The first guess (see this) was that parallel DNA or RNA strands could form braids. The problem is that the number of braid strands is limited and the computations are restricted within single cell nucleus. The need to establish the hardware for each computation separately can be also seen as a restriction.
One can imagine also other manners in which DNA or RNA could act as a topological quantum computer and it good to try to state clearly what one wants.
- Natural requirements are that the topological quantum computer programs can be naturally combined to larger programs and evolution means this kind of process; that the programs have a natural modular structure inherited from the previous stages of evolution; and that the computation is not restricted inside single nucleus.
- DNA and/or RNA defines the hardware of topological computation and at least for more advanced topological quantum computers this hardware should be static so that only programs would be dynamical. This leaves only DNA in consideration and the entangled initial and quantum states at the ends of braids quantum states would be assignable to static DNA structures.
- The program would be determined by different braidings connecting the states of DNA in time direction or in spatial direction. Since the genomes are identical in different nuclei, the strands could connect different nuclei or conjugate strands of double DNA strand.
1. The recent progress in quantum TGD and TGD inspired quantum biology
After the advent of the first model for topological quantum computation in TGD Universe (see this), the mathematical and physical understanding of TGD has developed dramatically and the earlier quite speculative picture can be replaced with a framework which leads to a rather unique view about topological quantum computations by DNA.
1.1 Universe as a topological quantum computer
One can say that the recent formulation of quantum TGD states that the entire Universe behaves like a topological quantum computer. This notion of topological quantum computer differs however from the standard one in many respects.
- The emergence of hierarchy of Planck constants realized as a generalization of the notion of imbedding space is now a basic piece of TGD allowing an elegant formulation of quantum TGD (see this and this). The phases of matter with large Planck constant are interpreted as dark matter. Large values of Planck constant make possible topological quantum computations in arbitrary long time scales so that the most fundamental objection against quantum computation can be circumvented.
- Zero energy ontology forces to unify S-matrix and density matrix to M-matrix - the product of the square root of density matrix and S-matrix-defined as time-like (or rather light-like) entanglement coefficients between positive and negative energy parts of zero energy state (see this and this). Connes tensor product emerging naturally from the notion of finite measurement resolution described in terms of inclusions of hyperfinite factors of type II1 defines highly uniquely the M-matrix. M-matrix would be natural candidate for defining topological quantum computation in light-like direction. Connes tensor product makes sense also in space-like direction and would define quantum storage of functions represented as entanglement coefficients.
- The notion of number theoretic braid (see this and this) is now well-understood and has become a basic element of the formulation of quantum TGD based on the requirement of number theoretical universality. As a matter fact, the notion of braid is generalized in the sense that braid strands can fuse and decay. The physical interpretation is as motion of minima of the generalization eigenvalue of the modified Dirac operator which is function of transversal coordinates of light-like partonic 3-surface and has interpretation as vacuum expectation of Higgs field. Fusion of braid strands corresponds to fusion of minima.
For generalized Feynman diagrams partonic light-like 3-surfaces meet at 2-dimensional vertices defined by partonic 2-surfaces (see this). This implies that braids replicate at vertices: the interpretation is as a copying of classical information. Quantum information is not copied faithfully. The exchange of partonic 2-surfaces in turn corresponds to quantum communications. Hence quantum communication and quantum copying emerge naturally as additional elements. Space-like Connes tensor product in turn defines quantum memory storage.
- Computation time is a fundamental restriction in both ordinary and quantum computation. Zero energy ontology makes possible communications in both directions of geometric time, which suggests the possibility of geometric time loops in topological quantum computations. Could this mean that computation time ceases to be a restriction and ordinary computations lasting for infinite amount of geometric time could be performed in a finite time interval of observer's time? This is perhaps too much to hope. The subjective time taken by the computation would be infinite if each step in the iteration corresponds to single quantum jump. If this is the case and if each quantum jump of observer corresponds to a finite increment of geometric time perceived by the observer, time loops would not allow miracles.
The evolution of ideas related to quantum biology provides also new valuable insights. In particular, the notion of magnetic body leads to a model of living system in which dark matter at magnetic flux quanta of the field body of biological system uses biological body as a motor instrument and sensory receptor (see this). Quantum control would be naturally via the genome and sensory input would be from cell membrane containing all kinds of receptors. This would suggest that magnetic flux sheets traverse through DNA strands and cell membranes.
The quantization of magnetic flux with unit defined by Planck constant having arbitrarily large values leads naturally to the notions of super-genome and hyper-genome (see this). Super-genome would consists of DNA strands of separate nuclei belonging to single magnetic flux sheet and these sequences of genomes would be like lines of text at the page of book. Super-genomes in turn can combine to form text lines at the pages of a bigger book, I have used the term hyper-genome. This hierarchy of genomes would give rise to a collective gene expression at the level of organs, individuals of a species, and at the collective level consisting of populations containing several species. Even biosphere could express itself coherently via all the genomes of the bio-sphere. The model of topological quantum computation performed by DNA should be consistent with this general picture.
2. Model for DNA based topological quantum computation
The most promising model of DNA as topological quantum computer relies on the hierarchy of genomes. The flux sheets or collections of parallel flux tubes assignable to a magnetic body would traverse the DNA strands of several nuclei so that strands would be analogous to lines of text on the page of a book.
DNA strands would define the intersections of magnetic or number theoretic braids with plane and braiding would be associated with with the magnetic field lines or flux tubes transversal to DNA. The M-matrix defining topological quantum computation would act on quantum states assignable to nucleotides.
2.1 The interpretation of nucleotides
The interpretation of the A,T,C,G degree of freedom is not obvious and one can consider several options.
1) The quantum numbers entangled by braids having nothing to do with (A,T,C,G) assignable to nucleotides and the braiding does not affect nucleotides.
2) The nucleotides (A,T,C,G) correspond to four different colors (a,t,c,g) for braid strands with conjugate nucleotides defining conjugate colors. The subgroup of allowed braidings would preserve the color patterns. The minimal assumption is that braid strands connect only identical nucleotides. A stronger - probably unrealistic - assumption is that braiding permutes nucleotides physically.
3) The entangled quantum numbers are in 1-1 correspondence with states A, T, C, G of nucleotide. In zero energy ontology this would be possible without breaking of fundamental conservation laws. One can even consider the possibility that A,T,C,G are these quantum numbers. Topological quantum computation in time direction would thus make it possible to replace the DNA strands with new ones and provide a purely quantal mechanism of genetic evolution. Only introns could be involved with topological quantum computations in this sense since they would not induce mutations visible at the level of amino-acids. The intronic portions of genome would not be evolutionary invariants: whether or not this is the case should be easily testable.
4) The combination of options 2) and 3) might make sense for topological quantum computations in time like direction. One would have superposition of topological quantum computations associated with various color patterns and the halting of the computation would mean in general the occurrence of a mutation.
The option 2) with braid strands connecting only identical nucleotides is rather attractive since it explains several facts about genome (as do also options 3) and 4)).
- The model requires that the genomes in different nuclei must be identical: otherwise it is not possible to realize braidings as symmetry transformations mapping portions of DNA to itself (as noticed, this map need not occur at the chemical level). An interesting question is whether also the permutations of nucleotides of different codons are allowed or whether only codons are permuted so that they would define fundamental sub-programs.
- One can understand why the minimum number of nucleotides in a codon is three. The point is that braid group is non-commutative only when the number of strands is larger than 2. The braidings acting as symmetries would correspond to a subgroup of ordinary braidings leaving the color pattern of braid invariant. Obviously the group is generated by some minimal number of combinations of ordinary braid generators. For instance, for two braid strands with different colors the generator is e12 rather than e1 (two exchange operations/full 2π twist). For codons one would have four different subgroups of full braid group corresponding to codons of type XXX, XYY, XXY, and XYZ. Each gene would be characterized by its own subgroup of braid group and thus by an M-matrix defining topological quantum computation.
- One could understand the "junk DNA" character of introns. Introns are the most natural candidates for the portions of genome participating topological quantum computations The transcription process would disturb topological quantum computation so that introns should be chemically passive. Since the portion of "junk DNA" increases with the evolutionary level of the species evolution would indeed correspond to an increase the amount of topological quantum computations performed.
One can imagine two basic realizations of topological quantum computation like processes- or to be more precise - entanglement by braiding. In TGD framework this entanglement could be interpreted in terms of Connes tensor product.
1. Space-like entanglement The first realization would rely space-like braids. Braid strands would connect identical lines of text at the page of book defined by sequences of genomes of different nuclei. Inside nucleus the strands would connect DNA and its conjugate. The braiding operation would take place between lines.
In this case it would be perhaps more appropriate to speak about quantum memory storage of a function realized as entanglement. These functions could represent various rules about the behavior of and survival in the physical world. For this option A,T,C,G cannot correspond to entangled quantum numbers and the interpretation as braid colors is natural. Braiding cannot correspond to a physical braiding of nucleotides so that (A,T,C,G) could correspond to braid color (strands would connect only identical nucleotides).
Strands would not connect strand and its conjugate like hydrogen bonds do but would be like long flux lines of dipole field starting from nucleotide and ending to its conjugate so that braiding would emerge naturally. Color magnetic flux tube structures of almost atom size appear in the TGD based model of nucleus and have light quarks and anti-quarks at their ends (see this). This could be the case also now since quarks and anti-quarks appear also in the model of high Tc superconductivity which should be present also in living matter (see this).
2. Light-like entanglement
Second realization would rely on light-like braids at the boundaries of light-like 3-surfaces connecting 2-surfaces assignable to single genome at different moments of time. Braiding would be dynamical and dance metaphor would apply. The light-like surface could intersect genomes only at initial and final moments and strands would connect only identical nucleotides. Light-likeness in the induced metric of course allows the partonic 3-surface to look static at the level of imbedding space. The fundamental number theoretic braids defined by the minima of the Higgs like field associated with the modified Dirac operator would be very natural in this case.
Genes would define only the hardware unless they code for the magnetic body of DNA too, which looks implausible. The presence of quantum memory and quantum programs would mean a breakdown of genetic determinism since the braidings representing memories and programs would develop quantum jump by quantum jump and distinguish between individuals with the same genome. Also the personal development of individual would take place at this level. It would be these programs (that is magnetic bodies) which would differentiate between us and our cousins with almost identical genome.
3. Biological evolution as an evolution of topological quantum computation
This framework allows to understand biological evolution as an evolution of topological quantum computation like processes in which already existing programs become building blocks of more complex programs.
- The transition from RNA era to DNA era (for TGD inspired model for pre-biotic evolution (see this) involving also the emergence of cell membrane bounded structures would mean the emergence of the topological quantum computation using a static hardware.
- For mono-cellulars double DNA strands define space-like topological quantum computations involving only single step if the braids connect the nucleotides of the two DNA strands: obviously a reason why for double DNA strands.
- For multicellular organisms more complex space-like topological quantum computations would emerge and could code rules about environment and multicellular survival in it. At this step also introns specialized to topological quantum computation would emerge.
- A further evolution as a generation of super-genomes in turn forming hyper-genomes and even higher structures would have a concrete counterpart as the organization of braids of lower level to form braids at higher level so that topological quantum computations would become increasingly complex and program module structure would emerge very naturally.