Development of ideas After required number of years however some concrete ideas began to emerge.
- The notion of magnetic body with fractal onionlike structure meant a decisive step of progress. Also the hierarchy of Planck constants and dark matter as controller of visible matter in living systems emerged. The function of EEG as communication and control tool of magnetic body using biological body as a motor instrument and sensory receptor looked very natural. This led also to a proposal that there is an entire hierarchy of EEGs and their variants. After several trials a vision about nerve pulses as concomitants of quantum level communications emerged as also a vision about DNA as topological quantum computer based on the flux tubes connecting DNA nucleotides with the lipid layers of cell membrane emerged and providing a function for the intronic portions of genome as carriers of quantum computer programs .
- Also a vision about the biochemical role of dark matter evolved. In particular, phase transitions reducing Planck constant for a magnetic flux tube would induce its contraction and force biomolecules near to each other. This would explain the miracles of DNA replication, translation, and transcription and quite generally the processes known as aggregation of proteins. The reconnection of magnetic flux tubes changing the topology of the biological Indra's net would be also a central mechanism.
- The model of nerve pulse and the vision about living matter as a kind of dynamical Indra's net led to a first clear idea about the role of neural transmitters. Transmitters are classified to inhibitory or excitatory depending on whether they increase or reduce the magnitude of the membrane potential. This property is however a property of the receptor rather than that of the transmitter. The same transmitter can have both excitatory and inhibitory receptors although often either receptor type dominates. The proposal was that neural transmitters are associated with the ends of the links of the 4-dimensional web connecting neurons to each other. Neurotransmitter attaches to the plug defined by the receptor connecting the communication wire from presynaptic neuron to the flux tube leading to the passive portion of postsynpatic DNA strand acting as sensory receptor. This would make possible rapid communications to DNA. The corresponding active portion of DNA strand could then respond by generating an activity at the level of cell membrane. This conforms with the general idea that proteins represent only one particular outcome of the gene expression. This left open the question whether the excitatory-inhibitory dichotomy could have some deeper meaning.
- Also it became clear the emotions and information are closely related and that peptides acting both as neurotransmitters and hormones are crucial for emotions . I proposed that emotions are "entropic" qualia. Although I realized the importance of negentropic entanglement I did not have time or I was not able to realize how far reaching this notion actually is.
Fractality replaces standard reductionism in TGD Universe. An old idea inspired by p-adic length scale hypothesis is that the binary structures associated with p-adic scales L(k) propto 2k/2 and L(k+2) define a fractal hierarchy. Brain hemispheres would represent one example of this kind of pair, lipid layers of the cell mebrane second one, and DNA double strand third one. Just for fun one could assume that the structure and functions of brain hemispheres have fractal analogs at the level of DNA double strand and vice versa and look what kind of questions this inspires.
- Could the identical structures of DNA strands correspond to the anatomical similarity of right and left brain and could the functional asymmetry of the strands correspond to the laterizalization of brain function? Could the genome act as the brain of cell? Could various brain areas have counterparts at the level of DNA? Could the hydrogen bonds between nucleotides serve as the counterpart of corpus callosum? Could the splitting of these bonds during transcription and replication correspond to what happens to a split brain patient?
- Before continuing it must be made clear that the global identification of right-left dichotomy with holistic-reductionistic dichotomy is wrong. One can however consider its local variant with holism and reductionism assigned do the pairs of right and left brain areas. For instance, emotional right (left) brain (amygdala) would be reductionistic (holistic, negentropic) and intellectual right (left) would be holistic (reductionistic, entropic). The practical reason to the division to the entropic and negentropic pieces could relate to the metabolism. The entropic regions could provide the binding energy as a usable energy to the positive energy negentropic entanglement. Good is not possible without Evil! There are no winners without loosers! Right brain is specialized in spatial thinking and left brain to verbal thinking and arithmetics: the geometry-algebra division of mathematics! Right brain is not so good in motor actions as left brain as any right-handed person knows. Right brain is however better in tactile sensing: right handed persons tend to use left hand for touching objects to get an idea about their shape. Also this can be understood in holistic-reductionistic picture.
- Apart from reflex actions almost all activities of the body seem to be controlled to a high degree by brain. Could also the activitites of cell be regarded as motor actions of the genome acting as the brain of cell receiving sensory imput from the cell membrane? Could one identify the analogs of sensory areas receiving information from cell membrane, processing, and sending it to the association areas? Could the analogs associative areas be identified as intronic portions of DNA performing topological quantum computations and communicating the outcome to the higher motor areas at the intronic portions of the of the complementary strand, wherefrom they would be communicated to the primary motor areas identifiable as the regions of DNA expressing themselves either chemically (RNA and proteins), as activitites generated directly at the level of cell membrane, or electromagnetically? For instance, could neurotransmitter in the receptor generate the feed of sensory input to the genome inducing the change of the membrane potential as the counterpart of motor action. Could prokaryotes without introns be analogous to brain with only primary sensory and motor areas
or to mere ladder-like nervous system?
- What right brain sings-left brain talks metaphor could mean in this picture? Pitch-rhythm dichotomy is more technical expression for this dichotomy. Function providing local data and its Fourier transform providing global data is more abstract representation for this dichotomy and Uncertainty Principle for momentum and position relates closely to these two representations of information. This dichotomy could reflect the presence of two different natural time scales and millisecond time scale for nerve pulses and .1 second time scale for moments of sensory experience are the natural candidates.
If so, this dichotomy could directly reflect the different time scales assignable to u and d type quarks (1 millisecond) and to electron (100 ms) and reduce to the level of elementary particle physics. This dichotomy would also have fractally scaled up variants made possible by the hierarchy of Planck constants. The analog of Fourier transform would be the negentropic unentanglement of sub-CDs (assignable to quarks) to single mental image inside electron's CD. The analog of function itself would be a collection of sub-CDs representing separate unentangled mental images assignable to individual nerge pulses in millisecond time scale. Also the topological quantum computations assigned to the intronic portions correspond to different time scales due and reflect quark-lepton dichotomy. The quarks in question could be the quarks assigned to the ends of flux tubes in the model of DNA as topological quantum computer.
- This raises some questions. Could the gene expressions of the two strands somehow reflect this dichotomy? For instance, could the flux tube structures assignable to the aminoacid sequences correspond to the millisecond and 100 ms scales assignable to quarks and electron have the property that also the functioning of these proteins is characterized by these typical time scales? The time scales of protein folding indeed appear in two typical ranges beginning from ms  and 100 ms respectively . There are also short proteins for which the folding takes place in microsecond time scales which might relate to the CD of proton.
What can one say about the function of neurotransmitters?
Can one say anything interesting about the the function of neurotransmitters if one combines this highly speculative picture- which can be defended only by the belief on fractality as universal principle- with the idea that bound state and negentropic entanglement make possible the fusion of mental images.
- Suppose that the fusion of neuronal mental images is required to build higher level mental images that we experience. Suppose that neuronal mental images involve DNA in an essential manner. Suppose that magnetic flux tubes serve as correlates for the entanglement so that the transmission of nerve pulse from pre-synaptic neuron to post-synaptic one creates a flux tube connection between neurons possibly extending to the genome of the post-synaptic neuron. The transmitter at the end of flux tube attached to the receptor acting as a plug would build this connection to some part of DNA specialized to receive particular kind of sensory data from a particular region of cell membrane with complementary strand activating as a response a motor function inducing gene expression at cell membrane level. Gene expression as build-up of proteins would not be necessary and is also too slow for neural activities.
- Suppose that the entanglement between neurons generated in this process is always negentropic as the interpretation as the idea about neural correlate for a conscious association suggests. One could also ask whether the neurons could entangled entropically and whether the entropic-inhibitory association could make sense. This does not lead to anything interesting and entropic entanglement between neurons should be regarded as a pathological condition. Note that neuron-neuron entanglemement would be naturally time-like and in this case only negentropic entanglement might be meaningful.
- To gain some perspective consider the activation of cell in general by some external perturbation from the resting state to the active state (here I have learned a lot from email correspondence with Vladimir Mateev) In the resting state the proteins inside cell are passive -or rather, forced to be passive- as one might expect on basis of the general vision about homeostasis. The unfolded proteins and unfolded portions of the folded proteins are connected by hydrogen bonds to ordered water so that the folding occurring otherwise spontaneously is prevented. One can say that the cellular winter prevails. The situation is however nearly critical and if external perturbation
occurs cell liberates metabolic energy melting the ice and spring comes. Also the outer surfaces of globular proteins are hydrogen bonded and when the ordered water melts, spontaneous melting of the protein takes place leading to a partial unfolding.
The resulting folded proteins and partially unfolded globular proteins interact by forming aggregates and this activity would naturally involve hbar reducing phase transitions and flux tube reconnections. In TGD based model the mechanism of both folding and melting would be the liberation of metabolic energy destroying the hydrogen bonds and the energy for this comes from the ATP containing positive energy negentropic bond between O=s of phosphates.
- Similar situation could prevail at the cell membrane. One can imagine that cell membrane is like a particle at the bottom of a small potential well. At the other side there is a deep well representing the generation of nerve pulse and at the other side a high wall corresponding to hyper-polarization requiring energy. Both polarization and hyperpolarization are prevented by the freezing of protein activities needed to induce them. The flux tubes connecting the presynaptic neuron and receptor and possibly genome are always negentropic and their formation can as such serve as the signal leading to the partial melting of the ordered water making possible to generate action leading to either depolarization or hyperpolarization. The signal could be just the additional metabolic energy making it possible for these transitions to occur.
- This picture does not require any communications from the receptor to the genome and in the simplest situation the resulting action could be seen as the analog of a reflex action. These communications could of course be present and the negentropic entanglement could make it easier to induce depolarization also now. Also the question whether excitatory-inhibitory dichotomy for the receptors has some deeper meaning apart from taking the neuron nearer to or farther from criticality for firing remains unanswered.
- To gain some perspective consider the activation of cell in general by some external perturbation from the resting state to the active state (here I have learned a lot from email correspondence with Vladimir Mateev) In the resting state the proteins inside cell are passive -or rather, forced to be passive- as one might expect on basis of the general vision about homeostasis. The unfolded proteins and unfolded portions of the folded proteins are connected by hydrogen bonds to ordered water so that the folding occurring otherwise spontaneously is prevented. One can say that the cellular winter prevails. The situation is however nearly critical and if external perturbation occurs cell liberates metabolic energy melting the ice and spring comes. Also the outer surfaces of globular proteins are hydrogen bonded and when the ordered water melts, spontaneous melting of the protein takes place leading to a partial unfolding.
- The chapter DNA as Topological Quantum Computer of "Genes and Memes".
- E. R. Kandel, J. H. Schwartz, T. M. Jessel (1991), Principles of Neural Science. Prentice-Hall International Inc..
- C. B. Pert (1997), Molecules of Emotion, Simon and Schuster Inc..
- T. E. Creighton (1993), Proteins: Structures and Molecular Properties. W.H. Freeman and Company. New York.
- Protein folding.
For background see the chapter TGD Inspired Model for Nerve Pulse.