Tuesday, May 17, 2016

One step further in 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 Quantum criticality and dark matter of "Hyper-finite factors, p-adic length scale hypothesis, and dark matter hierarchy" or the article One step further in the understanding the origins of life.

For a summary of earlier postings see Latest progress in TGD.

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