Short interspersed repetitive elements, or SINEs, are tRNA-derived retroposons that are dispersed throughout eukaryotic genomes and can be present in well over 104 total copies. The enormous volume of SINE amplifications per organism makes them important evolutionary agents for shaping the diversity of genomes, and the irreversible, independent nature of their insertion allows them to be used for diagnosing common ancestry among host taxa with extreme confidence. As such, they represent a powerful new tool for systematic biology that can be (...) strategically integrated with other conventional phylogenetic characters, most notably morphology and DNA sequences. This review covers the basic aspects of SINE evolution that are especially relevant to their use as systematic characters and describes the practical methods of characterizing SINEs for cladogram construction. It also discusses the limits of their systematic utility, clarifies some recently published misunderstandings, and illustrates the effective application of SINEs for vertebrate phylogenetics with results from selected case studies. BioEssays 22:148–160, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

It is well known that the modal logic S5 can be embedded in the classical predicate logic by interpreting the modal operator in terms of a quantifier. Wajsberg [10] proved this fact in a syntactic way. Mints [7] extended this result to the quantified version of S5; using a purely proof-theoretic method he showed that the quantified S5 corresponds to the classical predicate logic with one-sorted variable. In this paper we extend Mints' result to the basic modal logic S4; we (...) investigate the correspondence between the quantified versions of S4 (with and without the Barcan formula) and the classical predicate logic (with one-sorted variable). We present a purely proof-theoretic proof-transformation method, reducing an LK-proof of an interpreted formula to a modal proof. (shrink)

In this paper, we show the equivalence between the provability of a proof system of basic hybrid logic and that of translated formulas of the classical predicate logic with equality and explicit substitution by a purely proof–theoretic method. Then we show the equivalence of two groups of proof systems of hybrid logic: the group of labelled deduction systems and the group of modal logic-based systems.

Alcohol use disorder is a burden to society creating social and health problems. Detection of AUD and its effects on the brain are difficult to assess. This problem is enhanced by the comorbid use of other substances such as nicotine that has been present in previous studies. Recent machine learning algorithms have raised the attention of researchers as a useful tool in studying and detecting AUD. This work uses AUD and controls samples free of any other substance use to assess (...) the performance of a set of commonly used machine learning classifiers detecting AUD from resting state functional network connectivity derived from independent component analysis. The cohort used included 51 alcohol dependent subjects and 51 control subjects. Despite alcohol, none of the 102 subjects reported use of nicotine, cannabis or any other dependence or habit formation substance. Classification features consisted of whole brain rsFNC estimates undergoing a feature selection process using a random forest approach. Features were then fed to 10 different machine learning classifiers to be evaluated based on their classification performance. A neural network classifier showed the highest performance with an area under the curve of 0.79. Other good performers with similar AUC scores were logistic regression, nearest neighbor, and support vector machine classifiers. The worst results were obtained with Gaussian process and quadratic discriminant analysis. The feature selection outcome pointed to functional connections between visual, sensorimotor, executive control, reward, and salience networks as the most relevant for classification. We conclude that AUD can be identified using machine learning classifiers in the absence of nicotine comorbidity. (shrink)

Psychopathy is a disorder characterized by severe and frequent moral violations in multiple domains of life. Numerous studies have shown psychopathy-related limbic brain abnormalities during moral processing; however, these studies only examined negatively valenced moral stimuli. Here, we aimed to replicate prior psychopathy research on negative moral judgments and to extend this work by examining psychopathy-related abnormalities in the processing of controversial moral stimuli and positive moral processing. Incarcerated adult males (N = 245) completed a functional magnetic resonance imaging protocol (...) on a mobile imaging system stationed at the prison. Psychopathy was assessed using the Hare Psychopathy Checklist–Revised (PCL-R). Participants were then shown words describing three types of moral stimuli: wrong (e.g., stealing), not wrong (e.g., charity), and controversial (e.g., euthanasia). Participants rated each stimulus as either wrong or not wrong. PCL-R total scores were correlated with not wrong behavioral responses to wrong moral stimuli, and were inversely related to hemodynamic activity in the anterior cingulate cortex in the contrast of wrong > not wrong. In the controversial > noncontroversial comparison, psychopathy was inversely associated with activity in the temporal parietal junction and dorsolateral prefrontal cortex. These results indicate that psychopathy-related abnormalities are observed during the processing of complex, negative, and positive moral stimuli. (shrink)

Rearrest has been predicted by hemodynamic activity in the anterior cingulate cortex (ACC) during error-processing (Aharoni et al., 2013). Here, we evaluate the predictive power after adding an additional imaging modality in a subsample of 45 incarcerated males from Aharoni et al. (2013). Event-related potentials (ERPs) and hemodynamic activity were collected during a Go/NoGo response inhibition task. Neural measures of error-processing were obtained from the ACC and two ERP components, the error-related negativity (ERN/Ne) and the error positivity (Pe). Measures from (...) the Pe and ACC differentiated individuals who were and were not subsequently rearrested. Cox regression, logistic regression, and support vector machine (SVM) neuroprediction models were calculated. Each of these models proved successful in predicting rearrest and SVM provided the strongest results. Multimodal neuroprediction SVM models with out of sample cross-validating accurately predicted rearrest (83.33%). Offenders with increased Pe amplitude and decreased ACC activation, suggesting abnormal error-processing, were at greatest risk of rearrest. -/- . (shrink)

The Eton Latin Grammar, For Use in the Higher Forms. By Francis Hay Rawlins, M.A., and William Ralph Inge. London: Murray, 1888. 6s.The Revised Latin Primer. By Benjamin Hall Kennedy, D.D. Longmans, 1888. 2s. 6d.The New Latin Primer. Edited by J. P. Postgate, M.A., and C. H. Vince, M.A. Cassell, 1888. 2s. 6d.The Shorter Latin Primer, by Dr. Kennedy. Longmans, 1888. 1s.

Kruskal proved that finite trees are well-quasi-ordered by hom(e)omorphic embeddability. Friedman observed that this statement is not provable in predicative analysis. Friedman also proposed (see in [Simpson]) some stronger variants of the Kruskal theorem dealing with finite labeled trees under home(e)omorphic embeddability with a certain gap-condition, where labels are arbitrary finite ordinals from a fixed initial segment of ω. The corresponding limit statement, expressing that for all initial segments of ω these labeled trees are well-quasi-ordered, is provable in Π 1 (...) 1 -CA, but not in the analogous theory Π 1 1 -CA 0 with induction restricted to sets. Schutte and Simpson proved that the one-dimensional case of Friedman's limit statement dealing with finite labeled intervals is not provable in Peano arithmetic. However, Friedman's gap-condition fails for finite trees labeled with transfinite ordinals. In [Gordeev 1] I proposed another gap-condition and proved the resulting one-dimensional modified statements for all (countable) transfinite ordinal-labels. The corresponding universal modified one-dimensional statement UM 1 is provable in (in fact, is equivalent to) the familiar theory ATR 0 whose proof-theoretic ordinal is Γ 0 . In [Gordeev 1] I also announced that, in the general case of arbitrarily-branching finite trees labeled with transfinite ordinals, in the proof-theoretic sense the hierarchy of the limit modified statements $\mathbf{M}_{ (which are denoted by LM λ in the present note) is as strong as the hierarchy of the familiar theories of iterated inductive definitions (more precisely, see [Gordeev 1, Concluding Remark 3]). In this note I present a "positive" proof of the full universal modified statement UM, together with a short proof of the crucial "reverse" results which is based on Okada's interpretation of the well-established ordinal notations of Buchholz corresponding to the theories of iterated inductive definitions. Formally the results are summarized in $\S5$ below. (shrink)

' I heartily recommend it to any philosopher of language interested in the issues. [] Logicians, of course, will want to savour the whole thing.' Australian Journal of Philosophy, 71:3 (1993).

It is commonly believed that populist politics and social media pose a serious threat to our concept of truth. Philosophical pragmatists, who are typically thought to regard truth as merely that which is 'helpful' for us to believe, are sometimes blamed for providing the theoretical basis for the phenomenon of 'post-truth'. In this book, Sami Pihlström develops a pragmatist account of truth and truth-seeking based on the ideas of William James, and defends a thoroughly pragmatist view of humanism which gives (...) space for a sincere search for truth. By elaborating on James's pragmatism and the 'will to believe' strategy in the philosophy of religion, Pihlström argues for a Kantian-inspired transcendental articulation of pragmatism that recognizes irreducible normativity as a constitutive feature of our practices of pursuing the truth. James himself thereby emerges as a deeply Kantian thinker. (shrink)

Andy Clark has argued that language is “in many ways the ultimate artifact” (Clark 1997, p.218). Fuelling this conclusion is a view according to which the human brain is essentially no more than a patterncompleting device, while language is an external resource which is adaptively fitted to the human brain in such a way that it enables that brain to exceed its unaided (pattern-completing) cognitive capacities, in much the same way as a pair of scissors enables us to “exploit our (...) basic manipulative capacities to fulfill new ends” (Clark 1997, pp.193-4). How should we respond to this bold reconceptualization of our linguistic abilities? First we need to understand it properly. So I begin by identifying and unpacking (and making a small “Heideggerian” amendment to) Clark’s main language-specific claims. That done I take a step back. Clark’s approach to language is generated from a theoretical perspective which sees cognition as distributed over brain, body, and world. So I continue my investigation of Clark’s incursion into linguistic territory by uncovering and illustrating those key ideas from the overall distributed cognition research programme which are particularly relevant in the present context. I then use this analysis as a spring-board from which to examine a crucial issue that arises for Clark’s account of language, namely linguistic inner rehearsal. I argue that while there is much to recommend in Clark’s treatment of this issue, some significant difficulties remain to be overcome. Via this critique of Clark’s position, alongside some proposals for how the revealed problems might be addressed, I hope to edge us that bit closer to a full understanding of our linguistic abilities. (shrink)

In Contingent Computation, M. Beatrice Fazi offers a new theoretical perspective through which we can engage philosophically with computing. The book proves that aesthetics is a viable mode of investigating contemporary computational systems. It does so by advancing an original conception of computational aesthetics that does not just concern art made by or with computers, but rather the modes of being and becoming of computational processes. Contingent Computation mobilises the philosophies of Gilles Deleuze and Alfred North Whitehead in order to (...) address aesthetics as an ontological study of the generative potential of reality. Through a novel philosophical reading of Gödel’s incompleteness theorems and of Turing’s notion of incomputability, Fazi finds this potential at the formal heart of computational systems, and argues that computation is a process of determining indeterminacy. This indeterminacy, which is central to computational systems, does not contradict their functionality. Instead, it drives their very operation, albeit in a manner that might not always fit with the instrumental, representational and cognitivist purposes that we have assigned to computing. (shrink)

Wines with geographical indication can be classified and represented by such features as designations of origin, producers, vintage years, alcoholic strength, and grape varieties; these features allow us to define wines in terms of a set of necessary and/or sufficient conditions. However, wines can also be identified by other characteristics, involving their look, smell, and taste; in this case, it is hard to define wines in terms of necessary and/or sufficient conditions, as wine concepts exhibit typicality effects. This is a (...) setback for the design of computer science ontologies aiming to represent wine concepts, since knowledge representation formalisms commonly adopted in this field do not allow for the representation of concepts in terms of typical traits. To solve this problem, we propose to adopt a hybrid approach in which ontology-oriented formalisms are combined with a geometric representation of knowledge based on conceptual spaces. As in conceptual spaces, concepts are identified in terms of a number of quality dimensions. In order to determine those relevant for wine representation, we use the terminology developed by the Italian Association of Sommeliers to describe wines. This will allow us to understand typicality effects about wines, determine prototypes and better exemplars, and measure the degree of similarity between different wines. (shrink)

In this paper, I seek to provide building blocks for a reconciliation of the ethical care for heritage protection and nature restoration ethics. It will do so, by introducing a hermeneutic landscape philosophy that takes landscape as a multi-layered “text” in need of interpretation, and place identities as build upon certain readings of the landscape. I will argue that from a hermeneutic perspective, both approaches appear to complement each other. Renaturing presents a valuable correction to the anthropocentrism of many European (...) rural cultures. Yet, heritage protectionists rightly point to the value of narratives for Old World identities. I will conclude with a short reflection on how such a hermeneutic environmental ethic can be helpful in dealing with environmental conflicts. (shrink)

In their paper, “Helpful Lessons and Cautionary Tales: How Should COVID-19 Drug Development and Access Inform Approaches to Non-Pandemic Diseases?” Holly Fernandez Lynch and colleagues have present...

It is generally believed that the de Broglie-Bohm model does not admit a particle interpretation for massive relativistic spin-0 particles, on the basis that particle trajectories cannot be defined. We show this situation is due to the fact that in the standard representation of the Klein-Gordon equation the wavefunction systematically contains superpositions of particle and anti-particle contributions. We argue that by working in a Foldy-Wouthuysen type representation uncoupling the particle from the anti-particle evolutions, a positive conserved density for a particle (...) and associated density current can be defined. For the free Klein-Gordon equation the velocity field obtained from this current density appears to be well-behaved and sub-luminal in typical instances. As an illustration, Bohmian trajectories for a spin-0 boson distribution are computed numerically for free propagation in situations in which the standard velocity field would take arbitrarily high positive and negative values. (shrink)

This paper argues that consciousness can, and often does, extend beyond the confines of the skull and skin. Conscious acts can extend to the extent they are intentional. Intentionality is revealing activity, and revealing activity often straddles processes occurring both inside and outside the subject’s body. What makes a conscious act extended is identical with what makes it intentional.

Soviet attitude towards Bohr reflects changes in the ideological approach to science. During the last period before Stalin's death danov proclaimed the campaign against Western influence in Soviet philosophy and science. Nevertheless the physicist M. A. Markov tried to introduce complementarity as a materialistic interpretation of quantum-mechanics in 1948. He was officially condemned. This was followed by a period (1948-54) during which heavy attacks were made against the Copenhagen school. In 1958, after a personal exchange of thoughts with Bohr, academician (...) Fock declared complementarity and probability to be irreversible steps towards a new insight into physical reality, at the same time correcting some of Bohr's epistemological conceptions. (shrink)

The medieval Islamic philosophers held a certain conception of the divine unity that assumes the necessary existent to be both one and simple. The oneness of the necessary existent meant that it is the only necessary existent and its simplicity meant that it admits no composition whatsoever – it is pure essence and its essence is necessary existence. In The Incoherence of the Philosophers al-Ġazālī presents, with elaboration, an exposition of the philosophers' conception of the divine unity, several arguments for (...) its two components, and his critique of these arguments. In this paper I focus on six of the arguments attributed to the philosophers. Following the textual evidence, I reconstruct these arguments and offer two possible interpretations of them. The first interpretation, which I call the many-argument interpretation, sees one of the arguments as employing the simplicity of the necessary existent to establish its oneness and the other five arguments as invoking oneness to establish simplicity. The second interpretation, which I call the one-argument interpretation, doesn't offer a new reading for the first argument but sees the other five arguments as defending the simplicity of the necessary existent based on its basic concept. I argue for the superiority of the one-argument interpretation. Résumé Les philosophes de l'Islam classique ont une doctrine de l'unité divine selon laquelle l'existant nécessaire est à la fois unique et simple. Son unicité signifie qu'il est le seul existant nécessaire, sa simplicité qu'il n'admet aucune sorte de composition; il est pure essence et son essence est existence nécessaire. Dans la Destruction des Philosophes, al-Ġazālī présente avec force détails un exposé de la doctrine de l'unité divine des philosophes, plusieurs arguments en faveur de ses deux composantes, ainsi que sa critique de ces arguments. Je me concentre ici sur six des arguments qu'il attribue aux philosophes. En suivant les données textuelles, je reconstruis ces arguments et en propose deux interprétations possibles. La première, que j'appelle l'interprétation “à arguments multiples”, identifie l'un des arguments comme s'appuyant sur la simplicité de l'existant nécessaire pour établir son unicité, et les cinq autres comme s'appuyant sur son unicité pour établir sa simplicité. La seconde, que j'appelle l'interprétation “à argument unique”, conserve la première lecture du premier argument mais voit dans les cinq autres une défense de la simplicité de l'existant nécessaire fondée sur sa notion fondamentale. J'argumente en faveur de la supériorité de l'interprétation “à argument unique”. (shrink)

carrington places race and racism at the center of his densely written analysis of science fiction, fantasy, utopia, and other forms of popular culture. He moves easily between a broad range of forms, which include memoirs, television series, comic books, novels, novelizations, fandom and fanzines, and short fiction and fiction circulated on the Internet. Popular culture helps us to construct notions of identity and race, and for carrington many constituent groups, notably fans, develop its key concepts and values.Speculative fiction is (...) for carrington a framework that links these various forms of popular culture. Here, SF is a genre different from literature, as it is situated closer to, and is more deeply... (shrink)

Recognized in his day as a man of letters equaling Rousseau and Voltaire in France and rivaling Samuel Johnson, David Hume passed from favor in the Victorian age--his work, it seemed, did not pursue Truth but rather indulged in popularization. Although Hume is once more considered as one of the greatest British philosophers, scholars now tend to focus on his thought rather than his writing. To round out our understanding of Hume, M. A. Box in this book charts the interrelated (...) development of Hume's literary ambitions, theories of style, and compositional practice from his Treatise in 1739 through the Enquiries. In so doing, Box makes the case for Hume's career-long concern with the presentational modes of reaching an audience for his philosophical writings. Hume reacted to the popular failure of his masterpiece, A Treatise of Human Nature, Box suggests, by self-consciously exploring strategies in his subsequent works for agreeably bringing his readership to participate in the act of philosophizing. Combining a sensitive grasp of the ways Restoration period and eighteenth-century writers conceived the relations between rhetoric and philosophy with sound readings of particular texts, Box shows how Hume's literary concerns went beyond matters of style to involve persona, structure, and doctrine. While this book helps explain long-standing ambiguities surrounding Hume, especially by pointing out the tension between his created persona and his own voice, it also serves as an excellent introduction to his philosophy. (shrink)