In this review we highlight the importance of defining the untranslated parts of transcripts, and present a number of computational approaches for the discovery and quantification of alternative transcription start and poly-adenylation events in high-throughput transcriptomic data. The fate of eukaryotic transcripts is closely linked to their untranslated regions, which are determined by the position at which transcription starts and ends at a genomic locus. Although the extent of alternative transcription starts and alternative poly-adenylation sites has been revealed by sequencing (...) methods focused on the ends of transcripts, the application of these methods is not yet widely adopted by the community. We suggest that computational methods applied to standard high-throughput technologies are a useful, albeit less accurate, alternative to the expertise-demanding 5′ and 3′ sequencing and they are the only option for analysing legacy transcriptomic data. We review these methods here, focusing on technical challenges and arguing for the need to include better normalization of the data and more appropriate statistical models of the expected variation in the signal. We highlight the importance of defining the untranslated parts of transcripts, and present a number of computational approaches for the discovery and quantification of alternative transcription start site and alternative poly-adenylation events from standard high-throughput transcriptomic data. We discuss the challenges faced by these methods and argue for the use of better statistical models for dealing with biases in the data and variation in the signal. (shrink)

Canaanite Scribes in the Amarna Letters. By Juan-Pablo Vita. Alter Orient und Altes Testament, vol. 406. Münster: Ugarit-Verlag, 2015. Pp. xii + 179, 78 plates. €97.

As it is well known, Lakatos divided Popper's philosophy into three stages; he also identified successive stages of falsificationism. A lesser-known fact is that the Hungarian philosopher systematized Feyerabend's philosophy, too. This tripartite division might have been a joke; Lakatos was perhaps trying to lighten Feyerabend's mood when his colleague was struggling wit h publishers in Minnesota and in New Left. Not quite successfully the publishers had tried to adjust Feyerabend's style to the standards of scientific literature. No matter what (...) motivated Lakatos when he analysed Feyerabend's philosophy, he appropriately captured differences between the 1970 and the 1975 edition of Against Method. Discussions of both philosophers concerning the division also reflect convolutions of their intellectual encounters. The presented paper takes up these issues. (shrink)

The philosophical roots of Malinowski's functionalism are in the academic circles of Krakow, where three figures seem to have exerted a particularly strong influence: Pawlicki, Straszewski, and Heinrich. The predominant trend in philosophy at that time was empiriocriticism, as developed by Mach and Avenarius. Also important were F. A. Lange's interpretation of Marburg neo-Kantianism. It should be noted that the historical philosophy field was extremely broad and diverse. Functionalism, a philosophically open concept, cannot be subordinated to any one philosophical system, (...) although the "openness" of functionalism is not absolute but complemented by its "closedness" to certain other philosophies. Praxism pervades functionalist theory and even creates its foundation. Malinowski approach is entirely scientific, but functionalism is never just empirical. Malinowski realized that pure experience is as impossible as pure reasoning. (shrink)

This collection of current research on logic programming languages presents results from a three-year, ESPRIT-funded effort to explore the integration of the foundational issues of functional, logic, and object-oriented programming. It offers valuable insights into the fast-developing extensions of logic programming with functions, constraints, concurrency, and objects. Chapters are grouped according to the unifying themes of functional programming, constraint, logic programming, and object-oriented programming.

Herman J. Saatkamp’s _A Life of Scholarship with Santayana: Essays and Reflections_ gathers together his work of a lifetime. There are twenty-three pieces, in three sections: “Santayana and Philosophy,” “Editorship,” and “Genetic Concerns and the Future of Philosophy.”.

Choć teorie C.G. Junga i J. Hillmana były już dogłębnie analizowane w licznych tekstach, prezentowany artykuł ma na celu wprowadzenie nowego spojrzenia na genealogię ich koncepcji. Śledząc historię pojęć obrazu psychicznego oraz archetypu, tekst rekonstruuje ewolucję ich myśli na kanwie dwóch jakościowych podejść psychologii: freudowskiej Metapsychologii (pierwotnie rozumianej jako psychoanalityczną naukę skoncentrowaną na zastąpieniu metafizyki) oraz diltheyowskiej Psychologii Realnej (deskryptywnej psychologii badającej aktywność duszy). Prezentowane studium skupia się na okresie 1912-1979 rozciągającym się od ustanowienia integralnej szkoły jungowskiej do ustanowienia przez (...) J. Hillmana Psychologii Archetypowej. Tak też niniejszy test ma na celu przedstawienie krytycznego i historycznego podejścia do psychologii głębi oraz psychologii obrazu. (shrink)

Chciałem Go pożegnać. Kilkakrotnie próbowałem napisać choć parę słów. O Nim samym. Okazało się, że nie potrafię. Udało mi się tylko przedstawić Jego poglądy na reizm Tadeusza Kotarbińskiego, ale uczyniłem to gdzie indziej. Muszę tu poprzestać na ofiarowaniu Mu tego, co napisałem na Jego dziewięćdziesiąte urodziny, w osiemdziesięciolecie naszej przyjaźni.

Let [Formula: see text] be a monster model of an arbitrary theory [Formula: see text], let [Formula: see text] be any tuple of bounded length of elements of [Formula: see text], and let [Formula: see text] be an enumeration of all elements of [Formula: see text]. By [Formula: see text] we denote the compact space of all complete types over [Formula: see text] extending [Formula: see text], and [Formula: see text] is defined analogously. Then [Formula: see text] and [Formula: see (...) text] are naturally [Formula: see text]-flows. We show that the Ellis groups of both these flows are of bounded size, providing an explicit bound on this size. Next, we prove that these Ellis groups do not depend on the choice of the monster model [Formula: see text]; thus, we say that these Ellis groups are absolute. We also study minimal left ideals of the Ellis semigroups of the flows [Formula: see text] and [Formula: see text]. We give an example of a NIP theory in which the minimal left ideals are of unbounded size. Then we show that in each of these two cases, boundedness of a minimal left ideal is an absolute property and that whenever such an ideal is bounded, then in some sense its isomorphism type is also absolute. Under the assumption that [Formula: see text] has NIP, we give characterizations of when a minimal left ideal of the Ellis semigroup of [Formula: see text] is bounded. Then we adapt the proof of Theorem 5.7 in Definably amenable NIP groups, J. Amer. Math. Soc. 31 609–641 to show that whenever such an ideal is bounded, a certain natural epimorphism 863–932]) from the Ellis group of the flow [Formula: see text] to the Kim–Pillay Galois group [Formula: see text] is an isomorphism. We also obtain some variants of these results, formulate some questions, and explain differences which occur when the flow [Formula: see text] is replaced by [Formula: see text]. (shrink)

The "space" of Lascar strong types, on some sort and relative to a given complete theory T, is in general not a compact Hausdorff topological space. We have at least three aims in this paper. The first is to show that spaces of Lascar strong types, as well as other related spaces and objects such as the Lascar group Gal L of T, have well-defined Borel cardinalities. The second is to compute the Borel cardinalities of the known examples as well (...) as of some new examples that we give. The third is to explore notions of definable map, embedding, and isomorphism, between these and related quotient objects. We also make some conjectures, the main one being roughly "smooth if and only if trivial". The possibility of a descriptive set-theoretic account of the complexity of spaces of Lascar strong types was touched on in the paper [E. Casanovas, D. Lascar, A. Pillay and M. Ziegler, Galois groups of first order theories, J. Math. Logic1 305–319], where the first example of a "non-G-compact theory" was given. The motivation for writing this paper is partly the discovery of new examples via definable groups, in [A. Conversano and A. Pillay, Connected components of definable groups and o-minimality I, Adv. Math.231 605–623; Connected components of definable groups and o-minimality II, to appear in Ann. Pure Appl. Logic] and the generalizations in [J. Gismatullin and K. Krupiński, On model-theoretic connected components in some group extensions, preprint, arXiv:1201.5221v1]. (shrink)

Antyrealizm etyczny reprezentowany jest obecnie przez około 30% filozofów analitycznych. Podzielają oni przekonanie, że nie istnieją moralne własności, fakty czy wartości. Przez długi okres rozwijany był on zwłaszcza przez akognitywistów. Jednak od czasu publikacji książki J. Mackiego Ethics. Inventingright and wrong (1977) antyrealistyczny sceptycyzm został zradykalizowany, przybierając także formę teorii globalnego błędu. Przyjęcie powyższego przekonania prowadzi do trzech strategii postępowania: 1. fikcjonalizmu asertorycznego (J. Mackie), 2. fikcjonalizmu nieasertorycznego (R. Joyce) oraz 3. eliminatywizmu (I. Hinckfuss i R. Garner). W artykule, przyjmując (...) antyrealistyczny punkt wyjścia przedstawicieli teorii globalnego błędu, analizuję powody, dla których warto wyeliminować etykę, i powody, dla których moglibyśmy mieć z tym problem. Następnie przedstawiam argumenty, ze względu na które pomysł eliminacji etyki pośrednio wspiera zmianę myślenia o realizmie etycznym z paradygmatu ontologicznego na racjonalistyczny. W związku z tym prezentuję koncepcję rewizyjnego realizmu racji oraz dowodzę, że nie poddaje się ona argumentom zwolenników eliminacji etyki. (shrink)

Skorulski fut un des plus eminents professeurs de philosophie a l'Academie de Vihia au XVIIIe siecle et auteur de deux ouvrages philosophiques. Plus tard, il fut recteur de trois colleges des jesuites, provincial des jesuites en Lituanie et ensuite recteur de l'Academie de Viina. Cette dissertation constitue une breve monographie de Skorulski en tant que philosophe. Elle contient sa biographie, la description de ses ouvrages et la caracteristique de sa philosophie. La brochure contient en particuher: Conceptions philosophiques: Logique. Metaphysique. Physique (...) generale. Physique particulifere. Psychologie. Rapport au cartesianisme. Rapport a l'heliocentrisme. Conclusion. Supplements: 1. Lettre d'Antoine Skorulski au roi Stanislas Auguste Poniatowski, 1773. 2. Reponse du roi Stanislas Auguste Poniatowski. 3. Fragments du livre Commentariolum philosophiae, traduits en polonais. (shrink)

Skorulski fut un des plus eminents professeurs de philosophie a l'Academie de Vihia au XVIIIe siecle et auteur de deux ouvrages philosophiques. Plus tard, il fut recteur de trois colleges des jesuites, provincial des jesuites en Lituanie et ensuite recteur de l'Academie de Viina. Cette dissertation constitue une breve monographie de Skorulski en tant que philosophe. Elle contient sa biographie, la description de ses ouvrages et la caracteristique de sa philosophie. La brochure contient en particuher: Conceptions philosophiques: Logique. Metaphysique. Physique (...) generale. Physique particulifere. Psychologie. Rapport au cartesianisme. Rapport a l'heliocentrisme. Conclusion. Supplements: 1. Lettre d'Antoine Skorulski au roi Stanislas Auguste Poniatowski, 1773. 2. Reponse du roi Stanislas Auguste Poniatowski. 3. Fragments du livre Commentariolum philosophiae, traduits en polonais. (shrink)

We present the (Lascar) Galois group of any countable theory as a quotient of a compact Polish group by an F_σ normal subgroup: in general, as a topological group, and under NIP, also in terms of Borel cardinality. This allows us to obtain similar results for arbitrary strong types defined on a single complete type over ∅. As an easy conclusion of our main theorem, we get the main result of [K. Krupiński, A. Pillay and T. Rzepecki, Topological dynamics and (...) the complexity of strong types, Israel J. Math.228 (2018) 863–932] which says that for any strong type defined on a single complete type over ∅, smoothness is equivalent to type-definability. We also explain how similar results are obtained in the case of bounded quotients of type-definable groups. This gives us a generalization of a former result from the paper mentioned above about bounded quotients of type-definable subgroups of definable groups. (shrink)

Tytułowe zagadnienie jest w artykule analizowane w przestrzeni współmyślenia z Sebastianem Gałeckim, autorem książki pt. Etyka chrześcijańska dla postchrześcijańskiej epoki. Pytanie o model etyki dla współczesnych czasów, określanych nie bez racji jako postchrześcijańskie, jest jednym z ważniejszych zagadnień współczesnych poszukiwań etycznych. Autor wspomnianej monografii chce zbudować taki model poprzez scalenie trzech, jego zdaniem pozostających w izolacji, tradycji etyki: teorii prawa naturalnego, teorii cnót i teorii sumienia, w ich współczesnej wykładni dokonanej przez J. Finnisa, A. MacIntyre’a i J.H. Newmana. Czy taka (...) droga jest optymalna z punktu widzenia zagadnienia postawionego w tytule artykułu? Wątpliwości i pytania postawione w wyniku lektury rozprawy Gałeckiego kreślą zręby odpowiedzi na to pytanie, rysując jednocześnie pozytywne drogi refleksji nad kształtem etyki w czasach późnej nowoczesności. (shrink)

Organizational sensemaking is crucial for resource planning and crisis management since facing complex strategic problems that exceed their capacity and ability, such as crises, forces organizations to engage in inter-organizational collaboration, which leads to obtaining individual and diverse perspectives to comprehend the issues and find solutions. This online qualitative survey study examines how Norwegian Sea Rescue Society employees perceived the concept of an organizational crisis and how they sensed their co-workers react to it. The scope was the ongoing COVID-19 pandemic, (...) a global event affecting all countries and organizations and responding similarly globally. Data were collected during the Fall of 2020. The instrument of choice was the Internal Crisis Management and Crisis Communication survey. The results showed that the overall sample strongly believed in their organization’s overall resilience level. However, a somewhat vague understanding of roles and responsibilities in a crisis where detected, together with some signs of informal communication, rumor spreading, misunderstanding, frustration, and insecurity. This study contributes to the academic field of organizational research, hence crisis management and sensemaking, and could be valuable to managers and decision-makers across sectors. Increased knowledge about how employees react to a crisis may help optimize internal crisis management planning and utilize robust mitigation and response strategies. (shrink)

The aim of this paper is to consider the influence of the methodological status of the concept of the totalitarian syndrome on the strategy of its development. It is argued that the totalitarian syndrome as put forward by Carl J. Friedrich and Zbigniew Brzezinski represented a kind of social modelling. However, there are different approaches to modelling in the social sciences. Modelling, when perceived from a neo-Hegelian perspectives, leads to the elaboration of dependencies between social phenomenon and their main factors. (...) Modelling, when seen from a neo-Weberian perspective, relies on the construction of notions which systematize and order social phenomena. This hypothesis is illustrated by a methodological analysis of the extension of the totalitarian syndrome authored by Achim Siegel and Mark R. Thompson. (shrink)

W artykule proponuję nową wersję transcendentalizmu, uwzględniającą współczesny stan nauki oraz filozofii. Idee tego transcendentalizmu prezentuję w toku dyskusji z P. Churchlandem, J. Kimem, K. Popperem, J. Searlem, S. Pinkerem, E. Husserlem, I. Kantem i J. Konorskim.

A family $$\mathcal {I}$$ I of subsets of a set X is an ideal on X if it is closed under taking subsets and finite unions of its elements. An ideal $$\mathcal {I}$$ I on X is below an ideal $$\mathcal {J}$$ J on Y in the Katětov order if there is a function $$f{: }Y\rightarrow X$$ f : Y → X such that $$f^{-1}[A]\in \mathcal {J}$$ f - 1 [ A ] ∈ J for every $$A\in \mathcal {I}$$ A (...) ∈ I. We show that the Hindman ideal, the Ramsey ideal and the summable ideal are pairwise incomparable in the Katětov order, where The Ramsey ideal consists of those sets of pairs of natural numbers which do not contain a set of all pairs of any infinite set (equivalently do not contain, in a sense, any infinite complete subgraph), The Hindman ideal consists of those sets of natural numbers which do not contain any infinite set together with all finite sums of its members (equivalently do not contain IP-sets that are considered in Ergodic Ramsey theory), The summable ideal consists of those sets of natural numbers such that the series of the reciprocals of its members is convergent. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:The Works of George Santayana, volume IX, Winds of Doctrine: Studies in Contemporary Opinion ed. by Martin A. Coleman, David E. Spiech, and Faedra Lazar WeissKrzysztof (Chris) Piotr SkowrońskiEdited by Martin A. Coleman, David E. Spiech, and Faedra Lazar WeissThe Works of George Santayana, volume IX, Winds of Doctrine: Studies in Contemporary Opinion Cambridge, MA, and London, England: The MIT Press, 2023; 359 pp., incl.indexIt is not merely (...) a re-edition of Santayana’s book that is at stake here. This ninth volume of The MIT Critical Edition of The Works of George Santayana is a next step in showing us his vast output with extensive range, depth, and, most importantly, significant stimulation for our generation of scholars and non-scholars. Just to illustrate the scope of Santayana’s work: volume V of the present MIT Critical Edition, published in the years 2001–2008, consists of eight thick books with Santayana’s correspondence throughout seventy years of intellectual activity (around 3000 letters to roughly 350 recipients, William James, Josiah Royce, Bertrand Russell, Sidney Hook, Horace Kallen, B.A.G. Fuller, Hugo Münsterberg, among them), containing philosophical and cultural insights that substantially compliment the views he expressed in his published texts.The original idea of the MIT Critical Edition was to present the published and unpublished works, followed by an elaborate editorial apparatus. As we can read in the present volume, “The goal of the editors is to produce texts that accurately represent Santayana’s final intentions regarding his works while recording all evidence on which editorial decisions have been based” (p. 307). How complex and fascinating the whole project has been we can also learn from a recently published book by Herman Saatkamp, who edited the Santayana edition for twenty-six years (Charles Padrón and Chris Skowroński, eds., Herman J. Saatkamp Jr., A Life of Scholarship with George Santayana: [End Page 462] Essays and Reflections, Brill/Rodopi, 2021). As we can read in Saatkamp’s book (p. 139), the story goes back to 1976, when John Lachs, top Santayana expert, asked Saatkamp to write the National Endowment for the Humanities (NEH) and put forward a proposal for The Works of George Santayana. As the latest of its results today, we have the ninth volume just published, while future volumes are still being prepared for publication (twenty volumes are currently projected).More specific answers to questions: Do we need a critical edition to do this? Is it not enough just to publish the original volume anew? depend largely on the target audience. For those who are unfamiliar with Santayana, having in hand Volume IX shows that it is just a part, although an important part, of a much larger project, and Paul Forster’s lengthy introduction would be very helpful. Forster competently outlines Santayana’s work and life, and subsequently analyzes the book, chapter by chapter, so that we have a penetrating insight into its whole substance. Also, further down in the volume (pp. 303–306), we find a “Chronology of the Life and Work of George Santayana” that is informative to those unfamiliar with Santayana.I suspect that those audiences who are familiar with Santayana have been waiting for this volume impatiently. The original 1913 publication, by Charles Scribner’s Son (New York)—which itself was a collection of rather independent texts in the form of chapters—has been expanded with Santayana’s preface to the second edition, of 1926. Most importantly, however, the whole text (these two editions: 1913 and 1926) have been re-edited, revised, and corrected according to the criteria of a critical edition. Some terms, phrases, names, as well as other issues are explained extensively in a 140-page part entitled “Notes to the Text” (pp. 159–302). Some of these notes are instructive indeed, not only because they explain passages in the text, but also because they refer to other works by Santayana where he explains the issue at hand into more detail or from a different viewpoint. From these notes we learn much more about the ideas discussed and the figures to which Santayana refers in his reflections than we would by reading... (shrink)

Information can be public among a group. Whether or not information is public matters, for example, for accounts of interdependent rational choice, of communication, and of joint intention. A standard analysis of public information identifies it with (some variant of) common belief. The latter notion is stipulatively defined as an infinite conjunction: for p to be commonly believed is for it to believed by all members of a group, for all members to believe that all members believe it, and so (...) forth. This analysis is often presupposed without much argument in philosophy. Theoretical entrenchment or intuitions about cases might give some traction on the question, but give little insight about why the identification holds, if it does. The strategy of this paper is to characterize a practical-normative role for information being public, and show that the only things that play that role are (variants of) common belief as stipulatively characterized. In more detail: a functional role for “taking a proposition for granted” in non-isolated decision making is characterized. I then present some minimal conditions under which such an attitude is correctly held. The key assumption links this attitude to beliefs about what is public. From minimal a priori principles, we can argue that a proposition being public among a group entails common commitment to believe among that group. Later sections explore partial converses to this result, the factivity of publicity and publicity from the perspective of outsiders to the group, and objections to the aprioricity of the result deriving from a posteriori existential presuppositions. (shrink)

Living out of silence, out of a fully functioning, lovingly attentive mind, and not just out of thought, out of a partially functioning mind, is requisite for depth or profundity in living or relating. A fully attentive, truly silent or meditative mind sees that there is real dualism of time and the timeless and that time and the timeless each has its own unique value. The timeless, or real silence, that which alone can make for depth in one's living and (...) relating, can be there only when, in one's awareness, time and all that is related to time, have come to an end. An examination of a wide variety of statements made by writers, both past and present, shows that these understandings are seldom there in contemporary writings, just as they were not there in writings that have come down to us from the past. 'Living beyond the One and the Many' invites readers to consider the possibility that what is presented in it can bring deep meaning to one's way of living in the world"--Publisher's description, back cover. (shrink)

Stereological techniques allow biologists to create quantitative, three-dimensional descriptions of biological structures from two- dimensional images of tissue viewed under the microscope. For example, they can accurately estimate the size of a particular organelle, the total length of a mass of capillaries, or the number of neurons or synapses in a particular region of the brain. This book provides a practical guide to designing and critically evaluating stereological studies of the nervous system and other tissues. It explains the basic concepts (...) behind design-based stereology and how to get started. Also included are detailed descriptions of how to prepare tissue appropriately, perform pilot studies and decide on the appropriate sampling strategy, and account for phenomena such as tissue shrinkage. Numerous examples of applications of stereological methods that are applicable to studies of the central system and a wide variety of other tissues are explained. The book is therefore essential reading for neurobiologists and cell biologists interested in generating accurate representations of cell and tissue architecture. (shrink)