Argues for the primacy of the phylogenetic system as the general reference system in biology. This book, first published in 1966, generated significant controversy and opened possibilities for evolutionary biology.

The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as (...) the first, with many exciting developments yet to come. This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography—the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics. The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes: Parsimony and parsimony analysis Parametric phylogenetics including maximum likelihood and Bayesian approaches Phylogenetic classification Critiques of evolutionary taxonomy, phenetics, and transformed cladistics Specimen selection, field collecting, and curating Systematic publication and the rules of nomenclature Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology. (shrink)

I respond to the bad lot argument in the context of biological systematics. The response relies on the historical nature of biological systematics and on the availability of pattern explanations. The basic assumption of common descent enables systematic methodology to naturally generate candidate explanatory hypotheses. However, systematists face a related challenge in the issue of character analysis. Character analysis is the central problem for contemporary systematics, yet the general problem of which it is a case—what counts as evidence?—has not been (...) adequately discussed by proponents of inference to the best explanation. Facing this problem is the price of adopting abductive methods. I sketch an account of how systematists approach the problem of evidence. (shrink)

The concept of ‘phylogenetic inertia’ is routinely deployed in evolutionary biology as an alternative to natural selection for explaining the persistence of characteristics that appear sub-optimal from an adaptationist perspective. However, in many of these contexts the precise meaning of ‘phylogenetic inertia’ and its relationship to selection are far from clear. After tracing the history of the concept of ‘inertia’ in evolutionary biology, I argue that treating phylogenetic inertia and natural selection as alternative explanations is mistaken because phylogenetic inertia is, (...) from a Darwinian point of view, simply an expected effect of selection. Although Darwin did not discuss ‘phylogenetic inertia,’ he did assert the explanatory priority of selection over descent. An analysis of ‘phylogenetic inertia’ provides a perspective from which to assess Darwin’s view. (shrink)

Feinberg and Mallatt, in their presentation of neurobiological naturalism, have suggested that visual consciousness was acquired by early vertebrates and inherited by a wide range of descendants, and that its neural basis has shifted to nonhomologous nervous structures during evolution. However, their evolutionary scenario of visual consciousness relies on the assumption that visual consciousness is closely linked with survival, which is not commonly accepted in current consciousness research. We suggest an alternative idea that visual consciousness is linked to a specific (...) class of agency, consequently justifying their phylogenetic claim. We also examine the implication of their phylogenetic claim: visual consciousness is homologous across vertebrates, but its neural basis is not. This apparent incongruence illustrates a general phenomenon of homology, and that the resulting hierarchical view of visual consciousness and its neural basis can be straightforwardly accommodated by neurobiological naturalism. Throughout these discussions, we aim to address the potential theoretical issues in neurobiological naturalism and refine the picture illustrated by Feinberg and Mallatt regarding phylogenetic distribution and trajectories of visual consciousness. (shrink)

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon (...) names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names. (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.

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon (...) names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names. (shrink)

In this paper we propose a pragmatic approach to the evolution of language based on analysis of a particular element of human communication: discourse coherence. We show that coherence is essential for effective communication. Through analysis of a collection of neuropsychological and neurolinguistic studies, we maintain that the proper functioning of executive processes responsible for planning and executing actions plays a key role in the construction of coherent discourses. Studies that tested the discursive and conversational abilities of bonobos have showed (...) that apes are unable to construct a flow of discourse governed by coherence, and therefore, apes’ conversational interactions are quite different from those of humans. We then propose that the emergence of coherence in communication occurred after the split between great apes’ and humans’ lines of descendants and that this emergence might have been the result of a specific gradual development in the course of hominin evolution of the executive functions. (shrink)

Phylogenetics has inherent utility in evolutionary developmental biology (EDB) as it is an established methodology for estimating evolutionary relationships and for making comparisons between levels of biological organization. However, explicit phylogenetic methods generally have been limited to two levels of organization in EDB—the species and the gene. We demonstrate that phylogenetic methods can be applied broadly to other organizational levels, such as morphological structures or cell types, to identify evolutionary patterns. We present examples at and between different hierarchical levels (...) of organization to address questions central to EDB. We argue that this application of “hierarchical phylogenetics” can be a unifying analytical approach to the field of EDB. BioEssays 27:1158–1166, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

This chapter develops a subtle model that integrates environmental and internal factors. It describes the phylogenetic distribution of multicellular organisms in general and complex multicellular life in particular, clarifying the important distinction between the two. This chapter shows that the long apparent lag between the appearance of simple multicellularity in eukaryotes and the radiation of groups with complex multicellular organization has an environmental component that can be associated back to the consequences of life with interior and exterior cells. It suggests (...) that the evolutionary transition from unicells to complex multicellular organisms has several steps. (shrink)

The concept of ‘phylogenetic inertia’ is routinely deployed in evolutionary biology as an alternative to natural selection for explaining the persistence of characteristics that appear sub-optimal from an adaptationist perspective. However, in many of these contexts the precise meaning of ‘phylogenetic inertia’ and its relationship to selection are far from clear. After tracing the history of the concept of ‘inertia’ in evolutionary biology, I argue that treating phylogenetic inertia and natural selection as alternative explanations is mistaken because phylogenetic inertia is, (...) from a Darwinian point of view, simply an expected effect of selection. Although Darwin did not discuss ‘phylogenetic inertia,’ he did assert the explanatory priority of selection over descent. An analysis of ‘phylogenetic inertia’ provides a perspective from which to assess Darwin’s view. (shrink)

Cadherins are a multigene family of proteins which mediate homophilic calcium‐dependent cell adhesion and are thought to play an important role in morphogenesis by mediating specific intercellular adhesion. Different lines of experimental evidence have recently indicated that the site responsible for mediating adhesive interactions is localized to the first extracellular domain of cadherin. Based upon an analysis of the sequence of this domain, I show that cadherins can be classified into three groups with distinct structural features. Furthermore, using this sequence (...) information a phylogenetic tree relating the known cadherins was assembled. This is the first such tree to be published for the cadherins. One cadherin subtype, neural cadherin (N‐cadherin), shows very little sequence divergence between species, whereas all other cadherin subtypes show more substantial divergence, suggesting that selective pressure upon this domain may be greater for N‐cadherin than for other cadherins. Phylogenetic analysis also suggests that the gene duplications which established the main branches leading to the different cadherin subtypes occurred very early in their history. These duplications set the stage for the diversified superfamily we now observe. (shrink)

Philosophers examining mechanistic explanations in biology have identified heuristic strategies scientists use in discovering mechanisms. This paper examines the heuristic strategy of investigating phylogenetically distant model organisms, using research on sleep in fruit flies as an example. At the time sleep was discovered in flies in 2000 next to nothing was known about mechanisms regulating sleep in flies and what they could reveal about those in us. One relatively straightforward line of research focused on homologous genes in flies and humans, (...) using those in flies to understand what roles their homologs played in controlling sleep in us. But other research focused on a higher level of organization—the neural networks involved in homeostatic and circadian control of sleep. This raises a puzzle—given that fly and vertebrate brains are organized very differently, how could sleep regulation in flies serve as an informative model of vertebrate sleep? I argue that the basic design of mechanisms such as those regulating sleep can be conserved even as the composition of the mechanism changes and that researchers can hope to use the designs deciphered in flies as heuristic models for understanding sleep in humans. (shrink)

Nonhuman primates don’t have formal kinship systems, but genetic relatedness shapes patterns of residence, behavior, mating preferences, and cognition in the primate order. The goal of this article is to provide insight about the ancestral foundations on which the first human kinship systems were built. In order for evolution to favor nepotistic biases in behavior, individuals need to have opportunities to interact with their relatives and to be able to identify them. Both these requirements impose constraints on the evolution of (...) kinship bonds in primate species. For nonhuman primates and many other mammals, maternal care generates close ties between mothers and offspring and among littermates. For species in which mother–offspring bonds extend beyond weaning, associations with the mother also generate familiarity among siblings of different ages. For species with female philopatry, mother–offspring ties provide the foundation for lifelong relationships between mothers and daughters, and dense matrilineal kin networks. However, several factors constrain the development of kinship bonds in nonhuman primates. First, dispersal strategies, which are designed to reduce inbreeding, bias kinship networks in favor of the philopatric sex. Second, hostile relationships between groups mean that kin ties are usually severed when individuals move from one group to another. Third, in species with polygynandrous mating systems, uncertainty about paternity and restricted periods of male reproductive monopoly limit the scope for development of ties among fathers and offspring, paternal siblings, or extended paternal kin networks. In this article, I explore the impact of these factors on the evolution of ancestral human kinship systems. (shrink)

The phylogenetic data are inconsistent with the hypothesis that REM sleep duration is correlated with learning or learning ability. Humans do not have uniquely high amounts of REM sleep. The platypus, marsupials, and other mammals not generally thought to have extraordinary learning abilities have the largest amounts of REM sleep. The whales and dolphins (cetaceans) have the lowest amounts of REM sleep and may go without REM sleep for extended periods of time, despite their prodigious learning abilities. Vertes & Eastman].

The concept of a temporal phylogenetic network is a mathematical model of evolution of a family of natural languages. It takes into account the fact that languages can trade their characteristics with each other when linguistic communities are in contact, and also that a contact is only possible when the languages are spoken at the same time. We show how computational methods of answer set programming and constraint logic programming can be used to generate plausible conjectures about contacts between prehistoric (...) linguistic communities, and illustrate our approach by applying it to the evolutionary history of Indo-European languages. (shrink)

Biological racial realism (BRR) continues to be a much-discussed topic, with several recent papers presenting arguments for the plausibility of some type of “biological race.” In this paper, the focus will be on the phylogenetic conceptions of race, which is one of the most promising views of BRR, that define races as lineages of reproductively isolated breeding populations. However, I will argue that phylogenetic conceptions of race fail to prove that races are biologically real. I will develop and defend my (...) argument against the phylogenetic views of race by relying on current research in population genetics, human evolution, and social sciences. Ultimately, I will argue that (i) race is not a biologically legitimate category and (ii) philosophers should direct their resources to understand problems that arise due to racialization, and thereby they should find solutions to those problems. (shrink)

The aptationist program includes attempts at sorting adaptations from exaptations, and therefore requires knowledge of historical changes in biological character states (traits) and their effects or functions, particularly for nonoptimal aptations. Phylogenetic inference is a key approach for historical aspects of evolutionary hypotheses, particularly testing evolutionary scenarios, and such “tree-thinking” investigation is directly relevant to the aptationist program.

Three competing ‘methods’ have been endorsed for inferring phylogenetic hypotheses: parsimony, likelihood, and Bayesianism. The latter two have been claimed superior because they take into account rates of sequence substitution. Can rates of substitution be justified on its own accord in inferences of explanatory hypotheses? Answering this question requires addressing four issues: (1) the aim of scientific inquiry, (2) the nature of why-questions, (3) explanatory hypotheses as answers to why-questions, and (4) acknowledging that neither parsimony, likelihood, nor Bayesianism are inferential (...) actions leading to explanatory hypotheses. The aim of scientific inquiry is to acquire causal understanding of effects. Observation statements of organismal characters lead to implicit or explicit why-questions. Those questions, conveyed in data matrices, assume the truth of observation statements, which is contrary to subsequently invoking substitution rates within inferences to phylogenetic hypotheses. Inferences of explanatory hypotheses are abductive in form, such that some version of an evolutionary theory(ies) is/are included or implied. If rates of sequence evolution are to be considered, it must be done prior to, rather than within abduction, which requires renaming those putatively-shared nucleotides subject to substitution rates. There are, however, no epistemic grounds for renaming characters to accommodate rates, calling into question the legitimacy of causally accounting for sequence data. (shrink)

I address David Hull's theses about the process of science from the perspective of an evolutionary biologist, particularly emphasizing phylogenetic systematics, an area that has figured prominently in Hull's work as a source of both sociological data and metatheory. The goal is to carefully explore analogies and disanalogies between scientific process and comparative biology. There do seem to be remarkable analogies, indeed these lead to important insights that might not otherwise have been made, yet some possible analogies present novel problems: (...) Are "memes" like genes or like traits? What is the nature of replication in science? It is argued that the primary need is for some rigorously worked-out case studies. (shrink)

The occurrence of hiccoughs (hiccups) is very widespread and yet their neuronal origin and physiological significance are still unresolved. Several hypotheses have been proposed. Here we consider a phylogenetic perspective, starting from the concept that the ventilatory central pattern generator of lower vertebrates provides the base upon which central pattern generators of higher vertebrates develop. Hiccoughs are characterized by glottal closure during inspiration and by early development in relation to lung ventilation. They are inhibited when the concentration of inhaled CO2 (...) is increased and they can be abolished by the drug baclofen (an agonist of the GABAB receptor). These properties are shared by ventilatory motor patterns of lower vertebrates, leading to the hypothesis that hiccough is the expression of archaic motor patterns and particularly the motor pattern of gill ventilation in bimodal breathers such as most frogs. A circuit that can generate hiccoughs may persist in mammals because it has permitted the development of pattern generators for other useful functions of the pharynx and chest wall muscles, such as suckling or eupneic breathing. BioEssays 25:182–188, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

Cet article propose une étude conceptuelle d’une pratique scientifique. L’analyse phylogénétique, méthode phare en biologie de l’évolution, permet d’inférer les relations évolutives entre différentes espèces ou organismes. De nos jours, elle fait souvent intervenir l’usage de données moléculaires, dont les résultats sont appelés des phylogénies moléculaires. Comment caractériser cette pratique? Nous commençons par une présentation de la méthode, en la découpant en quatre étapes : (1) l’identification puis (2) l’alignement de séquences homologues (descendants d’un ancêtre commun) ; (3) la construction (...) puis (4) l’interprétation d’un arbre phylogénétique. Nous montrons que l’analyse phylogénétique n’est pas une expérimentation, et donc n’appartient pas au « style de laboratoire », tel que défini par Hacking. Elle ne correspond pas non plus à une méthode typique des sciences historiques, telle que décrite par Cleland. Bien que la correspondance de l’analyse phylogénétique avec ces catégorisations ne soit que partielle, nous défendons l’utilité de chacune de ces confrontations pour souligner des aspects distincts de cette pratique. Nous remettons aussi en cause l’idée d’une séparation méthodologique nette entre sciences expérimentales et sciences historiques. (shrink)

The author proposes a system of identification, positional, and phyletic numbers for taxa that makes possible a significant relationship between numerical classification and phylogeny.

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)

The most recent resurgence of philosophical attention to the so-called ‘functional talk’ in the sciences can be summarized in terms of the following questions: (Q1) What kind of restrictions, and in particular, what kind of evolutionary restrictions as well as to what extent, are involved in functional ascriptions? (Q2) How can we account for the explanatory import of function-ascribing statements? This paper addresses these questions on the basis of a modified version of Cummins’ functional analysis. The modification in question is (...) concerned with phylogenetical restrictions on causal role functions, and it stems from an analysis of some primary areas in molecular biology. I examine how evolutionary consideration affects the so-called “function-analytical explanatory strategy” (Cummins [1975] 1998, 2002). Finally, I argue that the neo-functional analysis here proposed accounts for a certain convergence between the main rival theories of biological function. (shrink)

A. W. F. Edwards is one of the most influential mathematical geneticists in the history of the discipline. One of the last students of R. A. Fisher, Edwards pioneered the statistical analysis of phylogeny in collaboration with L. L. Cavalli-Sforza, and helped establish Fisher's concept of likelihood as a standard of statistical and scientific inference. In this book, edited by philosopher of science Rasmus Grønfeldt Winther, Edwards's key papers are assembled alongside commentaries by leading scientists, discussing Edwards's influence on their (...) own research and on thinking in their field overall. In an extensive interview with Winther, Edwards offers his thoughts on his contributions, their legacy, and the context in which they emerged. This book is a resource both for anyone interested in the history and philosophy of genetics, statistics, and science, and for scientists seeking to develop new algorithmic and statistical methods for understanding the genetic relationships between and among species both extant and extinct. (shrink)

The most recent resurgence of philosophical attention to the so-called ‘functional talk' in the sciences can be summarized in terms of the following questions: (Q1) What kind of restrictions, and in particular, what kind of evolutionary restrictions as well as to what extent, is involved in functional ascriptions? (Q2) How can we account for the explanatory import of function-ascribing statements? This paper addresses these questions through a modified version of Cummins' functional analysis. The modification in question is concerned with phylogenetical (...) restrictions on causal role functions, and it stems from an analysis of some primary areas in molecular biology. I examine how evolutionary consideration affects the so-called ‘function-analytical explanatory strategy' (Cummins [1975] 1998, 2002). Finally, I argue that the neo-functional analysis here proposed accounts for a certain convergence between the main rival theories of biological function. ‡I wish to thank David Davies, Eva Jablonka, Thomas Reydon, and Marcel Weber for their helpful comments. †To contact the author, please write to: Department of Philosophy, University of Rijeka, Omladinska 14, 51000 Rijeka, Croatia; e-mail: [email protected]. (shrink)

This paper addresses the general problem of how to rationally choose an algorithm for phylogenetic inference. Specifically, the controversy between maximum likelihood (ML) and maximum parsimony (MP) perspectives is reframed within the philosophical issue of theory choice. A Kuhnian approach in which rationality is bounded and value-laden is offered and construed through the notion of a Style of Modeling. A Style is divided into four stages: collecting remnant models, constructing models of taxonomical identity, implementing modeling algorithms, and finally inferring and (...) confirming evolutionary trees or cladograms. The identification and investigation of styles is useful for exploring sociological and epistemological issues such as individuating scientific communities and assessing the rationality of algorithm choice. Regarding the last point, this paper suggests that the values motivating ML and MP perspectives are justified but only contextually; these algorithms also have normative force because they can be therapeutic by allowing us to rationally choose among several competing trees, nonetheless this force is limited and cannot be used in order to decide the controversy tout court. (shrink)

Methoden. Im obigen Artikel ist die „Phylogenie des Stammbaumes” untersucht worden. Beginnend mitHaeckel werden 26 Typen phylogenetischer Symbole kritisch besprochen, d.h. nicht die Resultate, sondern nur die Methoden, z.B. bezüglich Systematik und Phylogenie, lebender und ausgestorbener Organismen, geologischer Perioden, Stufen und homologer Variationen, geographischer Verbreitung, Diversität, etwaiger Bedeutung der Einzelheiten, Mono-, Bi- und Polyrheithrie , usw. Der Faktor Zeit wird dabei für phylogenetische Systeme als der wesentlichste betrachtet. Der Autor hat daher in seinen- neuen Darstellungen die Begriffe „Zeit-Stufen” oder „Zeit-Globen-Oberflächen” (...) eingeführt; diese stehen senkrecht zum „Zeit-Radius”. Auf diesem Grunde wird ein neues Kriterium zur Unterscheidung systematischer und phylogenetischer Vorstellungen denjenigen anderer Autoren hinzugefügt. Erläuterungen. Nach einer Übersicht über die besprochenen Schemen im 1. Teil werden die Verhältnisse zwischen systematischen und phylogenetischen Darstellungen sowie die Verbindung ihrer Symbole untersucht. Es wird gezeigt, dass viele Einzelheiten solcher Konstruktionen oft, wissentlich oder unwissentlich, keine bestimmte Bedeutung haben. Der Verfasser hat versucht zu zeigen, dass es erwünscht wäre, möglichst mit allen Einzelheiten einer symbolischen Darstellung irgendeine Bedeutung zu verbinden: Linien und Entfernungen in der Ebene, Winkel in räumlichen Schemen. Die letztgenannten werden besonders für solche Arten von phylogenetischen Systemen empfohlen, bei denen der Faktor Zeit stets eine der Dimensionen bildet. Dieser Grundsatz wird mit der Evolution systematischer Einzelheiten in Verbindung gebracht, und Merkmals-Phyletik, homologe Variationen, Stufen, Polyrheithrie, Analogie und Homologie, Konvergenz und Verwandtschaft, etc. werden kurz im Lichte der Vererbungslehre besprochen. Es istHayata's extrem dynamischen Ansichten zu verdanken, dass das Statische in den systematischen und phylogenetischen Darstellungen aufgelockert worden ist. Méthodes. Dans l'article inséré ci-dessus il s'agit de ce qu'on pourrait appeler „la phylogénie de l'arbre généalogique”. En commençant parHaeckel , l'auteur discute 26 types divers de symboles phylogénétiques, c.à.d. seulement les méthodes , par exemple en ce qui concerne la taxonomie et la phylogénie, les organismes récents et éteints, les périodes géologiques, les niveaux et les variations homologues, la distribution géographique, la diversité, la signification éventuelle des détails, la mono-, bi- et polyrheithrie , etc. Le Temps est considéré comme l'élément le plus essentiel dans tout système phylogénétique. Par conséquence, l'auteur a introduit dans ses nouvelles représentations les idées de „Niveaux” ou de „Surfaces des Sphères du Temps” qui sont imaginés perpendiculaires au Radius-Temps. Dans l'ordre de ces idées un nouveau critère est ajouté à ceux donnés par d'autres auteurs pour la distinction des systèmes taxonomiques et des représentations phylogénétiques. Justifications. Après une récapitulation des systèmes, énumérés dans la première partie, les relations des constructions taxonomiques et phylogénétiques, ainsi que les connections de leurs symboles sont discutées. Souvent plusieurs détails sont, sciemment ou insciemment, dépourvus de toutes signification. L'auteur a essayé de démontrer qu'il serait désirable d'attribuer autant que possible de significations définies au détails d'une représentation symbolique de la nature décrite: aux lignes et aux distances dans le plan, aux angles dans l'espace. Les constructions tridimensionales sont particulièrement recommandées pour plusieurs systèmes phylogénétiques; dans de tels systèmes le Temps devrait toujours remplir la fonction d'une des dimensions. Ce principe est mis en rapport avec l'évolution des unités taxonomiques; phylogénie des charactères, variations homologues, niveaux, polyrheithrie, analogie et homologie, convergence et relations héréditaires, tous ces sujets sont brièvement discutés dans leurs rapports avec la Génétique. Selon l'opinion de l'auteur, c'est aux idées ultra-dynamiques d'Hayata que la taxonomie et la phylogénie doivent la pénétration féconde du dynamisme dans leurs systèmes trop souvent statiques. (shrink)

David Hull’s approach to science, which culminated in his important book Science as a Process(1988), represents an unprecedented conjunction of philosophy of science with the results and concepts of a particular science. Hull takes an evolutionary approach to the conceptual development of science, importing much of his explanatory framework from comparative biology, the discipline where his empirical observations of scientists have been made. On the surface, such a cozy relationship between data, theory, and metatheory leads to worries about circular reasoning (...) (Mishler 1989). Nevertheless, I will argue here that Hull’s approach is basically sound, and that the strength of his arguments comes precisely from his recognition of key analogies between the evolution of organisms and the conceptual evolution of scientists; however, certain disanalogies must also be taken into account.Comparative biology can be divided into two distinct (although interrelated) halves based on differing orientations and types of questions asked. (shrink)

Phylogenetics is the study and reconstruction of evolutionary history and is filled with numerous foundational issues of interest to philosophers. This paper briefly introduces some central concepts in the field, describes some of the main methods for inferring phylogenies, and provides some arguments for the superiority of model-based methods such as Likelihood and Bayesian methods over nonparametric methods such as parsimony. It also raises some underdeveloped issues in the field of interest to philosophers.

Amine acetylation is a diverse topic with importance to the regulation of several physiological processes as well as the metabolism of drugs and environmental chemicals. Arylalkylamine N‐acetyltransferase is widely distributed in several species, where this enzyme plays an important role in the seasonal regulation of reproduction and photoperiodism in vertebrates through the pathway of melatonin formation. In insects, this enzyme is involved in monoamine neurotransmitter inactivation and the formation of catecholamine intermediates necessary for sclerotization of the insect cuticle.

A strong case has been made for the role and value of mechanistic explanation in neuroscience and molecular biology. A similar demonstration in other domains of scientific investigation, however, remains an important challenge of scope for the new mechanists. This article helps answer that challenge by demonstrating one valuable role mechanisms play in phylogenetics. Using the transition/transversion rate parameter as a case example, this article argues that models embedded with mechanisms produce stronger phylogenetic tree hypotheses, as measured by maximum (...) likelihood logL values. Two important implications for the new mechanistic account of explanation are considered. (shrink)

This chapter explores the idea that phylogenetic diversity plays a unique role in underpinning conservation endeavour. The conservation of biodiversity is suffering from a rapid, unguided proliferation of metrics. Confusion is caused by the wide variety of contexts in which we make use of the idea of biodiversity. Characterisations of biodiversity range from all-variety-at-all-levels down to variety with respect to single variables relevant to very specific conservation contexts. Accepting biodiversity as the sum of a large number of individual measures results (...) in an empirically intractable framework. However, large-scale decisions cannot be based on biodiversity variables inferred from local conservation imperatives because the variables relevant to the many systems being compared would be incommensurate with one another. We therefore need some general conception of biodiversity that would make tractable such large-scale environmental decision-marking. We categorise the large array of strategies for the measurement of biodiversity into four broad groups for consideration as general measures of biodiversity. We compare common moral justifications for the conservation of biodiversity and conclude that some form of instrumental value is the most plausible justification for biodiversity conservation. Although this is often interpreted as a reliance on option value, we opt for a broadly consequentialist characterisation of biodiversity conservation. We conclude that the best justified general measure of biodiversity will be some form of phylogenetic diversity. (shrink)

Ontological questions in biology have typically focused on the nature of species: what are species; how are they identified and individuated? There is an analogous, but much neglected concern: what are characters; how are they identified and individuated? Character individuation is significant because biological systematics relies on a parsimony principle to determine phylogeny and classify taxa, and the parsimony principle is usually interpreted to favor the phylogenetic hypothesis that requires the fewest changes in characters. But no character individuation principle identified (...) so far is adequate. For biological systematics we need a better way of conceiving characters. (shrink)