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 Tu-Bao Ho & Zhi-Hua Zhou (eds.), Pricai 2008: Trends in Artificial Intelligence. Springer 1104--1109.
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  2.  20
    Jeffry L. Ramsey (2007). Calibrating and Constructing Models of Protein Folding. Synthese 155 (3):307 - 320.
    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.  21
    Alan Levin (2010). A Top-Down Approach to a Complex Natural System: Protein Folding. [REVIEW] Axiomathes 20 (4):423-437.
    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.  11
    Alejandro Balbín & Eugenio Andrade (2004). Protein Folding and Evolution Are Driven by the Maxwell Demon Activity of Proteins. Acta Biotheoretica 52 (3):173-200.
    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.  1
    Jörg Martin & F.‐Ulrich Hartl (1994). Molecular Chaperones in Cellular Protein Folding. Bioessays 16 (9):689-692.
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  6.  6
    C. Robert Matthews & Mark R. Hurle (1987). Mutant Sequences as Probes of Protein Folding Mechanisms. Bioessays 6 (6):254-257.
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  7.  2
    Thomas E. Creighton (1992). What the Papers Say: Protein Folding Pathways Determined Using Disulphide Bonds. Bioessays 14 (3):195-199.
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  8.  2
    M. Januar, A. Sulaiman & L. T. Handoko (2010). Conformation Changes and Protein Folding Induced by Φ4 Interaction. In Harald Fritzsch & K. K. Phua (eds.), Proceedings of the Conference in Honour of Murray Gell-Mann's 80th Birthday. World Scientific 472.
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  9.  2
    Robert L. Baldwin (1994). Finding Intermediates in Protein Folding. Bioessays 16 (3):207-210.
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  10.  1
    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.
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  11. L. Angelani (2008). Energy Landscape Analysis of Protein Folding in an Off-Lattice Model. Philosophical Magazine 88 (33-35):3901-3905.
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  12. МОЛЕКУЛЯРНА БІОФІЗИКА (2004). Clustering Monte Carlo Simulations of the Hierarchical Protein Folding on a Simple Lattice Model. Complexity 7 (9):22-23.
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  13. P. Faccioli, M. Sega, F. Pederiva & H. Orland (2008). Stochastic Dynamics and Dominant Protein Folding Pathways. Philosophical Magazine 88 (33-35):4093-4099.
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  14. Peter Lund (1994). The Chaperonin Cycle and Protein Folding. Bioessays 16 (4):229-231.
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  15. 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.
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  16. Jeffry Ramsey (2007). Calibrating and Constructing Models of Protein Folding. Synthese 155 (3):307-320.
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  17.  4
    Michel Morange (2006). The Protein Side of the Central Dogma: Permanence and Change. History and Philosophy of the Life Sciences 28 (4):513 - 524.
    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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  18.  1
    Patrick W. K. Lee & Gustavo Leone (1994). Reovirus Protein?1: From Cell Attachment to Protein Oligomerization and Folding Mechanisms. Bioessays 16 (3):199-206.
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  19. G. V. Quicke (1972). The Problem of Protein Quality in Maize. Transactions of the Royal Society of South Africa 40 (2):71-79.
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  20.  25
    H. H. Pattee (2013). Epistemic, Evolutionary, and Physical Conditions for Biological Information. Biosemiotics 6 (1):9-31.
    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.  13
    Gustavo Caetano‐Anollés & Jay Mittenthal (2010). Exploring the Interplay of Stability and Function in Protein Evolution. Bioessays 32 (8):655-658.
  22.  6
    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.
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  23. Massimo Pigliucci (2010). Genotype–Phenotype Mapping and the End of the ‘Genes as Blueprint’ Metaphor. Philosophical Transactions Royal Society B 365:557–566.
    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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  24.  17
    C. K. Raju (2004). The Electrodynamic 2-Body Problem and the Origin of Quantum Mechanics. Foundations of Physics 34 (6):937-962.
    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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  25.  17
    Valeria Mosini (2013). Proteins, the Chaperone Function and Heredity. Biology and Philosophy 28 (1):53-74.
    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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  26.  11
    Shu Quan & James Ca Bardwell (2012). Chaperone Discovery. Bioessays 34 (11):973-981.
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  27.  3
    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.
    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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  28.  8
    Franco Giorgi, Luis Emilio Bruni & Roberto Maggio (2013). Semiotic Selection of Mutated or Misfolded Receptor Proteins. Biosemiotics 6 (2):177-190.
    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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  29.  10
    Hans-Jörg Rheinberger (1993). Experiment and Orientation: Early Systems of in Vitro Protein Synthesis. [REVIEW] Journal of the History of Biology 26 (3):443 - 471.
    The living world is one of complexity, the result of innumerable interactions among organisms, cells, molecules. In analyzing a problem, the biologist is constrained to focus on a fragment of reality, on a piece of the universe which he arbitrarily isolates to define certain of its parameters.In biology, any study thus begins with the choice of a “system.” On this choice depend the experimenter's freedom to maneuver, the nature of the questions he is free to ask, and even, often, (...)
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  30.  20
    Theodore J. Everett (2010). Observation and Induction. Logos and Episteme 1 (2):303-324.
    This article offers a simple technical resolution to the problem of induction, which is to say that general facts are not always inferred from observations of particular facts, but are themselves sometimes defeasibly observed. The article suggests a holistic account of observation that allows for general statements in empirical theories to be interpreted as observation reports, in place of the common but arguably obsolete idea that observations are exclusively particular. Predictions and other particular statements about unobservable facts can then (...)
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  31.  5
    Mehmet Ozansoy & Yagmur Denizhan (2009). The Endomembrane System: A Representation of the Extracellular Medium? [REVIEW] Biosemiotics 2 (3):255-267.
    Both prokaryotic and eukaryotic cells share the basic mechanisms of secretory protein synthesis. However, unlike prokaryotes, eukaryotic cells posses a system of compartments, the so-called endomembrane system, which are involved in the synthesis process. A comparison of the prokaryotic and eukaryotic protein synthesis processes and particularly the observation of the functional and structural similarity between the prokaryotic cell membrane (the interface to the cell exterior) and the membrane of the eukaryotic endoplasmic reticulum (one of the compartments within the (...)
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  32. 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.
    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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  33. Massimo Pigliucci & Maarten Boudry (2013). Why the Demarcation Problem Matters. In Massimo Pigliucci & Maarten Boudry (eds.), Philosophy of Pseudoscience: Reconsidering the Demarcation Problem.
    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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  34.  89
    Andreas Hüttemann & Alan C. Love (2011). Aspects of Reductive Explanation in Biological Science: Intrinsicality, Fundamentality, and Temporality. British Journal for the Philosophy of Science 62 (3):519-549.
    The inapplicability of variations on theory reduction in the context of genetics and their irrelevance to ongoing research has led to an anti-reductionist consensus in philosophy of biology. One response to this situation is to focus on forms of reductive explanation that better correspond to actual scientific reasoning (e.g. part–whole relations). Working from this perspective, we explore three different aspects (intrinsicality, fundamentality, and temporality) that arise from distinct facets of reductive explanation: composition and causation. Concentrating on these aspects generates new (...)
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  35. 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.
    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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  36. Theodore L. Brown (2008). Making Truth: Metaphor in Science. University of Illinois Press.
    How does science work? _Making Truth: Metaphor in Science_ argues that most laypeople, and many scientists, do not have a clear understanding of how metaphor relates to scientific thinking. With stunning clarity, and bridging the worlds of scientists and nonscientists, Theodore L. Brown demonstrates the presence and the power of metaphorical thought. He presents a series of studies of scientific systems, ranging from the atom to current topics in chemistry and biology such as protein folding, chaperone proteins, and (...)
     
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  37. Philippa Foot (1967). The Problem of Abortion and the Doctrine of Double Effect. Oxford Review 5:5-15.
    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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  38.  93
    Jonathan Birch (2012). Robust Processes and Teleological Language. European Journal for Philosophy of Science 3 (3):299-312.
    I consider some hitherto unexplored examples of teleological language in the sciences. In explicating these examples, I aim to show (a) that such language is not the sole preserve of the biological sciences, and (b) that not all such talk is reducible to the ascription of functions. In chemistry and biochemistry, scientists explaining molecular rearrangements and protein folding talk informally of molecules rearranging “in order to” maximize stability. Evolutionary biologists, meanwhile, often speak of traits evolving “in order to” (...)
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  39.  2
    Martha E. Keyes (1999). The Prion Challenge to the `Central Dogma' of Molecular Biology, 1965–1991. Studies in History and Philosophy of Science Part C 30 (2):181-218.
    Since the 1930s, scientists studying the neurological disease scrapie had assumed that the infectious agent was a virus. By the mid 1960s, however, several unconventional properties had arisen that were difficult to reconcile with the standard viral model. Evidence for nucleic acid within the pathogen was lacking, and some researchers considered the possibility that the infectious agent consisted solely of protein. In 1982, Stanley Prusiner coined the term `prion' to emphasize the agent's proteinaceous nature. This infectious protein hypothesis (...)
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  40.  11
    Martha E. Keyes (1999). The Prion Challenge to the `Central Dogma' of Molecular Biology, 1965–1991. Studies in History and Philosophy of Science Part C 30 (2):181-218.
    Since the 1930s, scientists studying the neurological disease scrapie had assumed that the infectious agent was a virus. By the mid 1960s, however, several unconventional properties had arisen that were difficult to reconcile with the standard viral model. Evidence for nucleic acid within the pathogen was lacking, and some researchers considered the possibility that the infectious agent consisted solely of protein. In 1982, Stanley Prusiner coined the term `prion' to emphasize the agent's proteinaceous nature. This infectious protein hypothesis (...)
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  41. E. M. (1999). The Prion Challenge to the `Central Dogma' of Molecular Biology, 1965-1991 - Part I: Prelude to Prions. Studies in History and Philosophy of Science Part C 30 (1):1-19.
    Since the 1930s, scientists studying the neurological disease scrapie had assumed that the infectious agent was a virus. By the mid 1960s, however, several unconventional properties had arisen that were difficult to reconcile with the standard viral model. Evidence for nucleic acid within the pathogen was lacking, and some researchers considered the possibility that the infectious agent consisted solely of protein. In 1982, Stanley Prusiner coined the term `prion' to emphasize the agent's proteinaceous nature. This infectious protein hypothesis (...)
     
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  42.  16
    J. P. Liautard (1999). Analytical Background and Discussion of the Chaperone Model of Prion Diseases. Acta Biotheoretica 47 (3-4):219-238.
    It is generally accepted that prion infection is due solely to a protein i.e. the protein-only hypothesis. The essential constituent of infectious prions is the scrapie prion protein (PrPSc) which is chemically indistinguishable from the normal, cellular protein (PrPC) but exhibits distinct secondary and tertiary structure. This very unusual feature seems to be in contradiction with a major paradigm of present structural biology stated by Anfinsen: a protein folds to the most stable conformation, this means (...)
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  43.  16
    Alexander Powell (2009). Molecules, Cells and Minds: Aspects of Bioscientific Explanation. Dissertation, University of Exeter
    In this thesis I examine a number of topics that bear on explanation and understanding in molecular and cell biology, in order to shed new light on explanatory practice in those areas and to find novel angles from which to approach relevant philosophical debates. The topics I look at include mechanism, emergence, cellular complexity, and the informational role of the genome. I develop a perspective that stresses the intimacy of the relations between ontology and epistemology. Whether a phenomenon looks mechanistic, (...)
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  44. Moti Mizrahi (2014). The Problem of Natural Inequality: A New Problem of Evil. Philosophia 42 (1):127-136.
    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 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 soul-making defense, are not (...)
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  45. Nate Charlow (2014). The Problem with the Frege–Geach Problem. Philosophical Studies 167 (3):635-665.
    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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  46. Massimo Pigliucci (2013). What Hard Problem? Philosophy Now (99).
    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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  47. Robert Francescotti (2013). The Problem of Animal Pain and Suffering. In Justin McBrayer Daniel Howard-Snyder (ed.), The Blackwell Companion to the Problem of Evil. 113-127.
    Here I discuss some theistic responses to the problem of animal pain and suffering with special attention to Michael Murray’s presentation in Nature Red in Tooth and Claw. The neo-Cartesian defenses he describes are reviewed, along with the appeal to nomic regularity and Murray’s emphasis on the progression of the universe from chaos to order. It is argued that despite these efforts to prove otherwise the problem of animal suffering remains a serious threat to the belief that an (...)
     
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  48.  26
    Ulrich E. Stegmann (2016). ‘Genetic Coding’ Reconsidered: An Analysis of Actual Usage. British Journal for the Philosophy of Science 67 (3):707-730.
    This article reconsiders the theoretical role of the genetic code. By drawing on published and unpublished sources from the 1950s, I analyse how the code metaphor was actually employed by the scientists who first promoted its use. The analysis shows that the term ‘code’ picked out mechanism sketches, consisting of more or less detailed descriptions of ordinary molecular components, processes, and structural properties of the mechanism of protein synthesis. The sketches provided how-possibly explanations for the ordering of amino acids (...)
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  49.  46
    Matthew Frise (forthcoming). Internalism and the Problem of Stored Beliefs. Erkenntnis:1-20.
    A belief is stored if it is in no way before the subject’s mind. The problem of stored beliefs is that of satisfactorily explaining how the stored beliefs which seem justified are indeed justified. In this paper I challenge the two leading internalist attempts to solve this problem. Internalism about epistemic justification, at a minimum, states that one’s mental life alone determines what one is justified in believing. First I dispute the attempt from epistemic conservatism, which states that (...)
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  50.  2
    Joachim Funke (2014). Analysis of Minimal Complex Systems and Complex Problem Solving Require Different Forms of Causal Cognition. Frontiers in Psychology 5.
    In the last 20 years, a stream of research emerged under the label of „complex problem solving“ (CPS). This research was intended to describe the way people deal with complex, dynamic, and intransparent situations. Complex computer-simulated scenarios were as stimulus material in psychological experiments. This line of research lead to subtle insights into the way how people deal with complexity and uncertainty. Besides these knowledge-rich, realistic, intransparent, complex, dynamic scenarios with many variables, a second line of research used more (...)
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