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  journal articles

genome ecology

Linquist, S. Cottenie, K. Elliott, T.A. Saylor, B. Kremer, S.C. and Gregory, T.R. (2015) Applying ecological models to communities 
of genetic elements: the case of neutral theory. Molecular Ecology, 24(13): 3232-3242.

Provides a critical overview of neutral theory in community ecology, and discusses how it should (and should not) be applied to communities of genetic elements. We also compare this application of genome-level neutral theory to other models of neutral evolution, in particular to Kimura's Neutral theory and Lynch's Mutational Hazard Model.

Linquist, S., B. Saylor, K.
Cottenie, T.A.. Elliott, S.C. Kremer & T.R. Gregory (2013). Distinguishing ecological from evolutionary approaches to transposable elements. Biological Reviews, 88(3): 573-584.

Identifies some key questions in transposon biology that are potentially illuminated by an ecological approach. Then offers a general distinction between ecology and evolution, which can be used to measure the extent to which a given pattern calls for each type of explanation. This distinction could in principle be applied at any level in biology (populations, communities, ecosystems, etc). We apply it here at the genomic level.

Saylor, B. T.A. Elliott, S. Linquist. S.C. Kremer, T.R.. Gregory & K Cottenie (2013). A novel application of ecological analyses to transposable element distributions in the Bos taurus genome. Genome, 56: 521-533.

Applies some of the thinking outlined in the former theoretical paper. Specifically, we conducted a transect analysis of transposable elements to assess whether "ecological" factors (within the genome) impact the spatial distribution of particular transposon families.

philosophy of ecology

Linquist, S. (forthcoming). Against Lawton's contingency thesis, or, why the demise of community ecology has been greatly exaggerated.  Proceedings of the Philosophy of Science Association.
By applying the distinction between evolution and ecology, developed by Linquist et al. (2013) to ecological communities, it becomes apparent that Lawton's Contingency Thesis --that ecological communities admit of no general "laws" --is based on the wrong kind of evidence.

Colyvan, M., S. Linquist, W. Grey, P. E. Griffiths, J. Odenbaugh and H. P. Possingham (2009). Philosophgical issues in ecology: recent trends and future directionsEcology and Society 14(2): 22-

Identifies some of the key philosophical issues in the discipline of ecology.

Linquist, S. (2008). But is it progress? On the alleged advances of conservation biology over ecology. Biology and Philosophy, 23: 529, 544.     

Argues that general ecological theories, such as Island Biogeography Theory, are equally (if not better) suited to conservation management than place prioritization algorithms.

function concepts in genomics

Elliott, T.A., S. Linquist and T.R. Gregory (2014).  
Conceptual and empirical challenges of ascribing functions to transposable elements.   the American Naturalist, 184 (1), 14-24.
Argues that the methods used by ENCODE to assign biochemical functions to genetic elements were illegitimate, not simply because they employed a CR as opposed to an SE concept, but because most of the elements that they investigated are (or once were) mobile --i.e. tranposons.  We provide a superior framework for determining when a mobile element can be legitimately viewed as functional.
Doolittle, W. F., T. Brunet, S. Linquist, & T.R. Gregory (2014).  Distinguishing between function and effect in genome biology.   Genome Biology and Evolution, 6, 1234-1237.  
Argues that geneticists should be more explicit in distinguishing CR and SE functions, and that a large portion of the effects that they currently identify as "functional" are  more accurately described as mere effects -i.e. non functional.

emotion, culture and neuroscience

Linquist, S.  & J. Bartol (2013). Two myths about somatic markers. The British Journal for the Philosophy of Science. 64(3): 455-484.

Provides a framework for classifying alternative versions of the (highly ambiguous) Somatic Marker Hypothesis. Then argues that chief proponents of SMH have favoured interpretations wherein somatic markers influence the core stages of decision making, when in fact their own evidence suggests a role in peripheral stages.

Bartol, J. & S. Linquist (forthcoming). How do somatic markers feature in decision making? Emotion Review.
Demonstrates that the scientific literature is replete with competing interpretations of the Somatic marker Hypothesis. And provides a basic computational model of decision making to help systematize these alternative interpretations.

innateness and human nature

Linquist, S. E. Machery, P. Griffiths & K. Stotz (2011). Exploring the folkbiological conception of innateness. Philosophical Transactions of the Royal Society B vol. 366,  issue 1563: 444-454.

Provides further empirical evidence for the Three Factor theory of the innateness concept. Also shows that judgments about traits being "in the genes" have the same structure. Argues that a multi-dimensional analysis of concepts is preferable because of the fine-grained analysis.

Griffiths, P. E. Machery and S. Linquist (2009). The vernacular concept of innateness. Mind and Language 24(5): 605-630.

Introduces the Three Factor theory of the innatenes concept, where evidence of fixity, species typicality or adaption are individually sufficient for the folk to judge that a trait is "innate." Provides empirical evidence that the three factors are also additive. 

Linquist, S. (2007). Prospects for a dual inheritance model of emotional evolution. Philosophy of Science, 74: 848�859.

Offers a dual inheritance (gene-culture coveolutionary) framework for understaning the evolution of complex human emotions (in this case, guilt).

Linquist, S. & A. Rosenberg, (2007), "Return of the Tabula Rasa. Philosophy and Phenomenological Research, 74(2): 476- 497.

A critical review essay of Kim Sterelny's Thought in a Hostile World.

Rosenberg, A. and S. Linquist (2006), On the original contract: Evolutionary game theory and human evolution.  Analyse & Kritik, 27(1): 136-157.
Draws together evidence from anthropology, primatology and other sources to assess the legitimacy of econbomic models of cooperation.

       books (edited volumes)

            Linquist, Stefan (2010), The Philosophy of Evolutionary Biology: Volume I. Ashgate Publishing: Surrey, England (616 pages).  

            Linquist, Stefan & Levy, Neil (2010), Evolutionary Psychology: Volume II. Ashgate Publishing: Surrey, England (456 pages).

            Linquist, Stefan (2010), The Evolution of Culture: Volume IV. Ashgate Publishing: Surrey, England (538 pages).

            chapters in books
Linquist, Stefan (2010), Introduction, The Philosophy of Evolutionary Biology: Volume I. Ashgate Publishing: Surrey, England. (p. 11-54).
            Linquist, Stefan & Levy, Neil (2010), Introduction, Evolutionary Psychology: Volume II.. Ashgate Publishing: Surrey, England
            (p. 11-45).

            Linquist, Stefan (2010), Introduction, The Evolution of Culture: Volume IV. Ashgate Publishing: Surrey, England (p. 11-41).

book reviews

Linquist, S. (2007) "If it feels good, believe it. Paul Thagard's Hot Thought: Mechanisms and Applications of Emotional Cognition", Notre Dame Philosophical Review.

Linquist, S. (2006) "When is an Orgasm just an Orgasm? Elizabeth Lloyd's The Case of the Female Orgasm: Bias in the Science of Evolution", Metascience, 15:411-419.

     Popular Articles

        "What makes a rockfish sexy?", appeared in The Westerley, Summer 2006 & 2009.

        "A day in the life of a sea cucumber", appeared in The Westerley, Summer 2009.      

        "Collector's log: A rare encounter with a crevice kelpfish", appeared in The Westerley, Summer 2006 & 2009.