Two metascientific concepts that have been ― and still are ― object of philosophical analysis are the concepts of model and theory. But while the concept of scientific theory was one of the concepts to which philosophers of science devoted most attention during the 20th century, it is only in recent decades that the concept of scientific model has come to occupy a central position in philosophical reflection. However, it has done so in such a way that, at present, as (...) Jim Bogen states in the back cover of the book Scientific Models in the Philosophy of Science, by Daniela Bailer-Jones, “[t]he standard philosophical literature on the role of models in scientific reasoning is voluminous, disorganized, and confusing”. In spite of this, one of the axes that would allow us to organize at least part of this literature, and with which Bailer-Jones’ book closes, is that which is identified as one of the “contemporary philosophical issues: how theories and models relate to each other” (Bailer-Jones 2009, p. 208).That is why, in this introduction to the special issues of Metatheoria devoted to the topic of “Models and Theories in Biology”, we will present the main advances that have been made in the philosophical analysis of the concepts of model and theory in general and in biology in particular, and we will also do the same with the answers that have been given to the problem of "how theories and models relate to each other”. (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)

The units or levels of selection debate concerns the question of what kind of biological systems are stable enough that part of their evolution is a result of the process of natural selection acting at their level. Traditionally, the debate has concerned at least two different, though related, questions: the question of the level at which interaction with the environment occurs, and the question of the level at which reproduction occurs. In recent years, biologists and philosophers have discussed a new (...) aspect of this debate, namely the possibility that certain multi-species consortia formed by a host and its microbiome may act as a unit of selection. This thesis, however, has not been without criticism, as it is doubtful that such consortia could meet the conditions required to achieve the degree of stability that would allow them to experience natural selection. The purpose of this paper is to systematically examine such criticisms and to defend the thesis that the holobiont/hologenome can act as a genuine level of selection both in the form of an interactor and in the form of a reproducer. To do so, it will be argued that the microbiome should be characterized in functional rather than taxonomic terms. (shrink)

We address the controversy in the literature concerning the definition of holobionts and the apparent constraints on their evolution using concepts from community population genetics. The genetics of holobionts, consisting of a host and diverse microbial symbionts, has been neglected in many discussions of the topic, and, where it has been discussed, a gene-centric, species-centric view, based in genomic conflict, has been predominant. Because coevolution takes place between traits or genes in two or more species and not, strictly speaking, between (...) species, it may affect some traits but not others in either host or symbiont. Moreover, when interacting species pairs are embedded in a larger community, indirect ecological effects can alter the expected pairwise dynamics. Mode of symbiont transmission and the degree of host inbreeding both affect the extent of microbial mixing across host lineages and thereby the degree to which selection on one trait of either partner affects other aspects of a holobiont phenotype. We discuss several potential defining criteria for holobionts using community genetics and population genetics models, suggesting their application and limitations. Using community genetics models, we show how conflict between genomes can be self-limiting, while cooperation and mutualism tend to be self-accelerating. It is likely that this bias in the evolutionary dynamics of interaction between hosts and symbionts is an important feature of holobionts. This bias in the evolutionary dynamic could contribute to explaining the absence of cheaters from natural mutualisms, although cheaters are predicted by gene-centered conflict theory to cause the evolutionary instability of mutualisms. Additionally, it may help explain the more frequent origin of mutualisms from parasitic than from free-living systems, an evolutionary trajectory opposite to that predicted by genome conflict theory. (shrink)

This Ph.D. thesis provides a pilosophical account of the structure of the evolutionary synthesis of the 1930s and 40s. The first, more historical part analyses how classical genetics came to be integrated into evolutionary thinking, highlighting in particular the importance of chromosomal mapping of Drosophila strains collected in the wild by Dobzansky, but also the work of Goldschmidt, Sumners, Timofeeff-Ressovsky and others. The second, more philosophical part attempts to answer the question wherein the unity of the synthesis consisted. I argue (...) that it exemplifies a weak of form of explanatory unification. (shrink)

Resumen -/- El objetivo de este trabajo consiste en analizar las relaciones entre los modelos de optimalidad y la selección natural. Defenderemos que esas relaciones pueden dividirse en dos tipos, en tanto hay dos tipos de explicaciones seleccionistas, que llamaremos “históricas” y “ahistóricas”. Las explicaciones históricas revelan como una población dada adquiere un rasgo que es adaptativo en ese ambiente e involucran muchas generaciones, variación, etc. Las explicaciones ahistóricas, explican por qué, en determinado momento, ciertos tipos de organismos tienen un (...) mayor éxito reproductivo que otros. Mostraremos que los modelos de optimalidad pueden jugar un rol en la determinación del explanandum de las explicaciones histórica seleccionistas, esto es, que ayudan a reconocer qué rasgos son adaptativos. Por otra parte, mostramos que los modelos de optimalidad nos permiten determinar a veces la parte del explanans de las explicaciones ahistóricas (particularmente, el concepto de fitness). -/- Abstract -/- The goal of this paper is to analyze the relations between optimality models and natural selection. We contend that these relationships can be divided into two kinds, as there are two kinds of natural selection explanations, which we call “historical” and “ahistorical”. Historical explanations reveal how a given population acquires a trait which is adaptive in its environment, and involves many generations, variations, etc. Ahistorical ones, explain why, at a given moment, certain kinds of organisms have a greater reproductive success than others. We show that optimality models can play a role in determining the explanandum of historical selectionist explanations, that is, they help us to recognize which traits are adaptive. And, on the other hand, that optimality models sometimes allow us to determine part of the explanans of ahistorical explanations (particularly, the concept of fitness). (shrink)

A strong case has been made for the role and value of mechanistic reasoning in process-oriented sciences, such as molecular biology and neuroscience. This paper shifts focus to assess the role of mechanistic reasoning in an area where it is neither obvious nor expected: population genetics. Population geneticists abstract away from the causal-mechanical details of individual organisms and, instead, use mathematics to describe population-level, statistical phenomena. This paper, first, develops a framework for the identification of mechanistic reasoning where it is (...) not obvious: mathematical and mechanistic styles of scientific reasoning. Second, it applies this framework to demonstrate that both styles are integrated in modern investigations of evolutionary biology. Characteristic of the former, applied population genetic techniques provide statistical evidence for associations between genotype, phenotype, and fitness. Characteristic of the latter, experimental interventions provide causal-mechanical evidence for associations between the very same relationships, often in the same model organisms. The upshot is a richer perspective of how evolutionary biologists build evidence for hypotheses regarding adaptive evolution and a general framework for assessing the scope of mechanistic reasoning across the sciences. (shrink)

In his recent bookThe Advancement of Science,Philip Kitcher endorses eliminative induction, or the view that confirmation of hypotheses proceeds by the elimination of alternatives. My intention here is to critically examine Kitcher's eliminativist view of confirmation, and his rejection of the widely held Bayesian position, according to which an hypothesis H is confirmed by evidence E just in case the probability of H conditional on E is greater than the simple unconditional probability of H [i.e. p(H/E) > p(H)]. Here, I (...) will maintain that while there are aspects of the eliminative approach which Bayesianism must incorporate, as has been argued by John Earman, the eliminativism advocated by Kitcher is unsatisfactory. In addition, I will suggest that Kitcher's reasons for rejecting Bayesian confirmation theory are unconvincing and depend on an overly restrictive version of the position and that indeed Bayesianism has resources needed by an eliminativist account of confirmation. (shrink)

The ecologist today finds scarce ground safe from controversy. Decisions must be made about what combination of data, goals, methods, and theories offers them the foundations and tools they need to construct and defend their research. When push comes to shove, ecologists often turn to philosophy to justify why it is their approach that is scientific. Karl Popper’s image of science as bold conjectures and heroic refutations is routinely enlisted to justify testing hypotheses over merely confirming them. One of the (...) most controversial theories in contemporary science is the Neutral Theory of Ecology. Its chief developer and proponent, Stephen Hubbell, presents the neutral theory as a bold conjecture that has so far escaped refutation. Critics of the neutral theory claim that it already stands refuted, despite what the dogmatic neutralists say. We see the controversy through a Popperian lens. But Popper’s is an impoverished philosophy of science that distorts contemporary ecology. -/- The controversy surrounding the neutral theory actually rests on a methodological fault. There is a strong but messy historical link between the concepts of being neutral and being null in biology, and Hubbell perpetuates this when he claims that the neutral theory is supplies the appropriate null for testing alternative theories. What method is being followed here? There are three contenders: -/- Null hypothesis testing tests for whether a there is a pattern to be explained. Null modeling tests for whether a process is causally relevant to a pattern. Baseline modeling apportions relative responsibility to multiple processes each relevant to a pattern. -/- Whether the neutral theory supplies an appropriate “null” depends upon whether null hypothesis, null modeling, or baseline model is intended. These methods prescribe distinct inference patterns. If they are null hypothesis testing or null modeling, the neutralists’s reasoning is invalid. If they are baseline modeling, the justification of a crucial assumption remains opaque. Either way, the neutral-null connection is being exploited rhetorically to privilege the neutral theory over its rivals. Clarifying the reasoning immunizes us against the rhetoric and foregrounds the underlying virtues of the neutralist approach to ecology. -/- The Popperian lens distorts theoretical development as dogmatism. Lakatos’s view of science as the development of research programmes clarifies the epistemology of the neutral theory. Focusing philosophical attention on the neutralist research programme illuminates (1) the synchronic uses of the neutral theory to make predictions and give descriptions and explanations; (2) its diachronic development in response to theoretical innovation and confrontation with data; (3) its complex relationships to alternative theories. For example, baseline modeling is now seen to be its primary explanatory heuristic. The justification for baseline modeling with the neutral theory, previously hidden from view, is seen in the logic of in the neutralist research programme. (shrink)

The concept of fitness has generated a lot of discussion in philosophy of biology. There is, however, relative agreement about the need to distinguish at least two uses of the term: ecological fitness on the one hand, and population genetics fitness on the other. The goal of this paper is to give an explication of the concept of ecological fitness by providing a reconstruction of the theory of natural selection in which this concept was framed, that is, based on the (...) way the theory was put to use in Darwin’s main texts. I will contend that this reconstruction enables us to account for the current use of the theory of natural selection. The framework presupposed in the analysis will be that of metatheoretical structuralism. This framework will provide both a better understanding of the nature of ecological fitness and a more complete reconstruction of the theory. In particular, it will provide what I think is a better way of understanding how the concept of fitness is applied through heterogeneous cases. One of the major advantages of my way of thinking about natural selection theory is that it would not have the peculiar metatheoretical status that it has in other available views. I will argue that in order to achieve these goals it is necessary to make several concepts explicit, concepts that are frequently omitted in usual reconstructions. (shrink)

I defend a radical interpretation of biological populations—what I call population pluralism—which holds that there are many ways that a particular grouping of individuals can be related such that the grouping satisfies the conditions necessary for those individuals to evolve together. More constraining accounts of biological populations face empirical counter-examples and conceptual difficulties. One of the most intuitive and frequently employed conditions, causal connectivity—itself beset with numerous difficulties—is best construed by considering the relevant causal relations as ‘thick’ causal concepts. I (...) argue that the fine-grained causal relations that could constitute membership in a biological population are huge in number and many are manifested by degree, and thus we can construe population membership as being defined by massively multidimensional constructs, the differences between which are largely arbitrary. I end by showing that positions in two recent debates in theoretical biology depend on a view of biological populations at odds with the pluralism defended here. (shrink)

Many standard philosophical accounts of scientific practice fail to distinguish between modeling and other types of theory construction. This failure is unfortunate because there are important contrasts among the goals, procedures, and representations employed by modelers and other kinds of theorists. We can see some of these differences intuitively when we reflect on the methods of theorists such as Vito Volterra and Linus Pauling on the one hand, and Charles Darwin and Dimitri Mendeleev on the other. Much of Volterra's and (...) Pauling's work involved modeling; much of Darwin's and Mendeleev's did not. In order to capture this distinction, I consider two examples of theory construction in detail: Volterra's treatment of post-WWI fishery dynamics and Mendeleev's construction of the periodic system. I argue that modeling can be distinguished from other forms of theorizing by the procedures modelers use to represent and to study real-world phenomena: indirect representation and analysis. This differentiation between modelers and non-modelers is one component of the larger project of understanding the practice of modeling, its distinctive features, and the strategies of abstraction and idealization it employs. (shrink)

Philosophy of science is positioned to make distinctive contributions to cognitive science by providing perspective on its conceptual foundations and by advancing normative recommendations. The philosophy of science I embrace is naturalistic in that it is grounded in the study of actual science. Focusing on explanation, I describe the recent development of a mechanistic philosophy of science from which I draw three normative consequences for cognitive science. First, insofar as cognitive mechanisms are information‐processing mechanisms, cognitive science needs an account of (...) how the representations invoked in cognitive mechanisms carry information about contents, and I suggest that control theory offers the needed perspective on the relation of representations to contents. Second, I argue that cognitive science requires, but is still in search of, a catalog of cognitive operations that researchers can draw upon in explaining cognitive mechanisms. Last, I provide a new perspective on the relation of cognitive science to brain sciences, one which embraces both reductive research on neural components that figure in cognitive mechanisms and a concern with recomposing higher‐level mechanisms from their components and situating them in their environments. (shrink)

I propose a distinct type of robustness, which I suggest can support a confirmatory role in scientific reasoning, contrary to the usual philosophical claims. In model robustness, repeated production of the empirically successful model prediction or retrodiction against a background of independentlysupported and varying model constructions, within a group of models containing a shared causal factor, may suggest how confident we can be in the causal factor and predictions/retrodictions, especially once supported by a variety of evidence framework. I present climate (...) models of greenhouse gas global warming of the 20th Century as an example, and emphasize climate scientists’ discussions of robust models and causal aspects. The account is intended as applicable to a broad array of sciences that use complex modeling techniques. (shrink)

The relatively new field of evolutionary developmental biology continues to attract considerable attention from biologists, philosophers, and historians, in part, because work in this field demonstrates that important changes are underway within biology. Though studies of development and evolution were closely connected during the 19th century, continued work in genetics fostered a general split between the two during the first decades of the twentieth century (e.g., Allen 1978; Gilbert 1978; Mayr and Provine 1980; Gilbert, Opitz and..

This chapter contains sections titled: Highlights of Past Literature Current Work Future Work.

Para algunos la selección natural se identifica con las diferencias de éxito de distintos organismos en la reproducción diferencial. Si esto fuese así, el principio de Hardy-Weinberg, por permitir determinar con bastante precisión bajo ciertos supuestos que la frecuencia génica en una población no es la esperada, podría ser visto como una versión cuantitativa de la selección natural cualitativa propuesta por Darwin. Es mi intención mostrar, a través del análisis de explicaciones dadas por Darwin, que la selección natural es más (...) que la mera diferencia en el éxito en la reproducción diferencial e investigar algunas relaciones entre la teoría de la selección natural y la genética de poblaciones. (shrink)

This chapter provides an introduction to the study of the philosophical notions of mechanisms and causality in biology and economics. This chapter sets the stage for this volume, Mechanism and Causality in Biology and Economics, in three ways. First, it gives a broad review of the recent changes and current state of the study of mechanisms and causality in the philosophy of science. Second, consistent with a recent trend in the philosophy of science to focus on scientific practices, it in (...) turn implies the importance of studying the scientific methods employed by researchers. Finally, by way of providing an overview of each chapter in the volume, this chapter demonstrates that biology and economics are two fertile fields for the philosophy of science and shows how biological and economic mechanisms and causality can be synthesized. (shrink)

Two controversies exist regarding the appropriate characterization of hierarchical and adaptive evolution in natural populations. In biology, there is the Wright-Fisher controversy over the relative roles of random genetic drift, natural selection, population structure, and interdemic selection in adaptive evolution begun by Sewall Wright and Ronald Aylmer Fisher. There is also the Units of Selection debate, spanning both the biological and the philosophical literature and including the impassioned group-selection debate. Why do these two discourses exist separately, and interact relatively little? (...) We postulate that the reason for this schism can be found in the differing focus of each controversy, a deep difference itself determined by distinct general styles of scientific research guiding each discourse. That is, the Wright-Fisher debate focuses on adaptive process, and tends to be instructed by the mathematical modeling style, while the focus of the Units of Selection controversy is adaptive product, and is typically guided by the function style. The differences between the two discourses can be usefully tracked by examining their interpretations of two contested strategies for theorizing hierarchical selection: horizontal and vertical averaging. (shrink)

climate scientists have been engaged in a decades-long debate over the standing of satellite measurements of the temperature trends of the atmosphere above the surface of the earth. This is especially significant because skeptics of global warming and the greenhouse effect have utilized this debate to spread doubt about global climate models used to predict future states of climate. I use this case from an under-studied science to illustrate two distinct philosophical approaches to the relation among data, scientists, measurement, models, (...) and theory. I argue that distinguishing between 'direct' empiricist and 'complex' empiricist approaches helps us understand and analyze this important scientific episode. I also introduce a complex empiricist account of testing and evaluation, and contrast it with the basic Hypothetico-Deductive approach to the climate models used by the direct empiricists. This more developed complex empiricist apporach will serve philosophy of science well, as computational models become more wide-spread in the sciences. (shrink)

The status of population genetics has become hotly debated among biologists and philosophers of biology. Many seem to view population genetics as relatively unchanged since the Modern Synthesis and have argued that subjects such as development were left out of the Synthesis. Some have called for an extended evolutionary synthesis or for recognizing the insignificance of population genetics. Yet others such as Michael Lynch have defended population genetics, declaring "nothing in evolution makes sense except in the light of population genetics" (...) (a twist on Dobzhansky's famous slogan that "nothing in biology makes sense except in the light of evolution"). Missing from this discussion is the use of population genetics to shed light on ecology and vice versa, beginning in the 1940s and continuing until the present day. I highlight some of that history through an overview of traditions such as ecological genetics and population biology, followed by a slightly more in-depth look at a contemporary study of the endangered California Tiger Salamander. I argue that population genetics is a powerful and useful tool that continues to be used and modified, even if it isn't required for all evolutionary explanations or doesn't incorporate all the causal factors of evolution. (shrink)

Philosophy can shed light on mathematical modeling and the juxtaposition of modeling and empirical data. This paper explores three philosophical traditions of the structure of scientific theory—Syntactic, Semantic, and Pragmatic—to show that each illuminates mathematical modeling. The Pragmatic View identifies four critical functions of mathematical modeling: (1) unification of both models and data, (2) model fitting to data, (3) mechanism identification accounting for observation, and (4) prediction of future observations. Such facets are explored using a recent exchange between two groups (...) of mathematical modelers in plant biology. Scientific debate can arise from different modeling philosophies. (shrink)

Theoretical biology and economics are remarkably similar in their reliance on mathematical models, which attempt to represent real world systems using many idealized assumptions. They are also similar in placing a great emphasis on derivational robustness of modeling results. Recently philosophers of biology and economics have argued that robustness analysis can be a method for confirmation of claims about causal mechanisms, despite the significant reliance of these models on patently false assumptions. We argue that the power of robustness analysis has (...) been greatly exaggerated. It is best regarded as a method of discovery rather than confirmation. (shrink)

The complexity and heterogeneity of causes influencing ecology’s domain challenge its capacity to generate a general theory without exceptions, raising the question of whether ecology is capable, even in principle, of achieving the sort of theoretical success enjoyed by physics. Weber has argued that competition theory built around the Competitive Exclusion Principle (especially Tilman’s resource-competition model) offers an example of ecology identifying a law-like causal regularity. However, I suggest that as Weber presents it, the CEP is not yet a causal (...) regularity. Instead, I argue that the scientific understanding in Tilman’s theory takes a different form. The theory explains through a structure I call “channeling explanation” which does not depend on deduction from general laws, but rather builds on constraints and trade-offs represented in state-space. Recognizing this structure supports the more general point that ecology and other so-called special sciences can reveal novel theoretical approaches to philosophy of science when approached with openness to their uniqueness. (shrink)

This essay analyzes and develops recent views about explanation in biology. Philosophers of biology have parted with the received deductive-nomological model of scientific explanation primarily by attempting to capture actual biological theorizing and practice. This includes an endorsement of different kinds of explanation (e.g., mathematical and causal-mechanistic), a joint study of discovery and explanation, and an abandonment of models of theory reduction in favor of accounts of explanatory reduction. Of particular current interest are philosophical accounts of complex explanations that appeal (...) to different levels of organismal organization and use contributions from different biological disciplines. The essay lays out one model that views explanatory integration across different disciplines as being structured by scientific problems. I emphasize the philosophical need to take the explanatory aims pursued by different groups of scientists into account, as explanatory aims determine whether different explanations are competing or complementary and govern the dynamics of scientific practice, including interdisciplinary research. I distinguish different kinds of pluralism that philosophers have endorsed in the context of explanation in biology, and draw several implications for science education, especially the need to teach science as an interdisciplinary and dynamic practice guided by scientific problems and explanatory aims. (shrink)

this requirement for adaptations. Emergent characters are always potential adaptations. Not all selection processes produce adaptations, however. The key issue, in delineating a selection process, is the relationship between a character and fitness. The emergent character approach is more restrictive than alternative schemas that delineate selection..

Schaffner’s model of theory reduction has played an important role in philosophy of science and philosophy of biology. Here, the model is found to be problematic because of an internal tension. Indeed, standard antireductionist external criticisms concerning reduction functions and laws in biology do not provide a full picture of the limits of Schaffner’s model. However, despite the internal tension, his model usefully highlights the importance of regulative ideals associated with the search for derivational, and embedding, deductive relations among mathematical (...) structures in theoretical biology. A reconstructed Schaffnerian model could therefore shed light on mathematical theory development in the biological sciences and on the epistemology of mathematical practices more generally. *Received November 2006; revised March 2009. †To contact the author, please write to: Philosophy Department, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064; e‐mail: [email protected]. (shrink)

Today's climate models are supported in a couple of ways that receive little attention from philosophers or climate scientists. In addition to standard 'model fit', wherein a model's simulation is compared to observational data, there is an additional type of confirmation available through the variety of instances of model fit. When a model performs well at fitting first one variable and then another, the probability of the model under some standard confirmation function, say, likelihood, goes up more than under each (...) individual case of fit alone. Thus, two instances of fit of distinct variables of a global climate model using distinct data sets considered collectively will provide stronger evidence for a model than either one of the instances considered individually. This has consequences for model robustness. Sets of models that produce robust results will, if their assumptions vary enough and they each are observationally sound, provide reasons to endorse common structures found in those models. Finally, independent empirical support for aspects and assumptions of the model provides an additional confirmational virtue for climate models, contrary to what is implied by some current philosophical writing on this topic. (shrink)

Multiply realizable properties are those whose realizers are physically diverse. It is often argued that theories which contain them are ipso facto irreducible. These arguments assume that physical explanations are restricted to the most specific descriptions possible of physical entities. This assumption is descriptively false, and philosophically unmotivated. I argue that it is a holdover from the late positivist axiomatic view of theories. A semantic view of theories, by contrast, correctly allows scientific explanations to be couched in the most perspicuous, (...) powerful language available. On a semantic view, traditional notions of multiple realizability are thus very hard to motivate. At best, one must abandon either the idea that multiple realizability is an interesting scientific notion, or else admit that multiply realizable properties do not automatically block scientific reductions. (shrink)

We review Evolution and the Levels of Selection by Samir Okasha. This important book provides a cohesive philosophical framework for understanding levels-of-selections problems in biology. Concerning evolutionary transitions, Okasha proposes that three stages characterize the shift from a lower level of selection to a higher one. We discuss the application of Okasha’s three-stage concept to the evolutionary transition from unicellularity to multicellularity in the volvocine green algae. Okasha’s concepts are a provocative step towards a more general understanding of the major (...) evolutionary transitions; however, the application of certain ideas to the volvocine model system is not straightforward. (shrink)

The fate of optimality modeling is typically linked to that of adaptationism: the two are thought to stand or fall together (Gould and Lewontin, Proc Relig Soc Lond 205:581–598, 1979; Orzack and Sober, Am Nat 143(3):361–380, 1994). I argue here that this is mistaken. The debate over adaptationism has tended to focus on one particular use of optimality models, which I refer to here as their strong use. The strong use of an optimality model involves the claim that selection is (...) the only important influence on the evolutionary outcome in question and is thus linked to adaptationism. However, biologists seldom intend this strong use of optimality models. One common alternative that I term the weak use simply involves the claim that an optimality model accurately represents the role of selection in bringing about the outcome. This and other weaker uses of optimality models insulate the optimality approach from criticisms of adaptationism, and they account for the prominence of optimality modeling (broadly construed) in population biology. The centrality of these uses of optimality models ensures a continuing role for the optimality approach, regardless of the fate of adaptationism. (shrink)

In this paper, a modest version of the Semantic View is motivated as both tenable and potentially fruitful for philosophy of science. An analysis is proposed in which the Semantic View is characterized by three main claims. For each of these claims, a distinction is made between stronger and more modest interpretations. It is argued that the criticisms recently leveled against the Semantic View hold only under the stronger interpretations of these claims. However, if one only commits to the modest (...) interpretation for all the claims, then the view obtained, the Modest Semantic View, is tenable and fruitful for the philosophy of science. (shrink)

Most models of generational succession in sexually reproducing populations necessarily move back and forth between genic and genotypic spaces. We show that transitions between and within these spaces are usually hidden by unstated assumptions about processes in these spaces. We also examine a widely endorsed claim regarding the mathematical equivalence of kin-, group-, individual-, and allelic-selection models made by Lee Dugatkin and Kern Reeve. We show that the claimed mathematical equivalence of the models does not hold. *Received January 2007; revised (...) April 2008. †To contact the authors, please write to: Elisabeth Lloyd, Department of History and Philosophy of Science, 130 Goodbody Hall, Indiana University, Bloomington, IN 47405; e-mail: [email protected]; Richard Lewontin, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138; Marcus Feldman, Department of Biological Sciences, Stanford University, Stanford, CA 94305; e-mail: [email protected]. (shrink)

In 1988, David Hull presented an evolutionary account of science. This was a direct analogy to evolutionary accounts of biological adaptation, and part of a generalized view of Darwinian selection accounts that he based upon the Universal Darwinism of Richard Dawkins. Criticisms of this view were made by, among others, Kim Sterelny, which led to it gaining only limited acceptance. Some of these criticisms are, I will argue, no longer valid in the light of developments in the formal modeling of (...) evolution, in particular that of Sergey Gavrilets’ work on adaptive landscapes. If we can usefully recast the Hullian view of science as being driven by selection in terms of Gavrilets’ and Kaufmann’s view of there being “giant components” of high-fitness networks through any realistic adaptive landscape, we may now find it useful to ask what the adaptive pressures on science are, and to extend the metaphor into a full analogy. This is in effect to reconcile the Fisherianism of the Dawkins–Hull approach to selection and replicators, with a Wrightean drift account of social constructionist views of science, preserving, it is to be hoped, the valuable aspects of both. (shrink)

Two alternative statistical approaches to modelling multi-level selection in nature, both found in the contemporary biological literature, are contrasted. The simple covariance approach partitions the total selection differential on a phenotypic character into within-group and between-group components, and identifies the change due to group selection with the latter. The contextual approach partitions the total selection differential into different components, using multivariate regression analysis. The two approaches have different implications for the question of what constitutes group selection and what does not. (...) I argue that the contextual approach is theoretically preferable. This has important implications for a number of issues in the philosophical debate about the levels of selection. Introduction Group selection and the covariance formulation of selection The contextual approach A modification of the simple covariance approach Consequences: frameshifting and additivity 5.1 Frameshifting 5.2 Additivity Conclusion. (shrink)

For a number of years, the debate in evolutionary biology over the ’levels of selection’ has attracted intense interest from philosophers of science. The main question concerns the level of the biological hierarchy at which natural selection occurs. Does selection act on organisms, genes, groups, colonies, demes, species, or some combination of these? According to traditional Darwinian theory the answer is the organism -- it is the differential survival and reproduction of individual organisms that drives the evolutionary process. But there (...) are alternative views too, including pluralist views which say that the choice between different levels of selection is often a matter of perspective, not empirical fact. (shrink)

David Hull's analysis of conceptual change in science, as presentedin his book, Science as a Process (1988), provides a useful framework for understanding one of the scientific controversies in which he actively and constructively intervened, the units of selectiondebates in evolutionary biology. What follows is a brief overview ofthose debates and some reflections on them.

In a previous study, using experimental metapopulations of the flour beetle, Tribolium castaneum, we investigated phase III of Wright's shifting balance process (Wade and Griesemer 1998). We experimentally modeled migration of varying amounts from demes of high mean fitness into demes of lower mean fitness (as in Wright's characterization of phase III) as well as the reciprocal (the opposite of phase III). We estimated the meta-populational heritability for this level of selection by regression of offspring deme means on the weighted (...) parental deme means.Here we develop a Punnett Square representation of the inheritance of the group mean to place our empirical findings in a conceptual context similar to Mendelian inheritance of individual traits. The comparison of Punnett Squares for individual and group inheritance shows how the latter concept can be rigorously defined and extended despite the lack of explicitly formulated, simple Mendelian laws of inheritance at the group level. Whereas Wright's phase III combines both interdemic selection and meta-populational inheritance, our formulation separates the issue of meta-populational heritability from that of interdemic selection. We use this conceptual context to discuss the controversies over the levels of selection and the units of inheritance. (shrink)

Accounts of the relation between theories and models in biology concentrate on mathematical models. In this paper I consider the dual role of models as representations of natural systems and as a material basis for theorizing. In order to explicate the dual role, I develop the concept of a remnant model, a material entity made from parts of the natural system(s) under study. I present a case study of an important but neglected naturalist, Joseph Grinnell, to illustrate the extent to (...) which mundane practices in a museum setting constitute theorizing. I speculate that historical and sociological analyses of institutions can play a specific role in the philosophical analysis of model-building strategies. (shrink)

Philosophical analysis of ecological theories has lagged behind the study of evolutionary theory. The semantic conception of scientific theories, which has been employed successfully in the analysis of evolutionary theory, is adopted here to analyse ecological theory. Two general problems in ecology are discussed. One arises from the continued use of covering law models in ecology, and the other concerns the applicability of ecological theory in conservation biology. The semantic conception of ecological theories is used to resolve these problems.

We argue that a fashionable interpretation of the theory of natural selection as a claim exclusively about populations is mistaken. The interpretation rests on adopting an analysis of fitness as a probabilistic propensity which cannot be substantiated, draws parallels with thermodynamics which are without foundations, and fails to do justice to the fundamental distinction between drift and selection. This distinction requires a notion of fitness as a pairwise comparison between individuals taken two at a time, and so vitiates the interpretation (...) of the theory as one about populations exclusively. (shrink)

This survey of major developments in North American philosophy of science begins with the mid-1960s consolidation of the disciplinary synthesis of internalist history and philosophy of science (HPS) as a response to criticisms of logical empiricism. These developments are grouped for discussion under the following headings: historical metamethodologies, scientific realisms, philosophies of the special sciences, revivals of empiricism, cognitivist naturalisms, social epistemologies, feminist theories of science, studies of experiment and the disunity of science, and studies of science as practice and (...) culture. A unifying theme of the survey is the relation between historical metamethodologists and scientific realists, which dominated philosophical work in the late 1970s. I argue that many of the alternative cognitive naturalisms, social epistemologies, and feminist theories that have been proposed can be understood as analogues to the differences between metamethodological theories of scientific rationality and realist accounts of successful reference to real causal processes. Recent work on experiment, scientific practice, and the culture of science may, however, challenge the underlying conception of the field according to which realism and historical rationalism (or their descendants) are the important alternatives available, and thus may take philosophy of science in new directions. (shrink)

I argue against theories that attempt to reduce scientific representation to similarity or isomorphism. These reductive theories aim to radically naturalize the notion of representation, since they treat scientist's purposes and intentions as non-essential to representation. I distinguish between the means and the constituents of representation, and I argue that similarity and isomorphism are common but not universal means of representation. I then present four other arguments to show that similarity and isomorphism are not the constituents of scientific representation. I (...) finish by looking at the prospects for weakened versions of these theories, and I argue that only those that abandon the aim to radically naturalize scientific representation are likely to be successful. (shrink)