# A 'Gamer Guide' To The Deeper Order And Connection In DNA

A ‘Gamer Guide’ To The Deeper Order And Connection In DNA

We have written a software program (for gamers) to show the deeper order and connection in DNA. We show how it is mathematically possible to describe separate ways for a codon to code for an amino acid.

This is one way. Thus the name: Collection One. There are 368,640 ways in all. Each way follows the same rules.

To make our software understandable, we have provided a purpose and meaning for each codon and for each amino acid it appears in.

Directions:

User Name: guest

There are two required inputs: weight and collection.
Pick any number between 0 and 63 and put it in the weight box. Each base-2 number relates to a DNA codon.

Choose 1 in the collection box.
Click on the begin button. You must click on the begin button or nothing will happen.

Enjoy!!!

Hi blubblub,
I looked at your link and it looks cool, but I don’t understand the purpose. How is this helpful for, say solving eterna puzzles?

I am sure that this is useful, but I just don’t understand it.

Thanks,
Matt

http://www.ringleins.com/rel8te/index…

Great question! Puzzles are combinations. RNA is the greatest puzzle of all time. It does not hurt to understand how it might be working mathematically.

We believe DNA is an adaption of RNA and explains why DNA needs RNA to make proteins.

This program shows how three primary colors – or their lack of and/or combination of – can show the deeper order and connection between RNA and DNA.

In short, the boxes you see around the center codon are (x) and (y) coordinates, forming two threesomes, that fold into the center box codon, no exceptions.

This bridges the Holy Grail of physics: All particles exist potentially (with a certain probability) as different combinations of other particles (no exceptions); with the Central Dogma of DNA: DNA Makes RNA Makes Protein.

Niels Bohr said ‘where there is pattern there is truth’.

If RNA adpated into DNA or DNA is an adaptation of RNA, how it fits together should be important to how it folds.

There seems to an existing assumption that nucleotide triplets represent DNA’s basic level and that each of the four nucleotides can therefore be assigned a ‘fixed’ color to make it easier to map the folding. As Eli Fisker and BerexNZ and Mat747 etc have been discovering, if this is proving not to be true at the simplest levels, how can it improve as designs become more complex? There are hidden patterns because there are deeper levels.

Our program shows mathematically how prefolding occurs before the DNA triplet level. If the folding algorithm for eteRNA puzzles is ever adapted to reflect how the colors really interact instead of the current assumption that these colors are fixed, then the folding should true up, become predictive, and therefore eliminate the errors in the algorithms.

I don’t get it. What is the weight? What does the collections do? please dumb it down

The weight is the base-2 value of the DNA codon.

Collection One represents the way in which ‘fractal’ amino acids can combine to create the codon triplet – with all the prefolding already in it. In short, DNA is a color balanced off centered base-2 system. RNA is embedded in it. The suggestion is RNA bridged to DNA and DNA is an adaptation of RNA. RNA is resonant and looks for relationships. DNA is digital and makes proteins.

All of this is on our picassa web album. There are screen shots of our program and caption explanations as well as the color templates.

Go to GOOGLE and put in transcription level prefolding characteristics, follow the links to our picassa web album.

What do you mean by “‘fractal’ amino acids”.

Also, I am still not understanding what is going on here.

Try an explain it as you would to a child, because I’m not getting it at all.

How do you use this to help find solutions to the labs?

Do you know that rna is not just a massager of dna but that it can act like a protein. it is a system which does not need to use codons for synthesis. a majority of the puzzles in eterna are trying to model these system not the codon protein folding system. This is call Non coding RNA it is more primitive then the protein folding but just as important it and works in parallel to protein synthesis. You might want read these http://protein3d.ncifcrf.gov/shuyun/W…

We do understand the mRNA, tRNA and ribosmal RNA aspect of all this. We believe they are manifestations of the same phenomena and rules.

I need to do a couple of things here but the biggest point we are making is that the DNA makes RNA makes protein is simply a mirror image of the deeper levels of RNA (which we believe preceeded DNA) where Proteins makes RNA makes DNA.

I will be happy to address both the ‘fractal’ comment (Matt) and how we think this applies to RNA folding (Joshua) in about six hours when I get back home.

By the way, the slide show of images with captions is simply to show the deeper levels. We know DNA has thymine and RNA has uracil; that RNA is a monomer and DNA is a polymer; and that RNA does not need DNA to make protein. However, we want to read the link you gave us Joshua so we can specifically address this in a language we can both agree on.

In the meantime, we appreciate the comments…

Let’s get right to it. Non-coding RNA that does not need DNA for synthesis is not ‘primitive’. To assume it is, is to miss an opportunity to understand how all of this fits together.

Should we accept that a bunch of random ‘loose’ nucleotides combine to create a ‘primitive’ RNA molecule that subsequently codes for an even higher level protein? This does not fit with what we know about molecules; mainly, that by the molecular level, an architecture is in place.

The most ‘primitive’ RNA molecule is not ‘primitive’ in the same way a DNA codon is never ‘degenerate’ and will never ‘wobble’ with uncertainty. We tend to give negative terms to phenomena we do not understand.

We need to understand that even at what has been termed the ‘primitive’ level of RNA, that an architecture is in place. What we think of as ‘random’ connections of ‘loose’ primordial nucleotides that form a ‘primitive’ RNA molecule is already has an elegant architecture that assigns every uracil or cytosine or adenine or guanine nucleotide its unique energy level and folding preference based on its context.

Our findings suggest that at these ‘primitive’ levels, the diagonal architecture of RNA enables the ‘loose’ nucleotides (what we call fractal nucleotides Matt) to bind to something like a protein by shape, like a key fits in a lock, creating the prefolding characteristics necessary for protein folding at higher levels.

Now how does this ‘primitive’ rna architecture help in the lab? The more accurate way to describe something is always preferred over the less accurate way. For starters, adenine is not always yellow, uracil is never blue, cytosine is not always green and guanine is not always red. Not every nucleotide in RNA is switched on (even at the primitive level). This will impact the folding pattern.

We took the time to put our math and our software out there. We created a web album with images and explanations of our math and software. The only way to understand it is to read the explanation and use the software. There are three reasons why this is not happening: #1 the assumption that ‘primitive’ RNA doesnot possess an architecture; #2 We are all busy; #3 Why would I want to spend time trying to understand something that has not been proven in a lab.

So we offer this olive branch: in order to produce the results we predict, we would need an open color pallette where we can assign any color to any nucleotide (to reveal deeper patterns) with the ability to turn off the energy level in any nucleotide at any time (which will impact the way it folds).

What we propose to do is take all eight of the accepted challenge designs and apply our color template. This is doable. The Dev’s could do it with four lines of code. Let A and U and C and G keepthere energy levels. We simply want to color them differently and also turn a few off.

Team blubblub

Joshua:

We work as a team here at blubblub.

When I say ‘we’, I am speaking of myself and my software programmer Charlie Ringlein. Charlie has over 13 years of specialized Information Technology (IT) experience. His IT-related experience is with application software, systems analysis, systems design, developing, coding, testing, debugging, and maintaining applications software. He has extensive experience creating newly restructured software development frameworks.

Software and Languages include:
Visual Studio
Flash
Dreamweaver
Photoshop
Visual Source Safe
Oracle 10g
Beyond Compare
ASP
HTML
Excel
C# / C Sharp
CSS
XML
XSLT
JavaScript / Java Script
ASP.Net

He is currently learning Silverlight.