I added several detailed examples about the application of TGD inspired theory of quantum biology so solve basic problems of quantum biology. The details of the solutions discussed below have emerged during the last year. I have not discussed all problems. For instance, I have not excluded the vision about pre-biotic evolution in TGD Universe for which the recent findings from Mars challenging the Maxwellian view about magnetic fields and characterized as "magnetic madness" provide support (see this).
I have picked up the following examples discussed in the chapter representing the new results related to biocatalysis with application to DNA replication, to the selection of bio-molecules, and genetic code. Second topic is metabolism: I have included also a universal purely thermodynamical model of remote metabolism relying on zero energy ontology. Also a discussion of replication is included.
1. Questions related to bio-chemistry
Bio-catalysis remains a total mystery in bio-chemical approach. Magnetic body carrying dark matter could provide the needed mechanisms. Actually these mechanism would be also basic mechanisms behind water memory and - dare I say it aloud? - homeopathy (see this).
According to TGD view about catalysis, reactants find each other by cyclotron resonance for dark cyclotron radiation assignable to massless extremals (MEs) possibly associated with U-shaped flux tubes. The U-shaped flux tubes of the molecules reconnect to a pair of flux tubes connecting the molecules. This occurs only if the flux tubes have same strength of magnetic field and therefore same thickness by flux quantization. The same value of heff guarantees resonance. The next step is the shortening of the flux tubes by a reduction of heff and liberating the energy kicking the reactants over the potential wall making the process extremely slow otherwise.
DNA replication, transcription to RNA, and translation of RNA to amino-acids are the fundamental processes in biology and TGD should provide a general model for them. Consider DNA replication as an example.
- The standard model assumes that DNA opens and nucleotides build up the DNA codons in ordered manner. Nucleotides would be caught one-by-one from the environment by U-shaped flux tubes from DNA reconnecting with similar flux tubes from nucleotides. In the proposed model however dark codons are the fundamental units and expected to induce the process at the level of chemistry. Dark codons do not allow a decomposition to letters. Therefore ordinary codons rather than nucleotides should serve as basic units in energy resonance binding them to dark codons (triple resonance or ordinary resonance with respect to the sum of resonance energies). This looks like a problem for both replication and transcription. Translation in which RNA codons are paired with amino-acids suggests a solution of the problem.
- Suppose that dark codons are the basic units also in the environment, and are connected by long flux tubes with rather large heff to ordinary nucleotides forming thus loose but actually strongly correlated triplets. Nucleotides would serve as basic units only apparently: the entities in question would be analogous to tRNA codons. In the replication and transcription the dark codons of opening DNA sequences would form flux tube contacts with dark codons in the environment coupled to ordinary loose codons by dark triple resonance.
After that the Planck constant heff associated with the connecting flux tubes would be reduced, the flux tubes would shorten and the complementary dark codon would be drawn near the the dark codon associated with DNA. Also the flux tubes connecting the dark codon to the nucleotides would shorten and the codon and complementary codon would form 3 base pairs. Shortening by a reduction of heff would provide the energy making the process fast enough. The loose codon property would allow to store the energy needed to make the reaction fast.
- This model can explain also the claim of Montagnier et al about remote DNA replication (see this and this). Gariaev et al have reported the same process much earlier and together with Peter Gariaev we have developed a model for the process (see this).
The situation is as follows. One has two vessels A and B: A contains genes and B only nucleotides. The vessels are connected by channels so narrow that the genes cannot leak through them. The system is irradiated at 7 Hz frequency, which is near the lowest Schumann frequency. The generation of the copies of genes in B is reported.
The proposed model suggest that the flux tubes emanating from the dark DNA codons associated with the opening DNA extend to the other side - possibly through the channels so that there is a strong correlation between the directions of flux tubes and their endpoints are close to each other. If they have same value of heff they would have same length. They would reconnect with dark codons at the other side connected to nucleotide triplets by long flux tubes and the process would continue in the same manner as in the ordinary replication.
1.2 What selected the biomolecules?
Now philosopher is asking why only very few candidates for relevant biomolecules are actually selected. Who/what selected and how? This leads to very unpleasant questions circumvented by deciding that the emergence of life was nothing but a thermodynamical fluctuation. It has however become clear that complex organic molecules are present even in interstellar and intergalactic space. The miraculous thermodynamical fluctuation explaining evolution without real evolution would have been really huge.
Philosopher tends to conclude that we simply have no clue about what selection at the bio-molecular level really is and continue that some new physics is involved so that it is time to think giving up the reductionistic narrative.
The selection problem appears also at the level of biochemical reaction pathways. One can imagine endless variety of "reaction vertices". If one assumes that only very few basic "reaction vertices" are allowed but the rest not, one can construct a limited number of reaction pathways. But this is an ad hoc assumption: this selection of allowed reaction pathways certainly occurs but we do not have a slightest idea about the physics behind it.
There is also an analogy with computer science. One can construct endless variety of linguistically correct computer programs: why only very few of them would be selected. And with neuroscience: from a huge array of behavioral patters only some are selected.
Here one can of course try a loophole: Darwinian selection. But there is no selection in the Universe of physicalist. This would require free will and intentionality. The trick does not work.
But what about this network in which biomolecules are connected by this something already mentioned?, asks philosopher. Could this something connect only biomolecules if they are in the same relationship as sender and receiver of radio signal. Could these somethings connect stably only systems possessing common resonance frequencies? Could this criterion could select both the preferred biomolecules and the "reaction vertices" and thus also reaction pathways.
One can develop this idea further.
- The resonance between systems with the same value of heff would be both frequency - and energy resonance. The resonance between systems with different values of heff requires change of heff of either system so that heff is same for the systems. Energy is conserved, which means that the frequency of the photon would change to satisfy E= heff,1f1=heff,2f2 . One would have only energy resonance.
The resonance of dark matter states with bio-molecules would be energy resonance and make it possible for long scales to control short scales by inducing molecular transitions. The transformed photons could have interpretation as bio-photons (see this and this).
- One can however argue that mere resonance is not enough to select bio-molecules. Magnetic flux tubes containing dark particles can vary their thickness and by the conservation of the monopole flux also magnetic field and cyclotron frequency so that they can get in resonance with any bio-molecule. A stronger condition is required.
The obvious idea is that also biomolecules can be in resonance and surviving bio-molecules are able to build networks. Selection would not be selection of mere individuals but that of networks able to co-operate. There would be a choir singing resonantly in unisono rather than only resonating pairs. The biomolecules involved would have common transition energies which would poses extremely strong conditions on survivors.
1.3 Genetic code
Genetic code definitely represents information. Is it really an outcome of thermodynamical fluctuation? Is there some deep mathematics associated with the genetic code?, asks the philosopher now. Be patient!
Genome contains also intronic portion: most of it consists of introns and the intronic portion is the larger the higher the evolutionary level is. The prevailing interpretation has been as "junk". Is it really junk?, wonders philosopher. Luckily, the attitude that trash bin represents the highest level of evolution has begun to slowly change to more rational one.
Could there be a beautiful mathematics behind genetic code? Could it be something similar to codes in computer science and have not only one representation - the chemical one - but numerous representations? If computer science would have developed before genetics - this question would have been completely natural and we would probably know a lot about these representations. Could this dark matter with large Planck constant at these mysterious somethings identified by our philosopher tentatively as magnetic flux tubes realize the really fundamental representation of the genetic code and also of of DNA, RNA, tRNA, and amino-acids (AAs) in information theoretic sense? And could also radiation provide realization of genetic code necessary for communications? This is what the philosopher claims (see this, this, this, and this).
The most plausible vision at this moment is that since magnetic body is the boss, chemical code should be incomplete secondary representation of more fundamental genetic code realized at the level of magnetic body controlling bio-matter. The realizations based on 3-proton triplets and dark light 3-chords defining icosa-tetrahedral representation of the genetic code in terms of Hamiltonian cycles (see this) would be the deeper realizations. There would be several Hamiltonian cycles distinguishing assignable to the same chemical representation of the genetic code. The analogy with music suggests that the realization in terms of 3-chords defining bio-harmony gives rise to quantum correlates of emotions assignable to magnetic body as kind of higher level sensory perceptions. Genetic codon as 6-bit unit would correspond to the "bitty" aspects of intelligence and harmony would correspond to emotional intelligence as the holistic aspect of intelligence (see this). Emotions would be realized already at the level of magnetic body (see this, this, and this) .
The recent findings that the RNA of a conditioned sea snail scattered over neurons of second sea snail in Petri dish generate neuronal correlates of conditioning supports the view that the magnetic body of the RNA of sea snail infects the emotion/mood related to the conditioning. The emotional state, mood, of DNA and RNA would affect gene expression. Epigenesis is a poorly understood in standard biology and could be based on emotional states lasting for several generations. This is natural in ZEO (see this and this).
How different representations of the genetic code relate to each other?
- The natural hypothesis is that given dark codon generates corresponding light 3-chord in communications and control. Alike likes alike rule of homeopathy suggests that triple resonance between identical codons is the basic mechanism of communications between various representations. Similar codons of DNA sequences would be in resonance if the mood defined by bio-harmony is same for them. For the same value of heff one would have both energy and frequency resonance for different values only energy resonance.
- The condition that all possible - or at least some - moods coded by Hamiltonian cycles are realized, poses additional conditions on ordinary DNA codons since given codon should be able to respond to several 3-chords resonantly. An open question is whether ordinary codons responds via triple resonance or to the energy associated with the sum of the three frequencies in which case one can consider the possibility that the sum of frequencies does not depend of bio-harmony.
- Since dark protons are entangled and do not allow a decomposition to letters, it is not possible to realize the correspondence with ordinary codons by assigning a frequency separately to each nucleotide: the chemical codon reacts as a holistic entity (see this). This gives highly non-trivial conditions on transcription and DNA replication: DNA and RNA nucleotides must form loose codons connected to dark codon by long flux tubes and in transcription/replication these flux tubes shorten. This allows to understand (see this) also the remote replication of DNA reported by Montagnier et al. The loose codons formed by nucleotides and dark codons would be very similar to tRNA codons except that the flux tubes connecting dark codon to nucleotide would be long.
Metabolism is one of the key aspects of biology. We must eat and plants must busily photosynthesize in order to survive. But why metabolic energy feed is needed? Again a mystery.
2.1 Non-equilibrium thermodynamics
Non-equilibrium thermodynamics is one attempt to answer this question. Thermodynamical equilibrium is completely uninteresting, entropy is maximal and in the case of local dynamics the state of system is completely determined by a small sample of it. However, if one has energy feed, situation changes since equilibrium becomes flow equilibrium. The energy feed guarantees that there is macroscopic dynamics rather than mere thermal motion at microscopic level.
Also in this case one has essentially the same situation everywhere unless one introduces macroscopic parameters - also energy flow - depending on time and position to get something more interesting. Simple reaction kinematics determined by differential equations can be replaced with that determined by partial differential equations obtained by allowing diffusion. Also temperature, pressure and other thermodynamical parameters can be allowed to depend on position and time. Turing proposed a model for the coloring of Zebra as outcome of this kind of dynamics. The model for neuronal membrane and nerve pulse generation is also a rough model trying to reproduce basic facts about nerve pulse generation using thermodynamics for neuronal membrane regarded as a capacitor. This is of course a mere parameterization of the situation. TGD leads to a quantum model for the situation (see this). Also the interpretation about the role of nerve pulse patterns at neuronal level changes dramatically (see this and this).
In non-equilibrium thermodynamics one speaks of self-organization. One can generalize this notion to quantum self-organization and the crucial criticality associated to the transitions between different self-organization patterns generalizes to quantum criticality (see this). Could these transitions correspond to spatio-temporal self organization patterns, behaviors, functions, programs. This in turn leads to deep connections with conformal symmetry (even its generalization in TGD), fractality, and universality of the dynamics. It is a pity that biologists do not seem to know much about these possibilities.
Now the philosopher starts to talk about ontology. Try to be patient. In standard physics the 3-D time= constant snapshot defines the state. This belief has led to weird proposals: in quantized general relativity one ends up with a proposal that there is no time at all.
2.2 ZEO based view about quantum self-organization
Could it be that 4-D deterministic time evolution between initial and final states could be more fundamental than the 3-D snapshot? Could superpositions of these 4-D evolutions define quantum states. If so, the state function reductions would occur between these superpositions and their non-determinism would be consistent with the determinism of field equations. Free will would not break laws of physics. It would be like starting new deterministic computer program. Our philosopher calls this ontology Zero Energy Ontology (ZEO) and claims that it leads to a theory of consciousness as a generalization of quantum measurement theory (see this). Irritating.
ZEO based quantum measurement theory predicts that in ordinary state function predicts that the arrow of time changes in ordinary state function reductions but is preserved in "small" state function reductions identifiable as analogs of so called weak measurements. The recent strange findings of Minev et al provide direct evidence for the change of the arrow of time in state function reductions of atomic systems (see this).
ZEO predicts also the possibility of signals propagating backwards in time. This led to the vision that episodal memories involve communications with the brain of geometric past (see this), to the idea that motor actions and sensory perception are time reversals of each other (see this): motor action would involve sending of negative energy control signals to the geometric past, and to the notion of remote metabolism based on quantum credit card mechanism. One can say that the system sends negative energy to a system able to receive it rather than receiving positive energy.
The energy of system as a function of heff increases when other parameters are kept constant. It costs energy build intelligence. heff for a given sub-system tends also to reduce spontaneously. Hence there must be continual energy feed to keep the level of conscious intelligence. A highly interesting possibility that this condition applies to all self-organizing systems. Self-organization generates long range coherence and requires energy feed. Could it be that dark matter makes itself visible by giving rise to long range correlations and coherence induced by dark matter at the magnetic body of the system (see this)?
Just as life also self-organization involves generation of coherence in long scales and requires energy feed. In the model for living system relying on dark matter as heff=n× h0 phases at magnetic body of the system coherence is induced by quantum coherence of the dark matter, and metabolic energy feed is required to increase heff tending to reduce spontaneously. Could self-organization be quite generally modelled in the same manner so that dark matter would make itself visible in everyday physics? Could the realizations of the genetic code in terms of dark nuclei and dark photon 3-chords be involved with the self-organization of water and be involved with morphogenesis?
2.3 Does metabolic energy feed generate conscious information?
The basic question about the role of metabolic energy remains, says the philosopher. What is its real role? Energy feed generates structures and structural complexity means information. It seems that metabolic energy feed involves also a feed of information or generation of information. And because living systems are in question, philosopher cannot avoid the question whether this information is actually conscious information. Is there any other kind of information than conscious information?!
To this question standard physics has no answer: it can only describe entropy mathematically and identification of information as lack of entropy is the easy answer suggested in lack of anything better. The question about a possible measure for conscious information analogous to Shannon entropy is one manner to end up with p-adic physics as a correlate of cognition and the necessary fusion of real and various p-adic physics leads to adelic physics (see this). Adelic physics in turn predicts - surprise- surprise - a hierarchy of phases of matter labelled by the value of Planck constant heff/h0=n defining the dimension of the extension of rationals defining the adele. These phases residing at these somethings defining the networks - magnetic flux tubes - make possible macroscopic quantum coherence inducing the coherence of living matter.
Quite generally, the energies of states as function of heff increase. For instance, atomic binding energy scales decreases like heff2 and cyclotron energies scale like heff. In order to generate phases with non-standard value of heff energy feed is needed. This energy is identifiable as metabolic energy.
In adelic physics heff serves as a measure for the IQ of the living system in well-defined system. The higher its value, the better changes the system has for generating conscious information - and also for destroying it. This leads to a rather concrete view about the origin of good and evil. The ethics and moral are simple: good deed increases the conscious information of the universe. Conscious entity can choose whether to increase the conscious information of the universe or reduce it. Evil deeds indeed lead to a reduction of conscious information of the universe since the doer cannot confess others or even himself what he did. Also the members of community become secretive - complex encryption schemes develop. The self-knowledge of the universe knows is reduced. Luckily, evolution unavoidably occurs in statistical sense and resources of conscious information increase in long enough time scale.
2.4 Remote metabolism as a purely thermodynamical universal mechanism in ZEO
Quite recently (towards end of 2019) I found a more precice formulation for the intuitive notion of remote metabolism, which strongly suggests that energy is conserved in ZEO. There is a decomposition to system and the energy energy source: call them A and B. Intuitively, A receives energy from B by sending negative energy to B. What does this really mean?
- A "big" (ordinary) state function reduction reversing arrow of time takes place: this would correspond to sending negative energy signal to past. The energy of A+B in the final time reversed state at new passive boundary of CD would be shared in new manner such that one can say that A has received from B the metabolic energy.
- Energy would be conserved. I have also considered the interpretation that the total energy of the system associated with CD increases (see this and this): since CD itself breaks Poincare invariance, it seems that one cannot exclude this. However, the Poincare invariance is realized at the level of moduli space for the positions of the either boundary of CD, and one can assume energy conservation. Even the wave functions at the boundary of CD can be taken to be in the representations of Lorentz group acting as its isometries. Plane waves correspond to wave functions in the moduli space for the boundary of CD keeping second boundary fixed.
- To make this more precise one must define metabolic energy more precisely by introducing the hierarchy of Planck constants and the fact that the increase of heff of sub-system keeping other parameters constant increases it energy. Second law means that A tends to loose energy due to the decrease of heff for its sub-systems. This is true also for the time-reversed state but in opposite direction of geometric time so that with respect to standard direction of time the energy increases. This would provide extremely general purely thermodynamical mechanism of remote metabolism.
For a summary of earlier postings see Latest progress in TGD.