Typology Reconfigured: From the Metaphysics of Essentialism to the Epistemology of Representation

The goal of this paper is to encourage a reconfiguration of the discussion about typology in biology away from the metaphysics of essentialism and toward the epistemology of classifying natural phenomena for the purposes of empirical inquiry. First, I briefly review arguments concerning 'typological thinking', essentialism, species, and natural kinds, highlighting their predominantly metaphysical nature. Second, I use a distinction between the aims, strategies, and tactics of science to suggest how a shift from metaphysics to epistemology might be accomplished. Typological thinking can be understood as a scientific tactic that involves representing natural phenomena using idealizations and approximations, which facilitates explanation, investigation, and theorizing via abstraction and generalization. Third, a variety of typologies from different areas of biology are introduced to emphasize the diversity of this representational reasoning. One particular example is used to examine how there can be epistemological conflict between typology and evolutionary analysis. This demonstrates that alternative strategies of typological thinking arise due to the divergent explanatory goals of researchers working in different disciplines with disparate methodologies. I conclude with several research questions that emerge from an epistemological reconfiguration of typology.     

The PhyloCode: a critical discussion of its theoretical foundation

The definition of taxon names as formalized by the PhyloCode is based on Kripke's thesis of "rigid designation" that applies to Millian proper names. Accepting the thesis of "rigid designation" into systematics in turn is based on the thesis that species, and taxa, are individuals. These largely semantic and metaphysical issues are here contrasted with an epistemological approach to taxonomy. It is shown that the thesis of "rigid designation" if deployed in taxonomy introduces a new essentialism into systematics, which is exactly what the PhyloCode was designed to avoid. Rigidly designating names are not supposed to change their meaning, but if the shifting constitution of a clade is thought to cause a shift of meaning of the taxon name, then the taxon name is not a "rigid designator". Phylogenetic nomenclature either fails to preserve the stability of meaning of taxon names that it propagates, or it is rendered inconsistent with its own philosophical background. The alternative explored here is to conceptualize taxa as natural kinds, and to replace the analytic definition of taxon names by their explanatory definition. Such conceptualization of taxa allows taxon names to better track the results of ongoing empirical research. The semantic as well as epistemic gain is that if taxon names are associated with natural kind terms instead of being proper names, the composition of the taxon will naturally determine the meaning of its name.
© The Willi Hennig Society 2006.     

Homology: Homeostatic Property Cluster Kinds in Systematics and Evolution

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.     

Genetic therapy, person-regarding reasons and the determination of identity -- a reply to Robert Elliot

I have outlined two ways of defending the claim that there are so-called person-regarding reasons for practising gene therapy on human conceptuses. One is metaphysical and concerns our nature and identity. The upshot of it is that, in cases of most interest, this therapy does not affect our identity, by bringing into existence anyone of our kind who would not otherwise have existed. The other defence is value theoretical and claims that even if genetic therapy were to affect the identity of beings our kind, there could still be person-regarding reasons for performing it, since we can be benefited and harmed by being caused to exist or not to exist. Robert Elliot has attacked both of these lines, and my present objective is to show how his criticisms can be deflected.     

Concepts of rational taxonomy

The problems are discussed related to development of concepts of rational taxonomy and rational classifications (taxonomic systems) in biology. Rational taxonomy is based on the assumption that the key characteristic of rationality is deductive inference of certain partial judgments about reality under study from other judgments taken as more general and a priory true. Respectively, two forms of rationality are discriminated--ontological and epistemological ones. The former implies inference of classifications properties from general (essential) properties of the reality being investigated. The latter implies inference of the partial rules of judgments about classifications from more general (formal) rules. The following principal concepts of ontologically rational biological taxonomy are considered: "crystallographic" approach, inference of the orderliness of organismal diversity from general laws of Nature, inference of the above orderliness from the orderliness of ontogenetic development programs, based on the concept of natural kind and Cassirer's series theory, based on the systemic concept, based on the idea of periodic systems. Various concepts of ontologically rational taxonomy can be generalized by an idea of the causal taxonomy, according to which any biologically sound classification is founded on a contentwise model of biological diversity that includes explicit indication of general causes responsible for that diversity. It is asserted that each category of general causation and respective background model may serve as a basis for a particular ontologically rational taxonomy as a distinctive research program. Concepts of epistemologically rational taxonomy and classifications (taxonomic systems) can be interpreted in terms of application of certain epistemological criteria of substantiation of scientific status of taxonomy in general and of taxonomic systems in particular. These concepts include: consideration of taxonomy consistency from the standpoint of inductive and hypothetico-deductive argumentation schemes and such fundamental criteria of classifications naturalness as their prognostic capabilities; foundation of a theory of "general taxonomy" as a "general logic", including elements of the axiomatic method. The latter concept constitutes a core of the program of general classiology; it is inconsistent due to absence of anything like "general logic". It is asserted that elaboration of a theory of taxonomy as a biological discipline based on the formal principles of epistemological rationality is not feasible. Instead, it is to be elaborated as ontologically rational one based on biologically sound metatheories about biological diversity causes.     

How to be a chaste species pluralist-realist: the origins of species modes and the synapomorphic species concept

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades.     

Assessing similarity: on homology,characters and the need for a semantic approach to non‐evolutionary comparative homology

The problem of homology has been a consistent source of controversy at the heart of systematic biology, as has the step of morphological character analysis in phylogenetics. Based on a clear epistemic framework and a characterization of “characters” as diagnostic evidence units for the recognition of not directly identifiable entities, I discuss the ontological definition and empirical recognition criteria of phylogenetic, developmental and comparative homology, and how these three accounts of homology each contribute to an understanding of the overall phenomenon of homology. I argue that phylogenetic homologies are individuals or historical kinds that require comparative homology for identification. Developmental homologies are natural kinds that ultimately rest on phylogenetic homologies and also require comparative homology for identification. Comparative homologies on the other hand are anatomical structural kinds that are directly identifiable. I discuss pre‐Darwinian comparative homology concepts and their problem of invoking non‐material forces and involving the a priori assumption of a stable positional reference system. Based on Young's concept of comparative homology, I suggest a procedure for recognizing comparative homologues that lacks these problems and that utilizes a semantic framework. This formal conceptual framework provides the much needed semantic transparency and computer‐parsability for documenting, communicating and analysing similarity propositions. It provides an essential methodological framework for generalizing over individual organisms and identifying and demarcating anatomical structural kinds, and it provides the missing link to the logical chain of identifying phylogenetic homology. The approach substantially increases the analytical accessibility of comparative research and thus represents an important contribution to the theoretical and methodological foundation of morphology and comparative biology.     

Species and kinds: a critique of Rieppel's "one of a kind" account of species

A major issue in philosophical debates on the species problem concerns the opposition between two seemingly incompatible views of the metaphysics of species: the view that species are individuals and the view that species are natural kinds. In two recent papers in this journal, Olivier Rieppel suggested that this opposition is much less deep than it seems at first sight. Rieppel used a recently developed philosophical account of natural kindhood, namely Richard Boyd's "homeostatic property cluster" theory, to argue that every species taxon can be conceived of as an individual that constitutes the single member of its own specific natural kind. In this paper I criticize Rieppel's approach and argue that it does not deliver what it is supposed to, namely an account of species as kinds about which generalized statements can be made.     

How to make oneself nature's spokesman? A latourian account of classification in eighteenth- and early nineteenth-century natural history

Classification in eighteenth-century natural history was marked by a battle of systems. The Linnaean approach to classification was severely criticized by those naturalists who aspired to a truly natural system. But how to make oneself nature's spokesman? In this article I seek to answer that question using the approach of the French anthropologist of science Bruno Latour in a discussion of the work of the French naturalists Buffon and Cuvier in the eighteenth and early nineteenth century. These naturalists followed very different strategies in creating and defending of what they believed to be a natural classification in zoology. Buffon failed, whereas Cuvier's work appeared to be very successful. My argument will be that, to explain Buffon's failure and Cuvier's success, we should not focus on the epistemological or theoretical concerns and justifications of these naturalists, but on the concrete and heterogeneous means or tools through which animals were mobilized, stabilized and combined into ever more comprehensive systems of classification.     

What is clinical effectiveness?

Clinical trials and other forms of evaluation of medical treatment are held to give an objective assessment of the ‘clinical effectiveness’ of the medical treatments under evaluation. This kind of evaluation is central to the evidence-based medicine movement, as it provides a basis for the rational selection of treatment. The ethical status of randomised clinical trials is widely agreed to depend crucially upon the state of equipoise regarding which of two (or more) treatments is more (or most) effective in a defined population. However, the meaning and nature of ‘clinical effectiveness’ are unclear. in this paper, I discuss the proposals to define clinical effectiveness as a relational property and as an intrinsic property, and the way effectiveness may supervene upon more fundamental physical properties of treatments. I discuss whether effectiveness is a single property or a family of properties; the types of outcome which can be explained by effectiveness properties; and the relationship between ‘objective’ and ‘preference’ outcomes. This paper suggests that while it may be possible to put clinical effectiveness on a proper metaphysical footing, in practice the language of clinical effectiveness is more properly a topic of the human sciences than of the natural sciences.     

Biodiversity is a chimera,and chimeras aren’t real

A recent article by Burch-Brown and Archer (Biol Philos, 2017) provides compelling arguments that biodiversity is either a natural kind or a pragmatically-valid scientific entity. I call into question three of these arguments. The first argument contends that biodiversity is a Homeostatic Property Cluster (HPC). I respond that there is no plausible homeostatic mechanism that would make biodiversity an HPC natural kind. The second argument proposes that biodiversity is a multiply-realizable functional kind. I respond that there is no shared function to ground this account. The final, and strongest, argument, is that biodiversity is an ineliminable explanans and explanandum in various subdisciplines of biology. I argue that once we look at the details of the relevant research, not only does biodiversity in a broad sense not function in explanatory roles, but we must eliminate biodiversity in favor of more specific concepts in order to make sense of the leading explanations in contemporary ecology and conservation science.     

Amorphic kinds: Cluster’s last stand?

I raise a puzzle case for “cluster” accounts of natural kinds—the homeostatic property cluster and stable property cluster accounts, especially—on the basis of their expected treatment of the metaphysics of certain disease kinds. Some kinds, I argue, fail to exhibit the co-instantiated property clusters these cluster views take to be (partly) constitutive of natural kinds. Some genetic diseases, for example, have archetypical instances with few or none of the pathological processes or symptoms associated with the kind: their instances are typified by a single dispositional property. I dub such kinds ‘amorphic’, owing to their limited morphology, and try out a number of ways in which these kinds might be treated in terms of property clusters, adapting responses cluster theorists have offered to the problem of polymorphic species. Finding these responses wanting, I conclude that cluster accounts are unlikely to be the best account of the metaphysics of amorphic kinds.     

Heuristics and Biases in Evolutionary Biology

Approaching science by considering the epistemological virtues which scientists see as constitutive of good science, and the way these virtues trade-off against one another, makes it possible to capture action that may be lost by approaches which focus on either the theoretical or institutional level. Following Wimsatt (1984) I use the notion of heuristics and biases to help explore a case study from the history of biology. Early in the 20th century, mutation theorists and natural historians fought over the role that isolation plays in evolution. This debate was principally about whether replication was the central scientific virtue (and hence the ultimate goal of science to replace non-experimental evidence with experimental evidence) or whether consilience of inductions was the central virtue (and hence, as many kinds of evidence as possible should be pursued).     

An Eliminativist Approach to Vulnerability

The concept of vulnerability has been subject to numerous different interpretations but accounts are still beset with significant problems as to their adequacy, such as their contentious application or the lack of genuine explanatory role for the concept. The constant failure to provide a compelling conceptual analysis and satisfactory definition leaves the concept open to an eliminativist move whereby we can question whether we need the concept at all. I highlight problems with various kinds of approach and explain why a satisfactory account of vulnerability is unlikely ever to be offered if we wish the concept to play a genuinely explanatory role in bioethical contexts. I outline why an eliminativist position should be taken with regard to this concept in light of these concerns but mitigate some of the severity of this position by arguing that we can still make sense of retaining our widespread use of the term by viewing it as nothing more than a useful pragmatic linguistic device that acts as a marker to draw attention to certain kinds of issue. These issues will be entirely governed by other, better understood ethical concepts and theories.     

Metagenomics and the niche concept

The metagenomics approach has revolutionised the fields of bacterial diversity, ecology and evolution, as well as derived applications like bioremediation and obtaining bioproducts. A further associated conceptual change has also occurred since in the metagenomics methodology the species is no longer the unit of study, but rather partial genome arrangements or even isolated genes. In spite of this, concepts coming from ecological and evolutionary fields traditionally centred on the species, like the concept of niche, are still being applied without further revision. A reformulation of the niche concept is necessary to deal with the new operative and epistemological challenges posed by the metagenomics approach. To contribute to this end, I review past and present uses of the niche concept in ecology and in microbiological studies, showing that a new, updated definition need to be used in the context of the metagenomics. Finally, I give some insights into a more adequate conceptual background for the utilisation of the niche concept in metagenomic studies. In particular, I raise the necessity of including the microbial genetic background as another variable into the niche space. Diana Marco is a member of the Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET).     

Organic Codes: A Unifying Concept for Life

Although the knowledge about biological systems has advanced exponentially in recent decades, it is surprising to realize that the very definition of Life keeps presenting theoretical challenges. Even if several lines of reasoning seek to identify the essence of life phenomenon, most of these thoughts contain fundamental problem in their basic conceptual structure. Most concepts fail to identify either necessary or sufficient features to define life. Here, we analyzed the main conceptual frameworks regarding theoretical aspects that have been supporting the most accepted concepts of life, such as (i) the physical, (ii) the cellular and (iii) the molecular approaches. Based on an ontological analysis, we propose that Life should not be positioned under the ontological category of Matter. Yet, life should be better understood under the top-level ontology of “Process”. Exercising an epistemological approach, we propose that the essential characteristic that pervades each and every living being is the presence of organic codes. Therefore, we explore theories in biosemiotics and code biology in order to propose a clear concept of life as a macrocode composed by multiple inter-related coding layers. This way, as life is a sort of metaphysical process of encoding, the living beings became the molecular materialization of that process. From the proposed concept, we show that the evolutionary process is a fundamental characteristic for life’s maintenance but it is not necessary to define life, as many organisms are clearly alive but they do not participate in the evolutionary process (such as infertile hybrids). The current proposition opens a fertile field of debate in astrobiology, epistemology, biosemiotics, code biology and robotics.