In this book Ron Amundson examines two hundred years of scientific views on the evolution-development relationship from the perspective of evolutionary developmental biology. This perspective challenges several popular views about the history of evolutionary thought by claiming that many earlier authors had made history come out right for the Evolutionary Synthesis. The book starts with a revised history of nineteenth-century evolutionary thought. It then investigates how development became irrelevant with the Evolutionary Synthesis. It concludes with an examination of the contrasts (...) that persist between mainstream evolutionary theory and evo-devo. This book will appeal to students and professionals in the philosophy and history of science, and biology. (shrink)

I develop an account of homology and homoplasy drawing on their use in biological inference and explanation. Biologists call on homology and homoplasy to infer character states, support adaptationist explanations, identify evolutionary novelties and hypothesize phylogenetic relationships. In these contexts, the concepts must be understood phylogenetically and kept separate: as they play divergent roles, overlap between the two ought to be avoided. I use these considerations to criticize an otherwise attractive view defended by Gould, Hall, and Ramsey & Peterson. By (...) this view, homology and homoplasy can only be delineated qua some level of description, and some homoplasies (parallelisms) are counted as homologous. I develop an account which retains the first, but rejects the second, aspect of that view. I then characterize parallelisms and convergences in terms of their causal role. By the Strict Continuity account, homology and homoplasy are defined phylogenetically and without overlaps, meeting my restriction. Convergence and parallelisms are defined as two types of homoplasy: convergent homoplasies are largely constrained by external factors, while parallelisms are due to internal constraints. (shrink)

Homology is a biological sameness relation that is purported to hold in the face of changes in form, composition, and function. In spite of the centrality and importance of homology, there is no consensus on how we should understand this concept. The two leading views of homology, the genealogical and developmental accounts, have significant shortcomings. We propose a new account, the hierarchical-dependency account of homology, which avoids these shortcomings. Furthermore, our account provides for continuity between special, general, and serial homology.

Taxa and homologues can in our view be construed both as kinds and as individuals. However, the conceptualization of taxa as natural kinds in the sense of homeostatic property cluster kinds has been criticized by some systematists, as it seems that even such kinds cannot evolve due to their being homeostatic. We reply by arguing that the treatment of transformational and taxic homologies, respectively, as dynamic and static aspects of the same homeostatic property cluster kind represents a good perspective for (...) supporting the conceptualization of taxa as kinds. The focus on a phenomenon of homology based on causal processes (e.g., connectivity, activity-function, genetics, inheritance, and modularity) and implying relationship with modification yields a notion of natural kinds conforming to the phylogenetic-evolutionary framework. Nevertheless, homeostatic property cluster kinds in taxonomic and evolutionary practice must be rooted in the primacy of epistemological classification (homology as observational properties) over metaphysical generalization (series of transformation and common ancestry as unobservational processes). The perspective of individuating characters exclusively by historical-transformational independence instead of their developmental, structural, and functional independence fails to yield a sufficient practical interplay between theory and observation. Purely ontological and ostensional perspectives in evolution and phylogeny (e.g., an ideographic character concept and PhyloCode’s ‘individualism’ of clades) may be pragmatically contested in the case of urgent issues in biodiversity research, conservation, and systematics. (shrink)

The study of similarity is fundamental to biological inquiry. Many homology concepts have been formulated that function successfully to explain similarity in their native domains, but fail to provide an overarching account applicable to variably interconnected and independent areas of biological research despite the monistic standpoint from which they originate. The use of multiple, explicitly articulated homology concepts, applicable at different levels of the biological hierarchy, allows a more thorough investigation of the nature of biological similarity. Responsible epistemological pluralism as (...) advocated herein is generative of fruitful and innovative biological research, and is appropriate given the metaphysical pluralism that underpins all of biology. (shrink)

Philosophical discussions of biological classification have failed to recognise the central role of homology in the classification of biological parts and processes. One reason for this is a misunderstanding of the relationship between judgments of homology and the core explanatory theories of biology. The textbook characterisation of homology as identity by descent is commonly regarded as a definition. I suggest instead that it is one of several attempts to explain the phenomena of homology. Twenty years ago the ‘new experimentalist’ movement (...) in philosophy of science drew attention to the fact that many experimental phenomena have a ‘life of their own’: the conviction that they are real is not dependent on the theories used to characterise and explain them. I suggest that something similar can be true of descriptive phenomena, and that many homologies are phenomena of this kind. As a result the descriptive biology of form and function has a life of its own—a degree of epistemological independence from the theories that explain form and function. I also suggest that the two major ‘homology concepts’ in contemporary biology, usually seen as two competing definitions, are in reality complementary elements of the biological explanation of homology. (shrink)

The so-called "adaptationism" of mainstream evolutionary biology has been criticized from a variety of sources. One, which has received relatively little philosophical attention, is developmental biology. Developmental constraints are said to be neglected by adaptationists. This paper explores the divergent methodological and explanatory interests that separate mainstream evolutionary biology from its embryological and developmental critics. It will focus on the concept of constraint itself; even this central concept is understood differently by the two sides of the dispute.

A un secolo e mezzo dalla pubblicazione dell'Origine delle specie, la nozione di omologia di Owen, che implica che due organi o due funzioni a confronto possono essere riconosciuti come “la stessa cosa” continua a dominare gli attuali approcci al problema dell’omologia. L'idea che i caratteri possano “rimanere se stessi” attraverso un numero indefinito (anche se finito) di stati alternativi che si susseguono nel corso dell'evoluzione è probabilmente basato su un'interpretazione idealistica di come gli organismi si evolvono. Se si dà (...) per scontata l'esistenza di caratteristiche del corpo che conservano la loro identità nel cambiamento, l'esistenza di omologhi può essere spiegata (i) in termini di leggi universali della forma, magari nella forma moderna dello strutturalismo di processo, o (ii) come il prodotto di discendenza comune, o (iii) in termini di cause prossime responsabili della comparsa di moduli di sviluppo conservati. Tuttavia, leggendo la storia della vita attraverso la lente dell’evoluzione, appare molto problematico descrivere un organismo come una somma di caratteri che, una volta apparsi come novità evolutive, rimangono poi come unità costruttive essenzialmente immutabili tra le quali possiamo predicare (o negare) omologia. Tutti i tratti sono meglio interpretati come incroci complessi e mutevoli di un numero indeterminato di elementi e dei processi che li modellano nel corso dell’ontogenesi e della filogenesi. Di conseguenza, appare raccomandabile un approccio fattoriale, o combinatorio, all’omologia. (shrink)

Homology is a natural kind concept, but one that has been notoriously elusive to pin down. There has been sustained debate over the nature of correspondence and the units of comparison. But this continued debate over its meaning has focused on defining homology rather than on its use in practice. The aim of this chapter is to concentrate on the practices of homologizing. I define “homologizing” to be a concept-in-use. Practices of homologizing are kinds of rule following, the satisfaction of (...) which demarcates a category—that of being a homologue. Identifying, explaining, discovering, and understanding are exchanges that connect practice to concept through the performance of a rule by practitioners. These practices are constitutive of natural kinding activities. If homologizing is a kind of kinding, consideration of these practices of discovery, tracking, and identification not only clarifies the meaning, use, and progression of the concept of homology, but provides further understanding of the processes and progression of natural kinds and kinding practices in general. (shrink)

Homology is a natural kind term and a precise account of what homology is has to come out of theories about the role of homologues in evolution and development. Definitions of homology are discussed with respect to the question as to whether they are able to give a non-circular account of the correspondence or sameness referred to by homology. It is argued that standard accounts tie homology to operational criteria or specific research projects, but are not yet able to offer (...) a concept of homology that does not presuppose a version of homology or a comparable notion of sameness. This is the case for phylogenetic definitions that trace structures back to the common ancestor as well as for developmental approaches such as Wagner's biological homology concept. In contrast, molecular homology is able to offer a definition of homology in genes and proteins that explicates homology by reference to more basic notions. Molecular correspondence originates by means of specific features of causal processes. It is speculated that further understanding of morphogenesis might enable biologists to give a theoretically deeper definition of homology along similar lines: an account which makes reference to the concrete mechanisms that operate in organisms. (shrink)

With the advent of evolutionary developmental research, or EvoDevo, there is hope of discovering the roles that the genetic bases of development play in morphological evolution. Studies in EvoDevo span several levels of organismal organization. Low-level studies identify the ultimate genetic changes responsible for morphological variation and diversity. High-level studies of development focus on how genetic differences affect the dynamics of gene networks and epigenetic interactions to modify morphology. Whereas an increasing number of studies link independent acquisition of homoplastic or (...) convergent morphologies to similar changes in the genomes, homoplasies are not always found to have identical low-level genetic underpinnings. This suggests that a combination of low- and high-level approaches may be useful in understanding the relationship between genetic and morphological variation. Therefore, as an empirical and conceptual framework, we propose the causality horizon to signify the lowest level that allows linking homoplastic morphologies to similar changes in the development. A change in a system below the causality horizon cannot be generalized. In more concrete terms, homoplastic morphologies cannot be reduced to the same change in gene regulation when that change occurs below the causality horizon; rather, a higher-level mechanism should be identified. (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)