Axiom: the derivation of amino acid codes in RNA and DNA develops within the dichotomy of purines/pyramidines.
Over the years a few publications have emerged noting the ease of making analogy between the sixty-four hexagrams of the I Ching and the sixty-four possible codes that occur in the genetic code for the linking of amino acids. (refs given at end of this page). The following introduces the wholes/aspects perspective to the analysis of the coding, working on the premise that the 'universal' concept of whole/aspects must manifest itself in the sequences; details on the inclusion of the I Ching follows this section.
There is a strong suggestion that in the DNA/RNA system in humans we have:
DNA - storage. (form bias - hierarchic structure (all contexts))
RNA - transfer and encoding/decoding. (aspectual bias - single context(gene))
A gene is cut from various parts of the storage area (DNA) and made into one gene sequence (mRNA). This passes through to the ribosomes where the sequence is read and matched to a free transfer codon (tRNA) that has attached an amino acid. This amino acid is tagged on to a growing amino acid chain that is the protein.
In the genetic code there is one start codon and three stop codons, with each codon being made-up of a three letter code sequence that is derived from four possible letters.
Some possibilities:
ACCACA
ACCACA this sequence functions differently to that in (1).
Thus, in any amino acid sequence which has several different code sequences, there is the implication that the same amino acid could work differently depending on context and this is set by the code.
Using the mixing template and the whole/parts dichotomy we can assign amino acid codons to generic 'meanings'. This is a simple one:one mapping that has no meaning at this time outside of the mapping.
Implied in this are the following groupings based on the template positions at level 6 of the template derived from applying the pyramidine/purine dichotomy:
Static-----------------------------------------------------Dynamic
Wholes Parts-to-Whole Relate. Parts Transition/
Transformation
(static aspects) (dynamic aspects)
AAA Lys AAC Asn AAT Asn AAG Lys
ACA Thr ACC Thr ACT Thr ACG Thr
ATA Ile ATC Ile ATT Ile ATG Met(START)
AGA Arg AGC Ser AGT Ser AGG Arg
CAA Gln CAC His CAT His CAG Gln
CCA Pro CCC Pro CCT Pro CCG Pro
CTA Leu CTC Leu CTT Leu CTG Leu
CGA Arg CGC Arg CGT Arg CGG Arg
TAA (STOPochre) TAC Tyr TAT Tyr TAG (STOPamber)
TCA Ser TCC Ser TCT Ser TCG Ser
TTA Leu TTC Phe TTT Phe TTG Leu
TGA (STOPopal) TGC Cys TGT Cys TGG Trp
GAA Glu GAC Asp GAT Asp GAG Glu
GCA Ala GCC Ala GCT Ala GCG Ala
GTA Val GTC Val GTT Val GTG Val
GGA Gly GGC Gly GGT Gly GGG Gly
The last member of the codon gives a clue to the overall explicit context of the codon and the first member gives the root context:
Using this information we can analyse codon changes. For example, the sickle -cell mutation, a deformity of blood cell structure, results from the change of a single base in a codon. This change is from an A to T/U (GAA to GUA). In the above classifications, we have gone from a whole to a part within the explicit context of a whole (xxA) developed within the root context of change (Gxx).
The amino acid codes listed above are in binary order. That is, using the template, they start at the contractive end (AAA) and finish at the expansive end (GGG) of level 6 of the template.
If this is of value or not is unknown, but the 'fact' that we can map an external coding system to a human coding system is interesting.
There is a faint possibility that there is 'something' going on since the DNA/RNA coding system is strongly based on dichotomy. The question is whether our classification of DNA/RNA results fron our method of classification or whether our method of classification is an extention of 'nature'. Life refines the basics despite the complexity of the system.
Of interest to the reader may be my observation, based on the published sequences of three genes, two human and one mammal (mouse), that within the coding sequence (intron area) there was a marked reduction in the number of amino acid codes that I have classified as 'Whole' biased. In the non-coding areas there seemed to be no strong difference. However, these 'results' could have been due to chance or a specific attribute of the genes that caused their sequences to be published. This all warrents further investigation.
One of the main elements in DNA/RNA is Carbon, and considering the discussion in this site on dichotomy, a look at the element, so strongly connected with life, shows some interesting characteristics.
What has been explicitly described so far is the emergence of a rich reality from the 'middle' space of any dichotomy. I have suggested that there is a fundamental process at work and thus our intuitive use of dichotomous analysis in our making of maps.
The question arises as to whether our maps are thus highly personal or whether we have adapted to the environment by internalizing one of it's fundamental characteristics - dichotomization - and thus our maps have some value outside of our heads. (especially 'public' maps which are based on a high degree of 'consensus' to make the maps as easy to read as possible - they are kept generic enough to allow for a large number of possible interpretations that still lead to the same 'conclusions' - X is west/left of Y. The template allows for this format and thus we find the rich 'generic' nature of the dichotomously-derived esoteric typologies.)
Of note is that some of the models of reality developed within physics continue to manifest this emergent property and one of the strongest models to date is that of quantum mechanics.
Quantum mechanics, besides being the 'flavour of the month' in physics, is the main tool used in chemestry and it is in chemestry that we find a shining example of dichotomous 'emergence' in the form of the carbon atom.
In chemestry, it is the outer shell of an atom that is concerned with the mixing of elements. This shell is restricted to having a maximum of eight electrons in it. The first five shells within the classification system follow the sequence 2 - 8 - 8 - 18 - 32... Thus the 18-shell only starts to fill up with more than 8 when the 32 shell is first created (with one electron). This is a function of maintaining stability and stresses the maximum-of-8-in-the-outer-shell rule. (The 'noble gases', that do not combine with anything, all have the maximum 8 electrons in their outer shells).
What is of interest (as far as life is concerned) is that the carbon atom has four electrons in it's outer shell and is found to be one of the most chemically active elements around within the context of possible variety as well as maintaining stability. It is this ability that leads to the emergence of carbon-based life forms since it is this ability that allows for a high degree of variation and thus the forming of complex structures. (The simplest organic material are hydrocarbons - combination of hydrogen and carbon atoms).
In Carbon, note that the number of electrons in the out shell are at the mid-point between the possible range of outer shell electrons (1-to-8). We can symbolize this dichotomously as min/max; 'rich reality' emerges from the middle:
min/max
^
'emergence'
This emergence is a natural phenomena and correlates with the mid point allowing for the highest degree of possible states. But, since this is the midpoint it suggests that a dualistic bias would be a 'natural' aspect, since all emergent states would be framed within the initial gross context of a 50/50 split.
As far as 'perception' is concerned, it would be favourable to maximize our abilities and thus the emergence of this 'balanced' point of view would be natural; Ashby's Law of Requisite Variety - the system with the most choices, rules.
Considering the concept of the Context Ratio, the initial frame (1) is akin to the above emergence but where there is no dependence. The development of hierarchy emerges when previous text and context becomes the context for the next degree of emergence and thus we have the most primitive form of hierarchic development in the form of the fibonacci sequence; a rather common developmental attribute found in many lifeforms.
All of this suggests that the most common lifeforms in the universe would be carbon-based, or else based on an element with four electrons in the outer shell:
1 2-4 (carbon - non metal) 2-8-4 (silicon - metalloid) 2-8-8-4 (germanium - metal) etc
This takes us back to the requisite variety concept (the system with the most choices controls the situation) and suggests that the concensus approach to map-making is akin to the allowing for as many possibilities that will still maintain the stability/integrity of the whole. And we find that the only state in which we can maximize the potential choices is in the 50/50 split.
Going from the micro to the macro, another example is Hubble's Law. Using a dichotomy of Speed of Recession / Distance, we find that the galaxies in the universe end-up bunched along the midpoint; this is in fact a 'map' of the expansion of the universe - a map of change. This law was derived by Hubble using a property of waves, specifically lightwaves in that moving away objects are seen as redshifted and coming towards as blueshifted; another dichotomy in which 'reality' would occupy the middle space, with the older the system the more central the data - no extremes.
In the context of humans,when we consider the claimed period of human evolution, it is easy to see how such a preference could emerge 'randomly' and then develop a degree of stability. Furthermore, the preference for this format in information processing gives the organism as rich a degree of choice as is statistically possible and so the optimum analysis of wholes, parts, and their aspects would appear to be based on dichotomous analysis with DNA/RNA coding being an example.
As mentioned, there have been a number of books that point out the correlation between hexagram creation and the codes for amino acids found in DNA and RNA. What this leads to is a model of thought based on strings of hexagrams, just as a coding sequence for a protein is based on strings of codons (a codon is a 'string' of three molecular bases that, taken as a group, lead to the insertion of a specific amino acid in a protein chain.) Using the DNA/RNA pattern, there is a suggestion that we can produce strings that map to thoughts (the normal process of building a hexagram is based on this, but here we replace yin/yang with a hexagram. Using the normal generation of a hexagram, we find that a hexagram links to a specific codon and so we use hexagrams to map strings of codons.).
As the template shows, at any one moment there is a specific state that corelates with(describes) the moment. We determine the state by the degree of dichotomization. Thus, if we only dichotomize to level 2 (4 states) then any moment has one of the possible states as context.
Since we wish to avoid generalities, we find that we can start to get good models from level 3 onwards (trigram level) and start to 'loose it', in that we enter the world of complexity and rich individual differences, after level 6 (hexagram level).
Using level 3, we find that at a specific moment one of the eight states is active, and it follows that any of the other states can be the next state. This follows for the hexagrams, but at that level we get a more refined state analysis.
Therefore the binary I Ching map can be read both vertically and horizontally, futhermore, the left edge wraps around and attaches to the right edge, and the top folds and joins the bottom (this is so because the top is the whole, and the more we cut, the more refined we get until we get to a point where we can cut no more - a continuum which is the whole). All this forms a torus.
In DNA/RNA systems, a gene string start with the sequence AUG. In the I Ching this links to hexagram 53, Development(Gradual Progress - 'With restraint comes influence'.).
A gene ends with one of three possible sequences - UAA (24), UAG (42), or UGA (55).
In the current model, these hexagrams deal with:
Note that the start hexagram is contractive (yin based) and the end hexagrams are all expansive (yang based). Using the mixing principle, the start is:
53 - contractive binding in the context of contractive bonding.
And the ends are:
In all four hexagrams, binding is predominant, setting the root context for two of the four, with bonding and bounding being the other root contexts.
(NOTE: my own mapping of the DNA/RNA codes to the I Ching falls in with that of Johnson Yan. See his "DNA and the I Ching : The Tao of Life" North Atlantic Books (1991) ISBN 1-55643-097-3.)
If we use the whole/parts dichotomy mappings we have:
This suggests a possible sequence pattern of endings: 55 <--> 42 <--> 24.
To me, there are some 'deep' connatations in this, but then the template can cause that without there being any 'fact'.
NOTES:
In DNA sequencing, RNApolymerase is required to detect a start position for a specific gene in a DNA sequence.
There are two such positions, the -35 sequence and the -10 sequence. It is presumed that the -35 sequence is for
the sigma factor of the RNApolymerase to link to and the -10 sequence is the pointer to the start position(+1).
Of note is the fact that the amino acids at the -10 sequence (also known as the 'Pribnow Box') are all of the A
or T type (A=wholes, P=parts) and the overall pattern (consensus sequence) is deemed TATAAT. The consensus sequence
for the -35 sequence is TTGACA (G=dynamic aspects, A = whole).
In the gene sequence, the start code is always AUG, a dynamics aspect marker and ends with UAA,UAG,UGA (whole,pAspect, or whole).
Given the discovery of 'inner details' of hexagrams being extractable using the XOR
operator, so the same mechanism would apply to DNA/RNA sequences, showing a level of detail in encoding not
covered before.
References: