plausibility of evidence to solve the religious conflicts

Big genomics and clinical data analytics strategies for precision cancer prognosis. Best Practices for Eradicating Religious Discrimination in the In E. N. Zalta (Ed. eCollection 2022. eCollection 2021. Raphael, B. J., Dobson, J. R., Oesper, L., & Vandin, F. (2014). Allen, J. F. (2001). Once a new resistance trait and gene emerges, it spreads rapidly among microbial communities. Worrall, J. Kaye, F. J. Pacific Philosophical Quarterly, 62(1), 1729. The problem of unconceived objections. Religious Conflict . Religious literacy is one of the "most urgent issues that anyone serious about social justice can undertake." An RPL fellowship gave Greg Khalil the space to critically think about his work. We conducted a scoping search using terms related to biological plausibility or mechanism to identify key references. PDF Conflict Prevention, Resolution and Reconstruction - United Nations Rethinking knowledge. On the classical concept of probability as ratio between favorable and possible cases, a conclusion obtained by (ISC) has zero probability when the number of possible cases is infinite. Bruno de Finetti) hold that initial or prior degrees of belief are largely a question of personal choice. Stevens (2013,p. 69): the computer becomes the crucial tool: efficiency is a product of bioinformatic statistical and data management techniques. The process of systematic review and its application in agri-food public-health. On the possible interpretations of probabilities, see Gillies (2000). Evaluating sources of information and claims they find has become more difficult in the post-truth era. This gene flow goes both ways. Moreover, people patients, visitors, and healthcare personnel -- move in and out of healthcare settings64. The American Mathematical Monthly, 48(7), 450465. Journal of Biosciences, 40(5), 955968. Identifying driver mutations from sequencing data of heterogeneous tumors in the era of personalized genome sequencing. LR provided appropriate guidance on data collection and interpretation according to public health informationist standards and requirements. We selected the adverse outcome pathway approach based on our interest in the application of these methods for supporting the evidence derived from observational studies. 6566): Bioinformatics can be understood [] as a kind of neo-Baconian science in which hypothesis-driven research is giving way to hypothesis-free experiments and data collection., Cf. Ertaylan G, Le Cornet C, van Roekel EH, Jung AY, Bours MJL, Damms-Machado A, et al. Frequentist vs. Bayesian clinical trials. R24 HD042854/HD/NICHD NIH HHS/United States, UG1 EY020522/EY/NEI NIH HHS/United States, NCI CPTC Antibody Characterization Program. I note that relative plausibility can be understood as probabilism under certain constraints that characterize a typical trial. a non-cogent argument, then Mizrahis argument against Stanford cannot even take off the ground, since it rests on a self-defeating argument. 64. Adverse outcome pathways: A conceptual framework to support ecotoxicology research and risk assessment. London: Routledge. Ellen Kovner Silbergeld, Johns Hopkins University, Bloomberg School of Public Health, Department of Environmental Health and Engineering, ude.uhj@2reblise. Are the somatic mutation and tissue organization field theories of carcinogenesis incompatible? Foreword; General principles and observations; 1.1 Credible or trustworthy evidence 1.2 Relevance of country conditions evidence 1.3 Benefit of the doubt 1.4 Notice to the claimant 1.5 Witnesses and examination of documents 1.6 Interlocutory decisions on credibility 1.7 Proper evidentiary basis for findings on credibility With expert consultation, we accessed papers describing general and detailed methods for organizing structural models representing biological plausibility through mechanisms that link exposures to health outcomes. These cassettes may be highly complex. \(c = 2\)), if we have \(k = 3\), then \({\gamma } = 8\). PubMedGoogle Scholar. The population genetics of antibiotic resistance: Integrating molecular mechanisms and treatment contexts, Evolutionary consequences of antibiotic use for the resistome, mobilome, and microbial pangenome, Managing waste from confined animal feeding operations in the United States: The need for sanitary reform. Galbraith D, Levy PE, Sitch S, Huntingford C, Cox P, Williams M, et al. Although his approach is distant from the view advocated here, there is nevertheless some similarity between the two. Religious conflicts on the rise in Africa - DW - 09/23/2017 Thus, if somatic mutations have been measured in m samples, the number of patients in which gene g is mutated is described by a binomial random variable B(m,Pg) with parameters m and Pg. Gillies, D. (2000). We utilized scoping reviews and expert consultation to identify two papers with general discussions of methods related to biological plausibility 11,12. Ankley GT, Bennett RS, Erickson RJ, Hoff DJ, Hornung MW, Johnson RD, et al. Indeed, if one maintains MA, one is clearly advocating for a philosophical position, i.e. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. New evidence from an . Prev Vet Med. Cellucci (2017a,p. 142): Methods can be divided into algorithmic and heuristic. Keywords: 3,4, and5. Life out of sequence. In E. N. Zalta (Ed. National Science Review, 1(2), 293314. This hypothesis has been empirically confirmed, see Soto and Sonnenschein (2011), Baker (2015a, b) and Bizzarri and Cucina (2016). Many criticisms can be raised to Mizrahis approach, but we cannot analyze them all here for reason of space. Silvia Bozza Abstract A comparison is made between probability and relative plausibility as approaches for the interpretation of evidence. Cabello FC, Godfrey HP, Tomova A, Ivanova L, Dlz H, Millanao A, et al. Studies in the logic of explanatory power. Until the end of the seventeenth century, all swans observed were white. Nature Genetics, 21(1 Suppl. Conclusions: Increases in antimicrobial resistance genes and class 1 integrons have been reported in animals fed antimicrobials and have been documented in studies of soils treated with animal wastes or veterinary antimicrobials47,54,55. Later experiments demonstrated mechanisms by which donor cells initiate plasmid mediated gene transfer and how antimicrobials stimulate intercellular signaling between susceptible and resistant bacterial strains to initiate events including gene transcription that facilitate horizontal gene transfer from chromosomal DNA within the donor cell and responses such as swarming within the susceptible recipient organisms3234. Becker RA, Dellarco V, Seed J, Kronenberg JM, Meek B, Foreman J, et al. Edwin Jaynes) hold that prior degrees of belief are fully determined by the evidence.. So, MA is self-defeating. When individuals have questions about scientific issues, they often search the Internet. ), Handbook of the philosophy of science. doi:10.1002/wsbm.1364. The evidence has been summarized in recent systematic reviews5,6,70, which reported associations observed between agricultural use of antimicrobials for all purposes and increased risks of AMR exposure of human populations. Momentum grows to make personalized medicine more precise. 201215). Lindley, D. V. (2000). Evidence-based medicine. This may also involve sublethal concentrations of antimicrobials45. Logic in relation to mathematics, evolution, and method. Aarestrup FM, Seyfarth AM, Emborg HD, Pedersen K, Hendriksen RS, Bager F. Effect of Abolishment of the Use of Antimicrobial Agents for Growth Promotion on Occurence of Antimicrobial Resistance in Fecal Entercocci from Food Animals in Denmark, Antimicrob Agents Chemother Agents Chemother. Why theres no cause to randomize. Empirically based subjectivists (e.g. One Reservoir: Redefining the Community Origins of Antimicrobial-resistant Infections, The impact of antibiotic use on resistance development and persistence, Horizontal Gene Transfer among Bacteria and Its Role in Biological Evolution. Proceedings of the National Academy of Sciences, 113(50), 1433014335. Resistance dissemination includes clonal expansion of resistant organisms as well as gene flow among organisms through horizontal gene transfer involving mobile genetic elements, conjugation, and other mechanisms. The Problem of Evil - Stanford Encyclopedia of Philosophy Stoner L, Barone Gibbs B, Meyer ML, Fryer S, Credeur D, Paterson C, Stone K, Hanson ED, Kowalsky RJ, Horiuchi M, Mack CP, Dave G. Front Cardiovasc Med. Lawrence, M. S., Stojanov, P., Polak, P., Kryukov, G. V., Cibulskis, K., Sivachenko, A., et al. Continental-scale pollution of estuaries with antibiotic resistance genes, Learning from agriculture: Understanding low-dose antimicrobials as drivers of resistome expansion. Longo, G. (2017). Biological plausibility in environmental health systematic reviews: a GRADE concept paper. This is the so-called problem of the external validity, see Worrall (2010). Leist M, Ghallab A, Graepel R, Marchan R, Hassan R, Bennekou SH, et al. Promise and Plausibility: Health Technology Adoption Decisions With Metascience, 18(3), 370379. In this case (i.e. Accessibility Indeed, according to Mizrahi (2014), it is possible to construct an argument, which is analogous to Stanfords argument against scientific realism, and so it is not easily refutable by those who accept Stanfords argument, according to which we should not believe our current philosophical theories, because history of philosophy shows that philosophers routinely failed to conceive of serious objections to their theories. We developed and populated a similar structure for this review based on a conceptual structure that represents a sequence of mechanisms involved in the emergence and dissemination of antimicrobial resistance1821To this model we added the routes that connect these events in agriculture to human exposure. Genomics 3.0: Big-data in precision medicine. We selected this latter model because of its applicability to observational studies and the substantial record of use in toxicology and ecology to support evidence based decisions related to risk assessment4,67,68. Generally, naturalness and simplicity are necessary for the success of such a theory. 205234). Moreover, ESBL resistance genes are frequently bundled with other resistance determinants in transposable gene cassettes51. Indeed, TOFT does not deny the existence of mutations in the genome of cancer cells. Causation and causal inference in epidemiology, USDA Chief Scientist Statement on WHO Guidelines on Antibiotics | USDA, WHO guidelines on use of medically important antimicrobials in food-producing animals, Systematic reviews to evaluate causation: an overview of methods and application. The logic of scientific discovery. ), The Stanford encyclopedia of philosophy. Chicago, La Salle: Open Court. Such a correlation does not convey any information on the correlated variables, nor on some other relevant aspect of the world, so it is useless, irrelevant, or worse, it may be lead us astray, if we do not correctly identify it as spurious. Carbapenemase-Producing Enterobacteriaceae Recovered from the Environment of a Swine Farrow-to-Finish Operation in the United States. An adverse outcome pathway as used in toxicology to define events in a causal sequence connecting exposures to outcomes at the population level 15. Dellsn, F. (2016). ES conducted literature searches and JD produced the original figures in the paper. Heuristic reasoning and the theory of probability. Antimicrobial resistance; Biological plausibility; Food-borne infections; Mechanisms; Systematic reviews. Since the isolation of the first of these drugs in 1948, there are now five generations of cephalosporins. An adverse outcome pathway as used in toxicology to define events in a causal sequence connecting exposures to outcomes at the population level . Do unborn hypotheses have rights? Evidence, probability, and relative plausibility: A response to Aitken A salmonella strain resistant to 13 antimicrobials was isolated from a child living on a farm who presented with ceftriazone resistance; all but one of the genes encoding multidrug resistance were on the same plasmid42. Human health risk assessment (HHRA) for environmental development and transfer of antibiotic resistance. Baral SD, Wirtz A, Sifakis F, Johns B, Walker D, Beyrer C. The Highest Attainable Standard of Evidence (HASTE) for HIV/AIDS Interventions: Toward a Public Health Approach to Defining Evidence [Internet]. Inclusion in an NLM database does not imply endorsement of, or agreement with, http://plato.stanford.edu/archives/spr2014/entries/scientific-discovery/. Indeed, Mizrahis argument against Stanford conveys in its turn a philosophical position, which implies a commitment to a given philosophical theory. A data-driven history of bioinformatics. Cham: Springer. As a service to our customers we are providing this early version of the manuscript. The environmental reservoirs of resistance may constitute the largest resources of these functions and are of specific concern in the context of agricultural uses through the release of untreated animal wastes containing resistance genes and antimicrobials that augment selection pressures within environmental microbiomes39. Date Written: January 12, 2023 Abstract In a recent article, Colin Aitken, Franco Taroni, and Silvia Bozza defend a probabilistic account of juridical proof and critique our "relative plausibility" account on both positive and normative grounds. Accessibility This discussion is divided into eight sections. We draw on a theoretical model of plausibility judgments and current theory and research in source evaluation to suggest that the post-truth era elevates the need for critical evaluation of online . As a library, NLM provides access to scientific literature. (2015). Weyl, H. (1949). Before WHO also provided support to EKS for participating in the guidelines development group. This review started as a background paper commissioned by the World Health Organization as part of the development of evidence supporting guidelines for reducing use of antimicrobials in food animal production. Volume 7. Synthese. doi:10.1007/s11229-016-1132-y. Jennifer Dailey, Johns Hopkins University, Whiting School of Engineering, Department of Materials Science, ude.uhj@4yeliadj. : 1814]. Crossref. The relationships within the global microbiome and its pangenome including the resistome and the mobilome that support horizontal gene transfer in response to antimicrobial pressure including those genes encoding resistance to clinically important antimicrobials. Vaux, D. L. (2011b). Isolated from Comemercial Poultry Production Environments. For a demonstration that no infinite sequence passes all tests of randomness, so that true randomness does not exist, see Calude (2002). The tissue organization field theory of cancer: A testable replacement for the somatic mutation theory. Illustration depicting complex relationships among and between multiple sources of AMR. Carcinogenesis explained within the context of a theory of organisms. This is of particular risk when crops are grown with animal wastes (as in organic production) or with irrigation by surface water sources contaminated by run off from land disposal of animal62,63. Promise of personalized omics to precision medicine. Young I, Waddell L, Sanchez J, Wilhelm B, McEwen SA, Raji A. Prev Vet Med. Inference to the Best Explanation, Relative Plausibility, and Adverse outcome pathways: opportunities, limitations and open questions. (2017). During the first years of experimentation by Fleming and others, resistance was recognized as a consequence of exposure. Bethesda, MD 20894, Web Policies Cf. C14.S1 Introduction C14.P1 In many areas of life, from hard science to managing one's everyday affairs, explanatory considerations help to guide inference. ), 3337. Evolutionary theory explained the emergence of antimicrobial resistance as a process of random genetic mutations that conferred biological resistance to drugs27. We populated our framework of adverse outcomes pathway analysis, using the literature on mechanisms of antimicrobial resistance and assigned mechanistic evidence to a sequential pathway linking antimicrobial exposure of microbial communities to human exposure to drug resistant pathogens. It is important to note that we are not denying that external factors may relevantly affect theoretical choices, we are just stressing that our perspective is able to account for relevant non-arbitrary epistemic factors that may lead to theoretical divergence or theory change in a rational way. National Library of Medicine Skurnik D, Clermont O, Guillard T, Launay A, Danilchanka O, Pons S, et al. Ph.D. thesis, University of Pittsburgh, School of Arts and Sciences, Department of History and Philosophy of Science, Pittsburgh. This is a preview of subscription content, access via Hypothesis (B) is a sufficient condition for solving the problem. Identifying driver mutations in sequenced cancer genomes: Computational approaches to enable precision medicine. Proceedings of the Biennial Meeting of the Philosophy of Science Association, 2, 325332. Wagner Group Russia's war in Ukraine Politics Religious conflicts on the rise in Africa 09/23/2017 A study by a German academic says religious conflicts in sub-Saharan Africa have been on the. These low dose and extended exposures to single or multiple antimicrobials condition networks of gene flow within the microbiome such that HGT is facilitated and role of mobile genetic elements in mediating resistance gene flow is enhanced within the gut microbiomes in animal hosts as well as in the environment46. The concept of plausibility is especially analyzed, in order to make clear the difference between that concept and the concept of probability (Sects. As noted in a recent review of cancer risks, information on biological plausibility is particularly important as a complement to associations observed in epidemiological studies3. Epub 2022 Mar 16. Classical, quantum and biological randomness as relative unpredictability. Current assessment methods based on GRADE are not appropriate because of the inherent limitations of public health studies. Teira, D. (2011). JLD was supported by the National Science Foundation through a Graduate Research Fellowship and the Center for a Livable Future through a CLF-Lerner Fellowship. 14 Conflict Resolution Strategies for the Workplace Google Scholar. The Algerian civil war stands out as one of most violent conflicts of the post-Cold War era. 2022 Jul 27;13:962791. doi: 10.3389/fphys.2022.962791. In F. Gifford (Ed. Lectures on logic. Rigo-Lemini, M., & Martnez-Navarro, B. They are exacerbated by animal stress and crowding during growth stages and transport60,61. SMT and TOFT integrable after all: A reply to Bizzarri and Cucina. In addition, multiple mobile genetic elements have also been measured in soils and sediments54. This first application requires validation by application to other systematic reviews where the criterion of biological plausibility is of value. Whaley P, Piggott T, Morgan RL, Hoffmann S, Tsaioun K, Schwingshackl L, Ansari MT, Thayer KA, Schnemann HJ. Now, it is MA which is a self-defeating argument. These multigene cassettes can include metal resistance genes such that co-selection and cross resistance can) also be driven by metals such as copper, cadmium, nickel. Some studies of ESBL+ genes in E coli isolates from animals, including carbapenemase, suggest that this may represent contamination of the agricultural environment by human wastes66. Science-based medicine, as envisioned by the creators of this blog, includes plausibility when . Cf. The two default states cannot be operational at the same time (Bizzarri and Cucina 2016,p. 232). Some authors prefer to speak of precision medicine rather than personalized medicine. Challenges of big data analysis. 8600 Rockville Pike The panproteome includes the gene products of the microbiome, including the parvome which includes clinically important antimicrobial molecules produced by humans22. An algorithmic method is a method that guarantees to always produce a correct solution to a problem. Wiley Interdisciplinary Reviews. Johns Hopkins University, Bloomberg School of Public Health, Department of Environmental Health and Engineering. SMT or TOFT? Worrall (2007a,pp. Ceftriaxone-Resistant Salmonella Infection Acquired by a Child from Cattle. The conclusions of systematic reviews of randomised controlled trials of homeopathy vary from 'comparable to conventional medicine' to 'no evidence of effects beyond placebo'. Cohen SP, McMurry LM, Hooper DC, Wolfson JS, Levy SB. But, this contrasts with the fact that, on the classical concept of probability, a conclusion obtained by (IMC) has non-zero probability when the number of possible cases is not infinite, and such is the case of the hypothesis that all swans are white (Cellucci 2013,p. 335). We argue that taking into account plausibility-based considerations can lead to clarify some epistemological shortcomings that afflict both these perspectives. The appraisal of theories: Kuhn meets Bayes. Assessment of the risk to public health due to use of antimicrobials in pigs an example of pleuromutilins in Denmark. Thus, de novo approaches do not really differ from other kinds of approaches developed to identify driver mutations, and cannot be said to be independent from previous knowledge. Epub 2006 May 24. In F. Gifford (Ed. To undertake this research, we utilized the example of the observed associations between antimicrobial use in food animals and increased risks of human exposures to antimicrobial resistant pathogens of zoonotic origin. Bird, A. Overhage J, Bains M, Brazas MD, Hancock REW. (2010). For this reason, there are no real barriers between the presence of AMR in agriculture and the entrance of these same AMR pathogens into healthcare settings. Patlewicz G, Simon TW, Rowlands JC, Budinsky RA, Becker RA. London: Routledge. Villeneuve DL, Crump D, Garcia-Reyero N, Hecker M, Hutchinson TH, LaLone CA, et al. Evaluating sources of scientific evidence and claims in the post-truth

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