Vito Balorda

Recent challenges to the new mechanistic framework argue that biological explanation involves causal structures, such as cascades, with different features, analogies, and investigative strategies, without explicitly claiming that they are ontologically distinct from mechanisms. I argue that cascades (e.g., blood coagulation) satisfy the same ontological commitments as mechanisms: they consist of organized entities engaging in activities and are embedded within hierarchical mechanistic architectures. Their distinctiveness is instead pragmatic: the cascade perspective foregrounds certain features, such as trigger sensitivity, amplification, and stable progression, for purposes of representation, discovery, and control without introducing a distinct kind of causal structure.

This thesis examines the causal explanation in molecular biology, particularly focusing on the predominant explanatory account in biology, namely, the new mechanistic account. According to this account, a phenomenon is explained by a mechanism, that is, a causal structure with a specific organization of entities and activities responsible for the phenomenon in question. For example, consider the mechanism of protein synthesis. It consists of entities (e.g., DNA) and activities (e.g., transcription) that are responsible for synthesizing proteins, that is, influencing the phenotypic traits of an organism. The thesis aims to further advance this debate by emphasizing three points. Firstly, it aims to structure and present the debate on the issue, particularly by focusing on the background concepts related to the new mechanistic account, such as: causation, explanation, mechanism, biological functions, and law of nature. In particular, it outlines the interventionist and production accounts of causal explanation, the causal role account of biological functions, and the mechanistic approach to laws of nature. Secondly, it presents various characterizations of the new mechanistic account, advocating for a consensus view on the concept of a mechanism. Additionally, it emphasizes alternative causal-explanatory structures, such as causal pathways and cascades. For each of these three structures, the thesis outlines their respective aspects regarding their corresponding explanation processes, namely the ontic, epistemic, and strategic aspects. The thesis argues that mechanisms, along with the aforementioned structures, are distinct in the strategic and epistemic aspects, while sharing certain features in the ontic aspect, asserting that mechanisms are the explanatory privileged causal structure. Thirdly, it aims to apply the interventionist account of causal explanation and the three aspects of mechanisms and pathways outlined above to two case studies from scientific practice, namely: (i) the intervention in the glycolytic pathway to prevent the growth of cancer cells, and (ii) the characterization of natural selection in terms of causal-explanatory structures. Regarding (i), the thesis argues that both the pathway’s epistemic aspect and the interventionist account can serve as useful conceptual frameworks. As for (ii), the thesis introduces a novel perspective, contending that natural selection could be partially characterized as a pathway.

U ovom radu razmatram pitanje: Postoji li razlika između korištenja pojma mehanizma kod ranih i novih mehanicista? Zastupam tezu prema kojoj se rani i novi mehanicisti razlikuju po sljedećim aspektima: 1) eksplanatornim ciljevima i 2) ontologiji. Ranim mehanicistima nazivam atomiste te novovjekovnog modernog filozofa Descartesa. U suvremenim filozofskim raspravama novim mehanicistima nazivaju se autori koji se koriste pojmom mehanizma kao uzročno-eksplanatornom strukturom u biologiji (npr. mehanizam sinteze proteina). Razlika između ranih i novih mehanicista u odnosu na prvi aspekt jest u tome što se rani koriste pojmom mehanizma s ciljem objašnjenja cjelokupnog funkcioniranja svijeta i korištenja analogije tijela sa strojem, a novi se koriste pojmom mehanizma u svrhu objašnjenja bioloških fenomena. Razlika u odnosu na drugi aspekt jest u tome što rani mehanicisti kao ontološku podlogu uzimaju atome i prazni prostor, a novi dualnu ontologiju, tj. entitete i aktivnosti kao nužne dijelove mehanizama.

In this paper, I address Max Delbrück’s conceptual and experimental importance for molecular biology (henceforth MB) origins. In particular, his complementarity approach and its antireductive implications on the (epistemic) reductionism debate in MB. Regarding Delbrück’s conceptual and experimental importance, I examine his influence on the development of MB by exploring a shift of his interests from physics to biology. Particularly, I outline his central role in “The Phage Group”, an informal group of scientists examining the origin of hereditary life using bacteriophages as their experimental model of choice. Delbrück and “The Phage Group” greatly influenced the development of MB, which culminated with the shared 1969 Nobel Prize for the discoveries regarding replication mechanism and genetic structure of viruses. Moreover, I examine Delbrück’s complementarity approach towards biological explanations. The complementarity in biology assumes that “biological phenomena might require the employment of descriptions that are mutually exclusive yet jointly necessary for understanding life processes” (McKaughan 2011, p. 11). I explore Delbrück’s complementarity approach, in particular the debate between the reductive and anti-reductive interpretations of it. I argue for the latter interpretation by suggesting that Delbrück advanced an anti-reductive view towards biological explanations by advocating for independent status of explanations of various biological disciplines. Furthermore, I address the complementarity approach in the light of the antireductive interpretation in the recent developments in MB, particularly, the potentiality of finding the complementarity approach in systems biology, epigenetics, and boundary selection.

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.

In the debate on causal explanation in biology, in the past two decades largely influenced by the new mechanist approach, the concept of a pathway has recently reemerged as a promising research agenda, 551-572, 2018; The British Journal for the Philosophy of Science, 72, 131-158, 2021). Ross’ account of biological explanation differentiates several autonomous types of causal structures that play explanatory and other roles across the life sciences. NM, however, prioritizes mechanisms as vehicles of biological explanations. According to this program, the causal architecture of biological pathways and other causal structures, such as cascades and processes, can be interpreted with at least one of the NM’s mechanism concepts. In other words, these alternative causal structures are not sufficiently distinctive to merit the explanatory autonomy with regard to the NM corresponding concepts. We examine the explanatory practice of molecular biology and concur with Ross that there are indeed distinct types of causal structures, not all falling under the concept of a mechanism. Nonetheless, we show that the concept of mechanism is referring to a privileged causal structure, at the center of explanatory efforts in molecular biology. Pathways and other causal concepts, while somewhat distinct from mechanisms themselves, are explanatorily relevant to the degree in which they exhibit mechanistic features, are parts of a mechanistic architecture, or may lead to a mechanistic arrangement. What emerges in that manner is a hierarchy of causal structures with mechanisms at the explanatory top, and lower levels differing in the degree in which they contribute to mechanistic arrangements.