The history of developmental biology is interwoven with debates as to whether mechanistic explanations of development are possible or whether alternative explanatory principles or even vital forces need to be assumed. In particular, the demonstrated ability of embryonic cells to tune their developmental fate precisely to their relative position and the overall size of the embryo was once thought to be inexplicable in mechanistic terms. Taking a causal perspective, this Element examines to what extent and how developmental biology, having turned (...) molecular about four decades ago, has been able to meet the vitalist challenge. It focuses not only on the nature of explanations but also on the usefulness of causal knowledge – including the knowledge of classical experimental embryology – for further scientific discovery. It also shows how this causal perspective allows us to understand the nature and significance of some key concepts, including organizer, signal and morphogen. This title is also available as Open Access on Cambridge Core. (shrink)

According to mainstream philosophical views causal explanation in biology and neuroscience is mechanistic. As the term ‘mechanism’ gets regular use in these fields it is unsurprising that philosophers consider it important to scientific explanation. What is surprising is that they consider it the only causal term of importance. This paper provides an analysis of a new causal concept—it examines the cascade concept in science and the causal structure it refers to. I argue that this concept is importantly different from the (...) notion of mechanism and that this difference matters for our understanding of causation and explanation in science. (shrink)

Many accounts of scientific modelling assume that models can be decomposed into the contributions made by their accurate and inaccurate parts. These accounts then argue that the inaccurate parts of the model can be justified by distorting only what is irrelevant. In this paper, I argue that this decompositional strategy requires three assumptions that are not typically met by our best scientific models. In response, I propose an alternative view in which idealized models are characterized as holistically distorted representations that (...) are justified by allowing for the application of various modelling techniques. (shrink)

An important strand in philosophy of science takes scientific explanation to consist in the conveyance of some kind of information. Here I argue that this idea is also implicit in some core arguments of mechanists, some of whom are proponents of an ontic conception of explanation that might be thought inconsistent with it. However, informational accounts seem to conflict with some lay and scientific commonsense judgments and a central goal of the theory of explanation, because information is relative to the (...) background knowledge of agents. Sometimes we make lay judgments about whether a model is an explanation simpliciter, not just an explanation relative to some particular agent. And as philosophers of explanation, we would like a philosophical account to tell us when a model is an explanation simpliciter, not just when a model is an explanation relative to some particular agent. Thus, even if one’s account of explanation is not concerned with explanation qua communicative or speech act, the account’s reliance on the concept of information generates a prima facie conflict between the claims that 1) explanation is the conveyance of information, 2) information is relative to the background knowledge of an agent, and 3) some models are explanations not relative to the background knowledge of any particular agent. I sketch a solution to this puzzle by distinguishing informationally what I call “explanation simpliciter” from what I call “explanation-to,” relativizing the latter to an individual’s background knowledge and the former to what I call “total scientific background knowledge”. (shrink)

The homeostatic property cluster theory is widely influential for its ability to account for many natural-kind terms in the life sciences. However, the notion of homeostatic mechanism has never been fully explicated. In 2009, Carl Craver interpreted the notion in the sense articulated in discussions on mechanistic explanation and pointed out that the HPC account equipped with such notion invites interest-relativity. In this paper, we analyze two recent refinements on HPC: one that avoids any reference to the causes of the (...) clustering of properties and one that replaces homeostatic mechanisms with causal networks represented by causal graphs. We argue that the former is too slender to account for some inductive inference in science and the latter, thicker account invites interest-relativity, as the original HPC does. This suggests that human interest will be an un-eliminative part of a satisfactory account of natural kindness. We conclude by discussing the implication of interest-relativity to the naturalness, reality, or objectivity of kinds and indicating an overlooked aspect of natural kinds that requires further studies. (shrink)

Although the analogy between macroscopic machines and biological molecular devices plays an important role in the conceptual framework of both neo-mechanistic accounts and nanotechnology, it has recently been claimed that certain complex molecular devices cannot be considered machines since they are subject to physicochemical forces that are different from those of macroscopic machines. However, the structural and physicochemical conditions that allow both macroscopic machines and microscopic devices to work and perform new functions, through a combination of elemental functional parts, have (...) not yet been examined. In order to fill this void, this paper has a threefold aim: first, to clarify the structural and organisational conditions of macroscopic machines and microscopic devices; second, to determine whether the machine-like analogy fits nanoscale devices; and third, to assess whether the machine-like analogy is appropriate for describing the behaviour of some biological macromolecules. Finally, the paper gives an account of ‘machine’ which, while acknowledging the physicochemical and organisational differences between man-made machines and biological microscopic devices, nevertheless identifies a common conceptual core that allows us to consider the latter ‘machines’. (shrink)

Ecological communities are seldom, if ever, biological individuals. They lack causal boundaries as the populations that constitute communities are not congruent and rarely have persistent functional roles regulating the communities’ higher-level properties. Instead we should represent ecological communities indexically, by identifying ecological communities via the network of weak causal interactions between populations that unfurl from a starting set of populations. This precisification of ecological communities helps identify how community properties remain invariant, and why they have robust characteristics. This respects the (...) diversity and aggregational nature of these complex systems while still vindicating them as units worthy of investigation. (shrink)

In this paper we identify six theses that constitute core results of philosophical investigation into the nature of mechanisms, and of the role that the search for and identification of mechanisms play in the sciences. These theses represent the fruits of the body of research that is now often called New Mechanism. We concisely present the main arguments for these theses. In the literature, these arguments are scattered and often implicit. Our analysis can guide future research in many ways: it (...) provides critics of New Mechanism with clear targets, it can reduce misunderstandings, it can clarify differences of opinion among New Mechanists and it helps to define a research agenda for New Mechanists. (shrink)

Biologists frequently draw on ideas and terminology from engineering. Evolutionary systems biology—with its circuits, switches, and signal processing—is no exception. In parallel with the frequent links drawn between biology and engineering, there is ongoing criticism against this cross-fertilization, using the argument that over-simplistic metaphors from engineering are likely to mislead us as engineering is fundamentally different from biology. In this article, we clarify and reconfigure the link between biology and engineering, presenting it in a more favorable light. We do so (...) by, first, arguing that critics operate with a narrow and incorrect notion of how engineering actually works, and of what the reliance on ideas from engineering entails. Second, we diagnose and diffuse one significant source of concern about appeals to engineering, namely that they are inherently and problematically metaphorical. We suggest that there is plenty of fertile ground left for a continued, healthy relationship between engineering and biology. (shrink)

Among the notions of levels invoked in accounts of biological phenomena, I focus on two: levels of production mechanisms and levels of control mechanisms. I argue that these two notions of level exhibit different characteristics: production mechanisms are organized hierarchically while control mechanisms are often organized heterarchically. I illustrate the differences in these modes of organization by examining production and control mechanisms involved in cell division in Escherichia coli and in circulation of blood in mammals. I conclude by exploring how (...) these two notions of levels can be integrated by adopting a perspective in which organisms are autonomous systems maintaining themselves far from equilibrium. (shrink)