This paper assesses the effect of DNA barcoding—the use of informative genetic markers to identify and discriminate between species—on taxonomy. Throughout, we interpret this in terms of _varipraxis_, a concept we introduce to make sense of the treatment of biological variation by scientists and other practitioners. From its inception, DNA barcoding was criticised for being reductive, in attempting to replace multiple forms of taxonomic evidence with just one: DNA sequence variation in one or a few indicative genes. We show, though, (...) how DNA barcoding has not narrowed or reduced taxonomy in the way it was projected to. We examine the development and implementation of DNA barcoding across three kingdoms of life: animals, plants, and protists. Through this, we demonstrate that for DNA barcoding to work, the range of acceptable intra-specific variation needs to be demarcated from variation deemed to be characteristic of inter-specific differences. Consequently, biological processes responsible for particular patterns of variation need to be investigated and understood. This encourages an integrative disposition towards understanding and explaining the evolutionary processes affecting the rate and nature of change at the nucleotide level. We detail how the impact of DNA barcoding has manifested differently across the three kingdoms we examine, assessing this in terms of the ontological commitments that are held and instantiated in practice. Based on this evaluation, we consider the problem of studying multi-kingdom communities, and assess the consequences of our analysis for understanding classification and taxonomy. (shrink)

Biologists who work on the pig (_Sus scrofa_) take advantage of its similarity to humans by constructing the inferential and material means to traffic data, information and knowledge across the species barrier. Their research has been funded due to its perceived value for agriculture and medicine. Improving selective breeding practices, for instance, has been a driver of genomics research. The pig is also an animal model for biomedical research and practice, and is proposed as a source of organs for cross-species (...) transplantation: xenotransplantation. Genomics research has informed transplantation biology, which has itself motivated developments in genomics. Both have generated models of correspondences between the genomes of pigs and humans. Concerning genomics, I detail how researchers traverse species boundaries to develop representations of the pig genome, alongside ensuring that such representations are sufficiently porcine. In transplantation biology, the representations of the genomes of humans and pigs are used to detect and investigate immunologically-pertinent differences between the two species. These key differences can then be removed, to ‘humanise’ donor pigs so that they can become a safe and effective source of organs. In both of these endeavours, there is a tension between practices that ‘humanise’ the pig (or representations thereof) through using resources from human genomics, and the need to ‘dehumanise’ the pig to maintain distinctions for legal, ethical and scientific reasons. This paper assesses the ways in which this tension has been managed, observing the differences between its realisations across comparative pig genomics and transplantation biology, and considering the consequences of this. (shrink)

From the 1980s onwards, the Roslin Institute and its predecessor organizations faced budget cuts, organizational upheaval and considerable insecurity. Over the next few decades, it was transformed by the introduction of molecular biology and transgenic research, but remained a hub of animal geneticists conducting research aimed at the livestock-breeding industry. This paper explores how these animal geneticists embraced genomics in response to the many-faceted precarity that the Roslin Institute faced, establishing it as a global centre for pig genomics research through (...) forging and leading the Pig Gene Mapping Project (PiGMaP); developing and hosting resources, such as a database for genetic linkage data; and producing associated statistical and software tools to analyse the data. The Roslin Institute leveraged these resources to play a key role in further international collaborations as a hedge against precarity. This adoption of genomics was strategically useful, as it took advantage of policy shifts at the national and European levels towards funding research with biotechnological potential. As genomics constitutes a set of infrastructures and resources with manifold uses, the development of capabilities in this domain also helped Roslin to diversify as a response to precarity. (shrink)

This paper aims to clarify the consequences of new scientific and philosophical approaches for the practical-theoretical framework of modern developmental biology. I highlight normal development, and the instructive-permissive distinction, as key parts of this framework which shape how variation is conceptualised and managed. Furthermore, I establish the different dimensions of biological variation: the units, temporality and mode of variation. Using the analytical frame established by this, I interpret a selection of examples as challenges to the instructive-permissive distinction. These examples include (...) the phenomena of developmental plasticity and transdifferentiation, the role of the microbiome in development, and new methodological approaches to standardisation and the assessment of causes. Furthermore, I argue that investigations into organismal development should investigate the effects of a wider range of kinds of variation including variation in the units, modes and temporalities of development. I close by examining various possible opportunities for producing and using normal development free of the assumptions of the instructive-permissive distinction. These opportunities are afforded by recent developments, which include new ways of producing standards incorporating more natural variation and being based on function rather than structure, and the ability to produce, store, and process large quantities of data. (shrink)

In this paper, rather than focusing on genes as an organising concept around which historical considerations of theory and practice in genetics are elucidated, we place genetic markers at the heart of our analysis. This reflects their central role in the subject of our account, livestock genetics concerning the domesticated pig, Sus scrofa. We define a genetic marker as a element existing in different forms in the genome, that can be identified and mapped using a variety of quantitative, classical and (...) molecular genetic techniques. The conjugation of pig genome researchers around the common object of the marker from the early-1990s allowed the distinctive theories and approaches of quantitative and molecular genetics concerning the size and distribution of gene effects to align in projects to populate genome maps. Critical to this was the nature of markers as ontologically inert, internally heterogeneous and relational. Though genes as an organising and categorising principle remained important, the particular concatenation of limitations, opportunities, and intended research goals of the pig genetics community, meant that a progressively stronger focus on the identification and mapping of markers rather than genes per se became a hallmark of the community. We therefore detail a different way of doing genetics to more gene-centred accounts. By doing so, we reveal the presence of practices, concepts and communities that would otherwise be hidden. (shrink)

Peter Abelard (1079–1142 ce) was the most wide‐ranging philosopher of the twelfth century. He quickly established himself as a leading teacher of logic in and near Paris shortly after 1100. After his affair with Heloise, and his subsequent castration, Abelard became a monk, but he returned to teaching in the Paris schools until 1140, when his work was condemned by a Church Council at Sens. His logical writings were based around discussion of the “Old Logic”: Porphyry's Isagoge, aristotle'S Categories and (...) On Interpretation and boethius'S textbook on topical inference. They comprise a freestanding Dialectica (“Logic”; probably c.1116), a set of commentaries (known as the Logica [Ingredientibus], c. 1119) and a later (c. 1125) commentary on the Isagoge (Logica Nostrorum Petititoni Sociorum or Glossulae). In a work Abelard called his Theologia, issued in three main versions (between 1120 and c.1134), he attempted a logical analysis of trinitarian relations and explored the philosophical problems surrounding God's claims to omnipotence and omniscience. The Collationes (“Debates,” also known as “Dialogue between a Christian, a Philosopher and a Jew”; probably c.1130) present a rational investigation into the nature of the highest good, in which the Christian and the Philosopher (who seems to be modeled on a philosopher of pagan antiquity) are remarkably in agreement. The unfinished Scito teipsum (“Know thyself,” also known as the “Ethics”; c.1138) analyses moral action. (shrink)

© 2017. The American Astronomical Society. All rights reserved.We present new observations of the low-mass companion to HD 984 taken with the Gemini Planet Imager as a part of the GPI Exoplanet Survey campaign. Images of HD 984 B were obtained in the J and H bands. Combined with archival epochs from 2012 and 2014, we fit the first orbit to the companion to find an 18 au orbit with a 68% confidence interval between 14 and 28 au, an eccentricity (...) of 0.18 with a 68% confidence interval between 0.05 and 0.47, and an inclination of 119°with a 68% confidence interval between 114°and 125°. To address the considerable spectral covariance in both spectra, we present a method of splitting the spectra into low and high frequencies to analyze the spectral structure at different spatial frequencies with the proper spectral noise correlation. Using the split spectra, we compare them to known spectral types using field brown dwarf and low-mass star spectra and find a best-fit match of a field gravity M6.5 ±1.5 spectral type with a corresponding temperature of K. Photometry of the companion yields a luminosity of log=2.88 ± 0.07 dex with DUSTY models. Mass estimates, again from DUSTY models, find an age-dependent mass of 34 ±1 to 95 ±4 M Jup. These results are consistent with previous measurements of the object. (shrink)

N- and O-linked glycan structures of cell surface and secreted glycoproteins serve a variety of functions related to cell–cell communication in systems affecting development and disease. The more sophisticated N-glycan biosynthesis pathway of metazoans diverges from that of yeast with the appearance of the medial-Golgi β-N-acetylglucosaminyltransferases (GlcNAc-Ts). Tissue-specific regulation of medial- and trans-Golgi glycosyltransferases contribute structural diversity to glycoproteins in metazoans, and this can affect their molecular properties including localization, half-life, and biological activity. Null mutations in glycosyltransferase genes positioned later (...) in the biosynthetic pathway disrupt expression of smaller subsets of glycan structures and are progressively milder in phenotype. In this review, we examine data on targeted mutations affecting glycosylation in mice and congenital mutations in man, with a view to understanding the molecular functions of glycan structures as modulators of glycoprotein activity. Finally, pathology associated with the expression of GlcNAc-Ts in cancer and diabetes-induced cardiac hypertrophy suggest that inhibitors of these enzymes may have therapeutic value. BioEssays 21:412–421, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

For many years there has been a debate about the role of the parietal lobe in the generation of behavior. Does it generate movement plans (intention) or choose objects in the environment for further processing? To answer this, we focus on the lateral intraparietal area (LIP), an area that has been shown to play independent roles in target selection for saccades and the generation of visual attention. Based on results from a variety of tasks, we propose that LIP acts as (...) a priority map in which objects are represented by activity proportional to their behavioral priority. We present evidence to show that the priority map combines bottom-up inputs like a rapid visual response with an array of top-down signals like a saccade plan. The spatial location representing the peak of the map is used by the oculomotor system to target saccades and by the visual system to guide visual attention. (shrink)

It has been acknowledged on numerous occasions that personal religiousness is a potential source of ethical norms, and consequently, an influence in ethical evaluations. An extensive literature review provides little in the way of empirical investigation of this recognized affect. This investigation conceptualizes religiousness as a motivation for ethical action, and discovers significant differences in ethical judgements among respondents categorized by personal religious motivation. Suggestions as to the source of these differences, and the implications which they offer to managers are (...) discussed and supported from the literature. (shrink)

The present study explored a multi‐construct model of moral development. Variables commonly seen in the moral development literature, such as family interactions, spiritual life, ascription to various sources of moral authority, empathy, shame, guilt and moral judgement competence, were investigated. Results from the current study support previous research that the three moral emotions of empathy, shame and guilt interrelate. Further, it was found that the relationship one has with a higher power (spirituality) involves empathy and guilt. Implications for moral education (...) are discussed. Future research should continue to explore a multi‐construct model of morality. (shrink)

Contextual learning pervades our perception and cognition and plays a critical role in adjusting to aversive and stressful events. Our ability to memorise spatial context has been studied extensive...

The theory of negation developed in the grammatical-philosophical system of later Vyākaraṇa remains almost entirely unstudied, despite its close links with the (widely studied) approaches to negation found in other philosophical schools such as Nyāya and Mīmāṃsā, and despite its consequent importance for a comprehensive understanding of the theory of negation in ancient India. In this paper we present an edition, translation and commentary of the relevant sections of Nāgeśa’s _Paramalaghumañjūṣā_, a concise presentation by the final authority of the Pāṇinian (...) tradition, together with an explanatory introduction outlining the grammarians’ theory of negation and its relations particularly with the Nyāya theory of negation. (shrink)

An early step in sporulation of the bacterium Bacillus subtilis, is the formation of two compartments in the developing sporangium: the mother cell and the forespore. These compartments differ in their programs of gene expression and developmental fate. The establishment of cell type within this simple developmental program, is accomplished by the compartmentalization of sigma subunits of RNA polymerase. The localization of these sigma factors results in compartment‐specific gene expression. Recent experiments have elucidated some of the early steps in the (...) establishment of 3V cell type. After septum formation, the activity of the sigma factor, σF, is confined to the forespore compartment. This, in turn, results in the localized expression of another developmental sigma factor, σG. The forespore localization of these two sigma factors, establishes the forespore line of gene expression. σF and σG also regulate mother cell events. σF activity in the forespore regulates the proteolytic processing of σE within the mother cell compartment. The localization σE activity leads to mother cell expression of another sigma factor, pro‐σK The proteolytic processing of pro‐σK to mature σK is controlled by the forespore sigma factor, σG Mature σK then directs the transcription of mother cell specific genes. Therefore, the initial localization of σF activity to the forespore compartment, orchestrates the establishment of cell type in both forespore and mother cell compartments. (shrink)

In this article, I discuss calls for access to empirical data within controversies about climate science, as revealed and highlighted by the publication of the e-mail correspondence involving scientists at the Climatic Research Unit at the University of East Anglia in 2009. I identify several arguments advanced for and against the sharing of scientific data. My conclusions are that, whereas transparency in science is to be valued, appeals to an unproblematic category of ‘empirical data’ in climate science do not reflect (...) the complexities of scientific practice in this field. (shrink)

The concept of reasonableness is essential to John Rawls’s political liberalism, and especially to its main ideas of public reason and liberal legitimacy. Yet the somewhat ambiguous account of reasonableness in Political Liberalism has led to concerns that the Rawlsian distinction between the reasonable and the unreasonable is arbitrary and ultimately indefensible. This paper attempts to advance a more convincing interpretation of reasonableness. I argue that the reasonable applies first to citizens, who then play an important role in determining which (...) comprehensive doctrines and political conceptions of justice are reasonable. In addition, while Rawls fails to specify explicitly the meaning of the reasonable in his standard of political justification (i.e. the liberal principle of legitimacy based on the criterion of reciprocity), I offer an interpretation of what it means for citizens to present reasonable claims and arguments to one another in public reason. (shrink)

SummaryThe Gainj of highland Papua New Guinea do not use contraception but have a total fertility rate of only 4·3 live births per woman, one of the lowest ever recorded in a natural fertility setting. From an analysis of cross-sectional demographic and endocrinological data, the causes of low reproductive output have been identified in women of this population as: late menarche and marriage, a long interval between marriage and first birth, a high probability of widowhood at later reproductive ages, low (...) effective fecundability and prolonged lactational amenorrhoea. These are combined with near-universal marriage, a low prevalence of primary sterility and a pattern of onset of secondary sterility similar to that found in other populations. Of all the factors limiting fertility, by far the most important are those involved in birth spacing, especially lactational amenorrhoea. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Dewey on Metaphysics, Meaning Making, and Maps James W. Garrison Blueprints and maps are propositions and they exemplify what it is to be propositional.1 [E]very characteristic trait is a quality.... produced and destroyed by existential conditions.2 John Dewey's claim that there are metaphysical generic traits of existence the theory of which provides "a ground-map" for cultural criticism remains controversial. I will work along two intertwining lines to try (...) and clear things up a bit. First, many assume that his reference to a metaphysical map is a metaphor. My paper will show that he uses the idea of a map consistently in many different places throughout his career. Second, my paper will examine how Dewey functionally coordinates ordinary existential traits and their maps within his theory of judgment. We will find that the generic traits and the ground-map of criticism connect in much the same way. Before examining Dewey's theory of judgment, I want to say something about where Dewey's metaphysics fits into his empirical "denotative method." In the conclusion, we wiU look at where metaphysics fits into the architectonic of his entire phUosophy. In between, we wiU examine maps functioning as propositions (especiaUy logical and mathematical universals) as weU as ever-evolving guides to unending inquiry in an unfinished and unfinishable universe. Eventually we wiU see why Dewey insists that "the social" is "The Inclusive PhUosophic Idea." Metaphysics, for Dewey, is simply one tool of cultural criticism among others. First and Last Philosophy in Dewey's Denotative Method Dewey's "denotative method" moves from the immediately given intuitive meanings of qualitative "having" of experience that impart a "sense" of a qualitative, organically whole TRANSACTIONS OFTHE CHARLES S. PEIRCE SOCIETY Vol. 41, No. 4 ©2005 O situation from whence we may select traits, through the experience of "significant " linguistic meanings, such as the propositions of judgment, to the experience of "knowing" as the product of the logical process of inquiry, and back again to primary experience.4 Each phase interpenetrates every 3 other. Here is how Dewey describes the trans-action between primary, noncognitive and secondary, cognitive experience in his original (1925) >■$ introduction to Experience and Nature: ^r There are two avenues of approach to the goal of philosophy. We may " begin with experience in gross, experience in its primary and crude forms ^ [e.g., traits].... Or, we may begin with refined selective products, the a most authentic statements of commended methods of science [e.g., ¿q maps], and work from them back to the primary facts of life. ^ P TT ϕ > Philosophy may start with either immediate existential experience or the 3 experience of mediating meanings. While we may distinguish these two L starting points, we should never construct a dualism from them since both jx occur within experience.6 Dewey explains that "the subject-matter of primary experience sets the problems and furnishes the first data of reflection ""O which constructs the secondary objects of reflection."7 Further, "crude or macroscopic experience" provides the "test and verification" of the secondary objects of reflection. Secondary objects "explain the primary objects, 2 they enable us to grasp them with understanding!'9 The two starting points " differ in direction, but eventually they close to form a circle of expanding? dence. They may then pioneer new pathways, or, having different values, D choose to construct different kinds of maps. ^ Douglas Browning distinguishes "three phases of discussion of the start- 0 ing point."23 The first concerns "the designation of a certain subject matter P1 referred to under the names 'experience' and 'my life'."24 Dewey's empirical « denotative method selects aspects from immediate qualitative experience. The >% second phase involves two things: First, "a reflective moving away from and looking back upon that subject-matter" and, second, "the bringing of a puta- S tive characterization against it." Browning's example of characterization is g "the catalogue of the generic traits of experience." The generic traits are not S antecedent to inquiry; rather they are the products of reflection used to char- 5 ' acterize primary experience. Browning observes that characterization is always ^ provisional; as we wiU find, Dewey insists that the theoretical map proposi- ^ tionaUy representing the existential... (shrink)

Several quantitative techniques for choosing among data models are available. Among these are techniques based on algorithmic information theory, minimum description length theory, and the Akaike information criterion. All these techniques are designed to identify a single model of a data set as being the closest to the truth. I argue, using examples, that many data sets in science show multiple patterns, providing evidence for multiple phenomena. For any such data set, there is more than one data model that must (...) be considered close to the truth. I conclude that, since the established techniques for choosing among data models are unequipped to handle these cases, they cannot be regarded as adequate. ‡I presented a previous version of this paper at the 20th Biennial Meeting of the Philosophy of Science Association, Vancouver, November 2006. I am grateful to the audience for constructive discussion. I thank Leiden University students Marjolein Eysink Smeets and Lenneke Schrier for suggesting the cortisol example, and Remko van der Geest for comments on a draft. †To contact the author, please write to: Faculty of Philosophy, University of Leiden, P.O. Box 9515, 2300 RA Leiden, The Netherlands; e-mail: [email protected]. (shrink)

For forty years, Harvey Mansfield has been worth reading. Whether plumbing the depths of MachiavelliOs Discourses or explaining what was at stake in Bill ClintonOs impeachment, MansfieldOs work in political philosophy and political science has set the standard. In Educating the Prince, twenty-one of his students, themselves distinguished scholars, try to live up to that standard. Their essays offer penetrating analyses of Machiavellianism, liberalism, and America., all of them informed by MansfieldOs own work. The volume also includes a bibliography of (...) MansfieldOs writings. (shrink)

Theories of consciousness have a long and controversial history. One well-known proposal — integrated information theory — has recently been labeled as ‘pseudoscience’, which has caused a heated open debate. Here we discuss the case and argue that the theory is indeed unscientific because its core claims are untestable even in principle.

This study examined within-person co-occurrence of self-focus, negative affect, and stress in a community sample of adolescents with or without emotional disorders. As part of a larger study, 278 adolescents were interviewed about emotional disorders. Later, they completed diary measures over three days, six times a day, reporting their current thoughts, affect, and levels of stress. Negative affect was independently related to both concurrent stress and self-focus. Importantly, the association between negative affect and self-focus was stronger among participants with a (...) recent unipolar mood disorder, compared to those with an anxiety disorder, comorbid anxiety and depression, or those without an emotional disorder. The implications of these findings to theories of self-focus and its role in emotional disorders are discussed. (shrink)

Certain philosophers have held the thesis of the unity of science. As often conceived, the thesis has two parts: the thesis of physicalism and the thesis of extensionality. For each of these two parts there is an outstanding problem, i.e. the problem of intentionality and the problem of intensionality respectively. The purpose of this paper is twofold: first, to make explicit the nature of these two problems, and second, to show to what extent they can be said to be the (...) same problem. Thus I am not at all interested here either to defend or attack this thesis or either of its parts. (shrink)

The dominant paradigm of experiments in the social and behavioral sciences views an experiment as a test of a theory, where the theory is assumed to generalize beyond the experiment's specific conditions. According to this view, which Alan Newell once characterized as “playing twenty questions with nature,” theory is advanced one experiment at a time, and the integration of disparate findings is assumed to happen via the scientific publishing process. In this article, we argue that the process of integration is (...) at best inefficient, and at worst it does not, in fact, occur. We further show that the challenge of integration cannot be adequately addressed by recently proposed reforms that focus on the reliability and replicability of individual findings, nor simply by conducting more or larger experiments. Rather, the problem arises from the imprecise nature of social and behavioral theories and, consequently, a lack of commensurability across experiments conducted under different conditions. Therefore, researchers must fundamentally rethink how they design experiments and how the experiments relate to theory. We specifically describe an alternative framework, integrative experiment design, which intrinsically promotes commensurability and continuous integration of knowledge. In this paradigm, researchers explicitly map the design space of possible experiments associated with a given research question, embracing many potentially relevant theories rather than focusing on just one. Researchers then iteratively generate theories and test them with experiments explicitly sampled from the design space, allowing results to be integrated across experiments. Given recent methodological and technological developments, we conclude that this approach is feasible and would generate more-reliable, more-cumulative empirical and theoretical knowledge than the current paradigm – and with far greater efficiency. (shrink)

Neutral monist, panpsychist, naturalist, and phenomenological interpretations of James's theory of mind are canvassed. Culling the true tenets from each, I make a case for a reconciling view on the basis of a distinction between mental and proto-mental properties. The resulting interpretation is compared to two forms of panpsychism identified by T Nagel in his essay of that name.