Progress in Biophysics and Molecular Biology 131 (2017) 354e368

Contents lists available at ScienceDirect

Progress in Biophysics and Molecular Biology

journal homepage: www.elsevier.com/locate/pbiomolbio

I-Ching, dyadic groups of binary numbers and the geno-logic coding in

living bodies
Zhengbing Hu a, Sergey V. Petoukhov b, c, *, Elena S. Petukhova b
a
Central China Normal University, No. 152 Louyu Road, 430079, Wuhan, China
b
Mechanical Engineering Research Institute of Russian Academy of Sciences, Malyi Kharitonievsky Pereulok, 4, Moscow, 101990, Russia
c
Moscow State Conservatory by P.I. Tchaikovsky, Bolshaya Nikitskaya, 13/6, Moscow, 125009, Russia

a r t i c l e i n f o a b s t r a c t

Article history: The ancient Chinese book I-Ching was written a few thousand years ago. It introduces the system of
Received 4 May 2017 symbols Yin and Yang (equivalents of 0 and 1). It had a powerful impact on culture, medicine and science
Received in revised form of ancient China and several other countries. From the modern standpoint, I-Ching declares the
25 August 2017
importance of dyadic groups of binary numbers for the Nature. The system of I-Ching is represented by
Accepted 29 August 2017
Available online 18 September 2017
the tables with dyadic groups of 4 bigrams, 8 trigrams and 64 hexagrams, which were declared as
fundamental archetypes of the Nature. The ancient Chinese did not know about the genetic code of
protein sequences of amino acids but this code is organized in accordance with the I-Ching: in partic-
Keywords:
Genetic code
ularly, the genetic code is constructed on DNA molecules using 4 nitrogenous bases, 16 doublets, and 64
I-Ching triplets. The article also describes the usage of dyadic groups as a foundation of the bio-mathematical
Binary numbers doctrine of the geno-logic code, which exists in parallel with the known genetic code of amino acids
Dyadic group but serves for a different goal: to code the inherited algorithmic processes using the logical holography
Walsh functions and the spectral logic of systems of genetic Boolean functions. Some relations of this doctrine with the I-
Hypercomplex numbers Ching are discussed. In addition, the ratios of musical harmony that can be revealed in the parameters of
DNA structure are also represented in the I-Ching book.
© 2017 Elsevier Ltd. All rights reserved.

Contents

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 354
2. About the I-Ching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 356
3. The genetic code systems and their matrix representations (“matrix-algebraic genetics”) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 357
4. The Ancient Chinese principle of cyclic changes and the matrices of DNA-alphabets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 359
5. Dyadic-shift matrices and hypercomplex numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361
6. Dyadic groups, Walsh functions and geno-logic coding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 362
7. The genetic code, linguistics and binary oppositions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 364
8. The genetic coding, oscillatory processes and musical harmony . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 365
9. Concluding remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 366
Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367

1. Introduction

Binary numbers and their dyadic groups occupy a very impor-

* Corresponding author. Mechanical Engineering Research Institute of Russian tant place in modern science and technology including computers,
Academy of Sciences, Malyi Kharitonievsky Pereulok, 4, Moscow, 101990, Russia. digital communication, systems of artificial intelligence, etc. But for
E-mail address: [email protected] (S.V. Petoukhov).

https://doi.org/10.1016/j.pbiomolbio.2017.08.018
0079-6107/© 2017 Elsevier Ltd. All rights reserved.
 Z. Hu et al. / Progress in Biophysics and Molecular Biology 131 (2017) 354e368 355

the first time binary numbers appeared in the Ancient Chinese The main table in the I-Ching book is the famous square table of
book “I-Ching”, which was written a few thousand years ago being 64 hexagrams in Fu-Xi's order (Fig. 1), which Chinese tradition
the oldest surviving book of human civilization (Legge, 1963; considers as a universal natural archetype. Each hexagram is a pile
Shchutskii, 1997; Wilhelm and Wilhelm, 1995). This book repre- of six broken and unbroken (solid) lines. According to the western
sents the Yin-Yang system where broken and unbroken (solid) lines tradition, these broken and unbroken lines are shown in the form of
symbolize Yin and Yang correspondingly. the binary symbols “0” and “1” and each hexagram represents a
By analogy with the alphabet of 4 nitrogenous bases (adenine, sequence of such six binary symbols. Fig. 1 demonstrates hexa-
cytosine, guanine and thymine) in the genetic DNA-molecules, the grams in both of these forms. Each position in all hexagrams has its
Yin-Yang system uses 4 bigrams with their conditional names: Old own individual number: in the western numeric presentation of a
Yang ( ), Old Yin ( ), Young Yang ( ) and Young Yin ( ). Fig. 1 hexagram, positions of its binary symbols are numbered left-to-
shows these bigrams in a possible form of the square matrix of the right by the numbers from 1 to 6; in the Chinese graphical pre-
second order. sentation, a numbering of the lines of each hexagram is read in the

Fig. 1. Left: the matrix representation of the 4 Chinese bigrams. Right: the table of 64 hexagrams in Fu-Xi's order where each of hexagrams is shown in the symbolic Chinese
tradition and also in a binary representation: each of solid or broken lines corresponds to 1 or 0 correspondingly. Chinese names of trigrams are also shown.
356 Z. Hu et al. / Progress in Biophysics and Molecular Biology 131 (2017) 354e368

sequence bottom-up. In the table of 64 hexagrams (Fig. 1) 8 tri- “transmitter-receiver” of information, the receiver knows the al-
grams (three-digit binary numbers or piles of three lines) indicate phabet of signals that can be transmitted to it by the transmitter.
its rows and columns. Each of hexagrams is a concatenation of 2 This knowledge is essential to provide noise-immune transmission
trigrams: the trigram of its row and the trigram of its column. of information.
Below we show that a quite similar table is realized for the genetic This paper develops the idea that the Yin-Yang system of the I-
set of 64 triplets. According to Ancient Chinese, “trigrams, hexa- Ching has deep analogies with the genetic code system and with
grams and their components in all possible combinatory combinations the basic structures in many fields of modern science, technology
form a universal hierarchy of classification schemes. These schemes in and culture.
visual patterns embrace any aspects of reality e spatial parts, time
intervals, the elements, numbers, colors, body organs, social and family 2. About the I-Ching
conditions, etc.” (Shchutskii, 1997, p. 10). The Ancient Chinese
claimed that this table of 64 hexagrams (Fig. 1) is the universal A great number of literature sources are devoted to I-Ching. Our
archetype of nature. The universality of this scheme, realized references include only a negligible part of a total quantity of these
independently from various interferences, implies that it possesses sources (Capra, 2000; Eremeev, 2005; Hesse, 1975; Kobzev, 1997;
the properties of noise-immunity. The Ancient Chinese knew McKenna and Mair, 1979; Needham, 1962; Petoukhov, 1999,
nothing about the genetic code, but the genetic code is arranged in 2008; Shchutskii, 1997; Schonberger, 1976; Stent, 1969; Swanson,
accordance with the I-Ching in many aspects (Petoukhov, 1999, 1984; Tusa, 1994; Vinogrodskiy, 2002; Wilhelm and Wilhelm,
2008; Petoukhov and He, 2010). 1995; Yan, 1991). Many of these sources label I-Ching as one of
A predecessor of the idea of computer Gottfried Leibniz, who the greatest and most mysterious human creations. From the
developed the concept of a universal language, was amazed by a viewpoint of the Chinese culture (the most ancient among all cul-
similarity of this table of 64 hexagrams with his own thoughts tures, which continue their existence on the Earth), I-Ching rep-
when he became acquainted with it: he considered himself as the resents something even more considerable: the creation made by
originator of the binary numeration system, which was already the Superperson, who embodied a secret of the Universe in special
presented in this ancient table. “Leibniz has seen in this similarity the symbols and signs.
evidence of the pre-established harmony and unity of the divine plan This book has a fundamental paradigmatic influence on the
for all epochs and for all people” (Shchutskii, 1997, p. 12). whole culture of the traditional China and the adjacent countries.
4 bigrams, 8 trigrams and 64 hexagrams of the I-Ching are The ideas expressed in it have created an original world-view and
connected with the notion “dyadic groups of binary n-bit numbers” methodology. They have influenced to a huge extent the develop-
(n ¼ 2,3,4, …), each of which contains 2n members (Harmuth, ment of philosophy, religion, natural sciences, literature and arts in
1989). For example, the dyadic group of 3-bit numbers contains 8 Ancient China. In view of this, the Chinese culture became abso-
members: lutely unique in the history of world culture. The symbols and
principles of I-Ching penetrated into all spheres of life of traditional
000, 001, 010, 011, 100, 101, 110, 111 (1) China e from theoretical conceptions and high art to household
subjects and decorations. Confucius said: “If it would be possible to
The known operation of the bitwise modulo-2 addition serves as extend my years, I would have given fifty of them for study of I-Ching“
the group operation in dyadic groups. It is denoted by the symbol 4 (Shchutskii, 1997). I-Ching declares a universality of the cyclic
and has the following rules: 0 4 0 ¼ 0; 0 4 1 ¼ 1; 1 4 0 ¼ 1; 1 4 principle of organization in nature. Traditional Oriental medicine is
1 ¼ 0. Modulo-2 addition is utilized broadly in the theory of discrete based on the viewpoints of this book.
signal processing as a fundamental operation for binary variables Many western scientists studied and used I-Ching. For example,
(Ahmed and Rao, 1975) . the creator of the analytical psychology C. Jung developed his
The modulo-2 addition of any two binary numbers from a doctrine about the collective unconscious in connection with this
dyadic group always results in a new number from the same group. book. According to Jung, the trigrams and the hexagrams of I-Ching
For example, modulo-2 addition of two binary numbers 110 and “fix a universal set of archetypes (innate psychic structures)”
101 from (1), which are equal to 6 and 5 respectively in decimal (Shchutskii, 1997, p. 12). Niels Bohr chose the Yin-Yang symbol as
notation, gives the result 110 4 101 ¼ 011, which is equal to 3 in his personal emblem. Many modern physicists, who feel the unity
decimal notation. The number 000 serves as the unit element of of the world, connect their theories with the ideas of traditional
this group: for example, 010 4 000 ¼ 010. The reverse element for Oriental culture, which unite all nature. For example, this has been
any number in this group is the number itself: for example, 010 4 reflected in the title “the eightfold way” of the famous book of Gell-
010 ¼ 000. Series (1) is transformed by modulo-2 addition of all its Mann and Ne'eman (1964). The intensive development of the self-
members with the binary number 001 into a new series of the same organizing and nonlinear dynamics of complex systems (syner-
numbers: 001, 000, 011, 010, 101, 100, 111, 110. Such changes in the getics) promotes the strengthening attention of western scientists
initial binary sequence, produced by modulo-2 addition of its to the traditional eastern world-view (e.g., see Capra, 2000). Special
members with any of binary numbers from (1), are termed dyadic groups study “Book of Changes” in many eastern and western
shifts (Ahmed and Rao, 1975; Harmuth, 1989). If any system of el- universities. Several conferences “I-Ching and modern sciences”
ements demonstrates its connection with dyadic shifts, it indicates were conducted in Moscow, Russia. The great number of sites in the
that the structural organization of the system is connected with the Internet is devoted to the similar studies. The influence of I-Ching is
logic modulo-2 addition. The works of (Petoukhov (2008, 2011); widely presented in modern life of Eastern countries. For example,
Petoukhov and He, 2010) show additionally that the structural or- the national flag of South Korea bears the symbols of trigrams. In a
ganization of the molecular-genetic system is connected with great number of specialized schools the instructors teach the stu-
dyadic shifts and correspondingly with modulo-2 addition. Dyadic dents about methodological aspects of practical application of
shifts are also involved in the patterns of molecular-genetic al- relevant ancient knowledge in medicine and in other fields. Ac-
phabets. In our work we pay special attention to non-trivial cording to some versions, I-Ching is a collection of knowledge,
structures of interrelated and structured alphabets of DNA which was obtained by Ancient well-trained individuals by means
and RNA since these alphabets are key elements in the noise- of their practices of meditations and inspirational conditions.
immune transmission of information. In the engineering systems One should note that I-Ching was written several thousand
 Z. Hu et al. / Progress in Biophysics and Molecular Biology 131 (2017) 354e368 357

years before the occurrence of modern Academies of sciences. It traits one can denote C ¼ T ¼ 1, A ¼ G ¼ 0. From the stand-
represents a set of statements of the unclear origin. From the point point of these traits any of DNA-sequences is represented by a
of view of a modern science, the book justifies a universal confor- corresponding binary sequence. For example, GCATGAAGT is
mity of these statements to the structure of nature without their represented by 010100001;
appropriate substantiation. Historically, the western academic sci- 2) two letters are amino-molecules (A and C) and the other two are
ence and its scientific laws (for example, Newton's laws, etc.) were keto-molecules (G and T). From the standpoint of these traits
developed without any connection with I-Ching by means of one can designate A ¼ C ¼ 1, G ¼ T ¼ 0. Correspondingly the
another methodology, though inspirational conditions, in which same sequence GCATGAAGT is represented by another binary
the person suddenly receives the complete picture of the answer to sequence 011001100;
his questions, are well-known in western science as well; it is 3) the pairs of complementary letters A-T and C-G are linked by 2
enough to recollect the famous history of the Periodic table of and 3 hydrogen bonds respectively. From the standpoint of
chemical elements which emerged to Mendeleyev in his sleep. For these binary traits one can designate C ¼ G ¼ 0, A ¼ T ¼ 1.
these reasons, many individuals consider I-Ching as a bright fact of Correspondingly the same sequence GCATGAAGT is read as
the Ancient Oriental culture but not as a valuable source of 001101101.
knowledge.
A well-known molecular geneticist (Stent (1969), p. 64) briefly Accordingly, each of DNA-sequences of nucleotides is the carrier
presented a hypothesis about possible connection between the of three parallel messages on three different binary languages. At
genetic code structures and the symbolic system of the I-Ching. the same time, these three types of binary representations form a
Several authors supported his hypothesis later. For example, the common logical set on the basis of logical operation of modulo-2
Nobel Prize winner in molecular genetics (Jacob (1974), p. 205) addition 4: modulo-2 addition of any two such binary represen-
wrote as well: “C'est peut-^ etre I Ching qu'il faudrait 
etudier pour saisir tations of the DNA-sequence coincides with the third binary rep-
les relations entre h
er
edit
e et langage” (it means in English: perhaps, resentation of the same DNA-sequence. The mentioned three
for revealing of relations between genetics and language it would representations of the sequence GCATGAAGT form a common
be necessary to study them through the Ancient Chinese I-Ching). logical set: for example, 010100001 4 011001100 ¼ 001101101.
In general, the viewpoint on the necessity of the profound analysis This fact is the initial evidence in favor that the system of genetic
of the named parallels and their possible expansion exists in mo- coding uses the Boolean algebra of logic with its binary tuples and
lecular genetics for 40 years. Our research on matrix-algebraic ge- logical operations such as modulo-2 addition. Profound analogies
netics (Petoukhov, 2008; Petoukhov and He, 2010; etc.) provides between genetic organization of living bodies and computers,
the additional materials to this area and to the hypothesis originally which are based on Boolean algebra, are described in (Petoukhov,
suggested by Stent. 2016b; Petoukhov and Petukhova, 2017a,b). In this article we
represent the analogies between the genetic organization and the
3. The genetic code systems and their matrix representations system of I-Ching.
(“matrix-algebraic genetics”) Information from the micro-world of genetic molecules dictates
the arrangement in the macro-world of living bodies under the
All living organisms are identical from the point of view of the conditions of strong noise and interference. This spanning is real-
molecular foundations of genetic coding of amino acid sequences in ized by means of unknown algorithms of multi-channel noise-
proteins. This coding is based on molecules of DNA and RNA. In DNA immunity coding. For example, in accordance with Mendel‘s laws
the genetic information is recorded using different sequences of of independent inheritance of traits, the colors of human skin, eye
four nitrogenous bases, which play the role of letters of the al- and hair are genetically defined independently. So, each living or-
phabet: adenine A, guanine G, cytosine C and thymine T (uracil U is ganism is an algorithmic machine of multi-channel noise-immune
used in RNA instead of thymine T) (Fig. 2, left). coding. To understand this machine one should use the theory of
Science does not know why the genetic alphabet of DNA has noise-immune coding, which is based on matrix representations of
been created by the Nature of just from four letters, and why just the digital information. This theory was developed by mathema-
these very simple molecules were chosen for DNA-alphabet (out of ticians for digital communication where similar problems of noise-
millions of possible molecules). But science knows (Petoukhov, immune transfer of information exist, for example, when we need
2008; Petoukhov and He, 2010; Stambuk, 1999; Fimmel et al., to transmit photos of the Martian surface to the Earth via electro-
2013) that these four molecules are interrelated by means of their magnetic signals traveling millions kilometers of interference.
symmetrical peculiarities into the united molecular ensemble with Below we borrow some formalisms of this mathematics to study
its three pairs of binary-oppositional traits (Fig. 2, right): genetic structures.
In noise-immune coding and also in quantum mechanics,
1) two letters are purines (A and G), and other two are pyrimidines Hadamard matrices play significant roles. By definition, a Hada-
(C and T). From the standpoint of these binary-oppositional mard matrix is a square matrix H with entries ±1, which satisfies

Fig. 2. Left: the four nitrogenous bases of DNA: adenine A, guanine G, cytosine C and thymine T. Right: three binary sub-alphabets of the genetic alphabet on the basis of three pairs
of binary-oppositional traits.
358 Z. Hu et al. / Progress in Biophysics and Molecular Biology 131 (2017) 354e368

H*HT ¼ n*E, where HT - transposed matrix, E  identity matrix. (Petoukhov, 2008). Entries of each columns are numerated in
Tensor (or Kronecker) exponentiation of Hadamard (2*2)-matrix H accordance with the first sub-alphabet in Fig. 1 (for example, the
generates a tensor family of Hadamard (2n*2n)-matrices H (n) triplet CAG and all other triplets in its column are combinations
(Fig. 2), rows and columns of which are Walsh functions (Ahmed “pyrimidine-purine-purine” and so this column is correspondingly
and Rao, 1975). Walsh functions are one of the main tools in numerated 011). By contrast, entries of each row are numerated in
communication technologies for noise-immunity coding. Below we accordance with the second sub-alphabet (for example, the same
use a known operation of tensor multiplication of genetic matrices triplet CAG and all other triplets in its row are combinations
by the following additional reason. DNA-molecules belong to the “amino-amino-keto” and so this row is correspondingly numerated
level of quantum mechanics, where the tensor multiplication is the 001).
important operation: when considering a quantum system con- Black and white cells of genetic matrices (C, A; T, G)(2) and (C, A;
sisting of two subsystems, the whole space of states is constructed T, G)(3) in Fig. 4 reflect the known phenomenon of segregation of
by the tensor product of their states. the set of 64 triplets into two equal sub-sets on the basis of strong
Hadamard (2n*2n)-matrices in Fig. 3 consist of 4, 16 and 64 en- and weak roots, i.e., the first two positions in triplets (Rumer, 1968;
tries. The DNA-alphabets also consist of 4 nitrogenous bases, 16 Fimmel and Strüngmann, 2016): a) black cells contain 32 triplets
doublets, and 64 triplets. By analogy we represent the system of with strong roots, i.e., with 8 “strong” doublets AC, CC, CG, CT, GC,
these alphabets in a form of the tensor family of square genetic GG, GT, TC; b) white cells contain 32 triplets with weak roots, i.e.,
matrices (C, A; T, G)(n) in Fig. 4 with additional binary numerations with 8 “weak” doublets AA, AG, AT, CA, GA, TA, TG, TT. Code
of their rows and columns on the basis of the following principle meanings of triplets with strong roots do not depend on the letters

Fig. 3. The beginning of the tensor (or Kronecker) family of Hadamard matrices H(n), where (n) means a tensor power. Black cells correspond to components “þ1”, white cells e to
“-1”.

Fig. 4. The tensor family of genetic matrices (C, A; T, G)(n) (n ¼ 1,2,3). Columns and rows of these matrices have binary numerations (see the explanation in text). Black cells of the
matrices contain 32 triplets with strong roots and also 8 doublets, which play the role of such strong roots.
 Z. Hu et al. / Progress in Biophysics and Molecular Biology 131 (2017) 354e368 359

on their third position; code meanings of triplets with weak roots theory of signal processing deals with multi-dimensional numbers
depend on their third letter (see details in (Petoukhov, 2016a)). and vector spaces by the following way. Signals are represented
Fig. 4 shows the unexpected phenomenological fact of a sym- there in the form of a sequence of the numeric values of their
metrical disposition of black and white triplets in the genetic ma- amplitude in reference points and they are interpreted as vectors of
trix (C, T; A, G)(3), which was constructed formally without any multi-dimensional spaces. In each tact time, a signal value is
mention about strong and weak roots, amino acids and the de- interpreted as the corresponding value of one coordinate of a multi-
generacy of the genetic code: dimensional vector in the space of signals. In this way, the theory of
discrete signals turns out to be the science of geometries of multi-
1) The left and right halves of the matrix mosaic are mirror-anti- dimensional spaces, where mathematics of matrices works effec-
symmetric each to other in its colors: any pair of cells, tively. On this geometrical basis, many methods and algorithms of
disposed by mirror-symmetrical manner in the halves, pos- recognition of signals and images, coding information, detections
sesses the opposite colors; and corrections of information errors, artificial intellect, and
2) both quadrants along each diagonals are identical from the training of robots are constructed. An investigation of symmetrical
standpoint of their mosaic; and structural analogies between computer informatics and ge-
3) the mosaics of all rows have meander configurations (each row netic informatics is one of the important tasks of modern science in
has black and white fragments of equal lengths) and they are connection with the creation of DNA-computers, DNA-robotics, and
identical to mosaics of some Walsh functions, which coincide the development of bioinformatics.
with Rademacher functions as the particular cases of Walsh Fig. 6 shows that the matrix V from Fig. 5 is a sum of 4 sparse
functions containing only numeric entries þ1 and 1 (Fig. 3); matrices: V ¼ v0 þ v1þ v2 þ v3. The set of these matrices v0, v1, v2, v3
4) each pair of adjacent rows of decimal numeration 0e1, 2e3, is closed under multiplication unexpectedly: multiplication of any
4e5, 6e7 has an identical mosaic (the realization of the prin- two matrices from this set gives a matrix from the same set. The
ciple “even-odd”). corresponding multiplication table of these 4 matrices (Fig. 6, right)
is identical to the multiplication table of the algebra of 4-
It should be noted that a huge quantity 64! z 1089 of variants dimensional hypercomplex numbers that are termed split-
exists for locations of 64 triplets in a separate (8*8)-matrix. For quaternions of J. Cockle and are well known in mathematics and
comparison, modern physics estimates the time of existence of the physics (Split-quaternion). From this point of view, the matrix V is
Universe in 4.35  1017 s. It is obvious that an accidental disposition the split-quaternion with unit coordinates.
of black and white triplets (and corresponding amino acids) in a Fig. 7 shows that the Walsh-representation W of the mosaic
(8*8)-matrix will almost never give symmetries. But in our matrix of 64 triplets from Fig. 4 is a sum of 8 sparse matrices,
approach this matrix of 64 triplets (Fig. 4) is not a separate matrix, W ¼ w0þw1þw2þw3þw4þw5þw6þw7, where w0 is the identity
but it is one of the members of the tensor family of matrices of matrix. The set of these sparse matrices is closed under multipli-
genetic alphabets, and in this case wonderful symmetries are cation and it defines the multiplication table (Fig. 7, bottom), which
revealed in the location of black and white triplets. These sym- is identical to the multiplication table of bi-split-quaternions of J.
metries testify that the location of black and white triplets in the set Cockle.
of 64 triplets is not accidental but reflects some hidden principles of Algebraic properties of the genetic matrices (Figs. 4 and 5) are
the genetic informatics. In particular these symmetrical matrices, not limited by the described ones in Figs. 6 and 7 but they include
schemes of which are analogical to the Ancient Chinese tables also the relations with the Yin-Yang algebra (Petoukhov, 2008;
(Fig. 1), are related with some kinds of hypercomplex numbers. Let Petoukhov and He, 2010) and multi-block united-hypercomplex
us consider this more attentively since genetic systems encode numbers (Petoukhov, 2017). These mathematical facts testify in
multi-parametric biosystems and this relation with hypercomplex favor that phenomenological structures of the genetic system,
numbers can be used in the mathematical models of bio- which are formally connected with tabular schemes of the I-Ching,
informational encoding. have their deep algebraic basis. The used type of decompositions of
Taking into account the phenomenological fact that each of rows genetic matrices (Figs. 6 and 7) is not arbitrary but is based on the
of the genetic matrices (C, A; T, G)(2) and (C, A; T, G)(3) (Fig. 4) co- principle of dyadic shifts and is called the dyadic-shift decompo-
incides with one of Walsh functions from the standpoint of their sition (see below).
meander-like mosaics, these symbolic matrices have their Walsh- Concerning the analogies between the genetic systems and
representations in a form of numeric matrices V and W (Fig. 5). Ancient Chinese notions, it is additionally interesting that four
The Walsh-representations differ from these symbolic matrices named bigrams (Fig. 1) were symbolized in Ancient China by the
only in the following: each of black (white) doublets and triplets is numbers 6, 7, 8, 9 (Shchutskii, 1997, p. 22, 522). But these four
replaced by decimal number þ1 (1). numbers characterize the quantity of protons in the chemical ele-
Below we show that these matrices (Fig. 5) are connected with ments, which form the molecules of the nitrogenous bases of DNA
some kinds of multidimensional numbers. It is interesting since the and RNA: carbon C has 6 protons (its ordinal number 6 in the pe-
riodic table), nitrogen N has 7 protons, oxygen O has 8 protons and
amino group (amides) NH2 has 9 protons.

4. The Ancient Chinese principle of cyclic changes and the

matrices of DNA-alphabets

I-Ching is devoted to cyclic changes and declares universality of

the cyclic principle of organization in nature. We show now that the
algebraic analysis of structured DNA-alphabets of 16 doublets and
64 triplets gives evidence of a connection of these phenomeno-
logical structures with the principle of cyclic permutations of po-
Fig. 5. Walsh-representations V and W of the mosaic matrices (C, A; T, G)(2) and (C, A; sitions inside doublets and triplets; figuratively speaking, the
T, G)(3) from Fig. 4, where each row is one of Walsh functions. principle of cyclic positional permutations is sewn into the genetic
360 Z. Hu et al. / Progress in Biophysics and Molecular Biology 131 (2017) 354e368

Fig. 6. Left: the matrix V from Fig. 5 is a sum of 4 sparse matrices v0, v1, v2, v3. Right: the multiplication table of the matrices v0, v1, v2, v3, where r0 is the identity matrix.

Fig. 7. Upper rows: the decomposition of the matrix W (from Fig. 5) into 8 sparse matrices: W ¼ w0þw1þw2þw3þw4þw5þw6þw7, where w0 is the identity matrix. Bottom row:
the multiplication table of these 8 matrices, which is identical to the multiplication table of bi-split-quaternions by J. Cockle.
 Z. Hu et al. / Progress in Biophysics and Molecular Biology 131 (2017) 354e368 361

structures. It should be added that modern technologies use cyclic variants of possible orders of positions inside triplets.
permutations as an important mathematical tool in discrete signal In each of these six matrices, each row has again a meander
processing (Ahmed and Rao, 1975; Boston, 2012). In modern studies configuration, which corresponds to one of Walsh functions for the
of genetic coding, a special attention is also paid to cyclic shifts eight-dimensional space. Correspondingly each of these matrices
connected with cyclic codes (Arque s and Michel, 1996; Michel, has its own Walsh-representation where black (white) cells
2012; Fimmel et al., 2014, 2016, 2015; Fimmel and Strüngmann, correspond to number þ1 (1). The same dyadic-shift decompo-
2015; Abo-Zahhad et al., 2014). sition of each of these matrices into 8 sparse matrices reveals that
Taking this into account, let us study cyclic changes of the ge- each set of 8 sparse matrices is closed under multiplication and
netic matrix of 64 triplets (Fig. 4) caused by cyclic permutations of corresponds to the same multiplication table in Fig. 7. In other
positions in triplets, which can be considered in parallel with cor- words, all 6 numeric matrices in Fig. 8 represent the same hyper-
responding cyclic changes of the Chinese table of 64 hexagrams complex number: bi-split-quaternion of J. Cockle with unit co-
caused by cyclic permutations in hexagrams (Fig. 1). The initial ordinates. In other words, under all these cyclical changes, the
order of positions 1-2-3 in triplets can be changed by permutations genetic matrices of 64 triplets retain their non-trivial algebraic
into the following orders: 1-2-3, 2-3-1, 3-1-2 under cyclic permu- essence.
tations in the direct reading of positions; 3-2-1, 2-1-3, 1-3-2 under
cyclic permutations under the reverse reading. For example, per-
5. Dyadic-shift matrices and hypercomplex numbers
mutations of positions in the triplet CAG transform it into the
triplets AGC, GCA, GAC, ACG, CGA.
As above mentioned, the dyadic groups of binary numbers are
Simultaneous identical permutations of positions in all triplets
connected with modulo-2 addition and matrices of dyadic shifts.
change black-and-white mosaic of the matrix of 64 triplets from
Fig. 9 shows an example of the matrices of dyadic shifts known in
Fig. 4. Fig. 8 shows mosaics of the matrix of 64 triplets for these 6
theory of digital signal processing (Ahmed and Rao, 1975). In this
matrix each row and column is binary numerated by analogy with
the Chinese table of 64 hexagrams (Fig. 1) and with the genetic
table of 64 triplets (Fig. 4).
Each row and each column of the matrix of dyadic shifts is
numerated by means of binary numbers from the dyadic group (1).
Each of matrix cells has its binary numeration from the same dyadic
group (1). This numeration of any cell is the result of modulo-2
addition of binary numerations of the column and the row of this
cell. For example, the cell from the column 110 and the row 101
obtains the binary numeration 011 by means of their modulo-2
addition. Such numerations of matrix cells are termed “dyadic-
shift numerations” (or simply “dyadic numeration”).
It is obvious that the Chinese table of 64 hexagrams and the
genetic matrix of 64 triplets can be also represented as the matrix of
dyadic shifts, if each of their cells is binary numerated by means of
modulo-2 addition of binary numerations of its row and column.
Ancient Chinese paid a special attention to a difference between
even and odd numbers, which are considered as Yin and Yang
numbers (or female and male numbers) correspondingly. Let us
also pay our attention to the location of even numbers 0, 2, 4, 6 and
odd numbers 1, 3, 5, 7 in the matrix of dyadic shifts (Fig. 9), which is
identical to the location of white and black cells in a chessboard.
Each row and each column of this black-and-white matrix has a
meander-like alternation of black and white cells, which coincides
with the meander alternation of elements þ1 and 1 in one of
Walsh functions in the Hadamard (8  8)-matrix (Fig. 3). Corre-
Fig. 8. The mosaics of 6 matrices of 64 triplets on the base of the matrix (C, A; T, G)(3)
(Fig. 4) in cases of different orders of positions in triplets: 1-2-3, 2-3-1, 3-1-2, 3-2-1, 1-
spondingly the dyadic-shift matrix (Fig. 9) has so called Walsh
3-2, 2-1-3. Numbers over each matrix show a relevant order of positions. Black (white) representation W123 in a form of the matrix with entries þ1 and 1
cells correspond to the triplets with strong (weak) roots. (Fig. 10). Here the index 123 means that this matrix is constructed

Fig. 9. The matrix of dyadic shifts. Parentheses contain expressions of binary numbers in decimal notation. Black color marks the cells with even numbers that is 0, 2, 4, 6 in decimal
notation.
362 Z. Hu et al. / Progress in Biophysics and Molecular Biology 131 (2017) 354e368

groups is defined in terms of Walsh functions for an application in

theory of switching functions in computers and digital technology
in the whole (Karpovsky et al., 2008). This section is devoted to the
additional data about a deep relation of Walsh functions with ge-
netic systems.
Walsh functions, which are rows of Hadamard matrices (Fig. 3),
are widely used in noise-immunity coding of information and in
many other tasks of digital signals processing (Ahmed and Rao,
1975; Seberry et al., 2005). For example, they are employed on
the spacecrafts “Mariner” and “Voyager” for the noise-immune
transfer of photos of Mars, Jupiter, Saturn, Uranus and Neptune to
Fig. 10. The Walsh representation W123 of the location of even and odd numbers in the Earth. Hadamard matrices are also used in quantum computers
dyadic-shift matrix (Fig. 9), which is connected with the Ancient Chinese table of 64 (“Hadamard gates”) and in quantum mechanics as unitary opera-
hexagrams (Fig. 1) and with the genetic matrix of 64 triplets (Fig. 4). tors. Complete systems of Walsh functions serve as a basis of the
“sequency theory” (Harmuth, 1989, 1977), which has led to effective
decisions in radio-engineering, acoustics, optics, etc. In particular,
for the case of the initial order of binary elements in triplets and
the problem of absorption of radio waves and acoustic waves,
hexagrams in Figs. 1 and 4 (below the matrices with cyclic per-
which is important for biological systems, is bypassed by means of
mutations of such order will be considered).
the “sequency analysis”. Hadamard matrices are employed in the
This Walsh representation W123 of the Ancient Chinese table of
logical holography (Morita and Sakurai, 1973) and in the spectral
64 hexagrams is connected with hypercomplex numbers widely
analysis of systems of Boolean functions (Karpovsky et al., 2008).
used in modern science. Fig. 7 shows an example of these con-
The following phenomenological fact testifies additionally about
nections where the matrix W123 (Fig. 10) is decomposed into 8
a hidden role of Walsh functions in the genetic systems. Inside the
sparse matrices v0, v1, v2, v3, v4, v5, v6, v7. The set of these 8 matrices
DNA-alphabet A, C, G and T, thymine T has a unique status and
is closed under multiplication: multiplication of any two matrices
differs from other three letters:
from this set gives a matrix from the same set. The multiplication
table (Fig. 11) of this set corresponds to one of kinds of hyper-
1. Only thymine T is replaced by another molecule U (uracil) in
complex numbers called as “hyperbolic matrions” (Petoukhov,
transferring from DNA to RNA;
2008; Petoukhov and He, 2010). One can additionally note that
2. Only thymine T does not have the functionally important amino
such special kind of decomposition of matrices is called as dyadic-
group NH2.
shift decompositions by the following reason. Each of these sparse
matrices vk (k ¼ 0,1,2, …,7) in Fig. 11 contains only those non-zero
This binary opposition can be expressed as: A ¼ C ¼ G ¼ þ1,
entries of the initial matrix W123, which belong to cells with
T ¼ 1. Correspondingly in each of the triplets its letters can be
appropriate decimal number k in the dyadic-shift matrix in Fig. 9.
replaced by these numbers to represent numerically the triplet as a
For example, all non-zero entries of the sparse matrix v0 are taken
product of these numbers (for example, the triplet CTA is repre-
from cells of W123 corresponded in their location to cells of the
sented by number 1*(-1)*1 ¼ 1). In this case the symbolic matrices
dyadic-shift matrix (Fig. 9) with decimal number 0; all non-zero
(C, A; T, G)(2) and (C, A; T, G)(3) in Fig. 4 become Hadamard matrices
entries of the matrix v1 are taken from cells of W123 corre-
H(2) and H(3) in Fig. 3. The sets of rows in H(2) and H(3) contain
sponded in their location to cells of the dyadic-shift matrix with the
complete orthogonal systems of Walsh function for 4-dimensional
decimal number 1, etc. Note that the useful decompositions in the
and 8-dimensional spaces correspondingly. The term “complete”
previous section (Figs. 10 and 11) were dyadic-shift ones. The dis-
means here that any numeric vector of 4-dimensional or 8-
covery of communications of the matrix W123 with basic elements
dimensional spaces can be represented in a form of a super-
of hypercomplex numbers - via its dyadic-shift decomposition e
position of these Walsh functions.
gives an additional evidence of the useful role of modulo-2 addition
The ideas of ancient Chinese about the structural kinship of the
for modeling of molecular-genetic systems and for analyzing the
microcosm and the macrocosm resemble the phenomenology of
ancient system of I-Ching.
modern holography, where it is possible to reconstruct a holistic
The simultaneous cyclic permutations of positions in all binary
image from a piece of a hologram. In biosciences many works are
3-bit numerations of rows and columns of the dyadic-shift matrix
devoted to the hypothesis about possible connections of hologra-
(Fig. 9) generate new mosaic matrices. Their dyadic-shift decom-
phy with brain and other functions including associative memory,
position into 8 sparse matrices reveals that each of them is con-
physiological processing visual information, etc. (see for example
nected with the same multiplication table of hyperbolic matrions
(Greguss, 1968; Petoukhov, 2016b; Petoukhov and Petukhova,
(Fig. 11). Other kinds of decompositions of the “chessboard” matrix
2017a,b; Pribram, 1971)). Here one should mention that the
W123, which is related with I-Ching, reveal its connection with so
dyadic groups and Walsh functions form a basis of the so-called
called systems of “multiblock united-hypercomplex numbers”
logical holography. Physical holography, which possesses the
introduced in Petoukhov (2017).
highest properties of noise-immunity, is based on a record of
standing waves from two coherent physical waves of the object
6. Dyadic groups, Walsh functions and geno-logic coding beam and of the reference beam (Soroko, 1980). But physical waves
can be modeled digitally. Correspondingly noise-immunity and
The described materials show the importance of binary other properties of optical and acoustical holography can be
numbers, their dyadic groups and modulo-2 addition for mathe- modeled digitally, in particular, using Walsh functions and logic
matical analysis and modeling significant genetic structures, which operations concerning the dyadic groups of binary numbers
are related with Yin-Yang schemes of I-Ching. As it is known, the because Walsh transforms are Fourier transforms on the dyadic
dyadic groups of binary numbers are connected with the complete groups. This can be made on the basis of discrete electrical or other
orthogonal systems of Walsh functions, which are their algebraic signals without any application of physical waves. A pioneering
characters (Fine, 1949). Therefore, the Fourier analysis on dyadic work about the “holography by Walsh waves” was performed by
 Z. Hu et al. / Progress in Biophysics and Molecular Biology 131 (2017) 354e368 363

Fig. 11. Upper rows: the dyadic-shift decomposition of the matrix W123 (Fig. 10) into 8 sparse matrices: W123 ¼ v0þv1þv2þv3þv4þv5þv6þv7. Bottom: multiplication table of 8-
dimensional hypercomplex numbers called as hyperbolic matrions.

Morita and Sakurai (1973). The work was devoted to Walsh waves For example, a supposition about the histone code is well known
(or Walsh functions), which propagate through electronic circuits (Histone Code, 2016). No mathematical approaches have been
(composed of logical and analog elements) by the analogy with the proposed to model such additional kinds of the genetic code.
optical Fourier transform holography. In this digital Walsh- It is obvious that the knowledge of regularities of the genetic
holography, the objects, whose digital holograms should be encoding of the structures of amino acid sequences is not sufficient
made, are represented in the forms of 2n-dimensional vectors. Each for understanding and explaining the enormous class of inherited
component of these vectors corresponds to one of 2n input chan- processes and principles of an algorithmic character: congenital
nels of appropriate electric circuits; the same is true for 2n output coordinated motions of living bodies, innate principles of sensory
channels, which are related with the components of resulting information processing, congenital instincts and spatial represen-
vectors. Due to the application of Walsh transformation, the in- tations, and so forth. We postulate that another kind of the bio-
formation about such vector is written in each component of the logical code exists in parallel with the genetic code of amino acid
appropriate hologram, which is also a 2n-dimensional vector, to sequences. We name conditionally this second code as “the geno-
provide a nonlocal character of storing information. logical code” since - on the basis of our research - we believe that
The epoch-making discovery of the genetic code of amino acid this biological code is connected with the logical operations and
sequences in proteins has revealed the molecular genetic com- logical functions, dyadic groups of binary numbers, Walsh func-
monality in the diversity of species of living organisms. Some au- tions, logical holography and the spectral logic of systems of
thors supposed that other kinds of genetic coding could also exist. Boolean functions (Petoukhov, 2016b; Petoukhov and Petukhova,
364 Z. Hu et al. / Progress in Biophysics and Molecular Biology 131 (2017) 354e368

2017a,b). We believe that DNA and RNA molecules are not only the system or separate kinds of proteins such as abovementioned
carriers of the genetic code of amino acid sequences but they are tubulin (Petoukhov, 2016b; Petoukhov and Petukhova, 2017a,b). It
also participants of the geno-logic code, which encodes logical is known that artificial intellect, which possesses an ability of
functions and which is connected with epigenetic mechanisms. reproducing features of biological intellect, cannot be constructed
DNA is an important part of this integrated coding system, pecu- without the usage of mathematical logic (Yaglom, 1980), therefore
liarities of which are reflected in the structures of DNA-alphabets the idea of the geno-logical coding is very natural. An example of a
and in the features of degeneracy of the genetic code of amino spider that is creating in an intellectual manner a spiderweb with
acids. The integrated coding system contains not only the code of up to 7 types of its threads and simultaneously solves the problem
amino acid sequences but also the code of sets of logic functions. of securing the edges of the spiderweb on adjacent supports,
We are developing a relevant mathematical doctrine about this speaks of the inheritance of intellectual properties in living bodies.
biological code. Below we describe our approaches to this theme. Modeling of such phenomena of inherited intelligence is one of the
As known, newborn turtles and crocodiles, when they hatch tasks of the theory of geno-logic coding.
from eggs, crawl with quite coordinated movements to water
without any training from anybody. Celled organisms, which have 7. The genetic code, linguistics and binary oppositions
no nervous systems and muscles, move themselves by means of
perfectly coordinated motions of cilia on their surfaces (the Our oral speech is a part of bioinformatics in a broad sense.
genetically inherited “dances of cilia”). In these inherited motions, a Many researchers have long associated the language of people's
huge number of muscle fibers, nerve cells, contractile proteins, communication with genetic coding.
enzymes and so forth are acting in concert by analogy with the Impressive discoveries in the field of the genetic code have been
coordinated work of multiple parts of computers. described by its researchers using the terminology borrowed from
Computers work on the basis of networks of two-positional linguistics and the theory of communications. As experts in mo-
switches (triggers), each of which can be in one of two states: lecular genetics remark, “the more we understand laws of coding of
“yes” or “no”. But in physiology, the similar law “all-or-none” (All- the genetic information, the more strongly we are surprised by their
or-None Law, 2016) for the components of excitable tissues exists: a similarity to principles of linguistics of human and computer lan-
nerve cell or a muscle fiber give only their answers “yes” or “no” guages” (Ratner, 2002, p. 203). Linguistics is one of the significant
under the action of different stimulus by analogy with the Boolean examples of existence and importance of ensembles of binary op-
variables and the Yin-Yang principle. If a stimulus is above a certain positions in information physiology.
threshold, a nerve or muscle fiber will fire with full response. Leading experts on structural linguistics believed for a long
Essentially, there will either be a full response or there will be no time that human languages were formed not from an empty place,
response (Igamberdiev and Shklovskiy-Kordi, 2017; Kaczmarek and but they represent a continuation of the genetic language or,
Levitan, 1987; Martini, 2005). A separate muscle, which contains somehow, they are closely connected with it, confirming the idea
many muscle fibers, can reduce its length in a different degree due of the information commonality of organisms. Analogies between
to the combined work of the multiplicity of its muscle fibers. Ner- the systems of genetic and linguistic information are the contents
vous system can also react differently to a stimulus of a different of a wide and important scientific sphere, which can be illustrated
force by means of combined excitations of its multiple nerve fibers here only briefly. We reproduce below some topical thoughts of
and also due to the ability to change the frequency of the genera- Jakobson (1985, 1987, 1999), who was one of the most famous
tion of nerve impulses at their fixed amplitude. experts and the author of a deep theory of binary oppositions in
Penrose (1996) in his thoughts about biological quantum com- linguistics. Jakobson and others share the same views that we
puters appeals to the known fact that tubulin proteins exist in two possess a language, which is as old as life and which is the most
different configurations, and they can switch between these con- alive among all languages. Among all systems of information
figurations like triggers to provide bio-computer functions. transfer, only the genetic code and linguistic codes are based on
Taking these known facts into account, we suggest considering a the use of discrete components, which in themselves have no
living organism as a genetically inherited huge network of triggers meaning, but serve for the construction of the minimum units,
of different types and different biological levels, including trigger which possess meaning. In both cases of the genetic language and
subnets of tubulin proteins, muscle fibers, neurons, etc. From this of a linguistic language, we deal with the separate units which
perspective, biological evolution can be represented as a process of have no meaning, but get a meaning after their special grouping. A
self-organization and self-development of the systems of biological similarity between both information systems is not depleted by
trigger networks. Correspondingly, the Darwinian principle of this fact at all. According to Jakobson, all relations among lin-
natural selection can be interpreted in a certain degree as a selec- guistic phonemes are decomposed into a series of binary oppo-
tion of biological networks of triggers together with the appro- sitions of elementary differential attributes (or traits). By analogy,
priate systems of Boolean functions for a coordinated work of these the set of the four letters of the DNA-alphabet contains three bi-
networks. In light of this it is not so surprising that the genetic nary sub-alphabets (Fig. 2), which allows to number columns and
system, that provides transmission of corresponding logic net- rows of the genetic matriсes (C A; T G)(n) (Fig. 4) in parallel with
works along the chain of generations, is also built on the principles the Ancient Chinese table (Fig. 1). As Jakobson stated, the genetic
of dyadic groups and operations of the Boolean algebra of logic. code system is the basic simulator, which underlines all verbal
Digital computers work on the basis of binary numbers and codes of human languages. “The heredity in itself is the fundamental
Boolean algebra. Hypotheses about the analogies between func- form of communications … Perhaps, the bases of language structures,
tioning of living organisms and computers exist long ago (see for which are imposed on molecular communications, have been con-
example (Penrose, 1996; Liberman, 1972; Hameroff and Penrose, structed by its structural principles directly” (Jakobson, 1985, p.
1996, 2014; Igamberdiev and Shklovskiy-Kordi, 2016, 2017; Ji, 396). These questions have arisen to Jakobson as a consequence of
2012)). Our results of studying molecular-genetic systems lead to its long-term researches of connections between linguistics,
the evidence that genetic systems function on the basis of logical biology and physics. Such connections were considered at the
operations of the Boolean algebra and the dyadic groups of binary united seminar of physicists and linguists, which was organized by
numbers. This is important since the level of the molecular-genetic Niels Bohr and Roman Jakobson jointly at the Massachusetts
system is deeper than the secondary levels of inherited nervous Institute of Technology.
 Z. Hu et al. / Progress in Biophysics and Molecular Biology 131 (2017) 354e368 365

“Jakobson reveals distinctly a binary opposition of sound attri- electrical oscillations is analogical (so called “electro-mechanical
butes as underlying each system of phonemes … The subject of analogies”). Taking these Eastern and Western materials into ac-
phonology has changed by him: the phonology considered count, we have conducted a special study, which revealed that the
phonemes (as the main subject) earlier, but now Jakobson has structural organization of the genetic code system corresponds to
offered that distinctive attributes should be considered as mathematics of resonances of oscillatory systems with many de-
“quantums” (or elementary units of language) … Jakobson was grees of freedom and that a living organism can be hypothetically
interested especially in the general analogies of language represented - from some standpoint - as a musical synthesizer with
structures with the genetic code, and he considered these an abundance of rearrangements of resonant modes (Petoukhov,
analogies as indubitable” (Ivanov, 1985). One can remind also of 2016a).
the title of the monograph “On the Yin and Yang nature of Ancient Chinese possessed the highest musical culture. Music
language” (Baily, 1982), which is characteristic for the subject of was the cornerstone in the Chinese civilization, which is the longest
binary oppositions in linguistics. living culture in history. Even the national system of measures and
weights has been constructed in connection with musical in-
struments. This fact has no precedents in history of civilizations
Similar questions about a connection of linguistics with the
(Needham, 1962; Eremeev, 2005, p. 76). According to the notions of
genetic code excite many researchers. In addition, many re-
Ancient Chinese, music is present at the origin of the world and
searchers perceive the linguistic language as a living organism. The
plays a spatiotemporal role: music represents a microcosm
book “Linguistic genetics” (Makovskiy, 1992) states: “The opinion
reflecting the structure of the Universe. Musical rules are repro-
about language as about a living organism, which is submitted to the
duced in different fields of culture. Briefly speaking, music in the
laws of a nature, ascends to a deep antiquity … Research of a nature, of
Ancient China was considered as a general natural archetype. Old
disposition and of reasons of isomorphism between genetic and lin-
Chinese music was used intensively in the ancient therapy with
guistic regularities is one of the most important fundamental problems
success according to many literature sources. It is interesting
for linguistics of our time”.
because this music is based on such a music scale, which is con-
In parallel with Jakobson's data on the key importance of binary
nected with the genetic code in its matrix form of presentation
oppositions in structural linguistics, we emphasize the key role of
(Darvas et al., 2012; Hu and Petoukhov, 2017; Petoukhov, 2008;
binary oppositions in genetic structures. But unlike his remarkable
Petoukhov and He, 2010).
studies, we pay attention not only to binary oppositions, but also
Long before Pythagoras the Ancient Chinese used the musical
develop matrix-algebraic analysis of genetic structures using such
system known in Europe under the name Pythagorean musical
mathematical notions and tools as dyadic groups, matrices and
scale (the analysis of these questions is presented in detail in the
their tensor products, Walsh functions, hypercomplex numbers,
book (Needham, 1962, v.4)). In the antique theory of music the
etc. We believe that the achievements of matrix-algebraic genetics
word “harmony” found its modern value - the consent of discor-
and its mathematical notions and tools will be useful for revealing
dant. Seven musical notes carry the names familiar to all: Do (C), Re
deep connections between genetic and linguistic languages. This
(D), Mi (E), Fa (F), Sol (G), La (A), Si (B). These seven notes are
matrix-genetic approach is capable of enriching its own arsenal of
interrelated among themselves by their frequencies not in an
structural linguistics as a roughly developing science and to clear a
accidental manner, but they form the regular uniform ensemble.
problem of the unified bases of biological languages. It can be
Really, it is well known that the seven notes of the Pythagorean
applied to researches on evolutionary linguistics, the analysis and
musical scale from appropriate octaves form the regular sequence
synthesis of poetic forms, cliodynamics (Igamberdiev, 2017), etc.
of the geometric progression on the base of the quint ratio 3:2
between frequencies of the adjacent members of this sequence
8. The genetic coding, oscillatory processes and musical (Fig. 12). The quint 3:2, which is the ratio between frequencies of
harmony the third and the second harmonics of an oscillated string, plays the
role of the factor of this geometrical progression. The frequency
The idea about the organization of the world, including living 293 Hz of the note Re (D1) of the first octave stays in the middle of
matter, on the basis of vibrations, is one of the oldest. It was this frequency series. The ratios of the frequencies of all notes to
manifested by the thinkers of Ancient India, Ancient China and this frequency of the note Re (D1) form the symmetrical series by
Ancient Greece. For example, in India, there was a doctrine of the signs and sizes of their powers of the quint: from the power “-3” up
highest sound “Nado-Brahman” as the germ of the whole Universe, to the power “þ3”.
which is the multitude of vibrations of particular frequencies. Due to the cosmic meaning of music in Ancient China, this quint
In our time many works are devoted to vibrations and reso- scale was preferable for ancient Chinese in comparison with an
nances in the organization of the world and living matter. For equal temperament scale, which was known for them many cen-
example, Nikola Tesla argued that all the connections between turies ago as well. This Chinese system was borrowed by Pythagoras
phenomena are established exclusively by various simple and in many aspects (Needham, 1962, v.4). The Pythagorean doctrine
complex resonances - the coordinated vibrations of physical sys- (that the world is arranged by the principles of musical harmony)
tems. The book “Vibration Medicine” (Gerber, 2001) calls resonance has arisen not at empty place. This doctrine was developed under
the key to understanding and managing any system that opens the an influence of the more ancient Oriental doctrines in some aspects.
door to the invisible world of life processes. Twice Nobel laureate
Linus Pauling created the theory of resonance interactions of mol-
ecules in a living organism; his book (Pauling, 1940) about it
became the most cited among the books of the 20th century.
The organism is a huge chorus of coordinated oscillatory pro-
cesses. Since ancient times, chronomedicine claims that all diseases
are a consequence of discrepancies in this chorus (desynchronosis). Fig. 12. The quint (or the fifth) sequence of the 7 notes of the Pythagorean musical
scale. The upper row shows the notes. The second row shows their frequencies. The
In living bodies mechanical and electrical oscillations are closely third row shows the ratios between the frequencies of these notes to the frequency
connected because many tissue are piezo-electrical: nucleic acids, 293 Hz of the note Re (D1). The designation of notes is given on Helmholtz system.
bone, actin, dentin, tendons, etc. Mathematics of mechanical and Values of frequencies are approximated to integers.
366 Z. Hu et al. / Progress in Biophysics and Molecular Biology 131 (2017) 354e368

The Pythagorean musical scale, which is based on the quint ratio by number 2*3*2 ¼ 12. In such approach, each of 64 triplets is
3:2, played the main role in these views. In Ancient China this quint represented by one of the following numbers of hydrogen bonds 8
music scale had a cosmic meaning connected with I-Ching: (¼23), 12 (¼22*3), 18 (¼2*32), 27 (¼33), the pairwise relations be-
numbers 2 and 3 were named “numbers of Earth and Heaven” tween which are equal to the quint 3/2 in integer powers, for
there. A connection of the basis of music with the numbers 2 and 3 example, 27/8 ¼ (3/2)3, 18/8 ¼ (3/2)2, etc. Accordingly, each DNA
is expressed in the classical work of literature “Spring and Autumn” molecule as a chain of the hydrogen bonds is characterized by its
by Lu Bu We: “The origins of music lie far back in the past. Music arises own sequence of the quint 3/2 in different integer powers.
from Measure and is rooted in the great Oneness. … Music is founded If pairs of adjacent triplets in DNA are considered, then DNA
on the harmony between heaven and earth, on the concord of molecule appears as a quint sequence of 7 kinds of numbers of
obscurity and brightness” (this citation is taken from the book of hydrogen bonds: 64 (¼26), 96 (¼25*3), 144 (¼24*32), 216 (¼23*33),
(Hesse (1975), p. 31), a Nobel Prize winner and an expert of I- 324 (¼22*34), 486 (¼2*35), 729 (¼36). Pairwise ratios in this series
Ching). These words about Earth and Heaven relate directly to the of numbers are equal to the quint 3/2 in the same powers as in the
numbers 2 and 3, which symbolized Earth and Heaven in Ancient Pythagoras 7-stage scale (Fig. 12). If, for example, the frequency of
China (including Chinese music) and which transform the table of 87 Hz of the note “F” (Fig. 12) is compared to the number 64, then
64 hexagrams into the quint matrix (3 2; 2 3)(3) (Petoukhov, 2008; all the rest numbers of this set will correspond to the other notes of
Petoukhov and He, 2010). The words about the concord of obscurity the Pythagoras scale. Then any sequence of triplet can be associated
and brightness correspond to the known fact that the Chinese uniquely with a sequence of notes of the Pythagoras scale (“genetic
musical system contained 12 sounds, each of which had a magic music in the Pythagoras scale”).
sense: the odd sounds personified brightness, active forces of The quint ratios are realized in DNA not only for the hydrogen
Heaven; the even sounds personified obscurity, passive forces of bonds of complementary bases, but also for several other param-
Earth (Eremeev, 2005). eters, such as quantities of atoms in the rings of purines and py-
After Ancient China, Pythagoreans considered numbers 2 and 3 rimidines (numbers 9 and 6 with the ratio 3/2), or the amount of
as the female and male numbers, which can give birth to new protons in the rings of complementary nitrogenous bases (numbers
musical tones in their interconnection. Ancient Greeks attached an 60 and 40 with the ratio 3/2), and others (Petoukhov, 2008). Chains
extraordinary significance to the search of the quint 3:2 in natural of these parameters in DNA form their own sequences of the quint,
systems because of their thoughts about musical harmony in the which correspond to sequences of notes of quint scales. In other
organization of the world. For example, the great mathematician words, Nature created DNA as a plexus of various sequences of the
and the engineer Archimedes considered as the best result of his quint in different integer powers (“quint polyphony of DNA”).
life the detection of the quint 3:2 between volumes and areas of a Our recent works (Hu and Petoukhov, 2017; Petoukhov, 2008;
cylinder and a sphere entered in it (Voloshinov, 2000). Just these Petoukhov and He, 2010) demonstrate that the quint musical scale
geometrical figures with the quint ratio were pictured on his is connected with the tensor family of so called quint matrices (3, 2;
gravestone according to Archimedes testament. And due to these 2, 3)(n), which represents the tensor family of genetic matrices (C, A;
figures Cicero found Archimedes grave later, 200 years after his T, G)(n) in the case of the replacement of nitrogenous bases by their
death. quantities of hydrogen bonds: C ¼ G ¼ 3, A ¼ T ¼ 2. If the square root
Many modern scientists paid their attention to relations of from any quint matrix is taken, the result is a “golden” matrix (4,
natural systems with musical harmony. For example, according to 41; 41, 4)(n), all elements of which are precisely equal to the
some prominent crystallographers - C.S. Weiss, J. Grassman, V. golden section 4¼(1þ50.5)/2 ¼ 1618 … in different integer powers
Goldschmidt - ratios of musical harmony are implemented in (quint matrices have a “backing” in the form of “golden” matrices).
structures of crystals (Berger, 2001; Hu and Petoukhov, 2017; The theme “the quint 3/2” and the theme “the golden section 4” are
Petoukhov, 2008; Petoukhov and He, 2010). When atomic physics interrelated. Using this mathematical relation, a new system of
revealed the spectral series in the hydrogen atom, A. Einstein and A. musical scales has been proposed under its name “Fibonacci-stage
Sommerfeld named them “the music of atomic spheres”. The scales” since many parameters of these scales are expressed by
prominent Russian biophysicist S. Shnoll (1989) wrote: “From Fibonacci-numbers (Petoukhov, 2008). Now this system is actively
possible consequences of interaction of macromolecules of enzymes, used in the Moscow State Conservatory by professional composers
which are carrying out conformational (cyclic) fluctuations, we shall to create pieces in new musical spaces on the basis of Fibonacci-
consider pulsations of pressure - sound waves. The range of numbers of stage scales. The Moscow Conservatory has already conducted a
turns of the majority of enzymes corresponds to acoustic sound fre- few concerts of this “genetic” music in Europe and Russia (their
quencies. We shall consider … a fantastic picture of “musical in- fragments are shown at sites http://youtu.be/gagKLDuO9z8, https://
teractions” among biochemical systems, cells, bodies, and a possible www.youtube.com/watch?v¼kxxH3-793WQ&feature¼youtu.be,
physiological role of these interactions. … It leads to pleasant thoughts http://pentagramon.com/video). Researches of a possible applica-
about nature of hearing, about an origin of musical perception and tion of genetic music in the field of musical therapy on the basis of
about many other things, which belong to area of biochemical aes- the mentioned musical scales, which are connected with the pa-
thetics already”. rameters of DNA and with schemes of I-Ching, are conducted by our
A few years ago an attention was drawn to the fact that the team in Moscow taking into account relevant data on musical
relationship of quint musical harmony is realized in a parametric therapy in Ancient China and in many modern countries. At this
structure of DNA molecules (Petoukhov, 2008). In DNA, comple- stage of our knowledge, the ideas developed in sections 7 and 8 on a
mentary pairs of nitrogenous bases exist: adenine-thymine (A-T) possible connection of musical therapy and linguistics with the
and cytosine-guanine (C-G) with 2 and 3 hydrogen bonds in them, genetic structures include assumptions, expectations and beliefs in
respectively. Correspondingly a numeric representation of these contrast to the exact scientific argumentation in the first sections of
code letters exists: A ¼ T ¼ 2, C ¼ G ¼ 3. From this point of view, the paper.
DNA is a chain of numbers 3 and 2 of the hydrogen bonds.
The genetic code encodes sequences of amino acids in proteins 9. Concluding remarks
by means of 64 triplets. Since A ¼ T ¼ 2, C ¼ G ¼ 3, each triplet has a
numeric representation as a product of number of hydrogen bonds The principle of the universal binary symbolization, which is
of its constituent letters. For example, the triplet ACT is represented presented in the Ancient Chinese book I-Ching in graphical forms,
 Z. Hu et al. / Progress in Biophysics and Molecular Biology 131 (2017) 354e368 367

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