The  binary  rule  of  DNA

Wenjian  Zhou

( The barley Center of Zhejiang Academy of Agriculture Science,

No.198 Shiqiao Road, Hangzhou,  Zhejiang province, China,  P C: 310021 )

Abstract

It is well known, life is composed of protein, and protein is composed of amino acid, amino acid is controled of DNA. Then, if we can make clear about the rule of sequence in DNA, secret of life will be discovered.

At present, two western biologists have gotten a macroscopical qualitative rule about DNA, -- the famous “ Double screw frame “. Base on it, almost all of biologists of different countries pay theirs attention into quantitative studying on pieces of DNA and studying genes quantitatively in the field of molecular biology. And the main study technique is analyzing sequence of genes through modern instrument-code of DNA., However, what can we gain from this scrap data of the research? How can we apply it into practice? Can we understand the essence of rule in DNA in a whole through it?

If we consider this question resorting to the eastern philosophy wisdom of whole eyesight, especially is the way from“ YiJing ”—a book discovering the change of nature, we will get a surprise result, that is, DNA code is a group of very exact and regular binary numbers. However, I don’t know how to use this discover till now, The further problem is, what control the code of DNA, and make it compose by binary rule? It is a kind of certain information, and information is something “invisible“.

Key word: protein, amino acid, DNA, binary.

A. Foreword

One time, when I was reading a book that is the best abstract about Chinese philosophy thought and culture headstream named “ YiJing “, found by chance that there is a few relation between it rule and DNA code, studied it carefully, and found that the DNA is a group of data code which is formed by binary rule.

It is why I wrote such a article, maybe it is not fitting requests of technical paper, but perhaps persons will get some elicitation from here and be benefit to their professional work.

Let’s have a simple review at some basic knowledge about DNA which was in middle school biology text.

We know, very important in cell is chromosome, it control the character and propagating of cell. But chromosome just is the carrier  what work really in it is. DNA molecule is existing as a frame of “ Double Screw Frame”, which list both side are phosphate molecule and to oxigenate ribose molecule, this is the same to all DNA, the part which control information are the different order of alkali-basis which hide in the middle. These four alkali-basis respectively are adenine A Bird-purin G cytidine C amd thymine T, and the rule of that they make a partnership are A to T and G to C, this is named “ the rule of alkali-basis partnership and supplementing each other.

In fact, alkali-basis is carrier too, the “list order” of alkali-basis is the real descendiblity information.  And we know, “ order” itself is “ empty, nothing” . it is obvious that it just is the “ empty, nothing” information control the tangible substance list and frame. This also show out the relation quiddity of image and number （ relation of Xiang and Shu saying in Chinese term ）:  It is nothing itself, but it control the image

One side, DNA distribute itself into two son-cells averagely through copy itself, so realize itself descendiblity, on the other side, it control the character of life-form through controlling protein composing DNA control protein composing by tansfering its information from karyon to cytoplasm through the course of re-record of RNA In messenger RNA, replace T with U to make partnership with A. in ribosome of cytoplasm, take the RNA as a model , carry the dissociative amino acid onto ribosome by transfer RNA , then list the amino-acid and compose it as protein according to the alkali-basis list order of RNA, there are three alkali-basis transfer make partnership with RNA, the other top load dissociative amino acid

Above is referencing the knowledge of descendiblity and aberrance of biology text of senior middle school  It wrote in the end of this chapter, protein is composed by 20 sorts amino acid which are being commonly thus take place a problem of that how four sorts anlali-basis to decide twenty sorts amino acid,  people have made this problem clear elementarily these years, that is, decide a amino acid by different list order of three alkali-basis Now people have checked out all the 20 sorts amino acid code as below table.

20  Sorts amino acid and their codes

Let’s look at this table, there are two obvious shortcoming on this table:

1. the codes of that decide amino acid are disorder and irregular, there is  1 , 2, 3, 4, and 6

2. the total number of codes in this table are 61, and according to mathematical calculate, the total feasibilities of that fetch 3 from 4 alkali-basis amino acids to make permutation and combination should be 64 sorts, it is possible here lost three codes. So this table is not orderly and complete in fact, according conclusion , there should be 64 sorts codes total.

B.  Ratiocination on binary

Say simply, there are two sorts of nucleotide : purin and pyrimidine, among them, purin are divided into adenine A and bird-purin G; pyrimidine are divided into afterbirth C and thymine pyrimidine T. might as well according to their order support : adenine A as 1,bird-purin G as 2, afterbirth C as 3, thymine pyrimidine T. as 4。

If we express them by binary number are below:

A = 00, G = 01, C = 10, T = 11.

Then we replace the corresponding nucleotide letters of the two tables into binary number.

20 amino acid and their codes

16 sorts amino acid and their codes ( cleaned up )

Then list the total codes according to its order, and express them by natural number and binary number respectively

That is to say, the 16 sorts amino acid what expressed by 64 nucleotides just are a list of natural number of 6 binary number which are composed by 4 alkali-basis, and it has 64 numbers from 1 to 64 total. Namely 2 ⁶ = 64 , this just is all of the secret of biology, and the secret of whole nature or world !

Let’s turn back to have a look at the old table, then express it as natural number , to see what secret is there:

We may see from above table, so-called amino acid codes, it is breaking the order of the 64 numbers from 1 — 64 then pick a piece of them put down casually.

Then it is who broken it in the end?  Only can be the God . But we are wrong again, the God hasn’t broken it himself , it is mankind ourselves who broken it when we study it, because the course of experimentation always are single and disorder. In fact, the God distribute every life including any life from virus to us person a only number for recognizing , just like ours citizen ID card number, just this ID number which the God give us is more long, but its basic unit is more simple in fact !  There just are 0 and 1 two numbers, and mankind citizen ID is 15 digit number composed by 0 to 9 these ten numbers. If the calculation speed of computer is fast enough , support we will have a kind of quanta computer, then whether we can find out all ID of life in the world? But I think the ID number of life is only, it is no use in fact. The most important is to sum up the rule of how the God compile these code, and the same part in this long coding, and in fact, this rule is showed clearly: all lift have their mutual forebear, and the ultimate of this mutual forbear is very simple really, that is 0 and 1 these two number, and it can be sum up to 0 , even the 0 is not exist too, this is the mutual thought of Chinese thinker, it perhaps will make those west scientists who are ambitious disappointed

C . Describe from the angle of Chinese philosophy thought--- TaiJi and YinYang

Let’s study this problem from the angle of Chinese philosophy thought---TaiJi and YinYang.

Why we think of this way?

1.  There are four alkali-basis total , and it were divided into two sorts of purin and pyridine this made us consider with 2 Yi and 4 Xiang saying with Chinese term.

2.      Transfer RNA use three alkali-basis to decide a amino acid, this make us consider with that the BaGua is composed by three double Bo. Compare to 4 Xiang picture( below picture 1), let’s support purin is Yang and pyridine is Yin, and adenine is the Yang in Yang named TaiYang, bird purin is the Yin in Yang named ShaoYin, cytidine is the Yang in Yin named ShaoYang, urine pyridine is the Ying in Ying named TaiYing, showed as below picture 1

figure 1

According to this suppose, a code is composed by three alkaline –basis just are 64 Gua, such as lysine AAA to Qian Gua.  According to this suppose, we divide every Gua of its 64 as three group from bottom to top taking two as a team, then express it with a letter of alkaline –basis respectively, get 64 codes, compare with the old table, we found that the 61 codes of them fit with the old table,   besides, there are else three Jian Gua UGA, Xian Gua UAG,Dun Gua UAA are lost. If we add these three codes, then it just can be corresponding with 64 Gua one by one. And after adding up these three codes , analyse its statistical result , we found it fit following three rule , this also can be found completely from TaiJi and 64 Gua picture in fact:

1,   A, G, C, U these four letters appeared 48 times respectively

2,   A, G, C, U the times of these four letters appeared at head, middle and end singly are 16 times.

3,   In a group of that stand for amino acid, the fore two digit letters must be the same the end digit appear according to the rule of alkaline-basis supplementing each other. and partnership.

Let’s analyse this rule comparing to the picture 2 below named “ Watching TaiJi 8Gua and amino acid codes together:

figure 2

1.   Why they appeared 48 times singly ?  Because  64×3÷4=48, among it, 64is the total number of Gua, 3 is the alkali - basis number of per code, 4 means there are 4 alkali basis take part in it.

2.   Why it is 16 times singly appearing head, middle and end digit?  Because from Qiao to Lin total 16 Gua, their first and second Bo both are Yang, namely it just stand for letter A, the else G, C, and U is for the same reason, namely  64÷4 = 16

3.  We can find from picture 2 that start from Qian along to the “ S” line back to Kun, the neighbor 4 Gua hteir first Bo to fourth Bo are the same, that is to say, the No. 1 and No. 2 letter must be same, and the final letter looking from picture is recycling according to the order of “ the rule of alkali-basis partnership and supplementing each other.  We can judge from here, a amino acid should be confirmed by 4 group code strictly , the rule of middle letter recycle according to 4 A,4 G,4 C and 4 U namely the “S” line.

Then, why the outer loop namely the end letter is according to the order of A G C U? Have a look at their character of Yin and Yang and list out their order, it is TaiYang, ShaoYin, ShaoYang, TaiYin, this just fit the positon of “ 2 Yi divide to 4 Xiang”. If we draw the “S” line straight , just is this order, thus this combination is the most suitable. This line is very important, it is the gist that I modified the amino acid code table. Now that s, we may modify the position of code in old table according above 3 rule

① Put the codes of TianDongXianAn and lysine together and compose a new amino acid : AAA、AAG、AAC、AAU, we named it TianLaiAnSuan;

② Put the codes of TianDongAnSuanand glutamic acid together: GAA、GAG、GAC、GAU,we named it TianGuAnSuan

③ Patch the lost Jian Gua UGA to back of tryptophan UGG--- this is fitting the rule in table, and put it together with cysteine, namely UGA, UGG, UGC, UGU, we named it BanSeAnSuan.

④ List the codes of GuAnXianAn with histidine together, namely CAA, CAG, CAC, CAU, we named it GuZuAnSuan.

⑤ Put the codes of YiLiangAnSuan and JiaLiuAnSuan together: AUA、AUG、AUC、AUU,we namedit YiJiaAnSuan.

⑥ Put the last two codes of leucine to the back of BenBingAnSuan, composed  UUA, UUG, UUC, UUU, we named it BenBingAnSuan yet.

⑦ Put the last two codes of arginine to the back of JiAnSuan together, namely AGA, AGG, AGC, AGU, we named it JingJiAnSuan.

⑧ Patch the lost Xian Gua UAG, Dun Gua UAA to the back of LaoAnSuan,  we named it LaoAnSuan yet.

16 sorts amino acid codes table ( modified )

So formed a new table of amino acid codes as above, here are 16 amino acid which composed by 64 codes.

We can find in this table, these 64 codes have very regular order and rule, if we make the 16 amino acid a complete permutation and combination, the imaginabale form will be  P₁₆¹⁶=16！≈20922789000000, about 20 million million, this haven’t considered combination numbers yet. And the inner hidden feasibilities in a DNA molecule perhaps are thousands upon thousands, so the real feasibilities almost is a infinite number. This just is the inner base of that the biology is rich and colorful ( multiformity ), and supply conditions for the species aberrance and anagenesis.

Now, there is a biology studying in the world, named “ mankind genome group plan “, among it, there is the part of “ China genome group “, say concretely, unite multitudinous biologist, use computer technology , try to analyse out the all pieces of mankind genome . this is a large work, even if depending computer technology, its work quantity is very large yet.

This plan started since 1989, there have been more than ten years till now, it was said it need five years yet to finish. I admire very much experts and their courage, but analyse genomes one by one, this like calculate sands, this way is not useful in fact. Because even they can make it clear, yet they are lacking holistic holding yet, besides, there are many genomes of early term that life evolvement intermix in it, so it will cost long time and large charge. This way is effected by the western thinking character, they are accustomed to analyse the microcosmic single digit.

Many people made figure of speech of change, development and advanced of this times, like to use the word “ knowledge blasting ”, say correctly is “ science and technology “ fly greatly. Among it, “ biology technology “ is an important thing, “ genome plan” just is one of them, there is “ clone technology “ and “ turning genome technology “ and combine the electronic technology and genome technology “ genome CMOS chip “ etc, besides, zoology and condition science which is related with biology.  In fact, nature science just are maths and physic two sorts, physic has included all of single subjects, such as chemistry, geography, and biology etc. biology have two direction: macroscopical sort outer of body is condition, microcosmic sort inner of body is genome. I think maybe condition is more pressing at present.

There is a problem of “revealable and hidden of genome and character“ in genetics, we may make a explanation and foretelling to this problem according to the theory of Taiji and YinYang of china.

32 doubles complex Gua namely 32 doubles amino acid which are supplementing each other, guess according to YinYang theory, the one wich are composed by Yang character amino acid in per double supplementing amino acid should be “ revealable “ genome, and the other one which composed by Yin character amino acid should be “ hidden “ genome, it is what mechanism should be studied in addition, but the code is Yin and Yang double, that is to say, in every life there exist two group of genomes Yin and Yang character face to face, as for what sort it will be showed in the end, it depend on the effect of conditions around, it is obvious that so called “ induce between conditon and persons “ in ancientry China is quite reasonable. The character of biology are decided by conditions at great degree in the end, because its “ inner placement models “ which may be chosen are infinite in fact.

Induction between persons and conditions is a external phenomenon, the most common such as women emmenia, just is effected by the gravitation of moon, Chinese name of this phenomenon “ month hemorrhage” is come from it. Not only persons, but also everything in this universe are inducting each other.  For example, many animal have their foreboding to natural disaster.  Everythings on earth induct each other,  there have induction between kinfolks on some great things. I ever read a report, it said, there is a mouse in a room, looked dysphoric very much before its master, after the master died, the mouse died too.

Besides, this just is why mankind usually have double character, why peoples have Split personality illness, and every character is possible to show under the prevail on the effect of conditions. Sometimes we have such a mind experience : certain a thing or scene, we felt clearly that it was going through before, but it is impossible if we consequence it according to common logic. Whether it showed there is a complete shadow world existing in man brain consciousness?  Sometimes it will rush into apparent consciousness by chance ?

Besides, there are many persons declared that they ever rush into” time tunnel “, such record was recorded in many authoritative information, such as army information, whether this is due to that shadow consciousness take up the leading station and formed a mistaken feeling ?

This character of Yin and Yang concomitant opposing of that everything showed, just confirmed that the theory of Chinese Tai Ji and Yin Yang is one of the truth in the universe which is all-pervading, scientific and basic,  this theory was used in Chinese medicine and got variety coming true just is a powerful proving.

Now that DNA code may be corresponding one by one with 64 Gua, and 64 Gua picture has been improved a binary code picture, that is to say, DNA codes list ought to be a binary list too, then where is the material relation in it ? How the DNA code incarnate this binary rule ?

We know, in DNA molecule, its list order just is the descendiblity  information,  one side, it get dexcendiblity by copy itself, the other side, it decide the character of biology by controlling proteins combine. DNA consist in karyon, and proteins were combined in the ribosome of cytoplasmic, this middle courses must be finished by help of another two medias. One is messenger RNA, after it copy a single chain according to the rule of “ alkali-basis patching each other and partnership “ and take one of DNA as model, come out from the hole of karyon to the ribosome, this course is called re-recorder. In ribosome, transferring RNA carry the dissociative amino acid into ribosome, and connect them as a protein according to the rule of “alkali-basis patching each other and partnership”. Because  transferring RNA carry amino acid with it’s an end, the other end are three alkalis,  partnership with messenger RNA in ribosome --- secret and mechanism just is in here !  When the three alkali-basis on transfering RNA make partnership with alkaline-basis on messenger RNA, there are two results only: match or not. This incarnate the binary rule in amino acid code into proteins. The secret of life, in the final analysis as if it is something moving according to certain rule. But there seem to be a certain spiritualism in this substance moving, as if it has certain aim, and don’t be so die and engine like mineral moving, theirs moving is controlled by certain information.

Then it is whom let it move so ? that is to say, it is whom to confirm these information and programme?  It is the God ? I don’t think so, if it is the God, then the universe just is the God, that is to say, the God just is the rule of that substance and its moving, and not a jin, not a life, not a person. Why say so ?  Transformism tell us some characters of life different to other common substances phenomenon, after it form a most simple modality, it will be effected by round conditions and change itself stage by stage, adjust itself, copy itself, and become more and more complex, more and more fit situation and effect situation at the same time. So want to make life clear, just need make it clear where its originalform come from ?

The most original form of life, just are some simple organic molecule, and organic molecule is coming from inorganic molecules.  The period of span of from inorganic to organic, is regarded as the most difficult tache to make clear in the course of life evolve. But it was proved later that it is due to the effect of conditions, simulation in lab re-showed this course, namely  by the effect of catalyzing of lightning in the early atmosphere on earth, made inorganic molecules combined some small organic molecules by chance. So the origin of life seems to be a hap, and it is certain too, a result must take place early or later. There also are persons think, the original organic molecules is a kind of substance of star come from out space, then we may ask further, where it is come from the original organic substance? It ought to be coming from inorganic substance under the effect of conditions. Why inorganic molecules can combine into organic molecules ?  Because it has such immanent molecule frame. Why it has such molecule frames ?  This is decided by its atom frame, atom frame is decided by the frame of more smaller particle, may run all long to quark or superstring. On the degree of quark or superstging, it yet is “ Tai Ji Yin Yang “ and its binary rule that make the definitive functionary! We may have a look at it:

There are two kinds superstring --- open and close, we may suppose the open superstring as Yang, close superstring as Yin. In the theory of electromagnetism, electric field is open and magnetic field is close, if there is a positive charge in space,, its electronic line may extend to infinite far saying on theory.

A magneton in space, its magnetic force line must be closed and form itself curve, of course this magnetic line ought to extend to infinite far, but it always is closing. But scientists have found “ Monopole “ too, just as bachelor hasn’t a consort pause. The character of electric field is similarly to Yang character, character of magnetic is similarly to Yin. And electric field and magnetic field themselves have  +  and  —  two ends, so it just like four shape, so may associate hertzian waves is a kind of Yin and Yang shape too. Is there a certain relation between open and close of superstring and electromagnetism field ?

We noticed: Quark have six sapors and three colors, it just is corresponding with total numbers of amino acid code are six Bo as Yin Yang three couble which was described in front. Another microcosmic theory “ quark “ also can’t escape rule of Yin and Yang. Quark have six kinds sapors at least, named respectively as “ top, below, Ji, Mei, bottom, top ”, there are red, green and blue three colors per sapor, here sapor and color just are signs, not real flavor and colors  We may think, these quark are not optional, and double.

Let’s come back to the frontal questions, in the course of organic molecules evolve, why it change and copy itself, is it a subjective aim？We have reason to think, this is effected by the choice effect of conditions. That is to say, under conditions of that time, there are thousands upon thousands of organic molecules which are formed by chance, it can be inspired by the list forms of amino acid is unlimited, but those organic molecules who can’t copy itself have been washed out and disappear after they formed, just some of them can copy and multiply themselves so kept, and the origin such copy just can be a kind of chance. From DNA to messenger RNA to transfer RNA, here is a problem, there is not found on text book, DNA molecules is a kind of “crew frame “, it is no problem of its course of copying, it is effected under the unfastening screw enzyme, divide into two single chains, then take one of single chain as model, according to “the rule of alkali-basis partnership and supplementing each other”, combine two same son-chains. Then how about the re-recorder course from DNA to RNA ?  RNA take a single chain of DNA as model, which chain in the end ? Because DNA is double chains, and these two son- chains are combined according to” the rule of alkali-basis partnership and supplementing each other “ that is to say, these two son-chains are contrary, suppose one of them is + , then another is --, another question, in the course from DNA to RNA, does DNA utie or not ? If untie, then there is the question of choice what son-chain of them; if not untie, then how it operate when it copy ? Or it were using both son- chains of them ? If so, then the proteins which are made must be divided into tow kinds of opposite on its character, how these two kinds of proteins are in a same life together ?

There is what use in the end the picture of 64 Gua and amino acid codes corresponding which were given by me in the front ?  We may think from this angle: Yin and Yang theory has been a mature complete duality theory system. In the course of old forebear use it to settle real problems, it not only can justify itself and with facility, and it fit the coming true and observation quite well. So we may use its description to Yin and Yang character to guess corresponding amino acid, and guide the direction of experiment on theory, just like the philosophy way do to idiographic sciences. Though Tai Ji and Yin Yang is the different phase of the same theory, but its application has different emphasis . Tai Ji model is more fitting to explain the origin and originating of everything , And after things are born, it must evolve with Yin and Yang duality form and rule, this time is fitting to use Yin Yang theory studying.

Let’s have a look, for example, AAA、AAG、AAC、AAU these four code combined a amino acid named “ Tian Dong An Suan “, it locate at the area of Yang Qian Qian, Jue, Dayou, Dazhuang four Gua. Then collate with many characters of Yang and many functions of Qian Gua, we may guess further many characters of amino acid locate at this area. Such as Qian is sky, belong to Yang, in charge of move, born, out, change into Qi, so the opposite amino acid, perhaps on its character is more moving,, more chances to combine proteins, the function in cell is wave, easy to locate the out floor etc. Of course, these just are my private guess, whether it can fit the observation and experiment , I don’t know now. Amino acid locate at other area, may be guessed by the same way according to different area they locate.. If such guess fit the observation and experiment, then in the field of applications, to search , control and fix unknown gene in lab, it all are useful.

Say on theory, its important meaning also is at: now that we improved that amino acid code are listed according to the binary rule by four alkaline basis, and this kind list can but educe the only 64 codes,, and protein sorts are thousands upon thousands. Then combine as amino acid according to code and combine protein by amino acid,  all can is but one kind of course of limited code list permutation and combination on cyc, namely: four alkaline basis list out 64 codes, 64 codes combine as 16 amino acid according to “ the rule of alkali-basis partnership and supplementing each other —— the standard element of protein, then combine our thousands upon thousands proteins.

So, gene list needn’t be analysed one by one use computer, and may be guessed out. There is the base of “ the rule of alkali-basis partnership and supplementing each other. in forebear thought, and the also are composed according to “ the rule of alkali-basis partnership and supplementing each other. We may see it on the picture “ Tai Ji derive from “: in the 64 Gua , take origin as center pot,  all double Gua which locate on the opposite position are “ the rule of alkali-basis partnership and supplementing each other.

Such wonderful and exact symmetry, it is not possible by a outlying chance at all !

Though it showed just form beautiful, there should be an internal exact rule in it !

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