matt mod of d9 jewel winner in a RNA 6x6 diagonal architecture

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Using the Octupus Spring Difficulty Level 4 -- (417 nucleotide ball template) from the ETERNA website, we plotted the first 12 nucleotides in "matt mod of d9 jewel" round four winner that scored a 99% synthesis rate. It created this design in our 6x6 RNA diagonal architecture. There is no wasted space and no overlapping. An AUG-like structure begins in slot three as it also does in C elegans and the drosophila fly sequences we analyzed.

The diagonal is stem-like and acts as a connection point that also separates function structures that prevent tangling and keep communication paths open. These points occur at: 0-45-63; 64-109-127; 127-172-190; 191-236-254 which are base-2 cohering and decohering shaping points. To view the screen shot go to: https://picasaweb.google.com/collinsm...
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blubblub

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  • retooling RNA synthesis

Posted 8 years ago

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JRStern

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y'see, now, that is very interesting, that design must use six different coloring conventions that I've never even tried - a lot more green! I've never understood why some puzzles have the limit of three C's in a row, as they almost never occur in my puzzle-solving algorithm.

as for the explanation - me no grok.
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blubblub

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JR -- please keep in mind that you can not learn anything from this screen shot that will help you solve current or possibly future puzzles. ETERNA puzzles are set up beautifully to introduce and walk people like you and me through the necessary steps to synthesize RNA. What we are doing is applying d9 and Matt's successfully synthesized submissions (a remarkable feat) into a mathematical model that may or may not have legs to stand on. So please do not look at our screen shot as alternative ways to do current puzzles. Look at our screenshot as an analog for what may or may not exist at deeper levels.
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Chris Cunningham [ccccc]

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@blubblub: You are going to have to try harder to explain what in the world you are talking about, if you actually expect anyone to get anything out of what you are saying. This looks like a lot of nonsense to me, although I imagine it actually isn't.

?
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blubblub

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Fair enough. We will try harder. Thanks to ETERNA templates we are able to apply our mathematical models to actual results from d9 and Matt's synthesized results and produce structures at deeper levels. These levels may or may nor be significant. All we know is that genomic study is stretched across biology, physics, engineering, mathematics, and chemistry and there has to be a deeper order and connection than what is currently proposed or we would have made more progress on the genome by now. We can talk all day on base-2 systems and we can say with confidence that both RNA and DNA are six place base-2 systems. We know that in base-2 systems what works at one level will not work at the next but then reemerge and work once more at another level. We know base-2 systems are combinatory, contain the transitive property, and can be color coded with a standard color template. This means we can trace behavior across dimensional lines, spaces and planes. We are seeing if our models work with what ETERNA is doing. When we look at this image we do not see nonsense but we do understand why you might. ETERNA is an incredibly important website for us. We read everything ETERNA posts -- including all of your posts. We will learn and grow like this website and we are confident we will find the bridge. Our sense is all pieces of the puzzle are important and ETERNA has the best shot at gathering all of the pieces together and solving the puzzle.
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dimension9

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Hi Blubblub

I have been reading all your posts and looking at all your online pics for several weeks now, and although I find your words and pictures extremely interesting, I have failed to achieve any significant understanding of what you are trying to communicate.

I have refrained from question or comment until now, hoping that I would eventually penetrate your meaning on my own - at least enough to be able to articulate some preliminary questions that might help illuminate where the communication seems to be failing for me - (and now, after reading Chris's post above - where I see it is failing for others as well) - but I have not thus far been able to discover even approximately where all this is falling short for me - enough to ask even a single cogent question.

You are obviously a very intelligent and articulate person, and just as obviously, both passionate and earnest about your studies. I also commend your willingness to share, and your calm patience with those of us who seem unable to follow your meaning.

But I must say, despite all these positives, all of your posts and pictures and explanations seem to constantly tremble just on the edge of some incredibly brilliant insight or revelation - but never quite deliver the crucial connective word or phrase or idea that would pull it all together! It results in a constant series of incredibly interesting and tantalizing hints - that never reach fruition - that then leave you with no satisfying resolution - much like being perpetually left at a cliff-hanger ending in a serial adventure - there is never any solid graspable conclusion - or for that matter, any conclusion whatsoever - not even a preliminary or partial one. It is very frustrating and disappointing to me (and I think to your other readers here on EteRNA as well).

I think that not only myself, but all of your readers here on EteRNA - really do want to understand, and are desperately seeking and hoping for that bit of an explanation that will suddenly (finally) illuminate your meaning, rather than further tanatalize without offering fulfillment.

Apologies, I do not mean to criticize, demean, belittle, malign, or otherwise deliver negative evaluations or feedback, but I do fear that even the most brilliant insights must inevitably suffer marginalization if not comunicated effectively.

For all I know, you and your colleagues and your research may hold the next "big breakthrough" in biochemistry globally. But for now, (most unfortunately), your promotions of your work here on the EteRNA forum have come across less with a ring of validity than with (please forgive me - I hesitate and regret to have to use the term) an aura of pseudo-scientific " tin-foil-hat" fringe-mentality.

I would humbly and respectfully submit, that even great genius - insufficiently articulated and communicated - is mere gibberish.

With great respect to you, I would - also humbly - counsel you to perhaps enlist the aid and services of a professional communicator or science-writer, to whom you could explain your ideas, and who could then translate them in a measured, step-by-step, organized fashion in such a way as to make them more accessible to your audience.

Please forgive me if any part of this has been in any way offensive - my intent has been only to elicit clarification, amidst repeated failures of my own sincere efforts at understanding.

I sincerely do wish to achieve understanding here.

-------------

Now, having gotten all of that off my chest, I just want to add that I also think your presence on the EteRNA forum is an extremely unique and very, very valuable positive addition.

Your posts bring a lot of color and personality to the dialog here, and present a completely fresh view and immensely interesting (if so-far mostly inscrutable) set of ideas and theories.

Your tone in your presentations is always, unfailingly positive, totally respectful of others, and completely engaging, and I always enjoy reading all of them (even if I do come away frustrated from not understanding).

I do hope you will continue to share your progress in your studies with all of us here at EteRNA. I only hope that - eventually - you will be able to explain it all, so that I may finally understand.

Thanks, and Best Regards,

-d9
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Chris Cunningham [ccccc]

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Agree. I've removed the link that went a bit too far because it wasn't really appropriate or fair.
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blubblub

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Excellent. Thankyou d9. As you know we follow all of your comments closely and used your jewel design to test our diagonal architecture. And who knows -- it may be well something you relate (or Fabian or Chris) on your side of the fence that allows us to begin to communicate in a far better level than we have so far which is obviously frustrating both to the ETERNA community and ourselves. We thought when we wrote our software everything would be self-explanatory. To us, that was the hard part. It is new but not without precedent. Thomas Wilhelm and a hand full of others have gotten results using the base-2 system approach. However, none of them could agree on a standard mathematical template. We introduced a standard mathematical template and used color to prove it. Everything we do is derived from our template which we then port over to the ETERNA template. There is no way to test what we have except for the ETERNA website. I do not wish to ramble but please know how appreciative we are to hear from you. It means alot to us. We agree with everything Fabian, Chris and now yourself have said to us. We take it to heart and we will follow your advice. What you are doing is 'top down' as Thomas Wilhelm puts it. What we do is bottom up. You guys take what you see and find out exactly how it operates. Then you expand your knowledge base and apply it to larger and larger challenges. In short, you can see, touch and feel your results -- you get instant feedback and instant gratification proportional to your goals and expectations. We envy you. And once more, we know you guys are on the verge of something huge. I can not stress that enough. From what we see -- RNA is the path.
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Matt Baumgartner [mpb21], Alum

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blubblub, I tend to agree with d9 and the others, in that I while the things that you have posted look super interesting, I simply do not understand them. If you could, please give us a very high level idea of what you are doing, and why it is important to EteRNA players or researchers.

Thanks,
Matt
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blubblub

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Hey Matt, how are you doing! As all of you have suggested but only d9 expressed with wit, logic and a poet's soul; we are currently enisting the aid of a science writer at the University of Wisconsin that will help us present our findings "in a measured, step-by-step, organized fashion" to make them more accessible EteRNA players and researchers. Meanwhile, we will keep reading and learning and growing with the aid of your website. The one thing you can never repay to anyone is the time you take. We feel we have a debt to repay to the EteRNA players and researchers.

Hopefully soon, you will be able to join in the discussion (if it makes sense), and expound, expand, and apply any area you see fit to whatever ends your imagination and talent leads.

We believe RNA is rooted in light, has a mathematical language that combines shape plus change and motion plus form; and exhibits the same order and connection as ideas.

How hard can it be to prove that?

But we have the five software programs written that is based on our math. It works. But is it real? We don't know.

So like each of you, with humor and humility, and with what we have and what we have learned, now go back to work.