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)

Gene–environment covariance is the phenomenon whereby genetic differences bias variation in developmental environment, and is particularly problematic for assigning genetic and environmental causation in a heritability analysis. The interpretation of these cases has differed amongst biologists and philosophers, leading some to reject the utility of heritability estimates altogether. This paper examines the factors that influence causal reasoning when G–E covariance is present, leading to interpretive disagreement between scholars. It argues that the causal intuitions elicited are influenced by concepts of agency (...) and blame-worthiness, and are intimately tied with the conceptual understanding of the phenotype under investigation. By considering a phenotype-specific approach, I provide an account as to why causal ascriptions can differ depending on the interpreter. Phenotypes like intelligence, which have been the primary focus of this debate, are more likely to spark disagreement for the interpretation of G–E covariance cases because the concept and ideas about its ‘normal development’ relatively ill-defined and are a subject of debate. I contend that philosophical disagreement about causal attributions in G–E covariance cases are in essence disagreements regarding how a phenotype should be defined and understood. This moves the debate from one of an ontological flavour concerning objective causal claims, to one concerning the conceptual, normative and semantic dependencies. (shrink)

Causation has multiple distinct meanings in genetics. One reason for this is meaning slippage between two concepts of the gene: Mendelian and molecular. Another reason is that a variety of genetic methods address different kinds of causal relationships. Some genetic studies address causes of traits in individuals, which can only be assessed when single genes follow predictable inheritance patterns that reliably cause a trait. A second sense concerns the causes of trait differences within a population. Whereas some single genes can (...) be said to cause population-level differences, most often these claims concern the effects of many genes. Polygenic traits can be understood using heritability estimates, which estimate the relative influences of genetic and environmental differences to trait differences within a population. Attempts to understand the molecular mechanisms underlying polygenic traits have been developed, although causal inference based on these results remains controversial. Genetic variation has also recently been leveraged as a randomizing factor to identify environmental causes of trait differences. This technique—Mendelian randomization—offers some solutions to traditional epidemiological challenges, although it is limited to the study of environments with known genetic influences. (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)

When explaining the causes of human behavior, genes are often given a special status. They are thought to relate to an intrinsic human 'essence', and essentialist biases have been shown to skew the way in which causation is assessed. Causal reasoning in general is subject to other pre-existing biases, including beliefs about normativity and morality. In this synthesis we show how factors which influence causal reasoning can be mapped to a framework of genetic essentialism, which reveals both the shared and (...) unique factors underpinning biases in causal reasoning and genetic essentialism. This comparison identifies overlooked areas of research which could provide fruitful investigation, such as whether normative assessments of behaviors influence the way that genetic causes are ascribed or endorsed. We also outline the importance of distinguishing reasoning processes regarding genetic causal influences on one's self versus others, as different cognitive processes and biases are likely to be at play. (shrink)

Purpose Genetic research, via the mainstream media, presents the public with novel, profound findings almost on a daily basis. However, it is not clear how much laypeople understand these presentations and how they integrate such new findings into their knowledge base. Genetic knowledge (GK), existing causal beliefs, and genetic essentialist tendencies (GET) have been implicated in such processes; the current study assesses the relationships between these elements and how brief presentations of media releases of scientific findings about genetics are consumed (...) and affect the readers. -/- Methods An Australian national survey of GK, GET, and existing causal beliefs about health phenomena (heart disease and obesity) was conducted. Participants were also exposed to news headlines that offered genetic and non-genetic partial explanations of the same health phenomena and reported their evaluations of these headlines, as well as the effects of the headlines on their personal understanding of the health phenomena. -/- Results GK was negatively-associated with GET. Whereas GK did not directly predict the evaluation and effects of the genetic headlines, GET did. GK predicted the effects of the headlines indirectly via GET and via GET and existing causal beliefs. -/- Conclusion GET seem to predict unwarranted effects of exposure to news headlines about genetic science, whereas GK seems to indirectly mitigate the same unwarranted effects. (shrink)

A high heritability estimate usually corresponds to a situation in which trait variation is largely caused by genetic variation. However, in some cases of gene-environment covariance, causal intuitions about the sources of trait difference can vary, leading experts to disagree as to how the heritability estimate should be interpreted. We argue that the source of contention for these cases is an inconsistency in the interpretation of the concepts ‘genotype’, ‘phenotype’, and ‘environment’. We propose an interpretation of these terms under which (...) trait variance initially caused by genetic variance is subsumed into a heritability for all cases of gene-environment covariance. (shrink)

We are less optimistic than Madole & Harden that family-based genome-wide association studies (GWASs) will lead to significant second-generation causal knowledge. Despite bearing some similarities, family-based GWASs and randomised controlled trials (RCTs) are not identical. Most RCTs assess a relatively homogenous causal stimulus as a treatment, whereas GWASs assess highly heterogeneous causal stimuli. Thus, GWAS results will not translate so easily into second-generation causal knowledge.

Effective altruism is a growing humanitarian movement with a track record of success in evaluating the effectiveness of charitable spending across a wide range of projects. We suggest ways in which the foundations of this movement can be applied to the complex world of conservation.

The concept of animal personality is based on consistent individual differences in behaviour, yet little is known about the factors responsible for such variation. Theory based on sex-specific selection predicts sexual dimorphism in personality-related traits and, in some cases, differences in trait variances between the sexes. In this study, we examined the sources of individual variation for boldness behaviour in guppies (Poecilia reticulata). We first demonstrated heightened boldness expression in males relative to females across feral wild types, artificially selected domestic (...) ‘designer’ guppies, and putative hybrids of the two. Boldness and body size covaried at the strain level but were not associated among individuals within strains. We also found high and repeatable behavioural differences among individuals (0.40 > intraclass r > 0.60) in all sex/strain groups except hybrid strain females. However, there was no evidence for the heightened inter-individual male variance anticipated for personality traits subject to certain forms of directional sex-specific selection. Domestic fish were boldest overall, and indicated the largest sex difference, which is consistent with genetic linkage between boldness and male ornamental colouration. Consistently high intrinsic variation in boldness behaviour, which extends to inbred domesticated fish, may in part underpin the invasive potential of this species. (shrink)

The aim of this virtual special issue is to bring together philosophical and historical perspectives to address long-standing issues in the interpretation, utility, and impacts of quantitative genetics methods and findings. Methodological approaches and the underlying scientific understanding of genetics and heredity have transformed since the field's inception. These advances have brought with them new philosophical issues regarding the interpretation and understanding of quantitative genetic results. The contributions in this issue demonstrate that there is still work to be done integrating (...) old and new methodological and conceptual frameworks. In some cases, new results are interpreted using assumptions based on old concepts and methodologies that need to be explicitly recognised and updated. In other cases, new philosophical tools can be employed to synthesise historical quantitative genetics work with modern methodologies and findings. This introductory article surveys three general themes that have dominated philosophical discussion of quantitative genetics throughout history: (1) how methodologies have changed and transformed our knowledge and interpretations; (2) whether or not quantitative genetics can offer explanations relating to causation and prediction; and (3) the importance of defining the phenotypes under study. We situate the contributions in this virtual special issue within a historical framework addressing these three themes. (shrink)

Much microbiota-gut-brain research focuses on the causal role of microbiomes as a whole, rather than their component parts: microbes. Hooks et al. find these whole-community explanations inadequate; however, they do not provide suggestions for better explanations. By appealing to proportionality – a criterion that can be used to develop more appropriate causal explanations – more accurate causal claims can be made.

RésuméCet article aborde la querelle comme un élément de la stratégie d’un philosophe vis-à-vis de la postérité. On pourrait évidemment penser à des querelleurs invétérés comme Pascal, Voltaire ou Rousseau, mais il sera question ici du cas plus complexe de Diderot et du dernier ouvrage publié de son vivant, l’Essai sur les règnes de Claude et de Néron et sur les moeurs et les écrits de Sénèque pour servir à l’introduction de la lecture de ce philosophe. L’article démontre que celui-ci (...) constitue un cas de « texte-querelle », c’est-à-dire un texte qui met en scène la querelle menée à son propre sujet et qui ainsi la fait redémarrer; il analyse la posture qu’adopte le philosophe-querelleur, surtout dans l’énoncé paradoxal « ne nous engageons point dans les querelles », dont il examine les qualités performatives. (shrink)

This volume is based on the 2004 series of the Oxford Amnesty Lectures, one of the world's leading name lecture series. In it major figures in philosophy, political science, law, psychoanalysis, sociology, and literature address the challenges that displacement, asylum, and migration pose to our notions of human rights.

This commentary focuses on the authors’ treatment of Koch’s postulates. It argues in favour of a modification of Koch’s postulates and their analysis in terms of necessary and sufficient conditions. This leads to a criticism of the authors’ treatment of the C. difficile case, and to query the need for the criteria of specificity and proportionality.

This commentary focuses on the authors’ treatment of Koch’s postulates. It argues in favour of a modification of Koch’s postulates and their analysis in terms of necessary and sufficient conditions. This leads to a criticism of the authors’ treatment of the C. difficile case, and to query the need for the criteria of specificity and proportionality.

In the life of any species, extinction is the final evolutionary process. It is a common one at present, as the world is entering a major extinction crisis. The pattern of extinction and threat is very non-random, with some taxa being more vulnerable than others. Explaining why some taxa are affected and some escape is a major goal of conservation biology. More ambitiously, a predictive model could, in principle, be built by integrating comparable studies of past and present extinctions. We (...) review progress towards both explanatory and predictive frameworks, comparing correlates of extinction in different groups at different times. Progress towards explanatory models for the current crisis is promising, at least in some well-studied taxa, but the development of a truly predictive model is hampered by the formidable difficulties of integrating studies of present and past extinctions. BioEssays 22:1123–1133, 2000. © 2000 John Wiley & Sons, Inc. (shrink)

Debates over the causes and consequences of the “Axial Age” – and its relevance for understanding and explaining “modernity” – continue to rage within and across a wide variety of academic disciplines, including anthropology, sociology, archaeology, history, social theory, and cognitive science. We present a computational model that synthesizes three leading theories about the emergence of axial civilizations. Although these theories are often treated as competitors, our computational model shows how their most important conceptual insights and empirically based causal claims (...) can be integrated within a single computational architecture. The plausibility of the latter is supported by the results of our simulation experiments, which were able to simulate the emergence and growth of an axial civilization. The model shows how the relevant theories can be rendered consistent, while challenging the claims of any one to comprehensiveness. (shrink)

Growth mindset is an important aspect of children’s socioemotional development and is subject to change due to environmental influence. Orchestral music education may function as a fertile context in which to promote growth mindset; however, this education is not widely available to children facing economic hardship. This study examined whether participation in a program of orchestral music education was associated with higher levels of overall growth mindset and greater change in levels of musical growth mindset among children placed at risk (...) by poverty. After at least 2 years of orchestral participation, students reported significantly higher levels of overall growth mindset than their peers; participating students also reported statistically significant increases in musical growth mindset regardless of the number of years that they were enrolled in orchestral music education. These findings have implications for future research into specific pedagogical practices that may promote growth mindset in the context of orchestral music education and more generally for future studies of the extra-musical benefits of high-quality music education. (shrink)

Attention Restoration Theory proposes that exposure to natural environments helps to restore attention. For sustained attention—the ongoing application of focus to a task, the effect appears to be modest, and the underlying mechanisms of attention restoration remain unclear. Exposure to nature may improve attention performance through many means: modulation of alertness and one’s connection to nature were investigated here, in two separate studies. In both studies, participants performed the Sustained Attention to Response Task before and immediately after viewing a meadow, (...) ocean, or urban image for 40 s, and then completed the Perceived Restorativeness Scale. In Study 1, an eye-tracker recorded the participants’ tonic pupil diameter during the SARTs, providing a measure of alertness. In Study 2, the effects of connectedness to nature on SART performance and perceived restoration were studied. In both studies, the image viewed was not associated with participants’ sustained attention performance; both nature images were perceived as equally restorative, and more restorative than the urban image. The image viewed was not associated with changes in alertness. Connectedness to nature was not associated with sustained attention performance, but it did moderate the relation between viewing the natural images and perceived restorativeness; participants reporting a higher connection to nature also reported feeling more restored after viewing the nature, but not the urban, images. Dissociation was found between the physiological and behavioral measures and the perceived restorativeness of the images. The results suggest that restoration associated with nature exposure is not associated with modulation of alertness but is associated with connectedness with nature. (shrink)

The primary purpose of Institutional Review Boards (IRBs) is to protect the rights and welfare of human research participants. Evaluation and measurement of how IRBs satisfy this purpose and other important goals are open questions that demand empirical research. Research on IRBs, and the Human Research Protection Programs (HRPPs) of which they are often a part, is necessary to inform evidence-based practices, policies, and approaches to quality improvement in human research protections. However, to date, HRPP and IRB engagement in empirical (...) research about their own activities and performance has been limited. To promote engagement of HRPPs and IRBs in self-reflective research on HRPP and IRB quality and effectiveness, barriers to their participation need to be addressed. These include: extensive workloads, limited information technology systems, and few universally accepted or consistently measured metrics for HRPP/irb quality and effectiveness. Additionally, institutional leaders may have concerns about confidentiality. Professional norms around the value of participating in this type of research are lacking. Lastly, obtaining external funding for research on IRBs and HRPPs is challenging. As a group of HRPP professionals and researchers actively involved in a research consortium focused on IRB quality and effectiveness, we identify potential levers for supporting and encouraging HRPP and IRB engagement in research on quality and effectiveness. We maintain that this research should be informed by the core principles of patient- and community-engaged research, in which members and key stakeholders of the community to be studied are included as key informants and members of the research team. This ensures that relevant questions are asked and that data are interpreted to produce meaningful recommendations. As such, we offer several ways to increase the participation of HRPP professionals in research as participants, as data sharers, and as investigators. (shrink)

People’s comfort with and acceptability of artificial intelligence (AI) instantiations is a topic that has received little systematic study. This is surprising given the topic’s relevance to the design, deployment and even regulation of AI systems. To help fill in our knowledge base, we conducted mixed-methods analysis based on a survey of a representative sample of the US population (_N_ = 2254). Results show that there are two distinct social dimensions to comfort with AI: as a peer and as a (...) superior. For both dimensions, general and technological efficacy traits—locus of control, communication apprehension, robot phobia, and perceived technology competence—are strongly associated with acceptance of AI in various roles. Female and older respondents also were less comfortable with the idea of AI agents in various roles. A qualitative analysis of comments collected from respondents complemented our statistical approach. We conclude by exploring the implications of our research for AI acceptability in society. (shrink)

Boyer suggests that laws cannot account for ownership intuitions, but there may be situations when intuitions hew to laws almost perfectly. Laws granting governments taxation powers provide an interesting case study. We report data here suggesting that people's intuitions track law very closely, and are unaffected by manipulating a P() tag input. We propose two hypotheses to explain this finding.

To prepare for potential human infection challenge studies involving SARS-CoV-2, we convened a multidisciplinary working group to address ethical questions regarding whether and how much SAR...

Increasingly, scholarship on moral injury is expanding to include non‐military personnel, and considers a violation of bodily integrity—for example, of civilian women who are targeted for sexual violence in warfare—as a particularly egregious harm. Moral injury discourse also extends beyond the individual to the social context in which moral injury arises, its relational effects, and its utterly devastating impact on personhood, an impact frequently characterized as a “soul wound.” The intersection of genocidal rape—both as an individual and a group harm—with (...) religion, as facilitating moral injury and restorative “soul repair,” exemplifies these trends. Although moral injury research rarely addresses the detrimental influences of religion or references the “soul” with precision, the discourse of moral injury does provide an opportunity for exploring the relationship between personhood and agency from the perspectives of those who inflict and are subjected to harm. (shrink)

The peer commentaries on our Target Article, “Promoting Ethical Payment in Human Infection Challenge Studies,” offer a number of insights that will help advance the co...

This paper makes a plea for more reflexive attempts to develop and anchor the emerging concept of responsible research and innovation. RRI has recently emerged as a buzzword in science policy, becoming a focus of concerted experimentation in many academic circles. Its performative capacity means that it is able to mobilise resources and spaces despite no common understanding of what it is or should be ‘made of’. In order to support reflection and practice amongst those who are interested in and (...) using the concept, this paper unpacks understandings of RRI across a multi-disciplinary body of peer-reviewed literature. Our analysis focuses on three key dimensions of RRI that remain particularly opaque. A total of 48 publications were selected through a systematic literature search and their content was qualitatively analysed. Across the literature, RRI is portrayed as a concept that embeds numerous features of existing approaches to govern and assess emerging technologies. Our analysis suggests that its greatest potential may be in its ability to unify and provide political momentum to a wide range of long-articulated ethical and policy issues. At the same time, RRI’s dynamism and resulting complexity may represent its greatest challenge. Further clarification on what RRI has to offer in practice—beyond what has been offered to date—is still needed, as well as more explicit engagement with research and institutional cultures of responsibility. Such work may help to realise the high political expectations that are attached to nascent RRI. (shrink)

The revised Common Rule includes a new option for the conduct of secondary research with identifiable data and biospecimens: regulatory broad consent. Motivated by concerns regarding autonomy and trust in the research enterprise, regulators had initially proposed broad consent in a manner that would have rendered it the exclusive approach to secondary research with all biospecimens, regardless of identifiability. Based on public comments from both researchers and patients concerned that this approach would hinder important medical advances, however, regulators decided to (...) largely preserve the status quo approach to secondary research with biospecimens and data. The Final Rule therefore allows such research to proceed without specific informed consent in a number of circumstances, but it also offers regulatory broad consent as a new, optional pathway for secondary research with identifiable data and biospecimens. In this article, we describe the parameters of regulatory broad consent under the new rule, explain why researchers and research institutions are unlikely to utilize it, outline recommendations for regulatory broad consent issued by the Secretary's Advisory Committee on Human Research Protections, and sketch an empirical research agenda for the sorts of questions about regulatory broad consent that remain to be answered as the research community embarks on Final Rule implementation. (shrink)