I cannot of course say anything interesting about this horribly complex molecular biology except that I believe that something immensely important could be missing: the notion of magnetic body carrying dark matter and controlling also biochemistry. My attempts to understand rely on the conceptual framework, which is the triple (magnetic body (MB), biological body (BB), environment) replacing the pair (BB, environment) in the usual approach. MBs are the intentional agents affecting other MBs or BBs and being affected by them. So I must try to understand these concepts in terms of these notions which I dare to regard as physical.
The first thing I can do is to assign my pet notions to words like behaviour, nutrient, pheromone, hormones, etc.. and try to understand whether these horrible biochemical complexities could reflect something very simple at the deeper level.
- TGD Universe obeys Zero Energy Ontology (ZEO) predicting that basic objects can be regarded as 4-dimensional surfaces associated with pairs of 3-surfaces at opposite boundaries of causal diamonds (CDs), which by strong form holography can be reduced to correspond pairs of collections partonic 2-surfaces and their 4-D tangent space data. Time-locality however remains and behavior is assigned to time evolution of magnetic body (MB).
Quantum self organisation replaces this 4-D magnetic body with new one in each quantum jump so that our geometric future and past are not fixed but evolve to an asymptotic self-organization pattern. In ZEO quantum jumps define sequences of state function reductions on fixed boundary of CD (and are analogous to repeated measurement which however affect only the part of zero energy state associated with this CD boundary fixed whereas in ordinary ontology the entire state would remain unaffected). The acts of free will have as quantum counterparts the quantum jumps in which state function reduction agains to the opposite boundary of CD and the arrow of geometric time changes at that particular level in the hierarchy of CDs. Self corresponds to a sequences of state function reductions at fixed boundary and dies when the boundary changes. There is entire hierarchy of selves corresponding to hierarchy of CDs and sub-selves correspond to mental images of self.
- Behavior pattern having as correlate 4-D magnetic body inside given CD is a very general notion: already DNA replication, transcription, translation, biochemical pathways, associations in nervous system, our behaviors,.. are all induced by behaviour patterns represented by 4-D magnetic bodies in appropriate time and length scales.
- If MB wants to affect behaviour it must affect MB at the lower level or BB directly. Reconnection by using U-shaped magnetic flux tubes to generate double flux tube connection is the basic mechanism for this and identifiable as correlate for directed attention. Stable reconnection requires that cyclotron frequencies of dark charge particles at flux tubes and therefore also the strengths of magnetic fields and thicknesses are same for the reconnected U-shaped flux tubes. The signalling is thus based on dark photons which can transform to ordinary photons identified as bio-photons. Dark photons can in this manner affect biochemistry since their energy spectrum is in the energy range of excitations of biomolecules (ranging from .5 eV (metabolic energy quantum) to visible and UV).
In the general situation several frequencies are involved and serve as kind of passwords. The model for musical harmony and genetic code in terms of bio-harmony relying on icosahedral Hamilton's cycles predicts that DNA codons and amino-acids correspond to 3-chords defining what might be called bio-harmony: in fact, 256 different bio-harmonies are predicted. The corresponding frequencies can be in the range of audible frequencies and it is quite possible that music of dark photons is realized in biology. Each molecule could correspond and produce its own collection of chords, maybe even melody somewhat like the characters in the operas of Wagner!
- This process would operate at all levels. Basic biomolecules are scanning their environment using these U shaped flux tubes and reconnecting. Immune system tries to detect invader molecules using reconnection followed by resonant exchange of dark photons, followed by the reduction of heff shortening the length of the flux tube and bringing the unlucky invader near the immune soldier to be mercilessly destroyed. This scanning can be done also with positive intentions: DNA replication, transcription to mRNA, translation, etc.. are examples
- This picture leads to an interpretation what happens , when biomolecule attaches to a receptor. Biomolecule - say neural transmitter or hormone - is the end of (a potential) communication line - plug formed by the U-shaped flux tube. When it attaches to the receptor, the owner of the receptor is plugged to the web and can send and receive dark photons resonantly to the receiver. Therefore bio-chemical communications are at deeper level not yet communications but only sending of plugs making possible real communication by dark photons.
- States have both armies and diplomats. Immune system is the counterpart of army trying to detect invaders and destroy them. There must be also a system trying to find potential friends and collaborators. We indeed co-operate with bacteria and the significance of this aspect seem to be increasingly realized. For instance, in Quantum Biology, coherence and decoherence there is a link to an article about collaboration some exotic sea animal with micro-organisms: the animal actively builds connections to the micro-organisms and here also reconnection mechanism is highly suggestive.
- Hormones are usually regarded as purely chemical means of communication. I have proposed that they make possible communication using dark photon signals propagating along communication lines defined by flux tubes. The attachment of biomolecule to a receptor in cell membrane is for plugging in: the biomolecule in receptor can be connected by flux tube pair to quite specific biomolecules or magnetic bodies.
- The effects of psychedelics and entheogens such as naturally occurring psylocybin (see also this) could involve even flux tubes connections to distant civilizations or higher level conscious entities! This sounds of course totally outlandish but is not my original proposal;-). In ZEO finite light velocity is not a problem since signals can travel also backwards in time). In this case the lengths of flux tubes would be very long and extend to distant galaxies.
- Pheromones (see this link as example) are like hormones except that they affect the behaviour of another member of the same species (or more generally?) by inducing epigenetic influences. Female butterfly emits pheromones and male receives them and connection is established by magnetic flux tube to the female's BB or MB. After than male flies to the direction in which the connection becomes stronger. This mechanism is same as used by birds in TGD Universe to find from Africa to the same place in Norther Finland every year;-). Also food odors have epigenetic influences. The same plugin model
applies also to these effects: chemical signals are actually plugs connecting to the web and making possible signalling
by dark photons.
- Also nutrients could fit nicely to this picture if also they are plugs connecting BB to some MB rather than just source of metabolic energy. To stay alive means is to stay connected to the web;-). Magnetic zombies die soon! The MB in question could be not only personal MB but also the dark MB of Mother Gaia as I have suggested (see this . The explanation of the Pioneer and Flyby anomalies (see this ) allow to consider a concrete identification as approximately spherical flux sheet carrying dark matter and having radius of Moon's orbital radius. The density of the dark matter would be universal and about .8 kg/m2. It would be approximately spherical and involve also a flux tube through the magnetic axis so that closed flux lines would result. This is of course just an innocent suggestion.
- Even mushrooms communicate via underground network analogous to neural networks and formed with roots and mycellium in forests (see this) and magnetic flux tube networks could be naturally at the background.
To sum up, communications would be a crucial aspect of being intelligent living system and the proposal is that magnetic body carrying dark matter and photons plays key role in these communications.