Year 2011

Another approach to protocell

In the previous posting I told about the highly interesting work of the group of Martin Hanczyc in attempts to build protocell. Also the group led by Jack. W. Szostak, who was the 2009 Nobel Prize winner in physiology or medicine - has carried out beautiful experiments in which they are able to create a candidate for protocell satisfying many of the basic requirements.

One such condition is the ability of protocell to transfer various nutrient molecules through the protocell membrane. In modern cell pumps and channels consisting of proteins are believed to serve that purpose (for a different view see the remark below). Genetically coded proteins were however absent during the primordial era. Therefore the membrane is constructed of branching lipids believed to exists during prebiotic era allowing sugars which are basic building bricks of DNA to permeate to the protocell. Given the DNA template , the basic building bricks of DNA molecule assemble to a copy of DNA in this protocell.

What is still lacking is the generation of the template strand of DNA itself and also the replication of protocell. If dark DNA in the form of dark nucleon strings is really there, the template could result as the assembly of the basic bricks of DNA around it and above a proposal for the analog of this kind of process is suggested. The replication of the dark genes would have been also present from the beginning and would have preceded the replication of genes and protocell. Biological evolution could be seen as a migration from dark space-time sheets to ordinary ones and somewhat analogous to the migration of life from sea to land.

Remark: There are puzzling experimental findings about quantal currents through cell membrane even in absence of metabolic sources. In many-sheeted space-time one could interpret these currents as various kinds of Josephson currents running between cell interior and exterior along current carrying space-time shees. Pumps and channels would be more like a diagnostic tool allowing cell to measure the concentrations of various important biomolecules and ions.

At first sight the approaches of Szostak and Martin Hanczyc look very different. These approaches have however a lot of common at deeper level if one accepts TGD based view as DNA-cell membrane system or its more primitive version as a topological quantum computer like system relying on the braiding of magnetic flux tubes connecting the counterpart of DNA nucleotides to the lipids of protocell membrane and on the prebiotic realization of genetic code at the level of dark nuclear physics.

One could also argue that the protocell of Hanczyk represents oil based life as opposed to life as we know it. In TGD framework this is a mis-interpretation. The protocells of Hanczyk live in an aqueous environment. Nitrobenzene oil is an aromatic compound as also sugars and contains nitrogen taking in the proposed scenario same role as phosphorus in ordinary life. Oleic anhydride is lipid and- would provide basic building brick for a particular variant of DNA like structure half-way between dark and completely chemical realization. Oleic anhydride would provide also the building bricks of protocell membrane and serve as a nutrient just like fat molecules- also lipids- serve in "real life".

For background see the chapter Evolution in Many-Sheeted Space-time of "Genes and Memes".

Oil droplets as a primitive life form

The origin of life is one the most fascinating problems of biology. The classic Miller-Urey experiment was carried out almost 60 years ago. In the experiment sparks were shooted through primordial atmosphere consisisting of methane, ammonia, hydrogen and water and the outcome was many of the aminoacids essential for life. The findings raised the optimism that the key to the understanding of the origins of life. After Miller's death 2007 scientists re-examined sealed test tubes from the experiment using modern methods found that well over 20 aminoacids-more than the 20 occurring in life- were produced in the experiments.

The Urey-Miller experiments have yielded also another surprise: the black tar consisting mostly of hydrogen cyanide polymer produced in the experiments has turned out to be much more interesting than originally thought and suggests a direction where the candidates for precursors of living cells might be found. In earlier experiments nitrobenzene droplets doped with oleic anhydride exhibited some signatures of life. The droplets were capable to metabolism using oleic anhydride as "fuel" making for the droplet to move. Droplets can move along chemical gradients, sense each other's presence and react to it and have also demonstrated rudimentary memory. Droplets can even "solve" a maze having "food" at its other end.

The basic objection against identification as primitive life form is that droplets have no genetic code and do not replicate. The model for dark nucleons however predicts that the states of nucleon are in one-one correspondence with DNA, RNA, tRNA, and aminoacid molecule and that vertebrate genetic code is naturally realized. The question is whether the realization of the genetic code in terms of dark nuclear strings might provide the system with genetic code and whether the replication could occur at the level of dark nucleon strings. TGD inspired quantum model of biology leads to a model for oil droplets as a primitive life form. In particular, a proposal for how dark genes could couple to chemistry of oil droplets is developed.

Intelligent oil droplets

New Scientist tells about a new twist related to the Urey-Miller experiment. Martin Hanczyc and his colleagues of University of Southern Denmark in Odense are doing research with a rather ambitious goal: the discovery of the recipe of life. The highly demanding challenge is to find candidates for the protocell that preceded the recent cell. What makes the task so difficult that it is not even clear what one should be searching for. For instance, what basic characteristics distinguishing living matter from inanimate systems protocell is expected to have before one can speak about primitive life form? And if one accepts the dogmas of standard biology, one encounters also the nasty hen-egg question which came first: metabolism or the genetic machinery.

Hanczyc and his colleagues have been experimenting with simple candidates for primitive life forms: oily nitrobenzene droplets doped with oleic anhydride immersed in alkaline aqueous solution (alkalinity is by definition an ability to reduce acidicity). They have found that these systems have some attributes generally associated with life. The recent experiments replaced oleic anhydrite with the black tar consisting of complex branched and fractal looking hydrogen cyanide (HCN) polymer produced by Urey-Miller experiments and found that also now the droplets exhibit lifelike behavior: they sense and respond their neighbors and move towards "food" sources.

The earlier experiments using nitrobenzene droplets doped with oleic anhydridge immersed in alkaline solution began immediately to move along straight lines. What happened that the oleic anhydrite at the surface of the droplet reacted with the water spilitting to two oleic acid molecules by hydration. This dropped the surface tension of the droplet and by a kind of spontaneous symmetry breaking the reaction rate had maximum at some point of the droplet and a "hot spot" was generated drawing oleic anhydride from the interior of the dropled and generating a convective flow. A pH gradient develops along the surface. The oleic acid in turn moved along the droplet surface from the hot spot to the diametrically opposite side of the droplet (see this). The net effect was a linear motion. pH gradient is claimed to be essential for the generation of motion but I must admit that I do not quite understand this point. A primitive metabolism liberating energy is obviously in question. By momentum conservation the total momentum for the convective flow and flow of oleic acid was compensated by a center of mass motion of the droplet.

One could claim that this process belongs to the same class of self-organization processes as the generation of convection patterns as one heats liquid from below. Other researchers have however discovered that the oil droplets can also travel along chemical gradients, something known as chemotaxis used by many bacteria to find food and void threats. One oil droplet managed even to "solve" a complex maze containing "food" at its other end. Whether this kind of behavior can be regarded as a mere chemistry is far from obvious to me. To me this a achievement look like a genuinely goal directed intentional behavior.

Hanczyc has also found that when the oil droplets approach each other they change course to avoid collision, or can circle each other-like partners in Viennese waltz! Oil droplets seem to have even memory. By videoing the paths of oil droplets Hanczyc found that the decision to stop or continue was not random but the behavior at any point of orbits was affected by the earlier behavior. This is by the way an elegant experimental manner to show that non-deterministic behavior is not just randomness. The experiments have been also carried using instead of oleic anhydrige mineral oil consisting of a mixture of alkanes having as building block polymeres from from CH₄ by dropping two hydrogen from each C as also lipids have (methane CH₄ is the simplest alkane). What distinguishes mineral oil molecules from the oleic anhydride molecules are the oxygen atoms in the middle of the reflection symmetric linear molecule. Also now the droplets move although the process takes place with a slower rate.

The basic objections against the identification of the oil droplets as a life form is that they do not replicate and there is no genetic code. One must be however very cautious with this kind of statetments. Maybe the primary life forms are not the droplets and the behavior of droplets reflects the control actions of these life forms on droplets. Perhaps also genetic code could be realized at at totally different level. The recent findings of the group of HIV Nobelist Montagnier indeed suggest a new realization of genetic code in water closely related to to water memory and TGD suggests a concrete realization of this code.

Some key ideas of TGD inspired quantum biology

Before proposing a model for intelligent oil droplets as a primitive life form its good to list some of the basic ideas of TGD inspired quantum biology.,

1. The basic hypothesis is that the dark matter at the magnetic flux tubes of the magnetic body assignable to any physical system serves as an intentional agent controlling the behavior of the ordinary matter (see this). Dark matter can correspond to just the ordinary p"../articles/- at least electrons and protons- in a phase with non-standard large value of Planck constant forming macroscopic quantum phases. Also biologically important ions could form this kind of phases.

   TGD inspired nuclear physics (see this) allows also the bosonic counterparts of fermionic with same nuclear charge so that every fermionic ion could be accompanied by exotic bosonic ion so that Bose-Einstein condensates could become possible.

2. The model for dark nucleons as entangled triplets of three quarks (see this and this) leads to the identification of the counterparts DNA, RNA, tRNA, and aminoacids as three-quark states and one can identify also vertebrate genetic code. DNA sequences correspond to dark nucleon sequences - dark nuclei - in this correspondence. The proposal is that dark proton sequences in water form dark nucleons with so large a Planck constant that nucleon size corresponds to size of singe DNA codon. There is indeed evidence that in attosecond time scale (time scale for corresponding causal diamonds) water obeys effective chemical formula H_1.5O as far as scattering of electrons and neutrons is considered (see R. A. Cowley, Physics 350, 243-245, 2004 and R. Moreh et al, Phys Rev. 94, 2005)).

   This would suggest that 1/4 of protons are in dark large Planck constant phase in the experiments. This proportion is expected to depend on temperature and pressure and should explain the rich spectrum of anomalies of water by regarding it as a two phase system (see this). Perhaps these protons could form dark nucleon sequences realizing genetic code. These sequences could replicate and evolve and could define at least the analog of DNA or RNA. Maybe even DNA-mRNa-aminoacids translation processing could take place. If a translation machinery transforming exotic DNA to ordinary has developed during evolution, this fundamental realization of genetic machinery might make possible kind of Research&Development making possible to experiment with different genomes. Evolution would not be a random process anymore (see this).

3. The proposal is that the ordered water layers associated with polar molecules dissolved in water are attached to the magnetic body of the molecule induced in water environment and that this magnetic body mimicking the original molecule is an essential element of this primitive life (see this). The self-organization processes of these layers induced by external perturbations could be the predecessor of processes like protein folding and de-folding. The mechanism of water memory could be based on dropping of the magnetic bodies of molecules as a result of repeated shaking involved with homepathic procedure inducing a sequence of catastrophes driving the evolution of these primitive life forms. One can also ask whethert these magnetic bodies could define the analog of proteins providing one realization of dark matter genetic code.

4. If dark nucleons have been the predecessors of chemical life forms, one can circumvent the hen-egg question about whether the genetic code or metabolism came first. In zero energy ontology negative energy signals propagating in the direction of geometric past would in turn provide fundamental mechanism of intentional action, metabolism, and memory. If this is the case, evolution would have only led to a refinement of the fundamental mechanisms of life already existing: there would be no need to pull anything out of hat. The mechanisms for chemical storage and utilization of energy are needed and moving oil droplets would provide a primitive realization of these mechanisms.

5. The notion of negentropic entanglement makes sense if one accepts the role of p-adic number fields and the vision about life as something residing in the intersection of real and p-adic worlds (see this). Entanglement probabilities for negentropic entanglement must be rational or algebraic numbers in the algebraic extension of p-adic numbers involved and there is unique prime for which this entanglement entropy is maximally negative. Negentropic entanglement makes possible new kind of many particle states which is not based on binding energy but the fact that negentropic entanglement is stable against state function reduction if Negentropy Maximization Principle determines its dynamics also in the case of negentropic entanglement. This makes it possible to have bound state like many particle states in which composite p"../articles/ are in well-defined sense free and binding energy is formally negative. The proposal is that the mysterious high energy phosphate bond corresponds to negentropic entanglement and carries both metabolic energy and information (see this). In this framework ATP-ADP cycle has also information theoretic interpretation as a transfer of conscious information.

The model for DNA as topological quantum computer (see this and this) led among other things to an identification of magnetic flux tubes connecting bio-molecules as a basic building bricks of living matter.

1. Flux tubes are assumed to connect DNA nucleotides to lipids of the nuclear and cell membranes. Flux tubes could begin from =O in the double bonds R=O or from negatively charged oxygens. In the case of DNA R would correspond to the basic unit in phosphate deoxiribose backbone consisting of aromatic 5-cycle and PO₄ containing one =O and one O^-. The lipid end would would contain =O and -OH and the flux tube could end to either of these or possibly -OH ionized to -O^- by a transformation of proton to dark proton.

2. The braiding of flux tubes makes topological quantum computation like processes possible (see this). The contractions and expansions of flux tubes induced by phase transitions changing the value of Planck constant would be a basic control mechanis allowing to understand how two biomolecules (say DNA and its conjugate) can find each other in the thick soup of organic molecules. The reconnections of the magnetic flux tubes would be second basic control mechanism and ATP→ADP process and its reverse would represent standardized reconnection.

3. The flux tube ends would contain quark and antiquark (u,d and their antiquarks are involved) coding for the four DNA letters A,T,C,G so that also dark quarks and their antiquarks would provide an elementary particle level realization for the codons. Note that topological quantum computation does not necessitate genetic code and therefore also the repeating DNA sequences regarded as junk could be used for topological quantum computations.

General ideas about oil droplets as a primitive life form

It is interesting to see what one obtains if one takes the dark nucleon realization of genetic code, the mechanism of water memory realized as magnetic bodies attached to the ordered water layers associated with polar molecules, the model for DNA as topological quantum computer, and the ideas about magnetic body with dark matter as fundamental bio-control as basic ingredients of the model of intelligent oil droplets.

1. A process resembling spontaneous symmetry breaking occurs for the droplet molecules as the hot spot is formed. The interpretation as a generation of magnetic body of approximately dipolar magnetic field is attractive. The magnetic body would control the droplet. The change of the direction of the motion of the oil droplet would correspond to the change of the orientation of the magnetic body and would thus reduce to a motor action of the magnetic body.

2. The flux tubes of the magnetic body would be most naturally parallel to the direction of the nitrobenzene polymer strands. Oleic anhydride molecules and the hydrogen cyanid polymers would be transferred along the magnetic flux tubes of an approximately dipolar magnetic field entering to the hot spot from interior and the oleic acid molecules could move along the flux tubes continuing along the surface of the droplet to the diametrically opposite point. The migration of birds along magnetic field lines is a fractal analog for this.

3. The dark matter at the magnetic body would give the oil drop its "intelligence". The dark nuclear genome could be realized at the magnetic body and the magnetic bodies might define the replicating life form as in the TGD based model of water memory for which the magnetic bodies represent molecules as far as low frequency electromagnetic fields characterized by cyclotron frequencies are considered. One could see intelligent oil droplets as a manifestation of control actions of a life form defined by dark matter at magnetic flux tubes and the first step in the process eventually leading to a complex control and coordination of the behavior of ordinary matter.

4. The ability of droplets to react to the presence of other droplets would be due to the communications between magnetic bodies based on low frequency photons at cyclotron frequencies but having energy above thermal energy if the value of Planck constant is large enough.

At least oleic anhydrite, hydrogen cyanide, and mineral oil can serve as a fuel of oil droplets and this raises the question what might be the common property shared by them. Certainly this property must relate to metabolism and the model for ordinary metabolism suggests that this property is shared also by the high energy phosphate bond.

1. Oleic anhydrite is a lipid formed by as a fusion of two oleic acids consisting of a sequence of CH₂ units and the characteristic (C=O)-(O-H) group at its end. The burning of the molecule splits it to two oleic acids by hydration meaning utilizing one water molecule. The formation of oleic acid in turn involves dehydration so that the burning process is analogous to depolymerization of DNA or aminoacid sequence by hydration.

2. Mineral oil is also a lipid and looks like oleic anhydride locally. In the ideal case however the crucial ..(C=O)-O-(C=O)-.. portions are lacking. Oxygenation could however produce this kind of defects to the mineral oil molecules so that the mechanism of burning would remain the same.

3. Hydrogen cyanide HCN involves valence bond of valence 3 between C and N. The polymers are constructed from H-C-N sequences with single valence bond between both C:s and N:s of two subsequent horizontal H-C-N units, which one can think of as being obtained from (H-C)-(H-C)... sequence and ..N-N-N... sequences with N and C connected by horizontal bonds. This polymer replaces oleic acid as a "fuel" reacting with water and liberating metabolic energy. These polymers -which would serve as primitive analogs of proteins- would be transferred along the magnetic flux tubes and burned at the hot spot by hydration. HCN has been proposed to have been a primitive precursor of both amino acids and nuclei acids. With motivations coming from the general vision about quantum biology, tt will beproposed that also hydrogen cyanide polymers contain in their C-backbone ..(C=O)-O-(C=O)-.. portions as local defects due to oxygenation so that the burning would occur via hydration in all three cases.

What are the prerequisites for metabolism and topological quantum computation like processes?

The basic question is whether metabolism interpreted in TGD framework as negentropy transfer and thus requiring the analogs of high energy phosphate bond and ATP-ADP cycle is possible. The high energy phosphate bonds make also possible flux tube structures serving as a prerequisite for topological quantum computation like process. Both oleic anhydride, hydrogen cyanide and mineral oil can serve as a metabolic source and one should identify the common property of them making. This property should be the analog of high energy phosphate bond.

1. High energy phosphate bond carries metabolic energy. This bond is poorly understood and I have proposed that high energy phosphate bond carries negentropic entanglement identified as the basic characteristic of life (see this. In the middle of oleic anhydride there =O-O-=O structure and its splitting in hydration liberates energy. This suggests that this structure also now carries the negentropic entanglement and the metabolic energy. The splitting process of oleic anhydrite occurring at the hotspot would be analogous to ATP→ ADP process involving splitting of PO₄ molecule from ATP.

2. Oleic acid is a lipid containing at its second end the characteristic (C=O)-OH group assumed to serve as a terminal for the magnetic flux tubes in the model of DNA-cell membrane system as quantum computer. In the presence energy feed one could imagine that the inverse process transforming oleic acid to oleic anhydride takes place and a primitive version of the metabolic cycle involving photosynthesis and cellular breathing can be imagined. Metabolic and quantum information processing would be very intimately related. By DNA as topological quantum computer analogy the magnetic flux tubes connecting oleic anhydride molecules would make be responsible for primitive topological quantum computation if present in the system.

3. Also when the tar from Urey-Miller experiment replaces oleic anhydrite small amount of oleic anhydride was used to build a film around oil droplet to lower surface tension. This suggests that the oleic anhydride has a deeper purpose and defines the analog of cell membrane and make possible for the magnetic flux tubes from the interior of the droplet to attach to the lipids? This could occur at least in the hot spot and at point opposite to it so that magnetic flux tubes would connect the diametrically opposite points of the droplet. Oleic anhydride would therefore serve a dual purpose serving both asa metabolic resource and a building brick of the protocell membrane: metabolic energy would be accompanied by information. Also in real life lipids -about which fats are a special case- have this double role.

4. The process occurs for both for hydrogen cyanide and mineral oil and and this raises obvious objections against the model since the energy and information carrying =O-C-O-C=O structures making also possible the flux tube connects are not present in the ideal situation. One must however remember that the situation in real life is far from ideal and the most obvious idea is that the polymers as such are not enough: oxygen is the basic metabolic resource and oxygenation serving as the loading of metabolic batteries might be the crucial element.
   1. The backbone of both lipids and of mineral oil polymers is CH₂ sequence. If some fraction of mineral oil polymers contain (C=O)-O -(C=O):s serving as carriers of metabolic energy and information the situation reduces to that for oleic anhydride apart from effects caused by the fact that the density of metabolic energy per volume is expected to be lower, which would explain why the motion is slower.
   2. Also in the case of hydrogen cyanide polymers one can imagine the presence of similar defect structures due to oxygenation. A portion of ...(H-C)-(H-C)-(H-C).... sequence would be replaced with ....(H-C)-(C=O)-O-(C=O)-(H-C)... with three carbons lacking. The nitrogen sequence ...N-N-N-N-N.. would split to ...N-OH and OH-N... so that three nitrogens would be lacking.

Under these assumptions the model explains all three cases using hydration as the basic mechanism of metabolism as well as the conditions required by DNA as topological quantum computer model. Note that the process consumes oxygen just as the ordinary breathing.

What about genetic code and counterpart of DNA?

Consider next the possible realization of the genetic code. The first thing to notice is that even in the case that genetic code is not realized the braiding would make possible topological quantum computation like processes and a realization of memory in terms of braiding patterns. Furthermore, chemical realization of the genetric code is not possible so that dark nucleons remain the only possibility in TGD framework. The challenge is to try imagine whether DNA like structures having flux tube connections with the counterparts of lipids in the cell membrane could exist. The following suggestion is a product of free imagination based on analogies and reflects my amateurish skills in biochemistry.

1. Aromatic rings are an essential element of both phosphate deoxiribose backbone of DNA and of DNA letters itself. Nitrobenzene molecule obeys chemical formula (C₆H-5)-NO₂ and contains benzene ring to which NO₂ nitro group is attached. The oily character is due to the benzene ring. Benzene rings could serve as a counterpart for the hydrocarbon 5-cycles appearing in phosphate deoxiribose backbone. Note however that in deoxiribose ring one carbon is replaced with O and two hydrogens with OH. Moreover, single benzene molecule would correspond to the counterpart of DNA triplet rather than single nucleoside. One could however argue that only a backbone is in question so that the differences might not matter.

2. One would naively expect that both nitrogen and phosphorus have same valence equal to three. In PO₄ phosporus has 5 valence bonds as a rule and the interpretation is that phosphorus tends to donate its valence electrons to get empty shell. This kind of states are known as oxidation states and are possible also for nitrogen: hydroxylamine NO₂H is one exmple of this kind of state. In fact, from the from structural formula of nitrobenzene one finds that nitrogen gives one electron to second oxygen so that also this state can be regarded as an oxidation state. This inspires the idea that nitrogen takes the role of phosphorus at least partially.

3. If one does not allow oxidation states, the simplest manner to construct the analog of phosphate deoxiribose backbone is as structure ...X-X-X..., with X= R-O- (R₁-N)-O, where R denotes oleic anhydride and R₁ is for benzene residue. The bridges connecting benzene rings would be reflection symmetric. The breaking of reflection symmetry is however essential since it determines the reading direction of DNA.

4. If one accepts oxidation states, the simplest option is that in benzene-NO₂ complex NO₂ is replaced with (N=0)-O and the counterpart of phosphate deoxiribose backbone would have the structure ...X-X-X-..., X=R- (R₁-N=0)-O with R denoting oleic anhydride and R₁ benzene. Oleic anhydride has valence bond to N so that N has 5 valence bonds as phosphorus in phosphate. Also the crucial =O is present. The units connecting subsequent benzene rings are not reflection symmetric anymore as indeed required. There is however no charged oxygen as in the case of ordinary DNA. Note that the analogs for AMP, ADP, ATP make sense since one can single replace P by N phosphate PO₄.

5. An interesting question is whether the nitrogen based metabolism could be realized as a primordial metabolism. Nitroglycerin is analogous to tri-phosphate although the nitrates are not arrranged linearly as in ATP and is used as both heart medicine and as an active incredient of explosives. The latter use conforms with the idea about the presence of high energy nitrate bond in NO⁴.
6. The two mirror image branches of oleic anhydride molecule consist of 15 carbon atoms and the structure is rather long as compared to the basic unit of phosphat edeoxiribose backbone so that the distance between subsequent benzene units would be rather long- of order 10 Angstroms. On the other hand, 10 DNA codons correspond to 10 nm length in a good accuracy so that one codon would take 1 nm length also in this case. If double strand is formed, twisting is possible so that the scales could be the same. The size scale of the dark nucleon representing single DNA codon should correspond to the size scale of single oleic anhydride molecule and the required value of Planck constant would be of order 10⁶ as the ratio of this scale and nucleon size of order 10^-15 meters.

7. The counterparts of DNA nucleotides forming a linear structure should join to the benzene rings. Dark nucleon sequences remain the only possibility if one wants a realization of genetic code. Each dark codon represented by dark nucleon would be connected by three flux tubes with quark and antiquark at their ends to single unit of the proposed structure. There would be three =O:s per single benzene ring. Since single benzene ring corresponds to single DNA codon three =O:s are indeed expected. Therefore =O:s could indeed correspond to terminals for flux tubes coming from single dark nucleon representing single DNA codon.

8. The division of oil droplet would be the analog of cell replication and would involve at the deeper level the replication of dark nucleon sequences. This requires the analog of DNA double strand and the analogs of DNA codons would be dark nucleons. Genetic codons could be realized in terms of flux tubes connecting dark nucleon sequences to the oleic acids or oleic anhydrides at the surface of the droplet. It remains to be seen whether the division can be achieve in real world.

To sum up, this model is rather direct application of TGD based vision about life and the killer test is whether the mineral oil oil molecules and hydrogen cyanide molecules are not ideal but actually contain the (C=O)-O-(C= O) pieces carrying energy and information and serve as terminals for the magnetic flux tubes.

For background see the chapter Evolution in Many-Sheeted Space-time.See also the article Oil droplets as a primitive life form?

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 for a discussion containing also additional references.

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