Stefan Linquist

Stefan Linquist
University of Guelph | UOGuelph · Department of Philosophy

PhD

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42
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676
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Publications

Publications (42)
Article
Full-text available
We compared two digital humanities methods in the analysis of a contested scientific term. “Epigenetics” is as enigmatic as it is popular. Some authors argue that its meaning has diluted over time as this term has come to describe a widening range of entities and mechanisms (Haig, International Journal of Epidemiology 41:13–16, 2012). Others propos...
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Wild Octopus tetricus frequently propel shells, silt, and algae through the water by releasing these materials from their arms while creating a forceful jet from the siphon held under the arm web. These "throws" occur in several contexts at a site in Jervis Bay, Australia, including in interactions with other octopuses. Material thrown in interacti...
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The distinction between causal role (CR) and selected effect (SE) functions is typically framed in terms of their respective explanatory roles. However, much of the controversy over functions in genomics takes place in an investigative, not an explanatory context. Specifically, the process of component-driven functional investigation begins with th...
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This correspondence responds to the critique by Butler et al. (BMC Genomics 22:241, 2021) of our recent paper on transposable element (TE) persistence. We address the three main objections raised by Butler et al. After running a series of additional simulations that were inspired by the authors’ criticisms, we are able to present a more nuanced und...
Preprint
Wild octopuses at an Australian site frequently propel shells, silt, and algae through the water by releasing these materials from their arms while creating a forceful jet from the siphon held under the arm web. These "throws" occur in several contexts, including interactions with conspecifics, and material thrown in conspecific contexts frequently...
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The recent explosion of interest in epigenetics is often portrayed as the dawning of a scientific revolution that promises to transform biomedical science along with developmental and evolutionary biology. Much of this enthusiasm surrounds what we call the epigenetic switch hypothesis, which regards certain examples of epigenetic inheritance as an...
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The applied discipline of agroecological design provides a useful case study for examining broader philosophical questions about the existence and importance of ecological generalizations or "laws." Recent developments in the availability and use of formal meta-analyses have led to the discovery of many resilient generalizations in ecology (Linquis...
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Background: The nuclear genomes of eukaryotes vary enormously in size, with much of this variability attributable to differential accumulation of transposable elements (TEs). To date, the precise evolutionary and ecological conditions influencing TE accumulation remain poorly understood. Most previous attempts to identify these conditions have foc...
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Pan-adaptationism is a theoretically problematic framework which assumes that most genetic and molecular structures have a function that was shaped by natural selection. Such an approach ignores plausible, non-selectionist explanations for the origins of those traits. Yet, the fields of molecular biology and genomics is often criticized for pan-ada...
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Why should governments or individuals invest time and resources in conserving biodiversity? A popular answer is that biodiversity has both instrumental value for humans and intrinsic value in its own right. Defending Biodiversity critically evaluates familiar arguments for these claims and finds that, at best, they provide good reasons for conservi...
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Defending Biodiversity exposes various weaknesses in recent scientific and ethical defenses of species and ecosystem conservation in the hope that those arguments can be improved upon. Jennifer Welchman’s critical review of our book embraces this challenge, focusing specifically on our discussion of aesthetic value. We argue that the best available...
Preprint
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The ability of a researcher to re-identify (re-ID) an animal individual upon re-encounter is fundamental for addressing a broad range of questions in the study of ecosystem function, community and population dynamics, and behavioural ecology. Tagging animals during mark and recapture studies is the most common method for reliable animal re-ID howev...
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Recent examples of rapid evolution under natural selection seem to require that the disciplines of ecology and evolution become better integrated. This inference makes sense only if one’s understanding of these disciplines is based on Hutchinson’s two-speed model of the ecological theater and the evolutionary play. Instead, these disciplines are mo...
Article
The proposed explanation for the evolution of shamanism is not the only viable option. I sketch an alternative commitment hypothesis that views shamanism as an adaptation at the level of biological individuals or cultural groups. To the extent that these hypotheses make overlapping predictions about the culturally shared features of shamanism, we l...
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It is widely recognized that the innate versus acquired distinction is a false dichotomy. Yet many scientists continue to describe certain traits as “innate” and take this to imply that those traits are not acquired, or “unlearned.” This article asks what cognitive role, if any, the concept of innateness should play in the psychological and behavio...
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We previously published a description of discovery of a site where octopuses live in an unusually dense collection of individual dens near one another in a bed of scallop shells amid a rock outcrop. We believe the shell bed is an extended midden, accumulated over time by individual octopuses returning to their dens with food. Here we consider what...
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We report wild octopuses (Octopus tetricus) living at high density at a rock outcrop, the second such site known. O. tetricus are often observed as solitary individuals, with the species known to exist at similar densities and exhibiting complex social behaviors at only one site other than that described here. The present site was occupied by 10–15...
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It is often argued that ecological communities admit of no useful generalizations or “laws” because these systems are especially prone to contingent historical events. Detractors respond that this argument assumes an overly stringent definition of laws of nature. Under a more relaxed conception, it is argued that ecological laws emerge at the level...
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The culture of honour hypothesis offers a compelling example of how human psychology differentially adapts to pastoral and horticultural environments. However, there is disagreement over whether this pattern is best explained by a memetic, evolutionary psychological, dual inheritance, or niche construction model. I argue that this disagreement stem...
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A promising recent development in molecular biology involves viewing the genome as a mini-ecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here we critically evaluate the prospects of Ecological Neutral Theory (ENT), a popular model in ecology, as...
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Several recent criticisms of the somatic marker hypothesis (SMH) identify multiple ambiguities in the way it has been formulated by its chief proponents. Here we provide evidence that this hypothesis has also been interpreted in various different ways by the scientific community. Our diagnosis of this problem is that SMH lacks an adequate computati...
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Lawton’s contingency thesis (CT) states that there are no useful generalizations (“laws”) at the level of ecological communities because these systems are especially prone to contingent historical events. I argue that this influential thesis has been grounded on the wrong kind of evidence. CT is best understood in Woodward’s (2010) terms as a claim...
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Abstract Media attention and the subsequent scientific backlash engendered by the claim by spokespeople for the Encyclopedia of DNA Elements (ENCODE) project that 80% of the human genome has a biochemical function highlight the need for a clearer understanding of function concepts in biology. This article provides an overview of two major function...
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There is renewed debate among biologists about the meaning of "function". Much of this has to do with the claim of ENCODE investigators to have at last disproven the 40-year-old notion that our genome is mostly informationally nonfunctional "junk" (ENCODE et al 2012; Graur et al 2013; Niu and Jiang 2013; Eddy 2012, 2013; Doolittle 2013). To the ext...
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Transposable elements (TEs) are among the most abundant components of many eukaryotic genomes. Efforts to explain TE abundance, as well as TE diversity among genomes, have led some researchers to draw an analogy between genomic and ecological processes. Adopting this perspective, we conducted an analysis of the cow (Bos taurus) genome using techniq...
Article
Considerable variation exists not only in the kinds of transposable elements (TEs) occurring within the genomes of different species, but also in their abundance and distribution. Noting a similarity to the assortment of organisms among ecosystems, some researchers have called for an ecological approach to the study of transposon dynamics. However,...
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Research on patients with damage to ventromedial frontal cortices suggests a key role for emotions in practical decision making. This field of investigation is often associated with Antonio Damasio’s Somatic Marker Hypothesis—a putative account of the mechanism through which autonomic tags guide decision making in typical individuals. Here we discu...
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Integrating the study of human diversity into the human evolutionary sciences requires substantial revision of traditional conceptions of a shared human nature. This process may be made more difficult by entrenched, 'folkbiological' modes of thought. Earlier work by the authors suggests that biologically naive subjects hold an implicit theory accor...
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Philosophy of ecology has been slow to become established as an area of philosophical interest, but it is now receiving considerable attention. This area holds great promise for the advancement of both ecology and the philosophy of science. Insights from the philosophy of science can advance ecology in a number of ways. For example, philosophy can...
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The proposal that the concept of innateness expresses a ‘folk biological’ theory of the ‘inner natures’ of organisms was tested by examining the response of biologically naive subjects to a series of realistic scenarios concerning the development of birdsong. Our results explain the intuitive appeal of many of the existing philosophical analyses of...
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As conservation biology has developed as a distinct discipline from ecology, conservation guidelines based on ecological theory have been largely cast aside in favor of theory-independent decision procedures for designing conservation reserves. I argue that this transition has failed to advance the field toward its aim of preserving biodiversity. T...
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Dual inheritance (DI) models of cultural evolution have been criticized for likening cultural transmission to genetic (lateral) transmission. I argue that although these objections might pertain to the cognitively sophisticated traits that DI theorists typically focus on (e.g. tool making and natural history knowledge), they do not undermine DI mod...
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Thought in a Hostile World 1 has four ostensible aims: …[1] to develop and vindicate a set of analytical tools for thinking about cognition and its evolution… [2] to develop a substantive theory of the evolution of human uniqueness… [3] to explore, from this evolutionary perspective, the relationship between folk psychology and an integrated scient...
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This paper considers whether the available evidence from archeology, biologi-cal anthropology, primatology, and comparative gene-sequencing, can test evolutionary game theory models of cooperation as historical hypotheses about the actual course of human prehistory. The examination proceeds on the assumption that cooperation is the product of cultu...
Article
Thesis (M.S.)--State University of New York at Binghamton, Biology Department, 2003. Includes bibliographical references (leaves 117-125).

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