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On the Role of Theory and Modeling in Neuroscience

Daniel Levenstein, Veronica A. Alvarez, Asohan Amarasingham, Habiba Azab, Zhe S. Chen, Richard C. Gerkin, Andrea Hasenstaub, Ramakrishnan Iyer, Renaud B. Jolivet, Sarah Marzen, Joseph D. Monaco, Astrid A. Prinz, Salma Quraishi, Fidel Santamaria, Sabyasachi Shivkumar, Matthew F. Singh, Roger Traub, Farzan Nadim, Horacio G. Rotstein and A. David Redish
Journal of Neuroscience 15 February 2023, 43 (7) 1074-1088; https://doi.org/10.1523/JNEUROSCI.1179-22.2022
Daniel Levenstein
1Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
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Veronica A. Alvarez
2Laboratory on Neurobiology of Compulsive Behaviors, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland 20892
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  • ORCID record for Veronica A. Alvarez
Asohan Amarasingham
3Departments of Mathematics and Biology, City College and the Graduate Center, City University of New York, New York, New York 10032
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Habiba Azab
4Department of Neuroscience, Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota 55455
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Zhe S. Chen
5Department of Psychiatry, Neuroscience & Physiology, New York University School of Medicine, New York, New York, 10016
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Richard C. Gerkin
6School of Life Sciences, Arizona State University, Tempe, Arizona 85281
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Andrea Hasenstaub
7Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, California 94115
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Ramakrishnan Iyer
8Allen Institute for Brain Science, Seattle, Washington 98109
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Renaud B. Jolivet
9Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands
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Sarah Marzen
10W. M. Keck Science Department, Pitzer, Scripps, and Claremont McKenna Colleges, Claremont, California 91711
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Joseph D. Monaco
11Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218
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Astrid A. Prinz
12Department of Biology, Emory University, Atlanta, Georgia 30322
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Salma Quraishi
13Neuroscience, Developmental and Regnerative Biology Department, University of Texas at San Antonio, San Antonio, Texas 78249
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Fidel Santamaria
13Neuroscience, Developmental and Regnerative Biology Department, University of Texas at San Antonio, San Antonio, Texas 78249
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Sabyasachi Shivkumar
14Brain and Cognitive Sciences, University of Rochester, Rochester, New York 14627
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Matthew F. Singh
15Department of Psychological & Brain Sciences, Department of Electrical & Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63112
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Roger Traub
16IBM T.J. Watson Research Center, AI Foundations, Yorktown Heights, New York 10598
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Farzan Nadim
1Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
7Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, California 94115
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Horacio G. Rotstein
1Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
7Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, California 94115
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A. David Redish
18Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455
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  • Forging Connections: Uniting Neuroscience and Philosophy of Science
    Marcin Milkowski and Daniel Kostic
    Submitted on: 16 June 2023
  • Submitted on: (16 June 2023)
    Page navigation anchor for Forging Connections: Uniting Neuroscience and Philosophy of Science
    Forging Connections: Uniting Neuroscience and Philosophy of Science
    • Marcin Milkowski, Philosopher of Science, Institute of Philosophy and Sociology, Polish Academy of Sciences
    • Other Contributors:
      • Daniel Kostic

    Levenstein et al. aptly highlight some of the foundational issues in theoretical neuroscience, such as the role of abstraction and idealization in providing scientific explanations and understanding, and distinguishing under which conditions neuroscientific models provide genuine explanations, or mere descriptions, predictions, or control.

    The authors rightly emphasize that philosophers of science can also gain valuable insights from the vast body of neuroscience literature, by employing methods of digital humanities, such as text mining, in line with the cognitive metascience approach (Miłkowski, 2023).

    Conversely, neuroscientists can benefit from the latest research in philosophy of science, particularly on the epistemic norms of diverse kinds of explanations in neuroscience, e.g., topological (Kostić, 2020), computational (Miłkowski, 2013; Chirimuuta, 2018), dynamical (Favela, 2020), and functional (Egan, 2017). Understanding the diverse goals of theories is conducive to fruitful exploratory and explanatory scientific practice. Some forms of scientific understanding are not always grounded in explanations, but also in diverse theoretical representations, e.g., diagrams, taxonomies, and diagnostic manuals (Miłkowski, 2023). Philosophical theories of understanding can also integrate different kinds of explanations in a single framework (Khalifa et al., 2022).

    The need for these interdisciplinary connections is particularly vivid in the case of net...

    Show More

    Levenstein et al. aptly highlight some of the foundational issues in theoretical neuroscience, such as the role of abstraction and idealization in providing scientific explanations and understanding, and distinguishing under which conditions neuroscientific models provide genuine explanations, or mere descriptions, predictions, or control.

    The authors rightly emphasize that philosophers of science can also gain valuable insights from the vast body of neuroscience literature, by employing methods of digital humanities, such as text mining, in line with the cognitive metascience approach (Miłkowski, 2023).

    Conversely, neuroscientists can benefit from the latest research in philosophy of science, particularly on the epistemic norms of diverse kinds of explanations in neuroscience, e.g., topological (Kostić, 2020), computational (Miłkowski, 2013; Chirimuuta, 2018), dynamical (Favela, 2020), and functional (Egan, 2017). Understanding the diverse goals of theories is conducive to fruitful exploratory and explanatory scientific practice. Some forms of scientific understanding are not always grounded in explanations, but also in diverse theoretical representations, e.g., diagrams, taxonomies, and diagnostic manuals (Miłkowski, 2023). Philosophical theories of understanding can also integrate different kinds of explanations in a single framework (Khalifa et al., 2022).

    The need for these interdisciplinary connections is particularly vivid in the case of network models that are increasingly being used in neuroscience (Kostić et al., 2020), and especially when it comes to evaluating their explanatory power (Kostić, 2020; Kostić and Khalifa, 2023).

    In conclusion, we strongly support Levenstein et al.'s call for greater collaboration between philosophers of science and neuroscientists on the foundational issues in neuroscience. Embracing this interdisciplinary approach is essential for advancing our knowledge of the brain and its function.

    Chirimuuta M (2018) Explanation in Computational Neuroscience: Causal and Non-causal. Br J Philos Sci 69:849–880.
    Egan F (2017) Function-Theoretic Explanation and the Search for Neural Mechanisms. In: Explanation and Integration in Mind and Brain Science (Kaplan DM, ed), pp 0. Oxford University Press. Available at: https://doi.org/10.1093/oso/9780199685509.003.0007 [Accessed June 16, 2023].
    Favela LH (2020) Dynamical systems theory in cognitive science and neuroscience. Philosophy Compass 15:e12695.
    Khalifa K, Islam F, Gamboa JP, Wilkenfeld DA, Kostić D (2022) Integrating Philosophy of Understanding With the Cognitive Sciences. Frontiers in Systems Neuroscience 16 Available at: https://www.frontiersin.org/articles/10.3389/fnsys.2022.764708 [Accessed June 16, 2023].
    Kostić D (2020) General theory of topological explanations and explanatory asymmetry. Philosophical Transactions of the Royal Society B: Biological Sciences 375:20190321.
    Kostić D, Hilgetag CC, Tittgemeyer M (2020) Unifying the essential concepts of biological networks: biological insights and philosophical foundations. Philosophical Transactions of the Royal Society B: Biological Sciences 375:20190314.
    Kostić D, Khalifa K (2023) Decoupling Topological Explanations from Mechanisms. Philosophy of Science 90:245–268.
    Miłkowski M (2013) Explaining the Computational Mind. Cambridge, Mass.: MIT Press.
    Miłkowski M (2023) Cognitive Metascience: A New Approach to the Study of Theories. Available at: https://psyarxiv.com/xvyz3/ [Accessed April 13, 2023].

    Show Less
    Competing Interests: None declared.
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Journal of Neuroscience
Vol. 43, Issue 7
15 Feb 2023
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On the Role of Theory and Modeling in Neuroscience
Daniel Levenstein, Veronica A. Alvarez, Asohan Amarasingham, Habiba Azab, Zhe S. Chen, Richard C. Gerkin, Andrea Hasenstaub, Ramakrishnan Iyer, Renaud B. Jolivet, Sarah Marzen, Joseph D. Monaco, Astrid A. Prinz, Salma Quraishi, Fidel Santamaria, Sabyasachi Shivkumar, Matthew F. Singh, Roger Traub, Farzan Nadim, Horacio G. Rotstein, A. David Redish
Journal of Neuroscience 15 February 2023, 43 (7) 1074-1088; DOI: 10.1523/JNEUROSCI.1179-22.2022

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On the Role of Theory and Modeling in Neuroscience
Daniel Levenstein, Veronica A. Alvarez, Asohan Amarasingham, Habiba Azab, Zhe S. Chen, Richard C. Gerkin, Andrea Hasenstaub, Ramakrishnan Iyer, Renaud B. Jolivet, Sarah Marzen, Joseph D. Monaco, Astrid A. Prinz, Salma Quraishi, Fidel Santamaria, Sabyasachi Shivkumar, Matthew F. Singh, Roger Traub, Farzan Nadim, Horacio G. Rotstein, A. David Redish
Journal of Neuroscience 15 February 2023, 43 (7) 1074-1088; DOI: 10.1523/JNEUROSCI.1179-22.2022
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Jump to comment:

  • Forging Connections: Uniting Neuroscience and Philosophy of Science
    Marcin Milkowski and Daniel Kostic
    Published on: 16 June 2023
  • Published on: (16 June 2023)
    Page navigation anchor for Forging Connections: Uniting Neuroscience and Philosophy of Science
    Forging Connections: Uniting Neuroscience and Philosophy of Science
    • Marcin Milkowski, Philosopher of Science, Institute of Philosophy and Sociology, Polish Academy of Sciences
    • Other Contributors:
      • Daniel Kostic

    Levenstein et al. aptly highlight some of the foundational issues in theoretical neuroscience, such as the role of abstraction and idealization in providing scientific explanations and understanding, and distinguishing under which conditions neuroscientific models provide genuine explanations, or mere descriptions, predictions, or control.

    The authors rightly emphasize that philosophers of science can also gain valuable insights from the vast body of neuroscience literature, by employing methods of digital humanities, such as text mining, in line with the cognitive metascience approach (Miłkowski, 2023).

    Conversely, neuroscientists can benefit from the latest research in philosophy of science, particularly on the epistemic norms of diverse kinds of explanations in neuroscience, e.g., topological (Kostić, 2020), computational (Miłkowski, 2013; Chirimuuta, 2018), dynamical (Favela, 2020), and functional (Egan, 2017). Understanding the diverse goals of theories is conducive to fruitful exploratory and explanatory scientific practice. Some forms of scientific understanding are not always grounded in explanations, but also in diverse theoretical representations, e.g., diagrams, taxonomies, and diagnostic manuals (Miłkowski, 2023). Philosophical theories of understanding can also integrate different kinds of explanations in a single framework (Khalifa et al., 2022).

    The need for these interdisciplinary connections is particularly vivid in the case of net...

    Show More

    Levenstein et al. aptly highlight some of the foundational issues in theoretical neuroscience, such as the role of abstraction and idealization in providing scientific explanations and understanding, and distinguishing under which conditions neuroscientific models provide genuine explanations, or mere descriptions, predictions, or control.

    The authors rightly emphasize that philosophers of science can also gain valuable insights from the vast body of neuroscience literature, by employing methods of digital humanities, such as text mining, in line with the cognitive metascience approach (Miłkowski, 2023).

    Conversely, neuroscientists can benefit from the latest research in philosophy of science, particularly on the epistemic norms of diverse kinds of explanations in neuroscience, e.g., topological (Kostić, 2020), computational (Miłkowski, 2013; Chirimuuta, 2018), dynamical (Favela, 2020), and functional (Egan, 2017). Understanding the diverse goals of theories is conducive to fruitful exploratory and explanatory scientific practice. Some forms of scientific understanding are not always grounded in explanations, but also in diverse theoretical representations, e.g., diagrams, taxonomies, and diagnostic manuals (Miłkowski, 2023). Philosophical theories of understanding can also integrate different kinds of explanations in a single framework (Khalifa et al., 2022).

    The need for these interdisciplinary connections is particularly vivid in the case of network models that are increasingly being used in neuroscience (Kostić et al., 2020), and especially when it comes to evaluating their explanatory power (Kostić, 2020; Kostić and Khalifa, 2023).

    In conclusion, we strongly support Levenstein et al.'s call for greater collaboration between philosophers of science and neuroscientists on the foundational issues in neuroscience. Embracing this interdisciplinary approach is essential for advancing our knowledge of the brain and its function.

    Chirimuuta M (2018) Explanation in Computational Neuroscience: Causal and Non-causal. Br J Philos Sci 69:849–880.
    Egan F (2017) Function-Theoretic Explanation and the Search for Neural Mechanisms. In: Explanation and Integration in Mind and Brain Science (Kaplan DM, ed), pp 0. Oxford University Press. Available at: https://doi.org/10.1093/oso/9780199685509.003.0007 [Accessed June 16, 2023].
    Favela LH (2020) Dynamical systems theory in cognitive science and neuroscience. Philosophy Compass 15:e12695.
    Khalifa K, Islam F, Gamboa JP, Wilkenfeld DA, Kostić D (2022) Integrating Philosophy of Understanding With the Cognitive Sciences. Frontiers in Systems Neuroscience 16 Available at: https://www.frontiersin.org/articles/10.3389/fnsys.2022.764708 [Accessed June 16, 2023].
    Kostić D (2020) General theory of topological explanations and explanatory asymmetry. Philosophical Transactions of the Royal Society B: Biological Sciences 375:20190321.
    Kostić D, Hilgetag CC, Tittgemeyer M (2020) Unifying the essential concepts of biological networks: biological insights and philosophical foundations. Philosophical Transactions of the Royal Society B: Biological Sciences 375:20190314.
    Kostić D, Khalifa K (2023) Decoupling Topological Explanations from Mechanisms. Philosophy of Science 90:245–268.
    Miłkowski M (2013) Explaining the Computational Mind. Cambridge, Mass.: MIT Press.
    Miłkowski M (2023) Cognitive Metascience: A New Approach to the Study of Theories. Available at: https://psyarxiv.com/xvyz3/ [Accessed April 13, 2023].

    Show Less
    Competing Interests: None declared.

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