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Mechanisms and generative material models

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Abstract

Mechanisms consist of component parts and processes organized in a specific way to produce changes that may give rise to one or more phenomena. I aim to examine the generative mechanism of generative material models in the production of new material models. A generative material model in biology is a living material model (such as model organisms) that is capable of generating new material models (e.g., new model organisms). I contend that generative mechanisms of a generative material model are not to be conflated with biological mechanisms: the former is a mechanism manipulated and altered by the modeler while the latter is a naturally occurring mechanism. I examine the ways in which idealization may contribute to the generative mechanism in generating new model organisms. I articulate that the component parts and activities in a generative mechanism are to a large extent shaped by idealization in generative material modeling. Although biological mechanisms do have a role to play in the generation of model organisms, I propose that we shall view the generative mechanism as a hybrid of biological mechanisms and modeling activities. I shall argue that the notion of generative mechanisms as hybrid mechanisms is different from the extant conceptions of mechanisms in various aspects.

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Notes

  1. Idealization in a generative material model involves distortion of the original component parts (e.g., changing genetic sequences and constitutions, protein–protein interactions, etc). Idealization as an activity of distortion has been discussed in McMullin (1985), Jones (2005) and Tee (2019). Weber (2014) claims that idealization can be applied to microorganisms by constructing isolated clone of bacteria which does not exist in nature. This process of idealization involves the manipulation of the bacteria grown in culture.

  2. My distinction between generative mechanisms and biological mechanisms is one that aims to demonstrate that the former (being a hybrid of biological mechanisms and modeling activities) is a distinct kind of biological mechanism that is capable of generating a new material model (organism); whereas the latter (viz. biological mechanisms) consists of naturally occurring component parts and processes which do not generate new material model (e.g., neurotransmission is a biological mechanism that does not generate new material model). Generative mechanisms are by no means unbiological in virtue of the intervention of modelers. In fact, generative mechanisms are biological in the first place (as many of its parts and processes are biological or biochemical)—which serves as the biological basis from which new material model (organism) such as new stem cells or yeasts could be generated under the manipulation of modelers. I am grateful to an anonymous reviewer for pushing me on this point.

  3. Peschard (2011) provides an account of a generative model for abstract mathematical models, which I shall call it a generative abstract model, which is to be distinguished from Fagan’s notion of a generative material model (to be discussed below). Both Fagan and Peschard contend that the objective of a generative model is to construct new models instead of representing the target phenomenon.

  4. To my best knowledge, Fagan’s (2016) account is the first account of generative material models. Though Peschard (2011) provides the first account of a generative model, hers is about generative abstract models because she focuses on abstract modeling.

  5. Fagan does not use the term ‘generative mechanism’. However, she does use the terms such as ‘mechanisms of cell development’ and ‘molecular mechanisms’ to elucidate the mechanisms by which a model organism produces new model organisms.

  6. Some philosophers view idealization introduced in stem cell biology as a methodological bias. For example, Minelli and Baedke (2014) reject the strategy of idealizing patterns of individual variation in modeling the developmental mechanism of a stem cell model. They argue that by preserving the developmental pattern of variation from idealization, our understanding of the developmental plasticity and evolvability of a model organism could be enhanced.

  7. Fagan does not deny the importance of modeling in the generation of new model organisms. What I am trying to show is that her account of generative mechanisms is complying with the extant received notions of biological mechanisms according to which a biological mechanism consists of naturally occurring material parts and the interaction between these parts.

  8. I anticipate that some critics may argue that hESCs should be treated as a biological entity rather than a model organism, therefore the generative mechanism of hESCs should also be viewed as a biological mechanism rather than a hybrid mechanism. To reply, it is important to bear in mind that hESCs are handled and cultured by biologists in the laboratory, and they are not naturally occurring biological entities. Besides, Fagan’s (2016) paper takes hESCs as a model organism despite her focus on the generative mechanism of hESCs is skewed towards biological mechanism.

  9. The first human embryonic stem cell line (hESCs) was created by James Thomson’s team (1998) in University of Wisconsin.

  10. Cf. Huber and Keuck (2013) who deny, in passing, the compatibility between the development of model organisms and idealization (p. 389).

  11. The integration of mathematical explanation and mechanistic explanation has also been recognized to be important in explaining qualitative explanandum, see Bechtel (2013) and Brigandt (2013).

  12. I do not take the generic account of a mechanism as a shortcoming.

  13. An external agent that plays a role in imposing induced organization, according to Glennan and Illari, is “like when a host arranges the seating of guests at a dinner party” (2018, p. 97).

  14. Brigandt (2013) states that the robustness of a biological system is “an evolved ability where the organismal system actively responds to disturbances, so as during embryonic development to permit the reliable generation of the adult phenotype in the face of perturbations to development, and subsequently to maintain functioning and an adaptive phenotype in a changing environment” (p. 486). This sentence on the characteristics of robustness during embryonic development of a biological system is quite relevant to the generative mechanism discussed in this paper, as generative mechanisms typically involve robust embryonic development of a new model organism. Brigandt further contends that the phenomenon of robustness shows that “sometimes the components of a mechanism cannot be clearly individuated (which also entails that the boundary between the mechanism and entities not belonging to the mechanism is blurry)” (p. 489. Original emphases).

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  1. Xiamen University Malaysia, Bandar Sunsuria, 43900, Sepang, Selangor, Malaysia

    Sim-Hui Tee

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Tee, SH. Mechanisms and generative material models. Synthese 198, 6139–6157 (2021). https://doi.org/10.1007/s11229-019-02454-9

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