21 found
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  1.  60
    Character identity mechanisms: a conceptual model for comparative-mechanistic biology.James DiFrisco, Alan C. Love & Günter P. Wagner - 2020 - Biology and Philosophy 35 (4):1-32.
    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 (...)
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  2. Time Scales and Levels of Organization.James DiFrisco - 2017 - Erkenntnis 82 (4):795-818.
    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 (...)
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  3.  43
    Genetic Causation in Complex Regulatory Systems: An Integrative Dynamic Perspective.James DiFrisco & Johannes Jaeger - 2020 - Bioessays 42 (6):1900226.
    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 (...)
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  4.  45
    Beyond networks: mechanism and process in evo-devo.James DiFrisco & Johannes Jaeger - 2019 - Biology and Philosophy 34 (6):54.
    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 (...)
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  5.  61
    Toward a Theory of Homology: Development and the De-Coupling of Morphological and Molecular Evolution.James DiFrisco - 2023 - British Journal for the Philosophy of Science 74 (3):771-810.
    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 (...)
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  6.  59
    Hylomorphism and the Metabolic Closure Conception of Life.James DiFrisco - 2014 - Acta Biotheoretica 62 (4):499-525.
    This paper examines three exemplary theories of living organization with respect to their common feature of defining life in terms of metabolic closure: autopoiesis, (M, R) 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 (M, R) systems—participate in a (...)
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  7.  25
    Reframing research on evolutionary novelty and co-option: Character identity mechanisms versus deep homology.James DiFrisco, G. P. Wagner & Alan Love - forthcoming - Seminars in Cell and Developmental Biology.
    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 (...)
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  8.  74
    Élan Vital Revisited: Bergson and the Thermodynamic Paradigm.James DiFrisco - 2015 - Southern Journal of Philosophy 53 (1):54-73.
    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 (...)
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  9.  63
    Levels of Organization in the Biological Sciences.Daniel Stephen Brooks, James DiFrisco & William C. Wimsatt (eds.) - 2021 - Cambridge, Massachusetts: MIT Press.
    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 (...)
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  10.  25
    Homology of process: developmental dynamics in comparative biology.James DiFrisco & Johannes Jaeger - forthcoming - Interface Focus.
    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 (...)
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  11.  12
    What is a trait? Lessons from the human chin.Andra Meneganzin, Grant Ramsey & James DIFrisco - 2024 - Journal of Experimental Zoology B 342 (2):65–75.
    The chin, a distinguishing feature of Homo sapiens, has sparked ongoing debates regarding its evolutionary origins and adaptive significance. We contend that these controversies stem from a fundamental disagreement about what constitutes a well-defined biological trait, a problem that has received insufficient attention despite its recognized importance in biology. In this paper, we leverage paleoanthropological research on the human chin to investigate the general issue of character or trait identification. First, we examine four accounts of the human chin from the (...)
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  12.  51
    Token physicalism and functional individuation.James DiFrisco - 2018 - European Journal for Philosophy of Science 8 (3):309-329.
    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 (...)
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  13.  37
    Functional explanation and the problem of functional equivalence.James DiFrisco - 2017 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 65:1-8.
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  14.  28
    The hierarchical basis of serial homology and evolutionary novelty.James DiFrisco, Alan Love & G. P. Wagner - 2023 - Journal of Morphology 284 (1):e21531.
    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 (...)
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  15.  31
    Adaptationism and Trait Individuation.James DiFrisco & Grant Ramsey - forthcoming - Philosophy of Science.
    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, (...)
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  16.  38
    Interdisciplinarity, epistemic pluralism, and unificationism.James DiFrisco - 2019 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 74:40-44.
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  17.  31
    Merleau-Ponty's Ontology of Life.James DiFrisco - 2012 - Pli 23:35-50.
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  18. Merleau-Ponty’s Ontology of Life.James Difrisco - 2012 - Pli 23.
     
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  19.  88
    Ontological Issues in the Life Sciences.James DiFrisco, Gaëlle Pontarotti, Federico Boem, Guillaume Schlaepfer, Ewelina Sokolowska & Eva Fernández-Labandera - 2015 - Biological Theory 10 (2):176-181.
  20.  29
    Process and Levels of Organization.James DiFrisco - 2015 - Dissertation, Ku Leuven
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  21.  26
    Nature Rendered "Intelligible": On Thomas Nagel's Mind and Cosmos. [REVIEW]James DiFrisco - 2015 - Journal of the British Society for Phenomenology 46 (1):79-86.
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