The Chern-Simons current in systems of DNA-RNA transcriptions

Question

Referee this paper: arXiv:1802.00314 by Salvatore Capozziello, Richard Pincak,

Kabin Kanjamapornkul, Emmanuel N. Saridakis

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Please use comments to point to previous work in this direction, and reviews to referee the accuracy of the paper. Feel free to edit this submission to summarise the paper (just click on edit, your summary will then appear under the horizontal line)

(Is this your paper?)

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Comments

This paper sounds insane because it proposes that supersymmetry, E8 x E8, and much more, are relevant to modeling something to do with a virus gene (a time series is involved). Mathematical techniques pioneered in physics sometimes have surprising applications elsewhere, but this paper exceeds my credibility. The goal should be to understand with some precision what is being done in this paper, and to identify specifically what is bad about it (if anything is bad).

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Really impressive but not surprising ... It is maths and as physicists they use the tools they know. Allmost anything with states, behaviors states dependent and competition may be modelized with physics tools.

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igael, I assure you that this paper is a masterpiece of insanity. How many absurd phrases of the form "theoretical physics concept applied to biological object" can we squeeze into one paper? So far we have the "BV cohomology of DNA", the "Seiberg-Witten docking equation" (and they mean something like HIV "docking" with its host cell), "the supersymmetry of the central dogma", "twistors in the hydrogen bonds", and it just goes on and on.

A cell is a complex dynamical system and so all sorts of concept like state, coupling, attractor, and many others make sense. Even supersymmetry and gauge symmetry can have surprising utility outside of physics. But this paper is crazy, like using general relativity to pay your phone bill, and I hope to make the craziness clear, once I have decoded the method in their madness.

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Mitchell, I agree with you that there are many shortcuts in this document. But the authors begin with "In this perspective, methods of Quantum Field Theory, and related results,
can be of high interest.".  Cautious ... I read something less ambitious based on stationary waves to explain the distribution of species in the placental and marsupial mammals classification. Not forgeting your important warnings, this contribution deserves some interest with a possible feed back to physics with the enlargement of the perspective. I believe that this approach can be perfected, it is one of the first attempts.

I found later that the work was made through this program . Perhaps it will make you more forgiving :)

Answer 1

I believe this bizarre paper is best understood as one of a collection of papers across several disciplines, whose common element appears to be the Slovak physicist Richard Pincak. Basically, there's a new 14-dimensional "theory", "G-theory", which has branes and other features in common with string theory, and which is "applied" not just to particle physics, but also to finance and, here, to molecular biology.

How can you "apply" a quantum geometric theory to bioinformatics? Here is a hint. As most people know, DNA is a polymer consisting of a sequence of nucleotide bases, drawn from an alphabet of four basic types, that are abbreviated A, C, G, T.

Begin with equation 1 in this paper. You will find a mapping in which these four nucleotides are represented by complex quaternions (and apparently the gene that contains them is also represented by an arbitrary complex phase, that's the beta_i appearing in an exponent in those formulas).

Now, jump ahead to page 13. You will find a reference to a "Hopf fibration over DNA molecule". What's going on? The nucleotides have already been mapped to quaternions. So now, the DNA sequence is being mapped to something like a bundle of oriented quaternionic manifolds along a line.

So, I now have some idea how this strange aggregate of ideas could get started. The base-4 sequences of nucleotides can get mapped to a geometric entity, and from there you can add dimensions corresponding to evolution, to chemical binding affinities, to fitness... and you can hope to apply numerous advanced concepts from algebraic geometry.

I strongly doubt that there is much here which makes sense. "Anti de Sitter" is confused with "anti self dual", the specifics of the quaternionic encoding of the nucleotides are introduced without motivation, on page 24 there's crazy talk about retrotransposon reincarnation via anti-ghost fields (I don't know if they just mean the re-expression of a silenced gene, or something weirder). And I've only scratched the surface.

Originally I thought this might be a cynical exercise in using higher-math jargon to create an illusion of science. But I now think it's earnest. In this and its companion papers, there's some real creativity. (For another example, see the title concept in this paper on machine learning.) But all the evidence suggests that it's ultimately incoherent. So I will recommend these papers only for people who like to explore that sort of thing.

Comments

This is amazing. I'm laughing out loud. Was worth it for the diagrams alone ;D

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More from one of the authors of G-theory.

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"Chern-Simons current" in Covid mutational lineages. 

The sensible part of the idea, is the observation that there are three nucleotides per codon, so codons form a discretized three-dimensional space (where each "coordinate" can take the values A, G, C, T), and so if you attach field values to the codons, you can indeed define a formal Chern-Simons current on this space. 

The problem is that the formal field values they associate with the codons, appear to be quite arbitrary, and yet they still think they can deduce something about geometries of molecules from them! Surely these "fields" should contain some information about the chemical affinities of the bases, if they are to tell us anything about actual chemistry...