•  34
    Despite numerous and increasing attempts to define what life is, there is no consensus on necessary and sufficient conditions for life. Accordingly, some scholars have questioned the value of definitions of life and encouraged scientists and philosophers alike to discard the project. As an alternative to this pessimistic conclusion, we argue that critically rethinking the nature and uses of definitions can provide new insights into the epistemic roles of definitions of life for different researc…Read more
  •  853
    Despite numerous and increasing attempts to define what life is, there is no consensus on necessary and sufficient conditions for life. Accordingly, some scholars have questioned the value of definitions of life and encouraged scientists and philosophers alike to discard the project. As an alternative to this pessimistic conclusion, we argue that critically rethinking the nature and uses of definitions can provide new insights into the epistemic roles of definitions of life for different researc…Read more
  •  512
    The Sum of the Parts: Large-Scale Modeling in Systems Biology
    Philosophy, Theory, and Practice in Biology 9 (10). 2017.
    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 livin…Read more
  •  87
    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 …Read more
  •  5
    Correction to: Precision medicine and the problem of structural injustice
    with Barbara Prainsack and Maya Sabatello
    Medicine, Health Care and Philosophy 27 (1): 133-133. 2024.
  •  11
    Precision medicine and the problem of structural injustice
    with Barbara Prainsack and Maya Sabatello
    Medicine, Health Care and Philosophy 26 (3): 433-450. 2023.
    Many countries currently invest in technologies and data infrastructures to foster precision medicine (PM), which is hoped to better tailor disease treatment and prevention to individual patients. But who can expect to benefit from PM? The answer depends not only on scientific developments but also on the willingness to address the problem of structural injustice. One important step is to confront the problem of underrepresentation of certain populations in PM cohorts via improved research inclu…Read more
  •  18
    Teaching philosophy of science that matters
    European Journal for Philosophy of Science 13 (2): 1-10. 2023.
  •  85
    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. T…Read more
  •  34
    Explanatory pluralism in biology
    Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 59 154-157. 2016.
  •  66
    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 expla…Read more
  •  7
    Book Forum
    Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 84 101325. 2020.
  •  84
    When one model is not enough: Combining epistemic tools in systems biology
    Studies in History and Philosophy of Biological and Biomedical Sciences 44 (2): 170-180. 2013.
    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 Rh…Read more
  •  21
    Top-down causation is often taken to be a metaphysically suspicious type of causation that is found in a few complex systems, such as in human mind-body relations. However, as Ellis and others have shown, top-down causation is ubiquitous in physics as well as in biology. Top-down causation occurs whenever specific dynamic behaviors are realized or selected among a broader set of possible lower-level states. Thus understood, the occurrence of dynamic and structural patterns in physical and biolog…Read more
  •  34
    Mesoscale modeling is often considered merely as a practical strategy used when information on lower-scale details is lacking, or when there is a need to make models cognitively or computationally tractable. Without dismissing the importance of practical constraints for modeling choices, we argue that mesoscale models should not just be considered as abbreviations or placeholders for more “complete” models. Because many systems exhibit different behaviors at various spatial and temporal scales, …Read more
  •  4
    The practical ethics of repurposing health data: how to acknowledge invisible data work and the need for prioritization
    with Line Hillersdal, Jette Holt, Klaus Hoeyer, and Sarah Wadmann
    Medicine, Health Care and Philosophy 26 (1): 119-132. 2023.
    Throughout the Global North, policymakers invest in large-scale integration of health-data infrastructures to facilitate the reuse of clinical data for administration, research, and innovation. Debates about the ethical implications of data repurposing have focused extensively on issues of patient autonomy and privacy. We suggest that it is time to scrutinize also how the everyday work of healthcare staff is affected by political ambitions of data reuse for an increasing number of purposes, and …Read more
  •  288
    The Quest for System-Theoretical Medicine in the COVID-19 Era
    with Felix Tretter, Olaf Wolkenhauer, Michael Meyer-Hermann, Johannes W. Dietrich, James Marcum, and Wolfram Weckwerth
    Frontiers in Medicine 8 640974. 2021.
    Precision medicine and molecular systems medicine (MSM) are highly utilized and successful approaches to improve understanding, diagnosis, and treatment of many diseases from bench-to-bedside. Especially in the COVID-19 pandemic, molecular techniques and biotechnological innovation have proven to be of utmost importance for rapid developments in disease diagnostics and treatment, including DNA and RNA sequencing technology, treatment with drugs and natural products and vaccine development. The C…Read more
  •  18
    Adapting practice-based philosophy of science to teaching of science students
    with Hanne Andersen, Kristian Danielsen, Claus Emmeche, Christian Joas, Mikkel Willum Johansen, Caio Nagayoshi, Joeri Witteveen, and Henrik Kragh Sørensen
    European Journal for Philosophy of Science 11 (3): 1-18. 2021.
    The “practice turn” in philosophy of science has strengthened the connections between philosophy and scientific practice. Apart from reinvigorating philosophy of science, this also increases the relevance of philosophical research for science, society, and science education. In this paper, we reflect on our extensive experience with teaching mandatory philosophy of science courses to science students from a range of programs at University of Copenhagen. We highlight some of the lessons we have l…Read more
  •  26
    Aging biomarkers and the measurement of health and risk
    with Line Hillersdal
    History and Philosophy of the Life Sciences 43 (1): 1-23. 2021.
    Prevention of age-related disorders is increasingly in focus of health policies, and it is hoped that early intervention on processes of deterioration can promote healthier and longer lives. New opportunities to slow down the aging process are emerging with new fields such as personalized nutrition. Data-intensive research has the potential to improve the precision of existing risk factors, e.g., to replace coarse-grained markers such as blood cholesterol with more detailed multivariate biomarke…Read more
  •  12
    Mouse avatars of human cancers: the temporality of translation in precision oncology
    with Mie S. Dam and Mette N. Svendsen
    History and Philosophy of the Life Sciences 43 (1): 1-22. 2021.
    Patient-derived xenografts are currently promoted as new translational models in precision oncology. PDXs are immunodeficient mice with human tumors that are used as surrogate models to represent specific types of cancer. By accounting for the genetic heterogeneity of cancer tumors, PDXs are hoped to provide more clinically relevant results in preclinical research. Further, in the function of so-called “mouse avatars”, PDXs are hoped to allow for patient-specific drug testing in real-time. This …Read more
  •  81
    Biology meets Physics: Reductionism and Multi-scale Modeling of Morphogenesis
    Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 7161 20-34. 2017.
    A common reductionist assumption is that macro-scale behaviors can be described "bottom-up" if only sufficient details about lower-scale processes are available. The view that an "ideal" or "fundamental" physics would be sufficient to explain all macro-scale phenomena has been met with criticism from philosophers of biology. Specifically, scholars have pointed to the impossibility of deducing biological explanations from physical ones, and to the irreducible nature of distinctively biological pr…Read more
  •  75
    Tracing Organizing Principles: Learning from the History of Systems Biology
    with Olaf Wolkenhauer
    History and Philosophy of the Life Sciences 35 (4): 553-576. 2013.
    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 app…Read more
  •  107
    Systems Biology and Mechanistic Explanation
    with Ingo Brigandt and Maureen O'Malley
    In Stuart Glennan & Phyllis McKay Illari (eds.), The Routledge Handbook of Mechanisms and Mechanical Philosophy, Routledge. pp. 362-374. 2017.
    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 organizat…Read more