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 participants to a series of realistic scenarios concerning the development of birdsong. Our results explain the intuitive appeal of existing philosophical analyses of the innateness concept. They simultaneously explain why these analyses are subject to compelling counterexamples. We argue that this explanation undermines the appeal of these analyses, whether understood as analyses of the (...) vernacular concept or as explications of that concept for the purposes of science. (shrink)

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 assist with the development of improved models of ecological hypothesis testing and theory choice. Philosophy can also help ecologists understand the role and limitations of (...) mathematical models in ecology. On the other side, philosophy of science will be advanced by having ecological case studies as part of the stock of examples. Ecological case studies can shed light on old philosophical topics as well as raise novel issues for the philosophy of science. For example, understanding theoretical terms such as “biodiversity” is important for scientific reasons, but such terms also carry political importance. Formulating appropriate definitions for such terms is thus not a purely scientific matter, and this may prompt a reevaluation of philosophical accounts of defining theoretical terms. We consider some of the topics currently receiving attention in the philosophy of ecology and other topics in need of attention. Our aim is to prompt further exchange between ecology and philosophy of science and to help set the agenda for future work in the philosophy of ecology. The topics covered include: the role of mathematical models, environmental problem formulation, biodiversity, and environmental ethics. (shrink)

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 according to which some traits are expressions of an animal's inner nature while others are imposed by its environment. In this paper, we report further studies that extend and refine our account (...) of this aspect of folkbiology. We examine biologically naive subjects' judgments about whether traits of an animal are 'innate', 'in its DNA' or 'part of its nature'. Subjects do not understand these three descriptions to be equivalent. Both innate and in its DNA have the connotation that the trait is species-typical. This poses an obstacle to the assimilation of the biology of polymorphic and plastic traits by biologically naive audiences. Researchers themselves may not be immune to the continuing pull of folkbiological modes of thought. (shrink)

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 behavioural sciences. I consider three arguments for eliminating innateness from scientific discourse. First, the classification of a trait as innate is thought to discourage empirical research (...) into its developmental origin. Second, this concept lumps together a number of different biological properties that ought to be treated as distinct. Third, innateness is associated with the outmoded folk biological theory of essentialism. In response to these objections, I consider two attempts to revise the concept of innateness which aim to make it more suitable for scientific explanation and research. One proposal is that innateness can be defined in terms of the biological property of environmental canalization. On this view, a trait is innate to the extent that it is developmentally buffered against a range of different environments. Another proposal is that innateness serves as an explanatory primitive for cognitive science. This view holds that there exist a sharp boundary between psychological and biological explanations and that to identify a trait as innate means that it falls into the latter explanatory domain. This essay ends with some questions for future research. (shrink)

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 stems from two shortcomings: lack of clarity about the theoretical commitments of these models and inadequate comparative data for testing them. To resolve the first problem, I offer a theoretical framework for deriving competing (...) predictions from each of the four models. In particular, this involves a novel interpretation of the difference between dual inheritance theory and cultural niche construction. I then illustrate a strategy for testing their predictions using data from the Human Relations Area File. Empirical results suggest that the aggressive psychological phenotype typically associated with honour culture is more common among pastoral societies than among horticultural societies. Theoretical considerations suggest that this pattern is best explained as a case of cultural niche construction. (shrink)

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 discuss two questionable assumptions—or ‘myths’—surrounding the direction and interpretation of this research. First, it is often assumed that there is a single somatic marker hypothesis. As others have noted, however, Damasio’s ‘hypothesis’ (...) admits of multiple interpretations (Dunn et al. [2006]; Colombetti [2008]). Our analysis builds upon this point by characterizing decision making as a multi-stage process and identifying the various potential roles for somatic markers. The second myth is that the available evidence suggests a role for somatic markers in the core stages of decision making, that is, during the generation, deliberation, or evaluation of candidate options. On the contrary, we suggest that somatic markers most likely have a peripheral role, in the recognition of decision points, or in the motivation of action. This conclusion is based on an examination of the past twenty-five years of research conducted by Damasio and colleagues, focusing in particular on some early experiments that have been largely neglected by the critical literature. 1 Introduction2 What is the Somatic Marker Model?3 Multiple Somatic Marker Hypotheses3.1 Are somatic markers necessary for practical decision making?3.2 Speed, accuracy, or both?3.3 At which of the five stages of decision making are somatic markers engaged?4 Anecdotal Evidence Suggests a Peripheral Role for Somatic Markers4.1 Chronic indecisiveness4.2 Extreme impulsiveness4.3 Enhanced decision making in the lab4.4 Lack of motivation. 5 Early Experiments Suggest that VMF Damage Leaves Core Processes Intact5.1 The evocative images study5.2 Five problem solving tasks6 Recent Experiments Fail to Discriminate among Alternate Versions of SMH7 Conclusion. (shrink)

The media attention and subsequent scientific backlash engendered by the claim, announced by spokespeople for the Encyclopedia of DNA Elements project, that 80% of the human genome has a “biochemical function” highlights the need for a clearer understanding of function concepts in biology. This article provides an overview of two major function concepts that have been developed in the philosophy of science – the “causal role” concept and the “selected effects” concept – and their relevance to ENCODE. Unlike some previous (...) critiques, the ENCODE project is not considered problematic because it employed a causal role definition of function, but because of how this concept was misused. In addition, several unique challenges that arise when dealing with transposable elements, but which were ignored by ENCODE, are highlighted. These include issues surrounding TE-level versus organism-level selection, the origins versus the persistence of elements, and accidental versus functional organism-level benefits. Finally, some key questions are presented that should be addressed in any studies aiming to ascribe functions to major portions of large eukaryotic genomes, the majority of which is made up of transposable elements. (shrink)

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 computational-level account of practical decision making. Such an account is necessary for drawing meaningful links between neurological- and psychological-level data. The paper concludes by providing a simple, five-step (...) model of practical decision making. Recasting SMH in terms of this model generates more precise and empirically tractable computational-level hypotheses about the various ways that somatic markers might influence practical decisions. (shrink)

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 adaptive organismal response to environmental change. This interpretation overlooks an alternative explanation in terms of coevolutionary dynamics between parasitic transposons and the host genome. This raises a question about whether epigenetics (...) researchers tend to overlook transposon dynamics more generally. To address this question, we surveyed a large sample of scientific publications on the topics of epigenetics and transposons over the past fifty years. We found that enthusiasm for epigenetics is often inversely related to interest in transposon dynamics across the four disciplines we examined. Most surprising was a declining interest in transposons within biomedical science and cellular and molecular biology over the past two decades. Also notable was a delayed and relatively muted enthusiasm for epigenetics within evolutionary biology. An analysis of scientific abstracts from the past twenty-five years further reveals systematic differences among disciplines in their uses of the term epigenetic, especially with respect to heritability commitments and functional interpretations. Taken together, these results paint a nuanced picture of the rise of epigenetics and the possible neglect of transposon dynamics, especially among biomedical scientists. (shrink)

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 conserving particular species or regions. However, they fail to provide a strong justification for conserving biodiversity per se. Hence, either environmentalists must develop more compelling arguments for conserving biodiversity or else (...) they should modify their agenda. This short precis is an overview of the central findings of our book. (shrink)

The distinction between causal role and selected effect 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 the designation of some genetic or epigenetic element as functional —i.e. not junk— because it possesses properties that, arguably, suggest some biologically interesting organismal effect. The investigative process then proceeds, in a bottom-up fashion, to (...) search for those effects. I argue that this process encounters a problem reminiscent of one that Gould and Lewontin associated with the adaptationist program. Just as their stereotypical adaptationst became trapped in the myopic pursuit of one selectionist hypothesis after another, so can the investigation of CR functions in genomics lead to an unending series putative organism-level CR functions for junk DNA. This is an acute problem for genomics, because eukaryotic genomes are littered with transposable elements and their deactivated descendants which often masquerade as interesting CR-functional components and it is experimentally onerous to determine whether they lack such a function. I further argue that selectionist reasoning about TE-host coevolutionary dynamics can greatly streamline the investigative process. Importantly, selectionist hypotheses need not be well confirmed to be illuminating in this context. Informed selectionist reasoning about the strategic roles of TEs in the genome offers a corrective to the idea that most of our DNA is somehow CR functional for the organism. (shrink)

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, there are several ways to adopt such an approach, and it is sometimes unclear what an ecological perspective will add to the existing co-evolutionary framework for explaining transposon-host interactions. This (...) review aims to clarify the conceptual foundations of transposon ecology in order to evaluate its explanatory prospects. We begin by identifying three unanswered questions regarding the abundance and distribution of TEs that potentially call for an ecological explanation. We then offer an operational distinction between evolutionary and ecological approaches to these questions. By determining the amount of variance in transposon abundance and distribution that is explained by ecological and evolutionary factors, respectively, it is possible empirically to assess the prospects for each of these explanatory frameworks. To illustrate how this methodology applies to a concrete example, we analyzed whole-genome data for one set of distantly related mammals and another more closely related group of arthropods. Our expectation was that ecological factors are most informative for explaining differences among individual TE lineages, rather than TE families, and for explaining their distribution among closely related as opposed to distantly related host genomes. We found that, in these data sets, ecological factors do in fact explain most of the variation in TE abundance and distribution among TE lineages across less distantly related host organisms. Evolutionary factors were not significant at these levels. However, the explanatory roles of evolution and ecology become inverted at the level of TE families or among more distantly related genomes. Not only does this example demonstrate the utility of our distinction between ecological and evolutionary perspectives, it further suggests an appropriate explanatory domain for the burgeoning discipline of transposon ecology. The fact that ecological processes appear to be impacting TE lineages over relatively short time scales further raises the possibility that transposons might serve as useful model systems for testing more general hypotheses in ecology. (shrink)

Lawton’s contingency thesis states that there are no useful generalizations 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 terms as a claim about the instability of certain causal dependencies across different background conditions. A recent distinction between evolution and ecology reveals what an adequate test of Lawton’s thesis would look like. To (...) date, CT remains untested. But developments in genome and molecular ecology point in a promising direction. (shrink)

A promising recent development in molecular biology involves viewing the genome as a miniecosystem, 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, a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of using ENT both as (...) an explanation of community dynamics and as a null hypothesis. We then analyze a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome-level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura’s Molecular Neutral Theory and Lynch’s Mutational Hazard Model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models which we dub ‘fitness-neutrality’ and ‘competitive neutrality’. This distinction helps to clarify the various roles for neutral models in genomics, for example, in explaining the evolution of genome size. (shrink)

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. The abandonment of island biogeography theory in favor of complementarity-based algorithms is a case in point. In what follows, I consider the four central objections raised against island biogeographic conservation guidelines, arguing (...) that they fail to undermine the credibility of this framework as a conservation tool. At best, these objections call for a more careful application of this framework to conservation problems, not its wholesale abandonment. At the same time, complementarily-based algorithms are biased in favor of networks of small reserves containing non-overlapping species. These conditions threaten to promote inbreeding depression, genetic drift and other factors that increase a population’s risk of extinction. Therefore, recent developments in the field of conservation biology have arguably not contributed to its ultimate aim of preserving the maximum amount of biodiversity in the long run. (shrink)

A common objection to adaptationist accounts of human emotions is that they ignore the influence of culture. If complex emotions like guilt, shame and romantic jealousy are largely culturally determined, how could they be biological adaptations? Dual inheritance models of gene/culture coevolution provide a potential answer to this question. If complex emotions are developmentally ‘scaffolded' by norms that are transmitted from parent to offspring with reasonably high fidelity, then these emotions can evolve to promote individual reproductive interests. This paper draws (...) on case studies of emotional development to illustrate how complex emotions satisfy these conditions. Many of the norms and parenting strategies influencing emotional development are absorbed during the early stages of life when a child is in primary contact with its parents and before the onset of complex cognition. These conditions make it likely that emotion-governing norms are transmitted vertically and with relatively little cognitive ‘contamination'. ‡Thanks to Mark Colyvan, Paul Griffiths, Alexander Rosenberg, and John Wilkins for helpful comments on previous drafts. †To contact the author, please write to: Department of Philosophy, University of Queensland, Brisbane, Queensland 4072, Australia; e-mail: [email protected]. (shrink)

I should like to offer my greatest thanks to Paul Griffiths for providing the opportunity for this exchange, and to commentators Gillian Brown, Steven Fuller, Stefan Linquist, and Erika Milam for their generous and thought-provoking comments. I shall do my best in this space to respond to some of their concerns.

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 more accurately viewed as occupying distinct “epistemic niches.” When so understood, we see that rapid evolution under selection, even if it is generally true, does not imply that evolutionary explanations are (...) improved by the inclusion of ecological details. Nor are ecological explanations necessarily improved by the inclusion of information about trait variation, heritability, effective population size, or other standard evolutionary factors. To illustrate, I develop a version of Kitcher’s “gory details” argument to show that, even for some trait that is under strong directional selection, a dynamically sufficient explanation of its ecological relationships should ignore most of the information explaining why that trait is evolving. The wholesale integration of ecology and evolution looks even less appealing when empirical sufficiency, a purely practical requirement, is taken into account. As a way forward, I propose an eco-evo partitioning framework. This strategy enables researchers to estimate the empirical sufficiency of a purely ecological, a purely evolutionary, or a combined eco-evo approach. (shrink)

Philosophical interest in ecology is relatively new. Standard texts in the philosophy of biology pay little or no attention to ecology (though Sterelny and Griffiths 1999 is an exception). This is in part because the science of ecology itself is relatively new, but whatever the reasons for the neglect in the past, the situation must change. A good philosophical understanding of ecology is important for a number of reasons. First, ecology is an important and fascinating branch of biology with distinctive (...) philosophical issues that arise from its study. Second, ecology is only one small step away from urgent political, ethical, and management decisions about how best to live in an apparently increasingly-fragile environment. Third, philosophy of ecology, properly conceived, can contribute directly to both our understanding of ecology and help with its advancement. Philosophy of ecology can thus be seen as part of the emerging discipline of “biohumanities”, where biology and humanities disciplines together advance our understanding and knowledge of biology (Stotz and Griffiths forthcoming). In this paper, we focus primarily on this third role of the philosophy of ecology and consider a number of places where philosophy can play an important role in ecology. In the process, we.. (shrink)

This paper considers whether the available evidence from archeology, biological 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 cultural selection and is not a genetically encoded trait. Nevertheless, we conclude that gene sequence data may yet shed signi cant light on the evolution of cooperation.

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 propose both a Waddingtonian “broad sense” and a mechanistic “narrow sense” definition to capture its various scientific uses (Stotz and Griffiths, History and Philosophy of the Life (...) Sciences 38:22, 2016). We evaluated these proposals by first replicating a recent analysis by (Linquist and Fullerton, Theoretical Medicine and Bioethics 42:137–154, 2021). We analyzed the 1100 most frequently cited abstracts on epigenetics across four disciplines: proximal biology, biomedicine, general biology, and evolution. Each abstract was coded for its heritability commitments (if any) and functional interpretation. A second study applied LDA topic modelling to the same corpus, thus providing a useful methodological comparison. The two methods converged on a discipline-relative ambiguity. Within such disciplines as biomedicine or molecular biology that focus on proximate mechanisms, “epigenetic(s)” refers to a range of molecular structures while specifying nothing in particular about their heritability. This proximal conception was primarily associated with the functions of gene regulation and disease. In contrast, a second relatively uncommon sense of “epigenetic(s)” is restricted to a small proportion of evolutionary abstracts. It refers to many of the same molecular structures, but regards them as trans-generationally inherited and associated with adaptive phenotypic plasticity. This finding underscores the benefit of digital tools in complementing traditional conceptual analysis. Philosophers should be cautious not to conflate the relatively uncommon evolutionary sense of epigenetics with the more widely used proximal conception. (shrink)

Recent years have seen a transformation in thinking about the nature of culture. Rather than viewing culture in opposition to biology, a growing number of researchers now regard culture as subject to evolutionary processes. Recent developments in this field have shifted some of the traditional academic fault lines. Alliances are forming between researchers trained in anthropology, evolutionary biology, psychology and philosophy. Meanwhile, several distinct schools of thought have appeared which differ in their vision of what an evolutionary approach to culture (...) should look like. This volume contains some of the most influential publications on these subjects from the past few decades. A theoretical background chapter and critical introduction identify the core issues at stake in the new study of cultural evolution. These chapters are followed by sections on each of the four dominant approaches: the phylogenetic approach, memetics, dual inheritance theory and niche construction. Following these are two chapters on closely related topics: the psychological mechanisms of culture and the existence of culture in non-human animals. Overall, this volume provides an up to date overview of some of the most exciting trends in contemporary evolutionary thought. (shrink)

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 (Linquist et al. 2016). However, these “laws” face numerous challenges when it comes to their practical application. Concerns about their reliability and scope might stem from unclear logical and epistemic connections to more foundational (...) or “unifying” generalizations (Lean in Philos Top 47(1), 2019) which, in ecology, tend to be derived from first principles and in association with highly abstract models. This raises questions about the nature of those foundational generalizations themselves. In particular, how resilient are they compared to the generalizations uncovered by empirically driven methods? Here we propose a procedure for evaluating the resilience of generalizations across five ecologically relevant dimensions. This procedure was applied to seven well known foundational generalizations in ecology. Surprisingly, it turned out to be impossible to estimate the resilience of these foundational generalizations based on the available literature. This points to the need for a more centralized repository of information about ecological generalizations, created with the explicit aim of evaluating such important dimensions as causal mechanism and predictive power. (shrink)