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  1. Asexual Organisms, Identity and Vertical Gene Transfer.Gunnar Babcock - 2020 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 81:101265.
    This paper poses a problem for traditional phylogenetics: The identity of organisms that reproduce through fission can be understood in several different ways. This prompts questions about how to differentiate parent organisms from their offspring, making vertical gene transfer unclear. Differentiating between parents and offspring stems from what I call the identity problem. How the problem is resolved has implications for phylogenetic groupings. If the identity of a particular asexual organism persists through fission, the vertical lineage on a phylogenetic tree (...)
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  2. The Animal Sexes as Historical Explanatory Kinds.Laura Franklin-Hall - 2020 - In Shamik Dasgupta, Ravit Dotan & Brad Weslake (eds.), Current Controversies in Philosophy of Science. Routledge. pp. 177-197.
    Though biologists identify individuals as ‘male’ or ‘female’ across a broad range of animal species, the particular traits exhibited by males and females can vary tremendously. This diversity has led some to conclude that cross-animal sexes (males, or females, of whatever animal species) have “little or no explanatory power” (Dupré 1986: 447) and, thus, are not natural kinds in any traditional sense. This essay will explore considerations for and against this conclusion, ultimately arguing that the animal sexes, properly understood, are (...)
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  3. Species in the Age of Discordance.Matthew H. Haber - 2019 - Philosophy, Theory, and Practice in Biology 11 (21).
    Biological lineages move through time, space, and each other. As they do, they diversify, diverge, and grade away from and into one another. One result of this is genealogical discordance; i.e., the lineages of a biological entity may have different histories. We see this on numerous levels, from microbial networks, to holobionts, to population-level lineages. This paper considers how genealogical discordance impacts our study of species. More specifically, I consider this in the context of three framing questions: (1) How, if (...)
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  4. Moving Past the Systematics Wars.Beckett Sterner & Scott Lidgard - 2018 - Journal of the History of Biology 51 (1):31-67.
    It is time to escape the constraints of the Systematics Wars narrative and pursue new questions that are better positioned to establish the relevance of the field in this time period to broader issues in the history of biology and history of science. To date, the underlying assumptions of the Systematics Wars narrative have led historians to prioritize theory over practice and the conflicts of a few leading theorists over the less-polarized interactions of systematists at large. We show how shifting (...)
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  5. Peeking Inside the Black Box: A New Kind of Scientific Visualization.Michael T. Stuart & Nancy J. Nersessian - 2018 - Minds and Machines 29 (1):87-107.
    Computational systems biologists create and manipulate computational models of biological systems, but they do not always have straightforward epistemic access to the content and behavioural profile of such models because of their length, coding idiosyncrasies, and formal complexity. This creates difficulties both for modellers in their research groups and for their bioscience collaborators who rely on these models. In this paper we introduce a new kind of visualization that was developed to address just this sort of epistemic opacity. The visualization (...)
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  6. Taxonomy for Humans or Computers? Cognitive Pragmatics for Big Data.Beckett Sterner & Nico M. Franz - 2017 - Biological Theory 12 (2):99-111.
    Criticism of big data has focused on showing that more is not necessarily better, in the sense that data may lose their value when taken out of context and aggregated together. The next step is to incorporate an awareness of pitfalls for aggregation into the design of data infrastructure and institutions. A common strategy minimizes aggregation errors by increasing the precision of our conventions for identifying and classifying data. As a counterpoint, we argue that there are pragmatic trade-offs between precision (...)
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  7. What’s in a Name? – Exploring the Definition of ‘Cultural Relict Plant’.Erik Persson - 2014 - In Anna Andréasson, Anna Jakobsson, Elisabeth Gräslund Berg, Jens Heimdahl, Inger Larsson & Erik Persson (eds.), Sources to the history of gardening. Swedish University of Agricultural Sciences. pp. 289-299.
    When working with garden archaeology and garden archaeobotany, the plant material is of great importance. It is important to be able to identify which plants have grown in a particular garden and which have not, which of the plants you find in the garden today that are newly introduced or have established themselves on their own, and which plants that may be remnants of earlier cultivation. During the past two years, my colleagues and I have been involved in a project (...)
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  8. The Normative Structure of Mathematization in Systematic Biology.Beckett Sterner & Scott Lidgard - 2014 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 46 (1):44-54.
    We argue that the mathematization of science should be understood as a normative activity of advocating for a particular methodology with its own criteria for evaluating good research. As a case study, we examine the mathematization of taxonomic classification in systematic biology. We show how mathematization is a normative activity by contrasting its distinctive features in numerical taxonomy in the 1960s with an earlier reform advocated by Ernst Mayr starting in the 1940s. Both Mayr and the numerical taxonomists sought to (...)
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  9. Integrating History and Philosophy of the Life Sciences in Practice to Enhance Science Education: Swammerdam’s Historia Insectorum Generalis and the Case of the Water Flea.Catherine Kendig - 2013 - Science & Education 22 (8):1939-1961.
    Abstract: Hasok Chang (Sci Educ 20:317–341, 2011) shows how the recovery of past experimental knowledge, the physical replication of historical experiments, and the extension of recovered knowledge can increase scientific understanding. These activities can also play an important role in both science and history and philosophy of science education. In this paper I describe the implementation of an integrated learning project that I initiated, organized, and structured to complement a course in history and philosophy of the life sciences (HPLS). The (...)
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  10. The Organic Whole: A Conception Worthy of Biological Life.Bhakti Madhava Puri - 2013 - The Harmonizer.
    All the central assumptions of the Modern Synthesis (Neo-Darwinism) have been disproven. [1, 2] An article with the title, "Rocking the foundations of molecular genetics,” appearing in the prestigious Proceedings of the National Academy of Sciences at the end of 2012 [3] would have not been possible a decade ago. Groundbreaking experimental evidence of epigenetic maternal inheritance over several generations was published in the same journal, throwing the whole foundation of 21st century molecular genetics into question. Neo-Darwinism attributed genetic change (...)
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  11. The Species Problem: A Philosophical Analysis. By Richard A. Richards. (Cambridge UP, 2010. Pp. X + 236. Price £50.00.).Catherine Kendig - 2012 - Philosophical Quarterly 62 (247):405-408.
    Book review of Richard A. Richards' The Species Problem: A Philosophical Analysis.
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  12. The Theoretical Costs of DNA Barcoding.Monika Piotrowska - 2009 - Biological Theory 4 (3):235-239.
    I begin with a description of the benefits and limits of DNA barcoding as presented by its advocates not its critics. Next, I argue that due to the mutually dependent relationship between defining and delimiting species, all systems of classification are grounded in theory, even if only implicitly. I then proceed to evaluate DNA barcoding in that context. In particular, I focus on the barcoders’ use of a sharp boundary by which to delimit species, arguing that this boundary brings along (...)
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  13. Organic Whole.Bhakti Madhava Puri - 2009 - Darwin Under Siege.
    There is a nested hierarchy of wholes that characterizes reality, and especially life. The most fundamental principle is that Reality in the Vedantic/Bhagavat conception is based on Personality, as mentioned in the very first aphorism of the Bhagavat Purana, “janmady asya yatho nvayat itaratas charteshu abhijnah svarat.” Here and in many other scriptures the foundation or origin of everything is centered upon the abhijna or cognizant (conscious) primordial Personality of Godhead. Modern science in the West has become centered on matter (...)
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  14. Why and How to Naturalize Semiotic Concepts for Biosemiotics.Tommi Vehkavaara - 2002 - Sign Systems Studies 30 (1):293-312.
    Any attempt to develop biosemiotics either towards a new biological ground theory or towards a metaphysics of living nature necessitates some kind of naturalization of its semiotic concepts. Instead of standard physicalistic naturalism, a certain kind of semiotic naturalism is pursued here. The naturalized concepts are defined as referring only to the objects of our external experience. When the semiotic concepts are applied to natural phenomena in biosemiotics, there is a risk of falling into anthropomorphic errors if the semiotic concepts (...)
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