Experiments are commonly thought to have epistemic privilege over simulations. Two ideas underpin this belief: first, experiments generate greater inferential power than simulations, and second, simulations cannot surprise us the way experiments can. In this article I argue that neither of these claims is true of experiments versus simulations in general. We should give up the common practice of resting in-principle judgments about the epistemic value of cases of scientific inquiry on whether we classify those cases as experiments or simulations, (...) per se. To the extent that either methodology puts researchers in a privileged epistemic position, this is context sensitive. (shrink)

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...) are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (shrink)

In a recent Target Article Naomi Scheinerman (2023a) has offered an important and compelling call to institutionalize popular participation for heritable genome engineering through the inclusion of...

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...) are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (shrink)

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...) are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (shrink)

In order to address the influence of unethical leader behaviors in the form of abusive supervision on subordinates’ retaliatory responses, we meta-analytically examined the impact of abusive supervision on subordinate deviance, inclusive of the role of justice and power distance. Specifically, we investigated the mediating role of supervisory- and organizationally focused justice and the moderating role of power distance as one model explaining why and when abusive supervision is related to subordinate deviance toward supervisors and organizations. With 79 independent sample (...) studies, we found that abusive supervision was more strongly related to supervisory-focused justice, compared to organizationally focused justice perceptions, and both types of justice perceptions were related to target-similar deviance. Finally, our results showed that the negative implications of abusive supervision were stronger in lower power distance cultures compared to higher power distance cultures. (shrink)

Koonin argues that CRISPR-Cas systems present the best-known case in point for Lamarckian evolution because they satisfy his proposed criteria for the specific inheritance of acquired adaptive characteristics. We see two interrelated issues with Koonin’s characterization of CRISPR-Cas systems as Lamarckian. First, at times he appears to confuse an account of the CRISPR-Cas system with an account of the mechanism it employs. We argue there is no evidence for the CRISPR-Cas system being “Lamarckian” in any sense. Second, it is unclear (...) whether the mechanism is more “Lamarckian” than many other forms of genetic change already well-characterized in Darwinian terms. We present three conceptually distinct senses in which the mechanism of IAC may be considered Lamarckian and argue that only the strongest sense of goal-directed IAC would be difficult to accommodate in a Darwinian account. As the CRISPR-Cas mechanism does not qualify as “Lamarckian” in this strong sense, we argue there is no conceptual value in calling it “Lamarckian”. Finally, we suggest that CRISPR-Cas systems do hold the potential for genuinely non-Darwinian, directed evolution in a way that Koonin did not discuss, involving their potential use as a human gene-editing tool. (shrink)

In this paper, I discuss the recent discovery of alleged arsenic bacteria in Mono Lake, California, and the ensuing debate in the scientific community about the validity and significance of these results. By situating this case in the broader context of projects that search for anomalous life forms, I examine the methodology and upshots of challenging biochemical constraints on living things. I distinguish between a narrower and a broader sense in which we might challenge or change our knowledge of life (...) as the result of such a project, and discuss two different kinds of projects that differ in their potential to overhaul our knowledge of life. I argue that the arsenic bacteria case, while potentially illuminating, is the kind of constraint-challenging project that could not—in spite of what was said when it was presented to the public—change our knowledge of life in the deeper sense. (shrink)

Francesco Redi’s seventeenth-century experiments on insect generation are regarded as a key contribution to the downfall of belief in spontaneous generation. Scholars praise Redi for his experiments demonstrating that meat does not generate insects, but condemn him for his claim elsewhere that trees can generate wasps and gallflies. He has been charged with rejecting spontaneous generation only to change his mind and accept it, and in the process, with failing as a rigorous experimental philosopher. In this paper I defend Redi (...) from both of these charges. In doing so, I draw some broader lessons for our understanding of spontaneous generation. ‘Spontaneous generation’ does not refer to a single theory, but rather a landscape of possible views. I analyze Redi’s theoretical commitments and situate them within this landscape, and argue that his error in the case of insects from plants is not as problematic as previous commentators have said it is. In his research on gall insects Redi was addressing a different question from that of his experiments on insect generation—the question was not “Can insects come from nonliving matter?,” but rather, “Can insects come from living organisms which are not their parents?” In the latter case, he gave an answer which we now know to be false, but this was not due to any failure in his rigor as an experimental philosopher. (shrink)

This article seeks to answer why North—South climate negotiations have gone on for decades without producing any substantial results. To address this question, we revisit and seek to integrate insights from several disparate theories, including structuralism (new and old), world systems theory, rational choice institutionalism, and social constructivism. We argue that the lack of convergence on climate grew almost inevitably from our starkly unequal world, which has created and perpetuated highly divergent ways of thinking (worldviews and causal beliefs) and promoted (...) particularistic notions of fairness (principled beliefs). We attempt to integrate structural insights about global inequality with the micro-motives of rational choice institutionalism. The structuralist insight that ‘unchecked inequality undermines cooperation’ suggests climate negotiations must be broadened to include a range of seemingly unrelated development issues such as trade, investment, debt, and intellectual property rights agreements. We conclude by reviewing the work of some ‘norm entrepreneurs’ bringing justice issues into climate negotiations and explore how these insights might influence ‘burden sharing’ discussions in the post-Kyoto world, where development is constrained by climate change. (shrink)

Dōgen Kigen (1200–1253 ce) is one of the most revered figures in the history of Japanese culture. A Zen master regarded by the Sōtō School as its spiritual founder, Dōgen is also considered by many to be Japan's greatest philosopher. (The other major contender is kūkai, with whose philosophy Dōgen's shares a number of features.) Possessed of a prodigious and subtle intellect, and master of a strikingly poetic style, he surely ranks among the world's most formidable thinkers.

Heidegger’s two modes of thinking, calculative and meditative, were used as the thematic basis for this qualitative study of physicians from seven countries . Focus groups were conducted in each country with 69 physicians who cared for the elderly. Results suggest that physicians perceived ethical issues primarily through the lens of calculative thinking with emphasis on economic concerns. Meditative responses represented 24% of the statements and were mostly generated by Canadian physicians whose patients typically were not faced with economic barriers (...) to treatment due to Canada’s universal health care system. (shrink)

Collaboration requires agents to coordinate their behavior on the fly, sometimes cooperating to solve a single task together and other times dividing it up into sub‐tasks to work on in parallel. Underlying the human ability to collaborate is theory‐of‐mind (ToM), the ability to infer the hidden mental states that drive others to act. Here, we develop Bayesian Delegation, a decentralized multi‐agent learning mechanism with these abilities. Bayesian Delegation enables agents to rapidly infer the hidden intentions of others by inverse planning. (...) We test Bayesian Delegation in a suite of multi‐agent Markov decision processes inspired by cooking problems. On these tasks, agents with Bayesian Delegation coordinate both their high‐level plans (e.g., what sub‐task they should work on) and their low‐level actions (e.g., avoiding getting in each other's way). When matched with partners that act using the same algorithm, Bayesian Delegation outperforms alternatives. Bayesian Delegation is also a capable ad hoc collaborator and successfully coordinates with other agent types even in the absence of prior experience. Finally, in a behavioral experiment, we show that Bayesian Delegation makes inferences similar to human observers about the intent of others. Together, these results argue for the centrality of ToM for successful decentralized multi‐agent collaboration. (shrink)

The intent of ethics is to establish a set of standards that will provide a framework to modify, regulate, and possibly enhance moral behaviour. Eleven focus groups were conducted with physicians from six culturally distinct countries to explore their perception of formalized, written ethical guidelines (i.e., codes of ethics, credos, value and mission statements) that attempt to direct their ethical practice. Six themes emerged from the data: lack of awareness, no impact, marginal impact, other codes or value statements supersede, personal (...) codes or values dictate, and ethical guidelines are useful. Overall, codes were valued only when they were congruent with existing personal morality. The findings suggest the need to re-evaluate the purpose, content, and delivery of codes for them to improve their function in promoting ethical conduct. (shrink)

Several technological developments, such as self-service technologies and artificial intelligence, are disrupting the retailing industry by changing consumption and purchase habits and the overall retail experience. Although AI represents extraordinary opportunities for businesses, companies must avoid the dangers and risks associated with the adoption of such systems. Integrating perspectives from emerging research on AI, morality of machines, and norm activation, we examine how individuals morally behave toward AI agents and self-service machines. Across three studies, we demonstrate that consumers’ moral concerns (...) and behaviors differ when interacting with technologies versus humans. We show that moral intention is less likely to emerge for AI checkout and self-checkout machines compared with human checkout. In addition, moral intention decreases as people consider the machine less humanlike. We further document that the decline in morality is caused by less guilt displayed toward new technologies. The non-human nature of the interaction evokes a decreased feeling of guilt and ultimately reduces moral behavior. These findings offer insights into how technological developments influence consumer behaviors and provide guidance for businesses and retailers in understanding moral intentions related to the different types of interactions in a shopping environment. (shrink)

Microbial model systems have a long history of fruitful use in fields that include evolution and ecology. In order to develop further insight into modelling practice, we examine how the competitive exclusion and coexistence of competing species have been modelled mathematically and materially over the course of a long research history. In particular, we investigate how microbial models of these dynamics interact with mathematical or computational models of the same phenomena. Our cases illuminate the ways in which microbial systems and (...) equations work as models, and what happens when they generate inconsistent findings about shared targets. We reveal an iterative strategy of comparative modelling in different media, and suggest reasons why microbial models have a special degree of epistemic tractability in multimodel inquiry. (shrink)

In this book, leading Christian political thinkers and practitioners critique the Rawlsian concepts of “justice as fairness” and “public reason” from the perspective of Christian political theory and practice. It provides a new level of analysis from Christian perspectives, including implications for such hot topics as the culture war.

The global pandemic needs to mark a turning point for the peoples of Aotearoa New Zealand. How can we make sure that our culturally diverse nation charts an equitable and sustainable path through and beyond this new world? In a less affluent future, how can we ensure that all New Zealanders have fair access to opportunities? One challenge is to preserve the sense of common purpose so critical to protecting each other in the face of Covid-19. How can we centre (...) what we have learnt about resilience within Māori and wider Pacific communities in our reforms? How can public understanding of Covid-19 science create a platform for the future social valuing of expertise? How can we ensure that the impact of Covid-19 in New Zealand results in a more sustainable, and inclusive workforce–for instance by expanding our perceptions of the value of our workers through promoting digital inclusion? To meet these challenges, we must reimagine our existing traditions of thought, breathing new life into perennial concepts and debates. Our paper indicates some of the ways that Philosophy is central to this collective reimagining, highlighting solutions to be found across our rich philosophical traditions. (shrink)

Autophagy and YAP1‐WWTR1/TAZ signalling are tightly linked in a complex control system of forward and feedback pathways which determine different cellular outcomes in differing cell types at different time‐points after perturbations. Here we extend our previous experimental and modelling approaches to consider two possibilities. First, we have performed additional mathematical modelling to explore how the autophagy‐YAP1 crosstalk may be controlled by posttranslational modifications of components of the pathways. Second, since analogous contrasting results have also been reported for autophagy as a (...) regulator of other transduction pathways engaged in tumorigenesis (Wnt/β‐catenin, TGF‐β/Smads, NF‐kB or XIAP/cIAPs), we have considered if such discrepancies may be explicable through situations involving competing pathways and feedback loops in different cell types, analogous to the autophagy‐YAP/TAZ situation. Since distinct posttranslational modifications dominate those pathways in distinct cells, these need to be understood to enable appropriate cell type‐specific therapeutic strategies for cancers and other diseases. (shrink)

BackgroundThere is increasing need for peer reviewers as the scientific literature grows. Formal education in biostatistics and research methodology during residency training is lacking. In this pilot study, we addressed these issues by evaluating a novel method of teaching residents about biostatistics and research methodology using peer review of standardized manuscripts. We hypothesized that mentored peer review would improve resident knowledge and perception of these concepts more than non-mentored peer review, while improving review quality.MethodsA partially blinded, randomized, controlled multi-center study (...) was performed. Seventy-eight neurology residents from nine US neurology programs were randomized to receive mentoring from a local faculty member or not. Within a year, residents reviewed a baseline manuscript and four subsequent manuscripts, all with introduced errors designed to teach fundamental review concepts. In the mentored group, mentors discussed completed reviews with residents. Primary outcome measure was change in knowledge score between pre- and post-tests, measuring epidemiology and biostatistics knowledge. Secondary outcome measures included level of confidence in the use and interpretation of statistical concepts before and after intervention, and RQI score for baseline and final manuscripts.ResultsSixty-four residents (82%) completed initial review with gradual decline in completion on subsequent reviews. Change in primary outcome, the difference between pre- and post-test knowledge scores, did not differ between mentored (−8.5%) and non-mentored (−13.9%) residents (p = 0.48). Significant differences in secondary outcomes (using 5-point Likert scale, 5 = strongly agree) included mentored residents reporting enhanced understanding of research methodology (3.69 vs 2.61; p = 0.001), understanding of manuscripts (3.73 vs 2.87; p = 0.006), and application of study results to clinical practice (3.65 vs 2.78; p = 0.005) compared to non-mentored residents. There was no difference between groups in level of interest in peer review (3.00 vs 3.09; p = 0.72) or the quality of manuscript review assessed by the Review Quality Instrument (RQI) (3.25 vs 3.06; p = 0.50).ConclusionsWe used mentored peer review of standardized manuscripts to teach biostatistics and research methodology and introduce the peer review process to residents. Though knowledge level did not change, mentored residents had enhanced perception in their abilities to understand research methodology and manuscripts and apply study results to clinical practice. (shrink)