Physicists: Desperate Acts

In TGD framework there are good reasons to believe that water contained the prebiotic life forms as dark analogs of various biomolecules consisting of dark proton sequences at magnetic flux tubes with the states of dark proton in 1-1 correspondence with various bio-polymers (DNA,RNA, amino-acids, tRNA). These string like objects would be dark nuclei but with a large value of Planck h_eff=n× h constant and with same size scale as biopolymers. The proposal is that they are present also in living matter and that is interaction between various levels based on dark photons which give bio-photons as decay products.

All the basic processes such as transcription, translation, and replication would be realized already at this level. The analogs of these processes assigning to dark analogs of biopolymers the biopolymers themselves would have evolved later. (ORP) suggests that ordinary biopolymers are accompanied by parallel flux tubes carrying dark protons sequences representing them. Ordinary manner would condense around dark matter. The strongest assumption is that dark processes induce their bio-chemical counterparts as biomolecules attach to the magnetic flux tubes for which they form images at the level of visible matter. This might explain why strong dehydration leads to denaturation of biomolecules and why denatured biomolecules are not biologically active. Dark DNA would represent the “soul” of DNA not present in denatured DNA! Same of course would apply to other biopolymers: the loss of dark matter would induce the in vivo → in vitro transformation. I have proposed the identification of dark counterparts of RNAs and amino-acids as complex braided and knotted structures with braiding carrying information making possible topological quantum computation like processes and topological realization of memory. DNA would provide a symbolic representation coding also the braiding characteristics of the dark amino-acid sequence. Dark amino-acid sequence would represent the braiding physically ad dark DNA as a sequence of symbols. Cyclotron frequencies are crucial for communication and the strength of magnetic field on flux tubes emanating transversally from dark amino-acid sequence would be determined by the state of dark proton. The correspondence between dark RNA and amino-acid would be determined by the condition that cyclotron frequencies are identical for the corresponding dark proton states (DNA and mRNA, RNA and amino-acid) so that resonant interaction is possible.

This picture conforms with the chemical properties of DNA, RNA and proteins.

RNA does not appear as double strands and in unfolded form is much less stable than DNA. This conforms with the fact that DNA serves as an information storage providing symbolic representation of RNA and amino-acids including their folding or at least braiding. RNA in turn would provide the concrete representation for braiding and folding.

DNA double strand is stable against hydrolysis but only inside cell – this could be due to the fact that the phase of water is ordered and ice-like so that it cannot induce hydrolysis by providing water molecules – perhaps the fourth phase of water discovered by Pollack and leading to the formation of dark proton sequences in TGD framework is in question.

The braiding structure of DNA is repetitive and carries no information. This conforms with the idea that DNA and its dark variant provide a purely symbolic representations in terms of genetic code for the corresponding amino-acid – and RNA polymers including also their braiding.

One can invent objections against the hypothesis that the dynamics of biopolymers is induced from that for their dark variants.

RNA is not stable against hydrolysis but it can gain stability by folding. Thus the shape of RNA molecule would not be determined by its dark variant in conflict with induction hypothesis. One can however consider the much weaker possibility that dark sector determines only topological dynamics. Only the braiding of the fold RNA molecules would determined by the braiding of dark variant.

DNA double strand is stable and braided in repetitive and very simple manner. If chemistry determines the stability of the DNA double strand then DNA double strand would induce the braiding of dark DNA strand rather than vice versa. Now one can argue that if dark DNA appears as double strand this forces the repetitive braiding.

[Next: Matti Pitkänen claims to resolve the chicken versus the egg problem in the context of their simultaneous emergence: “Hens and eggs emerged simultaneously.” I asked whether quantum level interactions were limited in scale, which they obviously cannot be when placed into the context of quantum biology.]

To how high level can one continue this parallelism. For instance, does it make sense to talk about dark variants of cell and cell membrane? Can one tell whether it was pro-cell or bio-molecules that emerged first? It seems that all these structures could have emerged simultaneously. What emerged was dark matter and its emergence involved the emergence of all the others. Hens and eggs emerged simultaneously.

Here the findings of Pollack about the generation of exclusion zones, which are negatively charged regions of water obeying exotic stoichiometry H_1.5O, are suggestive. The TGD based model assumes that a phase transition generating dark protons sequences at flux tubes of magnetic body outside the EZ takes place. The self-organization at the level of ordinary matter would generate dark matter at quantum criticality – a basic aspect of self-organization process leading to higher hierarchy levels taking the role of master. Dark matter would be the master or rather – there would be entire hierarchy of masters labelled by the values of h_eff. I have also considered the possibility that the generation of large h_eff phases happens at criticality quite universally so that life would be universal phenomenon rather than random thermodynamical fluctuation.

EZs with sizes about 200 microns (size of cell) could have been the prebiotic cells. There is also evidence that EZs consist of structures with size of order micron called coherent regions (CDs to be not confused with Causal Diamonds!). Could they have been the predecessors of the cell nuclei inside which dark DNA would be stable? The TGD model for the formation of EZs assumes that they are formed from CDs under irradiation. This picture leads also to a view about metabolism predict that UV radiation with energies about 12.6 eV must play a key role in metabolism. The proposal is that this radiation arrives as dark photons along magnetic flux tubes of the magnetic body and excites water molecules inside CDs so that they are energetically at distance of about .5 eV from the splitting of OH bond. The excitation of water molecules inside CDs by metabolic energy quantum of nominal value .5 eV transforms this phase to EZs of Pollack.

Next:Matti Pitkänen places everything currently known about the physics, chemistry and conserved molecular mechanisms that link nutrigenomics to pharmacogenomics via metabolic networks and genetic networks into the context of his theory about the simultaneous emergence of chickens and their eggs.]
Emergence of life as emergence of dark matter?
Many basic questions of biology seem to be hen-egg questions such as “genetics or metabolism?”, “cell membrane or biomolecules?”, “DNA or RNA?”, “RNA or amino-acids?”, etc.. This suggests that there exists a deeper level and emergence at this level induced the emergence at the level of biochemistry and cell biology. In TGD the emergence of living systems would reduce to the emergence of dark matter as large h_eff phases of ordinary matter taking place at quantum critical and perhaps even critical systems.

1. The question whether genetics or metabolism emerged first ceases to be relevant in this framework, where basic physics provides candidates for the fundamental mechanisms of metabolism (for instance liberation of zero point kinetic energy when the p-adic length scale of space-time sheet (magnetic flux tube) increases). Also genetic code would have been realized already before biochemistry if dark proton sequences provided the counterparts for the fundamental biomolecules. The dark biology as dark nuclear physics would make itself visible via biochemistry induced by it. We would see directly the dynamics of dark matter just by looking living systems!
2. If one takes this picture seriously, then also pre-RNA and various other pre-biopolymers could have been realized in terms dark proton sequences associated with dark magnetic flux tubes. The dark replication process could have been the arrangement of RNA and amino-acid flux tube portions in parallel and replication of the dark proton sequences with the help of the analog of tRNA attaching to the corresponding amino-acid. In this framework the notion of dark ribosome makes sense. It would however replicate only in cell replication.
3. In the biochemical scenarios also the emergence of DNA looks like mystery. In TGD framework dark DNA could have emerged at the same time as dark RNA and dark amino-acids as CDs and EZs emerged and make the stable presence of also ordinary DNA inside CDs and EZs. All basic biomolecules and prebiotic cell and metabolism would have accompanied the emergence of CDs and EZs under the irradiation of water feeding metabolic energy and giving rise to prebiotic photosynthesis (note that the negative net charge of DNAs could be due to the fact that part of protons is at dark flux tubes). Dark DNA could be interpreted as an information storage representing the braiding patterns of dark RNA and dark amino-acids symbolically.
4. In this framework the basic step of the replication is the generation of flux tube parallel to the flux tube from which one forms copy or map (say in DNA replication and and transcription). How this happens? A possible answer to the question relies on the earlier proposal that living system involves kind of coordinate grid formed from magnetic flux tubes serving as coordinate lines and meeting each other at the points of the grid. The replication process would involved translation of nearby flux parallel flux tube of the grid near to a given flux tube assignable to say DNA strand as a first step – maybe by h_eff reducing phase transition for flux tubes orthogonal the flux tube. After this the building bricks of the new biomolecule would be brought along either of the remaining locally orthogonal flux tubes – perhaps by h_eff reducing phase transition. The basic structure would be this Indras web containing visible matter at its nodes with dynamics consisting of magnetic motor actions.

This vision involves of course considerable challenges. One should model the dark ribosome counterparts of the replication process for dark DNA, transcription of dark DNA to dark mRNA, translation of dark mRNA to dark amino-acids, and also possible self-replication of dark ribosome.For background see the chapter Quantum gravity, dark matter, and prebiotic evolution of “Genes and Memes”. See also the article Was ribosome the first self-replicator?.

Here is the synopsis of Matti Pitkänen’s ridiculous claim:
Excerpt: “All basic biomolecules and prebiotic cell and metabolism would have accompanied the emergence of CDs and EZs under the irradiation of water feeding metabolic energy and giving rise to prebiotic photosynthesis (note that the negative net charge of DNAs could be due to the fact that part of protons is at dark flux tubes). Dark DNA could be interpreted as an information storage representing the braiding patterns of dark RNA and dark amino-acids symbolically.”
Matti Pitkänen’s answer to my question about water, which Joseph Klover linked to information about how it slows the speed of light. Joseph Klover seems to understand the fact that slowing the speed of light enable the transfer of information from the sun’s biological energy to the chemistry of protein folding via light-induced amino acid substitutions. In my model, the substitutions are linked to RNA-mediated cell type differentiation in plants and nutrient-dependent pheromone-controlled cell type differentiation in animals.
In Matti Pitkänen’s theory, information transfer from light to chemistry supports his claim that hens and their eggs simultaneously emerged. I think he has clarified the thoughts of most theoretical physicists and their ideas of how abiogenesis can be linked to mutations and the evolution of biodiversity, which is also clarified in this picture. Physicists seem to think that the bird and its eggs simultaneously emerged.

Ideas about cosmic rays with origins outside our solar system (Brian Cox) and ideas about beneficial mutations (Brian Cox) can now be compared to Matti Pitkänen‘s claims about the emergence of life in the context of the emergence of dark matter. Unfortunately, Matti Pitkänen took too much information from my model without learning what I had detailed and why I provided examples.
The examples established how the epigenetic landscape is linked to the physical landscape of DNA in the organized genomes of species from microbes to man via RNA-directed DNA methylation and amino acid substitutions. The substitutions differentiate the cell types of all individuals of all species. I provided details and examples so people like Brian Cox and Matti Pitkänen would continue to look like the the biologically uninformed physicists that they are. Clearly, anyone who tries to link deep space or simultaneous emergence of hens (female chickens) and their eggs to biologically-based cause and effect is wasting time and whatever money is funding their work.
The link must be from the sun’s biological energy to biologically-based cause and effect via the biophysically constrained chemistry of protein folding and differentiation of cell types that included the RNA-mediated sex differences in cell types that we explained in our 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior.
Physicists should stop making stuff up and start to learn about chemistry and biology. We wrote:
The Genome, positioning, timings. There are major structural differences between the X and Y chromosomes; e.g., centromeric aiphoid repeats sequences and distribution of heterochromatin (Graves, 1995; Wolfe et al., 1985). These structural differences correlate with sexually dimorphic chromosomal positioning within the nucleus and with male/female differences in replication timing of the active X, the inactive X, and the Y chromosomes, e.g., Boggs and Chinault (1994), Clemson and Lawrence (1996); Hansen, Canfield, and Gartler (1995). Increasingly the structure and timings within the nucleus are realized as contributing to gene expression regulation (Manders, Stap, Strackee, van Driel, and Aten, 1996; Stein, Stein, Lian, van Wijnen, and Montecino, 1996).”
The importance of that fact has since been placed into the context of cell type differentiaion and rejuvenative medicine.  See Making sense of amino acid sensing and Young blood reverses age-related impairments in cognitive function and synaptic plasticity in mice. 
The work of Christ et al (2013) extends these concepts to what is currently known about nutrigenomics and pharmacogenomics, which links metabolic networks to genetic networks via amino acid substitutions without the pseudoscientific nonsense of theories like Matti Pitkänen‘s that link the simultaneous emergence of birds and their eggs, which also links the the evolution of dinosaurs to birds.
See also: Experimental verification of Landauer’s principle linking information and thermodynamics and A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution
“In the fields of observation chance favors only the prepared mind.” — Louis Pasteur
Those who believe that abiogenesis and mutations can be linked to the evolution of biodiversty are not prepared to acknowledge that fact that “Life is physics and chemistry and communication.” Although Louis Pasteur could not explain the chicken and egg conundrum: “which came first, the chicken or the egg?” — there can be little doubt that he would never have thought that they simultaneously emerged.  Thank God, he was not a physicist like Matti Pitkänen.
 

The Nobel Prize in Physiology or Medicine 2004 was awarded jointly to Richard Axel and Linda B. Buck “for their discoveries of odorant receptors and the organization of the olfactory system”
They resolved the hen-egg conundrum by placing it into the context of what is known by serious scientists about biologically-based cause and effect.
They also showed how unimportant the ridiculous opinions of theoretical physicists are when it comes to discussions of biology. Matti Pitkänen reaffirmed how unimportant those opinions are and also he attested to how ridiculous the opinions of physicists are — at the same time.