Title: Proofs of life: molecular-biology reasoning simulates cell behaviors from first principles,
Abstract: 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.