Geologists, Paleontologists and other historical scientists are frequently concerned with narrative explanations targeting single cases. I show that two distinct explanatory strategies are employed in narratives, simple and complex. A simple narrative has minimal causal detail and is embedded in a regularity, whereas a complex narrative is more detailed and not embedded. The distinction is illustrated through two case studies: the ‘snowball earth’ explanation of Neoproterozoic glaciation and recent attempts to explain gigantism in Sauropods. This distinction is revelatory of historical (...) science. I argue that at least sometimes which strategy is appropriate is not a pragmatic issue, but turns on the nature of the target. Moreover, the distinction reveals a counterintuitive pattern of progress in some historical explanation: shifting from simple to complex. Sometimes, historical scientists rightly abandon simple, unified explanations in favour of disunified, complex narratives. Finally I compare narrative and mechanistic explanation, arguing that mechanistic approaches are inappropriate for complex narrative explanations. (shrink)

After having reconstructed a minimal biological characterisation of species, we endorse an “empirical approach” based on the idea that it is the peculiar evolutionary history of the species at issue—its peculiar origination process, its peculiar metapopulation structure and the peculiar mixture and strength of homeostatic processes vis à vis heterostatic ones—that determines species’ identity at a time and through time. We then explore the consequences of the acceptance of the empirical approach in settling the individuals versus kinds dispute. In particular, (...) while conceptual arguments have been proposed to show that species can be equally treated as individuals and kinds because mereology’s and set-theory’s languages are inter-translatable, we advance instead a causal argument to sustain the claim that each species is both a kind and an individual. (shrink)

It is widely acknowledged that metaphysical assumptions, commitments and presuppositions play an important role in science. Yet according to the empiricist there is no place for metaphysics as traditionally understood in the scientific enterprise. In this paper I aim to take a first step towards reconciling these seemingly irreconcilable claims. In the first part of the paper I outline a conception of metaphysics and its relation to science that should be congenial to empiricists, motivated by van Fraassen’s work on ‘stances’. (...) There has been a considerable amount of recent work devoted to van Fraassen’s ‘stance’ view, but it has not on the whole been noticed that the view has the potential to motivate a general empiricist conception of the relation between science and metaphysics. In the second and third sections I discuss two examples from biology to illustrate this conception: metaphysical punctuationism, and its relation to and influence on the thesis of punctuated equilibrium; and dialectical biology as defended by Levins and Lewontin. (shrink)

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)

There’s a general assumption that teleology and function do not exist in inanimate nature. Throughout biology, it is generally taken as granted that teleology (or teleonomy) and functions are not only unique to life, but perhaps even a defining quality of life. For many, it’s obvious that rocks, water, and the like, are not teleological, nor could they possibly have stand-alone functions. This idea - that teleology and function are unique to life - is the target of this paper. I (...) begin with an overview of McShea’s field theoretic account of teleology. I start with the field theoretic account because it presents a promising analysis of teleological systems. It is promising because, in not making any assumptions about life’s special status in teleological systems, it avoids counterexamples that have problematized other accounts. I then consider some of the prominent efforts that have been made to attempt to avoid ascribing functions or teleology to some form of inanimate nature. In my assessment, none of the efforts are successful. I conclude by offering mineral evolution as a case study to show how inanimate nature can be both teleological and functional. The evolution of mineral species reveals that teleology and function extend to inanimate nature, and that teleology and function come in degrees. (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)

Long-term vegetation dynamics based on paleo-pollen data display transient behaviour, often alternating in phase between predominant determinism and predominant 'turbulence', when viewed as a trajectory in a multivariate phase space. Given this, the metaphor of vegetation dynamics as a 'flowing stream', first introduced by Cooper in his classic 1926 paper entitled "The fundamentals of vegetation change", is re-examined and revealed to be not only useful, but strikingly realistic. Vegetation dynamic theory is reviewed and classic theories are found to reflect reality (...) poorly. It is suggested that vegetation dynamics is a far from equilibrium system, and that the application of nonequilibrium thermodynamic theory is appropriate. (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)

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)

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 Modern Synthesis has been receiving bad press for some time now. Back in 1983, in an article entitled “The Hardening of the Modern Synthesis” Stephen Jay Gould criticized the way the Modern Synthesis had developed since its inception in the 1930s and early 1940s (Gould 1983). Back then, those who would later become known as ‘architects’ of the synthesis were united in their call for explaining evolution at all levels in terms of causation at one level: genetics. What drove (...) changes in gene frequency remained an open question. It could be mainly selection, or drift, or some (other) form of constraint. But in the two decades that followed, the synthesis underwent a major change. By the late 1940s the synthesis had ‘hardened’ around adaptationism, according to Gould. Influential contributors like Dobzhansky, Simpson and Wright had increasingly expressed adaptationist views in the later editions of their landmark books. Not because evidence had piled up, showing that selection was in fact pervasive. Instead, Gould argued, adaptationist tendencies had been preserved by some kind of cultural inertia, and were now being revived. “Certain ‘national styles’ persisted from the eighteenth century, through Darwin’s era, and into our own time. Views on adaptation provide a good example” (Gould 1983). Gould did not just argue that some form of adaptationism had resurfaced. He became well-known for his efforts to intervene on this status quo by attempting to make evolutionary biology more ‘pluralistic’. In collaborative work with Richard Lewontin (Gould and Lewontin 1979), Elisabeth Vrba (Gould and Vrba 1982; Vrba and Gould 1986) and Niles Eldredge (Eldredge and Gould 1972; Gould and Eldredge 1977) he criticized the synthesis for its adaptationism and its lack of appreciation for hierarchical perspectives. Gould exerted his influence in a different way as well. Together with Eldredge, he had facsimiles reprinted of the first editions of two books that had shaped synthesis, but with their own critical introductions (Eldredge 1982; Gould 1982). Dobzhansky’s Genetics and the Origin of Species and Mayr’s Systematics and the Origin of Species appeared as reprints in the ‘Columbia Classics in Evolution’ series, sending an unambiguous message to the readers: these are foundational works, but they have been superseded. In the summer of 2008, some 25 years after Gould made his point about the hardening of the Modern Synthesis, a group of sixteen biologists and philosophers gathered at the Konrad Lorenz Institute for Evolution and Cognition Research (KLI) near Vienna, Austria, to discuss cutting-edge research that reaches beyond the synthesis framework. Before it even started, this workshop on the ‘Extended Synthesis’ had already attracted a fair share of attention in the blogosphere and had resulted in a news feature in Science (Pennisi 2008). After the meeting, Nature weighed in on the matter (Whitfield 2008). The results of over 3 days of presentations and extensive discussion have now been published as Evolution—The Extended Synthesis. 1 The publication of this collection of sixteen essays is accompanied by the republication of Julian Huxley’s Evolution: The Modern Synthesis; the book that introduced the term ‘Modern Synthesis’. Both books are introduced by the organizers of the KLI workshop, Massimo Pigliucci and Gerd Müller. Like Gould and Eldredge before them, Pigliucci and Müller did not reissue one of the canons of the Modern Synthesis without giving the readers some ‘guidance’. Starting with the cover, the editors proclaim boldly that this is ‘the definitive edition’ of Huxley’s book. In a new foreword, they sketch the context in which the book was written and assess some of its features. They voice some mild criticism of alleged ‘adaptationism’. But their tone is different from that of Gould and Eldredge. Pigliucci and Müller praise Huxley for his pluralistic outlook, which has again become essential in the forging of an Extended Synthesis. That makes Huxley’s book more than just an interesting but obsolete classic. Instead, it can teach valuable lessons about how to ‘soften up’ a synthesis that has become hardened over time. (shrink)

Ecological theory is built upon assumptions about the fundamental nature of organism-environment interactions. We argue that two mutually exclusive sets of such assumptions are available and that they have given rise to alternative approaches to studying ecology. The fundamentally different premises of these approaches render them irreconcilable with one another. In this paper, we present the first logical formalisation of these two paradigms.The more widely-accepted approach - which we label the demographic paradigm - includes both population ecology and community ecology (...) (synecology). Demographic ecology assumes that the environment is relatively stable and that biotic processes, governed predominantly by resource availability, are the most important of ecological and evolutionary influences. Moreover, ecological processes are assumed to translate into directional selection pressures that drive significant evolutionary change on a local scale through the process of optimisation. (shrink)

In his classic work The Mind and its Place in Nature published in 1925 at the height of the development of quantum mechanics but several years after the chemists Lewis and Langmuir had already laid the foundations of the modern theory of valence with the introduction of the covalent bond, the analytic philosopher C. D. Broad argued for the emancipation of chemistry from the crass physicalism that led physicists then and later—with support from a rabblement of philosophers who knew as (...) much about chemistry as etymologists—to believe that chemistry reduced to physics. Here Broad’s thesis is recast in terms more familiar to chemists. In the hard sell of particle physics, several prominent figures in chemistry—Hoffmann, Primas, and Pauling—have had their views interpreted to imply that they were sympathetic to greedy reductionism when in fact they were not. Indeed, being chemists without physicists as alter egos, they could not but side with Broad’s contention that chemistry, as a science that deals primarily in emergent phenomena which are beyond the purview of physicalism, owes no acquiescence to particle physics and its ethereal wares. Historically, among the most widely used expediencies in chemistry and materials science are additivity or mixture rules and their cohort transferability, all of which are devised and used under the mantle of naive reductionism. Here it is argued that while the transfer of functional groups between molecules works empirically to an extent, it is strictly outlawed by the no-cloning theorem of quantum mechanics. Several illustrative examples related to chemistry’s irreducibility to physics are presented and discussed. The failure of naive reductionism exhibited by the deep-inelastic scattering of leptons by A > 2 nuclei is traced to the same flawed reasoning that was the original basis of Moffitt’s ‘atoms in molecules’ hypothesis, the neglect of context, nuclei in the case of high-energy physics and molecules in the case of chemistry. A non-exhaustive list of other contexts from physics, chemistry, and molecular biology evidencing similar departures from the ideal of additivity or reductionism is provided for the perusal of philosophers. Had the call by the mathematician J. T. Schwartz for developments in mathematical linguistics possessed of a less single, less literal, and less simple-minded nature been met, perhaps it might have persuaded scientists to abandon their regressive fixation with unphysical reductionism and to adapt to new methodologies that engender a more nuanced handling of ubiquitous emergent phenomena as they arise in Nature than is the case today. (shrink)

Science is a very special form of storytelling, one in which the stories told have to be testable against empirical observation. But the world is a complicated place; and, to provide a coherent account of it, scientists often find themselves obliged to join up their observable dots using untestable or as-yet-untested lines. This is a necessary part of constructing many valuable and predictive scientific scenarios; and it is perfectly good procedure as long as the assumptions involved are fully compatible with (...) what is known and testable. But it also means that, in formulating their ideas about how the world works, scientists must remain keenly aware not only of what is and is not assumption in those complex ideas, but of how untested elements may color their beliefs. The contributions to this volume cover many interesting examples of how assumptions have affected ideas in diverse areas of the paleosciences, both practical and theoretical, and they serve together as a salutary reminder that vigilance and a willingness to rethink are always in order. (shrink)

I attempt to raise questions regarding elements of systematics—primarily in the realm of phylogenetic reconstruction—in order to provoke discussion on the current state of affairs in this discipline, and also evolutionary biology in general: e.g., conceptions of homology and homoplasy, hypothesis testing, the nature of and objections to Hennigian “phylogenetic systematics”, and the schism between Darwinian descendants of the “modern evolutionary synthesis” and their supposed antagonists, cladists and punctuationalists.

An earlier article described the mid-twentieth century origins of the method of “paradigms” in paleobiology, as a way of making testable hypotheses about the functional morphology of extinct organisms. The present article describes the use of “paradigms” through the 1970s and, briefly, to the end of the century. After I had proposed the paradigm method to help interpret the ecological history of brachiopods, my students developed it in relation to that and other invertebrate phyla, notably in Euan Clarkson’s analysis of (...) vision in trilobites. David Raup’s computer-aided “theoretical morphology” was then combined with my functional or adaptive emphasis, in Adolf Seilacher’s tripartite “constructional morphology.” Stephen Jay Gould, who had strongly endorsed the method, later switched to criticizing the “adaptationist program” he claimed it embodied. Although the explicit use of paradigms in paleobiology had declined by the end of the century, the method was tacitly subsumed into functional morphology as “biomechanics.”. (shrink)

Evolutionary developmental biology (evo-devo) offers both an account of developmental processes and also new integrative frameworks for analyzing interactions between development and evolution. Biologists and philosophers are keen on evo-devo in part because it appears to offer a comfort zone between, on the one hand, what some take to be the relative inability of mainstream evolutionary biology to integrate a developmental perspective; and, on the other hand, what some take to be more intractable syntheses of development and evolution. In this (...) article, I outline core concerns of evo-devo, distinguish theoretical and practical variants, and counter Sterelny's recent argument that evo-devo's attention to development, while important, offers no significant challenge to evolutionary theory as we know it. (shrink)

The extended evolutionary synthesis intends to offer a new framework for understanding evolution based mainly on empirical and theoretical findings of current studies, including heredity and evolutionary developmental biology. In this essay, we present and develop the following objections about the terminology associated with the EES literature: despite using the term "extension," EES protagonists claim new evolutionary processes, reformulate conceptual networks, and modify central assumptions of the evolutionary synthesis. Therefore, the difference between ES and EES should not be described in (...) terms of a set-subset relationship ; despite using the term "synthesis," the EES leads, at least in the short term, to a pluralism of approaches in evolutionary biology. Thus, we argue that the EES should not be described as a synthesis, but as a broad and plural interpretative framework encompassing different approaches. These objections are not directed to the proposed changes, but to the interpretation of these changes as a mere expansion of the previous evolutionary framework, as well as to the interpretation of the EES as a synthesis. Based on these objections, we seek to present some explanations for the use of the term "extended synthesis" among its protagonists. (shrink)

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)

Paul Hoyningen-Huene argues that what makes scientific knowledge special is its systematic character, and that this can be used to solve the demarcation problem. He labels this STDC: “Systematicity Theory’s Demarcation Criterion.” This paper argues that STDC fails, because there are areas of intellectual activity that are highly systematic, but that the great majority of scientists and historians and philosophers of science do not accept as scientific. These include homepathy, creationism, and climate change denial. I designate these activities “facsimile sciences” (...) because they mimic the appearance of science but are not, by the standards of philosophers and scientists, scientific. This suggests that we need additional criteria to demarcate science from non-science and/ or nonsense. (shrink)

Historians and philosophers of science agree that Darwin had an understanding of species which led to a workable theory of their origins. To Darwin species did not differ essentially from ‘varieties’ within species, but were distinguishable in that they had developed gaps in formerly continuous morphological variation. Similar ideas can be defended today after updating them with modern population genetics. Why then, in the 1930s and 1940s, did Dobzhansky, Mayr and others argue that Darwin failed to understand species and speciation? (...) Mayr and Dobzhansky argued that reproductively isolated species were more distinct and ‘real’ than Darwin had proposed. Believing species to be inherently cohesive, Mayr inferred that speciation normally required geographic isolation, an argument that he believed, incorrectly, Darwin had failed to appreciate. Also, before the sociobiology revolution of the 1960s and 1970s, biologists often argued that traits beneficial to whole populations would spread. Reproductive isolation was thus seen as an adaptive trait to prevent disintegration of species. Finally, molecular genetic markers did not exist, and so a presumed biological function of species, reproductive isolation, seemed to delimit cryptic species better than character-based criteria like Darwin’s. Today, abundant genetic markers are available and widely used to delimit species, for example using assignment tests: genetics has replaced a Darwinian reliance on morphology for detecting gaps between species. In the 150th anniversary of The Origin of Species , we appear to be returning to more Darwinian views on species, and to a fuller appreciation of what Darwin meant. (shrink)

Stephen Jay Gould is rightly remembered for many different kinds of contributions to our intellectual life. I focus on his criticisms of uses of evolutionary ideas to defend inegalitarian doctrines and on his attempts to expand the framework of Darwinian evolutionary theory. I argue that his important successes in the former sphere are applications of the idea of local critique, grounded in careful attention to the details of the inegalitarian proposals. As he became more concerned with the second project, Gould (...) was inclined to suggest that the abuses of evolutionary ideas rested on an insufficiently expanded Darwinism. I suggest that what is valuable in Gould's contribution to general evolutionary theory is the original claim about punctuated equilibrium (advanced, with Niles Eldredge in1972), and the careful defense of that claim through the accumulation of paleontological evidence. I try to show that the more ambitious program of a hierarchical expansion of neo-Darwinism is misguided, and that the endeavor to go beyond local critique fails. (shrink)

p. 13: But if Mayr himself was an unconscious 'physicalist', why did he argue so forcefully against the machine theory of life? In part his dissatisfaction with this approach can be explained as a residue of earlier experiences. When he started to argue for the autonomy of biology in the early 1960s, the unique, emergent characteristics of organisms were ignored by the philosophy of science which was dominated by physics (Greene 1994; Hull 1994). In this situation Mayr not only criticised (...) this particular neglect as reductionism, but questioned the usefulness of the physicalist approach for biology in general. In recent decades this situation has clearly changed and this was also due to Mayr's relentless fight for the recognition of the unique aspects of biology. Nevertheless he stuck to his broad rejection and ignored developments toward a more sophisticated view (cf. Emmeche, Koppe and Stjernfelt 1997). But there is probably more to it. His second motivation is an emotional aversion against connotations and implications of the word 'machine'. The view that organisms-including humans!-are 'survival machines', 'robot vehicles' programmed to preserve their genes conveys a deterministic and mechanistic view that is perceived by many persons as a gross 'narcissistic insult' (Freud 1917, pp. 6, 7). It is a view that Mayr definitely did not appreciate. (shrink)

In Greg Bear’s critically acclaimed science fiction novel Darwin’s Radio, the activation of an endogenous retrovirus (SHEVA), ironically located in a “noncoding region” of the human genome, causes extreme symptoms in women worldwide, including miscarriages. In the United States, a task force is assembled to control the pandemic crisis and to find out how SHEVA operates at the genomic level. However, as the story unfolds, it becomes manifest that SHEVA is too complex to decode in this way and, moreover, that (...) it is not a disease at all. Biologist Kay Lang speculates that SHEVA is triggered by signals from the environment, and that newborn SHEVA children will be a new variation or species of Man. In this essay I analyze Bear’s literary experiment with science along Deleuze and Guattari’s important, but largely overlooked, concepts of State science and nomad science. Bear’s novel gives narrative form to nomad-scientific ideas about life, notably Lynn Margulis’s theory of endosymbiogenesis, which holds that a species’ DNA is an assemblage of many genomes acquired in symbiotic relations. The import of Bear’s informed speculations, I argue, is not crass prediction but a nomadic vision of life as always already different (impure, infected) and in becoming—a counterpoint to the image of the double helix as the bedrock of human identity. Darwin’s Radio is a key example of how fiction can be an excellent partner for science, technology, and society, analyzing and intervening in debates about life and laying bare epistemological and biopolitical tensions of technoscience. (shrink)

The term adaptive radiation has been recurrently used to describe evolutionary patterns of several lineages, and has been proposed as the main driver of biological diversification. Different definitions and criteria have been proposed to distinguish an adaptive radiation, and the current literature shows disagreements as to how radiating lineages should be circumscribed. Inconsistencies increase when authors try to differentiate a clade under adaptive radiation from clades evolving under ‘regular’ speciation with adaptation, a pattern anticipated and predicted by the evolutionary theory (...) in any lineage. The most important disagreement is as to which evolutionary rate authors analyze to characterize a radiation; a discussion embedded in a prevailing inability to provide mechanistic explanations of the relationship among evolutionary rates. The union of pattern and process in the same term, the inadequacy of reported null hypotheses, and the frequent use of ad hoc comparisons between lineages have also contributed to the lack of consensus. A rigorous use of available terms and the articulation of solid criteria with objective methodologies in distinguishing evolutionary patterns are imperative. Given the difficulties in detecting adaptation, the use of the ‘adaptive’ term to qualify a radiation should be avoided unless methodologically tested. As an unambiguous method to distinguish radiating lineages, the statistical detection of significant increases in taxonomic diversification rates on monophyletic lineages can be considered a distinctive signature of a radiation. After recognizing this pattern, causal hypotheses explaining them can be stated, as well as correlates with other rates of evolution. (shrink)

As our understanding of biological evolution continues to deepen, tension still surrounds the relationship between competition and cooperation in the evolution of the biosphere, with rival viewpoints often associated with the Red Queen and Black Queen hypotheses respectively. This essay seeks to reconcile these viewpoints by integrating observations of some general trends in biosphere evolution with concepts from game theory. It is here argued that biodiversity and ecological cooperation are intimately related, and that both tend to cyclically increase over biological (...) history; this is likely due to the greater relative stability of cooperation over competition as a means of long-term conflict resolution within ecosystems. By integrating this view of the biosphere with existing models such as Niche Game Theory, it may be argued that competition and cooperation in ecosystems coexist at equilibria which shift preferentially towards increasing cooperation over biological history. This potentially points to a state of “cooperative equilibrium” as a limit or endpoint in long-term biosphere evolution, such that Black Queen and Red Queen behavior dominate different phases in an evolutionary movement towards optimal cooperative stability in ecological networks. This concept, if accepted, may also bear implications for developing future mathematical models in evolutionary biology, as well as for resolving the perennial debate regarding the relative roles of conflict and harmony in nature. (shrink)

This paper analyses the broad methodological structure of population-biological theorising. In it, I show that the distinction between initial exploratory, hypothesis-generating research and the subsequent process-reconstructing, hypothesis-testing type of research is not being made. Rather, the hypotheses generated in population biology are elaborated in such detail that students confound the initial research phase with the subsequent hypotheses-testing phase of research. In this context, I therefore analyse some testing procedures within the exploration phase and show that, as an extreme form of (...) confusion, statistical null-models are mistakenly given the status of causal population-biological theory. (shrink)

info:eu-repo/semantics/publishedVersion.

Evolution in modern life requires high replication fidelity to allow for natural selection. A simulation model utilizing simulated phenotype data on cellular probability of survival was developed to determine how self-replication fidelity could evolve in early life. The results indicate that initial survivability and replication fidelity both contribute to overall fitness as measured by growth rates of the cell population. Survival probability was the more dominant feature, and evolution was possible even with zero replication fidelity. A derived formula for the (...) relationship of survival probability and replication fidelity with growth rate was consistent with the simulated empirical data. Quantitative assessment of continuity and other evidence was obtained for a saltation evolutionary process starting from low to moderate levels of survival probability and self-replication fidelity to reach the high levels seen in modern life forms. (shrink)

Have the large-scale evolutionary patterns illustrated by the fossil record been driven by fluctuations in environmental opportunity, by biotic factors, or by changes in the types of phenotypic variants available for evolutionary change? Since the Modern Synthesis most evolutionary biologists have maintained that microevolutionary processes carrying on over sufficient time will generate macroevolutionary patterns, with no need for other pattern-generating mechanisms such as punctuated equilibrium or species selection. This view was challenged by paleontologists in the 1970s with proposals that the (...) differential sorting and selection of species and clades, and the effects of biotic crises such as mass extinctions, were important extensions to traditional evolutionary theory. More recently those interested in macroevolution have debated the relative importance of abiotic and biotic factors in driving macroevolutionary patterns and have introduced comparative phylogenetic methods to analyze the rates of change in taxonomic diversity. Applying Peter Godfrey-Smith’s distinction between distributional explanations and explanations focusing on the origin of variation, most macroevolutionary studies have provided distributional explanations of macroevolutionary patterns. Comparative studies of developmental evolution, however, have implicated the origin of variants as a driving macroevolution force. In particular, the repatterning of gene regulatory networks provides new insights into the origins of developmental novelties. This raises the question of whether macroevolution has been pulled by the generation of environmental opportunity, or pushed by the introduction of new morphologies. The contrast between distributional and origination scenarios has implications for understanding evolutionary novelty and innovation and how macroevolutionary process may have evolved over time. (shrink)

Published comments by American scientists on Darwin’s evolutionary theory are rather rare in the latter half of the 19th century. Clarence King, the founding director of the U.S. Geological Survey in 1879, and an experienced field geologist, focused on the relation between Darwin’s evolutionary concepts and the larger context of Hutton/Lyell’s uniformitarianism versus Cuvier’s catastrophism in his 1877 paper, “Catastrophism and Evolution.” King knew that the fossil record contains little or no data supporting Darwin’s vision of gradual evolutionary change. Instead, (...) using horse evolution seen in the rocks of the American West, the very example that by the 1920s had become the shining exemplar of gradual evolutionary change, King argued for catastrophic extinction and evolutionary replacement by “plastic” species that were able to survive in modified form as components of the succeeding biota. Though he could not see such change as involving natural selection, in this novel use of the term “plasticity,” there may well be adumbrations of modern evolutionary biology. King’s themes became muted as Americans began to embrace more fully Darwin’s work. But his version of catastrophism never entirely disappeared, especially in paleobiological circles. And it came back in more fully modern form with force beginning with the work of Norman D. Newell on mass extinctions in the mid-20th century—and with that of two of his students: Eldredge and Gould’s “Punctuated Equilibria.” This essay introduces King’s “Catastrophism and Evolution” for the journal’s “Classics in Biological Theory” collection; King’s article is available as supplementary material in the online version of this introduction. (shrink)

In a recent paper, Chris Haufe paints a provocative portrait of the late paleontologist Stephen Jay Gould. His principal aim is to resolve a “paradox” arising from a prima facie inconsistent pair of commitments: Gould believed that the biological facts could have been otherwise, and Gould believed that there are evolutionary laws. In order to resolve this paradox, Haufe makes two substantive claims: Gould was aware of the challenges that the Replay Thesis posed for a law-centered science of evolution, even (...) early in his career, and Gould endeavored to meet these challenges by deploying the “species-as-particles approach.” In this paper, I put pressure on both of these claims. By examining the goals and methods of Gould’s first “nomothetic research program,” the science of form, I show that it does not fit the picture of nomothetic science that Haufe illustrates. Additionally, I show that no straightforward connection exists between Gould’s understanding of contingency and his adoption of the species-as-particles approach. I propose that Gould’s career can be usefully split into three periods, each of which employed a distinct strategy for establishing distinctively paleontological contributions to evolutionary theory. (shrink)

Few of Stephen Jay Gould’s accomplishments in evolutionary biology have received more attention than his hierarchical theory of evolution, which postulates a causal discontinuity between micro- and macroevolutionary events. But Gould’s hierarchical theory was his second attempt to supply a theoretical framework for macroevolutionary studies—and one he did not inaugurate until the mid-1970s. In this paper, I examine Gould’s first attempt: a proposed fusion of theoretical morphology, multivariate biometry and the experimental study of adaptation in fossils. This early “macroevolutionary synthesis” (...) was predicated on the notion that parallelism and convergence dominate the history of higher taxa, and moreover, that they can be explained in terms of adaptation leading to mechanical improvement. In this paper, I explore the origins and contents of Gould’s first macroevolutionary synthesis, as well as the reasons for its downfall. In addition, I consider how various developments during the mid-1970s led Gould to identify hierarchy and constraint as the leading themes of macroevolutionary studies—and adaptation as a macroevolutionary red herring. (shrink)

This symposium discusses J.-L. Dessalles's account of the evolution of language, which was presented in Why we Talk (OUP 2007).

A theoretical framework is provided to explore teleonomy as a problem of self-causation, distinct from upward, downward and reticulate causation. Causality theories in biology are often formulated within hierarchy theories, where causation is conceptualized as running up or down the rungs of a ladder-like hierarchy or, more recently, as moving between multiple hierarchies. Research on the genealogy of cosmologies demonstrates that in addition to hierarchy theories, causality theories also depend upon ideas of time. This paper explores the roots and impact (...) of both time and hierarchy thinking on causal reasoning in the evolutionary sciences. Within evolutionary biology, the Neodarwinian synthesis adheres to a linear notion of time associated with linear hierarchies that portray upward causation. Eco-evo-devo schools recognize the importance of downward causation and consequently receive resistance from the standard view because downward causation is sometimes understood as backward causation, considered impossible by adherents of a linear time model. In contrast, downward causation works with a spatial or presential time notion. Hybridization, lateral gene transfer, infective heredity, symbiosis and symbiogenesis require recognition of reticulate causation occurring in both space and time, or spacetime, between distinct and interacting ontological hierarchies. Teleonomy is distinct from these types of causation because it invokes the problem of self-causation. By asking how the focal level in a hierarchy can persist through time, self-causation raises philosophical concerns on the nature of duration, identity and individuality. (shrink)

The year 2009 has been a year of numerous commemorations of both scientific and non-scientific achievements that contributed to the advancement of human kind. Protestants celebrated the 500th anniversary of the birth of Calvin; literary critics celebrated the 200th anniversary of the poet Edgar Allan Poe; and the musical genius Felix Mendelssohn-Bartholdy was also born 200 years ago. 2009 further marked the bicentennial of the birth of Louis Braille, the inventor of Braille; and Abraham Lincoln, the 16th president of the (...) United States, who founded the National Academy of Sciences. Pierre Curie, famous for his work on radioactivity that he conducted together with his wife Marie Curie, was born 150 ago; as was John Dewey, a philosopher and psychologist who is recognized as one of the founding fathers of both pragmatism as well as functional psychology. UNESCO and the International Astronomical Union dubbed 2009 the International Year of Astronomy. By doing so, astronomers celebrated the 400th anniversary of Galileo Galilei’s telescopic observations as well as the publication of Johannes Kepler’s Astronomia nova wherein he formulated the first two laws of planetary motion. 2009 also marked the last of a 3-year-long celebration of Planet Earth, another UNESCO-governed initiative. However, for evolutionary biologists and philosophers of science, 2009 will be largely remembered for its worldwide commemorations of the 200th anniversary of the birth of Charles Darwin, and the 150th anniversary of the publication of his magnum opus On the origin of species by means of natural selection. Footnote1 In order to pay tribute to Darwin’s major contribution to the advancement of evolutionary science, the International Union of Biological Sciences and the International Union of History and Philosophy of Science have called the year 2009 the Darwin Year. Given that so many scientific discoveries were commemorated, COPUS, the Coalition on the Public Understanding on Science, called out 2009 as the Year of Science, in the hope to pay equal tribute to both the field of biology as well as astronomy. 2009 was indeed a year of biology. Somewhat overshadowed by the big Darwin celebrations, smaller-scaled events were held to commemorate the 200th anniversary of the publication of Lamarck’s Philosophie Zoologique; and the 150th anniversary of the death of Alexander von Humboldt, the father of biogeography. In 1910, Constantin Mereschkowsky wrote his article on symbiogenesis entitled ‘The Theory of Two Plasmas as the Basis of Symbiogenesis, a New Study for the Origins of Organisms’. The article was published in the German Biologisches Zentralblatt, the journal that would later evolve into the current Theory in Biosciences. Somewhat forgotten, but equally important for the field of symbiogenesis, was the 200th anniversary of the birth of Pierre-Joseph Van Beneden, a Belgian paleontologist and zoologist famous for distinguishing parasitism from commensalism. Finally, Henry Bergson, known for inventing the currently rejected notion of élan vital, was born 150 years ago. In order to memorialize the important role these biologists played in the advancement of our understanding of the evolutionary process, a 2-day international conference was organized entitled: Evolution today and tomorrow, Darwin evaluated by contemporary evolutionary and philosophical theories. The conference was organized by The Centre for Philosophy of Science of the University of Lisbon (Portugal), in collaboration with the Centre for Environmental Biology of the same university, and the Lisbon Centre for Applied Psychology. The articles presented here are a spin-off of this conference. The current volumes contain the peer-reviewed articles of a selection of the plenary and invited speakers, as well as those of scholars who were additionally invited to contribute to the volumes. (shrink)

Traditionally defined as the science of the living, or as the field that beyond anatomical structure and bodily form studies functional organization and behaviour, physiology has long been excluded from evolutionary research. The main reason for this exclusion is that physiology has a presential and futuristic outlook on life, while evolutionary theory is traditionally defined as the study of natural history. In this paper, I re-evaluate these classic science divisions and situate physiology within the history of the evolutionary sciences, as (...) well as within debates on the Extended Evolutionary Synthesis and the need for a Third Way of Evolution. I then briefly point out how evolutionary physiology in particular contributes to research on function, causation, teleonomy, agency and cognition. (shrink)