Tuesday, December 28, 2010

The revolution taking place in genetics

I received an extremely interesting popular article (thanks to Kalle) about the profound revolution taking place in genetics. See this.

It is fair to say that genetic determinism is falling down and the revolution that is waiting just around the corner will be more profound that anything that has taken place before this in biology. The term "genome's dark matter" expresses what has been discovered during last years. The motivation for the term is the strong analogy with the dark matter of physics. In TGD framework this analogy might be much more than analogy.

The basic anomalies discussed in the article are following.

  1. Trans-generational inheritance. The stretches of DNA which were present in parent's or grand parents' genome but are not present in the genome of offspring affect the traits of offspring.
  2. Context sensitivity of gene's effect: the effect of gene is highly sensitive on its environment in DNA.
  3. Genes explain in many cases only 10 percent of the disease's inheritability: this is "missing heritability" problem.

What makes this so interesting from TGD point of view is that for a few years ago I developed a model of DNA as topological quantum computer (see this). I summarize the basic building bricks of the model before relating it to the Mendelian anomalies.

The notion of magnetic body

The notion of magnetic body as intentional agent using biological body as a motor instrument and sensory receptor with communications taking place in terms of fractal generalization of EEG is the key idea. Each physical system consisting of matter has magnetic body. Magnetic body of given living organism has a fractal onion like structure with layer sizes varying from sub-cellular scales to the scales assignable to EEG frequencies (Earth size) and even above up to the scale of light-life and maybe beyond to scales characterizing the evolution of species.

Immediate implications are the notion of collective DNA expression made possible by the interaction of DNA strands so that they belong to magnetic flux sheets: in this manner not only DNAs of cells and organelles, organs, single organism but also groups of organisms can form coherent structures expressing themselves in synchronous manner. This is a testable prediction.

DNA as topological quantum computer

Topological quantum computation is based on braiding: various braiding patters for braid strands define the tqc programs. There are two types of braids: time-like and space-like.

  1. Cell membrane is 2-D liquid and the flow of lipids affected by the flow of cellular liquid and also by nerve pulse patterns in case of neurons induce braiding. This braiding takes place dynamically at the 2-D parquette defined by the cell membrane in time direction and dance metaphor applies to it. Running tqc program can be seen as dancing.
  2. The magnetic flux tubes connecting DNA nucleotides to the lipids of nuclear membrane and cell membrane and possibly also to membranes of other cells define the space-like braid strands. Since the flux tubes connected to DNA strands are like threads connecting the feet of dancers to the walls of dance hall the resulting space-like braiding codes tqc program to memory, which is highly robust as a topological invariant.

There is a kind of duality between time-like and space-like braidings. This is a new element to the conventional quantum computation paradigm. Combined with the idea that memories are stored in geometric past in zero energy ontology this gives an extremely elegant memory storage mechanism.

Implications for genetics

This vision has profound implications for genetics.

  1. Genes define only the hardware of tqc. Software is defined by the braidings. Introns whose portion steadily increases as the evolutionary level becomes higher and is more than 95 per cent in humans, have been traditionally interpreted as junk DNA (this is true, believe or not!;-)). In this framework introns correspond naturally to that part of genome specialized in tqc: from the point of view of tqc it does matter much whether the intronic portions correspond to repeating sequences (interpreted as a signal for junk-ness) or not.
  2. The evolution of topological quantum computation programs would be far more important than the evolution of genome and the huge differences between species with almost the same genome (such as we and our cousins) could be understood in terms of cultural evolution due to the evolution of topological quantum computer programs. The evolution would have been for a long time evolution of tqc programs rather than that of hardware as the fact that the size of genome and details of does not matter much suggests. This suggests that the appearance of of prokaryotes (and multi-cellulars) meant the emergence of introns and perhaps also cultural evolution as the evolution of quantum software and collective magnetic bodies.

Implications for Mendelian anomalies

This vision also suggests how to understand the origin of the Mendelian anomalies.

  1. Trans-generational inheritance might be understood as an inheritance of tqc programs carrying indirectly information also about the genome of parents. If one accepts TGD vision about organisms as 4-D structures, one must of course be ready to even ask whether genetic effects could be also take place via the mediation of the magnetic bodies assignable to structures formed by several generations.
  2. The context sensitivity of the effect of particular gene could be understood in this picture since the programs are determined not only by a single gene but longer portions of DNA. Individual genes do not matter much when one tries to understand genetic correlates for autism, schizophrenia, and other complex diseases related to functions rather than mere structure. If one speaks about structure, such as the color of flowers situation is of course very simple and Mendelian approach works well. An interesting question is how closely the structure-function dichotomy, exon-intron dichotomy and hardware-software dichotomy correspond to each other.
  3. High level diseases would be much more programming errors than hardware problems. This would solve "missing heritability" problem.

What is amusing, that the physicist's dark matter would indeed be behind "genome's dark matter': magnetic flux tubes are indeed assumed to be carriers of dark matter- dark quarks in fact. In the proposed model quarks with large Planck constant meaning that their Compton length scales is scaled up and gives them size scale of order cell at least are in key role!

See the chapter DNA as Topological Quantum Computer of "Genes and Memes" for a discussion containing also additional references.


At 2:19 AM, Blogger Ulla said...

Happy New Year.

This is nothing new, only the pieces are brought together. I told you long ago. As a biologist it is hard to say that I don't believe in genetics :) You talked yourself of a physicists genes :) Nonsense.

Of course sometimes genes makes sence.


I can see the flux tubes in work...

The Big Book, maybe it has no back at all? It is only BE-condensators or solitons. No singularity, not even for selves. No back of the book.

I thought I would stop comment, but you are too sweet for a flie:) This one was such a goodie. You bastard :)

At 12:20 AM, Blogger Matti Pitkanen said...

This is not new for me since I predicted this for years ago in DNA as topological quantum computer model.

It certainly comes as a surprise for biologists who are routinely applying statistical methods to find genes as correlates for structure and function. It is really a cold shower to find that their basic paradigm of genes as units of inheritance is simply wrong. Individual genes do not matter much when one tries to understand genetic correlates for autism, schizophrenia, and other complex diseases related to functions rather than mere structure. If one speaks about structure, such as the color of flowers situation is of course very simple and Mendelian approach works well.

Genes of course make sense. They define the hardware and hardware determines to high extent how complex computations are possible. There is huge difference between the programs running Commodore 64 storing data to magnetic tape and the newest Mackintosh.

An interesting question is whether structure-function dichotomy corresponds in good approximation to hardware-software dichotomy.

The most horrible outcome of the identification of the genes- the hardware- as software, is the identification of more than 95 per cent of DNA as junk: it is incredible how long this idiotic identification in blatant conflict with simplest common sense has been taken seriously and is still taken by many biologists as a fact: just some time ago I saw a New Scientist story about evidence for this idea.

Note that this junk DNA identification follows completely logically from the basic premises. This shows how dangerous strictly logical approach is if one is not all the time testing for the possibility that basic assumptions are wrong.

It was interesting comment. Thank you.

At 12:25 AM, Blogger Matti Pitkanen said...

...and Good New Year;-).

At 2:07 AM, Blogger Ulla said...

In fact, the epigenetic mechanism, the RNA-silencing, was found from the color of a flower that didn't behave as it should. It was found this was some primitive immune system.

I want to be treated like a human. There are plenty of room for my comments here, as far as I can see. I cannot stand anything. I want a better New Year :)

At 2:54 AM, Blogger Ulla said...

In my mind I have been lecturing you for a couple of days now, and it helped. I am angry at you, Bastard. I don't deserve being treated like this, do I? You are not as nonchalant to anybody else, and still I promote TGD, Bastard. You are ridiculing me, do you realize that?

I had to say it. I have been silent too long. I have done nothing wrong, nor have you. You know that. Come out of your cage and start debate. Does it matter if it is only with me? The other will follow.

To your information I will take part in the Fqxi contest with the body-mind problem, and I will use your theory, but only partly. You know where you can reach me, if you have anything to say, my friend. (I am not so very angry).


At 3:09 AM, Blogger Ulla said...

You looked for Atiyah:
Mind, matter, mathemathics, but 2008.


At 11:33 AM, Blogger Ulla said...



At 1:43 PM, Blogger donkerheid said...

I would be surprised if scientists were not trying to understand these findings on purely conventional grounds and blame all this on complexity. Epigenetics and complicated gene regulations, for instance.
Sheldrake told though, that even adopted children are more likely to develop cancer, if their new family is genetically prone to cancer but the children themselves are not. That would challenge the 'complexity only' type of reasoning.

These new findings would mean that probably even more time and money will be spent on gene hunting and drug design, such as the genetic background of cancer. However, cancer might well be a nutritional disease. I'm not sure, of course, but I wouldn't be surprised at all.
There are good indications. Of course, to tell people to change their diet is not profitable for those who make loads of money from the cancer industry. More people are making a living on cancer than dying of it.

At 3:10 PM, Blogger Ulla said...

There was once a Norwegian doctor that tried alternatives against cance, and not only diets. He tried to stimulate their immune systems. And he had much better results than conventional treatment. Did they become happy because of this? Of course not. The forbid him to ever again do that kind of 'research'.

Or take the American doctor, expert on fatty acids. He injected pure fat in the bloodvessels of sick animals. What happened? They immidiately got better. He did his trials (on n-3), looked for a drug company that would manufacture his cures, got excellent results. What happened? The drug company withdraw. Reason: it was not pills easy to ingest. They thought they would not get so high profit.

So what will happen to this? No illusions, Donkerhead.

At 8:09 PM, Blogger Matti Pitkanen said...

Everything suggests that genes act as computer hardware also coding for its protein representation and introns define the programs. In principle the notion of magnetic body allows also to model for the interaction with community.

The progress is however slow. Increasingly complex regular or regulator of ... scenarios will be proposed in attempt to save the "More than 95 percent of human DNA pure trash" idea. The dogma about life as pure chemistry is behind this idiocy and it facts do not weigh much when entire community is on wrong track.

I have been listening lectures about alternative medicine, "energy medicine" as it is called. Energy medicine is the umbrella concept and has been chosen purposefully to be as neutral as possible.

I listened lectures about various forms of healing. First kind of healing involves interaction with healer: acupuncture, healing by touching, reiki, and so on. There is also interaction with the collective: group meditation, the active participation of relatives and friends in the healing,... The role of religion, rituals, and symbols in the healing was also discussed. There is also healing as a purely personal development: the patient lives in wrong manner and gradually develops a crisis and the crisis can lead to a healing through a profound change of value system.

The the work related to the effects of electro-magnetic fields on living matter represents more technical aspects of healing and promise to build a bridge between to existing biology and modify it appropriately.

The stories about the attitudes of the main stream scientists to simple scientific facts which do not fit do not give much hope: a friend of black humor can only laugh although one should be sad. And one must not forget that money is the decisive factor also in all kinds of science nowadays. Those who enjoy the funding do not want to lose it. In medicine this business aspect is especially important.

At 12:57 AM, Blogger Ulla said...

Once I tried to arrange a seminar in Energy Medicine - but nobody understood what it was, not even the doctors. So I never use the term again, although I am very fond of it, because it tells what it is about. As far as I know Becker was the one terming it.

Interesting that you too have noticed the body works through a creation of disturbance (not chaos as Prigogine said), as if it wants to draw attention to something.

One thing that now has come into my mind is that the divided beings between quantum and classic decoherenced states, that we are made us chose , or maybe better to say, compete within them. If we use one kind, say bodywork, we have extremely hard to use another at the same time, especially spiritual senses are far away. The competition between senses has also another story to tell us.

At 2:47 AM, Blogger Ulla said...

Stress affects our genes

At 8:49 AM, Blogger Ulla said...

Here we go again, as in TV on New Year...

This one is highly interesting, talks of biology as a big anomaly :)

Genomes for selfconstructing, selfmodifying informationprocessing architectures

At 12:22 PM, Blogger Ulla said...

Optimality properties of a proposed precursor to the genetic code by Butler T (Butler, Thomas)1, Goldenfeld N (Goldenfeld, Nigel)

Abstract: We calculate the optimality score of a doublet precursor to the canonical genetic code with respect to mitigating the effects of point mutations and compare our results to corresponding ones for the canonical genetic code. We find that the proposed precursor is much less optimal than that of the canonical code. Our results render unlikely the notion that the doublet precursor was an intermediate state in the evolution of the canonical genetic code. These findings support the notion that code optimality reflects evolutionary dynamics, and that if such a doublet code originally had a biochemical significance, it arose before the emergence of translation.

At 11:54 AM, Blogger donkerheid said...

Living in the wrong manner that leads to a crisis and then a transformation of values sounded familiar :). Though there was no healing involved.

I thought of learning some kind of healing myself. The basics can be taught in only 2 days.
They always talk of energies and frequencies so confidently that it is annoying. I would be surprised if these 'energies' made any sense in standard physics terms, or do they?

At 1:12 PM, Blogger Ulla said...

Ah, Donkerheid...

The healing IS the transormation.
People talk of frequencies and energies, but also of stress. You have no difficulty with the latter, or homeostasy, although it is only an ad hoc phrase.

What IS stress, what is energy/frequencies? What is resonances, vibrations, homeostasy, maximum negentropy principle...
What is information?

You can start by James Oschman as instance http://www.energyresearch.bizland.com/

I have done this for 10 y now, but I am still a novis, but I know a hell lot more than most.
An acupuncture doctor had studied this in 20 years and he still hold himself ignorant. In a lifetime you cannot learn everything.

A wast field of knowledge if you only start looking.
When I started I relied on the phrase "there is no research in the field" OOOPS there is lots and lots of it. Only you must use different search channels. It has nowadays also been seen at PubMed, so maybe something is changing.

The basic of TGD is in this field, and that is what is so good with TGD. You actually can LEARN something essential.

Hope you don't mind that I answered the question, Matti.

At 3:16 PM, Blogger Ulla said...

functional genomes and their interactions, not structural, are the important ones.

The human stem tree is also not explained by genes, but by 'islands of interaction' - stable groups mostly of introns (Svante Pääbo). There are often included genes for autism and schizophreny :) But that is no new aspect either.

At 8:53 PM, Blogger Matti Pitkanen said...

Dear Donkerheid,

as Ulla said, healing at the deepest level is a transformation. Something which changes both our past and future profoundly.

Much of the talk about frequencies and planes and so on must be taken as metaphoral and try to avoid irritation;-).

There is however a lot of support for quite concrete role of specific frequencies in bio-control and communication. Cyclotron frequencies flound already by seventies by pioneers of bio-electromagnetism to be important: there are still people who refuse to accept the fact that photons with say 15 Hz frequency could have any effects on biomatter because the photons have so low energies. If hbar is large form these photons, effects are possible since the energies can be above thermal energy. Here we collide with the wall of belief and can only wait. Luckily, dogmas are not inherited genetically;-).

In TGD framework also Josephson frequencies assignable cell membrane identified as Josephson junction play a key role and code for various sensory qualia in the model for sensory receptors. Among other things one can understand the correspondence between peak sensitivities of visual receptors as function of photon frequency and ends up
to model for lipid layer of cell membrane as an analog of computer monitor (liquid crystal actually!) in which each lipid represents a sensory pixel characterized by basic sensory qualia. These would be the analogs of sensory homunculi.

Communication between neurons and cells would take place via dark photons producing fractal variants of EEG photons or biophotons through the transformations to ordinary photons. Narrow frequency bands would be important as they are in ordinary radio communications. Narrow frequency bands are important also for communications between biological body and magnetic body.

The frequencies are just the beginning: the next question is what are the codes for the communication and in the case of hearing -and I would guess even more generally- frequency modulation seems to be one code (have heard whales singing?). Second mode would be based on temporal patterns. Rhythm and melody as in music.

At 12:43 PM, Blogger Ulla said...

Which makes time an active variable, seen in the quantum jump. But this quantum jump is nothing else than a symmetry breaking, giving decoherence and negentropy. So the consciousness is born in the measuring moment as a reduction and transformation of 'consciousness' (in the quantum coherent sea, or zero point). The whole is broken in parts and the information is changed.

But I still have problems with the Free Will. The factors acting on the decoherence are inner, and outer, if we don't have an emergent space. Can the created information change the quantum jump? It must be so, the computation and interpretation of the Self, also an decoherent structure, entangled within itself. That would make the differentation in itself would be an active factor too? Evolution is regulating itself, like some kind of living thing.

The hierarchy of frequencies, seen in the consciousness enlargement, as in the metaphysical chakras, are one big realization I like particularly much.

http://www.nature.com/news/2010/101105/full/news.2010.586.html RNA editing
DNA sequence may be lost in translation

http://www.nature.com/news/2010/101005/full/news.2010.510.html Focal dystonia is sometimes called 'musician's cramp', but it is not a primarily muscular problem: it begins in the brain. Whether or not music was therapeutic to these composers, it is clearly effective in treating both psychological and physiological disorders of the mind. It is thought that this is due, in part, to the way that music accesses the emotions.

At 12:32 AM, Blogger Ulla said...

I want also to point to the fact that even ordinary medical doctors are healers. You must come to them with an open mind and a hope and trust you will be better. It is in fact a kind of placebo.

If you go to doctors and are dam sure they cannot do anything, then what can they possibly do? Not even pills will help then. And what can a doctor do without his pills? The trust in medical doctors are big usually.

And what happen if the doctor tells you there is nothing to do? That is in fact anti-healing, or nocebo.

Quite off topic. Sorry.


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