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CURRENT RESEARCH ABSTRACTS

Note: The titles below are hyperlinked to downloadable articles.

Health, Ecology, and the Microbiome

eLife, Forthcoming

Advances in microbiomics have changed the way in which many researchers think about health and disease. These changes have also raised a number of philosophical questions around these topics, such as the types of living systems to which these concepts can be applied. Here, I discuss the human microbiome from two perspectives: the first treats the microbiome as part of a larger system that includes the human; the second treats the microbiome as an independent ecosystem that provides services to humans. Drawing on the philosophy of medicine and ecology, I explore two questions: i) how can we make sense of disease and dysfunction in these two perspectives? ii) are these two perspectives complimentary or do they compete with each other?

When Ecology Needs Economics and Economics Needs Ecology: Interdisciplinary Exchange During the Anthropocene

Ethics, Policy and the Environment, Forthcoming

(w DesRoches CT)

Abstract coming...​

Mutationism, not Lamarckism, captures the novelty of CRISPR-Cas

Biology and Philosophy, Forthcoming

(w JG Wideman, WF Doolittle, RJ Redfield)

Koonin, in an article in this issue, claims that CRISPR-Cas systems are mechanisms for the inheritance of acquired adaptive characteristics (IAAC), and that the operation of such systems comprises a "Lamarckian mode of evolution." We argue that viewing the CRISPR-Cas mechanism as facilitating a form of "directed mutation" more accurately represents how the system behaves and the history of neoDarwinian thinking, and is to be preferred.

Revamping the image of science for the Anthropocene

Philosophy, Theory, and Practice in Biology, Forthcoming

(w DesRoches CT)

Science is often described as a set of discipline-specific paradigms that share common concepts, theories, and practices. However, during the Anthropocene, this image of science has become inapplicable and is potentially damaging. Today, many natural and social scientists confront problems and systems that transgress traditional disciplinary boundaries—we focus on ecologists and economists. We claim that these changes justify rethinking the prevailing image of science, along with the relation between life scientists and social scientists. The time is ripe to recognize the new normal in Anthropocene science and spell out what transdisciplinary problems entail for research practice. We suggest three central issues should be recognized by any adequate characterization of the new normal. First, given the preponderance of natural-social systems in the Anthropocene, we claim that there are circumstances when analyzing such systems requires new methodological standards. Second, Anthropocene science will increasingly involve discussions that link the normative and the scientific, where questions of how and what we should study imply questions of value. Finally, because the vast majority of Anthropocene science will be interdisciplinary, we identify some of the mechanisms that allow researchers to engage with social scientists and scholars in the humanities.

Processes and patterns of interaction as units of selection: An introduction to ITSNTS thinking

Proceedings of the National Academy of Sciences (USA), 2018

(w WF Doolittle)

Many practicing biologists accept that nothing in their discipline makes sense except in the light of evolution, and that natural selection is evolution’s principal sense-maker. But what natural selection actually is (a force or a statistical outcome, for example) and the levels of the biological hierarchy (genes, organisms, species, or even ecosystems) at which it operates directly are still actively disputed among philosophers and theoretical biologists. Most formulations of evolution by natural selection emphasize the differential reproduction of entities at one or the other of these levels. Some also recognize differential persistence, but in either case the focus is on lineages of material things: even species can be thought of as spatiotemporally restricted, if dispersed, physical beings. Few consider—as “units of selection” in their own right—the processes implemented by genes, cells, species, or communities. “It’s the song not the singer” (ITSNTS) theory does that, also claiming that evolution by natural selection of processes is more easily understood and explained as differential persistence than as differential reproduction. ITSNTS was formulated as a response to the observation that the collective functions of microbial communities (the songs) are more stably conserved and ecologically relevant than are the taxa that implement them (the singers). It aims to serve as a useful corrective to claims that “holobionts” (microbes and their animal or plant hosts) are aggregate “units of selection,” claims that often conflate meanings of that latter term. But ITSNS also seems broadly applicable, for example, to the evolution of global biogeochemical cycles and the definition of ecosystem function.

Are Humans Disturbing Conditions in Ecology?

Biology and Philosophy, 2017

In this paper I argue, first, that ecologists have routinely treated humans—or more specifically, anthropogenic causal factors—as disturbing conditions. I define disturbing conditions as exogenous variables, variables "outside" a model, that when present in a target system, inhibit the applicability or accuracy of the model. This treatment is surprising given that (i) humans play a dominant role in many ecosystems and (ii) definitions of ecology contain no fundamental distinction between human and natural. Second, I argue that the treatment of humans as disturbing conditions is an idealization: since it is, and has long been, known that humans are pervasive, this treatment amounts to an intentionally introduced theoretical distortion. Finally, characterizing this treatment as idealization forces us to confront the question of its justification(s), and so, drawing on three different kinds of idealization, I evaluate how this treatment may be justified.

Demarcating Nature, Defining Ecology: Creating a Rationale for the Study of Nature’s ‘Primitive Conditions’

Perspectives on Science, 2017

The proper place of humans in ecological study has been a recurring issue. I reconstruct and evaluate an early twentieth century rationale in ecology that encouraged the treatment of humans as apart from natural processes, and I unearth the interests and assumptions, both epistemic and non-epistemic, that fostered it. This rationale was articulated during the early years of the Ecological Society of America, particularly through its Committee on the Preservation of Natural Conditions. Committee members advocated for the preservation of what they considered epistemologically foundational and functionally normal objects of study—nature’s “primitive conditions”—and in doing so collapsed two conceptually independent categories of unnaturalness: the artificial and the pathological. As these ecologists demarcated what counted as nature, they were, in the process, defining ecology as a science in ways that had lasting repercussions.

The Coupling of Taxonomy and Function in Microbiomes

Biology and Philosophy, 2017

(w Douglas GM, Brunet TDP, Leuschen K, Doolittle WF, Langille MGI)

Microbiologists are transitioning from the study and characterization of individual strains or species to the profiling of whole microbiomes and microbial ecology. Equipped with high-throughput methods for studying the taxonomic and functional characteristics of diverse samples, they are just beginning to encounter the conceptual, theoretical, and experimental problems of comparing taxonomy to (micro-ecological) function, and extracting useful measures from such comparisons (i.e. diversity, stability, or "health"). Although still unresolved, these problems are well studied in macro-ecology (the ecology of non-microbes) and are reiterated here as an historical precautionary for microbial ecologists. Beyond expected and unresolved terminological vagueness, we argue that assessments and comparisons of taxonomic and functional profiles in micro-ecology suffer from theoretically unresolvable arbitrariness and ambiguities. We divide these into problems of scale, individuation, and commensurability. We argue that there is no technically/theoretically "correct" scale, individuation, or comparison of taxonomy and function, but there are nonetheless better and worse methodologies for profiling.

The Eroding Artificial/Natural Distinction? Some Consequences for Ecology and Economics

In M Nagatsu and A Ruzzene (eds.), Philosophy and the Social Sciences: A Dialogue , forthcoming

(w DesRoches CT and Green TL)

Since Thomas Kuhn’s The Structure of Scientific Revolutions (1962), historians and philosophers of science have paid increasing attention to the implications of disciplinarity. In this chapter we consider restrictions posed to interdisciplinary exchange between ecology and economics that result from commitments to disciplinary purity. We argue that, when it comes to the objects of study in ecology and economics, ideas of disciplinary purity have been underwritten by the artificial-natural distinction. We then problematize this distinction, and thus disciplinary purity, both conceptually and empirically. Conceptually, the distinction is no longer tenable. Empirically, recent interdisciplinary research has shown the epistemological and policy-oriented benefits of dealing with models which explicitly link anthropogenic and non-anthropogenic factors. We conclude that, in the current age of the Anthropocene, it is to be expected that without interdisciplinary exchange, ecology and economics may relinquish global relevance because the distinct and separate systems to which each “pure” science was originally made to apply will only diminish over time.

Character displacement is an evolutionary pattern. So what causes it?

Biological Journal of the Linnean Society, 2017

(w Stuart YE, Hopkins R, and Bolnick DI)

Character displacement was originally defined simply as a pattern—divergence between two species in sympatry but not allopatry—and it was recognized that multiple processes might generate this pattern. However, over time, character displacement has come to be nearly synonymous with the process of adaptive divergence between species caused by selection stemming from resource-competitive interactions (and if not that, reproductive interactions). This tight link between character displacement and resource competition has generated, and continues to generate, imprecision and confusion in the literature. Here, to address this problem, we suggest unlinking character displacement the pattern from any specific process (e.g., natural selection arising from species interactions). That is, character displacement should be documented as a pattern, agnostically with respect to process. Purposeful, direct investigation of what process generated character displacement then naturally follows. This has the benefit of acknowledging that there can be many different avenues to divergence in sympatry.

Molecular Phylogenetics and the Perennial Problem of Homology

Journal of Molecular Evolution, 2016

(w Ford Doolittle)

The concept of homology has a long history, during much of which the issue has been how to reconcile similarity and common descent when these are not coextensive. Although thinking molecular phylogeneticists have learned not to say "percent homology" the problems are deeper than that, and unresolved.

Like Hercules and the Hydra: Trade-offs and Strategies in Ecological Model-Building and Experimental Design

Studies in History and Philosophy of Biological and Biomedical Sciences, 2016

Experimental ecologists often invoke trade-offs to describe the constraints they encounter when choosing between alternative experimental designs, such as between laboratory, field, and natural experiments. In making these claims, they tend to rely on Richard Levins' analysis of trade-offs in theoretical model-building. But does Levins' framework apply to experiments? In this paper, I focus this question on one desideratum widely invoked in the modelling literature: generality. Using the case of generality, I assess whether Levins-style treatments of modelling provide workable resources for assessing trade-offs in experimental design. I argue that, of four strategies modellers employ to increase generality, only one may be unproblematically applied to experimental design. Furthermore, modelling desiderata do not have obvious correlates in experimental design, and when we define these desiderata in a way that seem consistent with ecologists' usage, the trade-off framework falls apart. I conclude that a Levins-inspired framework for modelling does not provide the content for a similar approach to experimental practice; this does not, however, mean that it cannot provide the form.

The Art Itself is Nature’: Darwin, Domestic Varieties, and the Scientific Revolution

Endeavour, 2014

Common to both the scientific and Darwinian revolutions were discussions challenging the distinction between art and nature. Was art a part of nature? Could art be used as a model for nature? This intellectual congruence, however, is more than just nominal. Charles Darwin and Asa Gray, for example, were well-aware of the 17th century debates which preceded them through the works of such revered English writers as William Shakespeare and Thomas Browne. Furthermore, they used their understandings of these debates to inform and express their own thinking about the relation between artificial and natural selection.

Sex-specific foraging behaviors and growth rates in juveniles mediate the development of extreme sexual size dimorphism.

Open Ecology Journal, 2010

(w Foellmer M)

Character displacement was originally defined simply as a pattern—divergence between two species in sympatry but not allopatry—and it was recognized that multiple processes might generate this pattern. However, over time, character displacement has come to be nearly synonymous with the process of adaptive divergence between species caused by selection stemming from resource-competitive interactions (and if not that, reproductive interactions). This tight link between character displacement and resource competition has generated, and continues to generate, imprecision and confusion in the literature. Here, to address this problem, we suggest unlinking character displacement the pattern from any specific process (e.g., natural selection arising from species interactions). That is, character displacement should be documented as a pattern, agnostically with respect to process. Purposeful, direct investigation of what process generated character displacement then naturally follows. This has the benefit of acknowledging that there can be many different avenues to divergence in sympatry.

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