Science is now studying biodiversity on a massive scale. These studies are occurring not just at the scale of larger plants and animals, but also at the scale of minute entities such as bacteria and viruses. This expansion has led to the development of a specific sub-field of “microbial diversity”. In this paper, I investigate how microbial diversity faces two of the classical issues encountered by the concept of “ biodiversity ”: the issues of defining the units of biodiversity and (...) of choosing a mathematical measure of diversity. I also show that the extension of the scope of biodiversity to microbial entities such as viruses and many other not-clearly-alive entities raises yet another foundational issue: that of defining a “lower-limit” of biodiversity. (shrink)

In this paper, I critically assess Mark Richard’s interesting and important development of the claim that linguistic meanings can be fruitfully analogized with biological species. I argue that linguistic meanings qua cluster of interpretative presuppositions need not and often do not display the population-level independence and reproductive isolation that is characteristic of the biological species concept. After developing these problems in some detail, I close with a discussion of their implications for the picture that Richard paints concerning the dangers of (...) conceptual engineering and the prospects for dynamic notions of semantic stability. (shrink)

Biological science uses multiple species concepts. Order can be brought to this diversity if we recognize two key features. First, any given species concept is likely to have a patchwork structure, generated by repeated application of the concept to new domains. We illustrate this by showing how two species concepts (biological and ecological) have been modified from their initial eukaryotic applications to apply to prokaryotes. Second, both within and between patches, distinct species concepts may interact and hybridize. We thus defend (...) a semantic picture of the species concept as a collection of interacting patchwork structures. Thus, although not all uses of the term pick out the same kind of unit in nature, the diversity of uses reflects something more than mere polysemy. We suggest that the emphasis on the use of species to pick out natural units is itself problematic, because that is not the term’s sole function. In particular, species concepts are used to manage inquiry into processes of speciation, even when these processes do not produce clearly delimited species. (shrink)

Discusses the conditions of possibility for intercultural and comparative philosophy, and for crosscultural communication at large. This innovative book explores the preconditions necessary for intercultural and comparative philosophy. Philosophical practices that involve at least two different traditions with no common heritage and whose languages have very different grammatical structure, such as Indo-Germanic languages and classical Chinese, are a particular focus. Lin Ma and Jaap van Brakel look at the necessary and not-so-necessary conditions of possibility of interpretation, comparison, and other forms (...) of interaction and how we can speak of similarities and differences in this context. The authors posit that it is necessary to dissolve the question of universalism versus relativism by replacing the ideal language paradigm with a paradigm of family resemblances and that it is not necessary to share a common language to engage in comparison. Numerous case studies are presented, including many comparisons of Western and Chinese concepts. (shrink)

Several philosophers have recently tried to define natural kinds in epistemic terms only. Given the persistent problems with finding a successful metaphysical theory, these philosophers argue that we would do better to describe natural kinds solely in terms of their epistemic usefulness, such as their role in supporting inductive inferences. In this paper, I argue against these epistemology-only theories of natural kinds and in favor of, at least partly, metaphysical theories. I do so in three steps. In the first section (...) of the paper, I propose two desiderata for a theory of natural kinds. In the second section, I discuss one example of a ‘general’ epistemology-only theory, proposed by Marc Ereshefsky and Thomas Reydon, and argue that theories like theirs fail to provide adequate criteria of natural kinds. In the third section, I focus on one example of a ‘specific’ epistemology-only theory, proposed by P. D. Magnus, and use it to show why such theories cannot justify the claim that the proposed epistemic criteria account for the naturalness of kinds. (shrink)

This article uses the case study of ethnobiological classification to develop a positive and a negative thesis about the state of natural kind debates. On the one hand, I argue that current accounts of natural kinds can be integrated in a multidimensional framework that advances understanding of classificatory practices in ethnobiology. On the other hand, I argue that such a multidimensional framework does not leave any substantial work for the notion “natural kind” and that attempts to formulate a general account (...) of naturalness have become an obstacle to understanding classificatory practices. (shrink)

Which domains of biology do philosophers of biology primarily study? The fact that philosophy of biology has been dominated by an interest for evolutionary biology is widely admitted, but it has not been strictly demonstrated. Here I analyse the topics of all the papers published in Biology & Philosophy, just as the journal celebrates its thirtieth anniversary. I then compare the distribution of biological topics in Biology & Philosophy with that of the scientific journal Proceedings of the National Academy of (...) Science of the USA, focusing on the recent period 2003–2015. This comparison reveals a significant mismatch between the distributions of these topics. I examine plausible explanations for that mismatch. Finally, I argue that many biological topics underrepresented in philosophy of biology raise important philosophical issues and should therefore play a more central role in future philosophy of biology. (shrink)

Recently the functional model of reduction has become something like the standard model of reduction in philosophy of mind. In this paper, I argue that the functional model fails as an account of reduction due to problems related to three key concepts: functionalization, realization and causation. I further argue that if we try to revise the model in order to make it more coherent and scientifically plausible, the result is merely a simplified version of what in philosophy of science is (...) known as mechanistic explanation. Hence, instead of analyzing reduction in philosophy of mind in terms of functional reduction, it should be analyzed in terms of mechanistic explanation. (shrink)

This paper aims to offer a new argument in defence bacterial species pluralism. To do so, I shall first present the particular issues derived from the conflict between the non-theoretical understanding of species as units of classification and the theoretical comprehension of them as units of evolution. Secondly, I shall justify the necessity of the concept of species for the bacterial world, and show how medicine and endosymbiotic evolutionary theory make use of different concepts of bacterial species due to their (...) distinctive purposes. Finally, I shall show how my argument provides a new source of defence for bacterial pluralism. (shrink)

We argue that all general concepts are family resemblance concepts. These include concepts introduced by ostension, such as colour. Concepts of colour and of each of the specific colours are family resemblance concepts because similarities concerning an open-ended range of colour or of appearance features crop up and disappear. After discussing the notion of “same colour” and Wittgenstein's use of the phrase “our colours”, we suggest family resemblance concepts in one tradition can often be extended to family resemblance concepts in (...) another tradition, illustrated by Wittgenstein's use of the words Spiel and “game”. (shrink)

Pluralist and eliminativist positions have proliferated within both science and philosophy of science in recent decades. This paper asks the question why this shift of thinking has occurred, and where it is leading us. We provide an explanation which, if correct, entails that we should expect pluralism and eliminativism to transform other debates currently unaffected, and for good reasons. We then consider the question under what circumstances eliminativism will be appropriate, arguing that it depends not only on the term in (...) question, but also on the context of discussion and details of the debate at hand. The resultant selective eliminativism is an appealing compromise for various ‘pluralists’ and ‘eliminativists’ who are currently locking horns. (shrink)

The ontology of recipes is by and large unexplored. In this paper, I offer a three-steps account. After introducing some key terminology, I distinguish four main options for a theory of recipes: realism, constructivism, existentialism, and the naïve approach. Hence, I first argue that recipes are social entities whose identity depends on a process of identification, typically performed by means of a performative utterance on the part of a cook ; thus, the best theoretical framework for a theory of recipes (...) is a constructivist. Secondly, I argue that the identity of recipes can be grasped only by being suitably acquainted with the dishes that instantiate them, because of the impossibility to spell out recipes in details that would match a full-fledged dish; hence, the authority to establish the identity of a recipe rests on a process of apprenticeship. Finally, I argue that the identity of recipes and—vicariously—of the dishes that instantiate them, rest on three factors: the expertise required on the part of the cook; authenticity ; and the open-ended character of recipes. (shrink)

A number of areas of biology raise questions about what is of value in the natural environment and how we ought to behave towards it: conservation biology, environmental science, and ecology, to name a few. Based on my experience teaching students from these and similar majors, I argue that the field of environmental ethics has much to teach these students. They come to me with pent-up questions and a feeling that more is needed to fully engage in their subjects, and (...) I believe some exposure to environmental ethics can help focus their interests and goals. I identify three primary areas in which environmental ethics can con- tribute to their education. The first is an examination of who (or what) should be considered to be part of our moral community (i.e., the community to whom we owe direct duties). Is it humans only? Or does it include all sentient life? Or all life? Or ecosystems considered holistically? Often, readings implicitly assume one or more of these answers; the goal is to make the student more sensitive to these implicit claims and to get them to think about the different reasons that support them. The second area, related to the first, is the application of the different answers concerning the extent of the ethical community to real environmental issues and problems. Students need to be aware of how the different answers concerning the moral community can imply conflicting answers for how we should act in certain cases and to think about ways to move toward conflict resolution. The third area in which environmental ethics can contribute is a more conceptual one, focusing on central concepts such as biodiversity, sustainability, species, and ecosystems. Exploring and evaluating various meanings of these terms will make students more reflective and thoughtful citizens and biologists, sensitive to the implications that different conceptual choices make. (shrink)

The relation between method, concept and theory in science is complicated. I seek to shed light on that relation by considering an instance of it in systematics: The additional challenges phylogeneticists face when reconstructing phylogeny not at a single level, but simultaneously at multiple levels of the hierarchy. How does this complicate the task of phylogenetic inference, and how might it inform and shape the conceptual foundations of phylogenetics? This offers a lens through which the interplay of method, theory and (...) concepts may be understood in systematics, which, in turn, provides data for a more general account. (shrink)

Michael and has argued that species have intrinsic essences. This paper rebuts Devitt’s arguments, but in so doing it shores up the anti-essentialist consensus in two ways that have more general interest. First, species membership can be explanatory even when species have no essences; that is, Tamsin’s membership of the tiger species can explain her stripyness, without this committing us to any further claim about essential properties of tigers. Second, even the views of species that appear most congenial to essentialism—namely (...) phenetic and genotypic cluster accounts—do not entail strong forms of intrinsic essentialism. (shrink)

The pheneticist philosophy holds that biological taxa are clusters of entities united by a form of all-things-considered resemblance. This view of taxonomy has come in for almost universal criticism from philosophers, and has received little praise from biologists, over the past 30 years or so. This article defends a modest pheneticism, understood as part of a pluralist view of taxonomy. First, phenetic approaches to taxonomy are alive and well in biological practice, especially in the areas of microbiology and botany. Second, (...) the pheneticist notion of overall similarity is defensible, and is implicitly endorsed even by those (such as Quine) usually implicated in attacks on similarity. Third, there are limited biological domains within which pheneticism’s conception of species as kinds (rather than heterogeneous individuals) remains applicable. (shrink)

Species are considered the basic unit of biological classification and evolution. Hence, they are used as a benchmark in several fields, although the ontological status of such a category has always been a matter of debate. This paper aims to discuss the problem of the definition of species within the new mechanistic approach. Nevertheless, the boundary between entities, activities, and mechanisms remains difficult to establish and always requires an analysis of what is meant by explanation. As a case study, the (...) paper describes the debate concerning the species category by considering different kingdoms: Animals, Bacteria, and Fungi. The inherently biological differences between those groups prevent the use of a single, universally applicable concept of species that could fit the mechanisms responsible for the variability present in these kingdoms. The same issue is encountered within each group, as highlighted through a focus on mammals and microbes. This controversy has given rise to opposite approaches, namely: monism, which looks for a single definition that might account for all species, and pluralism, which admits that different groups of organisms require somewhat different definitions. In order to develop an adequate definition of species, we propose to apply a new mechanistic framework, which considers the ontic-epistemic dimensions of scientific explanation in close parallel. The apt correlation between epistemic and the ontic aspects highlights the way in which the concept of species and the reference to data are strictly co-determined. This suggests that the concept of species is better understandable within a dual ontic-epistemic approach. (shrink)

Evolution by natural selection has been extended to several supraorganismic levels, but whether it can apply to ecosystems remains controversial on two main counts. First, local ecosystems are loosely individuated, so that it is unclear how they manifest heredity and fitness. Second, even if they did, the meta-ecosystem formed by this population of local ecosystems will also suffer from a very low degree of cohesion, which will jeopardize any ENS. We suggest a way to overcome both issues, focusing on ecosystem (...) properties rather than on ecosystemic individuals. First, we follow recent theoretical developments which deny the centrality of reproduction in ENS. This leads us to merge heredity and fitness in a single process, in which a local ecosystem causally influences its neighbors, in a way responsible for their phenotypic similarity. Second, we suggest that the resulting meta-ecosystem need not meet the criteria of individuality. Instead, the evolving meta-ecosystem is best understood as a homeostatic property cluster, i.e., a set of phenotypes that together evolve by ENS at the ecosystem level. We illustrate this conceptual framework with a hypothetical example of local ecosystems that vary in terms of stability, productivity, diversity, and complementarity between species. Finally, we stress that our property-based account of ecosystemic ENS can help understand evolution at other biological levels, such as early life evolution and holobionts. (shrink)

Pluralism is popular among philosophers of biology. This essay argues that negative judgments about universal biology, while understandable, are very premature. Familiar life on Earth represents a single example of life and, most importantly, there are empirical as well as theoretical reasons for suspecting that it may be unrepresentative. Scientifically compelling generalizations about the unity of life must await the discovery of forms of life descended from an alternative origin, the most promising candidate being the discovery of extraterrestrial life. Nonetheless, (...) in the absence of additional examples of life, we are best off exploring the microbial world for promising explanatory concepts, principles, and mechanisms rather than prematurely giving up on universal biology. Unicellular microbes are by far the oldest, metabolically most diverse, and environmentally tolerant form of life on our planet. Yet somewhat ironically, much of our theorizing about life still implicitly privileges complex multicellular eukaryotes, which are now understood to be highly specialized, fragile latecomers to Earth. The problem with pursuing a pluralist approach to understanding life is that it is likely to blind us to the significance of just those entities and causal processes most likely to shed light on the underlying nature of life. (shrink)

After having reconstructed a minimal biological characterisation of species, we endorse an “empirical approach” based on the idea that it is the peculiar evolutionary history of the species at issue—its peculiar origination process, its peculiar metapopulation structure and the peculiar mixture and strength of homeostatic processes vis à vis heterostatic ones—that determines species’ identity at a time and through time. We then explore the consequences of the acceptance of the empirical approach in settling the individuals versus kinds dispute. In particular, (...) while conceptual arguments have been proposed to show that species can be equally treated as individuals and kinds because mereology’s and set-theory’s languages are inter-translatable, we advance instead a causal argument to sustain the claim that each species is both a kind and an individual. (shrink)

Common ancestry is a central feature of the theory of evolution, yet it is not clear what “common ancestry” actually means; nor is it clear how it is related to other terms such as “the Tree of Life” and “the last universal common ancestor”. I argue these terms describe three distinct hypotheses ordered in a logical way: that there is a Tree of Life is a claim about the pattern of evolutionary history, that there is a last universal common ancestor (...) is an ontological claim about the existence of an entity of a specific kind, and that there is universal common ancestry is a claim about a causal pattern in the history of life. With these generalizations in mind, I argue that the existence of a Tree of Life entails a last universal common ancestor, which would entail universal common ancestry, but neither of the converse entailments hold. This allows us to make sense of the debates surrounding the Tree, as well as our lack of knowledge about the last universal common ancestor, while still maintaining the uncontroversial truth of universal common ancestry. (shrink)

Biodiversity is a key concept in the biological sciences. While it has its origin in conservation biology, it has become useful across multiple biological disciplines as a means to describe biological variation. It remains, however, unclear what particular biological units the concept refers to. There are currently multiple accounts of which biological features constitute biodiversity and how these are to be measured. In this paper, I draw from the species concept debate to argue for a set of desiderata for the (...) concept of “biodiversity” that is both principled and coheres with the concept’s use. Given these desiderata, this concept should be understood as referring to difference quantified in terms of the phylogenetic structure of lineages, also known as the ‘tree of life’. (shrink)

We argue that all general concepts are family resemblance concepts. These include concepts introduced by ostension, such as colour(s). Concepts of colour and of each of the specific colours are family resemblance concepts because similarities concerning an open‐ended range of colour or of appearance features crop up and disappear. After discussing the notion of “same colour” and Wittgenstein's use of the phrase “our colours”, we suggest family resemblance concepts in one tradition can often be extended to family resemblance concepts in (...) another tradition, illustrated by Wittgenstein's use of the words Spiel and “game”. (shrink)

Can we be realists about a general category but pluralists about concepts relating to that category? I argue that paleobiological methods of delineating species are not affected by differing species concepts, and that this underwrites an argument that species concept pluralists should be species category realists. First, the criteria by which paleobiologists delineate species are ‘indifferent’ to the species category. That is, their method for identifying species applies equally to any species concept. To identify a new species, paleobiologists show that (...) interspecies processes, such as phenotypic plasticity, sexual dimorphism, or ontogenetic diversity, are a worse explanation of the variance between specimens than intraspecies processes. As opposed to operating under a single or plurality of species concepts, then, paleobiologists use abductive inferences, which would be required regardless of any particular species concept. Second, paleobiologists are frequently interested in large-scale, long-term morphological patterns in the fossil record, and resolving the fine-grained differences which result from different species concepts is irrelevant at those scales. I argue that this claim about paleobiological practice supports what I call ‘indifference realism’ about the species category. The indifference realist argues that when legitimate investigation is indifferent to a plurality of concepts, we should be realists about the category those concepts pertain to. (shrink)

Conceptual change can occur for a variety of reasons; some more scientifically significant than others. The 2006 definition of ‘planet’, which saw Pluto reclassified as a dwarf planet, is an example toward the more mundane end of the scale. I argue however that this case serves as a useful example of a related phenomenon, whereby what appears to be a single kind term conceals two or more distinct concepts with independent scientific utility. I examine the historical background to this case, (...) as a template for developing additional evidence for pluralist approaches to conceptual disputes within science and elsewhere. (shrink)

Ernst Mayr’s influence on philosophy of biology has given the field a particular perspective on evolution, phylogeny and life in general. Using debates about the tree of life as a guide, I show how Mayrian evolutionary biology excludes numerous forms of life and many important evolutionary processes. Hybridization and lateral gene transfer are two of these processes, and they occur frequently, with important outcomes in all domains of life. Eukaryotes appear to have a more tree-like history because successful lateral events (...) tend to occur among more closely related species, or at a lower frequency, than in prokaryotes, but this is a difference of degree rather than kind. Although the tree of life is especially problematic as a representation of the evolutionary history of prokaryotes, it can function more generally as an illustration of the limitations of a standard evolutionary perspective. Moreover, for philosophers, questions about the tree of life can be applied to the Mayrian inheritance in philosophy of biology. These questions make clear that the dichotomy of life Mayr suggested is based on too narrow a perspective. An alternative to this dichotomy is a multidimensional continuum in which different strategies of genetic exchange bestow greater adaptiveness and evolvability on prokaryotes and eukaryotes. (shrink)

The concept of nature in Western thought has been informed by the assumption of a categorical distinction between natural and artificial entities, which goes back to John Stuart Mill or even Aristotle. Such a way of articulating the natural/artificial distinction has proven unfit for conservation purposes mainly because of the extent and the pervasiveness of human activities that would leave no nature left to be conserved, and alternative views have been advanced. In this contribution, after arguing for the importance of (...) the concept of naturalness as a guide for conservation, I will try to provide an account of the natural/artificial distinction suited to contemporary conservation framing. Focusing on a particular kind of objects that I suggest to name “environmental objects”, I propose and defend the view of “naturalness as independence” according to which the more or less an environmental object's identity conditions and survival depend on human intervention, the more or less that object is artificial or natural, respectively. According to this view, conserving environmental objects will equate to maintaining or improving their naturalness or even originating artificial objects that may become new natural objects. This view has the advantage, on the one hand, of providing a rationale for a distinction which is not only part of how people think, but also pervasive in conservation practices and policies and, on the other hand, of accounting for the global pervasiveness of human intervention in the so-called natural world. (shrink)

This paper uses two case studies to explore an interest-relative view of taxonomy and how it complements kind pluralism in biology. First, I consider the ABC island bear, which can be correctly classified into more than one species. I argue that this classificatory pluralism can be explained by reference to the range of alternative explanatory interests in biology. In the second half of the paper, I pursue an interest-relative view of classification more generally. I then apply the resultant view to (...) a second case study: whether whales are fish. I argue that this question is not one about scientific vs folk usage, as has been assumed. I also develop a new view: that Fish should be rejected as a category, both from the point of view of biological science, and from the point of view of folk taxonomy. Along the way, I use the interest-relative view to shed light on the circumstances under which higher taxa should be accepted as legitimate categories for biological science. (shrink)

Contrary to the common-sense view and positivist aspirations, scientific concepts are often imprecise. Many of these concepts are ambiguous, vague, or have an under-specified meaning. In this paper, I discuss how imprecise concepts promote integration in biology and thus benefit science. Previous discussions of this issue focus on the concepts of molecular gene and evolutionary novelty. The concept of molecular gene helps biologists integrate explanatory practices, while the notion of evolutionary novelty helps them integrate research questions into an interdisciplinary problem (...) New directions in the philosophy of science, Springer, Dordrecht, 2014). In what follows, I compare molecular gene and evolutionary novelty to another imprecise concept, namely biological lineage. This concept promotes two other types of scientific integration: it helps biologists integrate theoretical principles and methodologies into different areas of biology. The concept of biological lineage facilitates these types of integration because it is broad and under-specified in ways that the concepts of molecular gene and evolutionary novelty are not. Hence, I use the concept of biological lineage as a case study to reveal types of integration that have been overlooked by philosophers. This case study also shows that even very imprecise concepts can be beneficial to scientific practice. (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.

There is an overriding orthodoxy amongst philosophers that attention is a ‘unified phenomenon’, subject to explanation by one monistic theory. In this article, I examine whether this philosophical orthodoxy is reflected in the practice of psychology. I argue that the view of attention that best represents psychological work is a variety of conceptual pluralism. When it comes to the psychology of attention, monism should be rejected and pluralism should be embraced. _1_ The Monistic Consensus _2_ The Varieties of Pluralism _3_ (...) Three Concepts _3.1_ Blindsight _3.2_ Executive attention _3.3_ Alerting _4_ Pluralism _4.1_ Methodological conceptual pluralism _4.2_ Three monist interpretations _5_ Philosophical Monism? _6_ Conclusion. (shrink)

Marc Ereshefsky’s project of eliminative pluralism holds that, as there is no unifying feature among all species concepts, we ought to doubt the existence of the species category. Here, I argue that one promising strategy for saving the species category is to reframe it as a natural kind after the practice turn. I suggest situating the species category within a recent account of natural kinds proposed by Marc Ereshefsky and Thomas Reydon called “scientific kinds”. Scientific kinds highlight ontological boundaries. More (...) importantly, they recognize boundaries drawn from the lab and the field, not only from the armchair. The point of this exercise is to situate the species category within an account of natural kinds that is sensitive to scientific practice. In order to argue for a realist interpretation of the species category, and not merely a pragmatic one, I rely on an approach to scientific metaphysics from Ken Waters that shifts the attention from “theory focused” to “practice-centered” analysis. (shrink)

Just like atomic physics seventy years ago, when it was realized that chain reaction could lead to medical applications as well as to the creation of atomic weapons, the life sciences have entered a grey zone. “Advances in biotechnology […]” a 2003 CIA document stated, “have the potential to create a much more dangerous biological warfare threat […] Engineered biological agents could be much worse than any disease known to man”. As sociologists of science have noted, contemporary life sciences have (...) dual use potential as they can be used to foster beneficial applications, for instance in health care, or generate harm, either intentionally or not, and possibly on an unprecedented.. (shrink)

The recent conception of biodiversity proposed by James Maclaurin and Sterelny was developed mostly with macrobiological life in mind. They suggest that we measure biodiversity by dividing life into natural units (typically species) and quantifying the differences among units using phenetic rather than phylogenetic measures of distance. They identify problems in implementing quantitative phylogenetic notions of difference for non-prokaryotic species. I suggest that if we focus on microbiological life forms that engage in frequent, promiscuous lateral gene transfer (LGT), and their (...) associated reticulated phylogenies, we need to rethink the notion of species as the natural unit, and we discover additional problems with phylogenetic notions of distance. These problems suggest that a phenetic approach based on morphospaces has just as much appeal, if not more, for microbes as they do for multi-cellular life. Facts about LGT, however, offer no new insight into the additional challenge of reconciling units and differences into a single measure of biodiversity. (shrink)

The history of biological systematics documents a continuing tension between classifications in terms of nested hierarchies congruent with branching diagrams (the ‘Tree of Life’) versus reticulated relations. The recognition of conflicting character distribution led to the dissolution of the scala naturae into reticulated systems, which were then transformed into phylogenetic trees by the addition of a vertical axis. The cladistic revolution in systematics resulted in a representation of phylogeny as a strictly bifurcating pattern (cladogram). Due to the ubiquity of character (...) conflict—at the genetic or morphological level, or at any level in between—some characters will necessarily have to be discarded ( qua noise) in favor of others in support of a strictly bifurcating phylogenetic tree. Pattern analysts will seek maximal congruence in the distribution of characters (ultimately of any kind) relative to a branching tree-topology; process explainers will call such tree-topologies into question by reference to incompatible evolutionary processes. Pattern analysts will argue that process explanations must not be brought to bear on pattern reconstruction; process explainers will insist that the reconstructed pattern requires a process explanation to become scientifically relevant, i.e., relevant to evolutionary theory. The core question driving the current debate about the adequacy of the ‘Tree of Life’ metaphor seems to be whether the systematic dichotomization of the living world is an adequate representation of the complex evolutionary history of global biodiversity. In ‘Questioning the Tree of Life’, it seems beneficial to draw at least four conceptual distinctions: pattern reconstruction versus process explanation as different epistemological approaches to the study of phylogeny; open versus closed systems as expressions of different kinds of population (species) structures; phylogenetic trees versus cladograms as representations of evolutionary processes versus patterns of relationships; and genes versus species as expressions of different levels of causal integration and evolutionary transformation. (shrink)