The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

Feminists of a philosophical sort, lovers of women and wisdom, political critics and witnesses! What unusual and important opportunities we face as we bring the lessons of the last few years to bear on complex theorizing, multi-issue praxis, and the work of twenty-first century democracy. We've been on the streets, in th classroom, and on the Internet, opposing war and occupation, protesting police brutality, demanding global peace and justice. We've helped organize teach-ins and lectures, meetings and potlucks, concerts and art (...) exhibitions. From the Revolutionary Association of the Women of Afghanistan to New Yorkers Say No to War, from Women in Black to Code Pink, feminists were some of the first vocal opponents of the Bush rush to war. In February 2003 we helped create the greatest global protest for peace in human history, proclaiming "The World Says No to War" under banners of the swirling blue earth, cracking open the hegemony of you're-either-with-us-or-you're-with-the-terrorists, and activating a phenomenal range of new coalitions. (shrink)

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

Some hold that musical works are fusions of, or coincide with, their performances. But if performances contain wrong notes, won't works inherit that property? We say ‘no’.

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

Daeley wrote good book. I wrote a tolerable review.

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (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)

Basic Formal Ontology (BFO) is a top-level ontology used in hundreds of active projects in scientific and other domains. BFO has been selected to serve as top-level ontology in the Industrial Ontologies Foundry (IOF), an initiative to create a suite of ontologies to support digital manufacturing on the part of representatives from a number of branches of the advanced manufacturing industries. We here present a first draft set of axioms and definitions of an IOF upper ontology descending from BFO. The (...) axiomatization is designed to capture the meanings of terms commonly used in manufacturing and is designed to serve as starting point for the construction of the IOF ontology suite. (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)

Public arguments can be good or bad not only as a matter of logic, but also in the sense that speakers can do good or bad things with arguments. For example, hate speakers use public arguments to contribute to the subordination of their targets. But how can ordinary speakers acquire the authority to perform subordinating speech acts? This is the ‘Authority Problem’. This paper defends a solution inspired by McGowan’s (Australas J Philos 87:389–407, 2009) analysis of oppressive speech, including against (...) concerns raised by McGowan (Just words: On speech and hidden harm, Oxford University Press, Oxford, 2019) herself. A deflated kind of authority can be gained from the hate speaker’s standing in a norm-governed ‘activity of oppression’. We should be wary about engaging with such speakers in public argument. Even if we counter their arguments, we may still elevate their standing within that activity and so enable them to perform more pernicious speech acts than was previously possible. (shrink)

Public arguments can be good or bad not only as a matter of logic, but also in the sense that speakers can _do_ good or bad things with arguments. For example, hate speakers use public arguments to contribute to the subordination of their targets. But how can ordinary speakers acquire the authority to perform subordinating speech acts? This is the ‘Authority Problem’. This paper defends a solution inspired by McGowan’s (Australas J Philos 87:389–407, 2009) analysis of oppressive speech, including against (...) concerns raised by McGowan (Just words: On speech and hidden harm, Oxford University Press, Oxford, 2019) herself. A _deflated_ kind of authority can be gained from the hate speaker’s standing in a norm-governed ‘activity of oppression’. We should be wary about engaging with such speakers in public argument. Even if we counter their arguments, we may still elevate their standing within that activity and so enable them to perform more pernicious speech acts than was previously possible. (shrink)

The author interprets three stories from recently Neolithic cultures (Melanesian, African Bushman, and Inuit) and a fourth story from an oral tradition of Haitian women. All four are about women and perhaps, judging by their content, composed by women. The author trained with Edward Whitmont and developed his interpretation technique in decades of practice with dreams as a Jungian analyst. He adds a new tool, the use of repetition, in which the same point is made by a series of different (...) details. Repetition provides an internal test for the accuracy of an interpretation. The author updates Jung’s concept of archetypes to incorporate an understanding of Darwinian evolution (which Jung lacked), new knowledge of the function of genes, and new knowledge of the emergence of complexity in dynamic and adaptive systems. He compares his interpretations of the four stories with other scholars’ interpretations, in particular the extraordinary work of Michael Wessels on African Bushman legends. Though Wessels criticized Jung for imposing his ‘colonial’ theory of universal archetypes, both Jung and Wessels insisted that interpretation requires a dialogue between two agents in which both are subjects, neither being dominated or objectified. In the four stories, the author shows, symbolic consciousness began with women. The anthropologist Chris Knight proposed something similar in 1991 in his controversial book Blood Relations: Menstruation and the Origins of Culture. (shrink)

What happens to the inner light of consciousness with the death of the individual body and brain? Reductive materialism assumes it simply fades to black. Others think of consciousness as indicating a continuation of self, a transformation, an awakening or even alternatives based on the quality of life experience. In this issue, speculation drawn from theoretic research are presented. -/- Table of Contents Epigraph: From “The Immortal”, Jorge Luis Borges iii Editor’s Introduction: I Killed a Squirrel the Other Day, Gregory (...) M. Nixon iv-xi Research Essays The Tilde Fallacy and Reincarnation: Variations on a "Skeptical" Argument Teed Rockwell 862-881 Death, Consciousness, and Phenomenology, Steve Bindeman 882-899 The Idealist View of Consciousness After Death, Bernardo Kastrup 900-909 Consciousness, a Cosmic Phenomenon—A Hypothesis, Eva Déli 910-930 The Theory of a Natural Afterlife: A Newfound, Real Possibility for What Awaits Us at Death, Bryon K. Ehlmann 931-950 Near-Death Cases Desegregating Non-Locality/Disembodiment via Quantum Mediated Consciousness: An Extended Version of the Cell-Soul Pathway, Contzen Pereira & J Shashi Kiran Reddy 951-968 On the Possible Existence of Quantum Consciousness After Brain Death, Massimo Pregnolato & Alfredo Pereira Jr. 969-991 Science and Postmortem Survival, Edward F. Kelly 992-1011 Explorations ISS Theory: Cosmic Consciousness, Self, and Life Beyond Death in a Hyperdimensional Physics, Chris H. Hardy 1012-1035 Does the Consciousness End, Remain Awake, or Transform After Death? Radivoj Stankovich (with Micho Durdevich) 1036-1050 Big Bang Spirituality, Life, and Death, Ken Bausch 1051-1063 Death, Consciousness and the Quantum Paradigm, Ronald Peter Glasberg 1064-1077 Living With Limits: The Continuum of Consciousness, Donald Brackett 1078-1098 Mysticism, Consciousness, Death, Mike Sosteric 1099-1118 What Dies? Eternalism and the Afterlife in William James, Jonathan Bricklin 1119-1140 Theories of Consciousness and Death: Does Consciousness End, Continue, Awaken, or Transform When the Body Dies? Roger Cook 1141-1153 It’s the Other Way Around: Matter is a Form of Consciousness and Death is the End of the Illusion of Life in the World, James P. Kowall & Pradeep B. Deshpande 1154-1208 Statements A Feminine Vision for the World Consciousness, & a New Outrageous Ontology, Lorna Green 1209-1217 The Mask of Eternity: The Quest for Immortality and the Afterlife, Iona Miller 1218-1228 Are We Really “such stuff as dreams are made on”? Chris Nunn 1229-1225 Is the Afterlife a Non-Question? (Let's Hope Not), Deepak Chopra 1226-1230 Life After Death? An Improbable Essay, Stuart Kauffman 1231-1236. (shrink)

NUTRIÇÃO SOBRE A AZOOSPERMIA EM BOVINOS -/- -/- E. I. C. da Silva Departamento de Agropecuária – IFPE Campus Belo Jardim Departamento de Zootecnia – UFRPE sede -/- AZOOSPERMIA EM BOVINOS -/- INTRODUÇÃO -/- A falta completa de esperma no ejaculado pode ser devido a uma falha no processo de espermatogênese ou relacionada a causas no transporte do esperma. Com relação ao transporte, o esperma pode ser impedido de ser ejaculado mediante bloqueios ou oclusões no sistema do ducto extragonadal, ou (...) por causa de uma disfunção ejaculatória. Nos cães, por exemplo, a possibilidade de oclusão ser a causa pode ser determinada por medições de fosfatase alcalina (ALP) no plasma seminal, já que a ALP se origina do epidídimo e seminífero epitélio tubular. Se a concentração de ALP no fluido seminal for superior a 5000 UI/l, a amostra ejaculada contém fluido desses tecidos e a oclusão pode ser descartada. -/- As causas testiculares da azoospermia incluem a falha da espermatogênese, que pode ser causada por uma série de fatores; estes incluem fatores hormonais, imunológicos, congênitos, tóxicos, patogênicos, traumáticos e nutricionais. Aqui, as supressões na região do AZF (que contém sub-regiões AZFa, AZFb e AZFc) no cromossoma Y desempenham um papel importante, representando 10-15% dos casos de azoo- e oligospermia. Na região AFZc, o gene DAZ, que é suprimido na azoospermia, é considerado importante no controle espermatogênico, uma vez que a sua eliminação é frequentemente detectada em homens e/ou animais inférteis. -/- A perda total da capacidade de formação de espermatozoides pelo epitélio testicular e, portanto, a ausência de espermatozoides viáveis ou não no volume ejaculado pelo animal é denominado como azoospermia (VARNER et al., 2000), um macho nessas condições deve ser imediatamente retirado dos processos produtivos e não é, de forma alguma, viável para fins reprodutivos. A origem da causa pode ter caráter nutricional, ou outras, sendo multifatoriais; em processos crônicos severos pode-se chegar à azoospermia reversível, que é diagnosticada e corrigida de forma oportuna. Entre os principais fatores de caráter nutricional temos: -/- 18.1 Nitratos (NO3-) e nitritos (NO2-) -/- Quando os ruminantes consomem uma alimentação com elevadas concentrações de nitratos (presente principalmente nas forrageiras) parte do nitrato não pode ser imediatamente convertido em nitrito e, por fim, em amoníaco (todas essas transformações acontecem no rúmen mediante a flora microbiana); isso faz com que nitrato e nitrito se acumulem no rúmen. A adição do nitrato no rúmen intensifica o problema. O envenenamento por nitrato ocorre quando o nível de nitrito presente no rúmen excede a capacidade do microbiota para convertê-lo em amoníaco. Quando isto acontece, o nitrato e o nitrito são absorvidos através da parede do rúmen e entram na circulação sanguínea. É o nitrito que causa a toxicidade. -/- Estudou-se o equilíbrio ácido-básico e sua relação com a reprodução e produção, postulando a hipótese de que esse equilíbrio afeta os mecanismos endócrinos e metabólicos, além dos reprodutivos. -/- 18.2 Relação energia:proteína -/- Quando a alimentação apresenta deficiências de energia aumenta-se a degradação das gorduras (provenientes do tecido adiposo), acompanhada pela redução da liberação de insulina (hipoinsulinemia) afetando-se a lipogênese, mobilizando-se mais gordura corporal do que se sintetiza. -/- Situações como a acidose ruminal (excesso de grão e deficiência em fibras) ou alcalose ruminal (excesso de ureia com baixa energia digerível) resultam em perturbações sobre a fertilidade; além disso, deficiências energéticas graves que levam à cetose causam estresse com a liberação de catecolaminas, ACTH e TSH que afetam a secreção de GnRH, afetando por fim, a espermiogênese. -/- -/- Uma diminuição de energia na alimentação gera hipoglicemia que, ao mesmo tempo, produz hipoinsulinemia incrementando assim a lipólise em tecidos, gerando como produtos as cetonas. -/- A hipoinsulinemia juntamente com a cetonemia e a geração de beta-endorfinas, por problemas na alimentação, reduzem notavelmente a síntese de GnRH. A GnRH reduz a liberação do LH e FSH. A diminuição da liberação do LH provoca azoospermia hipogonadotrópica com efeitos de estimulação hormonal anormais segundo a avaliação endócrina, bem como a obstrução testicular inexplicada. -/- Se houver um aumento significativo na liberação de FSH, a azoospermia hipogonadotrópica é refletida em diagnóstico como disfunção testicular. -/- 18.3 Minerais (Selênio Se) -/- Quando os níveis de Se na dieta são deficientes, ocorrem falhas na formação e maturação espermática. O Se mostra uma grande influência na fertilidade do macho afetando a qualidade do sêmen, o plasma seminal contém elevadas quantidades de GSH-Px, cuja função é proteger a membrana do espermatozoide do ataque peroxidativo; além disso, na cauda do gameta masculino há um selenopeptídeo que faz com que, em uma deficiência de Se, produza-se uma fratura no meio da cauda do espermatozoide. -/- O esperma dos animais com deficiência de Se apresentam pobre motilidade com características de desenvolvimento anormal na cauda do esperma. Demonstrou-se que a deficiência de Se, não somente precipita o problema em reprodutores, mas que o esperma deformado, foi menos efetivo na subsequente fertilização do ovócito ovulado (HAWKES et al., 2001), ou seja, animais que possuem deficiência desse mineral podem ter esperma inapropriado para a destinação de inseminação artificial ou mesmo a monta natural, uma vez que a taxa de concepção estará bastante baixa. -/- REFERÊNCIAS BIBLIOGRÁFICAS -/- BARRENHO, Gonçalo José Pinheiro. Nutrição e fertilidade em bovinos de leite. 2016. Dissertação de Mestrado. Universidade de Évora. -/- BINDARI, Yugal Raj et al. Effects of nutrition on reproduction-A review. Adv. Appl. Sci. Res, v. 4, n. 1, p. 421-429, 2013. -/- BOLAND, M. P. Efectos nutricionales en la reproducción del ganado. XXXI Jornadas Uruguayas de Buiatría, 2003. -/- CHENOWETH, Peter J.; LORTON, Steven (Ed.). Animal Andrology: Theories and Applications. Boston: Cabi, 2014. -/- -/- DEHNING, R. Interrelaciones entre nutrición y fertilidad. In: Curso Manejo de la Fertilidad Bovina18-23 May 1987Medellín (Colombia). CICADEP, Bogotá (Colombia) Universidad de La Salle, Medellín (Colombia) Instituto Colombiano Agropecurio, Bogotá (Colombia) Sociedad Alemana de Cooperación Técnica-GTZ (Alemania), 1987. -/- DE LUCA, Leonardo J. Nutrición y fertilidad en el ganado lechero. XXXVI Jornadas Uruguayas de Buiatría, 2008. -/- DIAS, Juliano Cesar et al. Alguns aspectos da interação nutrição-reprodução em bovinos: energia, proteína, minerais e vitaminas. PUBVET, v. 4, p. Art. 738-743, 2010. -/- FRAZER, Grant S. Bovine theriogenology. Veterinary Clinics: Food Animal Practice, v. 21, n. 2, p. xiii-xiv, 2005. -/- FRENEAU, G. E.; GUIMARÃES, J. D. Curso Teórico-Prático de Andrologia Bovina. Goiânia: Laboratório de andrologia e Tecnologia de Sêmen da Escola de Veterinária da Universidade Federal de Goiás, 2000. -/- GORDON, Ian. Controlled reproduction in farm animals series. Nova Iorque: CAB International, 1996. -/- HAWKES, WAYNE CHRIS; TUREK, PAUL J. Effects of dietary selenium on sperm motility in healthy men. Journal of Andrology, v. 22, n. 5, p. 764-772, 2001. -/- MAAS, John. Relationship between nutrition and reproduction in beef cattle. The Veterinary Clinics of North America. Food Animal Practice, v. 3, n. 3, p. 633-646, 1987. -/- SHORT, Robert E.; ADAMS, D. C. Nutritional and hormonal interrelationships in beef cattle reproduction. Canadian Journal of Animal Science, v. 68, n. 1, p. 29-39, 1988. -/- THATCHER, W. W. et al. Strategies for improving fertility in the modern dairy cow. Theriogenology, v. 65, n. 1, p. 30-44, 2006. -/- TEIXEIRA, J. C.; TEIXEIRA, LFAC. Alimentação de bovinos leiteiros. FAEPE, Lavras, 1997. -/- VARNER, D. D. et al. Techniques for evaluating selected reproductive disorders of stallions. Animal reproduction science, v. 60, p. 493-509, 2000. (shrink)

Online communication can often seem different to offline talk. Structural features of social media sites can shape the things we do with words. In this paper, I argue that the practice of ‘quote-tweeting’ can cause a single utterance that originally performed just one speech act to later perform several different speech acts. This describes a new type of illocutionary pluralism—the view that a single utterance can perform multiple illocutionary acts. Not only is this type more plural than others (if one (...) utterance can acquire many kinds of illocutionary force), but it also shows how illocutionary forces can be accumulated over time. This is not limited to online utterances—some offline contexts are similarly structured, and so offline utterances can also come to perform many different speech acts. (shrink)

This entry investigates the connections between neo-populism and neo-conspiracism in the USA. One central thread is the rhetoric of purity that fosters rigid dichotomies of thought about identities, contributing to both populism and conspiracism, eliciting a neologism: conspirapopulism.

Recent clinical trials show that psychedelics such as LSD and psilocybin can be given safely in controlled conditions, and can cause lasting psychological benefits with one or two administrations. Supervised psychedelic sessions can reduce symptoms of anxiety, depression, and addiction, and improve well-being in healthy volunteers, for months or even years. But these benefits seem to be mediated by "mystical" experiences of cosmic consciousness, which prompts a philosophical concern: do psychedelics cause psychological benefits by inducing false or implausible beliefs about (...) the metaphysical nature of reality? This book is the first scholarly monograph in English devoted to the philosophical analysis of psychedelic drugs. Its central focus is the apparent conflict between the growing use of psychedelics in psychiatry and the philosophical worldview of naturalism. Within the book, Letheby integrates empirical evidence and philosophical considerations in the service of a simple conclusion: this "Comforting Delusion Objection" to psychedelic therapy fails. While exotic metaphysical ideas do sometimes come up, they are not, on closer inspection, the central driver of change in psychedelic therapy. Psychedelics lead to lasting benefits by altering the sense of self, and changing how people relate to their own minds and lives-not by changing their beliefs about the ultimate nature of reality. The upshot is that a traditional conception of psychedelics as agents of insight and spirituality can be reconciled with naturalism (the philosophical position that the natural world is all there is). Controlled psychedelic use can lead to genuine forms of knowledge gain and spiritual growth-even if no Cosmic Consciousness or transcendent divine Reality exists. Philosophy of Psychedelics is an indispensable guide to the literature for researchers already engaged in the field of psychedelic psychiatry, and for researchers-especially philosophers-who want to become acquainted with this increasingly topical field. (shrink)

Users of psychedelic drugs often report that their sense of being a self or ‘I’ distinct from the rest of the world has diminished or altogether dissolved. Neuroscientific study of such ‘ego dissolution’ experiences offers a window onto the nature of self-awareness. We argue that ego dissolution is best explained by an account that explains self-awareness as resulting from the integrated functioning of hierarchical predictive models which posit the existence of a stable and unchanging entity to which representations are bound. (...) Combining recent work on the ‘integrative self' and the phenomenon of self-binding with predictive processing principles yields an explanation of ego dissolution according to which self-representation is a useful Cartesian fiction: an ultimately false representation of a simple and enduring substance to which attributes are bound which serves to integrate and unify cognitive processing across levels and domains. The self-model is not a mere narrative posit, as some have suggested; it has a more robust and ubiquitous cognitive function than that. But this does not mean, as others have claimed, that the self-model has the right attributes to qualify as a self. It performs some of the right kinds of functions, but it is not the right kind of entity. Ego dissolution experiences reveal that the self-model plays an important binding function in cognitive processing, but the self does not exist. (shrink)

Psychedelic ingestion and meditative practice are both ancient methods for altering consciousness that became widely known in Western society in the second half of the 20th century. Do the similarities begin and end there, or do these methods – as many have claimed over the years – share some deeper common elements? In this chapter I take a neurophilosophical approach to this question and argue that there are, indeed, deeper commonalities. Recent empirical studies show that psychedelics and meditation modulate overlapping (...) brain networks involved in the sense of self, salience, and attention; moreover, psychedelics can occasion lasting increases in “mindfulness-related capacities” for taking a non-reactive stance on one’s inner experience (e.g. Sampedro et al. 2017). The self-binding theory of psychedelic ego dissolution (Letheby and Gerrans 2017) offers a plausible explanation of these findings: by disrupting self-related beliefs implemented in high-level cortical networks, both psychedelics and meditation can “unbind” mental contents from one’s self-model, moving these contents along the continuum from phenomenal transparency to opacity (cf. Metzinger 2003). In other words, both psychedelics and meditation can expose and weaken our foundational beliefs about our own identity, allowing us to disidentify with these beliefs and see them as “just thoughts”. There are connections between these ideas and recent arguments suggesting that psychedelic use may have epistemic benefits consistent with philosophical naturalism (Letheby 2015, 2016, 2019). I conclude with a proposal: these connections may help in thinking about the putative epistemic benefits of meditation practice from a naturalistic perspective. (shrink)

This paper is an enquiry into the logical, metaphysical, and physical possibility of time travel understood in the sense of the existence of closed worldlines that can be traced out by physical objects. We argue that none of the purported paradoxes rule out time travel either on grounds of logic or metaphysics. More relevantly, modern spacetime theories such as general relativity seem to permit models that feature closed worldlines. We discuss, in the context of Gödel's infamous argument for the ideality (...) of time based on his eponymous spacetime, what this apparent physical possibility of time travel means. Furthermore, we review the recent literature on so-called time machines, i.e., of devices that produce closed worldlines where none would have existed otherwise. Finally, we investigate what the implications of the quantum behaviour of matter for the possibility of time travel might be and explicate in what sense time travel might be possible according to leading contenders for full quantum theories of gravity such as string theory and loop quantum gravity. (shrink)

The chapter introduces and characterizes the notion of fittingness. It charts the history of the relation and its relevance to contemporary debates in normative and metanormative philosophy and proceeds to survey issues to do with fittingness covered in the volume’s chapters, including the nature and epistemology of fittingness, the relations between fittingness and reasons, the normativity of fittingness, fittingness and value theory, and the role of fittingness in theorizing about responsibility. The chapter concludes with a brief discussion of issues to (...) do with fittingness that aren’t covered extensively by the volume’s chapters in order to indicate avenues for further research. (shrink)

This draft preprint presents a nine step argument for “Connectionist Structuralism” (CS), an account of the ontology of abstract objects that is neither purely nominalist nor purely platonist. CS is a common, often implicit assumption in parts of the artificial intelligence literature, but such discussions have not presented formal accounts of the position or engaged with metaphysical issues that potentially undermine it. By making the position legible and presenting an initial case for it, we hope to support a constructive dialogue (...) between AI researchers and philosophers of metaphysics that helps both sides to refine the position. -/- CS proposes that each abstract object we can draw on in human analysis corresponds to a particular subset of an individual person’s brain structure whose functionality is isomorphic to a subset of the nodes and connections in a suitable connectionist network. In other words, abstract objects are physically realised, but in individual brains, rather than only in the referent objects (pure nominalism) or in metaphysical universals (pure platonism). -/- This paper’s minimum claim is that CS can account for all abstract object predicables regarding sensible properties, such as “is red” or “is a square”. Using evidence from cognitive neuroscience, machine learning, and evolutionary biology, as well as a fully traceable toy example, we describe how CS can support our core cognitive uses of such sensible properties and can account for our core phenomenal experiences of them. In the former, CS provides sufficient albeit imperfect inferential safety, whose limitations are argued to strengthen rather than weaken the case for CS as describing human behaviour. In the latter, four target phenomenal features are accounted for – abstract objects as feeling intangible, non-located, transparent, and unchanging - along with accounts for further phenomena such as semantic refinement, the Stroop effect, synaesthesia, semantic clarity, sensory overload, and satiation. -/- Our minimum claim concerns the day-to-day usage and felt experience of abstract objects, but we suggest also an extended claim in which CS can form the basis of a pragmatic sufficient logic. As such, the initial outline of a response is provided for five common objections to positions that seek to ground abstract objects without reference to metaphysically stand-alone universals: referential opacity; identity of indiscernibles; infinite regression; non-physical concepts; and necessary truths. These outlines lay the foundation for (but do not seek to formally demonstrate) an extended CS account that addresses other abstract objects, including issues relating to their use in mathematics and formal logic. -/- The CS account leads to a four-layer hierarchy of similarity for whether your “red” is the same as mine. Considering both semantic and phenomenal similarity, we conclude that our “reds” are likely non-identical but can be made close enough for practical purposes. Finally, we describe how future work could elaborate CS as a metaphysical project and how confidence in it could be tested through empirical research. (shrink)

It is natural to think that many of our beliefs are rational because they are based on seemings, or on the way things seem. This is especially clear in the case of perception. Many of our mathematical, moral, and memory beliefs also appear to be based on seemings. In each of these cases, it is natural to think that our beliefs are not only based on a seeming, but also that they are rationally based on these seemings—at least assuming there (...) is no relevant counterevidence. This piece is an introduction to a volume dedicated to the question of what the connection is between seemings and justified belief: under what conditions, if any, can a seeming justify its content? (shrink)

Many philosophers sympathetic with a Humean understanding of laws of nature have thought that, in the final analysis, the fundamental laws will include not only the traditional dynamical equations, but also two additional principles: the Past Hypothesis and the Statistical Postulate. The former says that the universe began in a particular very-low-entropy macrostate M(0), and the latter posits a uniform probability distribution over the microstates compatible with M(0). Such a view is arguably vindicated by the orthodox Humean Best System Account (...) (BSA). However, I argue here that recent developments of the BSA render the Past Hypothesis otiose. In particular, the trend among Humeans toward a more pragmatic view of laws — according to which the best system is the one that is maximally effective at helping creatures like us amplify our information about the world — does not support the idea that the Past Hypothesis is a law of nature. (shrink)

L.S. Vygotsky’s “regulative” account of the development of human thinking hinges on the centralization of “directive” speech acts (commands or imperatives). With directives, one directs the activity of another, and in turn begins to “self-direct” (or self-regulate). It’s my claim that Vygotsky’s reliance on directives de facto keeps his account stuck at Tomasello's level of individual intentionality. Directive speech acts feature prominently in Tomasello’s developmental story as well. But Tomasello has the benefit of accounting for a functional differentiation in directive (...) communication—i.e., in collaborative activity, the command gives way to both the request and informational assertion. Lacking such differentiation, Vygotsky’s account runs the risk of playing to a rather strident conception of the socius, one more Machiavellian than Marxist. (shrink)

Siyaves Azeri (2020) quite well shows that arithmetical thinking emerges on the basis of specific social practices and material engagement (clay tokens for economic exchange practices beget number concepts, e.g.). But his discussion here is relegated mostly to Neolithic and Bronze Age practices. While surely such practices produced revolutions in the cognitive abilities of many humans, much of the cognitive architecture that allows normative conceptual thought was already in place long before this time. This response, then, is an attempt to (...) sketch the deep prehistory of human cognition in order to show the inter-social bases of normative thought in general. To do this, I will look first to the work of Vygotsky and Leontiev, two often neglected psychologists whose combined efforts culminate in a developmental account of human cognitive origins. Then, I will review some key insights from the contemporary comparative psychologist Michael Tomasello—whose project is admittedly a Vygotskian one—in order to further shed light on the social-practical basis of abstract thought, of which mathematical cognition is surely a part. (shrink)

This volume is the first systematic presentation of the work of Albert Einstein, comprising fourteen essays by leading historians and philosophers of science that introduce readers to his work. Following an introduction that places Einstein's work in the context of his life and times, the book opens with essays on the papers of Einstein's 'miracle year', 1905, covering Brownian motion, light quanta, and special relativity, as well as his contributions to early quantum theory and the opposition to his light quantum (...) hypothesis. Further essays relate Einstein's path to the general theory of relativity (1915) and the beginnings of two fields it spawned, relativistic cosmology and gravitational waves. Essays on Einstein's later years examine his unified field theory program and his critique of quantum mechanics. The closing essays explore the relation between Einstein's work and twentieth-century philosophy, as well as his political writings. (shrink)

What should we do when faced with powerful theoretical arguments that support a severe change in our personal beliefs and commitments? For example, what should new parents do when confronted by unanswered anti-natalist arguments, or two lovers vexed by social theory that apparently undermines love? On the one hand, it would be irrational to ignore theory just because it’s theory; good theory is evidence, after all. On the other hand, factoring in theory can be objectifying, or risks unraveling one's life, (...) fracturing one's identity or social relations. Sometimes, then, following the evidence where it apparently leads would mean not merely changing what we think but who we are. Some might say that there’s something right about the thought that theory can bear on what we ought to believe, it’s just that when we work with full beliefs, only then do we seriously risk having to substantially alter our doxastic economy when pressed by exceptional theoretical arguments. When we work with partial beliefs, however, this risk is greatly diminished. Others will say that we can advocate or champion revisionary positions whilst rationally retaining our pre-theoretical personal convictions. Still others will argue that we should adopt a Moorean posture towards the revisionary arguments. I argue that each response is inadequate, and argue instead that we are permitted to bracket certain kinds of theoretical evidence against our beliefs because of the personal and ethical risks born out of giving them serious consideration. In turn, some of philosophy's doxastic influence is constrained by its attendant ethical risks: the personal enjoys a partial insulation from the theoretical. I close by addressing what this means for practicing philosophers. (shrink)

Recent scientific research suggests that altered states of consciousness induced by classic psychedelic drugs can cause durable psychological benefits in both healthy and patient populations. The phenomenon of ‘psychedelic transformation’ has many philosophically provocative aspects, not least of which is the claim commonly made by psychedelic subjects that their transformation is centrally due to some kind of learning or knowledge gain. Can psychedelic experiences really be a source of knowledge? From the vantage point of philosophical materialism or naturalism, a negative (...) answer is tempting because psychedelic subjects often claim drug-facilitated knowledge of non-natural, transcendent realities. This fact, combined with common conceptions of these drugs as ‘hallucinogenic’ or ‘psychotomimetic’, invites the conclusion that claims of epistemic benefit from psychedelic experience are uniformly false. However, several recent proposals have been made in the literature about naturalistically acceptable epistemic benefits that might arise from psychedelic use. In this chapter I review these proposals, classifying them in accordance with standard epistemological categories, and discuss the arguments for and against them. I also offer some suggestions for future research. (shrink)

In this paper, we present a survey of the development of the technique of argument diagramming covering not only the fields in which it originated - informal logic, argumentation theory, evidence law and legal reasoning – but also more recent work in applying and developing it in computer science and artificial intelligence. Beginning with a simple example of an everyday argument, we present an analysis of it visualised as an argument diagram constructed using a software tool. In the context of (...) a brief history of the development of diagramming, it is then shown how argument diagrams have been used to analyze and work with argumentation in law, philosophy and artificial intelligence. (shrink)

In his wide-ranging study of architecture and cultural evolution, Chris Abel argues that, despite progress in sustainable development and design, resistance to changing personal and social identities shaped by a technology-based and energy-hungry culture is impeding efforts to avert drastic climate change. The book traces the roots of that culture to the coevolution of Homo sapiens and technology, from the first use of tools as artificial extensions of the human body to the motorized cities spreading around the world, whose (...) uncontrolled effects are fast changing the planet itself. Advancing a new concept of the meme, called the 'technical meme', as the primary agent of cognitive extension and technical embodiment, Abel proposes a theory of the 'extended self' as a complex and diffuse outcome of that coevolution. Challenging conventional ideas of the self as a separate and autonomous being, the extended self, he explains, encompasses material and spatial as well as psychological and social elements, including the built environment and artifacts, and now reaches out into the virtual world of cyberspace. Drawing upon research into extended cognition and embodied minds from philosophy, psychology and the neurosciences, the book presents a new approach to environmental and cultural studies. N.B. This book was the winner of the International Committee of Architectural Critics 2017 Bruno Zevi Book Award by unanimous decision of the international jury. (shrink)

Subjective theories of well-being claim that how well our lives go for us is a matter of our attitudes towards what we get in life rather than the nature of the things themselves. This article explains in more detail the distinction between subjective and objective theories of well-being; describes, for each approach, some reasons for thinking it is true; outlines the main kinds of subjective theory; and explains their advantages and disadvantages.

Philosophers often treat racist and sexist slurs as a special sort of puzzle. What is the difference between a slur and its correlates? In attempting to answer this question, a second distinction has been overlooked: that between slurs and insults. What makes a term count as a slur? This is not an unnecessary taxonomical question as long as ableist terms such as ‘moron’ are dismissed as mere insults. Attempts to resolve the insult/slur distinction by considering the communicative content of slurs (...) are not promising. A better solution is offered by speech act theory, and this paper develops a novel way to describe ordinary slurring utterances as oppressive speech acts. This can both explain the difference between slurs and insults, and challenge the dismissal of ableist terms. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

This essay aims to provide a self-contained introduction to time in relativistic cosmology that clarifies both how questions about the nature of time should be posed in this setting and the extent to which they have been or can be answered empirically. The first section below recounts the loss of Newtonian absolute time with the advent of special and general relativity, and the partial recovery of absolute time in the form of cosmic time in some cosmological models. Section II considers (...) the beginning and end of time in a broader class of models in which there is not an analog of Newtonian absolute time. As we will see, reasonable physical assumptions imply that the universe is finite to the past, and Section III turns to consideration of the “beginning” itself. We critically review conventional wisdom that a “singularity” reveals flaws in general relativity and briefly assess ways of avoiding the singularity. (shrink)