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Models in Context: Biological and Epistemological Niches

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Entangled Life

Part of the book series: History, Philosophy and Theory of the Life Sciences ((HPTL,volume 4))

Abstract

A model organism’s value depends on its biological and epistemological contexts. The biological context of a model species comprises all aspects of its environment in the research setting that may influence its biological characteristics. In contrast, the epistemological context is not a matter of the organism’s surroundings, but rather of what question it is supposed to help answer, and the assumptions about its “representativeness” that warrant broader application of results from a unique model. The biological context for model organisms in research is highly controlled and standardized. This strategy has often been productive; however, it risks eliminating essential environmental information and biological mechanisms, including organism-environment interactions that help shape phenotypes. Considering biological context helps us avoid experimental designs that simplify potentially important dimensions out of existence. Clarifying the epistemological context, from background assumptions to the ultimate goal of the research, lets us assess how the research approach we choose—such as employing a particular model—may constrain the range or utility of possible answers. Looking at models in context can enrich understanding of both the history and the practice of biology: how models are selected and evolve to fit questions, and how they in turn influence the direction of future work.

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Notes

  1. 1.

    Mammals are the exception that proves the rule: the blastocyst manipulates the intrauterine environment to permit implantation, thereby initiating a complex and dynamic maternal-fetal relationship with far-ranging developmental and evolutionary consequences.

References

  • Abzhanov, Arhat, Cassandra G. Extavour, Andrew Groover, Scott A. Hodges, Hopi E. Hoekstra, Elena M. Kramer, and Antonia Monteiro. 2008. Are we there yet? Tracking the development of new model systems. Trends in Genetics 24: 353–360.

    Article  Google Scholar 

  • Adams, Douglas. 1979. The Hitchhiker’s guide to the galaxy. New York: Random House.

    Google Scholar 

  • Albertson, R. Craig, William Cresko, H. William Detrich, and John H. Postlethwait. 2008. Evolutionary mutant models for human disease. Trends in Genetics 25: 74–81.

    Article  Google Scholar 

  • Atkinson, Mark A., and Edward H. Leiter. 1999. The NOD mouse model of type 1 diabetes: As good as it gets? Nature Medicine 5: 601–604.

    Article  Google Scholar 

  • Beckers, Johannes, Wolfgang Wurst, and Martin Hrabé de Angelis. 2009. Towards better mouse models: Enhanced genotypes, systemic phenotyping and envirotype modelling. Nature Reviews Genetics 10: 371–380.

    Article  Google Scholar 

  • Bedell, Mary A., Nancy A. Jenkins, and Neal G. Copeland. 1997. Mouse models of human disease. Part I: Techniques and resources for genetic analysis in mice. Genes & Development 11: 1–10.

    Article  Google Scholar 

  • Bolker, Jessica A. 2009. Exemplary and surrogate models: Two modes of representation in biology. Perspectives in Biology and Medicine 52: 485–499.

    Article  Google Scholar 

  • Burian, Richard M. 1992. How the choice of experimental organism matters: Biological practices and discipline boundaries. Synthese 92: 151–166.

    Article  Google Scholar 

  • Burian, Richard M. 1993. How the choice of experimental organism matters: Epistemological reflections on an aspect of biological practice. Journal of the History of Biology 26: 351–368.

    Article  Google Scholar 

  • Calvi, L.M., G.B. Adams, K.W. Weibrecht, J.M. Weber, D.P. Olson, M.C. Knight, R.P. Martin, E. Schipani, P. Divieti, F. Bringhurst, L. Milner, H. Kronenberg, and D. Scadden. 2003. Osteoblastic cells regulate the haematopoietic stem cell niche. Nature 425: 841–846.

    Article  Google Scholar 

  • Chung, Young, Colin E. Bishop, Nathan R. Treff, Stephen J. Walker, Vladislav M. Sandler, Sandy Becker, Irina Klimanskaya, et al. 2009. Reprogramming of human somatic cells using human and animal oocytes. Cloning and Stem Cells 11: 213–223.

    Article  Google Scholar 

  • Clair, La., J. James, John A. Bantle, and James Dumont. 1998. Photoproducts and metabolites of a common insect growth regulator produce developmental deformities in Xenopus. Environmental Science and Technology 32: 1453–1461.

    Article  Google Scholar 

  • Clarke, Adele E. 1992. The right tools for the job: At work in twentieth-century life sciences. Princeton: Princeton University Press.

    Google Scholar 

  • Collins, Francis S. 2011. Reengineering translational science: The time is right. Science Translational Medicine 3(90): 1–6.

    Article  Google Scholar 

  • Davidson, Carlos, and Roland A. Knapp. 2007. Multiple stressors and amphibian declines: Dual impacts of pesticides and fish on yellow-legged frogs. Ecological Applications 17: 587–597.

    Article  Google Scholar 

  • Davis, Mark M. 2008. A prescription for human immunology. Immunity 29: 835–838.

    Article  Google Scholar 

  • Engler, Adam J., Shamik Sen, H. Lee Sweeney, and Dennis E. Discher. 2006. Matrix elasticity directs stem cell lineage specification. Cell 126: 677–689.

    Article  Google Scholar 

  • Epstein, Michelle M. 2004. Do mouse models of allergic asthma mimic clinical disease? International Archives of Allergy and Immunology 133: 84–100.

    Article  Google Scholar 

  • Erickson, Robert P. 1996. Mouse models of human genetic disease: Which mouse is more like a man? BioEssays 18: 993–997.

    Article  Google Scholar 

  • Gilbert, Scott. 2001. Ecological developmental biology: Developmental biology meets the real world. Developmental Biology 233: 1–12.

    Article  Google Scholar 

  • Gilbert, Scott. 2003. Developmental biology, 7th ed. Sunderland: Sinauer.

    Google Scholar 

  • Gilbert, Scott, and Jessica A. Bolker. 2003. Ecological developmental biology: Preface to the symposium. Evolution and Development 5: 3–8.

    Article  Google Scholar 

  • Gilbert, Scott, and David Epel. 2009. Ecological developmental biology. Sunderland: Sinauer.

    Google Scholar 

  • Ginsburg, Benson. 1966. All mice are not created equal: Recent findings on genes and behavior. The Social Service Review 40: 121–134.

    Article  Google Scholar 

  • Ginsburg, Benson E. 1992. Muroid roots of behavior genetic research: A retrospective. In Techniques for the genetic analysis of brain and behavior: Focus on the mouse, ed. D. Goldowitz, D. Wahlsten, and R.E. Wimer, 3–16. New York: Elsevier.

    Google Scholar 

  • Haag, Eric S. 2009. Caenorhabditis nematodes as a model for the adaptive evolution of germ cells. Current Topics in Developmental Biology 86: 43–66.

    Article  Google Scholar 

  • Hackney, Jason A., Pierre Charbord, Brian P. Brunk, Christian J. Stoeckert, Ihor R. Lemischka, and Kateri A. Moore. 2002. A molecular profile of a hematopoietic stem cell niche. Proceedings of the National Academy of Sciences 99: 13061–13066.

    Article  Google Scholar 

  • Hardouin, Sylvie, and Andras Nagy. 2000. Mouse models for human disease. Clinical Genetics 57: 237–244.

    Article  Google Scholar 

  • Hesse, Mary B. 1963. Models and analogies in science. Notre Dame: University of Notre Dame Press.

    Google Scholar 

  • Hurst, Jane L., and Rebecca S. West. 2010. Taming anxiety in laboratory mice. Nature Methods 7: 825–826.

    Article  Google Scholar 

  • Jenner, Ronald A., and Matthew A. Wills. 2007. The choice of model organisms in evo-devo. Nature Reviews Genetics 8: 311–319.

    Article  Google Scholar 

  • Keller, Ray, Lance A. Davidson, and David R. Shook. 2003. How we are shaped: The biomechanics of gastrulation. Differentiation 71: 171–205.

    Article  Google Scholar 

  • Kilian, Kristopher A., Branimir Bugarija, Bruce T. Lahn, and Milan Mrksich. 2010. Geometric cues for directing the differentiation of mesenchymal stem cells. Proceedings of the National Academy of Sciences 107: 4872–4877.

    Article  Google Scholar 

  • Kohler, Robert E. 1994. Lords of the fly: Drosophila genetics and the experimental life. Chicago: Chicago University Press.

    Google Scholar 

  • Laland, Kevin N., F. John Odling‐Smee, and Scott F. Gilbert. 2008. EvoDevo and niche construction: Building bridges. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution 310: 549–566.

    Article  Google Scholar 

  • Lederman, Muriel, and Richard M. Burian. 1993. Introduction. Journal of the History of Biology 26: 235–237.

    Article  Google Scholar 

  • Leonelli, Sabina, and Rachel A. Ankeny. 2012. Re-thinking organisms: The impact of databases on model organism biology. Studies in History and Philosophy of Biological and Biomedical Sciences 43: 29–36.

    Article  Google Scholar 

  • Lewontin, Richard. 1983. The organism as the subject and object of evolution. Scientia 118: 65–95.

    Google Scholar 

  • Maher, Brendan. 2009. Evolution: Biology’s next top model? Nature 458: 695.

    Article  Google Scholar 

  • Mestas, Javier, and Christopher Hughes. 2004. Of mice and not men: Differences between mouse and human immunology. Journal of Immunology 172: 2731–2738.

    Google Scholar 

  • Moore, Kateri A., and Ihor R. Lemischka. 2006. Stem cells and their niches. Science 311: 1880–1885.

    Article  Google Scholar 

  • Nials, Anthony T., and Sorif Uddin. 2009. Mouse models of allergic asthma: Acute and chronic allergen challenge. Disease Models & Mechanisms 1: 213–220.

    Article  Google Scholar 

  • Odling-Smee, F. John, Kevin N. Laland, and Marcus W. Feldman. 2003. Niche construction: The neglected process in evolution. Princeton: Princeton University Press.

    Google Scholar 

  • Perera, Frederica, and Julie Herbstman. 2011. Prenatal environmental exposures, epigenetics, and disease. Reproductive Toxicology 31: 363–373.

    Article  Google Scholar 

  • Powell, Kendall. 2005. Stem-cell niches: It’s the ecology, stupid! Nature 435: 268–270.

    Article  Google Scholar 

  • Preuss, Todd M. 2000. Taking the measure of diversity: Comparative alternatives to the model-animal paradigm in cortical neuroscience. Brain, Behavior and Evolution 55: 287–299.

    Article  Google Scholar 

  • Rader, Karen. 2004. Making mice: Standardizing animals for American biomedical research. Princeton: Princeton University Press.

    Google Scholar 

  • Robert, Jason Scott. 2004. Model systems in stem cell biology. BioEssays 26: 1005–1012.

    Article  Google Scholar 

  • Robinson, Roy. 1965. Genetics of the Norway rat. New York: Pergamon Press.

    Google Scholar 

  • Russell, William, and Rex Leonard Burch. 1959. The principles of humane experimental technique. Springfield: Charles C. Thomas.

    Google Scholar 

  • Scadden, David T. 2006. The stem-cell niche as an entity of action. Nature 441: 1075–1079.

    Article  Google Scholar 

  • Schlichting, Carl D., and Massimo Pigliucci. 1998. Phenotypic evolution: A reaction norm perspective. Sunderland: Sinauer.

    Google Scholar 

  • Sonnenschein, Carlos, and Ana Soto. 1999. The society of cells: Control of cell proliferation and cancer. New York: Springer.

    Google Scholar 

  • Soto, Ana, and Carlos Sonnenschein. 2011. The tissue organization field theory of cancer: A testable replacement for the somatic mutation theory. BioEssays 33: 332–340.

    Article  Google Scholar 

  • Spradling, Allan, Daniela Drummond-Barbosa, and Toshie Kai. 2001. Stem cells find their niche. Nature 414: 98–104.

    Article  Google Scholar 

  • Thyagarajan, Tamizchelvi, Satish Totey, Mary Jo S. Danton, and Ashok B. Kulkarni. 2003. Genetically altered mouse models: The good, the bad, and the ugly. Critical Reviews in Oral Biology and Medicine 14: 154–174.

    Google Scholar 

  • Tollrian, Ralph, and C. Drew Harvell (eds.). 1999. The ecology and evolution of inducible defenses. Princeton: Princeton University Press.

    Google Scholar 

  • Travis, Joseph. 2006. Is it what we know or who we know? Choice of organism and robustness of inference in ecology and evolutionary biology. American Naturalist 167: 303–314.

    Article  Google Scholar 

  • Vanin, Stefano, Supriya Bhutani, Stefano Montelli, Pamela Menegazzi, Edward W. Green, Mirko Pegoraro, Federica Sandrelli, Rodolfo Costa, and Charalambos P. Kyriacou. 2012. Unexpected features of Drosophila circadian behavioural rhythms under natural conditions. Nature 484: 371–375.

    Article  Google Scholar 

  • Von Herrath, Matthias G., and Gerald T. Nepom. 2005. Lost in translation: Barriers to implementing clinical immunotherapeutics for autoimmunity. The Journal of Experimental Medicine 202: 1159–1162.

    Article  Google Scholar 

  • West-Eberhard, Mary Jane. 2003. Developmental plasticity and evolution. Oxford: Oxford University Press.

    Google Scholar 

  • Wilson, Paul A., and Ali Hemmati-Brivanlou. 1997. Vertebrate neural induction: Inducers, inhibitors, and a new synthesis. Neuron 18: 699–710.

    Article  Google Scholar 

  • Witkowsky, Jan. 1985. The hunting of the organizer: An episode in biochemical embryology. Trends in Biochemical Sciences 10: 378–381.

    Article  Google Scholar 

  • Xie, Ting, and Alan Spradling. 2000. A niche maintaining germ line stem cells in the Drosophila ovary. Science 290: 328–330.

    Article  Google Scholar 

  • Zhang, Jiwang, Chao Niu, Ling Ye, Haiyang Huang, Xi He, Wei-Gang Tong, Jason Ross, et al. 2003. Identification of the haematopoietic stem cell niche and control of the niche size. Nature 425: 836–840.

    Google Scholar 

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Acknowledgements

The author thanks Gillian Barker, Eric Desjardins, and Trevor Pearce for their helpful comments on the manuscript.

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Correspondence to Jessica A. Bolker .

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Bolker, J.A. (2014). Models in Context: Biological and Epistemological Niches. In: Barker, G., Desjardins, E., Pearce, T. (eds) Entangled Life. History, Philosophy and Theory of the Life Sciences, vol 4. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7067-6_8

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