Copyright © Lyuben Piperov December 2006

From Genesis to Genetics and Back

Part 2: Words, Flesh and History of the World

Lyuben Piperov

Abstract: More evidence for the analogy between the Word of God and the fundamental structure of all living has been found. The research has been extended to comprise RNA and the proteins. A significant proof has been found that the exact number of the letters in the Torah, 304 805, is unique if expressed in binary digits. A hypothesis has been developed that the Hebrew letters possess dual properties based on their position in the text and their numerical values, analogous to the quantum particle/wave dualism. Plausible evidence has been found that the letters of the Torah act as a quantum computer mapping through codes the real course of history. This has been verified in the link between the names of Aaron and Bulgaria and her long-term historical role for the current situation in the Middle East. Based on experimental data, a new level in the Bible code study is suggested, which is not deterministic but possesses emergent character. Finally, it is shown that the free will of every human is not only allowed but is required for the fulfillment of the Lord’s Plan. An example is given in the Appendix showing through an elementary computational problem the essential difference between classical and quantum computers.

Introduction

Part 1 of this study [1] started with the observation that the number of the letters in the Hebrew alphabet, 22, matches the number of the types of the human non-sex chromosomes. The overall number of chromosomes in a human sex, also called haploid, cell is 23, which matches the constant number characteristic for every alphabet – in our case the Hebrew – when it is used in an encoding method called atbash. Moreover, a surprising similarity was observed between the most famous atbash code in the Bible, that of Babylon-Sheshach in the book of Jeremiah, and the fundamental principle of encoding of DNA in its double helical structure. These facts inclined me to the thought that another well-known encoding principle - that of Gematria - may have been combined by the Creator with atbash for hiding even deeper secrets in His Word. To my surprise, it happened to be so and it appeared that the infamous number of the beast of Revelation, 666, was found to be encoded entirely in the Torah as a specific pattern applying occurrences at skip ±1 and numerical values of the complementary/reciprocal Babel-Sheshach (ששך-בבל) couple. This pattern corresponds exactly, even to such detail as the anti-parallelism of the strands in the double helix, to the pattern of the construction of DNA. Other details such as the links with number six led to the conclusion that what the code of 666 means is that the human flesh is sinful and always rebellious against God. Babylon is the archetype of all human kingdoms, which are to give way to the Kingdom of God, as prophesied in Daniel 2.

It is the right place here to elucidate an issue I rather hinted at in Part 1. I have received many questions and comments on whether finding out the number of the Beast should mean, or be equivalent to, identifying the man of sin, or Antichrist, or whoever human being representing the system inimical to God. Indeed, for centuries researchers have looked for a human being hidden behind this mysterious number. However, they have overlooked the unambiguous statement in Rev. 13:18:

... Let him that hath understanding count the number...

The challenge is to count, or calculate, a number, not to unmask a specific man! But what a challenge this one could be? The number is declared to be 666! How could we count a number already counted? ...

In my opinion, most researchers have been led astray because the ultimate value of the number is already given. For that reason, we cannot apply to this case the process of calculation as we do in our familiar mathematical processing, where we start with initial data and handle them to obtain the result. Here, we are given the result. Therefore, what other could ‘calculation’ mean but finding out a specific pattern for fitting numbers in a manner similar to arranging a jigsaw puzzle? The peculiarity of the 666-puzzle is that we have a framed picture and must pick up unknown number of pieces, out of enormously great number of scattered pieces, matching both each other and the picture in the frame.

We managed to find out ‘pieces’ that match perfectly each other. But isn’t there even deeper significance hidden in the picture and its frame. Isn’t the picture the whole history since the Creation and the frame ... time? It seems a reasonable assumption since the figures we found totalling 666 point to sin and rebelliousness characteristic of the human flesh. It is intertwined with the entire human history, at least since Nimrod. This interdependence could hardly be illustrated better than the huge human statue of the Nebuchadnezzar’s dream. Moreover, it could not require more mysterious revelation than in the basics of life: the double helix of DNA. This is not only indication that we, humans, have obtained the means for solving this problem but also that the Time of the End has come. Indeed, the words (םירבדה) had to be closed up and sealed until the Time of the End (Dan. 12:4, 9).

Having come across the strange but evident link between the structure and composition of DNA on one hand and the pattern of encoding of number 666 in the Torah on the other, I started contemplating on the reason of all this. DNA does not exist for itself. What DNA can make is copying itself within seconds and practically nothing else. The Lord God had designed everything for special purpose expressed in the next stage of His Creation. What are the ‘products’ of DNA in the reality? Proteins. DNA has no purpose without proteins. Proteins are ubiquitous. DNA is invisible in a certain sense. The invisibility is due to the fact that DNA is just a source of information. It is a molecule and the correctness of the information it contains can be determined on molecular level only. Proteins, or rather their functions, are visible on macro scale. Slight differences in proteins can lead to dramatic alterations in an organism, sometimes determining the margin between life and death. Proteins are responsible for carrying out all crucial functions in the organism. In fact, illnesses and ageing are due to changed, deficient, emerging or absent proteins. This is why at first scientists believed that life is a form of existence of proteins alone.

Within about a dozen years after the discovery of the genetic code, scientists established how DNA produces proteins. It is through molecules similar to DNA in composition. The only difference is that instead of thymine, they contain uracil and the sugar is ribose instead of deoxyribose [2].These molecules, which copy the blueprints in DNA and take part in the building up of proteins, are called ribonucleic acids (RNA). In fact, there are about 100 naturally modified nitrogenous bases in RNA, which determine its spatial characteristics. However, we will concentrate our attention on the role of RNA in the coding processes only. This process is so fundamental that it was labelled Central Dogma of Molecular Biology and is striking with its simplicity:

DNA → RNA → Protein

Why they have stamped this scheme with such a typical religious hallmark? No other law of nature has been called “dogma”, though there are many unshakable principles such as the gravitation law. I believe it is because the process of the transformation of the information in DNA into corporeal entities is very similar to issuing of decrees and fulfillment of prophecies. Here we have again words coming into effect through executors. The words in this case are written with a 4-letter alphabet in DNA, and then are ‘translated’ into another alphabet consisting of 4 letters too. This is the alphabet of the executors – the various types of RNA molecules. Three of the letters of the first alphabet are present in the RNA alphabet. The only difference is the fourth letter. This change results in significant dissimilarity of shape and functions between DNA and RNA.

Unlike DNA, whose double helical shape is similar in every living cell, different types of RNA are distinguished physically by shape according to the functions they have to execute. I will not discuss in details the chemistry of these substances. The reader can find them in many sources. However, before going further, let us reflect for a while on the alphabets of DNA and RNA.

Numbers, Letters and Words

The first fact, which impressed me, was that the overall number of the letters in both alphabets is five. This immediately reminded me of the finals in the Hebrew alphabet, whose number is also five. Keeping in mind that such coincidences are not due to the blind chance, I checked for deeper meaning hidden in this number.

The word for ‘man’ in the Bible, ish (שיא), has preserved its spelling in Modern Hebrew. On the other hand, a change in the spelling of ‘woman’ has occurred and today, the spelling in Modern Hebrew, השיא, differs from the spelling in the book of Genesis, השא.

The original spelling of both these words in Genesis provokes interesting conclusions. First, the total number of letters in these words is six. We have already discussed the significance of this number in Part 1. What is more interesting in respect to this study is that the overall number of letters from the Hebrew alphabet used for writing of man and woman is four: aleph (א), hey (ה), yod (י) and shin (ש). This number matches exactly the number of the letters in DNA and RNA alphabets. Interestingly, the two letters that are common for man and woman are aleph and shin. They form the word flame, שא. Flame is a mark of the divine. The Lord God placed flaming sword to keep the way to the tree of life from the man and the woman (Gen. 3:24). The letters that are found once in each name, yod (י) in man and hey (ה) in woman, form the concise Name of the Lord, הי. The Name of the Lord, mostly used in the Bible, YHVH, is a four-letter word, הוהי. However, it needs only one new letter, vav (ו) to be written out. Therefore, (1) the number of the final letters in the Hebrew alphabet, (2) the overall number of the nitrogenous bases - these are the ‘letters’ - in DNA and RNA as well as (3) the number of the types of letters in the three words: YHVH, man and woman, is the same in all three cases: five! Moreover, we have to add five to the numerical value of woman (1 + 300 + 5 = 306) to obtain the numerical value of man (1 + 10 + 300 = 311). This fact seems to be a good additional hint at the significance of Gematria in these studies.[1]

Then I studied the names of the first human couple: Adam (םדא) and Eve (הוח). At first glance, it is apparent that number six is here again: the overall number of the letters in both names as well as the types of the letters is six. The next step was to check the numerical values. The numerical value of Adam is 1 + 4 + 40 = 45. The value of Eve is 8 + 6 + 5 = 19. I was greatly surprised when obtained these figures because the difference between the numerical values is

45 – 19 = 26

26 is the numerical value of הוהי, the Holy Name of the Lord! How much this fact matches the reality! Indeed, the Lord God made the woman from the man. She did not possess a name by the time of her creation. Adam called her Eve = Living after the original sin, when man is become as one of us, to know good and evil… (Gen. 3:22). That is, when human flesh became mortal… Subtraction, the mathematical operation above, is in tune with the Biblical narration. The first woman had been made of a part taken out of the Adam’s body! The formula could not hint in more marvelous way at Him Who had performed this wonderful act! So, there are again three Names: YHVH, Adam and Eve, linked by their numerical values! The next question coming up to my mind was about the sum of the numerical values of Adam and Eve, 45 + 19 = 64. Is there something hidden in it? As we will see soon, there is a significance in this number too – significance pointing to biology…

From Blueprint to Construction

Proteins consist of a limited number of building blocks called alpha amino acids or simply amino acids. Each amino acid has a moiety, which is the same in all of them. This moiety allows them to be combined by strong chemical (so-called covalent) bonds in a manner similar to stringing beads of a necklace. The remaining part of each amino acid differs so that the presence of a particular amino acid in the “necklace” defines the form and the function of the whole string. Although proteins are linear strings of amino acids, once built, they start folding until obtain a specific shape determining their function. In most cases, proteins are complicated - sometimes composed of two or more separate strings - three-dimensional bodies.

The basic mechanism of building up of proteins starting with the information contained in DNA is much sophisticated. Here again, we will ignore specific details and will focus our attention entirely on the steps involved in the processes of encoding/decoding. The first stage is transferring the information contained in DNA to an RNA molecule called messenger RNA (mRNA). mRNA is the image of a specific protein! It copies and at the same time translates the information in DNA into a new four-letter ‘script’. The method of copying is based on the same atbash encoding principle discussed in Part 1. In this process, thymine (T) from DNA converts to adenine (A) in RNA, but A converts to uracil (U) instead of T. Guanine (G) converts to cytosine (C) and vice versa, exactly as in the reproduction of DNA. This process is actually unsealing of information sealed in DNA.

Unlike DNA, RNA is single-stranded. This is because it is not intended to reproduce but to take part in the construction of proteins. In addition, RNA is not as stable as DNA. It easily degrades in the cell environment. This characteristic is important for the control of the synthesis of proteins. Just imagine what would happen if RNA is indestructible to the extent DNA is: Proteins are synthesized in accordance with the needs of the cell. Suppose the latter has produced enough quantity of certain protein and needs to switch over to production of another one. The resources – the amino acids – are spread as solutes around the sites of production, which utilize the compounds available. Even if the cell had built “plants” for each specific protein, which would be unprofitable because the number of the proteins is extremely large, each “plant” would compete for the resources of amino acids. The mRNA would continue producing, like a tiny idiot, protein that is needed no more. Therefore, the only way to stop it from doing this is … destruction. I gave this example to show how destruction can be useful for the control of the events that are part of a greater plan, whose significance cannot be estimated on lower levels.[2] There is even deeper meaning in it. What happens in fact is turning mRNA into a protein! The mortal ‘image’ mRNA of the immortal DNA dies producing living structure. The seed dies yielding crop…

Like DNA and RNA, this real object is a linear string of amino acids. There are no side chains. The information encoded by the four-letter DNA alphabet transforms into the other four-letter RNA alphabet and then materializes in the string of amino acids unique for each particular protein. The mRNA is the blueprint, while another type of RNA called transfer RNA (tRNA), picks up a specific amino acid and “transfers” it to the site of protein building. There are as many types of tRNA as many are the amino acids. While mRNA specifies the sequence of the amino acids in the protein, tRNA provides the particular amino acid required for the precise location. We will outline the process stressing on its encoding facet.

After intense experimental work and applying great ideas, scientists established that each amino acid is encoded with three nitrogenous bases (nucleotides) in DNA. This code turns into another 3-nucleotide, that is three-letter code, in mRNA called codon. This codon binds with its counterpart in the tRNA, anticodon, in a way identical to the binding between the complementary bases from each strand of the double helix of DNA.

The codon specifies the letter of the new alphabet, that of the proteins. The sequence of the codons in mRNA is the spelling of the protein. The anticodon fixes the respective amino acid in the following way. The tRNA has two specific sites: the anticodon and the end that attaches the particular amino acid. In short, tRNA is e vehicle: it brings the right letter to the right place.

Figure 1 presents an example of a tRNA. It is one of the two tRNAs for phenylalanine. In this particular example, the codon in the mRNA is UUC (green, in the bottom). Note that the order of these letters is reversed in the picture! This is because the direction of the reading, as with DNA (see Part 1), is from the 5'- to the 3'-end. In the figure, the 5'-end of both mRNA and tRNA is in the right. The dots represent the nucleotides (base + sugar ribose + phosphate) forming tRNA. Black dots signify the non-specific part of the molecule. It is similar in the tRNAs for all amino acids. Note the peculiar, typical clover-like shape. The red dots near the 5'-end specify which particular amino acid will be attached to this end.

The codon (UUC) and the anticodon (AAG) are complementary, as discussed earlier and fix by the same hydrogen bonds as the bases in DNA. These bonds are among the weakest known intermolecular attraction forces and are very practical for the specific purpose of ensuring close proximity of the amino acid to the site of addition and then giving way to the next carrier as soon as possible.

Figure 1. The typical structure of transfer RNA (tRNA).

This universal three-letter code reminded me of a specific feature of the written Hebrew as well as the majority of the Semitic languages: the law of the triliteral stem. It states that all words are or derive from a three-letter root [3]. Could this law ensure the richness of Hebrew language? Yes, because the number of possible three-letter words increases dramatically with the number of the letters in the alphabet. For instance, a two-letter alphabet consisting of, say, A and B, generates eight three-letter words:

AAA	BBB
AAB	BBA
ABA	BAB
ABB	BAA

The reader can easily find that a three-letter alphabet, say, A B C, generates 27 three-letter words. The general formula for the maximum number of three-letter words, N, generated in any alphabet of L letters is

N = L³

Therefore, the maximum number of three-letter words generated by the four-letter alphabets of DNA and RNA is 4³ = 64. Now let us recall that 64 is the sum of the numerical values of Adam and Eve! This link between names and flesh made me check the effectiveness of the Hebrew alphabet. The maximum possible number of three-letter roots written in the 22-letter Hebrew alphabet is

22³ = 10 648

In the Strong’s Concordance, which contains all Hebrew roots used in the Old Testament, there are 8 674 words [3]. Not all of them are three-letter words, of course, but about two thirds of them (~ 5 500 to 6 000) are. Therefore, an alphabet of 18 letters (18³ = 5 832) may be insufficient to generate them, but 19 letters (19³ = 6 859) most probably will be enough. This fact bespeaks of the high effectiveness of the Hebrew alphabet – it consists of few letters more than the minimum required to ensure that each root of Hebrew language has its own three-letter code!

I have reviewed practically all phonetic alphabets. It is believed that all they derive from the 22-letter Phoenician alphabet, which in its turn derives from the Egyptian hieroglyphs [4-8].The alphabets derived from the Hebrew such as Greek, many Latin and Cyrillic alphabets as well as Coptic, Gothic, Armenian and Georgian scripts had been designed to match the phonetic requirements of the respective languages. I noticed that each “newborn” alphabet had more letters than the “mother” one.

An interesting example is the Cyrillic alphabets in use today. The original Cyrillic alphabet was designed in the 9^th century AD based on the specific Bulgarian speech. Contemporary Bulgarian alphabet has 30 letters. These are more than the letters in Greek and Hebrew alphabets, from which it was derived, as well as in basic Latin. However, being designed especially for Bulgarian language, I expected that Bulgarian alphabet would contain the lowest number of letters compared with all other languages using Cyrillic alphabet. I checked the number of letters in all alphabets given in [6] plus Mongolian. None of them has less than 30 letters. Among the seven Slavic languages, Bulgarian and Serbian only use 30 letters (~30%). Among the non-Slavic languages, two out of twelve alphabets use 30 letters (~17%). The highest number of letters in a Slavic Cyrillic alphabet turned out to be 37 (Russian and Ukrainian alphabets use 33 letters each), while with the non-Slavic ones it is 58. In my opinion, this is a good confirmation that the general scheme for derivation of different alphabets:

Hebrew (22) → Greek (24) → Bulgarian Cyrillic (30)

 ↓

 Basic Latin (26)

reflects also the route of derivation within the development and “branching” of the same alphabet when borrowed by languages for which it had not been intended originally. The general rule is that every new alphabet always adds and almost never discards letters from the parent alphabet. In rare cases, a letter is modified or replaced with another one.[3]

However, the foundation of the Egyptian hieroglyphic script consisted of 24 uniliterals. (A uniliteral is a symbol that stays for a single consonant). The earliest known Phoenician alphabet, which is considered as the progenitor of Hebrew alphabet, consists of 22 letters. Such reduction of a new alphabet derived from earlier script has not been observed with any other alphabet[4]. How, and what is more important, why, these 24 base signs were reduced to the 22 primary signs of the Hebrew script is an enigma whose solution, in my opinion, should be tried beyond pure linguistic analysis. It seems that number 22 had become a sacred number for letters in a script at the time of the origin of phonetic alphabets.

Once Hebrew alphabet has 22 letters, the immediate reasonable question would be: Is the protein chain similar to a text written in certain script? Then, is the protein alphabet similar to a phonetic alphabet in respect of number of letters? If “yes”, to which of the considered alphabets it is closest?

How Many Alpha Amino Acids are There in the Protein Alphabet?

As early as my first acquaintance with the Hebrew alphabet – about a decade ago - I noticed that the number of the alpha amino acids building up proteins cited in the books, 20[5], is close to the number of the letters in the Hebrew alphabet: 22. The latter number appeared to be the closest to 20 when compared with any other phonetic alphabet I knew. As we saw, all the other alphabets have more than 22 letters.

Between 1838, when the Swedish chemist Jöns Berzelius described the proteins chemically, and 1935, twenty amino acids had been discovered altogether to build the proteins of every living creature on the planet Earth. This number was believed to be settled once for all for two or three generations of biochemists. By the time the genetic code was clarified, in the 1960’s, there were still 20 amino acids known to be encoded. The establishment of the way the code works is among the highest achievements of the human intellect. What amazed the scientists was that the code is universal! Every amino acid is encoded in the same way from viruses and bacteria through plants and animals to humans. No exception of this rule has been observed! The table shown below was thought to be conclusive for about 20 years…

	U		C		A		G
U	UUU	Phe	UCU	Ser	UAU	Tyr	UGU	Cys
	UUC	Phe	UCC	Ser	UAC	Tyr	UGC	Cys
	UUA	Leu	UCA	Ser	UAA	Ochre	UGA	Umber
	UUG	Leu	UCG	Ser	UAG	Amber	UGG	Trp
C	CUU	Leu	CCU	Pro	CAU	His	CGU	Arg
	CUC	Leu	CCC	Pro	CAC	His	CGC	Arg
	CUA	Leu	CCA	Pro	CAA	Gln	CGA	Arg
	CUG	Leu	CCG	Pro	CAG	Gln	CGG	Arg
A	AUU	Ile	ACU	Thr	AAU	Asn	AGU	Ser
	AUC	Ile	ACC	Thr	AAC	Asn	AGC	Ser
	AUA	Ile	ACA	Thr	AAA	Lys	AGA	Arg
	AUG	Met	ACG	Thr	AAG	Lys	AGG	Arg
G	GUU	Val	GCU	Ala	GAU	Asp	GGU	Gly
	GUC	Val	GCC	Ala	GAC	Asp	GGC	Gly
	GUA	Val	GCA	Ala	GAA	Glu	GGA	Gly
	GUG	Val	GCG	Ala	GAG	Glu	GGG	Gly

This is the genetic vocabulary. The three-letter codes written in capital characters are all 64 codons. The bold characters in the left indicate the first letter/nucleotide in all codons in the respective row, while the same characters above the table indicate the second letter in the respective column. Each α-amino acid has also a three-letter code such as Phe for phenylalanine, Ser for serine etc. The encoded α-amino acid is to the right of each codon. Notice that the third letter, printed in bold character, is of less significance for the encoding of an amino acid compared to the first two letters. It is variable for many α-amino acids.

The three 3-nucleotide sets printed in bold coloured characters and having the exotic names have the function of ending the amino acid chain formation. (Sometimes they are called “nonsense” codons.)

The maximum theoretical number of encoded amino acids is 63. (We have to leave at least one three-letter code for the stop-codon.) There are only two amino acids encoded by a single codon: methionine (Met) encoded by AUG and tryptophan (Trp) encoded by UGG. All other amino acids are coded for by more than one codon: most of them by two codons and two amino acids are coded for by six codons.

Why there are 61 codons for only 20 amino acids? It is clear from the table above, that most of the codes allow for errors; in many cases, the third nucleotide is of no importance for the encoding of a particular amino acid. For instance, GUX, where X is any of the four letters, encodes valine; CCX encodes proline, etc. Therefore, a random error in the code would not cause fatal changes in the protein.

It was in the early 1980-s when, surprisingly, a new, rare amino acid was identified, which contains the microelement selenium. The new, 21^st member of the genetically encoded α-amino acids’ collection was called selenocysteine. It is encoded for by the codon UGA (coloured in red, for umber, in the table above) [9]. Then, in May 2002, another α-amino acid was reported to have been discovered. It was found in an enzyme called methanogen methyltransferase and is generated by the methane-producing microbe called Methanosarcina barkeri. The α-amino acid is called pyrrolysine and is genetically encoded by the codon UAG (coloured in amber in the table above) [10].

Is this number, 22, the ultimate number of genetically encoded alpha amino acids? The three coloured codons in the table are normally stop codons. The last two amino acids found to be genetically encoded by two of these codons are rare and, in addition, they require some specific modifications of mRNA so that certain codons may switch from their normal function to the expression of the respective amino acid. [11] These discoveries reveal that a codon can function either as a specific code for an alpha amino acid or as a stop codon. However, no instance has been observed so far of a codon encoding two or more amino acids. If this principle is preserved, there could be only one more genetically encoded amino acid – still not observed and encoded by the last coloured stop-codon, ochre. Therefore, the maximum possible number of genetically encoded amino acids is 23. A 24th amino acid found to be encoded by a codon which encodes another one, would destroy the universality of the code. There is of course, a way to escape from this catch. As we saw, the expression of the last two amino acids requires some modification of mRNA. Could another modification make these same coloured codons express other amino acids? Nobody knows. Some scientists believe that this could happen and there may be more amino acids in the genetic alphabet…

Nevertheless, the 22^nd amino acid was discovered recently. It is this fact that made me start this study. Were the number of the genetically encoded alpha amino acids different from 22, I would never put pen to paper…

Clusters of Letters, Clusters of Molecules

The core principle of the Bible code so far has been clustering of letters that are far from each other in the plain text in a close area. These letters must form a word or even a longer expression. The more and the longer are the items and the smaller is the area of the matrix the more significant is the code. There is a single rule that must be observed: the letters forming each item should be at equal distances in the plain text. This is the ELS (equidistant letter sequence) or skip. It is embedded in the computer programs searching items specified by the researcher.

As a pharmacist, I am well acquainted with the structures and the functions of the most important bio-molecules. I have noticed that the Bible code matrices are very similar to the picture of the distribution of active sites of some large polymeric molecules. This is especially valid for one of the two main types of proteins – globular proteins. [12] Globular proteins are soluble in water. Their proper function is vital for the organism. Globular proteins are all enzymes, many hormones and transporters. Globular protein is the well-known oxygen-carrier hemoglobin whose importance does not need emphasis. [13]

The basic rule, which is valid for a Bible code, is valid for the function of the globular proteins too: change, drop out or add a letter and the code/function is ruined. For example, sickle-cell anemia is caused by the replacing of one of the “letters”, glutamate, with another one, valine, in the 146-letter long text of the β-chain of hemoglobin…

A hazy idea of similarity and even analogism between the Tanakh, especially the Torah, and a globular protein started taking shape in my mind. The number of the letters in the Hebrew alphabet matches the number of genetically encoded alpha amino acids. In addition, the three-letter code is typical for both languages. Is there a distinctive feature of the proteins, which matches a similar characteristic of Hebrew texts?

The α-amino acids in the protein chain tend to form helices called alpha-helices [14]."Alpha" means that if we look down the length of the spring, the coiling is happening in a clockwise direction as it goes away from us. Under favourable conditions, these helices may be many residues long, which looked at from outside resemble tubes. These tubes bend in the space and form the so-called secondary structure of the protein. The α-helices are well-determined structures. Each complete turn of the helix has about 3.6 amino acids. But the characteristic frequency of three-letter words in the Hebrew language should mean that the average number of letters per word is relatively close to 3.6.

I checked the number of letters per word for the whole Tanakh. It appeared to be slightly below 4: 3.9; for the Torah alone, it is even lower: 3.81. Then I tried the Tanakh book by book, combining some of them in groups such as 1Samuel – 2 Kings, 1and 2Chronicles and the 12 “minor” prophets. The book with the lowest number of letters per word in the Torah is Leviticus: 3.74. However, the book in the Tanakh giving the lowest number appeared to be Ecclesiastes: 3.67! It practically matches the number of amino acid residues in a full turn of a protein α-helix! I wonder if there could be found a reasonably long text of Modern Hebrew (unless deliberately modified or created), which matches this number.

The finding that the number of letters per word in a whole book of the Tanakh matches a specific parameter of proteins conclusively assured me that there is a deeper relation between Word (information) and flesh (physical world; the Universe). Therefore, I started looking for suitable protein(s), which can be good model(s) for searching of analogies.

Most appropriate would be proteins with residues defined for specific function. Hemoglobin is not suitable for this purpose because the error causing sickle cell disease is due to a slight change in the overall behaviour of the molecule. It is not specific and could be likened to a mistake in a text, which changes the meaning of a word such as with protein and protean…

For the purpose of code breaking, more interesting appear to be enzymes. As with every other protein, the exact amino acid in each position in the chain is of invaluable importance. However, enzymes have something in addition. Their function is catching one or more molecules and fixing them in the space for a certain time, which must be enough for a chemical reaction to be carried out. Then they loose the product(s) and catch the next one(s). They do this either by means of a prosthetic group (it is not a part of the protein proper but a moiety which is fixed constantly to it to ensure its function [15]) or by a so-called active site. It is a specific spatial arrangement of the protein chain, which ensures specific amino acid residues in specific locations. These residues act as “hooks” and “pistons”.

Vital for facilitating of the three-dimensional stability of the protein are the so-called disulphide bridges [16]. Only one amino acid can form such bond. It is cysteine, which forms a disulphide bridge with another cysteine residue along the chain. It is a covalent bond and the protein chain, or tube, is like fastened with a dowel in the places where such bond is built up. Usually, there are about 4 to 6 such bridges in a typically long protein chain (~120 – 250 residues). [17]

It would be too naïve to expect that the residues forming an active site are distributed evenly (i.e., at equal intervals or skips). However, they may serve as a good analogue to the other main characteristic of the Bible code: clustering.

I had to choose a suitable protein for this purpose. It had to have well-established α-amino acid sequence and the residues forming the active site. I choose the enzyme lysozyme as a good model for verification of our ideas. It is an enzyme killing bacteria and is found in tears, saliva and even chicken egg white [18]. It consists of 129 amino acid residues and has four disulphide bridges shown in four different colours in Figure 2.

Figure 2. Lysozyme from white of hen egg [18]. The coloured lines show the location of disulphide bridges. The active site determining residues - circles coloured in red - are 19, located irregularly between the 34^th and the 114^th place.

Looking at the picture, I contemplated on what to do next. The simplest reasonable idea was to mark the active site defining residues and to arrange the whole protein formula in the manner a text is arranged for searching for codes. The question was: what will be the skip? The most apparent choice seemed to be the lowest number of residues between the two ends of a disulphide bridge – that coloured in red – 16. The picture I obtained is shown in Figure 3.

Figure 3. Lysozyme residues arranged at skip 16. The coloured capital letters are the respective ends of the disulphide bridges. Shadowed cells are the active-centre-defining amino acid residues.

I was surprised! Clustering is evident and it revealed itself at first attempt! Nine out of nineteen “active” residues – almost the half - are concentrated in less than 20% of the total area, in a 5×5 square bordered with thicker line. It also includes both ends of the G-G disulphide bridge. In addition, four out of the six remaining bridge residues are adjacent to the border of the area. Only a B and a Y residue are “scattered” away from the area. There is also the only occurrence of a column (11^th) containing “active letters” from three different rows.

The next step was to check if a better picture would occur with another skip. The next reasonable skip is that of the G-G bridge, 18. The result is shown in Figure 4.

Figure 4. Lysozyme residues arranged at skip 18.

Here, the 5×5 area is divided due to the peculiarity of the arrangement. However, it is evident that although the area is a little bit denser with active residues, ten, it does not include a disulphide bridge - the G-G bridge is adjacent to - and only one more cysteine residue, Y, “stuck” on the border. Moreover, this time the area of maximum density does not contain a column with active residues from three different rows. (A one-column extension to the left would add two active residues making them 12 altogether. Although the same operation with skip 16 would not add active residues, if performed to the right, the resulting 6×5 area would include two disulphide bridges vs. no one with skip 18.) There is also a strange similarity between the two “matrices”. In both cases, the disulphide bridge defining the skip is adjacent to the middle of the right border of the densest area.

Taking into account all parameters, I am inclined to think that the “matrix” obtained with the lower skip bears more significance. Thus, a very important requirement of the Bible code principles complies with it: higher significance obtained with a lower skip.

Trying with another “disulphide” skip is useless because the next one is… 85. Therefore, I tried with skips lower than 16. I observed nothing significant except at skip 13, where there was a column containing active residues from 5 rows. Then, at skip 12, the picture was astonishing! It is shown in Figure 5.

It is full of symmetries! Diagonals are marked with bold characters. The central vertical and horizontal lines are bold. Disulphide ends are located symmetrically both in relation to the vertical and the horizontal axes (with the exception of G-G, which are slightly off horizontal symmetry). They are symmetrical also in respect to both diagonals.

The active site defining amino acid residues also distribute symmetrically in relation to the same basic lines. Nine of them are to the left of the vertical axis and ten are to the right of it. Eleven are above the horizontal axis and eight are below it. (Notice that in both cases the lower number is in the area with less “letters”.) If we account for the halves cut by diagonals, there are 9 active residues to the upper left of the 12-122 diagonal and 10 to the down right of it. With the other diagonal, the ratio is also 9 to 10.

Figure 5. Symmetry found with lysozyme at skip 12.

The active residues distribute symmetrically also within the triangles defined by the half-diagonals and the sides of the matrix. There are seven of them in the left triangle and seven in the right one. There are two of them in the upper triangle and three in the bottom one. (The residues cannot distribute ideally because their number is odd.) R- R and G-G are positioned symmetrically into the left and the right triangles, while B- B and Y- Y are distributed in the same manner in the upper and bottom triangles.

What does this symmetry mean? It reminded me of x-ray diffraction patterns. They disclose the structure of the molecules. Images obtained consist of darker (usually dots) and lighter areas. This difference is due to the different contribution of each particle in scattering the incident beam to various directions. Dots indicate the positions of the tiny mirrors within a crystal as in Figure 6.

Figure 6. X-ray diagram of lysozyme crystal [19]

Notice the similarity between the two pictures above! Both contain pronounced cruciform symmetry. Often, especially close to the centre, dots on Figure 6 form squares. The letters in the matrix of Figure 5 also form a rectangle, which is close to a square. (The skip arranging the amino acids closest to a square is 11, but at this skip, the symmetry is not as clearly seen as with skip 12.) There are other techniques for taking x-ray diagrams. The cruciform may not be observable with them. However, the key aspect is that the x-ray diagram is a two-dimensional image of a three-dimensional object reflecting the spatial characteristics of the latter. Under certain conditions, the picture obtained shows specific cruciform characteristics obtained with a matrix analogous to the Bible code matrices.

There is something deeper in this. Suppose we know that at certain skip of the amino acid chain of a given protein, there is cruciform symmetry. Now if we have got the information about a part of the active centre building residues, we can predict with a probability exceeding the blind chance whether a certain residue is active forming residue or not. This is valid also for the disulphide ends and even for the non-active amino acids! For instance, if we know that the overall number of the active site forming residues is 19 and that 7 of them is in the left triangle, we will expect that more than 19/129, or about 15%, of the residues in the right triangle will be active centre forming ones. This reasoning is in the basis of the evaluation of Bible code matrices too! The only difference is that usually, symmetry there does not play such important role as distance. (I was lucky to find highly significant symmetrical occurrences of the three-letter word ישע (salvation) in the 2006 matrix [20]).

This analogy necessitates a very important consequence. Proteins are three-dimensional bodies. This suggests the notion that Bible codes are inherently three-dimensional. Both the Word and proteins are one-dimensional strings of 22 letters. Which factor raises the Bible codes and the proteins to three-dimensional level? I think this is the contribution of the non-active elements in both cases. They are not blind machines spitting out randomly active elements. These “inactive” members of the string have their own structure. With Bible codes, they are the letters of the plain, meaningful text. With proteins, these are the amino acid residues, which determine the spatial structure of the molecule. This is clear and easily understandable with proteins because they are physical bodies. We have the good example with mutations causing grave diseases such as sickle cell anemia.

On the other hand, this is not so much clear with the Bible code. Indeed, a substitution of a letter in the plain text, which is not encoded-term defining, would not change the code. So far, Bible code matrices deal with encoded terms and a single letter changed in the plain text in most cases is of no consequence. Even though the plain text in the most significant codes refers to the terms of the matrices, in many cases a letter in the plain text could be substituted with a suitable one so that the code and the general meaning of the plain text will remain unimpaired. Although there are differences in amino acid sequences in living organisms including humans, which are not fatal, the issue of the significance of particular letter for a code is unsolved.

Here is a hypothetical example to clarify my idea. Suppose we have a narration about someone and find significant encoded terms intersecting his name at certain letter. Let this man be Samuel שמואל. Let the intersection(s) occur(s) at one or both first two letters coloured in red. Now let us change his name in the plain text with Samson שמשון. We see that the length of both names is the same; therefore, the encoded terms and their intersections will remain untouched. In principle, this procedure is valid also for other words.

I must emphasize that I do not question the validity of the Bible! With this, deliberately naïve example I want to illustrate the significance of the letters, which do not take part directly in forming encoded items. In terms of ELS-obtained matrices, changes in these words or some parts of them in the plain text do not affect the particular code expressed in the matrix. Most Bible code researchers would say that certainly the importance of the plain text that is “missed out” with one matrix would be revealed with another one. I also believe that there are many ELS matrices, maybe practically infinitely many, containing significant encoded terms, which “scan” the plain text of the Word of God. Maybe there exist at least one encoded term linking every two letters in the plain text of the Torah or the whole Tanach However, I believe that we must look for another level of encoding for the following reason.

So far, we have observed a number of similarities between the clustering typical for significant Bible code matrices and the alpha amino acid residues of a protein when the sequence is arranged in the same way. We have observed the occurrence of symmetry with a protein matrix. Basically, symmetry is not considered as a requirement for a the evaluation of a Bible code matrix, although if present, it may add some significance. However, the most important conclusion of these similarities is the deterministic character common for both phenomena. We will make a short discourse in this very important subject.

Determinism and Free Will

Indeed, as with the proteins, where mutations sometimes predetermine the destiny of the individuals, the significance of a single letter in a Bible code is beyond discussion. There are diseases, which stagger with the accuracy of predicting the development of the affliction up to the time of death. Matt Ridley describes several diseases of this type in h