Microscopy has revealed tremendous diversity of bacterial and eukaryotic forms. Recent molecular analyses show discordance in estimates of biodiversity between morphological and molecular analyses. Moreover, phylogenetic analyses of the diversity of microbial forms reveal evidence of convergence at scales as deep as interdomain: morphologies shared between bacteria and eukaryotes. Here, we highlight examples of such discordance, focusing on exemplary lineages such as testate amoebae, ciliates, and cyanobacteria. These have long histories of morphological study, enabling deeper analyses on (...) both the molecular and morphological sides. We discuss examples in two main categories: (i) morphologically identical (or highly similar) individuals that are genetically distinct and (ii) morphologically distinct individuals that are genetically the same. We argue that hypotheses about discordance can be tested using the concept of neutral morphologies, or more broadly neutral phenotypes, as a null hypothesis. -/- . (shrink)

Sterner and Lidgard urge that philosophers of phylogenetics move beyond the “systematics wars”, referring to the 1960s–80s debates between numerical taxonomists, evolutionary taxonomists, and phylogenetic systematists. Indeed, philosophers would do well to move beyond those wars, and to focus even more recently than the parsimony versus likelihood debates of the 1980s–90s. In this paper I use integrated historical-philosophical analysis of those debates to clarify a contemporary dispute between proponents of coalescence-based methods and proponents of concatenation. My intent is to (...) illuminate the present state of the field of phylogenetics by tracing the use of one particular philosophical argument, “total evidence”, through several distinct scientific debates. (shrink)

Phylogenetic models traditionally represent the history of life as having a strictly-branching tree structure. However, it is becoming increasingly clear that the history of life is often not strictly-branching; lateral gene transfer, endosymbiosis, and hybridization, for example, can all produce lateral branching events. There is thus motivation to allow phylogenetic models to have a reticulate structure. One proposal involves the reconciliation of genealogical discordance. Briefly, this method uses patterns of disagreement – discordance – between trees of (...) different genes to add lateral branching events to phylogenetic trees of taxa, and to estimate the most likely cause of these events. I use this practice to argue for: (1) a need for expanded accounts of multiple-models idealization, (2) a distinction between automatic and manual de-idealization, and (3) recognition that idealization may serve the meso-level aims of science in a different way than hitherto acknowledged. (shrink)

Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree‐like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and (...) reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control. (shrink)

Considering the properties of mirror neurons (MNs) in terms of development and phylogeny, we offer a novel, unifying, and testable account of their evolution according to the available data and try to unify apparently discordant research, including the plasticity of MNs during development, their adaptive value and their phylogenetic relationships and continuity. We hypothesize that the MN system reflects a set of interrelated traits, each with an independent natural history due to unique selective pressures, and propose that there are (...) at least three evolutionarily significant trends that gave raise to three subtypes: hand visuomotor, mouth visuomotor, and audio–vocal. Specifically, we put forward a mosaic evolution hypothesis, which posits that different types of MNs may have evolved at different rates within and among species. This evolutionary hypothesis represents an alternative to both adaptationist and associative models. Finally, the review offers a strong heuristic potential in predicting the circumstances under which specific variations and properties of MNs are expected. Such predictive value is critical to test new hypotheses about MN activity and its plastic changes, depending on the species, the neuroanatomical substrates, and the ecological niche. (shrink)

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)

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.

_Teaching in a democracy is challenging and filled with dilemmas that have no easy answers._ For example, how do educators meet their responsibilities of teaching civic norms and dispositions while remaining nonpartisan? _Democratic Discord in Schools_ features eight normative cases of complex dilemmas drawn from real events designed to help educators practice the type of collaborative problem solving and civil discourse needed to meet these challenges of democratic education. Each of the cases also features a set of six commentaries written (...) by a diverse array of scholars, educators, policy makers, students, and activists with a range of political views to spark reflection and conversation. Drawing on research and methods developed in the Justice in Schools project at the Harvard Graduate School of Education (HGSE), _Democratic Discord in Schools_ provides the tools that allow educators and others to practice the deliberative skills they need in order to find reasonable solutions to common ethical dilemmas in politically fraught times. (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)

Robustness is a common platitude: hypotheses are better supported with evidence generated by multiple techniques that rely on different background assumptions. Robustness has been put to numerous epistemic tasks, including the demarcation of artifacts from real entities, countering the “experimenter’s regress,” and resolving evidential discordance. Despite the frequency of appeals to robustness, the notion itself has received scant critique. Arguments based on robustness can give incorrect conclusions. More worrying is that although robustness may be valuable in ideal evidential circumstances (...) (i.e., when evidence is concordant), often when a variety of evidence is available from multiple techniques, the evidence is discordant. †To contact the author, please write to: Jacob Stegenga, Department of Philosophy, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093; e‐mail: [email protected]. (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)

This article discusses a puzzle arising from the phenomenon of insight in obsessive–compulsive disorder. “Insight” refers to an awareness or understanding of obsessive thoughts as false or irrational. I argue that a natural and plausible way of characterizing insight in OCD conflicts with several different possible explanations of the epistemic attitude underlying insight‐directed obsessive thought. After laying out the puzzle for five proposed explanations of obsessive thought and then discussing several possible ways that the puzzle might be avoided, I close (...) the article by arguing that we can avoid the puzzle by adopting a new positive view of insight‐directed obsessive thought. (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)

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)

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)

Systematics based solely on structuralist principles is non-science because it is derived from first principles that are inconsistent in dealing with both synchronic and diachronic aspects of evolution, and its evolutionary models involve hidden causes, and unnameable and unobservable entities. Structuralist phylogenetics emulates axiomatic mathematics through emphasis on deduction, and “hypotheses” and “mapped trait changes” that are actually lemmas and theorems. Sister-group-only evolutionary trees have no caulistic element of scientific realism. This results in a degenerate systematics based on patterns of (...) fact or evidence being treated as so fundamental that all other data may be mapped to the cladogram, resulting in an apparently well-supported classification that is devoid of evolutionary theory. Structuralism in systematics is based on a non-ultrametric analysis of sister-group informative data that cannot detect or model a named taxon giving rise to a named taxon, resulting in classifications that do not reflect macroevolutionary changes unless they are sister lineages. Conservation efforts are negatively affected through epistemological extinction of scientific names. Evolutionary systematics is a viable alternative, involving both deduction and induction, hypothesis and theory, developing trees with both synchronic and diachronic dimensions often inferring nameable ancestral taxa, and resulting in classifications that advance evolutionary theory and explanations for particular groups. (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)

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)

Manila is one of the world’s most fragmented, privatized and un-public of cities. Why is this so? This paper contemplates the seemingly immutable privacy of the city of Manila, and the paradoxical character of its publicity. Manila is our prime exemplar of the 21st-century mega-city whose apparent disorder discloses a coherent order which we here call ‘neo-patrimonial urbanism’. Manila is a city where poor and rich alike have their own government, infrastructure, and armies, the shopping malls are the simulacra of (...) public congregations once found in cathedrals and plazas, and where household order is matched by streetside chaos, and personal cleanliness wars with public dirt. We nominate the key characteristics of this uncanny approximation of chaotic and discordant order – a polyphonous and polyrhythmic social order but one lacking harmony – and offer a historical sociology, a genealogy that traces an emblematic pattern across the colonizing periods of its emergent urban forms into the contemporary impositions of gated zones and territories. The enduring legacy of patrimonial power to Manila is to be found in the households and on the streets that undermine and devalue public forms of social power in favour of the patriarch and his householders (now relabelled as ‘shareholders’ in ‘public companies’) at the cost of harmonious, peaceable and just public order. Such a state of affairs is not only destructive of the historic built environment of the city, especially its public parks and plazas and heritage districts, its streets, footpaths, public transport and utilities, but is directly injurious of its citizens. To address the question of Manila’s private order and public chaos is to reopen the quest for the good city as the just polis. It is also to take us beyond arguments of indigenous versus colonial forms of urbanism that are mired in nationalist and modernization ideologies respectively, and it is to reject the reductive logics of globalization arguments that Asian mega-cities are but variations of American logics of urbanism. (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.

The concordance of results that are “robust” across multiple scientific modalities is widely considered to play a critical role in the epistemology of science. But what should we make of those cases where such multimodal evidence is discordant? Jacob Stegenga has recently argued that robustness is “worse than useless” in these cases, suggesting that “different kinds of evidence cannot be combined in a coherent way.” In this article I respond to this critique and illustrate the critical methodological role that robustness (...) plays as an aim of scientific inquiry. (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)

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 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]. (shrink)

This article explores the foundational place of disharmony in Deleuze's metaphysics and examines the consequences of this for the ethics that can be drawn from his work. For Deleuze, the space in which difference manifests itself is one of discord, monstrosity and violence. This becomes evident in his revision of Leibniz's notion of harmony in which he offers a “new harmony” based on the violent discords of differential relations, his evocation of the monstrosity of difference, and his theorization of the (...) violence of thought. This paper addresses the critically neglected juncture between Deleuze's violent metaphysics and the kinds of speculative ethics that this metaphysics calls forth. (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)

The one of goals that religious provisions aim to achieve is the preservation of the generation. For this reason, Islam recommends marriage and prohibits all illegitimate relationships outside of marriage. He also ordered the parties to respect each other's rights and fulfill their responsibilities in order to maintain the marriage union. He requested that all attitudes and behaviors that would disrupt the marriage union be avoided. How ever, from time to time, a word said or a behavior exhibited by one (...) or both spouses shakes the marriage union and even leads to its end. Situations that can be described as severe disagreements that occur between spouses and make the continuation of the marital union almost impossible are expressed with the concept of “shiqàq” in fiqh. Failure of the parties to observe marriage law in domestic relations is one of the main reasons that lead to “shiqàq”. Although the reasons for the “shiqàq” that leads the spouses to discord are not explained in the relevant verse, it is recommended that in case of “shiqàq”, the institution of arbitration should be applied and the arbitrators should first reconcile the relationship between the spouses and prevent the breakdown of the marital union. On the other hand, it is controversial among the sects whether arbitrators have the authority to terminate a marriage union that they do not find beneficial to continue. While the fuqaha, who argue that arbitrators are in the position of attorneys, say that referees cannot separate the spouses without the consent of the spouses, those who say that arbitrators are in the power of judges are of the opinion that arbitrators have the authority to separate husband and wife regardless of the consent of the spouses. In addition, in case of “shiqàq”, the man can directly divorce his wife, and the woman can request the judicial authorities to separate from her husband. In this study, which deals with the issue of “shiqàq” in the context of family law, first of all, the meaning of “shiqàq”, the issues that cause this situation and the legal consequences attached to this concept will be revealed. (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)

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)

Manila is one of the world’s most fragmented, privatized and un-public of cities. Why is this so? This paper contemplates the seemingly immutable privacy of the city of Manila, and the paradoxical character of its publicity. Manila is our prime exemplar of the 21st-century mega-city whose apparent disorder discloses a coherent order which we here call ‘neo-patrimonial urbanism’. Manila is a city where poor and rich alike have their own government, infrastructure, and armies, the shopping malls are the simulacra of (...) public congregations once found in cathedrals and plazas, and where household order is matched by streetside chaos, and personal cleanliness wars with public dirt. We nominate the key characteristics of this uncanny approximation of chaotic and discordant order – a polyphonous and polyrhythmic social order but one lacking harmony – and offer a historical sociology, a genealogy that traces an emblematic pattern across the colonizing periods of its emergent urban forms into the contemporary impositions of gated zones and territories. The enduring legacy of patrimonial power to Manila is to be found in the households and on the streets that undermine and devalue public forms of social power in favour of the patriarch and his householders (now relabelled as ‘shareholders’ in ‘public companies’) at the cost of harmonious, peaceable and just public order. Such a state of affairs is not only destructive of the historic built environment of the city, especially its public parks and plazas and heritage districts, its streets, footpaths, public transport and utilities, but is directly injurious of its citizens. To address the question of Manila’s private order and public chaos is to reopen the quest for the good city as the just polis. It is also to take us beyond arguments of indigenous versus colonial forms of urbanism that are mired in nationalist and modernization ideologies respectively, and it is to reject the reductive logics of globalization arguments that Asian mega-cities are but variations of American logics of urbanism. (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)

Specifically, Allan Franklin is concerned with two problems in the use of experimental results in science: selectivity of data or analysis procedures and the resolution of discordant results.

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)

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 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.

The purpose of this paper is to introduce the concept of social discord, based on the analysis of early chapters of Niccolo Machiavelli?s Discourses on Livy. I argue that, by deriving a broader philosophical concept from Machiavelli?s peculiar position that strife between the plebs and the senate made the Roman republic free and powerful, we can greatly enhance our understanding of not only some of the more original and controversial positions within the Florentine theorist?s magnum opus, but also of his (...) thought in general. Furthermore, by analyzing crucial moments within Machiavelli?s observation of the rise and fall of the Roman republic through the lens of social discord, I argue that the concept can be established as the foundation of his understanding of republicanism, while contesting his designation of the people as the guardians of liberty. Finally, I contrast the concept of social discord with that of social conflict - a subtle and seemingly negligible distinction that can, in my understanding of Machiavelli?s thought, nonetheless mean the difference between a republic?s development and prosperity and its untimely downfall. nema. (shrink)

Systematics based solely on structuralist principles is non-science because it is derived from first principles that are inconsistent in dealing with both synchronic and diachronic aspects of evolution, and its evolutionary models involve hidden causes, and unnameable and unobservable entities. Structuralist phylogenetics emulates axiomatic mathematics through emphasis on deduction, and “hypotheses” and “mapped trait changes” that are actually lemmas and theorems. Sister-group-only evolutionary trees have no caulistic element of scientific realism. This results in a degenerate systematics based on patterns of (...) fact or evidence being treated as so fundamental that all other data may be mapped to the cladogram, resulting in an apparently well-supported classification that is devoid of evolutionary theory. Structuralism in systematics is based on a non-ultrametric analysis of sister-group informative data that cannot detect or model a named taxon giving rise to a named taxon, resulting in classifications that do not reflect macroevolutionary changes unless they are sister lineages. Conservation efforts are negatively affected through epistemological extinction of scientific names. Evolutionary systematics is a viable alternative, involving both deduction and induction, hypothesis and theory, developing trees with both synchronic and diachronic dimensions often inferring nameable ancestral taxa, and resulting in classifications that advance evolutionary theory and explanations for particular groups. (shrink)

A 16-year-old adolescent who identifies as transgender wishes to consider fertility preservation prior to the use of gender-affirming hormones. The adolescent’s parents are divorced, and one parent supports fertility preservation while the other does not. This case explores the minor’s future reproductive autonomy and parental decision making in a field where there is limited evidence of known harms and benefits to the use of fertility preservation in the transgender population and about future potential regret from lack of consideration of fertility (...) preservation during the prime window of opportunity. This case is created from a composite of cases seen at multiple institutions. (shrink)

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)

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)

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.

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)

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)

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)