Explaining the behaviour of ecosystems is one of the key challenges for the biological sciences. Since 2000, new-mechanicism has been the main model to account for the nature of scientific explanation in biology. The universality of the new-mechanist view in biology has been however put into question due to the existence of explanations that account for some biological phenomena in terms of their mathematical properties (mathematical explanations). Supporters of mathematical explanation have argued that the explanation of the behaviour of ecosystems (...) is usually provided in terms of their mathematical properties, and not in mechanistic terms. They have intensively studied the explanation of the properties of ecosystems that behave following the rules of a non-random network. However, no attention has been devoted to the study of the nature of the explanation in those that form a random network. In this paper, we cover that gap by analysing the explanation of the stability behaviour of the microbiome recently elaborated by Coyte and colleagues, to determine whether it fits with the model of explanation suggested by the new-mechanist or by the defenders of mathematical explanation. Our analysis of this case study supports three theses: (1) that the explanation is not given solely in terms of mechanisms, as the new-mechanists understand the concept; (2) that the mathematical properties that describe the system play an essential explanatory role, but they do not exhaust the explanation; (3) that a non-previously identified appeal to the type of interactions that the entities in the network can exhibit, as well as their abundance, is also necessary for Coyte and colleagues’ account to be fully explanatory. From the combination of these three theses we argue for the necessity of an integrative pluralist view of the nature of behaviour explanation when this is given by appealing to the existence of a random network. (shrink)

Existing accounts of mechanistic causation are not suited for understanding causation in biological and neural mechanisms because they do not have the resources to capture the unique causal structure of control heterarchies. In this paper, we provide a new account on which the causal powers of mechanisms are grounded by time-dependent, variable constraints. Constraints can also serve as a key bridge concept between the mechanistic approach to explanation and underappreciated work in theoretical biology that sheds light on how biological systems (...) channel energy to actively respond to the environment in adaptive ways, perform work, and fulfill the requirements to maintain themselves far from equilibrium. We show how the framework applies to several concrete examples of control in simple organisms as well as the nervous system of complex organisms. (shrink)

Wegner, Giuliano, and Hertel (1985) defined the notion of a transactive memory system (TMS) as a group level memory system that “involves the operation of the memory systems of the individuals and the processes of communication that occur within the group (p. 191). Those processes are the collaborative procedures (“transactions”) by which groups encode, store, and retrieve information that is distributed among their members. Over the past 25+ years, the conception of a TMS has progressively garnered an increased interest among (...) social and organizational psychologists, communication scholars, and management theorists (Ren & Argote 2011). But there remains considerable disagreement about how exactly Wegner’s appeal to group memory should be understood. My goal in this paper is contribute to this debate, by articulating more clearly the value of conceptualizing groups as TMSs. This value, I argue, consists in providing us with a blueprint for how to explain group memory in terms of collective information-processing mechanisms. Collective information-processing mechanisms are dependent on, and interact with, the brain-bound information-processing of individuals, but cannot be reduced to the latter. In my analysis, I lean on extant accounts of mechanistic explanation in the philosophy of science (Bechtel & Richardson 1993; Machamer, Darden, & Craver 2000; Wimsatt 2007) that have been used to analyze the explanatory practices of psychology and cognitive neuroscience (Bechtel 2008, 2009). Based on my reconstruction of Wegner’s conceptualization of a TMS, I argue that the reality of emergent group cognition is compatible with its mechanistic explanation. More generally, my analysis shows that group cognition cannot be reduced to individual cognition, while avoiding the false dilemma between “wholism” and “nothing but-ism” which has hampered traditional construals of the “group mind” thesis (Allport 1968). (shrink)

Epigenetics investigates the dynamics of gene expression in various cells, and the signals from the internal and external environment affecting these dynamics. Neuroepigenetics extends this research into neurons and glia cells. Environmental-induced changes in gene expression are not only associated with the emerging structure and function of the nervous system during ontogeny, but are also fundamental to the wiring of neural circuitries responsible for learning and memory. Yet philosophers of science and neuroscience have so far paid little attention to these (...) findings. In this article, we describe some recent experimental work on the neuroepigenetics of fear and stress responses in rodents, its ingenious experimental translation into humans, and how this work seems not to be accurately described by popular “mechanist” accounts. Our final goal is to motivate broader philosophical attention to neuroepigenetics practices and findings, especially for how it considers environmentally driven and developmental plasticity in psychological explanations. (shrink)

This essay considers a mixed-effects modeling practice and its implications for the philosophical debate surrounding reductive explanation. Mixed-effects modeling is a species of the multilevel modeling practice, where a single model incorporates simultaneously two levels of explanatory variables to explain a phenomenon of interest. I argue that this practice makes the position of explanatory reductionism held by many philosophers untenable because it violates two central tenets of explanatory reductionism: single-level preference and lower-level obsession.

Philosophy of science is positioned to make distinctive contributions to cognitive science by providing perspective on its conceptual foundations and by advancing normative recommendations. The philosophy of science I embrace is naturalistic in that it is grounded in the study of actual science. Focusing on explanation, I describe the recent development of a mechanistic philosophy of science from which I draw three normative consequences for cognitive science. First, insofar as cognitive mechanisms are information‐processing mechanisms, cognitive science needs an account of (...) how the representations invoked in cognitive mechanisms carry information about contents, and I suggest that control theory offers the needed perspective on the relation of representations to contents. Second, I argue that cognitive science requires, but is still in search of, a catalog of cognitive operations that researchers can draw upon in explaining cognitive mechanisms. Last, I provide a new perspective on the relation of cognitive science to brain sciences, one which embraces both reductive research on neural components that figure in cognitive mechanisms and a concern with recomposing higher‐level mechanisms from their components and situating them in their environments. (shrink)

Evolutionary developmental biology (evo-devo) is considered a ‘mechanistic science,’ in that it causally explains morphological evolution in terms of changes in developmental mechanisms. Evo-devo is also an interdisciplinary and integrative approach, as its explanations use contributions from many fields and pertain to different levels of organismal organization. Philosophical accounts of mechanistic explanation are currently highly prominent, and have been particularly able to capture the integrative nature of multifield and multilevel explanations. However, I argue that evo-devo demonstrates the need for a (...) broadened philosophical conception of mechanisms and mechanistic explanation. Mechanistic explanation (in terms of the qualitative interactions of the structural parts of a whole) has been developed as an alternative to the traditional idea of explanation as derivation from laws or quantitative principles. Against the picture promoted by Carl Craver, that mathematical models describe but usually do not explain, my discussion of cases from the strand of evo-devo which is concerned with developmental processes points to qualitative phenomena where quantitative mathematical models are an indispensable part of the explanation. While philosophical accounts have focused on the actual organization and operation of mechanisms, properties of developmental mechanisms that are about how a mechanism reacts to modifications are of major evolutionary significance, including robustness, phenotypic plasticity, and modularity. A philosophical conception of mechanisms is needed that takes into account quantitative changes, transient entities and the generation of novel types of entities, feedback loops and complex interaction networks, emergent properties, and, in particular, functional-dynamical aspects of mechanisms, including functional (as opposed to structural) organization and distributed, system-wide phenomena. I conclude with general remarks on philosophical accounts of explanation. (shrink)

After a decade of intense debate about mechanisms, there is still no consensus characterization. In this paper we argue for a characterization that applies widely to mechanisms across the sciences. We examine and defend our disagreements with the major current contenders for characterizations of mechanisms. Ultimately, we indicate that the major contenders can all sign up to our characterization.

Cancer is not one, but many diseases, and each is a product of a variety of causes acting at distinct temporal and spatial scales, or ‘‘levels’’ in the biological hierarchy. In part because of this diversity of cancer types and causes, there has been a diversity of models, hypotheses, and explanations of carcinogenesis. However, there is one model of carcinogenesis that seems to have survived the diversification of cancer types: the multi-stage model of carcinogenesis. This paper examines the history of (...) the multistage theory, and uses the theory as a case study in the limits and goals of unification as a theoretical virtue, comparing and contrasting it with ‘‘integrative’’ research. (shrink)

Synthetic biology is often understood in terms of the pursuit for well-characterized biological parts to create synthetic wholes. Accordingly, it has typically been conceived of as an engineering dominated and application oriented field. We argue that the relationship of synthetic biology to engineering is far more nuanced than that and involves a sophisticated epistemic dimension, as shown by the recent practice of synthetic modeling. Synthetic models are engineered genetic networks that are implanted in a natural cell environment. Their construction is (...) typically combined with experiments on model organisms as well as mathematical modeling and simulation. What is especially interesting about this combinational modeling practice is that, apart from greater integration between these different epistemic activities, it has also led to the questioning of some central assumptions and notions on which synthetic biology is based. As a result synthetic biology is in the process of becoming more “biology inspired.”. (shrink)

The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models—which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation have failed to address how a mathematical model could contribute to such explanations. I discuss how mathematical (...) equations can be explanatorily relevant. Several cases from systems biology are discussed to illustrate the interplay between mechanistic research and mathematical modeling, and I point to questions about qualitative phenomena, where quantitative models are still indispensable to the explanation. Systems biology shows that a broader philosophical conception of mechanisms is needed, which takes into account functional-dynamical aspects, interaction in complex networks with feedback loops, system-wide functional properties such as distributed functionality and robustness, and a mechanism’s ability to respond to perturbations. I offer general conclusions for philosophical accounts of explanation. (shrink)

This essay analyzes and develops recent views about explanation in biology. Philosophers of biology have parted with the received deductive-nomological model of scientific explanation primarily by attempting to capture actual biological theorizing and practice. This includes an endorsement of different kinds of explanation (e.g., mathematical and causal-mechanistic), a joint study of discovery and explanation, and an abandonment of models of theory reduction in favor of accounts of explanatory reduction. Of particular current interest are philosophical accounts of complex explanations that appeal (...) to different levels of organismal organization and use contributions from different biological disciplines. The essay lays out one model that views explanatory integration across different disciplines as being structured by scientific problems. I emphasize the philosophical need to take the explanatory aims pursued by different groups of scientists into account, as explanatory aims determine whether different explanations are competing or complementary and govern the dynamics of scientific practice, including interdisciplinary research. I distinguish different kinds of pluralism that philosophers have endorsed in the context of explanation in biology, and draw several implications for science education, especially the need to teach science as an interdisciplinary and dynamic practice guided by scientific problems and explanatory aims. (shrink)

Accounts of mechanistic explanation have emphasized the importance of looking down—decomposing a mechanism into its parts and operations. Using research on visual processing as an exemplar, I illustrate how productive such research has been. But once multiple components of a mechanism have been identified, researchers also need to figure out how it is organized—they must look around and determine how to recompose the mechanism. Although researchers often begin by trying to recompose the mechanism in terms of sequential operations, they frequently (...) find that the components of a mechanism interact in complex ways involving positive and negative feedback and that the organization often exhibits highly interactive local networks linked by a few long-range connections (small-worlds organization) and power law distributions of connections. The mechanisms are themselves active systems that are perturbed by inputs but not set in motion by them. Researchers also need to look up —situate a mechanism in its context, which may be a larger mechanism that modulates its behavior. When looking down is combined with looking around and up, mechanistic research results in an integrated, multi-level perspective. (shrink)

Ongoing empirical discoveries in molecular biology have generated novel conceptual challenges and perspectives. Philosophers of biology have reacted to these trends when investigating the practice of molecular biology and contributed to scientific debates on methodological and conceptual matters. This article reviews some major philosophical issues in molecular biology. First, philosophical accounts of mechanistic explanation yield a notion of explanation in the context of molecular biology that does not have to rely on laws of nature and comports well with molecular discovery. (...) Second, reductionism continues to be debated and increasingly be rejected by scientists. Philosophers have likewise moved away from reduction toward integration across fields or integrative explanations covering several levels of organization. Third, although the gene concept has undergone substantial transformation and even fragmentation, it still enjoys widespread use by molecular biologists, which has prompted philosophers to understand the empirical reasons for this. At the same time, it has been argued the notion of ‘genetic information’ is largely an empty metaphor, which generates the illusion of explanatory understanding without offering an adequate explanation of molecular and developmental mechanisms. (shrink)

Philosophical discussions of systems biology have enriched the notion of mechanistic explanation by pointing to the role of mathematical modeling. However, such accounts still focus on explanation in terms of tracking a mechanism's operation across time (by means of mental or computational simulation). My contention is that there are explanations of molecular systems where the explanatory understanding does not consist in tracking a mechanism's operation and productive continuity. I make this case by a discussion of bifurcation analysis in dynamical systems, (...) articulating the distinctive way in which explanatory understanding is provided, especially about the reversibility or irreversibility of molecular processes. (shrink)

Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.

This paper is aimed at identifying how a model’s explanatory power is constructed and identified, particularly in the practice of template-based modeling (Humphreys, Philos Sci 69:1–11, 2002; Extending ourselves: computational science, empiricism, and scientific method, 2004), and what kinds of explanations models constructed in this way can provide. In particular, this paper offers an account of non-causal structural explanation that forms an alternative to causal–mechanical accounts of model explanation that are currently popular in philosophy of biology and cognitive science. Clearly, (...) defences of non-causal explanation are far from new (e.g. Batterman, Br J Philos Sci 53:21–38, 2002a; The devil in the details: asymptotic reasoning in explanation, reduction, and emergence, 2002b; Pincock, Noûs 41:253–275, 2007; Mathematics and scientific representation 2012; Rice, Noûs. doi:10.1111/nous.12042, 2013; Biol Philos 27:685–703, 2012), so the targets here are focused on a particular type of robust phenomenon and how strong invariance to interventions can block a range of causal explanations. By focusing on a common form of model construction, the paper also ties functional or computational style explanations found in cognitive science and biology more firmly with explanatory practices across model-based science in general. (shrink)

The question of specific properties of life compared to nonliving things accompanied biology throughout its history. At times this question generated major controversies with largely diverging opinions. Basically, mechanistic thinkers, who tried to understand organismic functions in terms of nonliving machines, were opposed by those who tried to describe specific properties or even special forces being active within living entities. As this question included the human body, these controversies always have been of special relevance to our self-image and also touched (...) practical issues of medicine. During the second half of the twentieth century, it seemed to be resolved that organisms are explainable basically as physicochemical machines. Especially from the perspective of molecular biology, it seemed to be clear that organisms need to be explained solely by the chemical functions of their component parts, although some resistance to this view never ceased. This research program has been working quite successfully, so that science today knows a lot about the physiological and chemical processes within organisms. However, again new doubts arise questioning whether the mere continuation of this analytical approach will finally generate a fundamental understanding of living entities. At the beginning of the twenty-first century the quest for a new synthesis actually comes from analytical empiricists themselves. The hypothesis of the present paper is that empirical research has been developed far enough today, that it reveals by itself the materials and the prerequisites to understand more of the specific properties of life. Without recourse to mysterious forces, it is possible to generate answers to this age-old question, just using recent, empirically generated knowledge. This view does not contradict the results of reductionistic research, but rather grants them meaning within the context of organismic systems and also may increase their practical usefulness. Although several of these properties have been discussed before, different authors usually concentrated on a single one or some of them. The paper describes ten specific properties of living entities as they can be deduced from contemporary science. The aim is to demonstrate that the results of empirical research show both the necessity as well as the possibility of the development of a new conception of life to build a coherent understanding of organismic functions. (shrink)

Mechanistic accounts of explanation have recently found popularity within philosophy of science. Presently, we introduce the idea of an extended mechanistic explanation, which makes explicit room for the role of environment in explanation. After delineating Craver and Bechtel’s account, we argue this suggestion is not sufficiently robust when we take seriously the mechanistic environment and modeling practices involved in studying contemporary complex biological systems. Our goal is to extend the already profitable mechanistic picture by pointing out the importance of the (...) mechanistic environment. It is our belief that extended mechanistic explanations, or mechanisms that take into consideration the temporal sequencing of the interplay between the mechanism and the environment, allow for mechanistic explanations regarding a broader group of scientific phenomena. (shrink)