The CRISPR-Cas systems of bacterial and archaeal adaptive immunity have become a household name among biologists and even the general public thanks to the unprecedented success of the new generation of genome editing tools utilizing Cas proteins. However, the fundamental biological features of CRISPR-Cas are of no lesser interest and have major impacts on our understanding of the evolution of antivirus defense, host-parasite coevolution, self versus non-self discrimination and mechanisms of adaptation. CRISPR-Cas systems present the best known case in point (...) for Lamarckian evolution, i.e. generation of heritable, adaptive genomic changes in response to encounters with external factors, in this case, foreign nucleic acids. CRISPR-Cas systems employ multiple mechanisms of self versus non-self discrimination but, as is the case with immune systems in general, are nevertheless costly because autoimmunity cannot be eliminated completely. In addition to the autoimmunity, the fitness cost of CRISPR-Cas systems appears to be determined by their inhibitory effect on horizontal gene transfer, curtailing evolutionary innovation. Hence the dynamic evolution of CRISPR-Cas loci that are frequently lost and acquired by archaea and bacteria. Another fundamental biological feature of CRISPR-Cas is its intimate connection with programmed cell death and dormancy induction in microbes. In this and, possibly, other immune systems, active immune response appears to be coupled to a different form of defense, namely, “altruistic” shutdown of cellular functions resulting in protection of neighboring cells. Finally, analysis of the evolutionary connections of Cas proteins reveals multiple contributions of mobile genetic elements to the origin of various components of CRISPR-Cas systems, furthermore, different biological systems that function by genome manipulation appear to have evolved convergently from unrelated MGE. The shared features of adaptive defense systems and MGE, namely the ability to recognize and cleave unique sites in genomes, make them ideal candidates for genome editing and engineering tools. (shrink)

Future-bias is the preference, all else being equal, for positive states of affairs to be located in the future not the past, and for negative states of affairs to be located in the past not the future. Three explanations for future-bias have been posited: the temporal metaphysics explanation, the practical irrelevance explanation, and the three mechanisms explanation. Understanding what explains future-bias is important not only for better understanding the phenomenon itself, but also because many philosophers think that which explanation is (...) the correct one has implications for our evaluation of the normative status of future-bias. In this paper we focus on the connection between future-bias and the temporal value asymmetry. The latter refers to the fact that people tend to assign more value to a state of affairs when it is located in the future, as opposed to being equidistant in the past. All three candidate explanations offered for future-bias proceed by explaining the temporal value asymmetry, and then supposing that future-bias is simply a manifestation of that asymmetry. Recently, however, it has been argued that the conditions under which people display the temporal value asymmetry and future-bias are different, and that this is reason to doubt that the latter is a manifestation of the former. In this paper we empirically test one response to this argument against the manifestation thesis—the simulation response—according to which once we control for the degree to which people can simulate the object of their preference, we find that people display future-bias and the temporal value asymmetry in the same conditions. We find no evidence in favour of the simulation response. Moreover, our results support some previous research that suggests that the temporal value asymmetry is less robust than previously thought, and this in itself casts doubt on the idea that future bias is just a manifestation of this asymmetry. (shrink)

I argue that influential recent discussions have whitewashed blame, characterizing it in ways that deemphasize or ignore its morally problematic features. I distinguish “definitional,” “creeping,” and “emphasis” whitewash, and argue that they play a central role in overall endorsements of blame by T.M. Scanlon, George Sher, and Miranda Fricker. In particular, these endorsements treat blame as appropriate by definition (Scanlon), or as little more than a wish (Sher), and infer from blame's having one useful function that it is a good (...) practice overall (Fricker). I use an analogy with revenge to illustrate the mechanisms of whitewashing, including broadening a concept to include available alternatives to it and inference from one feature of a practice to an overall conclusion about that practice. Several features of blame make it particularly prone to whitewashing, including blamers' personal or emotional stake in blaming and widespread disagreement about the nature of blame. I argue that a non‐whitewashing treatment of blame must pay closer attention both to blame's harms, and to comparisons between blame and alternative, non‐blaming reactions. (shrink)

Host‐pathogen arms race is a universal, central aspect of the evolution of life. Most organisms evolved several distinct yet interacting strategies of anti‐pathogen defense including resistance to parasite invasion, innate and adaptive immunity, and programmed cell death (PCD). The PCD is the means of last resort, a suicidal response to infection that is activated when resistance and immunity fail. An infected cell faces a decision between active defense and altruistic suicide or dormancy induction, depending on whether immunity is “deemed” capable (...) of preventing parasite reproduction and consequent infection of other cells. In bacteria and archaea, immunity genes typically colocalize with PCD modules, such as toxins‐antitoxins, suggestive of immunity‐PCD coupling, likely mediated by shared proteins that sense damage and “predict” the outcome of infections. In type VI CRISPR‐Cas systems, the same enzyme that inactivates the target RNA might execute cell suicide, in a case of ultimate integration of immunity and PCD. (shrink)

Eugene Marshall presents an original, systematic account of Spinoza's philosophy of mind, in which the mind is presented as an affective mechanism that, when rational, behaves as a spiritual automaton. He explores key themes in Spinoza's thought, and illuminates his philosophical and ethical project in a striking new way.

Nineteenth‐ and twentieth‐century North Atlantic theology has seen a succession of Trinitarian revivals. Some observers take as an index of a theologian's success whether he or she has much interesting to say about the Holy Spirit, and some, including Robert Jenson, have also noted a tendency to announce the Spirit and talk about the Son. While Rogers shares that concern, he qualifies the characterization to note that authors in three traditions sometimes admit the charge and demur, claiming that is how (...) it should be, citing passages in Calvin, Rahner, and Pavel Florensky. Of these the boldest is Florensky, who anticipates Jenson's critique but, writing in 1913, makes it not of Barth but of Eastern Orthodox theology , even in its liturgy. Rogers leaves this puzzle unresolved. (shrink)

Linguistics. Artificial intelligence. Related fields. Computation.

Most Artificial Intelligence theories of language either assume a syntactic component which serves as “front end” for the rest of the system, or else reject all attempts at distinguishing modules within the comprehension system. In this paper we will present an alternative which, while keeping modularity, will account for several puzzles for typical “syntax first” theories. The major addition to this theory is a “marker passing” (or “spreading activation”) component, which operates in parallel to the normal syntactic component.

A simple quantum relativistic model of ν µ − ντ neutrino oscillations in the OPERA experiment is presented. This model suggests that the two components in the neutrino beam are separated in space. After being created in a meson decay, the µ-neutrino moves 18 meters ahead of the beam’s center of energy, while the τ -neutrino is behind. Both neutrinos have subluminal speeds, however the advanced start of the ν µ explains why it arrives in the detector 60 ns earlier (...) than expected. Our model does violate the special-relativistic ban on superluminal signals. However, usual arguments about violation of causality are not applicable here. The invalidity of standard special-relativistic arguments is related to the interaction-dependence of the boost operator, which implies that boost-transformed space-time coordinates of events with interacting particles do not obey linear and universal Lorentz formulas. (shrink)

Common sense realism, by E. G. Bewkes.--Theology and religious experience, by Vergilius Ferm.--A reasoned faith, by G. F. Thomas.--Can religion become empirical? By J. S. Bixler.--Value theory and theology, by H. R. Niebuhr.--The truth in myths, by Reinhold Niebuhr.--Is subjectivism in value theory compatible with realism and meliorism? By Cornelius Krusé.--The semi-detached knower: a note on radical empiricism, by R. L. Calhoun.--The new scientific and metaphysical basis for epistemological theory, by F. S. C. Northrop.--A psychological approach to reality, by Hugh (...) Hartshorne.--A definition of religious liberalism, by D. S. Robinson. (shrink)

Margaret Atherton has written an excellent introduction to the work of George Berkeley, in which she systematically walks the reader through the various stages in his argument for immaterialism. By...

At the turn of the twentieth century, William James was America's most widely read philosopher. In addition to being one of the founders of pragmatism, however, he was also a leading psychologist and author of the seminal work, The Principles of Psychology. While scholars argue that James withdrew from the study of psychology after 1890, Eugene Taylor demonstrates convincingly that James remained preeminently a psychologist until his death in 1910.Taylor details James's contributions to experimental psychopathology, psychical research, and the psychology (...) of religion. Moreover, Taylor's work shows that out of his scientific study of consciousness, James formulated a sophisticated metaphysics of radical empiricism. In light of historical developments in psychology, as well as the current philosophic implications of the neuroscience revolution related to the biology of consciousness, Taylor argues that both the subject matter of James's investigations and his metaphysics of radical empiricism are just as important for psychology today as James believed they were in his own time.This book represents a major new contribution both to James scholarship and to the history of American psychology. Although philosophers have analyzed radical empiricism, this book is the first to trace the development of radical empiricism as a metaphysics addressed to psychologists. It is also the first to show James's involvement in depth-psychology and psychotherapeutics and to trace historical continuity between James's work on consciousness and subsequent developments in psychoanalysis, personality theory, and humanistic psychology. (shrink)

In partial fulfilment of the requirements for the degree of Master of Education, Department of Educational Administration.

Paper edition (unseen), $14.95. Annotation copyrighted by Book News, Inc., Portland, OR.

Empirical evidence shows that people have multiple time-biases. One is near-bias, another is future-bias, and a third is present-bias. Philosophers are concerned with the normative status of these time-biases. They have argued that, at least in part, the normative status of these biases depends on the extent to which they tend to promote, or frustrate, wellbeing, where “wellbeing” is taken to be of fundamental value. Since near-bias is thought to be associated with impulsivity, lack of self-control, and poor long-term health (...) and financial outcomes, it has often been supposed that it is associated with lower wellbeing. On those grounds, philosophers have argued that near-bias is rationally impermissible. By contrast, philosophical views about the normative status of future-bias have been mixed, with some arguing that future-bias is impermissible because, they think, it frustrates wellbeing, and others arguing that it is at least permissible (and perhaps obligatory) because it is the product of mechanisms whose functioning can be expected to promote wellbeing. However, to date there are no studies that have directly probed how time-biases correlate with wellbeing. Since it's not a settled matter which psychological mechanisms underlie time-biases, it is not uncontroversial which things serve as proxies for these preferences. We directly empirically investigate the connection between time-biases and measures of wellbeing, to see which of these biases is associated with promoting, or frustrating wellbeing. Contrary to expectation, we found no evidence that near-bias or present-bias are associated with frustrating wellbeing on any of the constructs we measured. On the other hand, and contrary to what some philosophers have supposed, we found that future-bias was associated with higher measures of wellbeing on several measures. We consider the implications of these findings for the evaluation of the normative status of these time biases. (shrink)

William James is best known for his Pragmatism , his Varieties of Religious Experience , and his Principles of Psychology , but little is known about his excursions into depth psychology, meaning a dynamic psychology of inner experience, despite the fact that he claimed in The Varieties that the subconscious was the primary avenue through which ultimately transforming mystical experiences occur. A survey of James's evolving conceptions of consciousness thorough the stages of his career reveals that his theories about the (...) subconscious emerged in the 1890s and became crystallized in his 1896 Lowell Lectures on Exceptional Mental States. While these lectures were never published, their content found a major place in various chapters in The Varieties, in addition to launching the so-called Boston School of Psychotherapy, experimental psychopathology at Harvard, and the popular era of psychotherapeutics that followed. As such, the Exceptional Mental States Lectures can be considered a bridge between the cognitive psychology in James's Principles and his emphasis on the primacy of the mystical experience in The Varieties . Finally, some of the more important implications of James's metaphysics of pure experience are broached for current directions in neuroscience today, regarding just what constitutes an adequate science of consciousness in light of what James had to say about depth psychology. (shrink)

The wide variety of blame presents two difficult puzzles. Why are instances of blame categorized under so many different mental kinds, such as judgment, belief, emotion, action, intention, desire, and combinations of these? Why is “blame” used to describe both interpersonal reactions and mere causal attributions, such as blaming faulty brakes for a car crash? I introduce a new conception of blame, on which blame is attention to something as a source of badness. I argue that this view resolves both (...) puzzles and offers an independently appealing conception of blame. (shrink)

Insufficient attention has been paid to the ethics of distributing costs of insurance risk. Seven approaches are articulated: the egalitarian model, the needs/ability model, the loss history model, the statistical model, the causality model, the moral fault model (avoidability interpretation and worldview interpretation), and eclectic models. The ethical dimensions of each model are explored. Although some reasons are given for preferring the eclectic model, the main purpose of the paper is to provide an ethical framework for further discussion of an (...) oft-neglected issue. (shrink)

The CRISPR-Cas systems of bacterial and archaeal adaptive immunity have become a household name among biologists and even the general public thanks to the unprecedented success of the new generation of genome editing tools utilizing Cas proteins. However, the fundamental biological features of CRISPR-Cas are of no lesser interest and have major impacts on our understanding of the evolution of antivirus defense, host-parasite coevolution, self versus non-self discrimination and mechanisms of adaptation. CRISPR-Cas systems present the best known case in point (...) for Lamarckian evolution, i.e. generation of heritable, adaptive genomic changes in response to encounters with external factors, in this case, foreign nucleic acids. CRISPR-Cas systems employ multiple mechanisms of self versus non-self discrimination but, as is the case with immune systems in general, are nevertheless costly because autoimmunity cannot be eliminated completely. In addition to the autoimmunity, the fitness cost of CRISPR-Cas systems appears to be determined by their inhibitory effect on horizontal gene transfer, curtailing evolutionary innovation. Hence the dynamic evolution of CRISPR-Cas loci that are frequently lost and acquired by archaea and bacteria. Another fundamental biological feature of CRISPR-Cas is its intimate connection with programmed cell death and dormancy induction in microbes. In this and, possibly, other immune systems, active immune response appears to be coupled to a different form of defense, namely, “altruistic” shutdown of cellular functions resulting in protection of neighboring cells. Finally, analysis of the evolutionary connections of Cas proteins reveals multiple contributions of mobile genetic elements to the origin of various components of CRISPR-Cas systems, furthermore, different biological systems that function by genome manipulation appear to have evolved convergently from unrelated MGE. The shared features of adaptive defense systems and MGE, namely the ability to recognize and cleave unique sites in genomes, make them ideal candidates for genome editing and engineering tools. (shrink)