This paper advances the development of a phylogeny-based psychology in which cognitive ability types are individuated as characters in the evolutionary biological sense. I explain the character concept and its utility in addressing (or dissolving) conceptual problems arising from discoveries of cognitive abilities across a wide range of species. I use the examples of stereopsis in the praying mantis, internal cell-to-cell signaling in plants, and episodic memory in scrub jays to show how anthropocentric cognitive ability types can be reformulated into (...) cognitive characters, thereby promoting the integration of psychology with other sciences of evolved traits. (shrink)

There have been several recent attempts to think about psychological kinds as homologies. Nevertheless, there are serious epistemic challenges for individuating homologous psychological kinds, or cognitive homologies. Some of these challenges are revealed when we look at competing claims of cognitive homology. This paper considers two competing homology claims that compare human anger with putative aggression systems of nonhuman animals. The competition between these hypotheses has been difficult to resolve in part because of what I call the boundary problem: boundaries (...) between instances of psychological kinds (e.g., anger and fear) cannot be directly observed. Thus, there are distinctive difficulties for individuating psychological kinds across lineages. I draw four conclusions from this case study: First, recent evidence from the neuroscience of fear suggests that one of the proposed homologies involves a straightforward conflation of anger and fear. Second, this conflation arises because of the boundary problem. Third, there is an implicit constraint on the operational criteria that is easy to overlook in the psychological case. In this case, ignoring the constraint is part of the problem. Fourth, this is a clear case in which knowledge of homology cannot be accumulated piecemeal. Identifying homologs of human anger requires identifying homologs of fear. (shrink)

Phylogenetics is the study and reconstruction of evolutionary history and is filled with numerous foundational issues of interest to philosophers. This paper briefly introduces some central concepts in the field, describes some of the main methods for inferring phylogenies, and provides some arguments for the superiority of model-based methods such as Likelihood and Bayesian methods over nonparametric methods such as parsimony. It also raises some underdeveloped issues in the field of interest to philosophers.

The evolutionary origin of consciousness has been a growing area of study in recent years. Nevertheless, there is intense debate on whether the existence of phenomenal consciousness without the cerebral cortex is possible. The corticocentrists have an empirical advantage because we are quasi-confident that we humans are conscious and have the well-developed cortex as the site of our consciousness. However, their prejudice can be an anthropic bias similar to the anthropocentric prejudice in pre-Darwinian natural history. In this paper, I propose (...) three basic principles to provide a conceptual basis for evolutionary studies of consciousness: the non-solipsistic principle, the evolution principle, and the anthropic principle. These principles collectively help us to avoid solipsism, anthropocentrism, and anthropomorphism to some degree, although we cannot be completely free from them. Also, the landscape metaphor associated with the anthropic principle provides an image of how different forms of consciousness can be acquired. (shrink)

This paper attempts to reconcile the conceptual conflict between typological and population thinking to provide a philosophical foundation for extended evolutionary synthesis. Typological thinking has been considered a pre-Darwinian, essentialist dogma incompatible with population thinking, which is the core notion of Darwinism. More recent philosophical and historical studies suggest that a non-essentialist form of typology has some advantages in the study of evolutionary biology. However, even if we adopt such an epistemological interpretation of typological thinking, there still remains an epistemological (...) and methodological conflict between these two styles of thinking. How can we relate typological thinking with population thinking in pursuit of more integrated or interconnected research into evolutionary biology? I propose that homology thinking, which is another style of thinking that recognizes homologous characters, provides a common basis for typological representations of character states and for character dynamics in an evolving population. Good examples of this bridging role are found in teratology and breeding, where variation and novelty are recognized in developmental and morphological traits, gene expression patterns, and so on. Essentialism-free, dynamic views of homology have great potential to reconcile typological and population thinking and to set the stage for the EES. (shrink)

Homology is a fundamental concept in biology. However, the metaphysical status of homology, especially whether a homolog is a part of an individual or a member of a natural kind, is still a matter of intense debate. The proponents of the individuality view of homology criticize the natural kind view of homology by pointing out that homologs are subject to evolutionary transformation, and natural kinds do not change in the evolutionary process. Conversely, some proponents of the natural kind view of (...) homology argue that a homolog can be construed both as a part of an individual and a member of a natural kind. They adopt the Homeostatic Property Cluster theory of natural kinds, and the theory seems to strongly support their construal. Note that this construal implies the acceptance of essentialism. However, looking back on the history of the concept of homology, we should not overlook the fact that the individuality view was proposed to reject the essentialist interpretation of homology. Moreover, the essentialist notions of natural kinds can, in our view, mislead biologists about the phenomena of homology. Consequently, we need a non-essentialist view of homology, which we name the “persistently reproducible module” view. This view highlights both the individual-like and kind-like aspects of homologs while stripping down both essentialist and anti-essentialist interpretations of homology. In this article, we articulate the PRM view of homology and explain why it is recommended over the other two views. (shrink)

I propose a new account of homology, according to which homology is a correspondence of developmental mechanisms due to common ancestry, formally defined as an isomorphism of causal graphs over lineages. The semiformal definition highlights the role of homology as a higher-order principle unifying evolutionary models and also provides definite meanings to concepts like constraints, evolvability, and novelty. The novel interpretation of homology suggests a broad perspective that accommodates evolutionary developmental biology and traditional population genetics as distinct but complementary approaches (...) to understand evolution, prompting further empirical and theoretical research. (shrink)

Feinberg and Mallatt, in their presentation of neurobiological naturalism, have suggested that visual consciousness was acquired by early vertebrates and inherited by a wide range of descendants, and that its neural basis has shifted to nonhomologous nervous structures during evolution. However, their evolutionary scenario of visual consciousness relies on the assumption that visual consciousness is closely linked with survival, which is not commonly accepted in current consciousness research. We suggest an alternative idea that visual consciousness is linked to a specific (...) class of agency, consequently justifying their phylogenetic claim. We also examine the implication of their phylogenetic claim: visual consciousness is homologous across vertebrates, but its neural basis is not. This apparent incongruence illustrates a general phenomenon of homology, and that the resulting hierarchical view of visual consciousness and its neural basis can be straightforwardly accommodated by neurobiological naturalism. Throughout these discussions, we aim to address the potential theoretical issues in neurobiological naturalism and refine the picture illustrated by Feinberg and Mallatt regarding phylogenetic distribution and trajectories of visual consciousness. (shrink)

Contrary to the common-sense view and positivist aspirations, scientific concepts are often imprecise. Many of these concepts are ambiguous, vague, or have an under-specified meaning. In this paper, I discuss how imprecise concepts promote integration in biology and thus benefit science. Previous discussions of this issue focus on the concepts of molecular gene and evolutionary novelty. The concept of molecular gene helps biologists integrate explanatory practices, while the notion of evolutionary novelty helps them integrate research questions into an interdisciplinary problem (...) New directions in the philosophy of science, Springer, Dordrecht, 2014). In what follows, I compare molecular gene and evolutionary novelty to another imprecise concept, namely biological lineage. This concept promotes two other types of scientific integration: it helps biologists integrate theoretical principles and methodologies into different areas of biology. The concept of biological lineage facilitates these types of integration because it is broad and under-specified in ways that the concepts of molecular gene and evolutionary novelty are not. Hence, I use the concept of biological lineage as a case study to reveal types of integration that have been overlooked by philosophers. This case study also shows that even very imprecise concepts can be beneficial to scientific practice. (shrink)

Researchers in the cognitive sciences often seek neural correlates of psychological constructs. In this paper, I argue that even when these correlates are discovered, they do not always lead to reductive outcomes. To this end, I examine the psychological construct of a critical period and briefly describe research identifying its neural correlates. Although the critical period is correlated with certain neural mechanisms, this does not imply that there is a reductionist relationship between this psychological construct and its neural correlates. Instead, (...) this case study suggests that there may be many-to-many psychological-neural mappings, not just one-to-one or even one-to-many relations between psychological kinds and types of neural mechanisms. (shrink)

This paper makes a distinction between ahistorical causal-functional kinds and historical kinds, which include both type- and token-historical kinds, some of which are “copied kinds.” After showing how these distinctions play out in various social sciences, a number of reasons are put forward for the historical individuation of some social kinds. As in the natural sciences, historical individuation in the social sciences can enable us to infer common causes, explain synchronic causal properties, and discover exceptions to causal regularities, among other (...) epistemic aims. (shrink)

Kinds that share historical properties are dubbed “historical kinds” or “etiological kinds,” and they have some distinctive features. I will try to characterize etiological kinds in general terms and briefly survey some previous philosophical discussions of these kinds. Then I will take a closer look at a few case studies involving different types of etiological kinds. Finally, I will try to understand the rationale for classifying on the basis of etiology, putting forward reasons for classifying phenomena on the basis of (...) diachronic features, thereby making a provisional case for considering at least some etiological kinds to be natural kinds. (shrink)

I will begin by proposing a taxonomy of taxonomic positions regarding the mind–brain: localism, globalism, revisionism, and contextualism, and will go on to focus on the last position. Although some versions of contextualism have been defended by various researchers, they largely limit themselves to a version of neural contextualism: different brain regions perform different functions in different neural contexts. I will defend what I call “environmental-etiological contextualism,” according to which the psychological functions carried out by various neural regions can only (...) be identified and individuated against an environmental context or with reference to a causal history. While this idea may seem innocuous enough, it has important implications for a structure-to-function mapping in the mind and brain sciences. It entails that the same neural structures can subserve different psychological functions in different contexts, leading to crosscutting psycho-neural mappings. I will try to illustrate how this can occur with reference to recent research on episodic memory. (shrink)

The relationship between statistical mechanics and population genetics has a long history. Both take advantage of statistics to address the behavior of large groups of entities. The main objective of this article is to assess the obstacles population genetics is meeting in its claim to explain biological phenomena from the conceptual apparatus of statistical mechanics according to two recent articles. Several tools available to the latter are missing in the former. Thus, in the absence of an adequate justification of the (...) relevance of the analogy and without the satisfaction of certain basic assumptions, I argue that the explanatory strategy of the analogously based model is seriously compromised. La relation entre mécanique statistique et génétique des populations a une longue histoire. À l’instar de la première, la seconde tire profit des statistiques afin de traiter le comportement des grands ensembles d’entités. L’objectif principal du présent article est d’identifier les obstacles que rencontre la génétique des populations dans sa prétention d’explication des phénomènes biologiques à partir de l’appareillage conceptuel de la mécanique statistique selon deux articles récents. Or, plusieurs outils dont dispose cette dernière manque à la première. Ainsi, en l’absence d’une justification adéquate de la pertinence de l’analogie et sans la satisfaction de certaines hypothèses fondamentales, je soutiens que la stratégie explicative du modèle analogue est sérieusement compromise. (shrink)

I spell out and update the individuality thesis, that species are individuals, and not classes, sets, or kinds. I offer three complementary presentations of this thesis. First, as a way of resolving an inconsistent triad about natural kinds; second, as a phylogenetic systematics theoretical perspective; and, finally, as a novel recursive account of an evolved character. These approaches do different sorts of work, serving different interests. Presenting them together produces a taxonomy of the debates over the thesis, and isolates ways (...) it has been productive. This goes to the larger point of this paper: a defense of the individuality thesis in terms of its utility, and an update of it in light of recent theoretical developments and empirical work in biology. (shrink)

I argue that there is a tension between the claim that at least some kinds in the special sciences are multiply realized and the claim that the reason why kinds are prized by science is that they enter into a variety of different empirical generalizations. Nevertheless, I show that this tension ceases in the case of ‘cultural homologues’—such as specific ideologies, religions, and folk wisdom. I argue that the instances of such special science kinds do have several projectable properties in (...) common due to their shared history of reproduction, and that the social learning involved means that we should also expect these kinds to be multiply realized. (shrink)

Natural kinds, real kinds, or, following J.S Mill simply, Kinds, are thought to be an important asset for scientific realists in the non-fundamental (or “special”) sciences. Essential natures are less in vogue. I show that the realist would do well to couple her Kinds with essential natures in order to strengthen their epistemic and ontological credentials. I argue that these essential natures need not however be intrinsic to the Kind’s members; they may be historical. I concentrate on assessing the merits (...) of historical essential natures in a paradigm case of Kinds in the non-fundamental sciences: species. I specify two basic jobs for essential natures: 1) offering individuation criteria, and 2) providing a causal explanation of the Kind’s multiple projectable properties. I argue that at least in the case of species historical essences are fit for both tasks. The principled resistance to Kinds with historical essences should also be cleared. (shrink)

I argue that an explicit distinction between cognitive characters and cognitive phenotypes is needed for empirical progress in the cognitive sciences and their integration with evolution-guided sciences. I elaborate what ontological commitment to characters involves and how such a commitment would clarify ongoing debates about the relations between human and nonhuman cognition and the extent of cognitive abilities across biological species. I use theoretical proposals in episodic memory, language, and sociocultural bases of cognition to illustrate how cognitive characters are being (...) introduced in scientific practice. (shrink)

Individuality is an important concept in biology, yet there are many non-equivalent criteria of individuality expressed in different kinds of biological individuals. This article evaluates these different kinds in terms of their capacity to support explanatory generalizations over the systems they individuate. Viewing the problem of individuality from this perspective promotes a splitting strategy in which different kinds make different epistemic trade-offs that suit them for different explanatory roles. I argue that evolutionary individuals, interpreted as forming a functional kind, face (...) difficulties of individuation and explanatory power that are mitigated by relying on more structurally based properties and non-evolutionary kinds. 1Introduction2Kinds of Biological Individuals3Evolutionary Individuals and Functional Kinds4Evolutionary versus Non-evolutionary Kinds of Individuals 4.1Physiological individuality4.2Ecological individuality4.3Developmental individuality5Conclusion. (shrink)

Path-dependence offers a promising way of understanding the role historicity plays in explanation, namely, how the past states of a process can matter in the explanation of a given outcome. The two main existing accounts of path-dependence have sought to present it either in terms of dynamic landscapes or branching trees. However, the notions of landscape and tree both have serious limitations and have been criticized. The framework of causal networks is both more fundamental and more general that that of (...) landscapes and trees. Within this framework, I propose that historicity in networks should be understood as symmetry breaking. History matters when an asymmetric bias towards an outcome emerges in a causal network. This permits a quantitative measure for how path-dependence can occur in degrees, and offers suggestive insights into how historicity is intertwined both with causal structure and complexity. (shrink)

This paper analyzes the relevance and interconnection of two forms of historicity in ecological restoration, namely historical fidelity and path dependence. Historical fidelity is the practice of attempting to restore an ecological system to some sort of idealized past condition. Path dependence occurs when a system can evolve in alternative local equilibria, and that the order and timing of the events that follow from the initial state influence which equilibrium is reached. Using theoretical examples and case studies, the following analysis (...) shows that path dependence can seriously impinge the feasibility of historical fidelity, thus reinforcing the idea that restoration ecology needs to move away from a rigid reliance on historical fidelity and is sometimes justified to endorse an interventionist agenda. Yet, contra recent criticisms, I argue that ecological restoration, directed by prudential and evidence-based reasoning, should maintain historical fidelity as one of its guiding objectives. (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)

The biological sciences have always proven a fertile ground for philosophical analysis, one from which has grown a rich tradition stemming from Aristotle and flowering with Darwin. And although contemporary philosophy is increasingly becoming conceptually entwined with the study of the empirical sciences with the data of the latter now being regularly utilised in the establishment and defence of the frameworks of the former, a practice especially prominent in the philosophy of physics, the development of that tradition hasn’t received the (...) wider attention it so thoroughly deserves. This review will briefly introduce some recent significant topics of debate within the philosophy of biology, focusing on those whose metaphysical themes (in everything from composition to causation) are likely to be of wide-reaching, cross-disciplinary interest. (shrink)

This thesis explores the use of the concept 'realization' in the philosophy of mind. The primary focus is on the role realization plays in assessing or opposing identity theory. The history of the use of the concept of realization in the philosophy of mind is reviewed, and from that a set of desiderata to be used for assessing accounts of realization is extracted. The desiderata are applied to a sample account of realization proposed by Sydney Shoemaker. (2007) Next the application (...) of 'realization' in contemporary contexts is considered, focusing on the idea that mental kinds are, potentially, multiply realized. Based on interpretations of results from research in the relevant sciences this thesis considers two kinds of strategies used to object to multiple realization, (1) arguments against the concept of multiple realization: the Grain Argument (Bechtel and Mundale 1999), and Shapiro's Dilemma (Shapiro 2000), and (2) defeaters for alleged cases/examples of multiple realization proposed by Lawrence Shapiro and Thomas Polger: unification, individual differences, kind splitting, and abstraction and idealization. (Polger and Shapiro 2016) The thesis argues that, ultimately, these arguments hinge on the claim that there is no empirical evidence of multiply realized mental kinds. In response to this claim, the fourth chapter presents novel examples of multiple realization drawn from research in the cognitive neuroscience of language. There are three aspects from the study of language that are presented as examples of multiple realization: (1) language lateralization, (2) reading acquisition, and (3) second/multi- language learning. The analysis of these case studies applies Shoemaker's account of realization as a framework for describing the empirical data as cases of multiple realization. Objections to, and defeaters for, these cases are considered and rejected. The thesis concludes by raising the possibility that mental kinds are realized by mechanisms. This proposal involves drawing connections between traditional questions/views from the philosophy of mind with a current research program from the philosophy of science; the view is particularly important in the philosophy of neuroscience and the philosophy of biology, known as 'new mechanism'. (shrink)

Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between (...) form and matter has yet to similarly earn its keep. In this chapter, I offer a first step toward showing that the hylomorphic framework is up to that task. To do so, I return to the birthplace of that doctrine - the biological realm. Utilising recent advances in developmental biology, I argue that the hylomorphic framework is an empirically adequate and conceptually rich explanatory schema with which to model the nature of organisms. (shrink)

A number of areas of biology raise questions about what is of value in the natural environment and how we ought to behave towards it: conservation biology, environmental science, and ecology, to name a few. Based on my experience teaching students from these and similar majors, I argue that the field of environmental ethics has much to teach these students. They come to me with pent-up questions and a feeling that more is needed to fully engage in their subjects, and (...) I believe some exposure to environmental ethics can help focus their interests and goals. I identify three primary areas in which environmental ethics can con- tribute to their education. The first is an examination of who (or what) should be considered to be part of our moral community (i.e., the community to whom we owe direct duties). Is it humans only? Or does it include all sentient life? Or all life? Or ecosystems considered holistically? Often, readings implicitly assume one or more of these answers; the goal is to make the student more sensitive to these implicit claims and to get them to think about the different reasons that support them. The second area, related to the first, is the application of the different answers concerning the extent of the ethical community to real environmental issues and problems. Students need to be aware of how the different answers concerning the moral community can imply conflicting answers for how we should act in certain cases and to think about ways to move toward conflict resolution. The third area in which environmental ethics can contribute is a more conceptual one, focusing on central concepts such as biodiversity, sustainability, species, and ecosystems. Exploring and evaluating various meanings of these terms will make students more reflective and thoughtful citizens and biologists, sensitive to the implications that different conceptual choices make. (shrink)