Monday, August 24, 2009

Three new physics realizations of the genetic code and the role of dark matter in bio-systems

TGD inspired quantum biology leads naturally to the idea that several realizations of genetic code exist. Besides the realizations based on temporal patterns of electromagnetic fields I have considered three different new physics realizations of the genetic code based the notions of many-sheeted space-time, magnetic body, and the hierarchy of Planck constants explaining dark matter in TGD framework.

  1. The first realization - proposed in the model for DNA as topological quantum computer (tqc) - maps the nucleotides A,G and T,C to dark quarks u,d and their anti-quarks assignable to the ends of magnetic flux tubes representing braid strands and connecting nucleotides to lipids of cell membrane.

  2. Second realization was discovered in the model of dark nuclei as strings of dark baryons. Dark baryons realize codons in terms of quantum entanglement and without decomposition to letters. Dark baryons are strings of 3 quarks connected by two color flux tubes. The neutral states of the dark baryon predicted by the model are in 1-1 correspondence with DNA, RNA, aminoacids. Candidates for the counterparts of tRNA anticodons are also obtained if one accepts that genetic code actually decomposes to 2 steps 64→40→20 such that there are 40 dark baryon counterparts for tRNA anticodons. The amazing finding is that vertebrate genetic code comes out correctly.

  3. The third realization is a physical realization for the divisor code proposed by Khrennikov and Nilsson. The realization relies on two integers labeling magnetic flux tubes containing dark matter. The dark magnetic flux tubes assignable to DNA codons and amino-acids could be labeled by these integers providing a representation of the genetic code consistent with the divisor code. Also a physical mechanism implying the physical equivalence of the dark baryon code and divisor code can be imagined.

The basic proposal is that dark baryon counterparts of basic bio-molecules and genetic code were present from beginning and gave rise to pre-biotic life at the magnetic flux tubes so that the evolution of biological life meant the development of translation and transcription mechanisms allowing to transform dark baryon variants of the codons to their chemical variants. These mechanisms would be still at work inside the living cell and allow the living matter to perform genetic engineering. This proposal is consistent with recent findings about large variations of genomes inside organism.

There is a strange experimental finding by a roup led by a HIV Nobel winner Montagnier giving support for this picture. A water solution containing human cells infected by bacteria is sterilized by a filtering procedure and healthy cells are added to the filtrate. Within few weeks the infected cells re-appear. A possible explanation is that dark baryon variant of the bacterial genome realized as nano-sized particles remains in the solution despite the filtering.

The codes are discussed from the point of view of DNA as tqc hypothesis and the model for protein folding and bio-catalysis. The basic selection rules of bio-catalysis could be based on the two integers assignable to the dark magnetic flux tubes. Only bio-molecules whose dark magnetic bodies contain a layer characterized by same integers can be connected by dark magnetic flux tubes. The reconnection of the dark magnetic flux tubes selecting the bio-molecules participating the catalytic reaction and the contraction of these flux tubes induced by a phase transition reducing Planck constant and forcing the bio-molecules near to each other would represent basic mechanisms of bio-catalysis.

For background see the new chapter Three new physics realizations of the genetic code and the role of dark matter in bio-systems of "Genes and Memes".

24 Comments:

At 8:19 AM, Blogger Zephir said...

Frankly, I don't understand your obsession by "dark matter variant" of whatever. Montagnier's finding can be explained by quantum mirage mechanism without involving any aditional unknown mechanism.

http://en.wikipedia.org/wiki/Quantum_mirage

Is there some tangible evidence for supersymmetry at large scale?

 
At 8:28 AM, Blogger Zephir said...

/*..strong force as a scaled and dark electro-weak force...*/

I'm basically convenient with this view. Though it's much easier to understand it as a surface tension force in analogy to Casimir force at even more expanded scale.

 
At 8:38 AM, Blogger Zephir said...

/*...In TGD framework this might be seen as an evidence for the presence of (wormhole) magnetic flux tubes as carriers of water molecules...*/
Apparently common crackpot strategy is to go from one experimental result into another without citations of authors, while claiming "yeah, it's the consequence of my framework, too" without any reproducible sequence of logic given and to pile ideas into undated PDF files periodically rewrited.

 
At 12:13 PM, Anonymous André K. said...

Hi Zephir,

you wrote:

"Montagnier's finding can be explained by quantum mirage mechanism without involving any aditional unknown mechanism."

Can you please give me the explanation? I don´t really get it just with the information from the wiki article. What exactly reappears in the filtrate?

André

 
At 2:20 AM, Blogger Matti Pitkanen said...

Dear Zephir,

I am not the only one whose patience you have been testing continually with you nonsensical comments (I remember your incredible behavior in Kea's blog recently, I remember your silly babbling in quite recent discussion about breaking of Lorentz invariance, etc).
And now same here. This quantum mirage comment has absolutely nothing to do with the topics discussed. Same can be about the remaining comments.

You know nothing about physics: why are you teasing people with your arrogant ignorance? I hate the term "crackpot" since it is so much mis-used but in your case I make exception. Since I do not want anyone to fill my blog with trash, I will moderate out your comments in the sequel if the continue to be similar nonsense.

 
At 2:24 AM, Blogger Matti Pitkanen said...

Dear Andre,

I am sorry for this stuff of Zephir. He is talking complete nonsense. I have not been forced earlier to censor out comments but this seems to be the only defense against trolls like Zephir.

 
At 7:48 AM, Blogger Matti Pitkanen said...

To Zephir:

Since you do not use your own name, I take the freedom to talk to you as your psychiatrist.

You seem to have personal problems and your behaviors in physics blogs do not seem to help to resolve them.

Your strategy in my case was obvious. You applied- or you thought that you were applying- Socratean method. You make a question and -instead of listening the answer as Socrates would have done- you make a second unrelated question. You of course have answers to all these questions so that this is just rhetoric.

The intended victim of you Socratian method of course realizes what you are aiming at. You are waiting for the glorious moment when you can say that your victim has not been able to give a single example about prediction of your theory! Socrates has once again demonstrated how little the companion knows!

In this Socratean process your comments get gradually more rude and -not surprisingly- also your intended victim starts to use heavier rhetoric. You get angry and represent direct personal insults. Sooner or later you initiate a whole flood of comments just to irritate. The outcome is that you are censored out and now Socrates is really really angry.

So: was this worth of it? Isn't a raging Socrates throwing insults a rather ridiculous character?

My suggestions for a more productive line of approach.

a) In blogs it might be good idea to stay in the topic of the discussion and leave Socratean method to Socrates.


b) If you have some ideas, why not document them and send them to viXra or some other open archive. The process of careful documentation might help you to realize that sending a jpeg file representing a randomly chosen image is not a justification for the claim that in General Relativity the notion of varying speed of light makes sense. And that a link to the word "Quantum Mirage" in Wikipedia is not quite enough to explain an anomaly in biology.

c) You might also find it useful to participate some basic physics courses. This might help you to realize that modern physics is not just blog rhetorics but an outcome of the lifework of intellectual giants of their time.

d) You could also try to reconsider what "simple" means in physics. It means conceptual simplicity, minimal number of principles. As far as mathematics is involved, conceptual simplicity implies just the opposite since Universe is indeed very complex, maybe it is as complex as it can be. Anyone who really thinks that modern physics can be done by using elementary college arithmetics, can be safely classified as a crackpot.

e) And finally: this painful question about ego. It is never too late to initiate a serious attempt to get rid of it. You never reach this goal but just this attempt makes gradually your life much more pleasant.

 
At 11:03 AM, Blogger Ulla said...

Oh, my God, what an explosion. I waited for something, but this! Bravo, Matti, you sing out at last, not one day too early.

But that with the ego you have missed. If you loose it you will be nothing, nothing worth to fight for. That is the end of the fight, the end of personal growing. To get rid of ego is too Buddhistian for me. Pleasant perhaps for the others, they can freely stamp at me.

Otherwise congratulation to a very interesting topic - again.

Fight on! It will be worth it!

 
At 11:54 AM, Anonymous André K. said...

"I have not been forced earlier to censor out comments[...]"

Too bad - I believe the explanation might have been interesting ;)

About the ego thing: I don´t think it´s a good idea to loose it or to get rid of the ego. It´s like most things: sometimes you need it and sometimes not. :D

André

 
At 5:00 PM, Blogger Zephir said...

[q] ..believe the explanation might have been interesting.. [/q]
Hi, Matti.

My explanation of autoinfection isn't based on "dark baryon theory", but on thixotropy of water clusters. Water clusters have interesting aspect of behavior: albeit elastic, they behave like tiny pieces of plasticine due the quantum mirage phenomena. This well known quantum effect is able to fill hole in large groups of atoms by quantum resonance effect of probability wave.

http://www.aetherwavetheory.info/images/chemistry/water/cluster_memory.gif

When we separate hydrogen ion from some random side of cluster, the cluster will get another ion from environment in such a way, the original shape of it will be retained - although whole cluster suffers by wild attacks of water molecules from all sides.

This model explains autothixotropy of water, Mpemba effect and even undeniable results of homeopathy and cluster medicine. We can imagine, in contact with foreign molecules water clusters will get modeled by charge density into mirror-like shape which can be retained even after removal of original molecules.

After then the quantum mirage phenomena can take place again, just in opposite way: in contact with polarized surface the repeated contact with clusters can model this surface into shape of original molecules. It can affect for example surface proteins, which are sensitive to particular geometry of electric charge density, which transforms them into activated complex.

So we can imagine, in environment formed by shaped water clusters the synthesis of proteins will be affected in the way, which replaces the physical presence of bacterial RNA from original solution. Here are even theories, organic life was transported into Earth from comets, in which existed supercooled water with stabilized clusters exists. The true is, supercooled water at -150 deg. is really behaving like solid gel, which keeps its shape after deformation, because water clusters are stabilized by low temperature here.

While I respect your theory from formal perspective, I cannot omit apparent lack of logical steps, in which you're trying to interpret various phenomena. Just try to ask someone else to reproduce your "explanations", and you'll see. Arrogance won't help you in such case.

 
At 5:18 PM, Blogger Zephir said...

/*..as far as mathematics is involved, conceptual simplicity implies just the opposite ...*/
I can fully agree with this stance, as my Aether Wave Theory is all about it. It just claims, whole complexity of Universe can be modeled by nested particle fluctuations of sufficiently (if not infinitely) dense environment.

Note that the formal math fails even at the case of deterministic description of motion of five to six particles, so I'm not developing formal model, just trying to find the cases, where it can be falsified at logical level. I'm really not insisting on assumption, observable universe must remain computable in deterministic way.

For me consecutive logics of formal math is too weak tool for understanding of complex phenomena in multicomponent systems and it can form a brake of further understanding of reality.

Currently we can model complex problems of turbulent flow just by using of particle simulations. I admit, it's not rigorous approach, but it's still used in industrial CFD. For example, we could model decay of atom nuclei by particle fluid without care about formal description of their interactions in similar way, like we can simulate turbulence by particles without dealing with unstable Navier-Stokes equations.

 
At 5:29 PM, Blogger Zephir said...

/*..I take the freedom to talk to you as your psychiatrist..*/
My freedom is to leave talks about psychiatry and ego without comment...;-)

I'm not pretending, I'm extraordinarily smart - on the contrary, my relative dumbness makes me quite effective in finding of the simplest possible models and explanations of reality. The problem of many brilliant experts (like you) is just too complex way of thinking. But this is not really an ego problem, rather professional deform.

Albert Einstein: If you can't explain something simply, you don't know enough about it.

"Simply" doesn't mean lack of reproducibility in sequence of logical steps, here. As a quite effective criterion of your understanding can serve the ability to predict new phenomena - not just to explain existing ones ex-post. Such approach requires to have robust logical model, rather then formal one.

 
At 5:42 PM, Blogger Zephir said...

/*..your silly babbling in quite recent discussion about breaking of Lorentz invariance..*/
Can you be more specific in this case, please? I summarized my opinion here:

http://aetherwavetheory.blogspot.com/2009/08/awt-and-grb090510-photon-controversy.html

Anyway, can you explain your "dark boson" theory of autoinfection in more details? Reproducible sequence of easy to follow logical steps is welcomed. Maybe we could get into something.

 
At 10:35 PM, Blogger Matti Pitkanen said...

To Zephir:


1. /*..I'm not pretending, I'm extraordinarily smart - on the contrary, my relative dumbness makes me quite effective in finding of the simplest possible models and explanations of reality. The problem of many brilliant experts (like you) is just too complex way of thinking. But this is not really an ego problem, rather professional deform...*/.

I understand.


2. You distinguish between formal math and logics and as a super logician you are able to see the simplest possible models of reality and you do not want to waste time to formal modelling. I can only congratulate.

Still I would strongly encourage you to see the trouble of developing formal model. This process is always a sequence of cold showers. Formal models make also possible quantitative tests so that it is not enough to fit a finite number of logical bits anymore but a frightening continuum of real numbers! Quantitative modeling killed the aether theories for century ago and also your aether wave theory might suffer the same fate.

3. Formal logical approach and formal modeling are of course not enough in science. Solving a gigantic high-dimensional crossword puzzle is a proper metaphor for what people are doing in theoretical physics. Besides formal modeling it involves guesses and checks and many of the guesses turn out to be wrong.


4. Your claim about the absence of sequence of logical steps in my arguments might reflect the fact that you did not have time to read. Of course, blog postings can serve only as summaries giving some impression about what is done. For this reason I have usually added links to the chapters of books where the details can be found.

5. "If you can't explain something simply, you don't know enough about it". This is one those statements of Albert Einstein which should be taken with precautions: Einstein should have specified what the audience is. For instance, time dilation cannot be explained "simply" for an audience without a considerable background in 4-D Minkowsky geometry. In the case of General Theory of Relativity the audience must be selected even more carefully.

 
At 10:39 PM, Blogger Matti Pitkanen said...

Dear Zephir,

this is a continuation to the previous posting.

6. /*..your silly babbling in quite recent discussion about breaking of Lorentz invariance..*/Can you be more specific in this case, please? I summarized my opinion here: http://aetherwavetheory.blogspot.com/2009/08/awt-and-grb090510-photon-controversy.html..*/.


I referred to your contributions to the discussion in Bee's blog.

a) The recent discussions have been about "Testing Einstein's special relativity with Fermi's short hard gamma-ray burst GRB090510" by Fermi GBM/LAT Collaborations, arXiv:0908.1832v1. The simultaneous observations of Fermi laboratory and MAGIC collaboration exclude breaking of Lorentz invariance as a deviation from dispersion relation E^2^-p^2=m^2 both predicted and not predicted by LQG approach as I learned.

I did not understand your photoball argument but I gathered that that photon mass could explain the dispersion which is now believed to be absent. In any case, you should check whether the dependence of arrival time on inverse energy (T= L/v= L/sqrt((m/E)^2+1)) is consistent with the dispersion relation for some value of photon mass and with known limits on photon mass. And does the prediction of shorter arrival time for photons with higher energy make sense. This MAGIC observation of 31 GeV photon combined with other observations might be enough to kill your theory.

b) The basic difference between TGD and GRT is that Poincare invariance is exact symmetry broken only globally: the basic structure in zero energy ontology is fractal hierarchy of causal diamonds (CD is intersection of future and past light-cones) and Poincare transformations can lead out from this causal diamond. This breaks Poincare globally but leaves E^2-p^2=m^2 (=0 for photons) intact.

c) The earlier MAGIC anomaly inspired the consideration of the possibility that the space-time sheet along which photon arrives depends on the energy of photon measured in the rest system of the space-time sheet so that the arrival time of photon would depend on energy as reported by MAGIC collaboration. This does not mean breaking of Lorentz invariance since this symmetry is realized at the level of imbedding space rather than space-time surface. The arrival time could be a piecewise constant function of energy of photon in the rest system of space-time sheet by p-adic length scale hypothesis. I have written a blog posting about this.

7. Dark matter theory of autoinfection is explained in earlier posting Genes and Water Memory. For a more detailed view about the logical steps you can look for the links to my books in this posting.

If experimental findings about re-appearance of the infection to sterilized solution are taken seriously, one must consider the possibility that genetic information is represented in some non-standard manner. Of course, many-sheeted space-time would allow also the possibility that some fraction of infected cells were at different space-time sheets and diffused to the standard one.

My abilities in logical thinking are so limited that I remain in total darkness concerning the question how the information about the genome of bacterium could be represented in terms of thixotropy of water clusters. The figure is nice but did not help me to fill in the details of the logical sequence.

 
At 11:17 PM, Blogger Zephir said...

/*..Dark matter theory of autoinfection is explained in earlier posting Genes and Water Memory...*/

Just reading:
"..during filtration part of the infected cells is "dropped" to large space-time sheets and diffused back to the original space-time sheets during the next week. This would explain why the micro-organisms were regenerated within few weeks..."

I see...

 
At 11:28 PM, Blogger Zephir said...

/*..how the information about the genome of bacterium could be represented in terms of thixotropy of water clusters...*/
Well, maybe whole the "dark boson" / "water cluster" stuff is redundant here. RNA could pass 20 nm filter without problem, it could penetrate health cells and to replicate viral proteins inside of them by some horizontal gene transfer mechanism. Or even viral proteins itself could infect health cells, because they could pass microfilter and reconstruct virions in solutions. Here are many experiments with water clusters and DNA interactions at distance, but I'd always prefer simplest explanation first.

 
At 11:36 PM, Blogger Zephir said...

/*..you should check whether the dependence of arrival time on inverse energy ..*/
Why not, but now it looks, like you have done such check already. You told me, it's a babbling. I'd expect, if you don't understand something, you'll ask first, just after then you'll judge my comment.

 
At 11:46 PM, Blogger Zephir said...

/*..time dilation cannot be explained "simply" for an audience without a considerable background in 4-D Minkowsky geometry..*/
Of course it can. At first, here's an applet.

http://superstruny.aspweb.cz/images/fyzika/relativity/twins.htm

and video (applet was written for MSIE 6.0, which is obsolete by now)

http://superstruny.aspweb.cz/images/fyzika/relativity/twins1.avi

 
At 12:05 AM, Blogger Matti Pitkanen said...

/*..you should check whether the dependence of arrival time on inverse energy ..*/

The high energy photons should arrive earlier. If I recall correctly, just the opposite happens. The proposed non new physics explanation is that the mechanism creating them is like high energy collision producing low energy photons first.

 
At 12:27 AM, Blogger Ulla said...

A fantasy figure? I really think the genome is much more complex than that. This is ridiculous.

 
At 12:31 AM, Blogger Matti Pitkanen said...

"RNA could pass 20 nm filter without problem, it could penetrate health cells and to replicate viral proteins inside of them by some horizontal gene transfer mechanism. Or even viral proteins itself could infect health cells, because they could pass microfilter and reconstruct virions in solutions."

This did not help to understand the role of thixotropy. If bacteria are really there, we are speaking about information coded by entire genome. How it leaks to the filtrate. If not, there are other possibilities. TGD based model of water memory predicts that water represents biologically relevant information about molecules in terms of electromagnetic field patterns at low frequencies associated with water cluster and also dark nuclei analogous to DNA, RNA and amino-acid sequences. The interaction with these field patterns could create the signatures used to conclude that infected cells are present. Similar mechanism explains the effect of homeopathic remedies.

The representation in terms of field patterns would apply also to genetic information and explain the other findings of Montagnier's group as I indeed suggest in the posting that I gave link to. Peter Gariaev reports that the temporal patterns for the orientation of linear polarization could code genetic information. I have proposed a model in TGD framework work this.

To conclude: the model of dark baryon predicts counterparts of DNA, RNA, aminoacids, and even tRNAs. Vertebrate genetic code is predicted exactly and genetic code is predicted to be composite of 60-->40 and 40-->20 codes. This picture would also solve the formidable problem about how the code evolved and lead to a completely new view about evolution.

I would be a complete idiot if I would forget this kind of results as funny coincidences when there are also experimental indications for new realizations of genetic code. Stupidity is a deadly sin for a theoretical physicist.

 
At 1:04 PM, Blogger Zephir said...

This comment has been removed by a blog administrator.

 
At 8:11 PM, Blogger Matti Pitkanen said...

Dear Zephir,

I removed your comment for hygienic reasons. I used many hours of my time to give you a lesson about what the term "quantitative" means in physics by demonstrating that all your "theories" formulated as random pictures, random links, or just nonsensical world salad were pure nonsense or in the best case wrong.

My hope was that this would help you to understand what is your problem. The lesson was in vain. To put it bluntly: you are simply crazy. I sincerely hope that you would not waste my time anymore and would share grains of your wisdom only at your own blog.

 

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