By Dr. Charles Ruark
Now that I have finished providing you with an introduction to the DNA molecule, I would like to go on to a more advanced topic that I have been alluding to in the previous teachings. Let me explain.
In the early 1990’s I became interested in “information” as a concept. It took me two years of searching for the books I wanted to read, which I found in the Vanderbilt student bookstore: “Digital Logic Circuit Analysis and Design” and “Structured Computer Organization.” It took me three years of intense study and many trips to the Vanderbilt School of Engineering in order to master the mathematics in these books which are very different from the math you and I learned in high school and college. Because of my contributions to Vanderbilt University and my position as chief of a large outlying hospital emergency department, an associate dean of the University allowed me to audit any engineering course I desired free of charge. The chairman of the engineering school was also very gracious, as were all the engineering professors, in allowing me to attend their classes along with the undergraduate engineering students.
“Lord, show me something about the DNA code that
no one else knows.”
In the mid-1990s, my prayer to Jesus was, “Lord, show me something about the DNA code that no one else knows.” I prayed this over and over.
Then, in probably 1997, I began my study of biochemistry very intensively. I conceived of the possibility of assigning bits (1’s and 0’s) to the DNA Code and developing logic equations describing the DNA code in about the year 1998, and I worked on this intensively for several years by myself. Finally, I gave up. I realized I couldn’t do it by myself and even worse, I didn’t even know how to phrase or explain the problem to get any help. Along with some accompanying articles and materials, I stored all my work in a large briefcase. Several years later, when I went back to revisit it, the briefcase was virtually empty. Somehow, I apparently had accidentally thrown my notes away.
After 22 years of practicing on the urgent side, I retired to the non-acute side of the ER and resigned my chiefship at the end of 2005. I had more time, but it wasn’t until I completely retired at the end of 2010 that I really had the time to pursue my scientific pursuits and my work on the Millennial Temple. However, from around 2005 onward I did do significant work on the Temple because I remember carrying my work to the hospital while working on the non-urgent side of the ER.
The fateful day came probably on about March 28 or 29, 2012, when I was very relaxed and on the treadmill in the middle of the afternoon. My mind returned once again to the stubborn problem of how to state my logic problem in order to get help in expressing the DNA Code in terms of digital logic equations and binary code. By then I had come to fully realize the enormous complexity of this problem and that even if I could state it (write it down), I could never in a million years solve it. Then suddenly, in a burst of insight, I saw how to do it, i.e., how to at least state it. I immediately got off the treadmill, went to my study, and wrote the problem down because I knew my mind could hold it only for an instant.
I have enclosed what I wrote down in the first attachment to Article 6 titled “Reply” and also the amazing reply to it by a professor of electrical engineering at Vanderbilt University Engineering School. He wishes his name to be withheld, and I will honor his request. Therefore, I will refer to him as Dr. S. I have also enclosed two more attachments, which are an excellent summary of his work. Teresa Benedetti was the secretary to the chief of the electrical engineering department at that time. The equations Dr. S eventually produced provide a theoretical cure for cancer because they provide, if implemented on the molecular level inside the cell, for the elimination of all mistakes/errors (mutations) at the levels of DNA replication, transcription, and translation (protein synthesis). I believe that this would effectively completely eliminate cellular mutation and, thus, cancer and all genetic diseases. It is a fact that a mutation or a set of mutations reside at the heart of every single cancer. A mutation in a critical gene causes a permanently defective protein. It is the defective protein’s deleterious effect on cell division that is the cause of cancer.
Unfortunately for humanity, these equations will be thoroughly suppressed by the scientific community because they eliminate all cellular errors, including the cherished concept of mutation. Since the scientific community maintains that mutation is how humanity arrived on the scene, it has far too much invested in mutation to ever admit that evolution never happened. Plainly stated, these equations and networks overturn the theory/paradigm of evolution because they eliminate all mutations. Evolution, as I have stated repeatedly, cannot occur without natural selection selecting out beneficial mutations over billions of years of time. They clearly show that the DNA code was once a binary code in the higher animals and humans. Therefore, humanity is currently using a substandard or backup DNA code that is the one used by the lower forms of life such as bacteria.
The first attachment, titled “Reply,” contains a concise statement of one of the most original math problems that you will, in my humble opinion, ever see. I don’t expect anyone to understand it. In the 1990’s the technology to solve it did not exist. It requires simplification of over 1,500 six-variable Boolean logic equations in order to arrive at the best solutions. Its solutions provide the optimum assignment of bits to the DNA code, something that has never been thought of before, much less actually done. It turns out that I could not simplify even one of these logic equations that the solutions to this problem must produce, much less 1,500. Furthermore, at the time I wrote the problem down in March of 2012, I did not even know how to begin the approach to solve it. It turns out that my original approach was only partially correct. I had made a critical mistake in setting up the problem, so it was actually best that my work was lost because I could have spent a lot of time trying to solve a flawed problem that, even in its flawed condition, I could not remotely begin to solve. Below is a synthesis of my understanding and Dr. S’s understanding (his approach) to this very difficult problem presented in language that I hope a few of you might understand.
The DNA Code is composed of 64 triplets (three molecules) called codons. The molecules (often referred to as either the bases or nucleotides) of the DNA code are the famous A G C and U or adenine, guanine, cytosine, and uracil. There are 64 possible codons, each codon being a unique combination of three of these four molecules. Therefore, it requires 6 bits (two bits per molecule) to properly assign bits to the molecules of a codon.
Which 6-bit combination did Jesus assign to
each codon of the DNA code?
Six bits creates 64 unique 6-bit binary combinations so that we can assign one 6-bit combination to one 3 molecule codon. The central question which must be answered is: “which 6-bits do we assign?”, since there are 24 different ways (or four factorial which is 4 x 3 x 2 x 1) to assign 6 bits to the 3 molecules comprising a codon. Theologically stated, we want to discover: Which 6-bit combination did Jesus assign to each codon of the DNA code? Let’s try to answer this question.
The Code consists of 4 molecules called nucleic acids or nucleotides (A G C U or adenine, guanine, cytosine, and uracil), so if you assign (00) to A then you are left with (01), (10), and (11) to assign to G, C, and U. It turns out that the solution to this math problem is 4! Which is 4 x 3 x 2 x 1 = 24. 4! is pronounced “four factorial”. There are 4 ways to assign 2-bits to adenine, leaving 3 ways to assign 2-bits to guanine, leaving 2 ways to assign 2-bits to cytosine, and finally 1 way to assign 2-bits to uracil. So, if the DNA code was, in its original state, a binary code, the question becomes: What was the optimum bit assignment (assignment of bits)? Or, to phrase the problem theologically: “What 2-bits did Jesus initially assign to each of these 4 molecules, i.e. the molecules of the DNA code, before its corruption in the Garden by the sin of Adam and Eve?” Let’s try to answer this question.
DNA — the Universal Code
In order to create all the proteins required for all life, Jesus created a Universal Code. Known as the DNA code by science, this Code employs 20 standard amino acids that are used by all Life and a stop or termination signal. In Boolean terms, the stop signal is equivalent to an additional amino acid. As we change the bit assignments to each molecule (A G C U) of the Code, although the codons assigned to these amino acids never change (they are fixed in nature by Jesus), the bits of the codons will change. Therefore, each unique bit assignment to the molecules A G C U, causes each of the 64 codons to have a different bit assignment and thus minterm assignment.
The Concept of a Minterm
At this point, I need to discuss the concept of a minterm. In exactly the same manner that amino acids are the building blocks of proteins and proteins the building blocks of Life, minterms are the building blocks of logic equations and logic equations, the building blocks of digital networks.
It is a fact that every Boolean logic equation can be expressed as a unique sum of minterms, and each output of a digital network is the output of a digital logic equation. Minterms are rudimentary logic equations possessing unique properties. They are the building blocks from which all Boolean logic equations and digital networks are formed. All minterms possess a unique base 10 number (base 10 value), and our problem requires 64 minterms numbered 0…63. In order to answer our question of “which bits” we must assign one minterm to each of the 64 codons. The minterm assigned to a codon is determined by the base 10 value of the codon as determined by the base 10 value of the bits assigned to A G C U. This base 10 value of the codon must match the base 10 number (value) of the minterm.
For example, let’s choose a codon at random by choosing a 6-bit binary number (we have 000000…..111111 or in base 10, 0….63 to choose from). Let’s choose (101101). We see the base 10 value of our codon is 45. Thus, in order to help you understand the complexity of our problem and also to discover the amino acid to which it is assigned, we must choose a bit assignment. Let’s choose for our bit assignment A = 00, G = 01, C = 10, and U = 11. The codon we chose at random would therefore, be codon CUG which specifies (codes for) in nature the amino acid leucine (leu).
In terms of codes, we can write m45 = (101101) = CUG = leu. Note that the codon has a base 10 value of 45. Thus, the minterm assigned to this codon would therefore be minterm45 or m45. In Boolean terms if we use as our variables JKLMNO, m45 = JK’LMN’O. Note that this Boolean expression evaluates to 1, if and only if, the above bit assignment is used. For any other bit assignment, it evaluates to 0. But now, at random, let’s change the bit assignment to the molecules A G C U to say A = 10, G = 11, C = 01, and U = 00. Then CUG = (010011) or in base 10, the number 19. This changes the minterm assigned to CUG to minterm19 or m19, but it does not change the fact that CUG is always assigned to leucine and codes for leucine. Thus, for this bit assignment, we can write m19 = (010011) = CUG = leu. Thus, since there are 24 unique 2-bit bit assignments for A G C and U, there are 24 different 6 variable minterms that we must assign to CUG in order to determine which one is the best for CUG, i.e., the one minterm out of the possible 64 that will help us produce the simplest logic equation possible for leucine.
A Daunting Math Problem
As I hope you are beginning to realize, it’s a daunting math problem. No human could ever remotely solve it without a powerful computer. I also believe that very few can really understand the math behind this problem. It would require someone like Dr. S, who has a Ph.D. in EE and a specialty in the field of digital networks and logic equation simplification, and also a Ph.D. in biochemistry. But I am going to proceed onward. If you are a college student interested in science, with some difficulty, with my help, you may be able to understand this extremely complex math problem. Your reward will be to clearly comprehend that the human being was once digital or the equivalent of digital.
Only digital networks or their equivalent possess the necessary ability to answer the trillions upon trillions of yes/no questions that must be asked and answered every second by the human body with 100% fidelity in order to eliminate cellular errors. I am also going to eventually explain why the culprit causing our demise is the chemical process known as diffusion and why the implementation of digital networks into the processes of DNA replication, transcription, and translation eliminate the process of diffusion from these critical processes. Also, please remember that I am a 75-year-old retired ER physician. If I can understand this, surely you can, and surely your college professors, who are evolutionists and in whom you may have blindly put your trust, can understand these equations and networks and explain why to you they wouldn’t work to theoretically eliminate all mutation, if implemented into human cells.
Let’s look carefully at leucine (leu) which is the amino acid of the above paragraph by examining Table 1 of the second attachment. Note that leu has 6 minterms assigned to it (m44, m45, m46, m47, m60, m61). Thus, we know immediately that Jesus assigned 6 codons to leu. As an example, let’s look at the minterm known as m47. The number 47 has a binary value of (101111). At the top of the table, you will see that the bit assignment to A G C U is A = 00 G = 01 C = 10 and U = 11. So, we know based on this bit assignment that the codon is C (10) U (11) U (11) or CUU. We also know that based on this bit assignment, Dr. S must assign m47 to CUU. However, if we change the bit assignment to the Code as we did in the above paragraph to A = 10, G = 11, C = 01 and U = 00, CUU becomes (010000 = 16), and the minterm assigned to CUU becomes m16. (101111 = 47) becomes codon AGG which Jesus assigned to the amino acid arginine.
If we follow our rule which we absolutely must do, the minterm assigned to AGG becomes m47 because 101111 = 47. Thus, you can see that changing the bit assignment to the Code does not change the codons that Jesus assigned to each amino acid. These were fixed in nature by Him. However, it does change the minterm assigned to each codon and, thus, the minterms assigned to each amino acid. Thus, changing the bit assignment to the Code creates 24 tables similar to Table 1 of the second attachment.
A Real Piece of Work!
Each of these tables are unique in the sense that they possess a unique set of minterms assigned to each amino acid as determined by the bits arbitrarily assigned to A G C and U. Since there are 24 ways to assign 2-bits to A G C and U, there are 24 of these tables. Table 1 shows the results of Dr. S’s work for the Universal Code and the Universal Code with Selenium. It shows at the top the optimum bit assignment to the Code and thus the optimum minterm assignment to each codon of the Code and thus the optimum minterm assignment to each amino acid of the Code. It’s really a piece of work! This bit assignment should be the bit assignment that Jesus originally assigned to the Code.
Note at the bottom of Table 1 that Jesus has assigned codon UGA to Sel (Selenium), which is sometimes referred to as the 21st amino acid. Most of the time, when He varies the Universal Code, He does it by reassigning a stop codon leaving the remainder of the Code untouched. It is recognized even by the most atheistic/evolutionary biochemistry texts that the Universal Code exhibits great intelligence in its design. Table 2 shows Dr. S’s optimum bit assignment and, thus, minterm assignment for the Vertebrate Mitochondrial Code.
Using Leucine as Our Example
Using leucine as our example, let’s examine leucine even more carefully. Every Boolean variable has a complement. To indicate that a variable has been complemented, Dr. S places a solid bar over it. However, we will use an apostrophe to indicate that a variable has been complimented. For example, the complement of J is J’. J + J’ = 1 and J x J’ = 0. The identity elements of the Boolean set are 1 and 0. For 1 and 0 the complement of 0 is 1 and the complement of 1 is 0. Thus, we can write: 0′ = 1 and 1′ = 0. For the bit assignment to the molecules of the Code let’s choose A (adenine) = 00, G (guanine) = 01, C (cytosine) = 10, U (uracil) =11 which is the optimal bit assignment to these molecules as determined by Dr. S.
Table 1 lists the minterms for leucine, which are the result of this optimum bit assignment. Therefore, in Boolean terms, we can write a logic equation for leucine in the form of a logical sum of minterms: leucine = m44 + m45 + m46 + m47 +m60 + m61. For variables JKLMNO, which are the variables used by Dr. S, let’s write out in long hand the minterms for leucine in terms of these variables. Recall that minterms are themselves rudimentary logic equations or logic functions. Minterms are the building blocks of all digital logic equations and digital networks.
m44 = f(JKLMNO) = JxK’xLxMxN’xO’, m45 = f(JKLMNO) = JxK’xLxMxN’xO, m46 = f(JKLMNO) = JxK’xLxMxNxO’, m47 = f(JKLMNO) = JxK’xLxMxNxO, m60 = f(JKLMNO) = JxKxLxMxN’xO’, m61 = f(JKLMNO) = JxKxLxMxN’xO
For the sake of brevity, the “x” sign (times sign or logical product sign) between the variables will be eliminated from now on.
Thus, we can write the logic equation for leucine as a logical sum of minterms: leu = f(JKLMNO) = JK’LMN’O’ + JK’LMN’O + JK’LMNO’ + JK’LMNO + JKLMN’O’ + JKLMN’O
As our example, let’s look at minterm45 or m45: 45 = (101101)
Note that for the above logic equation for leucine, f(101101) = 1, because m45 always evaluates to 1 for the binary number whose base 10 equivalent is 45. Let’s demonstrate this:
m45 = JK’LMN’O so based on the input value (101101) and substituting 1 or 0 for the variables we see that 1×0’x1x1x0’x1 = 1x1x1x1x1x1 =1. Recall that 0′ = 1 and 1′ = 0.
Now, as an example, let’s look at m47 which is JK’LMNO and substitute (101101 = 45) into it. Let’s see what happens. We get 1×0’x1x1x0x1 = 1x1x1x1x0x1 = 0. In Boolean algebra 1×0 = 0 and 1×1 = 1. So, after a substitution, if (0) appears in the logical product, the product becomes 0. We can do this same substitution for m44, m46, m60, and m61 and demonstrate that for (101101 = 45), they all evaluate to 0, but for the sake of brevity we won’t.
It is a fact that no other minterm in our network other than m45 will evaluate to 1 for the binary number (101101) which has a base 10 equivalent of 45. For example, m63 (m63 = JKLMNO = phenylalanine in our network) evaluates to 1 for the binary number (111111 = 63) and to 0 for any other 6-bit binary number in the range 000000…111111. This is a fundamental property of minterms. Electrical engineers like Dr. S can work with logic equations of many variables, but there is a practical limit to the number of variables because the more the variables composing the minterm the more complex the logic equations become and thus the more expensive the digital network and the heat it generates.
Every time you add a variable you double the number of minterms that you must work with in order to create your logic equations because all the minterms must be considered and possibly used. So, a 10 variable digital network requires 2 to the power of 10 or (1,024) 10 variable minterms. A 20 variable network would require 2 to the power of 20 or (1,048,576) 20 variable minterms! Simplifying over a million 20 variable minterms would, I suspect,t be a daunting task even for Dr. S.
Thus any 6 variable logic equation in the universe that contains the 6 variable minterm known as m45 will always evaluate to 1 when the binary number (101101) shows up at the input. And, most importantly, unless the equation contains m45, when (101101) is substituted for the variables of the equation, the logic equation will always evaluate to 0. All digital logic rests on these facts. There are 2 to the 64th power of possible unique 6-variable logic equations. That’s equal to the base 10 number 16 with 18 zeros after it or1.6 e + 19. Any of these logic equations containing m45 will evaluate to 1 when (101101) is substituted into the equation.
So, what would be the logic equation for leucine that contains the minterms m44, m45, m46, m47, m60, and m61 as expressed in simplest terms? This is where Dr. S. comes in. This is how he makes his living. As I mentioned, it takes a skilled electrical engineer and a powerful computer to reduce even one 6 variable logic equation to its simplest terms. Let me explain.
Below is the logic equation (or function) for leucine reduced to its simplest form as determined by Dr. S.:
Leu = (K N)’ JLM
Therefore, we can write leucine = (K N)’ JLM as a sum of the minterms JK’LMN’O’ + JK’LMN’O + JK’LMNO’ + JK’LMNO + JKLMN’O’ + JKLMN’O = (K N)’ JLM = leu
As a test of Dr. S’s competence, let’s see if f(101101) evaluates to 1 for (K N)’ JLM. It should because (KN)’JLM should contain m45 if Dr. S has done his job. We see that for (101101) J = 1, K = 0, L = 1, M =1, N = 0 and O = 1. Therefore, substituting we see that (0x0)’x1x1x1 = 1 because 0x0 = 0 and 0′ = 1. Therefore 1x1x1x1 = 1. Since the variable O has been eliminated its value can be ignored. As another example, let’s look at m61. m61 = JKLMN’O. 61 = (111101). Substituting (111101) into m61 we get 1x1x1x1x0’x1 = 1. Substituting (111101) into (KN)’JLM we get (1×0)’x1x1x1 = 0’x1x1x1 = 1. Thus, we see that whenever (101100 = 44), (101101 = 45), (101110 = 46), (101111 = 47 ), (111100 = 60), or (111101 = 61) shows up at the input of our network, since leucine = (KN)’JLM is formed by a logical sum of these minterms, leucine will evaluate to 1, because all that’s needed is for one minterm out of these six to be 1 for the equation to evaluate to 1. (In Boolean algebra 1 + 0 = 1). Otherwise, for all other possible 6-bit inputs (range is 000000….111111) leu will evaluate to 0. Thus, we see that (KN)’JLM is truly the logical sum of the above 6 minterms of 6 variables because if the outputs of the two equations/ functions are the same for each and every input, then the two equations/functions must be equal. All digital logic rests on this simple fact. It is absolutely amazing that this 6 minterm 6 variable equation reduces to a one-term equation of 5 variables!
I would challenge any Double E to design a meaningful 6 variable digital network containing more elegant logic equations, than those produced by the Universal DNA code.
The Numbers 40 and 4
The second attachment is a summary of Dr. S’s work. Below Tables 1 and 2 are his networks. His networks are extremely elegant. His networks show that the network for each Code (Universal, Universal with Selenium, and Mitochondrial) is composed of exactly 40 gates! 40 is the biblical number for judgment and indicates the judgment of Adam and Eve for their sin. Also, the third attachment shows that simple 4 gate networks located inside the cell nucleus will eliminate all mistakes in DNA replication and transcription.
Four is the number of creation and completeness. The DNA code became incomplete with the destruction of this network by the sin of Adam and Eve. I mention that replication and transcription occur in the cell nucleus. Translation occurs in the cytoplasm. It is extremely important for me to state that if these networks were reinserted into our cells, they would not interfere with the way our cells work right now. The only difference is that all cellular errors would cease immediately. All current biochemical processes would not change at all. Thus, the DNA code, as it exists in nature, appears to be designed to produce three extremely elegant digital networks all with the same optimum bit assignment and same number of gates (40). These networks also allow for a 2-bit DNA decoder (which is the optimum 4 gate network) to operate inside the cell nucleus for DNA replication and transcription. This 2-bit decoder would use same optimum 2-bit bit assignment that would be used in the cytoplasm for translation. Jesus chose His Code well!
Discovering the One Simplest, Most Elegant Digital Network
Ultimately, we are trying to discover the one simplest most elegant digital network (the one with the fewest number of gates) that will describe the DNA code, from the 24 possible digital networks that that will be produced by the 24 unique 2-bit bit assignments to the Code. This optimum network will consist of 21 digital logic equations, one for each of the twenty amino acids and a termination (stop signal) equation. The network with the fewest number of simple gates should be the Digital Network that Jesus would have implemented inside of every cell for all complex organisms.
Because Jesus is God and everything He does must be perfect, this Network should be as universal as the Standard or Universal DNA code as it now exists in nature. Also, the Network and its equations should be extremely elegant and simple once simplified. There should be one best bit assignment and this bit assignment should be essentially universal or standard inside the cells of all complex Life. In other words, if Adam and Eve were truly digital, in every respect and property, their Code should look like it was designed to be a Digital Code or Boolean Code. As I will explain below, there is a caveat: simple organisms do not need a digital code because mutations and errors in protein synthesis don’t harm them. In fact, mutations may actually be beneficial for them.
24 Variations
Therefore, for completeness sake I should mention that there are 24 variations found in nature to the Standard DNA code. These variations are unimportant to our analysis. Jesus may have had His own very important reasons for these minor variations. In my opinion these minor variations in no way diminish the universal properties of the DNA code for higher organisms. In fact, it is probable that Jesus did not supply simple organisms with digital networks because, as I mentioned, there is no evidence that mutations and errors in protein synthesis harm them.
The current Code, as it exists in nature, works fine for them. But for us, mutations and errors in protein synthesis can be extremely harmful. They are one of the main reasons we die. I believe that before the Fall, the bodies of Adam and Eve possessed very sophisticated cells, all with digital DNA Codes, digital chromosomes, and digital networks throughout their cells. I believe that the cells of simple organisms were much less sophisticated and did not possess these digital networks, etc.
It is very possible that many of the more complex multi-cellular organisms also possessed digital networks etc. The complexity of many organisms fall in between bacteria and humans, and we may never know the ones possessing digital networks before the Fall. It really makes no difference to us and poses no problem for our hypothesis concerning Adam and Eve. After the Fall, every organism on this planet possessed essentially the identical DNA Codes and herein is where the problem lies for us. Mutations have little to no effect on viruses, bacteria, algae, fungi, etc. In fact, they are critical for the survival of viruses. However, mutations kill us.
It is vitally important to understand that for protein synthesis, the codons assigned to each amino acid and termination signal have never changed. They were fixed in nature by Jesus before the Fall. However, in order to solve our problem, the minterms that can be assigned to these codons can and must change, because it is our job to determine which one of the 24 possible minterms (that can be assigned to each of the 64 codons) is best in terms of creating the digital networks that I believe Jesus originally created inside of every human cell.
As you can see, it is a daunting task which may be the reason no one has ever to my knowledge done it before. Before the Fall, there could have been thousands to millions of these networks floating in the cytoplasm and nucleus of every human cell. In addition, I believe that about 99% of the genes in our chromosomes were destroyed by the Fall. So, our bodies are now operating while missing 99% of our original genetic information.
The Fall Decimated the Human Genome
An E. Coli bacteria possess about 5,000 genes. Humans possess only about 20,000 genes. However, the number of base pairs or nucleotide pairs (A G C U) in our 46 linear chromosomes (the diploid genome) are 6 billion compared to 4.6 million for an E. Coli. The genome of an E. coli consists of one circular chromosome. Although the human body is far more complex than an E. Coli, our genomes possess only 4 times more genes than that of an E. Coli bacterium, but our chromosomes are 1,300 times larger. Now I think you can a little better understand why we die. The Fall decimated the human genome. It’s a wonder we are living at all.
Each of the 24 unique 2-bit bit assignments produces 21 unique 6 variable Boolean logic equations based on the minterms used to form them. These logic equations are the functions f(0)…..f(20) you see described in my statement of the problem in the first attachment. These functions are equivalent to the amino acids and stop signal.
In nature, there are actually 3 DNA Codes: Universal or Nuclear, Universal or Nuclear with Selenium (Selenium is sometimes considered the 21st amino acid), and Mitochondrial (mitochondria exist in the cytoplasm outside the cell nucleus). 21 x 24 = 504 and 504 x 2 = 1,008 6-variable logic equations for the Universal and Mitochondrial Codes that must be created and simplified in order to obtain the good/best networks and the optimum bit assignments for these Codes. For the Universal Code with Selenium there are 22 x 24 = 528 6-variable logic equations that must be formed and simplified for a total of 1,536 equations for the three Codes. There could be more than one good/best bit assignment and good/best set of equations. I could not simplify even one of these 6-variable equations, much less over 1,500. It takes an engineer very skilled in simplification of these types of equations and a powerful computer to do so.
That’s where Dr. S came in. He possessed the expertise, but I first had to figure out how to state the information contained in the above paragraphs very succinctly in Boolean terms, i.e., to pose the problem in terms of a theoretical digital logic problem, in order to find someone of his caliber and abilities. Dr. S has a PhD in electrical engineering. It took me about 10 years to bridge the gap between the information that I have shared with you in the above paragraphs and the theoretical digital logic problem posed in the first attachment, which is stated in terms of Boolean logic. His interest and response was quite miraculous. It is also miraculous that by the time I figured out how to correctly state the problem in terms of digital logic, the technology had become readily available in order to solve it. As you know, there have been tremendous advances in computer power over the last two decades.
I am sure you can imagine my excitement when I received an almost immediate positive response to my email. Over the next year, I met with Dr. S probably four times at a Starbucks close to Vanderbilt University. He is from Michigan, was about 35 years old at that time, and was probably an agnostic or atheist. However, we never discussed religion or our worldviews. He made it clear he didn’t want to. Once he understood my goals, for him it just became a matter of producing the best equations. I believe he was surprised at the elegance of the equations and that the very best equations all produced complementary bit assignments, but we never discussed their religious or scientific implications. He simply didn’t want to. I did ask him if, in his opinion, implementation of these equations and bit assignments inside the cell would eliminate cellular mutation and errors in protein synthesis. I also asked him if the digital networks produced by these equations could be made small enough to be feasible to be implemented inside the human cell. His answer was in the affirmative to both questions.
All It Takes Is One Mutation…In One Cell To Cause Cancer
During normal operation (no cell division) in order to produce proteins, I estimate that the human body with its 80 trillion cells must do 160 million trillion digital operations every second of everyday without possessing digital networks. In regard to cell division (DNA replication) as I will further explain below, mistakes pile up in the form of trillions and trillions of mutations over the course of a human lifetime. All it takes is one mutation (error) occurring in a critical area of a critical gene in one cell to cause cancer. However, since about 99% of the human genome (our 46 chromosomes) exists in the form of noncoding DNA, much of which (about 66%) is absolutely totally useless, mutations are, for the most part, fairly harmless. Also, the Codes in their present forms are carefully designed to mitigate potentially harmful mutations occurring in our genome. Nonetheless, extremely harmful mutations in the form of repetitive production of dangerously defective proteins obviously do occur despite the best efforts of the cells of our bodies to prevent them, correct them, or mitigate the effects of them. The results of these mutations that occur in critical genes take the form of cancers and genetic diseases. Digital networks simply don’t make the trillions upon trillions of mistakes that occur within our bodies over the course of a lifetime. They don’t make any mistakes.
In all cells as they exist today amino acids carried by transfer RNA arrive at the active site of the ribosome by diffusion by pure chance. The active site of the ribosome is where protein synthesis occurs. Each transfer RNA molecule has an anti-codon that must correctly bond to its codon or codons (see my explanation of the Wobble Hypothesis) for the correct amino acid to be added to the protein chain. The probability that the arriving amino acid will be the correct one for a correct bond to occur is only about 10-20% per bonding attempt. Thus, the ribosome must make multiple bonding attempts (about 40 to 80 per second) for one correct bond to occur. A ribosome typically adds about 8 amino acids per second to the growing protein chain.
To Make A Perfect Protein
To make a perfect protein typically requires about 400-500 correct bonds and probably 4,000 bonding attempts. One correct bond results in one correct amino acid being added to the protein chain. A human cell contains about 10 to the 10th power of proteins and up to ten million ribosomes. And that’s where the mistake or malfunction can occur.
Sometimes the enzyme makes a mistake. It allows an incorrect bond to occur and thus fails to reject the multiple incorrect amino acids arriving by random chance at the active site of the ribosome. The error rate of the enzyme is about 1 in one thousand to 1 in ten thousand. In regard to DNA replication, in the cell nucleus there are 4 possible nucleotides (adenine, guanine, cytosine, or thymine). Thus, there is about a 25% chance of the correct nucleotide arriving at the enzyme’s active site. Thus, for a correct bond to occur, the enzyme must accurately reject about 75% of the nucleotides arriving at its active site. The enzymes add about 50 bases per second and so must make about 200 bond attempts per second during DNA replication.
The error rate (mutation rate) of the enzymes under the best of circumstances is 1 in ten billion bonds and more typically, 1 in 6 billion bases. Therefore, every time a cell replicates one would expect about one mutation. The human body experiences about 80 trillion replications or cell divisions per year. Thus, over the course of 80 years, under the best of circumstances, the human body experiences about 6 quadrillion mutations because of faulty DNA replication. Therefore, one of the most important things a cell does is to at all times maintain the correct proportions of nucleotides inside the cell nucleus and also the correct proportions of amino acids in the cytoplasm. Imbalances in nucleotide or amino acid concentrations can result in greatly increased error rates, and this is why a balanced diet, maintaining the proper weight, and a solid exercise routine can greatly enhance your body’s ability to avoid cancer and genetic disease. In addition, I recommend finding out what the major carcinogens are and avoid them.
Digital networks properly implemented inside the cell would eliminate these mistakes and result in error free protein synthesis, error free transcription, and error free cellular replication (DNA replication). In digital protein synthesis in a digital cell when one of the 6 codons for leucine (our example) appears at the 6-bit input (JKLMNO) of the digital ribosome, the gate (channel in the cytoplasm) for leucine goes to 1 (leu = (KN)’JLM = 1) and is opened.
Leucine is transported to the active site via its tRNA molecule, and the enzyme makes the correct codon-anticodon bond 100% of the time. Thus, leucine is added to the protein chain. Inside the cell nucleus when (for example) on the parent strand of the digital chromosome adenine (00) appears at the 2-bit input (JK) of our DNA decoder (see third attachment), the gate (channel) for thymine goes to 1 (T = J’xK’ = 0’x0′ = 1×1 = 1).
The channel for thymine is opened and the enzyme adds thymine to the growing daughter strand of the replicating digital chromosome. Thus, the enzyme makes the correct bond 100% of the time. Based on the bit assignments we have discovered, a 4-gate network with a 2-bit input in the form of a 2-bit DNA Decoder inside the cell nucleus would eliminate all mutations occurring at the levels of DNA replication and transcription. More complex networks of 40 gates are necessary to eliminate all errors of translation and thus protein synthesis. Protein synthesis occurs in the cell cytoplasm.
Logic Problem?
In his spare time Dr. S produced the networks which are the solutions to this “logic problem”. I now possess these networks and know the optimum bit assignment to the molecules comprising the DNA code. I have prepared for you a summary of them in the second and third attachments. The optimum bit assignments are A = (00), G = (01), C = (10), and U = (11) for all three codes! This seems almost too good to be true, but it is. Who could have predicted it!
When I started out in the mid 1990’s studying digital logic, I had absolutely no idea the direction that any of my thoughts would go. All of my efforts could have been a complete bust. Each Code could have had its own optimum bit assignment completely different from the other two.
The best bit assignment could have been non complementary and therefore devoid of the wonderful Boolean complementary relationships that these best equations and bit assignment (that are a result of them) suggest once existed between the bonding molecules. The optimum equations themselves could have been cumbersome. In my opinion, Jesus would never do anything inelegant. Inelegant optimum equations/networks with inelegant optimum bit assignments as a result of them would be a clear indication that the DNA code never had a digital representation.
It is important to note that the optimum equations and bit assignment are strictly determined by the organization of each Code as it now exists in nature. Nevertheless, each of the three Codes miraculously has the identical best bit assignment as the other two and this assignment is complementary. In addition, the logic equations based on the optimum bit assignment are quite elegant as I have previously alluded to.
Also, the DNA code certainly didn’t have to qualify as a computer or Boolean Code in the first place. A code may be defined as the standardized systematic use of a given set of symbols used to represent information. As I have mentioned, the organization of the Code is fixed in nature.
All computer codes must meet the following quite rigorous requirements: 1) Every input can have one and only one output. 2) Every input must have an output and all the inputs and outputs must be accounted for. I can safely state that the DNA Code meets these stringent requirements. For every organism that has ever been in existence every codon codes for one and only one amino acid and there is not even one codon in all of Life that does not code for an amino acid. The Code never leaves a codon hanging out there undefined and unaccounted for. Think about that fact.
DNA: One of the Most Universal Codes in Existence
Every organism has a Code comprised of 64 codons and 20 or 21 amino acids and a stop signal and every codon has an existence and codes for one and only one amino acid or a stop signal. In this sense the DNA Code is truly one of the most universal codes in existence. Biochemistry texts call these properties “degenerate” because each amino acid possesses multiple codons when actually this property is the main way the current Code mitigates the effects of a harmful mutation.
The use of the word “degenerate” in relation to the DNA Code is a gross misuse of the word and is quite ridiculous. If the Code were not “degenerate” it could never qualify as a Boolean computer code and in addition, we would all very quickly die. Without question the DNA code is the most elegant, beautiful, and well-conceived code that has ever existed. Now let me discuss two topics. The first is the Wobble Hypothesis and the second is Complementarity as it is used in Boolean algebra.
The Wobble Hypothesis
Let’s discuss the Wobble Hypothesis first. As I have stated previously, the use of the word “degenerate” by the atheistic biochemical community demonstrates their ignorance and hypocrisy better than anything I know of regarding the utter elegance and sophistication of the DNA code.
In order to explain the Wobble Hypothesis, and since I have used leucine as my example, let’s use it to explain the famous “wobble” and in so doing, further demonstrate the inaccuracy and lack of understanding of the biochemists who refer to the Code as “degenerate”. As mentioned, in order to satisfy the requirements of qualifying for a Boolean computer code, every codon must code for one and only one amino acid. However, this creates the necessity of 64 tRNA’s with 64 unique anticodons, one for every codon, or does it?
To answer this question let’s examine leucine in detail in terms of the rules of the “wobble”.
First let’s list the codons for leucine fixed in nature by Jesus:
CUA CUG CUC CUU UUA UUG
Next, let’s look at the pairing UUA UUG. Now, you must remember that in a previous article I stated that the strands of the DNA molecule possessed the property of directionality so that the 3’ codon position (third position of the codon triplet) pairs with the 5’ anticodon position (first position of the anticodon triplet). Thus, the Watson-Crick base pairing for UUA would be the anticodon AAU and the anticodon for UUG is AAC . But according to the rules of the “wobble” AAU works for both UUA and UUG, allowing for the elimination of the anticodon AAC and the need for its tRNA molecule. In addition, if a mutation occurs involving the third position of the codon UUG, there is a distinct possibility that it will be rendered harmless by the Code.
Now let’s examine the codons CUC CUU according to the rules of the “wobble”. The traditional Watson Crick codon anticodon base pairing for CUC is GAG and for CUU the anticodon is GAA. However, according to the rules of the “wobble” the anticodon GAG works for both codons, thus eliminating the need for the anticodon GAA and its associated tRNA molecule. If a mutation occurs on the third of the CUU codon there is a distinct possibility the “wobble” will render it harmless.
Now let’s examine the codons CUA and CUG according to the rules of the “wobble”. The traditional Watson-Crick base pairing for CUA is the GAU anticodon and for CUG the anticodon GAC. However, according to the rules of the “wobble”, the anticodon GAU will bond to the CUG codon, thus eliminating the need for the GAC anticodon and also mitigating the effect of a mutation in the third position of the CUG codon.
Thus, the Code has effectively eliminated the AAC GAA and GAC anticodons and their associated tRNA’s while at the same time mitigated the effects of a harmful mutation in the third positions of the UUG CUU CUG codons.
An examination of our minterm table (table 2) for leucine shows that the wobble has had no effect on the minterms assigned to leucine nor will the wobble have any effect on any of the minterms assigned to the codons of table 2.
An exception to this statement should be methionine abbreviated as met. Why? The AUG codon codes for met (methionine). Thus, the Watson Crick anticodon is UAC for the met codon. However, by the rules of the wobble the anticodon UAU should suffice. But UAU will also bond to the AUA codon which codes for Ile (isoleucine). But this would violate the DNA code and also disqualify the Code as a computer code. And so, Jesus blessed met with its own unique tRNA anticodon UAC that, according to the rules of the wobble, should not exist as an anticodon inside the cell. He made this exception in order to maintain the fidelity of the Code. In other words, UAU will not bond with met according to the rules of the wobble, necessitating the existence of the UAC anticodon and its tRNA molecule. And since met has its own unique anticodon, Jesus also made it the start codon for the Universal Code.
What about the Mitochondrial Code for vertebrates? How does the “wobble” affect it regarding met. Here we see that AUA codes for met, so the UAU anticodon should suffice thus eliminating the need for the special UAC codon. UAU should suffice as the anticodon for both the AUG and AUA codons, according to the wobble rules. At this point I will point out that wobble rules can be complex for lower organisms; however, wobble rules never violate the fidelity of the particular genetic code which Jesus assigned the organism to. In all of Life there are 24 variations to the Universal Code. Every organism across the 5 taxonomic Kingdoms either uses the Universal Code or one of the 24 variations. The wobble rules never violate the fidelity of the particular Code to which it is assigned. Almost all organisms use the Standard or Universal Code. An examination of all the variations in the Standard Code on the NCBI website confirm that none of these variations violate the rules of the Standard Code which I will state again and add two additional rules:
1) Every codon has one and only one assigned amino acid
2) All 64 possible codons are accounted for
3) “Wobble” rules for codon anticodon bonding never violate rules 1 or 2
4) “Wobble” rules for codon anticodon bonding have no effect and do not change the optimum minterm assignments to codons as determined by Dr. S for the Standard Code in table 2.
A Strong Correlation
In fact, for the Standard Code there seems to be a strong correlation between the optimum minterm assignments and the “wobble” rules allowing for elimination of anticodons and their tRNA’s by means of non-traditional Watson Crick bonding in the third position of the codon with its anticodon. To better see this let’s again use leucine as our example. Below are the codon assignments and optimum minterm assignments for leu as depicted in our optimum minterm assignments (table 2) for the Universal Code.
Leu
CUA (101100) m44
CUG (101101) m45
CUC (101110) m46
CUU (101111) m47
UUA (111100) m60
UUG (111101) m61
I note that consecutive minterms when used in minterm sums often result in optimum simplification of these Boolean sums. On the left side of the column are the codons assigned to leu by the Code that allow for the elimination of three tRNA’s and their associated anticodons, according to the rules of the “wobble”.
On the right side of the column, are the optimum minterm assignments for leu as determined by Dr. S, thus creating the logic equation:
Leu = m44 + m45 + m46 + m47 + m60 + m61 = (KN)’JLM
I hope that you can appreciate this astounding simplification of six 6-variable minterms into a one term logic expression of five variables.
For the lay person, each minterm contains 6 variables for a total of 36 variables in the sum, which can be simplified to the 5-variable expression (KN)’JLM for a reduction of variables of 86%.
Likewise, the 6 minterms have been simplified to the one term (KN)’JLM resulting in an 84% reduction in the number of Boolean terms.
Thus, in regard to leu, the wobble rules of the Universal DNA Code seem to be optimized to reduce the need for tRNA anticodons by 50% and also optimized to reduce the number of Boolean variables by 86% and the number of Boolean terms by 84%.
Although the percentages will vary, I can generalize this observation to nearly every amino acid found in the Universal Code. This is a remarkable discovery.
The Double Helix
Within the double helix of the DNA molecule (chromosome), adenine bonds with thymine which is equivalent to uracil in the DNA Code and guanine bonds with cytosine. In Boolean algebra the complement of 0 equals 1 and the complement of 1 equal 0. Thus we write 0′ = 1 and 1′ = 0. Now look at the bit assignments for the Code: A (00)’ = U (11) and U (11)’ = A (00) which means that A’ = T = (11) and T’ = A = (00) inside the DNA molecule (chromosome) and also inside mitochondrial DNA (mitochondrial chromosomes). Also, G’ = C because (01)’ = (10) and C’ = G because (10)’ = (01).
These complementary relationships are extremely significant because it means that for every hydrogen bond across the double helix of the chromosome, complementarity must be maintained or there has been a mutation. Thus, not only will DNA replication, transcription, and translation always be perfect, if an error (mutation) occurs after these processes caused by a carcinogen or something else, then the bit assignment across the double helix of the chromosome will no longer be complementary. A very simple digital computation can detect this loss of complementarity. The fact that the optimum bit assignment is complementary is quite amazing. It certainly didn’t have to be this way, but it is!
10 to the 84th Power Possible Unique DNA Codes
There are 10 to the 84th power possible unique DNA Codes. This is an unbelievably large number. This number is larger than the number of photons in the universe. The three (typically known as Universal, Universal with Selenium, and Mitochondrial) currently used by every living thing on our planet show tremendous intelligence in their construction in order to minimize the harmful effects of a mutation when it does occur in the chromosomes of our genome. Nonetheless, even the remarkable designs of the DNA Codes cannot overcome the harmful effects of over six thousand trillion mutations that occur during the lifetime of an individual as a result of faulty DNA replication! This is not to mention errors in transcription and translation which in addition to mutations, also result is faulty proteins.
Also, in this polluted age mutations caused by carcinogens account for many harmful mutations. However, the digital logic equations produced by Dr. S provide digital networks that if properly implemented on a molecular level inside the cell, would eliminate all mutations and errors in protein synthesis and the mutation rate and error rate would become zero. Also, the mutations caused by carcinogens would become negligible. Thus, the current DNA Code(s) and chromosomes existing inside every human cell are formed in such a way as to strongly suggest that all the cells of Adam and Eve, before they ate the forbidden fruit, possessed a digital or binary representation; and also that their cells contained elegant digital networks or their equivalent, probably many thousands to millions of them.
I believe these networks were destroyed by their sin and thus physical death entered into the world. I believe the digital representation (the bit assignment) assigned to the molecules of the Code by Jesus was also destroyed. I believe this massive destruction of vital cellular machinery and information is the cause of cancer and is also one of the main reasons we die. This massive loss of information is also the cause of aging, but aging is another topic altogether. Aging is in itself a disease. Even if all errors in protein synthesis were eliminated and there was no mutation, we would still die of old age.
REPLY ATTACHMENT
Reply
Fri 3/30/2012, 5:36 PM
Charles,
I am a professional engineer at Vanderbilt. During my MSE, I worked with formal verification tools that solve problems similar to what you have proposed. I would be happy to discuss the details of your problem further.
Regards,
B. S. PhD
Institute for Space and Defense Electronics
Vanderbilt University
________________________________________
From: ee-grad [[email protected]] On Behalf Of Benedetti, Teresa P [[email protected]]
Sent: Friday, March 30, 2012 1:26 PM
To: [email protected]
Subject: FW: logic problem
FYI. If anyone is interested in helping to solve this problem.
Teresa Benedetti
Administrative Assistant
Electrical Engineering/Computer Science
VU Station B #351679
400 24th Avenue South
362 Jacobs Hall
Nashville TN 37235-1679
615.322.2796
Fax 615. 343.5459
From: CHARLES JR [mailto:[email protected]]
Sent: Friday, March 30, 2012 1:05 PM
To: Benedetti, Teresa P
Subject: logic problem
Teresa,
Here is the problem for a grad student to solve.
Given f0, f1, f2…….f20 for a total of twenty one 4 variable logic functions/equations give me a “good/best” solution for the following set of logic equations:
f0 = 4 (sum of) minterms, your choice of minterms (m0, m1, m2… m63)
f1 = 6 (sum of) minterms
f2 = 2 minterms
f3 = 2 ” ”
f4 = 2
f5 = 4
f6 = 2
f7 = 2
f8 = 2
f9 = 3
f10 = 6
f11 = 2
f12 = 1
f13 = 2
f14 = 4
f15 = 6
f16 = 4
f17 = 1
f18 = 2
f19 = 4
f20 = 3 (sum of) minterms
Please use for the variables AUGC so that the equations will be written (for example) in the form f0 = f(A,U,G,C) = sum of 4 minterms
Each minterm (0 through 63) may only be used once in deriving the 21 logic equations as is customary.
Work is to be done in detail so that I may see the minterms used to form each logic equation and the rational used in choosing them in order to arrive at a “good” or “best” solution.
I will remunerate the one that does the work for their efforts and will appreciate it very much also. My email is [email protected]<mailto:[email protected]> my cell is 289-8792.
Sincerely,
Charles S. Ruark, Jr., MD
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