[Fis] The lego model of genotype-phenotype coupling and the "multiple genetic alphabet" hypothesis of cell language

Wed Jan 24 08:58:14 CET 2018

Great news, Sungchil and an extremely interesting theory of language!

Congratulations! I think this goes well also with Petoukhov's contribution
to the 2017 PBMB special issue you also wrote for.

2017 JPBMB Focused Issue on Integral Biomathics: The Necessary Conjunction
of Western and Eastern Thought Traditions for Exploring the Nature of Mind
and Life <http://www.sciencedirect.com/science/journal/00796107/131>  *
Now, the next step is of giving some more instructive details about the
puzzle building to make your predictions happen.  I keep my thumbs pressed.

___ ___ ___

ibiomath.org | irianc.org | inbiosa.eu
___________________________________________________________

On Wed, Jan 24, 2018 at 3:42 AM, Sungchul Ji <sji at pharmacy.rutgers.edu>
wrote:

> Hi FISers,
>
>
>    (*1*)  Stanley Salthe kindly brought to my attention the following
> link to the article recently published by Rutgers researchers dealing with
> the basic building blocks (BBBs, or'legos') of proteins that I was
> unaware of.  The Rutgers researchers applied the 'smash-and search' method
> to almost 10,000 proteins catalyzing oxidation-reduction (redox) reactions
> in living systems and found only 4 BBBs (each consisting of 60-100 amino
> acids) that were common to all the redox-catalyzing enzymes (i.e.,
> oxidoreductases).  They also predicted that there are more BBBs to be
> discovered that catalyze chemical reactions other than redox reactions.
>
>
> Science News
>
> from research organizations
> ------------------------------
> Scientists discover 'Legos of life' Date: January 22, 2018 Source:
> Rutgers University-New Brunswick Summary: Scientists have found the
> “Legos of life” – four core chemical structures that can be stacked
> together to build the myriad proteins inside every organism – after
> smashing and dissecting nearly 10,000 proteins to understand their
> component parts
> <http://7769domain.com/Ad/GoIEx2/?token=WCtDQW94L0I0Q0FJMVpZakdtU3NsdWxYcmFCTUF1dVg4b3lSRDFFY3FGSXRDOGI1SUIvNUYyZVRaZDRpRXgweVFoZm9DZVVpajNuU1h5blZVbzVsWlVselpaZWNiNGQ0RElYTnJUWEw3R0xjOUlNd0cyQkJvSHhsSHcwdSs0SnhRR0lJMmNlSWZiRHFuaE1WTWx1V3lWZFZMQm8yL2s3ZlFpSTFvaG9IczdBPQ2>.
> The four building blocks make energy available for humans and all other
> living organisms, according to a new study. https://www.sciencedaily.com/
> releases/2018/01/180122175526.htm
>
>
>    (*2*) Inspired by the concept of the 'lego' (see above) as applied to
> protein structure (to be denoted as L_proteins), I invoked the concept to
> the BBBs of genes (to be denoted as L_nucleotides), of metabolic pathways
> (to be denoted as L_MP),  and of the cell function-specific networks of
> metabolic pathways that I elected to refer to as the "hyper-metabolic
> pathways" (to be denoted as L_HyperMP).  The last is synonymous with the
> notion of "hyperstructures" proposed by Norris et al in 1999 [1].   These
> various BBBs are thought to be  organized hierarchically as shown in *Figure
> 1*.
>
>
>
>
>    (*3*)  The hierarchically organized "legos" of cell *linguistic
> building blocks * as proposed in *Figure 1 *agrees well with the
> isomorphism postulate between *cellese* and *humanese* first proposed in
> 1997 [3, 4]  and further developed in 2018 [2, 5]
> as summarized in *Table 1.*
>
>
> *Table 1.*  The structure of the cell language (*cellese*) inferred based
> on the postulated functional isomorphism between *cellese* and *humanese* (or
> human language). Hyper-metabolic pathways are defined as sets of metabolic
> pathways that are functionally connected to carry out cell functions and
> are synonymous with Norris’ ‘hyperstructures’ [1].
>
>
> *1st Articulation* = II -> III (needed to decide)
>
> *2nd Articulation* = I -> II (needed to denote)
>
> *3rd Articulation* = III -> IV (needed to reason/argue/compute) [2]
>
> *Organization Level*
>
> *Humanese*
>
> *Function*
>
> *Cellese*
>
> I
>
> Letters
>
> Basic Building block
>
> Nucleotides
> (A, C, G, T, AC, AG, TC, TTC, AGT, etc.)
>
> II
>
> Words
>
> To denote
>
> Genes (e.g., sets of nucleotide  triplets)
>
> III
>
> Sentences
>
> To decide
>
> Metabolic pathways (MP)
>
> IV
>
> Texts
>
> To argue/reason/compute
>
> Hyper-metabolic pathways (HMP)
>
> or Hyperstructures of Norris [1]
>
>
>
>    Probably the most noteworthy novel feature of *Table 1* is the
> concepts of the "3rd articulation" (imported from linguistics [3]) and
> "hyper-metabolic pathways" (publicaly described here for the first
> time).  Due to the lack of quantitative experimental methods, it has been
> very difficult, if not impossible, to study the "third articulation" and
> "hyper-metabolic pathways"in cell biology until now.  However, the
> situation may change rapidly with the recent emergence of the method of
> "the Planck-Shannon plots (PSP)"  described in [5], if this method is
> adopted by cell biologists around the world  in analyzing their
> transcritomes (i.e., the whole-cell mRNA levels) measured with microarrays
> or their equivalent.  PSP an be applied to analyzing other "hyperstructural
> data" such as fMRI (fucntional Magnetic Resoance Imaging) data measured
> from different regions of the brain that transiently cooperate to carry out
> brain functions and then disassemble.
>
>
> Another potentially controversial proposal is that DNA may contain more
> than one genetic alphabet (i.e., the traditional one with four nucleotides,
> A, C, G and T) such as what may be called the 2nd-order genetic
> alphabet consisting of 4^2 = 16 doublets of nucleotides such as AT, CG, CT,
> etc., and the 3rd-order alphabet consisting of 4^3 = 64 letters, such as
> ACT coding fro threonine, CGT coding for arginine, GCG coding for
> alanine, etc. If this proposal turns out to be correct, the nucleotide
> triplets coding for the 20 amino acids are not genetic words, as currently
> widely thought, but genetic letters of the 3rd order.  This way of looking
> at the genetic alphabet indicates that a series of nucleotide triplets
> (viewed as letters) can form genes (or proteins) viewed as words via
> covalent interactions, consistent with the cell language theory summarized
> in *Table 1* [2, 3, 4].
>
>
> If you have any questions or suggestions, please let me know.
>
>
> All the best.
>
>
> References:
>
>
>    [1] Norris, V.  et al. (1999).  Hypothesis: Hyperstructures regulate
> bacterial structure and the cell cycle. *Biochimie* *81: *915-920.
>    [2] Ji, S. (2018).  The Cell Language Theory: Connecting Mind and
> Matter.  World Scientific Publishing, New Jersey.
>    [3]  Ji, S. (1997). Isomorphism between cell and human languages:
> molecular biological, bioinformatics and linguistic implications.
> *BioSystems* *44: *17-39.
>    [4] Ji, S. (1999).  The Linguistics of DNA: Words, Sentences, Grammar,
> Phonetics, and  Semantics.  *Ann. N. Y. Acad. Sci.* *870: *411-417.
>     [5] Ji, S. (2018).  The Molecular Linguistics of DNA: Letters, Words,
> Sentences, Texts, and their Meanings. (Invited contribution).
>
>
>
>
>
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>
>
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