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)
Homology is a natural kind term and a precise account of what homologyis has to come out of theories about the role of homologues in evolution anddevelopment. Definitions of homology are discussed with respect to the questionas to whether they are able to give a non-circular account of thecorrespondenceor sameness referred to by homology. It is argued that standard accounts tiehomology to operational criteria or specific research projects, but are not yetable to offer a concept of (...) class='Hi'>homology that does not presuppose a version ofhomology or a comparable notion of sameness. This is the case for phylogeneticdefinitions that trace structures back to the common ancestor as well as fordevelopmental approaches such as Wagner's biological homology concept. Incontrast, molecular homology is able to offer a definition of homology in genesand proteins that explicates homology by reference to more basic notions.Molecular correspondence originates by means of specific features of causalprocesses. It is speculated that further understanding of morphogenesis mightenable biologists to give a theoretically deeper definition of homology alongsimilar lines: an account which makes reference to the concrete mechanisms thatoperate in organisms. (shrink)
Recent work on inheritance systems can be divided into inclusive conceptions, according to which genetic and non-genetic inheritance are both involved in the development and transmission of nearly all animal behavioral traits, and more demanding conceptions of what it takes for non-genetic resources involved in development to qualify as a distinct inheritance system. It might be thought that, if a more stringent conception is adopted, homologies could not subsist across two distinct inheritance systems. Indeed, it is commonly assumed that (...) class='Hi'>homology relations cannot survive a shift between genetic and cultural inheritance systems, and substantial reliance has been placed on that assumption in debates over the phylogenetic origins of hominin behavioral traits, such as male-initiated intergroup aggression. However, in the homology literature it is widely accepted that a trait can be homologous—that is, inherited continuously in two different lineages from a single common ancestor—despite divergence in the mechanisms involved in the trait’s development in the two lineages. In this paper, we argue that even on an extremely stringent understanding of what it takes for developmental resources to form a separate inheritance system, homologies can nonetheless subsist across shifts between distinct inheritance systems. We argue that this result is a merit of this way of characterizing what it is to be an inheritance system, that it has implications for adjudicating between alternative accounts of homology, and that it offers an important cautionary lesson about how to reason with the homology concept, particularly in the context of cultural species. (shrink)
Günter Wagner’s Homology, Genes, and Evolutionary Innovation collects and synthesizes a vast array of empirical data, theoretical models, and conceptual analysis to set out a progressive research program with a central theoretical commitment: the genetic theory of homology. This research program diverges from standard approaches in evolutionary biology, provides sharpened contours to explanations of the origin of novelty, and expands the conceptual repertoire of evolutionary developmental biology. I concentrate on four aspects of the book in this essay review: (...) the genetic theory of homology and character identity networks; the implications for how we explain evolutionary novelties; the expanded set of concepts surrounding homology, and the epistemological conflicts between Wagner’s viewpoint and functionally-oriented evolutionary biology, as well as differences with other Evo–devo researchers. Together these have ramifications for how we interpret different explanatory approaches to evolutionary phenomena and understand relationships between the usefulness of concepts and the reality they represent. (shrink)
This paper responds to the essay reviews by David Haig, Alan Love and Rachel Brown of my recently published book “Homology, Genes and Evolutionary Innovation”. The issues addressed here relate to: the notion of classes and individuals, issues of explanatory value of adaptive and structuralist explanations in evolutionary biology, the role of homology in evolutionary theory, the limits of a pluralist stance vis a vis alternative explanations of homology, as well as the question whether and to what (...) extend the perspective laid out in HGEI can be or should be transferred to other branches of study, like comparative behavioral biology. (shrink)
Morphological elements, or structures, are sorted into four categories depending on their level of anatomical isolation and the presence or absence of intrinsically identifying characteristics. These four categories are used to highlight the difficulties with the concept of structure and our ability to identify or define structures. The analysis is extended to the concept of homology through a discussion of the methodological and philosophical problems of the current concept of homology. It is argued that homology is fundamentally (...) a similarity based concept rather than a phylogenetic concept, and a proposal is put forth to return to a comparative context for homology. It is shown that for both the concepts of structure and homology ana priori assumption of stable underlying patterns (i.e. archetypes) is essential. (shrink)
The concept of homology is the most solid theoretical basis elaborated by the morphological thinking during its history. The enucleation of some general criteria for the interpretation of homology is today a fundamental tool for life sciences, and for restoring their own opening to the question of qualitative innovation that arose so powerfully in the original Darwinian project. The aim of this paper is to verify the possible uses of the concept of compositional homology in order to (...) provide of an adequate understanding of the dynamics of creative thinking. (shrink)
Neural reuse theories suggest that, in the course of evolution, a brain structure may acquire or lose a number of cognitive uses while maintaining its cognitive workings (or low-level operations) fixed. This, in turn, suggests that homologous structures may have very different cognitive uses, while sharing the same workings. And this, essentially, is homology thinking applied to brain function.
Many of the current comparisons of taxic phylogenetic and biological homology in the context of morphology focus on what are seen as categorical distinctions between the two concepts. The first, it is claimed, identifies historical patterns of conservation and variation relating taxa; the second provides a causal framework for the explanation of this conservation and variation. This leads to the conclusion that the two need not be placed in conflict and are in fact compatible, having non-competing epistemic purposes or (...) mapping the same extensions in the form of monophyletic groupings. This article argues that moves in this direction miss the essential disagreement between these concepts as they have been developed in the context of the debate concerning the best concept for evolutionary investigation. We should rather see these concepts employing a common fundamental methodological approach to homology, but disagreeing about how to apply the methodology effectively. Both concepts employ class reasoning, which pursues homologies as units of generalization—more precisely, as sources of reliable and relevant group-bound information in the form of shared underlying causes. The dispute can be better understood by two poles that structure such reasoning: the need for a reliable basis for projections about the causal history of shared structures, and the desire to identify homologous characters with more informative and specific causal information relevant to generalizing about evolutionary processes. Judgments in favor of one or the other in turn have affected the scope or extension of these competing homology concepts. (shrink)
The repair of chromosomal double‐strand breaks (DSBs) by homologous recombination is essential to maintain genome integrity. The key step in DSB repair is the RecA/Rad51‐mediated process to match sequences at the broken end to homologous donor sequences that can be used as a template to repair the lesion. Here, in reviewing research about DSB repair, I consider the many factors that appear to play important roles in the successful search for homology by several homologous recombination mechanisms.
The aim of this article is to detail some reservations against the beliefs, claims, or presuppositions that current essentialist natural kind concepts (including homeostatic property cluster kinds) model grouping practices in the life sciences accurately and generally. Such concepts fit reasoning into particular preconceived epistemic and semantic patterns. The ability of these patterns to fit scientific practice is often argued in support of homeostatic property cluster accounts, yet there are reasons to think that in the life sciences kind concepts exhibit (...) a diversity of grouping practices that are flattened out by conceptualizing them as natural kinds. Instead this article argues that the process of understanding grouping practices needs to start from a more neutral position independent of any ontological account. Following Love (Acta Biotheor 57:51–75, 2009) this paper suggests that typical natural kind concepts should be broached in the first place as grouping strategies that use a variety of semantic and epistemic tactics to apply group-bound information to tasks of explanation and understanding. (shrink)
Scientists exhibit different styles in their reasoning about the natural world (e.g., experimental, historical, or statistical). These styles have been characterized, categorized, and combined in many ways throughout the history of science.
The ‘byproduct account’ of female orgasm, a subject of renewed debate since Lloyd (The case of the female orgasm, Harvard University Press, Cambridge, 2005), is universally attributed to Symons (The evolution of human sexuality, Oxford University Press, Oxford, 1979). While this is correct to the extent that he linked it to the adaptive value of male orgasm, I argue that the attribution of the theory as we understand it to Symons is based on a serious and hitherto unrecognised misinterpretation. Symons (...) had a different explanation of why women can orgasm, and beneath this explanation lies an obscure line of argument, including a particularly obscure use of the word ‘homologous’. (shrink)
I defend the view that many biological categories are defined by homology against a series of arguments designed to show that all biological categories are defined, at least in part, by selected function. I show that categories of homology are `abnormality inclusive'—something often alleged to be unique to selected function categories. I show that classifications by selected function are logically dependent on classifications by homology, but not vice-versa. Finally, I reject the view that biologists must use considerations (...) of selected function to abstract away from variation and pathology to form a canonical description of a class of biological systems. (shrink)
“Functional homology” appears regularly in different areas of biological research and yet it is apparently a contradiction in terms—homology concerns identity of structure regardless of form and function. I argue that despite this conceptual tension there is a legitimate conception of ‘homology of function’, which can be recovered by utilizing a distinction from pre-Darwinian physiology (use versus activity) to identify an appropriate meaning of ‘function’. This account is directly applicable to molecular developmental biology and shares a connection (...) to the theme of hierarchy in homology. I situate ‘homology of function’ within existing definitions and criteria for structural assessments of homology, and introduce a criterion of ‘organization’ for judging function homologues, which focuses on hierarchically interconnected interdependencies (similar to relative position and connection for skeletal elements in structural homology). This analysis of biological concepts has at least three broad philosophical consequences: (1) it provides the grounds for the study of behavior and psychological categories as homologues; (2) it demonstrates that philosophers who take selected effect function as primary effectively ignore large portions of comparative, structural, and experimental research, thereby misconstruing biological reasoning and knowledge; and, (3) it underwrites causal generalizations, which illuminates inferences made from model organisms in experimental biology. (shrink)
This paper explores an important type of biological explanation called ‘homology thinking.’ Homology thinking explains the properties of a homologue by citing the history of a homologue. Homology thinking is significant in several ways. First, it offers more detailed explanations of biological phenomena than corresponding analogy explanations. Second, it provides an important explanation of character similarity and difference. Third, homology thinking offers a promising account of multiple realizability in biology.
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)
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)
The present paper analyzes the use and understanding of the homology concept across different biological disciplines. It is argued that in its history, the homology concept underwent a sort of adaptive radiation. Once it migrated from comparative anatomy into new biological fields, the homology concept changed in accordance with the theoretical aims and interests of these disciplines. The paper gives a case study of the theoretical role that homology plays in comparative and evolutionary biology, in molecular (...) biology, and in evolutionary developmental biology. It is shown that the concept or variant of homology preferred by a particular biological field is used to bring about items of biological knowledge that are characteristic for this field. A particular branch of biology uses its homology concept to pursue its specific theoretical goals. (shrink)
In the last 10 years, several authors including Griffiths and Matthen have employed classificatory principles from biology to argue for a radical revision in the way that we individuate psychological traits. Arguing that the fundamental basis for classification of traits in biology is that of ‘homology’ (similarity due to common descent) rather than ‘analogy’, or ‘shared function’, and that psychological traits are a special case of biological traits, they maintain that psychological categories should be individuated primarily by relations of (...)homology rather than in terms of shared function. This poses a direct challenge to the dominant philosophical view of how to define psychological categories, viz., ‘functionalism’. Although the implications of this position extend to all psychological traits, the debate has centered around ‘emotion’ as an example of a psychological category ripe for reinterpretation within this new framework of classification. I address arguments by Griffiths that emotions should be divided into at least two distinct classes, basic emotions and higher cognitive emotions, and that these two classes require radically different theories to explain them. Griffiths argues that while basic emotions in humans are homologous to the corresponding states in other animals, higher cognitive emotions are dependent on mental capacities unique to humans, and are therefore not homologous to basic emotions. Using the example of shame, I argue that (a) many emotions that are commonly classified as being higher cognitive emotions actually correspond to certain basic emotions, and that (b) the “higher cognitive forms” of these emotions are best seen as being homologous to their basic forms. (shrink)
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 specialization of visual function within biological function is reason for introducing “homology thinking” into explanations of the visual system. It is argued that such specialization arises when organisms evolve by differentiation from their predecessors. Thus, it is essentially historical, and visual function should be regarded as a lineage property. The colour vision of birds and mammals do not function the same way as one another, on this account, because each is an adaptation to special needs of the visual (...) functions of predecessors—very different kinds of predecessors in each case. Thus, history underlies function. We also see how homology thinking figures in the hierarchical classification of visual systems, and how it supports the explanation of visual function by functional role analysis. (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)
There is long-standing conflict between genealogical and developmental accounts of homology. This paper provides a general framework that shows that these accounts are compatible and clarifies precisely how they are related. According to this framework, understanding homology requires both an abstract genealogical account that unifies the application of the term to all types of characters used in phylogenetic systematics and locally enriched accounts that apply only to specific types of characters. The genealogical account serves this unifying role by (...) relying on abstract notions of ‘descent’ and ‘character’. As a result, it takes for granted the existence of such characters. This requires theoretical justification that is provided by enriched accounts, which incorporate the details by which characters are inherited. These enriched accounts apply to limited domains, providing the needed theoretical justification for recognizing characters within that domain. Though connected to the genealogical account of homology in this way, enriched accounts include phenomena that fall outside the scope of the genealogical account. They therefore overlap, but are not nested within, the genealogical account. Developmental accounts of homology are to be understood as enriched accounts of body part homology. Once they are seen in this light, the conflict with the genealogical account vanishes. It is only by understanding the fine conceptual structure undergirding the many uses of the term ‘homology’ that we can understand how these uses hang together. (shrink)
The evolutionary embryologist Gavin Rylands de Beer can be viewed as one of the forerunners of modern evolutionary developmental biology in that he posed crucial questions and proposed relevant answers about the causal relationship between ontogeny and phylogeny. In his developmental approach to the phylogenetic phenomenon of homology, he emphasized that homology of morphological structures is to be identified neither with the sameness of the underlying developmental processes nor with the homology of the genes that are in (...) involved in the development of the structures. De Beer’s work on developmental evolution focused on the notion of heterochrony, arguing that paedomorphosis increases morphological evolvability and is thereby an important mode of evolution that accounts for the origin of many taxa, including higher taxa. (shrink)
In this article, I examine the issue of the alleged circularity in the determination of homologies within cladistic analysis. More specifically, I focus on the claims made by the proponents of the dynamic homology approach, regarding the distinction between primary and secondary homology. This distinction is sometimes invoked to dissolve the circularity issue, by upholding that characters in a cladistic data matrix have to be only primarily homologous, and thus can be determined independently of phylogenetic hypotheses, by using (...) the classical Owenian criteria or via multiple sequence alignment. However, since in the dynamic approach, sequence data can be analyzed without being pre-aligned, proponents have claimed that the distinction between primary and secondary homology has no place within cladistics. I will argue that this is not the case, since cladistic practice within the dynamic framework does presuppose primary homology statements at a higher level. (shrink)
The Mind-Brain Identity Theory lived a short life as a respectable philosophical position in the late 1950s, until Hilary Putnam developed his famous argument on the multiple realizability of mental states. The argument was, and still is, taken as the definitive demonstration of the falsity of Identity Theory and the foundation on which contemporary functionalist computational cognitive science was to be grounded. In this paper, in the wake of some contemporary philosophers, we reopen the case for Identity Theory and offer (...) a solution to the problem of multiple realizabilty. The solution is based on the necessity, at the time of establishing identity relations, of appealing to the notions of “homology” and “analogy” developed in the nineteenth century by Richard Owen. We also suggest that these notions are useful in order to correct certain shortcomings of some recent attempts at rebutting the Multiple Realizability argument. (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)
In his account of epistēmē, the highest level of understanding attainable in philosophical inquiry, Aristotle articulates standards for the ideal explanations that confer this level of understanding. I argue that Aristotle's key standard for epistēmē is of central importance for the biological homology concept. The explanatory shortcoming that results from violating this standard has been vaguely articulated in recent literature on homology; Aristotle's account offers a more neutral and precise formulation of the shortcoming and its antidote. Further, the (...) risk for this shortcoming has heightened with recent accounts of homology grounded in genetics, increasing the contemporary relevance of Aristotelian epistēmē. (shrink)
Homology is among the most important comparative concepts in biology. Today, the evolutionary reinterpretation of homology is usually conceived of as the most important event in the development of the concept. This paradigmatic turning point, however important for the historical explanation of life, is not of crucial importance for the development of the concept of homology itself. In the broadest sense, homology can be understood as sameness in reference to the universal guarantor so that in this (...) sense the different concepts of homology show a certain kind of “metahomology”. This holds in the old morphological conception, as well as in the evolutionary usage of homology. Depending on what is (or was) taken as a guarantor, different types of homology may be distinguished (as idealistic, historical, developmental etc.). This study represents a historical overview of the development of the homology concept followed by some clues on how to navigate the pluralistic terminology of modern approaches to homology. (shrink)
The present paper gives a philosophical analysis of the conceptual variation in the homology concept. It is argued that different homology concepts are used in evolutionary and comparative biology, in evolutionary developmental biology, and in molecular biology. The study uses conceptual role semantics, focusing on the inferences and explanations supported by concepts, as a heuristic tool to explain conceptual change. The differences between homology concepts are due to the fact that these concepts play different theoretical roles for (...) different biological fields. The specific theoretical needs and explanatory interests of different research approaches lead to different homology concepts. (shrink)
Comprehending the origin of marine invertebrate larvae remains a key domain of research for evolutionary biologists, including the repeated origin of direct developmental modes in echinoids. In order to address the latter question, we surveyed existing evidence on relationships of homology between the ectoderm territories of two closely related sea urchin species in the genus Heliocidaris that differ in their developmental mode. Additionally, we explored a recently articulated idea about homology called ‘organizational homology’ (Muller 2003. In: Muller (...) GB, Newman SA, editors. Origination of organismal form: beyond the gene in developmental and evolutionary biology. Cambridge, MA: A Bradford Book, The MIT Press. p 51–69. ) in the context of this specific empirical case study. Applying the perspective of organizational homology to our experimental system of congeneric echinoids has led us to a new hypothesis concerning the ectoderm evolution in these species. The extravestibular ectoderm of the direct developer Heliocidaris erythrogramma is a novel developmental territory that arose as a fusion of the oral and aboral ectoderm territories found in indirect developing echinoids such as Heliocidaris tuberculata. This hypothesis instantiates a theoretical principle concerning the origin of developmental modules, ‘integration’, which has been neglected because the opposite theoretical principle, ‘parcellation’, is more readily observable in events such as gene duplication and divergence (Wagner 1996. Am Zool 36:36–43). J. Exp. Zool. (Mol. Dev. Evol.) 306B:18– 34, 2006. (shrink)
American biologists in the late nineteenth century pioneered the descriptive-comparative study of all cell divisions from zygote to gastrulation -- the cell lineage. Data from cell lineages were crucial to evolutionary and developmental questions of the day. One of the main questions was the ultimate causation of developmental patterns -- historical or mechanical. E. B. Wilson's groundbreaking lineage work on the polychaete worm Nereis in 1892 set the stage for (1) an attack on Haeckel's phylogenetic-historical notion of recapitulation and (2) (...) support for mechanistic explanations of cleavage patterns. As more lineage work -- especially Lillie's work on "Unio" and Conklin's on "Crepidula" -- became available in the mid-late 1890s, mechanism was tempered with more evolutionary, homology-based views. However, as I show by focusing on three major issues -- homology, body plans and life history -- these views were primarily based on the precocious segregation and prospective significance -- what the cell became not what it was. Even on issues like adaptation, most lineagists argued teleologically from the adult backward. Most cell lineage workers, by 1900, were to varying degrees mechanist/experimentalist and recapitulationist simultaneously. The exception was E. G. Conklin, whose views were more akin to a Darwinian evolutionist than either mechanist or recapitulationist. Lineage work eventually declined and by 1907 published accounts of new lineages had basically stopped. I argue that established workers and younger researchers stopped wanting to take on cell lineage projects because the general patterns were the same for all the spiralians while the specifics showed too much variation. It was hard to theoretically encompass or analyze the minutiae of variation in a recapitulationist or mechanist framework. The only established worker who continued to do comparative lineage studies was E. G. Conklin, perhaps because the variation could best be accommodated by Darwinian evolution. (shrink)
This article reviews the recent reissuing of Richard Owen’s On the Nature of Limbs and its three novel, introductory essays. These essays make Owen’s 1849 text very accessible by discussing the historical context of his work and explaining how Owen’s ideas relate to his larger intellectual framework. In addition to the ways in which the essays point to Owen’s relevance for contemporary biology, I discuss how Owen’s unity of type theory and his homology claims about fins and limbs compare (...) with modern views. While the phenomena studied by Owen are nowadays of major interest to evolutionary developmental biology, research in evo-devo has largely shifted from homology (which was Owen’s concern) towards evolutionary novelty, e.g., accounting for fins as a novelty. Still, I argue that questions about homology are important and raise challenges even for explanations of novelty. (shrink)
Homology is a central concept of comparative and evolutionary biology, referring to the presence of the same bodily parts (e.g., morphological structures) in different species. The existence of homologies is explained by common ancestry, and according to modern definitions of homology, two structures in different species are homologous if they are derived from the same structure in the common ancestor. Homology has traditionally been contrasted with analogy, the presence of similar traits in different species not necessarily due (...) to common ancestry but due to a similar function or convergent evolution resulting from similar selective pressure in different species. (A more recent contrastive notion is homoplasy, the presence of similar traits in different species without common ancestry, i.e., as an instance of parallel evolution.) This sounds straightforward, but in fact the homology concept has a rich history and currently is the subject of extensive theoretical reflection, resulting in different contemporary approaches to homology. (shrink)
Recent philosophical work on biological homology has generally treated its conceptual fragmentation as a problem to be solved by new accounts that either unify disparate approaches to homology or specify sharp constraints on its meaning. I show that several proposed solutions either misunderstand or ignore central features of comparative biological research, despite attempts to capture scientific practice. I conclude that the problem is incorrectly framed and that disagreements about homology may be epistemically fruitful. Empirically tractable debates are (...) more likely to occur among biologists who share theoretical perspectives on homology. Philosophers should consider homology not merely as a generator of inductive generalizations but also as a scaffold for meaningful empirical comparisons. (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)
While it is generally agreed that the concept of homology refers to individuated traits that have been inherited from common ancestry, we still lack an adequate account of trait individuation or inheritance. Here I propose that we utilize a counterfactual criterion of causation to link each trait with a developmental-causal (DC) gene. A DC gene is made up of the genetic information (which might or might not be physically contiguous in the genome) that is needed for the production of (...) the organismic attributes that comprise the trait. I argue that individuated traits—phenes—correspond to organismic features that are caused by DC genes. Using such an approach, we can define a DC map, which shows the relations between each pair of phenes and provides a succinct summary of genotype-phenotype relationships and phenotypic complexity. Phenes in parents and offspring are judged to be homologous if their DC genes are composed of orthologous genetic factors. When comparing more distantly related organisms, traits are homologous when linked by a chain of parent-offspring homologs along the path of ancestry that links the two organisms. There are three possible ways to deal with the potential for multiple equivalent DC genes: maximal, minimal, and consensus homology. Whereas maximal homology has limited utility, the other two approaches have value and can help to guide research at the intersection of evolution and development. (shrink)
Current issues concerning the nature of ancestry and homology are discussed with reference to the evolutionary origin of the tetrapod limb. Homologies are argued to be complex conjectural inferences dependant upon a pre-existing phylogenetic analysisand a theoretical model of the evolutionary development of ontogenetic information. Ancestral conditions are inferred primarily from character (synapomorphy/homology) distributions within phylogeny, because of the deficiencies of palaeontological data. Recent analyses of tetrapod limb ontogeny, and the diverse, earliest morphologies known from the fossil record, (...) are inconsistent with typological concepts such as fixed ancestral patterns or bauplans, emphasising the incompatibility of these with evolutionary continuity. The evolutionary origin of the tetrapod limb is also examined in the light of its recent discussion in developmental genetics. While this field promises to reveal more of the fundamental ontogenetic content of homology (identity), at present it is concerned mostly with the abstraction of a new set of types, rather than investigating diversity and change. (shrink)
The meaning of the word homology has changed. From being a comparative concept in pre-Darwinian times, it became a historical concept, strictly signifying a common evolutionary origin for either anatomical structures or genes. This historical understanding of homology is not useful in classification; therefore I propose a return to its pre-Darwinian meaning.
Chris Arthur‟s body of work counts as a very important and original contribution to systematic dialectics, and I have profited immensely from his writings over the years. However we disagree on a number of points. Some have to do with the relatively secondary question of the intellectual relationship between Hegel and Marx; others involve more substantive matters. In his reply to my review of Joseph McCarney‟s Hegel on History Arthur distinguishes three different versions of the thesis that there is a (...) “homology” between the logic of capital (in a Marxian understanding of it) and Hegel‟s “idea.” I shall comment briefly on each and then conclude with a general remark. (shrink)
Most cognitive scientists nowadays tend to think that at least some of the mind’s capacities are the product of biological evolution, yet important conceptual problems remain for all scientists in order to be able to speak coherently of mental or cognitive systems as having evolved naturally. Two of these important problems concern the articulation of adequate, interesting, and empirically useful concepts of homology and variation as applied to cognitive systems. However, systems in cognitive science are usually understood as functional (...) systems of some sort. Thus, to be able to talk about functional systems being homologous requires having a solid, adequate, and empirically articulated concept of functional homology—and the same is true about functional variation. Here I construct an original concept of functional homology that, in my view, adequately systematizes a number of actual uses of the word “functional homology” in a variety of biological disciplines and in ethology. I also propose a number of criteria for the empirical application of the concept that are analogous to the criteria that are currently used in comparative biology, ethology, and molecular developmental genetics. Then I construct a concept of functional variation on the basis of this concept of homology. (shrink)
This work defines homology groups for proof-structures in multiplicative linear logic (see [Gir1], [Gir2], [Dan]). We will show that these groups characterize proof-nets among arbitrary proof-structures, thus obtaining a new correctness criterion and of course a new polynomial algorithm for testing correctness. This homology also bears information on sequentialization. An unexpected geometrical interpretation of the linear connectives is given in the last section. This paper exclusively focuses onabstract proof-structures, i.e. paired-graphs. The relation with actual proofs is investigated in (...) [Gir1], [Gir2], [Dan], [Ret] and [Tro]. (shrink)
Roffe et al. develop a rather creative line of response to Pearson’s :475–492, 2010) critique of pattern cladisma response centering on a structuralist approach to the homology concept. In this brief reply I attempt to demonstrate, however, that Roffe, and Ginnobili, and Blanco subtly mis-characterize the target of Pearson’s critique. The consequence of this mischaracterization is that even though the structuralist framework may help make sense of pattern cladism, it does not undermine Pearson’s critique of it.
This article reviews the recent reissuing of Richard Owen’s On the Nature of Limbs and its three novel, introductory essays. These essays make Owen’s 1849 text very accessible by discussing the historical context of his work and explaining how Owen’s ideas relate to his larger intellectual framework. In addition to the ways in which the essays point to Owen’s relevance for contemporary biology, I discuss how Owen’s unity of type theory and his homology claims about ﬁns and limbs compare (...) with modern views. While the phenomena studied by Owen are nowadays of major interest to evolutionary developmental biology, research in evo-devo has largely shifted from homology (which was Owen’s concern) towards evolutionary novelty, e.g., accounting for ﬁns as a novelty. Still, I argue that questions about homology are important and raise challenges even for explanations of novelty. (shrink)
While the homology concept has taken on importance in thinking about the nature of psychological kinds, no one has shown how comparative psychological and behavioral evidence can distinguish between competing homology claims. I adapt the operational criteria of homology to accomplish this. I consider two competing homology claims that compare human anger with putative aggression systems of nonhuman animals, and demonstrate the effectiveness of these criteria in adjudicating between these claims.
Homology continues to be a concept of central importance in the study of phylogenetic relations, but its relation to ontogenetic processes remains problematical. A definition of homology in terms of equivalent morphogenetic processes is defined and applied to the comparative study of tetrapod limbs. This allows for a consistent treatment of relations of similarity and difference of appendage structure in vertebrates, and the distinction between fishes fins and tetrapod limbs in terms of the concept of equivalence is described. (...) The role of genes can also be clarified in this context, in particular the influence of the Hox 4 complex in determining digit character and the homeotic transformations that arise from changes in their expression patterns. It is argued that these observations are not compatible with the notion of homology between individual digits (I, II, III, etc.) across the tetrapods, and that homology cannot be consistently identified with gene action. The relations between homology and the properties of the morphogenetic limb field are discussed. (shrink)
Neural reuse theories should interest developmental psychologists because these theories can potentially illuminate the developmental relations among psychological characteristics observed across the lifespan. Characteristics that develop by exploiting pre-existing neural circuits can be thought of as developmental homologues. And, understood in this way, the homology concept that has proven valuable for evolutionary biologists can be used productively to study psychological/behavioral development.