Function and organization: comparing the mechanisms of protein synthesis and natural selection

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Abstract

In this paper, we compare the mechanisms of protein synthesis and natural selection. We identify three core elements of mechanistic explanation: functional individuation, hierarchical nestedness or decomposition, and organization. These are now well understood elements of mechanistic explanation in fields such as protein synthesis, and widely accepted in the mechanisms literature. But Skipper and Millstein have argued (2005) that natural selection is neither decomposable nor organized. This would mean that much of the current mechanisms literature does not apply to the mechanism of natural selection.

We take each element of mechanistic explanation in turn. Having appreciated the importance of functional individuation, we show how decomposition and organization should be better understood in these terms. We thereby show that mechanistic explanation by protein synthesis and natural selection are more closely analogous than they appear—both possess all three of these core elements of a mechanism widely recognized in the mechanisms literature.

Section snippets

Introduction: the problem

There has been great progress in understanding mechanistic explanations in particular domains, but this progress needs to be extended to cover all sciences. We will advance that project here by comparing protein synthesis and natural selection. Both are called mechanisms, but the fields differ significantly, and Skipper and Millstein have recently argued that natural selection is not captured by the accounts of mechanisms currently available. They make the challenge:

We think the basic resources

Functional individuation

Mechanistic explanation begins with the identification of the phenomenon to be explained, and the mechanisms discovered are partially individuated by the phenomenon they are responsible for. Note that mechanisms are also individuated in other ways. Two different mechanisms that produce the same phenomenon will still be differentiated on the grounds of different parts, and their organization, as we will discuss. Nevertheless, the identification of the phenomenon to be explained is a crucial

Decomposition and mechanistic hierarchy

Once the phenomenon is identified, mechanistic explanation characteristically proceeds by decomposing the phenomenon into lower-level components. The activities of lower-level components are often regarded as further phenomena and further explanations are sought, so that decomposition moves to components another level down. This may iterate many times. So mechanisms discovered are usually located in just such a nested hierarchy, with relations to both lower-level and higher-level mechanisms in

Organization completes the explanation

Identifying the entities and their activities is not enough to explain the phenomenon. You have to understand how they produce the phenomenon of interest together—how they are organized. The importance of organization in the production of the phenomenon, and so in our full understanding of the phenomenon, is uncontroversial. MDC write: ‘The organization of these entities and activities determines the ways in which they produce the phenomenon’ (MDC, 2000, p. 3).

Conclusion

Mechanistic explanation begins with a specification of the phenomenon to be explained. At the least, this consists in an isolated description of a behaviour. Explanation then proceeds by identifying two kinds of parts—activities and entities—that contribute to producing that phenomenon. Entities and activities are both individuated in part by their roles in higher-level mechanisms, so that they have role-functions derived from the characterization of the phenomenon being explained. The

Acknowledgements

We would like to thank the Leverhulme Trust for funding this work on mechanisms. We are also grateful to numerous colleagues and students at Kent, Bristol, and internationally for discussion of ideas used here. Particular thanks are due to Tudor Baetu, Federica Russo, Erik Weber, and an anonymous referee.

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