Stefan Linquist

Philosophical Issues in Ecology: Recent Trends and Future Directions

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.

Distinguishing between “function” and “effect” in genome biology

Much confusion in genome biology results from conflation of possible meanings of the word “function.” We suggest that, in this connection, attention should be paid to evolutionary biologists and philosophers who have previously dealt with this problem. We need only decide that although all genomic structures have effects, only some of them should be said to have functions. Although it will very often be difficult or impossible to establish function (strictly defined), it should not automatically be assumed. We enjoin genomicists in particular to pay greater attention to parsing biological effects.

Exploring the folkbiological conception of human nature

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 animals 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.

Conceptual and Empirical Challenges of Ascribing Functions to Transposable Elements

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 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 in some previous critiques, the ENCODE project is not considered problematic here because it employed a causal role definition of function (which is relatively common in genetics) but because of how this concept was misused. In addition, several unique challenges that arise when dealing with transposable elements (TEs) but that 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 study aiming to ascribe functions to major portions of large eukaryotic genomes, the majorities of which are made up of transposable elements.

Distinguishing ecological from evolutionary approaches to transposable elements

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.

Applying ecological models to communities of genetic elements: the case of neutral theory

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 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 analyse 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: Kimuras molecular neutral theory and Lynchs 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.

Two Myths about Somatic Markers

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. 1u2003Introduction 2u2003What is the Somatic Marker Model? 3u2003Multiple Somatic Marker Hypotheses u2003u20033.1u2003Are somatic markers necessary for practical decision making? u2003u20033.2u2003Speed, accuracy, or both? u2003u20033.3u2003At which of the five stages of decision making are somatic markers engaged? 4u2003Anecdotal Evidence Suggests a Peripheral Role for Somatic Markers u2003u20034.1u2003Chronic indecisiveness u2003u20034.2u2003Extreme impulsiveness u2003u20034.3u2003Enhanced decision making in the lab u2003u20034.4u2003Lack of motivation. 5u2003Early Experiments Suggest that VMF Damage Leaves Core Processes Intact u2003u20035.1u2003The evocative images study u2003u20035.2u2003Five problem solving tasks 6u2003Recent Experiments Fail to Discriminate among Alternate Versions of SMH 7u2003Conclusion 1u2003Introduction 2u2003What is the Somatic Marker Model? 3u2003Multiple Somatic Marker Hypotheses u2003u20033.1u2003Are somatic markers necessary for practical decision making? u2003u20033.2u2003Speed, accuracy, or both? u2003u20033.3u2003At which of the five stages of decision making are somatic markers engaged? u2003u20033.1u2003Are somatic markers necessary for practical decision making? u2003u20033.2u2003Speed, accuracy, or both? u2003u20033.3u2003At which of the five stages of decision making are somatic markers engaged? 4u2003Anecdotal Evidence Suggests a Peripheral Role for Somatic Markers u2003u20034.1u2003Chronic indecisiveness u2003u20034.2u2003Extreme impulsiveness u2003u20034.3u2003Enhanced decision making in the lab u2003u20034.4u2003Lack of motivation. u2003u20034.1u2003Chronic indecisiveness u2003u20034.2u2003Extreme impulsiveness u2003u20034.3u2003Enhanced decision making in the lab u2003u20034.4u2003Lack of motivation. 5u2003Early Experiments Suggest that VMF Damage Leaves Core Processes Intact u2003u20035.1u2003The evocative images study u2003u20035.2u2003Five problem solving tasks u2003u20035.1u2003The evocative images study u2003u20035.2u2003Five problem solving tasks 6u2003Recent Experiments Fail to Discriminate among Alternate Versions of SMH 7u2003Conclusion

How Do Somatic Markers Feature in Decision Making

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 article 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.

A second site occupied by Octopus tetricus at high densities, with notes on their ecology and behavior

ABSTRACT 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 octopuses on eight different days. We recorded frequent interactions, signaling, mating, mate defense, eviction of octopuses from dens, and attempts to exclude individuals from the site. These observations demonstrate that high-density occupation and complex social behaviors are not unique to the earlier described site, which had been affected to some extent by remains of human activity. Behavior at this second site confirms that complex social interactions also occur in association with natural substrate, and suggest that social interactions are more wide spread among octopuses than previously recognized.

Yes! There are Resilient Generalizations (or “Laws”) in Ecology

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 of communities and elsewhere. A brief review of this debate reveals an issue with deep philosophical roots that is unlikely to be resolved by a better understanding of generalizations in ecology. We therefore propose a strategy for transforming the conceptual question about the nature of ecological laws into a set of empirically tractable hypotheses about the relative resilience of ecological generalizations across three dimensions: taxonomy, habitat type, and scale. These hypotheses are tested using a survey of 240 meta-analyses in ecology. Our central finding is that generalizations in community ecology are just as prevalent and as resilient as those in population or ecosystem ecology. These findings should help to establish community ecology as a generality-seeking science as opposed to a science of case studies. It also supports the capacity for ecologists, working at any of the three levels, to inform matters of public policy.