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Osimani B., Poellinger R. (2020) A Protocol for Model Validation and Causal Inference from Computer Simulation. In: Bertolaso M., Sterpetti F. (eds) A Critical Reflection on Automated Science. Human Perspectives in Health Sciences and Technology, vol 1. Springer, Cham. https://doi.org/10.1007/978-3-030-25001-0_9

Osimani, Barbara and Poellinger, Roland (2020) Osimani B., Poellinger R. (2020) A Protocol for Model Validation and Causal Inference from Computer Simulation. In: Bertolaso M., Sterpetti F. (eds) A Critical Reflection on Automated Science. Human Perspectives in Health Sciences and Technology, vol 1. Springer, Cham. https://doi.org/10.1007/978-3-030-25001-0_9. [Preprint]

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Abstract

The philosophical literature on modelling is increasingly vast, however clear formal analyses of computational modelling in systems biology are still lacking. We present a general, theoretical scheme which (i) visualizes the development and repeated refinement of a computer simulation, (ii) explicates the relation between different key concepts in modelling and simulation, and (iii) facilitates tracing the epistemological dynamics of model validation. To illustrate and motivate our conceptual scheme, we analyse a case study, the discovery of the functional properties of a specific protein, E-cadherin, which seems to have a key role in metastatic processes by way of influencing cell growth and proliferation signalling. To this end we distinguish two types of causal claims inferred from a computer simulation: (i) causal claims as plain combinations of basic rules (capturing the causal interplay of atomic behaviour) and (ii) causal claims on the level of emergent phenomena (tracing population dynamics). In formulating a protocol for model validation and causal inference, we show how, although such macro-level phenomena cannot be subjected to direct causal tests qua intervention (as, e.g., formulated in interventionist causal theories), they possibly suggest further manipulation tests at the basic micro-level. We thereby elucidate the micro-macro-level interaction in systems biology.


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Item Type: Preprint
Creators:
CreatorsEmailORCID
Osimani, Barbarabarbaraosimani@gmail.com
Poellinger, RolandRoland.Poellinger@outlook.com0000-0002-0487-4034
Keywords: Systems biology Micro-macro-level interaction Computer simulation Model validation Epistemology Emergent phenomena Causal inference
Subjects: Specific Sciences > Biology
Specific Sciences > Biology > Systematics
General Issues > Causation
General Issues > Computer Simulation
General Issues > Confirmation/Induction
General Issues > Evidence
General Issues > Formal Learning Theory
General Issues > History of Science Case Studies
Specific Sciences > Medicine
General Issues > Models and Idealization
Depositing User: Prof. Barbara Osimani
Date Deposited: 27 Jan 2021 15:13
Last Modified: 27 Jan 2021 15:13
Item ID: 18638
Subjects: Specific Sciences > Biology
Specific Sciences > Biology > Systematics
General Issues > Causation
General Issues > Computer Simulation
General Issues > Confirmation/Induction
General Issues > Evidence
General Issues > Formal Learning Theory
General Issues > History of Science Case Studies
Specific Sciences > Medicine
General Issues > Models and Idealization
Date: 2020
URI: https://philsci-archive-dev.library.pitt.edu/id/eprint/18638

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