Commentary on ‘How causal are microbiomes?’

This is a preview of subscription content, access via your institution.


  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.


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

    Google Scholar 

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

  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

    Google Scholar 

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

    Article  Google Scholar 

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

    Google Scholar 

  6. Lancaster M, Knoblich J (2014) Organogenesis in a dish: modeling development and disease using organoid technologies. Science.

    Article  Google Scholar 

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

    Article  Google Scholar 

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

    Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

  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.

  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

    Article  Google Scholar 

  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

    Article  Google Scholar 

  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

    Article  Google Scholar 

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

    Google Scholar 

Download references

Author information



Corresponding author

Correspondence to Melinda Bonnie Fagan.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This comment refers to the article available at

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Fagan, M.B. Commentary on ‘How causal are microbiomes?’. Biol Philos 34, 58 (2019).

Download citation