John Dupré

Natural Kinds and Biological Taxa

Travaux de Putnam et Kripke sur la taxonomie biologique. Aspects theoriques et philosophiques.

Varieties of Living Things: Life at the Intersection of Lineage and Metabolism

We address three fundamental questions: What does it mean for an entity to be living? What is the role of inter-organismic collaboration in evolution? What is a biological individual? Our central argument is that life arises when lineage-forming entities collaborate in metabolism. By conceiving of metabolism as a collaborative process performed by functional wholes, which are associations of a variety of lineage-forming entities, we avoid the standard tension between reproduction and metabolism in discussions of life – a tension particularly evident in discussions of whether viruses are alive. Our perspective assumes no sharp distinction between life and non-life, and does not equate life exclusively with cellular or organismal status. We reach this conclusion through an analysis of the capabilities of a spectrum of biological entities, in which we include the pivotal case of viruses as well as prions, plasmids, organelles, intracellular and extracellular symbionts, unicellular and multicellular life forms. The usual criterion for classifying many of the entities of our continuum as non-living is autonomy. This emphasis on autonomy is problematic, however, because even paradigmatic biological individuals, such as large animals, are dependent on symbiotic associations with many other organisms. These composite individuals constitute the metabolic wholes on which selection acts. Finally, our account treats cooperation and competition not as polar opposites but as points on a continuum of collaboration. We suggest that competitive relations are a transitional state, with multi-lineage metabolic wholes eventually outcompeting selfish competitors, and that this process sometimes leads to the emergence of new types or levels of wholes. Our view of life as a continuum of variably structured collaborative systems leaves open the possibility that a variety of forms of organized matter – from chemical systems to ecosystems – might be usefully understood as living entities.

Probability and causality: Why Hume and indeterminism don't mix

A basic assumption of this paper is that things and events have causal capacities: in virtue of the properties they possess, they have the power to bring about other events or states. If you want to bring about a certain outcome, it is a good idea to introduce something with the appropriate capacity. The Humean tradition downplays capacities, and conceives of them as no more than misleading ways of referring to lawlike regularities. We want to reverse this idea: it is better to think of lawlike regularities as misleading ways of referring to the exercise of capacities. If we try to tailor our causal claims to match the regularities we see in nature, we will miss a good deal of the causal structure. Much recent discussion of probabilistic causality may be seen as a neo-Humean attempt to explain probabilistic capacities as, in a way, reducible to probabilistic regularities. Causality is supposed to be a relation between events, a relation which holds in virtue of the empirically distinguishable properties that events have; the relation consists in, or at least is marked by, the regular association of these properties. For Hume the association needed to be universal; nowadays a probabilistic association of the right sort will do. This does not work, we want to argue, and the reason is that the right sort of connections between-capacities and properties do not exist. Capacities are carried by properties. That is, you cannot have the capacity without having one of the right properties. But the same property can carry mixed capacities, and so the true complexity of the situation cannot be revealed by the associations of properties. This is what we hope to show here.

Treatment of diabetes

Used of killed malaria parasites or an extract thereof in the preparation of a medicament for the treatment of non-insulin dependent diabetes mellitus (NIDDM).

In Defence of Classification

Abstract It has increasingly been recognised that units of biological classification cannot be identified with the units of evolution. After briefly defending the necessity of this distinction I argue, contrary to the prevailing orthodoxy, that species should be treated as the fundamental units of classification and not, therefore, as units of evolution. This perspective fits well with the increasing tendency to reject the search for a monistic basis of classification and embrace a pluralistic and pragmatic account of the species category. It also provides a diagnosis of the paradoxical but popular idea that species are individuals: Species are not individuals, but the units of evolution are.

Understanding Contemporary Genomics

Recent molecular biology has seen the development of genomics as a successor to traditional genetics. This paper offers an overview of the structure, epistemology, and (very briefly) history of contemporary genomics. A particular focus is on the question to what extent the genome contains, or is composed of anything that corresponds to traditional conceptions of genes. It is concluded that the only interpretation of genes that has much contemporary scientific relevance is what is described as the developmental defect gene concept. However, developmental defect genes typically only correspond to general areas of the genome and not to precise chemical structures (nucleotide sequences). The parts of the genome to be identified for an account of the processes of normal development are highly diverse, little correlated with traditional genes, and act in ways that are highly dependent on the cellular and higher level environment. Despite its historical development out of genetics, genomics represents a radically different kind of scientific project.

From molecules to systems: the importance of looking both ways

Although molecular biology has meant different things at different times, the term is often associated with a tendency to view cellular causation as conforming to simple linear schemas in which macro-scale effects are specified by micro-scale structures. The early achievements of molecular biologists were important for the formation of such an outlook, one to which the discovery of recombinant DNA techniques, and a number of other findings, gave new life even after the complexity of genotype-phenotype relations had become apparent. Against this background we outline how a range of scientific developments and conceptual considerations can be regarded as enabling and perhaps necessitating contemporary systems approaches. We suggest that philosophical ideas have a valuable part to play in making sense of complex scientific and disciplinary issues.

Towards a processual microbial ontology

Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely “processually equivalent” entities, “processually versatile” entities, and “stabilized” entities.

The Study of Socioethical Issues in Systems Biology

Systems biology is the rapidly growing and heavily funded successor science to genomics. Its mission is to integrate extensive bodies of molecular data into a detailed mathematical understanding of all life processes, with an ultimate view to their prediction and control. Despite its high profile and widespread practice, there has so far been almost no bioethical attention paid to systems biology and its potential social consequences. We outline some of systems biologys most important socioethical issues by contrasting the concept of systems as dynamic processes against the common static interpretation of genomes. New issues arise around systems biologys capacities for in silico testing, changing cultural understandings of life, synthetic biology, and commercialization. We advocate an interdisciplinary and interactive approach that integrates social and philosophical analysis and engages closely with the science. Overall, we argue that systems biology socioethics could stimulate new ways of thinking about socioethical studies of life sciences.

The polygenomic organism

Research supported by the Economic and Social Research Council (ESRC) and the Arts and Humanities Research Council (AHRC).