2. genesis of the genetic code for life

 

*by dr. bruce mclaughlin*

*this article presents evidence suggesting that god was the originator of the genetic code for life and that he encrypted messages about this code in the hebrew book of genesis.*

 

**introduction**

the infinitude of god permits him to instantly track all possible histories and futures of you, me and the universe with no more difficulty than it is for us to count the wheels on a bicycle.  a judeo-christian tradition is that god arranged the 304,805 character string of concatenated words in the torah to reveal not only a spiritual message but also to encrypt fundamental information about the beginning of the universe and its development over time including the entirety of physics, chemistry, biology and human history… a message within a message.

in **genesis of the reciprocal fine structure constant** by b. mclaughlin, several critical dimensionless numbers of physics/mathematics are predicted from the first 12 characters of the first verse of genesis.  is it possible that this same string of 12 characters provides information about the *codons* and corresponding amino acids of the genetic code?  given 64 *codons*, can the first 12 characters from the first verse of genesis suggest which sets of *codons* specify a particular amino acid?

 

**background**

the knowledge that genes consist of complex nucleotide sequences was a major breakthrough in the study of genetics.  however, in the early years of discovery, the number of nucleotides needed to code for one amino acid was unknown.  four types of nucleotides were known to code for the 20 amino acids of life.  four nucleotides taken two at a time provide only 16 different combinations which are insufficient to code for 20 amino acids.  four nucleotides taken three at a time provide 64 combinations.  each three-member combination of nucleotides is called a codon.  it was believed, at one time, that only 20 codons were used to specify amino acids.  however, it is now understood that as many as many as six different nucleotide triplets may specify the same amino acid.  the term degeneracy is used to describe the fact that a given amino acid may be specified by more than one codon.  the fundamental characteristics of the genetic code are now well established; it is a non-overlapping, triplet code without punctuation.  each triplet is called a codon comprising three adjacent nucleotides and specifying a specific amino acid.

 

**natural numerical order for codons and amino acids**

a codon can be defined equally well by: (1) an ordered set of 3 letters from the population [u, c, a, g], (2) a base 10 number (0 – 63), (3) a base 4 triplet (000 – 333) and (4) a base 3 quadruplet (0000 – 2100).  letting the base 4 triplets 000 to 333 represent uuu to ggg (by assigning u=0, c=1, a=2 and g=3) creates a natural numerical order for the 0 to 63 codons comprising the genetic code for life (table 1).  this numerical order can also be expressed as base 3 quadruplets (0000 to 2100).  each quadruplet can be viewed as lipschitz quaternion (a + b**i** + c**j** + d**k**) with a norm defined by a2 + b2 + c2 + d2.  these norms, like the numerical position of the codons, alternate from even to odd which facilitates even/odd classification when working with base 3 quadruplets.

based on observation, many amino acids of life are uniquely specified by two adjacent codons (even/odd) in the natural numerical order.  if this rule were followed throughout, each adjacent pair of even/odd codons would specify a different amino acid.  this is, in fact, the case for phe, tyr, cys, his, gln, asn, lys, asp and glu.  each amino acid is specified by two adjacent even/odd codons for a total of 18 codons.  but this pattern is not followed for the remaining 11 amino acids.  given the 46 remaining *codons*, can the first 12 characters from the first verse of genesis suggest which sets of *codons* specify the remaining 11 amino acids (and 3 stop positions)?           

 

cod   ba4   ba10   ama    ba3              norm

uuu   000      0          phe      0000                0

uuc   001      1          phe      0001                1

uua   002      2          leu      0002                4

uug   003      3          leu      0010                1

 

ucu   010      4          ser       0011                2

ucc    011      5          ser       0012                5

uca   012      6          ser       0020                4

ucg   013      7          ser       0021                5

 

uau   020      8          tyr       0022                8

uac   021      9          tyr       0100                1

uaa   022      10        stop     0101                2

uag   023      11        stop     0102                5

 

ugu   030      12        cys      0110                2

ugc   031      13        cys      0111                3

uga   032      14        stop     0112                6

ugg   033      15        trp       0120                5

 

cuu   100      16        leu      0121                6

cuc    101      17        leu      0122                9

cua   102      18        leu      0200                4

cug   103      19        leu      0201                5

 

ccu    110      20        pro       0202                8

ccc    111      21        pro       0210                5

cca    112      22        pro       0211                6

ccg    113      23        pro       0212                9

 

cau   120      24        his       0220                8

cac    121      25        his       0221                9

caa   122      26        gln      0222                12

cag   123      27        gln      1000                1

 

cgu   130      28        arg      1001                2

cgc    131      29        arg      1002                5

cga   132      30        arg      1010                2

cgg   133      31        arg      1011                3

 

auu   200      32        ile        1012                6

auc   201      33        ile        1020                5

aua   202      34        ile        1021                6

aug   203      35        met      1022                9

 

acu   210      36        thr       1100                2

acc    211      37        thr       1101                3

aca   212      38        thr       1102                6

acg   213      39        thr       1110                3

 

aau   220      40        asn      1111                4

aac   221      41        asn      1112                7

aaa   222      42        lys      1120                6

aag   223      43        lys      1121                7

 

agu   230      44        ser       1122                10

agc   231      45        ser       1200                5

aga   232      46        arg      1201                6

agg   233      47        arg      1202                9

 

guu   300      48        val      1210                6

guc   301      49        val      1211                7

gua   302      50        val      1212                10

gug   303      51        val      1220                9

 

gcu   310      52        ala      1221                10

gcc    311      53        ala      1222                13

gca   312      54        ala      2000                4

gcg   313      55        ala      2001                5

 

gau   320      56        asp      2002                8

gac   321      57        asp      2010                5

gaa   322      58        glu      2011                6

gag   323      59        glu      2012                9

 

ggu   330      60        gly      2020                8

ggc   331      61        gly      2021                9

gga   332      62        gly      2022                12

ggg   333      63        gly      2100                5

table 1. coding for the amino acids of life

 

**analysis**

for the purpose of analysis, consider the color coded 12 by 12 matrix, designated as **m** (figure 1); this matrix was central to the analysis in **genesis of the reciprocal fine structure constant** by b. mclaughlin.  **m** was constructed from the first 12 characters of the first verse of genesis.  

in this paper certain matrix elements are assigned non-black colors in accordance with specific rules.  the colors are non-overlapping and each color represents a single codon (i.e. 0120 or 1022) or multiple codons grouped together as intersecting strings.

 

**rules of color assignment**

 

* if two or more ***even****,* base 3 quadruplets, appear as intersecting strings in the matrix **m**, then the corresponding even/odd quadruplet pairs code for the same amino acid. a string may be read up, down, left, right or diagonally.  two intersecting strings may have no common elements or they may have multiple common elements but they must at least have one contiguous element.  also, equivalent intersecting string patterns may be found in more than one matrix location.

 

* any deviation from the even/odd pattern requires that a string be identified for each individual codon.

 

this will account for 46 codons and 11 amino acids (plus 3 stop).  each of the 9 remaining amino acids is specified by a single even/odd pair of codons.

 

**0   2   0****2****1****2** **0   2   0   1****2** **1**

**0****0** **0   0****0****1** **0   0   0   0****0** **0**

**1****1** **0****2** **0   0****1** **1   0   0****2****0**

**0****2** **0****2** **1****2****0****2****0** **0****2** **0**

**0****1** **0****0** **0****0****0****0** **0   0   0   1**

**0** **0   0****1** **0****1****1****2****1****1** **1   0**

**0****2****0****0** **0****0** **1   1   0   1   0   0**

**2****1****2** **0   0****1****2****0** **0   0   0   1**

**0****2****0****0** **0****0****1****1****0** **0   0   0**

**1****1****0****0** **2   0   1   0   0   0   1   0**

**0****0****1****0   0   0   0   0   1   0****0****1**

**0****2****0** **0   0   0   0   0   0****0****2****1**

 

figure 1.  matrix **m** with non-overlapping clusters of intersecting strings

 

the following non-overlapping collections of intersecting strings can be identified in figure 1.

 

* the **yellow** string designates 0120 which defines a stand-alone coding for trp.

 

* the **light green** string designates 1022 which defines a stand-alone coding for met.

 

* **brown** strings 1012, 1020 and 1021 intersect to define the three strings coding for ile.

 

* **light blue** strings 0202 and 0211 intersect to define the 2 corresponding even/odd pairs coding for pro.

 

* **orange** strings 1210 and 1212 intersect to define the 2 corresponding even/odd pairs coding for val.

 

* **gray** strings 2020 and 2022 intersect to define the 2 corresponding even/odd pairs coding for gly.

 

* **red** strings 0002, 0121 and 0200 intersect to define the 3 corresponding even/odd pairs coding for leu.

 

* **purple** strings 1001, 1010 and 1201 intersect to define the 3 corresponding even/odd pairs coding for arg.

 

* **dark green** strings 0011, 0020 and 1122 intersect to define the 3 corresponding even/odd pairs coding for ser. this string intersection also designates 1221 and 2000 which define the 2 corresponding even/odd pairs coding for ala.  the five even codons can be further separated by grouping the smallest three and the largest two.

 

* **dark blue** strings 1100 and 1102 intersect to define the 2 corresponding even/odd pairs coding for thr. this string intersection also designates 0101, 0102 and 0112 to define stand-alone coding for stop.  these five codons can be further separated by grouping the smallest three and the largest two.

 

table 2. corresponding amino acids for non-overlapping clusters of intersecting strings

 

 

**0   2   0   2   1   2   0   2   0   1   2   1**

**0   0   0   0   0   1   0   0   0   0   0   0**

**1   1   0   2   0   0   1   1   0   0   2   0**

**0   2   0   2   1   2   0   2   0   0   2   0**

**0   1   0   0   0   0   0   0   0   0   0   1**

**0   0   0   1   0   1   1   2   1   1   1   0**

**0** **2****0   0   0   0   1   1   0   1   0   0**

**2****1****2****0   0** **1****2****0   0   0   0   1**

**0****2****0****0****0   0** **1****1****0   0   0   0**

**1****1****0****0****2   0** **1****0   0   0   1   0**

**0   0** **1****0   0   0   0   0   1   0   0   1**

**0   2   0   0   0   0   0   0   0   0   2   1**

 

figure 2. matrix **m** with 2 clusters of intersecting strings containing all 64 codons

 

as an aside, a small portion of matrix **m** can be used to generate base three quadruplet strings for all 64 codons as shown in figure 2.  but, in figure 2, groups of strings cannot be connected to a particular protein.

 

**conclusion**

by reverse engineering the non-overlapping clusters of intersecting strings in figure 1 and using the rules for base 3 quadruplet (codon) assignment, the 64 codons point to 21 entities.  equivalently, the 64 base 4 triplets 000 to 333 (uuu to ggg) map onto 21 entities.  the fact that these 21 entities comprise 20 amino acids plus stop cannot be determined from figure 1;  nor can it be determined that the 64 codons are actually strings of nucleotides.  however, the information in figure 1 was obtained from only the first 12 hebrew characters in the first verse of genesis.  much additional information is encrypted in the remainder of the 304,805 characters of the torah.