Most recent philosophical thought about the scientific representation of the world has focused on dyadic relationships between language-like entities and the world, particularly the semantic relationships of reference and truth. Drawing inspiration from diverse sources, I argue that we should focus on the pragmatic activity of representing, so that the basic representational relationship has the form: Scientists use models to represent aspects of the world for specific purposes. Leaving aside the terms "law" and "theory," I distinguish principles, specific conditions, models, (...) hypotheses, and generalizations. I argue that scientists use designated similarities between models and aspects of the world to form both hypotheses and generalizations. (shrink)

This paper is an interpretation and defense of Richard Levins’ “The Strategy of Model Building in Population Biology,” which has been extremely influential among biologists since its publication 40 years ago. In this article, Levins confronted some of the deepest philosophical issues surrounding modeling and theory construction. By way of interpretation, I discuss each of Levins’ major philosophical themes: the problem of complexity, the brute-force approach, the existence and consequence of tradeoffs, and robustness analysis. I argue that Levins’ article is (...) concerned, at its core, with justifying the use of multiple, idealized models in population biology. (shrink)

Species pluralism gives us reason to doubt the existence of the species category. The problem is not that species concepts are chosen according to our interests or that pluralism and the desire for hierarchical classifications are incompatible. The problem is that the various taxa we call 'species' lack a common unifying feature.

Niche construction theory (NCT) aims to transform and unite evolutionary biology and ecology. Much of the debate about NCT has focused on construction. Less attention has been accorded to the niche: what is it, exactly, that organisms are constructing? In this paper I compare and contrast the definition of the niche used in NCT with ecological niche definitions. NCT’s concept of the evolutionary niche is defined as the sum of selection pressures affecting a population. So defined, the evolutionary niche is (...) narrower than the ecological niche. Moreover, when contrasted with a more restricted ecological niche concept, it has a slightly different extension. I point out three kinds of cases in which the evolutionary niche does not coincide with realized ecological niches: extreme habitat degradation, commensalism, and non-limiting or super-abundant resources. These conceptual differences affect the role of NCT in unifying ecology and evolutionary biology. (shrink)

The concept of niche (setting, context, habitat, environment) has been little studied by ontologists, in spite of its wide application in a variety of disciplines from evolutionary biology to economics. What follows is a first formal theory of this concept, a theory of the relations between objects and their niches. The theory builds upon existing work on mereology, topology, and the theory of spatial location as tools of formal ontology. It will be illustrated above all by means of simple biological (...) examples, but the concept of niche should be understood as being, like concepts such as part, boundary, and location, a structural concept that is applicable in principle to a wide range of different domains. (shrink)

A precise formulation of the structure of modern evolutionary theory has proved elusive. In this paper, I introduce and develop a formal approach to the structure of population genetics, evolutionary theory's most developed sub-theory. Under the semantic approach, used as a framework in this paper, presenting a theory consists in presenting a related family of models. I offer general guidelines and examples for the classification of population genetics models; the defining features of the models are taken to be their state (...) spaces, parameters, and laws. The suggestions regarding the various aspects of the characterization of population genetics models provide an outline for further detailed research. (shrink)

Neutral Theory is controversial in ecology. Ecologists and philosophers have diagnosed the source of the controversy as: its false assumption that individuals in different species within the same trophic level are ecologically equivalent, its conflict with Competition Theory and the adaptation of species, its role as a null hypothesis, and as a Lakatosian research programme. In this paper, I show why we should instead understand the conflict at the level of research programs which involve more than theory. The Neutralist and (...) Competitionist research programs borrow and construct theories, models, and experiments for various aims and given their home ecological systems. I present a holistic and pragmatic view of the controversy that foregrounds the interrelation between many kinds of practices and decisions in ecological research. (shrink)

Philosophers have studied mechanisms in many fields in biology. The focus has often been on molecular mechanisms in disciplines such as neuroscience, genetics and molecular biology, with some work on population-level mechanisms in ecology and evolution. We present a novel philosophical case study of individual-level mechanisms, mechanisms in ecology and evolution that concern the interactions between an individual and its environment. The mechanisms we analyze are called Niche Choice, Niche Conformance and Niche Construction (NC3) mechanisms. Based on a detailed analysis (...) of biologists’ research practices, we develop metaphysical claims about the components and organization of NC3 mechanisms, the phenomena they bring about and how these phenomena relate to individual differences, a major explanatory target in the field. We provide reasons for why processes of niche choice, conformance and construction are mechanisms and how they differ from molecular mechanisms underlying individual differences. Finally, we demonstrate that a general representation of NC3 mechanisms is highly abstract, with more specific types of NC3 mechanisms in particular study systems exhibiting more complex components organized in more complex ways. Our case study highlights some distinctive features of individual-level mechanisms in ecology and evolution, such as complex and heterogeneous organization and multiple phenomena. (shrink)

We here develop a concept of an individualized niche in analogy to Hutchison’s population-level concept of the ecological niche. We consider the individualized niche as the range of environmental conditions under which a particular individual has an expected lifetime reproductive success of ≥ 1. Our concept has primarily an ecological function, as it refers to the match of an individual phenotype to its contemporary environment while we discuss evolutionary fitness as an evaluative parameter of this fit. We address four specific (...) challenges that occur when scaling the niche down from populations to individuals. In particular, we discuss the consequences of uniqueness of individuals in a population and the corresponding lack of statistical replication, the dynamic nature of individualized niches and how they can be studied either as time-slice niches, as prospective niches or as trajectory-based niches, the dimensionality of the individualized niche, that is greater than the population niche due to the additional dimensions of intra-specific niche space, how the boundaries of individualized niche space can be defined by expected lifetime reproductive success and how expected reproductive success can be inferred by marginalizing fitness functions across phenotypes or environments. We frame our discussion in the context of recent interest in the causes and consequences of individual differences in animal behavior. (shrink)

The niche is allegedly the conceptual bedrock underpinning the most prominent, and some would say most important, theorizing in ecology. We argue this point of view is more aspirational than veridical. Rather than critically dissect existing definitions of the concept, the supposedly significant work it is thought to have done in ecology is our evaluative target. There is no denying the impressive mathematical sophistication and theoretical ingenuity of the ecological modeling that invokes ‘niche’ terminology. But despite the pervasive labeling, we (...) demonstrate that niche talk is nothing more than a gloss on theory developed without it, that doesn’t need it, and that doesn’t benefit from it. (shrink)

Two strategies for using a model as “null” are distinguished. Null modeling evaluates whether a process is causally responsible for a pattern by testing it against a null model. Baseline modeling measures the relative significance of various processes responsible for a pattern by detecting deviations from a baseline model. When these strategies are conflated, models are illegitimately privileged as accepted until rejected. I illustrate this using the neutral theory of ecology and draw general lessons from this case. First, scientists cannot (...) draw certain conclusions using null modeling. Second, these conclusions follow using baseline modeling, but doing so requires more evidence. (shrink)

We evaluate a common reasoning strategy used in community ecology and comparative psychology for selecting between competing hypotheses. This strategy labels one hypothesis as a “null” on the grounds of its simplicity and epistemically privileges it as accepted until rejected. We argue that this strategy is unjustified. The asymmetrical treatment of statistical null hypotheses is justified through the experimental and mathematical contexts in which they are used, but these contexts are missing in the case of the “pseudo-null hypotheses” found in (...) our case studies. Moreover, statistical nulls are often not epistemically privileged in practice over their alternatives because failing to reject the null is usually a negative result about the alternative, experimental hypothesis. Scientists should eschew the appeal to pseudo-nulls. It is a rhetorical strategy that glosses over a commitment to valuing simplicity over other epistemic virtues in the name of good scientific and statistical methodology. (shrink)

Perhaps no concept has been thought more important to ecological theorizing than the niche. Without it, technically sophisticated and well-regarded accounts of character displacement, ecological equivalence, limiting similarity, and others would seemingly never have been developed. The niche is also widely considered the centerpiece of the best candidate for a distinctively ecological law, the competitive exclusion principle. But the incongruous array and imprecise character of proposed definitions of the concept square poorly with its apparent scientific centrality. I argue this definitional (...) diversity and imprecision reflects a problematic conceptual indeterminacy that challenges its putative indispensability in ecology. (shrink)

This paper revisits the debate over whether the study of facilitation requires ecologists to revise their understanding of the relationship between realized and fundamental niches as conceptualized by Hutchinson. Following Rodriguez-Cabal et al., I argue against Bruno et al.’s claim that facilitation can make a species’ realized niche larger than its fundamental niche. However, I also maintain that the abstract Hutchinsonian conceptualization of the niche makes a whole range of facilitative interactions—which I propose to call ameliorative facilitation—invisible to niche-based approaches (...) to the study of ecological communities. I propose a way to incorporate ameliorative facilitation into such approaches. My proposal involves supplementing the Hutchinsonian realized/fundamental dyad with a third concept: the potential niche. This concept was introduced by ecologists studying the effects of environmental change on species distributions, but I show how it could also be fruitfully used in facilitation studies. I argue that this proposed solution is more appealing than Stachowicz’s suggestion that Hutchinson’s realized/fundamental contrast be applied to a spatial-geographical, as opposed to an abstract-conceptual, notion of the niche. (shrink)

Ecological communities around the world are under threat while a consensus theory of community structure remains elusive. In the last decade ecologists have struggled with two seemingly opposing theories: niche-based theory that explains diversity with species’ differences and the neutral theory of biodiversity that claims that much of the diversity we observe can be explained without explicitly invoking species’ differences. Although ecologists are increasingly attempting to reconcile these two theories, there is still much resistance against the neutral theory of biodiversity. (...) Here we argue that the dispute between the two theories is a classic example of the dichotomy between philosophical perspectives, realism and instrumentalism. Realism is associated with specific, small-scale and detailed explanations, whereas instrumentalism is linked to general, large-scale, but less precise accounts. Recognizing this will help ecologists get both niche-based and neutral theories in perspective as useful tools for understanding biodiversity patterns. (shrink)

This article characterizes various species concepts in terms of set-theoretic models that license biological inferences and illustrates the logical connections among different species concepts. Species in this construal are abstract models, rather than biological or even tangible entities, and relate to individual organisms via representation, rather than the membership or mereological whole/part relationship. The proposal sheds new light on vexed issues of species and situates them within broader philosophical contexts of model selection, scientific representation, and scientific realism.