Sunday, August 31, 2008

Could virtual DNAs allow a controlled development of the genome?

In the previous postings I have discussed TGD based model of homeopathy and phantom DNA based on the possibility that water molecules receiving the magnetic bodies of biomolecules in homeopathic manifacture process can mimick those aspects of these molecules most relevant for the biological functions. By combining these ideas with DNA as topological quantum computer hypothesis, one ends up with the idea that the evolution of DNA is not just random mutations plus selection, but takes place in controlled manner like the development of computer hardware in the virtual mimicry of internal chemical milieu in turn providing an abstract representation for the external world.

The fundamental question in the evolution biology is the question about the interaction between genome (G), phenotype (P), and environment (E).

  1. The standard dogma is that the information transfer from G to P is unidirectional and that environment acts on G by inducing random mutations of G, from which E selects the lucky survivors as those with the best ability to reproduce. Lamarckism represents a deviation from standard dogma by assuming direct information transfer from E to G.

  2. Genetic expression is controlled by environment, at least by silencing , which is like selecting only few books to be read from a big library. Cell differentiation represents basic example of selective gene expression. DNA methylation and transposition are accepted to reflect information transfer from E to G, perhaps via P. These modifications are however believed to be short lasting and not transferred to the offspring since it is difficult to imagine a mechanism transferring the mutations to the germ cells.

  3. The question however remains whether the G® P-E actually could complete to a closed loop G® P-E-G so that genome could directly respond to the changing physical environment and could transfer the successful response to the next generation .

In TGD framework the sequence G® P-E is replaced with a closed loop G-P-M-E to which E is attached at P by bidirectional arrow (organisms do also modify their environment actively). Magnetic body thus controls genome and receives information from cell membrane (P). The hierarchy of genomes (super-genome, hyper-genome,...) corresponding to the different levels of dark matter hierarchy allows this loop to be realized in different scales rather only at the level of single cell.

The question is whether the magnetic body of organism or higher level magnetic bodies could modify genomes, super-genomes, and hyper-genomes directly, perhaps by generating mutations of the genome in a short time scale; by monitoring how genetically modified organism survives in the environment; and -if the outcome of the experiment is successful - replacing the corresponding portion of DNA with the modified DNA both in ordinary germ cells. One can even ask whether the abstract model of the external environment provided by the internal chemical milieu might be mimicked by water magnetic bodies of water molecule clusters and provide a virtual world testing ground for a search of favorable mutations.

In DNA as a tqc vision essentially the development of a new computer hardware would be in question, and should take place in a controlled manner and involve an experimentation before going to the market rather than by random modifications taking place in computer CPUs. Second basic aspect of DNA as tqc paradigm is that water and bio-molecules live in symbiosis in the sense that self organization patterns of the cellular water flow define the tqc programs. The following first guess for how the development of computer hardware might be achieved is just a first guess but might have something to do with reality.

  1. What would be needed is a mechanism generating rapidly modifications of DNA. The mutations should be carried out using a kind of virtual DNA mimicking all the essential aspects of the symbolic dynamics associated with DNA. The magnetic bodies of DNA consisting of flux tubes connecting the nucleotides of DNA strands to cell membrane satisfy these conditions since A,T,G,C is coded to exotic light quarks u, d and anti-quarks `u, `d at the ends of flux tubes . DNA nucleotides could be replaced with clusters of water molecules but also other options can be imagined. Note that it does not matter when one speaks of mimicry of RNA or DNA molecules.

  2. If the proposed model of the phantom DNA and homeopathy is correct, this kind of virtual DNA exists and is generated in phantom DNA effect as magnetic bodies of DNA, including of course the magnetic flux tubes connecting the nucleotides to the cell membrane or conjugate strand of DNA.

  3. The crucial additional assumption would be that also the reversal of phantom DNA effect is possible and corresponds to the analog of DNA replication in which nucleotides attach to the virtual conjugate nucleotides of the virtual DNA strand or RNA strand in turn transformed to DNA strand be reverse transcription. The hypothesis would have rather strong implications for the genetic engineering since homeopathic remedies of genetically engineered DNA sequences could be transferred to cell nuclei just by drinking them.

  4. Phantom DNA sequences could form populations and - as far as their properties as a hardware of topological quantum computer are involved - evolve under selection pressures of the virtual world defined by the nuclear, cellular water, and intercellular water. A competition of components of tqc hardware developed by the higher level magnetic body to realize optimally tqc programs needed for survival would be in question. The simplest mutation of phantom DNA would replace the quark pairs at the ends the (wormhole-) magnetic flux tube with a new one and could occur in very short time scale. Also basic editing operations like cutting and pasting would be possible for these competing phantom DNA sequences. The winners in the competition would be transformed to actual DNA sequences by utilizing the reverse phantom DNA (or RNA -) effect and be inserted to genome. The genetic machinery performing cutting, gluing, and pasting of real DNA in a controlled manner exists. What is needed is the machinery monitoring who is the winner and making the decision to initiate the modification of the real DNA.

  5. The transfer of the mutations to germ cells could be achieved by allowing the population of the virtual DNA sequences to infect the water inside germ cells. The genetic program inducing the modification of DNA by using the winner of the tqc hardware competition should run automatically.

  6. One open question is whether the cellular or perhaps also extracellular water should represent the physical environment and - if answer is affirmative - how it achieves this. As a matter fact, considerable fraction of water inside cells is in gel phase and it might be that the intercellular water, which naturally defines a symbolic representation of environment, is where the virtual evolution takes place. Internal chemical milieu certainly reflects in an abstract manner the physical environment and the ability of the water molecule clusters to mimic bio-molecules would make the representation of the chemical environment possible. Also sudden changes of external milieu would be rapidly coded to the changes in internal milieu which might help to achieve genetic re-organization.

For details see chapters Homeopathy in Many-Sheeted Space-time of "Bio-Systems as Conscious Holograms" and The Notion of Wave-Genome and DNA as Topological Quantum Computer of "Genes and Memes"

2 Comments:

At 12:08 AM, Blogger Ulla said...

You write: DNA methylation and transposition are accepted to reflect information transfer from E to G, perhaps via P. These modifications are however believed to be short lasting and not transferred to the offspring since it is difficult to imagine a mechanism transferring the mutations to the germ cells.

This is not so sure. For diabetes there are strong indikations that these changes are inherited. See http://www.lakartidningen.se/07engine.php?articleId=10110

They write (august this year): Frågan om epigenetiska förändringar kan stå sig mer än en generation är fortfarande omstridd, men det finns djurförsök som ger starka belägg för att så kan vara fallet. Tydligast är en serie experiment av USA-forskaren Michael Skinner, där han under fosterstadiet utsatte råtthannar för ett växtgift med kända antiandrogena egenskaper. När hannarna blev vuxna fick de mycket riktigt sämre spermakvalitet och fruktsamhet – men det fick också deras avkomlingar i minst tre generationer till. Michael Skinner har visat att det inte rörde sig om en mutation men har däremot konstaterat att det växtgift han använde påverkar DNA-metyleringen.

and:

Han understryker att de ännu så länge bara visat att de här sambanden finns, inte vilka mekanismer som åstadkommer dem. Men vanlig genetisk selektion kunde uteslutas, säger han:

– Vi fann inget som tyder på det. I stället handlar det troligen om epigenetiska förändringar. Eftersom sambanden är könsbundna, sker överföringen sannolikt via y- och x-kromosomerna.

There is much science on this subject today. This is nature and nurture, in a concrete way.

By the way, I can only admire your analyzing skills.

 
At 1:31 AM, Blogger Matti Pitkanen said...

Thank you for links. I am not a professional biologist and any kind of information bit is more than welcome.

 

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