On January 22 at 11:45pm, discussion led me to ask whether biophotonic energy differences could be recognized by the photons at the quantum level of their interactions/energies. I thought the answer might explain biodiversity via a link from quantum level self – other recognition to immune system recognition and to macromolecular self – other recognition.
My focus has been on well-established macromolecular links from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms. For example, conserved molecular mechanisms link the sun’s biological energy via physical and chemical constraints to the ‘conditions of life’ that Darwin placed before consideration of natural selection.
The ‘conditions of life’ on earth require earthly biogenic origins that link immune system recognition at the quantum level of self – other recognition. For example, George F.R. Ellis posted a link to this article, which suggests that quantum physics may not extend to macromolecular interactions. Do Quantum Superpositions Have a Size Limit? That’s the type of question that I think leads physicists to unnecessary speculation about biologically-based cause and effect.
Their speculation supports the Big Bang cosmology industry but it has nothing do with what currently known about life. For example, serious scientists know that Life is physics and chemistry and communication. What serious scientists know can be traced back to what Charles Darwin learned by observations. What Darwin learned can be compared to what physicists have since learned about the chemistry of protein folding and biology of behavior. What some physicists have learned about biology may be simply stated in a picture that is worth 10,000 words.
This differences in these representations of birds appear to link quantum superpositions to macromolecular interactions. The difference also are linked to similarities in the interactions that link RNA-mediated cell type differentiation from quantum physics to cell type differentiation and all biodiversity.
Darwin’s ‘conditions of life’ require cell type differentiation. For example, cell types are different in different tissues of the bird and in different cell types of all other living organisms. Clearly, Darwin’s ‘condition of life’ were ignored when population geneticists bastardized his theory. Theorists used de Vries definition of mutation to make incomprehensible representations of biologically-based cause and effect that sometimes begin with abiogenesis in deep space.
For example, in this brief video, Brian Cox explains that cosmic rays and mutations and selection made him who he is, and what we are. Keep in mind that this is the type of experiment that many physicists may believe links deleterious mutations and beneficial mutations to the biodiversity of life on earth, which is manifested in morphological and behavioral phenotypes in species from microbes to man. Cox admits: “We don’t know but we can dream.” Serious scientists build their explanations of cause and effect on experimental evidence, not their dreams.
This experiment links cosmic rays and mutations to biodiversity but fails to link what is known about links from light perception to nutrient-dependent amino acid substitutions and self – other recognition differentiation of photo receptors and odor receptors that convert light energy and nutrient energy to chemical energy. Linking what is currently known about physics to what is known about biolgically-based cause and effect requires a link to the chemistry of RNA-mediated protein folding.
On January 24, 2015, I learned that one of the discussants in the secret group already had plagiarized my discussion comments as well as my Pheromones Reseach FB page comments and everything I have detailed during 20 years of published works on RNA-mediated cell type differentiation in blog posts here, like this one from January 10. Mutagenesis: Replacing facts with theories
Apparently, Matti Pitkänen decided to take my details and add his pseudoscientific nonsense to them. It would have been ethical for him to tell others where his information came from, but ethics are not required to move theoretical physics forward. The problem is that, until now, theoretical physicists have not attempted to link light-induced changes in amino acid substitutions to the creation of life on earth via direct links from the sun’s biological energy to RNA-mediated events.
To me, linking the sun’s biological energy to life makes more sense that anything I’ve heard from biophysicists. Theoretical physicists seem to not recognize the need to link metabolic networks to genetic networks in species from microbes to man.
Indeed, Pitkänen claims to have spent the last 37 years on a noble, but failed, attempt to use Topological Geometrodynamics (TGD) to construct a theory of everything, not forgetting consciousness. Could anyone blame him for his desperate attempt to use my model of RNA-mediated amino acid substitutions in plants and animals — without attribution?
I think he will do whatever it takes in attempts to salvage what he can from physics and stake his claim to knowing something about chemistry and biology — after learning about cell type differentiation from me. I also think others can recognize the material he plagiarized from my post here on January 10, 2015 Mutagenesis: Replacing facts with theories
He included it in a blog post linked to a pdf on January 11, 2015. A link to the pdf of the article opens here: Was ribosome the first self-replicator?
Unfortunately, what I thought would be open discussion among professionals has led to representations of my ideas by others. Some people without original ideas secretly steal ideas from others and claim the ideas as their own. Credit for the ideas does not matter. After his representations of my details about RNA-mediated events, all that matters whether or not he contributes to scientific progress.
In this case, however, Matti Pitkänen does not add any intelligible thoughts to discussion of light-induced amino acid substitutions and cell type differentiation. I’ve included his attempt to extend my model via its incorporation in TGD, to show that physicists understand virtually nothing about chemistry and biology. After an incoherent review of what I detailed on RNA-mediated cell type differentiation in, Was ribosome the first self-replicator? he adds more theory — with my emphasis below:
How the pre-ribosome as first replicator relates to TGD approach?
TGD framework predicts that replication as a splitting of 3-surfaces to two copies is a fundamental mechanism of quantum TGD analogous to the 1→ 2 decay of elementary particle and the replication of DNA, cells, etc… should reduce to a hierarchy of replications starting from long length scales and proceeding as replications at shorter length scales with master slave relationship between the subsequent levels of the scale hierarchy. This identification of replication as a mere splitting of 3-surfaces saying nothing about what happens for the quantum states associated with them is too general to allow to talk about unique primary replicator. If one however restricts the consideration to systems consisting of RNA and amino-acid sequences the idea about ribosome as primary replicator becomes highly non-trivial. In TGD framework it is possible that pre-biopolymers were not bio-polymers but their dark counterparts formed from dark protons sequences at magnetic flux tubes with states of dark proton in 1-1 corresponds with DNA ,RNA, amino-acids and tRNA. If so pre-ribosome was realized at the level of dark matter as dark ribosome – a complex formed by dark analogs of bio-polymers. If so, then pre-ribosome consisting of dark matter at flux quanta could be the primary replicator and the formation of its bio-molecular counterpart would be induced from that of dark pre-ribosome like the dynamics of slave in master slave hierarchy. This raises questions. How does this replication proceed? Does ribosome still replicate as all other biological structures do and induce replication of low ever level structures in the dark matter hierarchy? Does the ordinary biomatter induced at the lowest level of hierarchy would only make visible this replication? In the following I briefly summarize the basic TGD based notions involved in attempt to answer these questions.
[Note: a series of caveats that attest to what is not known are now linked to more theory that attempts to what’s known about the sun’s biological energy and nutrient-dependent self organization to quantum jump sequence that somehow leads to the emergence of self organization. The jumps were defined by Hugo de Vries as “mutations”. Matti Pitkänen tries to link the quantum jumps (i.e., the mutations) to 4-D behavioral patterns via quantum self-organization, instead of nutrient-dependent self-organization.]
4-D self-organization and magnetic body One class of questions concerns the roles of self-organization and genetices. Even the definition of the notion of self-organization is poorly defined. In TGD zero energy ontology (ZEO) forms the basic framework of both quantum TGD proper and its applications to consciousness and biology. In zero energy ontology (ZEO) self-organization is replaced with self-organization by quantum jump sequence leading to the emergence of not only 3-D spatial patters but also of 4-D behavioral patterns: one can say that living system is 4-dimensional and also its geometric past changes in quantum jumps (Libet’s findings).
Various motor actions of magnetic body appear as basic processes of the quantum self-organization. This includes braiding and knotting, heff changing phase transitions changing the lengths fo flux tubes, reconnections allowing to build connections between different system consisting of flux tube pairs, and also replication. Also signalling by dark photons is an essential part of the picture and the general hypothesis is that dark photons have same universal energy spectrum as bio-photons and thus in the energy range of molecular transition energies.
Replication in TGD framework occurs at the fundamental level as a replications of 3-surface and is completely analogous to 1→ 2 decay for point elementary particle. This replication could take place for the magnetic flux quanta representing various biopolymers and higher level structures and induced the replication at the level of visible matter. As noticed, this replication is not enough in biology and must be accompanied by the replication of the quantum states associated with 3-surfaces.
One key question is how the bio-molecular processes arranged into a functional network. Here the hypothesis that magnetic flux tubes form a 3-D grid analogous to coordinate grid with points of grid at intersections of 3 flux tubes and flux tubes as coordinate lines is very attractive. This Indra’s web would be behind the gel like structure of cellular water and make it single coherent unit. Behavioral modes would be time evolutions of this grid: motor actions of the magnetic body – or hierarchy of them.
[Next:Matti Pitkänen takes the discussion contributions on the biogenesis of achiral amino acid glycine by Joseph Klover and represents them as his own. Again, see my emphasis on the claim below: “I have proposed the identification of dark counterparts of RNAs and amino-acids as complex braided and knotted structures with braiding carrying information…” ]
Does dark matter induced the dynamics of visible biomatter?
The idea that dark matter induces the dynamics of biomatter is extremely attractive since the enormous complexity of biochemistry would be only adaptation to the dynamics of the much simple almost topological dynamics of the master represented as flux tubes carrying dark matter.
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 heff=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 H1.5O, 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 heff. I have also considered the possibility that the generation of large heff 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 heff phases of ordinary matter taking place at quantum critical and perhaps even critical systems.
- 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!
- 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.
- 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.
- 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 heff 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 heff 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.