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)

Mechanisms, in the prominent biological sense of the term, are historical entities. That is, whether or not something is a mechanism for something depends on its history. Put differently, while your spontaneously-generated molecule-for-molecule double has a heart, and its heart pumps blood around its body, its heart does not have a mechanism for pumping, since it does not have the right history. My argument for this claim is that mechanisms have proper functions; proper functions are historical entities; so, mechanisms are (...) historical entities, too. This thesis runs against the mainstream new mechanist way of thinking about mechanisms, where mechanisms are generally thought of in an ahistorical way. After arguing for this thesis, I draw out some consequences for philosophy of science and metaphysics. (shrink)

Much of the recent philosophical debate on causation and causal explanation in the biological and biomedical sciences has focused on the notion of mechanism. Mechanisms, their nature and epistemic roles have been tackled by a range of so-called neo-mechanistic theories, and widely discussed. Without denying the merits of this approach, our paper aims to show how lately it has failed to give proper credit to processes, which are central to the field, especially of contemporary molecular biology. Processes can be summed (...) up in the notion of ‘pathway’, which is far from being just equivalent to that of ‘mechanism’ and has a profound epistemological and explanatory relevance. It is argued that an adequate consideration of pathways impels some rethinking of scientific explanation in molecular biology, namely its functional and contextual features. A number of examples are given to suggest that the focus of philosophical attention in this disciplinary field should shift from the notion of mechanism to the notion of pathway. (shrink)

The article develops and justifies, on the basis of the epistemological argumentation theory, two central pieces of the theory of evaluative argumentation interpretation: 1. criteria for recognizing argument types and 2. rules for adding reasons to create ideal arguments. Ad 1: The criteria for identifying argument types are a selection of essential elements from the definitions of the respective argument types. Ad 2: After presenting the general principles for adding reasons (benevolence, authenticity, immanence, optimization), heuristics are proposed for finding missing (...) reasons, for deductive arguments, e.g., semantic tableaux are suggested. (shrink)

This paper makes use of the concepts and theoretical framework developed within the field of Argumentation Theory to account for the structure and characteristics of abduction and of the comparative processes of weighing explanatory hypothesis. It elaborates an analysis of abduction based on its consideration as a meta-explanatory argumentation scheme while elucidating its relations with abductive reasoning and inference. The conceptualization of comparative processes of weighing explanatory hypothesis as complex and varied argumentative structures is presented as an alternative to the (...) idea of providing a formally rigid and supposedly universal account of ‘inference to the best explanation’. (shrink)

This paper makes use of the concepts and theoretical framework developed within the field of Argumentation Theory to account for the structure and characteristics of abduction and of the comparative processes of weighing explanatory hypothesis. It elaborates an analysis of abduction based on its consideration as a meta-explanatory argumentation scheme while elucidating its relations with abductive reasoning and inference. The conceptualization of comparative processes of weighing explanatory hypothesis as complex and varied argumentative structures is presented as an alternative to the (...) idea of providing a formally rigid and supposedly universal account of ‘inference to the best explanation’. (shrink)

The idea that mechanisms are crucially important to differentiate between genuine and spurious causal relations is ubiquitous both in the philosophical and in the social scientific literature. Yet...

In this paper, we examine the issue of characterizing natural selection. Usually, natural selection is characterized as a force, as a statistical concept, and as a certain causal structure (e.g., a mechanism). We focus on the characterization of natural selection as a mechanism, and, considering the unsettled debate on the issue, particularly in the light of new mechanistic accounts, argue for a pathway characterization. We examine this issue by addressing the following three questions: (i) how does a strategic consideration of (...) mechanisms, according to which, roughly, is methodologically best to give primacy to the cognitive-epistemic power of mechanistic modelling and scientific methods even in evolutionary biology, relate to the extant interpretations of natural selection as a mechanism? (ii) Which part of the process of natural selection could be, if at all, characterized as a pathway, specifically, considering pathway’s strategic aspect, i.e., its modelling and methods? Accordingly, (iii) how do the concepts of mechanism and pathway relate to each other in this domain? In the present paper, we address primarily the first two questions. Thus, with regard to (i), we examine the characterization of natural selection as a mechanism. In particular, we apply the strategic consideration of mechanisms to other types of causal structures as well, such as that of a pathway. That discussion leads us to addressing question (ii), and to some extent (iii), where we argue that certain stages of natural selection conform to specific strategic pathway features. (shrink)

This work addresses biological explanations and aims to provide a philosophical account which brings together logical-procedural and historical-processual aspects when considering molecular pathways. It is argued that, having molecular features as explananda, a particular non-classical logical language – Zsyntax – can be used to formally represent, in terms of logical theorems, types of molecular processes, and to grasp how we get from one molecular interaction to another, hence explaining why a given outcome occurs. Expressing types of molecular biology processes in (...) terms of the Zsyntax language allows us to represent causal interactions by taking into account their context-sensitivity, and amounts to partly reviving the spirit of the so-called received view of explanation – which aimed to capture scientific explanatory accounts in terms of their logical structure and their appealing to nomological relations. Such a partial revival is pursued by invoking here non-classical deductions and empirical generalisations, which are called to provide the epistemic norms to explain the behavior of molecular pathways. (shrink)

Usually, the organization of living systems is explained by appealing to an intrinsic purpose that is based on the biological survival. However, paradigmatically, it is inevitable to observe that the final destiny of all living organisms is death. In this work, we defend that, from an organizational approach, there is a form of death—Regulatory Cell Death—that, far from being a mere "absence of life", is a process of biological regulation and a feature of self-maintenance in multicellular organisms.

The scope of this paper can be clarified by means of a well-known phenomenon that is usually called ‘industrial melanism’: the fact that the melanic form of the peppered moth became dominant in industrial areas in England in the second half of the nineteenth century. Such changes in relative phenotype frequencies are important explananda for population biologists. Apart from trying to explain such changes over time, population biologists also often try to explain differences between populations, e.g. why yellow shell colour (...) is dominant in certain colonies of land snails and almost absent in other colonies. The causal explanations that are given to address such explananda are the objects of analysis in this paper. Our primary aim is to explicate their structure: we want to capture the typical ingredients of causal explanations in population biology, and their organisation. Based on this explication, we discuss how natural selection fits into recent mechanical philosophy of science, and engage in the debate on the nature of evolutionary theory. (shrink)