Threesology Research Journal
Artificial Intelligence and 3sology (56K)

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AI and 3sology pages:

Artificial Intelligence and 3sology Introduction
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If we decide to adopt a usage of genetics as a model which will enable the application of a trinary formula, do we say that the presence of 1 "start" (UGA) and 3 "stop" codons (UAG, UGA, and UAA represent translation-termination signals) for RNA suggests a a process of "speaking and hearing", but overlook the presence of the 1 to 3 (or 3 to 1) ratio herein as being part of a trinary setup? The following are two representative charts illustrating the 3 to 1 ratios for the DNA and RNA dichotomy. While a discussion of these two illustrates a binary, the presence of the third bio-molecular substance known as proteins should not be overlooked. Proteins have a 3 to 1 configuration as well, but this proportioning illustration may not be easily recognized by the comments in the following Britannica excerpt on Proteins:


The terms secondary, tertiary, and quaternary structure are frequently applied to the configuration of the peptide chain of a protein. A nomenclature committee of the International Union of Biochemistry (IUB) has defined these terms as follows:


  1. The primary structure of a protein is determined by its amino acid sequence without any regard for the arrangement of the peptide chain in space.
  2. The secondary structure is determined by the spatial arrangement of the main peptide chain without any regard for the conformation of side chains or other segments of the main chain.
  3. The tertiary structure is determined by both the side chains and other adjacent segments of the main chain, without regard for neighbouring peptide chains.
  4. The term quaternary structure is used for the arrangement of identical or different subunits of a large protein in which each subunit is a separate peptide chain.


    Source: "Protein." Encyclopædia Britannica Ultimate Reference Suite, 2013.

Professional and lay scientists the world over have got it wrong. DNA and RNA do not (only) have a triplet codon (coding) system; each has a three-to-one ratio that may more easily be identified by describing as "three the same, one is different". But this relationship is not readily seen unless both DNA and RNA are placed side by side:


The RNA Codons:
U C A G
U UUU Phenylalanine (Phe) UCU Serine (Ser) UAU Tyrosine (Tyr) UGU Cysteine (Cys) U
UUC Phe UCC Ser UAC Tyr UGC Cys C
UUA Leucine (Leu) UCA Ser UAA    STOP UGA    STOP A
UUG Leu UCG Ser UAG    STOP UGG Tryptophan (Trp) G
C CUU Leucine (Leu) CCU Proline (Pro) CAU Histidine (His) CGU Arginine (Arg) U
CUC Leu CCU Pro CAC His CGC Arg C
CUA Leu CCA Pro CAA Glutamine (Gln) CGA Arg A
CUG Leu CCG Pro CAG Gln CGG Arg G
A AUU Isoleucine (Ile) ACU Threonine (Thr) AAU Asparagine (Asn) AGU Serine (Ser) U
AUC Ile ACC Thr AAC Asn AGC Ser C
AUA Ile ACA Thr AAA Lysine (Lys) AGA Arginine (Arg) A
AUG Methionine (Met) or
START
ACG Thr AAG Lys AGG Arg G
G GUU Valine Val GCU Alanine (Ala) GAU Aspartic acid (Asp) GGU Glycine (Gly) U
GUC (Val) GCC Ala GAC Asp GGC Gly C
GUA Val GCA Ala GAA Glutamic acid (Glu) GGA Gly A
GUG Val GCG Ala GAG Glu GGG Gly G



The Genetic Code (DNA): These are the codons as they are read on the (5' to 3') strand of DNA. Except that the nucleotide thymidine (T) is found in place of uridine (U), they read the same as RNA codons. However, mRNA is actually synthesized using the (3' to 5') as the template.


This table could well be called the Rosetta Stone of life.


The DNA Codons:
T C A G
T TTT Phe TCT Ser TAT Tyr TGT Cys
TTC Phe TCC Ser TAC Tyr TGC Cys
TTA Leu TCA Ser TAA STOP TGA STOP
TTG Leu TCG Ser TAG STOP TGG Trp
C CTT Leu CCT Pro CAT His CGT Arg
CTC Leu CCC Pro CAC His CGC Arg
CTA Leu CCA Pro CAA Gln CGA Arg
CTG Leu CCG Pro CAG Gln CGG Arg
A ATT Ile ACT Thr AAT Asn AGT Ser
ATC Ile ACC Thr AAC Asn AGC Ser
ATA Ile ACA Thr AAA Lys AGA Arg
ATG Met***    (START) ACG Thr AAG Lys AGG Arg
G GTT Val GCT Ala GAT Asp GGT Gly
GTC Val GCC Ala GAC Asp GGC Gly
GTA Val GCA Ala GAA Glu GGA Gly
GTG Val GCG Ala GAG Glu GGG Gly
*** When within gene; at beginning of gene, ATG signals start of translation.

Review: 3 stops to 1 start. 3 amino acids the same while 1 is different. Surely you can recognize these two examples as a repeating pattern. But is it merely a repeating cognitive pattern scribed out by the present evolutionary state of the human mind/brain, or is it in fact a recurring theme in nature that supercedes any cognitive-cultural imposition?

Item --- Three the same --- --- One is different ---
DNA = Adenosine- Cytosine- Guanine Thymine
RNA = Adenosine- Cytosine- Guanine Uracil

Source: Three "to" One ratios page A


DNA Protein synthesis (63K)

With respect to proteins and an inclusion of information regarding refraction, reflection, etc., as propagated physics properties, it is necessary that I include some information about the analysis of protein determination by way of light properties, as well as a mention chemical reactivity since it involves a specifice reference to a "three" example. I do so because it is necessary to think of the next generation of computation in terms of properties that run far afield of conventional binary thinking. Such thinking involves a transgression into areas once thought characteristic of Science Fiction only. For example, the typical person may think of time travel as a physics problem, while a few consider that it may involve the need for altering our genetic structure as well. But an understanding of the genetic structure with regards to origin and precipitate evolutionary influences involves uncommon intellectual sojourns.


Spectrophotometric behaviour


Spectrophotometry of protein solutions (the measurement of the degree of absorbance of light by a protein within a specified wavelength) is useful within the range of visible light only with proteins that contain coloured prosthetic groups (the nonprotein components). Examples of such proteins include the red heme proteins of the blood, the purple pigments of the retina of the eye, green and yellow proteins that contain bile pigments, blue copper-containing proteins, and dark brown proteins called melanins. Peptide bonds, because of their carbonyl groups, absorb light energy at very short wavelengths (185–200 nanometres). The aromatic rings of phenylalanine, tyrosine, and tryptophan (see Figure 1D), however, absorb ultraviolet light between wavelengths of 280 and 290 nanometres. The absorbance of ultraviolet light by tryptophan is greatest, that of tyrosine is less, and that of phenylalanine is least. If the tyrosine or tryptophan content of the protein is known, therefore, the concentration of the protein solution can be determined by measuring its absorbance between 280 and 290 nanometres.


Optical activity


It will be recalled that the amino acids, with the exception of glycine, exhibit optical activity (rotation of the plane of polarized light; see above, Physicochemical properties of the amino acids). It is not surprising, therefore, that proteins also are optically active. They are usually levorotatory (i.e., they rotate the plane of polarization to the left) when polarized light of wavelengths in the visible range is used. Although the specific rotation (a function of the concentration of a protein solution and the distance the light travels in it) of most L-amino acids varies from -30° to +30°, the amino acid cystine has a specific rotation of approximately -300°. Although the optical rotation of a protein depends on all of the amino acids of which it is composed, the most important ones are:


  1. Cystine

And the (3) aromatic amino acids:


  1. Phenylalanine
  2. Tyrosine
  3. Tryptophan

The contribution of the other amino acids to the optical activity of a protein is negligibly small.


Chemical reactivity of proteins


Information on the internal structure of proteins can be obtained with chemical methods that reveal whether certain groups are present on the surface of the protein molecule and thus able to react or whether they are buried inside the closely folded peptide chains and thus are unable to react. The chemical reagents used in such investigations must be mild ones that do not affect the structure of the protein.


The reactivity of tyrosine is of special interest. It has been found, for example, that only three of the six tyrosines found in the naturally occurring enzyme ribonuclease can be iodinated (i.e., reacted to accept an iodine atom). Enzyme-catalyzed breakdown of iodinated ribonuclease is used to identify the peptides in which the iodinated tyrosines are present. The three tyrosines that can be iodinated lie on the surface of ribonuclease; the others, assumed to be inaccessible, are said to be buried in the molecule. Tyrosine can also be identified by using other techniques; e.g., treatment with diazonium compounds or tetranitromethane. Because the compounds formed are coloured, they can easily be detected when the protein is broken down with enzymes.


Cysteine can be detected by coupling with compounds such as iodoacetic acid or iodoacetamide; the reaction results in the formation of carboxymethylcysteine or carbamidomethylcysteine, which can be detected by amino acid determination of the peptides containing them. The imidazole groups of certain histidines can also be located by coupling with the same reagents under different conditions. Unfortunately, few other amino acids can be labelled without changes in the secondary and tertiary structure of the protein.


Source: "Protein." Encyclopædia Britannica Ultimate Reference Suite, 2013.

Proteins, as the third biological component in a discussion with the presence of DNA and RNA must be identified with its own 3 to 1 ratio in terms of a primary- secondary- tertiary structure, and that the combination of these is called a quaternary structure. Clearly the 3 to 1 ratio has relevance to a discussion of computation based on a genetic model, just as an anthropomorphism of the involved circuitry. If we say that "stop and start" are somehow "heard", then what is the mechanism of hearing and communication? If electrical circuitry only affords us the (binary) speech pattern equivalent to the babbling of an infant, what sort of "circuitry" is needed for the word development stage? Instead of having to rely on the binary expressions comparable to ba-ba, na-na, da-da, etc., where the so-called level of intelligence capable of being achieved is that no better than a babbling infant; will either/or/and a genetic— physics model enable us to achieve a higher level of computational intelligence? In addition, will it be an intelligence of consciousness that exceeds the nonsense humans portray? Can humans create an intelligence superior to their own, thus creating a circumstance where human intelligence is recognized as the artificiality which it is; in terms of its design having been dependent on a decaying planetary environment?


However, you may not be yet convinced that the presence of a 3 to 1 ratio has any import for consideration in the development of a new type of computational design. You may be one who needs additional examples: the following chart provides a handful of so-called four-item references broken down into 3-to-1 characterizations (but you could also refer to them as a 1-to-3 ratio):


3 1
3 grouped (drumming) beats separated by 1 emphasized beat (Native American)
3 ordinary dimensions: Length ~ Width ~ Depth 1 Time dimension
3 fundamental gauge forces: Strong - Weak - Electromagnetic 1 fundamental non-gauge force: Gravity
3 "even" amino acids: Adenosine ~ Cytosine ~ Guanine 1 "odd": Uracil (RNA), Thymine (DNA)
3 basic protein structures: Primary - Secondary - Tertiary 1 composite protein structure: Quaternary
3 (metal) vending coins: Nickels ~ Dimes ~ Quarters 1 relational (paper) form: Dollar bill
3 numbered potatoes: 1 potato ~ 2 potato ~ 3 potato 1 un-numbered 4 (counting game)
3 numbered bits: 2 bits ~ 4 bits ~ 6 bits 1 un-numbered: a dollar (cheer-leading)
3 face cards: Kings ~ Queens ~ Jacks 1 related Ace card (faceless)
3 typically used face cards: Kings ~ Queens ~ Jacks 1 less commonly used face card: Joker
3 rhymes: eeny ~ meeny ~ miney separated by 1 (mo) of another 3: (mo ~ toe ~ go)
3 indoor coverings: Curtains ~ Blinds ~ Shades 1 related outdoor: Shutters
3 God labels: He ~ She ~ It 1 relational: Non-Entity (non-existence)
3 numbered bases: 1st ~ 2nd ~ 3rd related to 1 unnumbered: Home plate/base
3 customary years 1 relational: leap year
3 primary cycles: Intake ~ Compression ~ Power 1 relational: Exhaust
3 "element" A-U-M = "OM"
(Birth~ Being~ Dissolution)
1 relational: Silence
3 step shampooing: Wet hair ~ Lather ~ Rinse 1 relational: Repeat as desired
3 female desires for a man: Tall ~ Dark ~ Handsome 1 relational: Rich
3 part call: Hear Ye! Hear Ye! Hear Ye! 1 relational: The court is now in session
3 part game call: Apples ~ Peaches ~ Pumpkin Pie 1 relational: Who's not ready hollar I
3 basic forms of matter: Solids ~ Liquids ~ Gases
(Earth- Water- Air)
1 relational: Plasma
(Fire)
3 (metrical foot) stressed syllables 1 relational unstressed syllable
3 guitarists (Beatles): Paul ~ John ~ George 1 relational drummer: Ringo
3 regular U.S. forces: Army ~ Navy ~ Air force 1 relational: Marines (Navy Dept.)
[Coast Guard = Dept. of Transportation]
3 times repeated cadence: Gimme' (give me) your left 1 related: Right (military marching)
Gimme' your left- Gimme' your left- Gimme' your left----- Right
3 consonants to (four-letter) Cuss Words 1 related vowel
3 (numerical) feet: 1 foot + 1 foot + 1 foot equals 1 related (word): Yard
3 common body crossings: Legs ~ Arms ~ Fingers 1 uncommon related: Eyes
3 Europeans: D.L. George ~ V. Orlando ~ G. Clemenceau 1 (U.S.A): W. Wilson (Paris Peace Talks)
3 at-bat chances to run 1 relational mandatory walk (ball four)
3 microorganism "vats": Rumen ~ Reticulum ~ Omasum 1 "true" stomach: Abomasum (Ruminants)
3 Hurry! Hurry! Hurry! related to: 1 Step Right Up (Circus Barker)
3 synoptic gospels: Matthew - Mark - Luke 1 idiosyncratic gospel: John
Trinitarian (3) concept related to Unitarian (1) concept
3 original musketeers (Athos, Porthos, Aramis) 1 add-on (d'Artagnan)
3 active brain waves (Alpha, Beta, Theta) 1 inactive brain wave (Delta)
3 types of cones to the human eye 1 type of rod to the human eye
3 Piaget operational stages: Pre - Concrete - Formal 1 [non-operational] sensorimotor stage
3 Basic gaseous biological compounds:
Hydrogen- Oxygen- Nitrogen
1 Basic solid compound:
Carbon
3 rows of outer hair cells (mammalian ear) 1 row of inner hair cells
3 imagined places: Paradise - Purgatory - Inferno 1 actual place: Earth
3 common growing seasons: Spring - Summer - Fall 1 less typical growing season: Winter
3 metal ages: Silver - Bronze/Copper - Iron
[Bronze is an alloy of Copper]
1 non-metal age: Stone
(Was there a bone or stick age?)
3 common alternate milk (with fat) forms: 1% - 2% - Skim 1 common standard form: Whole milk
3 interactive identities: i - j - k = 1 resultant quaternion identity: -1
W. Hamilton's quaternion formula: i2 = j2 = k2 = ijk = -1
3 gasoline types: Unleaded - Regular - Premium 1 Diesel fuel oil
3 non-gasoline fuels: Diesel - Propane - Natural Gas 1 gasoline fuels
3 Earthly-bound Horsemen plagues:

War- Famine- Pestilence
1 Heaven/Hell-bound Horsemen plague:

Death
3 (physically labeled) psychosexual stages:
Oral - Anal - Genital
1 (non-physically labeled) stage:
Latency period
3 (OK Corral) Earp brothers: Wyatt - Morgan - Warren 1 (OK Corral) Doc Holiday
3 Stanley Miller Chemical Evolution experiment gases:
Methane ~ Hydrogen ~ Ammonia
1 Stanley Miller liquid:
Water
Art Maxim Percentages division:
Art is 75% perspiration (75% = 3)
"and" --- 25% inspiration (25% = 1)
3 basic tea types: Black - Green - Oolong 1 (basic) rare tea type: White
3 basic mathematical operations:
Addition- Subtraction- Multiplication
1 auxiliary mathematical operation:
Division
3 (DNA) bases code for: 1 amino acid
3 customary laws of Thermodynamics 1 Zeroth law of Thermodynamics
3 types of bone: Cortical - Compact - Trabecular 1 relational: Cartilage (pre-bone)
3 U.S. Presidential debates (2004) 1 relational: U.S. Vice President debate (2004)
3 compulsory schools: Elementary - Jr. High - High school 1 non-compulsory school: College (or Trade)
3 "human" cartoon characters: Fred - Wilma - Pebbles 1 animal character: Dino (family pet)
3 "human" cartoon characters: Barney - Betty - Bam Bam 1 animal character: Hoppy (family pet)
3 "regular" corners to a building 1 principal Corner Stone to a building
3 foot bones of ancient horses Fused together to make modern horse hoof
3 at-base runners: 1st base - 2nd base - 3rd base 1 at-home-plate grand slam hitter
3 "traditional" size proportions:
Small- Medium- Large
1 commercial profiteering size proportion:
Supersize
3 flexible downs in American football 1 play it safe or risk it all downs
3 word vulgar expression: God Damn It 1 (3 into 1) single word vulgar expression: Goddamnit
3 meal options: Sandwich - Sideorder - Drink called a (1) combo meal
3 single letter blood type designations: A - B - O 1 double letter blood type designation: AB
(positive or negative)
3 phase (U.S.) electric service is related to 1 phase (U.S.) electric service


If I've told you once (1), I've told you a thousand (1,000) times...
(The value "1,000" is a 1 with three zeros.)

3 to 1 expressions used by a soldier on guard duty:

Halt, who goes there?
Approach... and be recognized.

(There is a distinction that can be made between the first word and the 3 words which follow.)
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Mendelian inheritance is usually described as the process by which one of two alternate alleles of a gene is inherited from each parent so that the offspring has one of the following combinations: two dominant alleles, two recessive alleles, or one of each. If both parents are heterozygous, that is, have one of each allele, the three genotypes will occur among the offspring with the following probabilities: one homozygous dominant, two heterozygotes, and one homozygous recessive. Phenotypically the two heterozygotes will be indistinguishable from the homozygous dominant. This results in the famous 3:1 ratio

(James C. King, The Biology of Race, 1981, page 28)


Source: Three "to" One ratios page C


Subject page first Originated (saved into a folder): Thursday, November 13, 2014... 5:50 AM
Page re-Originated: Sunday, 24-Jan-2016... 08:51 AM
Initial Posting: Saturday, 13-Feb-2016... 10:59 AM
Updated Posting: Saturday, 09-Apr-2016... 12:16 PM

Your Questions, Comments or Additional Information are welcomed:
Herb O. Buckland
herbobuckland@hotmail.com