This paper is about a general methodology for pattern transformation. Patterns are network representations of the relations among structures and functions within an organism. Transformation refers to any realistic or abstract transformation relevant to biology, e.g. ontogeny, evolution and phenotypic clines. The main aim of the paper is a methodology for analyzing the range of effects on a pattern due to perturbing one or more of its structures and/or functions (transformation morphology). Concepts relevant to such an analysis of pattern transformation (...) are reviewed and several new ones introduced: pattern unit; direct and indirect functional demands; compatibility and trade-off; integrating, adding and decoupling; functional effectiveness; spatial, profile and other architectonic constraints; domains of structure-function relations; goal and process adaptability; multiple pathways. The paper is written from the the perspective of architectonic morphology, viz. functional morphology focusing on the relation between anatomical coherence and the compatibility of functions. The advantages and disadvantages of inductive and deductive approaches are discussed. (shrink)

Common ancestry is one of the pillars of Darwin’s theory of evolution. Today, the Tree of Life, which represents how all life is genealogically related, is often thought of as an essential component in the foundations of biological systematics and so therefore of evolutionary theory – and perhaps all of biology itself. It is an iconic representation in biology and even penetrates into popular culture.

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.

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)

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 theory of concepts advanced in the present discussion aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. To this end, I suggest that each scientific concept consists of three components of content: 1) the concept.

The paper discusses reference determination from the point of view of conceptual change in science. The first part of the discussion uses the homology concept, a natural kind term from biology, as an example. It is argued that the causal theory of reference gives an incomplete account of reference determination even in the case of natural kind terms. Moreover, even if descriptions of the referent are taken into account, this does not yield a satisfactory account of reference in the case (...) of the homology concept. I suggest that in addition to the factors that standard theories of reference invoke the scientific use of concepts and the epistemic interests pursued with concepts are important factors in determining the reference of scientific concepts. In the second part, I argue for a moderate holism about reference determination according to which the set of conditions that determine the reference of a concept is relatively open and different conditions may be reference fixing depending on the context in which this concept is used. It is also suggested that which features are reference determining in a particular case may depend on the philosophical interests that underlie reference ascription and the study of conceptual change. (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)

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)

Despite the traditional focus on metaphysical issues in discussions of natural kinds in biology, epistemological considerations are at least as important. By revisiting the debate as to whether taxa are kinds or individuals, I argue that both accounts are metaphysically compatible, but that one or the other approach can be pragmatically preferable depending on the epistemic context. Recent objections against construing species as homeostatic property cluster kinds are also addressed. The second part of the paper broadens the perspective by considering (...) homologues as another example of natural kinds, comparing them with analogues as functionally defined kinds. Given that there are various types of natural kinds, I discuss the different theoretical purposes served by diverse kind concepts, suggesting that there is no clear-cut distinction between natural kinds and other kinds, such as functional kinds. Rather than attempting to offer a unique metaphysical account of ‘natural’ kind, a more fruitful approach consists in the epistemological study of how different natural kind concepts are employed in scientific reasoning. (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)

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)

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)

This paper uses an example from biology, the homology concept, to argue that current versions of the causal theory of reference give an incomplete account of reference determination. It is suggested that in addition to samples and stereotypical properties, the scientific use of concepts and the epistemic interests pursued with concepts are important factors in determining the reference of natural kind terms.

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)

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 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)

Editors' introduction to the special issue on homology (Biology and Philosophy Vol. 22, Issue 5, 2007).

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)

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 importance of homology in biology is widely acknowledged. Wake (1994: 284) writes that “[h]omology is the central concept for all of biology.” Paterson (1987: 18) observes that “all useful comparisons in biology depend on the relation of homology.” Whenever we ask if two characters are the same character we are asking if they are homologous, regardless of whether those characters are genetic, morphological, anatomical, or behavioral. Yet like many central concepts in biology, our understanding of homology is plagued by (...) unresolved questions. For example, how should we define ‘homology’? There is no agreed upon definition in the literature. Or, how do we explain the fact that two homologous characters can be caused by non-homologous developmental factors (Hall 2007)? Or more fundamentally, what causes new homologues (Wagner 2001)? Then there are questions about the role of homologies in evolution. Homologues are quasi-independent, heritable units that selection acts on; they are units of evolvability (Laubichler 2000; Brigandt 2007). The idea of homologues as units of evolvability cries out for analysis. These are all pressing questions, but this paper will focus on just two of them. One is the possibility of a unified theoretical account of homology. The other is how homologues at one hierarchical level are caused by non-homologues at a lower level. As we shall see, recent work offers an emerging approach to homology that integrates phylogeny and development (Laubichler 2000). Such an approach provides the basis for a unified theoretical account of homology, and it sheds light on the hierarchical nature of homology. (shrink)

Biology and Philosophy, forthcoming 2007.

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)

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)

Many philosophers believe that 1) most uses of functional language in biology make implicit reference to natural selection and 2) the fundamental way in which biologists identify parts and processes in organisms is by their selected function(s). Both these claims are mistaken. Much functional language in biology refers to actual causal roles, and if this were not so, biology would be impossible. The extensive biological literature on the ‘character concept’ focuses on another principle of biological identity, namely homology. I outline (...) some of this work and use it to refute philosophical arguments for the importance and ubiquity of classification by adaptive function. (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)

Homology concepts are fundamental to the study of biological similarity. Monistic attempts to articulate an overarching homology concept, applicable to all areas of biology, have yet to succeed. Biology is fundamentally pluralistic, and multiple homology concepts, applicable at different levels of the biological hierarchy, allow a more thorough investigation of the nature of biological similarity. Articulating the definition and causes associated with any homology concept ensures that the pluralistic approach advocated here is neither relativistic nor defeatist, but generative of fruitful (...) biological research. (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)

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)

“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)

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)

Argues that biological organs, including mental capacities, should be identified by homology (not function).

I will argue that we cannot understand imitation unless we know more about its function. By comparing the two examples presented by Byrne & Russon I show how the imitative behaviour of orangutans can be interpreted as a homologue of human imitation during play. In contrast, the lack of data leave the role of imitation in gorillas doubtful.

I attempt to raise questions regarding elements of systematics—primarily in the realm of phylogenetic reconstruction—in order to provoke discussion on the current state of affairs in this discipline, and also evolutionary biology in general: e.g., conceptions of homology and homoplasy, hypothesis testing, the nature of and objections to Hennigian “phylogenetic systematics”, and the schism between (neo)Darwinian descendants of the “modern evolutionary synthesis” and their supposed antagonists, cladists and punctuationalists.

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)

The dangers of character reification for cladistic inference are explored. The identification and analysis of characters always involves theory-laden abstraction—there is no theory-free “view from nowhere.” Given theory-ladenness, and given a real world with actual objects and processes, how can we separate robustly real biological characters from uncritically reified characters? One way to avoid reification is through the employment of objectivity criteria that give us good methods for identifying robust primary homology statements. I identify six such criteria and explore each (...) with examples. Ultimately, it is important to minimize character reification, because poor character analysis leads to dismal cladograms, even when proper phylogenetic analysis is employed. Given the deep and systemic problems associated with character reification, it is ironic that philosophers have focused almost entirely on phylogenetic analysis and neglected character analysis. (shrink)

An accessible survey, this collection will enlighten historians of science, their students, practicing scientists, and anyone interested in the relationship ...

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 target article contains a number of distinct but interrelated claims about the cognitive nature of folk biology based in part on cross-cultural work with urbanized Americans and forest-dwelling Maya Indians. Folk biology consists universally of a ranked taxonomy centered on essence-based generic species. This taxonomy is domain-specific, perhaps an innately determined evolutionary adaptation. Folk biology also plays a special role in cultural evolution in general, and in the development of Western biological science in particular. Even in our culture, however, (...) it retains an autonomy from other domains of thought and from science. These claims are questioned and clarified. (shrink)

Sciences able to identify appropriate analytical units for their domain, their natural kinds, have tended to be more progressive. In the biological sciences, evolutionary natural kinds are adaptations that can be identified by their common history of selection for some function. Human brains are the product of an evolutionary history of selection for component systems which produced behaviours that gave adaptive advantage to their hosts. These structures, behaviour production systems, are the natural kinds that psychology seeks. We argue these can (...) be identified deductively by classing behaviour first according to its level of behavioural control. Early animals in our lineage used only reactive production, Vertebrates evolved motivation, and later Primates developed executive control. Behaviour can also be classified by the type of evolutionary benefit it bestows: it can deliver either immediate benefits (food, gametes), improvements in the individual’s position with respect to the world (resource access, social status), or improvements in the ability to secure future benefits (knowledge, skill). Combining history and function implies the existence of seven types of behaviour production systems in human brains responsible for reflexive, instinctual, exploratory, driven, emotional, playful and planned behaviour. Discovering scientifically valid categories of behaviour can provide a fundamental taxonomy and common language for understanding, predicting and changing behaviour, and a way of discovering the organs in the brain––its natural kinds––that are responsible for behaviour. (shrink)

Abstract Different concepts define species at the pattern-level grouping of organisms into discrete clusters, the level of the processes operating within and between populations leading to the formation and maintenance of these clusters, or the level of the inner-organismic genetic and molecular mechanisms that contribute to species cohesion or promote speciation. I argue that, unlike single-level approaches, a multi-level framework takes into account the complex sequences of cause-effect reinforcements leading to the formation and maintenance of various patterns, and allows for (...) revisions and refinements of pattern-based characterizations in light of the gradual elucidation of the causes and mechanisms contributing to pattern formation and maintenance. Content Type Journal Article Category Regular Article Pages 1-17 DOI 10.1007/s10441-011-9143-z Authors Tudor M. Baetu, Department of Philosophy, University of Maryland, 1125D Skinner Building, College Park, MD 20742, USA Journal Acta Biotheoretica Online ISSN 1572-8358 Print ISSN 0001-5342. (shrink)

Despite the traditional focus on metaphysical issues in discussions of natural kinds in biology, epistemological considerations are at least as important. By revisiting the debate as to whether taxa are kinds or individuals, I argue that both accounts are metaphysically compatible, but that one or the other approach can be pragmatically preferable depending on the epistemic context. Recent objections against construing species as homeostatic property cluster kinds are also addressed. The second part of the paper broadens the perspective by considering (...) homologues as another example of natural kinds, comparing them with analogues as functionally defined kinds. Given that there are various types of natural kinds, I discuss the different theoretical purposes served by diverse kind concepts, suggesting that there is no clear-cut distinction between natural kinds and other kinds, such as functional kinds. Rather than attempting to offer a unique metaphysical account of ‘natural’ kind, a more fruitful approach consists in the epistemological study of how different natural kind concepts are employed in scientific reasoning. (shrink)

To cite this Article: Ereshefsky, Marc , 'Foundational Issues Concerning Taxa and Taxon Names', Systematic Biology, 56:2, 295 - 301 To link to this article: DOI: 10.1080/10635150701317401 URL: http://dx.doi.org/10.1080/10635150701317401..

Many writers claim that human kinds are significantly different from biological and natural kinds. Some suggest that humans kinds are unique because social structures are essential for the etiology of human kinds. Others argue that human cultural evolution is decidedly different from other forms of evolution. In this paper I suggest that the gulf between humans and our biological relatives is not as wide as some argue. There is a taxonomic difference between human and nonhuman organisms, but such factors as (...) social structure and cultural evolution do not distinguish us from many other organisms. (shrink)

Most biologists use the Linnaean system for constructing classifications of the organic world. The Linnaean system, however, has lost its theoretical basis due to the shift in biology from creationist and essentialist tenets to evolutionary theory. As a result, the Linnaean system is both cumbersome and ontologically vacuous. This paper illustrates the problems facing the Linnaean system, and ends with a brief introduction to an alternative approach to biological classification.

Homeostatic Property Cluster (HPC) theory suggests that species and other biological taxa consist of organisms that share certain similarities. HPC theory acknowledges the existence of Darwinian variation within biological taxa. The claim is that “homeostatic mechanisms” acting on the members of such taxa nonetheless ensure a significant cluster of similarities. The HPC theorist’s focus on individual similarities is inadequate to account for stable polymorphism within taxa, and fails properly to capture their historical nature. A better approach is to treat distributions (...) of traits in species populations as irreducible facts, explained in terms of selection pressures, genealogy, and other evolutionary factors. We call this view Population Structure Theory (PST). PST accommodates the view, implicit in biological systematics, that species are identified by reference to particular historical populations. (shrink)

It is commonly held that objects in the world form natural kinds. Rabbits form a natural kind and so do all pieces of gold. The traditional account of natural kinds asserts that the members of a kind share a common essence. The essence of gold, for example, is its unique atomic structure. That structure occurs in all and only pieces of gold, and it is a property that all pieces of gold must have.

In this paper I explore Aristotle’s views on natural kinds and the compatibility of pluralism and realism, a topic that has generated considerable interest among contemporary philosophers. I argue that, when it came to zoology, Aristotle denied that there is only one way of organizing the diversity of the living world into natural kinds that will yield a single, unified system of classification. Instead, living things can be grouped and regrouped into various cross-cutting kinds on the basis of objective similarities (...) and differences in ways that subserve the explanatory context. Since the explanatory aims of zoology are diverse and variegated, the kinds it recognizes must be equally diverse and variegated. At the same time, there are certain constraints on which kinds can be selected. And those constraints derive more from the causal structure of the world than from the proclivities of the classifier (hence the realism). This distinguishes Aristotle’s version of pluralistic realism from those contemporary versions (like Dupré’s “promiscuous realism”) that treat all or most classifications of a given domain as equally legitimate and not just a sub-set of kinds recognized by the science that studies it. By contrast, Aristotle privileges scientifically important kinds on the basis of their role in causal investigations. On this picture natural kinds are those kinds with the sort of causal structure that allows them to enter into scientific explanations. In the final section I argue that Aristotle’s zoology should remain of interest to philosophers and biologists alike insofar as it combines a pluralistic form of realism with a rank-free approach to classification. (shrink)

This is the final draft of a paper written for a collection in honour of Ruth Millikan. Millikan has argued that biological taxa are historical kinds. Her argument is puzzling: it shows only that biological taxa are relational. And this conclusion has been challenged by Michael Devitt. Here, I argue that stable polymorphisms in kinds require underlying mechanisms that keep sub-groups separate. (This answers a criticism of my earlier views by Wilson, Barker, and Brigandt.) I argue that this condition brings (...) in a kind of historicity that Millikan wants, but that a further kind of historicity is dubious. (shrink)

Argues that biological organs, including mental capacities, should be identified by homology (not function).

Different chemical species are often cited as paradigm examples of structurally delimited natural kinds. While classificatory monism may thus seem plausible for simple molecules, it looks less attractive for complex biological macromolecules. I focus on the case of proteins that are most plausibly individuated by their functions. Is there a single, objective count of proteins? I argue that the vagaries of function individuation infect protein classification. We should be pluralists about macromolecular classification.

Many people argue that history makes a special difference to the subjects of biology and psychology, and that history does not make this special difference to other parts of the world. This paper will show that historical properties make no more or less of a difference to biology or psychology than to chemistry, physics, or other sciences. Although historical properties indeed make a certain kind of difference to biology and psychology, this paper will show that historical properties make the same (...) kind of difference to geology, sociology, astronomy, and other sciences. Similarly, many people argue that nonhistorical properties make a special difference to the nonbiological and the nonpsychological world. This paper will show that nonhistorical properties make the same difference to all things in the world when it comes to their causal behavior and that historical properties make the same difference to all things in the world when it comes to their distributions. Although history is special, it is special in the same way to all parts of the world. (shrink)

The vision of natural kinds that is most common in the modern philosophy of biology, particularly with respect to the question whether species and other taxa are natural kinds, is based on a revision of the notion by Mill in A System of Logic. However, there was another conception that Whewell had previously captured well, which taxonomists have always employed, of kinds as being types that need not have necessary and sufficient characters and properties, or essences. These competing views employ (...) different approaches to scientific methodologies: Mill’s class-kinds are not formed by induction but by deduction, while Whewell’s type-kinds are inductive. More recently, phylogenetic kinds (clades, or monophyletic-kinds) are inductively projectible, and escape Mill’s strictures. Mill’s version represents a shift in the notions of kinds from the biological to the physical sciences. (shrink)

Essentialism is widely regarded as a mistaken view of biological kinds, such as species. After recounting why (sections 2-3), we provide a brief survey of the chief responses to the “death of essentialism” in the philosophy of biology (section 4). We then develop one of these responses, the claim that biological kinds are homeostatic property clusters (sections 5-6) illustrating this view with several novel examples (section 7). Although this view was first expressed 20 years ago, and has received recent discussion (...) and critique, it remains underdeveloped and is often misrepresented by its critics (section 8). (shrink)

The dangers of character reification for cladistic inference are explored. The identification and analysis of characters always involves theory-laden abstraction—there is no theory-free “view from nowhere.” Given theory-ladenness, and given a real world with actual objects and processes, how can we separate robustly real biological characters from uncritically reified characters? One way to avoid reification is through the employment of objectivity criteria that give us good methods for identifying robust primary homology statements. I identify six such criteria and explore each (...) with examples. Ultimately, it is important to minimize character reification, because poor character analysis leads to dismal cladograms, even when proper phylogenetic analysis is employed. Given the deep and systemic problems associated with character reification, it is ironic that philosophers have focused almost entirely on phylogenetic analysis and neglected character analysis. (shrink)

This article began as a review of a conference, organized by Gerhard Schlosser, entitled “Modularity in Development and Evolution.” The conference was held at, and sponsored by, the Hanse Wissenschaftskolleg in Delmenhorst, Germany in May, 2000. The article subsequently metamorphosed into a literature and concept review as well as an analysis of the differences in current perspectives on modularity. Consequently, I refer to general aspects of the conference but do not review particular presentations. I divide modules into three kinds: structural, (...) developmental, and physiological. Every module fulfills none, one, or multiple functional roles. Two further orthogonal distinctions are important in this context: module-kinds versus module-variants-of-a-kind and reproducer versus nonreproducer modules. I review criteria for individuation of modules and mechanisms for the phylogenetic origin of modularity. I discuss conceptual and methodological differences between developmental and evolutionary biologists, in particular the difference between integration and competition perspectives on individualization and modular behavior. The variety in views regarding modularity presents challenges that require resolution in order to attain a comprehensive, rather than a piecemeal and fragmentary, evolutionary developmental biology. (shrink)

The concept of an ecological niche (econiche) has been used in a variety of ways, some of which are incompatible with a relational or functional interpretation of the term. This essay seeks to standardize usage by limiting the concept to functional relations between organisms and their surroundings, and to revise the concept to include epistemic relations. For most organisms, epistemics are a vital aspect of their functional relationships to their surroundings and, hence, a major determinant of their econiche. Rejecting the (...) traditional dualism of organism and environment, an econiche is defined as the reciprocal (dual) of a functionally specified class of organisms (FSTU). From this perspective, an econiche necessarily implies a certain type of organism, and a class of functionally similar organisms implies a special econiche.The econiche concept is also discussed in relation to other ecological terms that reflect the distributional patterns of organisms, such as habitat, and the concept of an empty niche is criticized. (shrink)

In response to the arguments of Bill McKibben and of Stephen Vogel that nature is at an end and that the very concept of nature should be discarded, I argue that, far from this being the case, the concept of nature is indispensable. A third sense of 'nature' besides the two distinguished by Vogel, that of the nature of an organism, is brought to attention and shown, through five arguments, to be indispensable for environmental philosophy and ethics, and for ethics (...) in general (veterinary and medical ethics included). But it is no coincidence that the same term is used for all three senses of'nature' in many languages. The indispensability of 'nature' in the third sense is used to suggest the indispensability of 'nature' in the second sense (things unaffected by human activity, a sense needed if we are to understand species whether wild or domesticated, because of their evolutionary history, and if we are to distinguish social systems from natural systems), and also of 'nature' in the first sense (things that are not supernatural, a sense needed if we are to ask metaphysical questions about whether 'nature' in this sense and in the other two might have a creator). (shrink)

The present study discusses the early theoretical development of Konrad Lorenz in the period from 1930 to 1937. In this period Lorenz developed his position on instinct in the first place, and thus his theoretical views were subject to change. Despite this change, the paper points to relatively stable features of Lorenz’s approach, which emerged relatively soon in his scientific career and guided his theoretical development in this and beyond this early phase.

Peculiar to Konrad Lorenz’s view of instinctive behavior is his strong innate-learned dichotomy. He claimed that there are neither ontogenetic nor phylogenetic transitions between instinctive and experience-based behavior components, thus contradicting all former accounts of instinct. The present study discusses how Lorenz came to hold this controversial position by examining the history of Lorenz’s early theoretical development in the crucial period from 1931 to 1937, taking relevant influences into account. Lorenz’s intellectual development is viewed as being guided by four theoretical (...) and practical commitments as to how to study and explain behavior. These four factors, which were part of the general approach of Lorenz but not of other animal psychologists, were crucial in bringing about his specific position on instinctive behavior. (shrink)

Biological research on race has often been seen as motivated by or lending credence to underlying racist attitudes; in part for this reason, recently philosophers and biologists have gone through great pains to essentially deny the existence of biological human races. We argue that human races, in the biological sense of local populations adapted to particular environments, do in fact exist; such races are best understood through the common ecological concept of ecotypes. However, human ecotypic races do not in general (...) correspond with ‘folk’ racial categories, largely because many similar ecotypes have multiple independent origins. Consequently, while human natural races exist, they have little or nothing in common with ‘folk’ races. (shrink)

The project of this chapter is to understand what a phylogenetic tree represents and to discuss some of the implications that this has for the practice of systematics. At least the first part of this task, if not both parts, might appear trivial – or perhaps better suited for a single page in a textbook rather than a scholarly research paper. But this would be a mistake. While the task of interpreting phylogenetic trees is often treated in this trivial way, (...) in fact their interpretation is tied to foundational conceptual questions at the heart of systematics – questions whose answers are hotly disputed. As I will argue, common practices for the interpretation and use of trees are actually in conflict and therefore some must be given up. Here I defend the view that unacceptable principles about species as units of phylogeny must be given up. According to the view that I will develop, all phylogenetic trees depict the history of populations. The branches on trees represent collections of population lineages through time and the splits represent population lineage splits. I will argue for this view by focusing on how we use phylogenetic trees for inferences about the evolutionary past. (shrink)

Abstract Different concepts define species at the pattern-level grouping of organisms into discrete clusters, the level of the processes operating within and between populations leading to the formation and maintenance of these clusters, or the level of the inner-organismic genetic and molecular mechanisms that contribute to species cohesion or promote speciation. I argue that, unlike single-level approaches, a multi-level framework takes into account the complex sequences of cause-effect reinforcements leading to the formation and maintenance of various patterns, and allows for (...) revisions and refinements of pattern-based characterizations in light of the gradual elucidation of the causes and mechanisms contributing to pattern formation and maintenance. Content Type Journal Article Category Regular Article Pages 1-17 DOI 10.1007/s10441-011-9143-z Authors Tudor M. Baetu, Department of Philosophy, University of Maryland, 1125D Skinner Building, College Park, MD 20742, USA Journal Acta Biotheoretica Online ISSN 1572-8358 Print ISSN 0001-5342. (shrink)