In his late years, Thomas Kuhn became interested in the process of scientific specialization, which does not seem to possess the destructive element that is characteristic of scientific revolutions. It therefore makes sense to investigate whether and how Kuhn’s insights about specialization are consistent with, and actually fit, his model of scientific progress through revolutions. In this paper, I argue that the transition toward a new specialty corresponds to a revolutionary change for the group of scientists involved in such a (...) transition. I will clarify the role of the scientific community in revolutionary changes and characterize the incommensurability across specialties as possessing both semantic and methodological aspects. The discussion of the discovery of the structure of DNA will serve both as an illustration of my main argument and as reply to one criticism raised against Kuhn—namely, that his model cannot capture cases of revolutionary yet non-disruptive episodes of scientific progress. Revisiting Kuhn’s ideas on specialization will shed new light on some often overlooked features of scientific change. (shrink)

I use a recent ‘experimental philosophy’ study of the concept of the gene conducted by myself and collaborators to discuss the broader epistemological framework within which that research was conducted, and to reflect on the relationship between science, history and philosophy of science, and society.Keywords: Experimental philosophy; Biohumanities; Representing Genes Project; Gene concept; Science criticism; Conceptual ecology.

I propose a systematic survey of the various attitudes proponents of enaction (or enactivism) entertained or are entertaining towards representationalism and towards the use of the concept “mental representation” in cognitive science. For the sake of clarity, a set of distinctions between different varieties of representationalism and anti-representationalism are presented. I also recapitulate and discuss some anti-representationalist trends and strategies one can find the enactive literature, before focusing on some possible limitations of eliminativist versions of enactive anti-representationalism. These limitations are (...) here taken as opportunities for reflecting on the fate of enactivism in its relations with representationalism and anti-representationalism. (shrink)

Natural kinds are often contrasted with other kinds of scientific kinds, especially functional kinds, because of a presumed categorical difference in explanatory value: supposedly, natural kinds can ground explanations, while other kinds of kinds cannot. I argue against this view of natural kinds by examining a particular type of explanation—mechanistic explanation—and showing that functional kinds do the same work there as traditionally recognized natural kinds are supposed to do in “standard” scientific explanations. Breaking down this categorical distinction between traditional natural (...) kinds and other kinds of kinds, I argue, delivers two goods: It provides us with a view of natural kindhood that does justice to the epistemic roles of kinds in scientific explanations. And it allows us to solve a problem that HPC theory, currently one of the more popular accounts of natural kindhood, confronts. (shrink)

According to a recent suggestion, the names of gene taxa should be conceived of as referring to individuals with concrete genes as their parts, just as the names of biological species are often understood as denoting individuals with organisms as their parts. Although prima facie this suggestion might advance the debate on gene concepts in a similar way as the species-are-individuals thesis advanced the debate on species concepts, I argue that the principal arguments in support of the gene-individuality thesis are (...) much less compelling than the parallel arguments in the species case. In addition, I argue that the notion of biological function invoked in the gene-individuality thesis (selected effect) is not the one that biologists actually use when individuating genes. Contra the gene-individuality thesis, I argue that gene names refer to kinds, defined primarily (though not exclusively) by causal-role functions. (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)

In this article we examine the “phenotype” concept in light of recent technological advances in Genome-Wide Association Studies . By observing the technology and its presuppositions, we put forward the thesis that at least in this case genotype and phenotype are effectively coidentifled one by means of the other. We suggest that the coidentiflcation of genotype-phenotype couples in expression-based GWAS also indicates a conceptual dependence, which we call “co-deñnition.” We note that viewing these terms as codeflned runs against possible expectations, (...) viz., that genotypes and phenotypes could ultimately be expressed independently from one another. In addition, the co-definition of genotypes and phenotypes in this context emphasizes the correlative character of both genotypes and phenotypes in GWAS. (shrink)

In recent years, a proliferation of books about empathy, cooperation and pro-social behaviours has significantly influenced the discourse of the life-sciences and reversed consolidated views of nature as a place only for competition and aggression. In this article I describe the recent contribution of three disciplines – moral psychology, primatology and the neuroscience of morality – to the present transformation of biology and evolution into direct sources of moral phenomena, a process here named the ‘moralization of biology’. I conclude by (...) addressing the ambivalent status of this constellation of authors, for whom today ‘morality comes naturally’: I explore both the attractiveness of their message, and the problematic epistemological assumptions of their research programmes in the light of new discoveries in developmental and molecular biology. (shrink)

In recent years, a proliferation of books about empathy, cooperation and pro-social behaviours (Brooks, 2011a) has significantly influenced the discourse of the life-sciences and reversed consolidated views of nature as a place only for competition and aggression. In this article I describe the recent contribution of three disciplines – moral psychology (Jonathan Haidt), primatology (Frans de Waal) and the neuroscience of morality – to the present transformation of biology and evolution into direct sources of moral phenomena, a process here named (...) the ‘moralization of biology’. I conclude by addressing the ambivalent status of this constellation of authors, for whom today ‘morality comes naturally’: I explore both the attractiveness of their message, and the problematic epistemological assumptions of their research programmes in the light of new discoveries in developmental and molecular biology. (shrink)

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)

Philosophical discussions of biological classification have failed to recognise the central role of homology in the classification of biological parts and processes. One reason for this is a misunderstanding of the relationship between judgments of homology and the core explanatory theories of biology. The textbook characterisation of homology as identity by descent is commonly regarded as a definition. I suggest instead that it is one of several attempts to explain the phenomena of homology. Twenty years ago the ‘new experimentalist’ movement (...) in philosophy of science drew attention to the fact that many experimental phenomena have a ‘life of their own’: the conviction that they are real is not dependent on the theories used to characterise and explain them. I suggest that something similar can be true of descriptive phenomena, and that many homologies are phenomena of this kind. As a result the descriptive biology of form and function has a life of its own—a degree of epistemological independence from the theories that explain form and function. I also suggest that the two major ‘homology concepts’ in contemporary biology, usually seen as two competing definitions, are in reality complementary elements of the biological explanation of homology. (shrink)

The concept of scaffolding has wide resonance in several scientific fields. Here we attempt to adopt it for the study of development. In this perspective, the embryo is conceived as an integral whole, comprised of several hierarchical modules as in a recurrent circularity of emerging patterns. Within the developmental hierarchy, each module yields an inter-level relationship that makes it possible for the scaffolding to mediate the production of selectable variations. A wide range of genetic, cellular and morphological mechanisms allows the (...) scaffolding to integrate these modular variations into a functionally coordinate unit. A genetic scaffolding accounts for the inherited invariance of pattern formation during the embryo’s growth. At higher level, cells behave as agents endowed with the capacity to interpret any scaffolding variation as signs. The full hierarchy of a multi-level scaffolding is eventually attained when the embryo acquires the capacity to impose a number of developmental constraints on its constituting parts in a top-down direction. The acquisition of this capacity allows a semiotic threshold to emerge between the living cellular world and the underlying non-living molecular world. As this boundary is gradually defined during development, cells enter into new functional relationships, while, at the same time, are relieved from their physical determinism. The resulting constraints can thus become the driving forces that upgrade embryonic scaffolding from the simple molecular signalling to the complexity of sign recognition proper of a cellular community. In this semiotic perspective, the apparent goal directness of any developmental strategy should no longer be accounted for by a predetermined genetic program, but by the gradual definition of the relationships selected amongst the ones historically explored. (shrink)

Developmental biology is a theory of interpretation. Developmental signals are interpreted differently depending on the previous history of the responding cell. Thus, there is a context for the reception of a signal. While this conclusion is obvious during metamorphosis, when a single hormone instructs some cells to proliferate, some cells to differentiate, and other cells to die, it is commonplace during normal development. Paracrine factors such as BMP4 can induce apoptosis, proliferation, or differentiation depending upon the history of the responding (...) cells. In addition, organisms have evolved to alter their development in response to differences in temperature, diet, the presence of predators, or the presence of competitors. This allows them to develop the phenotype, within the limits imposed by the genotype, best suited for the immediate habitat of the organism. Most developing organisms have also evolved to expect developmental signals from symbionts, and these organisms develop abnormally if the symbiont signals are not present. Thus Hoffmeyer’s “vertical semiotic system” of genetic communication and “horizontal semiotic system” of ecological communication are integrated during development. (shrink)

Conceptual change can occur for a variety of reasons; some more scientifically significant than others. The 2006 definition of ‘planet’, which saw Pluto reclassified as a dwarf planet, is an example toward the more mundane end of the scale. I argue however that this case serves as a useful example of a related phenomenon, whereby what appears to be a single kind term conceals two or more distinct concepts with independent scientific utility. I examine the historical background to this case, (...) as a template for developing additional evidence for pluralist approaches to conceptual disputes within science and elsewhere. (shrink)

Essentialism is widely regarded as a mistaken view of biological kinds, such as species. After recounting why (sections 2-3), we provide a brief survey of the chief responses to the “death of essentialism” in the philosophy of biology (section 4). We then develop one of these responses, the claim that biological kinds are homeostatic property clusters (sections 5-6) illustrating this view with several novel examples (section 7). Although this view was first expressed 20 years ago, and has received recent discussion (...) and critique, it remains underdeveloped and is often misrepresented by its critics (section 8). (shrink)

The discussion presents a framework of concepts that is intended to account for the rationality of semantic change and variation, suggesting that each scientific concept consists of three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept’s use. I argue that in the course of history a concept can change in any of these components, and that change in the concept’s inferential role and reference can be accounted for as being rational relative (...) to the third component, the concept’s epistemic goal. This framework is illustrated and defended by application to the history of the gene concept. It is explained how the molecular gene concept grew rationally out of the classical gene concept despite a change in reference, and why the use and reference of the contemporary molecular gene concept may legitimately vary from context to context. (shrink)

This essay analyzes and develops recent views about explanation in biology. Philosophers of biology have parted with the received deductive-nomological model of scientific explanation primarily by attempting to capture actual biological theorizing and practice. This includes an endorsement of different kinds of explanation (e.g., mathematical and causal-mechanistic), a joint study of discovery and explanation, and an abandonment of models of theory reduction in favor of accounts of explanatory reduction. Of particular current interest are philosophical accounts of complex explanations that appeal (...) to different levels of organismal organization and use contributions from different biological disciplines. The essay lays out one model that views explanatory integration across different disciplines as being structured by scientific problems. I emphasize the philosophical need to take the explanatory aims pursued by different groups of scientists into account, as explanatory aims determine whether different explanations are competing or complementary and govern the dynamics of scientific practice, including interdisciplinary research. I distinguish different kinds of pluralism that philosophers have endorsed in the context of explanation in biology, and draw several implications for science education, especially the need to teach science as an interdisciplinary and dynamic practice guided by scientific problems and explanatory aims. (shrink)

David Chalmers and Frank Jackson have promoted a strong program of conceptual analysis, which accords a significant philosophical role to the a priori analysis of concepts. They found this methodological program on an account of concepts using two-dimensional semantics. This paper argues that Chalmers and Jackson’s account of concepts, and the related approach by David Braddon-Mitchell, is inadequate for natural kind concepts as found in biology. Two-dimensional semantics is metaphysically faulty as an account of the nature of concepts and concept (...) possession. It is also methodologically flawed as a guideline for how to study scientific concepts. Proponents of two-dimensional semantics are criticized for not taking seriously semantic variation between persons and for failing to adequately account for the rationality of semantic change. I suggest a more pragmatic approach to natural kind term meaning, arguing that the epistemic goal pursued by a term’s use is an additional semantic property. (shrink)

Climate policy decisions are decisions under uncertainty and are, therefore, based on a range of future climate scenarios, describing possible consequences of alternative policies. Accordingly, the methodology for setting up such a scenario range becomes pivotal in climate policy advice. The preferred methodology of the Intergovernmental Panel on Climate Change will be characterised as ,,modal verificationism"; it suffers from severe shortcomings which disqualify it for scientific policy advice. Modal falsificationism, as a more sound alternative, would radically alter the way the (...) climate scenario range is set up. Climate science's inability to find robust upper bounds for future temperature rise in line with modal falsificationism does not disprove that methodology, rather, this very fact prescribes even more drastic efforts to curb CO2 emissions than currently proposed. (shrink)

Personalized genomics companies (PG; also called ‘direct-to-consumer genetics’) are businesses marketing genetic testing to consumers over the Internet. While much has been written about these new businesses, little attention has been given to their roles in science communication. This paper provides an analysis of the gene concept presented to customers and the relation between the information given and the science behind PG. Two quite different gene concepts are present in company rhetoric, but only one features in the science. To explain (...) this, we must appreciate the delicate tension between PG, academic science, public expectation, and market forces. (shrink)

The purpose of this article is to update and defend syntax-based gene concepts. I show how syntax-based concepts can and have been extended to accommodate complex cases of processing and gene expression regulation. In response to difficult cases and causal parity objections, I argue that a syntax-based approach fleshes out a deflationary concept defining genes as genomic sequences and organizational features of the genome contributing to a phenotype. These organizational features are an important part of accepted molecular explanations, provide the (...) theoretical basis for a large number of experimental techniques and practical applications, and play a crucial role in in annotating the genome, deriving predictions and constructing bioinformatics models. (shrink)

This paper explores early Australasian philosophy in some detail. Two approaches have dominated Western philosophy in Australia: idealism and materialism. Idealism was prevalent between the 1880s and the 1930s, but dissipated thereafter. Idealism in Australia often reflected Kantian themes, but it also reflected the revival of interest in Hegel through the work of ‘absolute idealists’ such as T. H. Green, F. H. Bradley, and Henry Jones. A number of the early New Zealand philosophers were also educated in the idealist tradition (...) and were influential in their communities, but produced relatively little. In Australia, materialism gained prominence through the work of John Anderson, who arrived in Australia in 1927, and continues to be influential. John Anderson had been a student of Henry Jones, who might therefore be said to have influenced both main strands of Australian philosophical thought. (shrink)

In this paper I first offer a systematic outline of a series of conceptual novelties in the life-sciences that have favoured, over the last three decades, the emergence of a more social view of biology. I focus in particular on three areas of investigation: (1) technical changes in evolutionary literature that have provoked a rethinking of the possibility of altruism, morality and prosocial behaviours in evolution; (2) changes in neuroscience, from an understanding of the brain as an isolated data processor (...) to the ultrasocial and multiply connected social brain of contemporary neuroscience; and (3) changes in molecular biology, from the view of the gene as an autonomous master of development to the ‘reactive genome’ of the new emerging field of molecular epigenetics. In the second section I reflect on the possible implications for the social sciences of this novel biosocial terrain and argue that the postgenomic language of extended epigenetic inheritance and blurring of the nature/nurture boundaries will be as provocative for neo-Darwinism as it is for the social sciences as we have known them. Signs of a new biosocial language are emerging in several social-science disciplines and this may represent an exciting theoretical novelty for twenty-first social theory. (shrink)

A number of areas of biology raise questions about what is of value in the natural environment and how we ought to behave towards it: conservation biology, environmental science, and ecology, to name a few. Based on my experience teaching students from these and similar majors, I argue that the field of environmental ethics has much to teach these students. They come to me with pent-up questions and a feeling that more is needed to fully engage in their subjects, and (...) I believe some exposure to environmental ethics can help focus their interests and goals. I identify three primary areas in which environmental ethics can con- tribute to their education. The first is an examination of who (or what) should be considered to be part of our moral community (i.e., the community to whom we owe direct duties). Is it humans only? Or does it include all sentient life? Or all life? Or ecosystems considered holistically? Often, readings implicitly assume one or more of these answers; the goal is to make the student more sensitive to these implicit claims and to get them to think about the different reasons that support them. The second area, related to the first, is the application of the different answers concerning the extent of the ethical community to real environmental issues and problems. Students need to be aware of how the different answers concerning the moral community can imply conflicting answers for how we should act in certain cases and to think about ways to move toward conflict resolution. The third area in which environmental ethics can contribute is a more conceptual one, focusing on central concepts such as biodiversity, sustainability, species, and ecosystems. Exploring and evaluating various meanings of these terms will make students more reflective and thoughtful citizens and biologists, sensitive to the implications that different conceptual choices make. (shrink)

The paper describes the change from molecular genetics to postgenomic biology. It focuses on phenomena in the regulation of gene expression that provide a break with the central dogma, according to which sequence specificity for a gene product must be template derived. In its place we find what is called here ‘constitutive molecular epigenesis’. Its three classes of phenomena, which I call sequence ‘activation’, ‘selection’ and ‘creation’, are exemplified by processes such as transcriptional activation, alternative cis- and trans-splicing, and RNA (...) editing. These phenomena support the following main theses of the paper: 1. Other molecular resources share the causal role of ‘genes’: the ‘causal specificity’ for the linear sequence of any gene product is distributed between the coding sequence, cis-acting sequences, trans-acting factors, environmental signals, and the contingent history of the cell (the cellular code) (thesis of distributed causal specificity). 2. These multiple and overlapping processing and targeting mechanisms amplify the repertoire of RNA and protein products specified through the eukaryotic genome, expanding the possibilities specified by the literal code of DNA (thesis of genetic underdeterminism). 3. These mechanisms of gene expression change the focus of postgenomic research from single molecules and their molecular, biochemical and intrinsic function to their cellular, constituent, component or contextual function due to their recruitment and organization in complex cellular networks. In other words, all agents involved in the regulation of gene expression, including DNA, must interact with other agents to achieve full specificity, which is imposed by regulated recruitment and combinatorial control (theses of regulated recruitment and of system analysis). I conclude from these three main theses that the complexity of higher organisms lies not in its number of genes but in the flexibility, versatility and reactivity of its whole genome. (shrink)