish that linguistics and psychology are distinct disciplines. (shrink)

Philosophy of immunology is a subfield of philosophy of biology dealing with ontological and epistemological issues related to the studies of the immune system. While speculative investigations and abstract analyses have always been part of immune theorizing, until recently philosophers have largely ignored immunology. Yet the implications for understanding the philosophical basis of organismal functions framed by immunity offer new perspectives on fundamental questions of biology and medicine. Developed in the context of history of medicine, theoretical biology, and medical anthropology, (...) philosophy of immunology differs from these related branches of study in its focus on traditional philosophical questions concerning identity, individuality, ecology, cognition, scientific methodology and theory construction. This broad agenda derives from immunology’s multifaceted research program that has developed from its initial clinical challenges of host defense, transplantation, autoimmunity, tumor immunology, and allergy. In addition to these well-established research areas, immunity is now understood to play a central role in other physiological functions, development, ecology, and evolutionary mechanics. Holding together these diverse domains of inquiry lie philosophical commitments oriented by organismal identity. In this regard, pertinent issues are raised concerning cognition (organization of immune perception and information processing), the character of individuality (framed by the ecological context of immune-mediated assimilation and rejection), and the dynamics of complex systems (understood as holistic systems biology). Indeed, immunology, in the context of cognitive science, evolutionary biology, environmental sciences, and development provides multi-focal perspectives for philosophy of science. (shrink)

In an important study, Lawrence Sklar has defended a doctrine of methodological conservatism (very roughly, the principle that a proposition derives some sort of epistemic warrant from being believed). I argue that Sklar's careful formulation of methodological conservatism remains too strong, and that a yet weaker version of the doctrine cannot be successfully defended. I also criticize Sklar's argument that the rejection of methodological conservatism would result in total skepticism. Finally, I turn to a closely related issue, and try (...) to show why different people with the same evidence should be justified in believing the same things. (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)

The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of data. To provide effective solutions computers need to integrate data deriving from myriad heterogeneous sources by bringing the data together within a single framework. The meeting brought together leaders in the field of what are called "top-level ontologies" to address this issue, and to establish strategies among (...) leaders in the field of biomedical ontology for the creation of interoperable biomedical ontologies which will serve the goal of useful data integration. (shrink)

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI (...) leverages established ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)