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  1. Bacterial Species Pluralism in the Light of Medicine and Endosymbiosis.Javier Suárez - 2016 - Theoria: Revista de Teoría, Historia y Fundamentos de la Ciencia 31 (1):91-105.
    This paper aims to offer a new argument in defence bacterial species pluralism. To do so, I shall first present the particular issues derived from the conflict between the non-theoretical understanding of species as units of classification and the theoretical comprehension of them as units of evolution. Secondly, I shall justify the necessity of the concept of species for the bacterial world, and show how medicine and endosymbiotic evolutionary theory make use of different concepts of bacterial species due to their (...)
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  • Trashing Life’s Tree.L. R. Franklin-Hall - 2010 - Biology and Philosophy 25 (4):689-709.
    The Tree of Life has traditionally been understood to represent the history of species lineages. However, recently researchers have suggested that it might be better interpreted as representing the history of cellular lineages, sometimes called the Tree of Cells. This paper examines and evaluates reasons offered against this cellular interpretation of the Tree of Life. It argues that some such reasons are bad reasons, based either on a false attribution of essentialism, on a misunderstanding of the problem of lineage identity, (...)
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  • Modern Synthesis is the Light of Microbial Genomics.Austin Booth, Carlos Mariscal & W. Ford Doolittle - 2016 - Annual Reviews of Microbiology 70 (1):279-297.
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  • Letting Go of “Natural Kind”: Toward a Multidimensional Framework of Nonarbitrary Classification.Ludwig David - 2018 - Philosophy of Science 85 (1):31-52.
    This article uses the case study of ethnobiological classification to develop a positive and a negative thesis about the state of natural kind debates. On the one hand, I argue that current accounts of natural kinds can be integrated in a multidimensional framework that advances understanding of classificatory practices in ethnobiology. On the other hand, I argue that such a multidimensional framework does not leave any substantial work for the notion “natural kind” and that attempts to formulate a general account (...)
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  • Individuating Population Lineages: A New Genealogical Criterion.Beckett Sterner - 2017 - Biology and Philosophy 32 (5):683-703.
    Contemporary biology has inherited two key assumptions from the Modern Synthesis about the nature of population lineages: sexual reproduction is the exemplar for how individuals in population lineages inherit traits from their parents, and random mating is the exemplar for reproductive interaction. While these assumptions have been extremely fruitful for a number of fields, such as population genetics and phylogenetics, they are increasingly unviable for studying the full diversity and evolution of life. I introduce the “mixture” account of population lineages (...)
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  • Methodology and Ontology in Microbiome Research.John Huss - 2014 - Biological Theory 9 (4):1-11.
    Research on the human microbiome has generated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units—the metagenome, core microbiome, and enterotype—have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statistical methods, coupled with a translational imperative, are the primary drivers of this new ontology. By reducing the dimensionality of variation (...)
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  • Gene Names as Proper Names of Individuals: An Assessment.Thomas A. C. Reydon - 2009 - British Journal for the Philosophy of Science 60 (2):409-432.
    According to a recent suggestion, the names of gene taxa should be conceived of as referring to individuals with concrete genes as their parts, just as the names of biological species are often understood as denoting individuals with organisms as their parts. Although prima facie this suggestion might advance the debate on gene concepts in a similar way as the species-are-individuals thesis advanced the debate on species concepts, I argue that the principal arguments in support of the gene-individuality thesis are (...)
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  • Model Organisms Are Not Models.Arnon Levy & Adrian Currie - 2015 - British Journal for the Philosophy of Science 66 (2):327-348.
    Many biological investigations are organized around a small group of species, often referred to as ‘model organisms’, such as the fruit fly Drosophila melanogaster. The terms ‘model’ and ‘modelling’ also occur in biology in association with mathematical and mechanistic theorizing, as in the Lotka–Volterra model of predator-prey dynamics. What is the relation between theoretical models and model organisms? Are these models in the same sense? We offer an account on which the two practices are shown to have different epistemic characters. (...)
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  • The Nature of Programmed Cell Death.Pierre M. Durand & Grant Ramsey - 2019 - Biological Theory 14 (1):30-41.
    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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  • Philosophy and the Microbe: A Balancing Act. [REVIEW]Maureen A. O’Malley - 2013 - Biology and Philosophy 28 (2):153-159.
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  • Darwin’s Solution to the Species Problem.Marc Ereshefsky - 2010 - Synthese 175 (3):405 - 425.
    Biologists and philosophers that debate the existence of the species category fall into two camps. Some believe that the species category does not exist and the term 'species' should be eliminated from biology. Others believe that with new biological insights or the application of philosophical ideas, we can be confident that the species category exists. This paper offers a different approach to the species problem. We should be skeptical of the species category, but not skeptical of the existence of those (...)
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  • Species, Genes, and the Tree of Life.Joel Velasco - 2010 - British Journal for the Philosophy of Science 61 (3):599-619.
    A common view is that species occupy a unique position on the Tree of Life. Evaluating this claim requires an understanding of what the Tree of Life represents. The Tree represents history, but there are at least three biological levels that are often said to have genealogies: species, organisms, and genes. Here I focus on defending the plausibility of a gene-based account of the Tree. This leads to an account of species that are determined by gene genealogies. On this view, (...)
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  • Evaluating Maclaurin and Sterelny’s Conception of Biodiversity in Cases of Frequent, Promiscuous Lateral Gene Transfer.Gregory J. Morgan - 2010 - Biology and Philosophy 25 (4):603-621.
    The recent conception of biodiversity proposed by James Maclaurin and Sterelny was developed mostly with macrobiological life in mind. They suggest that we measure biodiversity by dividing life into natural units (typically species) and quantifying the differences among units using phenetic rather than phylogenetic measures of distance. They identify problems in implementing quantitative phylogenetic notions of difference for non-prokaryotic species. I suggest that if we focus on microbiological life forms that engage in frequent, promiscuous lateral gene transfer (LGT), and their (...)
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  • What Is a Recipe?Andrea Borghini - 2015 - Journal of Agricultural and Environmental Ethics 28 (4):719-738.
    The ontology of recipes is by and large unexplored. In this paper, I offer a three-steps account. After introducing some key terminology, I distinguish four main options for a theory of recipes: realism, constructivism, existentialism, and the naïve approach. Hence, I first argue that recipes are social entities whose identity depends on a process of identification, typically performed by means of a performative utterance on the part of a cook ; thus, the best theoretical framework for a theory of recipes (...)
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  • The Current Status of the Philosophy of Biology.Peter Takacs & Michael Ruse - 2013 - Science & Education 22 (1):5-48.
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  • What Microbes Can Do: A Sensory Guide to MicrobiologyMarch of the Microbes: Sighting the UnseenJohn L. Ingraham Cambridge, MA: Belknap Press of Harvard University Press, 2010 (326 Pp; £21.95 Hbk; ISBN 978-0-67403582-9). [REVIEW]Maureen A. O'Malley - 2010 - Biological Theory 5 (2):182-186.
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  • Biodiversity Realism: Preserving the Tree of Life.Christopher Lean - 2017 - Biology and Philosophy 32 (6):1083-1103.
    Biodiversity is a key concept in the biological sciences. While it has its origin in conservation biology, it has become useful across multiple biological disciplines as a means to describe biological variation. It remains, however, unclear what particular biological units the concept refers to. There are currently multiple accounts of which biological features constitute biodiversity and how these are to be measured. In this paper, I draw from the species concept debate to argue for a set of desiderata for the (...)
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  • Microbiology and the Species Problem.Marc Ereshefsky - 2010 - Biology and Philosophy 25 (4):553-568.
    This paper examines the species problem in microbiology and its implications for the species problem more generally. Given the different meanings of ‘species’ in microbiology, the use of ‘species’ in biology is more multifarious and problematic than commonly recognized. So much so, that recent work in microbial systematics casts doubt on the existence of a prokaryote species category in nature. It also casts doubt on the existence of a general species category for all of life (one that includes both prokaryotes (...)
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  • Pluralism or Unity in Biology: Could Microbes Hold the Secret to Life?Carol E. Cleland - 2013 - Biology and Philosophy 28 (2):189-204.
    Pluralism is popular among philosophers of biology. This essay argues that negative judgments about universal biology, while understandable, are very premature. Familiar life on Earth represents a single example of life and, most importantly, there are empirical as well as theoretical reasons for suspecting that it may be unrepresentative. Scientifically compelling generalizations about the unity of life must await the discovery of forms of life descended from an alternative origin, the most promising candidate being the discovery of extraterrestrial life. Nonetheless, (...)
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  • What Microbes Can Do: A Sensory Guide to Microbiology.Maureen A. O’Malley - 2010 - Biological Theory 5 (2):182-186.
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