Arnon Levy

Analogies to machines are commonplace in the life sciences, especially in cellular and molecular biology — they shape conceptions of phenomena and expectations about how they are to be explained. This paper offers a framework for thinking about such analogies. The guiding idea is that machine-like systems are especially amenable to decompositional explanation, i.e., to analyses that tease apart underlying components and attend to their structural features and interrelations. I argue that for decomposition to succeed a system must exhibit causal orderliness, which I explicate in terms of differentiation among parts and the significance of local relations. I also discuss what makes a model depict its target as machine-like, suggesting that a key issue is the degree of detail with respect to the target’s parts and their interrelations.

Many biological investigations are organized around a small group of species, often referred to as ‘model organisms’, such as the fruit fly Drosophila melanogaster. The terms ‘model’ and ‘modelling’ also occur in biology in association with mathematical and mechanistic theorizing, as in the Lotka–Volterra model of predator-prey dynamics. What is the relation between theoretical models and model organisms? Are these models in the same sense? We offer an account on which the two practices are shown to have different epistemic characters. Theoretical modelling is grounded in explicit and known analogies between model and target. By contrast, inferences from model organisms are empirical extrapolations. Often such extrapolation is based on shared ancestry, sometimes in conjunction with other empirical information. One implication is that such inferences are unique to biology, whereas theoretical models are common across many disciplines. We close by discussing the diversity of uses to which model organisms are put, suggesting how these relate to our overall account. 1 Introduction2 Volterra and Theoretical Modelling3 Drosophila as a Model Organism4 Generalizing from Work on Model Organisms5 Phylogenetic Inference and Model Organisms6 Further Roles of Model Organisms6.1 Preparative experimentation6.2 Model organisms as paradigms6.3 Model organisms as theoretical models6.4 Inspiration for engineers6.5 Anchoring a research community7 Conclusion

Design thinking in general, and optimality modeling in particular, have traditionally been associated with adaptationism—a research agenda that gives pride of place to natural selection in shaping biological characters. Our goal is to evaluate the role of design thinking in non-evolutionary analyses. Specifically, we focus on research into abstract design principles that underpin the functional organization of extant organisms. Drawing on case studies from engineering-inspired approaches in biology we show how optimality analysis, and other design-related methods, play a specific methodological role that is tangential to the study of adaptation. To account for the role of these reasoning strategies in contemporary biology, we therefore suggest a reevaluation of the connection between design thinking and adaptationism

This paper offers a novel view of unity in neuroscience. I set out by discussing problems with the classical account of unity-by-reduction, due to Oppenheim and Putnam. That view relies on a strong notion of levels, which has substantial problems. A more recent alternative, the mechanistic “mosaic” view due to Craver, does not have such problems. But I argue that the mosaic ideal of unity is too minimal, and we should, if possible, aspire for more. Relying on a number of recent works in theoretical neuroscience—network motifs, canonical neural computations and design-principles—I then present my alternative: a “flat” view of unity, i.e. one that is not based on levels. Instead, it treats unity as attained via the identification of recurrent explanatory patterns, under which a range of neuroscientific phenomena are subsumed. I develop this view by recourse to a causal conception of explanation, and distinguish it from Kitcher’s view of explanatory unification and related ideas. Such a view of unity is suitably ambitious, I suggest, and has empirical plausibility. It is fit to serve as an appropriate working hypothesis for 21st century neuroscience.

Some philosophers of science – the present author included – appeal to fiction as an interpretation of the practice of modeling. This raises the specter of an incompatibility with realism, since fiction-making is essentially non-truth-regulated. I argue that the prima facie conflict can be resolved in two ways, each involving a distinct notion of fiction and a corresponding formulation of realism. The main goal of the paper is to describe these two packages. Toward the end I comment on how to choose among them.