Rules of thumb for judging ecological theories

An impressive fit to historical data suggests to biologists that a given ecological model is highly valid. Models often achieve this fit at the expense of exaggerated complexity that is not justified by empirical evidence. Because overfitted theories complement the traditional assumption that ecology is 'messy', they generally remain unquestioned. Using predation theory as an example, we suggest that a fit-driven appraisal of model value is commonly misdirected; although fit to historical data can be important, the simplicity and generality of a theory--and thus its ecological value--are of comparable importance. In particular, we argue that theories whose complexity greatly exceeds the complexity of the problem that they address should be rejected. We suggest heuristics for distinguishing between valuable ecological theories and their overfitted brethren.     

Save the planet: eliminate biodiversity

Recent work in the philosophy of biology has attempted to clarify and defend the use of the biodiversity concept in conservation science. I argue against these views, and give reasons to think that the biodiversity concept is a poor fit for the role we want it to play in conservation biology on both empirical and conceptual grounds. Against pluralists, who hold that biodiversity consists of distinct but correlated properties of natural systems, I argue that the supposed correlations between these properties are not tight enough to warrant treating and measuring them as a bundle. I additionally argue that deflationary theories of biodiversity don’t go far enough, since a large proportion of what we value in the environment falls outside bounds of what could reasonably be called “diversity”. I suggest that in current scientific practice biodiversity is generally an unnecessary placeholder for biological value of all sorts, and that we are better off eliminating it from conservation biology, or at least drastically reducing its role.     

The place of development in mathematical evolutionary theory

Development plays a critical role in structuring the joint offspring-parent phenotype distribution. It thus must be part of any truly general evolutionary theory. Historically, the offspring-parent distribution has often been treated in such a way as to bury the contribution of development, by distilling from it a single term, either heritability or additive genetic variance, and then working only with this term. I discuss two reasons why this approach is no longer satisfactory. First, the regression of expected offspring phenotype on parent phenotype can easily be nonlinear, and this nonlinearity can have a pronounced impact on the response to selection. Second, even when the offspring-parent regression is linear, it is nearly always a function of the environment, and the precise way that heritability covaries with the environment can have a substantial effect on adaptive evolution. Understanding these complexities of the offspring-parent distribution will require understanding of the developmental processes underlying the traits of interest. I briefly discuss how we can incorporate such complexity into formal evolutionary theory, and why it is likely to be important even for traits that are not traditionally the focus of evo-devo research. Finally, I briefly discuss a topic that is widely seen as being squarely in the domain of evo-devo: novelty. I argue that the same conceptual and mathematical framework that allows us to incorporate developmental complexity into simple models of trait evolution also yields insight into the evolution of novel traits.     

Developing unified theories in ecology as exemplified with diversity gradients

A scientific field matures as its theoretical underpinnings consolidate around unified theories: conceptual structures consisting of a few general propositions that encompass a wide domain of phenomena and from which can be derived an array of models. We demonstrate this process with a synthetic theory of ecological gradients and species richness. Our unified theory rests on four propositions. First, variation in some environmental factor effects variation in the number of individuals creating a gradient. Second, in a uniform environment of fixed area, more individuals lead to more species. Third, the variance of an environmental factor increases with its mean for sites of equal area. Fourth, all nonmonotonic relationships (i.e., hump shaped or U shaped) require a trade-off in organismal performance or in population characteristics with respect to the environmental gradient. We identify 17 models that link environmental gradients with diversity, show their relationship to our framework, and describe issues surrounding their empirical testing. We illustrate how a general theory can be used to build new models such as that for the U-shaped productivity-diversity relationship. Finally, we discuss how our theory could be unified further with other theories of diversity and indicate other areas of ecology that are ripe for unification. By providing an example of the process of theory unification, we hope to encourage such efforts throughout ecology.     

Assessing similarity: on homology,characters and the need for a semantic approach to non‐evolutionary comparative homology

The problem of homology has been a consistent source of controversy at the heart of systematic biology, as has the step of morphological character analysis in phylogenetics. Based on a clear epistemic framework and a characterization of “characters” as diagnostic evidence units for the recognition of not directly identifiable entities, I discuss the ontological definition and empirical recognition criteria of phylogenetic, developmental and comparative homology, and how these three accounts of homology each contribute to an understanding of the overall phenomenon of homology. I argue that phylogenetic homologies are individuals or historical kinds that require comparative homology for identification. Developmental homologies are natural kinds that ultimately rest on phylogenetic homologies and also require comparative homology for identification. Comparative homologies on the other hand are anatomical structural kinds that are directly identifiable. I discuss pre‐Darwinian comparative homology concepts and their problem of invoking non‐material forces and involving the a priori assumption of a stable positional reference system. Based on Young's concept of comparative homology, I suggest a procedure for recognizing comparative homologues that lacks these problems and that utilizes a semantic framework. This formal conceptual framework provides the much needed semantic transparency and computer‐parsability for documenting, communicating and analysing similarity propositions. It provides an essential methodological framework for generalizing over individual organisms and identifying and demarcating anatomical structural kinds, and it provides the missing link to the logical chain of identifying phylogenetic homology. The approach substantially increases the analytical accessibility of comparative research and thus represents an important contribution to the theoretical and methodological foundation of morphology and comparative biology.     

Anthropology and emotion

The centrality of emotion in thought and action is increasingly recognized in the human sciences, though basic questions of definition and scope remain unresolved. Where do emotions begin and end? How should we identify and analyse them? How should we write about them? Ethnographic fieldwork, as pioneered by Malinowski, offers powerful insights into the place of emotion in social life; but emotions are peculiarly difficult to capture in the generalizing format of case study and ethnographic summary. In this article I argue that semantic, structural, and discourse‐based approaches tend to miss what is most important – what counts for the persons concerned and therefore what makes the emotion. I review the conceptual and methodological issues and conclude that only a narrative approach can capture both the particularity and the temporal dimension of emotion, restoring verisimilitude and fidelity to experience.     

Digging through model complexity: using hierarchical models to uncover evolutionary processes in the wild

The growing interest for studying questions in the wild requires acknowledging that eco-evolutionary processes are complex, hierarchically structured and often partially observed or with measurement error. These issues have long been ignored in evolutionary biology, which might have led to flawed inference when addressing evolutionary questions. Hierarchical modelling (HM) has been proposed as a generic statistical framework to deal with complexity in ecological data and account for uncertainty. However, to date, HM has seldom been used to investigate evolutionary mechanisms possibly underlying observed patterns. Here, we contend the HM approach offers a relevant approach for the study of eco-evolutionary processes in the wild by confronting formal theories to empirical data through proper statistical inference. Studying eco-evolutionary processes requires considering the complete and often complex life histories of organisms. We show how this can be achieved by combining sequentially all life-history components and all available sources of information through HM. We demonstrate how eco-evolutionary processes may be poorly inferred or even missed without using the full potential of HM. As a case study, we use the Atlantic salmon and data on wild marked juveniles. We assess a reaction norm for migration and two potential trade-offs for survival. Overall, HM has a great potential to address evolutionary questions and investigate important processes that could not previously be assessed in laboratory or short time-scale studies.     

Some problems in the study of the origin of neotropical biodiversity using palaeoecological and molecular phylogenetic evidence

This study contends that progress in the understanding of the origin and maintenance of extant neotropical biodiversity by means of empirical evidence is hampered by the persistence of anachronistic conceptual approaches, notably the adherence to closed paradigms or ruling theories. The topic is discussed from three main perspectives: (1) the tendency to shift from one paradigm to another, (2) the use and abuse of broad generalizations from a single or a few case studies and (3) the use of inadequate phylogenetic dating (usually crown dating alone) for a sound appraisal of diversification timing. The origin of neotropical biodiversity is a complex subject that requires an open-minded attitude to be fully captured. The solution proposed is fairly easy, somewhat trivial, and rooted in the classical multiple working hypotheses (MWH) approach. The MWH seeks to explore any explanation possible for observed phenomena and develop every testable hypothesis in relation to their possible causes. The MWH approach promotes thoroughness, suggests lines of inquiry that might otherwise be overlooked and develops the habit of parallel and complex thought that, unfortunately, is not fully developed in the empirical study of neotropical biodiversity.     

Modeling abnormal priming in Alzheimer's patients with a free association network

Alzheimer's Disease irremediably alters the proficiency of word search and retrieval processes even at its early stages. Such disruption can sometimes be paradoxical in specific language tasks, for example semantic priming. Here we focus in the striking side-effect of hyperpriming in Alzheimer's Disease patients, which has been well-established in the literature for a long time. Previous studies have evidenced that modern network theory can become a powerful complementary tool to gain insight in cognitive phenomena. Here, we first show that network modeling is an appropriate approach to account for semantic priming in normal subjects. Then we turn to priming in degraded cognition: hyperpriming can be readily understood in the scope of a progressive degradation of the semantic network structure. We compare our simulation results with previous empirical observations in diseased patients finding a qualitative agreement. The network approach presented here can be used to accommodate current theories about impaired cognition, and towards a better understanding of lexical organization in healthy and diseased patients.     

From molecules to systems: the importance of looking both ways

Although molecular biology has meant different things at different times, the term is often associated with a tendency to view cellular causation as conforming to simple linear schemas in which macro-scale effects are specified by micro-scale structures. The early achievements of molecular biologists were important for the formation of such an outlook, one to which the discovery of recombinant DNA techniques, and a number of other findings, gave new life even after the complexity of genotype–phenotype relations had become apparent. Against this background we outline how a range of scientific developments and conceptual considerations can be regarded as enabling and perhaps necessitating contemporary systems approaches. We suggest that philosophical ideas have a valuable part to play in making sense of complex scientific and disciplinary issues.     

Neural coding of basic reward terms of animal learning theory, game theory, microeconomics and behavioural ecology

Neurons in a small number of brain structures detect rewards and reward-predicting stimuli and are active during the expectation of predictable food and liquid rewards. These neurons code the reward information according to basic terms of various behavioural theories that seek to explain reward-directed learning, approach behaviour and decision-making. The involved brain structures include groups of dopamine neurons, the striatum including the nucleus accumbens, the orbitofrontal cortex and the amygdala. The reward information is fed to brain structures involved in decision-making and organisation of behaviour, such as the dorsolateral prefrontal cortex and possibly the parietal cortex. The neural coding of basic reward terms derived from formal theories puts the neurophysiological investigation of reward mechanisms on firm conceptual grounds and provides neural correlates for the function of rewards in learning, approach behaviour and decision-making.     

The competition controversy in community ecology

There is a long history of controversy in ecology over the role of competition in determining patterns of distribution and abundance, and over the significance of the mathematical modeling of competitive interactions. This paper examines the controversy. Three kinds of considerations have been involved at one time or another during the history of this debate. There has been dispute about the kinds of regularities ecologists can expect to find, about the significance of evolutionary considerations for ecological inquiry, and about the empirical credentials of theoretical studies of competition. Each of these elements is examined with an eye toward gaining philosophical clarification of the issues involved. In the process, certain shortcomings of contemporary philosophical theories are revealed. In particular, I argue that plausibility arguments based on background considerations are an important part of the model building tradition, but that current accounts of the structure and evaluation of scientific theories do little to illuminate this side of theoretical ecology.     

Subjectivity and flexibility in invasion terminology: too much of a good thing?

Invasions biologists have frequently debated whether the definition of invasive should include ecological and economic impacts. More recent criticisms posit that objective definitions are impossible in any absolute sense, while subjectivity is desirable for its flexibility and motivational qualities. We argue that such criticisms underestimate the extent of subjectivity already present in invasion biology. Ecological questions may be methodological if they relate directly to other ecological theories and models, or motivational if they focus on issues important to society as a whole. Motivational questions are important for engaging scientists, improving public understanding of science, and often have applied benefits. In contrast, methodological questions are constrained by established scientific theories, and are therefore more efficient for the development of scientific knowledge. Contrary to recent critiques, we suggest that greater objectivity is both achievable and desirable for the discipline of invasion biology and ecology generally.     

Redefining disease? The nosologic implications of molecular genetic knowledge

How will developments in genetic knowledge affect the classification of disease? Leaders in genetics have suggested that knowledge of the role of genes in disease can determine nosology. Diseases might be defined by genotype, thus avoiding the limitations of more empirical approaches to categorization. Other commentators caution against disease definitions that are detached from the look and feel of disease, and argue for an interplay between genotypic and phenotypic information. Still others attribute nosologic change to social processes. We draw on an analysis of the scientific literature, our conversations with genetics clinicians, and reviews of patient organization Web sites to offer a revised interpretation of the nosologic implications of molecular genetic knowledge. We review the recent histories of three diseases--hemophilia, Rett syndrome, and cystic fibrosis--to argue that nosologic change cannot be explained by either biologic theories of disease etiology or sociologic theories of social tendencies. Although new genetic information challenges disease classifications and is highly influential in their redesign, genetic information can be used in diverse ways to reconstruct disease categories and is not the only influence in these revisions. Ironically, genetic information is likely to play a central role in producing a new, but still empirical, classification scheme.     

Character identification in evolutionary biology: The role of the organism

Summary In this article we argue that an organismic perspective in character identification can alleviate a structural deficiency of mathematical models in biology relative to the ones in the physical sciences. The problem with many biological theories is that they do not contain the conditions of their validity or a method of identifying objects that are appropriate instances of the models. Here functionally important biological characters are introduced as conceptual abstractions derived within the context of an ontologically prior object, such as a cell or an organism. To illustrate this approach, we present an analytical method of character decomposition based on the notion of the quasi-independence of traits. Two cases are analyzed: context dependent units of inheritance and a model of character identification in adaptive evolution. We demonstrate that in each case the biological process as represented by a mathematical theory entails the conditions for the individualization of characters. Our approach also requires a conceptual re-orientation in the way we build biological models. Rather than defining a set of biological characters a priori, functionally relevant characters are identified in the context of a higher level biological process.     

The graded and dichotomous nature of visual awareness

Is our visual experience of the world graded or dichotomous? Opposite pre-theoretical intuitions apply in different cases. For instance, when looking at a scene, one has a distinct sense that our experience has a graded character: one cannot say that there is no experience of contents that fall outside the focus of attention, but one cannot say that there is full awareness of such contents either. By contrast, when performing a visual detection task, our sense of having perceived the stimulus or not exhibits a more dichotomous character. Such issues have recently been the object of intense debate because different theoretical frameworks make different predictions about the graded versus dichotomous character of consciousness. Here, we review both relevant empirical findings as well as the associated theories (i.e. local recurrent processing versus global neural workspace theory). Next, we attempt to reconcile such contradictory theories by suggesting that level of processing is an often-ignored but highly relevant dimension through which we can cast a novel look at existing empirical findings. Thus, using a range of different stimuli, tasks and subjective scales, we show that processing low-level, non-semantic content results in graded visual experience, whereas processing high-level semantic content is experienced in a more dichotomous manner. We close by comparing our perspective with existing proposals, focusing in particular on the partial awareness hypothesis.     

Microcosm experiments can inform global ecological problems

Global-scale environmental problems are rarely regarded as amenable to traditional scientific experiment. We argue here that small-scale experiments using 'model organisms' in microcosms or mesocosms can be a useful approach for apparently intractable global problems, such as ecosystem responses to climate change or managing biodiversity through the design of nature reserves. An experimental, small-scale research programme can easily be coupled with the development of theory and act as a stimulus to further research, thereby hastening both understanding of the issues and development of practical solutions. This process--from microcosm experiment to the development of practical application--has previously been influential but also has a long time lag. We suggest short-cuts in an attempt to stimulate the use of small-scale experiments to address globally urgent issues with meaningful policy implications.