Abstract
Mathematical models applied in contemporary theoretical and systems biology are based on some implicit ontological assumptions about the nature of organisms. This article aims to show that real organisms reveal a logic of internal causality transcending the tacit logic of biological modeling. Systems biology has focused on models consisting of static systems of differential equations operating with fixed control parameters that are measured or fitted to experimental data. However, the structure of real organisms is a highly dynamic process, the internal causality of which can only be captured by continuously changing systems of equations. In addition, in real physiological settings kinetic parameters can vary by orders of magnitude, i.e., organisms vary the value of internal quantities that in models are represented by fixed control parameters. Both the plasticity of organisms and the state dependence of kinetic parameters adds indeterminacy to the picture and asks for a new statistical perspective. This requirement could be met by the arising Biological Statistical Mechanics project, which promises to do more justice to the nature of real organisms than contemporary modeling. This article concludes that Biological Statistical Mechanics allows for a wider range of organismic ontologies than does the tacitly followed ontology of contemporary theoretical and systems biology, which are implicitly and explicitly based on systems theory.
Highlights
On the Concept of the Organism10.3390/e24010066The term ‘organism’ first appears in biological texts in the late 17th century [1] (p. 777).Since the 19th century, it has represented a central concept of biology that together with the term ‘life’ defines the biological field of study
This article concludes that Biological Statistical Mechanics allows for a wider range of organismic ontologies than does the tacitly followed ontology of contemporary theoretical and systems biology, which are implicitly and explicitly based on systems theory
This article distinguishes between three successive levels of phenomenal analysis, in each of which the topic is treated on a higher level of abstraction: On the first and least abstract level, the term ‘organism’ refers to the body of a living being
Summary
The term ‘organism’ first appears in biological texts in the late 17th century [1] (p. 777). Departing from a critical consideration of mechanistic explanations within modern systems biology, which operate with differential equations, a ‘logic of systems biological mechanisms’ is formulated This logic can be seen as the abstract core of the system-ontological consideration of the organismic phenomenon. After the beginning of the decline of the gene-centered leveling of the concept of organism, both modern biology and the Anglo-Saxon philosophy of biology are increasingly dominated by different variants of systems-theoretical thinking This can be seen very clearly in the formalisms of systems biology. In view of this situation, the author is convinced that any attempt to introduce a mature logic of the organism on the basis of classical biophilosophy must begin with a critical examination of both systems-theoretical reductionism and the works of those philosophers of science, and in particular of biology, who follow the ‘New Mechanical. It aims to show the limits of systems-theoretical reductionism of the present in relation to this logic
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