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.