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Extended Mechanistic Explanations: Expanding the Current Mechanistic Conception to Include More Complex Biological Systems

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Abstract

Mechanistic accounts of explanation have recently found popularity within philosophy of science. Presently, we introduce the idea of an extended mechanistic explanation, which makes explicit room for the role of environment in explanation. After delineating Craver and Bechtel’s (2007) account, we argue this suggestion is not sufficiently robust when we take seriously the mechanistic environment and modeling practices involved in studying contemporary complex biological systems. Our goal is to extend the already profitable mechanistic picture by pointing out the importance of the mechanistic environment. It is our belief that extended mechanistic explanations, or mechanisms that take into consideration the temporal sequencing of the interplay between the mechanism and the environment, allow for mechanistic explanations regarding a broader group of scientific phenomena.

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Notes

  1. See Machamer et al. (2000), Glennan (1996, 2002), Bechtel and Abrahamsen (2005) and Craver (2007).

  2. Craver (2007) contrasts various meanings of ‘level’ with his account of a mechanistic level. For him, and other mechanists, levels of mechanisms are levels of composition, where the composition relation is not to be understood “at base” as spatial or material, but as the organization of acting entities (Craver 2007, 188–189). For instance, such levels are not to be confused with levels of scale—E. coli bacteria and a host do not count as being on different levels merely in virtue of differences in size.

  3. We focus our discussion on a particular suggestion made by Craver and Bechtel about how to think of multilevel systems in a mechanistic framework. We take their suggestion to be a flagship example for the New Mechanists. So, although our criticism focuses on their particular suggestion—mechanistically mediated effects—our concern may be generalizable to other suggestions that are relevantly similar.

  4. The term ‘mechanism environment’ will be discussed in detail in Sect. 3: Extended Mechanistic Explanations.

  5. It is important to note, William Bechtel is actively interested in just this, dynamic complex systems. See Bechtel (2009, 2010, 2012), Bechtel and Abrahamsen (2013) and Kaplan and Bechtel (2011), most notably. However, we wish to further this discussion by directly focusing on one possible component of a mechanism that may allow for both dynamic activity as well as robust mechanistic explanation, namely the mechanistic environment. That is to say, although the New Mechanists are aware that dynamic systems may be explainable via their accounts, we wish to draw attention to the possibility that the mechanism environment or initial conditions (more on this difference later) plays an important and overlooked part in the explanation of temporal dynamic systems.

  6. Please note that here we are being charitable. We do not think that light can be decomposed into wavelengths primarily because light just is at a wavelength. Instead, we utilize this example to show how Craver and Bechtel’s strategy ignores the importance of environmental features and how those features interact within and between levels in a model. Moreover, we utilize their very example to show that deficiency.

  7. Or, “an environmental condition that must remain present for the mechanism to achieve a particular phenomenon.” See Machamer et al. (2000), Darden (2002), Glennan (2002), Bechtel and Abrahamsen (2005), Craver (2007) and Craver and Darden (2013).

  8. See Machamer et al. (2000) regarding the initial argument for explanations being perspectival. Also note, this idea is echoed throughout the mechanism literature.

  9. It is important to note, we do not mean to imply that mechanisms necessarily have spatial boundaries. Instead, what is “outside” the mechanism is simply anything the scientist deems or discovers to be important for explanation that is not considered a component in the actual mechanism or “internal” to the mechanism. Again, what is considered the mechanism is not necessarily made up of component parts that are spatially closer to one another than entities that are external to the mechanism.

  10. Of course, there is a lot that is actually external to a particular mechanism. Mechanism and environment demarcation is a topic for further inquiry, but our concern here is its importance regarding specific complex mechanisms.

  11. It should be noted, both Zadnik (2011) and Kaplan (2012) use similar terminology, such as “extended mechanism”. However, these terms should be distinguished from our term, extended mechanistic explanations, as we focus specifically on the importance of the mechanism environment in combination with the mechanism itself.

  12. See Machamer et al. (2000), Darden (2002), Glennan (2002, 2010), Bechtel and Abrahamsen (2005, 2013), Bechtel (2006, 2009, 2010, 2012), Craver (2007) and Craver and Darden (2013).

  13. We use the popular term “initial conditions”, but it is important to note some New Mechanists use other terminology. For example, Carl Craver and others often speak of background conditions or mechanism having input and output functions (Craver 2007: 7). We believe our argument applies to these terms as well, in that some mechanistic explanations rely heavily on environmental features, or features not considered component parts of the mechanism. That is to say, we believe the New Mechanists will have to expand their conception of initial conditions or background assumptions to allow for more robust explanations found within contemporary biological science.

  14. Please note, we recognize that many of the New Mechanists have sophisticated ways of determining the components of a mechanism. For example, Craver supplies an account of constitutive relevance, one which is capable of denoting mechanism parts from the background conditions or initial conditions of the mechanisms (Craver 2007, 140–160). Also, see Kaplan (2012) for an alternate way to determine which environmental features ought to be considered internal to the mechanism. However, demarcating what is internal to the mechanism and what is external to the mechanism is not our concern here. At present, we are interested in showing the important role external features, or those already deemed non-component parts of a mechanism, play in explanation.

  15. It should be noted, we believe that the mechanism environment may also be important in sciences outside of biology, but have narrowed the scope of our present concern to better reflect the focus of the New Mechanists’.

  16. Also see Sect. 6 for further detail.

  17. It is often believed that quorum sensing can be divided into 4 steps: (1) the production of small biochemical signal molecules by the bacterial cell; (2) the release of the signal molecules, either actively or passively, into the surrounding environment; (3) the recognition of the signal molecules by specific receptors once they exceed a threshold concentration; and (4) changes in gene regulation (Sifri 2008).

  18. See Escherichia coli (2013) for information regarding E. coli.

  19. See Perna et al. (2001) and Vidovic et al. (2012) for more information on E. coli virulence.

  20. See Barnes and Chu (2010) for a general overview of using agent-based models in biology. See Grimm and Railsback (2005) for an overview that focuses on ecological applications.

  21. That’s not to say a population cannot be explicitly represented, just that the focus of agent-based modeling is on the individuals that make up a population.

  22. The verbal explanation that follows inevitably glosses over many details. For one, there are several places where randomness needs to be accounted for, including genetic mutations between parents and offspring, founder effects, genetic drift, and migrations between groups. See Barnes and Chu (2010, 56–77) for more details.

  23. One reason for this has to do with the explanatory role of the heterogeneity of switching rates between cells. For this reason a model cannot simply take the “mean” switching rate. Unlike heat, which can be defined as mean kinetic energy [see Wimsatt 2007 (chapter 12) for further discussion regarding aggregation]. Another reason why individuals can matter is that there are several interactions that are irreducible, including interactions between the bacteria and the host. For these reasons, some biologists are opting to use agent-based models to develop and simulate E. coli fimbriation (Barnes and Chu 2010, 56–77).

  24. Shapiro and Sober argue similarly (2007), regarding intra-level causation. They argue that there are very general circumstances in which macrocausation entails microcausation (2007, 256–259). This seems to go against the thesis that causation is solely intra-level.

  25. See Delehanty (2005) for criticisms of how the New Mechanists understand the boundaries of mechanisms.

  26. See Salmon (1984) for a similar argument in much more detail. Salmon argues that the question an investigator wants to answer fixes the area of nature that is under investigation. By getting clearer on the area of nature we want to explain, we can be far clearer on the details that matter. We argue that there might be relevant features within the mechanism environment (exterior to the mechanism) that are important to explanation, depending on exactly what one wants to explain.

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Acknowledgments

We would like to thank a great many people who have been instrumental in crafting this paper. First, we would like to thank Roberta Millstein for her ability to reread a paper countless times without complaint. We thank our many reviewers who were both diligent and helpful, a combination not praised enough. Thanks to James Griesemer and the Griesemer–Millstein Philosophy of Biology Lab for continual discussion, support, and helpful tips. Our thanks to Elliot Sober and the 2014 participants of POBAM who went out of their way to help hone our arguments. Finally, we give our appreciation to countless other conference and workshop attendees that have helped our project progress, including those at the Canadian Philosophical Association, the American Philosophical Association, and the Institute for Bioinformatics and Evolutionary Studies at the University of Idaho.

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  1. Department of Philosophy, Southern Connecticut State University, 501 Crescent Street, New Haven, CT, 06515, USA

    Sarah M. Roe

  2. Department of Philosophy, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844, USA

    Bert Baumgaertner

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  1. Sarah M. Roe
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Correspondence to Sarah M. Roe.

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Roe, S.M., Baumgaertner, B. Extended Mechanistic Explanations: Expanding the Current Mechanistic Conception to Include More Complex Biological Systems. J Gen Philos Sci 48, 517–534 (2017). https://doi.org/10.1007/s10838-016-9356-6

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