Microbes and microbiology are seldom encountered in philosophical accounts of the life sciences. Although microbiology is a well-established science and microbes the basis of life on this planet, neither the organisms nor the science have been seen as philosophically significant. This book will change that. It fills a major gap in the philosophy of biology by examining central philosophical issues in microbiology. Topics are drawn from evolutionary microbiology, microbial ecology, and microbial classification. These discussions are aimed at philosophers and scientists (...) who wish to gain insight into the basic philosophical issues of microbiology. (shrink)

In 1962, Donald Caspar and Aaron Klug published their classic theory of virus structure. They developed their theory with an explicit analogy between spherical viruses and Buckminster Fuller's geodesic domes. In this paper, I use the spherical virus-geodesic dome case to develop an account of analogy and deductive analogical inference based on the notion of an isomorphism. I also consider under what conditions there is a good reason to claim an experimentally untested analogy is plausible.

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.

The question “What is an organism?”, formerly considered as essential in biology, has now been increasingly replaced by a larger question, “What is a biological individual?”. On the grounds that i) individuation is theory-dependent, and ii) physiology does not offer a theory, biologists and philosophers of biology have claimed that it is the theory of evolution by natural selection which tells us what counts as a biological individual. Here I show that one physiological field, immunology, offers a theory, which makes (...) possible a biological individuation based on physiological grounds. I give a new answer to the question of the individuation of an organism by linking together the evolutionary and the immunological approaches to biological individuation. (shrink)

In this paper, I argue against John Beatty’s position in his paper “The Evolutionary Contingency Thesis” by counterexample. Beatty argues that there are no distinctly biological laws because the outcomes of the evolutionary processes are contingent. I argue that the heart of the Caspar–Klug theory of virus structure—that spherical virus capsids consist of 60T subunits (where T = k 2 + hk + h 2 and h and k are integers)—is a distinctly biological law even if the existence of spherical (...) viruses is evolutionarily contingent. (shrink)

The book presents a new way of understanding Darwinism and evolution by natural selection, combining work in biology, philosophy, and other fields.

Kant’s analysis of the concept of natural purpose in the Critique of judgment captured several features of organisms that he argued warranted making them the objects of a special field of study, in need of a special regulative teleological principle. By showing that organisms have to be conceived as self-organizing wholes, epigenetically built according to the idea of a whole that we must presuppose, Kant accounted for three features of organisms conflated in the biological sciences of the period: adaptation, functionality (...) and conservation of forms..Kant’s unitary concept of natural purpose was subsequently split in two directions: first by Cuvier’s comparative anatomy, that would draw on the idea of adaptative functions as a regulative principle for understanding in reconstituting and classifying organisms; and then by Goethe’s and Geoffroy’s morphology, a science of the general transformations of living forms. However, such general transformations in nature, objects of an alleged ‘archaeology of nature’, were thought impossible by Kant in the §80 of the Critique of judgment. Goethe made this ‘adventure of reason’ possible by changing the sense of ‘explanation’: scientific explanation was shifted from the investigation of the mechanical processes of generation of individual organisms to the unveiling of some ideal transformations of types instantiated by those organisms. (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)

In this paper I consider Kenneth Schaffner''s(1998) rendition of ''''developmentalism'''' from the point of viewof bacteriophage biology. I argue that the fact that a viablephage can be produced from purified DNA and host cellularcomponents lends some support to the anti-developmentalist, ifthey first show that one can draw a principled distinctionbetween genetic and environmental effects. The existence ofhost-controlled phage host range restriction supports thedevelopmentalist''s insistence on the parity of DNA andenvironment. However, in the case of bacteriophage, thedevelopmentalist stands on less firm (...) ground than when organismswith nervous systems, such as Schaffner''s C. elegans, areconsidered. (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)

Kant’s analysis of the concept of natural purpose in the Critique of judgment captured several features of organisms that he argued warranted making them the objects of a special field of study, in need of a special regulative teleological principle. By showing that organisms have to be conceived as self-organizing wholes, epigenetically built according to the idea of a whole that we must presuppose, Kant accounted for three features of organisms conflated in the biological sciences of the period: adaptation, functionality (...) and conservation of forms..Kant’s unitary concept of natural purpose was subsequently split in two directions: first by Cuvier’s comparative anatomy, that would draw on the idea of adaptative functions as a regulative principle for understanding in reconstituting and classifying organisms; and then by Goethe’s and Geoffroy’s morphology, a science of the general transformations of living forms. However, such general transformations in nature, objects of an alleged ‘archaeology of nature’, were thought impossible by Kant in the §80 of the Critique of judgment. Goethe made this ‘adventure of reason’ possible by changing the sense of ‘explanation’: scientific explanation was shifted from the investigation of the mechanical processes of generation of individual organisms to the unveiling of some ideal transformations of types instantiated by those organisms. (shrink)

College of Medicine, University of South Alabama Mobile, AL 36688-0002, USA wbp501{at}jaguar1.usouthal.edu ' + u + '@' + d + ' '//--> Abstract Recent work in viral genomics has shown that bacteriophages exhibit a high degree of mosaicism, which is most likely due to a long history of prolific horizontal gene transfer (HGT). Given these findings, we argue that each of the most plausible attempts to properly classify bacteriophages into distinct species fail. Mayr's biological species concept fails because there is (...) no useful viral analog to sexual reproduction. Phenetic species concepts fail because they obscure the mosaicism and the rich reticulated viral histories. Phylogenetic species concepts, even when extended to take into account reticulation, fail because there is no non-arbitrary distinction between recombination events that create a new viral species and those that do not. There is good reason to think that bacteriophages, arguably the Earth's most abundant biological agent, evolve without forming species. Introduction The Biology of Viruses 2.1 Bacteriophage life cycles 2.2 Mechanisms of HGT The Species Problem and Species Concepts 3.1 Phenetic species concepts 3.2 The biological species concept 3.3 Phylogenetic species concepts 3.4 The ecological species concept 3.5 Homeostatic property cluster species Viruses and Species Taxonomy Reticular Phylogenies Conclusion CiteULike Connotea Del.icio.us What's this? (shrink)

The Limits of the Self, will be essential reading for anyone interested in the definition of biological individuality and the understanding of the immune system.

The Australian scientist Frank Macfarlane Burnet—winner of the Nobel Prize in 1960 for his contributions to the understanding of immunological tolerance—is perhaps best recognized as one of the formulators of the clonal selection theory of antibody production, widely regarded as the ‘central dogma’ of modern immunology. His work in studies in animal virology, particularly the influenza virus, and rickettsial diseases is also well known. Somewhat less known and publicized is Burnet’s research on bacteriophages, which he conducted in the first decade (...) of his research career, immediately after completing medical school. For his part, Burnet made valuable contributions to the understanding of the nature of bacteriophages, a matter of considerable debate at the time he began his work. Reciprocally, it was while working on the phages that Burnet developed the scientific styles, the habits of mind and laboratory techniques and practices that characterized him for the rest of his career. Using evidence from Burnet’s published work, as well as personal papers from the period he worked on the phages, this paper demonstrates the direct impact that his experiments with phages had on the development of his characteristic scientific style and approaches, which manifested themselves in his later career and theories, and especially in his thinking regarding various immunological problems. (shrink)

Viruses are major drivers of global biogeochemistry and the etiological agents of many diseases. They are also the winners in the game of life: there are more viruses on the planet than cellular organisms and they encode most of the genetic diversity on the planet. In fact, it is reasonable to view life as a viral incubator. Nevertheless, most ecological and evolutionary theories were developed, and continue to be developed, without considering the virosphere. This means these theories need to be (...) to reinterpreted in light of viral knowledge or we need to develop new theory from the viral point-of-view. Here we briefly introduce our viral planet and then address a major outstanding question in biology: why is most of life viral? A key insight is that during an infection cycle the original virus is completely broken down and only the associated information is passed on to the next generation. This is different for cellular organisms, which must pass on some physical part of themselves from generation to generation. Based on this premise, it is proposed that the thermodynamic consequences of physical information (e.g., Landauer’s principle) are observed in natural viral populations. This link between physical and genetic information is then used to develop the Viral Information Hypothesis, which states that genetic information replicates itself to the detriment of system energy efficiency (i.e., is viral in nature). Finally, we show how viral information can be tested, and illustrate how this novel view can explain existing ecological and evolutionary theories from more fundamental principles. (shrink)