What methodological approaches do research programs use to investigate the world? Elisabeth Lloyd’s Logic of Research Questions (LRQ) characterizes such approaches in terms of the questions that the researchers ask and causal factors they consider. She uses the Logic of Research Questions Framework to criticize adaptationist programs in evolutionary biology for dogmatically assuming selection explanations of the traits of organisms. I argue that Lloyd’s general criticism of methodological adaptationism is an artefact of the impoverished LRQ. My Ordered Factors Proposal extends (...) the LRQ to characterize approaches with sequences of questions and factors. I highlight the importance that ordering one’s investigation plays in approaches at the level of adaptationism by analyzing two research programs in community ecology: competitionists and neutralists. Competitionists and neutralists take opposed starting points and use explanatory and developmental heuristics to consider more factors in due time. On the Ordered Factors Proposal, these approaches are not only the ecological factors they are open to considering but also the order in which they will consider them. My disagreement with Lloyd’s over how to characterize methodological approaches reflects different views about methodological monism and pluralism. (shrink)

Pluralism is widely appealed to in many areas of philosophy of science, though what is meant by ‘pluralism’ may profoundly vary. Because explanations of behaviour have been a favoured target for pluralistic theses, the sciences of behaviour offer a rich context in which to further investigate pluralism. This is what the topical collection The Biology of Behaviour: Explanatory pluralism across the life sciences is about. In the present introduction, we briefly review major strands of pluralist theses and their motivations. We (...) highlight three distinct types of pluralisms—type pluralism, fragmentation pluralism and insular pluralism—and introduce the articles of the topical collection. (shrink)

Evolutionary biology is a field currently animated by much discussion concerning its conceptual foundations. On the one hand, we have supporters of a classical view of evolutionary theory, whose backbone is provided by population genetics and the so-called Modern Synthesis (MS). On the other hand, a number of researchers are calling for an Extended Synthe- sis (ES) that takes seriously both the limitations of the MS (such as its inability to incorporate developmental biology) and recent empirical and theoretical research on (...) issues such as evolvability, modularity, and self-organization. In this article, I engage in an in-depth commentary of an influential paper by population geneticist Michael Lynch, which I take to be the best defense of the MS-population genetics position published so far. I show why I think that Lynch’s arguments are wanting and propose a modification of evolutionary theory that retains but greatly expands on population genetics. (shrink)

The dissertation criticizes two analogical applications of Darwinism to the spheres of mind and culture: the Darwinian approach to creativity and memetics. These theories rely on three basic analogies: the ontological analogy states that the basic ontological units of culture are so-called memes, which are replicators like genes; the origination analogy states that novelty in human creativity emerges in a "blind" Darwinian manner; and the explanatory units of selection analogy states that memes are "egoistic" and that they can spread independently (...) of our mind. The detailed philosophical analysis offered in the dissertation shows that these three analogies rely on either wrong or trivial statements: they provide either wrong or no new descriptions or explanations of the phenomena at hand. In Chapter One, I introduce the diverse ways, in which contemporary Darwinism is used today outside of evolutionary biology. Chapter Two explains what it means to claim that something evolves in a Darwinian manner. Chapter Three to Five address each of the three analogies separately. Darwinism applied to culture and mind, at least in the way discussed in this study, is not a dangerous idea. It leads either to wrong claims or to a re-telling in Darwinian terms of what we have already known. (shrink)

The theory of evolution by natural selection is, perhaps, the crowning intellectual achievement of the biological sciences. There is, however, considerable debate about which entity or entities are selected and what it is that fits them for that role. This article aims to clarify what is at issue in these debates by identifying four distinct, though often confused, concerns and then identifying how the debates on what constitute the units of selection depend to a significant degree on which of these (...) four questions a thinker regards as central. (shrink)

Genic selectionists (Williams 1966; Dawkins 1976) defend the view that genes are the (unique) units of selection and that all evolutionary events can be adequately represented at the genic level. Pluralistic genic selectionists (Sterelny and Kitcher 1988; Waters 1991; Dawkins 1982) defend the weaker view that in many cases there are multiple equally adequate accounts of evolutionary events, but that always among the set of equally adequate representations will be one at the genic level. We describe a range of cases (...) all involving stable equilibria actively maintained by selection. In these cases genotypic models correctly show that selection is active at the equilibrium point. In contrast, the genic models have selection disappearing at equilibrium. For deterministic models this difference makes no difference. However, once drift is added in, the two sets of models diverge in their predicted evolutionary trajectories. Thus, contrary to received wisdom on this matter, the two sets of models are not empirically equivalent. Moreover, the genic models get the facts wrong. (shrink)

Within the philosophy of science, the realism debate has been revitalised by the development of forms of structural realism. These urge a shift in focus from the object oriented ontologies that come and go through the history of science to the structures that remain through theory change. Such views have typically been elaborated in the context of theories of physics and are motivated by, first of all, the presence within such theories of mathematical equations that allow straightforward representation of the (...) relevant structures; and secondly, the implications of such theories for the individuality and identity of putative objects. My aim in this talk is to explore the possibility of extending such views to biological theories. An obvious concern is that within the context of the latter it is typically insisted that we cannot find the kinds of highly mathematised structures that structural realism can point to in physics. I shall indicate how the model-theoretic approach to theories might help allay such concerns. Furthermore, issues of identity and individuality also arise within biology. Thus Dupre has recently noted that there exists a ‘General Problem of Biological Individuality’ which relates to the issue of how one divides ‘massively integrated and interconnected’ systems into discrete components. In response Dupre advocates a form of ‘Promiscuous Realism’ that holds, for example, that there is no unique way of dividing the phylogenetic tree into kinds. Instead I shall urge serious consideration of those aspects of the work of Dupre and others that lean towards a structuralist interpretation. By doing so I hope to suggest possible ways in which a structuralist stance might be extended to biology. (shrink)

Organisms can be treated as optimizers when there is consensus among their genes about what is best to be done, but genomic consensus is often lacking, especially in interactions among kin because kin share some genes but not others. Grafen adopts a majoritarian perspective in which an individual’s interests are identified with the interests of the largest coreplicon of its genome, but genomic imprinting and recombination factionalize the genome so that no faction may predominate in some interactions among kin. Once (...) intragenomic conflicts are recognized, the individual organism can be conceptualized as an arbiter among competing interests within a collective. Organismal adaptation can be recognized without phenotypes being optimized. (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)

Okasha claims at the outset of his book "Evolution and the Levels of Selection" that the Price equation lays bare the fundamentals underlying all selection phenomena. However, the thoroughness of his subsequent analysis of multi-level selection theories leads him to abandon his fundamentalist commitments. At critical points he invokes cost benefit analyses that sometimes favors the Price approach and sometimes the contextual approach, sometimes favors MLS1 and sometimes MLS2. And although he doesn’t acknowledge it, even the Price approach breaks down (...) into a family of alternative equations that parse the causes in different ways, none of which is uniquely correct and none of which achieves the ultimate isolation of effects due to what Okasha believes are the fundamental causes. I argue that his book provides good reason to re-conceive our understanding of evolutionary theorizing in terms of a toolbox view and to stop subjecting the analyses of evolutionary concepts to a universalist standard. (shrink)

Okasha claims at the outset of his book "Evolution and the Levels of Selection" (2006) that the Price equation lays bare the fundamentals underlying all selection phenomena. However, the thoroughness of his subsequent analysis of multi-level selection theories leads him to abandon his fundamentalist commitments. At critical points he invokes cost benefit analyses that sometimes favors the Price approach and sometimes the contextual approach, sometimes favors MLS1 and sometimes MLS2. And although he doesn’t acknowledge it, even the Price approach breaks (...) down into a family of alternative equations that parse the causes in different ways, none of which is uniquely correct and none of which achieves the ultimate isolation of effects due to what Okasha believes are the fundamental causes. I argue that his book provides good reason to re-conceive our understanding of evolutionary theorizing in terms of a toolbox view (developed here) and to stop subjecting the analyses of evolutionary concepts to a universalist standard. (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)

Kerr and Godfrey-Smith argue that two mathematically equivalent, alternative formal representations drawn from population genetics, the contextualist and collectivist formalisms, may be equally good for quantifying the dynamics of some natural systems, despite important differences between the formalisms. I draw on constraints on causal representation from Woodward (Making things happen, Oxford University Press, New York, 2003) and Eberhardt and Scheines (Philos Sci 74(5):981–995, 2006) to argue that one or the other formalism will be superior for arbitrary natural systems in which (...) individuals form different types of groups. (shrink)

My general aim is to clarify the foundational difference between Stephen Jay Gould and Richard Dawkins concerning what biological entities are the units of selection in the process of evolution by natural selection. First, I recapitulate Gould’s central objection to Dawkins’s view that genes are the exclusive units of selection. According to Gould, it is absurd for Dawkins to think that genes are the exclusive units of selection when, after all, genes are not the exclusive interactors: those agents directly engaged (...) with, directly impacted by, environmental pressures. Second, I argue that Gould’s objection still goes through even when we take into consideration Sterelny and Kitcher’s defense of gene selectionism in their admirable paper “The Return of the Gene.” Third, I propose a strategy for defending Dawkins that I believe obviates Gould’s objection. Drawing upon Elisabeth Lloyd’s careful taxonomy of the various understandings of the unit of selection at play in the philosophy of biology literature, my proposal involves realizing that Dawkins endorses a different understanding of the unit of selection than Gould holds him to, an understanding that does not require genes to be the exclusive interactors. (shrink)

Group-structured populations, of the kind prominent in discussions of multilevel selection, are contrasted with ‘neighbor-structured’ populations. I argue that it is a necessary condition on multilevel description of a selection process that there should be a nonarbitrary division of the population into equivalence classes (or an approximation to this situation). The discussion is focused via comparisons between two famous problem cases involving group structure (altruism and heterozygote advantage) and two neighbor-structured cases that resemble them. Conclusions are also drawn about the (...) role of correlated interaction in the evolution of altruism. 1 Introduction 2 Two Kinds of Population Structure 3 Objections and Replies 4 Particles on a Line 5 Conclusion Appendix: Neighborhoods and Selection CiteULike Connotea Del.icio.us What's this? (shrink)

Formal methods developed for modeling levels of selection problems have recently been applied to the investigation of major evolutionary transitions. We discuss two new tools of this kind. First, the ‘near-variant test’ can be used to compare the causal adequacy of predictively equivalent representations. Second, ‘state-variable gestalt-switching’ can be used to gain a useful dual perspective on evolutionary processes that involve both higher and lower level populations.

In the first half of this dissertation, I develop a heuristic methodology for analyzing scientific solutions to the problem of underdetermination. Heuristics are rough-and-ready procedures used by scientists to construct models, design experiments, interpret evidence, etc. But as powerful as they are, heuristics are also error-prone. Therefore, I argue that they key to prudently using a heuristic is the articulation of meta-heuristics---guidelines to the kinds of problems for which a heuristic is well- or ill-suited. Given that heuristics will introduce certain (...) errors into our scientific investigations, I emphasize the importance of a particular category of meta-heuristics involving the search for robust evidence. Robustness is understood to be the epistemic virtue bestowed by agreement amongst multiple modes of determination. The more modes we have at our disposal, and the more these confirm the same result, the more confident can we be that a result is not a mere artifact of some heuristic simplification. Through an analysis of case-studies in the philosophy of biology and clinical trials, I develop a principled method for modeling and evaluating heuristics and robustness claims in a qualitative problem space. The second half of the dissertation deploys the heuristic methodology to address ethical and epistemological issues in the science of clinical trials. To that end, I develop a network model for the problem space of clinical research, capable of representing the various kinds of experiments, epistemic relationships, and ethical justifications intrinsic to the domain. I then apply this model to ongoing research with the antibacterial agent, moxifloxacin, for the treatment of tuberculosis, tracking its development from initially successful and promising in vitro and animal studies to its disappointing and discordant performance across five human efficacy trials. Given this failure to find a robust result with moxifloxacin across animal and human studies, what should researchers now do? While my final analysis of this case does not definitively answer that question, I demonstrate how my methodology, unlike a statistical meta-analysis, helps to clarify the directions for further research. (shrink)