In this paper I offer an analysis of causation based upon a theory of mechanisms-complex systems whose internal parts interact to produce a system's external behavior. I argue that all but the fundamental laws of physics can be explained by reference to mechanisms. Mechanisms provide an epistemologically unproblematic way to explain the necessity which is often taken to distinguish laws from other generalizations. This account of necessity leads to a theory of causation according to which events are causally related when (...) there is a mechanism that connects them. I present reasons why the lack of an account of fundamental physical causation does not undermine the mechanical account. (shrink)

Most recent philosophical thought about the scientific representation of the world has focused on dyadic relationships between language-like entities and the world, particularly the semantic relationships of reference and truth. Drawing inspiration from diverse sources, I argue that we should focus on the pragmatic activity of representing, so that the basic representational relationship has the form: Scientists use models to represent aspects of the world for specific purposes. Leaving aside the terms "law" and "theory," I distinguish principles, specific conditions, models, (...) hypotheses, and generalizations. I argue that scientists use designated similarities between models and aspects of the world to form both hypotheses and generalizations. (shrink)

Current analytic metaphysics has been claimed to be, at best, out of touch with modern physics, at worst, actually in conflict with the latter The continuum companion to the philosophy of science, Continuum, London, 2011; Ladyman and Ross Every thing must go: metaphysics naturalized, Oxford University Press, Oxford, 2007). While agreeing with some of these claims, it has been suggested that metaphysics may still be of service by providing a kind of ‘toolbox’ of devices that philosophers of science can access (...) in order to help provide an interpretation of theories in fundamental physics Metaphysics in contemporary physics, Rodopi, Amsterdam, 2015). In this context it has been argued that ‘standard’ forms of dispositionalism simply cannot be sustained in the context of modern physics but that certain ‘non-standard’ views may provide the resources to help explicate the sense in which physics may be regarded as ‘modally informed’. Here that suggestion will be further extended in order to consider the implications both with regard to the overall relevance of metaphysics given advances in science and for the prospects of a naturalised metaphysics more generally. In particular, this paper will focus on three concerns: that the particular tools identified are not, in fact, ‘scientifically disinterested’ and thus that the distinction between ‘naturalised’ and ‘non-naturalised’ metaphysics is at best vague or poorly drawn; that the usefulness of such tools depends on their being shaped to fit the relevant physics and thus the latter ‘guts’ metaphysics; that if metaphysics does prove to be useful in this sense then we have no reason to scorn non-naturalised metaphysics to begin with. (shrink)

A naturalistic account of the strengths and limitations of cladistic practice is offered. The success of cladistics is claimed to be largely rooted in the parsimony-implementing congruence test. Cladists may use the congruence test to iteratively refine assessments of homology, and thereby increase the odds of reliable phylogenetic inference under parsimony. This explanation challenges alternative views which tend to ignore the effects of parsimony on the process of character individuation in systematics. In a related theme, the concept of homeostatic property (...) cluster natural kinds is used to explain why cladistics is well suited to provide a traditional, verbal reference system for the evolutionary properties of species and clades. The advantages of more explicitly probabilistic approaches to phylogenetic inference appear to manifest themselves in situations where evolutionary homeostasis has for the most part broken down, and predictive classifications are no longer possible. (shrink)

Recent observations of power-law distributions in the connectivity of complex networks came as a big surprise to researchers steeped in the tradition of random networks. Even more surprising was the discovery that power-law distributions also characterize many biological and social networks. Many attributed a deep significance to this fact, inferring a “universal architecture” of complex systems. Closer examination, however, challenges the assumptions that (1) such distributions are special and (2) they signify a common architecture, independent of the system's specifics. The (...) real surprise, if any, is that power-law distributions are easy to generate, and by a variety of mechanisms. The architecture that results is not universal, but particular; it is determined by the actual constraints on the system in question. BioEssays 27:1060–1068, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

There is a worry that the ‘major transitions in evolution’ represent an arbitrary group of events. This worry is warranted, and we show why. We argue that the transition to a new level of hierarchy necessarily involves a nonselectionist chance process. Thus any unified theory of evolutionary transitions must be more like a general theory of fortuitous luck, rather than a rigid formulation of expected events. We provide a systematic account of evolutionary transitions based on a second-order regularity of chance (...) events, as stipulated by the ZFEL (Zero Force Evolutionary Law). And in doing so, we make evolutionary transitions explainable and predictable, and so not entirely contingent after all. (shrink)

How does evolution grow bigger brains? It has been widely assumed that growth of individual structures and functional systems in response to niche-specific cognitive challenges is the most plausible mechanism for brain expansion in mammals. Comparison of multiple regressions on allometric data for 131 mammalian species, however, suggests that for 9 of 11 brain structures taxonomic and body size factors are less important than covariance of these major structures with each other. Which structure grows biggest is largely predicted by a (...) conserved order of neurogenesis that can be derived from the basic axial structure of the developing brain. This conserved order of neurogenesis predicts the relative scaling not only of gross brain regions like the isocortex or mesencephalon, but also the level of detail of individual thalamic nuclei. Special selection of particular areas for specific functions does occur, but it is a minor factor compared to the large-scale covariance of the whole brain. The idea that enlarged isocortex could be a a by-product of structural constraints later adapted for various behaviors, contrasts with approaches to selection of particular brain regions for cognitively advanced uses, as is commonly assumed in the case of hominid brain evolution. (shrink)

I show that the recent account of levels in neuroscience proposed by Craver and Bechtel is unsatisfactory since it fails to provide a plausible criterion for being at the same level and is incompatible with Craver and Bechtel’s account of downward causation. Furthermore, I argue that no distinct notion of levels is needed for analyzing explanations and causal issues in neuroscience: it is better to rely on more well-defined notions such as composition and scale. One outcome of this is that (...) apparent cases of downward causation can be analyzed away. (shrink)

The idea of levels of organization plays a central role in the philosophy of the life sciences. In this article, I first examine the explanatory goals that have motivated accounts of levels of organization. I then show that the most state-of-the-art and scientifically plausible account of levels of organization, the account of levels of mechanism proposed by Bechtel and Craver, is fundamentally problematic. Finally, I argue that the explanatory goals can be reached by adopting a deflationary approach, where levels of (...) organization give way to more well-defined and fundamental notions, such as scale and composition. (shrink)

Richard Boyd’s Homeostatic Property Cluster Theory is becoming the received view of natural kinds in the philosophy of science. However, a problem with HPC Theory is that it neglects many kinds highlighted by scientific classifications while at the same time endorsing kinds rejected by science. In other words, there is a mismatch between HPC kinds and the kinds of science. An adequate account of natural kinds should accurately track the classifications of successful science. We offer an alternative account of natural (...) kinds that better recognizes the diversity of epistemic aims scientists have for constructing classifications. That account introduces the idea of a classificatory program and provides criteria for judging whether a classificatory program identifies natural kinds. (shrink)

Introduction: representationalismMost theorists of cognition endorse some version of representationalism, which I will understand as the view that the human mind is an information-using system, and that human cognitive capacities are representational capacities. Of course, notions such as ‘representation’ and ‘information-using’ are terms of art that require explication. As a first pass, representations are “mediating states of an intelligent system that carry information” (Markman and Dietrich 2001, p. 471). They have two important features: (1) they are physically realized, and so (...) have causal powers; (2) they are intentional, in other words, they have meaning or representational content. This presumes a distinction between a representational vehicle—a physical state or structure that has causal powers and is responsible for producing behavior—and its content. Consider the following characterization of a device that computes the addition functionReaders will recognize the similarity t. (shrink)

I argue that recent advances in developmental biology demonstrate the inadequacy of suborganismal mechanism. The category of the organism, construed as a ’natural purpose’ should play an ineliminable role in explaining ontogenetic development and adaptive evolution. According to Kant the natural purposiveness of organisms cannot be demonstrated to be an objective principle in nature, nor can purposiveness figure in genuine explain. I attempt to argue, by appeal to recent work on self-organization, that the purposiveness of organisms is a natural phenomenon (...) and, by appeal to the apparatus of invariance explanation, that biological purposiveness provides genuine, ineliminable biological explanations. (edited). (shrink)

Richard Goldschmidt was one of the most controversial biologists of the mid-twentieth century. Rather than fade from view, Goldschmidt's work and reputation has persisted in the biological community long after he has. Goldschmidt's longevity is due in large part to how he was represented by Stephen J. Gould. When viewed from the perspective of the biographer, Gould's revival of Goldschmidt as an evolutionary heretic in the 1970s and 1980s represents a selective reinvention of Goldschmidt that provides a contrast to other (...) kinds of biographical commemorations by scientists. (shrink)

We argue that intelligible appeals to interlevel causes (top-down and bottom-up) can be understood, without remainder, as appeals to mechanistically mediated effects. Mechanistically mediated effects are hybrids of causal and constitutive relations, where the causal relations are exclusively intralevel. The idea of causation would have to stretch to the breaking point to accommodate interlevel causes. The notion of a mechanistically mediated effect is preferable because it can do all of the required work without appealing to mysterious interlevel causes. When interlevel (...) causes can be translated into mechanistically mediated effects, the posited relationship is intelligible and should raise no special philosophical objections. When they cannot, they are suspect. (shrink)

Different sources of data on the evolution of segmentation lead to very different conclusions. Molecular similarities in the developmental pathways generating a segmented body plan tend to suggest a segmented common ancestor for all bilaterally symmetrical animals. Data from paleontology and comparative morphology suggest that this is unlikely. A possible solution to this conundrum is that throughout evolution there was a parallel co‐option of gene regulatory networks that had conserved ancestral roles in determining body axes and in elongating the anterior‐posterior (...) axis. Inherent properties in some of these networks made them easily recruitable for generating repeated patterns and for determining segmental boundaries. Phyla where this process happened are among the most successful in the animal kingdom, as the modular nature of the segmental body organization allowed them to diverge and radiate into a bewildering array of variations on a common theme. (shrink)

Social transmission is at the core of cultural evolutionary theory. It occurs when a demonstrator uses mental representations to produce some public displays which in turn allow a learner to acquire similar mental representations. Although cultural evolutionists do not dispute this view of social transmission, they typically abstract away from the multistep nature of the process when they speak of cultural variants at large, thereby referring both to variation and evolutionary change in mental representations as well as in their corresponding (...) public displays. This conflation suggests that differentiating each step of the transmission process is redundant. In this paper, I examine different forms of interplay between the multistep nature of social transmission and the metric spaces used by cultural evolutionists to measure cultural variation and to model cultural change. I offer a conceptual analysis of what assumptions seem to be at work when cultural evolutionists conflate the complex causal sequence of social transmission as a single space of variation in which populations evolve. To this aim, I use the framework of variation spaces, a formal framework commonly used in evolutionary biology, and I develop two theoretical concepts, ‘technique’ and ‘technical space’, for addressing cases where the complexity of social transmission defies the handy assumption of a single variation space for cultural change. (shrink)

Cultural evolutionists typically emphasize the informational aspect of social transmission, that of the learning, stabilizing, and transformation of mental representations along cultural lineages. Social transmission also depends on the production of public displays such as utterances, behaviors, and artifacts, as these displays are what social learners learn from. However, the generative processes involved in the production of public displays are usually abstracted away in both theoretical assessments and formal models. The aim of this paper is to complement the informational view (...) with a generative dimension, emphasizing how the production of public displays both enable and constrain the production of modular cultural recipes through the process of innovation by recombination. In order to avoid a circular understanding of cultural recombination and cultural modularity, we need to take seriously the nature and structure of the generative processes involved in the maintenance of cultural traditions. A preliminary analysis of what recombination and modularity consist of is offered. It is shown how the study of recombination and modularity depends on a finer understanding of the generative processes involved in the production phase of social transmission. Finally, it is argued that the recombination process depends on the inventive production of an interface between modules and the complex recipes in which they figure, and that such interfaces are the direct result of the generative processes involved in the production of these recipes. The analysis is supported by the case study of the transition from the Oldowan to the Early Acheulean flake detachment techniques. (shrink)

The cumulative open-endedness of human cultures represents a major break with the social traditions of nonhuman species. As traditions are altered and the modifications retained along the cultural lineage, human populations are capable of producing complex traits that no individual could have figured out on its own. For cultures to produce increasingly complex traditions, improvements and modifications must be kept for the next generations to build upon. High-fidelity transmission would thus act as a ratchet, retaining modifications and allowing the historical (...) buildup of complex traditions. Mechanisms acting against slippage are important, of course, but cultures also need to move forward for the ratchet to retain anything important. In this article, I argue that studies of modification-generating processes and the many ways they shape cumulative culture have been overlooked. Key to a better understanding of cultural modification processes is taking seriously that cultural traditions consist of complex, hierarchically structured recipes. Taking such structures seriously and assessing the different ways they can vary in cultural design space, a novel picture for the onset of cumulative cultural evolution emerges. I argue that a possible impediment for cumulative culture in nonhuman animals may in fact reside not so much in the fidelity of their social transmission but rather in the constraints, internal and external, on their capacity to modify complex, hierarchically structured cultural recipes. (shrink)

Leo Pardi was the initiator of ethological research in Italy. During more than 50 years of active scientific career, he gave groundbreaking contributions to the understanding of social life in insects, especially in Polistes wasps, an important model organism in sociobiology. In the 1940s, Pardi showed that Polistes societies are organized in a linear social hierarchy that relies on reproductive dominance and on the physiological and developmental mechanisms that regulate it, i.e. on the status of ovarian development of single wasps. (...) Pardi’s work set the stage for further research on the regulatory mechanisms governing social life in primitively eusocial organisms both in wasps and in other insect species. This article reconstructs Pardi’s investigative pathway between 1937 and 1952 in the context of European ethology and American animal sociology. This reconstruction focuses on the development of Pardi’s physiological approach and presents a new perspective on the interacting development of these two fields at the origins of our current understanding of animal social behavior. (shrink)

Like Laland et al., I think Mayr’s distinction is problematic, but I identify a further problem with it. I argue that Mayr’s distinction is a false dichotomy, and obscures an important question about evolutionary change. I show how this question, once revealed, sheds light on some debates in evo-devo that Laland et al.’s analysis cannot, and suggest that it provides a different view about how future integration between biological disciplines might proceed.

Understanding how cooperation evolves is central to explaining some core features of our biological world. Many important evolutionary events, such as the arrival of multicellularity or the origins of eusociality, are cooperative ventures between formerly solitary individuals. Explanations of the evolution of cooperation have primarily involved showing how cooperation can be maintained in the face of free-riding individuals whose success gradually undermines cooperation. In this paper I argue that there is a second, distinct, and less well explored, problem of cooperation (...) that I call the generation of benefit. Focusing on how benefit is generated within a group poses a different problem: how is it that individuals in a group can (at least in principle) do better than those who remain solitary? I present several different ways that benefit may be generated, each with different implications for how cooperation might be initiated, how it might further evolve, and how it might interact with different ways of maintaining cooperation. I argue that in some cases of cooperation, the most important underlying “problem” of cooperation may be how to generate benefit, rather than how to reduce conflict or prevent free-riding. (shrink)

This paper describes a pattern of explanation prevalent in the biological sciences that I call a ‘lineage explanation’. The aim of these explanations is to make plausible certain trajectories of change through phenotypic space. They do this by laying out a series of stages, where each stage shows how some mechanism worked, and the differences between each adjacent stage demonstrates how one mechanism, through minor modifications, could be changed into another. These explanations are important, for though it is widely accepted (...) that there is an ‘incremental constraint’ on evolutionary change, in an important class of cases it is difficult to see how to satisfy this constraint. I show that lineage explanations answer important questions about evolutionary change, but do so by demonstrating differences between individuals rather than invoking population processes, such as natural selection.1. Introduction2. Turning a ‘Scale’ into a ‘Plume’3. Lineage Explanations in Biology3.1. The evolution of eyes3.2. The evolution of feathers4. The Two Dimensions of a Lineage Explanation4.1. The production dimension4.2. The continuity dimension4.3. The dual role of the parts5. Constraining the Explanations6. Operational and Generative Lineages7. Explaining Change Without Populations8. Conclusion. (shrink)

In recent years, the concept of evolvability has been gaining in prominence both within evolutionary developmental biology (evo-devo) and the broader field of evolutionary biology. Despite this, there remains considerable disagreement about what evolvability is. This article offers a solution to this problem. I argue that, in focusing too closely on the role played by evolvability as an explanandum in evo-devo, existing philosophical attempts to clarify the evolvability concept have been overly narrow. Within evolutionary biology more broadly, evolvability offers a (...) robust explanation for the evolutionary trajectories of populations. Evolvability is an abstract, robust, dispositional property of populations, which captures the joint causal influence of their internal features on the outcomes of evolution (as opposed to the causal influence of selection, which is often characterized as external). When considering the nature of the physical basis of this disposition, it becomes clear that the many existing definitions of evolvability at play within evo-devo should be understood as capturing only aspects of a much broader phenomenon. 1 Introduction2 The Problem of Evolvability3 The Theoretical Role of Evolvability in Evolutionary Biology3.1 The explanatory targets of evolutionary biology3.2 Selection-based explanations3.3 Lineage explanations3.4 Evolvability-based explanations3.5 What properties must evolvability have?4 What Evolvability Really Is4.1 Making sense of ft4.2 Making sense of x and b5 What of the Limbs? The Power of E6 Conclusion. (shrink)

In recent years, the concept of evolvability has been gaining in prominence both within evolutionary developmental biology (evo-devo) and the broader field of evolutionary biology. Despite this, there remains considerable disagreement about what evolvability is. This article offers a solution to this problem. I argue that, in focusing too closely on the role played by evolvability as an explanandum in evo-devo, existing philosophical attempts to clarify the evolvability concept have been overly narrow. Within evolutionary biology more broadly, evolvability offers a (...) robust explanation for the evolutionary trajectories of populations. Evolvability is an abstract, robust, dispositional property of populations, which captures the joint causal influence of their internal features on the outcomes of evolution (as opposed to the causal influence of selection, which is often characterized as external). When considering the nature of the physical basis of this disposition, it becomes clear that the many existing definitions of evolvability at play within evo-devo should be understood as capturing only aspects of a much broader phenomenon. 1 Introduction2 The Problem of Evolvability3 The Theoretical Role of Evolvability in Evolutionary Biology 3.1 The explanatory targets of evolutionary biology 3.2 Selection-based explanations 3.3 Lineage explanations 3.4 Evolvability-based explanations 3.5 What properties must evolvability have?4 What Evolvability Really Is 4.1 Making sense of ft 4.2 Making sense of x and b5 What of the Limbs? The Power of E6 Conclusion. (shrink)

The concept of 'levels of organization' has come under fire recently as being useless for scientific and philosophical purposes. In this paper, we show that 'levels' is actually a remarkably resilient and constructive conceptual tool that can be, and in fact is, used for a variety of purposes. To this effect, we articulate an account of the importance of the levels concept seen in light of its status as a major organizing concept of biology. We argue that the usefulness of (...) ‘levels’ is best seen in the heuristic contributions the concept makes to treating and structuring scientific problems. We illustrate this with two examples from biological research. (shrink)

Despite its pervasiveness, the concept of ‘levels of organization’ has received relatively little attention in its own right. I propose here an emerging approach that posits ‘levels’ as a fragmentary concept situated within an interest-relative matrix of operational usage within scientific practice. To this end I propose one important component of meaning, namely the epistemic goal motivating the term’s usage, which recovers a remarkably conserved and sufficiently unifying significance attributable to ‘levels’ across different instances of usage. This epistemic goal, to (...) provide structure to scientific problems, delegates tasks whose execution generates the term’s expressed content in a given instance. This treatment of levels does not diminish the concept’s general importance to science, but rather allows for its use in, and usefulness for, scientific practice to be better contextualized to particular tasks encompassing varying breadths of activity. (shrink)

Essentialism is widely regarded as a mistaken view of biological kinds, such as species. After recounting why (sections 2-3), we provide a brief survey of the chief responses to the “death of essentialism” in the philosophy of biology (section 4). We then develop one of these responses, the claim that biological kinds are homeostatic property clusters (sections 5-6) illustrating this view with several novel examples (section 7). Although this view was first expressed 20 years ago, and has received recent discussion (...) and critique, it remains underdeveloped and is often misrepresented by its critics (section 8). (shrink)

By linking the concepts of homology and morphological organization to evolvability, this paper attempts to (1) bridge the gap between developmental and phylogenetic approaches to homology and to (2) show that developmental constraints and natural selection are compatible and in fact complementary. I conceive of a homologue as a unit of morphological evolvability, i.e., as a part of an organism that can exhibit heritable phenotypic variation independently of the organism’s other homologues. An account of homology therefore consists in explaining how (...) an organism’s developmental constitution results in different homologues/characters as units that can evolve independently of each other. The explanans of an account of homology is developmental, yet the very explanandum is an evolutionary phenomenon: evolvability in a character-by-character fashion, which manifests itself in phylogenetic patterns as recognized by phylogenetic approaches to homology. While developmental constraints and selection have often been viewed as antagonistic forces, I argue that both are complementary as they concern different parts of the evolutionary process. Developmental constraints, conceived of as the presence of the same set of homologues across phenotypic change, pertain to how heritable variation can be generated in the first place (evolvability), while natural selection operates subsequently on the produced variation. (shrink)

Despite the traditional focus on metaphysical issues in discussions of natural kinds in biology, epistemological considerations are at least as important. By revisiting the debate as to whether taxa are kinds or individuals, I argue that both accounts are metaphysically compatible, but that one or the other approach can be pragmatically preferable depending on the epistemic context. Recent objections against construing species as homeostatic property cluster kinds are also addressed. The second part of the paper broadens the perspective by considering (...) homologues as another example of natural kinds, comparing them with analogues as functionally defined kinds. Given that there are various types of natural kinds, I discuss the different theoretical purposes served by diverse kind concepts, suggesting that there is no clear-cut distinction between natural kinds and other kinds, such as functional kinds. Rather than attempting to offer a unique metaphysical account of ‘natural’ kind, a more fruitful approach consists in the epistemological study of how different natural kind concepts are employed in scientific reasoning. (shrink)

The paper works towards an account of explanatory integration in biology, using as a case study explanations of the evolutionary origin of novelties-a problem requiring the integration of several biological fields and approaches. In contrast to the idea that fields studying lower level phenomena are always more fundamental in explanations, I argue that the particular combination of disciplines and theoretical approaches needed to address a complex biological problem and which among them is explanatorily more fundamental varies with the problem pursued. (...) Solving a complex problem need not require theoretical unification or the stable synthesis of different biological fields, as items of knowledge from traditional disciplines can be related solely for the purposes of a specific problem. Apart from the development of genuine interfield theories, successful integration can be effected by smaller epistemic units (concepts, methods, explanations) being linked. Unification or integration is not an aim in itself, but needed for the aim of solving a particular scientific problem, where the problem's nature determines the kind of intellectual integration required. (shrink)

Evolutionary developmental biologists categorize many different kinds of things, from ontogenetic stages to modules of gene activity. The process of categorization—the establishment of “kinds”—is an implicit part of describing the natural world in consistent, useful ways, and has an essentially practical rather than philosophical basis. Kinds commonly serve one of three purposes: they may function (1) as practical tools for communication; (2) to support prediction and generalization; or (3) as a basis for theoretical discussions. Beyond the minimal requirement that classifications (...) reflect biological reality, what sorts of kinds or classification will be useful in advancing a research program depends on the epistemological context. Thus, the important meaning of “natural” in “natural kinds” is not “natural with respect to nature,” but “natural with respect to the question.” This conclusion arises from the recognition that the proper role of concepts (e.g. natural kind, module, homology, model) is not to answer biological questions, but rather to help frame them. From a scientist’s perspective, arguing about the wording (or existence) of a single definition of “natural” or “kind” is beside the point: we get more work done by letting the question at hand determine what kinds of kinds are natural, on the basis of their ability to help answer it. We should be content to let “natural kinds” remain vague, multivalent, and–therefore broadly useful. For a philosopher like Hacking, the diverse, disparate, and ultimately incommensurable uses of the term “natural kind” have diluted its value so far that it loses all meaning. For practicing scientists, however, defining useful kinds in the context of particular questions and systems remains a productive epistemological strategy. (shrink)

The practical criteria by which developmental biologists choose their model systems have evolutionary correlates. The result is a sample that is not merely small, but biased in particular ways, for example towards species with rapid, highly canalized development. These biases influence both data collection and interpretation, and our views of how development works and which aspects of it are important.

Two widely accepted assumptions within cognitive science are that (1) the goal is to understand the mechanisms responsible for cognitive performances and (2) computational modeling is a major tool for understanding these mechanisms. The particular approaches to computational modeling adopted in cognitive science, moreover, have significantly affected the way in which cognitive mechanisms are understood. Unable to employ some of the more common methods for conducting research on mechanisms, cognitive scientists’ guiding ideas about mechanism have developed in conjunction with their (...) styles of modeling. In particular, mental operations often are conceptualized as comparable to the processes employed in classical symbolic AI or neural network models. These models, in turn, have been interpreted by some as themselves intelligent systems since they employ the same type of operations as does the mind. For this paper, what is significant about these approaches to modeling is that they are constructed specifically to account for behavior and are evaluated by how well they do so—not by independent evidence that they describe actual operations in mental mechanisms. (shrink)

Ernst Mayr''s distinction between ultimate and proximate causes is justly considered a major contribution to philosophy of biology. But how did Mayr come to this philosophical distinction, and what role did it play in his earlier scientific work? I address these issues by dividing Mayr''s work into three careers or phases: 1) Mayr the naturalist/researcher, 2) Mayr the representative of and spokesman for evolutionary biology and systematics, and more recently 3) Mayr the historian and philosopher of biology. If we want (...) to understand the role of the proximate/ultimate distinction in Mayr''s more recent career as a philosopher and historian, then it helps to consider hisearlier use of the distinction, in the course of his research, and in his promotion of the professions of evolutionary biology and systematics. I believe that this approach would also shed light on some other important philosophical positions that Mayr has defended, including the distinction between essentialism: and population thinking. (shrink)

Skipper and Millstein (2005) argued that existing conceptions of mechanisms failed to "get at" natural selection, but left open the possibility that a refined conception of mechanisms could resolve the problems that they identified. I respond to Skipper and Millstein, and argue that while many of their points have merit, their objections can be overcome and that natural selection can be characterized as a mechanism. In making this argument, I discuss the role of regularity in mechanisms, and develop an account (...) of stochastic (i.e., probabilistic) mechanisms. Explaining the phenomenon of adaptation through the mechanism of natural selection illustrates the power and flexibility of using mechanistic strategies to explain natural phenomena. (shrink)

Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features (...) of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely “processually equivalent” entities, “processually versatile” entities, and “stabilized” entities. (shrink)

In this article we argue for an extension of Pere Alberch’s notion of developmental morphospace into the realm of cognition and introduce the notion of cognitive phenotype as a new tool for the evolutionary and developmental study of cognitive abilities.

This paper addresses the role of time scales in conceptualizing biological hierarchies. So far, the concept of hierarchies in philosophy of science has been dominated by the idea of composition and parthood, respectively. However, this view does not exhaust the diversity of hierarchical descriptions in the biosciences. Therefore, we highlight a type of hierarchy usually overlooked by philosophers of science. It distinguishes processes based on the different time scales (i.e. rates, frequencies, and rhythms) on which they occur. These time scale (...) hierarchies often are connected with assumptions defended in process ontology. Due to their ability to describe interlevel dynamics of various kinds, we call these hierarchies ‘dynamic hierarchies.’ In order to highlight and discuss their organization, explanatory roles, and epistemic virtues we focus on dynamic hierarchies in developmental biology and evolutionary developmental biology (evo-devo). In these fields, dynamic hierarchies offer crucial complementary information to descriptions of compositional hierarchies. (shrink)

Evolutionary developmental biology represents a paradigm shift in the understanding of the ontogenesis and evolutionary progression of the denizens of the natural world. Given the empirical successes of the evo-devo framework, and its now widespread acceptance, a timely and important task for the philosophy of biology is to critically discern the ontological commitments of that framework and assess whether and to what extent our current metaphysical models are able to accommodate them. In this paper, I argue that one particular model (...) is a natural fit: an ontology of dispositional properties coherently and adequately captures the crucial casual-cum-explanatory role that the fundamental elements of evo-devo play within that framework. (shrink)