This paper examines classification practices in the domain of plant data semantics, and particularly methods used to label plant traits to foster the collection, management, linkage and analysis of data about crops across locations—which crucially inform research and interventions on plants and agriculture. The efforts required to share data place in sharp relief the forms of diversity characterizing the systems used to capture the biological and environmental characteristics of plant variants: particularly the biological, cultural, scientific and semantic diversity affecting the (...) identification and description of plant traits, the methods used to generate and process data, and the goals and skills of those with relevant expertise—including farmers and breeders. Through a study of the Crop Ontology (which explicitly recognizes and negotiates diversity) and its application to cassava breeding, I argue for a process-sensitive approach to the naming of plant traits that focuses on documenting environmental processes instead of biological products. I claim that this approach can foster reliable linkage and robust re-use of plant data, while at the same time facilitating dialogue between data scientists, plant researchers, breeders, and other relevant experts in ways that crucially inform agricultural interventions. I conclude that the study of data semantics and related descriptors constitutes a productive and underexplored way to think about the epistemic import of naming traits within plant science. The effort to articulate semantic differences among plant varieties and methods of data processing can generate newly inclusive ways to develop and communicate biological knowledge. In turn, such practices have the potential to defy existing understandings of systematisation and hierarchies of expertise in biology, thus bolstering the extent to which plant science can support biodiversity and sustainable agriculture. (shrink)

The academic journal publishing model is deeply unethical: today, a few major, for-profit conglomerates control more than 50 of all articles in the natural sciences and social sciences, driving subscription and open-access publishing fees above levels that can be sustainably maintained by publicly funded universities, libraries, and research institutions worldwide. About a third of the costs paid for publishing papers is profit for these dominant publishers' shareholders, and about half of them covers costs to keep the system running, including lobbying, (...) marketing fees, and paywalls. The paywalls in turn restrict access of scientific outputs, preventing them from being freely shared with the public and other researchers. Thus, money that the public is told goes into science is actually being funneled away from it, or used to limit access to it. Alternatives to this model exist and have increased in popularity in recent years, including diamond open-access journals and community-driven recommendation models. These are free of charge for authors and minimize costs for institutions and agencies, while making peer-reviewed scientific results publicly accessible. However, for-profit publishing agents have made change difficult, by co-opting open-access schemes and creating journal-driven incentives that prevent an effective collective transition away from profiteering. Here, we give a brief overview of the current state of the academic publishing system, including its most important systemic problems. We then describe alternative systems. We explain the reasons why the move toward them can be perceived as costly to individual researchers, and we demystify common roadblocks to change. Finally, in view of the above, we provide a set of guidelines and recommendations that academics at all levels can implement, in order to enable a more rapid and effective transition toward ethical publishing. (shrink)

Scientific pluralism has become a household position within the philosophy of science literature. There are numerous accounts of plurality within various research fields. Most scientific pluralists, however, focus on the plurality of theories, explanations, or mechanisms, while other potential targets of plurality that the philosophy of scientific practice has particularly emphasized have so far not received extensive treatment. How should we approach such practice-based candidates of plurality? And what are potential pluralist positions concerning the objects of scientific practice? In this (...) article, I set out to answer these questions. I combine approaching a widely influential topic within the philosophy of science, scientific pluralism, with social science methodology. Using interview data combined with sociological analysis, I provide a nuanced picture of the dynamics of one particular research field that displays plurality. Focusing on how sociological configurations resonate with intellectual commitments within a research field, I disentangle practice-based from theoretical plurality. I consider how these empirical results should feedback on the scientific pluralism literature. (shrink)

This paper critiques the biological race realism of Quayshawn Spencer. Spencer's recent embrace of “radical race pluralism” (RRP) is welcome but incomplete, because it needs methods that distinguish different communicative contexts for how American English speakers use “race” and related terms. I offer a pragmatic approach to identifying such contexts that combines pragmatic argumentation theory, rhetorical polysemy, and a pragmatic approach to definition. One consequence of embracing RRP is that Spencer's theory of “OMB race talk” is unsupportable because it collapses (...) three distinct communicative contexts: genomic research, legal and regulatory governance, and ordinary talk. By so doing, OMB race talk blocks attempts to fight racism and violates ethical standards that should allow people the agency to define their own identities. (shrink)

Since at least the mid-2000s, political commentators, environmental advocates, and scientists have raised concerns about an “anti-science” approach to environmental policymaking in conservative governments in the US and Canada. This paper explores and resolves a paradox surrounding at least some uses of the “anti-science” epithet. I examine two cases of such “anti-science” environmental policy, both of which involve appeals to epistemic values that are widely endorsed by both scientists and philosophers of science. It seems paradoxical to call an appeal to (...) epistemic values “anti-science.” I develop an analysis that, I argue, can resolve this paradox. This analysis is a version of the “aims approach” to science and values, drawing on ideas from axiology and virtue ethics. I characterize the paradox in terms of conflicts or tensions between epistemic and pragmatic aims, and argue that there is a key asymmetry between them: epistemic aims are valuable, in part, because they are useful for pursuing pragmatic aims. Thus, when epistemic and pragmatic aims conflict, epistemic aims need to be reconceptualized in order to reconcile them to pragmatic aims. When this is done, in the “anti-science” cases, the epistemic values are scientific vices rather than virtues. Thus the “anti-science” epithet is apt. (shrink)

Historically, hypotheses failed in most cases to correctly forecast the workings of complex biological systems. Francis Crick’s adaptor hypothesis, however, stands out as an exceptional case of a confirmed abstract prediction. This hypothesis presciently anticipated the existence of RNA adaptors that function as bridges between amino acids and the chemically different nucleic acid template for proteins. Crick conjectured that the adaptors are enzymatically charged with cognate amino acids, they bind to complementary protein-coding nucleic acid, and their liberated amino acids are (...) incorporated into growing protein chains. Independently from and concomitantly with Crick’s hypothesis, Mahlon Hoagland and Paul Zamecnik conducted experiments with no guiding theory that culminated in discoveries of the actual adaptors, transfer RNA (tRNA) molecules, and their amino acids charging enzymes. This paper traces the parallel histories of Crick’s adaptor hypothesis and of the experimental discovery of tRNA and compares their relative impacts on the scientific community. Remarkably, despite the brilliance of Crick’s confirmed prognostication, it had marginal impact on practicing scientists. Conversely, Hoagland and Zamecnik’s experimental discoveries and their evidence-based model of protein synthesis had immediate and enduring impact. I discuss possible explanations for the different impacts of the theoretical prediction and experimental identifications of the same entities. (shrink)

The species comprising the fungal endophyte genus “Epichloë ”are symbionts of cool season grasses. About half the species in this genus are strictly vertically transmitted, and evolutionary theory suggests that these species must be mutualists. Nevertheless, Faeth and Sullivan (e.g., 2003) have argued that such vertically transmitted endophytes are ’usually parasitic,’ and Müller and Krauss (2005) have argued that such vertically transmitted endophytes fall along a mutualism-parasitism continuum. These papers (and others) have caused confusion in the field. We used a (...) systematic review to show that close to half of the published papers in this field incorrectly categorize the interaction. Here, we develop the argument that advantages and disadvantages are not the same things as mutualism and parasitism and that experimental evidence must be interpreted in the context of theory. We argue that, “contra ”Faeth and Sullivan, it is highly unlikely that such strictly vertically transmitted endophytes can be parasites, and that, “contra ”Müller and Krauss, it is inappropriate to apply the continuum concept to strictly vertically transmitted endophytes. We develop a mathematical model to support and illustrate our arguments. We use the model to clarify that parasitism “requires ”some degree of horizontal transmission, and that while it is appropriate to use the continuum concept when referring to the genus as a whole, or to species that possess horizontal transmission, we argue that it is inappropriate to use the concept when referring to species that are strictly vertically transmitted. (shrink)

Evolutionary and organismal biology have become inundated with data. At the same rate, we are experiencing a surge in broader evolutionary and ecological syntheses for which tree-thinking is the staple for a variety of post-tree analyses. To fully take advantage of this wealth of data to discover and understand large-scale evolutionary and ecological patterns, computational data integration, i.e., the use of machines to link data at large scale, is crucial. The most common shared entity by which evolutionary and ecological data (...) need to be linked is the taxon to which they belong. We propose a set of requirements that a system for defining such taxa should meet for computational data science: taxon definitions should maintain conceptual consistency, be reproducible via a known algorithm, be computationally automatable, and be applicable across the Tree of Life. We argue that Linnaean names, the most prevalent means of linking data to taxa, fail to meet these requirements due to fundamental theoretical and practical shortfalls. We argue that for the purposes of data-integration we should instead use phylogenetic definitions transformed into formal logic expressions. We call such expressions “phyloreferences”, and argue that, unlike Linnaean names, they meet all requirements for effective data-integration. (shrink)

A number of ecologists have put forward various proposals that ecology has laws, yet they have not explicated what role laws play in ecological explanations. Marcel Weber (1999), Lev Ginzburg and Mark Colyvan (2004) correct this deficiency and also make their case for laws of ecology: the principle of competitive exclusion and Malthus's law of exponential growth respectively. According to Weber, the principle of competitive exclusion explains phenomena (1) by direct application, or (2) by describing a default state from which (...) observed phenomena deviate and mechanisms are called to account for the discrepancy. Independently of Weber, Ginzburg and Colyvan articulate a role similar to (2) for Malthus's law. I argue that Weber's proposition of explanation by direct application is not consistent with Gause's account of ’bottle experiments’ that he uses to support it and does not do justice to ecologists' explanatory practice. To address these problems, I articulate an alternative account of explanation by direct application—the covering-law model—based on a proposal by Elgin and Sober (2002) and show that even in this proposal mechanisms play a key explanatory role. I also demonstrate how the covering-law model accounts for how Malthus's law can explain by direct application and for its role of descriptor of a default state. Finally, I argue that the views on laws as components in covering-law model explanations or as descriptors of default states do not give sufficient attention to the prominent explanatory role of mechanisms and to the demanding task of identifying and describing them, and ought to be corrected. (shrink)

One of the current problems in microbiology concerns the understanding of fitness in host-symbiont systems. A great deal of research and conceptual work has analysed how the host benefits from such associations; however, very little of this work has attempted to take the microbial perspective. Nevertheless, some scientists have argued that we should conduct more comparative studies of both microorganisms that interact with a host and their free-living counterparts in order to determine whether or not symbiosis is beneficial for these (...) microorganisms. In this paper, by means of analysing heritable symbiosis as a case study, I intend to provide a different perspective on this subject. Mainly, I argue that asking how the fitness of a given microorganism was changed during the evolution of heritable symbiosis may be theoretically unjustified at both the early and late stages of this process. The reason for this, I argue, is that, during the evolution of heritable symbiosis, the fitness of a microorganism becomes incommensurable with that of its free-living counterparts because their contexts become radically different; therefore, comparing their fitness makes little sense. My analysis is driven by the use of the ecological concept of fitness; accordingly, my conclusions are bound to this specific interpretation of fitness. (shrink)

Resident microorganisms, known as the microbiota, are essential for many physiological functions including protection against pathogens. Microbiota is indeed required for proper immune system development and function, and can also host-independently protect against infections. Thus, a co-constructed view of host protection involving both host and microbiota, named ’co-immunity,’ has been proposed, and the idea of an ’immunological holobiont’ has been suggested. Yet this view of co-immunity might be too limited, as experimental work has shown that the immune system is involved (...) in functions other than protection, essentially development and repair. Microbiota, through co-immunity, is thereby most likely involved in these functions, although strong evidence is currently lacking. Moreover, as our point of view is mainly host-centered, we may miss the implications of co-immunity at broader scales, including cellular and population levels. Intriguingly, co-immunity effects could be beneficial for one function and/or one level, while being detrimental for others. All these elements should be taken into consideration for microbiota manipulation, in order to avoid potentially harmful side effects. (shrink)

This paper develops the conceptual framework of ’sex contextualism’ for the study of sex-related variables in biomedical research. Sex contextualism offers an alternative to binary sex essentialist approaches to the study of sex as a biological variable. Specifically, sex contextualism recognizes the pluralism and context-specificity of operationalizations of ’sex’ across experimental laboratory research. In light of recent policy mandates to consider sex as a biological variable, sex contextualism offers constructive guidance to biomedical researchers for attending to sex-related biological variation. As (...) an alternative to and critique of biological binary sex essentialism, sex contextualism contributes to current debates in philosophy of biology, feminist science studies, and social ontology on the construction of categories of gender/sex differences in scientific research. (shrink)

Two welcome extensions of evolutionary thinking have come to prominence over the last thirty years: the so-called ’extended evolutionary synthesis’ (EES) and debate about biological kinds and individuals. These two agendas have, however, remained orthogonal to one another. The EES has mostly restricted itself to widening the explanations of adaptation offered by the preceding ’modern evolutionary synthesis’ by including additional mechanisms of inheritance and variation; while discussion of biological kinds has turned toward philosophical questions of essential vs. contingent properties of (...) life forms and realist vs. epistemological approaches to categorization and classification. Here we attempt to broaden the explanatory scope of evolutionary theory by linking these two agendas. We expand on the mechanistic orientation of the EES, using new understandings of networked systems of components in order to engage the distinct intellectual challenge of the origination of “historical kinds”. With this phrase we designate a subset of natural kinds that acquires, through evolutionary processes, a quasi-independent lineage-history. Such kinds emerge in both biology and culture, and we enlarge the limited number of historical kinds that have thus far been recognized in evolutionary biology in a series of paradigmatic exemplars, from genes and cell types to rituals and music. For each exemplar we discern specific mechanisms by which it arose and persists; comparing these, we suggest a general unity in the ways in which diverse historical kinds originate. (shrink)

What methodological approaches do research programs use to investigate the world? Elisabeth Lloyd’s Logic of Research Questions (LRQ) characterizes such approaches in terms of the questions that the researchers ask and causal factors they consider. She uses the Logic of Research Questions Framework to criticize adaptationist programs in evolutionary biology for dogmatically assuming selection explanations of the traits of organisms. I argue that Lloyd’s general criticism of methodological adaptationism is an artefact of the impoverished LRQ. My Ordered Factors Proposal extends (...) the LRQ to characterize approaches with sequences of questions and factors. I highlight the importance that ordering one’s investigation plays in approaches at the level of adaptationism by analyzing two research programs in community ecology: competitionists and neutralists. Competitionists and neutralists take opposed starting points and use explanatory and developmental heuristics to consider more factors in due time. On the Ordered Factors Proposal, these approaches are not only the ecological factors they are open to considering but also the order in which they will consider them. My disagreement with Lloyd’s over how to characterize methodological approaches reflects different views about methodological monism and pluralism. (shrink)