Search results for 'protein folding problem' (try it on Scholar)

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  1. Xiaolong Zhang & Wen Cheng (2008). An Improved Tabu Search Algorithm for 3D Protein Folding Problem. In. In Tu-Bao Ho & Zhi-Hua Zhou (eds.), Pricai 2008: Trends in Artificial Intelligence. Springer. 1104--1109.score: 90.0
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  2. Jeffry L. Ramsey (2007). Calibrating and Constructing Models of Protein Folding. Synthese 155 (3):307 - 320.score: 76.0
    Prediction is more than testing established theory by examining whether the prediction matches the data. To show this, I examine the practices of a community of scientists, known as threaders, who are attempting to predict the final, folded structure of a protein from its primary structure, i.e., its amino acid sequence. These scientists employ a careful and deliberate methodology of prediction. A key feature of the methodology is calibration. They calibrate in order to construct better models. The construction leads (...)
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  3. Alan Levin (2010). A Top-Down Approach to a Complex Natural System: Protein Folding. [REVIEW] Axiomathes 20 (4):423-437.score: 73.0
    We develop a general method for applying functional models to natural systems and cite recent progress in protein modeling that demonstrates the power of this approach. Functional modeling constrains the range of acceptable structural models of a system, reduces the difficulty of finding them, and improves their fidelity. However, functional models are distinctly different from the structural models that are more commonly applied in science. In particular, structural and functional models ask different questions and provide different kinds of answers. (...)
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  4. Alejandro Balbín & Eugenio Andrade (2004). Protein Folding and Evolution Are Driven by the Maxwell Demon Activity of Proteins. Acta Biotheoretica 52 (3).score: 56.0
    In this paper we propose a theoretical model of protein folding and protein evolution in which a polypeptide (sequence/structure) is assumed to behave as a Maxwell Demon or Information Gathering and Using System (IGUS) that performs measurements aiming at the construction of the native structure. Our model proposes that a physical meaning to Shannon information (H) and Chaitin's algorithmic information (K) parameters can be both defined and referred from the IGUS standpoint. Our hypothesis accounts for the interdependence (...)
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  5. M. Januar, A. Sulaiman & L. T. Handoko (2010). Conformation Changes and Protein Folding Induced by Φ4 Interaction. In. In Harald Fritzsch & K. K. Phua (eds.), Proceedings of the Conference in Honour of Murray Gell-Mann's 80th Birthday. World Scientific. 472.score: 42.0
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  6. Robert L. Baldwin (1994). Finding Intermediates in Protein Folding. Bioessays 16 (3):207-210.score: 42.0
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  7. Vishwanath R. Lingappa, D. Thomas Rutkowski, Ramanujan S. Hegde & Olaf S. Andersen (2002). Conformational Control Through Translocational Regulation: A New View of Secretory and Membrane Protein Folding. Bioessays 24 (8):741-748.score: 42.0
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  8. Jörg Martin & F.‐Ulrich Hartl (1994). Molecular Chaperones in Cellular Protein Folding. Bioessays 16 (9):689-692.score: 42.0
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  9. C. Robert Matthews & Mark R. Hurle (1987). Mutant Sequences as Probes of Protein Folding Mechanisms. Bioessays 6 (6):254-257.score: 42.0
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  10. МОЛЕКУЛЯРНА БІОФІЗИКА (2004). Clustering Monte Carlo Simulations of the Hierarchical Protein Folding on a Simple Lattice Model. Complexity 7 (9):22-23.score: 42.0
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  11. Thomas E. Creighton (1992). What the Papers Say: Protein Folding Pathways Determined Using Disulphide Bonds. Bioessays 14 (3):195-199.score: 42.0
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  12. Peter Lund (1994). The Chaperonin Cycle and Protein Folding. Bioessays 16 (4):229-231.score: 42.0
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  13. Gabriela Ochoa, Gabi Escuela & Natalio Krasnogor (2006). Artificial Life and Bioinformatics-Incorporating Knowledge of Secondary Structures in a L-System-Based Encoding for Protein Folding. In O. Stock & M. Schaerf (eds.), Lecture Notes in Computer Science. Springer-Verlag. 3871--247.score: 42.0
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  14. Michel Morange (2006). The Protein Side of the Central Dogma: Permanence and Change. History and Philosophy of the Life Sciences 28 (4):513 - 524.score: 38.0
    There are two facets to the central dogma proposed by Francis Crick in 1957. One concerns the relation between the sequence of nucleotides and the sequence of amino acids, the second is devoted to the relation between the sequence of amino acids and the native three-dimensional structure of proteins. 'Folding is simply a function of the order of the amino acids,' i.e. no information is required for the proper folding of a protein other than the information contained (...)
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  15. Valeria Mosini (2013). Proteins, the Chaperone Function and Heredity. Biology and Philosophy 28 (1):53-74.score: 37.0
    In this paper I use a case study—the discovery of the chaperon function exerted by proteins in the various steps of the hereditary process—to re-discuss the question whether the nucleic acids are the sole repositories of relevant information as assumed in the information theory of heredity. The evidence I here present of a crucial role for molecular chaperones in the folding of nascent proteins, as well as in DNA duplication, RNA folding and gene control, suggests that the family (...)
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  16. Gustavo Caetano‐Anollés & Jay Mittenthal (2010). Exploring the Interplay of Stability and Function in Protein Evolution. Bioessays 32 (8):655-658.score: 37.0
  17. Anna Jean Wirth & Martin Gruebele (2013). Quinary Protein Structure and the Consequences of Crowding in Living Cells: Leaving the Test‐Tube Behind. Bioessays 35 (11):984-993.score: 37.0
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  18. C. K. Raju (2004). The Electrodynamic 2-Body Problem and the Origin of Quantum Mechanics. Foundations of Physics 34 (6):937-962.score: 36.0
    We numerically solve the functional differential equations (FDEs) of 2-particle electrodynamics, using the full electrodynamic force obtained from the retarded Lienard–Wiechert potentials and the Lorentz force law. In contrast, the usual formulation uses only the Coulomb force (scalar potential), reducing the electrodynamic 2-body problem to a system of ordinary differential equations (ODEs). The ODE formulation is mathematically suspect since FDEs and ODEs are known to be incompatible; however, the Coulomb approximation to the full electrodynamic force has been believed to (...)
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  19. Patrick W. K. Lee & Gustavo Leone (1994). Reovirus Protein ?1: From Cell Attachment to Protein Oligomerization and Folding Mechanisms. Bioessays 16 (3):199-206.score: 36.0
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  20. H. H. Pattee (2013). Epistemic, Evolutionary, and Physical Conditions for Biological Information. Biosemiotics 6 (1):9-31.score: 35.0
    The necessary but not sufficient conditions for biological informational concepts like signs, symbols, memories, instructions, and messages are (1) an object or referent that the information is about, (2) a physical embodiment or vehicle that stands for what the information is about (the object), and (3) an interpreter or agent that separates the referent information from the vehicle’s material structure, and that establishes the stands-for relation. This separation is named the epistemic cut, and explaining clearly how the stands-for relation is (...)
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  21. Hong‐Fang Ji, Lei Chen, Ying‐Ying Jiang & Hong‐Yu Zhang (2009). Evolutionary Formation of New Protein Folds is Linked to Metallic Cofactor Recruitment. Bioessays 31 (9):975-980.score: 33.3
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  22. Minglei Wang, Simina Maria Boca, Rakhee Kalelkar, Jay E. Mittenthal & Gustavo Caetano-Anollés (2006). A Phylogenomic Reconstruction of the Protein World Based on a Genomic Census of Protein Fold Architecture. Complexity 12 (1):27-40.score: 33.3
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  23. Shu Quan & James Ca Bardwell (2012). Chaperone Discovery. Bioessays 34 (11):973-981.score: 28.0
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  24. Massimo Pigliucci (2010). Genotype–Phenotype Mapping and the End of the ‘Genes as Blueprint’ Metaphor. Philosophical Transactions Royal Society B 365:557–566.score: 27.0
    In a now classic paper published in 1991, Alberch introduced the concept of genotype–phenotype (G!P) mapping to provide a framework for a more sophisticated discussion of the integration between genetics and developmental biology that was then available. The advent of evo-devo first and of the genomic era later would seem to have superseded talk of transitions in phenotypic space and the like, central to Alberch’s approach. On the contrary, this paper shows that recent empirical and theoretical advances have only sharpened (...)
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  25. Aare Abroi & Julian Gough (2011). Are Viruses a Source of New Protein Folds for Organisms?–Virosphere Structure Space and Evolution. Bioessays 33 (8):626-635.score: 26.0
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  26. Franco Giorgi, Luis Emilio Bruni & Roberto Maggio (2013). Semiotic Selection of Mutated or Misfolded Receptor Proteins. Biosemiotics 6 (2):177-190.score: 23.0
    Receptor oligomerization plays a key role in maintaining genome stability and restricting protein mutagenesis. When properly folded, protein monomers assemble as oligomeric receptors and interact with environmental ligands. In a gene-centered view, the ligand specificity expressed by these receptors is assumed to be causally predetermined by the cell genome. However, this mechanism does not fully explain how differentiated cells have come to express specific receptor repertoires and which combinatorial codes have been explored to activate their associated signaling pathways. (...)
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  27. Daniel Howard-Snyder (2013). The Logical Problem of Evil: Mackie and Plantinga. In Justin McBrayer & Daniel Howard-Snyder (eds.), The Blackwell Companion to the Problem of Evil. Wiley-Blackwell. 19-33.score: 21.0
    J.L. Mackie’s version of the logical problem of evil is a failure, as even he came to recognize. Contrary to current mythology, however, its failure was not established by Alvin Plantinga’s Free Will Defense. That’s because a defense is successful only if it is not reasonable to refrain from believing any of the claims that constitute it, but it is reasonable to refrain from believing the central claim of Plantinga’s Free Will Defense, namely the claim that, possibly, every essence (...)
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  28. Massimo Pigliucci (2013). The Demarcation Problem: A (Belated) Response to Laudan. In Massimo Pigliucci & Maarten Boudry (eds.), Philosophy of Pseudoscience: Reconsidering the Demarcation Problem. University of Chicago Press. 9.score: 21.0
    The “demarcation problem,” the issue of how to separate science from pseu- doscience, has been around since fall 1919—at least according to Karl Pop- per’s (1957) recollection of when he first started thinking about it. In Popper’s mind, the demarcation problem was intimately linked with one of the most vexing issues in philosophy of science, David Hume’s problem of induction (Vickers 2010) and, in particular, Hume’s contention that induction cannot be logically justified by appealing to the fact (...)
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  29. Massimo Pigliucci & Maarten Boudry (2013). Why the Demarcation Problem Matters. In Philosophy of Pseudoscience: Reconsidering the Demarcation Problem.score: 21.0
    Ever since Socrates, philosophers have been in the business of asking ques- tions of the type “What is X?” The point has not always been to actually find out what X is, but rather to explore how we think about X, to bring up to the surface wrong ways of thinking about it, and hopefully in the process to achieve an increasingly better understanding of the matter at hand. In the early part of the twentieth century one of the most (...)
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  30. John N. Prebble (2013). Contrasting Approaches to a Biological Problem: Paul Boyer, Peter Mitchell and the Mechanism of the ATP Synthase, 1961–1985. [REVIEW] Journal of the History of Biology 46 (4):699-737.score: 21.0
    Attempts to solve the puzzling problem of oxidative phosphorylation led to four very different hypotheses each of which suggested a different view of the ATP synthase, the phosphorylating enzyme. During the 1960s and 1970s evidence began to accumulate which rendered Peter Mitchell’s chemiosmotic hypothesis, the novel part of which was the proton translocating ATP synthase (ATPase), a plausible explanation. The conformational hypothesis of Paul Boyer implied an enzyme where ATP synthesis was driven by the energy of conformational changes in (...)
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  31. Philippa Foot (1967). The Problem of Abortion and the Doctrine of Double Effect. Oxford Review 5:5-15.score: 18.0
    One of the reasons why most of us feel puzzled about the problem of abortion is that we want, and do not want, to allow to the unborn child the rights that belong to adults and children. When we think of a baby about to be born it seems absurd to think that the next few minutes or even hours could make so radical a difference to its status; yet as we go back in the life of the fetus (...)
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  32. Moti Mizrahi (2014). The Problem of Natural Inequality: A New Problem of Evil. Philosophia 42 (1):127-136.score: 18.0
    In this paper, I argue that there is a kind of evil, namely, the unequal distribution of natural endowments, or natural inequality, which presents theists with a new evidential (not logical or incompatibility) problem of evil. The problem of natural inequality is a new evidential problem of evil not only because, to the best of my knowledge, it has not yet been discussed in the literature, but also because available theodicies, such the free will defense and the (...)
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  33. Andrew M. Bailey, Joshua Rasmussen & Luke van Horn (2011). No Pairing Problem. Philosophical Studies 154 (3):349-360.score: 18.0
    Many have thought that there is a problem with causal commerce between immaterial souls and material bodies. In Physicalism or Something Near Enough, Jaegwon Kim attempts to spell out that problem. Rather than merely posing a question or raising a mystery for defenders of substance dualism to answer or address, he offers a compelling argument for the conclusion that immaterial souls cannot causally interact with material bodies. We offer a reconstruction of that argument that hinges on two premises: (...)
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  34. Massimo Pigliucci (2013). What Hard Problem? Philosophy Now (99).score: 18.0
    The philosophical study of consciousness is chock full of thought experiments: John Searle’s Chinese Room, David Chalmers’ Philosophical Zombies, Frank Jackson’s Mary’s Room, and Thomas Nagel’s ‘What is it like to be a bat?’ among others. Many of these experiments and the endless discussions that follow them are predicated on what Chalmers famously referred as the ‘hard’ problem of consciousness: for him, it is ‘easy’ to figure out how the brain is capable of perception, information integration, attention, reporting on (...)
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  35. James R. Beebe, Logical Problem of Evil. Internet Encyclopedia of Philosophy.score: 18.0
    The existence of evil and suffering in our world seems to pose a serious challenge to belief in the existence of a perfect God. If God were all-knowing, it seems that God would know about all of the horrible things that happen in our world. If God were all-powerful, God would be able to do something about all of the evil and suffering. Furthermore, if God were morally perfect, then surely God would want to do something about it. And yet (...)
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  36. David Robb (2013). The Identity Theory as a Solution to the Exclusion Problem. In S. C. Gibb, E. J. Lowe & R. D. Ingthorsson (eds.), Mental Causation and Ontology. Oxford University Press.score: 18.0
    This is about a proposed solution to the exclusion problem, one I've defended elsewhere (for example, in "The Properties of Mental Causation"). Details aside, it's just the identity theory: mental properties face no threat of exclusion from, or preemption by, physical properties, because every mental property is a physical property. Here I elaborate on this solution and defend it from some objections. One of my goals is to place it in the context of a more general ontology of properties, (...)
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  37. Nate Charlow (2014). The Problem with the Frege–Geach Problem. Philosophical Studies 167 (3):635-665.score: 18.0
    I resolve the major challenge to an Expressivist theory of the meaning of normative discourse: the Frege–Geach Problem. Drawing on considerations from the semantics of directive language (e.g., imperatives), I argue that, although certain forms of Expressivism (like Gibbard’s) do run into at least one version of the Problem, it is reasonably clear that there is a version of Expressivism that does not.
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  38. Alessandro Lanteri, Chiara Chelini & Salvatore Rizzello (2008). An Experimental Investigation of Emotions and Reasoning in the Trolley Problem. Journal of Business Ethics 83 (4):789 - 804.score: 18.0
    Elaborating on the notions that humans possess different modalities of decision-making and that these are often influenced by moral considerations, we conducted an experimental investigation of the Trolley Problem. We presented the participants with two standard scenarios (‹lever’ and ‹stranger’) either in the usual or in reversed order. We observe that responses to the lever scenario, which result from (moral) reasoning, are affected by our manipulation; whereas responses to the stranger scenario, triggered by moral emotions, are unaffected. Furthermore, when (...)
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  39. Kelly Becker (2008). Epistemic Luck and the Generality Problem. Philosophical Studies 139 (3):353 - 366.score: 18.0
    Epistemic luck has been the focus of much discussion recently. Perhaps the most general knowledge-precluding type is veritic luck, where a belief is true but might easily have been false. Veritic luck has two sources, and so eliminating it requires two distinct conditions for a theory of knowledge. I argue that, when one sets out those conditions properly, a solution to the generality problem for reliabilism emerges.
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  40. Nicholas Unwin (1999). Quasi-Realism, Negation and the Frege-Geach Problem. Philosophical Quarterly 50 (196):337-352.score: 18.0
    Expressivists, such as Blackburn, analyse sentences such as 'S thinks that it ought to be the case that p' as S hoorays that p'. A problem is that the former sentence can be negated in three different ways, but the latter in only two. The distinction between refusing to accept a moral judgement and accepting its negation therefore cannot be accounted for. This is shown to undermine Blackburn's solution to the Frege-Geach problem.
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  41. David J. Chalmers & Brian Rabern (2014). Two-Dimensional Semantics and the Nesting Problem. Analysis 74 (2):210-224.score: 18.0
    Graeme Forbes (2011) raises some problems for two-dimensional semantic theories. The problems concern nested environments: linguistic environments where sentences are nested under both modal and epistemic operators. Closely related problems involving nested environments have been raised by Scott Soames (2005) and Josh Dever (2007). Soames goes so far as to say that nested environments pose the “chief technical problem” for strong two-dimensionalism. We call the problem of handling nested environments within two-dimensional semantics “the nesting problem”. We show (...)
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  42. Marc Ereshefsky (2010). Darwin's Solution to the Species Problem. Synthese 175 (3):405 - 425.score: 18.0
    Biologists and philosophers that debate the existence of the species category fall into two camps. Some believe that the species category does not exist and the term 'species' should be eliminated from biology. Others believe that with new biological insights or the application of philosophical ideas, we can be confident that the species category exists. This paper offers a different approach to the species problem. We should be skeptical of the species category, but not skeptical of the existence of (...)
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  43. Anil Gomes (2011). Is There a Problem of Other Minds? Proceedings of the Aristotelian Society 111 (3pt3):353-373.score: 18.0
    Scepticism is sometimes expressed about whether there is any interesting problem of other minds. In this paper I set out a version of the conceptual problem of other minds which turns on the way in which mental occurrences are presented to the subject and situate it in relation to debates about our knowledge of other people's mental lives. The result is a distinctive problem in the philosophy of mind concerning our relation to other people.
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  44. Daan Evers (2014). Moral Contextualism and the Problem of Triviality. Ethical Theory and Moral Practice 17 (2):285-297.score: 18.0
    Moral contextualism is the view that claims like ‘A ought to X’ are implicitly relative to some (contextually variable) standard. This leads to a problem: what are fundamental moral claims like ‘You ought to maximize happiness’ relative to? If this claim is relative to a utilitarian standard, then its truth conditions are trivial: ‘Relative to utilitarianism, you ought to maximize happiness’. But it certainly doesn’t seem trivial that you ought to maximize happiness (utilitarianism is a highly controversial position). Some (...)
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  45. Chris Tucker (2009). Evidential Support, Reliability, and Hume's Problem of Induction. Pacific Philosophical Quarterly 90 (4):503-519.score: 18.0
    Necessity holds that, if a proposition A supports another B, then it must support B. John Greco contends that one can resolve Hume's Problem of Induction only if she rejects Necessity in favor of reliabilism. If Greco's contention is correct, we would have good reason to reject Necessity and endorse reliabilism about inferential justification. Unfortunately, Greco's contention is mistaken. I argue that there is a plausible reply to Hume's Problem that both endorses Necessity and is at least as (...)
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  46. Cameron Buckner (forthcoming). The Semantic Problem(s) with Research on Animal Mindreading. Mind and Language.score: 18.0
    Philosophers have worried that research on animal mind-reading faces a “logical problem”: the difficulty of experimentally determining whether animals represent mental states (e.g. seeing) or merely the observable evidence for those states (e.g. line-of-gaze). The most impressive attempt to confront this problem has been mounted recently by Robert Lurz (2009, 2011). However, Lurz’ approach faces its own logical problem, revealing this challenge to be a special case of the more general problem of distal content. Moreover, participants (...)
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  47. Earl Conee (2013). The Specificity of the Generality Problem. Philosophical Studies 163 (3):751-762.score: 18.0
    In “Why the generality problem is everybody’s problem,” Michael Bishop argues that every theory of justification needs a solution to the generality problem. He contends that a solution is needed in order for any theory to be used in giving an acceptable account of the justificatory status of beliefs in certain examples. In response, first I will describe the generality problem that is specific to process reliabilism and two other sorts of problems that are essentially the (...)
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  48. Graham Oddie & Dan Demetriou (2007). The Fictionalist's Attitude Problem. Ethical Theory and Moral Practice 10 (5):485 - 498.score: 18.0
    According to John Mackie, moral talk is representational (the realists go that bit right) but its metaphysical presuppositions are wildly implausible (the non-cognitivists got that bit right). This is the basis of Mackie’s now famous error theory: that moral judgments are cognitively meaningful but systematically false. Of course, Mackie went on to recommend various substantive moral judgments, and, in the light of his error theory, that has seemed odd to a lot of folk. Richard Joyce has argued that Mackie’s approach (...)
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  49. Michael Wheeler (2008). Cognition in Context: Phenomenology, Situated Robotics and the Frame Problem. International Journal of Philosophical Studies 16 (3):323 – 349.score: 18.0
    The frame problem is the difficulty of explaining how non-magical systems think and act in ways that are adaptively sensitive to context-dependent relevance. Influenced centrally by Heideggerian phenomenology, Hubert Dreyfus has argued that the frame problem is, in part, a consequence of the assumption (made by mainstream cognitive science and artificial intelligence) that intelligent behaviour is representation-guided behaviour. Dreyfus' Heideggerian analysis suggests that the frame problem dissolves if we reject representationalism about intelligence and recognize that human agents (...)
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  50. Qilin Li, Quine’s Naturalized Epistemology, Epistemic Normativity and the Gettier Problem.score: 18.0
    In this paper, it is argued that there are (at least) two different kinds of ‘epistemic normativity’ in epistemology, which can be scrutinized and revealed by some comparison with some naturalistic studies of ethics. The first kind of epistemic normativity can be naturalized, but the other not. The doctrines of Quine’s naturalized epistemology is firstly introduced; then Kim’s critique of Quine’s proposal is examined. It is argued that Quine’s naturalized epistemology is able to save some room for the concept of (...)
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