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.
- 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.
- Context sensitivity of gene's effect: the effect of gene is highly sensitive on its environment in DNA.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.