Despite the amount of work that has been produced on the subject over the years, the ‘transformation of cladistics’ is still a misunderstood episode in the history of comparative biology. Here, I analyze two outstanding, highly contrasting historiographic accounts on the matter, under the perspective of an influential dichotomy in the philosophy of science: the opposition between Scientific Realism and Empiricism. Placing special emphasis on the notion of ‘causal grounding’ of morphological characters in modern developmental biology’s theories, I arrive (...) at the conclusion that a ‘new transformation of cladistics’ is philosophically plausible. This ‘reformed’ understanding of ‘pattern cladistics’ entails retaining the interpretation of cladograms as ‘schemes of synapomorphies’, but in association to construing cladogram nodes as ‘developmental-genetic taxic homologies’, instead of ‘standard Darwinian ancestors’. The reinterpretation of pattern cladistics presented here additionally proposes to take Bas Van Fraassen’s ‘constructive empiricism’ as a philosophical stance that could properly support such analysis of developmental-genetic data for systematic purposes. The latter suggestion is justified through a reappraisal of previous ideas developed by prominent pattern cladists , which concerned a scientifically efficient ‘observable/non-observable distinction’ linked to the conceptual pair ‘ontogeny and phylogeny’. Finally, I argue that a robust articulation of Antirealist alternatives in systematics may provide a rational basis for its disciplinary separation from evolutionary biology, as well as for a critical reconsideration of the proper role of certain Scientific Realist positions, currently popular in comparative biology. (shrink)

The fundamental Hennigian principle, grouping solely on synapomorphy, is seldom used in modern phylogenetics. In the submitted paper, we apply this principle in reanalyzing five datasets comprising 197 complete plastid genomes (plastomes). We focused on the latter because plastome-based DNA sequence data gained dramatic popularity in molecular systematics during the last decade. We show that pattern-cladistic analyses based on complete plastid genome sequences can successfully resolve affinities between plant taxa, simultaneously simplifying both the genomic and analytical frameworks of phylogenetic (...) studies. We developed “Matrix to Newick” (M2N), a program to represent the standard molecular alignment of plastid genomes in the form of trees or relationships directly. Thus, massive plastome-based DNA sequence data can be successfully represented in a relational form rather than as a standard molecular alignment. Application of methods of median supertree construction (the Average Consensus method has been used as an example in this study) or Maximum Parsimony analysis to relational representations of plastome sequence data may help systematist to avoid the complicated assumption-based frameworks of Maximum Likelihood or Bayesian phylogenetics that are most used today in massive plastid sequence data analyses. We also found that significant amounts of pure genomic information that typically accommodate the majority of current plastid phylogenomic studies can be effectively dropped by systematists if they focus on the pattern-cladistics or relational analyses of plastome-based molecular data. The proposed pattern-cladistic approach is a powerful and straightforward heuristic alternative to modern plastome-based phylogenetics. (shrink)

Here, I consider the recent application of phylogenetic methods in historical linguistics. After a preliminary survey of one such method, i.e. cladistic parsimony, I respond to two common criticisms of cultural phylogenies: that cultural artifacts cannot be modeled as tree-like because of borrowing across lineages, and that the mechanism of cultural change differs radically from that of biological evolution. I argue that while perhaps remains true for certain cultural artifacts, the nature of language may be such as to side-step this (...) objection. Moreover, I explore the possibility that cladistic parsimony can be justified even if is true by appealing to the inference pattern known among philosophers as ‘Inference to the Best Explanation’. (shrink)

Quinn offered seven definitions of “cladist” and discussed the context in which they are used in relation to historical and current debates in systematics. As a member of her study taxon, I offer some contextual color commentary, clarifications on the views of “pattern cladists” regarding monophyly, ancestors, synapomorphy and other concepts, a definition of “syncretist”, and some thoughts on cladistics and philosophy in the twenty first century.

Summary The journal Systematic Zoology is studied in order to see what effect factionalism in the taxonomic community had on the refereeing process. Publication patterns in the journal were largely independent of changes in editorship. Although the taxonomic community was subdivided into feuding factions during the period under study, little bias along these lines was discernible in the refereeing process when studied statistically. Several explanations are suggested for the wide-spread impression at the time that bias was pervasive.

The phylogenetic species concept is applied for the first time to a major radiation of birds, the birds-of-paradise (Paradisaeidae) of Australasia. Using the biological species concept, previous workers have postulated approximately 40–42 species in the family. Of these, approximately 13 are monotypic and 27 are polytypic with about 100 subspecies. Phylogenetic species are irreducible (basal) clusters of organisms (terminal taxa) that are diagnosably distinct from other such clusters. Within the context of this concept, approximately 90 species of paradisaeids are postulated (...) to have diversified within Australasia. The phylogenetic species concept more accurately describes evolutionary diversity within the family and provides a better theoretical and empirical framework for analysing speciation, historical biogeography and patterns of morphological, behavioral and ecological diversification within this group than does the biological species concept. (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 (...) class='Hi'>pattern cladists. (shrink)

An interesting metatheoretical controversy took place during the 1980’s and 1990’s between pattern and phylogenetic cladists. What was always at stake in the discussion was not how work in systematics should be carried out, but rather how this practice should be metatheoretically interpreted. In this article, we criticize Pearson’s account of the metatheoretical factors at play in this discussion. Following him, we focus on the issue of circularity, and on the role that phylogenetic hypotheses play in the determination of (...) “primary homologies”. Pearson argues that the recognition of primary homologies cannot be achieved without recourse to previous phylogenetic knowledge, and that to claim otherwise is to state that primary homologies are observable. To show why that view would be inadequate, he appeals to Hanson’s views about theory-laden observation, alongside with a specific case study, which allegedly illustrates the more complex relation between observation and theory. We will argue that the pattern cladists’ point is better addressed by taking a quite different approach: instead of thinking in terms of observability, the topic can be tackled by paying attention to the way in which concepts are determined. We will take the notion of T-theoricity from metatheoretical structuralism and show that, once the issue is discussed with the appropriate metatheoretical framework, the alleged counterexample brought up by Pearson is not problematic at all for pattern cladism. (shrink)

Deduction leads to causal explanation in phylogenetic inference when the evidence, the systematic character, is conceptualized as a transformation series. Also, the deductive entailment of modus tollens is satisfied when those kinds of events are operationalized as patristic difference. Arguments to the contrary are based largely on the premise that character-states are defined intensionally as objects, in terms of similarity relations. However, such relations leave biologists without epistemological access to the causal explanation and explanatory power of historical statements. Moreover, the (...) prediction-making to which those kinds of relations are limited in practice can lead to a category error—the mental conversion of an abstraction into a thing . The latter practices and problems characterize pattern cladistics, taxa being interpreted as homeostatic property cluster natural kinds, and other instrumentalist research programs. (shrink)

Roffe et al. develop a rather creative line of response to Pearson’s :475–492, 2010) critique of pattern cladisma response centering on a structuralist approach to the homology concept. In this brief reply I attempt to demonstrate, however, that Roffe, and Ginnobili, and Blanco subtly mis-characterize the target of Pearson’s critique. The consequence of this mischaracterization is that even though the structuralist framework may help make sense of pattern cladism, it does not undermine Pearson’s critique of it.

The role of scientific theories in classifying plants and animals is traced from Hennig's phylogenetics and the evolutionary taxonomy of Simpson and Mayr, through numerical phenetics, to present-day cladistics. Hennig limited biological classification to sister groups so that this one relation can be expressed unambiguously in classifications. Simpson and Mayr were willing to sacrifice precision in representation in order to include additional features of evolution in the construction of classifications. In order to make classifications more objective, precise and quantitative, (...) numerical pheneticists limited themselves to representing degrees of phenetic similarity. Finally, present-day cladists can be separated into phylogenetic cladists, who retain much of Hennig's theory of classification, and pattern cladists, who have stripped Hennig's system down to its bare essentials. (shrink)

The role of scientific theories in classifying plants and animals is traced from Hennig's phylogenetics and the evolutionary taxonomy of Simpson and Mayr, through numerical phenetics, to present-day cladistics. Hennig limited biological classification to sister groups so that this one relation can be expressed unambiguously in classifications. Simpson and Mayr were willing to sacrifice precision in representation in order to include additional features of evolution in the construction of classifications. In order to make classifications more objective, precise and quantitative, (...) numerical pheneticists limited themselves to representing degrees of phenetic similarity. Finally, present-day cladists can be separated into phylogenetic cladists, who retain much of Hennig's theory of classification, and pattern cladists, who have stripped Hennig's system down to its bare essentials. (shrink)

Why has it been so difficult to integrate paleontology and mainstream evolutionary biology? Two common answers are: (1) the two fields have fundamentally different aims, and (2) the tensions arise out of disciplinary squabbles for funding and prestige. This paper examines the role of fossil data in phylogeny reconstruction in order to assess these two explanations. I argue that while cladistics has provided a framework within which to integrate fossil character data, the stratigraphic (temporal) component of fossil data has (...) been harder to integrate. A close examination of how fossil data have been used in phylogeny reconstruction suggests that neither explanation is adequate. While some of the tensions between the fields may be intellectual turf wars, the second explanation downplays the genuine difficulty of combining the distinctive data of the two fields. Furthermore, it is simply not the case that the two fields pursue completely distinct aims. Systematists do disagree about precisely how to represent phylogeny (e.g., minimalist cladograms or trees with varying levels of detail) but given that every tree presupposes a pattern of branching (a cladogram), these aims are not completely distinct. The central problem has been developing methods that allow scientists to incorporate the distinctive bodies of data generated by these two fields. Further case studies will be required to determine if this explanation holds for other areas of interaction between paleontology and neontology. (shrink)

This chapter contains sections titled: Introduction From Art to Science: An Introduction to Schools of Thought How to Infer Phylogeny, Or, Why Some Cladists Aren't “Cladists” Summary and Synthesis Acknowledgment References.

Many of the current comparisons of taxic phylogenetic and biological homology in the context of morphology focus on what are seen as categorical distinctions between the two concepts. The first, it is claimed, identifies historical patterns of conservation and variation relating taxa; the second provides a causal framework for the explanation of this conservation and variation. This leads to the conclusion that the two need not be placed in conflict and are in fact compatible, having non-competing epistemic purposes or mapping (...) the same extensions in the form of monophyletic groupings (see Roth, The biological basis of homology 1–26, 1988; Sluys, J Zool Syst Evol Res 34:145–152, 1996; Abouheif, Trends Ecol Evol 12:405–408, 1997; Brigandt, J Exp Zool 299:9–17, 2003, Biol Philos 22:709–725, 2007; Assis and Brigandt, Evol Biol 36:248–255, 2009). This article argues that moves in this direction miss the essential disagreement between these concepts as they have been developed in the context of the debate concerning the best concept for evolutionary investigation. We should rather see these concepts employing a common fundamental methodological approach to homology, but disagreeing about how to apply the methodology effectively. Both concepts employ class reasoning, which pursues homologies as units of generalization—more precisely, as sources of reliable and relevant group-bound information in the form of shared underlying causes. The dispute can be better understood by two poles that structure such reasoning: the need for a reliable basis for projections about the causal history of shared structures, and the desire to identify homologous characters with more informative and specific causal information relevant to generalizing about evolutionary processes. Judgments in favor of one or the other in turn have affected the scope or extension of these competing homology concepts. (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)

Although features of the dentition figure prominently in discussions of early hominid phylogeny, remarkably little is known of the developmental basis of the variations in occlusal morphology and dental proportions that are observed among taxa. Recent experiments on tooth development in mice have identified some of the genes involved in dental patterning and the control of tooth specification. These findings provide valuable new insight into dental evolution and underscore the strong developmental links that exist among the teeth and the jaws (...) and cranium. The latter has important implications for cladistic studies that traditionally consider features of the skull independently from the dentition. BioEssays 23:481–493, 2001. © 2001 John Wiley & Sons, Inc. (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)

Overview * Part I: Introduction * Philip Appleman, Darwin: On Changing the Mind * Part II: Darwin’s Life * Ernst Mayr, Who Is Darwin? * Part III: Scientific Thought: Just before Darwin * Sir Gavin de Beer, Biology before the Beagle * Thomas Robert Malthus, An Essay on the Principle of Population * William Paley, Natural Theology * Jean Baptiste Pierre Antoine de Monet Lamarck, Zoological Philisophy * Charles Lyell, Principles of Geology * John Herschell, The Study of Natural Philosophy (...) * William Whewell, Astronomy and General Physics Considered with Reference to Natural Theology * Alfred Russel Wallace, On the Tendency of Varieties to Depart Indefinitely from the Original Type * Part IV: Selections from Darwin’s Work * The Voyage of the Beagle * o Chapter I. St. Jago-Cape de Verd Island o Chapter XVII. Galapagos Archipelago * On the Tendency of Species to Form Varieties; and On the Perpetuation of Varieties and Species by Natural Means of Selection * o I. Extract from an unpublished Work on Species, by C. Darwin, Esq.... o II.of Letter from C. Darwin, Esq., to Prof. Asa Gray, Boston, U.S., dated Down, September 5th, 1857 * An Historical Sketch of the Progress of Opinion on the Origin of Species, previously to the : Publication of This Work The Origin of Species * o Introduction o Chapter I. Variation under Domestication o Chapter II. Variation under Nature o Chapter III. Struggle for Existence o Chapter IV. Natural Selection o Chapter VI. Difficulties on Theory o Chapter IX. On the Imperfections of the Geological Record o Chapter XIII. Mutual Affinities of Organic Beings: Morphology: Embryology: Rudimentary Organs o Chapter XIV. Recapitulation and Conclusion * The Descent of Man * o Introduction o Chapter I. The Evidence of the Descent of Man from Some Lower Form o Chapter II. On the Manner of Development of Man from Some Lower Form o Chapter III. Comparison of the Mental Powers of Man and the Lower Animals o Chapter VI. On the Affinities and Genealogy of Man o Chapter VIII. Principles of Sexual Selection o Chapter XIX. Secondary Sexual Characters of Man o Chapter XX. Secondary Sexual Characters of Man-continued o Chapter XXI. General Summary and Conclusion * Part V: Darwin’s Influence on Science * THE VICTORIAN OPPOSITION TO DARWIN * o David L. Hull, Darwin and His Critics o Adam Sedgwick, Objections to Mr. Darwin’s Theory of the Origin of Species o Sir Richard Owen, Darwin on the Origin of Species o Fleeming Jenkin, Review of the Origin of Species * VICTORIAN SUPPORTERS OF DARWIN * o Joseph Dalton Hooker, Flora Tasmaniae o Thomas Henry Huxley, On the Relations of Man to the Lowe Animals o Charles Lyell, Principles of Geology o Alfred Russel Wallace, The Debt of Science to Darwin * DARWIN AND THE SHAPING OF MODERN SCIENCE * o Scientific Method in Evolution o National Academy of Sciences, Evolution and the Nature of Science o Richard Dawkins, Explaining the Very Improbable o Lewis Thomas, On the Uncertainty of Science o Noretta Koetge, Postmodernisms and the Problem of Scientific Literary o Richard Dawkins, Science and Sensibility o The Neo-Darwinian Synthesis o Peter Bowler, The Evolutionary Synthesis o The Human Genealogy o Adam Kuper, The Chosen Primate o Ian Tattersall, Out of Africa Again... and Again? o Stephen Jay Gould, The Human Difference o Punctuated Equilibrium o Stephen Jay Gould, [On Punctuated Equilibrium] o Niles Eldredge, The Great Stasis Debate o Rethinking Taxonomy o Kevin Padian, Darwin’s Views of Classification o David L. Hull, Cladistic Analysis o Kevin Padian and Luis M. Chiappe, Cladistics in Action: The Origin of Birds and Their Flight o Evolution as Observable Fact o James L. Gould and William T. Keeton with Carol Grant Gould, How Natural Selection Operates o Peter r. Grant, Natural Selection and Darwin’s Finches o John A. Endler, Natural Selection in the Wild * Part VI: Darwinian Patterns in Social Thought * COMPETITION AND COOPERATION * o Richard Hofstadter, The Vogue of Spencer o Andrew Carnegie, The Gospel of Wealth o Peter Kropotkin, Mutual Aid o Martin A. Nowak, Robert M. May, and Karl Sigmund, The Arithmetics of Mutual Help * NATURE AND NURTURE * o Edward O. Wilson, Sociobiology: The New Synthesis o Stephen Jay Gould, Biological Potentiality vs. Biological Determination o Barbara Ehrenreich and Janet McIntosh, The New Creationism: Biology under Attack * EVOLUTION AND GENDER * o Elizabeth Cady Stanton, The Woman’s Bible o Nancy Makepeace Tanner, On Becoming Human o Evelleen Richards, Darwin and the Descent of Woman o James Eli Adams, Woman Red in Tooth and Claw * EVOLUTION AND OTHER DISCIPLINES * o Edward O. Wilson, [On Consilience] o Randolph H. Nesse and George C. Williams, Evolution and the Origin of Disease o Steven Pinker, How the Mind Works o Steve Jones, The Set within the Skull * Part VII: Darwinian Influences in Philosophy and Ethics * John Dewey, The Influence of Darwin on Philosophy * Daniel C. Dennett, Darwin’s Dangerous Idea: Natural Selection as an Algorithmic Process * Michael Ruse Darwinian Epistemology * Thomas Henry Huxley, Evolution and Ethics * Julian Huxley, Evolutionary Ethics * Michael Ruse and Edward O. Wilson, The Evolution of Ethics * Frans de Waal, Good Natured: The Origin of Right and Wrong in Humans and Other Animals * Matt Ridley, The Origins of Virtue * Part VIII: Evolutionary Theory and Religious Theory * MAINSTREAM RELIGIOUS SUPPORT FOR EVOLUTION * o Pope John Paul II, Message to the Pontifical Academy of Sciences o Central Conference of American Rabbis, On Creationism in School Textbooks o United Presbyterian Church in the U.S.A., Evolution and Creationsim o The Lutheran World Federation, [Statement on Evolution] o The General Convention of the Episcopal Church, Resolution on Evolutionism and Creationism o Unitariuan Universalist Association, Resolution Opposing "Scientific Creationism" * FUNDAMENTALIST CREATIONISM * o Eugene C. Scott, Antievolution and Creationism in the United States o The Scopes Trial o Thomas McIver, Orthodox Jewish Creationists o Harun Yahya, [Islamic Creationism] o Seami Srila Prabhupada, [A Hare Krishna on Darwinian Evolution] o Institute for Creation Research, Tenets of Creationism o Henry M. Morris, Scientific Creationism o Thomas J. Wheeler, Review of Morris o Richard D. Sjolund and Betty McCollister, Evolution at the Grass Roots o Richard D. Sjolund, [Creationism versus Biotechnology] o Betty McCollister, [The Politics of Creationism] o Molleen Matsumara, What Do Christians Really Believe about Evolution? o National Center for Science Education, Seven Significant Court Decisions Regarding Evolution/Creation Issues * PERSONAL INCREDULITY AND ANTIEVOLUTIONISM * o Richard Dawkins, [The Argument from Personal Incredulity] o Phillip E. Johnson, Darwin on Trial o Eugenie C. Scott, Review of Johnson o Michael Behe, Darwin’s Black Box o Robert Dorit, Review of Behe o Michael Ruse, Darwin’s New Critics on Trial * SCIENTISTS’ OPPOSITION TO CREATIONISM * o American Association for the Advancement of Science, Forced Teaching of Creationist Beliefs in Public School Science Education o American Institute of Biological Sciences, Resolution Oposing Creationism in Science Courses o National Association of Biology Teachers, Statement on Teaching Evolution o National Academy of Sciences, Frequently Asked Questions about Evolution and the Nature of Science * FUNDAMENTALIST CREATIONISM AND THE VALUE OF SATIRE * o Michael Shermer, Genesis Revisted: A Scientific Creation Story o Philip Appleman, Darwin’s Ark * Part IX: Darwin and the Literary Mind * DARWIN’S LITERARY SENSIBILITY * o Charles Darwin, Autobiography o L. Robert Stevens, Darwin’s Humane Reading o George Levine, Darwin and Pain: Why Science Made Shakespeare Nauseating o Gillian Beer, Darwin’s Plots * DARWIN’S INFLUENCE ON LITERATURE * o Lionel Stevenson, Darwin among the Poets o George Levine, Darwin among the Novelists o Joseph Wood Krutch, The Tragic Fallacy o Herbert J. Muller, Modern Tragedy o Philip Appleman, Darwin-Sightings in Recent Literature. (shrink)

Many contemporary race scholars reject the biological reality of race.Elsewhere I have argued that they have been too quick to do so. Part ofthe reason is that they have overlooked the possibility that races canbe defined cladistically. Since the publication of the cladistic raceconcept, a number of questions and objections have been raised. My aimin this paper is to address these objections.

Cladism, today the dominant school of systematics in biology, includes a classification component – the view that classification ought to reflect phylogeny only, such that all and only taxa are monophyletic (i.e. consist of an ancestor and all its descendants) - and a metaphysical component – the view that all and only real groups or kinds of organisms are monophyletic. For the most part these are seen as amounting to much the same thing, but I argue they can and should (...) be distinguished, in particular that cladists about classification need not accept the typically cladist view about real groups or kinds. Cladists about classification can and should adopt an explanatory criterion for the reality of groups or kinds, on which being monophyletic is neither necessary nor sufficient for being real or natural. Thus the line of reasoning that has rightly led to cladism becoming dominant within systematics, and the attractive line of reasoning in the philosophical literature that advocates a more liberal approach to natural kinds, are seen to be, contrary to appearances, compatible. (shrink)

I adopt a cladistic view of species, and explore the possibility that there exists an equally valuable cladistic view of organismic traits. This suggestion seems to run counter to the stress on functional views of biological traits in recent work in philosophy and psychology. I show how the tension between these two views can be defused with a multilevel view of biological explanation. Despite the attractions of this compromise, I conclude that we must reject it, and adopt an essentially cladistic (...) conception of biological traits. (shrink)

The goal of cladistic systematics is to discern sister-group relations (cladistic relations) by the methods of cladistic analysis and to represent them explicitly and unambiguously in cladograms and cladistic classifications. Cladists have selected cladistic relations to represent for two reasons: cladistic relations can be discerned with reasonable certainty by the methods of cladistic analysis and they can be represented with relative ease in cladograms and classifications. Cladists argue that features of phylogeny other than cladistic relations cannot be discerned with sufficient (...) certainty to warrant attempting to represent them in either cladograms or classifications and could not be represented if they could. I argue that a better alternative is to work toward improving methods of cladistic analysis (or else to supplement them with other methods) so that such features of phylogeny can be discerned and to devise methods of representation capable of representing them in both cladograms and classifications. However, cladograms and classifications cannot represent everything about phylogeny. It is better to represent one or two aspects of phylogeny explicitly and unambiguously than nothing at all. (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)

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)

In the article titled ‘A new perspective on the race debate’，Robin O. Andreasen argues that contrary to popular scientific belief, human races are biologically real—it is just that we are wrong about them. Andreasen calls her contemporary biological concept of race ‘the cladistic race concept’ (or CRC). Her theory uses theory from cladistics—a systematic school founded by entomologist Willi Hennig in 1950—to define human races genealogically as cladistic subspecies. In this paper I will argue that despite its promise as (...) a biological definition of human races, Andreasen's CRC is unconvincing. In particular, I will show that the central problem of the CRC is its attempt to apply cladistics below the species level. In other words, there is good reason to think that cladistic subspecies are not real, and therefore, they cannot be the target of a realist concept of race. (shrink)

In this article, I assess the prospects for the limitarian thesis that someone has too much wealth if they exceed a specific wealth threshold. Limitarianism claims that there are good political and/or ethical reasons to prevent people from having such ‘surplus wealth’, for example, because it has no moral value for the holder or because allowing people to have surplus wealth has less moral value than redistributing it. Drawing on recent literature on distributive justice, I defend two types of limitarian (...) principles of justice. First, limitarian midlevel principles draw on the limitarian thesis to specify normative commitments for guiding institutional design and individual actions. Second, the limitarian presumption draws on that thesis to specify what a just allocation of wealth requires under epistemic constraints. Such a presumption says that without substantive reasons to the contrary, we should regard a distribution as unjust if some people’s wealth exceeds the limitarian threshold. Furthermore, I will argue that we must reject a possible but implausible interpretation of limitarianism as an ideal distributive pattern. Yet both as a midlevel principle and as a presumption, limitarianism can play an important role in theorizing about justice in the real world. (shrink)

Ordinary people often make moral judgments that are consistent with philosophical principles and legal distinctions. For example, they judge killing as worse than letting die, and harm caused as a necessary means to a greater good as worse than harm caused as a side-effect (Cushman, Young, & Hauser, 2006). Are these patterns of judgment produced by mechanisms specific to the moral domain, or do they derive from other psychological domains? We show that the action/omission and means/side-effect distinctions affect nonmoral representations (...) and provide evidence that their role in moral judgment is mediated by these nonmoral psychological representations. Specifically, the action/omission distinction affects moral judgment primarily via causal attribution, while the means/side-effect distinction affects moral judgment via intentional attribution. We suggest that many of the specific patterns evident in our moral judgments in fact derive from nonmoral psychological mechanisms, and especially from the processes of causal and intentional attribution. (shrink)

Abstract I argue for a form of particularism from a reading of Wittgenstein's critique of the idea that word use is governed by rules. In place of the idea that word use is driven by rules, I show how the patterns of word use, in virtue of which we express our reasons, emerge from our ongoing practice, including our practice of seeing things as similar. I argue that the notion of seeing the similarities is primitive for Wittgenstein. The remark, ?this (...) and similar things are called ?games?? does not signal a form of ignorance. It signals the constitutive role that speakers, as judges, have to play in the metaphysics of the patterns of word use. (shrink)

In response to Quinn we identify cladistics to be about natural classifications and their discovery and thereby propose to add an eighth cladistic definition to Quinn’s list, namely the systematist who seeks to discover natural classifications, regardless of their affiliation, theoretical or methodological justifications.

Existing explanations of political intolerance and partisanship highlight how individuals’ ideological commitments and the homogeneity of their political environments foster intolerance toward other political groups. This article argues that cultural, interactional conditions play a crucial role in how personal and environmental factors work – or do not work – in local groups. Based on a four-year ethnographic study and 12 focus group discussions with two culturally distinct civic associations of American libertarians, I show how groups’ varying patterns of interaction, or (...) “styles,” establish distinct cultural settings, in which different attitudes and behaviors seem sensible and appropriate, particularly regarding other political groups. Thus, when libertarian groups established a “community style” of interaction, viewing the relationship among members in terms of friendship and community bonds, they also opened their social activities to non-libertarians, collaborated with them in political projects, and viewed politics as a matter of advancing shared interests with people from other political groups. Comparisons across and within field sites show how this relationship between style and political tolerance works in different libertarian groups and different social environments. These findings highlight the role of local factors in explaining variations in groups’ levels of political tolerance and present a key mechanism—centered on interaction patterns—to supplement existing analyses of the relationship between political intolerance and changing forms of civic organizing in the US. (shrink)

Pattern-based reasons are reasons for action deriving not from the features of our own actions, but from the features of the larger patterns of action in which we might be participating. These reasons might relate to the patterns of action that will actually be carried out, or they might relate to merely hypothetical patterns. In past work, I have argued that accepting merely hypothetical pattern-based reasons, together with a plausible account of how to weigh these reasons, can lead (...) to disastrous consequences. However, in this article, I argue that this problem is not limited to hypothetical pattern-based reasons: it turns out that there are analogous issues for reasons deriving from actual patterns. I then suggest that we can avoid this problem by adopting a different account of the weight of pattern-based reasons. (shrink)

The future of awake bruxism assessment will incorporate physiological data, possibly electromyography of the temporal muscles. But up to now, temporal muscle contraction patterns in awake bruxism have not been characterized to demonstrate clinical utility. The present study aimed to perform surface EMG evaluations of people assessed for awake bruxism to identify possible different subtypes. A 2-year active search for people with awake bruxism in three regions of the country resulted in a total of 303 participants. Their inclusion was confirmed (...) through non-instrumental approaches for awake bruxism: self-reported questionnaire and clinical exam, performed by three experienced and calibrated dentists. Also, 77 age- and sex-matched healthy controls were recruited. Temporalis surface EMG was performed with a portable device. EMG signals were sent to a computer via Bluetooth 4.0 at a sampling rate of 1,000 Hz. Digital signal processing was performed using the commercial neuroUP software, transformed in RMS and then normalized for peak detection, in a 10 min session. Cluster analysis revealed three distinct subtypes of awake bruxism: phasic, tonic, and intermediate. Individuals with a predominance of EMG peaks/min were classified as the “phasic” subtype. Those with the highest EMG rest power were classified as the “tonic” subtype. There was also an “intermediate” subtype, when both variables remained low. Characterization of awake bruxism physiology is important for future establishment of instrumental assessment protocols and treatment strategies. (shrink)

Are there really beliefs? Or are we learning (from neuroscience and psychology, presumably) that, strictly speaking, beliefs are figments of our imagination, items in a superceded ontology? Philosophers generally regard such ontological questions as admitting just two possible answers: either beliefs exist or they don't. There is no such state as quasi-existence; there are no stable doctrines of semi-realism. Beliefs must either be vindicated along with the viruses or banished along with the banshees. A bracing conviction prevails, then, to the (...) effect that when it comes to beliefs (and other mental items) one must be either a realist or an eliminative materialist. (shrink)

A solution to Gregg’s paradox is suggested in the spirit of cladistic taxonomy by inverting the usual order in which rank is assigned and working from the apex of the tree.

Via a hermeneutics focused on Chinese numerology and concentric arrangements, the book offers a novel construal of the textual universe proper to early China writings. The author lays bare distinguishable patterns of textual composition while relating them to corresponding patterns of thinking. He differentiates rhetorical variants through detailed studies of the Zhuangzi's Inner chapters, the Laozi, the Analects, and the Huainanzi. The philosophical depth and relevance of the Chinese ancient worldview appear in a fresh light when one unearths the patterns (...) into which its content is embedded. The focus on textual patterns and rhetorical arrangements also facilitates the reading of Chinese classics alongside other traditions. The book will be a valuable reference for scholars and graduate students studying Chinese literary criticism, Chinese philosophy, and comparative philosophy. (shrink)

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

The aims of this paper are to: (1) identify the best framework for comprehending multidimensional impact of deep brain stimulation on the self; (2) identify weaknesses of this framework; (3) propose refinements to it; (4) in pursuing (3), show why and how this framework should be extended with additional moral aspects and demonstrate their interrelations; (5) define how moral aspects relate to the framework; (6) show the potential consequences of including moral aspects on evaluating DBS’s impact on patients’ selves. Regarding (...) (1), I argue that the pattern theory of self can be regarded as such a framework. In realizing (2) and (3), I indicate that most relevant issues concerning PTS that require resolutions are ontological issues, including the persistence question, the “specificity problem”, and finding lacking relevant aspects of the self. In realizing (4), I identify aspects of the self not included in PTS which are desperately needed to investigate the full range of potentially relevant DBS-induced changes—authenticity, autonomy, and responsibility, and conclude that how we define authenticity will have implications for our concept of autonomy, which in turn will determine how we think about responsibility. Concerning (5), I discuss a complex relation between moral aspects and PTS—on one hand, they serve as the lens through which a particular self-pattern can be evaluated; on the other, they are, themselves, products of dynamical interactions of various self-aspects. Finally, I discuss (6), demonstrating novel way of understanding the effects of DBS on patients’ selves. (shrink)