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  1. 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 (...)
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  • Emergent Properties.Hong Yu Wong - 2015 - Stanford Encyclopedia of Philosophy.
    Emergence is a notorious philosophical term of art. A variety of theorists have appropriated it for their purposes ever since George Henry Lewes gave it a philosophical sense in his 1875 Problems of Life and Mind. We might roughly characterize the shared meaning thus: emergent entities (properties or substances) ‘arise’ out of more fundamental entities and yet are ‘novel’ or ‘irreducible’ with respect to them. (For example, it is sometimes said that consciousness is an emergent property of the brain.) Each (...)
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  • 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 (...)
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  • Heuristic Approaches to Models and Modeling in Systems Biology.Miles MacLeod - 2016 - Biology and Philosophy 31 (3):353-372.
    Prediction and control sufficient for reliable medical and other interventions are prominent aims of modeling in systems biology. The short-term attainment of these goals has played a strong role in projecting the importance and value of the field. In this paper I identify the standard models must meet to achieve these objectives as predictive robustness—predictive reliability over large domains. Drawing on the results of an ethnographic investigation and various studies in the systems biology literature, I explore four current obstacles to (...)
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  • Evolutionary Systems Biology: What It is and Why It Matters.Orkun S. Soyer & Maureen A. O'Malley - 2013 - Bioessays 35 (8):696-705.
  • Systems Biology Reveals Biology of Systems.Marta Bertolaso, Alessandro Giuliani & Laura De Gara - 2011 - Complexity 16 (6):10-16.
  • The Return of the Organism as a Fundamental Explanatory Concept in Biology.Daniel J. Nicholson - 2014 - Philosophy Compass 9 (5):347-359.
    Although it may seem like a truism to assert that biology is the science that studies organisms, during the second half of the twentieth century the organism category disappeared from biological theory. Over the past decade, however, biology has begun to witness the return of the organism as a fundamental explanatory concept. There are three major causes: (a) the realization that the Modern Synthesis does not provide a fully satisfactory understanding of evolution; (b) the growing awareness of the limits of (...)
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  • Gluing Life Together. Computer Simulation in the Life Sciences: An Introduction.Janina Wellmann - 2018 - History and Philosophy of the Life Sciences 40 (4):70.
    Over the course of the last three decades, computer simulations have become a major tool of doing science and engaging with the world, not least in an effort to predict and intervene in a future to come. Born in the context of the Second World War and the discipline of physics, simulations have long spread into most diverse fields of enquiry and technological application. This paper introduces a topical collection focussing on simulations in the life sciences. Echoing the current state (...)
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  • Systems Biology and the Integration of Mechanistic Explanation and Mathematical Explanation.Ingo Brigandt - 2013 - Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4):477-492.
    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 (...)
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  • Models, Mechanisms, and Coherence.Matteo Colombo, Stephan Hartmann & Robert van Iersel - 2015 - British Journal for the Philosophy of Science 66 (1):181-212.
    Life-science phenomena are often explained by specifying the mechanisms that bring them about. The new mechanistic philosophers have done much to substantiate this claim and to provide us with a better understanding of what mechanisms are and how they explain. Although there is disagreement among current mechanists on various issues, they share a common core position and a seeming commitment to some form of scientific realism. But is such a commitment necessary? Is it the best way to go about mechanistic (...)
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  • Evolutionary Developmental Biology and the Limits of Philosophical Accounts of Mechanistic Explanation.Ingo Brigandt - 2015 - In P.-A. Braillard & C. Malaterre (eds.), Explanation in Biology: An Enquiry into the Diversity of Explanatory Patterns in the Life Sciences. Springer. pp. 135–173.
    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 (...)
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  • Models in Systems Medicine.Jon Williamson - unknown
    Systems medicine is a promising new paradigm for discovering associations, causal relationships and mechanisms in medicine. But it faces some tough challenges that arise from the use of big data: in particular, the problem of how to integrate evidence and the problem of how to structure the development of models. I argue that objective Bayesian models offer one way of tackling the evidence integration problem. I also offer a general methodology for structuring the development of models, within which the objective (...)
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  • Model and movement: studying cell movement in early morphogenesis, 1900 to the present.Janina Wellmann - 2018 - History and Philosophy of the Life Sciences 40 (3):59.
    Morphogenesis is one of the fundamental processes of developing life. Gastrulation, especially, marks a period of major translocations and bustling rearrangements of cells that give rise to the three germ layers. It was also one of the earliest fields in biology where cell movement and behaviour in living specimens were investigated. This article examines scientific attempts to understand gastrulation from the point of view of cells in motion. It argues that the study of morphogenesis in the twentieth century faced a (...)
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  • Bridging the Gap: Does Closure to Efficient Causation Entail Quantum-Like Attributes?José Raúl Naranjo - 2011 - Axiomathes 21 (2):315-330.
    This paper explores the similarities between the conceptual structure of quantum theory and relational biology as developed within the Rashevsky-Rosen-Louie school of theoretical biology. With this aim, generalized quantum theory and the abstract formalism of (M,R)-systems are briefly presented. In particular, the notion of organizational invariance and relational identity are formalized mathematically and a particular example is given. Several quantum-like attributes of Rosen’s complex systems such as complementarity and nonseparability are discussed. Taken together, this work emphasizes the possible role of (...)
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  • Enabling Conditions for 'Open-Ended Evolution'.Kepa Ruiz-Mirazo, Jon Umerez & Alvaro Moreno - 2008 - Biology and Philosophy 23 (1):67-85.
    In this paper we review and argue for the relevance of the concept of open-ended evolution in biological theory. Defining it as a process in which a set of chemical systems bring about an unlimited variety of equivalent systems that are not subject to any pre-determined upper bound of organizational complexity, we explain why only a special type of self-constructing, autonomous systems can actually implement it. We further argue that this capacity derives from the ‘dynamic decoupling’ (in its minimal or (...)
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  • Systems, Autopoietic.Leonardo Bich & Arantza Etxeberria - 2013 - In Dubitzsky, Wolkenhauer, Cho & Yokota (eds.), Encyclopedia of Systems Biology. New York: Springer. pp. 2110-2113.
    Definition The authors’ definition of the autopoietic system has evolved through the years. One of them states that an autopoietic system is organized (defined as a unity) as a network of processes of production (transformation and destruction) of components that produces the components which: (1) through their interactions and transformations regenerate and realize the network of processes (relations) that produced them; and (2) constitute it (the machine) as a concrete unity in the space in which they exist by specifying the (...)
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  • A Philosophical Perspective on Evolutionary Systems Biology.Maureen A. O’Malley, Orkun S. Soyer & Mark L. Siegal - 2015 - Biological Theory 10 (1):6-17.
    Evolutionary systems biology is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis. We locate these discussions in the context (...)
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