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Commentary on ‘How causal are microbiomes?’

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Notes

  1. 1.

    Lynch et al. also discuss Koch’s principles for causality in microbiology, following Ross and Woodward (2016) in associating these with interventionist dimensions. As Koch’s principles play a secondary role in the paper’s argument, I set them aside here.

  2. 2.

    This is not to say that Woodward’s original interventionist account (2003) cannot be used to explicate the meaning of these and many other causal claims. On the contrary, “original flavor” interventionism is very well-suited to that task. My concern is with Lynch et al.’s treatment of the additional “dimensions” appended to interventionism to capture features of causal relations of scientific interest.

  3. 3.

    “…the key intervention of wiping out H. pylori with antibiotics is taken by many scientists, clinicians and physicians as the ultimate justification for causal claims about ulcers” (MS4; see also remarks on MS6, MS10).

  4. 4.

    A case could be made, I think, for one or the other sense of proportionality being a general desideratum for causal explanation. As the interventionist dimensions are treated en bloc in the paper, however, I will not pursue that idea here.

  5. 5.

    For more on this approach, see Schickore and Arabatzis (2012).

  6. 6.

    I discuss features of this approach in more detail in Fagan (2017, 2019).

  7. 7.

    “Pluripotency” refers to the ability to differentiate into all the main cell types of the organismal body, which is limited, in unmanipulated mammals, to early embryonic stages. Different kinds of stem cell have different degrees of potency, as well as different time-frames of self-renewal, organismal sources, and distinguishing characters (see Fagan 2019, on stem cell classification).

  8. 8.

    Such experiments could also be coupled with simulations, to virtually test the effects of different combinations of microbial taxa.

References

  1. Fagan MB (2013) Philosophy of stem cell biology. Palgrave-Macmillan, London

  2. Fagan MB (2017) Stem cell lineages: between cell and organism. Philos Theory Biol 9. Special Issue: The Ontologies of Living Beings http://www.philosophyandtheoryinbiology.org/

  3. Fagan MB (2019) Stem cell lineages and classification. In: Bursten J (ed) Perspectives on classification in synthetic sciences: unnatural kinds. Taylor and Francis, London

  4. Fortunel N et al (2003) Comment on ‘stemness’. Science 302:393

  5. Fox C (2006) Cell of cells. W.W. Norton, New York

  6. Lancaster M, Knoblich J (2014) Organogenesis in a dish: modeling development and disease using organoid technologies. Science. https://doi.org/10.1126/science.1247125

  7. Magnus T, Liu Y, Parker GC, Rao MS (2008) Stem cell myths. Philos Trans R Soc 363:9–22

  8. Maienschein Jane (2003) Whose view of life? Embryos, cloning, and stem cells. Harvard University Press, Cambridge

  9. Ross LN (2018) Causal selection and the pathway concept. Philos Sci 85:551–572

  10. Ross LN, Woodward J (2016) Koch’s postulates: an interventionist perspective. Stud Hist Philos Biol Biomed Sci 59:35–46

  11. Schickore J, Arabatzis T (eds) (2012) Special issue of Perspectives on Science, vol. 20, no. 4, with papers arising from the &HPS3 conference held in Bloomington. http://muse.jhu.edu/journals/perspectives_on_science/toc/posc.20.4.html

  12. Takahashi S, Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126:663–676

  13. Thomson J, Itskovitz-Eldor J, Shapiro S, Waknitz M, Swiergel J, Marshall V, Jones J (1998) Embryonic stem cell lines derived from human blastocysts. Science 282:1145–1147

  14. Warmflash A, Sorre B, Etoc F, Siggia ED, Brivanlou AH (2014) A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. Nat Methods 11:847–854

  15. Woodward J (2003) Making things happen. Oxford University Press, Oxford

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Correspondence to Melinda Bonnie Fagan.

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This comment refers to the article available at https://doi.org/10.1007/s10539-019-9702-2.

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Fagan, M.B. Commentary on ‘How causal are microbiomes?’. Biol Philos 34, 58 (2019) doi:10.1007/s10539-019-9711-1

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