Switch to: References

Add citations

You must login to add citations.
  1. Design Principles and Mechanistic Explanation.Wei Fang - 2022 - History and Philosophy of the Life Sciences 44 (4):1-23.
    In this essay I propose that what design principles in systems biology and systems neuroscience do is to present abstract characterizations of mechanisms, and thereby facilitate mechanistic explanation. To show this, one design principle in systems neuroscience, i.e., the multilayer perceptron, is examined. However, Braillard contends that design principles provide a sort of non-mechanistic explanation due to two related reasons: they are very general and describe non-causal dependence relationships. In response to this, I argue that, on the one hand, all (...)
    Direct download (3 more)  
     
    Export citation  
     
    Bookmark  
  • On the Structure and Epistemic Value of Function Ascriptions in Biology and Engineering Sciences.Erik Weber, Dingmar van Eck & Julie Mennes - 2019 - Foundations of Science 24 (3):559-581.
    In this paper we chart epistemological similarities between shared function talk in biology and the engineering sciences, focusing on the notions of biological advantage function and technical advantage function. We start by showing that biological advantage function ascriptions are common in biology and that technical advantage function ascriptions are common in engineering science. We then proceed to show that these ascriptions have a very similar structure and that their epistemic value also is similar: both biological advantage function and technical advantage (...)
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark   1 citation  
  • Mechanist Idealisation in Systems Biology.Dingmar van Eck & Cory Wright - 2020 - Synthese 199 (1-2):1555-1575.
    This paper adds to the philosophical literature on mechanistic explanation by elaborating two related explanatory functions of idealisation in mechanistic models. The first function involves explaining the presence of structural/organizational features of mechanisms by reference to their role as difference-makers for performance requirements. The second involves tracking counterfactual dependency relations between features of mechanisms and features of mechanistic explanandum phenomena. To make these functions salient, we relate our discussion to an exemplar from systems biological research on the mechanism for countering (...)
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark  
  • Mechanism Discovery and Design Explanation: Where Role Function Meets Biological Advantage Function.Dingmar van Eck & Julie Mennes - 2018 - Journal for General Philosophy of Science / Zeitschrift für Allgemeine Wissenschaftstheorie 49 (3):413-434.
    In the recent literature on explanation in biology, increasing attention is being paid to the connection between design explanation and mechanistic explanation, viz. the role of design principles and heuristics for mechanism discovery and mechanistic explanation. In this paper we extend the connection between design explanation and mechanism discovery by prizing apart two different types of design explanation and by elaborating novel heuristics that one specific type offers for mechanism discovery across species. We illustrate our claims in terms of two (...)
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark   2 citations  
  • Design Explanation and Idealization.Dingmar van Eck & Julie Mennes - 2016 - Erkenntnis 81 (5):1051-1071.
    In this paper we assess the explanatory role of idealizations in ‘design explanations’, a type of functional explanation used in biology. In design explanations, idealizations highlight which factors make a difference to phenomena to be explained: hypothetical, idealized, organisms are invoked to make salient which traits of extant organisms make a difference to organismal fitness. This result negates the view that idealizations serve only pragmatic benefits, and complements the view that idealizations highlight factors that do not make a difference. This (...)
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark   1 citation  
  • Integrative Pluralism for Biological Function.Beckett Sterner & Samuel Cusimano - 2019 - Biology and Philosophy 34 (6):1-21.
    We introduce a new type of pluralism about biological function that, in contrast to existing, demonstrates a practical integration among the term’s different meanings. In particular, we show how to generalize Sandra Mitchell’s notion of integrative pluralism to circumstances where multiple epistemic tools of the same type are jointly necessary to solve scientific problems. We argue that the multiple definitions of biological function operate jointly in this way based on how biologists explain the evolution of protein function. To clarify how (...)
    Direct download (3 more)  
     
    Export citation  
     
    Bookmark   4 citations  
  • Darwinian Functional Biology.Ginnobili Santiago - 2022 - Theoria : An International Journal for Theory, History and Fundations of Science 37 (2):233-255.
    Abstract One of the most important things that the Darwinian revolution affected is the previous teleological thinking. In particular, the attribution of functions to various entities of the natural world with explanatory pretensions. In this change, his theory of natural selection played an important role. We all agree on that, but the diversity and heterogeneity of the answers that try to explain what Darwin did exactly with functional biology are overwhelming. In this paper I will try to show how Darwin (...)
    Direct download (4 more)  
     
    Export citation  
     
    Bookmark  
  • Mechanism Discovery and Design Explanation: Where Role Function Meets Biological Advantage Function.Julie Mennes & Dingmar Eck - 2018 - Journal for General Philosophy of Science / Zeitschrift für Allgemeine Wissenschaftstheorie 49 (3):413-434.
    In the recent literature on explanation in biology, increasing attention is being paid to the connection between design explanation and mechanistic explanation, viz. the role of design principles and heuristics for mechanism discovery and mechanistic explanation. In this paper we extend the connection between design explanation and mechanism discovery by prizing apart two different types of design explanation and by elaborating novel heuristics that one specific type offers for mechanism discovery across species. We illustrate our claims in terms of two (...)
    Direct download  
     
    Export citation  
     
    Bookmark   1 citation  
  • Organizing Principles as Tools for Bridging the Gap Between System Theory and Biological Experimentation.Constantinos Mekios - 2016 - History and Philosophy of the Life Sciences 38 (1):65-89.
    Twentieth-century theoretical efforts towards the articulation of general system properties came short of having the significant impact on biological practice that their proponents envisioned. Although the latter did arrive at preliminary mathematical formulations of such properties, they had little success in showing how these could be productively incorporated into the research agenda of biologists. Consequently, the gap that kept system-theoretic principles cut-off from biological experimentation persisted. More recently, however, simple theoretical tools have proved readily applicable within the context of systems (...)
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark  
  • Causal Concepts Guiding Model Specification in Systems Biology.Dana Matthiessen - 2017 - Disputatio 9 (47):499-527.
    In this paper I analyze the process by which modelers in systems biology arrive at an adequate representation of the biological structures thought to underlie data gathered from high-throughput experiments. Contrary to views that causal claims and explanations are rare in systems biology, I argue that in many studies of gene regulatory networks modelers aim at a representation of causal structure. In addressing modeling challenges, they draw on assumptions informed by theory and pragmatic considerations in a manner that is guided (...)
    Direct download (3 more)  
     
    Export citation  
     
    Bookmark  
  • Strategies of Explanatory Abstraction in Molecular Systems Biology.Nicholaos Jones - 2018 - Philosophy of Science 85 (5):955-968.
    I consider three explanatory strategies from recent systems biology that are driven by mathematics as much as mechanistic detail. Analysis of differential equations drives the first strategy; topological analysis of network motifs drives the second; mathematical theorems from control engineering drive the third. I also distinguish three abstraction types: aggregations, which simplify by condensing information; generalizations, which simplify by generalizing information; and structurations, which simplify by contextualizing information. Using a common explanandum as reference point—namely, the robust perfect adaptation of chemotaxis (...)
    Direct download (7 more)  
     
    Export citation  
     
    Bookmark   1 citation  
  • The Phenomena of Homology.Paul Edmund Griffiths - 2007 - Biology and Philosophy 22 (5):643-658.
    Philosophical discussions of biological classification have failed to recognise the central role of homology in the classification of biological parts and processes. One reason for this is a misunderstanding of the relationship between judgments of homology and the core explanatory theories of biology. The textbook characterisation of homology as identity by descent is commonly regarded as a definition. I suggest instead that it is one of several attempts to explain the phenomena of homology. Twenty years ago the ‘new experimentalist’ movement (...)
    Direct download (7 more)  
     
    Export citation  
     
    Bookmark   34 citations  
  • In What Sense Does ‘Nothing Make Sense Except in the Light of Evolution’?Paul Edmund Griffiths - 2009 - Acta Biotheoretica 57 (1-2):11-32.
    Dobzhansky argued that biology only makes sense if life on earth has a shared history. But his dictum is often reinterpreted to mean that biology only makes sense in the light of adaptation. Some philosophers of science have argued in this spirit that all work in ‘proximal’ biosciences such as anatomy, physiology and molecular biology must be framed, at least implicitly, by the selection histories of the organisms under study. Others have denied this and have proposed non-evolutionary ways in which (...)
    Direct download (6 more)  
     
    Export citation  
     
    Bookmark   24 citations  
  • Revisiting Generality in Biology: Systems Biology and the Quest for Design Principles.Sara Green - 2015 - Biology and Philosophy 30 (5):629-652.
    Due to the variation, contingency and complexity of living systems, biology is often taken to be a science without fundamental theories, laws or general principles. I revisit this question in light of the quest for design principles in systems biology and show that different views can be reconciled if we distinguish between different types of generality. The philosophical literature has primarily focused on generality of specific models or explanations, or on the heuristic role of abstraction. This paper takes a different (...)
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark   21 citations  
  • ‘Extreme’ Organisms and the Problem of Generalization: Interpreting the Krogh Principle.Sara Green, Michael R. Dietrich, Sabina Leonelli & Rachel A. Ankeny - 2018 - History and Philosophy of the Life Sciences 40 (4):65.
    Many biologists appeal to the so-called Krogh principle when justifying their choice of experimental organisms. The principle states that “for a large number of problems there will be some animal of choice, or a few such animals, on which it can be most conveniently studied”. Despite its popularity, the principle is often critiqued for implying unwarranted generalizations from optimal models. We argue that the Krogh principle should be interpreted in relation to the historical and scientific contexts in which it has (...)
    No categories
    Direct download (6 more)  
     
    Export citation  
     
    Bookmark   4 citations  
  • Constraint‐Based Reasoning for Search and Explanation: Strategies for Understanding Variation and Patterns in Biology.Sara Green & Nicholaos Jones - 2016 - Dialectica 70 (3):343-374.
    Life scientists increasingly rely upon abstraction-based modeling and reasoning strategies for understanding biological phenomena. We introduce the notion of constraint-based reasoning as a fruitful tool for conceptualizing some of these developments. One important role of mathematical abstractions is to impose formal constraints on a search space for possible hypotheses and thereby guide the search for plausible causal models. Formal constraints are, however, not only tools for biological explanations but can be explanatory by virtue of clarifying general dependency-relations and patterning between (...)
    Direct download  
     
    Export citation  
     
    Bookmark   7 citations  
  • Can Biological Complexity Be Reverse Engineered?Sara Green - 2015 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 53:73-83.
    Concerns with the use of engineering approaches in biology have recently been raised. I examine two related challenges to biological research that I call the synchronic and diachronic underdetermination problem. The former refers to challenges associated with the inference of design principles underlying system capacities when the synchronic relations between lower-level processes and higher-level systems capacities are degenerate. The diachronic underdetermination problem regards the problem of reverse engineering a system where the non-linear relations between system capacities and lower-level mechanisms are (...)
    Direct download (4 more)  
     
    Export citation  
     
    Bookmark   7 citations  
  • Six Theses on Mechanisms and Mechanistic Science.Stuart Glennan, Phyllis Illari & Erik Weber - 2022 - Journal for General Philosophy of Science / Zeitschrift für Allgemeine Wissenschaftstheorie 53 (2):143-161.
    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 (...)
    Direct download (3 more)  
     
    Export citation  
     
    Bookmark  
  • Competition Theory and Channeling Explanation.Christopher H. Eliot - 2011 - Philosophy, Theory, and Practice in Biology 3 (20130604):1-16.
    The complexity and heterogeneity of causes influencing ecology’s domain challenge its capacity to generate a general theory without exceptions, raising the question of whether ecology is capable, even in principle, of achieving the sort of theoretical success enjoyed by physics. Weber has argued that competition theory built around the Competitive Exclusion Principle (especially Tilman’s resource-competition model) offers an example of ecology identifying a law-like causal regularity. However, I suggest that as Weber presents it, the CEP is not yet a causal (...)
    Direct download (9 more)  
     
    Export citation  
     
    Bookmark   5 citations  
  • Functional Explanation and the Problem of Functional Equivalence.James DiFrisco - 2017 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 65:1-8.
    No categories
    Direct download (3 more)  
     
    Export citation  
     
    Bookmark   1 citation  
  • Explanation in Computational Neuroscience: Causal and Non-Causal.M. Chirimuuta - 2018 - British Journal for the Philosophy of Science 69 (3):849-880.
    This article examines three candidate cases of non-causal explanation in computational neuroscience. I argue that there are instances of efficient coding explanation that are strongly analogous to examples of non-causal explanation in physics and biology, as presented by Batterman, Woodward, and Lange. By integrating Lange’s and Woodward’s accounts, I offer a new way to elucidate the distinction between causal and non-causal explanation, and to address concerns about the explanatory sufficiency of non-mechanistic models in neuroscience. I also use this framework to (...)
    Direct download (5 more)  
     
    Export citation  
     
    Bookmark   31 citations  
  • La ciencia de lo sustentable: razón de ser del discurso funcional en ecología.Gustavo Caponi - 2010 - Principia: An International Journal of Epistemology 14 (3):349-373.
    The main cognitive target of Ecology is the functional analysis of the ecological processes and systems. It does not suppose, meanwhile, that these processes and systems are designed systems and processes like individual leaving beings. The Ecology, likewise Physiology, is constitutively guided by the presupposition of a privileged state , to be explained, that it is the persistence of the systems and processes that she studied; and its functional analyses obey to this presupposition. Ecology supposes an ideal of natural order (...)
    Direct download (9 more)  
     
    Export citation  
     
    Bookmark   3 citations  
  • Handbook of Evolutionary Thinking in the Sciences.Thomas Heams, Philippe Huneman, Guillaume Lecointre & Marc Silberstein (eds.) - 2015 - Springer.
    The Darwinian theory of evolution is itself evolving and this book presents the details of the core of modern Darwinism and its latest developmental directions. The authors present current scientific work addressing theoretical problems and challenges in four sections, beginning with the concepts of evolution theory, its processes of variation, heredity, selection, adaptation and function, and its patterns of character, species, descent and life. The second part of this book scrutinizes Darwinism in the philosophy of science and its usefulness in (...)
  • Cajal’s Law of Dynamic Polarization: Mechanism and Design.Sergio Daniel Barberis - 2018 - Philosophies 3 (2):11-0.
    Santiago Ramón y Cajal, the primary architect of the neuron doctrine and the law of dynamic polarization, is considered to be the founder of modern neuroscience. At the same time, many philosophers, historians, and neuroscientists agree that modern neuroscience embodies a mechanistic perspective on the explanation of the nervous system. In this paper, I review the extant mechanistic interpretation of Cajal’s contribution to modern neuroscience. Then, I argue that the extant mechanistic interpretation fails to capture the explanatory import of Cajal’s (...)
    Direct download (6 more)  
     
    Export citation  
     
    Bookmark  
  • Representation in Cognitive Science.Nicholas Shea - 2018 - Oxford University Press.
    How can we think about things in the outside world? There is still no widely accepted theory of how mental representations get their meaning. In light of pioneering research, Nicholas Shea develops a naturalistic account of the nature of mental representation with a firm focus on the subpersonal representations that pervade the cognitive sciences.
  • International Handbook of Research in History, Philosophy and Science Teaching.Michael R. Matthews (ed.) - 2014 - Springer.
    This inaugural handbook documents the distinctive research field that utilizes history and philosophy in investigation of theoretical, curricular and pedagogical issues in the teaching of science and mathematics. It is contributed to by 130 researchers from 30 countries; it provides a logically structured, fully referenced guide to the ways in which science and mathematics education is, informed by the history and philosophy of these disciplines, as well as by the philosophy of education more generally. The first handbook to cover the (...)
  • Explanation in Biology: An Enquiry Into the Diversity of Explanatory Patterns in the Life Sciences.P.-A. Braillard and C. Malaterre (ed.) - 2015 - Springer.
  • Laws and Explanations in Biology and Chemistry: Philosophical Perspectives and Educational Implications.Zoubeida R. Dagher & Sibel Erduran - 2014 - In Michael R. Matthews (ed.), International Handbook of Research in History, Philosophy and Science Teaching. Springer. pp. 1203-1233.
    This chapter utilises scholarship in philosophy of biology and philosophy of chemistry to produce meaningful implications for biology and chemistry education. The primary purpose for studying philosophical literature is to identify different perspectives on the nature of laws and explanations within these disciplines. The goal is not to resolve ongoing debates about the nature of laws and explanations but to consider their multiple forms and purposes in ways that promote deep and practical understanding of biological and chemical knowledge in educational (...)
    Direct download  
     
    Export citation  
     
    Bookmark   3 citations  
  • Wiring Optimization Explanation in Neuroscience: What is Special About It?Sergio Daniel Barberis - 2019 - Theoria : An International Journal for Theory, History and Fundations of Science 1 (34):89-110.
    This paper examines the explanatory distinctness of wiring optimization models in neuroscience. Wiring optimization models aim to represent the organizational features of neural and brain systems as optimal (or near-optimal) solutions to wiring optimization problems. My claim is that that wiring optimization models provide design explanations. In particular, they support ideal interventions on the decision variables of the relevant design problem and assess the impact of such interventions on the viability of the target system.
    Direct download  
     
    Export citation  
     
    Bookmark  
  • Revisiting Generality in the Life Sciences: Systems Biology and the Quest for General Principles.Sara Green - unknown
    Due to the variation, contingency and complexity of living systems, biology is often taken to be a science without fundamental theories, laws or general principles. I revisit this question in light of the quest for design principles in systems biology and show that different views can be reconciled if we distinguish between different types of generality. The philosophical literature has primarily focused on generality of specific models or explanations, or on the heuristic role of abstraction. This paper takes a different (...)
    No categories
    Direct download (2 more)  
     
    Export citation  
     
    Bookmark   1 citation  
  • Environmental Ethics.Roberta L. Millstein - 2013 - In K. Kampourakis (ed.), The Philosophy of Biology: A Companion for Educators. Springer.
    A number of areas of biology raise questions about what is of value in the natural environment and how we ought to behave towards it: conservation biology, environmental science, and ecology, to name a few. Based on my experience teaching students from these and similar majors, I argue that the field of environmental ethics has much to teach these students. They come to me with pent-up questions and a feeling that more is needed to fully engage in their subjects, and (...)
    Direct download (4 more)  
     
    Export citation  
     
    Bookmark  
  • Systems Biology and Mechanistic Explanation.Ingo Brigandt, Sara Green & Maureen O'Malley - 2018 - In Stuart Glennan & Phyllis McKay Illari (eds.), The Routledge Handbook of Mechanisms and Mechanical Philosophy. New York: Routledge. pp. 362–374.
    We address the question of whether and to what extent explanatory and modelling strategies in systems biology are mechanistic. After showing how dynamic mathematical models are actually required for mechanistic explanations of complex systems, we caution readers against expecting all systems biology to be about mechanistic explanations. Instead, the aim may be to generate topological explanations that are not standardly mechanistic, or to arrive at design principles that explain system organization and behaviour in general, but not specific mechanisms. These abstraction (...)
    Direct download (4 more)  
     
    Export citation  
     
    Bookmark   7 citations