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The Differential Method and the Causal Incompleteness of Programming Theory in Molecular Biology

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Abstract

The “DNA is a program” metaphor is still widely used in Molecular Biology and its popularization. There are good historical reasons for the use of such a metaphor or theoretical model. Yet we argue that both the metaphor and the model are essentially inadequate also from the point of view of Physics and Computer Science. Relevant work has already been done, in Biology, criticizing the programming paradigm. We will refer to empirical evidence and theoretical writings in Biology, although our arguments will be mostly based on a comparison with the use of differential methods (in Molecular Biology: a mutation or alike is observed or induced and its phenotypic consequences are observed) as applied in Computer Science and in Physics, where this fundamental tool for empirical investigation originated and acquired a well-justified status. In particular, as we will argue, the programming paradigm is not theoretically sound as a causal(as in Physics) or deductive(as in Programming) framework for relating the genome to the phenotype, in contrast to the physicalist and computational grounds that this paradigm claims to propose.

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Authors and Affiliations

  1. Laboratoire d’Informatique, CNRS et École Normale Supérieure, Paris, France

    Giuseppe Longo & Pierre-Emmanuel Tendero

  2. CREA, École Polytechnique, Paris, France

    Giuseppe Longo

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  1. Giuseppe Longo
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  2. Pierre-Emmanuel Tendero
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Correspondence to Giuseppe Longo.

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A preliminary (and longer) French version of this paper is an invited paper in Evolution des concepts fondateurs de la biologie du XXIe siècle, (Miquel et al., eds) DeBoeck, Paris, 2007 (in press).

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Longo, G., Tendero, PE. The Differential Method and the Causal Incompleteness of Programming Theory in Molecular Biology. Found Sci 12, 337–366 (2007). https://doi.org/10.1007/s10699-007-9111-x

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