There have been repeated attempts in the history of comparative biology to provide a mechanistic account of morphological homology. However, it is well-established that homologues can develop from diverse sets of developmental causes, appearing not to share any core causal architecture that underwrites character identity. We address this challenge with a new conceptual model of Character Identity Mechanisms. ChIMs are cohesive mechanisms with a recognizable causal profile that allows them to be traced through evolution as homologues despite having a diverse (...) etiological organization. Our model hypothesizes that anatomical units at different levels of organization—cell types, tissues, and organs—have level-specific ChIMs with different conserved parts, activities, and organization. Relying on a methodology of conceptual engineering, we show how the ChIM concept advances our understanding of the developmental basis of morphological characters, while forging an important link between comparative and mechanistic biology. (shrink)

The logic of genetic discovery has changed little over time, but the focus of biology is shifting from simple genotype–phenotype relationships to complex metabolic, physiological, developmental, and behavioral traits. In light of this, the traditional reductionist view of individual genes as privileged difference‐making causes of phenotypes is re‐examined. The scope and nature of genetic effects in complex regulatory systems, in which dynamics are driven by regulatory feedback and hierarchical interactions across levels of organization are considered. This review argues that it (...) is appropriate to treat genes as specific actual difference‐makers for the molecular regulation of gene expression. However, they are often neither stable, proportional, nor specific as causes of the overall dynamic behavior of regulatory networks. Dynamical models, properly formulated and validated, provide the tools to probe cause‐and‐effect relationships in complex biological systems, allowing to go beyond the limitations of genetic reductionism to gain an integrative understanding of the causal processes underlying complex phenotypes. (shrink)

The concept of levels of organization, despite its widespread scientific currency, has recently been criticized by a number of philosophers of science. This paper diagnoses the main source of problems facing theories of levels. On this basis, the problems with the usual criteria for distinguishing levels are evaluated: compositional relations, organizational types, and spatial scales. Drawing on some work on hierarchies in ecology, I argue in favor of an alternative conception of levels defined by the criterion of rates or time (...) scales of processes. (shrink)

Explanation in terms of gene regulatory networks has become standard practice in evolutionary developmental biology. In this paper, we argue that GRNs fail to provide a robust, mechanistic, and dynamic understanding of the developmental processes underlying the genotype–phenotype map. Explanations based on GRNs are limited by three main problems: the problem of genetic determinism, the problem of correspondence between network structure and function, and the problem of diachronicity, as in the unfolding of causal interactions over time. Overcoming these problems requires (...) dynamic mechanistic explanations, which rely not only on mechanistic decomposition, but also on dynamic modeling to reconstitute the causal chain of events underlying the process of development. We illustrate the power and potential of this type of explanation with a number of biological case studies that integrate empirical investigations with mathematical modeling and analysis. We conclude with general considerations on the relation between mechanism and process in evo-devo. (shrink)

Advances in developmental genetics and evo-devo in the last several decades have enabled the growth of novel developmental approaches to the classic theme of homology. These approaches depart from the more standard phylogenetic view by contending that homology between morphological characters depends on developmental-genetic individuation and explanation. This article provides a systematic re-examination of the relationship between developmental and phylogenetic homology in light of current evidence from developmental and evolutionary genetics and genomics. I present a qualitative model of the processes (...) that cause de-coupling of morphological and molecular evolution by developmental system drift (DSD), and hypothesize that DSD is a widespread and regular stochastic process that is predictable from parameters such as population size, pleiotropy, and regulatory redundancy. These theoretical findings support an integrative approach in which models of DSD aid in determining when developmental-genetic explanations of homology apply and when other explanations such as stabilizing selection are needed. I argue that a phylogenetic monism about the definition and criteria of homology supports the integration of different explanations into a theory of homology better than pluralism does. (shrink)

This paper examines three exemplary theories of living organization with respect to their common feature of defining life in terms of metabolic closure: autopoiesis, systems, and chemoton theory. Metabolic closure is broadly understood to denote the property of organized chemical systems that each component necessary for the maintenance of the system is produced from within the system itself, except for an input of energy. It is argued that two of the theories considered—autopoiesis and systems—participate in a hylomorphist pattern of thinking (...) which separates the “form” of the living system from its “matter.” The analysis and critique of hylomorphism found in the work of the philosopher Gilbert Simondon is then applied to these two theories, and on the basis of this critique it is argued that the chemoton model offers a superior theory of minimal life which overcomes many of the problems associated with the other two. Throughout, the relationship between hylomorphism and the understanding of living things as machines is explored. The paper concludes by considering how hylomorphism as a background ontology for theories of life fundamentally influences the way life is defined. (shrink)

The received view of Bergson's philosophy of life is that it advances some form of vitalism under the heading of an “élan vital.” This paper argues against the vitalistic interpretation of Bergson's élan vital as it appears in Creative Evolution in favor of an interpretation based on his overlooked reflections on entropy and energetics. Within the interpretation developed here, the élan vital is characterized not as a spiritualistic “vital force” but as a tendency of organization opposed to the tendency of (...) entropic degradation. It is then shown how Bergson's view of evolution and living organization resonates with more contemporary scientific approaches belonging to a “thermodynamic paradigm” in theoretical biology in different respects, including the critique of neo-Darwinism and the positing of a driving force behind evolution. Finally, the special interest that Bergson's philosophical biology bears today is considered in terms of the connection between the concepts of élan vital and duration. (shrink)

Comparative biology builds up systematic knowledge of the diversity of life, across evolutionary lineages and levels of organization, starting with evidence from a sparse sample of model organisms. In developmental biology, a key obstacle to the growth of comparative approaches is that the concept of homology is not very well defined for levels of organization that are intermediate between individual genes and morphological characters. In this paper, we investigate what it means for ontogenetic processes to be homologous, focusing specifically on (...) the examples of insect segmentation and vertebrate somitogenesis. These processes can be homologous without homology of the underlying genes or gene networks, since the latter can diverge over evolutionary time, while the dynamics of the process remain the same. Ontogenetic processes like these therefore constitute a dissociable level and distinctive unit of comparison requiring their own specific criteria of homology. In addition, such processes are typically complex and nonlinear, such that their rigorous description and comparison not only requires observation and experimentation, but also dynamical modeling. We propose six criteria of process homology, combining recognized indicators with novel ones derived from dynamical systems modeling. We show how these criteria apply to animal segmentation and other ontogenetic processes. We conclude by situating our proposed dynamical framework for homology of process in relation to similar research programs, such as process structuralism and developmental approaches to morphological homology. (shrink)

Token physicalism is often viewed as a modest and unproblematic physicalist commitment, as contrasted with type physicalism. This paper argues that the prevalence of functional individuation in biology creates serious problems for token physicalism, because the latter requires that biological entities can be individuated physically and without reference to biological functioning. After characterizing the main philosophical roles for token physicalism, I describe the distinctive uses of functional individuation in models of biological processes. I then introduce some requirements on token identity (...) claims that arise from a position on individuation and identity known as sortalism. An examination of biological examples shows that these sortalist requirements cannot be plausibly met due to differences between individuation by functional biological criteria and by physical criteria. Even without assuming sortalism, token physicalism faces the more basic problem of excluding functionally irrelevant detail from the individuation of biological tokens. I close by suggesting that the philosophical roles for token identity are better fulfilled by a notion of token composition, which promotes a hierarchical picture of individuality. (shrink)

Given the pervasiveness of gene sharing in evolution and the extent of homology across the tree of life, why is everything not homologous with everything else? The continuity and overlapping genetic contributions to diverse traits across lineages seem to imply that no discrete determination of homology is possible. Although some argue that the widespread overlap in parts and processes should be acknowledged as “partial” homology, this threatens a broad base of presumed comparative morphological knowledge accepted by most biologists. Following a (...) long scientific tradition, we advocate a strategy of “theoretical articulation” that introduces further distinctions to existing concepts to produce increased contrastive resolution among the labels used to represent biological phenomena. We pursue this strategy by drawing on successful patterns of reasoning from serial homology at the level of gene sequences to generate an enriched characterization of serial homology as a hierarchical, phylogenetic concept. Specifically, we propose that the concept of serial homology should be applied primarily to repeated but developmentally individualized body parts, such as cell types, differentiated body segments, or epidermal appendages. For these characters, a phylogenetic history can be reconstructed, similar to families of paralogous genes, endowing the notion of serial homology with a hierarchical, phylogenetic interpretation. On this basis, we propose a five-fold theoretical classification that permits a more fine-grained mapping of diverse trait-types. This facilitates answering the question of why everything is not homologous with everything else, as well as how novelty is possible given that any new character possesses evolutionary precursors. We illustrate the fecundity of our account by reference to debates over insect wing serial homologs and vertebrate paired appendages. (shrink)

Adaptationism is often taken to be the thesis that most traits are adaptations. In order to assess this thesis, it seems we must be able to establish either an exhaustive set of all traits or a representative sample of this set. Either task requires a more systematic and principled way of individuating traits than is currently available. Moreover, different trait individuation criteria can make adaptationism turn out true or false. For instance, individuation based on natural selection may render adaptationism true, (...) but may do so by presupposing adaptationism. In this paper, we show how adaptationism depends on trait individuation and that the latter is an open and unsolved problem. (shrink)

A central topic in research at the intersection of development and evolution is the origin of novel traits. Despite progress on understanding how developmental mechanisms underlie patterns of diversity in the history of life, the problem of novelty continues to challenge researchers. Here we argue that research on evolutionary novelty and the closely associated phenomenon of co-option can be reframed fruitfully by: (1) specifying a conceptual model of mechanisms that underwrite character identity, (2) providing a richer and more empirically precise (...) notion of co-option that goes beyond common appeals to “deep homology”, and (3) attending to the nature of experimental interventions that can determine whether and how the co-option of identity mechanisms can help to explain novel character origins. This reframing has the potential to channel future investigation to make substantive progress on the problem of evolutionary novelty. To illustrate this potential, we apply our reframing to two case studies: treehopper helmets and beetle horns. (shrink)

The subject of this edited volume is the idea of levels of organization: roughly, the idea that the natural world is segregated into part-whole relationships of increasing spatiotemporal scale and complexity. The book comprises a collection of essays that raise the idea of levels into its own topic of analysis. Owing to the wide prominence of the idea of levels, the scope of the volume is aimed at theoreticians, philosophers, and practicing researchers of all stripes in the life sciences. The (...) volume’s contributions reflect this diversity, and draw from fields such as developmental biology, evolutionary biology, molecular biology, ecology, cell biology, and neuroscience. The book presents wide-ranging novel insights on causation and levels, the hierarchical structure of evolution, the role of levels in biological theory, and more. (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)

Structural realism is considered by many realists and antirealists alike as the most defensible form of scientific realism. There are now many forms of structural realism and an extensive literature about them. There are interesting connections with debates in metaphysics, philosophy of physics and philosophy of mathematics. This entry is intended to be a comprehensive survey of the field.

Moral philosophy is the study of what morality is and what it requires of us. As Socrates said, it's about "how we ought to live"-and why. It would be helpful if we could begin with a simple, uncontroversial definition of what morality is. Unfortunately, we cannot. There are many rival theories, each expounding a different conception of what it means to live morally, and any definition that goes beyond Socrates's simple formula-tion is bound to offend at least one of them. (...) This should make us cautious, but it need not paralyze us. In this chapter, I will describe the "minimum conception" of morality. (shrink)

"The lectures that follow were delivered at the Lowell Institute in Boston in November and December, 1906, and in January, 1907, at Columbia University, in New York."-Preface, pg. 3.

One of the most influential men of his time, philosopher, psychologist, educator, and author William James (1842-1910) helped lead the transition from a predominantly European-centered nineteenth-century philosophy to a new "pragmatic" American philosophy. Helping to pave the way was his seminal book Pragmatism (1907), in which he included a chapter on "Truth," an essay which provoked severe criticism. In response, he wrote the present work, an attempt to bring together all he had ever written on the theory of knowledge, (...) including an article on the function of cognition, later polemic and expository contributions, and some replies to previous criticism. The result was a full and definitive expression of the pragmatist "epistemology" from James' point of view. In the book, he urges the reader to "turn away from abstractions, verbal solutions, fixed principles, and pretended absolutes and look for concreteness and facts, action and power," arguing that "the ultimate test for us of what a truth means is the conduct it dictates or inspires." For students, scholars--anyone interested in William James or the history of American philosophical thought--this book offers an in-depth exposition of the influential ideas of one of the greatest American thinkers. Unabridged republication of the edition originally published by Longmans, Green and Co., New York and London, 1909. (shrink)

We have several intuitive paradigms of defeating evidence. For example, let E be the fact that Ernie tells me that the notorious pet Precious is a bird. This supports the premise F, that Precious can fly. However, Orna gives me *opposing* evidence. She says that Precious is a dog. Alternatively, defeating evidence might not oppose Ernie's testimony in that direct way. There might be other ways for it to weaken the support that Ernie's testimony gives me for believing F, without (...) the new evidence itself intuitively constituting reasons to believe one way or the other about Precious's flight ability. An example: Ursula tells me that Ernie has no idea what Precious's species is; he's just guessing. She may not herself want to or be in a position to weigh in about Precious's real species or flight ability. I call defeating evidence of this sort *undermining evidence. (shrink)

Two books bound together, from the religious period of one of the most renowned and representative thinkers. Written for laymen, thus easy to understand, it is penetrating and brilliant as well. Illuminations of age-old religious questions from a pragmatic perspective, written in a luminous style.

Consider the following facts about the average, philosophically untrained moral relativist: (1.1) The average moral relativist denies the existence of “absolute moral truths.” (1.2) The average moral relativist often expresses her commitment to moral relativism with slogans like ‘What’s true (or right) for you may not be what’s true (or right) for me’ or ‘What’s true (or right) for your culture may not be what’s true (or right) for my culture.’ (1.3) The average moral relativist endorses relativistic views of morality (...) without endorsing relativistic views about science or mathematics. (1.4) The average moral relativist takes moral relativism to be non-relatively true and does not think there is anything contradictory about doing so. (1.5) The average moral relativist adopts an egalitarian attitude toward a wide range of moral values, practices and beliefs, claiming they are all equally legitimate or correct. (1.6) The average moral relativist often admonishes others to be more tolerant of those who engage in alternative ethical practices and to refrain from making negative moral judgments about them. (1.7) The average moral relativist sometimes makes negative moral judgments about the behavior of others—e.g., by harshly judging moral absolutists to be intolerant—but is less inclined to do so when the relativist’s metaethical views are salient in a context of judgment. (1.8) The average moral relativist takes anthropological evidence concerning the worldwide diversity of ethical views and practices to support moral relativism. (shrink)

Noted psychologist and philosopher develops his own brand of pragmatism, based on theories of C. S. Peirce. Emphasis on "radical empiricism," versus the transcendental and rationalist tradition. One of the most important books in American philosophy. Note.

Experimental philosophy brings empirical methods to philosophy. These methods are used to probe how people think about philosophically interesting things such as knowledge, morality, and freedom. This paper explores the contribution that qualitative methods have to make in this enterprise. I argue that qualitative methods have the potential to make a much greater contribution than they have so far. Along the way, I acknowledge a few types of resistance that proponents of qualitative methods in experimental philosophy might encounter, and provide (...) reasons to think they are ill-founded. (shrink)

From the bestselling author of Assholes: A Theory, a book that--in the tradition of Shopclass as Soulcraft, Barbarian Days and Zen and the Art of Motorcycle Maintenance--uses the experience and the ethos of surfing to explore key concepts in philosophy. The existentialist philosopher Jean-Paul Sartre once declared "the ideal limit of aquatic sports...is waterskiing." The avid surfer and lavishly credentialed academic philosopher Aaron James vigorously disagrees, and in Surfing with Sartre he intends to expound the thinking surfer's view of (...) the matter, in the process elucidating such philosophical categories as freedom, being, phenomenology, morality, epistemology, and even the emerging values of what he terms "leisure capitalism." In developing his unique surfer-philosophical worldview, he draws from his own experience of surfing and from surf culture and lingo, and includes many relevant details from the lives of the philosophers, from Aristotle to Wittgenstein, with whose thought he engages. In the process, he'll speak to readers in search of personal and social meaning in our current anxious moment, by way of doing real, authentic philosophy. (shrink)

Louis Agassiz.--Address at the Emerson Centenary in Concord.--Robert Gould Shaw.--Francis Boott.--Thomas Davidson: a knight-errant of the intellectual life.--Herbert Spencer's autobiography.--Frederick Myers' services to psychology.--Final impressions of a psychical researcher.--On some mental effects of the earthquake.--The energies of men.--The moral equivalent of war.--Remarks at the peace banquet.--The social value of the college-bred.--The university and the individual: The Ph.D. octopus. The true Harvard. Stanford's ideal destiny.--A pluralistic mystic.

An approach to argument macrostructure -- The dialectical nature of argument -- Toulmin's problematic notion of warrant -- The linked-convergent distinction, a first approximation -- Argument structure and disciplinary perspective : the linked-convergent versus multiple-co-ordinatively compound distinctions -- The linked-convergent distinction, refining the criterion -- Argument structure and enthymemes -- From analysis to evaluation.

Recent empirical work on folk moral objectivism has attempted to examine the extent to which folk morality presumes that moral judgments are objectively true or false. Some researchers report findings that they take to indicate folk commitment to objectivism (Goodwin & Darley, 2008, 2010, 2012; Nichols & Folds-Bennett, 2003; Wainryb et al., 2004), while others report findings that may reveal a more variable commitment to objectivism (Beebe, 2014; Beebe et al., 2015; Beebe & Sackris, 2016; Sarkissian, et al., 2011; Wright, (...) 2018; Wright, Grandjean, & McWhite, 2013; Wright, McWhite, & Grandjean, 2014). However, the various probes that have been used to examine folk moral objectivism almost always fail to be good direct measures of objectivism. Some critics (Beebe, 2015; Pölzler, 2017, 2018) have suggested that the problems with existing probes are serious enough that they should be viewed as largely incapable of shedding any light on folk metaethical commitments. Building upon the work of Justin Khoo and Joshua Knobe (2018), I argue that many of the existing probes can be seen as good measures of the extent to which people think that the truth of one moral judgment excludes the possibility that a judgment made by a disagreeing party is also true and that the best explanation of the findings obtained using these measures is significant folk support for indexical moral relativism—the view that the content of moral judgments is context-sensitive. If my thesis is correct, many contemporary moral philosophers are deeply mistaken about the metaethical contours of folk morality in one very important respect. (shrink)

Yoga is hugely popular around the world today, yet until now little has been known of its roots. This book collects, for the first time, core teachings of yoga in their original form, translated and edited by two of the world's foremost scholars of the subject. It includes a wide range of texts from different schools of yoga, languages and eras: among others, key passages from the early Upanisads and the Mahabharata, and from the Tantric, Buddhist and Jaina traditions, with (...) many pieces in scholarly translation for the first time. Covering yoga's varying definitions across systems, models of the esoteric and physical bodies, and its most important practices, such as posture, breath control, sensory withdrawal and meditation, Roots of Yoga is a unique and essential source of knowledge. (shrink)

Background -- The moral manualists -- Initiating reform : Odon Lottin -- Retrieving Scripture and charity : Fritz Tillman and Gérard Gilleman -- Synthesis : Bernard Häring -- The neo-manualists -- New foundations for moral reasoning, 1970-89 -- New foundations for a theological anthropology, 1980-2000 -- Toward a global discourse on suffering and solidarity -- Afterword: The encyclicals of Pope Benedict XVI.

In 1896 William James published an essay entitled The Will to Believe, in which he defended the legitimacy of religious faith against the attacks of such champions of scientific method as W.K. Clifford and Thomas Huxley. James's work quickly became one of the most important writings in the philosophy of religious belief. James Wernham analyses James's arguments, discusses his relation to Pascal and Renouvier, and considers the interpretations, and misinterpretations, of James's major critics. Wernham shows (...) convincingly that James was unaware of many destructive ambiguitities in his own doctrines and arguments, although clear and consistent in his view that our obligation to believe in theism is not a moral but a prudential obligation -- a foolish-not-to-believe doctrine, rather than a not-immoral-to-believe one. Wernham also shows that the doctrine is best read as affirming the wisdom of gambling that God exists, a notion which James failed to distinguish from believing and which, among other things, he explicitly identified with faith. James's pragmatism, a theory concerning the meaning of truth, is shown to be quite distinct from the doctrine of The Will to Believe. In concentrating on a careful analysis of this doctrine of the will-to-believe, Wernham not only makes a major contribution to understanding James's philosophy, but also clarifies issues in the philosophy of religion and in the analysis of belief and faith. (shrink)

Episodic memory is usually regarded in a Conceptualist light, in the sense of its being dependent upon the grasp of concepts directly relevant to the act of episodic recollection itself, such as a concept of past times and of the self as an experiencer. Given this view, its development is typically timed as being in the early school‐age years (Perner, 2001;Tulving, 2005). We present a minimalist, Non‐Conceptualist approach in opposition to this view, but one that also exists in clear contrast (...) to the kind of minimalism (‘episodic‐like’) espoused byClayton and Dickinson (1998)with regard to memory in food‐caching birds. While emphasising the nonconceptual elements of episodic memory (in common with the ‘episodic‐like’ approach) we also insist on the essentially phenomenological nature of the memory (as does the Conceptualist approach). We propose the third year of life as a plausible onset period. Our view is rooted in Kantian assumptions about the spatiotemporal content of experience (and thus of re‐experience) and about the synthetic unity of experience—and thus of re‐experience. We answer two objections to this position. (shrink)

This new critical edition is an examination of William James's Essays in Radical Empiricism in light of the scientific naturalism prominent in James's Principles of Psychology (1890) and the subsequent development of Darwinian, functional psychology and functionalism in psychology, the philosophy psychology and the philosophy of mind.

Emotion regulation has the odd distinction of being a wildly popular construct whose scientific existence is in considerable doubt. In this article, we discuss the confusion about whether emotion generation and emotion regulation can and should be distinguished from one another. We describe a continuum of perspectives on emotion, and highlight how different (often mutually incompatible) perspectives on emotion lead to different views about whether emotion generation and emotion regulation can be usefully distinguished. We argue that making differences in perspective (...) explicit serves the function of allowing researchers with different theoretical commitments to collaborate productively despite seemingly insurmountable differences in terminology and methods. (shrink)

Anthology of readings in moral philosophy.