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Further evidence of scientists’ recognition of metaphor’s importance: Olson, M. E., Arroyo-Santos, A., and Vergara-Silva, F. (2019). A user’s guide to metaphors in ecology and evolution. Trends in Ecology & Evolution 34(7): 605–615.CrossRefGoogle ScholarPubMed

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See also Nicholson’s critique of the machine conception of the cell and organism: Nicholson, D. J. (2019). Is the cell really a machine? Journal of Theoretical Biology 477: 108–126.CrossRefGoogle ScholarPubMed

Quotation “Some enzyme complexes function literally as machines …”: Block, S. M. (1997). Real engines of creation. Nature, 386(6622): 217–218.CrossRefGoogle ScholarPubMed

On “the molecular storm”: Hoffmann, P. M. (2012). Life’s Ratchet: How Molecular Machines Extract Order from Chaos. New York: Basic Books.Google Scholar

Boudry and Pigliucci’s critique of engineering metaphors: Boudry, M. and Pigliucci, M. (2013). The mismeasure of machine: synthetic biology and the trouble with engineering metaphors. Studies in History and Philosophy of Biological and Biomedical Sciences 44: 660–668.Google Scholar

Johannes Jaeger’s YouTube Channel Beyond Networks: The Evolution of Livings Systems is a series of videos critical of the machine conception of cells and organisms.Google Scholar

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For the history of cell theory and metaphor, this chapter draws on my earlier book: Reynolds, A. S. (2018). The Third Lens: Metaphor and the Creation of Modern Cell Biology. Chicago, IL: University of Chicago Press.Google Scholar

For additional discussion of metaphors in the history of biochemistry: Reynolds, A. S. (2018). In search of cell architecture: General Cytology and early twentieth-century conceptions of cell organization. In Matlin, K. S., Maienschein, J., and Laubichler, M. D. (eds.), Visions of Cell Biology: Reflections Inspired by Cowdry’s General Cytology. Chicago, IL: University of Chicago Press, pp. 46–72.Google Scholar

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The section on metaphor and cell death draws on: Reynolds, A. S. (2014). The deaths of a cell: how language and metaphor influence the science of cell death. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 48: 175–184. Quotation from Lockshin “Because computers were just beginning to be talked about … ”: Maghsoudi, N., Zaketi, Z., and Lockshin, R. A. (2012). Programmed cell death and apoptosis – where it came from and where it is going: from Elie Metchnikoff to the control of caspases. Experimental Oncology 34(3): 146–152, 146.Google Scholar

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For a very clear and accessible exposition of evolutionary biology, I recommend: Kampourakis, K. (2020). Understanding Evolution. Cambridge: Cambridge University Press.Google Scholar

A pioneering analysis of Darwin’s use of metaphor is found in Young, R. M. (1985). Darwin’s Metaphor: Nature’s Place in Victorian Culture. Cambridge: Cambridge University Press.Google Scholar

Quotation from Ruse “starting with the key notions of selection and struggle …”: Ruse, M. and Richards, R. J. (2016). Debating Darwin. Chicago, IL: University of Chicago Press, p. 48.Google Scholar

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For the history of Woese and the molecular approach to the Tree of Life I rely on Quammen, D. (2018). The Tangled Tree: A Radical New History of Life. New York: Simon & Shuster.Google Scholar

Quotation from Doolittle “we must now admit that any tree … ”: Doolittle, W. F. (2000). Uprooting the tree of life. Scientific American February: 90–95, 94.Google Scholar

On trees as networks: Morrison, D. A. (2014). Is the tree of life the best metaphor, model, or heuristic for phylogenetics? Systematic Biology 63(4): 628–638.Google Scholar

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Quotation from Doolittle: “The tree of life is not something that exists in nature …” Doolittle, W. F. (1999). Phylogenetic classification and the universal tree. Science 284: 2124–2128.Google Scholar

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Quotation from Dawkins “swarm in huge colonies, safe inside gigantic lumbering robots … ”: Dawkins, R. (1989 [1976]). The Selfish Gene, new ed. Oxford: Oxford University Press, pp. 19–20.Google Scholar

On the cooperative gene: Dawkins, R. (2006) The Selfish Gene, 30th anniversary ed. Oxford: Oxford University Press, pp. ix–x.Google Scholar

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Quotation from Ruse “One has to transcend dichotomies of objective/subjective, discovered/created, description of reality/social construction …”: Ruse, M. (2006). Darwinism and Its Discontents. Cambridge: Cambridge University Press, p. 212.Google Scholar

Readers might also find of interest: Radick, G. (2009). Is the theory of natural selection independent of its history? In Hodge, J. and Radick, G. (eds.), The Cambridge Companion to Darwin, 2nd ed. Cambridge: Cambridge University Press, pp. 147–172.Google Scholar

For scientific objectivity metaphorically construed as the view from nowhere: Nagel, T. (1986). The View from Nowhere. Oxford: Oxford University Press.Google Scholar

Especially relevant for the themes of this chapter and the last is: Olson, M. E., Arroyo-Santos, A., and Vergara-Silva, F. (2019). A user’s guide to metaphors in ecology and evolution. Trends in Ecology & Evolution 34(7): 605–615.Google Scholar

For the history of ecology, this chapter draws chiefly on: Kricher, J. (2009). The Balance of Nature: Ecology’s Enduring Myth. Princeton, NJ: Princeton University Press. Allaby, M. (1996). Basics of Environmental Science. New York: Routledge.Google Scholar

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Quotation from Engels: “The whole Darwinian theory of the struggle for existence is simply the transference from society to animate nature of Hobbes’ theory …”: Radick, G. (2009). Is the theory of natural selection independent of its history? In Hodge, J. and Radick, G. (eds.), The Cambridge Companion to Darwin, 2nd ed. Cambridge: Cambridge University Press, pp. 147–172, 158–159.Google Scholar

For Darwin and the economy of nature: Pearce, T. (2010). “A great complication of circumstances”: Darwin and the economy of nature. Journal of the History of Biology 43(3): 493–528.Google Scholar

For ecology as defined by Haeckel: “the collective science of the relations of organisms to their environment”: Haeckel, E. (1866). Generelle Morphologie, vol. 2. Berlin: Reimer, p. 286.Google Scholar

On ecological niches: Pocheville, A. (2015). The ecological niche: history and recent controversies. In Heams, T., Huneman, P., Lecointre, P., and Silberstein, M. (eds.), Handbook of Evolutionary Thinking in the Sciences, Dordrecht: Springer, pp. 547–586.Google Scholar

Quotations from Lewontin “the use of the metaphor of a niche implies a kind of ecological space with holes in it …” and “Just as there can be no organism without an environment … ”: Lewontin, R. C. (2000). The Triple Helix: Gene, Organism and Environment. Cambridge, MA: Harvard University Press, pp. 45, 48.Google Scholar

On niche-construction theory: Odling-Smee, J., Laland, K., and Feldman, M. (2003). Niche Construction: The Neglected Process in Evolution. Princeton, NJ: Princeton University Press.Google Scholar

On the ecosystem concept: Tansley, A. G. (1935). The use and abuse of vegetational concepts and terms. Ecology 16(3): 284–307.Google Scholar

“to include with the biome all the physical and chemical factors … ”: Allaby, M. (1996). Basics of Environmental Science. New York: Routledge, p. 150.Google Scholar

Quotation from Tansley “In an ecosystem the organisms and the inorganic factors alike are components …”: Tansley, A. G. (1935). The use and abuse of vegetational concepts and terms. Ecology 16(3): 284–307, 306.Google Scholar

Quotation from Cuddington “nature is orderly and beneficent …”: Cuddington, K. (2001). The “balance of nature” metaphor and equilibrium in population ecology. Biology & Philosophy 16: 463–479, 466.Google Scholar

Larson on the “balance of nature”: Larson, B. M. H. (2011). Metaphors for Environmental Sustainability: Redefining Our Relationship with Nature. New Haven, CT: Yale University Press, p. 6.Google Scholar

Kricher on the “balance of nature”: Kricher, J. (2009). The Balance of Nature: Ecology’s Enduring Myth. Princeton, NJ: Princeton University Press, p. 16.Google Scholar

Quotations from Kricher that the balance of nature “has always been a fuzzy, poorly defined idea …” and of “little value in evolution and ecology”: Kricher, J. (2009). The Balance of Nature: Ecology’s Enduring Myth. Princeton, NJ: Princeton University Press, pp. 19, 23.Google Scholar

On current tensions about the language of global warming and climate change: Brown, T. L. (2003). Making Truth: Metaphor in Science. Chicago, IL: University of Illinois Press, chapter 9.Google Scholar

Quotation from Allaby “To some non-scientists, however, ‘ecology’ suggests a kind of stability … ”: Allaby, M. (1996). Basics of Environmental Science. New York: Routledge, p. 9.Google Scholar

“Ecological health is a nebulous concept that should be expunged from the vocabulary …”: Lancaster, J. (2000). The ridiculous notion of assessing ecological health and identifying the useful concepts underneath. Human and Ecological Risk Assessment: An International Journal 6(2): 213–222, 214.Google Scholar

On category mistakes: Ryle, G. (2002 [1949]). The Concept of Mind. Chicago, IL: University of Chicago Press.Google Scholar

For criticism of “ecological health”: Lackey, R. (2001). Values, policy, and economic health. BioScience 51(6): 437–443.Google Scholar

Quotations from Hutton “solid body of earth, an aqueous body of sea …”: Hutton, J. (1795). Theory of the Earth: With Proofs and Illustrations, Vol. 1. Edinburgh: www.gutenberg.org/files/12861/12861-h/12861-h.htm.Google Scholar

On Hutton’s metaphors: Norwick, S. (2002). Metaphors of Nature in James Hutton’s “Theory of the Earth with Proofs and Illustrations.” Earth Sciences History 21(1): 26–45.Google Scholar

On the Gaia hypothesis: Lovelock, J. E. (1979). Gaia: A New Look at Life on Earth. Oxford: Oxford University Press.Google Scholar

Quotations from Lovelock, “Organisms and their environment evolve as a single, self-regulating system” and “organisms and their material environment evolve as a single, coupled system”: Lovelock, J. E. (2003). The living Earth. Nature 426(18): 769–770, 769.Google Scholar

On Daisyworld: Watson, A. J. and Lovelock, J. E. (1983). Biological homeostasis of the global environment: the parable of Daisyworld. Tellus Series B 35(4): 286–289.Google Scholar

Lovelock, J. E. and Margulis, L. (1974). Atmospheric homeostasis by and for the biosphere: the Gaia hypothesis. Tellus Series A 26(1–2): 2–10.Google Scholar

On Darwinizing Gaia: Doolittle, W. F. (2017). Darwinizing Gaia. Journal of Theoretical Biology 434: 11–19.Google Scholar

Doolittle, W. F. and Inkpen, S. A. (2018). Processes and patterns of interaction as units of selection: an introduction to ITSNTS thinking. PNAS 115(16): 4006–4014.Google Scholar

The Great Law of Peace of the Iroquois/Haudenosaunee Confederacy, Wampum #28: www.ganienkeh.net/thelaw.html.Google Scholar

For the nature of biomedicine: Valles, S. (2020). Philosophy of biomedicine. In Zalta, E. N. (ed.), The Stanford Encyclopedia of Philosophy (summer 2020 ed.): https://plato.stanford.edu/archives/sum2020/entries/biomedicine.Google Scholar

On metaphors of illness, medicine, and pandemic: Sontag, S. (2001). Illness as Metaphor and AIDS and Its Metaphors. New York: Farrar, Strauss and Giroux, and Picador. Van Rijn-van Tongeren, G. W. (1997). Metaphors in Medical Texts. Amsterdam: Rodopi. Nerlich, B. (2020). Metaphors in times of a global pandemic. In Wuppuluri, S. and Grayling, A. C. (eds.), Words and Worlds: Use and Abuse of Analogies and Metaphors within Sciences and Humanities. New York: Springer.Google Scholar

Readers should be aware of Brigitte Nerlich’s blog, Making Science Public, where she writes regularly about the role of metaphors in communicating genomics, synthetic biology, climate change, and other science to the public: https://blogs.nottingham.ac.uk/makingsciencepublic.Google Scholar

Some of the first attempts to address ethical issues involving genetic engineering of human embryos are: Glover, J. (1984). What Sort of People Should There Be? New York: Penguin. Glover, J. (2007). Choosing Children: The Ethical Dilemmas of Genetic Intervention. Oxford: Oxford University Press.Google Scholar

For a more recent discussion, see Baylis, F. (2019). Altered Inheritance: CRISPR and the Ethics of Human Genome Editing. Cambridge, MA: Harvard University Press.Google Scholar

For the perspective of a scientist involved in the creation of a new powerful genome editing technology, see Doudna, J. and Sternberg, S. H. (2017). A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution. New York: Houghton Mifflin Harcourt.Google Scholar

For the history of genetic engineering and related developments, I have relied largely on Morange, M. (2020). The Blackbox of Biology: A History of the Molecular Revolution, translated by M. Cobb. Cambridge, MA: Harvard University Press.Google Scholar

Stevens, H. (2016). Biotechnology and Society: An Introduction. Chicago, IL: University of Chicago Press.Google Scholar

On genome editing and gene targeting: Urnov, F. D., Rebar, E. J., Holmes, M. C., Zhang, H. S., and Gregory, P. D. (2010). Genome editing with engineered zinc finger nucleases. Nature Reviews Genetics 11(9): 636–646. See also Bak, R., Gomez-Espina, N., and Porteus, M. (2018). Gene editing on center stage. Trends in Genetics 34(8): 600–611.Google Scholar

Quotation from Doudna and Charpentier, “Our study further demonstrates that the Cas9 endonuclease family can be programmed …”: Jinek, M., Chylinski, K., Fonfara, I., et al. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816–820, 816.Google Scholar

Quotations from Doudna, J. (2015). How CRISPR lets us edit our DNA. TED Talk: www.youtube.com/watch?v=TdBAHexVYzc.Google Scholar

Doudna quotations, “malleable as a piece of literary prose … ” in Baylis, F. (2019). Altered Inheritance: CRISPR and the Ethics of Human Genome Editing. Cambridge, MA: Harvard University Press, p. 11; original in Doudna, J. and Sternberg, S. H. (2017). A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution. New York: Houghton Mifflin Harcourt, p. 90.Google Scholar

For criticism of the molecular scissors description of CRISPR: Hortle, E. (2019). Why the “molecular scissors” metaphor for understanding CRISPR is misleading. The Conversation: https://theconversation.com/why-the-molecular-scissors-metaphor-for-understanding-crispr-is-misleading-119812.Google Scholar

On the “fruitful friction” of multiple metaphors: Larson, B. M. H. (2009). Optimizing friction between alternative genomic metaphors: how much plurality is enough? Genomics, Society and Policy 5(3): 20–28.Google Scholar

Morange on the implications of the genome editing metaphor: Morange, M. (2020). The Blackbox of Biology: A History of the Molecular Revolution, translated by M. Cobb. Cambridge, MA: Harvard University Press, p. 308.Google Scholar

On Cas9 as a molecular scalpel: Mummidivarapu, N. (2020). The promise of CRISPR: a rhetorical analysis of dominant metaphors in an emerging technology. Unpublished MPhil. thesis, Department of History and Philosophy of Science, University of Cambridge.Google Scholar

On CRISPR and targeting metaphors: O’Keefe, M., Perrault, S., Halpern, J., et al. (2015). “Editing” genes: a case study about how language matters in bioethics. The American Journal of Bioethics 15(12): 3–10. Oftedal, G. (2018). The role of “missile” and “targeting” metaphors in nanomedicine. Philosophia Scientiae, Travaux d’Histoire des Sciences et Philosophie/Studies in History of Sciences and Philosophy 23(1): 39–55.Google Scholar

Quotation from Urnov: “If human embryo editing for reproductive purposes or germline editing were space flight”: Ledford, H. (2020). CRISPR gene editing in human embryos wreaks chromosomal mayhem. Nature 583: 17–18.Google Scholar

For the scientific response to editing of human twin embryos: Lanphier, E., Urnov, F., Haecker, S. E., Werner, M., and Smolenski, J. (2015). Don’t edit the human germline. Nature 519(7544): 410–411.Google Scholar

On programmable enzymes: Abudayyeh, O. O., Gootenberg, J. S., Franklin, B., et al. (2019). A cytosine deaminase for programmable single-base RNA editing. Science 365(6451): 382–386. Reardon, S. (2020). A new twist on gene editing. Nature 578: 25–27.Google Scholar

On metaphors in drug design, the following blog post by Derek Lowe (and comments) is very informative: Lowe, D. (2011). Block that metaphor: metaphors, good and bad. In the Pipeline blog, March 17: https://blogs.sciencemag.org/pipeline/archives/2011/03/17/block_that_metaphor.Google Scholar

On the renaming of the journal Cloning to Cloning and Stem Cells: Wilmut, I. and Taylor, J. (2018). Cloning after Dolly: editorial. Cellular Reprogramming 20(1): DOI: 10.1089/cell2018.29011.psiw.Google Scholar

On the epigenetic landscape metaphor, see: Baedke, J. (2018). Above the Gene, Beyond Biology: Toward a Philosophy of Epigenetics. Pittsburgh, PA: University of Pittsburgh Press.Google Scholar

Squier, S. M. (2017). Epigenetic Landscapes: Drawings as Metaphor. Durham, NC: Duke University Press.Google Scholar

Description of reprogramming from www.nature.com/subjects/reprogramming.Google Scholar

Developmental landscape and reprogramming illustration from: Takahashi, K. (2012). Cellular reprogramming: lowering gravity on Waddington’s epigenetic landscape. Journal of Cell Science 125(11): 2553–2560.Google ScholarPubMed

CRISPR used to create “programmable artificial transcription factors”: Lo, A. and Qi, L. (2017). Genetic and epigenetic control of gene expression by CRISPR-Cas systems. F1000Research 6: DOI: 10.12688/f1000research.11113.1.Google Scholar

For a current and informative example of engineering, reprogramming, and circuit metaphors: Wang, N. B., Beitz, A. M., and Galloway, K. E. (2020). Engineering cell fate: applying synthetic biology to cellular reprogramming. Current Opinion in Systems Biology 24: 18–31.Google Scholar

For more on metaphors in immunology: Swiatczak, B. and Tauber, A. I. (2020). Philosophy of Immunology. In Zalta, E. N. (ed.), The Stanford Encyclopedia of Philosophy (summer 2020 ed.): https://plato.stanford.edu/archives/sum2020/entries/immunology.Google Scholar

On Microsoft computer scientists collaborating with cancer biologists: Linn, A. (n.d.). How Microsoft computer scientists and researchers are working to “solve” cancer: https://news.microsoft.com/stories/computingcancer.Google Scholar

For the “hallmarks of cancer”: Hanrahan, D. and Weinberg, R. (2011). Hallmarks of cancer: the next generation. Cell 144(5): 646–674.Google Scholar

On rewiring immune cells to attack cancer: Tometz, K. (2016). Northwestern researchers rewire cells to attack cancer. Wttw Chicago PBS: https://news.wttw.com/2016/12/13/northwestern-researchers-rewire-cells-attack-cancer.Google Scholar

On rewiring/rerouting/hijacking cell signal pathways and GEARS: Krawczyk, K., Scheller, L., Kim, H., and Fussenegger, M. (2020). Rewiring of endogenous signaling pathways to genomic targets for therapeutic cell reprogramming. Nature communications 11(1): 1–9.Google Scholar

“all metaphors may be ultimately wrong, but some of them are surely (very) useful”: De Lorenzo, V. (2018). Evolutionary tinkering vs. rational engineering in the time of synthetic biology. Life Sciences, Society and Policy 13(13): 16: DOI: 10.1186/s40504-018-0086-x. This is an adaptation of a famous expression attributed to the statistician George Box that “All models are wrong, but some are useful.” Box, G. E. P. (1976). Science and statistics. Journal of the American Statistical Association 71(356): 791–799: DOI: 10.1080/01621459.1976.1048094.Google Scholar

On different aims of science: Hacking, I. (1983). Representing and Intervening: Introductory Topics in the Philosophy of Natural Science. Cambridge: Cambridge University Press. Potochnik, A. (2017). Idealization and the Aims of Science. Chicago, IL: University of Chicago Press.Google Scholar

Dennett and Levin on treating cells and other things as cognitive agents: Levin, M. and Dennett, D. C. (2020). Cognition all the way down: biology’s next great horizon is to understand cells, tissues and organs as agents with agendas (even if unthinking ones). Aeon, October 13: https://aeon.co/essays/how-to-understand-cells-tissues-and-organisms-as-agents-with-agendas.Google Scholar

For films depicting subcellular molecules as agents, see: Journey Inside the Cell, produced by the Discovery Institute, a creationist think tank that promotes “intelligent design” theory as a religion-friendly alternative to evolutionary accounts of cellular and organismal origins; Cell Signals, created by Cold Spring Harbor Laboratory and Interactive Knowledge, Inc.; and Genome Editing with CRISP-Cas9, created by the McGovern Institute. All are easily found on YouTube.Google Scholar

On the impact of editing, engineering, and agency metaphors on medicine and society: Nelson, S. C., Yu, J.-H., and Ceccarelli, L. (2015). How metaphors about the genome constrain CRISPR metaphors: separating the “text” from its “editor.” The American Journal of Bioethics 15(12): 60–62. Ceccarelli, L. (2018). CRISPR as agent: a metaphor that rhetorically inhibits the prospects for responsible research. Life Sciences, Society and Policy 14: 24. McLeod, C. and Nerlich, B. (2017). Synthetic biology, metaphors and responsibility. Life Sciences, Society and Policy 13(13); and all the articles in McLeod, C., and Nerlich, B. (eds.) (2018). Synthetic biology: how the use of metaphors impacts on science, policy and responsible research. Special Issue of Life Sciences, Society and Policy 14.Google Scholar

On the influence of environmental factors (and their interaction with genetics): Kampourakis, K. (2020). Understanding Genes. Cambridge: Cambridge University Press.Google Scholar

Quotations from Ball: Ball, P. (2011). A metaphor too far. Nature: DOI: 10.1038/news.2011.115.Google Scholar

Ball, P. (2019). How to Grow a Human: Adventures in Who We Are and How We Are Made. London: William Collins, p. xi.Google Scholar

Quotation from Lewontin “ … the price of metaphor is eternal vigilance”: Lewontin, R. C. (2001). In the beginning was the word. Science 291(5507): 1263–1264. (A review of Kay, L. (2000). Who Wrote the Book of Life? Stanford, CA: Stanford University Press.)Google Scholar

Quotation from Larson “Diverse metaphors … act as a prophylactic against reification”: Larson, B. M. H. (2009). Optimizing friction between alternative genomic metaphors: how much plurality is enough? Genomics Society and Policy 5(3): 20–28, 22.Google Scholar

On the similarity between science and map-making: Winther, E. (2020). When Maps Become the World. Chicago, IL: University of Chicago Press.Google Scholar

Quotation from Nerlich “public understanding of science is …”: Nerlich, B., Dingwell, R., and Clarke, D. D. (2002). The book of life: how the completion of the Human Genome Project was revealed to the public. Health: An Interdisciplinary Journal for the Social Study of Health, Illness and Medicine 6(4): 445–469, 465.Google Scholar