Wednesday, July 13, 2011

Quantum model for remote replication of DNA

The idea about remote replication, transcription and translation of genes in terms of electromagnetic field patterns is very attractive and would be in accordance with the wave DNA vision. This requires a coding of DNA nucleotides. I have proposed several codings of this kind.

  1. In DNA as topological quantum computer model quark and anti-quark at the ends of a flux tube connecting DNA nucleotide to a lipid of the nuclear or cell membrane takes care of the coding. Also sequences of dark nucleons giving rise to dark nuclei realize the analogs of DNA, RNA, tRNA, and amino-acids as well as vertebrate genetic code (see this). Dark nucleons sequences could correspond to the phantom DNA discovered by Gariaev's group.

  2. Quantum antenna hypothesis represents one of the oldest ideas of TGD inspired quantum biology: molecules would act like quantum antennas. Frequency coding would be very natural for groups of molecules participating in the same reaction: the flux tubes connecting the molecules would carry the radiation inducing resonant antenna interaction and phase transitions reducing Planck constant would bring the reacting molecules near to each other. Magnetic flux tubes connecting the molecules would be essential element of the mechanism. Remote replication would represent an example about a situation in which hbar changing phase transition does not take place. If one wants coding of individual molecules -such as DNA nucleotides- by frequency in turned coded by the value of hbar for given photon energy (E= hf), one is forced to make ad hoc assumptions and it is difficult to find any plausible scenario. Quantum antenna mechanism could make possible remote replication for which the findings of Montagnier's group as well as remote transcription for which the work of Gariaev's group gives some evidence.

In the sequel a model for the coding of DNA in terms of radiation patterns is discussed. There are three experimental guidelines: the phantom DNA identified as dark nucleon sequences in TGD framework and the evidence for remote activation of DNA transcription - both discovered by Gariaev's group - are assumed as the first two key elements of the model. The remote replication of DNA suggested by the experimental findings of Montagnier's group serves as a further guideline in the development of the model.

Polymerase chain reaction (PCR) is the technique used in the experiments of Montagnier's group. DNA polymerase catalyzes the formation of DNA from existing DNA sequences serving as a template. Since the catalytic interaction of DNA polymerase takes place with already existing DNA sequence, the only possibility is that first some conjugate DNA sequences are generated by remote replication after which DNA polymerase uses these sequences as templates to amplify them to original DNA sequences. Whether the product consists of original DNA or its conjugate can be tested.

The model inspires the proposal that the magnetic body of a polar molecule codes for it using dark nucleon sequences assignable to the hydrogen bonds between the molecule and surrounding ordered water layer. Quantum antenna mechanism would allow the immune system to modify itself by developing ordinary DNA coding for amino-acids attaching to and thus "catching" the polar molecule. The mechanism could be behind water memory and homeopathic healing. Every polar molecule in living matter would have dark nucleon sequence or several of them (as in the case of amino-acids) serving as its name. This would also associate unique dark nucleon sequence also with the magnetic body of DNA so that DNA-dark DNA association would be automatic. Same applies to mRNA and tRNA and amino-acids.

Before continuing I want to express my gratitude to Peter Gariaev for posing a question which led to the realization of the connection between quantum antenna hypothesis, remote replication, and genetic code and its generalization.

1. The findings that one should understand

It is good to start by summarizing the experimental findings that the model should explain.

  1. One should be able to identify phantom DNA. This identification explains the findings about phantom DNA if ordinary and dark DNA have common resonance frequencies and therefore behave like resonantly interacting quantum antennae.

  2. The earlier findings of Gariaev's group suggesting remote gene expression, which becomes also possible if the DNAs of the sender can activate the DNA of the receiver by radiation. Direct activation could be based on electromagnetic signal between DNA of the sender and ordinary conjugate DNA of the receiver. Scattering from ordinary and possibly also phantom DNA and would generate this kind of signal. The challenge is to explain why the activation obeys genetic code in the sense that a given DNA sequence activates only similar DNA sequence.

  3. The claim of Montagnier's team is that the radiation generated by DNA affects water in such a manner that it behaves as if it contained the actual DNA. A brief summary of experiment of Montagnier and collaborators is in order.

    1. Two test tubes containing 100 bases long DNA fragments were studied. Both tubes were subjected to 7 Hz electromagnetic radiation. Earth's magnetic field was eliminated to prevent its possible inteference (the cyclotron frequencies of Earth's magnetic field are in EEG range and one of the family secrets of biology and neuroscience since seventies is that cyclotron frequencies in magnetic fields have biological effects on vertebrate brain). The frequencies around 7 Hz correspond to cyclotron frequencies of some biologically important ions in the endogenous magnetic field of .2 Tesla explaining the findings. This field is 2/5 of the nominal value of the Earth's magnetic field.

    2. What makes the situation so irritating for skeptics who have been laughing for decades for homepathy and water memory is that the repeated dilution process used for the homeopathic remedies was applied to DNA in the recent case. The solution containing no detectable amounts DNA (dilution factor was 10-12) was placed in second test tube whereas the first test tube contained 100 bases long DNA in the original concentration.

    3. After 16 to 18 hours both tubes were subjected to polymerase chain reaction (PCR), which builds DNA from its basic building bricks using DNA polymerase enzyme. What is so irritating from the point of view of skeptic was that DNA was generated also in the test tube containing the highly diluted water. Water in presence of second test tube seems to be able to cheat the polymerase by mimicking the presence of the actual DNA serving in the usual situation as a template for builing copies of DNA. One could also speak about the analog quantum teleportation. Note that the presence of both test tubes - and therefore some kind of communication between the samples - is absolutely esential for the process to take place: repeated dilution is not enough.

2. The model of remote replication consistent with DNA as topological quantum computer model

The basic assumptions are that the scattered radiation, the flux tubes of the magnetic body of DNA along which the radiation propagates, and quarks and antiquarks at the ends of the flux tubes from system able to serve as a template for the formation of conjugate of ordinary DNA. To understand how remote remote replication could take place, some further assumptions are necessary.

  1. The flux tubes emanating from DNA are parallel and condensed at 2-D flux sheet having DNA at is first boundary so that DNA nucleotides can attach to the flux tubes at the second boundary. The attached nucleotides would be along the same line and would form DNA sequence in remote replication process.

  2. Quantum antenna interaction takes place between group of molecules participating a given reaction so that they have common antenna frequency as resonance frequency. The frequencies characterize the radiation propagating along magnetic flux tubes connecting the molecules, and could come as sub-harmonics of the frequency of (in the case considered) visible light from the formula

    E= hnf, hn=n h , n=1,2,3,... .

    Here E is the fixed energy of photon. hn denotes value of Planck constant which in TGD Universe can have infinite number of values coming as multiplies of the ordinary Planck constant h.

    For a given photon energy E one obtains harmonics of the basic wavelength

    λ=c/f(n)= nλ0 .

    Wave length would correspond to the length of the flux tube proportional to n. DNAs with flux tubes characterized by different values of n would correspond to different levels in the evolutionary hierarchy. In TGD inspired theory of consciousness the value of hn serves as the measure for the time scale of planned action and memory span and neurons of frontal lobe would represent the highest level in the hierarchy,

  3. If resonance frequency is same for all nucleotides, frequency cannot distinguish between DNA nucleotides. In the model of DNA as topological quantum computer the quark (u or d) and antiquark (kenooverlineu or kenooverlined ) at the ends of the flux tube code for A,T,C,G. This model is the simplest one and does not require any additional assumptions about frequency coding. It also allows resonant interaction at several frequencies: the scattering of visible light from DNA indeed produces a wide spectrum of frequencies interpreted in terms of dark variants of visible photons.

    One can criticize the assumption that particular quark or antiquark is associated with the flux tube ending at particular nucleotide. At this moment this assumption does not have a convincing dynamical explanation. Presumably this explanation would rely on the minimization of the interaction energy.

  4. What is needed is a model explaining why the resonant antenna frequency does not depend on nucleotide: obviously the frequency should relate to something shared by all nucleotides. An energy level associated with sugar-phosphate backbone of DNA is what comes first in mind. A more exotic option is transition involved with quark-antiquark pair. Since electromagnetic field for non-vacuum extremals is accompanied by classical color field, the exchange of gluons between quark and antiquark suggests itself as the quantum antenna interaction distinguishing between nucleotides.

Quantum antenna mechanism is extremely general and flexible and might be a fundamental mechanism of bio-catalysis allowing also communication between visible and dark matter sectors. Antenna mechanism is of course central also in ordinary communications. If the biologically most relevant interactions of biomolecules via quantum antenna mechanism then also water memory and the claimed effects of homeopathically treated water might be understood (see this). The testing of the dark photon aspect of the hypothesis would require the detection of the dark photons somehow: the decay to a bunch of n ordinary photons with same wavelength is the obvious manner to achieve this.

1. Identification of phantom DNA

The observed residual coherent scattering from a chamber from which ordinary DNA is removed inspired the notion of phantom DNA. The questions are what phantom DNA is and is it relevant to remote replication of the ordinary DNA.

Phantom DNA identified observed in the scattering experiments could correspond to dark nucleon sequences realizing vertebrate genetic code with dark nucleons consisting of three quarks representing both DNA,RNA, tRNA, and aminoacids as particular nucleon states (see this). The resonant interaction between ordinary and dark DNA would explain why light at same frequencies scatters also from dark DNA in phantom DNA experiments. In Montagnier's experiments it could give rise to a positive feedback amplifying the radiation from second sample containing DNA. Water would be living in the sense that it contains "dark DNA" and dark DNA might allow remote transcription to ordinary DNA sequences in presence of ordinary DNA codons (triplets) and vice versa.

Skeptic can of course ask whether one could explain the experimental findings without assuming phantom DNA.

  1. In Gariaev's experiments which inspired the notion of phantom DNA part of DNA could "drop" to parallel space-time sheets and have the same effect on the scattered radiation as the ordinary DNA. This explanation would however require the many-sheeted space-time of TGD - probably equally abominable to skeptic as phantom DNA.

  2. In Montagnier's experiment the ordinary DNA contained by water droplet could diffuse to dark space-time sheets and enter the target along the same magnetic flux tubes as radiation propagates. DNA polymerase would allow to amplify this leaking DNA and produce conjugate DNA. Irradiation of the original DNA would generate the flux sheets serving as a route for the transfer. The killer test is to check whether it is indeed conjugate of the original DNA which is produced. Again many-sheeted space-time is required.

  3. For the option based on DNA as topological quantum computer hypothesis discussed above the remote replication would take place via the direct formation of conjugate DNA template and DNA polymerase produces from this copies of the original DNA whereas for "trivial" option conjugate DNA is produced. Phantom DNA would not be absolutely necessary. It is however questionable whether the intensity of the radiation is high enough and the resonant interaction with phantom DNA which could give rise to a positive feedback might be needed to amplify the radiation.

2. Dark DNA and frequency coding by quantum antenna mechanism

The remote transcription of dark DNA (phantom DNA) to ordinary DNA and vice versa would have quite far reaching implications for evolution since dark DNA/RNA/tRNA/amino-acids could define a virtual world serving as Rkeno&D lab where new DNAs could be developed and if needed translated to ordinary DNA. The dark DNA could be also transferred through cell membranes without difficulty, in particular to germ cells. Also the genetic transfer between different organisms would become possible. Second possibility is that the magnetic flux tubes mediating the dark photons traverse the cell membranes so that even the transfer of dark nucleons through the cell membrane is un-necessary. The implications for genetic engineering would be obvious.

Could one generalize the quantum antenna mechanism to the interaction between dark nucleons representing DNA triplets as entangled states of three quarks and ordinary DNA codons consisting of three unentangled nucleotides? Could similar mechanism realize genetic code assigning to dark DNA dark variants of RNA, tRNA and amino-acids via the analogs of transcription and translation processes? It seems that frequency coding, which - somewhat disappointingly - did not look natural for remote replication of ordinary DNA, is ideal for these processes so that the original idea of wave DNA would be realized at the level of dark-visible and dark-dark interactions.

The flux tubes would be associated with entire codons -DNA triplets - rather than individual nucleotides. Different DNA triplets do not form interacting groups in the sense that they should be connected by flux tubes. Therefore the simplest possibility would be frequency coding with specific resonance frequency for each DNA triplet. No quarks at the ends of the flux tubes connecting codons (not nucleotides) are needed. If one assumes that octaves correspond to the same frequency this would require odd multiples

λ(n)= (2n+1)λ0 , n=0,...,63

of λ0 so that the longest wavelength would be 127λ0. In the number theoretic model of the genetic code based on the notion of Combinatorial Hierarchy (see this codons are indeed labeled by 64 integers in the range 0,...,127=27-1. These integers are however not assumed to be odd. One can also consider the possibility that the frequencies are coded by the value of Planck constant and this option leads to an interpretation of the earlier proposed TGD inspired realization of the so called divisor code suggested by Khrennikov and Nilsson in terms of quantum antenna hypothesis. This will be discussed later on.

Support for this option comes from the phenomenon of phantom DNA demonstrating that resonant scattering of light from DNA and dark DNA occurs for the same frequencies.

Can one imagine remote transcription of dark DNA to ordinary DNA using only nucleotides as building bricks? This process would require coupling of DNA nucleotides to dark nucleons representing DNA triplets and it is not easy to imagine any simple mechanism making this possible. Already existing DNA triplets seem to be necessary.

3. Common explanation for the recent findings of Montagnier and earlier findings of Gariaev

In the experiments of Montagnier's group the outcome is remote replication whereas the earlier experiments Gariaev's group give evidence for remote activation of DNA transcription. Hence one expects a common underlying mechanism.

  1. The TGD based explanation of Montagnier's findings relies on the assumption that the homeopathic procedure generated a population of dark DNA nucleotides in the diluted system. The sequence of dilutions and shakings was like a series of environmental catastrophes driving the evolution of dark DNA and also feeding metabolic energy to the system. The outcome was dark DNA population mimicking the original DNA in the test tube B. In the presence of DNA polymerase in tube B and second test tube A containing ordinary DNA the dark DNA was somehow able to generate ordinary DNA in tube B. The detailed mechanism for this remained open.

  2. Could the scattered laser light have the same effect as the homeopathic procedure? This would require a direct transcription of dark DNA to ordinary DNA in the presence of DNA polymerase and nucleotides (only them!). It is very difficult to understand how this could happen. DNA polymerase very probably does not have the same catalyzing effect on dark DNA sequences as on ordinary DNA sequences. It is also difficult to imagine the build-up of ordinary DNA from nucleotides using dark nucleon sequences as templates: if frequency coded codons would serve as building bricks, situation would be simpler as already found.

  3. One must not forget that the presence of the test tube A was essential in the experiment of Montagnier: communications between the test tubes crucial for the outcome must have taken place. The consistency between the two experiments could be achieved if the DNA in test tube A generated the counterpart of the scattered laser signal in Gariaev's experiments but certainly as a much weaker signal.

  4. This signal should have been amplified somehow by the presence the dark DNA sequences in tube B so that it would have been able to generate critical amounts of conjugate of the original DNA amplified by DNA polymerase to the copy of the original. What suggests itself is a positive feedback loop ordinary DNA sequences → dark DNA sequences → ordinary DNA sequences..... causing the amplification of the weak signal so that it is able to induce remote replication by the proposed mechanism. This kind of feedback of signals propagating between magnetic bodies was assumed also in the model for the strange images produced by the irradiation of DNA sample by ordinary light interpreted as photographs of magnetic flux tubes containing dark matter (see this) .

What is nice from TGD point of view that the consistency between the two experiments give support also for the notion of dark DNA and its identification as phantom DNA.

4. Summary

The basic assumptions of the model of remote replication deserve a short summary.

  1. Bio-molecules would serve as receiving and sending quantum antennas forming populations with communications between members just like higher organisms. The molecules participating the same reaction would naturally have same antenna frequencies. Quarks and antiquarks at the ends of the flux tubes would code for different nucleotides and the frequencies associated with the nucleotides would be identical. The character of classical electromagnetic field would code for a particular nucleotide.

  2. Remote replication and other remote polymerization processes would differ from the ordinary one only in that the phase transition reducing the value of Planck constant for the flux tube would not take place and bring the molecules near each other.

  3. The immediate product of remote replication would be the conjugate of the original DNA sequence and DNA polymerase would amplify it to the copy of the original DNA sequence. This prediction could be tested by using very simple DNAs sequences- say sequences consisting two nucleotides which are not conjugates. For instance, one could check what happens if conjugate nucleotides are absent from the target (neither conjugate nor original DNA sequence should be produced). If the target contains conjugate nucleotides but no originals, only conjugate DNA sequences would be produced - one might hope in sufficiently large amounts to be detectable.

  4. Frequency coding would be natural for quantum antenna interactions between ordinary DNA and its dark variant and also between dark variants of DNA, RNA, tRNA, and amino-acids. The reason is that dark nucleons represent the genetic code by entanglement and it is not possible to reduce the codon to a sequence of letters.

3. Possible implications

The proposed realization of remote replication seems to have rather far reaching implications for the understanding of the mechanism of homeopathy and basic mechanisms of immune system as well as to the understanding of how DNA-dark nucleon sequence association. One can also interpret the proposed TGD based realization of the divisor code suggested by Khrennikov (see this) as frequency coding of DNA triplets by the value of Planck constant assignable to flux tubes emerging from DNA triplets.

1. Possible relevance for homeopathy and immune system

TGD inspired vision about water memory assumes that the magnetic bodies of molecules dis-solved into water represent the molecules in terms of cyclotron frequencies characterizing its magnetic body. Molecules can lose their magnetic bodies as the hydrogen bonds connecting the molecule to the magnetic body are split. The population of these lost magnetic bodies would define a representation for the dissolved substance able to mimic it.

The hitherto unanswered questions concern the detailed structure of the magnetic body of the molecule and how it codes for the molecule. The hydrogen bonds connecting the molecule to the ordered water forming a kind of ice covering the molecule in the inactive state should be crucial aspect of the coding. If dark nucleon sequences are associated with the hydrogen bonds of this "ice layer" or generated in their splitting as I have proposed, one can ask whether dark nucleon sequences could characterize the molecular magnetic body. If so, cyclotron resonance frequencies or more general frequencies associated with the dark DNA sequences could code for the molecule. DNA sequences would define a universal language allowing for the system to name for polar molecules.

Quantum antenna mechanism would in turn associate ordinary DNA sequences with the dark nucleon sequences coding for the molecule. Hence one can imagine a development of a mechanism allowing the organism to modify its DNA by adding to it genes coding for proteins characterized by the same resonance frequencies as the magnetic bodies of the invader molecules. These proteins would couple strongly to the invader molecules via quantum antenna mechanism and the phase transition reducing Planck constant would allow them to catch the invader molecules by attaching to them. The fact that the DNA of immune system evolves very rapidly conforms with this vision.

2. Frequency coding for DNA sequences by the value of Planck constant as a realization of divisor code

The realization of dark magnetic bodies of polar molecules in terms of dark nucleon sequences allows to understand the association of dark DNA with ordinary DNA, RNA, and tRNA making among other things possible the transcription of dark DNA to DNA and vice versa. Dark nucleon sequences would be associated with the magnetic bodies of DNA, mRNA, and tRNA. This would apply also to amino-acid sequences. Dark DNA would separate from ordinary DNA as it loses its magnetic body in the splitting of hydrogen bonds and suffers denaturation. Similar mechanism would cause denaturation of other biomolecules and would mean that they "lose their names" and thus information content and become mere organic molecules instead of living bio-molecules. This kind of association would make the emergence of the genetic code and its generalization to the naming of molecules by DNA sequences trivial.

Genetic code can be understood from the proposed natural correspondence between dark nucleon sequences and DNA, RNA, tRNA, and acmino-acids). I have however developed also another realizaton based on TGD based realization of so called divisor code first suggested by Khrennikov and Nilsson and the following argument allows to interpret in terms of frequency for fixed value of photon energy with frequencies coded by the value of Planck constant.

  1. The observation of Khrennikov and Nilsson is following. Consider the integers n in the range 1,...,21 and obviously labeling amino-acids and let k(n) the number of divisors of n. Define B(k) as the number of integers n for which the number of divisors is k. It turns out that the numbers B(k) are rather near to the numbers A(k) of amino-acids coded by k codons. This suggests that given amino-acid A is coded by a product of prime p(A), which alone characterizes it, and integer n(A) in the range 1,...,21. The product of integers characterizing the codon coding for A would be characterized by the product of p(A) and some factor r(A) of n(A). With these assumptions given codon would code for only single amino-acid and the number of DNAs coding for amino-acid A is the number of the factors r(A) of n(A). The codons coding for A would be coded by integers p(A)r(A) such that r(A) divides n(A). The safest assumption would be that the primes p(A) satisfy p(A)>19 so that the p(A) does not divide n(A) for any A. If p(A) is as small as possible the value spectrum of p(A) is

    {23,29,31,37, 41,43,47,53, 59,61,67,71, 73,79,83,89, 97,101,103,107, 109}.

    What is interesting is that Mersenne prime M7=27-1 = 217 appears in the model of genetic code based on the notion of Combinatorial Hierarchy (see this). This model assumes that DNA codons correspond to 64 integers in the range 1,...,127. This realization of the genetic code cannot however be consistent with the divisor code realized in the proposed manner since it would require that the integers n(A)p(A) would belong to the range 1,..,127. The prime factors of these integers can however belong to this range.

  2. The TGD inspired proposal was that the flux tube assignable to amino-acid A corresponds to hbar =p(A)× n(A)hbar0 whereas the DNA triplet (for quark-antiquark coding nucleotide rather than triplet) coding for it is characterized by hbar =p(A)× r(A)hbar0 such that r(A) divides n(A).

  3. This proposal could be interpreted in terms of frequency coding by quantum antenna mechanism. For a given photon energy E wave length would be coded by the value of hbar and one would have λn=n λ0, n=p(A)n(A) for amino-acids and n=p(A)r(A) for codons. The condition that flux tube lengths are same for different DNA triplets would be satisfied if the common length of the flux tubes is an integer multiple of λ0 proportional to the product of all integers appearing as factors in the integers coding for amino-acids. The common length of the flux tubes would be therefore proportional to the product ∏A p(A)∏ArA.

For background see the chapter Homeopathy in Many-Sheeted Space-time of "Biosystems as Conscious Holograms".

13 Comments:

At 4:22 PM, Blogger ThePeSla said...

Matti,

I gave this matter some thought this afternoon and present to you a draft (I tried to keep my own terms down) of a project to suggest how you might consider applying these questions of computation to your framework, since you are heading that way anyway.

So see my post in pesla.blogspot called Noether and Noetics.

Essentially you should apply your many sheet idea to a hierarchy to the spectrum of these numbers for purposes of computation I suspect.

The PeSla

 
At 1:53 AM, Blogger Ulla said...

http://www.sciencedaily.com/releases/2011/07/110706113450.htm

"Chromosome Size in Diploid Eukaryotic Species Centers on the Average Length with a Conserved Boundary," was recently published in the journal Molecular Biology and Evolution 28:1901-11. It details a project that compared 886 chromosomes in 68 random species of eukaryotes - organisms whose cells contain a nucleus and are enclosed by cellular membranes. The researchers found that the chromosome sizes within each eukaryotic species are actually similar rather than drastically different as previously believed. They also found that the chromosomes of these different organisms share a similar distribution pattern.

http://images.sciencedaily.com/2011/07/110706113450.jpg

The team found that nearly every genome perfectly formed an S-curve of ascending chromosomal lengths when placed on a standardized X-Y axis. That meant the genome from a species of rice expressed the same pattern as the genome from a species of maize, sorghum, fruit fly, dog, chimpanzee, etc. "It eliminated a scale effect and made it possible to compare a species with several dozen chromosomes to a species with much fewer chromosomes," Birds are unique because in addition to their usual chromosome sequences, they contain one additional set of minichromosome sequences,

DOI: 10.1093/molbev/msr011

Mitochondrias also contain additional female DNA. And the Nuture-effect can also be heredical.

The genome isn't structure itself. Only its products are. One gene can produce many structures.

Dark information? Action at a distance?

 
At 10:15 AM, Blogger ThePeSla said...

Matti,

the link paper on the issue of degeneracy and number theoretic code I find rather simplistic and not up to the level of your deeper thoughts on this matter. And certainly not the way I treat binary systems in my quasical theories.

Also it is not clear to me that Ullas comment relates here- nor that that result is showing anything spectacular other than some things are random that correspond to some things patterned.

The questions you raise are much more interesting than the terms used (as with my terminology). Now do I understand there was no genetic material at all and it was not diluted to very little of it?

I hope you have been following my thoughts lately - I have a rather simple one today called Tetrons. These, structurally at least, may represent something scaleless where you can think of degeneracy as if some mechanism of quarks and wormholes etc.

Of course things once connected remain so like two bottles of supersaturated solutions moved far apart and one crystallized the other other will too if disturbed. But if we see this as action at a distance it is quantum theory is it not? And so is such ideas of memory say in water. If we can influence by mere choice what we see that changes what others see who never knew us directly- is that not dark information? Was that really a question Ulla? I remind you snowflakes can look like carbon stuctures, six fold.

Matti, we need to go a little deeper in these fundamentals.

ThePeSla

 
At 3:39 AM, Anonymous matpitka@luukku.com said...

Ulla,

the results you mention fit with the vision that DNA defines hardware for quantum computation and that braiding of magnetic flux tubes defines the programs. This also explains why the amount of "junk" DNA- the part of DNA responsible for quantum computer programs- increases with the evolutionary level.


Dear Pesla,

I do am note quite sure what you mean with the link to the paper on the issue about degeneracy and number theoretic code.

In any case, I would not be the first to call "simplistic" the discovery that vertebrate genetic code and counterparts of DNA,RNA,tRNA, and aminoacids are realized as states of dark nucleons!;-).

Someone might regard this kind of discovery as sensational since it has a potential of revolutionizing completely the views about the relationship between living and inanimate matter!;-).

Maybe some very important context is lacking and leads to misinterpretation of what I am saying;-).

 
At 5:47 AM, Blogger Ulla said...

http://zone-reflex.blogspot.com/2011/04/complexity-and-evolution.html

http://www.genomicron.evolverzone.com/2007/09/whats-wrong-with-this-figure/

No, simplistic is maybe not the word. Dark nucleons are very hard to sell on the market :)

 
At 10:44 AM, Blogger ThePeSla said...

Ulla, in Matti's article above a link to:
http://arxiv.org/abs/q-bio/0612022

"the chromosome sizes within each eukaryotic species are actually similar rather than drastically"

It an interesting but not surprising result. The DNA acts like a reverse rubber band at some point in the scale to our normal experience of rubber bands.

The arteries and vein are a cable system that conveys information of structure if you must have a physical concept. And the frequency Matti talks about is experimentally connected to the general structure (as well as the position of things) for it can regrow muscle nerve bones, the whole works over three inches or so- thus some limbs do not need to be amputated since this (Pearsons, the guy who said you can say anything in a text book and he who passed out nobel prizes). Is this DNA related? Some vague field with lines of force? Some correspondence of chromosome size and random data? Or the general picture of things as point positions and position complexes?

Hmmmm, perhaps this frequency coming from the HAARP program is playing with the context of our perception in our heads and making our skulls rather thick. :-)

The PeSla

 
At 1:25 AM, Blogger Ulla said...

"This also explains why the amount of "junk" DNA- the part of DNA responsible for quantum computer programs- increases with the evolutionary level." - my links meant a contradiction to this statement. The figure showed a small increase in eucaryotic DNA. Junk-DNA is still unclear.

Your "The arteries and vein are a cable system that conveys information of structure" would need a link.

One of the earliest books that treats this frequency coding problem (DC-electricity)is Beckers 'the Body Electric'- a fascinating book. DNA also react to frequencies like a rubber band, as you say. The problem in this case is regeneration, methylation, the Nurture. Not only "Junk".

I think you had better not advice us, it is very irritating. Better with only questions. This is a very long process, and I have been lucky to help Matti with this to a small part. I don't need advice. Links, yes.

 
At 2:37 AM, Anonymous matpitka@luukku.com said...

To Ulla;

In higher organisms the portion of "junk" DNA certainly increases: as you know it is something like 95-98 per cent for humans. I have strong temptation to argue that the situation is same for lower species.
Also the number of chromosomes increases with evolutionary level.

What the reference says is that for *a given species* the sizes of chromosomes do not vary much. This is just what I expect. The emergence of new species would mean the gradual emergence of more and more "junky" genomes and also of new "junky" chromosomes.


Also the emergence of flux tubes with higher Planck constant making possible intercellular communications in longer length scales would be involved. The same DNA sequence could have several evolutionary levels according to the value of Planck constant. DNA alone would not tell too much. This "dark evolution" would give rise to "cultural evolution" as the emergence of collective gene expression. Typically it would make flock of birds an independent organism.


The constancy of (*chemically*) expressed portion of DNA conforms with the idea that the evolution of hardware is slow. Also in the evolution of computers the evolution of software is much faster than the evolution of hardware.

Concerning the selling of dark nucleon DNA everything is a matter of time: the implications of these simple mathematical observations are so profound that this idea will make a five minute breakthrough when a correct combination of physics and biology background meets influential enough position in science community. I cannot of course help much since no-one in community listens to a heretic without academic power.

Second problem is that many of my theoretical physicist colleagues really manage to believe that everything about physics is understood in everyday length scales. Personally I find it extremely difficult to really believe that "everyday length scales" is meant to include also life. Sean Carroll is one of the numerous helpless victims of this cognitive disorder whose causes are difficult to understand even when one knows how horrible damage specialization can do for a young brisk brain. Not much can be done to help these individuals;-).

 
At 1:52 AM, Blogger Ulla said...

The functions of noncoding
RNA’s have linked gene expression with the smallest covalent modifications, methylation and acetylation.
Building a dynamic model of multiple dimensional composite functions at each moment by approximating negativity as a function of mass change is what may be necessary for discovering the causative force underlying oscillations in concentrations and states of small molecules and therefore populations. Is there a mechanism to define species’ variability through the physics of small molecules relative to the origin of carbon signaling?

Negativity = 'negative' part of ZEO, the interference/strings between waves and particles.

http://www.wseas.us/e-library/conferences/2011/Cambridge/MEDICAL/MEDICAL-09.pdf

You should look at this guy. And answer his questions, although his language is not usual. He may be 'the Prince' :)

 
At 6:32 AM, Blogger Ulla said...

I forgot the transposons, the part of the 'junk' DNA that is movable 'jumping genes'. They are of two types: DNA-transposons (cut and paste), c 3% and retrotransposons (copy and paste), c.42% of the genome. These (L1) are one reason for growing genome, and also behind some cancers (subsystem). Another important part is Alu-sequencies.

Hairpin loops are correlated? And the palindromic part of genome with duplications, insertions, deletions etc. Transposons also deliver material for building of telomers and centrosomes, so they are highly active (electromagnetic?). Telomers are also important for cancers, centromers for celldivision.

The cell tries to calm down the transposons through modifications of histones, metylation (primitive immune system) and epigenetics, RNA-interferense, so that only a small part can 'jump' (0,05%).

http://www.sciencedirect.com/science/article/pii/S1568786406001753

... the PATRR adopts a cruciform structure in male meiotic cells, creating genomic instability...

http://en.wikipedia.org/wiki/Palindromic_sequence
Restriction enzymes recognize a specific sequence of nucleotides and produce a double-stranded cut in the DNA. While recognition sequences vary widely, with lengths between 4 and 8 nucleotides, many of them are palindromic, which correspond to nitrogenous base sequences (expanding) between complementary strands, which, when read from the 5' to 3' direction, are identical sequences.

The 'junk-DNA' is used for remodelling, and is closely related to immunology (which is related to homeopathy), and immunology is probably one of the eearliest modelling factors for life, creating the membranes and genome.

Fast growth (much insuline?), temp., stress and diseases activate these (acetylation), short people doesn't have cancers, or very seldom.

They must be very important for this mechanism. I can see the fluxtubes and dark information at work:)

See Scott Devine, Barbara McClintock, John Pace II and Cedric Feschotte (for the evolution, these are maybe more important than mutations, because they are already there).

http://www.genetics.org/content/168/2/933.full

Epigenetics was first found in diabetics in humans.

 
At 9:11 PM, Blogger Matti Pitkanen said...

Immune system represents he fastest evolving part of genome and here direct transcription of dark nucleon sequences coding for invader molecules to DNA sequences attached to DNA coding for proteins in turn attaching to invader molecules by quantum antenna mechanism, is an attractive proposal to me.

Evolution would have a Lamarckian aspect: instead of applying a mere random change plus natural selection the bio-system would actively react on the invader molecules developing proteins catching them (just as we do in longer length scales, no one tries to fix the computer by modifying its circuits randomly!). The mechanism would apply also in the homeopathic healing. It would be really amusing if the despised homeopathy would be the Golden Road to quantum biology!

 
At 1:07 AM, Blogger Ulla said...

Ye, Lamarck represent the alchemical path of wisdom, and homeopathy the non-molecular, energetic. Really amusing. I must grin at it. Advanced science :D

Look how nicely it fits with the advanced science. We would only need new glasses.

 
At 10:11 AM, Anonymous Anonymous said...

The negative results with
vacuum tubes at the experiments
with Nina Kulagina show that
the Psy or its carrier is
intrinsic even for the inanimate
matter.

Dark Knight

 

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