John Dupr explores recent revolutionary developments in biology and considers their relevance for our understanding of human nature and society. He reveals how the advance of genetic science is changing our view of the constituents of life, and shows how an understanding of microbiology will overturn standard assumptions about the living world.

John Dupré explores recent revolutionary developments in biology and considers their relevance for our understanding of human nature and human society. Epigenetics and related areas of molecular biology have eroded the exceptional status of the gene and presented the genome as fully interactive with the rest of the cell. Developmental systems theory provides a space for a vision of evolution that takes full account of the fundamental importance of developmental processes. Dupré shows the importance of microbiology for a proper understanding (...) of the living world, and reveals how it subverts such basic biological assumptions as the organisation of biological kinds on a branching tree of life, and the simple traditional conception of the biological organism. (shrink)

This chapter connects the major transitions to evolvability and its evolution. It reviews a three-pulse model of the conditions that make the evolution of complexity possible. It specifically outlines the life up to the evolution of fully equipped prokaryote cells, the phase of microbial evolution, and the third phase that sees the evolution of complex development. It compares the prokaryote and multicellular evolvability. The deeply obscure problem of precellular evolution is also evaluated. This chapter shows that individual properties of developmental (...) mechanisms are significant to evolvability, but they are not all that is important. (shrink)

Philosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy (...) of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations. (shrink)

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. (shrink)

Metagenomics is an emerging microbial systems science that is based on the large-scale analysis of the DNA of microbial communities in their natural environments. Studies of metagenomes are revealing the vast scope of biodiversity in a wide range of environments, as well as new functional capacities of individual cells and communities, and the complex evolutionary relationships between them. Our examination of this science focuses on the ontological implications of these studies of metagenomes and metaorganisms, and what they mean for common (...) sense and philosophical understandings of multicellularity, individuality and organism. We show how metagenomics requires us to think in different ways about what human beings are and what their relation to the microbial world is. Metagenomics could also transform the way in which evolutionary processes are understood, with the most basic relationship between cells from both similar and different organisms being far more cooperative and less antagonistic than is widely assumed. In addition to raising fundamental questions about biological ontology, metagenomics generates possibilities for powerful technologies addressed to issues of climate, health and conservation. We conclude with reflections about process-oriented versus entity-oriented analysis in light of current trends towards systems approaches. (shrink)

This paper will begin with some very broad and general considerations about the kind of biological entities we are. This exercise is motivated by the belief that the view of what we—multicellular eukaryotic organisms—are that is widely assumed by biologists, medical scientists and the general public, is an extremely limited one. It cannot be assumed a priori that a more sophisticated view will make a major difference to the science or practice of medicine, and there are areas of medicine to (...) which it is probably largely irrelevant. However, in this case there are important implications for medicine, or so I shall argue. In particular, it enables us to appreciate fully the potential medical significance of some of the most exciting contemporary advances in general biology, in such fields as epigenetics, metagenomics, and systems biology; and part of this significance is that these advances have raised serious doubts about how we should understand the biological individuals that medicine is generally assumed to aim to treat. (shrink)

Sometimes themes can be found in common across very different systems in which change occurs. Imre Lakatos developed a theory of change in science, and one involving entities visible at different levels. There are theories defended at a particular time, and there are also research programs, larger units that bundle together a sequence of related theories and within which many scientists may work. Research programs are competing higher-level units within a scientific field. Scientific change involves change within research programs, and (...) change in the ensemble of research programs present at a time, where some will be growing, some shrinking, some progressing, some degenerating. These are also themes in biological evolution. Recent biology has often found itself dealing with the relation between change at a level of "collectives" – such as organisms like us – and change at a lower level – the level of cells, genes, and other evolving parts. This work is continuous with an older discussion, one that arose when biological evolution was no more than a vague speculation, round the beginning of the 19th century. What is the living individual? What is the basic unit of life or living organization? Questions like this were pursued by Goethe, by Erasmus Darwin, the grandfather of Charles, and many others. Initially it was plants, especially, that were seen to raise these problems, and then newly described marine animals with strange life cycles. The discussion was influenced by the rise of the cell theory in the early 19th century, but some writers looked for individuals well below the level of the cell. (shrink)