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Philosophy of Biology

Edited by John Wilkins (University of Sydney, University of Melbourne)
Assistant editor: Justin Bzovy (University of Western Ontario)
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  1. added 2015-07-03
    Robert Arp, Barry Smith & Andrew Spear (forthcoming). Building Ontologies with Basic Formal Ontology. MIT Press, August 7, 2015.
    In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...)
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  2. added 2015-07-02
    Olivier Rieppel (2007). Species: Kinds of Individuals or Individuals of a Kind. Cladistics 23:373-384.
    The “species-as-individuals” thesis takes species, or taxa, to be individuals. On grounds of spatiotemporal boundedness, any biological entity at any level of complexity subject to evolutionary processes is an individual. From evolutionary theory flows an ontology that does not countenance universal properties shared by evolving entities. If austere nominalism were applied to evolving entities, however, nature would be reduced to a mere flow of passing events, each one a blob in space–time and hence of passing interest only. Yet if there (...)
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  3. added 2015-07-02
    David B. Kitts (1978). Theoretics and Systematics: A Reply to Cracraft, Nelson, and Patterson. Systematic Zoology 27 (2):222-224.
  4. added 2015-07-02
    Ernst Mayr (1978). Evolution. Scientific American 239:46-55.
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  5. added 2015-07-02
    David B. Kitts (1977). Karl Popper, Verifiability, and Systematic Zoology. Systematic Zoology 26 (2):185-194.
  6. added 2015-06-28
    Chris F. Taylor, Dawn Field, Susanna-Assunta Sansone, Jan Aerts, Rolf Apweiler, Michael Ashburner, Catherine A. Ball, Pierre-Alain Binz, Molly Bogue, Tim Booth, Alvis Brazma, Ryan R. Brinkman, Adam Michael Clark, Eric W. Deutsch, Oliver Fiehn & Jennifer Fostel, Promoting Coherent Minimum Reporting Guidelines for Biological and Biomedical Investigations: The MIBBI Project.
    Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...)
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  7. added 2015-06-26
    Beckett Sterner (forthcoming). Pathways to Pluralism About Biological Individuality. Biology and Philosophy:1-20.
    What are the prospects for a monistic view of biological individuality given the multiple epistemic roles the concept must satisfy? In this paper, I examine the epistemic adequacy of two recent accounts based on the capacity to undergo natural selection. One is from Ellen Clarke, and the other is by Peter Godfrey-Smith. Clarke’s position reflects a strong monism, in that she aims to characterize individuality in purely functional terms and refrains from privileging any specific material properties as important in their (...)
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  8. added 2015-06-26
    Susana Monsó (forthcoming). Empathy and Morality in Behaviour Readers. Biology and Philosophy:1-20.
    It is tempting to assume that being a moral creature requires the capacity to attribute mental states to others, because a creature cannot be moral unless she is capable of comprehending how her actions can have an impact on the well-being of those around her. If this assumption were true, then mere behaviour readers could never qualify as moral, for they are incapable of conceptualising mental states and attributing them to others. In this paper, I argue against such an assumption (...)
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  9. added 2015-06-26
    Marc Ereshefsky (2014). Consilience, Historicity, and the Species Problem. In R. Paul Thompson & Denis Walsh (eds.), Evolutionary biology: conceptual, ethical, and religious issues. Cambridge. 65-86.
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  10. added 2015-06-25
    Hannes Rusch & Eckart Voland (forthcoming). Human Agricultural Economy is, and Likely Always Was, Largely Based on Kinship. Why? Behavioral and Brain Sciences.
    Commentary on J. Gowdy & L. Krall "The economic origins of ultrasociality": We question the sequence of evolutionary transitions leading to ultrasociality in humans proposed by Gowdy & Krall. Evidence indicates that families are, and likely always have been, the primary productive units in human agricultural economies, suggesting that genetic relatedness is key to understanding when the suppression of individual autonomy to the benefit of subsistence groups, i.e. extended families, evolved.
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  11. added 2015-06-24
    Robert Böhm, Hannes Rusch & Özgür Gürerk (forthcoming). What Makes People Go to War? Defensive Intentions Motivate Retaliatory and Preemptive Intergroup Aggression. Evolution and Human Behavior.
    Although humans qualify as one of the most cooperative animal species, the scale of violent intergroup conflict among them is unparalleled. Explanations of the underlying motivations to participate in an intergroup conflict, however, remain unsatisfactory. While previous research shows that intergroup conflict increases individually costly behavior to the benefit of the in-group, it has failed to identify robust triggers of aggressive behavior directed at out-groups. Here, we present a controlled laboratory experiment which demonstrates that such aggression can be provoked systematically (...)
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  12. added 2015-06-24
    Yu Gao, Adrian Raine & Robert A. Schug (2012). Somatic Aphasia: Mismatch of Body Sensations with Autonomic Stress Reactivity in Psychopathy. Biological Psychology 90:228–233.
    Background— Although one of the main characteristics of psychopaths is a deficit in emotion, it is unknown whether they show a fundamental impairment in appropriately recognizing their own body sensations during an emotion-inducing task. Method— Skin conductance and heart rate were recorded in 138 males during a social stressor together with subjective reports of body sensations. Psychopathic traits were assessed using the Psychopathy Checklist – Revised (PCL-R) 2nd edition (Hare, 2003). Results— Nonpsychopathic controls who reported higher body sensations showed higher (...)
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  13. added 2015-06-24
    Koshy Tharakan (2011). Anthropocentrism and Ecocentrism: On the Metaphysical Debate in Environmental Ethics. Jadavpur Journal of Philosophy 21 (2):27-42.
  14. added 2015-06-23
    Tano S. Posteraro (forthcoming). Deleuze's Larval Subject and the Question of Bodily TIme. Symposium: The Canadian Journal of Continental Philosophy.
    This paper treats Deleuze's first synthesis of time and the corresponding concept of larval subjectivity by routing it through a biophilosophy of organism. I develop, out of my reading of Deleuze, a temporal concept of organismic subjectivity.
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  15. added 2015-06-23
    Franck Varenne, Pierre Chaigneau, Jean Petitot & René Doursat (2015). Programming the Emergence in Morphogenetically Architected Systems. Acta Biotheoretica 63 (3).
    Large sets of elements interacting locally and producing specific architectures reliably form a category that transcends the usual dividing line between biological and engineered systems. We propose to call them morphogenetically architected complex systems (MACS). While taking the emergence of properties seriously, the notion of MACS enables at the same time the design (or “meta-design”) of operational means that allow controlling and even, paradoxically, programming this emergence. To demonstrate our claim, we first show that among all the self-organized systems studied (...)
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  16. added 2015-06-23
    Tano S. Posteraro (2014). Organismic Spatiality: Toward a Metaphysic of Composition. Environment and Planning D 32 (4):739-752.
    The task of this paper is the construction of a theory of organismic spatiality. I take as a starting point Gilles Deleuze’s reference in The Logic of Sense to Gilbert Simondon’s concept of the membrane. The membrane is a dynamically topological limit between the organism’s milieus of interiority and exteriority—the first moment of organismic spatiality. It is the foundation of the organism as an entity spatially distinct from its environment. The membrane is discriminatory and asymmetric—a concept, I claim, best understood (...)
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  17. added 2015-06-22
    Jack Birner (2015). F. A. Hayek’s The Sensory Order: An Evolutionary Perspective? Biological Theory 10 (2):167-175.
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  18. added 2015-06-22
    Vidyanand Nanjundiah & Michel Morange (2015). Aging, Sex Ratio, and Genomic Imprinting: Functional and Evolutionary Explanations in Biology. Biological Theory 10 (2):125-133.
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  19. added 2015-06-22
    James DiFrisco, Gaëlle Pontarotti, Federico Boem, Guillaume Schlaepfer, Ewelina Sokolowska & Eva Fernández-Labandera (2015). Ontological Issues in the Life Sciences. Biological Theory 10 (2):176-181.
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  20. added 2015-06-22
    William Yaworsky, Mark Horowitz & Kenneth Kickham (2015). Gender and Politics Among Anthropologists in the Units of Selection Debate. Biological Theory 10 (2):145-155.
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  21. added 2015-06-22
    Emanuele Archetti (2015). Three Kinds of Constructionism: The Role of Metaphor in the Debate Over Niche Constructionism. Biological Theory 10 (2):103-115.
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  22. added 2015-06-22
    Stuart A. Newman (2015). Notes on Stepping In. Biological Theory 10 (2):101-102.
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  23. added 2015-06-22
    Brian McLoone (2015). Some Criticism of the Contextual Approach, and a Few Proposals. Biological Theory 10 (2):116-124.
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  24. added 2015-06-22
    Yoshinari Yoshida & Hisashi Nakao (2015). EvoDevo as a Motley Aggregation: Local Integration and Conflicting Views of Genes During the 1980s. Biological Theory 10 (2):156-166.
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  25. added 2015-06-19
    Masayuki Hirano (forthcoming). Evolution of Vertebrate Adaptive Immunity: Immune Cells and Tissues, and AID/APOBEC Cytidine Deaminases. Bioessays:n/a-n/a.
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  26. added 2015-06-18
    David Ellerman, On Adjoint and Brain Functors.
    There is some consensus among orthodox category theorists that the concept of adjoint functors is the most important concept contributed to mathematics by category theory. We give a heterodox treatment of adjoints using heteromorphisms (object-to-object morphisms between objects of different categories) that parses an adjunction into two separate parts (left and right representations of heteromorphisms). Then these separate parts can be recombined in a new way to define a cognate concept, the brain functor, to abstractly model the functions of perception (...)
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  27. added 2015-06-16
    Ray Scott Percival (1995). Science Evolving. [REVIEW] Nature 376 (6536):131-132.
    MICHAEL Ruse aims to describe what scientists actually do in their research and how they arrive at their theories — a mixed bag of false starts, fallacious reasoning, the cultivation of followers, the marketing of ideas and so on. His approach, evolutionary naturalism, rejects the traditional distinction between the normative and the descriptive analysis of science. For him the path of discovery to, say, Darwin's theory of natural selection makes a difference to the theory itself, whereas for the normative analyst (...)
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  28. added 2015-06-16
    Ray Scott Percival (1994). Natural Selections. [REVIEW] Nature 371 (6499):666-667.
    How do you put both physicists and biologists on their guard? Answer: propound a philosophical theory that ignores Darwin's demolition of essentialism in species and brands any physicist who denies your theory of natural kinds as an anti-realist. A traditional division in philosophy is between metaphysics (what sorts of things exist) and epistemology (what and how we know). Some think that the core of realism is the metaphysical assumption that there is a world independent of our minds. But this core (...)
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  29. added 2015-06-15
    Guy Bennett-Hunter (forthcoming). Emergence, Emergentism and Pragmatism. Theology and Science.
    In this paper, I argue for the usefulness of pragmatism as a framework within which to develop the theological application of emergentist theory. I consider some philosophical issues relevant to the recent revival of interest, across various disciplines, in the concept of emergence and clarify some of the conceptual issues at stake in the attempts to formulate the philosophical position of emergentism and to apply it theologically. After highlighting some major problems arising from the main existing ways of formulating emergentism, (...)
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  30. added 2015-06-15
    Laura Perini (2013). Diagrams in Biology. The Knowledge Engineering Review 28 (3):273-286.
    Biologists depend on visual representations, and their use of diagrams has drawn the attention of philosophers, historians, and sociologists interested in understanding how these images are involved in biological reasoning. These studies, however, proceed from identification of diagrams on the basis of their spare visual appearance, and do not draw on a foundational theory of the nature of diagrams as representations. This approach has limited the extent to which we under- stand how these diagrams are involved in biological reasoning. In (...)
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  31. added 2015-06-15
    Laura Perini (2012). Form and Function: A Semiotic Analysis of Figures in Biology Textbooks. In Nancy Anderson & Michael Dietrich (eds.), The Educated Eye Visual Culture and Pedagogy in the Life Sciences. 235-254.
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  32. added 2015-06-11
    on the Integrated Frameworks (2011). On the Integrated Frameworks of Species Concepts: Mayden's Hierarchy of Species Concepts and de Queiroz's Unified Concept of Species. Journal of Zoological Systematics and Evolutionary Research 49 (3):177-184.
    Richard L. Mayden and Kevin de Queiroz have devised and developed ‘a hierarchy of species concepts’ and ‘a unified species concept’, respectively. Although their integrated frameworks of species concepts are rather different as to how to integrate the diverse modern concepts of species, the end result is that they are likely to agree on species recognition in nature, because they virtually share the same major components (i.e. evolutionary or lineage concept of species; same way of delimiting species), and have the (...)
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  33. added 2015-06-11
    Richard L. Mayden (1999). Consilience and a Hierarchy of Species Concepts: Advances Toward Closure on the Species Puzzle. Journal of Nematology 31 (2):95–116.
    Numerous concepts exist for biological species. This diversity of ideas derives from a number of sources ranging from investigative study of particular taxa and character sets to philosophical aptitude and world view to operationalism and nomenclatorial rules. While usually viewed as counterproductive, in reality these varied concepts can greatly enhance our efforts to discover and understand biological diversity. Moreover, this continued "turf war" and dilemma over species can be resolved if the various concepts are viewed in a hierarchical system and (...)
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  34. added 2015-06-11
    Richard L. Mayden & R. M. Wood (1995). Systematics, Species Concepts, and the Evolutionarily Significant Unit in Biodiversity and Conservation Biology. In J. L. Nielson (ed.), Evolution and the aquatic ecosystem: Defining unique units in population conservation. Special Publication No. 17. American Fisheries Society. 58–113.
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  35. added 2015-06-11
    David L. Hull (1980). Individuality and Selection. Annual Review of Ecology and Systematics 11:311-332.
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  36. added 2015-06-09
    Ernst Mayr (1940). Speciation Phenomena in Birds. American Naturalist 74 (752):249-278.
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  37. added 2015-06-05
    Christine James (2015). Data Science and Mass Media: Seeking a Hermeneutic Ethics of Information. Proceedings of the Society for Phenomenology and Media, Vol. 15, 2014, Pages 49-58 15 (2014):49-58.
    In recent years, the growing academic field called “Data Science” has made many promises. On closer inspection, relatively few of these promises have come to fruition. A critique of Data Science from the phenomenological tradition can take many forms. This paper addresses the promise of “participation” in Data Science, taking inspiration from Paul Majkut’s 2000 work in Glimpse, “Empathy’s Impostor: Interactivity and Intersubjectivity,” and some insights from Heidegger’s "The Question Concerning Technology." The description of Data Science provided in the scholarly (...)
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  38. added 2015-06-05
    Daniel S. Brooks (2014). The Role of Models in the Process of Epistemic Integration: The Case of the Reichardt Motion Detector. History and Philosophy of the Life Sciences 36 (1):90-113.
  39. added 2015-06-04
    Miles MacLeod (forthcoming). Heuristic Approaches to Models and Modeling in Systems Biology. Biology and Philosophy:1-20.
    Prediction and control sufficient for reliable medical and other interventions are prominent aims of modeling in systems biology. The short-term attainment of these goals has played a strong role in projecting the importance and value of the field. In this paper I identify the standard models must meet to achieve these objectives as predictive robustness—predictive reliability over large domains. Drawing on the results of an ethnographic investigation and various studies in the systems biology literature, I explore four current obstacles to (...)
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  40. added 2015-06-04
    Alberto Acerbi & Alex Mesoudi (2015). If We Are All Cultural Darwinians What’s the Fuss About? Clarifying Recent Disagreements in the Field of Cultural Evolution. Biology and Philosophy 30 (4):481-503.
    Cultural evolution studies are characterized by the notion that culture evolves accordingly to broadly Darwinian principles. Yet how far the analogy between cultural and genetic evolution should be pushed is open to debate. Here, we examine a recent disagreement that concerns the extent to which cultural transmission should be considered a preservative mechanism allowing selection among different variants, or a transformative process in which individuals recreate variants each time they are transmitted. The latter is associated with the notion of “cultural (...)
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  41. added 2015-06-01
    Silvia Menchón (2015). The Effect of Intrinsic and Acquired Resistances on Chemotherapy Effectiveness. Acta Biotheoretica 63 (2):113-127.
    Although chemotherapy is one of the most common treatments for cancer, it can be only partially successful. Drug resistance is the main cause of the failure of chemotherapy. In this work, we present a mathematical model to study the impact of both intrinsic and acquired resistances on chemotherapy effectiveness. Our simulations show that intrinsic resistance could be as dangerous as acquired resistance. In particular, our simulations suggest that tumors composed by even a small fraction of intrinsically resistant cells may lead (...)
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  42. added 2015-06-01
    Chris Buskes (2015). Darwinizing Culture: Pitfalls and Promises. Acta Biotheoretica 63 (2):223-235.
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  43. added 2015-06-01
    Ibrahim Seini, Oluwole Makinde & Baba Seidu (2015). Mathematical Analysis of the Effects of HIV-Malaria Co-Infection on Workplace Productivity. Acta Biotheoretica 63 (2):151-182.
    In this paper, a nonlinear dynamical system is proposed and qualitatively analyzed to study the dynamics and effects of HIV-malaria co-infection in the workplace. Basic reproduction numbers of sub-models are derived and are shown to have LAS disease-free equilibria when their respective basic reproduction numbers are less than unity. Conditions for existence of endemic equilibria of sub-models are also derived. Unlike the HIV-only model, the malaria-only model is shown to exhibit a backward bifurcation under certain conditions. Conditions for optimal control (...)
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  44. added 2015-06-01
    Khalid Hattaf, Abdelhadi Abta & Hassan Laarabi (2015). Optimal Control of a Delayed SIRS Epidemic Model with Vaccination and Treatment. Acta Biotheoretica 63 (2):87-97.
    This article deals with optimal control applied to vaccination and treatment strategies for an SIRS epidemic model with logistic growth and delay. The delay is incorporated into the model in order to modeled the latent period or incubation period. The existence for the optimal control pair is also proved. Pontryagin’s maximum principle with delay is used to characterize these optimal controls. The optimality system is derived and then solved numerically using an algorithm based on the forward and backward difference approximation.
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  45. added 2015-06-01
    Forogh Tavakoli, Nastaran Khodadad, Behzad Dehghani & Afagh Moattari (2015). In Silico Functional and Structural Characterization of H1N1 Influenza A Viruses Hemagglutinin, 2010–2013, Shiraz, Iran. Acta Biotheoretica 63 (2):183-202.
    Hemagglutinin is a major virulence factor of influenza viruses and plays an important role in viral pathogenesis. Analysis of amino acid changes, epitopes’ regions, glycosylation and phosphorylation sites have greatly contributed to the development of new generations of vaccine. The hemagglutinins of 10 selected isolates, 8 of 2010 and 2 of 2013 samples were sequenced and analyzed by several bioinformatic softwares and the results were compared with those of 3 vaccine isolates. The study detected several amino acid changes related to (...)
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  46. added 2015-06-01
    Vyacheslav Kalmykov & Lev Kalmykov (2015). A Solution to the Biodiversity Paradox by Logical Deterministic Cellular Automata. Acta Biotheoretica 63 (2):203-221.
    The paradox of biological diversity is the key problem of theoretical ecology. The paradox consists in the contradiction between the competitive exclusion principle and the observed biodiversity. The principle is important as the basis for ecological theory. On a relatively simple model we show a mechanism of indefinite coexistence of complete competitors which violates the known formulations of the competitive exclusion principle. This mechanism is based on timely recovery of limiting resources and their spatio-temporal allocation between competitors. Because of limitations (...)
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  47. added 2015-06-01
    Holger Teismann, Richard Karsten & Michael Deveau (2015). The Modellers’ Halting Foray Into Ecological Theory: Or, What is This Thing Called ‘Growth Rate’? Acta Biotheoretica 63 (2):99-111.
    This discussion paper describes the attempt of an imagined group of non-ecologists to determine the population growth rate from field data. The Modellers wrestle with the multiple definitions of the growth rate available in the literature and the fact that, in their modelling, it appears to be drastically model-dependent, which seems to throw into question the very concept itself. Specifically, they observe that six representative models used to capture the data produce growth-rate values, which differ significantly. Almost ready to concede (...)
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  48. added 2015-06-01
    Hadise Bazmara, Abolfazl Jahangiri, Iraj Rasooli & Fatemeh Sefid (2015). Functional Exposed Amino Acids of BauA as Potential Immunogen Against Acinetobacter Baumannii. Acta Biotheoretica 63 (2):129-149.
    Multidrug-resistant Acinetobacter baumannii is recognized to be among the most difficult antimicrobial-resistant gram negative bacilli to control and treat. One of the major challenges that the pathogenic bacteria face in their host is the scarcity of freely available iron. To survive under such conditions, bacteria express new proteins on their outer membrane and also secrete iron chelators called siderophores. Antibodies directed against these proteins associated with iron uptake exert a bacteriostatic or bactericidal effect against A. baumanii in vitro, by blocking (...)
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  49. added 2015-05-31
    Ronald J. Planer (forthcoming). Gene-Concept Pluralism, Causal Specificity, and Information. [REVIEW] Studies in History and Philosophy of Science Part C.
  50. added 2015-05-31
    Jessica Isserow (2015). Empathy and Morality. Biology and Philosophy 30 (4):597-608.
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