[FOM] "Proofs of life"

José Manuel Rodriguez Caballero josephcmac at gmail.com
Wed Nov 7 15:55:34 EST 2018

Dear Dr. Vestergaard,

  I would like to suggest you to apply your approach to cancer cells,
following Warburg’s theory. There are many controversies about Warburg’s
point of view, but as far as I know, all the attempt of refutations were
counterattacked by Warburg himself and by his followers.

Here is the main reference:

Warburg, O. (1956). On the origin of cancer cells. Science, 123(3191),


Sincerely yours,
José Manuel Rodriguez Caballero

El mar., 6 nov. 2018 a las 20:39, Rene Vestergaard (<renevestergaard at acm.org>)

> "Proofs of life: molecular-biology reasoning simulates cell behaviors
> from first principles" is now available at http://arxiv.org/abs/1811.02478
> The work springs from computer-verified reasoning and establishes wider
> utility by means of a reasoning-computation correspondence, including
> for long-standing critical problems in biology that have defied standard
> approaches.
> Sincerely,
> Rene
> -----
> Mathematics-style correctness works for molecular biology and enables
> phenotype and life-cycle prediction from genotypes. Formally,
> reductionist science involves constructive reasoning, i.e., executable
> simulation.
> Axiomatic reasoning provides an alternative perspective that allows us
> to address long-standing open problems in biology. Our approach is
> supported by meta-theory and likely applies to any reductionist discipline.
> Science relies on external correctness: statistical analysis and
> reproducibility, with ready applicability but inherent false
> positives/negatives. Mathematics uses internal correctness: conclusions
> must be established by detailed reasoning, with high confidence and deep
> insights but not necessarily real-world significance. Here, we formalize
> the molecular-biology reasoning style; establish that it constitutes an
> executable first-principle theory of cell behaviors that admits
> predictive technologies, with a range of correctness guarantees; and
> show that we can fully account for the standard reference: Ptashne, A
> Genetic Switch. Everything works for principled reasons and is presented
> within an open-ended meta-theoretic framework that seemingly applies to
> any reductionist discipline. The framework is adapted from a
> century-long line of work on mathematical reasoning. The key step is to
> not admit reasoning based on an external notion of truth but work only
> with what can be justified from considered assumptions. For molecular
> biology, the induced theory involves the concurrent running/interference
> of molecule-coded elementary processes of physiology change over the
> genome. The life cycle of the single-celled monograph organism is
> predicted in molecular detail as the aggregate of the possible
> sequentializations of the coded-for processes. The difficult question of
> molecular coding, i.e., the specific means of gene regulation, is
> addressed via a detailed modeling methodology. We establish a
> complementary perspective on science, complete with a proven correctness
> notion, and use it to make progress on long-standing and critical open
> problems in biology.
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