Because of the problems associated with ecological concepts, generalizations, and proposed general theories, applied ecology may require a new "logic" of explanation characterized neither by the traditional accounts of confirmation nor by the logic of discovery. Building on the works of Grunbaum, Kuhn, and Wittgenstein, we use detailed descriptions from research on conserving the Northern Spotted Owl, a case typical of problem solving in applied ecology, to (1) characterize the method of case studies; (2) survey its strengths; (3) summarize and (...) respond to its shortcomings; and (4) investigate and defend its underlying "logic". (shrink)

In his criticism of my paper on the concept of race (Sesardic, 2010), Adam Hochman raises many issues that deserve further clarification. First, I will comment on Hochman’s claim that I attack a straw man version of racial constructionism. Second, I will try to correct what I see as a distorted historical picture of the debate between racial naturalists and racial constructionists. Third, I will point out the main weaknesses in Hochman’s own defense of constructionism about race. And fourth, I (...) will briefly comment on why I think that Hochman unjustifiably dismisses one of the potential sources of racial differentiation that were suggested in my paper. Before I start, though, a preliminary clarification is in order. Hochman kindly calls my article ‘‘one of the strongest defenses of racial naturalism in recent times’’, which might suggest to the reader that my goal was to offer a full-fledged biological explication of the concept of race. But in fact my ambition was more limited. As I explained: My aim in this paper was not to prove the biological reality of race. Rather, more modestly, I have tried to show that typical attempts to disconnect the concept of race from genetics have too quickly and too uncritically been accepted by many ‘‘race critics’’. (Sesardic, 2010, p. 160; italics added) I will continue defending the same position in this article. (shrink)

This article discusses the contribution to evolutionary theory of Leonard Darwin, the eighth child of Charles Darwin. By analysing the correspondence Leonard Darwin maintained with Ronald Aylmer Fisher in conjunction with an assessment of his books and other written works between the 1910s and 1930s, this article argues for a more prominent role played by him than the previously recognised in the literature as an informal mentor of Fisher. The paper discusses Leonard’s efforts to amalgamate Mendelism with both Eugenics and (...) Darwinism in order for the first to base their policies on new scientific developments and to help the second in finding a target for natural selection. Without a formal qualification in biological sciences and as such mistrusted by some “formal” scientists, Leonard Darwin engaged with key themes of Darwinism such as mimicry, the role of mutations on speciation and the process of genetic variability, arriving at important conclusions concerning the usefulness of Mendelian genetics for his father’s theory. (shrink)

During the 1970s, a "revolution" in American paleobiology took place. It came about in part because a group of mostly young, ambitious paleontologists adapted many of the quantitative methodologies and techniques developed in fields including biology and ecology over the previous several decades to their own discipline. Stephen Jay Gould, who was then just beginning his career, joined others in articulating a singular vision for transforming paleontology from an isolated and often ignored science to a "nomothetic discipline" that could sit (...) at evolution's "high table." Over the course of a single decade, between 1970 and 1980, this transformation had in large part been accomplished. Among those most centrally involved in this process were Gould, Thomas Schopf, David Raup, and Gould's graduate student Jack Sepkoski, all of whom made major contributions in theoretical and quantitative analysis of the fossil record and evolutionary history. Recognizing that an ideological agenda was not enough, Gould and others developed and promoted new outlets, technologies, and pedagogical strategies to nurture their new discipline. This paper describes this process of transformation, and presents Sepkoski's education and participation as exemplary of the "new model paleontologist", which Gould hoped to produce. (shrink)

In this paper we argue that ecological evolutionary developmental biology accounts of cognitive modernity are compatible with cultural evolution theories of language built upon iterated learning models. Cultural evolution models show that the emergence of near universal properties of language do not require the preexistence of strong specific constraints. Instead, the development of general abilities, unrelated to informational specificity, like the copying of complex signals and sharing of communicative intentions is required for cultural evolution to yield specific properties, such as (...) language structure. We argue that eco-evo-devo provides the appropriate conceptual background to ground an account for the many interconnected genetic, environmental and developmental factors that facilitated the emergence of an organic system able to develop language through the iterated transmission of information. We use the concept of niche construction to connect evolutionary developmental accounts for sensory guided motor capacities and cultural evolution guided by iterated learning models. This integrated theoretical model aims to build bridges between biological and cultural approaches. (shrink)

In this paper, I propose two theses, and then examine what the consequences of those theses are for discussions of reduction and emergence. The first thesis is that what have traditionally been seen as robust, reductions of one theory or one branch of science by another more fundamental one are a largely a myth. Although there are such reductions in the physical sciences, they are quite rare, and depend on special requirements. In the biological sciences, these prima facie sweeping reductions (...) fade away, like the body of the famous Cheshire cat, leaving only a smile.... The second thesis is that the "smiles" are fragmentary patchy explanations, and though patchy and fragmentary, they are very important, potentially Nobel-prize winning advances. To get the best grasp of these "smiles," I want to argue that, we need to return to the roots of discussions and analyses of scientific explanation more generally, and not focus mainly on reduction models, though three conditions based on earlier reduction models are retained in the present analysis. I briefly review the scientific explanation literature as it relates to reduction, and then offer my account of explanation. The account of scientific explanation I present is one I have discussed before, but in this paper I try to simplify it, and characterize it as involving field elements and a preferred causal model system abbreviated as FE and PCMS. In an important sense, this FE and PCMS analysis locates an "explanation" in a typical scientific research article. This FE and PCMS account is illustrated using a recent set of neurogenetic papers on two kinds of worm foraging behaviors: solitary and social feeding. One of the preferred model systems from a 2002 Nature article in this set is used to exemplify the FE and PCMS analysis, which is shown to have both reductive and nonreductive aspects. The paper closes with a brief discussion of how this FE and PCMS approach differs from and is congruent with Bickle's "ruthless reductionism" and the recently revived mechanistic philosophy of science of Machamer, Darden, and Craver. (shrink)

Current Perspectives in Philosophy of Biology.

This paper aims to uncover the explanatory profile of an idealized version of Karl Ernst von Baer’s notion of individuation, wherein the special develops from the general. First, because such sequences can only be exemplified by a multiplicity of causally-related events, they should be seen as the topics of historical why-questions, rather than initial condition why-questions. Second, because historical why-questions concern the diachronic unity or genidentity of the events under consideration, I argue that the von Baerian pattern elicits a distinctive (...) response to such questions, wherein we are inclined to simultaneously affirm and reject the temporal unity of these events. I buttress this claim by considering non-biological expressions of the von Baerian principle, drawn from institutional history and literature. In the second half of the paper, I consider the implications of my findings for ontogenetic and phylogenetic sequences. I argue that the explanatory profile of von Baer’s principle neatly describes the distinctive speciation events that characterize deep metazoan phylogeny, as described by Stuart Newman. I also argue that parallel considerations should move us to accept a sense in which ontogenetic stages are not diachronically unified. (shrink)

Modern biology is ambivalent about the notion of evolutionary progress. Although most evolutionists imply in their writings that they still understand large-scale macroevolution as a somewhat progressive process, the use of the term “progress” is increasingly criticized and avoided. The paper shows that this ambivalence has a long history and results mainly from three problems: (1) The term “progress” carries historical, theoretical and social implications which are not congruent with modern knowledge of the course of evolution; (2) An incongruence exists (...) between the notion of progress and Darwin’s theory of selection; (3) It is still not possible to give more than a rudimentary definition of the general patterns that were generated during the macroevolution of organisms. The paper consists of two parts: the first is a historical overview of the roots of the term “progress” in evolutionary biology, the second discusses epistemological, ontological and empirical problems. It is stated that the term has so far served as a metaphor for general patterns generated amongst organisms during evolution. It is proposed that a reformulation is needed to eliminate historically imported implications and that it is necessary to develop a concept for an appropriate empirical description of macroevolutionary patterns. This is the third way between, on the one hand, using the term indiscriminately and, on the other hand, ignoring the general patterns that evolution has produced. (shrink)

Evolutionary theory assumed that mutations occur constantly, gradually, and randomly over time. This formulation from the “modern synthesis” of the 1930s was embraced decades before molecular understanding of genes or mutations. Since then, our labs and others have elucidated mutation mechanisms activated by stress responses. Stress‐induced mutation mechanisms produce mutations, potentially accelerating evolution, specifically when cells are maladapted to their environment, that is, when they are stressed. The mechanisms of stress‐induced mutation that are being revealed experimentally in laboratory settings provide (...) compelling models for mutagenesis that propels pathogen–host adaptation, antibiotic resistance, cancer progression and resistance, and perhaps much of evolution generally. We discuss double‐strand‐break‐dependent stress‐induced mutation in Escherichia coli. Recent results illustrate how a stress response activates mutagenesis and demonstrate this mechanism's generality and importance to spontaneous mutation. New data also suggest a possible harmony between previous, apparently opposed, models for the molecular mechanism. They additionally strengthen the case for anti‐evolvability therapeutics for infectious disease and cancer. (shrink)

Kincaid argues that molecular biology provides little support for the reductionist program, that biochemistry does not reveal common mechanisms, indeed that biochemical theory obstructs discovery. These assertions clash with biologists' stated advocacy of reductionist programs and their claims about the consequent unity of experimental biology. This striking disagreement goes beyond differences in meaning granted to the terms. More significant is Kincaid's misunderstanding of what biochemists do, for a closer look at scientific practice-- and one of Kincaid's examples--reveals substantial progress toward (...) explaining biological function with biochemical models. With the molecular detail emerge unifying generalizations as well as further aspects of the functional processes. (shrink)

There are several interpretations of the argument structure of Darwin's Origin of Species, representing Covering-Law, Inference-to-the-Best-Explanation, and (more recently) Semantic models. I argue that while all three types of interpretation enjoy some textual support, none succeeds in capturing the overall strategy of the Origin, consistent with Darwin's claim that it is 'one long argument'. I provide detailed criticisms of all three current models, and then offer an alternative interpretation based on the view that there are three main argument strategies in (...) the Origin, all supporting the 'causal efficacy' of Darwin's theory. This interpretation provides both a more unified treatment of the text, and some important implications concerning the relation between general philosophical models of scientific theory support and specific historical cases. (shrink)

Morphological EvoDevo is a field of biological inquiry in which explicit relations between evolutionary patterns and growth or morphogenetic processes are made. Historically, morphological EvoDevo results from the coming together of several traditions, notably Naturphilosophie, embryology, the study of heterochrony, and developmental constraints. A special feature binding different approaches to morphological EvoDevo is the use of formalisms and mathematical models. Here we will introduce anatomical network analysis, a new approach centered on connectivity patterns formed by anatomical parts, with its own (...) concepts and tools specifically designed for the study of morphological EvoDevo questions. Riedl’s concept of burden is tightly related to the use of anatomical networks, providing a nexus between the evolutionary patterns and the structural constraints that shape them. (shrink)

Starting from the early decades of the twentieth century, evolutionary biology began to acquire mathematical overtones. This took place via the development of a set of models in which the Darwinian picture of evolution was shown to be consistent with the laws of heredity discovered by Mendel. The models, which came to be elaborated over the years, define a field of study known as population genetics. Population genetics is generally looked upon as an essential component of modern evolutionary theory. This (...) article deals with a famous dispute between J. B. S. Haldane, one of the founders of population genetics, and Ernst Mayr, a major contributor to the way we understand evolution. The philosophical undercurrents of the dispute remain relevant today. Mayr and Haldane agreed that genetics provided a broad explanatory framework for explaining how evolution took place but differed over the relevance of the mathematical models that sought to underpin that framework. The dispute began with a fundamental issue raised by Mayr in 1959: in terms of understanding evolution, did population genetics contribute anything beyond the obvious? Haldane's response came just before his death in 1964. It contained a spirited defense, not just of population genetics, but also of the motivations that lie behind mathematical modelling in biology. While the difference of opinion persisted and was not glossed over, the two continued to maintain cordial personal relations. (shrink)

I respond to the bad lot argument in the context of biological systematics. The response relies on the historical nature of biological systematics and on the availability of pattern explanations. The basic assumption of common descent enables systematic methodology to naturally generate candidate explanatory hypotheses. However, systematists face a related challenge in the issue of character analysis. Character analysis is the central problem for contemporary systematics, yet the general problem of which it is a case—what counts as evidence?—has not been (...) adequately discussed by proponents of inference to the best explanation. Facing this problem is the price of adopting abductive methods. I sketch an account of how systematists approach the problem of evidence. (shrink)

Early nineteenth century systematists sought to describe what they called the Natural System or the Natural Classification. In the nineteenth century, there was no agreement about the basis of observed patterns of similarity between organisms. What did these systematists think they were doing, when they named taxa, proposed relationships between taxa, and arranged taxa into representational schemes? In this paper I explicate Charles Frederic Girard’s (1822–1895) theory and method of systematics. A student of Louis Agassiz, and subsequently (1850–1858) a collaborator (...) with Spencer Baird, Girard claimed that natural classificatory methods do not presuppose either a special creationist or an evolutionary theory of the natural world. The natural system, in Girard’s view, comprises three distinct ways in which organisms can be related to each other. Girard analyzed these relationships, and justified his classificatory methodology, by appeal to his embryological and physiological work. Girard offers an explicit theoretical answer to the question, what characters are evidence for natural classificatory hypotheses? I show that the challenge of simultaneously depicting the three distinct types of relationship led Girard to add a third dimension to his classificatory diagrams. (shrink)

This paper explores the ways in which Wilbur and Orville Wright thought as they tackled the problem of designing and constructing a heavier-than-air craft that would fly under its own power and under their control. It argues that their use of analogy and their use of knowledge in diagnostic reasoning lies outside the scope of current psychological theories and their computer implementations. They used analogies based on mental models of one system, such as the wings, to help them to develop (...) theories of another system, such as the propellers. They were also skilled reasoners, who were adept at finding counterexamples to arguments. (shrink)

The project of treating knowledge as an empirical object of study has gained popularity in recent naturalistic epistemology. It is argued here that the assumption that such an object of study exists is in tension with other central elements of naturalistic philosophy. Two hypotheses are considered. In the first, “knowledge” is hypothesized to refer to mental states causally responsible for the behaviour of cognitive agents. Here, the relational character of truth creates a problem. In the second hypothesis “knowledge” is hypothesized (...) to refer to mental states causally responsible for the evolutionarily successful behaviour of cognitive agents. Here, the problem lies in the fact that evolution by natural selection is not necessarily conducive to truth. The result does not necessarily amount to eliminativism, however, since the naturalist may consistently reject the condition of truth that lies behind these problems. (shrink)

The history of helminthology in the Early Modern Period has been characterized as a debate between two camps, the internalists and the externalists. The internalists believed that helminths are spontaneously generated within the body of the host, whereas the externalists claimed that helminths enter the host from the external environment. According to the this account, the debate between these two camps ended in the nineteenth century with the victory of the externalist viewpoint. Here, we redefine these two terms, as well (...) as the beliefs that the two groups upheld. We suggest that internalists were not necessarily committed to the theory of spontaneous generation, nor were externalists committed to its rejection. These terms only refer to the place where helminths supposedly originate, but not to the process by which they are generated. Thus, some internalists rejected the theory of spontaneous generation, while others held externalist viewpoints and at the same time accepted this theory. We claim that the debate did not end with the victory of the externalist camp; rather, a new position which we call “life-cyclism”, emerged and incorporated some elements of the two earlier positions. (shrink)

ArgumentThe spread of Darwinian ideas by the late nineteenth century in Argentina transformed the intellectual elites' notion of progress and civilization. While before Darwin, union, harmony, and assimilation were the ideas most commonly associated with the civilizatory process; variation, struggle, and divergence dominated the post-Darwin discussion. More importantly, unlike in Europe, in Argentina the theory not only triggered interest in the process of speciation, but also its relationship with extinction. Extinction became the benchmark of progress, and the sign of success (...) for the nation. If the country was civilizing itself, the “natural” elimination of inferior individuals, unfit for the struggle for existence, had to be proved and displayed. The origin of modernity was here associated with the existence of evolutionary waste that revealed the work of natural selection on behalf of national improvement. (shrink)

In The Variation of Animals and Plants under Domestication, published in 1868, Darwin used the metaphor of the architect to argue in favor of natural autonomy and to clarify the role of chance in his theory of adaptive change by variation and natural selection. In this article, I trace the history of this important heuristic instrument in Darwin's writings and letters and suggest that this metaphor was important to Darwin because it helps him to explain the role of chance, and (...) gives an argument in favor of the free will. (shrink)

An important historical relation that has hardly been addressed is the influence of Prosper Lucas's Treatise on Natural Inheritance on the development of Charles Darwin's concepts related to inheritance. In this article we trace this historical connection. Darwin read Lucas's Treatise in 1856. His reading coincided with many changes concerning his prior ideas on the transmission and expression of characters. We consider that this reading led him to propose a group of principles regarding prepotency, hereditary diseases, morbid tendencies and atavism; (...) following Lucas, he called these principles: laws of inheritance. (shrink)

The book presents the case that cognitive science should turn its attention to developing theories of human cognition that cover the full range of human perceptual, cognitive, and action phenomena. Cognitive science has now produced a massive number of high-quality regularities with many microtheories that reveal important mechanisms. The need for integration is pressing and will continue to increase. Equally important, cognitive science now has the theoretical concepts and tools to support serious attempts at unified theories. The argument is made (...) entirely by presenting an exemplar unified theory of cognition both to show what a real unified theory would be like and to provide convincing evidence that such theories are feasible. The exemplar is SOAR, a cognitive architecture, which is realized as a software system. After a detailed discussion of the architecture and its properties, with its relation to the constraints on cognition in the real world and to existing ideas in cognitive science, SOAR is used as theory for a wide range of cognitive phenomena: immediate responses ; discrete motor skills ; memory and learning ; problem solving ; language ; and development. The treatments vary in depth and adequacy, but they clearly reveal a single, highly specific, operational theory that works over the entire range of human cognition, SOAR is presented as an exemplar unified theory, not as the sole candidate. Cognitive science is not ready yet for a single theory – there must be multiple attempts. But cognitive science must begin to work toward such unified theories. (shrink)