Results for 'Systems biology'

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  1. 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. (...)
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  2.  25
    Explanatory Integration Challenges in Evolutionary Systems Biology.Sara Green, Melinda Fagan & Johannes Jaeger - 2015 - Biological Theory 10 (1):18-35.
    Evolutionary systems biology aims to integrate methods from systems biology and evolutionary biology to go beyond the current limitations in both fields. This article clarifies some conceptual difficulties of this integration project, and shows how they can be overcome. The main challenge we consider involves the integration of evolutionary biology with developmental dynamics, illustrated with two examples. First, we examine historical tensions between efforts to define general evolutionary principles and articulation of detailed mechanistic explanations (...)
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  3. The Epistemology of Causal Selection: Insights From Systems Biology.Beckett Sterner - forthcoming - In C. Kenneth Waters (ed.), Causal Reasoning in Biology. University of Minnesota Press.
    Among the many causes of an event, how do we distinguish the important ones? Are there ways to distinguish among causes on principled grounds that integrate both practical aims and objective knowledge? Psychologist Tania Lombrozo has suggested that causal explanations “identify factors that are ‘exportable’ in the sense that they are likely to subserve future prediction and intervention” (Lombrozo 2010, 327). Hence portable causes are more important precisely because they provide objective information to prediction and intervention as practical aims. However, (...)
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  4.  37
    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 (...)
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  5.  51
    Systems Biology: Philosophical Foundations.Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.) - 2007 - Elsevier.
    Systems biology is a vigorous and expanding discipline, in many ways a successor to genomics and perhaps unprecendented in its combination of biology with a ...
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  6.  2
    The Sum of the Parts: Large-Scale Modeling in Systems Biology.Fridolin Gross & Sara Green - 2017 - Philosophy, Theory, and Practice in Biology 9 (10).
    Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole.” Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call “modular reductionism” and “bottom-up reductionism.” Much knowledge in molecular biology has been gained by decomposing living systems into functional modules (...)
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  7.  14
    Disciplinary Baptisms: A Comparison of the Naming Stories of Genetics, Molecular Biology, Genomics and Systems Biology.Alexander Powell, Maureen A. O'Malley, Staffan Mueller-Wille, Jane Calvert & John Dupré - 2007 - History and Philosophy of the Life Sciences 29 (1):5-32.
    Understanding how scientific activities use naming stories to achieve disciplinary status is important not only for insight into the past, but for evaluating current claims that new disciplines are emerging. In order to gain a historical understanding of how new disciplines develop in relation to these baptismal narratives, we compare two recently formed disciplines, systems biology and genomics, with two earlier related life sciences, genetics and molecular biology. These four disciplines span the twentieth century, a period in (...)
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  8.  18
    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 (...)
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    Interdisciplinary Problem- Solving: Emerging Modes in Integrative Systems Biology.Miles MacLeod & Nancy J. Nersessian - 2016 - European Journal for Philosophy of Science 6 (3):401-418.
    Integrative systems biology is an emerging field that attempts to integrate computation, applied mathematics, engineering concepts and methods, and biological experimentation in order to model large-scale complex biochemical networks. The field is thus an important contemporary instance of an interdisciplinary approach to solving complex problems. Interdisciplinary science is a recent topic in the philosophy of science. Determining what is philosophically important and distinct about interdisciplinary practices requires detailed accounts of problem-solving practices that attempt to understand how specific practices (...)
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  10.  57
    Robert Rosen's Work and Complex Systems Biology.I. C. Baianu - 2005 - Axiomathes 16 (1-2):25-34.
    Complex Systems Biology approaches are here considered from the viewpoint of Robert Rosen’s (M,R)-systems, Relational Biology and Quantum theory, as well as from the standpoint of computer modeling. Realizability and Entailment of (M,R)-systems are two key aspects that relate the abstract, mathematical world of organizational structure introduced by Rosen to the various physicochemical structures of complex biological systems. Their importance for understanding biological function and life itself, as well as for designing new strategies for (...)
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  11.  5
    Systems Biology and Predictive Neuroscience: A Double Helical Approach.Wiseman Harris - 2017 - Zygon 52 (2):516-537.
    This article explores the overlap between systems biology and predictive neuroscience, placing them in their larger context, the contemporary trend of bioinformatic convergence across the sciences. These two domains overlap with respect to their interest in data accumulation and data integration; their reliance on computational statistical correlation; and their translational goals, that is, producing practical fruits and applications from the interscientific cross-pollination that contemporary data-integrative approaches make possible. The interventions that such translational conversations generate are medical and social (...)
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  12.  25
    Systems Bioethics and Stem Cell Biology.Jason Scott Robert, Jane Maienschein & Manfred D. Laubichler - 2006 - Journal of Bioethical Inquiry 3 (1-2):19-31.
    The complexities of modern science are not adequately reflected in many bioethical discussions. This is especially problematic in highly contested cases where there is significant pressure to generate clinical applications fast, as in stem cell research. In those cases a more integrated approach to bioethics, which we call systems bioethics, can provide a useful framework to address ethical and policy issues. Much as systems biology brings together different experimental and methodological approaches in an integrative way, systems (...)
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  13.  8
    Systems Biology Reveals Biology of Systems.Marta Bertolaso, Alessandro Giuliani & Laura De Gara - 2011 - Complexity 16 (6):10-16.
  14.  10
    A Systems Biology View of Evolutionary Genetics.Jonathan Bard - 2010 - Bioessays 32 (7):559-563.
  15.  45
    Mechanistic Explanations and Models in Molecular Systems Biology.Fred C. Boogerd, Frank J. Bruggeman & Robert C. Richardson - 2013 - Foundations of Science 18 (4):725-744.
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  16.  21
    Systems Engineering Without an Engineer: Why We Need Systems Biology.C. Way Jeffrey & A. Silver Pamela - 2007 - Complexity 13 (2):22-29.
  17.  2
    Bioactive Peptides, Networks and Systems Biology.Kurt Boonen, John W. Creemers & Liliane Schoofs - 2009 - Bioessays 31 (3):300-314.
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  18.  52
    Some Thoughts on A. H. Louie's “More Than Life Itself: A Reflection on Formal Systems and Biology”. [REVIEW]Claudio Gutiérrez, Sebastián Jaramillo & Jorge Soto-Andrade - 2011 - Axiomathes 21 (3):439-454.
    We review and discuss A. H. Louie’s book “More than Life Itself: A Reflexion on Formal Systems and Biology” from an interdisciplinary viewpoint, involving both biology and mathematics, taking into account new developments and related theories.
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  19.  48
    Waddington Redux: Models and Explanation in Stem Cell and Systems Biology.Melinda Fagan - 2012 - Biology and Philosophy 27 (2):179-213.
    Stem cell biology and systems biology are two prominent new approaches to studying cell development. In stem cell biology, the predominant method is experimental manipulation of concrete cells and tissues. Systems biology, in contrast, emphasizes mathematical modeling of cellular systems. For scientists and philosophers interested in development, an important question arises: how should the two approaches relate? This essay proposes an answer, using the model of Waddington’s landscape to triangulate between stem cell and (...)
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  20.  41
    Systems Biology and Mechanistic Explanation.Ingo Brigandt, Sara Green & Maureen O'Malley - forthcoming - 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 (...)
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  21.  33
    Calculating Life? Duelling Discourses in Interdisciplinary Systems Biology.Jane Calvert & Joan H. Fujimura - 2011 - Studies in History and Philosophy of Science Part C 42 (2):155-163.
    A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores (...)
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  22.  18
    Coupling Simulation and Experiment: The Bimodal Strategy in Integrative Systems Biology.Miles MacLeod & Nancy J. Nersessian - 2013 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4):572-584.
    The importation of computational methods into biology is generating novel methodological strategies for managing complexity which philosophers are only just starting to explore and elaborate. This paper aims to enrich our understanding of methodology in integrative systems biology, which is developing novel epistemic and cognitive strategies for managing complex problem-solving tasks. We illustrate this through developing a case study of a bimodal researcher from our ethnographic investigation of two systems biology research labs. The researcher constructed (...)
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  23.  30
    When One Model is Not Enough: Combining Epistemic Tools in Systems Biology.Sara Green - 2013 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (2):170-180.
    In recent years, the philosophical focus of the modeling literature has shifted from descriptions of general properties of models to an interest in different model functions. It has been argued that the diversity of models and their correspondingly different epistemic goals are important for developing intelligible scientific theories . However, more knowledge is needed on how a combination of different epistemic means can generate and stabilize new entities in science. This paper will draw on Rheinberger’s practice-oriented account of knowledge production. (...)
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  24.  29
    The Study of Socioethical Issues in Systems Biology.Maureen O'Malley, Jane Calvert & John Dupré - 2007 - American Journal of Bioethics 7 (4):67-78.
    Systems biology is the rapidly growing and heavily funded successor science to genomics. Its mission is to integrate extensive bodies of molecular data into a detailed mathematical understanding of all life processes, with an ultimate view to their prediction and control. Despite its high profile and widespread practice, there has so far been almost no bioethical attention paid to systems biology and its potential social consequences. We outline some of systems biology's most important socioethical (...)
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  25.  59
    Ins and Outs of Systems Biology Vis-À-Vis Molecular Biology: Continuation or Clear Cut?Philippe De Backer, Danny De Waele & Linda Van Speybroeck - 2010 - Acta Biotheoretica 58 (1):15-49.
    The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems (...) ‘revolutionizes’ molecular biology and ‘transcends’ its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology’s use of modelling and bioinformatics, and by its scale enlargement. (shrink)
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  26.  12
    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 (...)
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  27.  44
    Tracing Organizing Principles-Learning From the History of Systems Biology.Sara Green & Olaf Wolkenhauer - forthcoming - History and Philosophy of the Life Sciences.
    With the emergence of systems biology the notion of organizing principles is being highlighted as a key research aim. Researchers attempt to ‘reverse engineer’ the functional organization of biological systems using methodologies from mathematics, engineering and computer science while taking advantage of data produced by new experimental techniques. While systems biology is a relatively new approach, the quest for general principles of biological organization dates back to systems theoretic approaches in early and mid-20th century. (...)
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  28.  15
    Towards Philosophical Foundations of Systems Biology: Introduction.Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff - 2007 - In Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.), Systems Biology: Philosophical Foundations. Elsevier.
  29.  1
    Systems Biology and the Integration of Mechanistic Explanation and Mathematical Explanation.Ingo Brigandt - 2013 - Studies in History and Philosophy of Science Part C 44 (4a):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. (...)
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  30.  5
    The Creative Industry of Integrative Systems Biology.Miles MacLeod & Nancy J. Nersessian - 2013 - Mind and Society 12 (1):35-48.
    Integrative systems biology is among the most innovative fields of contemporary science, bringing together scientists from a range of diverse backgrounds and disciplines to tackle biological complexity through computational and mathematical modeling. The result is a plethora of problem-solving techniques, theoretical perspectives, lab-structures and organizations, and identity labels that have made it difficult for commentators to pin down precisely what systems biology is, philosophically or sociologically. In this paper, through the ethnographic investigation of two ISB laboratories, (...)
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  31.  23
    On Building Reliable Pictures with Unreliable Data: An Evolutionary and Developmental Coda for the New Systems Biology.William C. Wimsatt - 2007 - In Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.), Systems Biology: Philosophical Foundations. Elsevier. pp. 103--20.
  32.  9
    The Conceptual Challenge of Systems Biology.Linda Van Speybroeck, Philippe De Backer, Joris Van Poucke & Danny De Waele - 2005 - Bioessays 27 (12):1305-1307.
    Report of the symposium 'Towards a Philosophy of Systems Biology' held at the Vrije Universiteit of Amsterdam (VUA), the Netherlands, from 2 to 3 June 2005.
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  33.  20
    Theories, Models, and Equations in Systems Biology.Kenneth F. Schaffner - 2007 - In Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.), Systems Biology: Philosophical Foundations. Elsevier. pp. 145--162.
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  34.  9
    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 (...)
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  35.  9
    Afterthoughts as Foundations for Systems Biology.Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff - 2007 - In Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.), Systems Biology: Philosophical Foundations. Elsevier.
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  36.  17
    Systems Biology: At Last an Integrative Wet and Dry Biology.Frank J. Bruggeman - 2007 - Biological Theory 2 (2):183-188.
    The progress of the molecular biosciences has been so enormous that a discipline studying how cellular functioning emerges out of the behaviors of their molecular constituents has become reality. Systems biology studies cells as spatiotemporal networks of interacting molecules using an integrative approach of theory , experimental biology , and quantitative network-wide analytical measurement . Its aim is to understand how molecules jointly bring about life. Systems biology is rapidly discovering principles governing the functioning of (...)
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  37.  1
    Coupling Simulation and Experiment: The Bimodal Strategy in Integrative Systems Biology.Miles Macleod & Nancy Nersessian - 2013 - Studies in History and Philosophy of Science Part C 44 (4a):572-584.
    The importation of computational methods into biology is generating novel methodological strategies for managing complexity which philosophers are only just starting to explore and elaborate. This paper aims to enrich our understanding of methodology in integrative systems biology, which is developing novel epistemic and cognitive strategies for managing complex problem-solving tasks. We illustrate this through developing a case study of a bimodal researcher from our ethnographic investigation of two systems biology research labs. The researcher constructed (...)
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  38.  6
    A Day of Systems and Synthetic Biology for Non‐Experts.Andrew Moore - 2009 - Bioessays 31 (1):119-124.
  39.  3
    Towards a Constructivist Systems Biology? Review Of: F. C. Boogerd Et Al. (Eds.) (2006) Systems Biology.H. Goorhuis - 2007 - Constructivist Foundations 3 (1):57-57.
    Summary: Based on the book, the overall impression is that systems biology struggles with the limits of first-order cybernetics and tries to overcome it by mixing bottom up and top down methods from classical approaches such as genetics, molecular biology and enzymology. However, the contributors avoid the step from first-order to second-order cybernetics.
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  40.  8
    Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity.Sara Green, Maria Şerban, Raphael Scholl, Nicholaos Jones, Ingo Brigandt & William Bechtel - 2017 - Synthese.
    The increasing application of network models to interpret biological systems raises a number of important methodological and epistemological questions. What novel insights can network analysis provide in biology? Are network approaches an extension of or in conflict with mechanistic research strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples (...)
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  41.  26
    The Roles of Integration in Molecular Systems Biology.Maureen A. O'Malley & Orkun S. Soyer - 2012 - Studies in History and Philosophy of Science Part C 43 (1):58-68.
  42.  11
    Evolution and RNA Relics. A Systems Biology View.Jacques Demongeot, Nicolas Glade & Andrés Moreira - 2008 - Acta Biotheoretica 56 (1-2):5-25.
    The genetic code has evolved from its initial non-degenerate wobble version until reaching its present state of degeneracy. By using the stereochemical hypothesis, we revisit the problem of codon assignations to the synonymy classes of amino-acids. We obtain these classes with a simple classifier based on physico-chemical properties of nucleic bases, like hydrophobicity and molecular weight. Then we propose simple RNA ring structures that present, overlap included, one and only one codon by synonymy class as solutions of a combinatory variational (...)
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  43.  12
    Genomics, "Discovery Science," Systems Biology, and Causal Explanation: What Really Works?Eric H. Davidson - 2015 - Perspectives in Biology and Medicine 58 (2):165-181.
    In my field, animal developmental biology, and in what could be regarded as its “deep time derivative,” the evolutionary biology of the animal body plan, there exist two kinds of experimentally supported causal explanation. These can be described as “rooted” and “unrooted.” Rooted causal explanation provides logical links to and from the genomic regulatory code, extending right into the genomic sequences that control regulatory gene expression. The genomic regulatory code ultimately determines the developmental process in a direct way, (...)
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  44.  41
    Fundamental Issues in Systems Biology.Maureen A. O'Malley & John Dupré - 2005 - Bioessays 27 (12):1270-1276.
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  45.  20
    Mechanistic Explanation in Systems Biology: Cellular Networks.Dana Matthiessen - 2017 - British Journal for the Philosophy of Science 68 (1):1-25.
    It is argued that once biological systems reach a certain level of complexity, mechanistic explanations provide an inadequate account of many relevant phenomena. In this article, I evaluate such claims with respect to a representative programme in systems biological research: the study of regulatory networks within single-celled organisms. I argue that these networks are amenable to mechanistic philosophy without need to appeal to some alternate form of explanation. In particular, I claim that we can understand the mathematical modelling (...)
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  46.  32
    Putting the Systems Back Into Systems Biology.Athel Cornish-Bowden - 2006 - Perspectives in Biology and Medicine 49 (4):475-489.
  47.  28
    Building Simulations From the Ground Up: Modeling and Theory in Systems Biology.Miles MacLeod & Nancy J. Nersessian - 2013 - Philosophy of Science 80 (4):533-556.
  48.  35
    Health as Intra-Systemic Integrity: Rethinking the Foundations of Systems Biology and Nanomedicine.George Khushf - 2008 - Perspectives in Biology and Medicine 51 (3):432-449.
  49. Molecular and Systems Biology and Bioethics.Jason Scott Robert - 2007 - In David L. Hull & Michael Ruse (eds.), The Cambridge Companion to the Philosophy of Biology. Cambridge University Press.
  50.  38
    Mechanistic Explanation in Systems Biology: Cellular Networks.D. Matthiessen - 2015 - British Journal for the Philosophy of Science:axv011.
    It is argued that once biological systems reach a certain level of complexity, mechanistic explanations provide an inadequate account of many relevant phenomena. In this article, I evaluate such claims with respect to a representative programme in systems biological research: the study of regulatory networks within single-celled organisms. I argue that these networks are amenable to mechanistic philosophy without need to appeal to some alternate form of explanation. In particular, I claim that we can understand the mathematical modelling (...)
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