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The ontology of organisms: Mechanistic modules or patterned processes?

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Abstract

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best conceptualisation of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles.

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Notes

  1. Bapteste and Dupré (2013: 380–381); my emphasis.

  2. In order to retain sufficient generality, this definition encapsulates both the phylogenetic and developmental concepts of ‘homologue’.

  3. It may even be the case, as has recently been argued, that the generative robustness inherent in developmental systems is in fact a necessary requirement for their ability to evolve. See Edelman and Gally (2001), and Whitacre and Bender (2010).

  4. As Rosenberg (2001) argues, if the process of natural selection is in a certain sense “blind” to structure, operating instead primarily on function, it’s not at all surprising that one and the same functional homologue might, over time, and in successive generations, be underpinned by distinct sets of GRNs (that is, given mutational robustness, and the accumulation of cryptic variation, etc.).

  5. Recently, there’s been a surge of compelling evidence that homologues in a wide range of taxa might be principally underwritten by shared, “core” GRN elements—see Davidson and Erwin’s (2006) ‘kernel’ concept, and Wagner’s (2014) concept of ‘character identity networks’. It’s important to note that even if a particular homologue does share some central GRN elements in all of its instances, the generative capacity of each instance to produce its specific variation on that homologous structure must also be grounded in that GRN being highly integrated with both upstream and downstream regulatory cassettes, and these elements will be substantially variable across these instances.

  6. The description just offered will no doubt strike a fair few as a fundamentally unfair reading of the ontological picture painted by the data of evo-devo – and, to my mind, it certainly is. However, in taking a naïve view of that picture, the aim of this part of the paper is to understand the prima facie, conceptual motivations one might have for finding the process theory attractive (or the mechanistic picture unattractive). The critique of this naïve view, in defence of the mechanistic ontology, is the focus of the rest of the paper.

  7. See Alon (2006) for an excellent overview of the “regulatory logic” used to construct models of these networks.

  8. As far as I’m concerned, these difficulties are being adequately addressed outside of a strictly conceptual, philosophical account, within empirical studies on ‘modularity’ in developmental systems. There, a sub-system is considered ‘modular’ just in case it satisfies certain criteria on regulatory connectivity. This type of modularity is no doubt central to the evolutionary process (Callebaut and Rasskin-Gutman 2005), and recent evidence with respect to the processes involved in shaping the developmental hourglass lends credence to this conception (Raff 1996; Galis and Metz 2001; Kalinka et al. 2010).

  9. For specific critiques of a mechanistic ontology which stem the homeostatic properties of developmental systems, see Woese (2004), McManus (2012) and Dupré (2013). It’s interesting to note that even Woodward (2013), a card-carrying mechanist, thinks that the phenomenon of robustness (in an important class of cases) lies outside the explanatory remit of a mechanism ontology.

  10. As Dupré (2013: 27) puts it, the worry is that, for many cases “…there is no unique and definitive sequence of molecular events” by which these mechanisms might be individuated.

  11. These ‘pathway features’ are the comparative basis of so-called developmental homologies; see Gilbert and Bolker (2001), Rosa and Etxeberria (2011) and Nathan and Borghini (2014) for recent discussions of the conceptual distinctions between phylogenetic and developmental homology.

  12. One might also consider the higher-order, patterned-based nature of Goodwin’s (Webster and Goodwin 1996) ‘morphogenetic fields’ as another instructive example. See Levin (2012) for some interesting recent work inspired by this approach.

  13. A principle derived from Plato’s Sophist, but more recently articulated by Armstrong (1997).

  14. There are now a number of specialist journals which focus on holistic treatments of developmental phenomena—see, for instance, Molecular Systems Biology and BMC Systems Biology.

  15. Contemporary forms of DST represent the theoretical union of Waddington’s (1957) geometrical-dynamical models and Kauffman’s (1969) Boolean network configurations.

  16. Note that this is true even in the case of non-autonomous systems (Corson and Siggia 2012) where that topology changes over developmental time.

  17. That process ontology and DST are natural bedfellows has been pointed out before. Waddington (1969) himself professed to being deeply influenced by Whitehead, the founder of modern process ontology, as Gilbert and Bolker (2001) note. More recently, Hall (2013) has characterised the contemporary, mathematical models of DST as having a natural home within a Whiteheadean ontology.

  18. There is a lively and interesting debate concerning whether higher-order, dynamic models can be genuinely explanatory—see Brigandt (2015) and Kaplan (2015) for opposing views. Even if one isn’t convinced that they are so, the point can be granted for the sake of argument.

  19. See for instance Dupré (2013) argument that a process ontology is required for the phenomenon of robustness, Jaeger and Monk’s (2015) claim that a process ontology is the required to utilise the explanatory power of DST with respect to regulatory networks, or Gilbert and Bolker’s (2001) argument that a process ontology is required to understand the embryonic organising prowess of homologous structures.

  20. Elevation levels can also be conceptualised as (inversely) representing probability measures—see Huang (2009) and Zhou et al. (2012).

  21. One could hold a hybrid view according to which both mechanisms and processes are understood as ontologically robust, and in which no process is without some mechanistic configuration which operates as its metaphysical ground by specifying its higher-order dynamic profile. The argument just offered was not meant to take this sort of view off the table, but it may very well serve to undercut its motivation: if the conceptual resources of a mechanistic ontology are capable of performing this grounding role, and higher-order explanatory power need not be attributed to any higher-order entities, what do we stand to gain by positing the existence of (ontologically robust) processes? Thanks to an anonymous reviewer for raising this point.

  22. It’s worth noting that it’s conceptually open to the mechanist to simply deny that any such stability exists, understanding it instead as a heuristic abstraction from the underlying metaphysical state of novel mechanisms popping in and out of existence whenever reconfiguration events take place. I don’t think this is an attractive view, for a variety of reasons, but notice that adopting it doesn’t require any novel ontology: even if which mechanisms underlie a particular phenomenon becomes a matter of relative indiscernibility, this doesn’t commit the ontology to countenancing anything other than mechanisms as the performers of that causal work.

  23. Even on evolutionary time-scales, the higher-order stability of developmental systems qua the canalization of phenotypic traits is a long-term reflection of their mechanistically explicable network robustness. See Flatt (2005).

  24. For a more full discussion of the relationship between ‘ontology’ and ‘models’, see Bechtel and Abrahamsen (2005).

  25. Of course, this preference is only relevant if it’s the case that the phenomenon in question is able to be given some further metaphysical analysis, and if only one of our competitors is capable of doing so. Below, I argue that both of these conditions are met.

  26. Cf. Mitchell’s (2012) excellent discussion of accounting for the phenomenon of ‘emergence’ in the physical sciences.

  27. This is true at least in principle. In practice, the only examples I know of that explicitly discuss the identity conditions of particular processes focus on comparing ‘homologous processes’ (in Gilbert and Bolker 2001, Rosa and Etxeberria 2011)—but their homology seems to implicitly rely on a shared mechanistic underpinning. In Gilbert and Bolker (ibid.: 3–5) for instance, the ‘Wnt pathway’ is conceived as a “modular unit of process” which has many distinct instances, but each of these instances are acknowledged to feature homologous sets of genes, proteins, and a certain set of interactions between them: this looks like individuation via mechanistic constitution, as already discussed.

  28. For comparison, consider the analogous point which Dispositionalists raise against their Humean opponents in the debate on the ‘laws of nature’: while regularity-based accounts get the right laws, they can’t explain how or why the these are the ‘laws’. See Mumford (2004) for an excellent in-depth discussion.

  29. It’s worth noting that there are DST models of robustness as well—see, for instance, Kitano (2004) and Huneman (2010). Though as I have already argued, even if they possess explanatory power in this respect, it is ultimately (ontologically) derived from the features of underlying operative mechanisms. For related discussions, see Kaplan and Craver (2011), Brigandt (2015) and Kaplan (2015).

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I am grateful for the generous support of the Analysis Trust.

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    Christopher J. Austin

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Austin, C.J. The ontology of organisms: Mechanistic modules or patterned processes?. Biol Philos 31, 639–662 (2016). https://doi.org/10.1007/s10539-016-9533-3

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