Ontology Project Research Articles

Merleau-Ponty nos arquivos Husserl: uma entrevista com Emmanuel de Saint Aubert

Silvana de Souza Ramos and Iracy Ferreira dos Santos Junior’s interview with Emmanuel de Saint Aubert explores the history and role of the Husserl Archives (Paris) in fostering multidisciplinary research in phenomenology. Saint Aubert clarifies Merleau-Ponty’s engagement with Husserl’s manuscripts, describing the situated and complex reading he undertook not only of these manuscripts but also of Husserl’s work as a whole. This aspect is particularly significant for contemporary French philosophical studies, as Merleau-Ponty played a pivotal role in introducing Husserl’s ideas into French thought. This clarification allows us to show the originality of Merleau-Ponty’s philosophy, as it reveals that he was not merely an exegete of Husserl, but a restless and multifaceted thinker, deeply involved in the intellectual and political debates of his time. If he cannot be reduced to a mere reader of Husserl, neither can his later ontology be simply attributed to Heidegger’s influence. Once engaged in a meticulous study of the unfinished manuscripts that Merleau-Ponty left behind due to his premature death, which were drafts for a new book, Saint Aubert conducted a thorough investigation of Merleau-Ponty’s use of key terms in his ontology – chair, Leib, empiétement, chiasmi – showing that these terms do not literally translate or express concepts derived from Husserl or Heidegger. On the contrary, these terms acquire a multifaceted range of meanings in Merleau-Ponty’s writings, nourished by his philosophical readings and meditations, by his scientific and literary refinement, as well as his ethical and political concerns. Saint Aubert’s research, dedicated to the interpretation of Merleau-Ponty’s so-called “unpublished” works, resulted in the publication of five books by Vrin, all guided by a transversal genetic reading of Merleau-Ponty’s work. Additionally, with the help of other researchers, Saint Aubert carefully edited and published several volumes of Merleau-Ponty’s manuscripts. This material, made available in an organized and contextualized manner, is of incomparable richness, allowing for a more precise understanding of Merleau-Ponty’s role in contemporary thought, while also illuminating the meaning of his ontological project.

Le forme dello spirito nell'ontologia critica di Nicolai Hartmann. Per una lettura critico-­genetica de Il problema dell'essere spirituale

The Author critically discusses the theoretical assumptions underlying Nicolai Hartmann's 1933 The Problem of Spiritual Being. The Author deals with the main categorial problems involved in the Hartmannian discussion about the spiritual being, also looking at his previous production. In particular, the Author analyzes the position of the ontic level of spiritual being with respect to the previous three real ontic levels (inorganic, organic, psychological) and the mutual relationship between the three fundamental forms of spiritual being identified by Hartmann (personal, objective, objectified). The Author believes that the 1933 volume has been poorly considered in its direct links with the overall project of critical ontology.

Генезис науки XVII века: опыты по «приручению» бесконечности

The author of the article considers the problem of actual infinity to be the meta-basis of the genesis of New European science. The author shows the advantages of this approach to identify the internal logic of the genesis of science of the XVII century, as well as to clarify the prospects of modern science, experiencing a crisis of its foundations. The author shows that Nikolai Kuzansky’s ontological project reveals the conditions necessary for the mathematization of nature for the transformation of the finite into the actually infinite, which overcomes the hopelessness of Zeno’s similar attempts. Zeno showed that there is no transition from the finite to the actually infinite. To transform the fi nite into the actually infi nite, the latter must already be given. This kind of presence is revealed by Kuzansky in the apophatic idea of the divine minimum coinciding with the maximum. But at the same time, Kuzansky speaks only about the imaginary, and not the real possibility of transforming nature on the basis of actual infinity. And in order to turn ‘scientific ignorance’ into ‘scientific knowledge’, it was necessary to present, outside the theological context, the possibility of transforming nature on the basis of actual infinity, discovered by Kuzansky. This task was set by the founders of the New European science. The author of the article analyzes and compares the attempts of Galileo and Descartes to ‘tame’ the actual infinity. The author shows that the difference in their positions on the question of the achievability of reliable knowledge, which laid important milestones in the history of the genesis of New European science (the transition from the scholastic tradition to probabilistic epistemology), is due to the awareness of the complexity of the problem of actual infinity. As a result, the author shows that neither the theoretical speculations of the founders of science, nor the attraction of modern additional resources unknown to antiquity or the Middle Ages (experiment, pinhole camera) were unable to change anything in the ratio of the finite and the infinite.

Reading for post qualitative inquiry

This paper advocates reading philosophy and using its concepts in educational and social science research. The lengthy engagement with the various concepts and conceptual orders of poststructuralism required for post qualitative inquiry exceeds the scope of reading required for a conventional literature review at the beginning of a typical empirical research project. Reading that spans many years of an academic career does not serve the epistemological project of stabilizing what is known through recognition, representation, and summary but attends to an ontological project of re-orienting thought through experimentation, invention, and creation to enable what does not yet exist but might.

Ideal Type and Essential Type — They Need Each Other

In light of the ongoing validity crisis in psychiatric classification, phenomenologically oriented psychiatric study has gained traction. This paper assesses two modes of investigation proposed by phenomenologists in studying mental disorders: the ideal type approach and the essential type approach. Despite the recent suggestion that they are antithetical approaches, I argue that they should constantly constrain and inform each other. In short, I advance a mutual complementarity thesis. Having established this thesis, I conclude by demonstrating how this proposal can function as an heuristic strategy for effectively facilitating the recently proposed psychiatric research initiative, i.e. the ontological project of phenomenological psychopathology.

Interpreting Gene Ontology Annotations Derived from Sequence Homology Methods.

The Gene Ontology (GO) project describes the functions of the gene products of organisms from all kingdoms of life in a standardized way, enabling powerful analyses of experiments involving genome-wide analysis. The scientific literature is used to convert experimental results into GO annotations that systematically classify gene products' functions. However, to address the fact that only a minor fraction of all genes has been characterized experimentally, multiple predictive methods to assign GO annotations have been developed since the inception of GO. Sequence homologies between novel genes and genes with known functions help to approximate the roles of these non-characterized genes. Here we describe the main sequence homology methods to produce annotations: pairwise comparison (BLAST), protein profile models (InterPro), and phylogenetic-based annotation (PAINT). Some of these methods can be implemented with genome analysis pipelines (BLAST and InterPro2GO), while PAINT is curated by the GO consortium.

Single-Molecule Real-Time Sequencing for Identifying Sexual-Dimorphism-Related Transcriptomes and Genes in the Chinese Soft-Shelled Turtle (Pelodiscus sinensis)

The Chinese soft-shelled turtle (Pelodiscus sinensis), an economically important aquatic species in China, displays considerable sexual dimorphism: the male P. sinensis is larger and, thus, more popular in the market. In this study, we obtained the full-length (FL) transcriptome data of P. sinensis by using Pacific Biosciences (PacBio)’s isoform sequencing and analyzed the transcriptome structure. In total, 1,536,849 high-quality FL transcripts were obtained through single-molecule real-time (SMRT) sequencing, which were then corrected using Illumina sequencing data. Next, 89,666 nonredundant FL transcripts were generated after mapping to the reference genome of P. sinensis; 291 fusion genes and 17,366 novel isoforms were successfully annotated using data from the nonredundant protein sequence database (NR), eukaryotic orthology groups (KOG), the Gene Ontology (GO) project, and the KEGG Orthology (KO) database. Additionally, 19,324 alternative polyadenylation sites, 101,625 alternative splicing events, 12,392 long noncoding RNAs, and 5916 transcription factors were identified. Smad4, Wif1, and 17-β-hsd were identified as female-biased genes, while Nkd2 and Prp18 held a higher expression level in males than females. In summary, we found differences between male and female P. sinensis individuals in AS, lncRNA, genes, and transcripts, which relate to the Wnt pathway, oocyte meiosis, and the TGF-β pathway. Female-biased genes such as Smad4, Wif1, and 17-β-hsd and male-biased genes such as Nkd2 and Prp18 played important roles in the sex determination of P. sinensis. FL transcripts are a precious resource for characterizing the transcriptome of P. sinensis, laying the foundation for further research on the sex-determination mechanisms of P. sinensis.

“The Music of Being”: a note on a metaphor from Giorgio Agamben’s last volume of <i>Homo Sacer</i>.

The article attempts to clarify the place and meaning of musical-acoustic metaphors that appear in the last volume of Homo Sacer, The Use of Bodies, in connection with the project of modal ontology. The definition of philosophy as the “supreme music,” increasingly common in the pages of his later texts, suggests that this is not just a figurative meaning of musical images but an attempt to give them conceptual weight. To clarify the musical basis of philosophy, the article offers an analysis of a number of statements from The Use of Bodies in the context of Agamben’s early reflections on language and voice (most notably in Language and Death). The analysis allows us to show that musical metaphors mark the direction of Agamben’s positive program, particularly the project of modal ontology, which seeks to resolve the aporia of the ontological apparatus thattraces back to Aristotle. Although the aim of the article is mainly technical — to fit only apparently incidental musical metaphors into the logic of Agamben’s entire philosophical project — it seems that this analysis may be useful in clarifying the basis for understanding and critiquing the thought of the Italian philosopher.

“Education is a white woman’s world”: theorizing race, gender, and geography in a liberatory Black pedagogical space

ABSTRACT In this Black feminist critical inquiry, I theorize the politics of race, gender, and geography in the context of a liberatory Black pedagogical space located in the United States. Using curated interview and observation data, I position an anti-racist pedagogue as a cartographer who employed method, content, style, and technique to map freedom routes away from schooling, a Dumasian site of suffering for Black students. I paint a narrative portrait that foregrounds sights, sounds, and felt tensions emerging from two manifestations of Black affective networks that constellated in the Black male critical pedagogue’s classroom. Ultimately, I call for attention to the construction of liberatory education spaces created to address the comfort and needs of not only racially minoritized learners but also students who embody sexes, genders, and gender performances marginalized in white-dominant culture. Such pedagogical spaces, I argue, can be a refusal to indulge the ontological, epistemological, and existential project of whiteness.

A Rebel against the Volk

This paper discusses Hannah Arendt’s model of the Jewish pariah, developed in her study of Jewish assimilation. The argument is that Arendt’s model represents her early efforts to move beyond Martin Heidegger’s philosophy. The paper focuses on Arendt’s concept of a conscious pariah as a model for political resistance, independence, and agency. It shows how Arendt infused elements of Heidegger’s philosophy into her early vision of Jewish politics, while also transcending the limits of Heidegger’s ontological project with her political vision. The paper suggests that Arendt’s book on Rahel Varnhagen shares similarities with Heidegger’s work on Mitsein in Being and Time, while her 1944 model of the conscious pariah, especially the focus on the pariah as a rebel, illustrates her concerns with Heidegger’s work on the Volk.

Heidegger and Plato's idea of the Good

The article deals with the question of Plato's reception in Heidegger's philosophy. In particular, the research focuses on the question of how Heidegger interpreted the idea of the good from Plato's "State". Here a number of difficulties important for the history of philosophy arise. What is the ontological status of the idea of good? How is the idea of the good connected with the demiurge from the dialogue "Timaeus"? On the one hand, it is well known that the late Heidegger criticized Plato and all European metaphysics, which was and remains Platonism. On the other hand, the early Heidegger clearly presents an attempt to master the shining heights of Platonism: the question of the meaning of being needs an angle from which a definite answer can be highlighted – and Heidegger borrows this angle from Plato. Just as the good endows existence with being and truth, so the understanding of being is possible from time, because it is temporality that is the condition for understanding being, it highlights its meaning. And if Plato's being "pounces" on the good, or on the one, then for Heidegger, time is such a condition. This line of thought, fundamental to the whole project of fundamental ontology, is directly related to the philosophy of Plato, who for the first time was able to rise so high as to become ἐπέκεινα τῆς οὐσίας, to see things as if from the outside, i.e. in the light of the transcendent idea of good. Nevertheless, Heidegger criticizes Plato, which allows us to raise the question: how did Heidegger understand Platonic ἐπέκεινα τῆς οὐσίας and the doctrine of the good? It is impossible to answer this question unequivocally, since Heidegger approached this question from different sides and at different times interpreted this most important position of the Greek thinker in different ways. Nevertheless, the main remarks can be reduced to two: (1) the good was conceived by Plato as something moral and therefore mixed with the existing, (2) the good subordinates the being, brings it under fitness.

Tags for Tears: The Obstetric Anal Sphincter Injury Hashtag Ontology Project.

Social media is a powerful outlet for the dissemination of health care information. Adoption of a hashtag ontology-a standardized list of terms-may help better organize information and improve access to educational materials for health care providers (HCPs) and patients. The primary objective was to create a hashtag ontology specific to obstetric anal sphincter injuries (OASIS) based on Twitter usage. Secondary objectives included (1) performing a thematic analysis of OASIS-related tweet content and (2) reporting the type of users posting about OASIS. This study was an analysis of tweets related to OASIS posted between June 1, 2019, and June 1, 2022. Symplur Signals (a Twitter analytics software) (Symplur LLC, Los Angeles, CA) was used to identify relevant tweets based on predetermined search terms. Hashtags were reviewed by social media influencers to create a finalized ontology list. The top 100 tweets underwent thematic analysis and were grouped based on emergent themes. Types of users posting about OASIS were also analyzed. Symplur identified 660 tweets related to OASIS. The final ontology included the following 8 hashtags: #OASIS, #perinealtrauma, #birthtrauma, #3rddegreetear, #4thdegreetear, #episiotomy, #operativedelivery, and #postpartumbody. Major tweet content themes included education, self-promotion, patient experience, medical-legal, research, and opinions. Educational tweets surrounded prevention, risk factors, complications, and educational events related to OASIS and perineal trauma. Of the educational tweets, only 30% were posted by HCPs. This study created a standardized hashtag ontology related to OASIS. Less than one third of educational tweets were posted by HCPs.

Higher expression of PLEK and LY86 as the potential biomarker of carotid atherosclerosis.

Carotid atherosclerosis (AS) occurs in atherosclerotic lesions of the carotid artery, which can lead to transient ischemic attack and stroke in severe cases. However, the relationship between pleckstrin (PLEK) and lymphocyte antigen 86 (LY86) and carotid AS remains unclear. The carotid AS datasets GSE43292 and GSE125771 were downloaded from the gene expression omnibus database. Differentially expressed genes (DEGs) were screened and weighted gene co-expression network analysis was performed. Construction and analysis of protein-protein interaction network. Functional enrichment analysis, gene set enrichment analysis and comparative toxicogenomics database analysis were performed. TargetScan screened miRNAs that regulated central DEGs. A total of 305 DEGs were identified. According to gene ontology analysis, they were mainly enriched in immune system processes, extracellular regions and cytokine binding. Kyoto encyclopedia of genes and genomes analysis showed that the target cells were mainly enriched in Rap1 signal pathway, B cell receptor signal pathway and PPAR signal pathway. In the enrichment project of metascape, the reaction to bacteria, cell activation and chemotaxis can be seen in the enrichment project of gene ontology. Total 10 core genes (TYROBP, FCER1G, PLEK, LY86, IL10RA, ITGB2, LCP2, FCGR2B, CD86, CCR1) were obtained by protein-protein interaction network construction and analysis. Core genes (PLEK, LY86, IL10RA, ITGB2, and LCP2) were highly expressed in carotid AS samples and lowly expressed in normal samples. Comparative toxicogenomics database analysis showed that 5 genes were associated with pneumonia, inflammation, necrosis, and drug allergy. PLEK and LY86 genes are highly expressed in carotid AS. The higher the expression of PLEK and LY86, the worse the prognosis is.

Network Pharmacology to Explore the Mechanism of Prunella vulgaris L. Against Prolactinoma

Objectives Prolactinoma is a common intracranial tumor with a high incidence and serious harm to human health. At present, there is only one therapeutic drug in China, bromocriptine, and the Chinese herb Prunella vulgaris L. ( P. vulgaris)(PV) has shown certain anti-prolactinoma effects in the early stage. We expect to develop a candidate drug against prolactinoma. Materials and Methods First, the extracts of P. vulgaris L.(PVE)were extracted with water, and the cell proliferation test of rat pituitary tumor cells MMQ was checked by the Cell Counting Kit-8 (CCK-8) assay. Then, core targets and correlative pathways were selected by the “protein–protein interaction” (PPI) network and the “PV–Target–Prolactinoma” network. The core targets and main components simulate the binding by molecular docking. Finally, the PVE and MMQ cells were used to verify the results. Results Through the CCK-8 assay, the PVE inhibited the proliferation of MMQ cells. From the network pharmacology, the 21 targets, 9 signaling pathways, and 20 gene ontology (GO) projects were attained ( p < 0.05). As a result the estrogen receptor α (ESR1), RAC-alpha serine/threonine-protein kinase(AKT1), and mitogen-activated protein kinase 3(MAPK3)were the core targets of protein against prolactinomas, which was in line with western blotting analysis. Conclusion Our findings demonstrate that the PVE was verified against prolactinomas through the ESR1, MAPK3 targets, and the phosphoinositide 3-kinase/protein kinase B pathway.

Enacting the pluriverse in the West: contemplative activism as a challenge to the disenchanted one-world world

Within IR, scholars are starting to consider difference on the level of ontology rather than epistemology. Other worlds are introduced into IR’s political pluriverse, however, these are often encountered in faraway places, thereby playing into the colonial narrative that ontological difference does not exist in the ‘West’. This paper introduces another real from within the ‘disenchanted North’ that is shaped by contemplative activists: people using contemplation as a form of protest. An engagement with contemplative activism challenges our commonly held assumptions about what contemplation and social change are, thereby undermining the institutions of ‘science’ and ‘religion’ underlying the universe. It argues that the project of political ontology in IR should consist of two moves: drawing in other, in particular spiritual, realities into the political imaginations of IR and challenging the ontological assumptions underpinning concepts. Consequently, it suggests that the pluriverse in IR should be a methodological rather than an ontological commitment.

Consummate Phenomena: Oskar Becker’s “Hyperontological” Aesthetics

ABSTRACTThis essay reconstructs Oskar Becker’s idiosyncratic conception of aesthetics and its importance for phenomenology. For Becker, the aesthetic is not simply one type of phenomenon among others; rather, it occupies a privileged position as, first, that phenomenon which is itself “wholly phenomenal,” and, second, that phenomenon which discloses the ontological structure of phenomenality itself (and is thus what he calls “hyperontological”). The paper first reconstructs Becker’s descriptive phenomenology of the aesthetic (which he restricts to the realm of masterpieces of fine art). For Becker, the key characteristic for understanding the givenness of beauty is its sense of fragility, which he uses to reveal a complicated interweaving of temporality and modality at the heart of the aesthetic. This essay then shows how this is rooted in Becker’s larger ontological project of developing a phenomenology of the non-historical in dialogue with Heidegger’s early work, a project which began in 1927 with the publication of his magnum opus Mathematical Existence.

The stakes of abyssal geography. Response to commentaries on David Chandler and Jonathan Pugh's ‘Abyssal geography’.

The stakes of abyssal geography. Response to commentaries on David Chandler and Jonathan Pugh's ‘Abyssal geography’.

The Problem of the Actual Infinity and the Path of the New European Classical Epistemology: from Genesis to the Modern Crisis

Introduction. The purpose of the paper is to show the prospects of the problem of actual infinity for understanding the ways of New European classical epistemology. The relevance of the work is due to the need to fill a gap in the history of New European epistemology, which today makes it difficult to understand the essence of its crisis. Such a lacuna was formed by the lack of grounds for the transition from the probabilistic concept of natural science, which takes into account apophaticism associated with the idea of actual infinity, to positive science, which presupposes a positive understanding of actual infinity.Methodology and sources. The author of the paper reconstructs and critically analyzes the attempts of the founders of New European science (Galileo and Descartes) to reform the ontological project of Nikolai Kuzansky due to the need for a positive understanding of the actual infinity. The author distinguishes between the reception of the problem of actual infinity in the New European philosophy and its objective state. Based on a comparative analysis, the author of the article establishes the identity of the logic of the development of the problem of actual infinity in the studies of Zeno of Elea and in New European epistemology, thereby testifying to its enduring significance.Results and discussion. The author shows that in the development of the problem of actual infinity, an objective regularity manifests itself, consisting in the fact that an unjustified assumption of the possibility of changing physical nature on the basis of the actual infinite really leads to a change in nature, but only the basis for this change is not actual, but potential infinity. This logic was reproduced in the history of New European epistemology. Thereby, mathematical natural science really turned out to be possible, but not on what its creators put in the basis (actual infinity), but on a derivative of it (potential infinity), and as a result it strengthens the position of supporters of non-classics.Conclusion. The problem of actual infinity makes it possible to understand the logic of the development of New European epistemology from its genesis to the modern crisis, and shows a deep interconnection between these two points.

A systematic comparison and evaluation of building ontologies for deploying data-driven analytics in smart buildings

Ontologies play a critical role in data exchange, information integration, and knowledge sharing across diverse smart building applications. Yet, semantic differences between the prevailing building ontologies hamper their purpose of bringing data interoperability and restrict the ability to reuse building ontologies in real-world applications. In this paper, we propose and adopt a framework to conduct a systematic comparison and evaluation of four popular building ontologies (Brick Schema, RealEstateCore, Project Haystack, and Digital Buildings) from both axiomatic design and assertions in a use case, namely the Terminological Box (TBox) evaluation and the Assertion Box (ABox) evaluation. In the TBox evaluation, we use the SQuaRE-based Ontology Quality Evaluation (OQuaRE) framework and concede that Project Haystack and Brick Schema are more compact with respect to the ontology axiomatic design. In the ABox evaluation, we apply an empirical study with sample building data that suggests Brick Schema and RealEstateCore have greater completeness and expressiveness in capturing the main concepts and relations within the building domain. The results indicate that there is no universal building ontology for integrating Linked Building Data (LBD). We also discuss ontology compatibility and investigate building ontology design patterns (ODPs) to support ontology matching, alignment, and harmonisation.

Vasily Sesemann’s Review of “Being and Time” of Martin Heidegger: analytical commentary

In my paper, I give an analytical commentary on Vasily Sesemann’s review of Martin Heidegger's treatise Being and Time (1927) published in the journal entitled The Way in 1928. The aim of this commentary is to evaluate the adequacy of Sesemann’s perception of Heidegger’s thought and the acceptability of his review for today’s reception of the Heideggerian ontological project. In my text, I state that Sesemann accurately fixes the transcendent essence of Heidegger’s ontological investigation, its basic theme and the main stages of its explication. In this regard, the Sesemann’s evaluation of the project of fundamental ontology in Heidegger is much closer to the very idea of this project in comparison to the evaluations of it given by both Edmund Husserl and Nicolai Hartmann. Sesemann also offered several successful or - at least - original translations of Heideggerian terms into Russian. Since he understands the incompleteness of the project, the results of which were presented in the initial divisions of Being and Time, Sesemann remains very far from being able to provide a final judgement about it. And yet, he points out the key achievements of Heidegger: the special significance of the differentiation of the ways of being of Dasein and the inner-worldly entities, emphasis of care-structure, which allows to grasp Dasein in its integrity and systemic essence of Heidegger’s work. I also acknowledge that although the interpretation proposed by Sesemann contains some weaknesses, f.i., the interpretation of Dasein as being-awareness and the neo-Kantian understanding of the systematic essence of the ontology of Heidegger, the review written by Vasily Sesemann is highly keen and may be valid for reception of Heideggerian philosophy up to nowadays.