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Genes and Memes
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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".
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.,
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.
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.
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.
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.
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.
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.
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.
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.
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.
Implications for Mendelian anomalies
This vision also suggests how to understand the origin of the Mendelian anomalies.
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.