Prepared By:
Dr. Charles Ruark, Jr.
February 21, 2024
*Reference “DNA Analysis- A PDF” for this article.
The First Table (first two pics) is the comprehensive work from which I derived the Second Table (second two pics). The First Table allows you to see the massive scope of the math problem necessary to obtain the solutions necessary to eliminate all protein errors and mutations from vertebrate cells. For now, I will just make a few comments concerning the First and Second Tables. At the bottom of page 2 of the First Table on the left note that typically adenine (A) bonds with uracil (U) and guanine (G) bonds with cytosine (C). That’s why the short horizonal arrows run from A to U and G to C. However, when a codon sets on the bonding site (A-site) of the ribosome, in the third codon position which is the one to the right of the middle position, it bonds according to the rules of the Wobble Base Pairing Code (WC). The long horizontal arrows show the bonding scheme of the WC. The table at the bottom of page 2 of the Second Table on the left also shows the bonding scheme of the Wobble Code (WC). The WC is vital to our existence. I will thoroughly explain the WC below and give examples, so bear with me.
Human cells are defective in four primary regards:
- Our cells create mutations (errors) as a result of defective DNA replication.
- Our cells produce defective proteins as a result of errors in protein synthesis.
- Our cells age. Human cells can only divide 70-80 times, then become senile and eventually self-destruct. Human cells have the gene for the enzyme telomerase but with the Fall in the Garden, it became inactive. The DNA molecule is directional. Human cells lack the ability to replicate their DNA in both directions, going from right to left and left to right or more precisely, from the 3′ to 5′ direction and the other way, i.e., the 5′ to 3′ direction. The enzymes necessary to replicate DNA in both directions were also lost with the Fall. If human cells could replicate their DNA in both directions, their telomeres would not shorten, and their cells would become immortal. Active telomerase would ensure that any accidental damage done to the ends of the chromosomes would be quickly repaired. Re-implementation of both these systems would eliminate the aging process. The following slightly modified (for readability) quote taken off the internet is given as the reason as to why DNA is replicated in only one direction: “The need for accuracy probably explains why DNAreplication occurs only in the 5′-to-3′ direction. If there were a DNA polymerase that added deoxyribonucleoside triphosphates in the 3′-to-5′ direction, the growing 5′-chain end, rather than the incoming mononucleotide, would carry the activating triphosphate. In this case, the mistakes in polymerization could not be simply hydrolyzed away, because the bare 5′-chain end thus created would immediately terminate DNA synthesis. It is therefore much easier to correct a mismatched base that has just been added to the 3′ end than one that has just been added to the 5′ end of a DNA chain. Although the mechanism for DNA replication seems at first sight much more complex than the incorrect mechanism described earlier, it is much more accurate because all DNA synthesis occurs in the 5′-to-3′ direction.” However, as you will see below, digital DNA replication will eliminate the need for this immediate error correction, since the DNA polymerase will always be presented with the correct base by the digital system, i.e., by the 2-bit DNA Decoder (see attached decoder.pdf). It’s also interesting that this article never mentions that it is the cell’s inability to synthesize DNA in both directions that is the cause of aging. Every time there is a cell division, the ends of our chromosomes shorten by a significant amount until the cell can no longer divide. This shortening is caused by our cells’ inability to synthesize DNA in the 3′-to-5″ direction. As the length of our telomeres shortens because of cell division, the ends of our chromosomes become more and more exposed and eventually damaged, thus our cells become senile and eventually self-destruct or may become cancerous. For our cells to divide our chromosomes must have a telomere the length of at least one Ozaki fragment on both ends, i.e. telomeres a total length of about 100-200 nucleotides (bases) on both ends.
- Our cells employ simple diffusion as the method used to transport critical molecules such as the DNA bases (A, G, C, U/T), messenger RNA (mRNA), and transfer RNA (t-RNA) to their respective bonding sites.
The logic equations that you see in the First and Second Tables, if implemented inside human cells, would eliminate 100% of errors in protein synthesis. Using the same optimal bit assignments (A = 00, G = 01, C = 10, U = 11) that are for protein synthesis, the attached 2-bit DNA Decoder, if implemented in the nucleus of human cells, would eliminate 100% of all human mutations. In the DNA Decoder, T (thymine) is substituted for U (uracil). All DNA in nature (no exceptions) uses AGCT as its bases. All RNA uses AGCU, no exceptions. However, the DNA Code is typically represented on the internet and in biochemistry books using U (uracil) as the base, so I will follow convention.
The first digital network titled RNA Logic Network and Synthesis shows the digital network whose outputs have implemented these equations. If this network was inserted into every cell in the human body at the ribosome, it would eliminate 100% of errors in protein synthesis. It is amazing that this network requires 40 simple AND/OR gates. I have counted them many times. I have two other networks, one for the Mitochondrial Code and one for the Standard Code with Selenium. Selenium is often referred to as the 21st amino acid. It is amazing that these networks use the identical optimal bit assignment and also require 40 gates. Neither had to. It’s just the way the math worked out. I did not include these networks and their explanations. They are beyond our scope.
The second network is titled 2-Bit DNA Decoder. No simpler digital network can exist. It is remarkable that the insertion of this simple network into the nucleus of every human cell would eliminate 100% of errors in DNA replication and thus eliminate all mutations. I believe that Jesus can implement these equations in human cells. Jesus is an amazing engineer.
These logic equations will not eliminate aging. However, I believe that by greatly reducing the need for cell division and protein synthesis, these equations would greatly slow down the aging process to the point that we might live for thousands of years. With the reactivation of telomerase to replenish the ends of our chromosomes our cells would again regain immortality, and we would become physically immortal again, just like Adam and Eve before the Fall.
It is a fact that any Boolean logic equation equals a unique minterm sum. Consequently, any logic equation can be expanded to its unique minterm sum and any minterm sum can be simplified to its unique optimal logic equation.
Minterms are specially designed one term Boolean logic functions, hence they are “minterms.” Using the amino acid alanine in the First Table as an example note that it is equal to the minterm sum m24 + m25 + m26 + m27 that equals the logic equation on the extreme right that you see for alanine. Look at the first minterm for alanine which is minterm 24 (m24). The codon found in nature for this minterm is GCA. The code based on the optimal bit assignment (A = 00, G = 01, C = 10, U = 11) is 011000. When this code is entered into this minterm, the minterm evaluates to 1. 011000 = the decimal number 24, so that a minterm always evaluates to 1 when the binary code equals the decimal value of the minterm. Now for another example, look at the GCU codon for alanine. The code is 011011 and the decimal value of the code is 27. When this code is entered into m27 the minterm evaluates to 1. 011011 = the decimal number 27. This is the way minterms work, so that the four codes for alanine evaluate to 1 for the logic equation that you see for alanine, which equals the minterm sum m24 + m25 +m26 + m27. None of the other binary codes that you see in the First Table, or the Second Table, will evaluate to 1, when entered into the logic equation for alanine, but only these 4 codes. And ditto for each amino acid and its logic equation.
This is why we can say that each amino acid equals its logic equation. If you examine Dr. S’s networks, you will discover that he agrees with me. Truly, for example, phenylalanine (Phe) = JKLMN . Why? When this logic equation evaluates to 1, a pathway or gate is opened just as in a computer, that transports the AAG anticodon to the aminoacyl site (A-site) of the ribosome where the anticodon/codon bond is made. The codon is either UUC or UUU and the code for these codons is 111110 and 111111 respectively. This is done with 100% accuracy.
About every fifth protein (20%) in human protein synthesis contains an error, i.e., an incorrect amino acid. The average human body synthesizes 3.0e+ 20 proteins per hour. This is 3 times 10 raised to the 20th power so that the number of defective proteins per hour is about 6.0e + 19 proteins. This is an enormous number of potentially defectives proteins per hour. Only a digital system can produce this number of proteins per hour (3.0e + 20) with perfect fidelity.
The next paragraph is not critical so you can skip it, but I hope that you won’t.
The difficulty of solving the math problem lies in determining the optimal assignments of the 64 minterms to the 20 amino acids and stop signal. The optimal assignment of the minterms to the 20 amino acids and the stop signal will provide the optimal bit assignments to the four bases AGCU. There are 24 different ways to assign 2-bits to the four bases (AGCU). Every time the bit assignment changes the code and the corresponding minterms change for each amino acid. Optimal simplification of 6-variable minterm sums can only be accomplished by a specialist like Dr. S. In order to optimize the minterm sums for each amino acid meant that Dr. S. had to optimize 24 times 21 = 504, 6-variable minterm sums and then determine which one of the 24 possible sets of 21 logic equations was the optimal or best set. This best set will provide the optimal bit assignment to the bases. Best or optimal equals the fewest number of gates necessary to create the corresponding digital network. Next, he had to actually create the digital network to represent these best/optimal 21 logic equations. I have attached again his tables and digital network for the Universal Code, Universal Code with Selenium, and Mitochondrial Code. It’s a piece of work to say the least. The above Tables are only for the Standard or Universal Nuclear DNA Code.
It took me ten years to phrase the logic problem on which these tables are based. I hope that by now you might get a glimpse of why I had so much difficulty in phrasing this problem. It took a year to get Dr. S. to refine his work so that it might be understandable. If I hadn’t thoroughly mastered digital logic and Boolean algebra, I would have been lost. The final tables and networks are beautiful in their simplicity, and there are no mistakes. I checked everything. He was impressed that I checked all his work.
I would like to shift to the Second Table. To the left of the Amino Acid column are the anticodon/codon assignments for each amino acid for the nuclear DNA Code in vertebrate cells. Mitochondria have a slightly different DNA Code. The Wobble Base Paring Code (see bottom left second page of the Second Table) reduces the anticodons to twenty-five anticodons (out of a possible 64), and thus there is the need for only 25 t-RNA molecules out of a possible 64. The forty-four codons for the twenty amino acids and three Stop Codons eliminate 17 codons out of a possible 64. Each amino acid has its own unique binary code and logic function seen to the right of the amino acid column.
Below are some conclusions:
- Locate the “Amino Acid” column Second Table. For protein synthesis our current cells operate on the Anticodon/Codon column to the left of the Amino Acid column. Everything to the right of this column including the Code column and Logic Equation column was destroyed in the Garden of Eden when Adam and Eve ate the poison fruit. Our cells are operating on a DNA Code that Jesus designed for single cell organisms.
- Note how there are about half as many anticodons as there are codons. Jesus carefully assigned to each amino acid a cadre of codons based on the base pairing code internal to the DNA Code that I call the Wobble Code (WC). The bonding rules provided by the Wobble Code greatly reduce the genomic damage done when a mutation (error) occurs during DNA replication at the third base (3′ base in the codon) position of the codon. In addition, the Wobble Code, by elimination of 50% of the t-RNA anticodon molecules andtheir attached anticodons, that are necessary for protein synthesis, greatly increases cellular efficiency and greatly reduces errors in protein synthesis. Essentially, the Wobble Code allows us to live our allotted 80-90 years.
- Even though most of you don’t know Boolean algebra, I believe that you can still appreciate the incredible simplicity of the logic equations that are the result of the Super Mind that simultaneously created an optimal biochemical internal bonding code for the DNA Code, i.e., the Wobble Code (WC) and these incredibly simple logic equations. The incredible reduction of anticodons for each amino acid and the incredible reduction of terms and variables resulting in the incredibly elegant logic equation for each amino acid is the result of the Mind of the Deity (Jesus) that possessed the super knowledge to optimally assign to each amino acid a unique group of codons that achieved both goals.
- The DNA Code as it exists in nature is a thing of beauty beyond words to describe it. The so-called “degeneracy” of the Code allows the digital half of the Code to exist. The DNA Code is referred to as being “degenerate” because most of its amino acids are assigned multiple codons, but it is the very “degeneracy” that creates the beautiful logic equations while the WC eliminates any problems caused by “degeneracy” and also minimizes a mutation in the 3′ base (3rd base position) of the codon. For example, in the GCA codon that codes for alanine, the 3′ base or third base position of the codonis occupied by the base adenine (A). If there is a mutation in an exon in the genome that changes the A to G in this codon, it will still bond with CGU which is the anticodon for alanine. This is because of the rules of the WC that allow the GCA codon or GCG codon to bond with the CGU anticodon.
- No one knows why the bonding scheme of the Wobble Code even works. That’s why it’s called the Wobble Hypothesis. It works because Jesus upholds the execution of the DNA Code so that we can live. Life is a miracle. Living cells are miracles. No one can understand Life. Life is beyond the human mind to understand. Having said this, let’s explain the Wobble Code (WC) known as the Wobble Hypothesis. Although there may be multiple codons assigned to one amino acid (see the left side of the First Table), no codon codes for or outputs more than one amino acid. There are no exceptions to this rule for any living organism, but we are only concerned with the Vertebrate Code. The WC demonstrates the incredible intelligence and power of the Deity. What does “wobble” mean? Using the alanine codon GCA as an example, according to the bonding rules of the DNA Code, the anticodon CGU should only bond to the GCA codon. However, the WC rules state that if G occupies the third codon position (the 3′ base in the codon), it can “wobble,” and thus G can also bond with U. So the anticodon CGU can bond with both the GCA and GCG codons that Jesus assigned to alanine, thus eliminating the need for a CGC anticodon. Jesus organized the codon assignments to each amino acid so that the WC rules can be applied to almost every pair of codons in the DNA Code!This thus eliminates almost 50% of the anticodons necessary for protein synthesis and also mitigates the harmful effects of a genomic mutation in the base occupying the third codon position, with no violation of the rules of the DNA Code. I said “almost” because there are exceptions that defy a good explanation. I think the most important exception involves the AUG codon that codes for methionine (Met). The (Met) codon is quite important because it is the Start Codon that initiates the translation process as well as coding for methionine. The codons for isoleucine (Ile) are AUU, AUC, and AUA. The anticodon for AUA is UAU. Because the AUG codon has G in its third base position, according to the rules of the WC, theoretically it should also bond with the UAU anticodon which is an anticodon for Ile. However, this would violate the fundamental rule of the DNA Code which states that a codon/anticodon bond cannot output more than one amino acid. But the WC does not apply here because the G occupying the third codon position of the AUG codon doesn’t “wobble,” for some reason. Why? No one knows why. It just doesn’t. The AUG codon that Jesus assigned to (Met) has its own unique anticodon UAC. The AUA anticodon UAU of the t-RNA molecule that could theoretically transport (Ile) to the A-site simply will not bond with the AUG codon assigned to (Met). I say “theoretically” because the WC can eliminate the AUA codon from usage inside the cell (see Second Table). This is a clear example of the fact that there are mysteries of life that are beyond human understanding and the Wobble Code (WC) is one of them. In Adam’s cells before the Fall, the WC worked in tandem with the amazingly elegant (simple) logic equations to provide absolutely optimum cellular efficiency and elimination of cellular errors at all levels, i.e., DNA replication, RNA transcription, and protein synthesis. In addition, the digital networks that Adam’s cells possessed did not interfere in the least with the execution of the chemical DNA Code as it exists today. Using the GCA and GCG codons for (Ala) as an example (see Second Table), when the logic equation for (Ala) goes to 1, the gate in the digital network of the Universal Code for (Ala) is opened and the CGU anticodon for (Ala) is instantaneously transported to the GCA or GCG codon setting on the A-site of the ribosome. The enzyme makes the correct chemical bond according to the bonding rules of both the DNA Code and WC, which is the CGU anticodon. But suppose there are multiple anticodons. Arginine has four codons and two anticodons (see Second Table). When any of the four (Arg) codons set on the A-site, the digital network will instantaneously present the two anticodons GCG or UCU for (Arg) to the enzyme that makes the codon/anticodon bond at the A-site. The enzyme will choose the correct anticodon to make the correct bond almost every time, but suppose it makes an extremely rare mistake? It doesn’t matter because both anticodons code for (Arg). Therefore, this digital process provides 100% fidelity, and diffusion cannot cause a mistake. A digital network eliminates the error caused by diffusion in DNA replication, RNA transcription, and protein synthesis. Diffusion is the culprit that introduces error into the cell.
- There appears to be one optimal bit assignment for the Universal Code, the Universal Code with Selenium, and the Mitochondrial Code, for all vertebrates. This is for DNA replication, transcription to messenger RNA, and translation into protein. This bit assignment is A = 00, G = 01, C =10, U/T = 11. If our cells were once digital, it would make no sense for there to be more than one universal cellular bit assignmentfor all cellular digital networks for all vertebrate cells. Optimally, all cellular digital networks should use identical bit assignments, and they do.
- In addition, the optimalbit assignments should theoretically be complementary, and they are. The complement of (00, A) is (11, U/T). The complement of (01, G) is (10, C). This is for the entire cell. It allows for excellent error correction for the binary code assigned to the DNA and RNA molecules. This is quite remarkable. Only a Super Mind could accomplish such a feat.
- Our current cells operate on the diffusion principle to achieve DNA replication, transcription to messenger RNA, and protein synthesis. At the level of replication and transcription there is only a 25% chance that the correct base will arrive (diffuse into the replication site) to make the correct bond. This is because there are four bases (A,G,C,U/T). This works out to about one mutation per cell division for DNA replication. The human body experiences 80 trillion mutations per year as a result of defective DNA replication under the best of conditions. Diffusion results in an error rate (mutation rate) of about one mutation in a billion, to one mutation in ten billion bases, under the best of circumstances. Because you may not eat the right diet, don’t exercise enough, get the right amount of sleep, and expose yourselves to carcinogens, your mutation rate is probably significantly higher than this. This is why you get cancer. The more mutations you accumulate the more likely you are to develop cancer.
- At the translation level at the ribosome, since there are at least 25 anticodons competing for bonding with the codon that sets of the A-site, the error rate for an incorrect bond is much higher than for DNA replication and RNA transcription. Because of diffusion, the error rate for protein synthesis is about one incorrect amino acid per 1,000 to 10,000 codons under the best of circumstances or about one incorrect amino acid for every five proteins. Thus about 20% of your proteins will contain an incorrect amino acid. This doesn’t sound like much, but it is. The number of proteins per hour synthesized by the human body is 3.0e + 20, so the number of defectiveproteins per hour equals 6.0e + 19 or 6 times 10 raised to the 19th Because you may not eat the right diet, exercise enough, get the right amount of sleep, and may expose yourselves to carcinogens, your error rate is probably significantly higher than this. Diseases like Alzheimer’s dementia are a result of defective synthesis of proteins. The defective proteins accumulate inside the neurons causing them to malfunction.
- How does a 2-bit DNA Decoder work? DNA replication is semiconservative. To occur it requires the preexistence of a functioning intact DNA molecule. The enzymes do not exist in nature to synthesize DNA de novo. This alone should be enough to disprove evolution.In current human cells at the replication fork where the daughter strand is being created using the parent strand as a template, the DNA polymerase because of diffusion stands only a 25% chance of receiving the correct base. If the base that diffuses in is an incorrect base to make the bond, the polymerase must reject it and hope that the next base that arrives by diffusion will be the base for the correct bond and so on until the correct base finally arrives. The more rejections that occur the more likely for an incorrect bond to occur and thus a mutation. Why all this? It is because there are four bases, A, G, C, or T and each one arrives by chance by diffusion. However, if you are not eating the right diet and there is a paucity of a particular base, the chances of a mutation because of a mistake are much higher. Therefore, to accurately replicate twelve billion bases (diploid number of bases or your 46 chromosomes), under the best of circumstances, the polymerase must answer an average of 48 billion yes/no questions with 100% accuracy for a successful replication without a mutation, i.e., to accomplish one cell division with 100% accuracy. It simply cannot do it. Mistakes are inevitable. A mistake in DNA replication is a mutation. A 2-bit DNA Decoder inserted into the replication fork guarantees 100% accuracy in DNA replication. Pull the Decoder attachment up and look at it. For example, when A (00) sets on the active site where the polymerase makes the bond, which is the JK input of the Decoder, JK = 00, M0 evaluates to 1 (0’ x 0’ = 1 x 1 = 1) and the gate for T (thymine) is opened. The digital system instantaneously supplies the polymerase with a thymine molecule and the correct bond to adenine is made with 100% accuracy. But what if the polymerase makes a mistake and decides that thymine is not the correct base to bond with adenine? It doesn’t matter. The Decoder simply supplies another thymine molecule until the polymerase accepts adenine and does make the correct bond. However, it would be an extremely rare occurrence for this to even happen. Diffusion is eliminated from the replication process. There can be no mutations. Since the current human body requires 80 trillion cell divisions per year to maintain itself, this works out to a minimum of 80 trillion x 48 billion = 3.84e + 24 yes/no questions that must be asked and answered correctly for the human body to accurately replicate its DNA each year. This is an enormous number. One mutation per cell division under the best of conditions works out to 80 trillion mutations per year. This is why you die of cancer. Only a digital system in the form of a simple 2-bit digital decoder can be up to successfully accomplishing this demanding task. And this doesn’t take carcinogens into account. 80% of all human mutations are caused by carcinogens.
- If you are not a bacterium or a lower organism, diffusion is a terrible way to design a cell. Diffusion means that our cells have error built into them. Bacteria and viruses thrive off of mutations. They are not bothered by defective proteins. However, mutations and defective proteins kill us. Implementation into our cells of the right side of the Second Table by Jesus would replace diffusion with digital networks. These networks would eliminate all cellular errors. A cell that doesn’t create error and that doesn’t age is immortal. If all the cells in the human body are immortal, the human body is immortal.Our immortality that was lost in the Garden can therefore be regained by the omnipotent power of the Deity. In fact, I would argue that it is easier for Jesus to re-implement our immortality than it was for Him to destroy it and still leave a profane, but adequately functioning human body.
In sum literally everything points to the fact that the cells of Adam and Eve before the Fall were light years superior to human cells of today. We are missing 99% of our original genome. 67% of our genome is retroviral in origin because it contains the enzyme reverse transcriptase. It is known as junk DNA. 30% is intronic containing no coding information. Out of the remaining 3%, only 1% is exonic. The exons are the genes that contain the code for our proteins. The bodies of Adam and Eve were immortal. They possessed a complete set of genes and could metabolize fats, proteins, and carbohydrates to carbon dioxide, nitrogen, and water. They also had all the genes, hence the metabolic pathways, found in nature in the various bacteria and lower organisms and also marvelous genes that we can know nothing about. The disastrous loss of this genetic information as a result of the genetic poison is why they became ashamed of their nakedness after the Fall and why they died. Their bodies almost immediately began to produce the human waste that our bodies produce today, and they began to age.
Now you might argue that implementation of digital networks into human cells is all but impossible. But consider this. The haploid human genome contains about 6 billion bits of information (three billion base pairs, consisting of sense and nonsense strands with each sense stand worth 2-bits) or about 750 megabytes. A CD is worth 750 megabytes. A four-minute song on a CD is worth about 37.5 megabytes. Only about 1% of our genome codes for protein which is 7.5 megabytes. Of these 7.5 megabytes a typical cell, because of a process known as differentiation, utilizes only 10-20% of this or about 1.5 megabytes. This amounts to about ten seconds of a song on a CD. I would maintain that this fact is more “impossible” for Jesus to accomplish and still keep us alive for 80 years, than re-implementation by Jesus of these digital networks into our cells. It is a miracle that we are alive at all. We are living off of an incredibly small amount of genetic information.
I have always had a fascination with the DNA Code. I have my original biochemistry book dating back to the early 1970’s. I have a stack of reference biochemistry books. In medical school you learn all the metabolic pathways for metabolism of fats, proteins, carbohydrates, etc. I got A’s in biochemistry in medical school. I have successfully treated many cases of diabetic ketoacidosis (DKA) in the ER. I have not forgotten my cellular metabolism. If I have a question about it, I know where to find the answer. I’m interested in all things DNA including the organization of the human genome. The back third of the biochemistry textbooks is where all the interesting stuff resides. In the 1990’s I, for some reason, had a hunch that the DNA Code was originally misrepresented by Watson and Crick and that it was originally a binary code with each of its bases worth 2-bits. I was incorrect but only partly so. The DNA Code as it exists in nature was once both a chemical code for the lower organisms such as bacteria and a digital computer code for the higher organisms like us. I think these above Tables together with my explanations hopefully provide you more than a glimpse of the Super Mind of Jesus who has the power to re-implement the right side of these Tables inside our cells, and thereby eliminate all mutations and errors in protein synthesis. Thus, cancer and all human disease become horrors of the past tense associated with our sinful past. He also has the power to reactivate telomerase and provide our DNA with the enzymes necessary to replicate itself in both directions, thus eliminating aging.
The coming Millennium will be the age of enduring peace. The immortals of the age will reside within the Millennial Temple as the Lord’s personal servants and priests. The people of the land will continue to possess common or profane physical bodies until the fulfillment of Isaiah 25:6-8 and 1 Cor 15:26 at which time the human genome will again become immortal, and our race will regain the immortality that was lost in the Garden.