Proofs of life: molecular-biology reasoning simulates cell behaviors from first principles

• Published in: arXiv.org
• Main Authors: Vestergaard, René, Pietriga, Emmanuel
• Format: Paper
• Language: English
• Published: Ithaca Cornell University Library, arXiv.org 22.01.2019
• Subjects: Biology; Computation; Computer simulation; Deoxyribonucleic acid; DNA; Domain specific languages; First principles; Reasoning
• ISSN: 2331-8422

We axiomatize the molecular-biology reasoning style, verify compliance of the standard reference: Ptashne, A Genetic Switch, and present proof-theory-induced technologies to predict phenotypes and life cycles from genotypes. The key is to note that `reductionist discipline' entails constructive reasoning, i.e., that any argument for a compound property is constructed from more basic arguments. Proof theory makes explicit the inner structure of the axiomatized reasoning style and allows the permissible dynamics to be presented as a mode of computation that can be executed and analyzed. Constructivity and executability guarantee simulation when working over domain-specific languages. Here, we exhibit phenotype properties for genotype reasons: a molecular-biology argument is an open-system concurrent computation that results in compartment changes and is performed among processes of physiology change as determined from the molecular programming of given DNA. Life cycles are the possible sequentializations of the processes. A main implication of our construction is that technical correctness provides a complementary perspective on science that is as fundamental there as it is for pure mathematics, provided mature reductionism exists.