This paper aims to identify the key characteristics of model organisms that make them a specific type of model within the contemporary life sciences: in particular, we argue that the term “model organism” does not apply to all organisms used for the purposes of experimental research. We explore the differences between experimental and model organisms in terms of their material and epistemic features, and argue that it is essential to distinguish between their representational scope and representational target. We also examine (...) the characteristics of the communities who use these two types of models, including their research goals, disciplinary affiliations, and preferred practices to show how these have contributed to the conceptualization of a model organism. We conclude that model organisms are a specific subgroup of organisms that have been standardized to fit an integrative and comparative mode of research, and that it must be clearly distinguished from the broader class of experimental organisms. In addition, we argue that model organisms are the key components of a unique and distinctively biological way of doing research using models.Keywords: Experimental organism; Genetics; Model organism; Modeling; Philosophy of biology; Representation. (shrink)

In this article, we discuss epistemological limitations relating to the use of ethnoracial categories in biomedical research as devised by the Office of Management and Budget’s institutional guidelines. We argue that the obligation to use ethnoracial categories in genomics research should be abandoned. First, we outline how conceptual imprecision in the definition of ethnoracial categories can generate epistemic uncertainty in medical research and practice. Second, we focus on the use of ethnoracial categories in medical genetics, particularly genomics-based precision medicine, where (...) ethnoracial identity is understood as a proxy for medically relevant differences among individuals. Notably, extensive criticisms have been made already against the genetic interpretation of races, but, nonetheless, the concept of race remains a key element of contemporary genomics. This motivates us to explore possible reasons why such criticisms may have been ineffective in redirecting attention to other (non-race-based) ways of controlling for human variability. We contend that popular arguments against the idea that human races have a genetic basis, though convincing in many respects, are not sufficient to exclude the pragmatic use of race and ethnicity as proxies for genetic variability related to complex phenotypes. Finally, we provide two further arguments to support the idea that ethnoracial categories are unlikely to provide meaningful insights into medical genetics, which implies that even the interpretation of race as a useful tool to stratify disease risk is unwarranted. (shrink)

This paper challenges the common assumption that some phenotypic traits are quantitative while others are qualitative. The distinction between these two kinds of traits is widely influential in biological and biomedical research as well as in scientific education and communication. This is probably due to both historical and epistemological reasons. However, the quantitative/qualitative distinction involves a variety of simplifications on the genetic causes of phenotypic variability and on the development of complex traits. Here, I examine three cases from the life (...) sciences that show inconsistencies in the distinction: Mendelian traits, Mendelian diseases, and polygenic mental disorders. I show that these traits can be framed both quantitatively and qualitatively depending, for instance, on the methods through which they are investigated and on specific epistemic purposes. This suggests that the received view of quantitative and qualitative traits has a limited heuristic power—limited to some local contexts or to the specific methodologies adopted. Throughout the paper, I provide directions for framing phenotypes beyond the quantitative/qualitative distinction. I conclude by pointing at the necessity of developing a principled characterisation of what phenotypic traits, in general, are. (shrink)

Um alinhamento responsável à alguma versão do naturalismo filosófico requer a articulação explicita e cuidadosa de um argumento em sua defesa. Em quatro passos, o texto que segue abaixo expande e examina a validade de um argumento que é frequentemente rascunhado em favor do naturalismo. Como veremos, contudo, a versão do naturalismo que esse argumento nos permite é um pouco diferente dos naturalismos filosóficos mais populares.

Voles are attracting attention because genetic variation at a single locus appears to have a profound impact on a complex social behavior, namely monogamy. After briefly reviewing the state of the most relevant scientific literature, I examine the way that this research gets taken up by the popular media, by scientists, and by the notable philosopher of neuroscience Patricia Churchland and interpreted as having deeply revisionary implications for how we ordinarily understand ourselves as persons. We have all these big questions (...) we would like to resolve about free will, consciousness, our understanding of persons, and the nature of morality and there is a tendency to ask more of neuroscience than it can yet answer. I do not deny that advances in neuroscience may eventually bear on important philosophical issues. However, it is not at all clear that this research has many of the sweeping implications being claimed for it and, in communicating science responsibly to the public, there is reason to be cautious about suggesting that it does. (shrink)

With an increasing number of ways to ‘assist’ reproduction, some bioethicists have started to wonder what it takes to become a genetic parent. It is widely agreed that sharing genes is not enough to substantiate the parent–offspring relation, but what is? Without a better understanding of the concept of reproduction, our thinking about parent–offspring relations and the ethical issues surrounding them risk being unprincipled. Here, I address that problem by offering a principled account of reproduction—the Overlap, Development and Persistence account—which (...) I believe best captures the meaning of ‘genetic parenthood’. (shrink)

Colombo’s (Phenomenology and the Cognitive Sciences, 2013) plea for neural representationalism is the focus of a recent contribution to Phenomenology and Cognitive Science by Daniel D. Hutto and Erik Myin. In that paper, Hutto and Myin have tried to show that my arguments fail badly. Here, I want to respond to their critique clarifying the type of neural representationalism put forward in my (Phenomenology and the Cognitive Sciences, 2013) piece, and to take the opportunity to make a few remarks of (...) general interest concerning what Hutto and Myin have dubbed “the Hard Problem of Content.”. (shrink)

Although much has been learned about hereditary mechanisms since Gregor Mendel’s famous experiments, gene concepts have always remained vague, notwithstanding their central role in biology. During over hundred years of genetic research, gene concepts have often and dynamically changed to accommodate novel experimental findings, without ever providing a generally accepted definition of the ‘gene.’ Yet, the distinction between ‘regulatory genes’ and ‘structural genes’ has remained a common theme in modern gene concepts since the definition of the operon-model. This distinction is (...) now challenged by recent findings which suggest that, at least in eukaryotes, structural genes may in many situations have a regulatory function that is independent of the function of the gene product (protein or non-coding RNA molecule). This brief paper discusses these new findings and some possible implications for the notion of the ‘regulatory gene.’. (shrink)

The status of risk factors and disease remains a disputed question in the theory and practice of medicine and healthcare, and so does the related question of delineating disease boundaries. I present a framework based on Bernard Lonergan’s account of emergent probability for differentiating (1) generically distinct levels of systematic function within organisms and between organisms and their environments and (2) the methods of functional, genetic, and statistical investigation. I then argue on this basis that it is possible to understand (...) disease in terms of biological or higher intra-level dysfunction, risk factors—including genetic risk factors—in terms of statistical inter-level conditioning of a given stage or developmental sequence of systematic functioning, and the empirical boundaries of disease in terms of the limits of both functional categorization (from an epistemic standpoint) and upper-level integration of lower-level processes and events (from an ontological standpoint). (shrink)

Abstract A lot of science has passed under the bridge since the classic definition of evolution as a change in gene frequencies in a population became common. Much knowledge has accumulated since then about evolution, heredity, ecology, development, phenotypic plasticity, niche construction and genetic drift. Building on Van Valen’s description of evolution as “the control of development by ecology,” it is suggested that the classic definition be replaced by a updated ‘eco‐evo-evo’ definition of evolution by natural selection which acknowledges this (...) accumulation. (shrink)

Many degree programs in science and engineering aim at enabling their students to perform interdisciplinary problem solving. In this paper we present three types of expertise that are involved in different ways in interdisciplinary problem solving. In doing so we shall first characterise two important epistemological challenges commonly faced in interdisciplinary problem solving, namely the communication challenge that arises from the use of different concepts within different scientific domains, and the integration challenge that arises from the differences between domain-specific epistemological (...) standards. Next, drawing on recent work on expertise developed within science studies, we characterize the interactional expertise that is a precondition for scientists to communicate across scientific domains, and the integrational expertise that is a precondition for scientists to be able to integrate cognitive resources originating in different domains. Finally, we shall analyse how different types of interdisciplinary problem solving sets different requirements for interactional and integrational expertise and discuss the implications for science and engineering programs in higher education. (shrink)

Christopher Boorse’s Health care ethics: an introduction, Temple University Press, Philadelphia, pp 359–393, 1987; in Humber, Almeder, Totowa What is disease?, Humana Press, New York City, pp 1–134, 1997; J Med Philos, 39:683–724, 2014) Bio-Statistical Theory comprehends diseases in terms of departures from natural norms, which involve an objectively describable deviation from the proper physiological or psychological functioning of parts of the human organism. I argue that while recent revisions and additional considerations shield the BST from a number of issues (...) raised by critics, they give rise to significant new challenges. These are related to the attribution of epistemic authority, the possibility of multiple concepts in the authoritative literature, and the framing of BST as “philosophical explication.” The conclusion is that, in its current form, the BST is unable to provide a robust framework for a naturalist classification. (shrink)

The dialectic discourse of the ‘gene’ as the unit of heredity deduced from the phenotype, whether an intervening variable or a hypothetical construct, appeared to be settled with the presentation of the molecular model of DNA: the gene was reduced to a sequence of DNA that is transcribed into RNA that is translated into a polypeptide; the polypeptides may fold into proteins that are involved in cellular metabolism and structure, and hence function. This path turned out to be more bewildering (...) the more the regulation of products and functions were uncovered in the contexts of integrated cellular systems. Philosophers struggling to define a unified concept of the gene as the basic entity of genetics confronted those who suggested several different ‘genes’ according to the conceptual frameworks of the experimentalists. Researchers increasingly regarded genes de facto as generic terms for describing their empiric data, and with improved DNA-sequencing capacities these entities were as a rule bottom-up nucleotide sequences that determine functions. Only recently did empiricists return to discuss conceptual considerations, including top-down definitions of units of function that through cellular mechanisms select the DNA sequences which comprise ‘genomic-footprints’ of functional entities. (shrink)

In the advertising discourse of human genetic database projects, of genetic ancestry tracing companies, and in popular books on anthropological genetics, what I refer to as the anthropological gene and genome appear as documents of human history, by far surpassing the written record and oral history in scope and accuracy as archives of our past. How did macromolecules become "documents of human evolutionary history"? Historically, molecular anthropology, a term introduced by Emile Zuckerkandl in 1962 to characterize the study of primate (...) phylogeny and human evolution on the molecular level, asserted its claim to the privilege of interpretation regarding hominoid, hominid, and human phylogeny and evolution vis-à-vis other historical sciences such as evolutionary biology, physical anthropology, and paleoanthropology. This process will be discussed on the basis of three key conferences on primate classification and evolution that brought together exponents of the respective fields and that were held in approximately ten-years intervals between the early 1960s and the 1980s. I show how the anthropological gene and genome gained their status as the most fundamental, clean, and direct records of historical information, and how the prioritizing of these epistemic objects was part of a complex involving the objectivity of numbers, logic, and mathematics, the objectivity of machines and instruments, and the objectivity seen to reside in the epistemic objects themselves. (shrink)

Reliability and external validity are two fundamental values that pose incompatible constraints on neurobiological experiments. The more reliability an experimental result achieves, the less external validity it earns, and vice versa. In this article, I propose an externalist interpretation of external validity: the external validity of an experimental result depends not only on how much complexity is built into an experimental design, but also on the relationship between the experimental result and other related experiments. This externalist interpretation, which explains how (...) a neurobiological experiment can be reliable and externally valid simultaneously, suggests a new way to understand the epistemology of neurobiological experimentation. (shrink)

This article argues, in opposition to a common interpretation of Wittgenstein deriving from Winch, that there is nothing especially problematic about the social sciences. Familiar Wittgensteinian theses about language, notably on the open-endedness of linguistic rules and on the importance of family resemblance concepts, have great relevance not only to the social sciences but also to much of the natural sciences. The differences between scientific and ordinary language are much less sharp than Winch, and probably Wittgenstein, supposed.