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  1. CRISPR: A New Principle of Genome Engineering Linked to Conceptual Shifts in Evolutionary Biology.Eugene V. Koonin - 2019 - Biology and Philosophy 34 (1):9.
    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 (...)
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  2. How Biological Technology Should Inform the Causal Selection Debate.Janella Baxter - 2019 - Philosophy, Theory, and Practice in Biology 11.
    Causal selection is the widespread practice of singling out some causal variables from a set of causally relevant factors as explanatorily significant. The debate in the philosophy of biology literature has to do with what, if anything, justifies this practice in biology. Philosophers of biology have referred to the view that there is no explanatory justification for this practice as the causal parity thesis. Causal selection, by contrast, is the rejection of causal parity. On this view, biologists are at least (...)
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  3. Evolving Across the Explanatory Gap.Peter Godfrey-Smith - 2019 - Philosophy, Theory, and Practice in Biology 11.
    One way to express the most persistent part of the mind-body problem is to say that there is an “explanatory gap” between the physical and the mental. The gap is not usually taken to apply to all of the mental, but to subjective experience, the mind’s “qualitative” features, or what is now referred to as “phenomenal consciousness.” The “gap” formulation is due to Joseph Levine. He acknowledged the appeal of intuitions of separability between physical facts, of any kind we can (...)
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  4. Revamping the Image of Science for the Anthropocene.S. Andrew Inkpen & C. Tyler DesRoches - 2019 - Philosophy, Theory, and Practice in Biology 11.
    In 2016, a multidisciplinary body of scholars within the International Commission on Stratigraphy—the Anthropocene Working Group—recommended that the world officially recognize the Anthropocene as a new geological epoch. The most contested claim about the Anthropocene, that humans are a major geological and environmental force on par with natural forces, has proven to be a hotbed for discussion well beyond the science of geology. One reason for this is that it compels many natural and social scientists to confront problems and systems (...)
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  5. The Role of Assessor Teaching in Human Culture.Laureano Castro, Miguel Ángel Castro-Nogueira, Morris Villarroel & Miguel Ángel Toro - forthcoming - Biological Theory:1-10.
    According to the dual inheritance theory, cultural learning in our species is a biased and highly efficient process of transmitting cultural traits. Here we define a model of cultural learning where social learning is integrated as a complementary element that facilitates the discovery of a specific behavior by an apprentice, and not as a mechanism that works in opposition to individual learning. In that context, we propose that the emergence of the ability to approve or disapprove of offspring behavior, orienting (...)
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  6. Can Vestibular Stimulation Be Used to Treat Obesity?Paul D. McGeoch - forthcoming - Bioessays.
    It is hypothesized that repeated, non‐invasive stimulation of the vestibular (balance) system, via a small electrical current to the skin behind the ears, will cause the brain centers that control energy homeostasis to shift the body toward a leaner physique. This is because these centers integrate multiple inputs to, in effect, fix a set‐point for body fat, which though difficult to alter is not immutable. They will interpret repeated stimulation of the parts of the vestibular system that detect acceleration as (...)
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  7. Let's Stop the Sloppy Use of “Lamarckian”.Dave Speijer - forthcoming - Bioessays.
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  8. CRISPR-Cas Immunity: Beyond Nonself and Defence.Thomas Pradeu & Jean-François Moreau - 2019 - Biology and Philosophy 34 (1):6.
    In this commentary of Koonin’s target paper, we defend an extended view of CRISPR-Cas immunity by arguing that CRISPR-Cas includes, but cannot be reduced to, defence against nonself. CRISPR-Cas systems can target endogenous elements and tolerate exogenous elements. We conclude that the vocabulary of “defence” and “nonself” might be misleading when describing CRISPR-Cas systems.
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  9. Haben menschliche Embryonen eine Disposition zur Personalität?Anne Sophie Meincke - 2018 - In Markus Rothhaar, Martin Hähnel & Roland Kipke (eds.), Der manipulierbare Embryo. Münster, Germany: pp. 147-171.
    Do human embryos have a disposition to personhood? This has been argued within recent attempts to reformulate the classical argument from potentiality for the protection of human embryos with the help of the concept of disposition. In this paper, I analyse the central ontological premise of this new approach and show that any hopes of rehabilitating in dispositionalist terms the idea of a potential to personhood inherent in human embryos are mistaken. The dispositionalist version of the potentiality argument navigates in (...)
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  10. Potentialität und Disposition in der Diskussion über den Status des menschlichen Embryos: Zur Ontologie des Potentialitätsarguments.Anne Sophie Meincke - 2015 - Philosophisches Jahrbuch 122 (2):271-303.
    The argument from potentiality for embryo protection relies on the assumption of a specific developmental potential of human embryos: as human embryos under normal conditions naturally developing into beings whose strong moral status is uncontroversial, namely into human persons, they likewise enjoy strong moral status. In my paper, I endeavour to spell out the ontological foundations of the argument from potentiality and to discuss them critically in the light of new empirical findings in embryology. Particular attention is hereby paid to (...)
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  11. Persons as Biological Processes: A Bio-Processual Way Out of the Personal Identity Dilemma.Anne Sophie Meincke - 2018 - In Daniel J. Nicholson & John Dupre (eds.), Everything Flows. Towards a Processual Philosophy of Biology. Oxford, UK: pp. 357-378.
    Human persons exist longer than a single moment in time; they persist through time. However, so far it has not been possible to make this natural and widespread assumption metaphysically comprehensible. The philosophical debate on personal identity is rather stuck in a dilemma: reductionist theories explain personal identity away, while non-reductionist theories fail to give any informative account at all. This chapter argues that this dilemma emerges from an underlying commitment, shared by both sides of in the debate, to an (...)
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  12. The Many Meanings of “Cost” and “Benefit:” Biological Altruism, Biological Agency, and the Identification of Social Behaviours.Peter J. Woodford - 2019 - Biology and Philosophy 34 (1):4.
    The puzzle of how altruism can evolve has been at the center of recent debates over Hamilton’s Rule, inclusive fitness, and kin-selection. In this paper, I use recent debates over altruism and Hamilton’s legacy as an example to illustrate a more general problem in evolutionary theory that has philosophical significance; I attempt to explain this significance and to draw a variety of conclusions about it. The problem is that specific behaviours and general concepts of organism agency and intentionality are defined (...)
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  13. “Memetic Engineering”, Please! Thought, Values and Behaviour Are as Important as Technology!Andrew Moore - 2019 - Bioessays 41 (1):1800242.
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  14. Can All Major ROS Forming Sites of the Respiratory Chain Be Activated By High FADH2 /NADH Ratios?Dave Speijer - 2019 - Bioessays 41 (1):1800180.
    Aspects of peroxisome evolution, uncoupling, carnitine shuttles, supercomplex formation, and missing neuronal fatty acid oxidation (FAO) are linked to reactive oxygen species (ROS) formation in respiratory chains. Oxidation of substrates with high FADH2/NADH (F/N) ratios (e.g., FAs) initiate ROS formation in Complex I due to insufficient availability of its electron acceptor (Q) and reverse electron transport from QH2, e.g., during FAO or glycerol‐3‐phosphate shuttle use. Here it is proposed that the Q‐cycle of Complex III contributes to enhanced ROS formation going (...)
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  15. A Perspective on the Potential Utility of a Viscosupplement Multifunctional Biotherapeutic.James Melrose - 2019 - Bioessays 41 (1):1800215.
  16. Scientific Knowledge in the Age of Computation: Explicated, Computable and Manageable?Sophia Efstathiou, Rune Nydal, Astrid Lægreid & Martin Kuiper - forthcoming - Theoria: Revista de Teoría, Historia y Fundamentos de la Ciencia.
    Through an empirical account of Knowledge Management-enabled research in systems biology, we argue that computational KM helps produce new first-order biological knowledge, in new ways. KM is enabled by conceiving of ‘knowledge’ as an object for computational science: explicated in the text of biological articles and computable via appropriate data and metadata. These founded concepts risk underestimating practice-based knowing in ensuring the validity of ‘manageable’ knowledge as knowledge.
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  17. Multidrug Therapy for HIV Infection: Dynamics of Immune System.Deepmala Kamboj & M. D. Sharma - forthcoming - Acta Biotheoretica.
    A mathematical model of the dynamics of the immune system is considered to illustrate the effect of its response to HIV infection, i.e. on viral growth and on T-cell dynamics. The specific immune response is measured by the levels of cytotoxic lymphocytes in a human body. The existence and stability analyses are performed for infected steady state and uninfected steady state. In order to keep infection under control, roles of drug therapies are analyzed in the presence of efficient immune response. (...)
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  18. Toward a Macroevolutionary Theory of Human Evolution: The Social Protocell.Claes Andersson & Petter Törnberg - forthcoming - Biological Theory:1-17.
    Despite remarkable empirical and methodological advances, our theoretical understanding of the evolutionary processes that made us human remains fragmented and contentious. Here, we make the radical proposition that the cultural communities within which Homo emerged may be understood as a novel exotic form of organism. The argument begins from a deep congruence between robust features of Pan community life cycles and protocell models of the origins of life. We argue that if a cultural tradition, meeting certain requirements, arises in the (...)
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  19. Review of Other Minds: The Octopus, the Sea and the Deep Origins of Consciousness. [REVIEW]Daniel Dennett - 2019 - Biology and Philosophy 34 (1):2.
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  20. Code Biology, Peircean Biosemiotics, and Rosen’s Relational Biology.Marcello Barbieri - forthcoming - Biological Theory:1-9.
    The classical theories of the genetic code claimed that its coding rules were determined by chemistry—either by stereochemical affinities or by metabolic reactions—but the experimental evidence has revealed a totally different reality: it has shown that any codon can be associated with any amino acid, thus proving that there is no necessary link between them. The rules of the genetic code, in other words, obey the laws of physics and chemistry but are not determined by them. They are arbitrary, or (...)
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  21. The Concept of Innateness as an Object of Empirical Enquiry.Richard Samuels - 2016 - In Justin Sytsma & Wesley Buckwalter (eds.), Blackwell Companion to Experimental Philosophy. Blackwell. pp. 504-519.
  22. Sabina Leonelli, Data-Centric Biology: A Philosophical Study , 288 pp., $35.00, Paperback, ISBN: 9780226416472. [REVIEW]Youjung Shin - 2018 - Journal of the History of Biology 51 (4):887-889.
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  23. Philosophy in the Trenches: Reflections on The Eugenic Mind Project.Alan C. Love - 2018 - Philosophy, Theory, and Practice in Biology 10.
    Robert Wilson’s The Eugenic Mind Project is a major achievement of engaged scholarship and socially relevant philosophy and history of science. It exemplifies the virtues of interdisciplinarity. As principal investigator of the Living Archives on Eugenics in Western Canada project, while employed in the Department of Philosophy at the University of Alberta, Wilson encountered a proverbial big ball of mud with questions and issues that involved local individuals living through a painful set of memories and implicated his institutional home in (...)
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  24. Correction To: A Critique of Barbieri’s Code Biology Through Rosen’s Relational Biology: Reconciling Barbieri’s Biosemiotics with Peircean Biosemiotics.Federico Vega - 2018 - Biological Theory 13 (4):280-280.
    In the ‘Barbieri’s Concept of Mechanisms’ section on page 12 of above mentioned article.
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  25. On Calcott’s Permissive and Instructive Cause Distinction.Pierrick Bourrat - 2019 - Biology and Philosophy 34 (1):1.
    I argue that Calcott :481–505, Calcott 2017) mischaracterizes in an important way the notion of causal specificity proposed by Woodward :287–318, Woodward 2010). This leads him to rely too heavily on one single aspect of Woodward’s analysis on causal specificity; propose an information-theoretic measure he calls ‘precision’ which is partly redundant with, but less general than one of the dimensions in Woodward’s analysis of specificity, without acknowledging Woodward’s analysis; and claim that comparing the specificities of two or more causes under (...)
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  26. On the State of Scientific English and How to Improve It − Part 12: Keeping It Simple When Under Time Pressure….Andrew Moore - 2018 - Bioessays 40 (12):1800218.
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  27. Have Causal Claims About the Gut Microbiome Been Over‐Hyped?Pierrick Bourrat - 2018 - Bioessays 40 (12):1800178.
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  28. Human Endogenous Formaldehyde as an Anticancer Metabolite: Its Oxidation Downregulation May Be a Means of Improving Therapy.Yuri L. Dorokhov, Ekaterina V. Sheshukova, Tatiana E. Bialik & Tatiana V. Komarova - 2018 - Bioessays 40 (12):1800136.
    Malignant cells are characterized by an increased content of endogenous formaldehyde formed as a by‐product of biosynthetic processes. Accumulation of formaldehyde in cancer cells is combined with activation of the processes of cellular formaldehyde clearance. These mechanisms include increased ALDH and suppressed ADH5/FDH activity, which oncologists consider poor and favorable prognostic markers, respectively. Here, the sources and regulation of formaldehyde metabolism in cancer cells are reviewed. The authors also analyze the participation of oncoproteins such as fibulins, FGFR1, HER2/neu, FBI‐1, and (...)
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  29. Finding Wealth in Waste: Irreplicability Re‐Examined.Bart Penders & A. Cecile J. W. Janssens - 2018 - Bioessays 40 (12):1800173.
    Irreplicability is framed as crisis, blamed on sloppy science motivated by perverse stimuli in research. Structural changes to the organization of science, targeting sloppy science (e.g., open data, pre‐registration), are proposed to prevent irreplicability. While there is an unquestionable link between sloppy science and failures to replicate/reproduce scientific studies, they are currently conflated. This position can be understood as a result of the erosion of the role of theory in science. The history, sociology, and philosophy of science reveal alternative explanations (...)
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  30. Moral Talk and Indirect Reciprocity: Direct Observation Enables the Evolution of ‘Moral Signals’.Connor Robinson-Arnull - 2018 - Biology and Philosophy 33 (5-6):42.
    A prominent explanation of the evolution of altruism is ‘indirect reciprocity’ where the tracking of reputations in a population promotes altruistic outcomes. This paper investigates the conditions under which the meaning of reputation-tracking signals can co-evolve with altruistic behaviours. Previous work on this question suggests that such a co-evolution is unlikely. In our model, we introduce a mixture of direct and indirect information: individuals directly observe the actions and signals of others with some probability, rather than individuals always relying only (...)
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  31. The Descent of Preferences.David Spurrett - manuscript
    More attention has been devoted to providing evolutionary scenarios accounting for the development of beliefs, or belief-like states, than for desires or preferences. Here I articulate and defend an evolutionary rationale for the development of psychologically real preference states. Preferences token or represent the expected values of discriminated states, available actions, or action-state pairings. The argument is an application the ‘environmental complexity thesis’ found in Godfrey-Smith and Sterelny, although my conclusions differ from Sterelny’s. I argue that tokening expected utilities can, (...)
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  32. Evolutionary Arguments Against Moral Realism: Why the Empirical Details Matter (and Which Ones Do).Jeroen Hopster - 2018 - Biology and Philosophy 33 (5-6):41.
    The aim of this article is to identify the strongest evolutionary debunking argument against moral realism and to assess on which empirical assumptions it relies. In the recent metaethical literature, several authors have de-emphasized the evolutionary component of EDAs against moral realism: presumably, the success or failure of these arguments is largely orthogonal to empirical issues. I argue that this claim is mistaken. First, I point out that Sharon Street’s and Michael Ruse’s EDAs both involve substantive claims about the evolution (...)
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  33. Permanence and Extinction of a Diffusive Predator–Prey Model with Robin Boundary Conditions.M. A. Aziz-Alaoui, M. Daher Okiye & A. Moussaoui - 2018 - Acta Biotheoretica 66 (4):367-378.
  34. Proceedings of the First Vietnamese-French Joint Conference on Applications of Mathematics to Ecology, Bio-Economics, Epidemiology and Health Care: Hanoi and Tuanchau, Vietnam, December 12–15, 2016. [REVIEW]Doanh Nguyen-Ngoc & Tri Nguyen-Huu - 2018 - Acta Biotheoretica 66 (4):255-256.
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  35. Drug Repositioning by Integrating Known Disease-Gene and Drug-Target Associations in a Semi-Supervised Learning Model.Duc-Hau Le & Doanh Nguyen-Ngoc - 2018 - Acta Biotheoretica 66 (4):315-331.
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  36. The Nature of Programmed Cell Death.Pierre M. Durand & Grant Ramsey - forthcoming - Biological Theory:1-12.
    In multicellular organisms, cells are frequently programmed to die. This makes good sense: cells that fail to, or are no longer playing important roles are eliminated. From the cell’s perspective, this also makes sense, since somatic cells in multicellular organisms require the cooperation of clonal relatives. In unicellular organisms, however, programmed cell death poses a difficult and unresolved evolutionary problem. The empirical evidence for PCD in diverse microbial taxa has spurred debates about what precisely PCD means in the case of (...)
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  37. S Cott L Idgard and L Ynn K. N Yhart , Biological Individuality: Integrating Scientific, Philosophical and Historical Perspectives.Javier Suárez - 2018 - History and Philosophy of the Life Sciences 40 (4):67.
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  38. G Iovanni B Oniolo & M Arco J. N Athan , Philosophy of Molecular Medicine. Foundational Issues in Research and Practice, New York and London: Routledge, 2017, 287 Pp., £115. [REVIEW]Sara Green - 2018 - History and Philosophy of the Life Sciences 40 (4):66.
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  39. Individual Essentialism in Biology.Michael Devitt - 2018 - Biology and Philosophy 33 (5-6):39.
    A few philosophers of biology have recently explicitly rejected Essential Membership, the doctrine that if an individual organism belongs to a taxon, particularly a species, it does so essentially. But philosophers of biology have not addressed the broader issue, much discussed by metaphysicians on the basis of modal intuitions, of what is essential to the organism. In this paper, I address that issue from a biological basis, arguing for the Kripkean view that an organism has a partly intrinsic, partly historical, (...)
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  40. Rethinking the Role of Theory in Exploratory Experimentation.David Colaço - 2018 - Biology and Philosophy 33 (5-6):38.
    To explain their role in discovery and contrast them with theory-driven research, philosophers of science have characterized exploratory experiments in terms of what they lack: namely, that they lack direction from what have been called “local theories” of the target system or object under investigation. I argue that this is incorrect: it’s not whether or not there is direction from a local theory that matters, but instead how such a theory is used to direct an experiment that matters. Appealing to (...)
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  41. Neural Reuse and the Modularity of Mind: Where to Next for Modularity?John Zerilli - forthcoming - Biological Theory:1-20.
    The leading hypothesis concerning the “reuse” or “recycling” of neural circuits builds on the assumption that evolution might prefer the redeployment of established circuits over the development of new ones. What conception of cognitive architecture can survive the evidence for this hypothesis? In particular, what sorts of “modules” are compatible with this evidence? I argue that the only likely candidates will, in effect, be the columns which Vernon Mountcastle originally hypothesized some 60 years ago, and which form part of the (...)
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  42. Task Allocation and the Logic of Research Questions: How Ants Challenge Human Sociobiology.Ryan Ketcham - forthcoming - Biological Theory:1-17.
    After biologist Deborah Gordon made a series of experimental discoveries in the 1980s, she argued that a change in terminology regarding the division of labor among castes of specialists was needed. Gordon’s investigations of the interactive effects of ants in colonies led her to believe that the established approach Edward O. Wilson had pioneered was biased in a way that made some alternative candidate adaptive explanations invisible. Gordon argued that this was because the term “division of labor” implied a division (...)
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  43. Cancer Ecology: The Intracellular Interactome Makes Little Sense Without the Intercellular One.Andrew Moore - 2018 - Bioessays 40 (11):1800202.
  44. Evidence for a Neogenic Niche at the Periphery of Pancreatic Islets.Mark O. Huising, Sharon Lee & Talitha van der Meulen - 2018 - Bioessays 40 (11):1800119.
    We recently discovered a novel subset of beta cells that resemble immature beta cells during pancreas development. We named these “virgin” beta cells as they do not stem from existing mature beta cells. Virgin beta cells are found exclusively at the islet periphery in areas that we therefore designated as the “neogenic niche.” As beta cells are our only source of insulin, their loss leads to diabetes. Islets also contain glucagon‐producing alpha cells and somatostatin‐producing delta cells, that are important for (...)
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  45. Visions of Eye Commensals: The Known and the Unknown About How the Microbiome Affects Eye Disease.Anthony J. St Leger & Rachel R. Caspi - 2018 - Bioessays 40 (11):1800046.
    Until recently, the ocular surface is thought by many to be sterile and devoid of living microbes. It is now becoming clear that this may not be the case. Recent and sophisticated PCR analyses have shown that microbial DNA‐based “signatures” are present within various ethnic, geographic, and contact lens wearing communities. Furthermore, using a mouse model of ocular surface disease, we have shown that the microbe, Corynebacterium mastitidis (C. mast), can stably colonize the ocular mucosa and that a causal relationship (...)
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  46. How the Hippocampus Represents Memories: Making Sense of Memory Allocation Studies.Thiago F. A. França & José M. Monserrat - 2018 - Bioessays 40 (11):800068.
  47. Missed Druggable Cancer Hallmark: Cancer–Stroma Symbiotic Crosstalk as Paradigm and Hypothesis for Cancer Therapy.Eugene Sverdlov - 2018 - Bioessays 40 (11):1800079.
    During tumor evolution, cancer cells use the tumor‐stroma crosstalk to reorganize the microenvironment for maximum robustness of the tumor. The success of immune checkpoint therapy foretells a new cancer therapy paradigm: an effective cancer treatment should not aim to influence the individual components of super complex intracellular interactomes (molecular targeting), but try to disrupt the intercellular interactions between cancer and stromal cells, thus breaking the tumor as a whole. Arguments are provided in favor of a hypothesis that such interactions include (...)
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  48. Promoting an “Auteur Theory” for Young Scientists: Preserving Excitement and Creativity ….Arshad Desai & Suckjoon Jun - 2018 - Bioessays 40 (11):1800147.
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  49. How Does a Memory Find Its Neurons?Christoph Schmidt‐Hieber - 2018 - Bioessays 40 (11):1800189.
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  50. Précis of A Tapestry of Values: An Introduction to Values in Science.Kevin C. Elliott - 2018 - Philosophy, Theory, and Practice in Biology 10.
1 — 50 / 10752