How could the TQC programs representing basic bio-reactions emerge?

The basic bio-chemical processes such as replication, transcription, translation have remained mysteries in standard biology. My conviction is that a lot of new physics is needed. Bio-chemistry is not enough, even QFT is not enough. Even standard views about space-time and classical fields, QM, and basic ontology are not enough.

TGD approach indeed brings in several new physics elements.

1. The notion of magnetic body (MB). MB carrying dark matter identified as dark variants of charged particles having non-standard value h_eff= n×h₀ of Planck constant is central in TGD inspired quantum biology. MB is the intentional agent receiving sensory input from biological body and controlling it. The interactions at the level of ordinary bio-matter would be governed by the MBs of molecules, and bio-chemistry would be a shadow of this much simpler dynamics.
   

   MB of water entrains to the cyclotron frequencies of the MBs of the basic biomolecules by varying flux tube thickness. This makes possible water memory (see this) and implies homeopathy like mechanisms serving as basic quantal building bricks in the functioning of the immune system. Dark variants of DNA, etc.. realized as dark proton sequences would be one aspect of this representation.
   
   

2. The braiding of the magnetic flux tubes makes possible realization of topological quantum computer (TQC) programs. Biological functions should correspond to TQC programs and the challenge is to understand how they emerge naturally. A possible answer to this question will be proposed in the sequel.
   
   
3. There are also other central notions such as zero energy ontology (ZEO) predicting that the arrow of time is not fixed. The following arguments suggests that ZEO is absolutely essential for the understanding of the miracles of bio-chemistry. TQC programs running backwards in time would generate as output various biological functions such as DNA transcription and other basic processes.
   
   

What are the big problems?

It is best to start from the problems that one should solve. At bio-molecular level the basic problem is to understand how complex temporal sequences of bio-chemical reactions involving bio-catalysts are possible as highly deterministic sequences.

1. How the reacting molecules - including catalysts - are able to find each other in the molecular soup?
   

   TGD answer: Contraction of flux tubes connecting molecules very selectively as h_eff is reduced brings molecules together. Connections between molecules are generated by reconnection of U-shaped flux tubes scanning enviroment and producing pair of flux tubes connecting the two systems provided they have the same cyclotron frequency. Resonant em coupling by dark photons is in question.
   
   

2. How the attached molecules are able to attach to just the correct spot and orient just in the correct manner?
   

   TGD answer: the contraction mechanism for flux tubes automatically guarantees also this.
   
   

3. How the rate of reaction can exceed the expected rate by so huge factor?
   

   TGD answer: Reactants are connected by flux tubes so that the probability that they find each other is much higher and depends on the occurrence of h_eff reducing transition which occurs spontaneously. The energy liberated in the contraction of flux tube allows to overcome potential wall in the reaction and exponential increase in the rate is achieve.
   
   

4. How bio-catalysis can proceed in time ordered manner like deterministic computer program so that very many initial states can lead to the same outcome?
   

   Here the initial states would correspond to positions orientations, etc of input molecules. Huge number of initial states lead to the same outcome.
   

   I think that this is the really difficult question. I am highly skeptic about the possibility to understand this in QFT framework. In the following I propose TGD inspired solution of this problem requiring ZEO, which means a revolutionary modification of basic ontology and of views about time.
   
   

How bio-catalysis can proceed in time ordered manner like deterministic computer program so that very many initial states can lead to the same outcome?

Apparently a breaking of second law is involved. Very many initial states lead to the same outcome rather than vice versa. As if the process would be controlled by the time reversal of the original process and entropy would increase but in opposite time direction as usually but at the control level! The notion of syntropy introduced by Fantappie comes in mind!

TGD answer would involve at least the following pieces.

1. Dark DNA and dark variant associated with enzyme should be part of the story. Large h_eff brings in conscious information realized as algebraic complexity and large scale quantum coherence.
   
   
2. ZEO allowing time reversed processes should be essential. ZEO predicts both directions of time and motor actions are postulated to correspond to sensory perception in opposite arrow of time (see this). What this precisely means is not however clear.
   
   
3. Magnetic body (MB) should be the boss controlling dynamics. This dynamics should be very simple. Biochemistry should be shadow dynamics and apparently extremely complex.
   
   
4. Topological quantum computational aspect(TQC) is also central but I have not been able to articulate what TQC programs emerge: the following ZEO arguments suggests an astonishingly simple mechanism for this.
   

   The complex reaction sequences like transcription should correspond to a running of topological quantum computer (TQC) program coded by the braiding. I just made a big step of progress in the understanding of sensory memories. Memory recall would be like a quantum computer program running backwards in time and producing sensory experience as output (see this).
   

   There is a strong temptation to believe that this is completely general aspect of all also motor actions. By fractality also DNA transcription, translation, etc... are analogs of motor actions. Somehow they should be coded to TQC programs realized as braidings of flux tubes of MB.
   

   The output of the TQC program running backwards with respect to the standard direction of time would be motor action as we observe it. All basic bio-processes involving several steps be coded to braidings. One can imagine a hierarchical structure: programs, subprograms, etc... for the TQC programs. Braidings of braidings of.... This conforms with the hierarchical many-sheeted structure of space-time.
   
   

How to realize motor actions as outputs of TQC programs running in non-standard direction of time?

1. Assume that when some process - such as DNA transcription or its time reversal occurs - it induces braiding of flux tubes - topological quantum computer (TQC) program at the level of MB.
   

   As this TQC program runs backwards in time, the time reversal of the original process is generated as output at the level of ordinary bio-matter.
   
   

2. For instance, in the case of transcription, one should assume that the time reversal of transcription meaning the decay of mRNA back to its building bricks generates the TQC program as braiding. Running of this TQC problem in the reverse time direction should generate transcription.
   
   
3. What looks strange that the time reversal of the assembly process - essentially a decay process occurring in very manners - would code for the highly deterministic TQC program for the assembly process. But this is actually just what one wants!!
   

   The decay process is highly unpredictable but its time-reversal is highly predictable! There are very many TQC programs, which give rise to the desired output! The ways from Rome lead to all possible directions but all ways lead to Rome! In ZEO butterfly effect transforms to extreme predictivity in opposite time direction!
   
   

4. How MB and space-time sheets assignable to ordinary matter and having opposite arrows of time - or more generally two levels of h_eff hierarchy with different values of h_eff and different arrow of time - could interact? If the arrows of time are opposite, the intersection of space-time sheets should have dimension smaller than D=4. Since the classical dynamics determined by twistor lift breaks T symmetry (the analog of Kähler action in M⁴ degrees of freedom is the reason), 3-D intersection does not imply that the surfaces co-incide for the space-time surface and its time reversal.
   

   The interaction should be via common boundary conditions: the space-time sheets with different arrow of time should intersect along 3-D or even lower-dimensional surfaces at the boundaries of CD and perhaps also at the 3-D light-like orbits of partonic 2-surfaces at which the signature of the induced metric changes. Magnetic flux tubes induce braiding, which suggests that magnetic flux tubes of MB as 4-D surfaces should have at most 3-D intersection with the space-time surfaces representing ordinary bio-matter and defining the nodes of tensor network (see this). These 3-D - possibly light-like - intersections would mediate the interaction. For the usual arrow of time for MB interaction would be sensory input to MB and induce braiding. For the opposite arrow of time for MB it would be motor action in which MB would be the controller forcing bio-matter to follow in the un-braiding process.
   

   In the generic case the intersection of two 4-surfaces in M⁴× CP₂ is discrete. Could the intersection of space-time surfaces with different arrow of time consist of a discrete set of points? Could this be enough for MB to control bio-matter? Note that cognitive representations identified as intersections of real space-time surfaces and their p-adic variants consist of a discrete set of points (see this).
   
   

5. The connection with Sheldrake's vision about morphogenetic fields, in particular the genereration of "habits" even at the level of so called dead matter is rather obvious. TQC programs would indeed code for habits and would be generated by Nature without a need of a programmer writing the code. I have discussed Sheldrake's vision from a slightly different viewpoint here.
   
   

There are interesting connections to ancient Indian philosophy and Christianity. ZEO has analog in ancient Indian philosophy as I learned from a discussion with Savyasanchi Ghose while writing this. As notions doer and un-doer are analogous to self and time reversed self. MB would be in the role of supreme observer although it would not be outsider to the Universe. The undoing the time reversal of deed by MB would serve as a template for the dynamics of deed at the level of ordinary matter.

Building braids and opening them are the basic operations in TQC according to ZEO. A visit to web using "undoer" reveals that it appears also in Christianity, Mary the undoer of knots! Knots are now a metaphor for sins and undoing them means mercy. In Christianity God would be the counterpart of MB and we would be 4-D dynamical images of God.

To sum up, this sounds like mystics and brings strongly in my mind a french movie about time that I saw decades ago. It was very poetic and somehow caught at the emotional level something very deep about the mysteries of time, life, and consciousness in a manner not expressible using the vocabulary of scientist. It seems that TGD is providing the language that I did not have at that time and that ZEO is starting to demonstrate its magnificent explanatory power.

See the chapter Sensory Perception and Motor Action as Time Reversals of Each Other: a Royal Road to the Understanding of Other Minds? or the article with the same title.

For a summary of earlier postings see Latest progress in TGD.

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