What if nucleotides are switched on or off like genes?

In light of the recent lab results where ‘branches’ fell short of its RNA synthesis goal, we want to offer an observation and hopefully some insight into our shared pursuit. What we are posting today has been said before and thought of before. It just has not been presented like we present it. We suggest that sometimes a fresh way of presenting proven ideas resonates with a new generation of men and women not trying to follow in the footsteps of the men of old, but seeking what they sought.

Something Ben Goertzel said strikes us as important to our shared pursuit: ‘Biological evolution doesn’t work by forcing organisms to satisfy highly specific constraints in order to survive. Rather, it demands that they give rise to emergent patterns displaying certain broad qualities. Searching for systems that satisfy specific ‘constraints’ is both ‘unnatural’ and very hard. The big question is: How do we go backwards from the desired emergent patterns to the underlying rules?

This is what we see in EteRNA with Adrian, Jeehjung, Mat47, D9, Berex NZ, Eli Fisker, Madde, Donald, lroppy, mpb21, AnticNoise, Ding, Boganis, iojp et al (we can’t list everyone we read, sorry).

Evolutionary Biology holds that the forces and processes that caused the Big Bang, cosmic constants, the universe to expand, galaxies to spiral, and solar systems to form, are identical to the forces that caused life to emerge on earth. Physics holds that all particles exist potentially (with a certain probability) as different combinations of other particles.

Our own work is inspired by Wheeler Families; a type of Base-2 system expressing E=MC2 in layman’s terms. For example: Wheeler families describe proton ‘collision’ behavior and express what happens when matter tells space how to curve; space tells matter how to move; and acceleration is equivalent to gravity. More important though to EteRNA is that the ‘glue’ that holds molecules like DNA and RNA together are the same patterns formed by Wheeler Families.

Work already has been done in labs as well as EteRNA have proven that RNA synthesis is more and more about discernible mathematical relationships – in particular patterns and symmetries (least common denominators) that remain invariant under different circumstances and viewpoints but give rise to emergent behavior which apparently follow a few simple rules.

But what are these rules? Is there a toolbox to find them? If the rules are simple, does that not infer that the tools we need are simple as well? Are there ‘larger picture’ clues in nature we can draw on?

We like something Moebius once said, that the area inside of a Moebius Strip is as important as the shape of the Moebius Strip itself. One of our findings in our base-2 model is that the nucleotides in a codon triplet (DNA or RNA) can be switched on or off.

The question is: Is the nucleotide switched on as important as the nucleotide switched off? The work done by scientists like Steve Paddock and Sean Carroll prove --at least with genes – that this is indeed the case. Maybe the same thing is happening at a simpler level with RNA nucleotides. Like a neutron in an atom, the nucleotide still holds value in the sense it contributes to the RNA structure but it does not carry charge and does not bond. It is like the pauses in music that allows us to hear the overall melody. This would also effect the folding.

The EteRNA puzzles and challenge winners consistently show every nucleotide as ‘turned on’. The colors are ‘fixed’. Maybe this is correct and maybe it isn’t. We have spent a considerable amount of our time exploring this idea. Our work suggests there is an alternative way. Jeehjung opined that our work is similar to a pseudocode. We had to look that up but – yes – it may well be a pseudocode.

EteRNA was announced almost exactly to the moment we decided we had taken our ‘pseudocode’ as far as we can go. It only took two seconds of reading posts on the EteRNA website to come to the realization we do not possess the intelligence, the background, the language or the resources EteRNA has at its disposal. We applaud this effort and know it will succeed because it is open to all kinds of thinking and that is what will be required to solve the puzzles and unravel the genome.

This is why we gladly offer our work and insights to EteRNA. We may be right and we may be wrong. We may be reading our data incorrectly. We may be howling at the moon. But we offer it nonetheless. We believe EteRNA has the right approach.

Team blubblub