ponedjeljak, 31. kolovoza 2015.
srijeda, 1. travnja 2015.
The Atomic Genetic Code
ABSTRACT
The modern science
mainly treats the biochemical basis of sequencing in biomacromolecules and
processes in biochemistry. One can ask weather the language of biochemistry is
the adequate scientific language to explain the phenomenon in that science. Is
there maybe some other language, out of biochemistry, that determines how the
biochemical processes will function and what the structure and organization of
life systems will be? The research results provide some answers to these
questions. They reveal to us that the process of sequencing in biomacromolecules
is conditioned and determined not only through biochemical, but also through
cybernetic and information principles.
Keywords: Digital Genetics,
Genetics Code, RNA Code, Amino acids Code,
Evolution
METHODS
The genetic code
tables used by the modern science are characterized and determined by
principles of biochemistry. However, if in those tables, instead of the UCAG
nucleotides we put the number of atoms of those nucleotides, we will get the
new tables of the genetic code characterized and determined by programmatic and
information principles. Therefore, biochemistry can be explained through a
phenomenon out of biochemistry. Particularly interesting results we will get
when determining numeric values for the information content of atoms and molecules.
We will then find out that those values express physical and chemical
characteristics of molecules. For example: in a DNA molecule, the
polynucleotide chains are connected through an exact cyberinformation
connections. In those molecules there are also mathematical matrixes of DNA,
represented by the number of atoms of four ATCG bases. These matrixes determine
the positioning of nucleotides in that molecule. With this, the biological
particularities of DNA are determined. Similar mathematical matrixes determine
the positioning of nucleotides in the RNA molecule. In the amino acid proteins,
they are interconnected into the respective mathematical chains. In those
chains are also matrixes where particular mathematical principles apply, the
principles that determine the positioning of each amino acid in the chain.
RESULTS
The herewith discussed research results show
that the process of sequencing in biomacromolecules is conditioned and
determined not only through biochemical, but also through cybernetic
information principles.
We would
particularly like to stress here that the genetic, as well as biochemical
information in a broader sense of the word, is determined and characterized by
very complex cybernetic and information principles. The constantans in those
principles are: the number of atoms and molecules, atomic numbers, atomic
weight, physical and chemical parameters, even and odd values, codes and
analogue codes, standard deviations, frequencies, primary and secondary values,
and many other things. How functioning of biochemistry is determined through
cybernetic information principles, will be discussed further in this text.
The Atomic Genetic Code (RNA)
A = 15
atoms; U = 12 atoms; C = 13 atoms; G = 16 atoms;
Number
of atoms
UUU=36
Phe=23

UUC=37
Phe=23

CUC=38
Leu=22

UUA=39
Leu=22

UUG=40
Leu=22

CUG=41
Leu=22

CGC=42
Arg=26

GAU=43
Asp=16

GAC=44
Asp=16

CGG=45
Arg=26

AGA=46
Arg=26

AGG=47
Arg=26

GGG=48
Gly=10


UCU=37
Ser=14

UCC=38
Ser=14

AUU=39
Ile=22

AUC=40
Ile=22

UGC=41
Cys=14

AUA=42
Ile=22

AUG=43
Met=20

UGG=44
Trp=27

AAA=45
Lys=24

AAG=46
Lys=24

GGA=47
Gly=10



CUU=37
Leu=22

CCU=38
Pro=17

CCC=39
Pro=17

CUA=40
Leu=22

CCA=41
Pro=17

CCG=42
Pro=17

AAC=43
Asn=17

ACG=44
Thr=17

GGC=45
Gly=10

GAA=46
Glu=19

GAG=47
Glu=19





UAU=39
Tyr=24

GUU=40
Val=19

GUC=41
Val=19

GCC=42
Ala=13

GUA=43
Val=19

GUG=44
Val=19

GCG=45
Ala=13








UCA=40
Ser=14

UCG=41
Ser=14

UAA=42
STOP

AGU=43
Ser=14

AGC=44
Ser=14









ACU=40
Thr=17

ACC=41
Thr=17

AAU=42
Asn=17

ACA=43
Thr=17

GGU=44
Gly=10









UAC=40
Tyr=24

GCU=41
Ala=13


UAG=43
STOP

GCA=44
Ala=13









CAU=40
His=20

CAC=41
His=20


CAA=43
Gln=20

CAG=44
Gln=20









UGU=40
Cys=14

CGU=41
Arg=26


UGA=43
STOP

CGA=44
Arg=26





Number
of atoms in triplets UCAG
UUU
36

UUC
37

CUC
38

UUA
39

UUG
40

CUG
41

CGC
42

GAU
43

GAC
44

CGG
45

AGA
46

AGG
47

GGG
48


UCU
37

UCC
38

AUU
39

AUC
40

UGC
41

AUA
42

AUG
43

UGG
44

AAA
45

AAG
46

GGA
47



CUU
37

CCU
38

CCC
39

CUA
40

CCA
41

CCG
42

AAC
43

ACG
44

GGC
45

GAA
46

GAG
47





UAU
39

GUU
40

GUC
41

GCC
42

GUA
43

GUG
44

GCG
45








UCA
40

UCG
41

UAA
42

AGU
43

AGC
44









ACU
40

ACC
41

AAU
42

ACA
43

GGU
44









UAC
40

GCU
41


UAG
43

GCA
44









CAU
40

CAC
41


CAA
43

CAG
44









UGU
40

CGU
41


UGA
43

CGA
44





.(36+48)
= (37+47) = (38+46) = (39+45) = (40+44) = (41+43)
etc.
In fact, we discovered that the mathematical
balance in the distribution of
codons and amino acids in the genetic code is achieved.
Mathematical
position of the nucleotides in codon
The development of
prediction methods based on digital theory is focused on the exploration of new
digital formulas and algorithms. The genetic code is stored in DNA molecules as
sequences of bases: adenine (A) which pairs with thymine (T), and cytosine (C)
which pairs with guanine (G), The analog of DNA in a digital genetic algorithm
is a number of atoms, atomic numbers, analog codes, etc.
At mathematical
evolution of genetic processes, nucleotides TCAG are being transformed to
codons UCAG and later to amino acids and various organic composition.
Number of atoms
Second
Position of Codon



T

C

A

G



163

183

179

183

708


183

179

171

175

708


179

171

187

171

708


183

175

171

179

708


708

708

708

708


Diagonal
D1 = 708; Diagonal D2 = 708;
The digital genetic
code describe a genotype, which is translated into an organism a phenotype by
the processes of cell division.
Mathematical
evolution of genetic processes is manifested in different ways. Evolution of
groups of atoms is especially interesting.
Here are some examples
Digital codon square
A digital
codon square of order n is an arrangement of n² numbers,
usually distinct integers,
in a square, such that the n numbers in all
rows, all columns, and both diagonals sum to the same constant. A digital square contains the integers
from 1 to n². The term "digital square" is also sometimes used
to refer to any of various types of word square.
Number
of atoms
163

183

179

183

708

183

179

171

175

708

179

171

187

171

708

183

175

171

179

708

708

708

708

708


D1 = (163+179+187+179) = 708;
D2 = (183+171+171+183) = 708;
The
constant sum in every row, column and diagonal is called the magic
analogue constant or magic sum, M.
163

183

179

183

183

179

171

175

179

171

187

171

183

175

171

179

(163+183+183+179) = 708;
(179+183+171+175) = 708;
(179+171+183+175) = 708;
187+171+171+179) =708;
163

183

179

183

183

179

171

175

179

171

187

171

183

175

171

179

ê
708
163

183

179

183

183

179

171

175

179

171

187

171

183

175

171

179

ê
708
etc.
Analogue Atomic Genetic Code
How could we adapt
the program, ciberfnetic, and informational system to convey more
information? Here’s one way. This is an
analogue code
“Theoretically the ancient book of DNA could have
been analogue. But, for the same reason as for our analogue armada beacons, any
ancient book copied and recopied in analogue language would degrade to
meaninglessness in very few scribe generations. Fortunately, human writing is
digital, at least in the sense we care about here. And the same is true of the
DNA books of ancestral wisdom that we carry around inside us. Genes are
digital, and in the full sense not shared by nerves”(20).
Correlation of the Code and Analogue Code
The atomic and analogue genetic code is the set of rules by which information encoded in
genetic material (DNA
or RNA sequences)
is translated into proteins
(amino acid
sequences) by living cells. Specifically, those codes defines a
mapping between trinucleotide sequences called codons and amino acids; every triplet of nucleotides in a nucleic
acid sequence specifies a single amino acid. Because the vast majority of genes are encoded with
exactly the same code.
Those codes are universal. The same codons are
assigned to the same amino acids and to the same START and STOP signals in the
vast majority of genes in animals, plants, and microorganisms.
Analogue
CodeCode Code
Example:
Analogue
Code of the number 12 is number 21:
21 12;
Analogue
Code of the number 15 is number 51:
51 15;
etc.
At this stage of our research we replaced nucleotides from the Amino
Acid Code Matrix with analogue numbers of the atoms in those nucleotides.
A = 15 atoms; T = 15 atoms; C = 13
atoms; G = 16 atoms
A = 51; T = 51; C = 31; G = 61;
Analogue codon table
Mathematical position of the nucleotides in codon
Second Position of Codon



T

C

A

G



442

642

602

642

2328


642

602

522

562

2328


602

522

682

522

2328


642

562

522

602

2328


2328

2328

2328

2328


Diagonal D1 = 2328; Diagonal D2 = 2328;
Row 1 = Column 1; Row 2 = Column
2; Row 3 = Column 3; Row 4 = Column 4;
Analogue codon square
A analogue codon square of
order n is an arrangement of n² numbers, usually distinct integers,
in a square, such that the n numbers in all
rows, all columns, and both diagonals sum to the same constant
442

642

602

642

2328

642

602

522

562

2328

602

522

682

522

2328

642

562

522

602

2328

2328

2328

2328

2328


D1 = (442+602+682+602) = 2328;
D2 = (642+522+522+642) = 2328;
The
constant sum in every row, column and diagonal is called the magic
analogue constant or magic sum, M = 2328;
Correlation:
442

642

602

642

642

602

522

562

602

522

682

522

642

562

522

602

(442+642+642+602) = 2328;
(602+642+522+562) = 2328;
etc.
442

642

602

642

642

602

522

562

602

522

682

522

642

562

522

602

ê
2328
442

642

602

642

642

602

522

562

602

522

682

522

642

562

522

602

ê
2328
Determinsants in
Digital analogue Genetic Code
DET (4
x 4)
442

642

602

642

642

602

522

562

602

522

682

522

642

562

522

602

ê
2681856000
2681856000 = (2328 + 2328 + 2328…,
+ 2328);
There is a
mathematical balance within all of the phenomena in the analogue genetic code
matrix.
Mathematical
correlation of groups of nucleotides are a proof that genetic processes have
evolved from one mathematical shape to another one. They are a proof that we
can uncover some of hidden secrets in that science, with the help of
mathematics.


Atomic
numbers




U

C

A

G


F
i r s t P o s i t i o n 
U

728

856

776

808


C

856

728

776

808


A

776

776

888

728


G

808

808

728

824




3168

3168

3168

3168

Diagonal
D1 = 3168; Diagonal D2 = 3168;
The atomic genetic
code describe a genotype, which is translated into an organism a phenotype by
the processes of cell division.
Mathematical
evolution of genetic processes is manifested in different ways. Evolution of
groups of atoms is especially interesting.
Here are some examples
Digital codon square
A atomic
codon square of order n is an arrangement of n² numbers,
usually distinct integers,
in a square, such that the n numbers in all
rows, all columns, and both diagonals sum to the same constant. A digital square contains the integers
from 1 to n². The term "digital square" is also sometimes used
to refer to any of various types of word square.
Number of atoms
728

856

776

808

3168

856

728

776

808

3168

776

776

888

728

3168

808

808

728

824

3168

3168

3168

3168

3168


D1 = (728+856+776+808) = 3168; D2 =
(808+776+776+808) = 3168;
The
constant sum in every row, column and diagonal is called the magic
analogue constant or magic sum, M.
728

856

776

808

856

728

776

808

776

776

888

728

808

808

728

824

ê
3168
728

856

776

808

856

728

776

808

776

776

888

728

808

808

728

824

ê
3168
728

856

776

808

856

728

776

808

776

776

888

728

808

808

728

824

ê
3168
etc.
At this stage of our research we replaced nucleotides from the Amino
Acid Code Matrix with analogue of the atomic numbers in those nucleotides.
A = 70; U = 58 atoms; G = 78 atoms; C = 58
atoms
A = 7; U = 85; G = 87; C = 85;
Analogue codon table


Atomic
numbers




U

C

A

G


F
i r s t P o s i t i o n 
U

944

640

632

952


C

640

944

632

952


A

632

632

960

944


G

952

952

944

320




3168

3168

3168

3168

Diagonal D1 = 3168; Diagonal D2 = 3168;
Row 1 = Column 1; Row 2 = Column
2; Row 3 = Column 3; Row 4 = Column 4;
Analogue codon square
A analogue codon square of
order n is an arrangement of n² numbers, usually distinct integers,
in a square, such that the n numbers in all
rows, all columns, and both diagonals sum to the same constant
944

640

632

952

3168

640

944

632

952

3168

632

632

960

944

3168

952

952

944

320

3168

3168

3168

3168

3168


D1 = (944+944+960+320) = 3168;
D2 = (952+632+632+952) = 3168;
The
constant sum in every row, column and diagonal is called the magic
analogue constant or magic sum, M = 3168;
Correlation:
944

640

632

952

640

944

632

952

632

632

960

944

952

952

944

320

ê
3168
944

640

632

952

640

944

632

952

632

632

960

944

952

952

944

320

ê
3168
944

640

632

952

640

944

632

952

632

632

960

944

952

952

944

320

ê
3168
Determinsants in
Digital analogue Genetic Code
DET (4
x 4)
944

640

632

952

640

944

632

952

632

632

960

944

952

952

944

320

ê
197237145600
197237145600 = (3168+ 3168 + 3168…, + 3168);
There is a
mathematical balance within all of the phenomena in the analogue genetic code
matrix.
Mathematical
correlation of groups of nucleotides are a proof that genetic processes have
evolved from one mathematical shape to another one. They are a proof that we
can uncover some of hidden secrets in that science, with the help of
mathematics.
Atomic weight

C

H

N

O

S


A

5

5

5

0

0

15

U

4

4

2

2

0

12

C

4

5

3

1

0

13

G

5

5

5

1

0

16

C = 12,0111;
H = 1,00797; N = 14,0067; O = 15,9994;
S = 32,064;
A = 135; U = 112; C = 111; G = 151;
The
Digital Genetic Code
At the first stage of our research we replaced nucleotides from the
Genetic Code with atomic weight of those nucleotides.
Mathematical
position of the nucleotides in codon
The development of
prediction methods based on digital theory is focused on the exploration of new
digital formulas and algorithms. The genetic code is stored in DNA molecules as
sequences of bases: adenine (A) which pairs with thymine (T), and cytosine (C)
which pairs with guanine (G), The analog of DNA in a digital genetic algorithm
is a number of atoms, atomic numbers, analog codes, etc.
At mathematical
evolution of genetic processes, nucleotides TCAG are being transformed to
codons UCAG and later to amino acids and various organic composition.


Second
Position of Codon




U

C

A

G


F
i r s t P o s i t i o n 
U

1401

1653

1493

1561


C

1653

1401

1493

1561


A

1497

1497

1717

1397


G

1557

1557

1405

1589




6108

6108

6108

6108

Diagonal
D1 = 6108; Diagonal D2 = 6108
The atomic genetic
code describe a genotype, which is translated into an organism a phenotype by the
processes of cell division.
Mathematical
evolution of genetic processes is manifested in different ways. Evolution of
groups of atoms is especially interesting.
Here are some examples
Atomic codon square
A atomic
codon square of order n is an arrangement of n² numbers,
usually distinct integers,
in a square, such that the n numbers in all
rows, all columns, and both diagonals sum to the same constant. A digital square contains the integers
from 1 to n². The term "digital square" is also sometimes used
to refer to any of various types of word square.
Number of atoms
1401

1653

1493

1561

6108

1653

1401

1493

1561

6108

1497

1497

1717

1397

6108

1557

1557

1405

1589

6108

6108

6108

6108

6108


D1 = (1401+1401+1717+1589) = 6108; D2 =
(1561+1493+1497+1557) = 6108;
The
constant sum in every row, column and diagonal is called the magic
analogue constant or magic sum, M.
1401

1653

1493

1561

1653

1401

1493

1561

1497

1497

1717

1397

1557

1557

1405

1589

ê
6108
1401

1653

1493

1561

1653

1401

1493

1561

1497

1497

1717

1397

1557

1557

1405

1589

ê
6108
1401

1653

1493

1561

1653

1401

1493

1561

1497

1497

1717

1397

1557

1557

1405

1589

ê
6108
etc.
At this stage of our research we replaced nucleotides from the Amino
Acid Code Matrix with analogue of the atomic weight in those nucleotides.
A = 135; U = 112; C = 111; G = 151;
A = 531; U = 211; C = 111; G = 151;
Analogue codon table


Second
Position of Codon




U

C

A

G


F
i r s t P o s i t i o n 
U

2292

3732

3572

2452


C

3732

2292

3572

2452


A

3972

3972

2212

1892


G

2052

2052

2692

5252




12048

12048

12048

12048

Diagonal D1 = 3168; Diagonal D2 = 3168;
Analogue codon square
A analogue codon square of
order n is an arrangement of n² numbers, usually distinct integers,
in a square, such that the n numbers in all
rows, all columns, and both diagonals sum to the same constant
2292

3732

3572

2452

12048

3732

2292

3572

2452

12048

3972

3972

2212

1892

12048

2052

2052

2692

5252

12048

12048

12048

12048

12048


D1 = 12048; D2 = 12048
The
constant sum in every row, column and diagonal is called the magic analogue
constant or magic sum, M = 12048;;
Correlation:
2292

3732

3572

2452

3732

2292

3572

2452

3972

3972

2212

1892

2052

2052

2692

5252

ê
12048
2292

3732

3572

2452

3732

2292

3572

2452

3972

3972

2212

1892

2052

2052

2692

5252

ê
12048
2292

3732

3572

2452

3732

2292

3572

2452

3972

3972

2212

1892

2052

2052

2692

5252

ê
12048
etc
Determinsants in
Digital analogue Genetic Code
DET (4
x 4)
944

640

632

952

640

944

632

952

632

632

960

944

952

952

944

320

ê
74615095296000
ê
(12048+ 12048 + 12048…,
+ 12048);
There is a
mathematical balance within all of the phenomena in the analogue genetic code
matrix.
Mathematical
correlation of groups of nucleotides are a proof that genetic processes have
evolved from one mathematical shape to another one. They are a proof that we
can uncover some of hidden secrets in that science, with the help of
mathematics.
It is obvious that digital matrix of amino acid code evolved from
digital matrix of nucleotide code.
Mathematical
correlation of groups of nucleotides are a proof that genetic processes have
evolved from one mathematical shape to another one. They are a proof that we
can uncover some of hidden secrets in that science, with the help of
mathematics.
Perspectives
1. About importance
of the proposal
Development of science in following period will be based on contemporary
digital technology. To conquer new technology it would be far more efficient to
use method of reverse engineering for comprehension of phenomen in genetics. We'll
give a brief description of that method:
The genetic code tables used by the modern
science are characterized and determined by principles of biochemistry.
However, if in those tables, instead of the UCAG nucleotides we put the number
of atoms of those nucleotides, we will get the new tables of the genetic code
characterized and determined by programmatic and information principles.
Therefore, biochemistry can be explained through a phenomenon out of
biochemistry,
Particularly interesting results we will get when
determining numeric values for the information content of atoms and molecules.
We will then find out that those values express physical and chemical
characteristics of molecules. For example: in a DNA molecule, the
polynucleotide chains are connected through an exact cyberinformation
connections. In those molecules there are also mathematical matrixes of DNA,
represented by the number of atoms of four ATCG bases. These matrixes determine
the positioning of nucleotides in that molecule. With this, the biological
particularities of DNA are determined. Similar mathematical matrixes determine
the positioning of nucleotides in the RNA molecule. In the amino acid proteins,
they are interconnected into the respective mathematical chains. In those chains
are also matrixes where particular mathematical principles apply, the
principles that determine the positioning of each amino acid in the chain.
Therefore, the herewith discussed research results show that the process of
sequencing in biomacromolecules is conditioned and determined not only through
biochemical, but also through cybernetic information principles. The hypothesis
here is that the processes in an organism occur only when certain mathematical
conditions are met, i.e. when there is a certain mathematical correlation
between parameters in those processes. That correlation is expressed by the
respective methodology.
We would particularly like to stress here that
the genetic, as well as biochemical information in a broader sense of the word,
is determined and characterized by very complex cybernetic and information
principles. The constantans in those principles are: the number of atoms and
molecules, atomic numbers, atomic weight, physical and chemical parameters,
even and odd values, codes and analogue codes, standard deviations,
frequencies, primary and secondary values, and many other things
2. Where it might be useful
In view of this,
our findings might have a series of
impacts to the aforementioned work. We are devoted to provide a digital code
for each of 20 native amino acids. These digital codes should more complete and
better reflect the essence of each of the 20 amino acids. Therefore, it might
stimulate a series of future work by using the author’s digital codes to
formulate the pseudo amino acid composition for predicting protein structure
class, subcellular location, membrane protein type, enzyme family class, GPCR
type, protease type, proteinprotein interaction, metabolic pathways, protein
quaternary structure, and other protein attributes.
We can expect that
this discovery will significantly speed up the research of mutational genesis
of humans, molecular etymology, in applied biology and genetic engineering, and
also it will provide discoveries in new medicines and methods of medicinal
treatments.
3. Future
steps required
 Establish
scientificresearch project team for development of advanced
technologies in genetics, medicine and biochemistry.
 Project team
should make concrete program of scientificresearch work, where
they should define goals of research,
indispensable facilities for implementation of project, project duration,
budget, and other conditions.
3. Define rights and duties of all participants
in implementation of project.
4. To implement project defined by project
documentation.
Research in the field of fundamental sciences
 Decode matrix
of amino acid code and on the experimental way prove that the matrix
really exists. And after that, use that matrix to conquer top technologies
in the field of genetics.
 Decode matrix
of nucleotide code and digital codes which connect that matrix with matrix
of amino acid code. And use that matrix to conquer top technologies in the
field of biochemistry.
 Decode matrix
code in Tables of periodic system of chemical elements, and use that
matrix to conquer top technologies in the field of chemistry.
 Decode matrix
code in the nature, and use that matrix to conquer top technologies in the
field of all natural sciences.
 Decode matrix
code of chromosomes in human body.
 With the help
of above mentioned matrixes, decode map of human DNA.
 Decode matrix
code of processes in the field of nuclear physics.
 Decode
insulin matrix code, as well as all other codes from the field of
biochemistry.
 Other
research (Matrix code in Pascal's triangle, Matrix code in astronomy,
Matrix code in theoretical physics, determinism, etc.)
4.Paragraph
of limitations
1. Confirm that the manuscript has been
submitted solely to this journal and is not
published, in press, or submitted
elsewhere.
2.
Confirm that all the research meets the ethical guidelines, including
adherence to
the legal requirements of the study
country.
3. Confirm that you have completed and sent a Copyright Transfer
Agreement
(CTA) to the Editorial Office.
5.The
obtained results
The obtained results are
valid. In this manuscript, we proposed the universal genetic code. Mathematics
could confirm this fact with 100% scientific accuracy. For example, Table mathematical position of
the nucleotides in codon, Digital codon square, Analogue atomic genetic code,
Correlation of the code and analogue code Analogue codon table, Analogue codon square,
Determinsants in Digital analogue Genetic Code, Determinsants in Digital
analogue Genetic Code, Atomic weight Atomic codon square, etc.This mathematic system represents
that very universal formula of the genetic code which 100%
scientific accuracy. was looking for.
.
C O N C L U S I O N
It is a rewarding work to translate the biochemical language of amino acids into a digital language because it may be very useful for developing new methods for predicting protein sub cellular localization, membrane protein type, protein structure secondary prediction or any other protein attributes.
This is because ever since the concept of Chou's pseudo amino acid composition was proposed many efforts have been made trying to use various digital numbers to represent the 20 native amino acids in order to better reflect the sequenceorder effects through the vehicle of pseudo amino acid composition. Some investigators used complexity measure factor some used the values derived from the cellular automata, some used hydrophobic and/or hydrophilic values, some were through Fourier transform, and some used the physicochemical distance.
Now, it is going to
be possible to use the completely new strategy of research in genetics.
However, observation of all these relations which are the outcome of the
periodic law (actually, of the law of binary coding) is necessary, because it
can be of great importance for decoding conformational forms and
stereochemical and digital structure of proteins.
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