Despite an enormous philosophical literature on models in science, surprisingly little has been written about data models and how they are constructed. In this paper, I examine the case of how paleodiversity data models are constructed from the fossil data. In particular, I show how paleontologists are using various model-based techniques to correct the data. Drawing on this research, I argue for the following related theses: first, the ‘purity’ of a data model is not a measure of its epistemic reliability. (...) Instead it is the fidelity of the data that matters. Second, the fidelity of a data model in capturing the signal of interest is a matter of degree. Third, the fidelity of a data model can be improved ‘vicariously’, such as through the use of post hoc model-based correction techniques. And, fourth, data models, like theoretical models, should be assessed as adequate for particular purposes. (shrink)

Estimating whether the Earth’s biota is in the middle of a crisis relies heavily on comparisons between present and past data about biodiversity or biodiversity surrogates. Although the past is a crucial source of information to assess the severity of the current biodiversity crisis, substantive conceptual and methodological questions remain about how paleodiversity and biodiversity are to be properly compared. I argue that to justify claims of a current biodiversity crisis is harder than it appears. More precisely, I claim that (...) paleodiversity measurements are incommensurable with contemporary measurements, given the different ways that biodiversity is conceptualized and operationalized. I conclude by proposing three possible ways of overcoming this incommensurability problem. (shrink)

Summary Based on Clausius’ phrasing of a “transformational content” and the resulting 2nd law of thermodynamics, I demonstrated that Gilbert Simondon’s On the Mode of Existence of Technical Objects is historically situated at the threshold of understanding open systems thermodynamics and the related concepts of balance. Furthermore, I showed that Gestalt theory, as represented by Wolfgang Köhler, at least reproduced, if not partially anticipated or even prepared this development of 20th century thinking. Finally, I gave some short examples of how (...) Simondon applied the figure/ground distinction to human perception, memory, and a general theory of becoming and I introduced his proposal to analyse “the grounds” just as thoroughly as the laws of figuration. (shrink)

This paper brings needed clarity to the influential view that species are cohesive entities held together by gene flow, and then develops an empirical argument against that view: Neglected data suggest gene flow is neither necessary nor sufficient for species cohesion. Implications are discussed. ‡I'm grateful to Rob Wilson, Alex Rueger and Lindley Darden for important comments on earlier drafts, and to Joseph Nagel, Heather Proctor, Ken Bond, members of the DC History and Philosophy of Biology reading group, and audience (...) members at the November 2006 meeting of the PSA, for helpful comments or discussion. Social Sciences and Humanities Research Council of Canada fellowship 752-2005-1208 supported research. †To contact the author, please write to: Philosophy Department, University of Wisconsin–Madison, 5185 Helen C. White Hall, 600 North Park Street, Madison, WI 53706; e-mail: [email protected]. (shrink)

We review the various factors that limit adaptation by natural selection. Recent discussion of constraints on selection and, conversely, of the factors that enhance “evolvability”, have concentrated on the kinds of variation that can be produced. Here, we emphasise that adaptation depends on how the various evolutionary processes shape variation in populations. We survey the limits that population genetics places on adaptive evolution, and discuss the relationship between disparate literatures. BioEssays 22:1075–1084, 2000. © 2000 John Wiley & Sons, Inc.

Focusing primarily on papers and books discussing the evolutionary and systematic interpretation of the Cambrian animal fossils from the Burgess Shale fauna, this paper explores the role of epistemic values in the context of a discipline striving to establish scientific authority within a larger domain of epistemic problems and issues . The focal point of this analysis is the repeated claims by paleontologists that the study of fossils gives their discipline a unique ‘historical dimension’ that makes it possible for them (...) to unravel important aspects of evolution invisible to scientists who study the extant biosphere. The first part of the paper explores the shifting of emphasis in the writings of paleontologists between two strategies that employ opposing views on the classical positivist and physicalist ideal of science. The second part analyzes paleontologists’ claims of privileged access to life’s historical dimension in a situation where a theoretical upheaval occurring independent of the epistemical problem at hand completely shifts the standards for evaluating the legitimacy of various knowledge claims. Though the various strategies employed in defending the privileged historical perspective of paleontology have been disparate and, to an extent contradictory, each impinges on the acceptance of a specific epistemic ideal or set of values and success or failure of each depends on the compatibility of this ideal with the surrounding community of scientists. (shrink)

Using the Burgess Shale controversies as a case-study, this paper argues that controversies within different domains may interact as to create a situation of "complicated intricacies," where the practicing scientist has to navigate through a context of multiple thought collectives. To some extent each of these collectives has its own dynamic complete with fairly negotiated standards for investigation and explanation, theoretical background assumptions and certain peculiarities of practice. But the intellectual development in one of these collectives may "spill over" having (...) far reaching consequences for the treatment of apparently independent epistemic problems that are subject of investigation in other thought collectives. For the practicing scientist it is necessary to take this complex web of interactions into account in order to be able to navigate in such a situation. So far most studies of academic science have had a tendency to treat the practicing scientist as members of a single (enclosed) thought collective that stands intellectually isolated from other similar entities unless the discipline was in a state of crisis of paradigmatic proportions. The richness and complexity of Burgess Shale debate shows that this encapsulated kind of analysis is not enough. (shrink)

Although Bayesian methods are widely used in phylogenetic systematics today, the foundations of this methodology are still debated among both biologists and philosophers. The Bayesian approach to phylogenetic inference requires the assignment of prior probabilities to phylogenetic trees. As in other applications of Bayesian epistemology, the question of whether there is an objective way to assign these prior probabilities is a contested issue. This paper discusses the strategy of constraining the prior probabilities of phylogenetic trees by means of the Principal (...) Principle. In particular, I discuss a proposal due to Velasco (Biol Philos 23:455–473, 2008) of assigning prior probabilities to tree topologies based on the Yule process. By invoking the Principal Principle I argue that prior probabilities of tree topologies should rather be assigned a weighted mixture of probability distributions based on Pinelis’ (P Roy Soc Lond B Bio 270:1425–1431, 2003) multi-rate branching process including both the Yule distribution and the uniform distribution. However, I argue that this solves the problem of the priors of phylogenetic trees only in a weak form. (shrink)

(2000). Machines and meaning: Technological autonomy and social adaptation. World Futures: Vol. 55, Challenges of Evolution at the Turn of the Millennium: Part II: The Chllenges of Civilizational Transition, pp. 71-90.

Sewall Wright introduced the metaphor of evolution on “adaptive landscapes” in a pair of papers published in 1931 and 1932. The metaphor has been one of the most influential in modern evolutionary biology, although recent theoretical advancements show that it is deeply flawed and may have actually created research questions that are not, in fact, fecund. In this paper I examine in detail what Wright actually said in the 1932 paper, as well as what he thought of the matter at (...) the very end of his career, in 1988. While the metaphor is flawed, some of the problems which Wright was attempting to address are still with us today, and are in the process of being reformulated as part of a forthcoming Extended Evolutionary Synthesis. (shrink)

The role of paleontology in evolutionary biology between the publication of The Origin of Species in 1859 and the Evolutionary Synthesis of the 1940s is frequently described as mostly misguided failure. However, a significant number of American and British PDPS invertebrate paleontologists of this period did devote considerable attention to evolution, and their evolutionary theories and conclusions were a good deal more diverse and nuanced than previous histories have suggested. This paper brings into focus a number of important but underrecognized (...) aspects of the history of paleontology within the history of biology, including that PDPS paleontologists were not all as theoretically backward as they have been portrayed; that the post-Synthesis narrative of the history of evolution should be continually reevaluated, in part to decouple historical understanding from the agendas of authors who have used history to advance particular views of evolution; and that there is a much richer story to be told about the history of evolutionary biology in both the pre- and post-Synthesis eras. (shrink)

The contemporary use of the term ‘complexity’ frequently indicates that it is considered a unified concept. This may lead to a neglect of the range of different theories that deal with the implications related to the notion of complexity. This paper, integrating both the English and the Latin traditions of research associated with this notion, suggests a more nuanced use of the term, thereby avoiding simplification of the concept to some of its dominant expressions only. The paper further explores the (...) etymology of ‘complexity’ and offers a chronological presentation of three generations of theories that have shaped its uses; the epistemic and socio‐cultural roots of these theories are also introduced. From an epistemological point of view, this reflection sheds light on the competing interpretations underlying the definition of what is considered as complex. Also, from an anthropological perspective it considers both the emancipatory as well as the alienating dimensions of complexity. Based on the highlighted ambiguities, the paper suggests in conclusion that contributions grounded in contemporary theories related to complexity, as well as critical appraisals of their epistemological and ethical legitimacy, need to follow the recursive feedback loops and dynamics that they constitute. In doing so, researchers and practitioners in education should consider their own practice as a learning process that does not require the reduction of the antagonisms and the complementarities that shape its own complexity. (shrink)

The evolutionary synthesis of the 1930s and 1940s integrated the study of biological microevolution and biological macroevolution into the theoretically consistent and hugely productive field of evolutionary biology. A similar synthesis has yet to occur for the study of culture, and the social sciences remain fragmented and theoretically incompatible. Here, it is suggested that a Darwinian theory of cultural evolution can promote such a synthesis. Earlier non-Darwinian theories of cultural evolution, such as progress theories, lacked key elements of a Darwinian (...) theory of cultural evolution that are necessary to promote a synthesis, while other contemporary theories of cultural evolution, such as memetics, make too stringent neo-Darwinian assumptions that are inconsistent with evidence regarding cultural transmission. Several examples are given which indicate the beginnings of an evolutionary synthesis for culture, where patterns of cultural macroevolution have been explained in terms of underlying cultural microevolutionary forces. Finally, it is argued that experimental simulations of cultural evolution can play an important role in this emerging synthesis. (shrink)

El proyecto del ‘Darwinismo Formal’ de Alan Grafen propone una formulación matemática de la teoría de Darwin que pretende demostrar que la selección natural moldea los rasgos fenotípicos a través de la maximización de la eficacia. El proyecto de Grafen reposa sobre tres premisas: la selección natural es la única fuerza que moldea los fenotipos; la eficacia es la única medida de le evolución; y el diseño biológico surge como resultado de un proceso de optimización selectiva. En este trabajo argumentamos (...) que estas tres premisas limitan la aplicabilidad del modelo a los hechos evolutivos más simples. Esto se debe a que Grafen implícitamente presupone un concepto de eficacia que es a la vez causa y efecto de las novedades fenotípicas; lo que, por un lado, vacía la teoría de Darwin de poder explicativo y, por el otro, lleva a ignorar la potencial contribución de fuerzas evolutivas no selectivas en la configuración de la complejidad biológica. Para superar estos escollos del proyecto de del Darwinismo Formal - que son además comunes a todos los modelos formales adaptacionistas - proponemos sustituir el concepto causal de eficacia por el de robustez, definiendo así el diseño biológico como forma y función en lugar de como maximización de la eficacia. (shrink)

The assumption that natural selection alone is sufficient to explain not only which traits get fixed in a population/species, but also how they develop, has been questioned since Darwin’s times, and increasingly in the last decades. Alternative theories, linked to genetic and phenotypic processes, or to the theory of complex systems, have been proposed to explain the rise of the phenotypic variety upon which natural selection acts. In this article, we illustrate the current state of the issue and we propose (...) a logical space based on phenotypic robustness that allows a classification of evolutionary phenomena and can provide a framework for unifying all these accounts. (shrink)

In his recent book on Darwinism, Daniel Dennett has offered up a species of a priori selectionism that he calls algorithmic. He used this view to challenge a number of positions advocated by Stephen J. Gould. I examine his algorithmic conception, review his unqualified enthusiasm for the a priori selectionist position, challenge Dennett's main metaphors (cranes vs. skyhooks and a design space), examine ways in which his position has lead him to misunderstand or misrepresent Gould (spandrels, exaptation, punctuated equilibrium, contingency (...) and disparity), and discuss recent results in developmental biology that suggest that an a priori position does not fill the demands of an evolutionary biology. I conclude by insisting that evolutionary biology is many leveled, complicated, and is carried on an ever shifting and expanding empirical base that when disregarded results in caricature. (shrink)

A number of authors argue that while species are evolutionary units, individuals and real entities, higher taxa are not. I argue that drawing the divide between species and higher taxa along such lines has not been successful. Common conceptions of evolutionary units either include or exclude both types of taxa. Most species, like all higher taxa, are not individuals, but historical entities. Furthermore, higher taxa are neither more nor less real than species. None of this implies that there is no (...) distinction between species and higher taxa; the point is that such a distinction is more subtle than many authors have claimed. (shrink)

Evolutionary stasis is discussed in light of the idea that the common output of every successful evolution is the creation of the entities that are increasingly resistant to further change. The moving force of evolution is entropy. This general aspiration for chaos is a cause of the mortality of organisms and extinction of species. However, being a prerequisite for any motion, entropy generates (by chance) novelties, which may happen to be (by chance) more resistant to further decay and thus survive. (...) The entities that change rapidly disappear. All existing entities are endowed with an ability to resist further change. In simple organisms, the stasis is primarily achieved by means of the high fidelity of DNA reproduction. In organisms with a large genome and complex development, the achievable fidelity of genome reproduction fails to guarantee homeorhetic reproduction: there is more mutation than reproduction. Such species must be capable of surviving and remain phenotypically unchanged at continuous changes of their genes. This capability (canalization or robustness) reflects a global degeneracy of the link structure-function: there are more genotypes than phenotypes. Hence, function (i.e. meaning), not structure, is selected. The selection for successful ontogenesis in a varying environment creates developmental robustness to mutational and environmental perturbations and, consequently, to the halt of evolution. Evolution is resistance to entropy, the adaptation to environment being only one of the means of this resistance. Everything essential in biology is determined not by physical causality but by semantic rules and goal-directed programs. This principal operates on various levels of biological organization. (shrink)

The traditional practice of establishing morphological types and investigating morphological organization has found new support from evolutionary developmental biology (evo-devo), especially with respect to the notion of body plans. Despite recurring claims that typology is at odds with evolutionary thinking, evo-devo offers mechanistic explanations of the evolutionary origin, transformation, and evolvability of morphological organization. In parallel, philosophers have developed non-essentialist conceptions of natural kinds that permit kinds to exhibit variation and undergo change. This not only facilitates a construal of species (...) and higher taxa as natural kinds, but also broadens our perspective on the diversity of kinds found in biology. There are many different natural kinds relevant to the investigative and explanatory aims of evo-devo, including homologues and developmental modules. (shrink)

This paper examines a new challenge to neo-Darwinism, a movement known as process structuralism. The process structuralist critique of neo-Darwinism holds 1) that there are general laws in biology and that biologists should search for these laws; 2) that there are general forms of morphology and development and that biologists should attempt to uncover these forms; 3) that organisms are unified wholes that cannot be understood without adopting a holistic perspective; and 4) that no special, causal primacy should be given (...) to the genes in development and morphology. This paper places process structuralism in its historical context, examines the philosophical underpinnings of the movement, and discusses some of the evidence used to support its claims. (shrink)

The allegedly alternative theories of Phyletic Gradualism and Punctuated Equilibria are examined as regards the nature of their differences. The explanatory value of both models is determined by establishing their actual connection with reality. It is concluded that they are to be considered complementary rather than mutually exclusive at all levels of infraspecific, specific, and supraspecific evolution. So, in order to be described comprehensively, the pathways of evolution require at least two distinct models, each based on a discrete range of (...) real phenomena. [Phyletic Gradualism; Punctuated Equilibria; evolutionary theories; divergence models; additive speciation; microevolution; macroevolution; anagenesis.]. (shrink)

Classifying is a fundamental operation in the acquisition of knowledge. Taxonomic theory can help students of cognition, evolutionary psychology, ethology, anatomy, and sociobiology to avoid serious mistakes, both practical and theoretical. More positively, it helps in generating hypotheses useful to a wide range of disciplines. Composite wholes, such as species and societies, are “individuals” in the logical sense, and should not be treated as if they were classes. A group of analogous features is a natural kind, but a group of (...) homologous features is not. Imposing hypotheses justified only on the basis of nominalist, realist, phenomenalist, or conceptualist metaphysics upon the neurophysiology of organisms or upon the causes of behavior exemplifies the “psychologist's fallacy” of William James. Levels should be distinguished from their members and from classes of levels, and the ontological status of entities ranked at levels should be made clear. It is important not to confuse such categories as substance and process with one another. Several genetical terms, such as “gene” and chromosome,” are even more equivocal than has been realized. Discussions about units of selection, behavior, and thinking suffer from the ambiguity of a “unit of” an entity. An important source of misunderstanding about natural selection is the habit of treating it as an “agent”: in an important sense, natural selection does not “act” at all. (shrink)