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Molecular pathways and the contextual explanation of molecular functions

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Abstract

Much of the recent philosophical debate on causation and causal explanation in the biological and biomedical sciences has focused on the notion of mechanism. Mechanisms, their nature and epistemic roles have been tackled by a range of so-called neo-mechanistic theories, and widely discussed. Without denying the merits of this approach, our paper aims to show how lately it has failed to give proper credit to processes, which are central to the field, especially of contemporary molecular biology. Processes can be summed up in the notion of ‘pathway’, which is far from being just equivalent to that of ‘mechanism’ and has a profound epistemological and explanatory relevance. It is argued that an adequate consideration of pathways impels some rethinking of scientific explanation in molecular biology, namely its functional and contextual features. A number of examples are given to suggest that the focus of philosophical attention in this disciplinary field should shift from the notion of mechanism to the notion of pathway.

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Notes

  1. A wide survey of neo-mechanism as a philosophical movement is provided in Glennan and Illari (2017a).

  2. Such features as isolability, organization and sequentiality are taken to situate processes along some “multidimensional gradient”. This is opposed to an analysis on the basis of discrete entities (Skillings 2015, p. 1140).

  3. Discussing biomedical discovery, Paul Thagard too states: “biochemical pathways are a kind of mechanism. […] In biochemical pathways, the entities are the molecules and the activities are the chemical reactions that transform a molecule into other molecules” (2002, pp. 237–238, italics added).

  4. According to Ioannides and Psillos, the three major metaphysical accounts of mechanisms nowadays are Machamer et al. (2000), Glennan’s (2002) and Bechtel and Abrahamsen’s (2005). We already introduced Glennan’s most recent definition above, and will refer to the other two works below. Psillos’ work on mechanistic causation has not only addressed most recent theories and trends, but also thoroughly investigated the historical roots of the philosophy of mechanisms. See e.g. Psillos (2011).

  5. Dowe’s account has been amended in Boniolo et al. (2011).

  6. On the suggestion of an overall rethinking of the living world in processual terms, up to a renewed philosophy of biology, see Dupré and Nicholson (forthcoming). For some arguments against the metaphysical replacement of mechanisms with processes, see Austin (2016).

  7. A large number of papers demonstrate this. Just to mention a few, see: Giovannetti et al. (2013), Kimball and Jefferson (2016), Nethi et al. (2015), Wang et al. (2016) and Nosrati et al. (2017).

  8. We are far from denying that functions have also been addressed within philosophical discussions of mechanisms. Just to recall some very recent work, Justin Garson (2017), e.g., stresses that mechanisms are sometimes described in terms of their functions. However, he remains faithful to the notion of mechanism: “the class of functional mechanisms is [taken as] an interesting proper subset of the class of minimal mechanisms” (Garson 2017, p. 105), where “minimal mechanisms” are understood according to Glennan’s (2017) definition. We hence believe that this analysis is not immune to the shortcomings of the far too broad notion of minimal mechanism.

  9. See Boniolo et al. (2010, 2013, 2015) and Boniolo and Lanfrancone (2016).

  10. As is known, many genes and the encoded proteins have different names. We follow the nomenclature indicated by the HUGO Gene Nomenclature Committee, (www.genenames.org).

  11. Melanoma, as is known, is a type of skin cancer. MAPK is a mitogen-activated protein kinase (originally called ERK—extracellular signal-regulated kinase—as in the figure) and PI3 K is another protein: phosphatidylinositol-4,5-bisphosphate 3-kinase.

  12. c-KIT is a tyrosine kinase receptor and RAS (Rat sarcoma protein) is a serine/threonine-protein kinase.

  13. Commenting on that, Dupré continues: “The problem with this kind of teleological system, or system with a robust tendency to end up in particular preferred states, is that the relation between functions and mechanisms is more complex than that supposed by standard mechanistic theories” (ibidem).

  14. Amongst most recent works on this, see e.g. Darden et al. (2018).

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Acknowledgments

We would like to thank the referees and J. Dupré for their very useful comments on a previous version of this paper.

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Author notes

  1. Giovanni Boniolo and Raffaella Campaner have contributed equally to this paper.

Authors and Affiliations

  1. Dipartimento di Scienze Biomediche e Chirurgico Specialistiche, Università di Ferrara, Via Fossato di Mortara, 64a, 44121, Ferrara, Italy

    Giovanni Boniolo

  2. Department of Philosophy and Communication, University of Bologna, Via Zamboni, 38, 40126, Bologna, Italy

    Raffaella Campaner

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  1. Giovanni Boniolo
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  2. Raffaella Campaner
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Correspondence to Giovanni Boniolo.

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Boniolo, G., Campaner, R. Molecular pathways and the contextual explanation of molecular functions. Biol Philos 33, 24 (2018). https://doi.org/10.1007/s10539-018-9634-2

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