scholarly journals Network explanations and explanatory directionality

2020 ◽  
Vol 375 (1796) ◽  
pp. 20190318 ◽  
Author(s):  
Lina Jansson

Network explanations raise foundational questions about the nature of scientific explanation. The challenge discussed in this article comes from the fact that network explanations are often thought to be non-causal, i.e. they do not describe the dynamical or mechanistic interactions responsible for some behaviour, instead they appeal to topological properties of network models describing the system. These non-causal features are often thought to be valuable precisely because they do not invoke mechanistic or dynamical interactions and provide insights that are not available through causal explanations. Here, I address a central difficulty facing attempts to move away from causal models of explanation; namely, how to recover the directionality of explanation. Within causal models, the directionality of explanation is identified with the direction of causation. This solution is no longer available once we move to non-causal accounts of explanation. I will suggest a solution to this problem that emphasizes the role of conditions of application. In doing so, I will challenge the idea that sui generis mathematical dependencies are the key to understand non-causal explanations. The upshot is a conceptual account of explanation that accommodates the possibility of non-causal network explanations. It also provides guidance for how to evaluate such explanations. This article is part of the theme issue ‘Unifying the essential concepts of biological networks: biological insights and philosophical foundations’.

2020 ◽  
Vol 375 (1796) ◽  
pp. 20190316 ◽  
Author(s):  
Maria Serban

Network theoretical approaches have shaped our understanding of many different kinds of biological modularity. This essay makes the case that to capture these contributions, it is useful to think about the role of network models in exploratory research. The overall point is that it is possible to provide a systematic analysis of the exploratory functions of network models in bioscientific research. Using two examples from molecular and developmental biology, I argue that often the same modelling approach can perform one or more exploratory functions, such as introducing new directions of research, offering a complementary set of concepts, methods and algorithms for individuating important features of natural phenomena, generating proofs of principle demonstrations and potential explanations for phenomena of interest and enlarging the scope of certain research agendas. This article is part of the theme issue ‘Unifying the essential concepts of biological networks: biological insights and philosophical foundations’.


2020 ◽  
Vol 375 (1796) ◽  
pp. 20190319 ◽  
Author(s):  
Claus C. Hilgetag ◽  
Alexandros Goulas

Concepts shape the interpretation of facts. One of the most popular concepts in systems neuroscience is that of ‘hierarchy’. However, this concept has been interpreted in many different ways, which are not well aligned. This observation suggests that the concept is ill defined. Using the example of the organization of the primate visual cortical system, we explore several contexts in which ‘hierarchy’ is currently used in the description of brain networks. We distinguish at least four different uses, specifically, ‘hierarchy’ as a topological sequence of projections, as a gradient of features, as a progression of scales, or as a sorting of laminar projection patterns. We discuss the interpretation and functional implications of the different notions of ‘hierarchy’ in these contexts and suggest that more specific terms than ‘hierarchy’ should be used for a deeper understanding of the different dimensions of the organization of brain networks. This article is part of the theme issue ‘Unifying the essential concepts of biological networks: biological insights and philosophical foundations’.


2020 ◽  
Vol 375 (1796) ◽  
pp. 20190326 ◽  
Author(s):  
Nathalie Niquil ◽  
Matilda Haraldsson ◽  
Télesphore Sime-Ngando ◽  
Philippe Huneman ◽  
Stuart R. Borrett

Network analyses applied to models of complex systems generally contain at least three levels of analyses. Whole-network metrics summarize general organizational features (properties or relationships) of the entire network, while node-level metrics summarize similar organization features but consider individual nodes. The network- and node-level metrics build upon the primary pairwise relationships in the model. As with many analyses, sometimes there are interesting differences at one level that disappear in the summary at another level of analysis. We illustrate this phenomenon with ecosystem network models, where nodes are trophic compartments and pairwise relationships are flows of organic carbon, such as when a predator eats a prey. For this demonstration, we analysed a time-series of 16 models of a lake planktonic food web that describes carbon exchanges within an autumn cyanobacteria bloom and compared the ecological conclusions drawn from the three levels of analysis based on inter-time-step comparisons. A general pattern in our analyses was that the closer the levels are in hierarchy (node versus network, or flow versus node level), the more they tend to align in their conclusions. Our analyses suggest that selecting the appropriate level of analysis, and above all regularly using multiple levels, may be a critical analytical decision. This article is part of the theme issue ‘Unifying the essential concepts of biological networks: biological insights and philosophical foundations'.


Author(s):  
Brad Skow

This chapter argues that the notion of explanation relevant to the philosophy of science is that of an answer to a why-question. From this point of view it surveys most of the historically important theories of explanation. Hempel’s deductive-nomological, and inductive-statistical, models of explanation required explanations to cite laws. Familiar counterexamples to these models suggested that laws are not needed, and instead that explanations should cite causes. One theory of causal explanation, David Lewis’s, is discussed in some detail. Many philosophers now reject causal theories of explanation because they think that there are non-causal explanations; some examples are reviewed. The role of probabilities and statistics in explanation, and their relation to causation, is also discussed. Another strategy for dealing with counterexamples to Hempel’s theory leads to unificationist theories of explanation. Kitcher's unificationist theory is presented, and a new argument against unificationist theories is offered. Also discussed in some detail are Van Fraassen’s pragmatic theory, and Streven’s and Woodward’s recent theories of causal explanation.


2020 ◽  
Vol 375 (1796) ◽  
pp. 20190321 ◽  
Author(s):  
Daniel Kostić

In this paper, I present a general theory of topological explanations, and illustrate its fruitfulness by showing how it accounts for explanatory asymmetry. My argument is developed in three steps. In the first step, I show what it is for some topological property A to explain some physical or dynamical property B . Based on that, I derive three key criteria of successful topological explanations: a criterion concerning the facticity of topological explanations, i.e. what makes it true of a particular system; a criterion for describing counterfactual dependencies in two explanatory modes, i.e. the vertical and the horizontal and, finally, a third perspectival one that tells us when to use the vertical and when to use the horizontal mode. In the second step, I show how this general theory of topological explanations accounts for explanatory asymmetry in both the vertical and horizontal explanatory modes. Finally, in the third step, I argue that this theory is universally applicable across biological sciences, which helps in unifying essential concepts of biological networks. This article is part of the theme issue ‘Unifying the essential concepts of biological networks: biological insights and philosophical foundations'.


2020 ◽  
Vol 375 (1796) ◽  
pp. 20190320 ◽  
Author(s):  
William Bechtel

Network representations are flat while mechanisms are organized into a hierarchy of levels, suggesting that the two are fundamentally opposed. I challenge this opposition by focusing on two aspects of the ways in which large-scale networks constructed from high-throughput data are analysed in systems biology: identifying clusters of nodes that operate as modules or mechanisms and using bio-ontologies such as gene ontology (GO) to annotate nodes with information about where entities appear in cells and the biological functions in which they participate. Of particular importance, GO organizes biological knowledge about cell components and functions hierarchically. I illustrate how this supports mechanistic interpretation of networks with two examples of network studies, one using epistatic interactions among genes to identify mechanisms and their parts and the other using deep learning to predict phenotypes. As illustrated in these examples, when network research draws upon hierarchical information such as provided by GO, the results not only can be interpreted mechanistically but provide new mechanistic knowledge. This article is part of the theme issue ‘Unifying the essential concepts of biological networks: biological insights and philosophical foundations’.


2020 ◽  
Vol 375 (1796) ◽  
pp. 20190325 ◽  
Author(s):  
Ricard Solé ◽  
Sergi Valverde

A common trait of complex systems is that they can be represented by means of a network of interacting parts. It is, in fact, the network organization (more than the parts) that largely conditions most higher-level properties, which are not reducible to the properties of the individual parts. Can the topological organization of these webs provide some insight into their evolutionary origins? Both biological and artificial networks share some common architectural traits. They are often heterogeneous and sparse, and most exhibit different types of correlations, such as nestedness, modularity or hierarchical patterns. These properties have often been attributed to the selection of functionally meaningful traits. However, a proper formulation of generative network models suggests a rather different picture. Against the standard selection–optimization argument, some networks reveal the inevitable generation of complex patterns resulting from reuse and can be modelled using duplication–rewiring rules lacking functionality. These give rise to the observed heterogeneous, scale-free and modular architectures. Here, we examine the evidence for tinkering in cellular, technological and ecological webs and its impact in shaping their architecture. Our analysis suggests a serious consideration of the role played by selection as the origin of network topology. Instead, we suggest that the amplification processes associated with reuse might shape these graphs at the topological level. In biological systems, selection forces would take advantage of emergent patterns. This article is part of the theme issue ‘Unifying the essential concepts of biological networks: biological insights and philosophical foundations’.


2020 ◽  
Vol 375 (1796) ◽  
pp. 20190314
Author(s):  
Daniel Kostić ◽  
Claus C. Hilgetag ◽  
Marc Tittgemeyer

Over the last decades, network-based approaches have become highly popular in diverse fields of biology, including neuroscience, ecology, molecular biology and genetics. While these approaches continue to grow very rapidly, some of their conceptual and methodological aspects still require a programmatic foundation. This challenge particularly concerns the question of whether a generalized account of explanatory, organizational and descriptive levels of networks can be applied universally across biological sciences. To this end, this highly interdisciplinary theme issue focuses on the definition, motivation and application of key concepts in biological network science, such as explanatory power of distinctively network explanations, network levels and network hierarchies. This article is part of the theme issue ‘Unifying the essential concepts of biological networks: biological insights and philosophical foundations’.


2020 ◽  
Vol 1 (7) ◽  
pp. 152-158
Author(s):  
N. M. BURYKINA ◽  

This article discusses the role of the family in the social development of children with special needs in an inclusive educational environment, in connection with which the study addresses a new aspect of the interaction between the teacher and the child’s family, the interaction of the teacher (teacher) and parents of children with developmental disabilities is highlighted in a variety of areas, students in secondary schools or attending kindergartens. The purpose of the study is to assess the role of the family in the adaptation of children with developmental disabilities, studying in secondary schools or attending kindergartens. To achieve this goal, the author defines a range of research tasks: to study the historical and philosophical foundations of the role of the family in raising children with special needs; highlight the role of the family in implementing early intervention programs in secondary schools; substantiate the main stages that any school must go through, striving to create a more fruitful relationship between the school, family and community. The author stated the following results as a scientific novelty: general recommendations have been developed so that parents feel confident, competent and can work more productively together with teachers (educators) when children visit kindergarten groups (classes). As a result of the study, the author came to the conclusion that the process of teaching children with special needs in a comprehensive school is most effective in the interaction of the teacher and the family of the child.


2010 ◽  
Vol 42 (8) ◽  
pp. 834-844
Author(s):  
Ting-Ting WANG ◽  
Lei MO

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