Nobel-price winning atmospheric chemist Paul Crutzen introduced in 2000 the concept of the Anthropocene as the name for the successor geological period to the Holocene. The Holocene started about 12,000 years ago and is characterized by the relatively stable and temperate climatic and environmental conditions that were conducive to the development of human societies. Until recently, human development had relatively little impact on the dynamics of geological time. Although disagreement exists over the exact birth date of the Anthropocene, it is (...) indisputable that the impact of human activity on the geo-climatic environment became more pronounced from the industrial revolution onwards, leading to a situation in which humans are now widely considered to have an eco-geologically critical impact on the earth's bio-physical system. The most obvious example is the accumulation of greenhouse gases like CO2and Methane in the atmosphere and the changes this induces in climatic dynamics. Others are the growing homogenization of biodiversity as a result of human-induced species migration, mass extinction and bio-diversity loss, the manufacturing of new species through genetic modification, or the geodetic consequences resulting from, for example, large dam construction, mining and changing sea-levels. (shrink)

The development of culture-independent strategies to study microbial diversity and function has led to a revolution in microbial ecology, enabling us to address fundamental questions about the distribution of microbes and their influence on Earth’s biogeochemical cycles. This article discusses some of the progress that scientists have made with the use of so-called “omic” techniques (metagenomics, metatranscriptomics, and metaproteomics) and the limitations and major challenges these approaches are currently facing. These ‘omic methods have been used to describe the taxonomic structure (...) of microbial communities in different environments and to discover new genes and enzymes of industrial and medical interest. However, microbial community structure varies in different spatial and temporal scales and none of the ‘omic techniques are individually able to elucidate the complex aspects of microbial communities and ecosystems. In this article we highlight the importance of a spatiotemporal sampling design, together with a multilevel ‘omic approach and a community analysis strategy (association networks and modeling) to examine and predict interacting microbial communities and their impact on the environment. (shrink)

Health economists claim to use market economics combined with the microeconomic concepts of opportunity cost and the margin to advise on priority setting. However, they are advising on setting priorities through a macro-economic analysis using the costs of the supplier, thus prioritising the producer and not the consumer as the dynamic of economic activity. For health economists any contention within priority setting is due to lack of data not their confusion over fundamental concepts.

A scientific explanatory project, part-whole explanation, and a kind of science, part-whole science are premised on identifying, investigating, and using parts and wholes. In the biological sciences, mechanistic, structuralist, and historical explanations are part-whole explanations. Each expresses different norms, explananda, and aims. Each is associated with a distinct partitioning frame for abstracting kinds of parts. These three explanatory projects can be complemented in order to provide an integrative vision of the whole system, as is shown for a detailed case study: (...) the tetrapod limb. My diagnosis of part-whole explanation in the biological sciences as well as in other domains exploring evolved, complex, and integrated systems (e.g., psychology and cognitive science) cross-cuts standard philosophical categories of explanation: causal explanation and explanation as unification. Part-whole explanation is itself one essential aspect of part-whole science. (shrink)

I analyze the importance of parts in the style of biological theorizing that I call compositional biology. I do this by investigating various aspects, including partitioning frames and explanatory accounts, of the theoretical perspectives that fall under and are guided by compositional biology. I ground this general examination in a comparative analysis of three different disciplines with their associated compositional theoretical perspectives: comparative morphology, functional morphology, and developmental biology. I glean data for this analysis from canonical textbooks and defend the (...) use of such texts for the philosophy of science. I end with a discussion of the importance of recognizing formal and compositional biology as two genuinely different ways of doing biology – the differences arising more from their distinct methodologies than from scientific discipline included or natural domain studied. Ultimately, developing a translation manual between the two styles would be desirable as they currently are, at times, in conflict. (shrink)

Levins and Lewontin have contributed significantly to our philosophical understanding of the structures, processes, and purposes of biological mathematical theorizing and modeling. Here I explore their separate and joint pleas to avoid making abstract and ideal scientific models ontologically independent by confusing or conflating our scientific models and the world. I differentiate two views of theorizing and modeling, orthodox and dialectical, in order to examine Levins and Lewontin’s, among others, advocacy of the latter view. I compare the positions of these (...) two views with respect to four points regarding ontological assumptions: (1) the origin of ontological assumptions, (2) the relation of such assumptions to the formal models of the same theory, (3) their use in integrating and negotiating different formal models of distinct theories, and (4) their employment in explanatory activity. Dialectical is here used in both its Hegelian–Marxist sense of opposition and tension between alternative positions and in its Platonic sense of dialogue between advocates of distinct theories. I investigate three case studies, from Levins and Lewontin as well as from a recent paper of mine, that show the relevance and power of the dialectical understanding of theorizing and modeling. (shrink)

Darwin's ideas on variation, heredity, and development differ significantly from twentieth-century views. First, Darwin held that environmental changes, acting either on the reproductive organs or the body, were necessary to generate variation. Second, heredity was a developmental, not a transmissional, process; variation was a change in the developmental process of change. An analysis of Darwin's elaboration and modification of these two positions from his early notebooks (1836-1844) to the last edition of the /Variation of Animals and Plants Under Domestication/ (1875) (...) complements previous Darwin scholarship on these issues. Included in this analysis is a description of the way Darwin employed the distinction between transmission and development, as well as the conceptual relationship he saw between heredity and variation. This paper is part of a larger project comparing commitments regarding variation during the latter half of the nineteenth century. (shrink)

This paper opens with a presentation of the philosophical underpinning and rationale of the concept of physical literacy. This is followed by an articulation of the concept of physical literacy. Three subsequent sections then consider aspects of the concept in a little more detail. The first investigates the relationship of the physical literacy to the development of a sense of self and to establishing interaction with others. Here the philosophical approach is informed by writings on cognitive development and recent neurological (...) insights. The second considers the universality of the concept and looks briefly at the views of existentialists and of contemporary sociologists. The third section addresses the place of propositional knowledge in being physically literate. The implications of objectifying the body in descriptive language are weighed against the fact that verbally expressed understanding and knowledge are an integral part of Western culture. The debate presented is one of a series that has, over the last five years, mapped the author's work on developing the concept of physical literacy. The aspects chosen to be discussed here are three that have generated considerable interest and debate. In conclusion, there is a short reflection on the implications of the views discussed for education and physical education. (shrink)

This paper is an interpretation and defense of Richard Levins’ “The Strategy of Model Building in Population Biology,” which has been extremely influential among biologists since its publication 40 years ago. In this article, Levins confronted some of the deepest philosophical issues surrounding modeling and theory construction. By way of interpretation, I discuss each of Levins’ major philosophical themes: the problem of complexity, the brute-force approach, the existence and consequence of tradeoffs, and robustness analysis. I argue that Levins’ article is (...) concerned, at its core, with justifying the use of multiple, idealized models in population biology. (shrink)

Over the past fifteen years there has been a considerable amount of debate concerning what theoretical population dynamic models tell us about the nature of natural selection and drift. On the causal interpretation, these models describe the causes of population change. On the statistical interpretation, the models of population dynamics models specify statistical parameters that explain, predict, and quantify changes in population structure, without identifying the causes of those changes. Selection and drift are part of a statistical description of population (...) change; they are not discrete, apportionable causes. Our objective here is to provide a definitive statement of the statistical position, so as to allay some confusions in the current literature. We outline four commitments that are central to statisticalism. They are: 1. Natural Selection is a higher order effect; 2. Trait fitness is primitive; 3. Modern Synthesis (MS)-models are substrate neutral; 4. MS-selection and drift are model-relative. (shrink)

Debates about the relationship between agricultural technology and the conservation of crop genetic diversity are often hampered by unclear vocabulary and imprecise data. Various interpretations of the terms “modern variety,” “local variety,” “hybrid,” and “green revolution” are first explored, and then evidence is examined regarding the effect of modern varieties on intra- and intercrop diversity, risk, input use, and farmer decision-making. The objective is to urge a more reasoned debate about the future of plant genetic resources.

Different explanations of color vision favor different philosophical positions: Computational vision is more compatible with objectivism (the color is in the object), psychophysics and neurophysiology with subjectivism (the color is in the head). Comparative research suggests that an explanation of color must be both experientialist (unlike objectivism) and ecological (unlike subjectivism). Computational vision's emphasis on optimally prespecified features of the environment (i.e., distal properties, independent of the sensory-motor capacities of the animal) is unsatisfactory. Conceiving of visual perception instead as the (...) visual guidance of activity in an environment that is determined largely by that very activity suggests new directions for research. (shrink)

In biology, the ‘ecological orientation' rests on a commitment to examining systems, and the conceptual challenge of defining that system now employs techniques and concepts adapted from diverse disciplines (i.e., systems philosophy, cybernetics, information theory, computer science) that are applied to biological simulations and model building. Immunology has joined these efforts, and the question posed here is whether the discipline will remain committed to its theoretical concerns framed by the notions of protecting an insular self, an entity demarcated from its (...) environment, or will shift its focus of interest to a wider context. An ecological perspective emphasizes the interchange between the organism and its environment, the processing of information, and the regulation arising from responses to this larger context. Moving from the first attempts at modeling the immune system as a closed network, immunologists have joined the general interest in systems analysis, and that move might portend a significant shift to an open, more holistic consideration of immune regulation. *Received December 2006; revised August 2007. †To contact the author, please write to: Center for Philosophy and History of Science, Boston University, 745 Commonwealth Ave., Boston, MA 02215; e-mail: [email protected] (shrink)

Residual categories are those which cannot be formally represented within a given classification system. We examine the forms that residuality takes within our information systems today, and explore some silences which form around those inhabiting particular residual categories. We argue that there is significant ethical and political work to be done in exploring residuality.

. Reproducible results and repeatable measurements at the same location are fundamental to science, yet of grave concern to scientists. Involvement in biological re-surveys under MVZ-Berkeley, Harvard-LTER and Hamaarag elucidated “replication” and “location” and untangled “incommensurability” from “no fact of the matter” and “indeterminacy.” All cases revealed incommensurability without indeterminacy on the smallest scale and indeterminacy without incommensurability on higher scales, with communication failure in the former and successful workarounds in the latter. I argue that an involved philosophy helps clarify (...) fundamental concepts in this case, and since it could also help other cases it therefore should be examined in every case before being ruled out. (shrink)

Edward O. Wilson's forays into human sociobiology have been the target of persistent, vehement attack by his Harvard colleague in evolutionary biology, Richard C. Lewontin. Through examination of existing documents in the case, together with in-depth personal interviews of Wilson, Lewontin, and other biologists, the reasons for Wilson's stance and Lewontin's criticisms are uncovered. It is argued that the dispute is not primarily personally or politically motivated, but involves a conflict between long-term scientific-cum-moral agendas, with the reductionist program as a (...) key issue. It is concluded that it is in the interest of both disputants to keep the controversy alive. (shrink)

The Gaia hypothesis emerged from two interpenetrating traditions, the mechanist and the organicist, with the former tending to reductionism and the latter to holism. While mechanist James Lovelock is the acknowledged father, he collaborated with the organicist Lynn Margulis in the early 1970s when the first papers appeared in the scientific literature. Both continued to be active in Gaia-related conferences until Margulis’s premature death in late 2011. In a very readable exposition, Michael Ruse succeeds brilliantly in tracing the philosophical roots (...) of this concept continuing in the histories of modern geology and biology to its formulation in the late twentieth century.This is Lovelock and Margulis’s definition of the Gaia hypothesis quoted in this book: “We conclude from the fact that the temperature and certain other environmental conditions on the earth have not altered very much from what is an optimum for life on surface, that life must actively maintain these conditions”. (shrink)

The environmental degradation caused by industrial agriculture, as well as the resulting social and health consequences, creates an urgency to rethink food production by expanding the moral imagination to include agricultural practices. Agricultural practices presume human use of the earth and acknowledge human dependence on the biotic community, and these relations mean that agriculture presents a separate set of considerations in the broader field of environmental ethics. Many scholars and activists have argued persuasively that we need new stories to rethink (...) agricultural practice, however, the link—the story that does and can shape agricultural practice—has not yet been fully articulated in environmental discourse. My analysis explores how language has shaped existing agricultural models and, more important, the potential of story to influence agricultural practice. To do this, I draw upon cognitive theory to illustrate how metaphoric and narrative language structures thought and influences practice, beginning with my contention that industrial agriculture relies on a discourse of mechanistic relations between humans and a passive earth, language that has naturalized the chemically intensive monocultures prevalent in much of the American Midwest. However, alternative agricultures, including organic agriculture, agro-ecology, and ecological agriculture, emphasize qualities such as interdependence and reciprocity and do so as a deliberate response to the perceived inadequacies of industrial agriculture and its governing narrative. Exploring the different discourses of agricultural systems can help us think through different modalities for human relations with the biotic community and demonstrate story’s potential role in altering practice. (shrink)

: A central claim of Longino's contextual empiricism is that scientific inquiry, even when "properly conducted", lacks the capacity to screen out the influence of contextual values on its results. I'll show first that Longino's attack against the epistemic integrity of science suffers from fatal empirical weaknesses. Second I'll explain why Longino's practical proposition for suppressing biases in science, drawn from her contextual empiricism, is too demanding and, therefore, unable to serve its purpose. Finally, drawing on Bourdieu's sociological analysis of (...) scientific communities, I'll sketch an alternative view of scientific practice reconciling a thoroughly social view of science (such as Longino's) with a defense of its epistemic integrity. (shrink)

Astonishing changes have occurred to agricultural production systems since WWII. As such, many people tend to date the origins of industrial chemical agricultural to the early 1940s. The origins of industrial chemical agriculture, however, both on and off the field, have a much longer history. Indeed, industrial agriculture’s much discussed chemical dependency—in particular its need for toxic chemicals—and the development of the industries that feed this fix, have a long and diverse past that extend well back into the nineteenth century. (...) In this paper, through the narrative of a late nineteenth century creation story, I go in search of a crucial linchpin in that longer history. I argue that industrial pest control has been imbued with the practices, discourse, materials, and ethics of modern chemical warfare since its inception. Faced with pest-induced collapse, Los Angeles citrus growers and scientists of the USDA and UC Agricultural Extension chemically fixed the citrus pest problem by developing and utilizing the cyanide gas chamber. Cyanide fumigation quickly became the toxic cornerstone of the citrus industry, enabling its intensification and expansion as the pest infection became systemic. By the turn the century, furnished with an economic poison made cheap and weapons-grade due to changes in the world gold mining industry, growers transformed cyanide fumigation into a necessary agricultural input. In chemically overriding an agro-ecological contradiction of capitalist agriculture, growers, scientists, and government officials amalgamated industrially organized agriculture to accelerating and endless chemical warfare. These suddenly necessary agricultural practices signaled a state change in world-ecology and agroindustrial organization, thus, the discovery of effective industrial control for citrus pests was not only a pivotal moment in the history of Southern California but it was also an event that has had world-historical implications. (shrink)