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)

Recent work has suggested that conservation efforts such as restoration ecology and invasive species eradication are largely value-driven pursuits. Concurrently, changes to global climate are forcing ecologists to consider if and how collections of species will migrate, and whether or not we should be assisting such movements. Herein, we propose a philosophical framework which addresses these issues by utilizing ecological and evolutionary interrelationships to delineate individual ecological communities. Specifically, our Evolutionary Community Concept recognizes unique collections of species that interact and (...) have co-evolved in a given geographic area. We argue this concept has implications for a number of contemporary global conservation issues. Specifically, our framework allows us to establish a biological and science-driven context for making decisions regarding the restoration of systems and the removal of exotic species. The ECC also has implications for how we view shifts in species assemblages due to climate change and it advances our understanding of various ecological concepts, such as resilience. (shrink)

In addition to the distinction between species as a category and speciesas a taxon, the word species is ambiguous in a very different butequally important way, namely the temporal distinction between horizontal andvertical species. Although often found in the relevant literature, thisdistinction has thus far remained vague and undefined. In this paper the use ofthe distinction is explored, an attempt is made to clarify and define it, andthen the relation between the two dimensions and the implications of thatrelation are examined. (...) Using Darwin's analogy of language evolution forspeciesevolution, and by appealing to a major change in the conception of languagebetween 19th- and 20th-century linguistics, it is argued that the horizontaldimension has priority (pragmatic, epistemological, logical, and ontological)over the vertical dimension. This has immense ramifications for the modernspecies problem. Fundamentally, it favors horizontal species concepts oververtical ones. In so doing it places species realism on a much more securefoundation and largely undercuts species pluralism. In addition it raises aserious problem for the increasingly popular family of phylogenetic speciesconcepts, which generally suffer from a dimensionality confusion. However,thereis a recent trend within this family that attempts to restore the priority ofthe horizontal dimension. It is concluded that this trend should be affirmedandthat the species-as-individuals view should be abandoned. (shrink)

I argue for accepting a pluralist approach to species, while rejecting the realism about species espoused by P. Kitcher and a number of other philosophers of biology. I develop an alternative view of species concepts as divisions of organisms into groups for study which are relative to the systematic explanatory interests of biologists at a particular time. I also show how this conception resolves a number of difficult puzzles which plague the application of particular species concepts.

Gayon's recent claim that Buffon developed a concept of species as physical individuals is critically examined and rejected. Also critically examined and rejected is Gayon's more central thesis that as a consequence of his analysis of Buffon's species concept, and also of Darwin's species concept, it is clear that modern evolutionary theory does not require species to be physical individuals. While I agree with Gayon's conclusion that modern evolutionary theory does not require species to be physical individuals, I disagree with (...) his reasons and instead provide logical rather than historical reasons for the same conclusion. (shrink)

The purpose of this paper is to test the contemporary concept of biological species against some of the problems caused by treating species as spatiotemporally extended entities governed by criteria of persistence, identity, etc. After outlining the general problem of symmetric division in natural objects, I set out some useful distinctions (section 1) and confirm that species are not natural kinds (section 2). Section 3 takes up the separate issue of species definition, focusing on the Biological Species Concept (BSC). Sections (...) 4 and 5 examine the matter of species identity over space and time respectively, as determined by the BSC. Both gradualistic and punctuated equilibrium models of speciation are discussed. In section 6 I argue that the BSC fails to determine adequate criteria for dealing with certain kinds of speciation. Section 7 moves speculatively beyond the BSC to a brief examination of alternatives. (shrink)

When philosophers discuss the topic of explanation, they usually have in mind the following question: given the beliefs one has and some proposition that one wishes to explain, which subset of the beliefs constitutes an explanation of the target proposition? That is, the philosophical ‘problem of explanation’ typically has bracketed the issue of how one obtains the beliefs; they are taken as given. The problem of explanation has been the problem of understanding the relation ‘x explains y’. Since Hempel did (...) so much to canonize this way of thinking about explanation, it deserves to be called ‘Hempel's problem’. (shrink)

When philosophers discuss the topic of explanation, they usually have in mind the following question: given the beliefs one has and some proposition that one wishes to explain, which subset of the beliefs constitutes an explanation of the target proposition? That is, the philosophical ‘problem of explanation’ typically has bracketed the issue of how one obtains the beliefs; they are taken as given. The problem of explanation has been the problem of understanding the relation ‘x explains y’. Since Hempel did (...) so much to canonize this way of thinking about explanation, it deserves to be called ‘Hempel's problem’. (shrink)

A method of phylogenetic reconstruction as proposed by a number of scientists of the Senckenberg Research Institute is discussed. The method is based on functional-morphological studies, the evolutionary adaptation principle of Bock and Von Wahlert (1965) and so-called model reconstruction. It is argued in this paper that direction of the adaptation process cannot be determined because of lack of knowledge about particular selective forces and that theories of model reconstruction are not open to contradiction in the sense of Popperian falsification. (...) Although it has been claimed that the method provides the only valid directional argument for morphoclines in cladistic studies, it remains unclear how to proceed when morphoclines show contradictory polarities. Moreover, it is doubtful whether polarities of morphoclines can be determined independently of phylogenetic hypotheses, and also whether the use of multistate morphoclines is methodologically valid. By relying on a particular evolutionary theory, i.e. the neo-Darwinian theory, and consequently assigning natural selection as the major agent of directional progress, the Senckenburg method of phylogenetic reconstruction restricts itself to microevolutionary change and, therefore, cannot be used when other hypotheses on the evolutionary process appear to explain the speciation process more plausibly, i.e. hypotheses on macroevolution. Furthermore, it is an unproved statement that evolution always proceeds according to the principle of economy. (shrink)

Over the past decade, it has been discovered that disparate aspects of morphology – often of distantly related groups of organisms – are regulated by the same genetic regulatory mechanisms. Those discoveries provide a new perspective on morphological evolutionary change. A conceptual framework for exploring these research findings is termed ‘deep homology’. A comparative framework for morphological relations of homology is provided that distinguishes analogy, homoplasy, plesiomorphy and synapomorphy. Four examples – three from plants and one from animals – demonstrate (...) that homologous developmental mechanisms can regulate a range of morphological relations including analogy, homoplasy and examples of uncertain homology. Deep homology is part of a much wider range of phenomena in which biological (genes, regulatory mechanisms, morphological traits) and phylogenetic levels of homology can both be disassociated. Therefore, to understand homology, precise, comparative, independent statements of both biological and phylogenetic levels of homology are necessary. (shrink)

Morphology and its relevance for systematics is a promising field for the application of biosemiotic principles in scientific practice. Genital coupling in spiders involves very complex interactions between the male and female genital structures. As exemplified by two spider species,Nephila clavipesandNephila pilipes ssp. fenestrata, from a biosemiotic point of view the microstructures of the male bulb’s embolus and the corresponding female epigynal and vulval parts form the morphological zone of an intraspecific communication and sign-interpreting process that is one of the (...) prerequisites for sperm transfer. Hence these morphological elements are of high taxonomic value, as they play an essential role in mating and fertilization and consequently in establishing and preserving a reproductive community. Morphology clearly benefits from a biosemiotic approach, as biosemiotics helps to sort out species-specific morphological characters and to avoid problematic typological interpretations. (shrink)

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 Darwinian descendants of the “modern evolutionary synthesis” and their supposed antagonists, cladists and punctuationalists.

Morphogenetische Untersuchungen ermöglichen eine zuverlässige Ermittlung der homologen Elemente in der Lobenlinie der Ammonoidea. Umgekehrt lehrt eine Analyse hypothetischer Vorstellungen, die man sich über die phylogenetischen Zusammenhänge gewisser Ammoneen-Gruppen gebildet hatte, daß sich daraus die Homologie-Beziehungen nicht herleiten lassen. Es besteht keine Konkordanz zwischen den morphologischen Tatbeständen und den stammesgeschichtlichen Konstruktionen, die sich in diesen Fällen als falsch erweisen. Daraus wird der Schluß gezogen, daß der Homologie-Begriff nur unvoreingenommen morphologisch definiert und interpretiert werden kann. Die auf morphologischer Grundlage ermittelten Homologien (...) entscheiden über die Möglichkeit stammesgeschichtlicher Verknüpfungen, nicht aber umgekehrt phylogenetische Deutungen über die Homologie. Ebenso kann die stets unsichere Phylogenie nicht zur Grundlage der Systematik gemacht werden. Auch da liegen die logisch-methodischen Zusammenhänge umgekehrt: Die im System ausgedrückte Formverwandtschaft ist die Basis der Phylogenie und nicht die Phylogenie die der Morphologie. Die Theorie eines Phylogenetischen Systems der Organismen wird abgelehnt.Morphogenetic investigations provide a firm basis for an exact identification of homologous elements in the suture line of ammonoids. On the other hand an analysis of current phylogenetic connections of certain ammonoid groups demonstrates that they give no clue for tracing homologies. There is no agreement between the morphological facts and the phylogenetic fictions, the latter in these cases being definitely wrong. Therefrom it is concluded that the concept of homology can only be defined and interpreted on a morphological basis. The established homologies are decisive for the admissibility of phylogenetic connections and not phylogenetic inferences for the recognition of homologies. In the same manner systematics cannot be based on the always unsafe phylogeny, but only on the actual facts of morphology. The concept of a phylogenetic classification of organisms is rejected. (shrink)

In this article, I examine the issue of the alleged circularity in the determination of homologies within cladistic analysis. More specifically, I focus on the claims made by the proponents of the dynamic homology approach, regarding the distinction (sometimes made in the literature) between primary and secondary homology. This distinction is sometimes invoked to dissolve the circularity issue, by upholding that characters in a cladistic data matrix have to be only primarily homologous, and thus can be determined independently of phylogenetic (...) hypotheses, by using the classical Owenian criteria (for morphological characters) or via multiple sequence alignment (for sequence data). However, since in the dynamic approach, sequence data can be analyzed without being pre-aligned, proponents have claimed that the distinction between primary and secondary homology has no place within cladistics. I will argue that this is not the case, since cladistic practice within the dynamic framework does presuppose primary homology statements at a higher level. (shrink)

The 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)

Species are generally considered to be the basic units of evolution, and hence to constitute spatio-temporally bounded entities. In addition, it has been argued that species also instantiate a natural kind. Evolution is fundamentally about change. The question then is how species can remain the same through evolutionary change. Proponents of the species qua individuals thesis individuate species through their unique evolutionary origin. Individuals, or spatio-temporally located particulars in general, can be bodies, objects, events, or processes, or a combination of (...) these. It is here argued that species are best understood as open or closed, causally integrated processual systems that also instantiate an historically conditioned homeostatic property cluster natural kind. (shrink)

The architects of the modern synthesis banned essentialism from evolutionary theory. This rejection of essentialism was motivated by Darwin’s theory of natural selection, and the continuity of evolutionary transformation. Contemporary evolutionary biology witnesses a renaissance of essentialism in three contexts: “origin essentialism” with respect to species and supraspecific taxa, the bar coding of species on the basis of discontinuities of DNA variation between populations, and the search for laws of evolutionary developmental biology. Such “new essentialism” in contemporary biology must be (...) of a new kind that accommodates relational (extrinsic) properties as historical essences and cluster concepts of natural kinds. (shrink)

The philosophy of pattern cladism has been variously explained by reference to the work of Louis Agassiz. The present study analyzes Agassiz's attempt to combine an empirical approach to the study of nature with an idealistic philosophy. From this emerges the problem of empiricism and of the isomorphy between the order of nature and human thinking. The analysis of the writings of Louis Agassiz serves as the basis for discussion of the reality of natural groups as postulated by pattern cladists.

The correct explanation of why species, in evolutionary theory, are individuals and not classes is the cladistic species concept. The cladistic species concept defines species as the group of organisms between two speciation events, or between one speciation event and one extinction event, or (for living species) that are descended from a speciation event. It is a theoretical concept, and therefore has the virtue of distinguishing clearly the theoretical nature of species from the practical criteria by which species may be (...) recognized at any one time. Ecological or biological (reproductive) criteria may help in the practical recognition of species. Ecological and biological species concepts are also needed to explain why cladistic species exist as distinct lineages, and to explain what exactly takes place during a speciation event. The ecological and biological species concepts work only as sub-theories of the cladistic species concept and if taken by themselves independently of cladism they are liable to blunder. The biological species concept neither provides a better explanation of species indivudualism than the ecological species concept, nor, taken by itself, can the biological species concept even be reconciled with species individualism. Taking the individuality of species seriously requires subordinating the biological, to the cladistic, species concept. (shrink)

The taxa that appear in biological classifications are commonly seen as representing information about the traits of their member organisms. This paper examines in what way taxa feature in the storage and retrieval of such information. I will argue that taxa do not actually store much information about the traits of their member organisms. Rather, I want to suggest, taxa should be understood as functioning to localize organisms in the genealogical network of life on Earth. Taxa store information about where (...) organisms are localized in the network, which is important background information when it comes to establishing knowledge about organismal traits, but it is not itself information about these traits. The view of species and higher taxa that is proposed here follows from examining three problems that occur in contemporary biological systematics and are discussed here: the problem of generalization over taxa, the problem of phylogenetic inference, and the problematic nature of the Tree of Life. (shrink)

The taxa that appear in biological classifications are commonly seen as representing information about the traits of their member organisms. This paper examines in what way taxa feature in the storage and retrieval of such information. I will argue that taxa do not actually store much information about the traits of their member organisms. Rather, I want to suggest, taxa should be understood as functioning to localize organisms in the genealogical network of life on Earth. Taxa store information about where (...) organisms are localized in the network, which is important background information when it comes to establishing knowledge about organismal traits, but it is not itself information about these traits. The view of species and higher taxa that is proposed here follows from examining three problems that occur in contemporary biological systematics and are discussed here: the problem of generalization over taxa, the problem of phylogenetic inference, and the problematic nature of the Tree of Life. (shrink)

The term “cladist” has distinct meanings in distinct contexts. Communication between philosophers, historians, and biologists has been hindered by different understandings of the term in various contexts. In this paper I trace historical and conceptual connections between several broadly distinct senses of the term “cladist”. I propose seven specific definitions that capture distinct contemporary uses. This serves to disambiguate some cases where the meaning is unclear, and will help resolve apparent disagreements that in fact result from conflicting understandings of the (...) term. (shrink)

We analyze the relationship between evolutionary theory and classification of higher taxa in the work of three ichthyologists: Albert C.L.G. Günther (1830–1914), Edward Drinker Cope (1840–1897), and Theodore Gill (1837–1914). The progress of ichthyology in the early years following the Origin has received little attention from historians, and offers an opportunity to further evaluate the extent to which evolutionary theorizing influenced published views on systematic methodology. These three ichthyologists held radically different theoretical views. The apparent commensurability of claims about relationships (...) among groups of fishes belies differences in what the relationships actually were supposed to be. As well, interpreting classification as genealogical did not lead to agreement about taxonomic methodology; instead, applying evolutionary theory raised new axes of disagreement. (shrink)

Roderic Page’s new book, Tangled Trees: Phylogeny, Cospeciation and Coevolution (2003), is a worthwhile read for anyone interested in either methodological issues in systematics, or how organisms shape one another’s selective environments. “Cospeciation,” for the uninitiated, is the concurrent speciation of two or more lineages that are ecologically associated (e.g. host-parasite associations, as well as mutualistic or symbiotic associations). “Coevolution,” in contrast, is the reciprocal adaptation of hosts and parasite taxa. The main focus of Page’s book is thus when, how (...) and why the branching process of host taxa mirrors that of parasite taxa. “Parasite” here is broadly conceived to be anything from a louse to a virus to a retrotransposon, and “host” may be anything from a genome to a whale. (shrink)

All biologists use classifications to one degree or another, and those of us who work on classifications use the results of all other biologists to one degree or another, so you might reasonably expect that biologists in general would share some common conception of how classifications should be constructed and how they can be used. Certainly one might expect that all taxonomists, at least, would share such a perspective. But this is not the case; in fact, the theory of taxonomy (...) is at present a very controversial subject, with much of the controversy revolving around the question of how to go about constructing an ideal classification.Surprisingly, there is relatively little controversy about what properties an ideal classification would have. Admittedly, different terms are used to describe these properties, various workers arguing that classifications should be maximally stable, or maximally useful, or maximally informative, or maximally testable, or maximally refutable, or maximally predictive, and so on. (shrink)

Although emotion is closely associated with motivation, and interacts with perception, cognition, and action, many conceptualizations still treat emotion as separate from these domains. Here, a comparative/evolutionary anatomy framework is presented to motivate the idea that long-range, distributed circuits involving the midbrain, thalamus, and forebrain are central to emotional processing. It is proposed that emotion can be understood in terms of large-scale network interactions spanning the neuroaxis that form “functionally integrated systems.” At the broadest level, the argument is made that (...) we need to move beyond a Newtonian view of causation to one involving complex systems where bidirectional influences and nonlinearities abound. Therefore, understanding interactions between subsystems and signal integration becomes central to unraveling the organization of the emotional brain. (shrink)

Determining whether a homoplastic trait is the result of convergence or parallelism is central to many of the most important contemporary discussions in biology and philosophy: the relation between evolution and development, the importance of constraints on variation, and the role of contingency in evolution. In this article, I show that two recent attempts to draw a black-or-white distinction between convergence and parallelism fail, albeit for different reasons. Nevertheless, I argue that we should not be afraid of gray areas: a (...) clarified version of S. J. Gould's earlier account, based on a separation of underlying developmental mechanisms from the realized trait, still represents a useful approach. (shrink)

This article characterizes various species concepts in terms of set-theoretic models that license biological inferences and illustrates the logical connections among different species concepts. Species in this construal are abstract models, rather than biological or even tangible entities, and relate to individual organisms via representation, rather than the membership or mereological whole/part relationship. The proposal sheds new light on vexed issues of species and situates them within broader philosophical contexts of model selection, scientific representation, and scientific realism.

Phylogenies are increasingly prominent across all of biology, especially as DNA sequencing makes more and more trees available. However, their utility is compromised by widespread misconceptions about what phylogenies can tell us, and improved tree thinking is crucial. The most-serious problem comes from reading trees as ladders from left to right - many biologists assume that species-poor lineages that appear early branching or basal are ancestral - we call this the primitive lineage fallacy. This mistake causes misleading inferences about changes (...) in individual characteristics and leads to misrepresentation of the evolutionary process. The problem can be rectified by considering that modern phylogenies of present-day species and genes show relationships among evolutionary cousins. Emphasizing that these are extant entities in the 21st century will help correct inferences about ancestral characteristics, and will enable us to leave behind 19th century notions about the ladder of progress driving evolution. (shrink)

The idea that clades might be units of selection, defended by a number of biologists and philosophers of biology, is critically examined. I argue that only entities which reproduce, i.e. leave offspring, can be units of selection, and that a necessary condition of reproduction is that the offspring entity be able, in principle, to outlive its parental entity. Given that clades are monophlyetic by definition, it follows that clades do not reproduce, so it makes no sense to talk about a (...) clade's fitness, so clade selection is impossible. Three possible responses to this argument are examined and found wanting. (shrink)

There is long-standing conflict between genealogical and developmental accounts of homology. This paper provides a general framework that shows that these accounts are compatible and clarifies precisely how they are related. According to this framework, understanding homology requires both an abstract genealogical account that unifies the application of the term to all types of characters used in phylogenetic systematics and locally enriched accounts that apply only to specific types of characters. The genealogical account serves this unifying role by relying on (...) abstract notions of ‘descent’ and ‘character’. As a result, it takes for granted the existence of such characters. This requires theoretical justification that is provided by enriched accounts, which incorporate the details by which characters are inherited. These enriched accounts apply to limited domains, providing the needed theoretical justification for recognizing characters within that domain. Though connected to the genealogical account of homology in this way, enriched accounts include phenomena that fall outside the scope of the genealogical account. They therefore overlap, but are not nested within, the genealogical account. Developmental accounts of homology are to be understood as enriched accounts of body part homology. Once they are seen in this light, the conflict with the genealogical account vanishes. It is only by understanding the fine conceptual structure undergirding the many uses of the term ‘homology’ that we can understand how these uses hang together. (shrink)

Recent work in the philosophy of scientific concepts has seen the simultaneous revival of operationalism and development of patchwork approaches to scientific concepts. We argue that these two approaches are natural allies. Both recognize an important role for measurement techniques in giving meaning to scientific terms. The association of multiple techniques with a single term, however, raises the threat of proliferating concepts (Hempel, 1966). While contemporary operationalists have developed some resources to address this challenge, these resources are inadequate to account (...) for the full range of complex behaviors of scientific concepts. We adopt show how the patchwork approach’s repertoire of inter-patch relations can expand the resources available to the operationalist. We focus on one especially important type of inter-patch relation: sharing a general reasoning strategy. General reasoning strategies serve two important functions: (1) they bind together distinct patches of scientific concepts, and (2) they provide normative guidance for extending concepts to new domains. (shrink)

This article defends lineage pluralism; the view that biological lineages are not a single, unified type of entity. I analyze aspects of evolutionary theory, phylogenetics, and developmental biology to show that these areas appeal to distinct notions of lineage. I formulate three arguments for lineage pluralism. These arguments undercut the main motivations for lineage monism; the view that biological lineages are a single, unified type of entity. Although this view is rarely made explicit, it is often assumed in philosophy and (...) biology. Hence, this article sheds light on this monistic assumption and shows why lineage pluralism should be adopted instead. (shrink)

According to the species-as-individuals thesis(hereafter S-A-I), species are cohesive entities. Barker and Wilson recently pointed out that the type of cohesion exhibited by species is fundamentally different from that of organisms (paradigmatic individuals), suggesting that species are homeostatic property cluster kinds. In this article, I propose a shift in how to approach cohesion in the context of S-A-I: instead of analyzing the different types of cohesion and questioning whether species have them, I focus on the role played by cohesion in (...) the identity of individuals. This shift allows us to recognize why cohesion matters to S-A-I, as well as to reconceive the analogy between species and organisms (paradigmatic individuals), and also allows us to highlight the context sensitivity of both ‘‘cohesion’’ and ‘‘individuals.’’ From this perspective, I identify two problems in Barker and Wilson’s argumentation. Firstly, the authors fail to recognize that species are individuals even if they do not have the same type of cohesion that organisms have. Secondly, their argument relies on a misinterpretation of S-A-I. I conclude that species cohesion is still best framed as a feature of species individuality rather than a feature of species as homeostatic property cluster kinds. The arguments presented here contribute to the re-articulation and reevaluation of S-A-I in the face of contemporary discussions. (shrink)

Ontological understanding of biological units is crucial to their use in experimental design, analysis, and interpretation. Conceptualizing fundamental units in biology as individuals or classes is important for subsequent development of discovery operations. While the criteria for diagnosing individuals are acknowledged, temporal boundedness is often misinterpreted and temporal minima are applied to units in question. This results in misdiagnosis or abandonment of ontological interpretation altogether. Biological units such as areas of endemism in biogeography and species in evolutionary biology fall victim (...) to such problems. Our goal here is to address the misconception that biological individuals such as species and areas of endemism have a temporal minimum. Areas of endemism can persist within small temporal boundaries in the context of metapopulation dynamics, island biogeography, and range expansion and contraction. Similarly, lineage reticulation illustrates examples of short-lived species. Here, examples of known entities are provided to illustrate their persistence on short time scales in attempt to rescue future interpretation of biological units from ontological misdiagnosis, elucidate the philosophical individuality of areas of endemism and species with short lifespans, and provide justification for the “snapshot in time” diagnostic approach. (shrink)

Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those who (...) created them, and unable to serve as inputs for automated reasoning. This volume shows, in a nontechnical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends. (shrink)

The biogeographic contributions of Léon Croizat (1894–1982) and the conflictive relationships with his intellectual descendants and critics are analysed. Croizat’s panbiogeography assumed that vicariance is the most important biogeographic process and that dispersal does not contribute to biogeographic patterns. Dispersalist biogeographers criticized or avoided mentioning panbiogeography, especially in the context of the “hardening” of the Modern Synthesis. Researchers at the American Museum of Natural History associated panbiogeography with Hennig’s phylogenetic systematics, creating cladistic biogeography. On the other hand, a group of (...) New Zealand biologists formalized Croizat’s original concepts and soon began arguing with cladistic biogeographers over the relative merits of their approaches. In Latin America, panbiogeography and cladistic biogeography were incorporated as parts of an integrative approach. A recent development, molecular panbiogeography, is based on the use of molecular phylogenetic data. The current practice shows that some authors insist on considering panbiogeography as the only appropriate approach and vicariance as the only relevant process, whereas others accept Croizat’s dictum “Earth and life evolve together” as a useful guide to understanding broad, general patterns, but recognize that dispersal also contributes substantially to biotic assembly. The framework of integrative pluralism allows to explain the complexities of the biogeographic processes involved in biotic assembly without the need of unification on a large scale. This historical analysis intersects with the existing historiography of the Modern Synthesis and may provide some insights on the dynamics of integrative pluralism, which may be especially relevant in the current development of the Extended Synthesis. (shrink)

The concept of individuality as applied to species, an important advance in the philosophy of evolutionary biology, is nevertheless in need of refinement. Four important subparts of this concept must be recognized: spatial boundaries, temporal boundaries, integration, and cohesion. Not all species necessarily meet all of these. Two very different types of pluralism have been advocated with respect to species, only one of which is satisfactory. An often unrecognized distinction between grouping and ranking components of any species concept is necessary. (...) A phylogenetic species concept is advocated that uses a grouping criterion of monophyly in a cladistic sense, and a ranking criterion based on those causal processes that are most important in producing and maintaining lineages in a particular case. Such causal processes can include actual interbreeding, selective constraints, and developmental canalization. The widespread use of the biological species concept is flawed for two reasons: because of a failure to distinguish grouping from ranking criteria and because of an unwarranted emphasis on the importance of interbreeding as a universal causal factor controlling evolutionary diversification. The potential to interbreed is not in itself a process; it is instead a result of a diversity of processes which result in shared selective environments and common developmental programs. These types of processes act in both sexual and asexual organisms, thus the phylogenetic species concept can reflect an underlying unity that the biological species concept can not. (shrink)

Changes in the methodology of the historical sciences make them more vulnerable to unjustifiable speculations being passed off as scientific results. The integrity of historical science is in peril due the way speculative and often unexamined causal assumptions are being used to generate data and underpin the identification of correlations in such data. A step toward a solution is to distinguish between plausible and speculative assumptions that facilitate the inference from measured and observed data to causal claims. One way to (...) do that is by comparing these assumptions against a well-attested set of aspects of causation, such as the so-called “Bradford Hill Criteria”. The BHC do not provide a test for causation or necessary and sufficient conditions for causation but do indicate grounds for further investigation. By revising the BHC to reflect the needs and focus of historical sciences, it will be possible to assess the cogency of methods of investigation. These will be the Historical Sciences Bradford Hill Criteria. An application to one area in historical science is used to demonstrate the effectiveness of the HSBHC, namely biogeography. Four methods are assessed in order to show how the HSBHC can be used to examine the assumptions between our data and the causal biogeographical processes we infer. (shrink)