What's new in

Genes and Memes

Note: Newest contributions are at the top!



Year 2018



Expanding Earth hypothesis, Platonic solids, and plate tectonics as a symplectic flow

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.

  1. The expansion would have started from or generated decomposition of the Earth's crust to an icosahedral lattice with 20 faces, which contain analogs of what is known as cratons and having a total area equal to that of Earth before expansion. The prediction for the recent land area fraction is 25 per cent is 4.1 per cent too low. The simplest explanation is that expansion still continues but very slowly.
  2. The craton like objects (hereafter cratons) would move like 2-D rigid bodies and would fuse to form continents.
  3. The memory about the initial state should be preserved: otherwise there would exist no simple manner to reproduce the observation of Adams by simple motions of continents combined with downwards scaling. This might be achieved if cratons are connected by flux tubes to form a network. For maximal connectivity given triangular face is connected by flux tube to to all 3 nearest neighbour faces. Minimal connectivity corresponds to an essentially unique dodecahedral Hamiltonian cycle connecting cratons to single closed string. At least for maximal connectivity this memory would allow to understand the claim of Adams stating that the reduction of radius by factor 1/2 plus simple motions for the continents allow to transform the continents to single continent covering the entire surface of the scaled down Earth.
  4. The dynamics in scales longer than that of craton would be naturally a generalization of an incompressible liquid flow to area preserving dynamics defined by symplectic flow. The assumption that Hamilton satisfies Laplace equation and is thus a real or imaginary part of analytic function implies additional symmetry: the area preserving flow has dual.
For details see the chapter Expanding Earth hypothesis or the article Expanding Earth hypothesis, Platonic solids, and plate tectonics as a symplectic flow .



Did RNA replicate in codon-wise manner during RNA era?

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).

  1. During RNA era amino-acids associated with pre-tRNA molecules would served as catalysts for replication of RNA codons. The linguistic mode would have been "holistic" during RNA er in accordance with the findings of the above experiments. RNA codon would have been the basic unit.
  2. This would have led to a smaller number of RNAs since RNA and RNA like molecules in tRNA are not in 1-1 correspondence. A more realistic option could have been replication of subset of RNA molecules appearing in tRNA in this manner.
  3. Then a great evolutionary leap leading from RNA era to DNA era would have occurred. AA catalyzed replication of RNA would have transformed to a translation of RNA to proteins and the roles of RNA and AA in tRNA would have changed. [Perhaps the increase of heff in some relevant structure as quantum criticality was reached led to the revolution?]
  4. At this step also (subset of) DNA and its transcription to (a subset of) mRNA corresponding to tRNA had to emerge to produce mRNA in transcription. In the recent biology DNA replicates and is transcribed nucleotide by nucleotide rather than using codon as a unit so that DNA and RNA polymerases catalyzing replication and transcription should have emerged at this step. An alternative option would involve the "tDNA" as the analog of "tRNA" and the emergence of polymerases later: this does not however look attractive if one accepts the idea about the transition from holistic to analytic mood.

    The ability of DNA to unwind is essential for the emergence of the "analytic linguistic mode" as an analog of written language (DNA) decomposing codons to triplets of letters. This must have been a crucial step in evolution comparable to the emergence of written language based on letters. Also the counterpart of RNA polymerase and separate RNA nucleotides for transcription should have emerged if not already present.

    The minimal picture would be emergence of a subset of DNA codons corresponding to RNAs associated with pre-tRNA and the emergence of the analogs of DNA and RNA polymerases as the roles of amino-acid and RNA codon in tRNA were changed.

  5. How DNA could have emerged from RNA? The chemical change would have been essentially the replacement of ribose with de-oxiribose to get DNA from RNA and U→ T. Single O-H in ribose was replaced with H. O forms hydrogen bonds with water and this had to change the hydrogen bonding characteristics of RNA.

    If the change of heff =n×h0 (one has h= 6× h0 in the most plausible scenario, see this and this) was involved, could it have led to stabilization of DNA. Did cell membrane emerge and allow to achieve this? I have proposed (see this) that the emergence of cell membrane meant the emergence of new representation of dark genetic code based on dark nuclei with larger value of heff.

The communication between dark and ordinary variants of biomolecules involves resonance mechanism and would also involve genetic code represented as 3-chords, music of light, and it is interesting to see whether this model provides additional insights.
  1. The proposal is that 3-chords assignable to nucleotides as music of light with allowed 64 chords defining what I have called bio-harmony is essential for the resonance (see this, this, and this). The 3 frequencies must be identical in the resonance: this is like turning 3 knobs in radio. This 3-fold resonance would correspond to the analytic mode. The second mode could be holistic in the sense that it would involve only the sum only the sum of the 3 frequencies modulo octave equivalence assigning a melody to a sequence of 3-chords.
  2. The proposal is that amino-acids having not triplet decomposition are holistic and couple to the sum of 3 frequencies assignable to tRNA and mRNA in this manner. Also the RNAs in tRNA could couple to mRNA in this manner. One could perhaps say that tRNA, mRNA and amino-acids codons sing whereas DNA provides the accompaniment proceeding as 3-chords. The couplings of DNA nucleotides to RNA nucleotides would realy on the frequencies assignable to nucleotides.
  3. If the sum of any 3 frequencies associated with mRNA codons is not the same except when the codons code for the same amino-acids, the representation of 3-chords with the sum of the notes is faithful. The frequencies to DNA and RNA nucleotides cannot be however independent of codons since the codons differing only by a permutation of letters would correspond to the same frequency and therefore code for the same amino-acid. Hence the information about the entire codon would be needed also in transcription and translation and could be provided either by dark DNA strand associated with DNA strand or by the interactions between the nucleotides of the DNA codon.
  4. The DNA codon itself would know that if is associated with dark codon and the frequencies assignable to nucleotides are determined by the dark DNA codon. It would be enough that the frequency of the letter depends on its position in the codon so that there would be 3 frequencies for every letter: 12 frequencies altogether.

    What puts bells ringing is that this the number of notes in 12-note scale for which the model of bio-harmony (see this and this) based on the fusion of icosahedral (12 vertices and 20 triangular faces) and tetrahedral geometries by gluing icosahedron and tetrahedron along one face, provides a model as Hamiltonian cycle and produces genetic code as a by-product. Different Hamiltonian cycles define different harmonies identified as correlates for molecular moods.

    Does each DNA nucleotide respond to 3 different frequencies coding for its position in the codon and do the 4 nucleotides give rise to the 12 notes of 12-note scale? There are many choices for the triplets but a good guess is that the intervals between the notes of triplet are same and that fourth note added to the triplet would be the first one to realize octave equivalence. This gives uniquely CEG #, C#FA,DF#/B b, and DG#B as the triplets assignable to the nucleotides. The emergence of 12-note scale in this manner would be a new element in the model of bio-harmony.

    There are 4!=24 options for the correspondence between {A, T, C, G} as the first letter and {C,C#,D,D#}. One can reduce this number by a simple argument.

    1. Letters and their conjugates form pyrimidine-purine pairs T, A and C,G. The square of conjugation is identity transformation. The replacement of note with note defining at distance of half-octave satisfies this condition (half-octave - tritonus - was a cursed interval in ancient music and the sound of ambulance realizes it). Conjugation could correspond to a transformation of 3-chords defined as

      CEG# ↔ DF#Bb , C#FA↔ D#GB .

    2. One could have

      {T, C} ↔ {CEG #, C#FA} , {A,G}↔ {DF#Bb,D#GB}

      or

      {T, C} ↔ {DF#Bb,D#GB} , {A,G}↔ {CEG#, C#FA} .

    3. One can permute T and C and A and G in these correspondences. This leaves 8 alternative options. Fixing the order of the image of (T, C) to say (C,C#) fixes the order of the image of (A, G) to (D,D#) by the half-octave conjugation. This leaves 4 choices. Given the bio-harmony and having chosen one of these 4 options one could therefore check what given DNA sequence sounds as a sequence of 3-chords (see this).

      Anyone willing to do this kind of experimentation obtains from me the program modules used the Garage band programs to produce a sequence of chords. A further interesting experiment would be check what kind of melodies come out if one assigns to a chord a note as the sum of frequencies of the chord reduced by octave equivalence to basic octave.

    That the position the frequency associated with the nucleotide depends on its position in the codon would also reflect the biochemistry of the codon and this kind of dependence would be natural. In particular, different frequencies associated with the first and third codon would reflect the parity breaking defining orientation for DNA.
See the chapter About the Correspondence of Dark Nuclear Genetic Code and Ordinary Genetic Code or the article with the same title.



Homonymy of the genetic code from TGD point of view

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.



About the Correspondence of Dark Nuclear Genetic Code and Ordinary Genetic Code

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.

Insights

The above observations inspire several speculative insights.

  1. The emergence of dark nuclei identified as dark proton sequences would relate to Pollack's effect in which irradiation of water generates in presence of gel phase bounding the water what Pollack calls exclusion zones (EZs). EZs are negatively charged and water has effective stoichiometry H1.5O. EZs deserve their name: somehow they manage to get rid of various impurities: this might be very important if EZs serve as regions carrying biologically important information. The protons of water molecules must go somewhere and the proposal is that they go to the magnetic body of some system consisting of flux tubes. The flux tubes contain the dark protons as sequences identifiable as dark nuclei.
  2. Since nuclear physics precedes chemistry, one can argue that prebiotic life is based on these dark biomolecules serving as a template for ordinary biomolecules. To some degree biochemistry would be shadow dynamics and dark dynamics would be extremely simple as compared to the biochemistry induced by it. In particular, DNA replication, transcription, and translation would be induced by their dark variants. One can even extend this vision: perhaps also ordinary nuclear physics and its scaled up counterpart explaining "cold fusion" are parts of evolutionary hierarchy of nuclear physics in various scales.
  3. Nature could have a kind of R&D lab allowing to test various new candidates for genes by using transcription and translation at the level of dark counterparts of the ordinary basic biomolecules.
Conditions on the model

The model must satisfy stringent conditions.

  1. Both the basis A, T, C, G and A, U, C, G as basic chemical building bricks of RNA and DNA must have emerged without the help of enzymes and ribozymes. It is known that the biochemical pathway known as pentose-phosphate pathway generates both ribose and ribose-5-phosphate defining the basic building brick of RNA. In DNA ribose is replaced with de-oxiribose obtained by removing one oxygen.

    Pyrimidines U, T and C having single aromatic ring are are reported by NASA to be generated under outer space conditions (see this). Carell et al have identified a mechanism leading to the generation of purines A and G, which besides pyrimidines C,T (U) are the basic building bricks of DNA and RNA. The crucial step is to make the solution involved slightly acidic by adding protons. TGD inspired model for the mechanism involves dark protons (see this).

    Basic amino-acids are generated in the Miller-Urey type experiments. Also nucleobases have been genererated in Miller-Urey type experiments.

    Therefore the basic building bricks can emerge without help of enzymes and ribozymes so that the presence of dark nuclei could lead to the emergence of the basic biopolymers and tRNA.

  2. Genetic code as a correspondence between RNA and corresponding dark proton sequences must emerge. Same true for DNA and also amino-acids and their dark counterparts. The basic idea is that metabolic energy transfer between biomolecules and their dark variants must be possible. This requires transitions with same transition energies so that resonance becomes possible. This is also essential for the pairing of DNA and dark DNA and also for the pairing of say dark DNA and dark RNA. The resonance condition could explain why just the known basic biomolecules are selected from a huge variety of candidates possible in ordinary biochemistry and there would be no need to assume that life as we know it emerges as a random accident.
  3. Metabolic energy transfer between molecules and their dark variants must be possible by resonance condition. The dark nuclear energy scale associated with biomolecule could correspond to the metabolic energy scale of .5 eV. This condition fixes the model to a high extent but also other dark nuclear scales with their own metabolic energy quanta are possible.
Vision

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.



To the index page