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  1. A Framework for Philosophical Biology.Sepehr Ehsani - manuscript
    Advances in biology, at least over the past two centuries, have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. The field of theoretical biology used to primarily provide a basis, similar to theoretical physics in the physical sciences, to rationally examine the frameworks within which biological experiments were carried out and to shed light on overlooked gaps in understanding. Today, however, theoretical biology has generally become synonymous with computational and mathematical biology. (...)
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  2. Causal Specificity, Biological Possibility and Non-Parity About Genetic Causes.Marcel Weber - manuscript
    Several authors have used the notion of causal specificity in order to defend non-parity about genetic causes (Waters 2007, Woodward 2010, Weber 2017, forthcoming). Non-parity in this context is the idea that DNA and some other biomolecules that are often described as information-bearers by biologists play a unique role in life processes, an idea that has been challenged by Developmental Systems Theory (e.g., Oyama 2000). Indeed, it has proven to be quite difficult to state clearly what the alleged special role (...)
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  3. Causal Selection Versus Causal Parity in Biology: Relevant Counterfactuals and Biologically Normal Interventions.Marcel Weber - forthcoming - In C. Kenneth Waters & James Woodward (eds.), Philosophical Perspectives on Causal Reasoning in Biology. Minnesota Studies in Philosophy of Science. Vol. XXI. Minneapolis: University of Minnesota Press.
    Causal selection is the task of picking out, from a field of known causally relevant factors, some factors as elements of an explanation. The Causal Parity Thesis in the philosophy of biology challenges the usual ways of making such selections among different causes operating in a developing organism. The main target of this thesis is usually gene centrism, the doctrine that genes play some special role in ontogeny, which is often described in terms of information-bearing or programming. This paper is (...)
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  4. Beyond Descriptive Accuracy: The Central Dogma of Molecular Biology in Scientific Practice.M. Polo Camacho - 2021 - Studies in History and Philosophy of Science Part A 86:20-26.
    There is no denying the Central Dogma’s impact on the biological sciences. Since the Dogma’s formulation by Francis Crick in 1958, however, many have debated the Dogma’s empirical adequacy. My aim is to move beyond these discussions, and instead consider the Central Dogma’s significance to contemporary biological practice. To do this, I consider four distinct approaches for determining the non-descriptive methodological significance of a scientific principle. I argue that these approaches fail to vindicate the Central Dogma, and that, under many (...)
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  5. What’s All the Fuss About? The Inheritance of Acquired Traits is Compatible with the Central Dogma.M. Polo Camacho - 2020 - History and Philosophy of the Life Sciences 42 (3):1-15.
    The Central Dogma of molecular biology, which holds that DNA makes protein and not the other way around, is as influential as it is controversial. Some believe the Dogma has outlived its usefulness, either because it fails to fully capture the ins-and-outs of protein synthesis (Griffiths and Stotz, 2013; Stotz, 2006), because it turns on a confused notion of information (Sarkar, 2004), or because it problematically assumes the unidirectional flow of information from DNA to protein (Gottlieb, 2001). This paper evaluates (...)
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  6. Genomic Stress Responses Drive Lymphocyte Evolvability: An Ancient and Ubiquitous Mechanism.Bartlomiej Swiatczak - 2020 - Bioessays 42 (10):2000032.
    Somatic diversification of antigen receptor genes depends on the activity of enzymes whose homologs participate in a mutagenic DNA repair in unicellular species. Indeed, by engaging error-prone polymerases, gap filling molecules and altered mismatch repair pathways, lymphocytes utilize conserved components of genomic stress response systems, which can already be found in bacteria and archaea. These ancient systems of mutagenesis and repair act to increase phenotypic diversity of microbial cell populations and operate to enhance their ability to produce fit variants during (...)
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  7. The Central Dogma Is Empirically Inadequate…No Matter How We Slice It.M. Polo Camacho - 2019 - Philosophy, Theory, and Practice in Biology 11.
    Roughly, the Central Dogma of molecular biology states that DNA codes for protein, not the other way around. This principle, which is still heralded as an important element of contemporary biological theory, has received much critical attention since its original formulation by Francis Crick in 1958. Some have argued that the principle should be rejected, on the grounds that it fails to fully capture the ins-and-outs of protein synthesis, while others have argued that the Dogma is predicated on notions of (...)
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  8. Grounding Knowledge and Normative Valuation in Agent-Based Action and Scientific Commitment.Catherine Elizabeth Kendig - 2018 - In Hauke Riesch, Nathan Emmerich & Steven Wainwright (eds.), Philosophies and Sociologies of Bioethics: Crossing the Divides. Cham, Switzerland: pp. 41-64.
    Philosophical investigation in synthetic biology has focused on the knowledge-seeking questions pursued, the kind of engineering techniques used, and on the ethical impact of the products produced. However, little work has been done to investigate the processes by which these epistemological, metaphysical, and ethical forms of inquiry arise in the course of synthetic biology research. An attempt at this work relying on a particular area of synthetic biology will be the aim of this chapter. I focus on the reengineering of (...)
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  9. Which Kind of Causal Specificity Matters Biologically?Marcel Weber - 2017 - Philosophy of Science 84 (3):574-585.
    Griffiths et al. (2015) have proposed a quantitative measure of causal specificity and used it to assess various attempts to single out genetic causes as being causally more specific than other cellular mechanisms, for example, alternative splicing. Focusing in particular on developmental processes, they have identified a number of important challenges for this project. In this discussion note, I would like to show how these challenges can be met.
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  10. Metaanalysis of psychoanalysis.Andrej Poleev - 2016
  11. Towards a Notion of Intervention in Big-Data Biology and Molecular Medicine.Emanuele Ratti & Federico Boem - 2016 - In Marco Nathan & Giovanni Boniolo (eds.), Philosophy of Molecular Medicine - Foundational Issues in Research and Practice. Routledge.
    We claim that in contemporary studies in molecular biology and biomedicine, the nature of ‘manipulation’ and ‘intervention’ has changed. Traditionally, molecular biology and molecular studies in medicine are considered experimental sciences, whereas experiments take the form of material manipulation and intervention. On the contrary “big science” projects in biology focus on the practice of data mining of biological databases. We argue that the practice of data mining is a form of intervention although it does not require material manipulation. We also (...)
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  12. What is so Special About Smell? Olfaction as a Model System in Neurobiology.Ann-Sophie Barwich - 2015 - Postgraduate Medical Journal 92:27-33.
    Neurobiology studies mechanisms of cell signalling. A key question is how cells recognise specific signals. In this context, olfaction has become an important experimental system over the past 25 years. The olfactory system responds to an array of structurally diverse stimuli. The discovery of the olfactory receptors (ORs), recognising these stimuli, established the olfactory pathway as part of a greater group of signalling mechanisms mediated by G-protein-coupled receptors (GPCRs). GPCRs are the largest protein family in the mammalian genome and involved (...)
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  13. Big Data Biology: Between Eliminative Inferences and Exploratory Experiments.Emanuele Ratti - 2015 - Philosophy of Science 82 (2):198-218.
    Recently, biologists have argued that data - driven biology fosters a new scientific methodology; namely, one that is irreducible to traditional methodologies of molecular biology defined as the discovery strategies elucidated by mechanistic philosophy. Here I show how data - driven studies can be included into the traditional mechanistic approach in two respects. On the one hand, some studies provide eliminative inferential procedures to prioritize and develop mechanistic hypotheses. On the other, different studies play an exploratory role in providing useful (...)
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  14. Serendipity and the Discovery of DNA.Áurea Anguera de Sojo, Juan Ares, María Aurora Martínez, Juan Pazos, Santiago Rodríguez & José Gabriel Zato - 2014 - Foundations of Science 19 (4):387-401.
    This paper presents the manner in which the DNA, the molecule of life, was discovered. Unlike what many people, even biologists, believe, it was Johannes Friedrich Miescher who originally discovered and isolated nuclein, currently known as DNA, in 1869, 75 years before Watson and Crick unveiled its structure. Also, in this paper we show, and above all demonstrate, the serendipity of this major discovery. Like many of his contemporaries, Miescher set out to discover how cells worked by means of studying (...)
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  15. Genetics and Philosophy: An Introduction.Monika Piotrowska - 2014 - International Studies in the Philosophy of Science 28 (2):223-226.
    Much of the book is aimed at persuading the reader that genes are not ‘the prime movers in all biological processes’ and that ‘postgenomic genes’ are better understood in a functional sense, as ‘things an organism can do with its genome.' With the main argument in place, the authors examine its impact on a number of philosophical debates. I will discuss three of them: causation, information, and reduction.
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  16. Re-Examining the Gene in Personalized Genomics.Jordan Bartol - 2013 - Science & Education 22 (10):2529-2546.
    Personalized genomics companies (PG; also called ‘direct-to-consumer genetics’) are businesses marketing genetic testing to consumers over the Internet. While much has been written about these new businesses, little attention has been given to their roles in science communication. This paper provides an analysis of the gene concept presented to customers and the relation between the information given and the science behind PG. Two quite different gene concepts are present in company rhetoric, but only one features in the science. To explain (...)
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  17. Distinguishing Ecological From Evolutionary Approaches to Transposable Elements.Stefan Linquist, Brent Saylor, Karl Cottenie, Tyler A. Elliott, Stefan C. Kremer & T. Ryan Gregory - 2013 - Biological Reviews 88 (3):573- 584.
    Considerable variation exists not only in the kinds of transposable elements (TEs) occurring within the genomes of different species, but also in their abundance and distribution. Noting a similarity to the assortment of organisms among ecosystems, some researchers have called for an ecological approach to the study of transposon dynamics. However, there are several ways to adopt such an approach, and it is sometimes unclear what an ecological perspective will add to the existing co-evolutionary framework for explaining transposon-host interactions. This (...)
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  18. Age of Proto-Human.Ningombam Bupenda Meitei - 2013 - viXra.Org:15.
    The paper intends to find the more probable age of proto-human, which in turn could help in finding the timeline of proto-language. In the hominid line of evolution, the rise of modern humans plays a significant role and its role is also owing to the fact of their uniqueness due to language. Different disciplines are put together to solve the mystery of language of human. In an attempt to understand how old, language could be, the paper makes an attempt to (...)
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  19. Francis Crick: Hunter of Life's Secrets. [REVIEW]Angela Creager - 2011 - Isis 102:202-204.
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  20. Psychiatric Molecular Genetics and the Ethics of Social Promises.John Z. Sadler - 2011 - Journal of Bioethical Inquiry 8 (1):27-34.
    A recent literature review of commentaries and ‘state of the art’ articles from researchers in psychiatric genetics (PMG) offers a consensus about progress in the science of genetics, disappointments in the discovery of new and effective treatments, and a general optimism about the future of the field. I argue that optimism for the field of psychiatric molecular genetics (PMG) is overwrought, and consider progress in the field in reference to a sample estimate of US National Institute of Mental Health funding (...)
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  21. Who Owns What? Private Ownership and the Public Interest in Recombinant DNA Technology in the 1970s.Doogab Yi - 2011 - Isis 102 (3):446-474.
    This essay analyzes how academic institutions, government agencies, and the nascent biotech industry contested the legal ownership of recombinant DNA technology in the name of the public interest. It reconstructs the way a small but influential group of government officials and university research administrators introduced a new framework for the commercialization of academic research in the context of a national debate over scientific research's contributions to American economic prosperity and public health. They claimed that private ownership of inventions arising from (...)
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  22. Genomes and What to Make of Them. [REVIEW]Mike Fortun - 2010 - Isis 101:917-918.
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  23. Oswald T. Avery: Nobel Laureate or Noble Luminary?Frank Portugal - 2010 - Perspectives in Biology and Medicine 53 (4):558-570.
    The fact that Oswald T. Avery (1877-1955) did not become a Nobel Laureate for his discovery of DNA as the genetic material has frequently been cited as a prime example of a mistake made in the awarding of the Nobel Prizes. The late Nobel Laureate Arne Tiselius explained the oversight away by saying that Avery "was an old man when he made his discovery" (Litell 1967)—although Avery was actually younger than several others who won the Nobel Prize around the same (...)
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  24. Essay on Science and GMO.Valerije Vrček - 2010 - Filozofska Istrazivanja 30 (1-2):231-235.
  25. Noncoding RNAs: Persistent Viral Agents as Modular Tools for Cellular Needs.Witzany Guenther - 2009 - Annals of the New York Academy of Sciences 1178:244-267.
    It appears that all the detailed steps of evolution stored in DNA that are read, transcribed, and translated in every developmental and growth process of each individual cell depend on RNA-mediated processes, in most cases interconnected with other RNAs and their associated protein complexes and functions in a strict hierarchy of temporal and spatial steps. Life could not function without the key agents of DNA replication, namely mRNA, tRNA, and rRNA. Not only rRNA, but also tRNA and the processing of (...)
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  26. What Does It Mean to Be 75% Pumpkin? The Units of Comparative Genomics.Monika Piotrowska - 2009 - Philosophy of Science 76 (5):838-850.
    Comparative genomicists seem to be convinced that the unit of measurement employed in their studies is a gene that drives the function of cells and ultimately organisms. As a result, they have come to some substantive conclusions about how similar humans are to other organisms based on the percentage of genetic makeup they share. I argue that the actual unit of measurement employed in the studies corresponds to a structural rather than a functional gene concept, thus rendering many of the (...)
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  27. Taxonomy and Why History of Science Matters for Science.Andrew Hamilton & Quentin Wheeler - 2008 - Isis 99:331-340.
    The history of science often has difficulty connecting with science at the lab-bench level, raising questions about the value of history of science for science. This essay offers a case study from taxonomy in which lessons learned about particular failings of numerical taxonomy in the second half of the twentieth century bear on the new movement toward DNA barcoding. In particular, it argues that an unwillingness to deal with messy theoretical questions in both cases leads to important problems in the (...)
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  28. Embodied Anomaly Resolution in Molecular Genetics: A Case Study of RNAi.John J. Sung - 2008 - Foundations of Science 13 (2):177-193.
    Scientific anomalies are observations and facts that contradict current scientific theories and they are instrumental in scientific theory change. Philosophers of science have approached scientific theory change from different perspectives as Darden (Theory change in science: Strategies from Mendelian genetics, 1991) observes: Lakatos (In: Lakatos, Musgrave (eds) Criticism and the growth of knowledge, 1970) approaches it as a progressive “research programmes” consisting of incremental improvements (“monster barring” in Lakatos, Proofs and refutations: The logic of mathematical discovery, 1976), Kuhn (The structure (...)
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  29. Molecular Genetics.Ken Waters - 2008 - Stanford Encyclopedia of Philosophy.
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  30. DNA Replication and Models for the Origin of piRNAs.Jack R. Bateman & Chao-Ting Wu - 2007 - Bioessays 29 (4):382-385.
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  31. Systems Biology: Philosophical Foundations.Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.) - 2007 - Elsevier.
    Systems biology is a vigorous and expanding discipline, in many ways a successor to genomics and perhaps unprecendented in its combination of biology with a ...
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  32. Data Without Models Merging with Models Without Data.Ulrich Krohs & Werner Callebaut - 2007 - In Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.), Systems Biology: Philosophical Foundations. Elsevier. pp. 181--213.
    Systems biology is largely tributary to genomics and other “omic” disciplines that generate vast amounts of structural data. “Omics”, however, lack a theoretical framework that would allow using these data sets as such (rather than just tiny bits that are extracted by advanced data-mining techniques) to build explanatory models that help understand physiological processes. Systems biology provides such a framework by adding a dynamic dimension to merely structural “omics”. It makes use of bottom-up and top-down models. The former are based (...)
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  33. Does EvoDevo Equal Regulatory Evolution?: Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom Sean B. Carroll New York and London : Norton , 2005 (350 Pp; $25.95 Hbk; ISBN 0393060160); From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design (2nd Ed.) Sean B. Carroll , Jennifer K. Grenier , Scott D. Weatherbee Malden, MA : Blackwell , 2004 (258 Pp; $49.95 Pbk; ISBN 1405119500).Manfred D. Laubichler - 2006 - Biological Theory 1 (1):102-103.
  34. “Molecular Gene”: Interpretation in the Right Context. [REVIEW]Degeng Wang - 2005 - Biology and Philosophy 20 (2-3):453-464.
    How to interpret the “molecular gene” concept is discussed in this paper. I argue that the architecture of biological systems is hierarchical and multi-layered, exhibiting striking similarities to that of modern computers. Multiple layers exist between the genotype and system level property, the phenotype. This architectural complexity gives rise to the intrinsic complexity of the genotype-phenotype relationships. The notion of a gene being for a phenotypic trait or traits lacks adequate consideration of this complexity and has limitations in explaining the (...)
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  35. Superficial? Not Us--We Men Are Born Molecular Geneticists!Thiruchandurai V. Rajan - 2004 - Perspectives in Biology and Medicine 47 (3):422-429.
  36. From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design (Review).Manfred D. Laubichler - 2003 - Perspectives in Biology and Medicine 46 (1):148-153.
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  37. Molecular Biology of Fanconi Anaemia—an Old Problem, a New Insight.Shamim I. Ahmad, Fumio Hanaoka & Sandra H. Kirk - 2002 - Bioessays 24 (5):439-448.
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  38. Molecular Genetics and the Transformation of Medicine.Mary Ann G. Cutter - 2002 - Journal of Medicine and Philosophy 27 (3):251 – 256.
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  39. The Recombinant Dna Controversy: A Memoir: Science, Politics, And The Public Interest. [REVIEW]Sally Hughes - 2002 - Isis 93:530-531.
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  40. Bioethics and Medical Practice in the Age of Molecular Genetics.Ruth Chadwick - 2000 - .
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  41. Molecular Genetics of Color Vision and Color Vision Defects.Maureen Neitz & Jay Neitz - 2000 - Arch Ophthalmol 118 (5):691-700.
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  42. Severo Ochoa and the Biomedical Sciences in Spain Under Franco, 1959-1975.Maria Santesmases - 2000 - Isis 91:706-734.
  43. The Strands of a Life: The Science of DNA and the Art of Education by Robert L. Sinsheimer. [REVIEW]Hugh Hawkins - 1997 - Isis 88:365-366.
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  44. Color Categories and Biology: Considerations From Molecular Genetics, Neurobiology, and Evolutionary Theory.Stephen L. Zegura - 1997 - Behavioral and Brain Sciences 20 (2):211-212.
    Evidence from molecular genetics bolsters the claim that color is not a perceptuolinguistic and behavioral universal. Neurobiology continues to fill in many details about the flow of color information from photon reception to central processing in the brain. Humans have the most acute color vision in the biosphere because of natural selection and adaptation, not coincidence.
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  45. Ethical Issues of Molecular Genetics in Psychiatry.C. Howard - 1994 - Journal of Medical Ethics 20 (2):119-120.
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  46. Molecular Genetics, Reductionism, and Disease Concepts in Psychiatry.Herbert W. Harris & Kenneth F. Schaffner - 1992 - Journal of Medicine and Philosophy 17 (2):127-153.
    The study of mental illness by the methods of molecular genetics is still in its infancy, but the use of genetic markers in psychiatry may potentially lead to a Virchowian revolution in the conception of mental illness. Genetic markers may define novel clusters of patients having diverse clinical presentations but sharing a common genetic and mechanistic basis. Such clusters may differ radically from the conventional classification schemes of psychiatric illness. However, the reduction of even relatively simple Mendelian phenomena to molecular (...)
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  47. Explanations of the Structure of DNA.Masayuki Obayashi - 1992 - Annals of the Japan Association for Philosophy of Science 8 (2):111-116.
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  48. Nobelesse Oblige: Lives of Molecular Biologists.Pnina G. Abir-Am - 1991 - Isis 82 (2):326-343.
  49. Correspondences Between Classifications and Between Classes of Entities in Molecular Genetics.Gavril Acalugaritei - 1990 - Acta Biotheoretica 38 (2):103-111.
    Certain correspondences appear between the classifications and between the classes of various entities at molecular genetic level: types of fundamental correspondences between classifications and between classes of normal entities, on the one hand, and of mutant entities on the other hand; ranks of correspondences between classifications and between classes of entities. The concept of universality of the genetic code was reformulated on the basis of the above correspondences.
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  50. Molecular Genetic Aspects of Sex Determination in Drosophila.Bruce S. Baker, Rodney N. Nagoshi & Kenneth C. Burtis - 1987 - Bioessays 6 (2):66-70.
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