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  1. Robin O. Andreasen & Milo J. Aukerman (2002). The Human Genome Project: A Reply to Rosenberg. [REVIEW] Biology and Philosophy 17 (5):673-678.
    In this paper we discuss the scientific value of the human genome project. To what extent is the data obtained by sequencing the entire human genome useful in the gene dicovery process? Responding to Alex Rosenberg' skepticism about the value of such data, we maintain that brute sequence data is much more useful than he suggests.
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  2. R. I. X. Andreassen (1991). Should Ethical Concerns Regulate Science? The European Experience with the Human Genome Project. A Report Form Denmark. Bioethics 5 (3):250–256.
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  3. Rachel A. Ankeny (2001). Model Organisms as Models: Understanding the 'Lingua Franca' of the Human Genome Project. Proceedings of the Philosophy of Science Association 2001 (3):S251-.
    Through an examination of the actual research strategies and assumptions underlying the Human Genome Project (HGP), it is argued that the epistemic basis of the initial model organism programs is not best understood as reasoning via causal analog models (CAMs). In order to answer a series of questions about what is being modeled and what claims about the models are warranted, a descriptive epistemological method is employed that uses historical techniques to develop detailed accounts which, in turn, help to reveal (...)
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  4. Giuseppe Attardi (1986). The Elucidation of the Human Mitochondrial Genome: A Historical Perspective. Bioessays 5 (1):34-39.
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  5. T. M. Baetu (2012). Genomic Programs as Mechanism Schemas: A Non-Reductionist Interpretation. British Journal for the Philosophy of Science 63 (3):649-671.
    In this article, I argue that genomic programs are not substitutes for multi-causal molecular mechanistic explanations of inheritance, but abstract representations of the same sort as mechanism schemas already described in the philosophical literature. On this account, the program analogy is not reductionistic and does not ignore or underestimate the active contribution of epigenetic elements to phenotypes and development. Rather, genomic program representations specifically highlight the genomic determinants of inheritance and their organizational features at work in the wider context of (...)
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  6. Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.) (2007). Systems Biology: Philosophical Foundations. 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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  7. Susanne Boshammer, Matthias Kayss, Christa Runtenberg & Johann S. Ach (1998). Discussing Hugo: The German Debate on the Ethical Implications of the Human Genome Project. Journal of Medicine and Philosophy 23 (3):324 – 333.
    The current German criticism of HUGO centers around the term ‘human dignity’; consenquentialist and autonomy-based arguments are used. The debate culminates in questioning the integrity of bioethics as a scholarly discipline and has created a heterogeneous coalition of disparate political and social groups that oppose any research that would facilitate genetic pre-selection of human characteristics.
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  8. Teresa Brady (1995). The Ethical Implications of the Human Genome Project for the Workplace. International Journal of Applied Philosophy 10 (1):47-56.
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  9. Christian Byk (1992). The Human Genome Project and the Social Contract: A Law Policy Approach. Journal of Medicine and Philosophy 17 (4):371-380.
    For the first time in history, genetics will enable science to completely identify each human as genetically unique. Will this knowledge reinforce the trend for more individual liberties or will it create a ‘brave new world’? A law policy approach to the problems raised by the human genome project shows how far our democratic institutions are from being the proper forum to discuss such issues. Because of the fears and anxiety raised in the population, and also because of its wide (...)
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  10. Ruth Chadwick & Charles Ngwena (1995). The Human Genome Project, Predictive Testing and Insurance Contracts: Ethical and Legal Responses. [REVIEW] Res Publica 1 (2):115-129.
    The economic costs to the insurers of complementary routine genetic testing would outweigh the benefits. However, should testing technology in future be refined so as to produce a cheap and reliable test, there is no reason why insurers might not take up predictive testing as part of the normal underwriting process. It is this possibility which justifies formulating a pre-emptive policy. At the very least, there are reasons for promoting and protecting the welfare of the proposer so as to redress (...)
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  11. Laurel Cooper, Ramona Walls, Justin Elser, Maria A. Gandolfo, Dennis W. Stevenson & Barry Smith (2013). The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses. Plant and Cell Physiology 54:1-23..
    The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...)
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  12. Frank C. Dukepoo (1998). Commentary on “Scientific Limitations and Ethical Ramifications of a Non-Representative Human Genome Project: African American Responses” (F. Jackson). [REVIEW] Science and Engineering Ethics 4 (2):171-180.
  13. Lisa Gannett, The Human Genome Project. Stanford Encyclopedia of Philosophy.
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  14. Patricia S. Greenspan (1993). Free Will and the Genome Project. Philosophy and Public Affairs 22 (1):31-43.
    Popular and scientific accounts of the U.S. Human Genome Project often express concern about the implications of the project for the philosophic question of free will and responsibility. However, on its standard construal within philosophy, the question of free will versus determinism poses no special problems in relation to genetic research. The paper identifies a variant version of the free will question, free will versus internal constraint, that might well pose a threat to notions of individual autonomy and virtue in (...)
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  15. Frederick Grinnell (2000). Philosophy of Biology and the Human Genome Project. Biology and Philosophy 15 (4):595-601.
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  16. M. Nizam Isa (2002). Ethical Issues of the Human Genome Project. In Abu Bakar Abdul Majeed (ed.), Bioethics: Ethics in the Biotechnology Century. Institute of Islamic Understanding Malaysia.
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  17. Fatimah Jackson (1998). Scientific Limitations and Ethical Ramifications of a Non-Representative Human Genome Project: African American Response. [REVIEW] Science and Engineering Ethics 4 (2):155-170.
    The Human Genome Project (HGP) represents a massive merging of science and technology in the name of all humanity. While the disease aspects of HGP-generated data have received the greatest publicity and are the strongest rationale for the project, it should be remembered that the HGP has, as its goal the sequencing of all 100,000 human genes and the accurate depiction of the ancestral and functional relationships among these genes. The HGP will thus be constructing the molecular taxonomic norm for (...)
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  18. David O. Jones, Ian G. Cowell & Prim B. Singh (2000). Mammalian Chromodomain Proteins: Their Role in Genome Organisation and Expression. Bioessays 22 (2):124-137.
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  19. Eric T. Juengst (1996). Self-Critical Federal Science? The Ethics Experiment Within the U.S. Human Genome Project. Social Philosophy and Policy 13 (02):63-.
    On October 1, 1988, thirty-five years after co-discovering the structure of the DNA molecule, Dr. James Watson launched an unprecedented experiment in American science policy. In response to a reporter's question at a press conference, he unilaterally set aside 3 to 5 percent of the budget of the newly launched Human Genome Project to support studies of the ethical, legal, and social implications of new advances in human genetics. The Human Genome Project , by providing geneticists with the molecular maps (...)
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  20. Michael M. Kaback (2001). The "Asilomar Process" and the Human Genome Project. Perspectives in Biology and Medicine 44 (2):230-234.
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  21. Rainer Kattel & Margit Suurna (2008). The Rise and Fall of the Estonian Genome Project. Studies in Ethics, Law, and Technology 2 (2).
    This paper presents the case study of the Estonian Genome Project during its initial phase from 2001 to 2007. In these years, the EGP was an independent foundation established by the Estonian government and almost fully financed by foreign and local private venture capital. In essence, it was a public-private partnership in science, research and development. At the end of 2004, this governance structure broke down and private funding was pulled from the project. The paper discusses what went wrong with (...)
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  22. Ulrich Krohs & Werner Callebaut (2007). Data Without Models Merging with Models Without Data. In Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.), Systems Biology: Philosophical Foundations. Elsevier. 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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  23. Graciela Kuechle & Diego Rios (2012). A Game-Theoretic Analysis of the Baldwin Effect. Erkenntnis 77 (1):31-49.
    The Baldwin effect is a process by which learnt traits become gradually incorporated into the genome through a Darwinian mechanism. From its inception, the Baldwin effect has been regarded with skepticism. The objective of this paper is to relativize this assessment. Our contribution is two-fold. To begin with, we provide a taxonomy of the different arguments that have been advocated in its defense, and distinguish between three justificatory dimensions—feasibility, explanatory relevance and likelihood—that have been unduly conflated. Second, we sharpen the (...)
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  24. Eric S. Lander (1998). Scientific Commentary: The Scientific Foundations and Medical and Social Prospects of the Human Genome Project. Journal of Law, Medicine & Ethics 26 (3):184-188.
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  25. Andrew B. Lane & Duncan J. Clarke (2012). Genome Instability: Does Genetic Diversity Amplification Drive Tumorigenesis? Bioessays 34 (11):963-972.
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  26. Abby Lippman (1999). The Human Genome Project: Perilous Promises? Medicine, Health Care and Philosophy 2 (1):47-49.
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  27. Darryl Macer (1991). Whose Genome Project? Bioethics 5 (3):183–211.
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  28. Mark A. Musen, Natalya F. Noy, Nigam H. Shah, Patricia L. Whetzel, Christopher G. Chute, Margaret-Anne Story & Barry Smith (2012). The National Center for Biomedical Ontology. Journal of the American Medical Informatics Association 19 (2):190-195.
    The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...)
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  29. Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu (2011). The Protein Ontology: A Structured Representation of Protein Forms and Complexes. Nucleic Acids Research 39 (1):D539-D545.
    The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...)
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  30. Bo Andreassen Rix (1991). Should Ethical Concerns Regulate Science? The European Experience with the Human Genome Project. Bioethics 5 (3):250-256.
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  31. Alex Rosenberg (2001). Careless Reading About the Human Genome Project. Biology and Philosophy 16 (2):281-284.
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  32. Alexander Rosenberg (1996). The Human Genome Project: Research Tactics and Economic Strategies. Social Philosophy and Policy 13 (02):1-.
    In the Museum of Science and Technology in San Jose, California, there is a display dedicated to advances in biotechnology. Most prominent in the display is a double helix of telephone books stacked in two staggered spirals from the floor to the ceiling twenty-five feet above. The books are said to represent the current state of our knowledge of the eukaryotic genome: the primary sequences of DNA polynucleotides for the gene products which have been discovered so far in the twenty (...)
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  33. Mary Rosner & T. R. Johnson (1995). Telling Stories: Metaphors of the Human Genome Project. Hypatia 10 (4):104 - 129.
    Scientists of the Human Genome Project tend to rely on three metaphors to describe their work, each of which implicitly tells much the same story. Whether they claim to interpret the ultimate "book," to fix a flawed "machine," or to map a mysterious "wilderness," they invariably cast the researcher as one who dominates and exploits the Other. This essay, which explores the ways such a story conflicts with feminist values, proposes an alternative.
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  34. Daniel L. Rubin, Noy N. F. and Musen M. A. Lewis, Chris J. Mungall, Sima Misra, Monty Westerfield, Michael Ashburner, Ida Sim, Christopher G. Chute, Harold Solbrig, Margaret A. Storey, Barry Smith, John D. Richter, Natasha F. Noy & Mark A. Musen (2006). The National Center for Biomedical Ontology: Advancing Biomedicine Through Structured Organization of Scientific Knowledge. Omics: A Journal of Integrative Biology, 10(2), 2006, 10 (2):185-198.
    The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...)
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  35. Richard R. Sharp & J. Carl Barrett (1999). The Environmental Genome Project and Bioethics. Kennedy Institute of Ethics Journal 9 (2):175-188.
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  36. Raymond Spier (1998). The Human Genome Project Under the Microscope. Science and Engineering Ethics 4 (2):131-134.
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  37. Marga Vicedo (1992). The Human Genome Project: Towards an Analysis of the Empirical, Ethical, and Conceptual Issues Involved. [REVIEW] Biology and Philosophy 7 (3):255-278.
    In this paper I claim that the goal of mapping and sequencing the human genome is not wholly new, but rather is an extension of an older project to map genes, a central aim of genetics since its birth. Thus, the discussion about the value of the HGP should not be posed in global terms of acceptance or rejection, but in terms of how it should be developed. The first section of this paper presents a brief history of the project. (...)
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  38. Ramona Walls, Balaji Athreya, Laurel Cooper, Justin Elser, Maria A. Gandolfo, Pankaj Jaiswal, Christopher J. Mungall, Justin Preece, Stefan Rensing, Barry Smith & Dennis W. Stevenson (2012). Ontologies as Integrative Tools for Plant Science. American Journal of Botany 99 (8):1-13.
    Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...)
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  39. David Wasserman (1999). Thomas H. Murray, Mark A. Rothstein, and Robert F. Murray, Ed., The Human Genome Project and the Future of Health Care:The Human Genome Project and the Future of Health Care. [REVIEW] Ethics 109 (4):911-914.
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  40. D. Weatherall (1992). Mapping the Code. The Human Genome Project and the Choices of Modern Science. Journal of Medical Ethics 18 (2):109-110.
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  41. David L. Wiesenthal & Neil I. Wiener (1996). Privacy and the Human Genome Project. Ethics and Behavior 6 (3):189 – 202.
    The Human Genome Project has raised many issues regarding the contributions of genetics to a variety of diseases and societal conditions. With genetic testing now easily conducted with lowered costs in nonmedical domains, a variety of privacy issues must be considered. Such testing will result in the loss of significant privacy rights for the individual. Society must now consider such issues as the ownership of genetic data, confidentiality rights to such information, limits placed on genetic screening, and legislation to control (...)
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  42. Adam S. Wilkins (1995). Variation in the Human Genome. Bioessays 17 (10):905-906.
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  43. Adam S. Wilkins (1993). The Human Genome: Dispelling the Fogg Travelling Around the Human Genome (1993). By Bektkand Jokdak. Les Editions Inserm and John Libbey Eurotext: Paris. IX+188pp. 210 Ff; $45. Isbn Inserm 2‐85598‐572‐2 and Isbn John Libbey Eurolext 2‐7420‐0030‐5. [REVIEW] Bioessays 15 (12):842-842.
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  44. Rasmus Grønfeldt Winther (forthcoming). Race and Biology. In Linda Alcoff, Luvell Anderson & Paul Taylor (eds.), The Routledge Companion to the Philosophy of Race. Routledge.
    The ontology of race is replete with moral, political, and scientific implications. This book chapter surveys proposals about the reality of race, distinguishing among three levels of analysis: biogenomic, biological, and social. The relatively homogeneous structure of human genetic variation casts doubt upon the practice of postulating distinct biogenomic races that might be mapped onto socially recognized race categories.
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