In this sequence of philosophical essays about natural science, the author argues that fundamental explanatory laws, the deepest and most admired successes of modern physics, do not in fact describe regularities that exist in nature. Cartwright draws from many real-life examples to propound a novel distinction: that theoretical entities, and the complex and localized laws that describe them, can be interpreted realistically, but the simple unifying laws of basic theory cannot.

One of intuitions driving the acceptance of a neat structured tree of life is the assumption that organisms and the lineages they form have somewhat stable spatial and temporal boundaries. The phenomenon of symbiosis shows us that such ‘fixist’ assumptions does not correspond to how the natural world actually works. The implications of lateral gene transfer (LGT) have been discussed elsewhere; I wish to stress a related point. I will focus on lateral function transfer (LFT) and will argue, using examples (...) of what many would call ‘superorganisms’, that the emergence of symbiotic individuals revives the importance of functional and adaptationist thinking in how we conceptualize the lineages of biological individuals. The consequence of the argument is that, if we really want to hold onto tree of life thinking, we had better accept that new saplings appear and disappear all the time. (shrink)

Recently improved understanding of evolutionary processes suggests that tree-based phylogenetic analyses of evolutionary change cannot adequately explain the divergent evolutionary histories of a great many genes and gene complexes. In particular, genetic diversity in the genomes of prokaryotes, phages, and plasmids cannot be fit into classic tree-like models of evolution. These findings entail the need for fundamental reform of our understanding of molecular evolution and the need to devise alternative apparatus for integrated analysis of these genomes. We advocate the development (...) of integrative phylogenomics for analyzing these genomes and their histories, with tools suited to analyzing the importance of lateral gene transfer (LGT) and of DNA evolution in extra-cellular mobile genetic elements (e.g., viruses, plasmids). These phenomena greatly increase the complexity of relationships among interacting genetic partners, as they exchange functional genetic units. We examine the ontology of functional genetic units, interacting genetic partners, and emergent genetic associations, argue that these three categories of entities are required for a successful integrated phylogenomics. We conclude with arguments to suggest that the proposed new perspective and associated tools are suitable, and perhaps required, as a replacement for the bifurcating trees that have dominated evolutionary thinking for the last 150 years. (shrink)

Woodward's long awaited book is an attempt to construct a comprehensive account of causation explanation that applies to a wide variety of causal and explanatory claims in different areas of science and everyday life. The book engages some of the relevant literature from other disciplines, as Woodward weaves together examples, counterexamples, criticisms, defenses, objections, and replies into a convincing defense of the core of his theory, which is that we can analyze causation by appeal to the notion of manipulation.

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)

Recent discoveries of geographical patterns in microbial distribution are undermining microbiology’s exclusively ecological explanations of biogeography and their fundamental assumption that ‘everything is everywhere: but the environment selects’. This statement was generally promulgated by Dutch microbiologist Martinus Wilhelm Beijerinck early in the twentieth century and specifically articulated in 1934 by his compatriot, Lourens G. M. Baas Becking. The persistence of this precept throughout twentieth-century microbiology raises a number of issues in relation to its formulation and widespread acceptance. This paper will (...) trace the conceptual history of Beijerinck’s claim that ‘everything is everywhere’ in relation to a more general account of its theoretical, experimental and institutional context. His principle also needs to be situated in relationship to plant and animal biogeography, which, this paper will argue, forms a continuum of thought with microbial biogeography. Finally, a brief overview of the contemporary microbiological research challenging ‘everything is everywhere’ reveals that philosophical issues from Beijerinck’s era of microbiology still provoke intense discussion in twenty-first century investigations of microbial biogeography. (shrink)

The Tree of Life hypothesis frames the evolutionary process as a series of events whereby lineages diverge from one another, thus creating the diversity of life as descendent lineages modify properties from their ancestors. This hypothesis is under scrutiny due to the strong evidence for lateral gene transfer between distantly related bacterial taxa, thereby providing extant taxa with more than one parent. As a result, one argues, the Tree of Life becomes confounded as the original branching structure is gradually superseded (...) by reticulation, ultimately losing its ability to serve as a model for bacterial evolution. Here we address a more fundamental issue: is there a Tree of Life that results from bacterial evolution without considering such lateral gene transfers? Unlike eukaryotic speciation events, lineage separation in bacteria is a gradual process that occurs over tens of millions of years, whereby genetic isolation is established on a gene-by-gene basis. As a result, groups of closely related bacteria, while showing robust genetic isolation as extant lineages, were not created by an unambiguous series of lineage-splitting events. Rather, a temporal fragmentation of the speciation process results in cognate genes showing different genetic relationships. We argue that lineage divergence in bacteria does not produce a tree-like framework, and inferences drawn from such a framework have the potential to be incorrect and misleading. Therefore, the Tree of Life is an inappropriate paradigm for bacterial evolution regardless of the extent of gene transfer between distantly related taxa. (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)

Extreme variation in the meaning of the term “species” throughout the history of biology has often frustrated attempts of historians, philosophers and biologists to communicate with one another about the transition in biological thinking from the static species concept to the modern notion of evolving species. The most important change which has underlain all the other fluctuations in the meaning of the word “species” is the change from it denoting such metaphysical entities as essences, Forms or Natures to denoting classes (...) of individual organisms. Several authors have taken notice of the role of metaphysics in the work of particular biologists. An attempt will be made in this paper to present a systematic investigation of the role which metaphysics has played in the work of representative biologists throughout the history of biology, especially as it relates to their species concepts. (shrink)

Extreme variation in the meaning of the term “species” throughout the history of biology has often frustrated attempts of historians, philosophers and biologists to communicate with one another about the transition in biological thinking from the static species concept to the modern notion of evolving species. The most important change which has underlain all the other fluctuations in the meaning of the word “species” is the change from it denoting such metaphysical entities as essences, Forms or Natures to denoting classes (...) of individual organisms. Several authors have taken notice of the role of metaphysics in the work of particular biologists. An attempt will be made in this paper to present a systematic investigation of the role which metaphysics has played in the work of representative biologists throughout the history of biology, especially as it relates to their species concepts. (shrink)

This paper examines David Hull’s and Peter Godfrey-Smith’s accounts of biological individuality using the case of biofilms. Biofilms fail standard criteria for individuality, such as having reproductive bottlenecks and forming parent-offspring lineages. Nevertheless, biofilms are good candidates for individuals. The nature of biofilms shows that Godfrey-Smith’s account of individuality, with its reliance on reproduction, is too restrictive. Hull’s interactor notion of individuality better captures biofilms, and we argue that it offers a better account of biological individuality. However, Hull’s notion of (...) interactor needs more precision. We suggest some ways to make Hull’s notion of interactor and his account of individuality more precise. Generally, we maintain that biofilms are a good test case for theories of individuality, and a careful examination of biofilms furthers our understanding of biological individuality. (shrink)

With this manifesto, John Dupré systematically attacks the ideal of scientific unity by showing how its underlying assumptions are at odds with the central conclusions of science itself.

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)

Comprehensive evaluation and study of man's theories and knowledge of genetical characteristics and the evolutionary processes.

Causation is everywhere in the world: it features in every science and technology. But how much do we understand it? Mumford and Anjum develop a new theory of causation based on an ontology of real powers or dispositions. They provide the first detailed outline of a thoroughly dispositional approach, and explore its surprising features.

This fine collection of essays by a leading philosopher of science presents a defence of integrative pluralism as the best description for the complexity of scientific inquiry today. The tendency of some scientists to unify science by reducing all theories to a few fundamental laws of the most basic particles that populate our universe is ill-suited to the biological sciences, which study multi-component, multi-level, evolved complex systems. This integrative pluralism is the most efficient way to understand the different and complex (...) processes - historical and interactive - that generate biological phenomena. This book will be of interest to students and professionals in the philosophy of science. (shrink)

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

This book offers a philosophy for error-prone humans trying to understand messy systems in the real world.