Pitfalls of Science

[Charles]

Test
RUARK-RNA-001.pdf This pdf is fairly self explanatory. It is for the Universal DNA Code and the Universal Code with Selenium

RUARK-MTDNA-001.pdf This pdf is for the Mitochondrial Code

RUARK-RNA-003.pdf This pdf shows the optimum digital networks for all three codes and the optimum bit assignment which is A = 00, G = 01, C = 10, U = 11. So there is one optimum bit assignment for Translation.

decoder.pdf This optimum bit assignment also works for DNA Replication and Transcription in the form of a simple 2-bit Decoder

Implementation of these networks inside human cells would eliminate all mutations and errors in proteins that occur during Translation.

I will have significant comments to follow.

[Charles]

I hope the last post was not confusing. It was not meant to impress. Overall it demonstrates the DNA Code can be described as an elegant Boolean Code. Let's examine the first two pdf's. They are quite important.

Attachment 62416

Attachment 62418


The first pdf (62416) represents an incredible amount of math condensed to an elegant table. This table shows that there are two optimum bit assignments for the Universal Code (00011011) and (01001110) and also for the Universal Code including Selenium. Either of these bit assignments requires 37 gates. When these gates actually form the networks, their respective networks require 40 gates. It may be optimal/beneficial for each network to possess its own unique optimum bit assignment but not necessary.

In looking at the second pdf (62418) which is the table for the Mitochondrial Code we see there are three optimal bit assignments: (00011011), (01001110), and (11100100). Note that this includes the same bit assignments for the Universal Code and Universal Code with Selenium. When the gates of Mitochondrial Code actually form its network, it (the network) too requires 40 gates.

Folks, that's just they way it is. These Codes are fixed in nature. These are their optimum bit assignments. It's quite a piece of work. No human mathematician or group of mathematicians working by hand could crunch the numbers necessary to arrive at these solutions even if they worked a lifetime and then would their equations be reliable? The equations determine the number of gates and the gates determine the optimum bit assignments. It amounts to over 1,500 6-variable multiple term minterm sums. On the best day I ever lived as a mathematician (I was a math major), I could not simplify one of these minterm sums. I didn't think it could be done. One of the reasons I spent so much time (over a year) researching this project, before employing an engineer to solve the math was the expense and not to embarrass myself.

It seemed like an impossible problem, a dream if you will. I've always been a dreamer. It took about 20 years to conceive (began in the early 1990's) and about 10 years before I could concisely state it (2012) so that an engineer might understand it, i.e. what I wanted him to do. I had no hope it could be done and had no idea what the outcome might be.

I've had to send off a batch of emails on my Project and have the treadmill before me but I have some very important comments to make on this work.

These networks in the pdf (Ruark RNA 003) would probably require 40 enzymes (proteins) to implement inside human cells to perfect protein Translation. Probably 4 enzymes (proteins) to perfect DNA Replication and Transcription. These networks that would be enzyme (protein) based not transistor based would eliminate all cellular error including all mutations that is built-in or inherent to cells and make cells much more resistant to carcinogens. These networks would be the active process previously mentioned that would supply the eftu or the DNA polymerase with the correct tRNA or nucleotide for bonding 100% of the time. Only digital networks are capable of handling with 100% accuracy the extremely large numbers you have seen in my previous posts.

"A eukaryotic ribosome is composed of nucleic acids and about 80 proteins and has a molecular mass of about 4,200,000 Da. About two-thirds of this mass is composed of ribosomal RNA and one third of about 50+ different ribosomal proteins."

Ribosomes are composed of two subunits (Large subunit and Small subunit). They are considered large molecular machines. A human cell can contain up to 10 million ribosomes. The digital networks you see in the Ruark RNA 003 pdf would be composed of about 40 proteins equal to 40 gates. Conformational changes in the proteins would be the equivalent of off/on, no/yes, 0/1. The network (protein complex) would be a third ribosomal subunit. I believe this subunit once existed but the genes for it have been lost or destroyed.

That's what these networks and equations suggest. The DNA Code is an elegant compact Boolean code averaging an incredible 2 gates per amino acid! I will have more to say about this but I am stressed for time. A structure (the cell) that could develop the densest most compact digital storage media theoretically possible (DNA molecule) should have no difficulty developing a 40 gate digital network, particularly since the code it developed is undeniably an elegant Boolean code. But this network is missing.

Bacteria don't need this network. They thrive on mutations. Protein errors don't concern them in the least. They are immortal. They can divide forever. The human cell in its current state is greatly inferior to the bacterial cell. Human cells are programmed to die. Bacteria are programmed to live

The reactivation of telomerase and the insertion of the digital networks you see here including the Replication Decoder would render human cells cancer free and immortal. I will have more to say about this later.

[Charles]

I watch every episode of "How the Universe Works" for entertainment. When I was a kid I read every sci-fi book I could get my hands on and all the classics. One summer when I was about 15 I read the entire Lensman Series by E.E. Doc Smith. I was usually an outdoors kid. I remember my mother coming in the living room where my father's Bozak Concert Grands were and asking me if anything was wrong. Because I hadn't been out of the house for a week reading those novels.

Recently Michelle Thaller made a statement I totally agree with: "The universe continues to lead us down a rabbit hole". I believe the episode was "Monsters of the Milky Way". I agree. Question to Michelle: Is this deliberate? Is the Universe doing this to you deliberately?

So before I give an explanation of a minterm let me state a few of my conclusions regarding the cell.

The human cell once was digital with a microprocessor and full array of digital networks. These networks existed as sets of enzymes. The gates of these networks were enzymes.

The DNA Code is and was a Boolean Code.

The DNA molecule (our chromosomes) was coded in binary code.

The human cell once was immortal.

The human cell has been severely damaged and is now programmed to die.

The human genome is missing about by my estimate 97% of its genes.

The human cell is running on a backup system the equivalent of a set of run flat tires.

The human body once was 100% "green", meaning that it produced no pollution of any kind.

[Charles]

Now let's discuss the minterm. I will do it by using threonine as an example. There's nothing special about threonine. I pulled it out of the hat. I remember when I was in geometry class in the 10th grade, my teacher said about proof: "You either get it or you don't." This really scared me because I wondered, "Would I get it?"

Boolean algebra is like this. You either get it or you don't. For me its ridiculously easy but it may not be that way for you.

Here are some facts about it:

Any Boolean function can be expressed as a Truth Table. A Truth Table is a powerful thing.

Any Boolean function can be expressed as a sum of minterms, i.e. as a minterm sum.

Using the Truth Table I can write any Boolean function as a minterm sum and then simplify the minterm sum to form my desired function.

The outputs of any digital network are Boolean functions.

I am using this understanding to use the DNA Code as it exists in nature to express each amino acid as a minterm sum that is based on the codons nature has assigned to it. These codons cannot change but the minterm sum can change based on the assignment of bits to the molecules A, G, C, U. Discovering the optimum sum of minterms for each amino acid is a devilishly complex math problem. No human being could by hand remotely solve it in a lifetime.

So now specifically let's look at threonine:

As mentioned you will frequently see in biochem texts this type expression:

Thr = ACU, ACC, ACA, ACG where these triplets are the codons of the DNA Code asigned to the amino acid threonine. This is really as far as the biochem text can go. It can't write the true Boolean expression because it doesn't recognize the Code as Boolean. Let me say this expression thr = ACU, ACC, ACA, ACG is crude.

The true expression is much more elegant:

Thr = ACU + ACC + ACA + ACG where "+" is the logical sum operator of the Boolean set is much more elegant and is the correct way to write the Code.

I have to adjourn. Wife has Dr.'s appointment.

[Charles]

My wife had a very successful appointment. I am thankful.

The minterm is a very useful one term Boolean logic function, hence the terminology "min" term. I have looked at the definition on the internet. As with most stuff written about Boolean algebra on the internet, I find it very unsatisfactory.

Consequently, I'd like to give you a practical definition by showing you its utility and how to use them to design a digital network. I have studied science and mathematics for many years. When I was in college I always wanted to understand "how" or "why". I wasted a lot of time. My advice is to memorize. The how and why George Boole came up with his postulates I still don't know and really don't care. I marvel over them because his algebra describes the laws of thought. Think about that: the laws of thought. His set does not contain any numbers; thus the laws of information obey the rules of a set that does not intersect with the laws of physics, since every equation of physics can be made to be equal to zero, which is a real number.

We are going to use the optimum bit assignment A = 00, G = 01, C = 10, U = 11 for our bit assignment to demonstrate the remarkable utility of the minterm.

ACA, ACG, ACC, ACU are the codons nature assigns to threonine (Thr). Therefore the binary code for ACA is 001000, for ACG is 001001 and so on for the four codons as listed below.

Each minterm is assigned a unique base ten number.

(Note that the binary code for each of these codons evaluates to a base 10 number and so we must choose for our minterm, the minterm associated with that identical base 10 number. Below you see the codon, its binary code, and its minterm. Don't try to understand why it works this way. It's irrelevant. It just does.)

ACA 001000 m8; ACG 001001 m9; ACC 001010 m10; ACU 001011 m11

Let's examine m8 to see how this works. Note that ACA has the binary code 001000 based on our bit assignment. Therefore it must be assigned minterm m8. m8 is the 6-variable Boolean function:

J'K'LM'N'O' so we write m8 = f(JKLMNO) = J'K'LM'N'O'. This function has the property: f(001000) = 1 Why?: 0'x0'x1x0'x0'x0' =1x1x1x1x1x1 = 1. Consider m11. m11 = f(JKLMNO) = J'K'LM'NO = f(001011) = 1 because 0'x0'x1x0'x1x1 = 1x1x1x1x1x1 =1. Likewise for m9 = J'K'LM'N'0 and m10 = J'K'LM'NO'. So we can say Thr = m8 + m9 +m10 +m11 which is a minterm sum that equals Thr = J'K'LM'N'O' + J'K'LM'N'0 + J'K'LM'NO' +J'K'LM'NO. This minterm sum simplifies to Thr = L · M' · J' · K' which is an incredibly slick one term Boolean product.

Thus our optimum bit assignment groups together the minterms m8, m9, m10, and m11. It almost looks contrived. Too good to be true. But I just pulled Thr out of the hat. When I did, I could tell already that these minterms would simplify to a really slick Boolean function and in fact it does: Thr = L · M' · J' · K'. Thus when any of the four inputs 001000; 001001; 001010; 001011, sets on the peptidyl site of the ribosome, i.e. the input of the digital network, the output of the digital network equal to Thr goes to 1 or positive/open and the network reaches out and grabs the thr-tRNA that has the correct thr anticodon and the amino acid threonine with 100% specificity. The network then presents this thr-tRNA to the peptidyl site of the ribosome where the codon is and the enzyme (eftu) makes the bond. There's no more guesswork, no more dependence on the second law (diffusion), or random chance.

A digital system like this would guarantee 100% accurate Translation of all proteins. This is a fact.

It appears that out of the 1.5e+84 unique DNA Codes, the Code chosen by nature was the optimum Boolean Code (fewest number of gates and thus the simplest digital network and best optimum bit assignment) and the best Code simultaneously optimized for the fewest number of harmful mutations, when the digital network is not operating. Nature also chose the densest, most rugged, most reliable digital storage medium in the universe in which to store its digital data, the DNA molecule, also, known as our chromosome.

Next I will discuss why a complementary bit assignment is so important. Note that A bonds to U or T. Thus 00 + 11 = 1 and 00x11 =0. G bonds to C thus 01 +10 = 1 and 01x10 = 0. It certainly did not have to be this way. The DNA Code is arranged so that the optimum bit assignments are all complementary. Quite incredible that out of the 1.5e+84 possible Codes a Code(s) requiring only 40 gates also has optimum bit assignment(s) that are complementary. And that these optimum bit assignment(s) work for Transcription and Replication, in addition to Translation. In other words the human cell has an optimum bit assignment that works for Replication, Transcription, and Translation and is complimentary.