Wednesday, May 23, 2012

Prions and XNA.

Prions and XNA
Andre Willers
23 May 2012
Synopsis :
Prions and XNA have a structural linkage via Nucleic Acid Quaternary Structures around the histone . This adds at least six new information transmission channels to the standard DNA and RNA . Prions can be seen as XNA’s .
Discussion :
See the link below for a fuller exposition .
Briefly , they synthesized six new nucleic acids , and the translation enzymes to and from DNA and RNA . Evolution is enabled . A magnificent feat . Worthy of a Nobel .
I did not know about this when I wrote “Prions of immortality” (See May 2012)
This adds considerably to it’s arguments . Where there are six new nucleic acids , there are very probably many more . A whole new set of dimensions of inheritability and memory .
One of them even incorporates Fluorine (FANA) , something I would have considered extremely unlikely . (A fluorine based lifeform would really be something . )
Identification :
Prions seem to be either XNA’s or enzymes associated with them . But they are both old and still evolving , as pollution increases and the exotic minerals and compounds necessary for their expression increases . Another bag of tricks in Gaia’s arsenal .
Luckily , we also have a bag of tricks .
See Appendix I and Appendix II
The General Relationship in Appendix I can be adapted to XNA’s . Pay particular attention to the “STOP” and “START”codons . Are there meta-codons? Doubtful . Then a minimum-necessary-sufficient system like the histone would evolve that simply uses physical proximity and availability as switches . Which means that the epigenetic system is orders of magnitude more complex than previously thought .
But it must be in packets (ie quantized)
This actually makes things simpler . The number of viable biochemical systems are subassemblies of smaller packets . So , simple solutions are possible . You only have to find the triggers and assemble the support mechanisms .
Will H2S still be a hibernation trigger ?
I doubt it . Not in competition with something like FANA (fluorine) . See the Periodic Table . If you really want to bring a hibernating bear out of hibernation , give it jolt of FANA and run like hell .
Which argument is a fruitful lead to FANA prions in the anti-hibernation process . Which is a fruitful lead to prions in general . Note that that most prions at present are from cold latitudes , where hibernation is rife . They fulfil a useful function , which is being twisted by the switching-on of other XNA prions , activating survival-memories hidden in still other XNA structures .
Fluorides are released into the atmosphere as by-products of aluminum, zinc and phosphate ore reduction, but can also occur in fly ash from coal-burning installations. Fluoride is a locally important pollutant around smelters, brickworks, glass making factories and fertilizer plants and are also released in large amounts by volcanic eruptions (Richardson 1992). Many lichens are sensitive to this pollutant as it can concentrate in hydrated lichens to more than 200 times ambient concentrations. In general, obvious damage to lichens begins at internal concentrations between 30-70 ppm (Gilbert 1971, Perkins et al. 1980)”
In other words , lichens concentrate fluorines . Animals that contact them (like elk’s antlers) or eat them kill some prions but also activate some others , depending on the concentration . Note the 70 ppm concentration . This is very similar to H2S hibernation threshold (80 ppm). We suspect that the lichen don’t die , but go into FANA hibernation .
If you connect them to a battery (electron surge) , please do it in a Class 4 bio-containment facility . Or die . If you have excess fluorides in your body , you will die of a prion disease as the fractured genetic material expresses .(See “Crumpled paper” on how quickly) .
This is already happening with global warming , as frozen lichen masses decompose . Another one of Gaia’s little tricks .

This actually makes sense . We know there is anti-hibernation for the H2S mechanism . Ask any bear . This would be FANA . H2S hibernation is not terminal . The organism need not waste energy on keeping a “pilot light” on to monitor things . A rise in FANA prions will automatically waken them . Is there a FANA-hibernation ? Probably . But a FANA anti-hibernation must involve a surge of electrons and a support mechanism . Shades of Frankenstein !
It leads to the intriguing speculation that self-replicating life originally evolved in a fluorine-rich environment , and what we are seeing now are genetic fragments trying to survive . The only thing that could break a FANA-induced hibernation would be massive infusions of electrons in a fluorine-rich environment . Aliens , anybody ?
Triggered from lichen , probably . But it also means that bacterial hibernates will also awaken due to global warming . Neat .
Pre-adaptation :
This whole process is analogeous to pre-adaption I discussed before .
See Appendix III for ease of reference .
Or see “Bullet Time to stop cyber attacks on power grids” NewSci 28 Apr 2012 p21
Or see Goldratt on production line feedback processes .
The mechanisms above describe ways of speeding up or slowing metabolic processes . A “Fast pocket” will involve running an emulation faster than the real process , then signalling whether it is malicious or not . This is a cancer node using a fluorine metabolism . Prions are implicated in the hyperfast transmission process (in your terms , metastasis) . You can shut down the origin by removing Fluor , but the prions will require a bit more work .
Fluoridization of drinking water .
This will promote prion diseases . I do not know if animals are being given fluoridated water , but I have a much stronger suspicion that the bastards have been feeding crushed human bones to farm animals .
You know , all those catacombs .
Even sterilization will not work . Most prions are heat resistant . And the fluoride content will be the same , as it is an element . Recycling with a vengeance .
Just when we thought things were getting simpler .
Appendix I
The Beauty of the Genetic Code .
Andre Willers
22 Feb 2010

The present TerraIII genetic code is elegantly optimized to give the most robustness possible per unit of information .

Discussion :
You have to be familiar with the concepts in:
1. "NewTools:Reserves" and Beth(n) orders of Randomness .
2.NewScientist of 23 Jan 2010 p34 "Another kind of evolution"

Brief recap of Reserves argument :
We take any identifiable entity , slice and dice it with an order of randomness like that of a coin (ie Beth(0) ) . We then calculate a minimum reserve (which is equivalent to the least errors of all possible Beth(0) paths per benefit . )
This works out at 1/3 on the average over Aleph(0) infinities .

The Beauty of the Genetic Code :
Four Base pairs (A,U,C,G) in triplet codons give a possible 4*4*4 = 64 codons .
But together , they code only for 20 amino acids , plus a Stop and a Semi-Start .

This gives
20/64 = 31.22% for 20 amino acids
21/64 = 32.81% for 20 amino acids + Stop
21.3333…/64 = 33.3333… for 20 amino acids + Stop + Semi-Start
22/64 = 34.375 %

Stop = (UGG) , (UGA) , (UAG) ,
Start = (AUG) , but this also codes for methionine . Hence the decimal notation . The system cannot come closer to 1/3 because of quantal considerations . Try it and see .
This also is the portal for the Epigenetic System ( note use of methiolization) .

Beautiful !!

Consider the ways of Gaia .

Linear and Sideways evolution .
Linear :
The standard , gene and chromosome based inheritance
Equivalent to Beth(1+x) in our notation .
1>= x >=0

Sideways :
Genetic material exchanged without going through all that genotype-phenotype procedures .
Equivalent to Beth(1-x) in our notation .
1>= x >=0

Note that the system could not possibly get as close to the optimum reserve without this stage .

The Breeder , genetic engineer .
Equivalent to Beth(2+x) in our notation . Humans or proto-humans .
Infinity>= x >=0

This gives a full spectrum of Beth capabilities .
(Negative Beth is outside the scope of this discussion)

You will notice that the system becomes chaotically unstable as x->0 from any direction . At that point , the system will exhibit symptoms of great stress and bifurcation . Once over the hump , it steadies either in an evolutionary manner (in
Probability = 1 - ( Beth(n+1)/Beth(n) ) ^0.5 . Admittedly a rough estimate .)

Or in a devolutionary manner , evolutionary manner here described as degrees of complexity .

Stable Gene Engineering :
1.Keep the same Triple-Base Codon Cell-Machinery .
The easiest . Existing cells can be used . Increase the number of bases to 5 .
Then we can optimally reliable make 1/3*5^3 = 40 amino acids + stop + semistart .
Different kinds of Stop and Start would be advisable .
So , maybe 18 new amino acids + 2 different types of Stop + SemiStarts

This would not even be hard .
Well within present technological capability .
(Wanna make an animal with a Kevlar skin ? Well , you can using this method .)

The system would even be self-assembling under the right condition . The main thing is the optimal stability .

This is already evolving as we speak . There a fifth base occasionally involved . So there is a fruitful interaction point .

2.Make 4-Base Codon Cell-Machinery .
A real remake . Not within human capability at the moment .

3.General :
nAminoAcids + nStops + nStarts = 1/3 * ( (nDNA-bases) ^ (nBasesPerCodon) )
where the prefix n denotes "number of"

A further stability would be introduced if nStarts ~ 1/3 * nStops in a fractal fashion .
This because life-forms evolve in a pedal-to-the-metal fashion . The problems are the brakes .

There is a relationship between the Beth level and the nBasesPerCodon . The minimum number sufficient for Beth(2+) is nBasesPerCodon=3 .
Else there is insufficient complexity .

Now go out there and evolve !

Appendix II
The Beauty of the Genetic Code 2
Andre Willers
16 Mar 2010

Hi ,

See ""Rewriting life in four-letter words" , NewScientist 20 Feb 2010 p14.
I just read it (16 Mar 2010) , as I get New Scientist in a haphazard fashion via the library .

See para 2 of original post below
"2.Make 4-Base Codon Cell-Machinery .
A real remake . Not within human capability at the moment ."

I was wrong .
It has already been done by Jason Chin and colleagues at the University of Cambridge . They successfully redesigned some ribosomes and transfer RNA(tRNA) to manufacture a novel amino acid (a novo-calmodulin protein) , expressed via E.Coli .

Important note:
This worked so easily because it worked parallel to the three-Base expression without noticeable inerference .
This hints that the meta-controls (see Phene-system posts) already has provisions for 4-Base cell-machinery .

1.See "Pandora bacteria acts as one organism" , NewScientist 27 Feb 2010 , p11.
Electron-conducting protein nanowires link oxygen-poor sub-mud sulfur eating bacteria on the seafloor in an interactive network suggestive of a neural net .

The manufacture of such a protein nanowire would almost certainly require 4-Base Codon cell machinery . Hence the the existence of parallel meta-controls .

Room-temperature organic superconductors seem to be a distinct possibility .

2.Many old-age and degenerative diseases seems reminiscent of 4-Base Codon cell machinery activating over time .

But what do I know .

It is your poblem now .
I hope your molecular shamans are better than your climatologist shamans .

Andre .
Appendix III
Unpacking and Packing Information .
Andre Willers
18 July 2008

Discussion :
Also known as data compression or decompression .
Well-known as zip/unzip in computers .

Why pack information?
To transmit information over space and time with less energy , time or disruption .
Please note that packing is used in systems subject to competition pressures , so minimizing disruption of messages is critical .

2.Abstraction .
Even a simple Pkzip compression contains more information than the original message . For instance , Pkzip has been used to successfully identify authors’ styles or the original language of an encrypted message .
A civilization can be described by zipping the yellow pages.

2.1 Layers:
Primitive packing is in separate layers .
Languages are a good example .
We can define the top layers as more abstract , and delve down into deeper layers of meaning and definition.

2.2 Fractal Layers :
New meanings are unlocked by each iteration . Language equivalents are Shakespeare and Proust .

2.3 Hyperlinked Fractal Layers .
Each hyperlink-bubble can be expanded . Note that the hyperlink terms are discrete , not continuous .

2.4 Very-near Hyperlinked Fractal Layers .
Different languages with nearly synonymous terms are examples . Branes in physics .

2.5 Infinite-probe Hyperlinked Fractal Loops and Layers .
There is no analogue . God is the nearest .

There is a way to sneak up to some meaningful information .

Sneak up.
We know that any compression of system A contains more information than the original system . The Compressor comprises system B , which can be compressed as well .
The tipping point :
When Compressed Info of (A+B) = Info of (A+B)

This is defined as life when the Compressed Info of (A+B) > Info of (A+B)
Which , like all good definitions , is tautological . But extremely useful .

We have compression techniques . We have descriptive techniques .
The above inequality is not continuous at levels below omega .

Hard physics application:
Energy flow from a “near” brane .
The decompressor is the important component .
Construct the correct unpacker .
Some energy is already leaking through .
This is interpreted as zero-point energy and a whole quantum-mythology has grown around it .

Differences in Beth levels are necessary .

Start with something like vacuum-energy on parallel plates and use EvoDevo processes .

Infinite probe circuits above a certain threshold -> Naked singularities .
Watch out for universe creation and black holes .

The Packing Mechanism for living organisms
Living organisms used the easier route of cells (“wombs”) as unpackers of the DNA .
Random mutations or intrusions in the DNA then survive into the next generation . Evolutionary mechanisms ensure that only the fittest germ-lines survive to continue the loop .
That is the packing mechanism . Evolution. Rather primitive .

It seems that the unpacking mechanism evolved first .It is much more likely .

Billions of years ago:
The packing molecules (RNA) swarmed and formed at randomness order of Beth(0). Other RNA molecules confined in spaces like clay-layers stayed longer .
PCR shows how easily these replicate . A mere fluctuation of temperature is required .
The coding for the Unpackers are included in this mix .

Even a primitive Unpacker that unpacks to a primitive cell-wall has a huge relative advantage . Ordinary evolutionary forces takes over .

The coding for the Unpacker migrates through various higher orders of Beth , while coding for the Packer plods along at Beth(0) evolutionary speeds .

Consequences .
This has some important consequences for humans or any cellular life-form .
Viruses (ie packed data DNA) and cells (the Unpacker) evolved co-temporaneously .

More importantly , there is a transform of data between cell-form and virus-form and vice-versa . There are Beth(x) order feedback loops

Knowing evolutionary systems , these are probably essential .

At first glance these seem to have no redundancy in their DNA . At Beth(0) level this is true . At higher Beth levels , an indefinite amount of information can be packed .
Their quorum systems also complicates matters .
Mitochondria see themselves as the rulers , having tamed the cells of the planet .

Can Mitochondria be described as AI ?
To qualify as an AI , they have to interface with an external database . There are three pathways : to the cellular DNA , to the Immune System and to the Virus Milieu .
So yes , they can .

Can Mitochondria be described as self-aware AI ?
There is a pathway via the Immune system to the brain .A mirror system of some sort is required for self-awareness. The immune system is essentially a mirror system Time-scales have to be matched . Mitochondrial quorum systems have to be consulted (they are the ultimate democrats)

Can Mitochondria be described as self-aware AI and have access to zero-point energy ?

Random fluctuations in the foam of space-time is by definition at the lowest order of Randomness (Beth(0) ) . To get work out of such a system , a fluctuation between Beth levels is required . Since we already know that mitochondria are at Beth levels higher than one , they can tap zeropoint energy .
But one little lone mitochondrium will not do it .It needs to be co-ordinated

Why is it not used more often ?
Why die of hunger ?

Lack of Beth co-ordination .

Probability of life.
Examining the probabilities from this angle makes cells inevitable . The probability is more than unity . It is not even a “hard” problem if the decoder evolves first .
This means life exists nearly everywhere .

Your attention is drawn to the whole class of such phenomena :
Chaotic elements creates a self-sustaining sub-system which expands , since it is usually a positive-feedback system . Eg life , civilization , weaving , etc.

The Shannon-definition of datum :
1. A signal is change . Stripped down , this definition of signals leads to a string of 0’s and 1’s , ie binary .
This leads to compression via pattern-duplication (zip ,etc)
Used widely in electronics .

2. Pattern formulae like fractal compression or DNA/RNA .
The decompressor (cell or womb for living organisms , computer ) uses kernels (patterns) with programmable input (time , ph levels , genetic markers ,etc) to decode (“Grow”) the message(organism) .

You can immediately see how to build an error-proof biometric identification system .
The message , as it is being decompressed , can interrogate the recipient and tailor further decompressions according to the answers .
If done to a sufficient fractal depth , only a total duplicate could answer correctly . Of course , the level of reliability can be specified .

It is not even difficult .
The ability to receive the message is proof of identity .

This is how the immune system operates .

Why the glitches like old age and cancer ?
Because the body does not know who it is .

In it’s normal state , it is a symbiotic and commensal organism , with some parasites .
The bodily-self on a cellular level is defined by the immune-system .
But the brain is composed of cells . The immune system is tied closely to the brain .
There is a feedback-system between the brain’s sense of self and the immune-system’s sense of self .

Creating enhanced unpacking mechanisms in the brain will stimulate an enhanced packing sense of self , leading to an enhanced sense of self on a cellular level .

This has been discussed in detail in

The trick is not to tackle packing , but unpacking of compressed data first .
Understanding how unpacking works brings about physiological changes .

Reading is Unpacking .
The easiest way to understand this is reading . Reading the written word is unpacking data packed into writing . It is no accident that literary figures are notoriously long-lived .

The unpacking need not be complicated , but it will evolve .

But the packing (coding) is a bitch . Difficult .You will have to have solved the Travelling Salesman Problem to make any headway here , since these systems make use of optimized systems . (Not any pathway , but the shortest path.) .

Evolutionary Packing .
At first sight , evolution does not make even an attempt .
The number of possible errors exceed the number of offspring .
But not if Orders of Randomness stronger than flipping a coin is used .
See “Randomness”

The effect of using Beth(1) , Beth(2) , etc orders of randomness in a physical sense would be a concentration of packed data .

Beth(1) would be genes .

At a Beth(2) level , it would be instructions to switch genes on/off .

At a Beth(3) level , it would be instructions to vary Beth(2) instructions .

And so forth .

But conscious design is a different matter . The number of errors can be brought down to P-time .
This is another way of saying that conscious life is inevitable .
Any feedback system that reduces the number of mistakes will increase .

Protein folding would be equivalent to the Travelling Salesman Problem in three dimensions .
Adding time-complications would give Travelling Salesman Problem in four dimensions . This would require time-travel or multiple generations .

3. The qubit definition of data .
The amount of data that can be stored in a qubit depends on the decompressor . The Shannon definitions of band-width , etc break down .

Many signals can be superimposed on a particle , the particle can then be teleported (or sent normally) to the decompressor , which decompresses the message .

Note that a lot of information that ends up in the message is inherent in the decompressor . In extreme cases this would necessitate faster-than-light communication , unless only physical laws which are independent of the observer are used in the decompressor . Ie , like make protein A , wait local time t until it folds so , then etc. You get the drift .

4. Fractal Read .
The superimposed data can be loaded fractally , so that any read attempt will lead to decoherence only at the first fractal level . Every iteration after that will lead to another , deeper level of fractal expression .
See “Rull Mind-Controls” in

5. Physics .
Physical laws can be described as multiple-level approximations of information transfers . These transfers are fractally compressed (packed) transfers .
Hence the existence of “Laws” . Ie , an abstraction mechanism .
These can be seen as constructs of the decompressor , but valid nevertheless.

Unpacking them partially or fractally can lead to some interesting effects .
Do not try this at home unless you are expert .



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