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One step further in the understanding the origins of life

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Abstract

The group led by Thomas Carell has made an important step in the understanding the origins of life. They have identified a mechanism leading to the generation of purines A and G which besides pyrimidines A,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. In TGD based model of quantum biology this suggest that the protons in the acidic water are dark and that the attachment of the dark protons to the amines of the amino-pyrimidine transforms them to ordinary protons and makes the amino-pyrimidine non-reactive. There would be however one exception: the amine which reacts further to give purines as a reaction product. In this case the proton would remain dark and the chemical properties of the amine would remain intact. The TGD based model for cold fusion and the recent results about superdense phase of hydrogen identifiable in TGD framework as dark proton sequences giving rise to dark nuclear strings provides support for this picture.
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One step further in the understanding the origins of life
M. Pitk¨anen
Email: matpitka6@gmail.com.
http://tgdtheory.com/.
June 20, 2019
Abstract
The group led by Thomas Carell has made an important step in the understanding the
origins of life. They have identified a mechanism leading to the generation of purines A and
G which besides pyrimidines A,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. In TGD based
model of quantum biology this suggest that the protons in the acidic water are dark and that
the attachment of the dark protons to the amines of the amino-pyrimidine transforms them
to ordinary protons and makes the amino-pyrimidine non-reactive. There would be however
one exception: the amine which reacts further to give purines as a reaction product. In this
case the proton would remain dark and the chemical properties of the amine would remain
intact. The TGD based model for cold fusion and the recent results about superdense phase of
hydrogen identifiable in TGD framework as dark proton sequences giving rise to dark nuclear
strings provides support for this picture.
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 (see https://en.wikipedia.
org/wiki/Pyrimidine) have single carbon 6-cycle. Purines A and G (see https://en.
wikipedia.org/wiki/Purine) in turn have single 6-single and 5-cycle fused attached to-
gether 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 plau-
sible mechanism [I2] (see http://tinyurl.com/z65kpyo).
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 https://en.wikipedia.org/wiki/Formamide
and for the class of chemical compounds known as amines see https://en.wikipedia.org/
wiki/Amine).
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 acid (see
https://en.wikipedia.org/wiki/Formic_acid) or formamide. Hence it seems that one
big problem has been solved.
1
2
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 [K1, K2]
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 sequen-
cies - dark nuclear strings - serving as a dynamical template for the biological replication.
Also transcription and translation would be induced by dark process. Actually all bio-
chemical 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 [C1] (see http://tinyurl.com/hxbvfc7) 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 [L2]. 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 http://tgdtheory.fi/public_
html/articles/geesink.pdf) 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 [L1] [L1]: 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 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 en-
ergy 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 [L3]!
PARTICLE AND NUCLEAR PHYSICS 3
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?
REFERENCES
Particle and Nuclear Physics
[C1] Holmlid L and Kotzias B. Phase transition temperatures of 405-725 K in superfluid ultra-
dense hydrogen clusters on metal surfaces. AIP Advances. Available at: http://tinyurl.
com/hxbvfc7, 6(4), 2016.
Biology
[I1] The Fourth Phase of Water : Dr. Gerald Pollack at TEDxGuelphU. Available at: https:
//www.youtube.com/watch?v=i-T7tCMUDXU, 2014.
[I2] Carell T et al. A high-yielding, strictly regioselective prebiotic purine nucleoside formation
pathway. Science. Available at:http://science.sciencemag.org/content/352/6287/833,
352(6287):833–836, 2016.
Books related to TGD
[K1] Pitk¨anen M. Homeopathy in Many-Sheeted Space-Time. In Bio-Systems as Conscious
Holograms. Online book. Available at: http://www.tgdtheory.fi/tgdhtml/holography.
html#homeoc, 2006.
[K2] Pitk¨anen M. Nuclear String Hypothesis. In Hyper-finite Factors and Dark Matter Hier-
archy. Online book. Available at: http://www.tgdtheory.fi/tgdhtml/neuplanck.html#
nuclstring, 2006.
Articles about TGD
[L1] Pitk¨anen M. Pollack’s Findings about Fourth phase of Water : TGD View. Available at:
http://tgdtheory.fi/public_html/articles/PollackYoutube.pdf, 2014.
[L2] Pitk¨anen M. Cold Fusion Again . Available at: http://tgdtheory.fi/public_html/
articles/cfagain.pdf, 2015.
[L3] Pitk¨anen M. More Precise TGD Based View about Quantum Biology and Prebiotic Evolution.
Available at: http://tgdtheory.fi/public_html/articles/geesink.pdf, 2015.
ResearchGate has not been able to resolve any citations for this publication.
Phase transition temperatures of 405-725 K in superfluid ultra-dense hydrogen clusters on metal surfaces
Article
Full-text available
  • Apr 2016
Ultra-dense hydrogen H(0) with its typical H-H bond distance of 2.3 pm is superfluid at room temperature as expected for quantum fluids. It also shows a Meissner effect at room temperature, which indicates that a transition point to a non-superfluid state should exist above room temperature. This transition point is given by a disappearance of the superfluid long-chain clusters H2N(0). This transition point is now measured for several metal carrier surfaces at 405 - 725 K, using both ultra-dense protium p(0) and deuterium D(0). Clusters of ordinary Rydberg matter H(l) as well as small symmetric clusters H4(0) and H3(0) (which do not give a superfluid or superconductive phase) all still exist on the surface at high temperature. This shows directly that desorption or diffusion processes do not remove the long superfluid H2N(0) clusters. The two ultra-dense forms p(0) and D(0) have different transition temperatures under otherwise identical conditions. The transition point for p(0) is higher in temperature, which is unexpected.
View
More Precise TGD Based View about Quantum Biology and Prebiotic Evolution
Research
Full-text available
  • Aug 2015
In this work I try to clarify the relation of the basic notions of TGD and of TGD inspired biology to the ordinary bio-chemistry. I also try to improve my understanding about work of Fr\"ohlich, Del Giudice, and Pollack using the notions of TGD. The key idea is the notion of coherence induced by weak em fields with preferred frequencies, which in ordinary quantum theory correspond to energies much below the thermal energy in quantum theory - this creates what is called kT paradox. In TGD framework one can do without coherence regions (one could perhaps identify them as special cases of Pollacks EZs), which can be much larger. The basic observation is that for a pair of hydrogen bonded water molecules the reaction 2H$_2$O$\rightarrow$ H$_3$O$_2^{-}$ + dark proton require UV photon with energy of O-H bond of about 5.15 eV. Water clathrates are good candidates for the precursors of EZs since they have size scale in the same range as EZs and contain hydrogen bonded water. Quantum criticality suggests that this process should occur spontaneously as a chain reaction. This is achieved in the same manner as in nuclear fusion if the dark protons at the flux tube fused to nuclear strings giving rise to dark nuclei. If dark nuclear binding energy transforms as Coulomb energy, the nuclear energy scale of MeV scales down to 1-10 eV - depending on the value of $h_{eff}$. An attractive guess is that the energy range of bio-photons corresponds to that for dark nuclear binding and excitation energies. Their spontaneous transformation back to ordinary nuclei would liberate energy could at least partially explain the evidence for bio-transmutations. Also the relation to cold fusion is interesting. Dark nuclear binding energy is liberated as dark photons decaying into bunches of ordinary photons inducing further reactions {\it hydrogen bonded 2H$_2$O$\rightarrow$ H$_3$O$_2^{-}$ + dark proton} also other kind of dark ionizations. If the size of EZs varies from about 1 micron to 100 microns and if the the size scale of EZ corresponds to the wavelength of dark gamma photon $h_{eff}/h$ varies in the range $10^6-10^8$. This would be the total number of dark photons resulting in the decay to ordinary photons. Water clathrates have same size scale range as EZs and consist of hydrogen bonded water molecules and could serve as precursors of EZs: EZ would have different lattice structure than clathrates. In this process ordinary protons transform dark protons at magnetic flux tubes outside EZ. Dark ionization differs from ordinary ionization only in that the proton is dark. The difference between dark and ordinary ionization would define the borderline between ordinary and bio-chemistry (or dark chemistry). Chemical quantum criticality is possible also for other cations and also anions and all biologically important ions can appear as dark ions. The Urey-Miller experiment was very successful: it produced a large variety of amino-acids crucial for life from simple basic constituents. The variant of this experiment has even produced adenosine, DNA nucleotide fundamental for ATP. There is however a severe problem. The prebiotic atmosphere was not reducing as in the Urey-Miller experiment simulating it. Clays are good candidates for the key structures in prebiotic evolution since they can replicate. One can even speculate with an analog of genetic code. Phyllosilicates containing -O-H groups are especially interesting: they can adsorb basic biomolecules and induce their polymerization to oligomers. They also induce a formation of vesicles formed from lipid bilayer and serving as a candidate for a predecessor of cell. DNA is the problem and has led to a scenario known as RNA world. Phyllosilicates are also known to generate radiation with positive health effects. The natural and testable hypothesis is that the presence of EZs allows to circumvent the difficulties of the standard RNA world scenario and also generate DNA and biologically active phosphates containing the mysterious phosphate bond as ionized dark proton. The dark magnetic flux tubes and UV photon energy needed to generate EZs could be provided by gel in Pollacks's experiments and by electric discharges in Urey-Miller experiment. Also dark photons from the formation of dark nuclei decaying to bunches of bio-photons can be considered. Water chlathrates can contain atoms and even micrometer sized phyllosilicate crystals, which could catalyze the formation of biomolecules at their surfaces as dark nuclear fusion chain reaction. Chlathrate could also develop phospholipid bilayer around it - kind of primitive cell membrane. TGD inspired proposal for prebiotic evolution was inspired by the TGD based realization of Expanding Earth hypothesis and assumes that life evolved in underground oceans and burst on the surface of Earth in Cambrian explosion. This view leads to a more precise view about prebiotic evolution. Possible technological implications of this picture - if true - are quite impressive. Cold biofusion could make possible artificial generation of technologically important elements and the mechanism generating EZs could make possible creation of artificial intelligent life forms involving silicates and water.
View
View
A high-yielding, strictly regioselective prebiotic purine nucleoside formation pathway
Article
  • May 2016
Making RNA in the prebiotic world The RNA World hypothesis posits that RNA was one of the first self-replicating molecules leading to the origin of life. The nucleotide bases of RNA—A, U, C, and G—are chemically complex, and it has been unclear how the large purine bases A and G might have arisen on prebiotic Earth. Becker et al. show that the A and G bases can be synthesized easily and in high yield from prebiotically reasonable precursors, lending further support to the RNA World hypothesis. Science , this issue p. 833
View
Nuclear String Hypothesis. In Hyper-finite Factors and Dark Matter Hierarchy. Online book
  • Jan 2006
  • M Pitkänen
Pitkänen M. Nuclear String Hypothesis. In Hyper-finite Factors and Dark Matter Hierarchy. Online book. Available at: http://www.tgdtheory.fi/tgdhtml/neuplanck.html# nuclstring, 2006. Articles about TGD
Pollack's Findings about Fourth phase of Water : TGD View
  • Jan 2014
  • M Pitkänen
Pitkänen M. Pollack's Findings about Fourth phase of Water : TGD View. Available at: http://tgdtheory.fi/public_html/articles/PollackYoutube.pdf, 2014.