List: Further inquiry into the structure of proteins reveals that this table is incomplete with respect to the identities of amino acids in proteins.
Several more amino-acids are now known to be parts of proteins (hydroxy-proline and hydroxy-lysine are two examples.) On a more general level, the concept that a single physical feature of a chemical molecule can explain biology is problematic, to say the least. Cheers Jerry On Nov 23, 2015, at 7:34 PM, Sungchul Ji wrote: > Hi, > > (1) In response to my PEIRCE-L post dated 11/22/2015, Petoukhov wrote to me > this morning: > > > "From the formal standpoint, our voice apparatus is a vibro-system with many > degrees of freedom (112315-1) > and with its resonant frequencies." > > This statement, when combined with his earlier theoretical results [1, 2], > naturally leads to the following generarization: > > "All living systems and their components are vibro-systems with many degrees > of freedom (112315-2) > with their resonant frequencies." > > With Petoukhov's permission and for reasons of convenience, I decided to > refer to Statement (112315-2) as the 'Petoukhov hypothesis'. > > (2) One experimental evidence supporting the Petoukhov hypothesis is that 3 > of the 64 codons shown in Table 1 below (i.e., TAA, TAG, and TGA) encode the > "actions" of stopping the transcriptional process rather than any amino acids > (when viewed superficially). One plausible way to account for this fact > would be that the 3 nucleotide triplets located along the the DNA double > helix, i.e., the stop codons, may transfer their 'resonant frequencies' > (i.e., their associated vibrational energies) to an RNA polymerase molecule > thereby stopping its motions along the DNA tracks, preventing transcription. > In fact the same molecular mechanism may be responsible for transcribing the > amino acid-coding codons on DNA to its conjugate mRNA product. That is, these > amino acid-coding codons may transfer their resonant frequencies to a mRNA > polymerase molecule so that it can carry out the transcriptional process > rather than stopping it, unlike the stopping action-coding codons. > > > Table 1. 64 Codons connect nucleotide triplets to amino acid actions > (i.e., their resonant vibrational frequencies) mediated by transcriptional > and translational processes. > > CCC > Pro > CCA > Pro > CAC > His > CAA > Gln > ACC > Thr > ACA > Thr > AAC > Asn > AAA > Lys > CCT > Pro > CCG > Pro > CAT > His > CAG > Gln > ACT > Thr > ACG > Thr > AAT > Asn > AAG > Lys > CTC > Leu > CTA > Leu > CGC > Arg > CGA > Arg > ATC > Ile > ATA > Met > AGC > Ser > AGA > Arg > CTT > Leu > CTG > Leu > CGT > Arg > CGG > Arg > ATT > Ile > ATG > Met > AGT > Ser > AGG > Arg > TCC > Ser > TCA > Ser > TAC > Tyr > TAA > Stop > GCC > Ala > GCA > Ala > GAC > Asp > GAA > Glu > TCT > Ser > TCG > Ser > TAT > Tyr > TAG > Stop > GCT > Ala > GCG > Ala > GAT > Asp > GAG > Glu > TTC > Phe > TTA > Leu > TGC > Cys > TGA > Stop > GTC > Val > GTA > Val > GGC > Gly > GGA > Gly > TTT > Phe > TTG > Leu > TGT > Cys > TGG > Trp > GTT > Val > GTG > Val > GGT > Gly > GGG > Gly > > > (3) Let us remember that the resonant frequencies, ν, of an oscillator is > related to its energy, E, via the "Planck–Einstein relation" > (https://en.wikipedia.org/wiki/Planck_constant): > > > > (112315-3) > > Of curse, a codon on DNA carry not only the resonant vibrational energy > determined by (112315-3) but also the 'genetic information' encoded in the > molecular shape of the codon that is essential for recognizing (and > transferring resonant energy to) its binding partner on an RNA polymerase. > In other words, we must be careful not to be blinded by the elegance of the > Planck-Einstein relation, Eq. (112315-3), and forget the equally important > 'genetic information' stored in a codon, since the action of a codon depends > on both its vibrational ENERGY and genetic INFORMATION, in agreement with the > Principle of Information-Energy complementarity or the Gnergy Principle of > Organization [3]. The Petoukhov hypothesis, (112315-2), is consistent with > the information-energy requirement for the action of a codon because the > resonant frequencies of a codon embody both the vibrational energy and the > information about the molecular mass and shape of the codon that determine > its resonant waves. > > All the best. > > Sung > > -- > Sungchul Ji, Ph.D. > > Associate Professor of Pharmacology and Toxicology > Department of Pharmacology and Toxicology > Ernest Mario School of Pharmacy > Rutgers University > Piscataway, N.J. 08855 > 732-445-4701 > > www.conformon.net > > > References: > [1] Petoukhov, S. V. (2015). The system-resonance approach in modeling > genetic structures. BioSystem (n press). The pre-print at > http://www.sciencedirect.com/science/journal/aip/03032647 . > [2] Petoukhov, S. D. (2015). Music and the Modeling Approach to Genetic > Systems of Biological Resonances (Genetic System and Vibrational Mechanics). > The 4th ISIS Summit, Vienna, 2015. Power Point slides at > http://sciforum.net/conference/70/paper/2812. > [3] Ji, S. (2012). Information-Energy Complementarity as the Principle of > Organization. In: Molecular Theory of the Living Cell: concepts, Molecular > Mechanisms, and Biomedical Applicaitons. Springber, New York. Pp. 110-113. > PDF at http://www.conformon.net under Publications > Book Chapters. > > > > ----------------------------- > PEIRCE-L subscribers: Click on "Reply List" or "Reply All" to REPLY ON > PEIRCE-L to this message. PEIRCE-L posts should go to peirce-L@list.iupui.edu > . To UNSUBSCRIBE, send a message not to PEIRCE-L but to l...@list.iupui.edu > with the line "UNSubscribe PEIRCE-L" in the BODY of the message. More at > http://www.cspeirce.com/peirce-l/peirce-l.htm . > > > >
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