The Adverse Outcome Pathway (AOP) concept is a knowledge assembly and communication tool to facilitate the transparent translation of mechanistic information into outcomes meaningful to the regulatory assessment of chemicals. The AOP framework and associated knowledgebases (KBs) have received significant attention and use in the regulatory toxicology community. However, it is increasingly apparent that the potential stakeholder community for the AOP concept and AOP KBs is broader than scientists and regulators directly involved in chemical safety assessment. In this paper we (...) identify and describe those stakeholders who currently—or in the future—could benefit from the application of the AOP framework and knowledge to specific problems. We also summarize the challenges faced in implementing pathway-based approaches such as the AOP framework in biological sciences, and provide a series of recommendations to meet critical needs to ensure further progression of the framework as a useful, sustainable and dependable tool supporting assessments of both human health and the environment. Although the AOP concept has the potential to significantly impact the organization and interpretation of biological information in a variety of disciplines/applications, this promise can only be fully realized through the active engagement of, and input from multiple stakeholders, requiring multi-pronged substantive long-term planning and strategies. (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)

Critical notice of R. Mayhew's, The Female In Aristotle's Biology.

REPRODUÇÃO EM NOVILHAS LEITEIRAS -/- INTRODUÇÃO -/- O principal objetivo da criação de substitutos em gado leiteiro é produzir uma novilha que tenha seu parto aos dois anos de idade (23 a 25 meses) e com um peso de 550 a 580 kg. O manejo reprodutivo das novilhas começa quando estas atingem 14 ou 15 meses de idade e um peso de 350 a 370 kg. A produção de novilhas deve ser suficiente para substituir as vacas descartadas anualmente (25 a (...) 35%), e para contribuir com o crescimento do rebanho. Espera-se que em um gado leiteiro deva haver uma população de animais de reposição, desde um dia de vida até à fase de novilha ao parto, correspondendo pelo menos a 70 % do total das vacas (figura 1). -/- Figura 1: A meta do programa de produção de substitutos ou fêmeas de reposição consiste em uma novilha que chegue ao seu primeiro parto aos 24 ou 25 meses de idade, entre um peso de 550 a 580 kg. Elaborado pelo autor. -/- A produção de novilhas depende basicamente de três fatores: da fertilidade das vacas, ou seja, do número de bezerras nascidas anualmente; da mortalidade durante a criação e desenvolvimento; e da eficiência reprodutiva das novilhas. O manejo reprodutivo moderno das novilhas é orientado para a utilização da inseminação artificial, seja em um estro natural ou sincronizado. As novilhas representam a população animal geneticamente mais avançada no rebanho, portanto, o mérito genético de suas crias obtidas por inseminação é maior do que o das crias das vacas adultas. Além disso, as crias das novilhas obtidas mediante a inseminação aceleram o avanço genético, uma vez que contribuem com uma proporção maior de substituições do rebanho em comparação com as crias das vacas de outras faixas etárias. Além disso, as novilhas são as fêmeas mais férteis do rebanho (porcentagem de concepção: 60 a 70% vs 30 a 40% em vacas), pelo que o custo do sêmen por gestação é menor em comparação com as vacas adultas, o que permite investir em melhores touros e em sêmen sexado. -/- 1. PUBERDADE -/- A puberdade é definida como a fase de desenvolvimento em que a fêmea apresenta o seu primeiro estro fértil. Regularmente as novilhas leiteiras, sob condições ótimas de manejo, chegam à puberdade entre 11 e 12 meses de idade, ou seja, antes de alavancar o peso recomendado para receber o primeiro serviço. Vale salientar que as novilhas podem ficar gestantes após a puberdade; no entanto, isto não é conveniente porque ainda não completou-se o seu desenvolvimento. Se ficarem gestantes nos primeiros ciclos estrais, as novilhas poderiam chegar ao parto com pouco desenvolvimento físico, o que provocaria distocias e baixa produção de leite (figura 2). A ativação do sistema neuroendócrino para que a bezerra atinja a puberdade é regulada principalmente pelo estado nutricional (condição corporal). A transição do anestro pré-puberal à ciclicidade puberal coincide com um aumento da condição corporal e das concentrações de insulina, IGF-I e leptina. Estes hormônios agem como sinais metabólicos no hipotálamo e hipófise que modificam a frequência de secreção das gonadotropinas, resultando na maturação folicular e ovulação. O atraso em relação à puberdade está diretamente relacionado com deficiências na alimentação; esta condição verifica-se em criações pouco tecnificadas, principalmente de pequenos e médios produtores. As novilhas que já atingiram o peso para receber o primeiro serviço e não apresentaram estro, devem ser examinadas por via retal para excluir possíveis anormalidades do desenvolvimento, tais como freemartinismo ou hipoplasia genital. -/- Figura 2: O fator mais importante que determina a puberdade é a nutrição. Bezerras bem alimentadas apresentam ciclos estrais aos 11 meses de idade e devem ser inseminadas aos 14 ou 15 meses de idade, com um peso de 350 a 370 kg. Acervo pessoal do autor. -/- 2. DETECÇÃO DE ESTRO E INSEMINAÇÃO ARTIFICIAL -/- A baixa eficiência na detecção de estros é o problema que mais afeta a eficiência reprodutiva das novilhas. De acordo com a duração do estro (8 a 18 horas), a observação das novilhas em períodos de 30 minutos durante a manhã e à tarde, permite detectar em estro até 70% das fêmeas, enquanto a observação contínua (24 horas) aumenta a eficiência na detecção até 95% (figuras 3 e 4). No manejo tradicional dos rebanhos leiteiros, as novilhas recebem pouca atenção por parte dos trabalhadores, o que resulta em baixa eficiência na detecção de estros (50 a 60%). Em diferença das vacas adultas em lactação, as novilhas estão menos expostas a fatores que diminuem a expressão do estro, portanto, com uma rotina de observação, de pelo menos duas horas na manhã (6h a 8h da manhã) e duas horas pela tarde até a noite (17h da tarde a 19h da noite), pode-se detectar até 90% das fêmeas no estro (figura 5). -/- Figura 3: O fator que mais influencia a idade ao primeiro parto é a baixa eficiência na detecção de estros, pelo que é recomendável a observação de estros com pessoal qualificado, em períodos de pelo menos duas horas pela manhã e duas à tarde. Acervo pessoal do autor. -/- Figura 4: Com a observação contínua é possível alcançar de 90 a 95% de eficiência na detecção de estros. Acervo pessoal do autor. -/- Figura 5: A inseminação deve ser realizada durante o período de receptividade sexual. Com boa eficiência na detecção de estros, a inseminação pode ser praticada no programa AM-PM e PM-AM, ou em apenas um turno de inseminação pela manhã (10:00), com bons resultados. -/- 3. TAXA DE PRENHEZ -/- O melhor indicador de eficiência reprodutiva é a taxa de prenhez. Este indicador refere-se à proporção de animais gestantes do total elegível para inseminação, num período equivalente a um ciclo estral. Como já se descreveu no trabalho Fisiologia do Estro e do Serviço na Reprodução Bovina, este indicador considera a eficiência na detecção de estros e a porcentagem de concepção, e reflete com maior objetividade a eficácia do manejo reprodutivo. Este parâmetro pode ser melhorado através de um aumento da proporção de novilhas detectadas em estro, o que se obtém aumentando o tempo de observação e aplicando técnicas de sincronização do estro (figura 6). -/- 4. INSEMINAÇÃO DE NOVILHAS COM SÊMEN SEXADO -/- A utilização de sêmen sexado é uma boa opção para a produção de novilhas de reposição. Com a nova tecnologia disponível para a separação de espermatozoides com o cromossomo x, é possível alcançar até 90% de crias fêmeas; no entanto, o processo de separação de espermatozoides tem baixa eficiência, o que limita o número de espermatozoides por palheta. As palhetas de inseminação com sêmen sexado contém de dois a três milhões de espermatozoides (doses de sêmen não sexado têm de 20 a 30 milhões). De acordo com os dados de fertilidade de gados comerciais, as novilhas inseminadas com sêmen sexado mostram de 10 a 20% menor concepção que novilhas inseminadas com sêmen não sexado, o que desencoraja o seu uso. Causas de baixa fertilidade não são conhecidas, no entanto, estão associadas com a menor concentração espermática e com alguns danos nos espermatozoides provocados pelo processo de separação. No entanto, o uso de sêmen sexado é uma opção viável para aumentar a produção de novilhas no rebanho, e com o melhoramento dos processos de separação espermática em pouco tempo se converterá em uma prática de rotina nos estábulos (figura 7). -/- Figura 6: Uma técnica que aumenta a eficiência na detecção dos estros consiste em pintar a região da grupa. Quando esta pintura desaparece ou se nota que as novilhas estão "talhadas", devem ser apalpadas via retal para determinar se existem sinais genitais de estro. Acervo pessoal do autor. -/- Figura 7: As novilhas são as fêmeas mais férteis do rebanho, por isso o custo do sêmen por gestação é menor em comparação com as vacas adultas, o que permite investir em melhores touros e em sêmen sexado. Acervo pessoal do autor. 5. MONTA DIRIGIDA -/- A monta dirigida ou direta é uma opção prática e eficaz para emprenhar as novilhas. Neste sistema se introduz um touro com um grupo de novilhas, para que ele se encarregue de encontrar as fêmeas em estro e proceder a monta. Em rebanhos comerciais, o ideal é a utilização de um touro para 25 fêmeas. No entanto, com este manejo perde-se a oportunidade de utilizar a inseminação artificial e, com isso, a possibilidade de melhoria genética. -/- 6. PROGRAMAS DE SINCRONIZAÇÃO DE ESTROS -/- Os tratamentos para sincronizar o estro das novilhas possuem os mesmos fundamentos que os utilizados nas vacas. -/- 6.1 Prostaglandina F2a -/- A PGF2α é utilizada para a sincronização de estros em grupos de novilhas, e também é utilizada para a indução do estro individualmente, nas fêmeas que são examinadas por via retal e têm um corpo lúteo. A resposta dos animais tratados é variável; em novilhas pode-se alcançar até 95% de animais em estro. O tempo de manifestação do estro após a injeção é de 48 a 120 horas. -/- 6.1.1 Dupla injeção de PGF2a -/- Além da sincronização dos animais selecionados pela presença de um corpo lúteo diagnosticado por palpação retal, existem dois programas que não incluem a palpação retal. Por exemplo, na segunda-feira, ou no dia preferido, injeta-se PGF2α em todas as novilhas que se deseja inseminar. Cerca de 50% das novilhas manifestarão estro nas próximas 48 a 120 horas. As fêmeas que não mostrarem estro receberão uma segunda injeção na segunda-feira seguinte (intervalo de sete dias). As que apresentaram estro com a primeira injeção teriam um corpo lúteo nesse momento, enquanto as que não o manifestaram estavam em estro ou em metaestro; assim, ao repetir o tratamento sete dias depois, estas últimas novilhas teriam um corpo lúteo e responderiam à PGF2α (figura 8). No outro programa, é administrada duas doses de PGF2α com 11 dias de separação/intervalo. As novilhas podem ser inseminadas no estro observado, após qualquer uma das duas injeções. Este programa oferece uma boa sincroniza- ção após a segunda injeção e é o programa de escolha na sincronização das novilhas receptoras de embriões (figura 9). -/- Figura 8: Sincronização do estro com dupla injeção de PGF2a com 7 dias de diferença/intervalo. Elaborado pelo autor. -/- Figura 9: Sincronização do estro com dupla injeção de PGF2a com 11 dias de diferença/intervalo. Elaborado pelo autor. -/- 6.2 Progestágenos -/- Existe um tratamento que consiste na inserção, na parte externa da orelha, de um implante que contém norgestomet, que permanece na região auricular por nove dias. Além disso, o tratamento é complementado com a injeção intramuscular de valerato de estradiol e norgestomet, no momento da colocação do implante. O tempo de apresentação do estro a partir da remoção do implante é de 48 a 72 horas e a proporção de animais em estro muitas vezes se torna maior do que 80%. Outro tratamento é baseado na inserção intravaginal de dispositivos de liberação de progesterona. O dispositivo pode ser utilizado durante 12 dias ou o período de exposição pode ser encurtado, desde que seja acompanhado da injeção de uma dose luteolítica de PGF2α, um dia antes ou no momento da remoção do dispositivo. A fertilidade global conseguida após o serviço no estro sincronizado é similar à obtida no estro natural; porém, algumas novilhas são menos férteis, o que está associado com alterações no desenvolvimento folicular e alterações na relação temporal entre o estro e a ovulação. Observou-se que o tratamento com implantes de norgestomet combinados com a injeção de valerato de estradiol pode induzir comportamento estral em animais que não estão ciclando normalmente. Isso ocorre porque os níveis de estradiol, administrados no primeiro dia, persistem até o momento da remoção do implante. Assim, ao remover a fonte do progestágeno e ao haver concentrações altas de estradiol se desencadeia o estro, o qual em novilhas anéstricas não é acompanhado de ovulação, enquanto que em novilhas ciclando se altera a relação temporal entre o estro, pico pré-ovulatório de LH e ovulação. Bons resultados são alcançados quando o valerato de estradiol não é administrado e é substituído por uma injeção de PGF2α no momento da remoção do implante. Outro fator que tem sido associado com baixa fertilidade é o dia do ciclo em que o tratamento começa. Observou-se que quando coincide com a presença de um corpo lúteo (diestro), a porcentagem de concepção é maior do que quando não há um corpo lúteo (proestro). Isto ocorre porque a concentração sérica do progestágeno, por si só, não é capaz de suprimir a secreção pulsátil de LH, o que faz com que o folículo dominante presente no momento de iniciar o tratamento não sofra atresia e persista até o dia da retirada do progestágeno, convertendo-se no folículo ovulatório. Com isso, o folículo já envelheceu e o ovócito já sofreu alterações que reduzem o seu potencial para desenvolver um embrião viável. Quando o tratamento coincide com a presença de um corpo lúteo, a secreção de LH é efetivamente suprimida devido ao efeito aditivo da progesterona secretada pelo corpo lúteo e do progestágeno exógeno, inserido na vaca, o que provoca a reposição folicular. Em condições de campo, a seleção das vacas pela presença de um corpo lúteo antes de iniciar o tratamento com progestágenos é impraticável, uma vez que não é possível visualizá-lo, além disso essa prática/seleção não faria sentido, já que seria mais fácil tratar estes animais com dose ou doses de PGF2α. Atualmente existem tratamentos para eliminar folículos dominantes e promover uma nova onda folicular. -/- 6.3 Progestágenos orais -/- O acetato de melengestrol (MGA) é um progestágeno administrado por via oral. Em fêmeas bovinas é utilizado para melhorar a eficiência alimentar nos currais de engorda, o que se consegue através da inibição da apresentação do estro. Como todos os progestágenos, o MGA inibe a secreção de LH, eliminando assim a maturação do folículo e a ovulação. Após a remoção do MGA, o folículo dominante termina o seu desenvolvimento e as fêmeas apresentam estro em forma sincronizada. A dose de MGA por novilha é de 0,5 a 1 mg por dia, em tratamentos que variam de 9 a 14 dias. A apresentação comercial de MGA contém 0,22 mg do hormônio por 1 g do produto. O MGA pode ser facilmente misturado com qualquer concentrado ou grão moído. Após o último dia de tratamento, o estro se apresenta de dois a seis dias. O intervalo de remoção do MGA ao estro é mais longo quando comparado com outros progestágenos. Isto deve-se ao tempo de remoção do MGA, uma vez que enquanto um implante ou dispositivo intravaginal é removido abruptamente, o MGA pode continuar a ser absorvido enquanto é removido do trato gastrointestinal. Com tratamentos de 14 dias podem-se obter porcentagens de concepção menores em comparação com o estro natural, o que se deve em grande parte à ovulação de folículos persistentes. Um tratamento eficaz, que também melhora a fertilidade, consiste na administração de MGA durante 14 dias, seguido de uma injeção de PGF2α 15 ou 17 dias após a remoção do progestágeno. Com este programa, uma alta proporção de fêmeas teriam um corpo lúteo no momento da injeção da PGF2α e apresentariam estro com boa sincronização. Outro tratamento eficaz consiste na administração do MGA durante nove dias, mais uma dose de PGF2α ao nono dia; com este programa também se obtêm bons resultados em sincronização do estro e fertilidade. Este tratamento foi avaliado com novilhas holandesas e a porcentagem de fêmeas sincronizadas é elevada (95%). A porcentagem de concepção é semelhante à obtida no estro natural. Estes resultados são comparáveis aos obtidos com outros programas, como implantes de norgestomet ou dispositivos intravaginais de liberação de progesterona, mas com um custo significativamente menor (figura 10). -/- 6.4 Sincronização da ovulação e inseminação em tempo fixo -/- Em contraste com o observado em vacas em lactação, a resposta das novilhas aos programas de sincronização da ovulação e inseminação a tempo fixo é deficiente, o que se reflete em porcentagens de concepção de 20 a 35% menores que as novilhas inseminadas no estro natural. A causa desta resposta está relacionada com diferenças no desenvolvimento folicular; assim, nas novilhas o tempo de desenvolvimento do folículo dominante é mais rápido e o tempo de domínio é mais curto do que nas vacas em lactação. Desta forma, o folículo da onda folicular sincronizada com a injeção de GnRH sofre atresia antes da injeção de PGF2α, de tal forma que quando se induz a ovulação com a segunda injeção de GnRH, as novilhas têm folículos em diferentes estádios de desenvolvimento, o que provoca assincronia entre a ovulação e a inseminação artificial. -/- Figura 10: Programa de sincronização do estro com Acetato de Melengestrol (MGA). Elaborado pelo autor. -/- 7. MANEJO DO ANESTRO -/- Uma vez que as novilhas atingem a puberdade, apresentam ciclos estrais em intervalos de 21 dias que só são interrompidos pela gestação ou por alguma patologia. O anestro patológico é raro em novilhas; no entanto, surgem casos de piometra e cistos luteinizados, que são tratados com uma dose de PGF2α. Também se observam anormalidades de desenvolvimen- to, tais como freemartinismo e hipoplasia genital, patologias que não têm tratamento; somente 8% das novilhas freemartin são férteis. O anestro funcional (as novilhas manifestam estro, mas não são detectadas) é frequen- te e está diretamente relacionado com a eficiência na detecção de estros. As novilhas com idade e peso para se integrarem no programa reprodutivo e não apresentarem sinais de estro devem ser examinadas retalmente para diagnosticar a causa do anestro. Se, durante a palpação retal, as novilhas tiverem um corpo lúteo são tratadas nesse momento com PGF2α, os animais sem corpo lúteo podem receber uma injeção de PGF2α, sete dias depois. Este programa sincroniza o estro e aumenta a probabilidade de o detectar (figura 11). -/- Figura 11: As novilhas com idade e peso para se integrarem no programa reprodutivo e não mostrarem sinais de estro devem ser verificadas via retal para diagnosticar a causa do anestro. Arquivo pessoal do autor. -/- 8. MANEJO DA NOVILHA INFÉRTIL -/- A fertilidade das vacas leiteiras diminuiu nos últimos 30 anos, enquanto a fertilidade das novilhas não se alterou; após a primeira inseminação, entre 60 e 70% das novilhas emprenham. O objetivo do programa reprodutivo é conseguir que 90% das novilhas gestem nos primeiros três serviços. Desta forma, esta proporção de animais daria à luz antes dos 25 meses de idade. É comum que 10% das novilhas se transformem em animais repetidores, ou seja, novilhas com mais de três serviços inférteis. A causa da falha na concepção de novilhas deve-se principalmente à morte embrionária precoce. Uma causa importante da falha na concepção das novilhas repetidoras são as patologias adquiridas no aparelho reprodutivo; é comum encontrar aderências ovarianas e salpingite. Provavelmente, esses problemas são consequência de alguma infecção adquirida durante a criação. Diversos tratamentos hormonais têm sido testados para resolver o problema de infertilidade em novilhas repetidoras e os resultados obtidos ainda são deficientes. Como estes tratamentos não apresentam resultados consistentes, a melhor forma de mitigar o problema de infertilidade nas novilhas é melhorando as práticas de inseminação, ou seja, o momento da inseminação, o manejo do sêmen e a técnica de inseminação empregada. Além disso, a melhor técnica para aumentar a proporção de novilhas prenhes no rebanho é aumentar a eficiência da detecção de estros. -/- 9. RESUMO -/- As novilhas devem parir aos dois anos de idade (23 a 25 meses). O peso ao parto deve ser de 550 a 580 kg. O manejo reprodutivo começa aos 14 ou 15 meses de idade, com um peso de 350 a 370 kg. As palhetas de sêmen sexado contêm de 2 a 3 milhões de espermatozoides. As doses de sêmen não sexado contêm de 20 a 30 milhões de espermatozoides. A porcentagem de concepção das novilhas inseminadas com sêmen sexado é 10 a 20% menor do que com sêmen não sexado. Com sêmen sexado se obtém entre 90 e 95% de fêmeas. A porcentagem de concepção com programas de IATF é de 20 a 35% menor que nas novilhas inseminadas no estro natural. Cerca de 90% das novilhas devem ficar prenhes nos primeiros três serviços. Devem ser produzidas novilhas para substituir as vacas que são descartadas anualmen- te (25 a 35%). Espera-se que um gado leiteiro tenha ao dispor uma população de animais de reposição, desde um dia de vida até a etapa de novilha ao parto, correspondente a, pelo menos, 70 % do total das vacas. -/- REFERÊNCIAS BIBLIOGRÁFICAS -/- AUAD, Alexander Machado et al. Manual de bovinocultura de leite. Brasília: LK Editora, 2010. BRICKELL, J. S.; MCGOWAN, M. M.; WATHES, D. C. Effect of management factors and blood metabolites during the rearing period on growth in dairy heifers on UK farms. Domestic animal endocrinology, v. 36, n. 2, p. 67-81, 2009. DE VRIES, A. et al. Exploring the impact of sexed semen on the structure of the dairy industry. Journal of Dairy Science, v. 91, n. 2, p. 847-856, 2008. Fertilidade em Vacas Leiteiras: Fisiologia e Manejo. Fisiologia do Estro e do Serviço na Reprodução Bovina. FERREIRA, A. M. Manejo reprodutivo de bovinos leiteiros: práticas corretas e incorretas, casos reais, perguntas e respostas. Edição do autor, Juiz de Fora, 2012. FERREIRA, A. de M. Reprodução da fêmea bovina: fisiologia aplicada e problemas mais comuns (causas e tratamentos). Juiz de Fora: Minas Gerais–Brasil, p. 422, 2010. GALINA, Carlos; VALENCIA, Javier. Reproducción de los animales domésticos. 2006. GONÇALVES, J. N. Manual do produtor de leite. Viçosa, MG: Aprenda Fácil, 2012. HEINRICHS, A. J. Raising dairy replacements to meet the needs of the 21st century. Journal of dairy science, v. 76, n. 10, p. 3179-3187, 1993. HOFFMAN, P. C. Optimum body size of Holstein replacement heifers. Journal of Animal Science, v. 75, n. 3, p. 836-845, 1997. NEIVA, R. S. Criação eficiente de bezerros e novilhas. Lavras: Autor, 2013. NEIVA, Rogério Santoro. Produção de bovinos leiteiros. Lavras: UFLA, 1998. PEREIRA, E. S. et al. Novilhas leiteiras. Graphiti Gráfica e Editora LTDA, Fortaleza, Ceará, 2010. CARVALHO, B. C. Manejo reprodutivo de novilhas leiteiras. In. SENAR. Curso de reprodução e genética em bovinocultura de leite. Coronel Pacheco: Senar, 2021. YOUNGQUIST, Robert S.; THRELFALL, W. R. Large animal theriogenology. 2007. (shrink)

À propos de : Catherine et Raphaël Larrère, Penser et agir avec la nature : Une enquête philosophique, Paris, La Découverte, 2015. -/- L’idée d’une nature sauvage à protéger des avancées techniques ne prend en compte ni la complexité des artefacts, ni ce qu’implique aujourd’hui la protection de la nature. En mettant l’accent sur la notion de biodiversité, C. et R. Larrère cherchent à donner un nouveau fondement à l’écologie politique.

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Apoha, a Sanskrit term meaning exclusion, was used by the late fifth- to early sixth-century Buddhist philosopher Dignā ga as a keystone in his theory of denotation. According to Dignā ga, a word denotes its meaning through the exclusion of what is other (anyā poha). This idea provoked celebration and controversy that would last through the end of Sanskritic Indian Buddhism. In the hands of Dignā ga’s successor Dharmakīrti (seventh century), who developed what became the normative version of this theory, (...) apoha leverages the fact that a causally efficacious real thing is different from everything else to describe how the interaction between living beings and their worlds produces judgements that are either shared or not in accord with the various factors contributing to the judgement’s formation. Dharmakīrti argues that there’s an infinite number of ways that a real thing could be conceptualised since each real thing is different from the infinite expanse of other real things. Acting toward a real thing requires delimiting the scope of what one ignores so that just some of the differences are left over. A living being can afford to ignore the differences between the differences that are left over in this exclusion because these differences don’t impact the specific goal based on which the living being judges an object to be efficacious or not. (shrink)

Diversity is often announced as a solution to ethical problems in artificial intelligence (AI), but what exactly is meant by diversity and how it can solve those problems is seldom spelled out. This lack of clarity is one hurdle to motivating diversity in AI. Another hurdle is that while the most common perceptions about what diversity is are too weak to do the work set out for them, stronger notions of diversity are often defended on normative grounds that fail to (...) connect to the values that are important to decision-makers in AI. However, there is a long history of research in feminist philosophy of science and a recent body of work in social epistemology that taken together provide the foundation for a notion of diversity that is both strong enough to do the work demanded of it, and can be defended on epistemic grounds that connect with the values that are important to decision-makers in AI. We clarify and defend that notion here by introducing emergent expertise as a network phenomenon wherein groups of workers with expertise of different types can gain knowledge not available to any individual alone, as long as they have ways of communicating across types of expertise. We illustrate the connected epistemic and ethical benefits of designing technology with diverse groups of workers using the examples of an infamous racist soap dispenser, and the millimeter wave scanners used in US airport security. (shrink)

The experimental turn in philosophy has reached several sub-fields including ethics, epistemology, and metaphysics. This paper is among the first to apply experimental techniques to questions in the philosophy of law. Specifically, we examine Lon Fuller's procedural natural law theory. Fuller famously claimed that legal systems necessarily observe eight principles he called "the inner morality of law." We evaluate Fuller's claim by surveying both ordinary people and legal experts about their intuitions about legal systems. We conclude that, at best, we (...) should be skeptical of Fuller's inner morality of law in light of the experimental data. (shrink)

Feminists note an association of arguing with aggression and masculinity and question the necessity of this connection. Arguing also seems to some to identify a central method of philosophical reasoning, and gendered assumptions and standards would pose problems for the discipline. Can feminine modes of reasoning provide an alternative or supplement? Can overarching epistemological standards account for the benefits of different approaches to arguing? These are some of the prospects for argumentation inside and outside of philosophy that feminists consider. -/- (...) The further concern is that the academic study of argumentation – in philosophy and other disciplines – has failed to account for the type of reasoning needed for social justice movements. What resources for addressing these concerns can be found in informal logic and interdisciplinary argumentation theory? Since part of the perceived problem derives from assuming that arguing is a contest, are more collaborative epistemological frameworks better? Can regular politeness or civility hedge against undesirable tendencies of argumentation? Can “critical thinking” pedagogy involving argument educations answer the needs of social justice? (shrink)

This paper explores how Charles Peirce’s habit-based epistemology leads him to theorise perception. I show how Peirce’s triadic semiotic analysis of perceptual judgment renders his theory of perception neither a representationalism nor a relationism /direct realism, but an interesting hybrid of the two. His view is also extremely interesting, I argue, in the way that by analysing symbols as habits it refuses the common assumption that perception is an affair best understood synchronically, as a ‘language-entry event’. Relatedly, I extend previous (...) work (Legg 2008) which argues that Peirce’s epistemology counts as a ‘hyperinferentialism’ in Robert Brandom’s terms, but this does not mean that Peirce’s theory of perception cannot accommodate unmediated contact with reality - what Peirce called ‘the outward clash’. (shrink)

Much mainstream analytic epistemology is built around a sceptical treatment of modality which descends from Hume. The roots of this scepticism are argued to lie in Hume’s (nominalist) theory of perception, which is excavated, studied and compared with the very different (realist) theory of perception developed by Peirce. It is argued that Peirce’s theory not only enables a considerably more nuanced and effective epistemology, it also (unlike Hume’s theory) does justice to what happens when we appreciate a proof in mathematics.

I defend the thesis that friendship can constitutively require epistemic irrationality against a recent, forceful challenge, raised by proponents of moral and pragmatic encroachment. Defenders of the “encroachment strategy” argue that exemplary friends who are especially slow to believe that their friends have acted wrongly are simply sensitive to the high prudential or moral costs of falsely believing in their friends’ guilt. Drawing on psychological work on epistemic motivation (and in particular on the notion of “need for closure”), I propose (...) a different picture of what friendship requires in the doxastic realm. I argue that contrary to what the encroachment strategy suggests, exemplary friends’ belief formation ought not be guided by a concern with accuracy or error avoidance, but instead by a need to avoid a “specific closure” – namely, a need to avoid concluding in their friends’ guilt. I propose that exemplary friendship often generates a defeasible, doxastic obligation to exemplify such a need, despite its inherent corrupting effects on exemplary friends’ epistemic faculties. (shrink)

This correlational study investigated the relationship between preservice teachers’ math self-concept, self-efficacy, and attitude with their math achievement. Participants were chosen using stratified random sampling from BEEd and BSEd mathematics majors (n = 117). From the findings, preservice teachers had moderate to high math self-concept, self-efficacy, and attitude. These variables were statistically correlated with each other and with math achievement. The inclusion of training programs for developing the preservice teachers’ math self-concept, self-efficacy, and attitude, as well as designing curricula that (...) engage and encourage them to do mathematics and problem-solving, must be considered among teacher education institutions. (shrink)

This paper argues that an addressee's failure to recognize a speaker's authority can constitutes another form of silencing.

Ecological Psychology and Enactivism both challenge representationist cognitive science, but the two approaches have only begun to engage in dialogue. Further conceptual clarification is required in which differences are as important as common ground. This paper enters the dialogue by focusing on important differences. After a brief account of the parallel histories of Ecological Psychology and Enactivism, we cover incompatibility between them regarding their theories of sensation and perception. First, we show how and why in ecological theory perception is, crucially, (...) not based on sensation. We elucidate this idea by examining the biological roots of work in the two fields, concentrating on Gibson and Varela and Maturana. We expound an ecological critique of any sensation-based approach to perception by detailing two topics: classic retinal image theories and perception in single-celled organisms. The second main point emphasizes the importance of the idea of organism-environment mutuality and its difference from structural coupling of sensations and motor behavior. We point out how ecological - phenomenological methods of inquiry grow out of mutualism and compare Gibson’s idea of visual kinesthesis to Merleau-Ponty’s idea of the lived body. Third, we conclude that Ecological Psychology and varieties of Enactivism are laying down different paths to pursue related goals. Thus, convergence of Ecological Psychology and Enactivism is not possible given their conflicting assumptions, but cross-fertilization is possible and desirable. (shrink)

(Added April 2023: This draft is superseded by Briggs, R.A., & George, B.R. (2023). 'What Even Is Gender?'. Routledge. DOI 10.4324/9781003053330, and in particular by the first three chapters thereof. While this much earlier draft remains available for archival purposes, you are encouraged to read and cite the 2023 book and to use its terminology.) -/- This paper presents a new taxonomy of sex/gender concepts based on the idea of starting with a few basic components of the sex/gender system, and (...) exhausting the possible types of simple associations and identities based on these. The resulting system is significantly more fine-grained than most competitors, and helps to clarify a number of points of confusion and conceptual tension in academic and activist conversations about feminism, transgender politics, and the social analysis of gender. (shrink)

Discussions of psychiatric nosology focus on a few popular examples of disorders, and on the validity of diagnostic criteria. Looking at Anorexia Nervosa, an example rarely mentioned in this literature, reveals a new problem: the DSM has a strict taxonomic structure, which assumes that disorders can only be located on one branch. This taxonomic assumption fails to fit the domain of psychopathology, resulting in obfuscation of cross-category connections. Poor outcomes for treatment of Anorexia may be due to it being pigeonholed (...) as an Eating Disorder, when a disturbance of body perception may be a more central symptom than food restriction. This paper explores the possibility of restructuring the DSM taxonomy to allow for a pluralist classification of disorders. This change could improve treatment and research without requiring any changes to diagnostic criteria. (shrink)

Homology is a natural kind concept, but one that has been notoriously elusive to pin down. There has been sustained debate over the nature of correspondence and the units of comparison. But this continued debate over its meaning has focused on defining homology rather than on its use in practice. The aim of this chapter is to concentrate on the practices of homologizing. I define “homologizing” to be a concept-in-use. Practices of homologizing are kinds of rule following, the satisfaction of (...) which demarcates a category—that of being a homologue. Identifying, explaining, discovering, and understanding are exchanges that connect practice to concept through the performance of a rule by practitioners. These practices are constitutive of natural kinding activities. If homologizing is a kind of kinding, consideration of these practices of discovery, tracking, and identification not only clarifies the meaning, use, and progression of the concept of homology, but provides further understanding of the processes and progression of natural kinds and kinding practices in general. (shrink)

The account of natural kinds as stable property clusters is premised on the possibility of separating the epistemic value of natural kinds from their underlying metaphysics. On that account, the co-instantiation of any sub-cluster of the properties associated with a given natural kind raises the probability of the co-instantiation of the rest, and this clustering of property instantiation is invariant under all relevant counterfactual perturbations. We argue that it is not possible to evaluate the stability of a cluster of properties (...) without taking stock of the metaphysical picture used to account for that stability. Thus, even on the stable property cluster account, the epistemic value of natural kinds remains partly grounded in their metaphysical status. (shrink)

A commonly raised criticism against celebrity culture is that it celebrates people who become famous without any connection to their skills, talents or achievements. A culture in which people become famous simply for being famous is criticized for being shallow and inauthentic. In this paper we offer a defence of celebrity by arguing against this criticism. We begin by outlining what we call the Talent Argument: celebrity is a negative cultural phenomenon because it creates and sustains fame without any connection (...) to the accomplishments that arise from an expression of talent or skill. By appealing to the metaphysics of talent and skill, we argue against the Talent Argument and propose that being a celebrity requires the skills that are necessary to acquire and maintain one’s status as a celebrity. A celebrity is more likely to be talented and successful in their expression of these skills, and even celebrities who are ‘famous for being famous’ will often display talents and skills that give rise to their fame. This means that those who critique celebrity culture should not do so by appealing to the Talent Argument. We show how our account of celebrity, talent and skill works to reject both the strong version of the Talent Argument, as well as a weaker and more plausible version of the argument we call the Valuable Talents argument. We conclude by noting that our analysis has demonstrated the need to explore more closely the kinds of skills that are necessary to cultivate celebrity status. This allows for a more nuanced understanding of what a celebrity is, and the values that are attached to celebrity culture. (shrink)

In this paper, we argue that to properly understand our commitment to a principle of free speech, we must pay attention to what should count as speech for the purposes of such a principle. We defend the view that ‘speech’ here should be a technical term, with something other than its ordinary sense. We then offer a partial characterization of this technical sense. We contrast our view with some influential views about free speech , and show that our view has (...) distinct advantages. Finally, we consider racist hate speech. Here, we argue that if certain theorists are right about what some racist hate speech does, then such speech should fall outside the scope of the free speech principle, and so, should be as regulable as any non-speech action. (shrink)

“Proof of concept” is a phrase frequently used in descriptions of research sought in program announcements, in experimental studies, and in the marketing of new technologies. It is often coupled with either a short definition or none at all, its meaning assumed to be fully understood. This is problematic. As a phrase with potential implications for research and technology, its assumed meaning requires some analysis to avoid it becoming a descriptive category that refers to all things scientifically exciting. I provide (...) a short analysis of proof of concept research and offer an example of it within synthetic biology. I suggest that not only are there activities that circumscribe new epistemological categories but there are also associated normative ethical categories or principles linked to the research. I examine these and provide an outline for an alternative ethical account to describe these activities that I refer to as “extended agency ethics”. This view is used to explain how the type of research described as proof of concept also provides an attendant proof of principle that is the result of decision-making that extends across practitioners, their tools, techniques, and the problem solving activities of other research groups. (shrink)

Despite the enormity of the financial losses flowing from the 2008 financial crisis and the outrageousness of the conduct that led up to it, almost no individual involved has been prosecuted for criminal conduct, much less actually gone to prison. What this chapter argues is that the failure to punish those in management for their role in this misconduct stems from a misunderstanding of the need to prove that they personally knew of this wrongdoing and harbored an intent to defraud. (...) But not only would negligence be a sufficient legal and moral basis for imposing terms of imprisonment in these cases, mere causal responsibility would also be enough, for causal responsibility has embed in it all we need to find those causally responsible morally responsible too, and once some basis for moral responsibility is established, the imposition of terms of imprisonment is both legally permitted and morally just. (shrink)

Discussions over whether these natural kinds exist, what is the nature of their existence, and whether natural kinds are themselves natural kinds aim to not only characterize the kinds of things that exist in the world, but also what can knowledge of these categories provide. Although philosophically critical, much of the past discussions of natural kinds have often answered these questions in a way that is unresponsive to, or has actively avoided, discussions of the empirical use of natural kinds and (...) what I dub “activities of natural kinding” and “natural kinding practices”. The natural kinds of a particular discipline are those entities, events, mechanisms, processes, relationships, and concepts that delimit investigation within it—but we might reasonably ask: How are these natural kinds discovered?, How are they made?, Are they revisable?, and Where do they come from? A turn to natural kinding practices reveals a new set of questions open for investigation: How do natural kinds explain through practice?, What are natural kinding practices and classifications and why should we care?, What is the nature of natural kinds viewed as a set of activities?, and How do practice approaches to natural kinds shape and reconfigure scientific disciplines? Natural kinds have traditionally been discussed in terms of how they classify the contents of the world. The metaphysical project has been one which identifies essences, laws, sameness relations, fundamental properties, and clusters of family resemblances and how these map out the ontological space of the world. But actually how this is done has been less important in the discussion than the resultant categories that are produced. I aim to rectify these omissions and suggest a new metaphysical project investigating kinds in practice. (shrink)

John Wilkins and Malte Ebach respond to the dismissal of classification as something we need not concern ourselves with because it is, as Ernest Rutherford suggested, mere ‘‘stamp collecting.’’ They contend that classification is neither derivative of explanation or of hypothesis-making but is necessarily prior and prerequisite to it. Classification comes first and causal explanations are dependent upon it. As such it is an important (but neglected) area of philosophical study. Wilkins and Ebach reject Norwood Russell Hanson’s thesis that classification (...) relies on observation that is theory-laden and deny the need for aetiological assumptions and historical reconstruction to justify its arrangement. What they offer instead is a significant (albeit controversial) contribution to the philosophical literature on classification, a pre-theoretic natural classification based on the observation of patterns in data of ready-made phenomena. Their notion of ready-made phenomena rests on a conception of tacit knowledge or know-how. This is evident in their distinction between strong Theory-dependence and na ̈ıve theory-dependence. Their small t-theory-dependence permits patterns of observation that facilitate know-how but does not rely on a domain-specific explanatory theory of their aetiology. Wilkins and Ebach suggest classification differs from theory building in that it is passive (whereas theory building is active). Classification is possible just because it does not require the sieve of theory to capture classes that are ‘‘handed to you by your cognitive dispositions and the data that you observe’’ (p. 18). Finding regularities sans-theory is just something we do and can do without any prior theory about the underlying causes or origins of the resultant regularities. Luke Howard’s classification of clouds serves as an exemplar of a passive, theory-free classification system and the periodic table and the DSM help to illustrate this type of non-aetiological patterning. A recurrent theme is the nature of naturalness. For Wilkins and Ebach, the conception of naturalness is not one that is based on the generation or discovery of natural kind categories popular in both the traditional metaphysics of Mill and Wittgenstein as well as updated notions within philosophy of biology such as Boyd’s Homeostatic Property Cluster kinds. Instead, Wilkins and Ebach define the naturalness of classification as the falling into hierarchical patterns, aligning the search for natural arrangement with the aim of systematics, and as something that is grounded in a cognitive task or activity. However, they leave the question of realism v. antirealism open. ‘‘In natural classification...we must have real relations no matter how we might interpret ‘real’’’ (p. 70). There is tension with regard to their ontological commitments as they vacillate between constructive, operationalist, and realist approaches. Wilkins and Ebach initially define real as that which is causal and important (pp. 70–71), and later as that which ‘‘depends in no way upon a mind or observer’’ (p. 122). This makes their claim that there was ‘‘no real theory involved [in the pre-Darwinian classifications of Jussieu and Adanson]’’ (p. 64) difficult to interpret. Cont’d……. (shrink)

This entry explores Charles Peirce's account of truth in terms of the end or ‘limit’ of inquiry. This account is distinct from – and arguably more objectivist than – views of truth found in other pragmatists such as James and Rorty. The roots of the account in mathematical concepts is explored, and it is defended from objections that it is (i) incoherent, (ii) in its faith in convergence, too realist and (iii) in its ‘internal realism’, not realist enough.

This paper addresses some apparent philosophical tensions between realism and enactivism by means of Charles Peirce’s pragmatism. Enactivism’s Mind-Life Continuity thesis has been taken to commit it to some form of anti-realist ‘world-construction’ which has been considered controversial. Accordingly, a new realist enactivism is proposed by Zahidi (_Phenomenology and the Cognitive Sciences,_ _13_(3), 461–475, 2014 ), drawing on Ian Hacking’s ‘entity realism’, which places subjects in worlds comprised of the things that they can successfully manipulate. We review this attempt, and (...) argue that whilst Zahidi rightly urges enactivists towards ‘internal realism’, he cannot sustain a non-negotiable aspect of realism that is crucial for scientific progress – the claim that multiple subjects inhabit _the same world_. We explore Peirce’s pragmatism as an alternative solution, foregrounding his distinction between existence and reality, and his inquiry-based account of cognition. These theoretical innovations, we argue, fruitfully generalize Zahidi’s _manipulation-based_ enactivist realism to a richer, _inquiry-based_ enactivist realism. We explore how this realism’s pan-species monism about truth encourages and supports the investigation of non-human animal cognition, and conclude by considering some implications of our discussion for long-standing realism debates within pragmatism. (shrink)

"Although I think it is far to say that in what natives of this part of the world call 'downunder,' Peirce is still a minority interest, appreciation of his work appears to be growing slowly but surely...".

Pursuing difficult long-term goals typically involves encountering substantial evidence of possible future failure. If decisions to pursue such goals are serious only if one believes that one will act as one has decided, then some of our lives’ most important decisions seem to require belief against the evidence. This is the puzzle of difficult action, to which I offer a solution. I argue that serious decisions to φ do not have to give rise to a belief that one will φ, (...) but can instead be accompanied by a hope to φ. Hope can motivate and rationalize the various actions that we associate with serious commitment. It can also account for the existence of special pressures to adopt an agential stance toward one’s future. Because hope can be cognitively rational when belief is not, there is no problematic tension between the ideal of epistemic rationality and the phenomenon of difficult action. (shrink)

Although Kant had a high regard for Jesus as a moral teacher, interpreters typically assume that his philosophy disallows belief in Jesus as God. Those who regard Kant as a moral reductionist are especially likely to offer a negative construal of the densely-argued subsection of his 1793 Religion that relates directly to this issue. The recent “affirmative” trend in Kant-scholarship provides the basis for an alternative reading. First, theologians must regard Jesus as human so that belief in Jesus can empower (...) believers to become good. Second, theologians may refer to Jesus as divine by identifying his disposition as exemplifying the “archetype of perfect humanity.” Third, Judeo-Christian history poses an empirical problem that theologians can solve by interpreting Jesus’s divinity according to the schematism of analogy. While this does not constitute a robust (identifiably Christian) doctrine of Jesus’s divinity, it does provide clear guidelines for formulating such a tenet of historical faith. (shrink)

We often form intentions to resist anticipated future temptations. But when confronted with the temptations our resolutions were designed to withstand, we tend to revise our previous evaluative judgments and conclude that we should now succumb—only to then revert to our initial evaluations, once temptation has subsided. Some evaluative judgments made under the sway of temptation are mistaken. But not all of them are. When the belief that one should now succumb is a proper response to relevant considerations that have (...) newly emerged, can acting in line with one’s previous intention nonetheless be practically rational? To answer this question, I draw on recent debates on the nature of higher-order evidence and on what rationally responding to such evidence involves. I propose that agents facing temptation often have evidence of “deliberative unreliability”, which they ought to heed even when it is “misleading” (that is, even when their evaluative judgments are in fact proper responses to the relevant considerations then available). Because evidence of deliberative unreliability can “dispossess” agents of normative reasons for evaluative judgments and actions that they would otherwise have, being continent despite judging that one should now succumb can often be more rational than giving in. (shrink)

A review of the life and work of the Australian philosopher Huw Price.

This paper assesses the state of research ethics in low- and middle-income countries and the achievements of the Fogarty International Center's bioethics training program since 2000. The vision of FIC for the next decade of research ethics education is encapsulated in four proposed goals: (1) Ensure sufficient expertise in ethics review by having someone with long-term training on every high-workload REC; (2) Develop LMIC capacity to conduct original research on critical ethical issues by supporting doctoral and postdoctoral training and career (...) paths for research ethicists; (3) Make research training and review at LMIC institutions sustainable by identifying additional funding mechanisms and models; (4) Make institutional research systems more ethical and efficient through context-specific training integrated into all levels of scientific training. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

A conspicuous feature of contemporary modelling practices is the use of the same mathematical forms and modelling methods across different scientific domains. This model transfer raises many philosophical questions concerning, for example, the exact object of transfer, the relationship between the model and the target domain, the specific challenges such transfer confronts, and the ways in which model transfer relates to scientific progress. While the interest in studying model transfer has increased among philosophers of science in recent years, the phenomenon (...) has not yet received its due attention. The literature is scattered and much of it has addressed questions around the factors that might explain model transfer, such as whether the different target phenomena to which a model is applied eventually prove to be structurally and dynamically similar, or whether they have to share more fundamental ontological features that explain the interdisciplinary success of distinct models. This chapter surveys the existing literature on model transfer with the main goal of highlighting the main findings of existing discussions and pointing out open issues whose discussion would improve our understanding of this highly relevant phenomenon in science. (shrink)

In economics, thought experiments are frequently justified by the difficulty of conducting controlled experiments. They serve several functions, such as establishing causal facts, isolating tendencies, and allowing inferences from models to reality. In this paper, I argue that thought experiments served a further function in economics: facilitating the quantitative definition and measurement of the theoretical concept of utility, thereby bridging the gap between theory and statistical data. I support my argument by a case study, the “hypothetical experiments” of the Norwegian (...) economist Ragnar Frisch (1895-1973). Frisch aimed to eliminate introspection and a subjective concept of utility from economic reasoning. At the same time, he sought behavioral foundations for economic theory that enabled quantitative reasoning. By using thought experiments to justify his set of choice axioms and facilitating the operationalization of utility, Frisch circumvented the problem of observing utility via actual experiments without eliminating the concept of utility from economic theory altogether. As such, these experiments helped Frisch to empirically support the theory’s most important results, such as the laws of demand and supply, without the input of new empirical findings. I suggest that Frisch’s experiments fulfill the main characteristics of thought experiments. (shrink)

Ethnobotanical research provides ample justification for comparing diverse biological nomenclatures and exploring ways that retain alternative naming practices. However, how (and whether) comparison of nomenclatures is possible remains a subject of discussion. The comparison of diverse nomenclatural practices introduces a suite of epistemic and ontological difficulties and considerations. Different nomenclatures may depend on whether the communities using them rely on formalized naming conventions; cultural or spiritual valuations; or worldviews. Because of this, some argue that the different naming practices may not (...) be comparable if the ontological commitments employed differ. Comparisons between different nomenclatures cannot assume that either the naming practices or the object to which these names are intended to apply identifies some universally agreed upon object of interest. Investigating this suite of philosophical problems, I explore the role grey nomenclatures play in classification. ‘Grey nomenclatures’ are defined as those that employ names that are either intentionally or accidentally non-Linnaean. The classification of the lichen thallus (a symbiont) has been classified outside the Linnaean system by botanists relying on the International Code of Nomenclature for algae, fungi, and plants (ICN). But, I argue, the use of grey names is not isolated and does not occur exclusively within institutionalized naming practices. I suggest, ‘grey names’ also aptly describe nomenclatures employed by indigenous communities such as the Samí of Northern Finmark, the Sherpa of Nepal, and the Okanagan First Nations. I pay particular attention to how naming practices are employed in these communities; what ontological commitments they hold; for what purposes are these names used; and what anchors the community’s nomenclatural practices. Exploring the history of lichen naming and early ethnolichenological research, I then investigate the stakes that must be considered for any attempt to preserve, retain, integrate, or compare the knowledge contained in both academically formalized grey names and indigenous nomenclatures in a way that preserves their source-specific informational content. (shrink)

The premise of biological modularity is an ontological claim that appears to come out of practice. We understand that the biological world is modular because we can manipulate different parts of organisms in ways that would only work if there were discrete parts that were interchangeable. This is the foundation of the BioBrick assembly method widely used in synthetic biology. It is one of a number of methods that allows practitioners to construct and reconstruct biological pathways and devices using DNA (...) libraries of standardized parts with known functions. In this paper, we investigate how the practice of synthetic biology reconfigures biological understanding of the key concepts of modularity and evolvability. We illustrate how this practice approach takes engineering knowledge and uses it to try to understand biological organization by showing how the construction of functional parts and processes can be used in synthetic experimental evolution. We introduce a new approach within synthetic biology that uses the premise of a parts-based ontology together with that of organismal self-organization to optimize orthogonal metabolic pathways in E. coli. We then use this and other examples to help characterize semisynthetic categories of modularity, parthood, and evolvability within the discipline. (shrink)

We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices. If properly developed and extended, we believe the VSO (...) will find applications for the EMR, clinical informatics, and medical device communities. (shrink)

Charles Peirce's diagrammatic logic — the Existential Graphs — is presented as a tool for illuminating how we know necessity, in answer to Benacerraf's famous challenge that most ‘semantics for mathematics’ do not ‘fit an acceptable epistemology’. It is suggested that necessary reasoning is in essence a recognition that a certain structure has the particular structure that it has. This means that, contra Hume and his contemporary heirs, necessity is observable. One just needs to pay attention, not merely to individual (...) things but to how those things are related in larger structures, certain aspects of which relations force certain other aspects to be a certain way. (shrink)

Mainstream philosophy has seen a recent flowering in discussions of intellectualism which revisits Gilbert Ryle’s famous distinction between ‘knowing how’ and ‘knowing that’, and challenges his argument that the former cannot be reduced to the latter. These debates so far appear not to have engaged with pragmatist philosophy in any substantial way, which is curious as the relation between theory and practice is one of pragmatism’s main themes. Accordingly, this paper examines the contemporary debate in the light of Charles Peirce’s (...) habit-based epistemology. We argue both that knowing-that can be understood as a particularly sophisticated form of knowing-how, and that all bodily competencies—if sufficiently deliberately developed—can be analysed as instantiating propositional structure broadly conceived. In this way, intellectualism and anti-intellectualism are seen to be not opposed, and both true, although Peirce’s original naturalistic account of propositional structure does lead him to reject what we shall call ‘linguistic intellectualism’. (shrink)

In many diagrams one seems to perceive necessity – one sees not only that something is so, but that it must be so. That conflicts with a certain empiricism largely taken for granted in contemporary philosophy, which believes perception is not capable of such feats. The reason for this belief is often thought well-summarized in Hume's maxim: ‘there are no necessary connections between distinct existences’. It is also thought that even if there were such necessities, perception is too passive or (...) localized a faculty to register them. We defend the perception of necessity against such Humeanism, drawing on examples from mathematics. (shrink)

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)

We undeniably live in an information age—as, indeed, did those who lived before us. After all, as the cultural historian Robert Darnton pointed out: ‘every age was an age of information, each in its own way’ (Darnton 2000: 1). Darnton was referring to the news media, but his insight surely also applies to the sciences. The practices of acquiring, storing, labeling, organizing, retrieving, mobilizing, and integrating data about the natural world has always been an enabling aspect of scientific work. Natural (...) history and its descendant discipline of biological taxonomy are prime examples of sciences dedicated to creating and managing systems of ordering data. In some sense, the idea of biological taxonomy as an information science is commonplace. Perhaps it is because of its self-evidence that the information science perspective on taxonomy has not been a major theme in the history and philosophy of science. The botanist Vernon Heywood once pointed out that historians of biology, in their ‘preoccupation with the development of the sciences of botany and zoology… [have] diverted attention from the role of taxonomy as an information science’ (Heywood 1985: 11). More specifically, he argued that historians had failed to appreciate how principles and practices that can be traced to Linnaeus constituted ‘a change in the nature of taxonomy from a local or limited folk communication system and later a codified folk taxonomy to a formal system of information science [that] marked a watershed in the history of biology’ (ibid.). A similar observation could be made about twentieth-century philosophy of biology, which mostly skipped over practical and epistemic questions about information management in taxonomy. The taxonomic themes that featured in the emerging philosophy of biology literature in the second half of the twentieth century were predominantly metaphysical in orientation. This is illustrated by what has become known as the ‘essentialism story’: an account about the essentialist nature of pre- Darwinian taxonomy that used to be accepted by many historians and philosophers, and which stimulated efforts to document and interpret shifts in the metaphysical understanding of species and (natural) classification (Richards 2010; Winsor 2003; Wilkins 2009). Although contemporary debates in the philosophy of taxonomy have moved on, much discussion continues to focus on conceptual and metaphysical issues surrounding the nature of species and the principles of classification. Discussions centring on whether species are individuals, classes, or kinds have sprung up as predictably as perennials. Raucous debates have arisen even with the aim of accommodating the diversity of views: is monism, pluralism, or eliminativism about the species category the best position to take? In addition to these, our disciplines continue to interrogate what is the nature of these different approaches to classification: are they representational or inferential roles of different approaches to classification (evolutionary taxonomy, phenetics, phylogenetic systematics)? While there is still much to learn from these discussions—in which we both actively participate—our aim with this topical collection has been to seek different entrypoints and address underexposed themes in the history and philosophy of taxonomy. We believe that approaching taxonomy as an information science prompts new questions and can open up new philosophical vistas worth exploring. A twenty-first century information science turn in the history and philosophy of taxonomy is already underway. In scientific practice and in daily life it is hard to escape the imaginaries of Big Data and the constant threats of being ‘flooded with data’. In the life sciences, these developments are often associated with the socalled bioinformatics crisis that can hopefully be contained by a new, interdisciplinary breed of bioinformaticians. These new concepts, narratives, and developments surrounding the centrality of data and information systems in the biological and biomedical sciences have raised important philosophical questions about their challenges and implications. But historical perspectives are just as necessary to judge what makes our information age different from those that preceded us. Indeed, as the British zoologist Charles Godfray has often pointed out, the piles of data that are being generated in contemporary systematic biology have led to a second bioinformatics crisis, the first being the one that confronted Linnaeus in the mid-18th century (Godfray 2007). Although our aim is to clear a path for new discussions of taxonomy from an information science-informed point of view, we continue where others in the history, philosophy, and sociology of science have already trod. We believe that an appreciation of biological taxonomy as an information science raises many questions about the philosophical, theoretical, material, and practical aspects of the use and revision of biological nomenclatures in different local and global communities of scientists and citizen scientists. In particular, conceiving of taxonomy as an information science directs attention to the temporalities of managing an accumulating data about classified entities that are themselves subject to revision, to the means by which revision is accomplished, and to the semantic, material, and collaborative contexts that mediate the execution of revisions. (shrink)

Enactivism has influentially argued that the traditional intellectualist ‘act-content’ model of intentionality is insufficient both phenomenologically and naturalistically, and minds are built from world-involving bodily habits – thus, knowledge should be regarded as more of a skilled performance than an informational encoding. Radical enactivists have assumed that this insight must entail non-representationalism concerning at least basic minds. But what if it could be shown that representation is itself a form of skilled performance? I sketch the outline of such an account (...) from the perspective of Peirce’s pragmatist semiotics, which theorises signs as habits of associating specific cues with appropriate acts and schemas of ensuing experience. Within this framework, I argue, a naturalistic account of propositional structure can be constructed which transcends the symbolic – and in some instances even the linguistic – sphere, and offers new insights regarding the Information Processing Challenge, and the Hard Problem of Content. (shrink)

Although there is a growing recognition that older adults and those with extensive comorbid conditions undergo cancer screening too frequently, there is little information about patients’ perceptions regarding cessation of cancer screening. Information on older adults’ views of screening cessation would be helpful both for clinicians and for those designing interventions to reduce overscreening.