James DiFrisco

• PhD
• Group Leader at The Francis Crick Institute

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, we reexamine the traditional reductionist view of individual genes as privileged difference-making causes of phen...

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...

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 expla...

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 wide...

Developmental system drift (DSD) occurs when the genetic basis for homologous traits diverges over time despite conservation of the phenotype. In this Review, we examine the key ideas, evidence and open problems arising from studies of DSD. Recent work suggests that DSD may be pervasive, having been detected across a range of different organisms an...

This paper evaluates recent work purporting to show that the “agency” of organisms is an important phenomenon for evolutionary biology to study. Biological agency is understood as the capacity for goal-directed, self-determining activity—a capacity that is present in all organisms irrespective of their complexity and whether or not they have a nerv...

Although evolutionary transitions of individuality have been extensively theorized, little attention has been paid to the origin of levels of organization within organisms. How and why do specialized cells become organized into specialized tissues or organs? What spurs a transition in organizational level in cases where the function is already pres...

Organoids and stem-cell-based embryo models (SEMs) are imperfect organ or embryo representations that explore a much larger space of possible forms, or morphospace, compared to their in vivo counterparts. Here, we discuss SEM biology in light of seminal work by Pere Alberch, a leading figure in early evo-devo, interpreting SEMs as developmental ‘mo...

Although evolutionary transitions of individuality have been extensively theorized, little attention has been paid to the origin of levels of organization within organisms. How and why do specialized cells become organized into specialized tissues or organs? What spurs a transition in organizational level in cases where the function is already pres...

Although evolutionary transitions of individuality have been extensively theorized, little attention has been paid to the origin of levels of organization within organisms. How and why do specialized cells become organized into specialized tissues or organs? What spurs a transition in organizational level in cases where the function is already pres...

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 impo...

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,...

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 close...

A body plan is a stable configuration of characters for a major taxonomic group, such as chordates or arthropods. Despite widespread casual reliance on the concept for guiding comparisons within and between groups, the nature of body plans as well as the biological causes underlying their evolution have remained elusive. This paper proposes an abst...

Scientific philosophers examine the nature and significance of levels of organization, a core structural principle in the biological sciences. This volume examines the idea of levels of organization as a distinct object of investigation, considering its merits as a core organizational principle for the scientific image of the natural world. It appr...

This volume examines the idea of levels of organization as a distinct object of investigation, considering its merits as a core organizational principle for the scientific image of the natural world. It approaches levels of organization—roughly, the idea that the natural world is segregated into part–whole relationships of increasing spatiotemporal...

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...

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 i...

What does it mean to be the same organism over time? This chapter develops an understanding of diachronic identity of organisms from an organizational perspective. We argue that a necessary condition for diachronic identity is organizational continuity, i.e., the presence of a continuous causal process linking successive organizational regimes, irr...

Scientific philosophers examine the nature and significance of levels of organization, a core structural principle in the biological sciences. This volume examines the idea of levels of organization as a distinct object of investigation, considering its merits as a core organizational principle for the scientific image of the natural world. It appr...

Explanation in terms of gene regulatory networks (GRNs) has become standard practice in evolutionary developmental biology (evo-devo). 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 thre...

This essay takes Lidgard and Nyhart's (2017) recent volume on biological individuality as a starting point for a general discussion of interdisciplinarity, epistemic pluralism, and unification across scientific perspectives. I identify some common obstacles to interdisciplinary communication and trace their presence in Lidgard and Nyhart's (2017) b...

Homology is the fundamental determinant of the sameness of biological characters or traits. When two characters stand in a relation of homology, they belong to the same character kind. For example, the eyes of humans and birds are homologous as vertebrate eyes-that is, they are the same kind of character: vertebrate eyes. Although the concept of ho...

Life cycle traits, such as metagenesis and metamorphosis, often take on functionally varied forms in evolution. Like other biological traits, life cycle traits can be classified phylogenetically under a dual aspect, as homologies or homoplasies. Several examples of indeterminate boundaries between metamorphosis, metagenesis, and asexual reproductio...

This collection of essays explores the metaphysical thesis that the living world is not ontologically made up of substantial particles or things, as has often been assumed, but is rather constituted by processes. The biological domain is organized as an interdependent hierarchy of processes, which are stabilized and actively maintained at different...

This essay investigates the identity and persistence conditions for processes as a task of biological process ontology. I argue that the problem of intrinsic variation in evolution, development, and metabolism motivates viewing biological individuals as processes rather than as substances. Different criteria of identity for processes are then evalu...

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 refe...

The legitimacy of functional explanations in biology is threatened by a problem first identified by Hempel: the problem of functional equivalence. In order for the prevalence of a trait to be explained by its function, the function would have to explain why that very trait is prevalent and not some other functionally equivalent trait. But functions...

Individuality is an important concept in biology, yet there are many non-equivalent criteria of individuality expressed in different kinds of biological individuals. This paper evaluates these different kinds in terms of their capacity to support explanatory generalizations over the systems they individuate. Viewing the problem of individuality fro...

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, orga...

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 t...

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 ideas on entropy and energetics. Within the interp...