Incommensurability and theory comparison in experimental biology

Incommensurability of scientific theories, as conceived by Thomas Kuhnand Paul Feyerabend, is thought to be a major or even insurmountable obstacletothe empirical comparison of these theories. I examine this problem in light ofaconcrete case from the history of experimental biology, namely the oxidativephosphorylation controversy in biochemistry (ca. 1961-1977). After a briefhistorical exposition, I show that the two main competing theories which werethe subject of the ox-phos controversy instantiate some of the characteristicfeatures of incommensurable theories, namely translation failure,non-corresponding predictions, and different claims about what kinds ofentitiesexist in the world. By examining how the controversy was eventually resolved, Ithen show that at least this pair of incommensurable theories couldneverthelessbe empirically compared.     

Exploring Scientific Misconduct: Isolated Individuals,Impure Institutions,or an Inevitable Idiom of Modern Science?

This paper identifies three distinct narratives concerning scientific misconduct: a narrative of “individual impurity” promoted by those wishing to see science self-regulated; a narrative of “institutional impropriety” promoted by those seeking greater external control of science; and a narrative of “structural crisis” among those critiquing the entire process of research itself. The paper begins by assessing contemporary definitions and estimates of scientific misconduct. It emphasizes disagreements over such definitions and estimates as a way to tease out tension and controversy over competing visions of scientific research. It concludes by noting that each narrative suggests a different approach for resolving misconduct, and that the difference inherent in these views may help explain much of the discord concerning unethical behavior in the scientific community.     

Performing abstraction: two ways of modelling<Emphasis Type="Italic"> Arabidopsis thaliana</Emphasis>

What is the best way to analyse abstraction in scientific modelling? I propose to focus on abstracting as an epistemic activity, which is achieved in different ways and for different purposes depending on the actual circumstances of modelling and the features of the models in question. This is in contrast to a more conventional use of the term ‘abstract’ as an attribute of models, which I characterise as black-boxing the ways in which abstraction is performed and to which epistemological advantage. I exemplify my claims through a detailed reconstruction of the practices involved in creating two types of models of the flowering plant Arabidopsis thaliana, currently the best-known model organism in plant biology. This leads me to distinguish between two types of abstraction processes: the ‘material abstracting’ required in the production of Arabidopsis specimens and the ‘intellectual abstracting’ characterising the elaboration of visual models of Arabidopsis genomics. Reflecting on the differences between these types of abstracting helps to pin down the epistemic skills and research commitments used by researchers to produce each model, thus clarifying how models are handled by researchers and with which epistemological implications.     

Anthropological Knowledge and Scientific Fact

In 1967 Ward Goodenough described two performance-based measures that many of us use to judge the quality of anthropological knowledge. Do we understand events in another community as its members understand them? Can we act there in ways that people will accept as conforming to their expectations? Judged by these standards, the famous hoax that the physicist Alan Sokal published in 1996 in the non-refereed journal Social Text would pass as good anthropology (however shameless). I look at a different—yet similar—scientific controversy, one that began in 1998 at the editorial offices of the British science weekly Nature. This controversy, which I call "The Little Lizard Controversy," and in which I have played a role, may show us how scientists sometimes misunderstand one another and why anthropological knowledge about the practice of science may be crucial in nurturing interdisciplinary research "collaboratories" in the twenty-first century, [science, interdisciplinary, controversies, miscommunication, symbols]     

Role of the undergraduate student research assistant in the new millennium

In this study, we analyze the contribution of the undergraduate student who participates in the process of generating scientific data and developing a research project using Brazilian research as an example. Historically, undergraduate students have performed the critical role of research assistants in developing countries. This aspect has been underappreciated as a means of generating scientific data in Brazilian research facilities. Brazilian educational institutions are facing major age-related generational changes among the science faculty within the next 5-10 yr. A lack of adequate support for graduate students leads to a concern that undergraduates will not be interested in choosing research assistant programs and, subsequently, academic research careers. To remedy this situation it is important to focus on ways to encourage new research careers and enhance university-industry collaborations.     

Interpreting evidence: why values can matter as much as science

Despite increasing awareness of the ways in which non-epistemic values play roles in science, many scientists remain reluctant to acknowledge values at stake in their own work. Even when research clearly relates to risk assessment and establishing public policy, contexts in which the presence of values is less likely to be contentious, scientists tend to present such research as merely involving empirical questions about what the evidence is. As a result, debates over policy-related science tend to be framed as purely epistemic debates over the state of the evidence. We argue that this neglects the important ways that ethical and social values play legitimate roles in judgments about what we take to be evidence for a particular policy. Using the case of recent disputes about the relative safety of home birth, we argue that although the debate has been framed as a purely scientific one about the empirical evidence for home birth, it actually involves disagreements about underlying value assumptions. If our claims are correct, then in order to move the debate forward, scientists will need to engage in a critical discussion about the values at stake.     

The emerging structure of the Extended Evolutionary Synthesis: where does Evo-Devo fit in?

The Extended Evolutionary Synthesis (EES) debate is gaining ground in contemporary evolutionary biology. In parallel, a number of philosophical standpoints have emerged in an attempt to clarify what exactly is represented by the EES. For Massimo Pigliucci, we are in the wake of the newest instantiation of a persisting Kuhnian paradigm; in contrast, Telmo Pievani has contended that the transition to an EES could be best represented as a progressive reformation of a prior Lakatosian scientific research program, with the extension of its Neo-Darwinian core and the addition of a brand-new protective belt of assumptions and auxiliary hypotheses. Here, we argue that those philosophical vantage points are not the only ways to interpret what current proposals to ‘extend’ the Modern Synthesis-derived ‘standard evolutionary theory’ (SET) entail in terms of theoretical change in evolutionary biology. We specifically propose the image of the emergent EES as a vast network of models and interweaved representations that, instantiated in diverse practices, are connected and related in multiple ways. Under that assumption, the EES could be articulated around a paraconsistent network of evolutionary theories (including some elements of the SET), as well as models, practices and representation systems of contemporary evolutionary biology, with edges and nodes that change their position and centrality as a consequence of the co-construction and stabilization of facts and historical discussions revolving around the epistemic goals of this area of the life sciences. We then critically examine the purported structure of the EES—published by Laland and collaborators in 2015—in light of our own network-based proposal. Finally, we consider which epistemic units of Evo-Devo are present or still missing from the EES, in preparation for further analyses of the topic of explanatory integration in this conceptual framework.     

Popper,Laws, and the Exclusion of Biology from Genuine Science

The primary purpose of this paper is to argue that biologists should stop citing Karl Popper on what a genuinely scientific theory is. Various ways in which biologists cite Popper on this matter are surveyed, including the use of Popper to settle debates on methodology in phylogenetic systematics. It is then argued that the received view on Popper--namely, that a genuinely scientific theory is an empirically falsifiable one--is seriously mistaken, that Popper's real view was that genuinely scientific theories have the form of statements of laws of nature. It is then argued that biology arguably has no genuine laws of its own. In place of Popperian falsifiability, it is suggested that a cluster class epistemic values approach (which subsumes empirical falsifiability) is the best solution to the demarcation problem between genuine science and pseudo- or non-science.     

Measuring Laypeople’s Trust in Experts in a Digital Age: The Muenster Epistemic Trustworthiness Inventory (METI)

Given their lack of background knowledge, laypeople require expert help when dealing with scientific information. To decide whose help is dependable, laypeople must judge an expert’s epistemic trustworthiness in terms of competence, adherence to scientific standards, and good intentions. Online, this may be difficult due to the often limited and sometimes unreliable source information available. To measure laypeople’s evaluations of experts (encountered online), we constructed an inventory to assess epistemic trustworthiness on the dimensions expertise, integrity, and benevolence. Exploratory (n = 237) and confirmatory factor analyses (n = 345) showed that the Muenster Epistemic Trustworthiness Inventory (METI) is composed of these three factors. A subsequent experimental study (n = 137) showed that all three dimensions of the METI are sensitive to variation in source characteristics. We propose using this inventory to measure assignments of epistemic trustworthiness, that is, all judgments laypeople make when deciding whether to place epistemic trust in–and defer to–an expert in order to solve a scientific informational problem that is beyond their understanding.     

Rational Disagreements in Phylogenetics

This paper addresses the general problem of how to rationally choose an algorithm for phylogenetic inference. Specifically, the controversy between maximum likelihood (ML) and maximum parsimony (MP) perspectives is reframed within the philosophical issue of theory choice. A Kuhnian approach in which rationality is bounded and value-laden is offered and construed through the notion of a Style of Modeling. A Style is divided into four stages: collecting remnant models, constructing models of taxonomical identity, implementing modeling algorithms, and finally inferring and confirming evolutionary trees or cladograms. The identification and investigation of styles is useful for exploring sociological and epistemological issues such as individuating scientific communities and assessing the rationality of algorithm choice. Regarding the last point, this paper suggests that the values motivating ML and MP perspectives are justified but only contextually; these algorithms also have normative force because they can be therapeutic by allowing us to rationally choose among several competing trees, nonetheless this force is limited and cannot be used in order to decide the controversy tout court.     

Not null enough: pseudo-null hypotheses in community ecology and comparative psychology

We evaluate a common reasoning strategy used in community ecology and comparative psychology for selecting between competing hypotheses. This strategy labels one hypothesis as a “null” on the grounds of its simplicity and epistemically privileges it as accepted until rejected. We argue that this strategy is unjustified. The asymmetrical treatment of statistical null hypotheses is justified through the experimental and mathematical contexts in which they are used, but these contexts are missing in the case of the “pseudo-null hypotheses” found in our case studies. Moreover, statistical nulls are often not epistemically privileged in practice over their alternatives because failing to reject the null is usually a negative result about the alternative, experimental hypothesis. Scientists should eschew the appeal to pseudo-nulls. It is a rhetorical strategy that glosses over a commitment to valuing simplicity over other epistemic virtues in the name of good scientific and statistical methodology.     

Forensic culture as epistemic culture: The sociology of forensic science

This paper explores whether we can interpret the notion of ‘forensic culture’ as something akin to what Knorr-Cetina called an ‘epistemic culture’. Can we speak of a ‘forensic culture’, and, if so, how is it similar to, or different from, other epistemic cultures that exist in what is conventionally called ‘science’? This question has important policy implications given the National Academy Science’s (NAS) recent identification of ‘culture’ as one of the problems at the root of what it identified as ‘serious deficiencies’ in U.S. forensic science and ‘scientific culture’ as an antidote to those problems. Finding the NAS’s characterisation of ‘scientific culture’ overly general and naïve, this paper offers a preliminary exploration of what might be called a ‘forensic culture’. Specifically, the paper explores the way in which few of the empirical findings accumulated by sociologists of science about research science seem to apply to forensic science. Instead, forensic science seems to have developed a distinct culture for which a sociological analysis will require new explanatory tools. Faithful sociological analysis of ‘forensic culture’ will be a necessary prerequisite for the kind of culture change prescribed by external reformist bodies like the NAS.     

Graduate Students and Knowledge Exchange with Local Stakeholders: Possibilities and Preparation

Tropical biologists are exploring ways to expand their role as researchers through knowledge exchange with local stakeholders. Graduate students are well positioned for this broader role, particularly when supported by graduate programs. We ask: (1) how can graduate students effectively engage in knowledge exchange during their research; and (2) how can university programs prepare young scientists to take on this partnership role? We present a conceptual framework with three levels at which graduate students can exchange knowledge with stakeholders (information sharing, skill building, and knowledge generation) and discuss limitations of each. Examples of these strategies included disseminating preliminary research results to southern African villages, building research skills of Brazilian undergraduate students through semester‐long internships, and jointly developing and implementing a forest ecology research and training program with one community in the Amazon estuary. Students chose strategies based on stakeholders' interests, research goals, and a realistic evaluation of student capacity and skill set. As strategies became more complex, time invested, skills mobilized, and strength of relationships between students and stakeholders increased. Graduate programs can prepare students for knowledge exchange with partners by developing specialized skills training, nurturing external networks, offering funding, maximizing strengths of universities in developed and developing regions through partnership, and evaluating knowledge exchange experiences. While balancing the needs of academia with those of stakeholders is challenging, the benefits of enhancing local scientific capacity and generating more locally relevant research for improved conservation may be worth the risks associated with implementing this type of graduate training model.     

Police epistemic culture and boundary work with judicial authorities and forensic scientists: the case of transnational DNA data exchange in the EU

The exchange of forensic DNA data is seen as an increasingly important tool in criminal investigations into organised crime, control strategies and counter-terrorism measures. On the basis of a set of interviews with police professionals involved in the transnational exchange of DNA data between EU countries, this paper examines how forensic DNA evidence is given meaning within the various different ways of constructing a police epistemic culture, it is, a set of shared values concerning valid knowledge and practices normatively considered adequate and legitimate. The police epistemic culture is fuelled by multiple dynamics of boundary work, revealing how police professionals involved in international cooperation (i) define their specific core activities and competencies; (ii) construct particular understandings of valid knowledge and how it should be produced; (iii) enact the police epistemic culture in contrast to the epistemic cultures of the judicial authorities and forensic scientists.     

What's the matter with HIV-directed killer T cells?

That HIV-specific cytotoxic T-lymphocytes (CTLs) might be defective in some way has stimulated much controversy and research. We use mathematical models to explore the predictions of two competing CTL-defect theories: "defective memory" and "defective activation". We discuss whether these models are consistent with adoptive-transfer experiments in HIV-infected patients and vaccine trials in simian immunodeficiency virus (SIV)-infected monkeys. Finally, we describe experimental tests that could decide among these two theories and a competitor: CTL exhaustion.     

Gender on the Brain: A Case Study of Science Communication in the New Media Environment

Neuroscience research on sex difference is currently a controversial field, frequently accused of purveying a ‘neurosexism’ that functions to naturalise gender inequalities. However, there has been little empirical investigation of how information about neurobiological sex difference is interpreted within wider society. This paper presents a case study that tracks the journey of one high-profile study of neurobiological sex differences from its scientific publication through various layers of the public domain. A content analysis was performed to ascertain how the study was represented in five domains of communication: the original scientific article, a press release, the traditional news media, online reader comments and blog entries. Analysis suggested that scientific research on sex difference offers an opportunity to rehearse abiding cultural understandings of gender. In both scientific and popular contexts, traditional gender stereotypes were projected onto the novel scientific information, which was harnessed to demonstrate the factual truth and normative legitimacy of these beliefs. Though strains of misogyny were evident within the readers’ comments, most discussion of the study took pains to portray the sexes’ unique abilities as equal and ‘complementary’. However, this content often resembled a form of benevolent sexism, in which praise of women’s social-emotional skills compensated for their relegation from more esteemed trait-domains, such as rationality and productivity. The paper suggests that embedding these stereotype patterns in neuroscience may intensify their rhetorical potency by lending them the epistemic authority of science. It argues that the neuroscience of sex difference does not merely reflect, but can actively shape the gender norms of contemporary society.     

A survey of the scientific data and training methods utilized by collegiate strength and conditioning coaches

The purpose of this study was to determine the extent to which scientific research influences college strength and conditioning coaching practices and to determine the training methods utilized. A total of 321 surveys were mailed to Division I strength and conditioning coaches, and the response rate was 42.7% (137 of 321 surveys). Results indicate that all subjects held a baccalaureate degree, the majority in a human performance-related field, and that 75% were Certified Strength and Conditioning Specialist (CSCS) certified. The respondents' most widely utilized professional resources were the Strength and Conditioning Journal (94%) and other collegiate coaches and programs (93%). Forty-seven percent of respondents indicated that other collegiate coaches and their programs were the most important sources of knowledge outside of formal education. The majority indicated that they used a periodization protocol (93%) utilizing multiple sets (97%), plyometrics (90%), explosive movements (88%), and Olympic lifts (85%). Respondents tend to rely on sources of information that may not be defined as scientific, as evidenced by the low priority given to peer-reviewed literature. Respondents also tend to employ the methods they utilized as athletes. Reliance on these sources may not take advantage of advances made through scientific research in exercise physiology, biomechanics, and more specifically the area of strength and conditioning.     

Factors facilitating research: a survey of zoo and aquarium professionals

The purpose of this survey was to assess the background, training, and perceptions of professionals conducting and coordinating research at North American zoos and aquariums accredited by the Association of Zoos and Aquariums (AZA) and to identify the factors they considered critical to successful scientific programs. We analyzed responses to a 57‐item questionnaire from 231 professionals at AZA zoos and aquariums. The majority of those surveyed conducted behavioral research, conducted research only in a captive setting, held curatorial positions, had their salaries supported by their institutions' operating budget, and considered themselves part of a successful scientific program. About 30% of those we surveyed possessed a doctoral research degree in comparison to 55% possessing lesser level degrees—19% with master's, 34% with bachelor's, and 2% with other degrees. Support from the chief executive officer and personnel dedicated to conducting scientific programs were judged as the two most important factors contributing to the successful scientific programs. The information provided in this report may be used to develop and improve both established and newly initiated scientific programs in zoos and aquariums. Zoo Biol 29:663–675, 2010. © 2010 Wiley‐Liss, Inc.