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Magnetospheric Consciousness

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Year 2016

Could the replication of mirror DNA teach something about chiral selection?

I received a link to a very interesting popular article from which I learned that short strands of mirror DNA and mirror RNA - known as aptamers - have been be produced commercially for decades - a total surprise to me. Aptamers bind to targets like proteins and block their activity and this ability can be utilized for medical purposes.

Now researchers at Tsinghua University of Beijing have been able to create a mirror variant of an enzyme - DNA polymeraze - catalyzing the transcription of mirror DNA to mirror RNA also replication of mirror DNA. What is needed are the DNA strand to be replicated or transcribed, the mirror DNA nucleotides, and short primer strand since the DNA polymeraze starts to work only if the primer is present. This is like recalling a poem only after hearing the first few words.

The commonly used DNA polymerase containing about 600 amino-adics is too long to be built up as a right-handed version and researchers used a much shorter version: African swine fever virus having only 174 amino-acids. The replication turned out to be very slow. A primer of 12 nucleotides was extended to a strand of 18 nucleotides in about 4 hours: 3/2 nucleotides per hour. The extension to a strand of 56 nucleotides took 36 hours making 44/36= 11/9 nucleotides per hour. DNA and its mirror image co-existed peacefully in a solution. One explanation for the absence of mirror life is that the replication and transcription of mirror form was so slow that it lost the fight for survival. Second explanation is that the emergence of mirror forms of DNA polymerase and other enzymes was less probable.

Can one learn anything about this?

  1. Chiral selection is one of the deep mysteries of biology. Amino-acids are left-handed and DNA and RNA double strands form a right-handed screw. One can assign handedness with individual DNA nucleotides and with DNA double strand but web sources speak only about the chirality of double strand. If the chirality of the DNA nucleotides were not fixed, it would have been very probably discovered long time ago as an additional bit doubling the number of DNA letters.
  2. What could be the origin of the chirality selection? Second helicity could have been loser in the fight for survival and the above finding supports this: fast ones eat the slow ones like in market economy. There must be however a breaking of mirror symmetry. Weak interactions break of mirror symmetry but the breaking is extremely small because the weak bosons mediating weak interaction are so massive that the length scale in which the breaking of mirror symmetry matters is of order 1/100 times proton size. This breaking is quite too small to explain chiral selection occurring in nano-scales: there is discrepancy of 8 orders of magnitude. The proposal has been that the breaking of mirror symmetry has been spontaneous and induced by a very small seed. As far as I know, no convincing candidate for the seed has been identified.
According to TGD inspired model chiral selection would be induced from that in dark matter sector identified in terms of phases of ordinary matter with non-standard value of Planck constant heff/h= n. In living matter dark matter would reside at magnetic flux tubes and control ordinary matter. TGD predicts standard model couplings, in particular weak parity breaking. For heff/h= n the scale below which weak bosons behave as massless particles implying large parity breaking is scaled up by n. Large parity breaking for dark matter becomes possible in even biological length scales for large enough heff.

The crucial finding is that the states of dark proton regarded as part of dark nuclear string can be mapped naturally to DNA, RNA, tRNA, and amino-acid molecules and that vertebrate genetic code can be reproduced naturally. This suggests that genetic code is realized at the level of dark nuclear physics and induces its chemical variant. More generally, biochemistry would be kind of shadow of dark matter physics. A model for dark proton sequences and their helical pairing is proposed and estimates for the parity conserving and breaking parts of Z0 interaction potential are deduced.

For details see the article Could the replication of mirror DNA teach something about chiral selection? or the chapter Evolution in many-sheeted space-time of "Magnetospheric Consciousness".

One step further in the understanding the origins of life

I learned about very interesting discovery related to the problem of understanding how the basic building bricks of life might have emerged. RNA (DNA) has nucleotides A,G,C,U (T) as basic building bricks.

The first deep question is how the nucleotides A,G,C,U, and T emerged.

  1. There are two types of nucleotides. Pyrimidines C and T/U ) have single carbon 6-cycle. Purines A and G in turn have single 6-single and 5-cycle fused attached together along one side. Purines are clearly more complex than pyrimidines.
  2. U.K. chemist John Sutherland demonstrated a plausible sequence of steps leading to the emergence of pyrimidines. Purines turned out to be more problematic. Leslie Orgel and colleagues suggested a possible pathway but it produces purines in too tiny amounts.
Now a group led by Thomas Carell in Ludwig Maximilian University have found a more plausible mechanism.
  1. Carell and colleagues studied the interaction of biomolecule formamido-pyrimidine (FaPy) with DNA and found that it also reacts to produce purines. Could FaPys have served as predecessors of purines? (For formamide see this and for the class of chemical compounds known as amines see this).
  2. The first step would have been a copious production of amino-pyrimidines containing several chemical groups known as amines. The problem is that the are so many amines and they normally react indiscriminantly to produce many different compounds. One wants mostly purines so that only one critical amine is wanted.
  3. When Carell and his team added some acid to the solution to decrease its pH, a miracle happened. The extra protons from acid attached to the amines of the amino-pyrimidine and made them non-reactive. There was however one exception: just the amine giving rise to purine in its reactions! The reactive amine also readily bonded with formic acid or formamide. Hence it seems that one big problem has been solved.
The second challenge is to understand how the building bricks of RNA and DNA combined to form longer polymers and began to replicate.
  1. One prevailing vision is that so called RNA world preceded the recent biology dominated by DNA. The goal has been to achieve generation of RNA sequence in laboratory. Unlike DNA RNA sequences are not stable and long sequences are difficult to generate. DNA in turn replicates only inside cell and the presence of what is known as ordered water seems to be essential for this.
  2. This step might involve new physics and chemistry and I have considered the possibility that the new physics involves magnetic bodies and dark proton sequences as a representation of the genetic code at the level of dark nuclear physics. There is no need to add that the fact that dark proton states provide representations for RNA, DNA, tRNA, and amino-acids (see this) looks like a miracle and I find still difficult to believe that it is true and for genetic code. Also the representation of vertebrate code emerges in terms of correspondences of dark proton states.

    This suggests that the replication of DNA and takes place at the level of dark proton sequencies - dark nuclear strings - serving as a dynamical template for the biological replication. Also transcription and translation would be induced by dark process. Actually all biochemical processes could have as template the dynamics of molecular magnetic bodies and biochemistry would be kind of shadow of deeper dynamics.

  3. There is actually support for dark proton sequences. Quite recently I learned about the article of Leif Holmlid and Bernhard Kotzias (see this) about the superdense phase of hydrogen. In TGD superdense phase has interpretation as dark proton sequences at magnetic flux tubes with the Compton length of dark proton coded by heff/h≈ 211 to electron's Compton length (see this). Remarkably, it is reported that the superdense hydrogen is super-conductor and super-fluid at room temperatures and even above: this is just what TGD predicts.

    The dark protons in TGD inspired quantum biology (see this) should have much longer Compton length of order of the distance between nucleotides in DNA sequences in order to serve as templates for chemical DNA. This gives a dark Compton length of order ≈ 3.3 Angstroms from the fact that there are 10 codons per 10 nm. This gives heff/h≈ 218 .

One can return back to the first step in the genesis of DNA and RNA. The addition of protons to the solution used to model prebiotic environment to make it slightly acidic was the key step. Why?
  1. Here cold fusion might help. Cold fusion is claimed to take place in electrolysis involving ionization and charge separation. The electric fields used in electrolysis induce ionization and thus charge separation. For me it has however remained a mystery how electric fields, which are extremely tiny using the typical strength of molecular electric field as standard are able to induce a charge separation. Of course, every chemist worth of his salt regards this as totally trivial problem. I am however foolish enough to consider the possibility that some new physics might be involved.
  2. The mechanism causing charge separation could be analogous to or that discovered by Pollack as he irradiated water bounded by a gel phase (see this): in the recent case the electric field would take the role of irradiation as a feeder of energy. Negatively charged exclusion zones (EZs) were formed and 1/4 of protons went somewhere.

    The TGD proposal (see this) is that part of protons went to magnetic flux tubes and formed dark proton sequences identifiable as dark nuclear strings. The scaled down nuclear binding energy favours the formation of dark nuclear strings perhaps proceeding as analog of nuclear chain reaction. This picture allows to ask whether dark proton sequences giving rise to a fundamental representation of the genetic code could have been present already in water (see this).

  3. How DNA/RNA could have then formed? Could the protons making the solution acidic be dark so that the proton attaching to the amine would be dark? Could it be that for all amines except the right one the proton transforms to ordinary proton and destroys the chemical reactivity. Could the attached dark proton remain dark just for the correct amine so that the amine would remain reactive and give rise to purine in further reactions? Could A,G,C,T and U be those purines and pyrimidines - or even more general biomolecules - for which the attachment to dark proton does not transform it to ordinary proton and in this manner affect dramatically the chemical properties of the molecule? What is the condition for the preservation of the darkness of the proton?

See the chapter Prebiotic evolution in many-sheeted space-time or the article One step further in the understanding the origins of life.

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