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  1. #71
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    Shcherbak's patterns

    Background

    As you know, there are 4 bases or "letters" that make up the genetic code - these are T, G, A, C

    These 4 letters combine to form 64 codons, or "words", each codon consisting of 3 letters.

    These 64 codons code for the 20 amino acids.

    Each amino acid is made of two parts - a part that is common to all amino acids, called a "standard block", and a part that differs from one amino acid to the next - called a "radical part"


    3 Groups of Codons

    These 64 codons divide naturally into 3 groups -

    1. Codons made of identical letters, eg TTT, GGG, AAA, CCC

    2. Codons made of unique letters, eg TGA, CAG, AGT etc

    3. Codons made of 2 identical letters and one unique letter, eg TTA, AAC etc


    So the 64 codons divide as follows -

    4 codons have identical bases

    24 codons have unique bases

    36 codons have 2 identical bases and one unique base


    Numerical pattern in these groups

    The codons with identical bases + the codons with unique bases create amino acids with where the sum of the nucleons in the radical part = 2 x 703, and the total number of nucleons in both radical + standard block = 5 x 666


    The codons with two identical bases and one unique base create amino acids with 3 x 666 nucleons in the radical part and 2590 nucleons in the standard block.

    These relationships can be seen more clearly in the diagram below -



    The whole pattern is based around multiples of 37, in particular 703, 666 and 259

    Actually, this pattern is only the surface pattern. Within each group there are symmetrical subdivisions that also sum to multiples of 37.


    Shcherbak is quite clear in his conclusion that the entire genetic code is based on arithmetic. It is a pure construction of mathematical precision.

    Regards

    Craig
    Last edited by Craig.Paardekooper; 02-23-2011 at 09:02 AM.

  2. #72
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    New Paper on Shcherbak's patterns

    I have just come across a new paper on Shcherbak's patterns.

    The self-similar numbers as a special case of cyclic numbers and their relation to the cyclic (genetic) codes (29th Nov 2010)

    Abstract
    The genetic code is analyzed as one of the major natural codes, which as such can reveal the deeper principles of optimal coding. The analysis is based on a discovery that the symmetrical architecture of genetic code and the nucleon number of its constituents - the free canonical amino acids and bases, are strictly determined by the prime number with a cycling digit property -037. A detailed derivation for all types of analogues of 037 is given and shown that they represent a special case of cyclic numbers whose digits and multipliers are equidistant. The derived generic formula for analogues of 037 is correlated with cyclotomic and generalized Golden Mean polynomials, by which is shown their relation with discrete self-similarity, why author named them the Self-similar Numbers. Also it is given their relationship with the cyclic codes, which is with fact that the genetic code is arranged in multiple ways at different levels as a cyclic code, generally indicate that the hierarchically nested cyclicality is one of the principles of fractal organization of the genetic code, as well as the other organic codes in the living organisms.

    This paper appears in: Neural Network Applications in Electrical Engineering (NEUREL), 2010 10th Symposium on
    Issue Date: 23-25 Sept. 2010
    On page(s): 97 - 102
    Location: Belgrade
    Print ISBN: 978-1-4244-8821-6
    INSPEC Accession Number: 11676971
    Digital Object Identifier: 10.1109/NEUREL.2010.5644099
    Date of Current Version: 29 November 2010

    I found a website were you can access this paper - Paper


    A good way to locate the latest papers on this subject is to google -

    "Shcherbak arithmetic in the genetic code pdf"


    Regards

    Craig
    Last edited by Craig.Paardekooper; 02-23-2011 at 04:50 PM.

  3. #73
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    Quote Originally Posted by Craig.Paardekooper View Post
    Background

    As you know, there are 4 bases or "letters" that make up the genetic code - these are T, G, A, C

    These 4 letters combine to form 64 codons, or "words", each codon consisting of 3 letters.

    These 64 codons code for the 20 amino acids.

    Each amino acid is made of two parts - a part that is common to all amino acids, called a "standard block", and a part that differs from one amino acid to the next - called a "radical part"


    3 Groups of Codons

    These 64 codons divide naturally into 3 groups -

    1. Codons made of identical letters, eg TTT, GGG, AAA, CCC

    2. Codons made of unique letters, eg TGA, CAG, AGT etc

    3. Codons made of 2 identical letters and one unique letter, eg TTA, AAC etc


    So the 64 codons divide as follows -

    4 codons have identical bases

    24 codons have unique bases

    36 codons have 2 identical bases and one unique base


    Numerical pattern in these groups

    The codons with identical bases + the codons with unique bases create amino acids with where the sum of the nucleons in the radical part = 2 x 703, and the total number of nucleons in both radical + standard block = 5 x 666


    The codons with two identical bases and one unique base create amino acids with 3 x 666 nucleons in the radical part and 2590 nucleons in the standard block.

    These relationships can be seen more clearly in the diagram below -



    The whole pattern is based around multiples of 37, in particular 703, 666 and 259

    Actually, this pattern is only the surface pattern. Within each group there are symmetrical subdivisions that also sum to multiples of 37.


    Shcherbak is quite clear in his conclusion that the entire genetic code is based on arithmetic. It is a pure construction of mathematical precision.

    Regards

    Craig
    Hi Craig,

    Fascinating stuff... Thanks for keeping us posted...
    Blessings,
    Rose
    Never trust anything you are afraid to question ~

    To know oneself is to know the universe...


    Live Fully...Love Extravagantly...For the sake of Goodness

    Be ye therefore wise as serpents, and harmless as doves. Matt.10:16

    Come let us reason together...Isa.1:18
    ********************************
    My new Blog site: God and Butterfly

  4. #74
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    Rakocevics paper is online

    Here is the link to the paper by Rakocevic

    Rakocevic Paper

    Chavez paper
    Last edited by Craig.Paardekooper; 02-24-2011 at 03:59 AM.

  5. #75
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    Here is a link to a paper I have written about Rakocevic. It is not quite complete yet.

    http://www.craigdemo.co.uk/geneticscode1.pdf

  6. #76
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    Paper by Stephen Coneglan

    Stephen Coneglan just emailed to me his latest research on the Rakocevic patterns.

    Stephen has rearranged Rakocevics 4 x 5 matrix of the 20 amino acids, so that the amino acids are arranged symmetrically according to their properties.

    When he did this, Stephen discovered that the new arrangement shows precise symmetry not just in the columns but also in the rows.

    Further more, Stephen discovered that a "doublet" pattern has emerged centred on the number 55.

    Stephen's paper

  7. #77
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    Email from Paul Milligan

    Craig

    Enjoy reading your work on DNA & threads on Biblewheel. Have been reading Richard’s site since long before he brought his biblewheel book out. Though I haven’t contributed to it. My other love is molecular biology and looking for the imprint of the creator in our own cellular make-up. cr

    Your interest has largely been in the translation of RNA codons into Amino-Acids.

    Just wanted to add for your interest a few things that have suggested to me that the creator may have left His imprint.


    [1] - DNA distribution.
    DNA in cells could be divided into 3 arenas :
    --- 1 pair of sex chromosomes ....................... does this hint of the Hebrew ALEPH and father
    --- 22 autosome pairs ........................................ does this hint to the Hebrew TAV, a mark, cross & written word - maybe Jesus, the Word
    - from Aleph to Tav represented in the nucleus
    --- together with circular DNA in the powerhouse of cells - the mitochondria -- wheels of DNA a little like the Hebrew word for wheel Galgal from 3rd Hebrew letter. Each mitochondrion in humans and many animals having one circular DNA with 37 genes.

    Guess I see metaphorical hints of Father, Son & Holy Spirit in the overall layout. The 3 hebrew letters associated with the above being A,T,& G. Is it a coincidence that the beginning codon of every protein to be made in the protein factory is methionine = ATG ............... even though they stand for english named nucleosides. (If cytosine C was replaced by the Hebrew letter kaph K=11 as there is no letter C in Hebrew, then the sum of the Hebrew Letters A,T,G,K = 37 ........ 1+22+3+11 with ATG summing to 26 - elohim )

    [2]
    Each DNA rung is made up of :
    - a 5 ringed ribose
    - a 6 ringed pyramidine ---- T or C
    - a purine ------- a combination of a 6 ring and 5 ring to make a double ringed structure that has 10 struts with a middle bond like a waist belt ------ A or G
    - a 5 ring ribose


    As the 2 strands of DNA open up and swing out then it is possible for the ring structure count of each DNA rung to become 10,5,6,5 similar to the tetragrammaton. Metaphorically the maker can be said to have hidden his name in each and every strand of DNA in every living thing.


    5 elements are used to make up DNA - P,O,N,C,H -- their atomic numbers sum to 37 [ 15+8+7+6+1] and their nucleons sum to 74


    [3]
    Strange to me that we humans should run at 37* centigrade - ie 37 / 100ths of the temperature difference between water freezing and steaming. Funny the places that the old 37 crops up.


    [4]
    HISTONES
    To coil and store the 2 metres of DNA in each human cell the molecule is wrapped around little spools called NUCLEOSOMES which allows the DNA to be further compacted and twisted, eventually the compression process becoming a visible chromosome. 147 base pairs of DNA [ 7x3x7] are wrapped around a nucleosome consisting of histone protein spool of 8 histone protein spokes in a 1.65 Left handed super-helical turn. Though some studies suggest 146 base pairs [73 x 2] are coiled.


    {A study of the geometry of the organelles within a cell is also an interesting study. I have put a diagram below of the DNA clamp that goes along each double strand as it is replicated - an interesting symbol !


    If you are interested to look at protein geometry in cells - http://beautifulproteins.blogspot.com/


    Anyway this email was really just to suggest our Maker has left imprints in other parts of biology as well as the codon-amino acid code ........... which IS amazing in its own right as you suggest.


    Regards - Paul Millican

  8. #78
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    Quote Originally Posted by Craig.Paardekooper View Post
    Craig

    Enjoy reading your work on DNA & threads on Biblewheel. Have been reading Richard’s site since long before he brought his biblewheel book out. Though I haven’t contributed to it. My other love is molecular biology and looking for the imprint of the creator in our own cellular make-up. cr

    Your interest has largely been in the translation of RNA codons into Amino-Acids.

    Just wanted to add for your interest a few things that have suggested to me that the creator may have left His imprint.


    [1] - DNA distribution.
    DNA in cells could be divided into 3 arenas :
    --- 1 pair of sex chromosomes ....................... does this hint of the Hebrew ALEPH and father
    --- 22 autosome pairs ........................................ does this hint to the Hebrew TAV, a mark, cross & written word - maybe Jesus, the Word
    - from Aleph to Tav represented in the nucleus
    --- together with circular DNA in the powerhouse of cells - the mitochondria -- wheels of DNA a little like the Hebrew word for wheel Galgal from 3rd Hebrew letter. Each mitochondrion in humans and many animals having one circular DNA with 37 genes.

    Guess I see metaphorical hints of Father, Son & Holy Spirit in the overall layout. The 3 hebrew letters associated with the above being A,T,& G. Is it a coincidence that the beginning codon of every protein to be made in the protein factory is methionine = ATG ............... even though they stand for english named nucleosides. (If cytosine C was replaced by the Hebrew letter kaph K=11 as there is no letter C in Hebrew, then the sum of the Hebrew Letters A,T,G,K = 37 ........ 1+22+3+11 with ATG summing to 26 - elohim )

    [2]
    Each DNA rung is made up of :
    - a 5 ringed ribose
    - a 6 ringed pyramidine ---- T or C
    - a purine ------- a combination of a 6 ring and 5 ring to make a double ringed structure that has 10 struts with a middle bond like a waist belt ------ A or G
    - a 5 ring ribose


    As the 2 strands of DNA open up and swing out then it is possible for the ring structure count of each DNA rung to become 10,5,6,5 similar to the tetragrammaton. Metaphorically the maker can be said to have hidden his name in each and every strand of DNA in every living thing.


    5 elements are used to make up DNA - P,O,N,C,H -- their atomic numbers sum to 37 [ 15+8+7+6+1] and their nucleons sum to 74


    [3]
    Strange to me that we humans should run at 37* centigrade - ie 37 / 100ths of the temperature difference between water freezing and steaming. Funny the places that the old 37 crops up.


    [4]
    HISTONES
    To coil and store the 2 metres of DNA in each human cell the molecule is wrapped around little spools called NUCLEOSOMES which allows the DNA to be further compacted and twisted, eventually the compression process becoming a visible chromosome. 147 base pairs of DNA [ 7x3x7] are wrapped around a nucleosome consisting of histone protein spool of 8 histone protein spokes in a 1.65 Left handed super-helical turn. Though some studies suggest 146 base pairs [73 x 2] are coiled.


    {A study of the geometry of the organelles within a cell is also an interesting study. I have put a diagram below of the DNA clamp that goes along each double strand as it is replicated - an interesting symbol !


    If you are interested to look at protein geometry in cells - http://beautifulproteins.blogspot.com/


    Anyway this email was really just to suggest our Maker has left imprints in other parts of biology as well as the codon-amino acid code ........... which IS amazing in its own right as you suggest.


    Regards - Paul Millican
    Hi Craig,

    Thanks for posting Paul Millican's e-mail.... Also, I went to the Beautiful Proteins Blogspot and was amazed at the stunning symmetries of many proteins....

    Thanks again,
    Rose
    Never trust anything you are afraid to question ~

    To know oneself is to know the universe...


    Live Fully...Love Extravagantly...For the sake of Goodness

    Be ye therefore wise as serpents, and harmless as doves. Matt.10:16

    Come let us reason together...Isa.1:18
    ********************************
    My new Blog site: God and Butterfly

  9. #79
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    Latest amino acid findings

    On 12th March 2011, Stephen Coneglan emailed me his latest research on mathematical patterns in the amino acids.

    What he has discovered is that the arrangement of the amino acids that gives rise to the numerical symmetries is not a random arrangement - rather the numerical patterns appear when the amino acids are arranged symmetrically according to their various chemical properties.

    Here is his latest updated paper, which includes much new info in the appendices.

    http://www.craigdemo.co.uk/stephenbook.doc

    In order to review Stephens findings I will email his findings to Rakocevic, Shcherbak and Perez tomorrow. Their feedback will be invaluable.

    Craig
    Last edited by Craig.Paardekooper; 03-12-2011 at 02:47 PM.

  10. #80
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    Email from Shcherbak

    Vladimir Shcherbak has replied to the papers that we submitted to him for review.

    Here is his response -

    Dear Craig,

    thank for your longstanding interest to my research. You have attached two articles. Article by Stephen Coneglan updates 5x4 table of 20 canonical amino acids published by Miloje Rakocevic in JTB while your article gives geometrical interpretation to these results. I think that Miloje Rakocevic finding became even more brilliant due to your scrupulous research.

    However, pure mathematical approach to the genetic code and its numerical parameters threatens to be the scholastic one. To avoid scholasticism I try, for example, to interpret my results as instruction on possible universal arithmetic grammar of genomes. By the way, I recommend you to pay attention to the second Chargaff's rule (see attached articles). This phenomenon and its total power may be a continuation of the genetic code arithmetical order, this time in genomes. Therefore we – I and my young colleague Maxim Makukov – are searching now for analogous numerical grammar in genomes.

    There are two squared numbers of total sum 2x37^2=2738 in your articles. On the other hand there is equation 12^2+35^2=37^2 among Pythagorean numbers. I would like to ask you and Stephen: is it possible to bisect regularly 5x4 table and its total sum producing the same equations 12^2+35^2=37^2 and 12^2+35^2=37^2? I ask this question because the genetic code has shown already the first Pythagorean number.

    Yours sincerely

    Vladimir
    Mr Shcherbak also attached two documents that he thought would be of interest. Shcherbak and his colleague Maxim Makukov, are now searching for similar patterns in genomes.

    Document1

    Document1


    It has always been my hope that through work such as this we leave behind something beautiful - a pure pattern of meaning and purpose - a foundation stone.
    Last edited by Craig.Paardekooper; 03-19-2011 at 08:45 PM.

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