196 Photos - Jan 18, 2014
Photo: Model of the structure of penicillin, by Dorothy Hodgkin, Oxford, c. 1945
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Biophysicists and biochemists are yielding more and more examples of biochemical entanglement patterns every day, particularly in the area of 'systems chemistry'.

The smallest units of organization in systems chemistry are not physical objects in the ordinary sense; they are forms, ideas which can be expressed unambiguously only in mathematical language. 

Recent discoveries suggest information is in some sense made of information which comes in bits -- irreducible yes-no, on-off decisions -- that can be modeled with the '0's and '1's that comprise base-2 systems.Photo: All atoms emit a distinct pattern of light called a spectrum.

The Turing machine can be viewed as a least common denominator -- a translation between sequence in time and pattern in space -- lying at the foundation of mathematics and suggesting the possibilities of a communications medium we have only just begun to explore. -- Frank Dyson

Using Cellular Automata, Wolfram’s Rule 110 is the smallest Turing machine on record. It has only two states and five possible colors.

Wolfram demonstrated that Cellular Automaton Rule 110 is capable of universal computation (given the right software).

Any CA Rule can be represented as a base2 system half state base2 cross section.

Operating similarly to Wolfram’s CA Rule 110, RNA and DNA nucleotide Base2 System Half State Color Cross Sections also have only two states ‘0’ and ‘1’ and five possible colors (the 3 primary colors and black and white).

We hypothesize that the half state color of a nucleotide base base2 cross section corresponds to the information in its place values,
similar to how the different spectra in starlight indicate what elements are in a star.Photo: "Systems chemistry" allows researchers to outline the chemistry-biology connection.

Addy Pross, explains in his book 'What Is Life? 'How Chemistry Becomes Biology', that the emergence of life on earth and classical Darwinian theory are intimately related.

Pross explains that Darwinian theory is just the biological expression of a more general chemical principle, one that Darwin himself predicted would likely be uncovered in time.

Pross explains that 'biogenesis' may be the inevitable result of chemical reactions in nucleic acids creating a feedback loop that results in a greater ability for more and more complex biochemical reactions.

At each level of genomic complexity a different kind of genetic change becomes relevant… with the result that DNA allows for less leeway to unpredictability. -- Janet Browne, from her review of Jay Gould's book, 'Vital Dust'.

Bioinformatics and computational biology are related fields that focus on the development or application of quantitative tools to address modern biological problems.Photo: Base-2 Systems are at the mathematical foundation of balance, and occupy a center position in physics, biology, and chemistry.

In fact, matter, gravity and the simplest symmetry of life lead directly to Base-2 Systems'. -- Phyllis and Phillip Morrison.

Base-2 System language consists of the elements ‘0’ and ‘1’, the only two numbers that remain the same when squared. In an Einstein Universe where E = MC2, that means '0' and '1' are the mathematical memes of Relativity.

The base-2 language in a mathematical system is able to be expressed in cross sections and show which place value is contributing to the overall weight or value of its unique composition.

In Base-2 Systems and Venn diagrams are interrelated. Venn diagrams add a further level of interpretation by indicating the half-state 'variance' or 'co-variance' between mRNA relationships.Photo: A newly discovered design feature of the DNA molecule called topologically associating domains, or TADs, suggests the informational expanse of the genome is divvied up into a series of manageable, parochial and law-abiding neighborhoods with strict nucleic partitions between them — each one a TAD. -- Natalie Angier, NYTimes Science Section.

“DNA is a super-long molecule packed into a very small space, and it’s clear that it’s not packed randomly. It follows a very intricate and controlled packing mechanism, and TADs are a major part of the folding protocol.” -- Dr. Stefan Mundlos of the Max Planck Institute for Molecular Genetics.

Through chromosome conformation studies and related research, scientists have discovered the genome is organized into about 2,000 jurisdictions, and they are beginning to understand how these TADs operate.

TAD boundaries dictate the rules of genetic engagement. As with city neighborhoods, TADs come in a range of sizes, from a few dozen DNA subunits long to TADs that sprawl over tens of thousands of bases. TAD borders serve as folding instructions for DNA. The new research indicates that switches and enhancers act only on those genes, those protein codes, stationed within their own precincts. In other words, what happens in a TAD stays in a TAD.

This is where Quantum Computing comes in. Using the uniqueness of each TAD, a quantum computer can map and profile the unique base2 system half state cross section color pattern of each DNA codon in 3D space (similar to a biochemical GPS) to literally follow DNA and Protein Folding when 'DNA Makes RNA Makes Protein".Photo: Mathematics goes hand in hand with science, for the key hallmark of science is that it yields verifiable predictions, and mathematical models allow this.

Mathematics is useful precisely because it allows large scale summary of a system, in a manner which may admit prediction of the behavior of that system.

Does the the ability to use mathematically derived base-2 color progression to emulate particle interactions -- the most basic events in biochemistry -- open up the bridge between chemistry and biology?Photo: Self-assembling RNA molecules play critical roles throughout biology and bioengineering. Can the inherent  'transformative' nature in the universality, scaling, self-similarity and flow of RNA elemental information represented in a mathematically derived Base-2 System Color Progression half-state architecture identify how and where its information occurs?

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'Universality means that different systems will behave identically. 'Scaling means that some quality is being preserved while everything else changes; 'self-similarity is symmetry across scales. Flow is defined as 'shape plus change, motion plus form.'

'Each change of scale brings new phenomena and new kinds of behavior... every extension seems to bring new information.'

'Flow assumes some reality independent of the particular instant'. 'Flow wants to realize itself, regardless of its surrounding material'.

Quotes from Chaos: A New Science', James Gleick.Photo: Image: Diagram of 'Modern Science' from one of Cliff Pickover's books appendices. Cliff is the head of IBM Thomas Watson Labs.

If biogenesis is the inevitable result of chemical reactions in nucleic acids creating a feedback loop that results in a greater ability for more and more complex biochemical reactions, then
shouldn't two changes be made?

Replace  Pythagoreans near the center of the
page with Base2 System Progression and have
L-Systems directly connect to it.

Locate the chemical elements box -- center-left -- as you look at the diagram and replace it with biogenesis and take out the question mark.Photo: Angular momentum is a measurement of how something rotates around its own axis, which light is known to do. Essentially, as photons -- tiny particles of light -- travel through space, they twist and turn around their axes.

Previously it was thought that light's angular momentum was a constant, but the team at Trinity College in Dublin, Ireland discovered that under certain conditions, it only spins around its axis half as much as it should -- in a 'half state' if you will.

This is critical to using light in measurement because it explains how color can combine or be muted but never lose its energy color value across point, line, plane, shape, scale and dimension.

Everything stops light but nothing pollutes it. 1/2 of red is still red. 1/2 of blue is still blue. 1/2 of yellow is still yellow. Photons have an 'emptiness to change' and all matter 'reflects' it. Our Universe, and Nature itself is meant to change.

Anything not “0” is off center and nothing but zero is zero. Nothing exists without a center around which it revolves, whether the nucleus of the atom, the heart of the body, the sun and our solar system…when the center does not hold the pattern collapses. P.8 Schneider, How To Create The Universe Out Of Nothing.Photo: See our Poster at Drop Box: www.dropbox.com/s/lunsfdi3s5z2t2t/mark-qbio-poster.psd?dl=0

Encoded in shape are the most basic features of reality that can be calculated — it's volume -- which consists of the probabilities of outcomes of lower level particle interactions. In short: the scattering amplitude equals the volume.  The details of a particular scattering amplitude can dictate the dimension and facets of the corresponding shape.

In the 1990's, Sean Carroll and Steve Paddock (UW-Madison / HHMI) -- pioneered a process that visualized 'Biogenetic Flow' -- and proved that there are 'preexisting patterns' with a 'sequence-in-time-and-pattern-in-space' at deeper genetic levels: a self assembling 'preexisting pattern' responding to a ‘sequence in time-pattern in space’ -- as 'shape-plus-change-motion-plus- form' -- and assuming some reality independent of the particular instant - trying to realize itself regardless of its surrounding material; possessing properties that do not seem to be random but inherent in the deeper genetic architecture itself as the outcome of rules that yield the shape of the value.

Carroll and Paddock hypothesized and pioneered in the lab ways of how this is done.Photo: Why is mathematically derived base2 system color progression important to genomic pattern and relationships?

How we perceive color is the same as how we perceive events. Any motion, event, change, succession, simultaneity or cause/effect in light is a single point of interest; a point that is certainly going to have other relationships that can be seen and measured with the naked eye.

Humans can detect the presence of a single photon, the smallest measurable unit of light.

Light consists of photons, the smallest physical entity with quantum properties which is interacting biogenetically in our billions of cells.The response that the photon generates survives all the way to the level of our awareness.
Research has shown that one photon "primes" the system to register the next.

Read more at: http://phys.org/news/2016-07-humans-smallest.html#jCpPhoto: Chemist John Sutherland and his team at the University of Manchester, England has created the conditions in which the building blocks of RNA, one of the key molecules of life and the probable precursor to DNA, assemble themselves naturally. Cytosine (C), in its 'half-state', possesses the genetic material ('1' in base-2) and combines with its other half-state possessing no genetic material ('0' in base-2). When exposed to sunlight, the now complete (C) cytosine creates Uracil.

Sutherland and his team's discovery begins to solve one of the central hard questions in prebiotic chemistry -- establishing a pathway from simple to more complex chemicals, where chemistry becomes biology.

But there used to be one big problem with that theory: The ingredients present on prebiotic Earth – Earth before life – don't mesh together to make RNA. That problem has been solved.

In a study published in Nature Communications, researchers found convincing candidates for the nucleotides that may have formed the "N" in a pre-RNA polymer – something that looks and acts very much like RNA, but is built from materials readily available in our planet's prebiotic days.

The researchers found that two molecules known as barbituric acid and melamine readily combined with the sugar ribose (the "R" in RNA) and with each other when left alone in lukewarm water.

They even bonded into structures like the ladder-rung pattern seen in RNA and DNA, forming long strands of polymers that turned their watery incubators into a jelly-like substance.Photo: The base2 system half state color progression is built up from '0', one entangled half state at a time. 'U' is always 00; 'C' is always 01;
'A' is always 10; 'G' is always 11. The color depends on its context in the base2 system cross section pattern.

The image is of the first eight RNA molecules -- first as nucleotides, then pairs and then nested inside a DNA/mRNA (0-63) architecture. The key word is 'backfilling'. Base2 systems buildup but they also backfill to bring the past into the present that is an emptiness to change.
(0) U (000) is black,
(1) C (001) is blue,
(2) A (010) is yellow,
(3) G (011) is green.

the base2 cross section inverse of green and its color complement is red.
(4) CU (100) red,
which allows the full color palette (0-7) to take shape -- a half state triplet with eight fundamental building blocks the Chinese called Trigrams.
(5) CC (101) purple,
(6) CA (110) orange,
(7) CG (111) white

(7) CG (111) white is the result of perfect color balance between the three primary colors.With this palette, I can color the genome.Photo: This sets the stage for a Genomic Biochemical Base-2 System Color Progression.

Quotes from Sutherland's Lab: http://www.bioinf.manchester.ac.uk/resources/phase/manual/node72.html.

'There are 16 possible RNA base-pairings, however of these, only six (2) UA, (3) UG (7) CG), (8) AU, (12) GU, (13) GC, are stable enough to form actual base-pairs.

The rest are called 'mismatches' and occur at very low frequencies in helices.' 'It helps explain why the primary structure of the RNA stems (i.e., their nucleotide sequence) can still vary and in fact we observe that RNA helical regions are quite variable in sequence'...'The nature of the bases is not important and substitutions are possible as long as they preserve the secondary structure.'

NOTE: The RNA (0-15) Base-2 System cross sections representing these stable bases: UA and GC, UG and GU, CG and AU are all Base-2 System inverse cross sections. 

This symmetry raises a question: Are the ten weaker 'mismatches' playing a role in amino acid formation through entanglement at this and deeper levels?Photo: In order to comprehensively understand the RNA's function, the better similarity measure among RNA's should be designed to consider their structure features (RNA nucleotides, RNA base pairs and mRNA codon triplet bases).

Using a context driven phonemic Base-2 System half-state base-2 color progression, it is possible to demonstrate how the RNA base half state with the least value -- the non-coding 'half-state' as chemist John Sutherland and his team at the University of Manchester, England puts it -- becomes entangled with the next RNA base-2 system cross section half state in the base-2 progression and is 'purposed' with the information in it.
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Mathematically, RNA pairs are a four place base-2 half state system (0-15) 'nested' within DNA and mRNA's six place base-2 system (0-63).

RNA pairs have a base-2 progression of:
08/0; 04/0; 02/0; and 01/0.
DNA and mRNA have a base-2 progression of:
32/0; 16/0; 08/0; 04/0; 02/0; and 01/0.Photo: T/U = 00,      C = 01      A = 10      G = 11 

Does each type of RNA molecule consist of the elements it itself appears in at deeper levels?

When plotted, (the red boxes) the deeper elements in the RNA molecule create the patterns and relationships seen in this image. Each molecule follows one mathematical formula where V=volume or value and (BP) = base pair.

Observation:
The architecture possesses properties that do not seem to be random, but inherent in the deeper architecture itself, as the outcome of rules that yield the shape of the value itself.

#V  (BP)  four red box elements in each line:
(00) xU: (01) xC, (02) xA (04) CU and (08) AU.
(01) xC: (00) xU, (03) xG, (05) CC and (09) AC.
(02) xA: (00) xU, (03) xG, (06) CA and (10) AA.
(03) xG: (01) xC, (02) xA (07) CG and (11) AG.
(04) CU: (00) xU, (05) CC (06) CA and (12) GU.
(05) CC: (01) xC, (04) CU (07) CG and (13) GC.
(06) CA: (02) xA, (04) CU (07) CG and (14) GA.
(07) CG: (03) xG, (05) CC (06) CA and (15) GG.
(08) AU: (00) xU, (09) AC (10) AA and (12) GU.
(09) AC: (01) xC, (08) AU (11) AG and (13) GC.
(10) AA: (02) xA, (08) AU (11) AG and (14) GA.
(11) AG: (03) xG, (09) AC (10) AA and (15) GG.
(12) GU: (04) CU, (08) AU (13) GC and (14) GA.
(13) GC: (05) CC, (09) AC (12) GU and (15) GG.
(14) GA: (06) CA, (10) AA (12) GU and (15) GG.
(15) GG: (07) CG, (11) AG (13) GC and (14) GA.

Conclusion:
Mathematics creates a path to study underlying visual genomic geometry in order to simulate, find, and define genomic biochemical preexisting patterns.Photo: 'At least one of the six RNA base-pairings stable enough to form actual base-pairs: (2) UA, (3) UG, (7) CG), (8) AU, (12) GU, and (13) GC; appears in and consists of the very 'mismatches' John Sutherland identifies in his lab website.
http://www.bioinf.manchester.ac.uk/resources/phase/manual/node72.html.

  #    BP    four red box elements in each line:
(00) xU: (01) xC, (02) xA (04) CU and (08) AU.
(01) xC: (00) xU, (03) xG, (05) CC and (09) AC.
(02) xA: (00) xU, (03) xG, (06) CA and (10) AA. 
(03) xG: (01) xC, (02) xA (07) CG and (11) AG.
(04) CU: (00) xU, (05) CC (06) CA and (12) GU.
(05) CC: (01) xC, (04) CU (07) CG and (13) GC.
(06) CA: (02) xA, (04) CU (07) CG and (14) GA.
(07) CG: (03) xG, (05) CC (06) CA and (15) GG.
(08) AU: (00) xU, (09) AC (10) AA and (12) GU.
(09) AC: (01) xC, (08) AU (11) AG and (13) GC.
(10) AA: (02) xA, (08) AU (11) AG and (14) GA.
(11) AG: (03) xG, (09) AC (10) AA and (15) GG.
(12) GU: (04) CU, (08) AU (13) GC and (14) GA.
(13) GC: (05) CC, (09) AC (12) GU and (15) GG.
(14) GA: (06) CA, (10) AA (12) GU and (15) GG.
(15) GG: (07) CG, (11) AG (13) GC and (14) GA.Photo: Early Predictions:

Each mRNA codon (a DNA codon codes for to make an amino acid to make a protein) has a unique meaning, function, and purpose -- even when coding for the same amino acid.

An mRNA codon that codes for one amino acid can share the same attraction repulsion pattern as another mRNA codon that codes for a different amino acid, suggesting a deeper relationship.

In every gene sequence (including repetitive gene sequences), the total number of codon occurrences provide new clues as to the purpose of a gene sequence and how it folds into a specific protein shape.

In every gene sequence, any missing codon not found in the primary gene sequence, will occur in abundance at deeper levels; suggesting a scaffolding underlying all protein folding.

Things get more ordered at deeper levels, not less, suggesting that codons are not 'degenerate' and the 'Wobble Theory' is incorrect.Photo: Patterns in data lead to predictive models of molecular function and mechanism. An mathematically derived Base-2 System half state color progression will allow accurate and more detailed comparisons between current genome sequences; require less resource, speed up analysis, reduce inaccuracies and suggest new and rewarding areas of discovery.

How do we visually represent deeper 'intra' and 'inter' networking relationships in the order and connection of genetic information found in protein sequences that fit known scientific models of DNA and Protein folding behavior?

Base-2 system half state color progression used in conjunction with real time genetic modeling may help answer why, when, where and how genetic information behaves in self-similar ways across scaled genetic network architectures.Photo: The structural polymorphism of chromatin appears to be reconfigurable from the nucleosomal to the nuclear level.

We hypothesize that base-2 system half state color progression would not only apply to a small proportion of complex genomes that encode protein, it would also be relevant to all of the DNA in these genomes.



.Photo: In any biology textbook, when you look at a diagram of how genes are depicted, it is invariably a one-dimensional line.

In reality, genes are arranged in such a way that two parts of the gene may be distal to each other linearly, but very close in three dimensions.

While scientists have developed an understanding of the one-dimensional structure of DNA, little is known about the basic principles of DNA folding and its role in gene regulation.

Even less is known about how different parts of DNA are folded next to each other inside the nucleus.

What we do know is that the spatial organization of the regulatory process of formation is intimately linked to its role in the body.
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Note: The colors in this example are out of color context because they are not mathematically derived. Every 'A' is red, every 'G' is yellow, every 'T' is blue, and every 'C' is green. This obscures patterns and relationships that are there.

'WHEN DNA MAKES RNA MAKES PROTEIN' THE COLOR OF A CODON BASE DEPENDS ON THE CONTEXT OF THE BASE IN THE CODON TRIPLET.
IT SEEMS COUNTER INTUITIVE BUT IT IS EASILY PROVEN.Photo: Examples of past attempts to use base2 systems to decipher the genome not only failed to assign a Base-2 System color progression to nucleotide bases, they did not agree on a standard base-2 representation of the nucleotides -- Thymine, Uracil, Cytosine, Adenine, and Guanine.Photo: Current genomic software programs only use color to differentiate one codon base from another; assigning only one 'fixed' color value to each codon base (like in this image where 'A' can only be red, or 'G' can only be yellow, or 'T' can only be blue or 'C' can only be green).

This means genomic data sets using fixed color values for  each  codon base miss key transitive patterns and relationships nested inside larger genomic patterns.

There is a treasure trove of archived genomic data sets that can be revisited to find these patterns and relationships.

When codon bases are assigned their Base-2 System half state color based on their relative context in the linear gene sequence, the patterns and relationships that 'emerge' provide clues to the relationships between RNA base pairs, DNA and the mRNA codons DNA codes for to make a protein.Photo: Note: In a mathematically derived Base2 System Progression:

The 'T' for Thymine in DNA and
The 'U' for Uracil in RNA both = 00;
The 'C' for Cytosine = 01;
The 'A' for Adenine = 10;
The 'G' for Guanine = 11.

The U, C, A, and G nucleotide codon base in an RNA's Base-2 system's color progression depends on its context in the codon triplet. No specific color can be assigned to a codon base until its context in the codon triplet is known.

It is necessary to assign place value first to a codon triplet base before assigning color based on its context.Photo: In base2 systems: T/U = 00, C = 01, A = 10, G = 11.

Base-2 color progression nucleotide codon base half state cross section values switch 'on' or 'off' to create all of the possible codon possibilities:
each of the 16 RNA pairs, the 64 DNA codon triplets and the 64 mRNA codons DNA codes for to make a protein is unique in pattern and function -- and yet part of the same system which can be mapped across point, line. plane, shape, scale and dimension with a base2 system color progression.

The balances are interesting.

The RNA base pairs considered stable enough to code for an RNA are all base2 system inverses. And when DNA Makes mRNA: 27 mRNA codons (3³) do not have a uracil in them. 27 mRNA codons (3³) have one uracil in them. And 09 mRNA codons have two uracils in them (3²).
One RNA codon (0) UUU, has 3 uracils.

Question: Does (0) UUU 000000 act as a biological constant or mathematical morphism which triggers a system comprised in perfect thirds in a base2 system: 1-21, 22-42, 43 to 63?Photo: T/U=00      C=01      A=10      G=11.

Using mathematical correct base-2 system cross sections, is there one universal rule to explain how RNA codon base half-states switch 'on' or 'off' to create the larger scaffolding for the protein shape that houses the specific meaning and function of the gene -- the way a key opens a lock?

Is signaling with light or biochemicals occurring at RNA levels?

How might it work? Is it emergent?

Is it like a 'wave' pattern or 'time cones' or similar to  ripples from a rock being thrown into a pond?Photo: Fact: All atoms emit a distinct pattern of light called a spectrum.

Mathematically derived base2 system color progression suggests nucleotide half-states use two states '0' or '1', and three primary colors -- operating similar to the smallest Turing Machine on record; Wolfram's CA Rule 110.

The result is at the mRNA codon level, every center base in an mRNA codon triplet is either red or black. Every 1st and 3rd nucleotide base in an mRNA codon triplet base is either black, blue yellow or green.

The combination of primary color nucleotide half states in the bases (1st with 2nd, 2nd with 3rd, 1st with 3rd) create the secondary colors.  The black (no color) and white (combined color) families are Hox codons which we hypothesize regulate the gene sequence and direct the folding of the linear gene sequence into its 3D shape.Photo: T/U=00      C=01      A=10      G=11.

All waves, including light, have a common property: if two waves combine, the waves can meet each other crest-to-crest, adding up and reinforcing the effect of each other, or they can meet crest-to-trough, cancelling each other out so that they have no effect. When they meet crest-to-trough, for every "up" vibration in one wave, there is a corresponding "down" vibration in the other wave.

One universal rule undelies the context driven phonemic Base-2 System color progression.

When two same color Base-2 system mirror value columns are switched on at the same time [Blue: 32 and 01; Yellow: 16 and 02; Red: 08 and 04], the color is muted in both value columns but the value remains -- similar to how combinations of up and down quarks make either a neutron or a proton.

Could RNA pairs and the mRNA DNA codes for to make a protein be using something similar to light to indicate where the 'active', 'inactive' and 'muted' information occurs in a codon triplet?Photo: Hand drawn image of photon half-states in a six place base-2 system. The refracted light from the different patterns create mathematically derived color that can be ported to real-time images.
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'1' means information is there'. '0' means information is 'not there' -- but its place is held allowing interaction, flow, change, transfer, and transformation.

Until chemist John Sutherland and his team at the University of Manchester, England discovered half-states in RNA, it was difficult to demonstrate that context driven phonemic Base-2 System color progression applies to RNA, DNA and mRNA and mathematically demonstrate RNA entanglement.

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In physics; when a laboratory apparatus was developed that could reliably fire one electron at a time through a double slit, the emergence of an interference pattern suggested that each electron was interfering with itself, and therefore in some sense the electron had to be going through both slits at once.

This phenomenon has also been shown to occur with atoms and EVEN SOME MOLECULES, including buckyballs. Does it ocur in RNA?Photo: Image: This is the order (0-63) of a context driven phonemic Base-2 System color progression where each numeral represents an mRNA codon that DNA codes for to make a protein. 

For example: the base2 system cross section for UUU is (0) 00 00 00 where:
T/U= 00       C= 01       A= 10       G= 11
in base-2 language.

Each number corresponds to a unique cross section pattern (0-63); where it can be further broken down into the portion of the mRNA nucleotide base element that is contributing to the mRNA's overall numeric value, meaning and color.
Ven Diagrams can then be used to measure 'variances' and 'co-variances'.

Even at this 1st of six levels the color family pattern relationships are apparent.Photo: T/U=00     C=01     A=10     G=11.

This is the context driven phonemic RNA CODON color progression (0-63).

Is the only difference between DNA and RNA
that the T for thymine in DNA is replaced by U for uracil in RNA?

Or does this change also conform effortlessly to a balanced RNA architecture where uracil acts like a mathematical 'morphism'?Photo: Does the sequential order of a base-2 system 
(0-63) context driven phonemic mRNA color progression reveal an internal symmetry and relationship between DNA and mRNA codons?

First Level Findings:
Why do same color codons have the same base2 cross section  folding preference yet retain an ability to code for different amino acids? How might same color family mRNA codons be related?

Why do complementary color RNA codons like black and white, blue and orange, yellow and purple, and green and red have mirror image positions that are diagonally oriented opposites?

Why are all 64 mRNA codons oriented to either
the right diagonal or left diagonal ? 

Why do only the black mRNA codons produce perfect stand-alone base-2 cross section palindromic symmetry patterns? Why do only white mRNA codons consist of cross section internal inverse patterns? Why don't the color family codons (blue, yellow, green, red, purple, orange) have any of these patterns?Photo: Gottfried Leibniz was Albert Einstein's favorite mathematician and philosopher.

Why did Leibniz call the right and left diagonals of a squared system 'relative' zeroes? How did finding the diagonal of a square subsequently lead Leibniz to inventing calculus, and solving the problem of 'infitesimals' and imaginary numbers?

Dark grey = black codons (also base-2 system palindrome patterns. Light Grey = white codons.

Black trifold:     00, 12, 18, 30, 33, 45, 51, 63.
Blue trifold:        01, 13, 19, 31, 32, 44, 50, 62.
Yellow trifold:   02, 14, 16, 28, 35, 47, 49, 61.
Green trifold:    03, 15, 17, 29, 34, 46, 48, 60.
Red trifold:        04, 08, 22, 26, 37, 41, 55, 59.
Purple trifold:    05, 09, 23, 27, 36, 40, 54, 58.
Orange trifold:   06, 10, 20, 24, 39, 43, 53, 57.
White trifold:      07, 11, 21, 25, 38, 42, 52, 56.

When (x) + (y) = 63, why are the two variables always same color family RNA codons and base-2 system pattern inverses of one another?Photo: U=00      C=01      A=10      G=11.

The current genomic mRNA model can be laid out in a Base-2 System half state color progression mathematically portrayed in the values that appear beneath the current model. 

In a base-2 half state color progression 'U' (uracil) is the only codon base letter value that is fixed and is always '0'.

'U' (uracil) can only have a value of '0'.
However, depending on the codon base context:
'C' (cytosine) can have values of '16', '04' or '01'.
'A' (adenine) can have values of '32', '08' or '02'.
'G' (guanine) can have values of '48', '12' or '03'.

Converting this mRNA chart into a place driven base-2 half state color progression architecture allows mathematically derived color to be assigned to each mRNA base half-state to find the deeper patterns and relationships.

RESULT:
Each mRNA codon is unique in value, meaning and purpose, even when coding for the same amino acid.

Base-2 system cross section patterns show how and where each codon base half switched 'on' or 'off' to create one of the amino acids.Photo: A context driven base-2 half state RNA color progression architecture demonstrates how each codon has an overall mathematically derived color. 

One of the new relationships discovered is that same color codons, even when coding for different amino acids, will always have the same base2 system cross section attraction/repulsion pattern which may  be important to protein folding.

A mathematically derived context driven base-2 half state color can be assigned to each codon half-state place value in the RNA pair, DNA and mRNA architecture. The combination of these color half states will always combine to create the overall codon color.

Even at this first level the symmetry is evident even though it is in sequential form.Photo: T/U = 00       C = 01       A = 10       G = 11.

Observation: Uracil driven codons (0-15) contain all three stop codons: UAA, UAG, and UGA. Further, UAG has an mathematical relationship with AUG, the start codon that codes for MET. Uracil driven UGG [trp] is also a uracil driven codon and the only other single codon amino acid group besides AUG.

The numeric color value indicates the color family the RNA belongs. RNA codon base half states with color carry the 'active' information.

Same color family codons carry the same attraction-repulsion pattern but can code for different amino acids. 

Example: Red Family Codons (37) ACC, Thr and (41) AAC Asn. ACC and AAC are base-two system mirror images of each other. ACC thr is important in providing access to the essential and AAC Asn enables this access in confined spaces.

The (8) black and (8) white Hox codons are enlarged. There is one black or one white Hox codon for each one of the 16 uracil driven codon foursomes.


.Photo: This slide is a companion to the previous slide. illustrating how symmetry is even more evident at deeper levels.

This is the pattern of the elements that mRNA codons (0-31) consists. Each line has six dots which represent the elements at deeper levels. mRNA codons 32-63 are a mirror image of (0-31) that would appear in the space at the bottom of this page.

The meanings remain unique to each of the 64 mRNA codons because the 'sequence-in-time-pattern-in-space' is different for each. This is because the (32-63) mirror image elements -- while not having the same meaning or purpose -- do belong to the same color family. Interestingly, each color family exhibits logical AEIO internal family relationships.

In other words, each mRNA codon is unique and consists of and appears in different elements at deeper levels.

An mathematically derived base2 system color progression can track each of the uniquely patterned and purposed 64 mRNA codons DNA codes for to make a protein using cross sections (0-63) and port to real time graphical representations.Photo: The image was created by shooting a pulse of laser light at a metallic nanowire to make its charged particles vibrate. Next the scientists fired a stream of electrons past the wire holding the trapped light. When the two collided, it created an energy exchange that could be photographed from the electron microscope.

So what does this mean when looking at the photograph?

When the photons and electrons collide, they either slow down or speed up, which creates a visualization of a light wave.

At the same time the speed change appears as a quanta - packets of energy - transferred between the electrons and photons as particles.

In other words, it's the first case of observing light particles and waves simultaneously.

An 'entangled' Base2 system half state color progression can take full advantage of this method.Photo: We hypothesize that what a DNA codon consists of is what that DNA codon's elements appear in at deeper levels.

RNA codons consist of the probabilities of outcomes of deeper level particle interactions. In short: the volume of an amino acid an RNA codes for equals its scattering amplitude. The details of a particular scattering amplitude can dictate the dimension and facets of the corresponding shape.

A Fourier Series is based on a simple fact: 'every curve consists of piling up waves'. Each of the 64 RNA codons is unique with a specific weight, purpose and value. Each of the 64 RNA codons codes for a unique wave.

The number of occurrences of any RNA codon in a gene sequence can be expressed as amplitude which shapes the gene; this may explain why the RNA codons in each of the 20 amino acid codon families do not have to be the same size, weight, or tasked for the same purpose, even when coding for the same amino acid.

Source	https://commons.wikimedia.org/wiki/File:SquareWaveFourierArrows.gif
Author	Bob K.Photo: Proteins can not fold into their unique shapes to make a gene until an exact balance unique to that protein is reached.

This balance can be emulated in a base2 system color progression.

All matter comes from light. Light consists of photons (the definition of which is 'a particle the opposite of itself', or 1-1). Photons have an 'emptiness to change' and matter 'reflects' this. All of Nature itself -- all of life -- has 'an emptiness to change'.

Nothing reflects this 'emptiness to change' more than 'biogenetic flow'. Anything not “0” is by definition off center and seeks balance. Nothing exists without a center around which it revolves, whether it is the nucleus of the atom, the heart of the body, or the sun in our solar system…when the center does not hold the pattern collapses. P.8 Schneider, 'How To Create The Universe Out Of Nothing'.Photo: What are the practical applications?

Encoded in shape are the most basic features of reality that can be calculated — it's volume -- which consists of the probabilities of outcomes of lower level particle interactions.

In short: the scattering amplitude equals the volume.  The details of a particular scattering amplitude can dictate the dimension and facets of the corresponding shape.

Protein shape is coded into a gene's sequence-in-time-pattern-in-space and can provide important insight into solving  how protein folding occurs from a linear gene sequence.
------------
FIRST IMAGE: A sound sculpture (image) exists for a fraction of a second and is created when paint is perturbed by a burst of sound waves.

Variations in the viscosity and the pattern of paint, along with variations in the frequencies used to put the paint in motion, produce a unique image that exhibits a natural balance.

SECOND IMAGE: a scattering amplitude we plan to base around a base2 system color progression.Photo: Complex shapes have the same pattern at different scales. It all relates to transporting energy in the most efficient way possible. Each successfully crafted and unique shape is like a hanging mobile.

Encoded in shape are the most basic features of reality that can be calculated -- it's volume -- which consists of the probabilities of outcomes of particle interactions.

RNA's 'shape-plus-change-motion-plus-form' force combines with a unique 'sequence in time and pattern in space' force to create a masterpiece of biogenetic energy transfer using one universal law across point, line, plane, scale, shape and dimension.

‘At each level of complexity a different kind of genetic change becomes relevant…with the result that DNA allows for less leeway to unpredictability’.Photo: The deeper elemental mRNA energy color pairs are interchangeable (entangled), and join ‘0’ to create nature’s architecture.

Any diagonal in a balanced squared system is associated with Pi in three dimensions.

Mathematically, it appears that each mRNA codon uses its diagonal as a frame of reference to organize its bilateral information and keep it from tangling or losing information.

Mathematically, the space in which a protein folds is a mathematical expression of interrelationships among events that can be mapped.

It is always the case that the tetrahedral shape of an amino acid formed by connecting points on a regular square grid must have areas in the ratios of whole numbers. 

Using color, which obeys one universal rule, it can be shown how a polypeptide amino acid chain transitions into the protein’s unique final shape.Photo: Like DNA and RNA when balanced, the whorl pattern of a sunflower seed pattern can be viewed as a latticed base2 system color progression.

There is no repetition of a color in any row or column 0-40. Is this coincidence or evidence that mathematics, color and folding are connected and have an underlying preexisting order?

The seed color conversion string value in a base-2 color progression is in progressions of 8 whereas, for example, mRNA is in a progression of 16.

(0)black(8)red(16)yellow(24)orange(32) blue (3)green(11)white(19)blue(27)purple(35) yellow
(6)orange(14) yellow(22)red(30)black(38) white
(1)blue(9)purple(17)green(25)white(33)black
(4)red(12)black(20)orange(28)yellow(36) purple
(7)white(15)green(23)purple(31)blue(39) orange
(2)yellow(10)orange(18) black(26)red(34) green
(5)purple(13) blue(21)white(29)green(37)red

00      08      16      24      32 = 80
03      11      19      27      35 = 95
06      14      22      30      38 = 110
01      09      17      25      33 = 85
04      12      20      28      36 = 100
07      15      23      31      39 = 125
02      10      18      26      34 = 90
05      13      21      29      37 = 105

28       92    156    220    284(click on text to adjust)

Add each column and the progression sum from column to column is +64. Add each row and the progression sum from row to row is +5 where the progression is in the form of a +2 latticing.Photo: A gene is a protein's way of making another protein. A protein is a gene's way of making another gene. -- 'Genome', by Matt Ridley.

A protein knows what it is a 'part-of' and 'apart from', meaning each gene sequence is a unique 'sequence in time and pattern in space'. The primary sequence of a gene has multiple relational deeper layers.

This suggests that 'biogenesis' is more mathematically ordered at deeper levels, not less.
It also suggests an exquisite balance, a symmetry, a synergy, a symbiosis exists between all levels.

'Flow wants to realize itself, regardless of its surrounding material. Flow assumes some reality INDEPENDENT of the particular instant'. -- Gleick: Chaos: A New Science, 1989.

Proteins can not fold into their unique shapes to make a gene until an exact balance unique to that protein is reached. In other words, take out the sequence-in-time-pattern-in-space and watch it fold.

Life itself can not evolve until an exact balance is reached within an ecosystem.

Balance is key.Photo: T/U=00     C=01     A=10     G=11.

The choice of codons can influence local translation kinetics during protein synthesis. Universal patterns of conserved optimal and nonoptimal codons, often in clusters, associate with the secondary structure of the translated polypeptides independent of the levels of expression; suggesting an evolved function for codon optimality.

Do the 'missing' RNA codons in a gene's linear primary sequence when 'DNA Makes RNA Makes Protein' play an role (possibly equal) in shaping the protein?

If so, on how many levels of scaling does this occur on? How does this change the way we view DNA transcription which creates genes and proteins for cell continuity; or replicates itself, ensuring the process of life itself? 

Can this be shown with fractal genomic mathematics?

--Photo: A cell is like a seed that has everything that it needs to reach fruition if it is nurtured. Does elemental RNA work on the local cellular level to balance the cell's needs? In that sense, is RNA co-determinant with DNA.

Much would be explained if when DNA Made RNA to make a Protein it was simply coding for one of many possible assemblages of mRNA codons to make the 'type' of gene(s) the cell needs.

This flexibility would lead to diversification. This would also help to explain why no two mRNA codons are exactly alike, even when coding for the same amino acid. The pattern, shape, size and centered imbalance of each of the 64 mRNA codon's (an analog would be a mobile) is different.

It would also begin to explain in a genomic progression how each primary sequence's 'inactive', 'muted' and 'missing' mRNA codon triplet half states provide its scaffolding at deeper levels.

NOTHING IS WASTED.

Meaning the genomic biochemical architecture is more elegant at deeper levels not less, meaning there is not any 'wobble' or degenerate DNA codons when they code for mRNA to make a Protein.

DNA is not redundant.
.Photo: In RNA base-2:   U = 00    C = 01   A = 10    G = 11.
In DNA base-2:   T = 00    C = 01   A = 10    G = 11.
In mRNA base-2: T/U = 00, C = 01; A = 10 G = 11.

Do Sutherland mirror pair palindromes in single stranded RNA play a significant role in how a linear gene sequence coalesces into its three dimensional shape? Does the diagonal that naturally cuts through the ribose (the R in RNA) to infinity facilitate this process? The RNA base mirror pair palindrome values (0) UU to (15) GG:

(01) 0001 UC mirrors (08) 1000 AU;
(02) 0010 UA mirrors (04) 0100 CU;
(03) 0011 UG mirrors (12) 1100 GU;
(05) 0101 CC mirrors (10) 1010 AA;
(07) 0111 CG mirrors (14) 1110 GA.

Is DNA the stable evolutionary advance of the fluid volatile early RNA? Does this explain why DNA still needs mRNA to code for the amino acids to make protein?

When DNA codes for RNA to make a Protein, base-2 cross section palindromes in mRNA codon triplets play a significant role in directing the linear gene sequence coalescing into its unique three dimensional protein shape.

mRNA codon triplet stand alone palindromes are:
(00) 000000 UUU phe; (12) 110011 UGU cys;
(18) 010010 CUA leu; (30) 011110 CGA arg;
(33) 100001 AUC ile; (45) 101101 AGC ser;
(51) 110011 GUG val; (63) 111111 GGG gly.

Internal inverse mRNA codon triplet cross sections also play a role in protein folding:

(07) 000111 UCG ser; (11) 001011 UAG stop;
(21) 010101 CCC pro; (25) 011001 CAC his;
(38) 100110 ACA thr; (42) 101010 AAA lys;
(52) 110100 GCU ala; (56) 111000 GAU asp.Photo: Is information density in nucleotide codon bases similar to how areas of gene density are located on a chromosome?

Can a mathematically correct Base-2 System half state color progression indicate where this 'active' and 'inactive' information occurs in each nucleotide codon base?

Do RNA codon half-states switch ‘on’ and ‘off’ to create each of the 64 unique RNA codons?

In Genomic Biochemistry, is each of the uniquely patterned RNA codon half state already reacting or anticipating local cell conditions to create the scaffolding for a 'targeted' protein before 'DNA Makes RNA Makes Protein'?Photo: Question:
What specific leucine codons are being used in this gene sequence? Which serines? Which phenylalanine? Which alanines? Which prolines?

The assumption seems to be it doesn't matter.

Mathematically:
We hypothesize that it can in some instances it make a difference. For example, It matters with isoleucine. AUA and AUC code for isoleucine but AUC's function and purpose is different than AUA's. And AUA may not be an isoleucine at all but works intimately with the 'version' of Methionine (AUG) that isn't the start codon.

Mathematically:
DNA is more elegant at deeper levels, not less. DNA does not 'wobble' and codons are not 'degenerate'. DNA is not 'redundant'. Each codon has a specific pattern, meaning and purpose.

Mathematically:
The current model of the 20 amino acids is outdated.Photo: Half-states in RNA codon bases can be illustrated using two states '0' or '1', the three primary colors, and their combinations.

Every center nuclotide base in a DNA or RNA codon triplet is either red or black. Every 1st and 3rd nucleotide base in a DNA or RNA codon triplet is either black, blue yellow or green.

The combination of primary color nucleotide bases (1st with 2nd, 2nd with 3rd, 1st with 3rd) create the secondary colors. All three switched on primary color nucleotide bases in RNA create white, as do any combination of a a red and green nucleotide base.

Hox codons are any codon whose combinatory overall dominant color is black or white.Photo: Data sets assigning fixed color values to mRNA codon bases miss key transitive patterns and relationships nested inside larger genomic patterns. Assigning one color to each of the mRNA nitrogenous bases (for example where 'A' can only be red, or 'G' can only be yellow, or 'T' can only be blue or 'C' can only be green) does not produce meaningful output in graphical systems.

This is the alphabetical listing of the 20 amino acids by amino acid group with each mRNA triplet codon letter assigned its mathematically driven color.

Mathematically, each of the unique 64 mRNA triplet codon bases consist of two half-states that can be turned ''on' or 'off' and still hold place value, functioning similar to the way quarks make either a proton or a neutron in an atom.

The autonomous color of each half-state determines the overall 'dominant' color of the codon base. The combination of the mRNA codon triplet bases determine the overall color of the codon as well as what color family it belongs and is always reflected in the codon's numeral value.

One surprise already is that same color mRNA codon families can code for different amino acids.

One Universal Rule creates this pattern: the middle mRNA codon triplet base letter is always either black or red while the 1st and 3rd mRNA codon triplet base letter can be black, blue, yellow, or green based on its context.

An overall mRNA triplet codon color of white is the result of perfectly balanced half state color frequencies. The palindromic cross section pattern of black mRNA codons mute color at the half state level.
-------------------
Note: Glutamic acid and Glutamine are juxtaposed.



--Photo: T/U = 00,     C = 01,     A = 10,     G = 11.

The (0-31) RNA base-2 cross section patterns in the above chart depict the overall dominant color of the codon. The color of the bases is expressed in the codon base color columns.

Blue 1 and 32 are binary (base2) mirrors in a 6 place fractal base2 system.
Yellow 2 and 16 are binary base2 mirrors in a 6 place fractal base2 system.
Red 4 and 8 are binary (base2) mirrors in a 6 place fractal base2 system.

A codon whose dominant color is orange, purple or green is the result of two primary color column active place values being switched on creating the mathematical dominant secondary color.Photo: T/U = 00,     C = 01,     A = 10,     G = 11.

The (32-63) RNA base-2 cross section patterns in the above chart depict the overall dominant color of the codon. The color of the bases is expressed in the codon base color columns.

Blue 1 and 32 are binary (base2) mirrors in a 6 place fractal base2 system.
Yellow 2 and 16 are binary base2 mirrors in a 6 place fractal base2 system.
Red 4 and 8 are binary (base2) mirrors in a 6 place fractal base2 system.

A codon whose dominant color is orange, purple or green is the result of two primary color column active place values being switched on creating the mathematical dominant secondary color.Photo: Using a water droplet as his muse, Sidney Nagel and his Lab at the University of Chicago discovered that as long as a water droplet is 'unperturbed', microscopic water droplets follow the same universal laws as celestial formations, and nuclear fission.

As important, the Nagel Lab also discovered that when a water droplet is 'perturbed' it is fundamentally different than a water droplet in an 'unperturbed system'.

Thanks to Nagel's documented work, we now know that a 'perturbed' water droplet has an inherent ability to 'retain' almost all of its 'relevant' information. So... does this have implications for the genome?

'DNA Makes RNA Makes Protein' by replacing thymine with uracil; but is there something deeper going on here? Is water a pathway? There are quite a few hydrophobic codons in the genome.

With Nagel's 'pertubations', the differentiation of codon group 'types' seems clearer.

Question: When a cell is 'perturbed', is it able to tap into multiple levels of retained biochemical information at myriad biochemical levels in an attempt to return the cell to an unperturbed balanced system?

Is RNA its vehicle?

How do we study that?Photo: Using a mathematically derived Base-2 System Progression, this is the alphabetical listing of the 20 amino acids and suggests that the current organization of the 20 amino acid groups is incorrect in that the color families they belong to are oriented to one diagonal or another or both (white or black) and can consist of different amino acids.

Black and blue codons code for the same amino acids; as do red and purple codons, and orange and white codons. Black and white codons are Hox codons. Red codons are 'hinges'. Yellow and green codons code for the same amino acids with the exception of the relationships between yellow 14 [ter] and 35 [met] (aka stop and start codons); which have an intimate relationship with green 15 [W] trp and 34 [I] ile.

The designation 'both' under the heading 'diagonal' means that different color family codons in the same amino acid group can also be oriented to both the right diagonal and left diagonal.

There are 21 codons that are hydrophobic and oriented to both diagonals which is exactly one-third of the 63 mRNA codons DNA codes for to make an amino acid in a DNA linear gene sequence: isoleucine, leucine, valine, alanine, and proline.

Note: glutamic acid and glutamine are juxtaposed.Photo: T/U=00       C=01       A=10       G=11.

When a '1' appears in the '32' column, it adds blue to the 1st letter of an RNA codon triplet; AND when a '1' appears in '16' column it adds the color yellow to the 1st letter of an RNA codon triplet.

When a '1' appears in the '08' column it adds red to the 2nd letter of the RNA codon triplet; AND when a '1' appears in the '04' column it also adds red to the 2nd letter of the RNA codon triplet.

When a '1' appearing in the '02' column adds yellow to the 3rd letter of an RNA codon triplet; AND a '1' in the '01' column adds the color blue to the 3rd letter of an RNA codon triplet.

And when a '1' appears simultaneously in same color columns: blue 32 and 01; yellow 16 and 02; red 08 and 04; the color is muted (appearing black).Photo: 0 to 7.

A Base-2 System architecture suggests how RNA evolved, remaining independent at its fractal half-state levels, nesting within the DNA architecture, while maintaining its RNA integrity and fluidity.

When a '1' populates same color columns [for example]:

blue 32 and 1;
yellow 16 and 2;
or red 8 and 4;

the value remains but the color is muted.

If an (1) is in one same color column and not the other; then the color in the column with the (1) is switched 'on'. 

Each  pattern holds unique information
and a '1' indicates what codon triplet base half-state is entangled and contains the active nucleotide information.Photo: 8 to 15.

When a '1' populates same color columns:

blue 32 and 1;
yellow 16 and 2;
or red 8 and 4;

the value remains but the color is muted.

If an (1) is in one same color column and not the other; then the color in the column with the (1) is switched 'on'. 

Each  pattern holds unique information
and a '1' indicates what codon triplet base half-state is entangled and contains the active nucleotide information.Photo: 16 to 23.

When a '1' populates same color columns:

blue 32 and 1;
yellow 16 and 2;
or red 8 and 4;

the value remains but the color is muted.

If an (1) is in one same color column and not the other; then the color in the column with the (1) is switched 'on'. 

Each  pattern holds unique information
and a '1' indicates what codon triplet base half-state is entangled and contains the active nucleotide information.Photo: 24 to 31.

When a '1' populates same color columns:

blue 32 and 1;
yellow 16 and 2;
or red 8 and 4;

the value remains but the color is muted.

If an (1) is in one same color column and not the other; then the color in the column with the (1) is switched 'on'. 

Each  pattern holds unique information
and a '1' indicates what codon triplet base half-state is entangled and contains the active nucleotide information.Photo: 32 to 39.

When a '1' populates same color columns:

blue 32 and 1;
yellow 16 and 2;
or red 8 and 4;

the value remains but the color is muted.

If an (1) is in one same color column and not the other; then the color in the column with the (1) is switched 'on'. 

Each  pattern holds unique information
and a '1' indicates what codon triplet base half-state is entangled and contains the active nucleotide information.Photo: 40 to 47.

When a '1' populates same color columns:

blue 32 and 1;
yellow 16 and 2;
or red 8 and 4;

the value remains but the color is muted.

If an (1) is in one same color column and not the other; then the color in the column with the (1) is switched 'on'. 

Each  pattern holds unique information
and a '1' indicates what codon triplet base half-state is entangled and contains the active nucleotide information.

Note: (46) should be 10 11 10 which is why it is green.Photo: 48 to 55.

When a '1' populates same color columns:

blue 32 and 1;
yellow 16 and 2;
or red 8 and 4;

the value remains but the color is muted.

If an (1) is in one same color column and not the other; then the color in the column with the (1) is switched 'on'. 

Each  pattern holds unique information
and a '1' indicates what codon triplet base half-state is entangled and contains the active nucleotide information.Photo: 56 to 63.

When a '1' populates same color columns:

blue 32 and 1;
yellow 16 and 2;
or red 8 and 4;

the value remains but the color is muted.

If an (1) is in one same color column and not the other; then the color in the column with the (1) is switched 'on'. 

Each  pattern holds unique information
and a '1' indicates what codon triplet base half-state is entangled and contains the active nucleotide information.

48-63 are guanine driven codons.

1 has two uracils: (48) GUU.

6 have one uracil: (49) GUC, (50) GUA, (51) GUG, (52) GCU, (56) GAU, (60) GGU.

9 codons do not have uracil in them: (53) GCC, (54) GCA, (55) GCG, (57) GAC (58) GAA, (59) GAG, (61) GGC, (62) GGA, (63) GGG.Photo: If there are Hox genes are there Hox codons? 

Do Hox codons regulate protein organization in multiple levels of relational space?

Would combinations of RNA be produced by local changes in the mode of interaction at lower centers? Would higher centers within the organization tune or adjust the interactions at lower enters suggesting that protein synthesis (within the foregoing style of organization) consists of acquiring a convenient synergy, thus lowering the number of parameters requiring independent control?

Does a black Hox codon's position in any primary sequence of a gene regulate the purpose of that particular segment; while white Hox codons fractal nucleotide elements  'shepherd' the black Hox codon driven segments into a final protein shape?Photo: T/U = 00,       C = 01,       A = 10,       G = 11.

All black family codons are palindrome pattern Hox codons meaning they are the same base2 pattern forwards and backwards.

It is interesting that Hox codons almost always occur the most in gene sequences we have studied.

Why in every case do member pairs in same color families that code for the same amino acids break out into 81:45 or 77:49 relationships?

--------------------------
Note: 51 GUG val should be 110011 not 101011.Photo: T/U = 00,       C = 01,       A = 10,       G = 11.

Blue family codons code for the same amino acids as black Hox codons but do not have the regulatory influence or palindrome pattern like black Hox codons.

Why in every case do member pairs in same color families that code for the same amino acids break out into 81:45 or 77:49 relationships?
-------------------------
Note: 50 GUA should be 110010 not 101010.Photo: T/U = 00,       C = 01,       A = 10,       G = 11.

Is it correct to state that a codon is 'degenerate' or 'wobbles' when it can be demonstrated mathematically how each codon is unique in pattern, meaning and function and is intricately networked with codons in other amino acid groups?

It is interesting that black and white Hox codons almost always occur the most in gene sequences we have studied.

Black Hox codons are palindromic patterns and code for both an amino acid AND regulate the linear DNA segment where they appear in a gene.

Blue color family codons code for the same name amino acids as black Hox codons do but lack the regulatory influence.

Why in every case do member pairs in same color families that code for the same amino acids break out into 81:45 or 77:49 relationships? 

Does it relate to their base2 cross section pattern that portrays its 'active' and 'inactive' attraction repulsion states.

[Note: GUG 51 should be 110011 valine].
[Note: GUA 50 should be 110010 valine].Photo: T/U = 00,       C = 01,       A = 10,       G = 11.

Yellow family codons code for the same amino acids as green color family codons but the patterns and purpose differ.

Of interest here is the relationship between the start/methionine codon (35) AUG and the stop codon (14) UGA, and their relationship to green color family codons (34) AUA ile and (15) UGG trp.

Why in every case do member pairs in same color families that code for the same amino acids break out into 81:45 or 77:49 relationships?Photo: T/U = 00,       C = 01,       A = 10,       G = 11.

Green family codons code for the same amino acids as yellow color family codons but the patterns and purpose differ. There is no wobbling or uncertainty or degenerate codons involved here.

Of interest here is the relationship between the start/methionine codon (35) AUG and the stop codon (14) UGA, and their relationship to green color family codons (34) AUA ile and (15) UGG trp.

Why in every case do member pairs in same color families that code for the same amino acids break out into 81:45 or 77:49 relationships?Photo: T/U = 00,       C = 01,       A = 10,       G = 11.

Of interest here is the relationship between the start/methionine codon (35) AUG and the stop codon (14) UGA, and their relationship to green color family codons (34) AUA ile and (15) UGG trp.

Otherwise, yellow and green color families code for the same name amino acids but differ in pattern and purpose.

Why in every case do member pairs in same color families that code for the same amino acids break out into 81:45 or 77:49 relationships? 

Does it relate to their base2 cross section pattern that portrays its 'active' and 'inactive' attraction repulsion states.
----------------------------------
Note: GUU 48 valine should be 110000 not 101000.Photo: T/U = 00,       C = 01,       A = 10,      G = 11.

Red color family codons: 
UCU ser,
UAU tyr,
CCA pro,
CAA gln,
ACC thr,
AAC asn,
GCG ala,
GAG glu;
are codon triplet middle base 'hinge' patterns and may be critical to protein folding.

Red and purple color family codons code for the same name amino acids but the patterns and purpose differ.

This is not redundancy. The purpose, function and folding patterns between the color families differ.
---------------------
Why in every case do member pairs in same color families that code for the same amino acids break out into 81:45 or 77:49 relationships?

Note: GAG 59 glu should be 111011 not 101011.Photo: T/U = 00,       C = 01,       A = 10,       G = 11.

Purple and red color family codons code for the same name amino acids but the patterns and purpose differ.

There is no wobbling, uncertainty or degenerate codons involved here.

This is not redundancy. The purpose, function and folding patterns between the color families differ.

Why in every case do member pairs in same color families that code for the same amino acids break out into 81:45 or 77:49 relationships?
-----------------------------
Note: GAA 58 glu should be 111010 not 101010.Photo: T/U = 00,       C = 01,       A = 10,      G = 11.

Red codons (UCU ser, UAU tyr, CCA pro, CAA gln, ACC thr, AAC asn, GCG ala, GAG glu) are codon triplet middle base 'hinge' patterns which are critical to protein folding.

Red and purple color family codons code for the same name amino acids but the patterns and purpose differ.

This is not redundancy. The purpose, function and folding patterns between the color families differ.

Why in every case do member pairs in same color families that code for the same amino acids break out into 81:45 or 77:49 relationships?
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Note: 59 GAG should be 111011 not 101011.
Note: 58 GAA should be 111010 not 101010.Photo: T/U = 00,       C = 01,       A = 10,       G = 11.

Orange color family codons code for the same amino acids as white color family Hox codons but the patterns and purpose differ.

There is no wobbling, uncertainty or degenerate codons involved here.

Why in every case do member pairs in same color families that code for the same amino acids break out into 81:45 or 77:49 relationships?
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Note: GAC 57 asp should be 110001 not 101001.Photo: T/U = 00,       C = 01,       A = 10,       G = 11.

White color family codons code for the same amino acids as orange color family codons do but the patterns and purpose differ.

Do the the white Hox codons carry the rules for shepherding and bridging amino acid segments together?

In other words, do white Hox codons coordinate the scaffolding for the unique protein shape?

In every gene sequence we have studied black and white Hox codons were either the most occurring or near the top of the most occurring codons in the gene sequence.

This may signal that palindrome pattern black Hox codons and internal inverse pattern white Hox codons work together in directing the morphogenesis in Hox genes.

Why in every case do member pairs in same color families that code for the same amino acids break out into 81:45 or 77:49 relationships?
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Note: 56 GAU should be 111 000 not 101 000.Photo: T/U = 00,       C = 01,       A = 10,       G = 11.

Do the the white Hox codons carry the rules for shepherding and bridging amino acid segments together?

In other words, do white Hox codons coordinate the scaffolding for the unique protein shape?

Orange and white color family codons code for the same amino acids but the white Hox codons have a regulatory function as well.

Why in every case do member pairs in same color families that code for the same amino acids break out into 81:45 or 77:49 relationships?
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Note: 56 GAU should be 111 000 not 101 000.Note: 57GAC should be 111 001 not 101 001.Photo: This is an image of a 'morphism'. Morphisms are structure-preserving functions. The notion of morphism recurs in much of contemporary mathematics as well as topology, and continuous functions.

Morphisms are related to time-translation symmetry which can be broken indefinitely without violating the second law of thermodynamics which remains intact (a crucial stipulation to exist within the laws of physics), the significance of which is: (a) Nature is not immune to being spontaneously broken; (b) Non-equilibrium systems can host many interesting states of matter that cannot exist in equilibrium systems.

The entire genome itself is mostly a non-equilibrium system that hosts many interesting states of matter that can gain an equilibrium which may be providing an epigenetic or homological function.Photo: This is a NUMERICALLY BALANCED context driven phonemic RNA configurations.

Every row, column and diagonal sums to 252.

An mRNA codon can be expressed in a numerical values that correspond to one of 64 RNA base-2 cross sections (0-63).Photo: T/U=00       C=01       A=10       G=11.

This is the same BALANCED RNA Base-2
(0-63) systems in its CODON configuration.






No exceptions.Photo: T/U=00     C=01     A=10     G=11.

How it works: The RNA a DNA codon codes for to make a protein consists of the RNA bases it itself appears in at deeper levels.

The 64 RNA codons expressed numerically in a balanced system reveal these relationship patterns and connections.The RNA codon elements of any RNA codon chosen will always be found latticed in the binary (base-2) inverse of the codon selected in this image.

For example: the binary (base-2) inverse of (0) UUU, phenylalanine is (63) 111111, GGG glycine.

The balanced (y-axis) vertical elements are 4+8+51 = (63). The balanced (x-axis) horizontal elements are 18+1+44 = (63).

Both (x) and (y) coordinate threesomes have the same sum but different (base-2) progression values that attract repulse back to (0) UUU.

Each of the 64 RNA codons have a unique color and folding pattern that follows one universal rule.Photo: Image: In this configuration, UUU (0) 000000, (phe) base codon (x) and (y) coordinates are found in the vertical column and horizontal row of its base-2 inverse: GGG (63) 111111, gly.

Mathematically, the (x) and (y) coordinates not only account for a one step translation and transcription process but also identify the three different energy color pairs involved each codon consists of and where the 'active' and inactive information is in each.

Each fractal nitrogenous same color family energy pair consists of one (y) axis pair; one (x) axis pair, and one hinge pattern pair consisting of one (y) and one (x) fractal nucleotide element coordinate.

Is the hinge pattern a key to how and where an amino acid folds in the polypeptide chain, allowing two parts of the gene distal to each other linearly, to be close in three dimensions, before it morphs into the final protein shPhoto: Mathematically, three same color energy pair elements are not only what phenylalanine (0) UUU [F] phe consists of but what phenylalanine appears in at its deeper levels.

QUESTIONS: Why do the three same color energy pairs create two equal sum threesomes? Why do the two threesomes consist of elements that code for completely different amino acids? [In this case: 01+44+18 and 04+08+51 sum to the base-2 inverse of '0' -- before attracting and repulsing into (0) UUU [F] phe, phenylalanine. All 64 RNA codons share a similar architecture. How is it that this architecture is already present before 'DNA Makes RNA Makes Protein'?

Why do the three same color energy pair elements organize bilaterally along the diagonal at an even deeper level? Is a deeper bilateral architecture significant? Does a diagonal architecture facilitate the scaffolding for protein folding? Does it insure the information holds the correct position and does not tangle?Photo: T/U=00.     C=01.     A=10.     G=11.

DNA TTT codes for mRNA (0) UUU [F] phe.

mRNA (0) UUU [F] phe, consists of three energy pair codon elements (plotted on the 8x8 grid on the left as you look at the image) which seem random until their deeper level energy pair codon elements are added (plotted in the image on the right as you look at it). Each mRNA codon has a unique pattern.

Why does this pattern seem organized? Why is there a triangular relationship in both quadrilateral centers? Why is this true for all 64 DNA codons when they code for mRNA?

Why does each DNA codon that codes for an mRNA consist of three element color energy pairs? Why do the relationships in each mRNA a DNA codes for appear organized?

Why are the triangular 'islands' of information in the relationships diagonally oriented? Are the quadrilateral shapes in each unique organization significant?Photo: Diagonals, Venn diagrams and Cartesian (x) and (y) axis coordinate systems are mathematically related.

A Venn diagram displays the degree of variance and co-variance of  its fractal elements [IN THIS CASE: (0) UUU phe]. 

The vertical (y) Cartesian coordinates [04, 08, 51] are to the left and the horizontal (x) coordinates
[01, 44, 18] are to the right.

The sum of any two covariant elements will be the inverse of the remaining covariant element in the Venn diagram:

08+04 = (12) 001100 -- the inverse of (51) 110011;
01+44 = (45) 101101 -- the inverse of (18) 010010.

As evidenced in the symmetry, the math is precise, allowing an additional layer of information to be studied.Photo: All light consists of photons -- the definition of which is -- 'a particle the opposite of itself'.

Place a '+1' in circle 'A', '0' in circle 'B', '-1' in circle C and you have the mathematical representation of a photon that (for example) allows the Fibonacci Series to flow backward and forward:
...5 -...3 -...2 -...1 -...(1-0+1)...+1...+2...+3...+5...

A, B and C are intersecting circles of deeper amino acid elements of various levels of size and intent.

A∩B is the co-variant of circles A and B.
A∩C is the co-variant of circles A and C.
B∩C is the co-variant of circles B and C.

A∩B∩C is the intersection of AB, AC and BC and would be the mRNA codon that is being dissected (example: UUU phe [F].

Venn Diagrams dovetail with Base2 System cross sections which already detail which nucleotide base is contributing to its value.

It is precisely the nucleotide invariant 'value' of uracil (always '0') that triggers the 'coherence' and 'decoherence',  'attraction' and 'repulsion', and 'variance' and 'covariance',  in the deeper level amino acid elements.Photo: These are the sequentially ordered three energy pairs in (0) UUU, phenylalanine with their numeric values. They appear to be randomly placed but they are not.Photo: This is the same three (0) UUU phenylalaine fractal nitrogenous color codon energy pairs in one of hundreds of thousands of possible balanced configurations.

The three color energy pairs that once seemed random are symmetrically spaced and latticed Cartesian coordinates.

Do neutral (non-active) nucleotide base elements in RNA codon triplets hold place (like a neutron in an atom)?

How are they switched 'on' and 'off'?

Why do the switched 'on' codon base elements always sum to the inverse of the base-2 value of the nitrogenous bases switched off?

Is this is a both a predictive and self-correcting system?Photo: T/U = 00,      C = 01,      A = 10,      G = 11.

These are the (0-63) sequentially ordered three nucleotide color energy pairs with their CODON values. They appear to be randomly placed but they are not.Photo: T/U = 00,      C = 01,      A = 10,      G = 11.

This is the same three (0) UUU, phenylalanine  color codon energy pairs in one of hundreds of thousands possible configurations.

The three color energy pairs that once seemed random are Cartesian coordinates. 

In this configuration, any RNA (x) or (y) coordinate is interchangeable and joins the ‘0’ coordinate to create amino acid scaffolding for the protein structure.Photo: ABCabc numeric color energy pair configuration of (0) UUU phenylalanine within one of six uniquely shaped possibilities.

Is this shape within a shape emergent behavior?

Why does it scale? Why is it consistent?

At the top is the 1st level sequential numerical order and dominant color of the 64 RNA codons. The RNA fractal architecture is found by plotting the three color energy pairs that the RNA consists of and appears in at the deeper level in a vertical column on the left and then plotting each one of their three color energy pairs  in horizontal rows to the right.

Notice how the codon being analyzed (in this case (0) 000000, phe) always forms the diagonal.Photo: T/U = 00,     C = 01,     A = 10,     G = 11.

ABCabc codon configuration for (0) UUU phenylalanine.

Notice how (0) UUU forms a natural diagonal in the bilateral pattern.

Does a diagonal architecture organize the codon color pairs into bilateral mirror image patterns along its (0) UUU diagonal similar to complex conformation dynamics in the condensed phase?

The times required to cross the barrier for the folding and unfolding of different nucleic acids are consistently about a few microseconds, despite many orders of magnitude differences in rate coefficients.

At the top is the sequential codon order of the 64 RNA codons with each RNA codon numerical order dominant color.Photo: Why is the numerically depicted codon color energy pairs genetic information for black Hox codon (0) UUU [phe] phenylalanine bilaterally organized around the diagonal in this AaBbCc configuration?

Do diagonally driven color energy pair elements suggest how the spatial organization of the regulatory process of genes -- which is intimately linked to its role in the body -- begins here.

The sequential context driven phonemic RNA base-2 color progression is at the top in numeric (dominant color) form. The three RNA energy color pairs are in the vertical column to the left. The three RNA color pairs in each of them appear in the horizontal rows to the right.

Each of the 64 RNA codons and each of its potential configurations can be expressed in this way.Photo: T/U=00     C=01     A=10     G=11.

AaBbCc configuration of (0) UUU phenylalanine with their codon values.

At the top is the sequential numerical order and dominant color of the 64 RNA codons. The RNA diagonal architecture is found by plotting the three color energy pairs that the RNA consists of and appears in at the deeper level in a vertical column on the left and then plotting each one of their three color energy pairs  in horizontal rows to the right.

Note the genetic information is bilaterally organized along the diagonal (0) UUU, phe.Photo: ABCcba numeric configuration of (0) UUU phenylalanine.

At the top is the sequential numerical order and dominant color of the 64 RNA codons. The RNA diagonal architecture is found by plotting the three color energy pairs that the RNA consists of and appears in at the deeper level in a vertical column on the left and then plotting each one of their three color energy pairs  in horizontal rows to the right.

Note the genetic information is bilaterally organized along the diagonal (0) UUU, phe.Photo: T/U=00     C=01     A=10     G=11.

ABCcba configuration of (0) UUU phenylalanine with their codon values.

This architecture is found by plotting the three color energy pairs that the RNA consists of and appears in at the deeper level in a vertical column on the left and then plotting each one of their three energy pairs  in horizontal rows to the right.

Note the genetic information bilaterally organized along the diagonal (0) UUU, phe.Photo: T/U=00      C=01      A=10      G=11.

We hypothesize that what an RNA base pair, DNA codon, and the mRNA it codes for consists of -- is what it appears in at deeper levels. This means each of the 64 DNA codons (via the mRNA it codes for) is more dynamic than previously thought. It suggests that it is the cell that helps co-determine which DNA sequence possibility responds to the cell's needs.

The image has 7 blocks. The center mRNA codon that DNA codon ATU codes (34) AUA [I] ile, and consists of three pair elements at deeper levels. Now consider that this is only one of thousands of possibilities.

This means that any one of the 64 DNA codons can code for an mRNA codon that has thousands of versions.

Questions: Why does the center block mRNA codon (in this case (34) AUA [I] ile always consist of three elemental pairs? Why do these pairs always combine to form two equal sum threesomes that consist of completely different amino acids (in this case: 14/35/48 = 38/42/17)? Why do the two same sum threesomes always attract and repulse into the center box mRNA codon value?

(14) UGA [ter]  001110 /// (38) ACA [T] 100110
(35) AUG [M]   100011 /// (42) AAA [K] 101010
(48) GUU [V]    110000 /// (17) CUC [L]  010001
cancel out the '0' and '1''s in each value column.
Both threesomes attract/repulse into (34) AUA.

Could one energy threesome have an internal purpose and function and the other threesome an external purpose and function? Is it tied to 'sequence in time' and 'pattern in space'? Why do the six amino acid elements in each mRNA codon organize along a diagonal? Why is there a bilateral architecture? Does the diagonal (which represents a mean) prevent tangling? Does a diagonal architecture facilitate protein folding?Photo: (34) AUA [I] ile, consists of three pairs of codon elements (plotted on the sequential 8x8 grid on the left as you look at the image) which seem random until their deeper 1st level relationships are added (plotted in the image on the right as you look at it). 

What a DNA codon is -- is what the mRNA it codes for consists of and appears in at its deeper levels. Notice its diagonal orientation.

T/U = 00.     C = 01.     A = 01.     G = 11.

The horizontal elements of (34) AUA [I] ile are 14+35+48=97.
(14) 00 11 10 UGA
(35) 10 00 11 AUG
(48) 11 00 00 GUU
which attract and repulse into (34) AUA [I] ile.

The vertical elements of (34) AUA [I] ile are 38+42+17=97.
(38) 10 01 10 ACA
(42) 10 10 10 AAA
(17) 01 00 01 CUC
which attract and repulse into (34) AUA [I] ile.

Does the fact that I can cancel '0' and '1' two different ways in every place value significant?
What is the relationship between the parallel quadrilaterals?
.Photo: This is a numeric sequential ordering of the seemingly 'random' three mRNA color pairs that fold into (34) AUA [I] ile.Photo: T/U = 00,      C = 01,      A = 10,      G = 11.

These are the same three pairs in (34) AUA [I] ile, as in the previous screenshot in their mRNA codon format. Like the numeric sequence, they appear to be random when plotted in a linear alignment.Photo: T/U = 00,      C = 01,      A = 10,      G = 11.

In a balanced system, randomness disappears and the order and relationships emerge.

A mathematicall driven context driven base2 system mRNA color progression reveals an underlying order to the three pairs that (34) AUA 100010 [I] ile consists of and appears in at this deeper levels.

The  mRNA elemental (x) and (y) pair coordinates can be mathematically plotted and ported to graphical tools.Photo: T/U = 00,      C = 01,      A = 10,      G = 11.

In a balanced system, randomness disappears and the order and relationships emerge.

This is the striated configuration of (34) AUA [I] ile 6x6 diagonal architecture.
This architecture is found by plotting the three pairs that the mRNA consists of and appears in at deeper levels in a vertical column on the left and then plotting each one of their own three pairs in horizontal rows to the right.Photo: T/U = 00,      C = 01,      A = 10,      G = 11.

In a balanced system, randomness disappears and the order and relationships emerge.

This is the center square configuration of (34) AUA [I] ile 6x6 diagonal architecture.

This architecture is found by plotting the three pairs that the mRNA consists of and appears in at deeper levels in a vertical column on the left and then plotting each one of their three pairs  in horizontal rows to the right.Photo: T/U = 00,      C = 01,      A = 10,      G = 11.

In a balanced system, randomness disappears and the order and relationships emerge.

This is the four square structure of (34) AUA [I] ile 6x6 diagonal architecture.This architecture is found by plotting the three color energy pairs that the mRNA consists of and appears in at the deeper level in a vertical column on the left and their plotting each one of their three pairs in the horizontal rows to the right.Photo: T/U = 00,      C = 01,      A = 10,      G = 11.

In a balanced system, randomness disappears and the order and relationships emerge.

This is the Aa yellow Bb white Cc green nine square configuration of (34) AUA ile 6x6 biochemical elements.

This architecture is found by plotting the three pairs that the mRNA consists of and appears in at deeper levels in a vertical column on the left and then plotting each one of their three pairs  in horizontal rows to the right.Photo: T/U = 00,      C = 01,      A = 10,      G = 11.

In a balanced system, randomness disappears and the order and relationships emerge.

This is the upper left square configuration of (34) AUA [I] ile 6x6 diagonal architecture.

This architecture is found by plotting the three color pairs that the mRNA consists of and appears in at deeper levels in a vertical column on the left and then plotting each one of their three pairs in horizontal rows to the right.Photo: T/U = 00,      C = 01,      A = 10,      G = 11.

In a balanced system, randomness disappears and the order and relationships emerge.

This is the lower right square configuration of
(34) AUA [I] ile 6x6 diagonal architecture.

This architecture is found by plotting the three pairs that the mRNA consists of and appears in at deeper levels in a vertical column on the left and then plotting each one of their three pairs  in horizontal rows to the right.Photo: Without RNA -- there would be no DNA.

RNA existed without DNA for Eons.

In a biogenetic ceding of power for the overall benefit of RNA. DNA logically evolved.

A base-2 System half-state architecture suggests an RNA 'progression' to DNA while remaining independent at its deeper levels to maintain its RNA integrity and fluidity.

The benefit: 'When DNA Makes RNA Makes Protein', each mRNA codon a DNA codon codes for holds unique pattern and specialized function information, even if and when it codes for the same amino acid.Photo: Current thinking is a chain of amino acids can only change from one shape to another by mechanically passing though various shapes in between (like an assembly line). This has an Industrial Age flavor to it. 

What if the shape changes by quantum transition, meaning that the protein ‘jumps’ from one shape to another without having to form the shapes in between?Photo: Quantum transition, like (QED) is part of a Base-2 System progression -- like DNA and RNA. The DNA transcription and translation process is similar to a concept in physics known as superposition. What differs is that in physics, there is not an assembly line, superposition happens in an instant -- more important, the variables 'a' and 'b' are co-determinant.

Three essential ingredients are necessary for dynamic preexisting fractal patterns to superimpose two 'states' (eg. transcription and translation) into one process:

First, there has to be a sufficiently large density of interacting elements or 'degrees of freedom'.

Second, the interactions have to be 'non-linear'.

Third, the free energy has to be 'dissipated'.

Superposition consists of precisely these three ingredients.

The result of superposition is always a diagonal.Photo: Each of the 64 mRNA codons that codes for one of the 20 amino acid is unique in meaning and purpose.

Hiding within any particular system is more than one stable solution -- as one equilibrium or the other -- but not both.

All particles in a system exist potentially (with a certain probability) as different combinations of other particles. -- Wu Li Masters.
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The image shows two different symmetrical configurations, each row, column and diagonal the same sum.

What if a cell signaled an imbalance that required the relationships appearing in the 1st of these 3 configurations, then, during another time, signaled for the relationships found in the 2nd or 3rd configuration?

Isn't this similar to a gene sequence? The cell would develop a 'go to' solution (a bias) for different situations in the same manner neuron paths strenthen with use.

If cell imbalance varies -- if a cell's needs vary due to age, stress, nutrition, or disease to give four examples -- then perhaps it would ask for different relationships to meet different conditions using the same 20 amino acids but choosing a different 'flavor' codon of that amino acid.

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Image: Using an mRNA base2 system color progression, three pandiagonal 8x8 squares produce three different color configurations, each of which produce a mirror symmetry pattern. There are 368,640 such possibilities.



.Photo: T/U = 00,       C = 01,       A = 10,       G = 11.

Two questions:

Are the 20 amino acid groups better represented with 16 logical uracil driven codon function foursomes whose place values switch on and off to create the 64 mRNA codons DNA codes for to make a protein?

 Is RNA (at the local cellular level) co-determinant with DNA?Photo: Using each of the 16 uracil driven mRNA codons (0-15 in base2 systems) as the cornerstone of a foursome, it is possible to construct all 64 mRNA codons that DNA codes for to make a protein.

Click on the link below to see the entire base-2 system color progression for mRNA codons 0-63.

https://docs.google.com/document/d/1s8f6rOkj5r0pzDy8Um74xJMq1bA7vNbtFAif9q5GVFY/edit?usp=sharingPhoto: T/U=00.         C=01.         A=10.         G=11.

Unencumbered (decohering) energy always whorls -- seeking balance -- yet can be attracted, repulsed, directed and joined in this state.

This is an image of the sixteen (0-15) uracil driven mRNA codons (in 16 blocks of four) with each of the 16 uracil driven codons serving as a cornerstone for the other three codons in the foursome -- a 3:1 ratio -- the same ratio as the shape of the tetrahedron shape of an amino acid.

The resulting whorl patterns from the +16 progression in each foursome create a symmetric visual geometric whorl pattern. [Example: uracil driven (15) UGG curves around (31) CGG and up to (47) AGG and around (63) GGG].

This allows transition and transformation.

This hand drawn illustration of the 16 RNA codons (0-15) illustrate how RNA codons are nested within the 64 (0-63) DNA codons in a Base-2 System. 

Black palindrome pattern Hox codons: 0, 12, 18, 30, 33, 45, 51 and 63; are unchanging, oscillating base-2 patterns that code for an amino acid AND regulate the function and purpose of the gene segment it appears in.

White Hox codons: 7, 11, 21, 25, 38, 42, 52 and 56 are non-palindromic but internal inverse pattern base-2 patterns that facilitate the forming and shaping of the 48 RNA 'color' codons (blue, yellow, green, red, purple and orange) with each color family consisting of 8 RNA codons which code for unique amino acids.Photo: This is the same image of the sixteen (0-15) uracil driven mRNA codons (in 16 blocks of four) with each of the 16 uracil driven codons serving as a cornerstone for the other three codons in the foursome -- a 3:1 ratio -- the same ratio as the shape of the tetrahedron shape of an amino acid.
The resulting whorl patterns from the +16 progression in each foursome create a symmetric visual geometric whorl pattern. [Example: uracil driven (15) UGG curves around (31) CGG and up to (47) AGG and around (63) GGG].

Inherent in Base-2 System genomic geometry is the ability to mathematically describe the changeability of information; creating a common frame of reference for discussing, interpreting, and manipulating genomic information to improve understanding, cooperation and collaboration between scientists across professional boundaries such as physics, chemistry, engineering, mathematics, biology and genetics.

At least mathematically, each codon conveys its unique meaning and function using ‘active’ coding information base-2 system half-states. The base color of a codon indicates how information can be turned  'on' or 'off' and still hold a place value, functioning similar to the way quarks make either a proton or a neutron in an atom.

Every center nuclotide base in an mRNA codon triplet it codes for is either red or black. Every 1st and 3rd nucleotide base in an mRNA codon triplet is either black, blue yellow or green.

The combination of primary color half-states yellow and blue in a codon base create a green triplet codon base. Internal inverse base2 system cross sections primary color balance create white codons. All base2 system cross section palindromic patterns mute the primary colors creating black.Photo: T/U=00      C=01      A=10      G=11.

(0) UUU [F] phenylalanine is a black Hox codon. It is to the genome what '0' is to morphisms in mathematics -- a constant by which each an RNA codon retains its specific place value information and in doing so can create in a greater architecture.

Switching nucleotide energy pair fractal elements 'on' or 'off' in uracil driven codons accounts for all 64 possibilities. Blue, yellow or red color is the result of changing place values; the final color depending on the Base-2 System cross section pattern created.

In this image: switching (0) UUU [F] phe nucleotide fractal energy half-states 'on' and 'off' create three other RNA related codons [starting bottom right and moving clockwise]: (16) CUU [L] leucine; (32) AUU [I] ile; and (48) GUU [V] val.

(0) UUU [F] phenylalanine is a stand alone palindromic pattern, as are all black Hox codons: UUU, UGU, CUA, CGA, AUC, AGC, GUG, GGG. The black Hox codon color family codes for the same amino acids blue color family codons code for but include Hox regulatory functions and meanings.Photo: T/U=00      C=01      A=10      G=11.

IMAGE:
(1) UUC [F] phenylalanine is a blue color family codon. It codes for the same amino acid as (0) UUU [F] but has a different pattern and meaning.  UUC re-solves and diverges directions from the invariant UUU.

(1) UUC [F] phe, other blue color family members are: UGC, CUG, CGG, AAU, AGU, GUA, GGA.

Switching the nucleotide half-states 'on' and 'off' create three other RNA codons [starting top left and moving clockwise]: (17) CUC [L] leucine; and (49) GUC [V] val; and (33) AUC [I] ile, which is black because the color value columns half-states mirror each other and therefore are are muted.

AUC is a stand alone palindromic black color family Hox codon.Photo: T/U=00      C=01    A=10      G=11.

IMAGE:
(2) UUA [L] leucine is a yellow color family codon. It codes for 6 of the same 8 amino acids the green color family does but has different patterns and meanings. 

(2) UUA [L] leu other yellow color family codon members are: (14) UGA, (16) CUU, (28) CGU,
(35) AUG, (47) AGG, (49) GUC, and (61) GGC.

Switching the nucleotide half-states 'on' and 'off' create three other RNA codons [starting top right and moving counter clockwise]: (34) AUA [I] ile; and (50) GUA [V] val; and (18) CUA [L] leu; whose half-states mirror each other and are muted. CUA is a stand alone palindromic black color family Hox codon. 

Data shows that, in addition to insulin, amino acids and particularly leucine cause a marked suppression of proteolysis. Availability of all amino acids to prevent hypoaminoacidemia is necessary to sustain basal rates of protein synthesis. The infusion of leucine alone resulted in significant stimulation of leucine oxidation.Photo: T/U=00      C=01    A=10      G=11.

IMAGE:
(3) UUG [L] leucine is a green color family codon. It codes for 6 of the 8 same amino acids as the yellow color family but has different patterns and meanings. 

(3) UUG [L] leucine other green color family codon members are: (15) UGG, (17) CUC, (29) CGC,
(34) AUA, (46) AGA, (48) GUU, (60) GGU.

Switching the nucleotide half-states 'on' and 'off' create three other RNA codons [starting bottom left and moving counter clockwise]: (19) CUG [L] leu; and (35) AUG [M], the START codon; and (51) GUG whose mirror pattern means the color is muted. GUG is a stand alone palindromic black Hox codon.

Data shows that, in addition to insulin, amino acids and particularly leucine cause a marked suppression of proteolysis. Availability of all amino acids to prevent hypoaminoacidemia is necessary to sustain basal rates of protein synthesis. The infusion of leucine alone resulted in significant stimulation of leucine oxidation.Photo: T/U=00      C=01    A=10      G=11.

IMAGE:
(4) UCU [S] serine is a red color family codon. It codes for the same amino acids purple color family RNA codons do but has different patterns and meanings. 

(4) UCU [S] ser, other red color family codon members are: (8) UAU, (22) CCA, (26) CAA, 
(37) ACC, (41) AAC, (55) GCG, (59) GAG.

Switching the nucleotide energy half-states 'on' and 'off' create the three other RNA codons [starting top left and moving clockwise]: (20) CCU [P] pro; (36) ACU [T], and (52) GCU [A] alanine;
and (52) GCU [A] alanine, which is a member of the white Hox codon color family. The combination of the three primary color fractal half-states create white light. White Hox codons are involved in regulating by sheperding protein formation.Photo: T/U=00      C=01    A=10      G=11.

IMAGE:
(5) UCC [S] serine is a purple color family codon. It codes for the same amino acids as red family RNA codons do but has different patterns and meanings. 

(5) UCC [S] ser other purple color family codon members are: (9) UAC, (23) CCG, (27) CAG, 
(36) ACU, (40) AAU, (54) GCA, (58) GAA.

Switching half-states 'on' and 'off' create the three other RNA codons [starting bottom right and moving clockwise]: (21) CCC [P] pro; (37) ACC [T]; and (53) GCC [A] alanine.

(21) CCC [P] pro is a white Hox codon because its three primary color half states combine together; CCC belongs to the white Hox codon color family and is involved in regulating protein formation.Photo: T/U=00      C=01    A=10      G=11.

IMAGE:
(6) UCA [S] serine is an orange color family codon. It codes for the same amino acids as white family RNA codons but has different patterns and meanings. 

(6) UCA [S] ser other orange color family codon members are: (10) UAA, (20) CCU, (24) CAU, 
(39) ACG, (43) AAG, (53) GCC.

Switching the nucleotide energy half-states 'on' and 'off' create the three other RNA codons [starting bottom left and moving counter clockwise]: (22) CCA [P] pro; (38) ACA [T], and (54) GCA [A] alanine; (38) ACA [T] is a white Hox codon and belongs the to white Hox color family beause its three primary color half-states combine to create white; it is involved in regulating protein formation.Photo: T/U=00      C=01    A=10      G=11.

(39) should be ACG not UCG.

IMAGE:
(7) UCG [S] serine is a white color family codon. It codes for the same amino acids as orange family RNA codons but has different patterns and meanings due to its regulatory influence on protein formation.

(7) UCG [S] ser other white color family codon members are: (11) UAG, (21) CCC, (25) CAC, 
(38) ACA, (42) AAA, (52) GCU.

Switching the nucleotide energy half-states 'on' and 'off' create the three other RNA codons [starting top right and moving counter clockwise]:
(23) GCG [P] pro; (39) UCG [T], and (55) GCG [A] alanine.

(07) UCG ser is a white Hox codon, belongs to the white Hox color family and is involved in regulating protein formation.Photo: T/U=00      C=01    A=10      G=11.

IMAGE:
(8) UAU [Y] tyrosone is a red color family codon. It codes for the same amino acids purple color family RNA codons do but has different patterns and meanings. 

(8) UAU [Y] tyr, other red color family codon members are: (4) UCU, (22) CCA, (26) CAA, 
(37) ACC, (41) AAC, (55) GCG, (59) GAG.

Switching the nucleotide energy half-states 'on' and 'off' create the three other RNA codons [starting top left and moving clockwise]:
(24) CAU his; (40) AAU asn, and (56) GAU [D] asp, which is a member of the white Hox codon color family. The combination of the three primary color nucleotide half-states create white light. White Hox codons are involved in regulating protein formation.Photo: T/U=00      C=01    A=10      G=11.

IMAGE:
(9) UAC [Y] tyrosine is a purple color family codon. It codes for the same amino acids as red family RNA codons but has different patterns and meanings. 

(9) UAC [Y] tyrosine other purple color family codon members are: (5) UCC, (23) CCG, (27) CAG, 
(36) ACU, (40) AAU, (54) GCA, (58) GAA.

Switching the fractal nucleotide half-states 'on' and 'off' create the three other RNA codons [starting bottom right and moving clockwise]:
(25) CAC [H] his; (41) AAC [N], and 
(57) GAC [D] asp.

(25) CAC [H] his, is a white Hox codon because the three primary color half-states combine; CAC his, belongs to the white Hox codon color family and is involved in regulating protein formation.Photo: T/U=00      C=01    A=10      G=11.

IMAGE:
(10) UAA [ter] stop codon is an orange color family codon. It codes for the same amino acids as white family RNA codons but has different patterns and meanings. 

(10) UAA [ter] STOP, other orange color family codon members are: (06) UCA, (20) CCU, (24) CAU, (39) ACG, (43) AAG, (53) GCC.

Switching the nucleotide energy half-states 'on' and 'off' create the three other RNA codons [starting bottom left and moving counter clockwise]: (26) CAA [Q] gln; (42) AAA [K] lys,
(58) GAA [E] glu.

(42) AAA [K] is a white Hox codon because the three primary color half-states combine. AAA [K] belongs  to the white Hox color family and is involved in regulating protein formation.Photo: T/U=00      C=01    A=10      G=11.

IMAGE:
(11) UAG [ter] stop codon is a white color family codon. It codes for the same amino acids as orange family RNA codons but has different patterns and meanings. 

(11) UAG [ter] stop codon other white color family codon members are: (07) UCG, (21) CCC, (25) CAC, (38) ACA, (42) AAA, (52) GCU.

Switching the nucleotide energy half-states 'on' and 'off' create the three other RNA codons [starting top right and moving counter clockwise]:
(27) CAG [Q] gln; (43) AAG [K] lys; (59) GAG [E] glu.

(11) UAG [ter] STOP, is a white Hox codon because three primary half-states combine. UAG belongs to the white color family and is involved in regulating protein formation.Photo: T/U=00     C=01     A=10     G=11.

IMAGE:
(12) UGU [C] cysteine is a black Hox codon. The black Hox codon color family codes for the same amino acids blue color family codons code for but have different patterns and meaning due to its regulatory functions.

In this image: switching (12) UGU [C] cysteine nucleotide half-states 'on' and 'off' create three other RNA codons [starting bottom right and moving clockwise]: (28) CGU [R] arg;
(44) AGU [S] ser; and (60) GGU [G] gly.

(12) UGU [C] cys nucleotide energy half-states have a stand alone palindromic pattern, as do all black color family Hox codons:(0) UUU, (18) CUA, (30) CGA, (33) AUC, (45) AGC, (51) GUG, (63)GGG.Photo: T/U=00      C=01      A=10      G=11.

IMAGE:
(13) UGC [C] cysteine is a blue color family codon which code for the same amino acids black Hox codons do. UGU codes for the same amino acid as UGU [C] cys, but has a different pattern and meaning. 

(13) UGC [C] cys other blue color family members are: (1) UUC, (19) CUG, (31) CGG, (32) AAU,
(44) AGU, (50) GUA, (62) GGA.

In this image: switching (13) UGU [C] cys, nucleotide half-states 'on' and 'off' create three other RNA codons [starting top left and moving clockwise]: (29) CGC [R] arg; (45) AGC [S] ser; and (61) GGC [G] gly.

(45) AGC [S] ser, is a stand alone palindromic black color family Hox codon. Its perfectly symmetrical pattern mutes the three primary colors.Photo: T/U=00      C=01    A=10      G=11.

IMAGE:
(14) UGA [ter] STOP, belongs to the yellow color family codon which code for 6 of the 8 same amino acids as the green color family but have different patterns and meanings. 

(14) UGA [ter] STOP, other yellow color family codon members are: (02) UUA, (16) CUU, (28) CGU, (35) AUG, (47) AGG, (49) GUC, and (61) GGC.

Switching the nucleotide energy half-states 'on' and 'off' create three other RNA codons [starting top right and moving counter clockwise]: (46) AGA [R] arg; and (62) GGA [G] gly]; and (30) CGA [R] arg, which has a symmetrical pattern meaning the primary colors are muted. It is a stand alone palindromic black color family Hox codon.Photo: T/U=00      C=01    A=10      G=11.

IMAGE:
(15) UGG [W] trp is a green color family codons which code for 6 of the 8 same amino acids as the yellow color family but have different patterns and meanings. 

(15) UGG [W] trp other green color family codon members are: (03) UUG, (17) CUC, (29) CGC,
(34) AUA, (46) AGA, (48) GUU, (60) GGU.

Switching the nucleotide energy half-states 'on' and 'off'create three other RNA codons [starting bottom left and moving counter clockwise]: (31) CGG [R] arg; and (47) AGG [R] arg; and (63) GGG [G] gly, whose three primary colors are muted. GGG is a stand alone palindromic black Hox codon.Photo: T/U=00       C=01       A=10       G=11.

EXPLANATION OF STRUCTURE:
using Base-2 System value (15) 001111,UGG [W] , trp and the Base-2 System Color progression.

A mathematically correct context driven phonemic Base-2 System color progression can be used to predict where information is in RNA codons. It lends itself to a new mathematical model of RNA.

All 64 RNA codons can be depicted in 16 (0-15) codon foursomes with a uracil driven codon at its core (meaning the 1st base letter is always uracil). In the example chosen, (15) UGG (00 1111), tryptothan -- is one of the 16 uracil driven RNA codons -- at the core of one of 16 (0-15) RNA codon foursomes.

Tryptophan is a crystalline essential amino acid C11H12N2O2 that is widely distributed in proteins. 

Tryptophan's ability to 'approach' and 'get near to' plays a pivotal row in protein formation.
(continued on next slide)Photo: T/U=00       C=01       A=10       G=11.

Each of the 16 (0-15) uracil driven base-2 progression foursomes have either one black Hox codon or one white Hox codon in them. 

In the (15) UGG tryptophan foursome, the Hox codon is black (63) GGG glycine. Glycine is important for biological energy, providing a receptive, structuring, stabilizing formative force.

Replacing uracil with cytosine creates
blue (31) CGG arginine;
Replacing uracil with adenine creates
yellow (47) AGG arginine;
Replacing uracil with glycine creates
black (63) GGG glycine.

All 64 RNA codons, including start and stop codons, can be depicted this way
(continued on next slide)Photo: T/U=00       C=01       A=10       G=11.

Each numerical value in a box is the overall dominant color of that RNA cross section at the primary sequence level. 

In order to have color (blue, yellow  green, red, purple, orange) a Base-2 System half-state value column has to be populated by a '1'.

(63) GGG is black because '32' blue and '01' blue; '16' yellow and '02' yellow; and  '08' red and '04' red; are populated with a '1' and therefore mute each other.

(47) A G G is yellow because '32' blue and '01' blue are populated with a '1' and mute each other.
The same is true for '08' red and '04' red.

(31) C G G is blue because '16' yellow and '02' yellow mute each other; as does '08' red and '04' red.

(15) U G G is green because '08' red' mutes '04' red.

This means in (15) UGG tryptophan, the '02' yellow and '1' blue base-2 column value half-states are switched on meaning the 3rd nucleotide letter in RNA codon UGG is green and the overall dominant color of the codon is also green.Photo: mRNA UAA is a STOP codon or (10) 001010 in binary (base2).

In a balanced system, randomness disappears and the order and relationships emerge.

It means its horizontal (x) axis threesome and its vertical (y) axis threesome elements will be found in its binary (base2) inverse (53) GCC. This is a built-in transcription-translation process.

(53) GCC 110101 means this codons elements provide the ability to shift gears.

The horizontal (x) axis threesome UAG + CAU + ACA = 73.
The vertical (y) axis threesome is UAA + GAC + UGA = 73.

Both threesomes nucleotide elements attract and repulse into UAA [ter] (10) 001010.

Is UAA similar to the polarization that occurs between two same charged magnetic fields which are essentially connected but can not join?

Is the fact that the other two stop codons are two of UAA''a six elements significant?Photo: This is stop codon UAG ter or (11) 001011 in binary (base2).

In a balanced system, randomness disappears and the order and relationships emerge.

Stop codon (10) UAA and Stop codon (11) UAG may work together. (10) may be lightning and (11) may be thunder.

UAG's horizontal (x) axis threesome and its vertical (y) axis threesome elements will be found in its binary (base2) inverse (52). This is a built-in transcription-translation process.

The horizontal (x) axis threesome UAA + CAC + ACG = 74.
The vertical (y) axis threesome is UUG + GAU + UGG = 74.

Both threesomes nucleotide elements attract and repulse into to UAG [ter] (11) 001011.

UAG imposes change on something that can not change itself.Photo: This is stop codon UGA ter or (14) 001110 in binary (base2).

In a balanced system, randomness disappears and the order and relationships emerge.

STOP codon (14) UGA and START codon (35) AUG MET, work together. (14) UGA, is similar to slowing down to make a turn and (35) is similar to continuing on with the route.

UGA's horizontal (x) axis threesome and its vertical (y) axis threesome elements will be found in its binary (base2) inverse (49) GUC, which means to the influence individual parts have on the the whole. This is a built-in transcription-translation process.
The horizontal (x) axis threesome UGG + CGU + AUA = 77.
The vertical (y) axis threesome is UCA + GGC + UAA = 77.

Both threesomes nucleotide elements attract and repulse into UGA -- STOP (14) 001110 which means to diminish.Photo: This is Start codon AUG or (35) AUG methionine, 100011 in binary (base2).

In a balanced system, randomness disappears and the order and relationships emerge.

Start codon (35) UGA Start codon and  
(14) UAG Stop codon work together.

AUG will 'continue' on and persevere until signaled by UAG to 'diminish' the action.

UGA's horizontal (x) axis threesome and its vertical (y) axis threesome fractal elements will be found in its binary (base2) inverse (28) CGU. This is a built-in transcription-translation process.

The horizontal (x) axis threesome UGG + GUC + AUA = 98.
The vertical (y) axis threesome is ACG + CUU + AAG = 98 .

Both threesomes fractal nucleotide elements attract and repulse into AUG -- met (35) 100011.Photo: A balanced but off-centered architecture is efficient and eliminates the need for DNA to be fully meshed when it codes for RNA.

There are three different color pairs involved in the palindrome black Hox codon (0) UUU [F] phe.

The deeper elements of an RNA codon are found in the vertical column and the horizontal row of its binary (base-2) inverse. There is one (y) axis color pair; one (x) axis color pair, and one hinge pattern color pair that consists of one (y) and one (x) coordinate element. The hinge pattern is the key to how and where the amino acid folds in the protein. There is no order to the threesome. 

(18) 010010 CUA leu,
(44) 101100 AGU ser,
(01) 000001 UUC phe.
attract and repulse into (00) 000000 UUU phe.

(51) 110011 GUG val,
(08) 001000 UAU tyr,
(04) 000100 UCU ser.
attract and repulse into (00) 000000 UUU phe.

The (y) axis column threesome will always sum to the same total as the (x) axis row threesome; in this eaxample (63) 111111 GGG [G] gly.Photo: A balanced but off-centered architecture is efficient and eliminates the need for DNA to be fully meshed when it codes for RNA.

There are three different color pairs involved in the palindrome black Hox codon (12) UGU [C] cys.

The deeper elements of an RNA codon are found in the vertical column and the horizontal row of its binary (base-2) inverse. There is one (y) axis color pair; one (x) axis color pair, and one hinge pattern color pair that consists of one (y) and one (x) coordinate element. The hinge pattern is the key to how and where the amino acid folds in the protein. There is no order to the threesome. 

(30) 011110 CGA arg,
(32) 100000 AUU ile,
(13) 001101 UGC cys.
attract and repulse into (12) UGU [C] cys.

(63) 111111 UGU cys,
(08) 001000 UAU tyr,
(04) 000100 UCU ser.
attract and repulse into (12) UGU [C] cys.

The (y) axis column threesome will always sum to the same total as the (x) axis row threesome.Photo: A balanced but off-centered architecture is efficient and eliminates the need for DNA to be fully meshed when it codes for RNA.

There are three different color pairs involved in the palindrome black Hox codon (18) CUA [L] leu.

The deeper elements of an RNA codon are found in the vertical column and the horizontal row of its binary (base-2) inverse. There is one (y) axis color pair; one (x) axis color pair, and one hinge pattern color pair that consists of one (y) and one (x) coordinate element. The hinge pattern is the key to how and where the amino acid folds in the protein. There is no order to the threesome. 

(00) 000000 UUU phe,
(62) 111110 GGA gly,
(19) 010011 CUG leu.
attract and repulse into (18) CUA [L] leu.

(33) 100001 AUC ile,
(26) 011010 CAA gln,
(22) 010110 CCA pro.
attract and repulse into (18) CUA [L] leu.

The (y) axis column threesome will always sum to the same total as the (x) axis row threesome.Photo: A balanced but off-centered architecture is efficient and eliminates the need for DNA to be fully meshed when it codes for RNA.

There are three different color pairs involved in the palindrome black Hox codon (30) CGA [R] arg.

The deeper elements of an RNA codon are found in the vertical column and the horizontal row of its binary (base-2) inverse. There is one (y) axis color pair; one (x) axis color pair, and one hinge pattern color pair that consists of one (y) and one (x) coordinate element. The hinge pattern is the key to how and where the amino acid folds in the protein. There is no order to the threesome. 

(12) 001100 UGU cys,
(50) 110010 GUA val,
(31) 011111 CGG arg.
attract and repulse into (30) CGA [R] arg.

(45) 101101 AGC ser,
(26) 011010 CAA gln,
(22) 010110 CCA pro.
attract and repulse into (30) CGA [R] arg.

The (y) axis column threesome will always sum to the same total as the (x) axis row threesome.Photo: A balanced but off-centered architecture is efficient and eliminates the need for DNA to be fully meshed when it codes for RNA.

There are three different color pairs involved in the palindrome black Hox codon (33) AUC [I] ile.

The deeper elements of an RNA codon are found in the vertical column and the horizontal row of its binary (base-2) inverse. There is one (y) axis color pair; one (x) axis color pair, and one hinge pattern color pair that consists of one (y) and one (x) coordinate element. The hinge pattern is the key to how and where the amino acid folds in the protein. There is no order to the threesome.  

(51) 110011 GUG val,
(32) 100000 AUU ile,
(13) 001101 UGC cys.
attract and repulse into (33) AUC [I] ile.

(18) 010010 CUA leu,
(41) 101001 AAC asn,
(37) 100101 ACC thr.
attract and repulse into (33) AUC [I] ile.

The (y) axis column threesome will always sum to the same total as the (x) axis row threesome.Photo: A balanced but off-centered architecture is efficient and eliminates the need for DNA to be fully meshed when it codes for RNA.

There are three different color pairs involved in the palindrome black Hox codon (45) AGC [S] ser.

The deeper elements of an RNA codon are found in the vertical column and the horizontal row of its binary (base-2) inverse. There is one (y) axis color pair; one (x) axis color pair, and one hinge pattern color pair that consists of one (y) and one (x) coordinate element. The hinge pattern is the key to how and where the amino acid folds. in the protein. There is no order to the threesome. 

(63) 111111 GGG gly,
(44) 101100 AGU ser,
(01) 000001 UUC phe.
attract and repulse into (45) AGC [S] ser.

(30) 011110 CGA arg,
(41) 101001 AAC asn,
(37) 100101 ACC thr.
attract and repulse into (45) AGC [S] ser.

The (y) axis column threesome will always sum to the same total as the (x) axis row threesome.Photo: A balanced but off-centered architecture is efficient and eliminates the need for DNA to be fully meshed when it codes for RNA.

There are three different color pairs involved in the palindrome black Hox codon (51) GUG [V] val.

The deeper elements of an RNA codon are found in the vertical column and the horizontal row of its binary (base-2) inverse. There is one (y) axis color pair; one (x) axis color pair, and one hinge pattern color pair that consists of one (y) and one (x) coordinate element. The hinge pattern is the key to how and where the amino acid folds. 

(33) 100001 AUC ile,
(50) 110010 GUA val,
(31) 011111 CGG arg.
attract and repulse into (51) GUG [V] val.

(00) 000000 UUU phe,
(59) 111011 GAG glu,
(55) 110111 GCG ala.
attract and repulse into (51) GUG [V] val.

The (y) axis column threesome will always sum to the same total as the (x) axis row threesome.Photo: A balanced but off-centered architecture is efficient and eliminates the need for DNA to be fully meshed when it codes for RNA.

There are three different color pairs involved in the palindrome black Hox codon (63) GGG [G] gly.

The deeper elements of an RNA codon are found in the vertical column and the horizontal row of its binary (base-2) inverse. There is one (y) axis color pair; one (x) axis color pair, and one hinge pattern color pair that consists of one (y) and one (x) coordinate element. The hinge pattern is the key to how and where the amino acid folds. 

(45) 101101 AGC ser,
(62) 111110 GGA gly,
(19) 010011 CUG leu.
attract and repulse into (63) GGG [G] gly.

(12) 001100 UGU cys,
(59) 111011 GAG glu,
(55) 110111 GCG ala.
attract and repulse into (63) GGG [G] gly.

The (y) axis column threesome will always sum to the same total as the (x) axis row threesome.Photo: (07) UCG ser, white Hox codon.

In a balanced system, randomness disappears and the order and relationships emerge.

(21) 010101 CCC pro,
(06) 000110 UCA ser,
(43) 101011 AAG lys,
attract/repulse to (07) 000111 UCG ser.

(52) 110100 GCU ala,
(03) 000011 UUG leu,
(15) 001111 UGG trp,
attract/repulse to (07) 000111 UCG ala.

The biochemical paired elements of a RNA codon are found in the vertical column
and the horizontal row of its binary (base2) inverse.

The (y) axis column threesome will always sum to the same total as the (x) axis row threesome.
A balanced but off-centered architecture is efficient and eliminates the need for DNA to be fully meshed when it codes for mRNA to make the amino acids.

There will be three different color pairs involved:
one (y) axis pair; one (x) axis pair, and one hinge pattern pair consisting of one (y) and one (x) coordinate elements. The hinge pattern may be the key to how and where the amino acid folds.Photo: This is stop codon UAG ter or (11) 001011 in binary (base2).

In a balanced system, randomness disappears and the order and relationships emerge.

Stop codon (10) UAA and Stop codon (11) UAG work together. (10) is lightning and (11) is thunder.

UAG's horizontal (x) axis threesome and its vertical (y) axis threesome biochemical elements will be found in its binary (base2) inverse (52).

The horizontal (x) axis threesome UAA + CAC + ACG = 74.
The vertical (y) axis threesome is UUG + GAU + UGG = 74.

Both threesomes biochemical nucleotide elements attract and repulse into to UAG -- ter (11) 001011.

UAG imposes change on something that can not change itself.Photo: (21) CCC pro, white Hox codon.

In a balanced system, randomness disappears and the order and relationships emerge.
(07) 000111 UCG ser,
(20) 010100 CCU pro,
(57) 111001 GAC asp,
attract/repulse to (21) 010101 CCC pro.

(17) 010001 CUC leu,
(29) 011101 CGC arg,
(38) 100110 ACA thr,
attract/repulse to (21) 010101 CCC pro.

The biochemical paired elements of a RNA codon are found in the vertical column and the horizontal row of its binary (base2) inverse.

The (y) axis column threesome will always sum to the same total as the (x) axis row threesome.
A balanced but off-centered architecture is efficient and eliminates the need for DNA to be fully meshed when coding for mRNA.

There will be three different color pairs involved:
one (y) axis pair; one (x) axis pair, and one hinge pattern pair consisting of one (y) and one (x) coordinate elements. The hinge pattern may be the key to how and where the amino acid folds.Photo: (25) CAC his, white Hox codon.

In a balanced system, randomness disappears and the order and relationships emerge.

(11) 001011 UAG ter,
(24) 011000 CAU his,
(53) 110101 GCC ala,
attract and repulse into (25) CAC his.

(17) 010001 CUC leu,
(29) 011101 CGC arg,
(42) 101010 AAA lys,
attract and repulse into (25) CAC his.

The biochemical paired elements of a RNA codon are found in the vertical column
and the horizontal row of its binary (base2) inverse.

The (y) axis column threesome will always sum to the same total as the (x) axis row threesome.
A balanced but off-centered architecture is efficient and eliminates the need for DNA to be fully meshed when coding for mRNA.

There will be three different color pairs involved:
one (y) axis pair; one (x) axis pair, and one hinge pattern pair
consisting of one (y) and one (x) coordinate elements.
The hinge pattern may be key to how and where the amino acid folds.Photo: (38) ACA thr, white Hox codon.

In a balanced system, randomness disappears and the order and relationships emerge.

(52) 110100 CCU ala,
(10) 001010 UAA ter,
(39) 100111 ACG thr,
attract and repulse into (38) 100110 ACA thr.

(21) 010101 CCC pro,
(34) 1000010 AUA, ile,
(46) 101110 AGA arg,
attract and repulse into (38) 100110 ACA thr.

The biochemical paired elements of a RNA codon are found in the vertical column and the horizontal row of its binary (base2) inverse.

The (y) axis column threesome will always sum to the same total as the (x) axis row threesome.
A balanced but off-centered architecture is efficient and eliminates the need for DNA to be fully meshed when coding for mRNA.

There will be three different color pairs involved:
one (y) axis pair; one (x) axis pair, and one hinge pattern pair
consisting of one (y) and one (x) coordinate element.
The hinge pattern may be the key to how and where the amino acid folds.Photo: (42) AAA lys, white Hox codon.

In a balanced system, randomness disappears and the order and relationships emerge.

(56) 111000 GAU asp,
(06) 000110 UCA ser,
(43) 101011 AAG lys,
attract and repulse into (42) 101010 lys.

(34) 100010 AUA ile,
(46) 101110 AGA arg,
(25) 011001 CAC lys,
attract and repulse into (42) 101010 lys.

The biochemical paired elements of a RNA codon are found in the vertical column and the horizontal row of its binary (base2) inverse.

The (y) axis column threesome will always sum to the same total as the (x) axis row threesome.
A balanced but off-centered architecture is efficient and eliminates the need for DNA to be fully meshed when coding for mRNA.

There will be three different color pairs involved:
one (y) axis pair; one (x) axis pair, and one hinge pattern pair
consisting of one (y) and one (x) coordinate element.
The hinge pattern maybe the key to how and where the amino acid folds.Photo: (52) GCU ala, white Hox codon.

In a balanced system, randomness disappears and the order and relationships emerge.

(38) 100110 ACA thr,
(24) 011000 CAU his,
(53) GCC 110101 ala,
attract and repulse into (52) GCU ala.

(48) 110000 GUU val,
(60) 111100 GGU gly,
(07) 000111 UCG ser,
attract and repulse into (52) GCU ala.

The biochemical  paired elements of a RNA codon are found in the vertical column and the horizontal row of its binary (base2) inverse.

The (y) axis column threesome will always sum to the same total as the (x) axis row threesome.
A balanced but off-centered architecture is efficient and eliminates the need for DNA to be fully meshed when coding for mRNA.

There will be three different color pairs involved:
one (y) axis pair; one (x) axis pair, and one hinge pattern pair
consisting of one (y) and one (x) coordinate element.
The hinge pattern may be the key to how and where the amino acid folds.Photo: (56) GAU asp, white Hox codon.

In a balanced system, randomness disappears and the order and relationships emerge.

(42) 101010 AAA lys,
(20) 010100 CCU pro,
(57) 111001 GAC asp,
attract and repulse into (56) GAU asp.

(48) 110000 GUU val,
(60) 111100 GGU gly,
(11) 001011 UAG ter,
attract and repulse into (56) GAU asp.

The biochemical paired elements of a RNA codon are found in the vertical column and the horizontal row of its binary (base2) inverse.

The (y) axis column threesome will always sum to the same total as the (x) axis row threesome.
A balanced but off-centered architecture is efficient and eliminates the need for DNA to be fully meshed when coding for mRNA.

There will be three different color pairs involved:
one (y) axis pair; one (x) axis pair, and one hinge pattern pair
consisting of one (y) and one (x) coordinate element.
The hinge pattern may be the key to how and where the amino acid folds.Photo: T/U = 00,       C = 01,       A = 10,       G = 11.

This is a DNA repetitive sequence of CELE#4 found in C elegans. C elegans is a roundworm genomic scientists study in the laboratory because they can watch every one of its 959 cells develop. 

Why does C elegans need repetitive sequences?
More to the point...why are repetitive sequences 8% of the human genome? Is a repetitive sequence to a genome what a rest is to music?

Given: every RNA codon that codes for an amino acid belongs to one of the amino acid groups;

and any RNA codon that codes for a specific amino acid in one amino acid group can share the same attraction repulsion pattern as another RNA codon that belongs to a different amino acid group;

then,

does that suggest that a repetitive sequence may provide a similar type of invariance that RNA codon UUU provides during transcription, or provides a constant pattern on a larger scale similar to the white and black palindrome patterned Hox codons provide?Photo: T/U=00       C=01       A=10       G=11.

Image: Cele#4 repetitive sequence in the C.Elegans genome from the Sanger Collection.

Do the missing codons in the primary sequence of this gene play a spatial role in the way the protein it is coding for folds and attains its shape? 

Does the total occurrence codon count of any codon in a primary sequence provide a glimpse as to the overall meaning and purpose of the gene itself?

Does the primary sequence codon Base-2 System cross section patterns and family color indicate the possible function of the codons?

For example, why are all black codon Base-2 System cross section patterns palindromes?

Why are the sum of black and white codon occurrences always the most plentiful in all of the gene sequences found in the Sanger Collection?Photo: IMAGE: This is a chart listing specific codons not mentioned in the cele#4 repetitive sequence found in the C.elegans genome primary sequence in the Sanger Collection.

It mathematically represents an 'entanglement' Nagel has found in water droplets and the 'entanglement' Sutherland and his lab have found between cystosine and uracil at the biochemical prebiotic level.

The zero in Column ‘A’ means these RNA codons do not appear in the cele #4 primary sequence at all. Interestingly, all ‘missing’ codons in its primary sequence appear in abundance in its RNA fractal scaffolding layers 'B' and 'C'.Column ‘B’ is the number of times the once 'missing' primary sequence codon occurs as one of six RNA fractal nucleotide element subcodons (in the form of three energy pairs) in other codons in the primary sequence. Column ‘C’ is the number of times the once 'missing' codon occurs in the gene's diagonally driven 6x6 bilateral nucleotide element pattern.Photo: In base-2:      T/U=00     C=01     A=10     G=11.

Homo sapiens tumor necrosis factor receptor superfamily, member 21 (TNFRSF21), mRNA [1220 codon triplets]. 

Recently scientists have discovered that the most dangerous cancer of the uterine lining closely resembles the worst ovarian and breast cancers, providing the most telling evidence yet that cancer will increasingly be seen as a disease defined primarily by its genetic fingerprint (pattern)
rather than just by the organ where it originated.

This finding confirms the idea that cancers are more usefully classified by their Pre-Existing DNA GENE PATTERN than by where they originate.Photo: FOXP2, important in human speech and communication may also have a critical function in the development and evolution of neural circuitry in humans.

T = U as RNA. T or U = 00; C = 01; A = 10; G = 11.

The first eight most occurring codons in FoxP2 are assembled entirely of T and A bases. The top two most occurring codons are Hox codons.

The top 8 most occurring codon occurrences in the first 12,973 codon triplets are:

TTT (P) -- is a black Hox codon and has 674 occurrences.
AAA (K) -- is a white Hox codon and has 481 occurrences.
ATT (I) -- is a blue family codon and has 415 occurrences.
TTA (L) -- is a yellow family codon and has 369 occurrences.
AAT (N) is a blue family codon and has 353 occurrences.
TAA (ter) is an orange family codon and has 319 occurrences.
ATA (I) is a green family codon and has 313 occurrences.
TAT (Y) is a yellow family codon and has 313 occurrences.Photo: T/U = 00,        C = 01,        A = 10,        G = 11.

ADSS adenylosuccinate synthase [Homo sapiens] Gene ID: 159, updated on 14-Jul-2012 has 14,347 codon triplets.

(0) TTT is a black Hox codon and has the most occurrences. 0) TTT is invariant, unchanging persistence  causing change around it.

(42) AAA is a white Hox codon has the 2nd most occurrences. (42) AAA creates the pause that creates the rhythm.

Note: There are only A'a and all T's in the first five most occurring codons.Photo: T/U = 00,        C = 01,        A = 10,        G = 11.

Homo sapiens nerve growth factor (beta polypeptide) (NGF), mRNANCBI Reference Sequence: NM_002506.2 has 350 codon triplets.

(27) CAG (purple codon) and (26) CAA (red codon) both code for glutamine (gln) but have a different purpose and meaning.

In fact balck and blue; red and purple; and orange and white codons code for the same amino acid but mean separate things. 

(27) CAG has 16 occurrences and (26) CAA has 15 occurrences. (27) CAG stirs things to activity while (26) CAA bites through a layer or level to reveal the essence.

(45) AGC (black Hox codon) has 12 occurrences and (25) CAC (white Hox codon) has 12 occurrences. The black and white Hox codon occurrences combine to exceed any other color codon count.
The 1st five most occurring codons in Homo sapiens nerve growth factor (beta polypeptide) (NGF), mRNA are combinations of C's A's and G's.Photo: A biocomputer uses the power of ATP, the chemical Myosin codes for to provide energy to the cells in human bodies. 

This image is of the first 96 RNA codons in gene sequence of [Myosin light chain 1]: Saccharomyces cerevisiae S288c Mlc1p (MLC1), mRNA, which has 150 codon triplets. Scrolling down (in the actual program) would show all of it.

The codons can be broken out into their base2 system color progression families. Important, because same color codon families share a common purpose yet can consist of different amino acids. Findings include each codon is unique in pattern and meaning and codon occurrences are an indicator of their importance in the gene sequence. To convert the codons below into their base2 values shown above each codon:
T/U = 00,     C = 01,     A = 10,     G = 11.

AAG (43) 101011 tension released;
GAC (57) 111001 share a common feeling;
GAA (58) 111010 contributing;
TTG (03) 000011 invigorating;
ATT (32) 100000 connecting with;
GAT (56) 111000 rarity;
TTC (01) 000001 re-cohering;
AAC (41) 101001 maneuver in a tight place;
GCC (53) 110101 shifting gears.


.Photo: It is the brief arrangement of codons in a homeodomain that allow different interpretations for anatomical development (morphogenesis) in animals, fungi and plants; the same as codons in other arrangements carry out other protein behavior.

A homeobox gene family is a logical place to look for mathematically derived  mRNA base-2 color progression patterns and relationships.

What follows are some examples.Photo: “The mathematical properties of persistence and permanence are very closely related to the stability and homeostasis properties of biological interaction networks.” Gheorghe Cracium, Professor Mathematics, University of Wisconsin -- Madison.
craciun at math dot wisc dot edu

This image is of the breakout of codon occurrences and what color family each codon belongs to for Hox Gene Homo sapiens parkinson protein 7 (PARK7), transcript variant 2, mRNA has 307 codon triplets.

Hox genes infer the existence of Hox codons. Mathematics proves their existence. Black and White Hox Codons direct the regulatory function and folding in genes.

T/U=00.        C=01.        A=10.        G=11.

(42) 101010 AAA (white Hox codon) has the most occurrences at 19.
(52) 110100 GCT (white Hox codon) is 2nd with 13 occurrences.
(19) 010011 CTG (blue color family) is 3rd with 12 occurrences.
(51) GTG (black Hox codon) is 4rth with 11 occurrences.

(42) AAA (white Hox codon) has the most occurrences at 19.
(52) GCT (white Hox codon) is 2nd with 13 occurrences.
(19) CTG (blue) is 3rd with 12 occurrences.
(51) GTG (black Hox codon) is 4rth with 11 occurrences.

(42) AAA creates the pause that allows you feel the rhytym.
(52) GCT is a white Hox codon that maintains a steady progression.
(19) CTG is blue and exuberantly brings things to fruition.
(51) 110011 GTG is a black Hox codon that manages a immense variety of small details.Photo: T/U = 00,        C = 01,        A = 10,        G = 11.

Homo sapiens chromosome 1, GRCh37.p5 Primary Assembly has 18,813 triplets.

This is its snapshot at 4000 triplets.It is interesting that in the first 96 codon triplets of Homo sapiens chromosome 1, GRCh37 pictured in this image, that three color families quickly announce themselves: orange [17] occurrences;  white Hox codons  [17] occurrences; and black Hox codons [16] occurrences.

Combined, white and black  Hox codons have the most occurrences at this point.Photo: T/U = 00,       C = 01,       A = 10,       G = 11.

Homo sapiens chromosome 1, GRCh37.p5 Primary Assembly at 8000 triplets (continued)...

(63) GGG (a black Hox codon) now has 283 occurrences.

(21) CCC (a white Hox codon) now has 279 occurrences.

(20) CCT ( an orange codon) has dropped to 4rth with 264 occurrences.

(19) CUG (a blue codon) has risen to 3rd with 271 occurrences.Photo: T/U = 00,       C = 01,       A = 10,       G = 11.

Homo sapiens chromosome 1, GRCh37.p5 Primary Assembly at 12000 triplets (continued)...

GGG (black Hox codon) has 405 occurrences.

CTG (blue codon) has 396 occurrences.

CCC (white Hox codon) has 394 occurrences.

CCT (orange codon) has 376 occurrences.

CTC (green codon) has 353 occurrences.

C's, T's, and G's, dominate the 1st five most occurring codons at this point.Photo: T/U = 00,       C = 01,       A = 10,       G = 11.

Homo sapiens chromosome 1, GRCh37 Primary Assembly 18,813 triplets. [SUMMARY].

Why is either a black Hox codon or a white Hox codon have the most occurrences.

CCC (white Hox codon) finish with 634.
CTG (blue codon) finishes with 611.
GGG (black Hox codon) finish with 604.
CCT (orange codon) finish with 590.
TGG (green codon) finish with 564.
CAG (purple codon) finish with 556.
CTC (green codon) finish with 526.

Orange, yellow and green codons are oriented to the white Hox codon diagonal. 

Blue, purple and red codons are oriented to black Hox codon diagonal.

Neither yellow or red color family codons are among the top seven most occurring codons? 

Yellow codons enthusiastically 'respond' to the over riding idea and red codons 'adjust and adapt' rather than change. Evidently, Homo sapiens chromosome 1, GRCh37 Primary Assembly is not heavily focused on either.Photo: T/U = 00,        C = 01,        A = 10,        G = 11.

Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial is an enzyme that in humans is encoded by the DBT gene.

(42) AAA is a white Hox codon and has the most occurrences. (42) AAA creates the pause that creates the rhythm.

(0) TTT is a black Hox codon and has the 2nd most occurrences. (0) TTT is invariant, unchanging persistence causing change around it.

The first six most occurrences are composed of combinations of A's and T's.Photo: T/U = 00,        C = 01,        A = 10,        G = 11.

Homo sapiens carnitine palmitoyltransferase 2 (CPT2), RefSeqGene on chromosome 1NCBI Reference Sequence: NG_008035.1 has 8,256 codon triplets.

(0) TTT is a black Hox codon and has the most occurrences.
(42) AAA is white Hox codon and has the 2nd most occurrences.Photo: T/U=00        C=01        A=10        G=11

Homo sapiens thyroid stimulating hormone, beta (TSHB), mRNANCBI Reference Sequence: NM_000549.3 has 192 codon triplets.

Over 1/3rd of the codons are bunched between 5 and [10]occurrences.

CTG (blue) [10] , exuberantly bring to fruition.
CCA (red) [08] cautiously make a way.
ATA (green) [07] transform.
GCA (purple) [07] acknowledge a presence.
TTT (black) [07] persist and provide constancy.
AGT (blue) [06] clear confusion away.
TAA (orange) [06] polarizing tension.
TCA (orange) [06] define value.
ACT (purple) [05] provide subtle support.
ATG (yellow) [05] persevere and continue.
ATT (blue) [05] connect with.
CTC (green) [05] strip away a protective cover.
CTT (yellow) [05] cooperate with.
GTG (black) [05] manage a variety of details.
TGT (black) [05] occurrences, conform with.

2 more codons have 5 occurrences and 8 more codons have 4 occurrences.Photo: T/U = 00,         C = 01,         A = 10,        G = 11.

Homo sapiens interferon regulatory factor 6 (IRF6), transcript variant 2, mRNANCBI Reference Sequence: NM_001206696.1 has 1,418 codon triplets. This a gene is for connective tissue.

GGA (blue) [48] eliminate the unusable.
TTT (black) [46] constancy and persistence.
CTT (yellow) [43] cooperate with.
GAA (purple) [41] actively contributing.
TGG (green) [38] come to meet.
CTG (blue) [37] exuberantly coming to fruition.

All 64 codons are used in the primary sequence which does not always happen, even with a gene this size. However, even when all 64 codons are not used in a primary sequence, the 'missing codons' always appear in abundance in the fractal layers, providing the fractal scaffolding that underlies protein shape.Photo: T/U = 00,         C = 01,         A = 10,         G = 11.

Homo sapiens collagen, type XI, alpha 1 (COL11A1), transcript variant E, mRNANCBI Reference Sequence: NM_001190709.1 has 2,397 codon triplets.

GGT (most occurrences),  GGA (3rd), GGG (8th). GGC (9th), all code for glycine (gly).

Every color codon family is represented in the top nine most occurring codons:
GGT -- green (188), CCT -- orange (143), GGA -- blue (131), CCA -- red (124), AAA -- white (110), GAA -- purple (103), GAT -- white (79), GGG -- black (65), GGC -- yellow (61).

The combination of black and white color family Hox codons sum to the most occurrences (313).

Once again, all 64 codons are used in the primary sequence which does not always happen, even with a gene this size. However, even when all 64 codons are not used in a primary sequence, the 'missing codons' always appear in abundance in the fractal layers.Photo: T/U = 00,           C = 01,           A = 10,           G = 11.

[Myosin light chain 1]: Saccharomyces cerevisiae S288c Mlc1p (MLC1), mRNA.

Myosins are best known for their role in muscle contraction. The '0's and '1's in the base-2 system patterns below can be viewed as attraction-repulsion patterns.

AAG (43) 101011 tension released;
GAC (57) 111001 share a common feeling;
GAA (58) 111010 contribute;
TTG (03) 000011 invigorate;
ATT (32) 100000 connect with;
GAT (48) 111000 being vigilant;
TTC (01) 000001 resolve;
AAC (41) 101001 maneuver in a tight place;
GCC (53) 110101 shift gears.

No single value of a black or white color family Hox codon appears as one of the first nine most occurring codons; yet the combination of all of the black and white color family Hox codons surpass any other color family codon total.Photo: T/U = 00,       C = 01,       A = 10,       G = 11.

#1 ALX4 gene

The ALX4 gene provides instructions for producing a protein that is necessary for proper development throughout the body, especially in the skull and limb bones.

The ALX4 protein is a transcription factor, which means it attaches (binds) to specific regions of DNA and helps control the activity of certain genes.

The presence of the ALX4 protein seems to be particularly critical for the complete development of the skull.

CONTINUED...Photo: T/U=00         C=01         A=10         G=11.

(continued from previous page)
Homo sapiens ALX homeobox 4 (ALX4), mRNANCBI Reference Sequence: NM_021926.3 consists of 1822 RNA codon triplets. Note the number of triple and double codon bases.

White Hox codon (21) CCC 010101 in process.
Blue (19) CTG 010011 exuberant, bringing to fruition.
The black Hox codon (63) GGG 111111 formative structuring power.
Yellow (47) AGG 101111 organize  into functional units.
Orange (20) CCT 010100 share space.
Purple (27) CAG 011011 rouse things to action. Red (22) CCA 010110 differentiate.
Yellow (61) GGC 111101 group essential qualities together.
Black Hox codon (45) AGC 101101 venture forth without reserve.
Orange (53) GCC 110101 shift gears.
Purple (05) TCC 000101 wait until the right moment to act.
Green (17) CTC 010001 peel away a protective cover.
Red (55) GAG 110111 following fundamentals.Photo: T/U=00       C=01       A=10       G=11.

Human cartilage-specific homeodomain protein Cart-1 mRNA, complete cds GenBank: U31986.1

(xx) = base-2 value (0-63).
[xx] = occurrences.

Red (22) CCA 010110 differentiates one 'something' from another [17].
White Hox codon (38) ACA 100110 possessing the emptiness to change [15].
Yellow (35) ATG 100011 start codon or can mean continue and persevere [14].
Blue (32) ATT 100000 means connecting [14].
Green (17) CTC 010001 strips away a protective cover [14].
White Hox codon (42) AAA 101010 pause that allows us to hear the note [13].
Purple (27) CAG 011011 rouses something to action [13].
Green (46) AGA 101110 means protected environment in order to develop [12].
Blue (62) GGA 111110 eliminating the unusable [12].
Black Hox codon (0) TTT 000000 black Hox codon unchanging [12].
Orange (43) AAG 101011 release from tension [11].
Black Hox codon (45) AGC 101101 venture forth without reserve [11].
Blue (44) AGT 101100 clear away confusion [11].
White Hox codon (21) CCC 010101 maintaining correct position [11].Photo: 31468.1 Public Homo sapiens 11 ALX4 11 103 68. Assembly GRCh37.p9 (GCF_000001405.21)
On '-' strand of Chromosome 11 (NC_000011.9).

Top 14:
Purple (27) CAG 011011 rouse to action 						[31].
Orange (53) GCC 110101 ability to change gears 				[26].
Red (59) GAG 111011 following fundamentals 					[20].
Black Hox codon (45) AGC 101101 venturing forth without reserve 		[19].
Yellow (61) GGC 111101 grouping essential qualities together 		[18].
Orange (43) AAG 101011 an understanding that releases tension 		[17].
Purple (23) CCG 010111 hidden intelligence 					[16].
Orange (57) GAC 111001 sharing a bond and clustering together 		[16].
White Hox codon (21) CCC 010101 maintaining correct position 			[14].
Green (17) CTC 010001 stripping away a protective cover 			[11].
Blue (19) CTG 010011 exhuberant increase 						[11].
Purple (09) TAC 001001 stimulate and interact with 				[11].
Black Hox codon (63) GGG 111111 formative structuring power 		[10].
Black Hox codon (51) GTG 110011 managing a variety of small details 		[10].Photo: 31468.1	Public	Homo sapiens	11	ALX4	11	103	68 (cont).

Total color codon occurrences:
black codons [39] reglate and white codons [54] sheperd segments together and shape = [93].
purple [77] are ombudsman.
orange [71] define values.
red [58] adjust and adapt.
blue [41] decohere and cohere.
yellow [41] harmonize and organize.
green [24] invigorate and transform.

No occurrences for stop codons orange
(10) 001010 TAA and white Hox codon
(11) 001011 TAG .

In fact, there is only one stop codon in the entire gene sequence: yellow (14) TGA 001110; the ninth codon from the end with one occurrence.

No occurrences for
black Hox codon (18) CTA 010010,
white Hox codon (56) GAT 111000, 
green (46) AGA 101110,
green (34) ATA 100010 or
blue (50) GTA 110010; but they all occur in abundance at the fractal scaffolding level.Photo: T/U = 00         C = 01         A = 10          G = 11

Rat protein kinase C zeta-subspecies 'memory' gene has 887 triplets. 

Most occurring:
orange (57) GAC [D] asp -- sharing a bond;
blue (19) CTG 01 [L] leu -- exuberant increase culminating;
purple (27) CAG [Q] gln -- stirring to activity;
black Hox codon (33) ATC [I] ile -- pushing beyond normal limits;
orange (43) AAG [K] lys -- release from tension;red homeobox
red (59) GAG [E] glu -- providing what is needed to meet the future;
yellow (61) GGC [G] gly -- grouping essential qualities together;
yellow (47) AGG [R] arg -- organizing into functional units;
blue (01) TTC [F] phe -- diverging;
white Hox codon (57) GAT [D] asp -- pivoting;
orange (53) GCC [A] ala -- shifting gears;
white Hox codon (21) CCC [P] pro -- in process;
white Hox codon (25) CAC [H] his -- compelled to move forward;
purple (58) GAA [E] glu -- actively contributingPhoto: T/U=00     C=01     A=10     G=11
uracil 'U' replaces thymine 'T' in RNA.
BHC = black Hox codon / WHC = white Hox codon
PSK9 protein has 443 codon triplets. In its tightly bunched and self-contained meaning it uses all 64 codons; meaning 'WYSIWYG' and all of its scaffolding occurs as a secondary function which is an exception in any protein and not the rule.
PSK9's 16 most occurring codons represent 45% of the protein sequence and a clue to how it works:
TGA -- [ter] diminish action (stop codon)
GAA -- [E] visibly thriving an contributing
TGT -- [C] relationship of inner to outer (BHC)
AAT -- [N] expressing presence or claim
ATT -- [I] a coupling, connective energy
TGG -- [W] coming to meet
AAA -- [K] establishing a rhythm (WHC))
TTT -- [F] unchanging (BHC)
CAT -- [H] graceful, unencumbered movement
GGA -- [G] eliminate what is unusable
TAG -- [ter] imposing a new status (stop codon) 
TAT -- [Y] making a way step by step
TGC -- [C] testing limits and connections
GCA -- [A] stopping an acknowledging boundaries
AGA -- [R] accepting envelopment
AGT -- [S] dispersing what is blocking the way

Hox codons, both black and white, regulate the segments they appear in and sheperd the segments into its final protein shape.Photo: All primary gene sequences can be viewed as part of a balanced Cartesian coordinate system on a spherical scaffolding; providing a deeper insight into the 'distal' nature of gene linear sequences.

Each Base-2 System numerical value (0-63) is equivalent to one RNA codon. Each RNA codon codes for a unique 'function, meaning and fold' amino acid.

EXAMPLE: If a primary gene sequence has 2081 codons and the black Hox codon (12) UGU occurs as one of those 2081 occurrences 159 times, then UGU has159 separate layers interleaved throughout a 2081 layer deep spherical configuration.

In this view: (12) UGU appears in the same spot in each layer with the same base-2 attraction-repulsion pattern but the '0' and '1' attraction-repulsion patterns of UGU can conform differently to what layer is above and below it.

CONCLUSION: Any gene sequence can be plotted on balanced scaffolded (x) and (y) grids, and observed -- as it folds into its primary sequence occurrence shape first before expanding (according to its occurrences) into its tertiary and then -- if needed -- quaternary forms.Photo: Dr. Borenstein, Metagenomics Systems Biology, University of Washington, addresses a diverse set of central questions in evolutionary and systems biology.

His research interests lie in the interplay between evolutionary processes and the organization of biological, ecological and social systems; identifying fundamental, universal, and generic links between the structure of complex systems and their generative dynamics, and developing methods to draw novel insights from these links.

One such insight is how two microbial species -- too much alike or too different from one another -- will not interact to create emergent behavior ????
-- but will create emergent behavior if not too much alike and not too different from one another.

Is this suggesting attraction/repulsion patterns!?!Photo: This is a simple 3D mix of the 64 RNA fractal codon elements with base-2 system color progression. The black and white Hox codon elements are not pictured to better show the natural relationships which already exist before we look for the mathematical patterns underlying it all.Photo: This is a simple 3D mix of the 64 mRNA codon elements with base-2 system color progression. The black and white Hox codon elements are not pictured to better show the natural relationships which already exist before we look for the mathematical patterns underlying it all.

Information contained within each mRNA codon element is organized along a diagonal.

In this slide: A black Hox codon's diagonal color preferences are red, blue and purple.

Hox codons are responsible for creating the unique behavior of organized clusters in certain segments of genes called a homeobox and the specific homeodomain.

It is the brief arrangement of Hox codons in a homeodomain that allow different interpretations for anatomical development (morphogenesis) in animals, fungi and plants; the same as Hox codons in other arrangements carry out other protein behavior.Photo: This is a simple 3D mix of the 64 mRNA codon elements with base-2 system color progression. The black and white Hox codon elements are not pictured to better show the natural relationships which already exist before we look for the mathematical patterns underlying it all.

Information contained within each mRNA codon element is organized along a diagonal.

In this slide: A white's Hox codon diagonal color preferences are yellow, green and orange.

Hox codons are responsible for creating the unique behavior of organized clusters in certain segments of genes called a homeobox and the specific homeodomain.

It is the brief arrangement of Hox codons in a homeodomain that allow different interpretations for anatomical development (morphogenesis) in animals, fungi and plants; the same as Hox codons in other arrangements carry out other protein behavior.Photo: From simple chemical substances to compounds like DNA, nearly all assemblages of atoms are linked together by electronic bonds. The quest to understand these tiny bonds -- the very glue of material existence -- is the heart of chemical science.

Sharp direct images of electronic bonds (known as orbitals) reveal shapes described as doughnut-like rings, dumbbell-shaped lobes and arrays suggestive of butterfly wings. These shapes fit theoretical predictions. -- Browne, NYTimes.Photo: The three shapes of orbitals in the electrical bond of matter (rings, wings, and dumb bells), are similar to the shapes formed by connecting Wheeler Family mirror image Base-2 System progression (0-15) cross section patterns.

A Wheeler Family consists of the probabilities of what happens when Matter Tells Space How To Curve and Space Tells Matter How To Move. John Wheeler gave us this 'layman's' definition of Relativity in a show hosted by Peter Ustinov about Nigel Calder's book: 'Einsteins Universe', in 1976.

*The butterfly pattern Wheeler Family consists of [1, 7, 8 and 14]. (1 and 8) and (7 and 14) are base-2 mirror images. (1 and 14) and (7 and 8) are base-2 inverses. 
*The dumbbell shape Wheeler Family consists of
[2, 4, 11, 13]. (2 and 4) and (11 an 13) are base-2 mirror images. (2 and 13) and (4 and 11) are base-2 inverses.
* The doughnut-like Wheeler Family consists of
[3,  5, 10, 12]. (3 and 12) and (5 an 10) are both
base-2 mirror images and inverses.

*A fourth Wheeler Family consists of parallel line palindromic cross sections [0, 6, 9, 15]. (0 and 15) and 6 and 9) are base-2 inverses.Photo: In 1978, working with my brother Kevin, we designed a Thinking Analysis we later turned into two software programs -- one in Fortran (1979) and one in BASIC (1984). By then, I had already expanded the Thinking Analysis to 64 cross sections. We have the printout of the fortran program and an operating version of the 1984 program along with this explanation.

I mention it because no one can ever accuse of us of jumping on the band wagon. This has been our passion for almost 40 years.






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Note: I spelled environment wrong on the image.Photo: The same as there is a spectrum of color, a scale of music, and a periodic table of elements -- so too is there a Genomic Biochemical Base-2 system half state color progression.

This underlying genomic biochemical architecture possesses the characteristics of the color spectrum; the wave amplitude of music, and the specificity of the Periodic Table of Elements.





.Photo: A bird's feathers, a reptile's scales, and a mammal's hairs may seem like very distinct features, but feathers, scales, and hairs are homologous as appendages in that these features share a developmental origin. They each use the same initial ‘decision center signaling system’, called a placode, a genetic mechanism that decides to create the ‘place’ where a feather, scale or hair can grow out of the skin.

And that 'decision center' doesn't just dictate where a hair, scale, or feather should emerge from the skin, it also transmits information about how much space should be between each appendage or any patterning, like the swirls in the fur of a dog.Photo: Our quest to use a mathematically derived  context driven base2 system color progression to find the hidden patterns in the genome is now over six years old.

Color is relative: each base in each RNA base pair, DNA triplet codon or mRNA triplet codon has a specific color mathematically driven by its context in the base2 progression it is in.

Our approach is very different than current approaches that assign one 'fixed' color to each of the five nucleotide bases (T, U, C, A, G) resulting in camouflaging  key transitive and nesting patterns common to different genes that are there and readily visible to the naked eye and image recognition programs using context driven color.

The eteRNA player community submission shows our early confusion on the difference between RNA pairs, mRNA codons and the DNA codons that code for mRNA codons to make amino acids.

For example, gene sequences are never 10 million bases long. Our point there was how can any linear gene sequence fold into a protein in less than a second, over and over in our billions of cells 24/7 our entire lives? The answer (we hypothesize) is that RNA pairs, mRNA and have a diagonal architecture.

Since this entry six years ago Sutherland's MRC Lab has found a prebiotic bridge from Chemistry to Biology that can be expressed in a mathematically derived  base-2 system half state color progression.Photo: We thought eteRNA was on the verge of introducing a standard 'relative' color palette six years ago. They did not so we did  and made it public like we promised.

https://docs.google.com/document/d/1s8f6rOkj5r0pzDy8Um74xJMq1bA7vNbtFAif9q5GVFY/edit?usp=sharingPhoto: Photo: I wish I could be at your seminar tomorrow: [Quantbio] Qbio Mini-Forum, Wed (12/14); Challenges and Opportunities for Qbio at UW-Madison.