Ingo Brigandt

Ethology brought some crucial insights and perspectives to the study of behavior, in particular the idea that behavior can be studied within a comparative-evolutionary framework by means of homologizing components of behavioral patterns and by causal analysis of behavior components and their integration. Early ethology is well-known for its extensive use of qualitative observations of animals under their natural conditions. These observations are combined with experiments that try to analyze behavioral patterns and establish specific claims about animal behavior. Nowadays, there is still disagreement about the significance of observation and experiments and their relation.

This essay discusses Elliott Sober’s Evidence and Evolution: The Logic Behind the Science. Valuable to both philosophers and biologists, Sober analyzes the testing of different kinds of evolutionary hypotheses about natural selection or phylogenetic history, including a thorough critique of intelligent design. Not at least because of a discussion of different schools of hypothesis testing (Bayesianism, likelihoodism, and frequentism), with Sober favoring a pluralism where different inference methods are appropriate in different empirical contexts, the book has lessons for philosophy of science beyond its evolutionary focus. I criticize Sober for not including epistemic values and social aspects of scientific practice in his epistemological framework.

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.

The discussion presents a framework of concepts that is intended to account for the rationality of semantic change and variation, suggesting that each scientific concept consists of three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept’s use. I argue that in the course of history a concept can change in any of these components, and that change in the concept’s inferential role and reference can be accounted for as being rational relative to the third component, the concept’s epistemic goal. This framework is illustrated and defended by application to the history of the gene concept. It is explained how the molecular gene concept grew rationally out of the classical gene concept despite a change in reference, and why the use and reference of the contemporary molecular gene concept may legitimately vary from context to context.

Understanding the organization of an organism by individuating meaningful parts and accounting for organismal properties by studying the interaction of bodily parts is a central practice in many areas of biology. While structures are obvious bodily parts and structure and function have often been seen as antagonistic principles in the study of organismal organization, my tenet is that structures and functions are on a par. I articulate a notion of function (functions as activities), according to which functions are bodily parts just as structures are. Recognizing part-whole relations among an organism’s various structures and functions permits fruitful investigation and multilevel explanation of organismal properties and functioning, across both developmental and evolutionary time. I show how my perspective clarifies debates surrounding homology and evolutionary novelty that stem from an alleged structure-function dichotomy. My approach favors a pluralism about individuation, where the criteria of what counts as a meaningful bodily part depend on the particular epistemic aims pursued in a scientific context.

We give an answer to the question as to whether quantifier elimination is possible in some infinite algebraic extensions of Qp (‘infinite p-adic fields’) using a natural language extension. The present paper deals with those infinite p-adic fields which admit only tamely ramified algebraic extensions (so-called tame fields). In the case of tame fields whose residue fields satisfy Kaplansky’s condition of having no extension of p-divisible degree quantifier elimination is possible when the language of valued fields is extended by the power predicates Pn introduced by Macintyre and, for the residue field, further predicates and constants. For tame infinite p-adic fields with algebraically closed residue fields an extension by Pn predicates is sufficient.

In this chapter I lay out a notion of philosophical naturalism that aligns with pragmatism. It is developed and illustrated by a presentation of my views on natural kinds and my theory of concepts. Both accounts reflect a methodological naturalism and are defended not by way of metaphysical considerations, but in terms of their philosophical fruitfulness. A core theme is that the epistemic interests of scientists have to be taken into account by any naturalistic philosophy of science in general, and any account of natural kinds and scientific concepts in particular. I conclude with general methodological remarks on how to develop and defend philosophical notions without using intuitions.

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.

The paper works towards an account of explanatory integration in biology, using as a case study explanations of the evolutionary origin of novelties-a problem requiring the integration of several biological fields and approaches. In contrast to the idea that fields studying lower level phenomena are always more fundamental in explanations, I argue that the particular combination of disciplines and theoretical approaches needed to address a complex biological problem and which among them is explanatorily more fundamental varies with the problem pursued. Solving a complex problem need not require theoretical unification or the stable synthesis of different biological fields, as items of knowledge from traditional disciplines can be related solely for the purposes of a specific problem. Apart from the development of genuine interfield theories, successful integration can be effected by smaller epistemic units (concepts, methods, explanations) being linked. Unification or integration is not an aim in itself, but needed for the aim of solving a particular scientific problem, where the problem's nature determines the kind of intellectual integration required.

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.

The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models—which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation have failed to address how a mathematical model could contribute to such explanations. I discuss how mathematical equations can be explanatorily relevant. Several cases from systems biology are discussed to illustrate the interplay between mechanistic research and mathematical modeling, and I point to questions about qualitative phenomena, where quantitative models are still indispensable to the explanation. Systems biology shows that a broader philosophical conception of mechanisms is needed, which takes into account functional-dynamical aspects, interaction in complex networks with feedback loops, system-wide functional properties such as distributed functionality and robustness, and a mechanism’s ability to respond to perturbations. I offer general conclusions for philosophical accounts of explanation.

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

The purpose of the paper is twofold. I first outline a philosophical theory of concepts based on conceptual role semantics. This approach is explicitly intended as a framework for the study and explanation of conceptual change in science. Then I point to the close similarities between this philosophical framework and the theory theory of concepts, suggesting that a convergence between psychological and philosophical approaches to concepts is possible. An underlying theme is to stress that using a non-atomist account of concepts is crucial for the successful study of conceptual development and change.

The present paper discusses Kitcher’s framework for studying conceptual change and progress. Kitcher’s core notion of reference potential is hard to apply to concrete cases. In addition, an account of conceptual change as change in reference potential misses some important aspects of conceptual change and conceptual progress. I propose an alternative framework that focuses on the inferences and explanations supported by scientific concepts. The application of my approach to the history of the gene concept offers a better account of the conceptual progress that occurred in the transition from the Mendelian to the molecular gene than Kitcher’s theory.

Evolutionary developmental biology (evo-devo) is considered a ‘mechanistic science,’ in that it causally explains morphological evolution in terms of changes in developmental mechanisms. Evo-devo is also an interdisciplinary and integrative approach, as its explanations use contributions from many fields and pertain to different levels of organismal organization. Philosophical accounts of mechanistic explanation are currently highly prominent, and have been particularly able to capture the integrative nature of multifield and multilevel explanations. However, I argue that evo-devo demonstrates the need for a broadened philosophical conception of mechanisms and mechanistic explanation. Mechanistic explanation (in terms of the qualitative interactions of the structural parts of a whole) has been developed as an alternative to the traditional idea of explanation as derivation from laws or quantitative principles. Against the picture promoted by Carl Craver, that mathematical models describe but usually do not explain, my discussion of cases from the strand of evo-devo which is concerned with developmental processes points to qualitative phenomena where quantitative mathematical models are an indispensable part of the explanation. While philosophical accounts have focused on the actual organization and operation of mechanisms, properties of developmental mechanisms that are about how a mechanism reacts to modifications are of major evolutionary significance, including robustness, phenotypic plasticity, and modularity. A philosophical conception of mechanisms is needed that takes into account quantitative changes, transient entities and the generation of novel types of entities, feedback loops and complex interaction networks, emergent properties, and, in particular, functional-dynamical aspects of mechanisms, including functional (as opposed to structural) organization and distributed, system-wide phenomena. I conclude with general remarks on philosophical accounts of explanation.

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.

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

This essay analyzes and develops recent views about explanation in biology. Philosophers of biology have parted with the received deductive-nomological model of scientific explanation primarily by attempting to capture actual biological theorizing and practice. This includes an endorsement of different kinds of explanation (e.g., mathematical and causal-mechanistic), a joint study of discovery and explanation, and an abandonment of models of theory reduction in favor of accounts of explanatory reduction. Of particular current interest are philosophical accounts of complex explanations that appeal to different levels of organismal organization and use contributions from different biological disciplines. The essay lays out one model that views explanatory integration across different disciplines as being structured by scientific problems. I emphasize the philosophical need to take the explanatory aims pursued by different groups of scientists into account, as explanatory aims determine whether different explanations are competing or complementary and govern the dynamics of scientific practice, including interdisciplinary research. I distinguish different kinds of pluralism that philosophers have endorsed in the context of explanation in biology, and draw several implications for science education, especially the need to teach science as an interdisciplinary and dynamic practice guided by scientific problems and explanatory aims.

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).

The ‘death of evidence’ issue in Canada raises the spectre of politicized science, and thus the question of what role social values may have in science and how this meshes with objectivity and evidence. I first criticize philosophical accounts that have to separate different steps of research to restrict the influence of social and other non-epistemic values. A prominent account that social values may play a role even in the context of theory acceptance is the argument from inductive risk. It maintains that the more severe the social consequences of erroneously accepting a theory would be, the more evidence is needed before the theory may be accepted. However, an implication of this position is that increasing evidence makes the impact of social values converge to zero; and I argue for a stronger role for social values. On this position, social values may determine a theory’s conditions of adequacy, which among other things can include co..

Whereas an inference (deductive as well as inductive) is usually viewed as being valid in virtue of its argument form, the present paper argues that scientific reasoning is material inference, i.e., justified in virtue of its content. A material inference is licensed by the empirical content embodied in the concepts contained in the premises and conclusion. Understanding scientific reasoning as material inference has the advantage of combining different aspects of scientific reasoning, such as confirmation, discovery, and explanation. This approach explains why these different aspects (including discovery) can be rational without conforming to formal schemes, and why scientific reasoning is local, i.e., justified only in certain domains and contingent on particular empirical facts. The notion of material inference also fruitfully interacts with accounts of conceptual change and psychological theories of concepts

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