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Genes and Memes
Note: Newest contributions are at the top!
A FB discussion inspired by the recent findings of NASA suggesting the presence of life under the surface of Mars raised the question whether the TGD based Expanding Earth model is consistent with plate tectonics and with the motivating claim of Adams that the continents fit together nicely to cover the entire surface of Earth if its radius were one half of the recent radius. The outcome was what one might call Platonic plate tectonics.
There was a very interesting popular article in Spacedaily with title "Scientists crack how primordial life on Earth might have replicated itself" (see this). The research paper "Ribozyme-catalysed RNA synthesis using triplet building blocks" is here.
It is possible to replicate unfolded RNA strands in Lab by using enzymes known as ribozymes, which are RNA counterparts of enzymes, which are amino-adic sequences. In the presence of folding the replication is however impossible. Since ribozymes are in general folded, they cannot catalyze their own replication in this manner. The researchers however discovered that the replication using RNA triplets - genetic codons - as basic unit can be carried out in laboratory even for the folded RNA strands and with rather low error rate. Also the ribozyme involved can thus replicate. For units longer than 3 nucleotides the replication becomes prone to errors.
These findings are highly interesting in TGD framework. In TGD chemical realization of genetic code is not fundamental. Rather, dark matter level would provide the fundamental realizations of analogs of DNA, RNA, tRNA, and amino-acids as dark proton sequences giving rise to dark nuclei at magnetic flux tubes. Also ordinary nuclei correspond in TGD Universe to sequences of protons and neutrons forming string like entities assignable to magnetic flux tubes.
The basic unit representing DNA, RNA and tRNA codon and amino-acid would consist of 3 entangled dark protons. The essential aspect is that by entanglement the dark codons do not decompose to products of letters. This is like words of some languages, which do not allow decomposition to letters. This representation is holistic. As we learn to read and write, we learn the more analytic western view about words as letter sequences. Could the same hold true in evolution so that RNA triplets would have come first as entities pairing with dark RNA codons from from dark proton triplets as a whole? Later DNA codons would have emerged and paired with dark DNA codons. Now the coupling would have have been letter by letter in DNA replication and transcription to mRNA.
It is intriguing that tRNA consists of RNA triplets combined from amino-acids and analogs of mRNA triplets! The translation of mRNA to amino-acids having no 3-letter decomposition of course forces the holistic view but one can ask whether something deeper is involved. This might be the case. I have been wondering whether during RNA era RNA replicated using a prebiotic form of translational machinery, which replicated mRNA rather than translated RNA to protein formed from amino-acids (AAs).
Peter Gariaev and colleagues have applied the linguistic notions of synonymy and homonymy to genetic code. Also the notion of syhomy fusing these concepts is introduced. Homonymy is visible in mRNa-tRNA pairing and induced by the 1-to-many pairing of the third mRNA nucleotide with tRNA nucleotide. The homonymy in mRNA-AA (AA for amino-acid) pairing is also present albeit rare.
The codons for the standard code can be divided to two classes. For 32 codons the first two letters fix AA completely. For the remaining 32 codons this is not the case. There is however almost unbroken symmetry in that U and C resp. A and G code for the same AA. The breaking of this symmetry is minimal appearing only for 3 4-columns of the code table and present for A-G only. The deviations from the standard code as a rule break A-G or T-C symmetry or re-establish it.
The notion of homonymy is highly interesting from TGD point of view. TGD leads to two basic proposals for non-chemical realization of genetic code predicting the numbers of DNA codons coding for amino-acid (AA) rather successfully. The first proposal relies on TGD based view about dark matter as heff/h=n phases of ordinary matter and identifies counterparts of DNA, RNA, tNRA, and AAs as entangled dark proton triplets.
Second proposal emerged from the model of music-harmony based on fusion of icosahedral and tetrahedral geometries. Codons are represented as photon triplets (dark or ordinary) defining the allowed 3-chords of given harmony defined by Hamilton cycle at icosahedron extended to Hamilton cycle to the fusion of icosahedron with tetrahedron along common face. Photon triplets give rise to resonant coupling giving rise to physical pairing of biomolecule and its dark counterpart. Remarkably, there are 3 different realizations of tRNA in terms of 3-chords. There is large number of bio-harmonies corresponding to Hamiltonian cycles. Since music expresses and creates emotions, the proposal is that a realization of emotions at molecular level adding additional degrees of freedom not visible at the level of chemistry is in question. This might give rise to a context dependence of the code.
The proposal is that genetic code at dark level extends to a sequence DDNA → DmRNA → DtRNA → DAA of horizontal pairings analogous to projections is fundamental one. Codon-codon pairings are realized via dark photon triplet resonance and mRNA-AA pairing by resonant coupling to the sum fXYZ=f1+f2+f3 of 3-chord frequencies: the codons coding same AA would have frequencies fXYZ differing only by a multiple of octave. One might perhaps say that AA sequence defines melody and mRNA sequence the accompaniment.
There is context dependence and homonymies already in DmRNA-DtRNA pairing and due the fact that DtRNA corresponds to a 2-harmony which is sub-harmony of 3-harmony and can be chosen in 3 different manners. The vertical pairings DDNA → DNA, DmRNA → mRNA, etc. also mediated by frequency couplings induce ordinary genetic code and horizontal pairings in DNA → mRNA → tRNA → AA. DAA → AA pairing dictates mRNA → AA pairing and mRNA → tRNA homonymy does not matter and actually makes the translation safer by increasing the number of tRNAs performing the same task.
The rather rare homonymies in DNA-AA pairing can be understood as accidental degeneracies. AA couples resonantly to the sum fXYZ=f1+f2+f2 of frequencies associated with codon XYZ and it can occur that the sum frequencies can be identical for two codons.
See the chapter Homonymy of the genetic code from TGD point of view or the article with the same title.
The idea about the realization of genetic code in terms of dark proton sequences giving rise to dark nuclei is one of the key ideas of TGD inspired quantum biology (see this). This vision was inspired by the totally unexpected observation that the states of three dark protons (or quarks) can be classified to 4 classes in which the number of states are same as those of DNA, RNA, tRNA, and amino-acids. Even more, it is possible to identify genetic code as a natural correspondence between the dark counterparts of DNA/RNA codons and dark amino-acids and the numbers of DNAs/RNAs coding given amino-acid are same as in the vertebrate code. What is new is that the dark codons do not reduce to ordered products of letters.
During years I have considered several alternatives for the representations of genetic code. For instance, one can consider the possibility that the letters of the genetic code correspond to the four spin-isospin states of nucleon or quark or for spin states of electron pair. Ordering of the letters as states is required and this is problematic from the point of view of tensor product unless the ordering reflects spatial ordering for the positions of particles representing the letters. One representation in terms of 3-chords formed by 3-photon states formed from dark photons emerges from the model of music harmony (see this). By octave equivalence the ordering of the notes is not needed.
The above observations inspire several speculative insights.
The model must satisfy stringent conditions.
The basic problem in the understanding of the prebiotic evolution is how DNA, RNA, amino-acids and tRNA and perhaps even cell membrane and microtubules . The individual nucleotides and amino-acids emerge without the help of enzymes or ribozymes but the mystery is how their polymers emerged. If the dark variants of these molecules served as templates for their generation one avoids this hen-and-egg problem. The problem how just the biomolecules were picked up from a huge variety of candidates allowed by chemistry could be solved by the resonance condition making possible metabolic energy transfer between biomolecules and dark nuclei.
Simple scaling argument shows that the assumption that ordinary genetic code corresponds to heff/h=n=218 and therefore to the p-adic length scale L(141)≈ .3 nm corresponding to the distance between DNA and RNA bases predicts that the scale of dark nuclear excitation energies is .5 eV, the nominal value of metabolic energy quantum. This extends and modifies the vision about how prebiotic evolution led via RNA era to the recent biology. Unidentified infrared bands (UIBs) from interstellar space identified in terms of transition energies of dark nuclear physics support this vision and one can compre it to PAH world hypothesis.
p-Adic length scale hypothesis and thermodynamical considerations lead to ask whether cell membrane and microtubules could correspond to 2-D analogs of RNA strands associated with dark RNA codons forming lattice like structures. Thermal constraints allow cell membrane of thickness about 5 nm as a realization of k=149 level with n= 222 in terms of lipids as analogs of RNA codons. Metabolic energy quantum is predicted to be .04 eV, which corresponds to membrane potential. The thickness of neuronal membrane in the range 8-10 nm and could correspond to k=151 and n=223 in accordance with the idea that it corresponds to higher level in the cellular evolution reflecting that of dark nuclear physics.
Also microtubules could correspond to k=151 realization for which metabolic energy quantum is .02 eV slightly below thermal energy at room temperature: this could relate to the inherent instability of microtubules. Also a proposal for how microtubules could realize genetic code with the 2 conformations of tubulin dimers and 32 charges associated with ATP and ADP accompanying the dimer thus realizing the analogs of 64 analogs of RNA codons is made.
See the chapter About the Correspondence of Dark Nuclear Genetic Code and Ordinary Genetic Code or the article with the same title.