Sunday, March 22, 2015

Cell memory and magnetic body

In Ulla's "Thinking Allowed" there was a very interesting link to a popular article telling about claimed discovery of mechanism of cell memory. In the case considered memory means now the ability of mother and daughter cell to remember what was or what should should be their identity as highly differentiated cells. In the division this information seems to be completely forgotten in the sense of standard biochemistry. How is it regained: this is the problem!

Transcription factor proteins bound to DNA guarantee that cell expresses itself according to its differentiation. I have never asked myself what the mechanism of differentiation is (I should have a proper emoticon to describe this unpleasant feeling)! Transcription factors is it: they guarantee that correct genes are expressed.

As cell replicates the transcription factors disappear temporarily but are restored in mother and daughter cell later. How this happens looks like a complete mystery in the ordinary biochemistry in which one has soup of all kinds stupid molecules moving randomly around and making random collisions with similar idiots;-).

This problem is much more general and plagues all biochemistry. How just the correct randomly moving biomolecules of the dense molecular soup find each other - say say DNA and mRNA in transcription process and DNA and its conjugate in replication?

The TGD based answer is that reacting molecules are connected or get connected by rather long magnetic flux tubes, which actually appear as pairs (this is not relevant for the argument). Then magnetic flux tubes contract and force the reacting molecules close to each other. The contraction of the dark magnetic flux tube is induced by a reduction of Plankc constant heff=n×h: this does not occur spontaneously since one ends up to a higher criticality. This conclusions follows by accepting the association of a hierarchy of criticalities to a hierarchy of Planck constants and fractal hierarchy of symmetry breakings for what I call supersymplectic algebra possessing natural conformal structure and the hierarchy of isomorphic sub-algebras for which the conformal weights of the original algebra are multipled by integer n characterizing the sub-algebra. Metabolic energy would be needed at this stage.

As a matter fact, the general rule would be that anything requiring reduction of Planck constant demands metabolic energy. Life can be seen as an endless attempt to bet back to higher criticality and spontaneous drifting to lower criticality. Buddhists understood this long time ago and talked about Karma's law: the purpose of life is to keep heff low and fight with all means to avoid spiritual awakening;-). In biological death we have again the opportunity to get rid of this cycle and get enlightened. Personally I do not dare to be optimistic;-).

In the case of cell replication also the transcription factors replicate just as the DNA but stay farther away from DNA during the replication: the value of heff has spontaneously increased during replication period as it happens as conscious entity "dies";-). When the time is ripe, their heff is reduced and they return to their proper place near DNA and the fight with Karma's law continues again. Note that this shows also that death is not a real thing at molecular level. Same should be true at higher levels of fractal self hierarchy.


Ulla said...

"the purpose of life is to keep heff low and fight with all means to avoid spiritual awakening;-)."

I have been asking lately what really the 'enlarged consciousness' so many talk of means. If you take it literally it would mean a path away from knowledge, learned things, education. Maybe what we see today in the world?

As a rule consciousness cannot but diminish, as we make cognates out of it.

'Enlightment' is the same, we shred off old learnings and sins that have distorted our minds, old memes disappear etc. This is the essence of 'only a child can see heaven'.

Generally these words are used in the opposite meaning. As some 'knowing' state, some 'truths' etc. This 'knowledge or truth' is however not learned, but 'sensed', a bit along the Sheldrake line of thought.

So, in essence the 'enlarged consciousness' would be enlarged Plancks constant. There are some meditation techniques that can do this, in a way 'link in to a bigger brain'. Also Karma (old sins and distortions) belong here :) The purpose would be to undo, neutralize these things to be able to learn the truth/get 'enlarged consciousness'? This is growing, one purpose of evolution.

The messing of consciousness and awareness is so common, and so hard to get right back again. said...

Enlightment means a way off from what we call "learned" wisdom to personal discovery and real understanding or at least honest attempt to understand. Learned things are very often only behaviours that we learn to gain acceptance. No real understanding is involved. Sad ti sat that most of the learning in academic environments is just this.

Saying it more quantitatively. Large h_eff means also better measurement resolution and cognitive resolution. Maybe what is lost is concreteness when state function reductions do not occur and one has negentropicentanglement representing abstractions.

One must give something away to achieve it and letting it go to larger h_eff means loss of the earlier ego- biological death at extreme. The paradoxical thing is that increase of h_eff tends to occur spontaneously - assuming that my interpretations are correct: but do not take it as word of God!;-). And even Gods cannot be trusted!

Anonymous said...

What the heff?! said...

heff was not the meaning I had in mind originally;-). I was not quite sure whether the hierarchy is real or not and decided to be cautious the possibly existing remnants of my academic reputation and added the subscript _eff - effective. As a matter fact, the interpretations as real thing and effective thing are both possible.

Anonymous said...

so are the cells Markovian or not? :) said...

Abstract talks about Markovian process with long term memory. I understand this as presence of long range correlations in time. This is one manner to give some content to the word "memory". Memories can be also identified as learned skills or as associations as behaviourists do. There are also episodal memories: this is what memory in layman language often means . Neither Markov nor behaviourism can give much here.

Markovian process is very special kind of statistical modelling tool assuming randomness at the bottom. What I am talking about is something much more general. For me cell is conscious intentional agent rather than Markovian random walker. By answering yes or no I would do violence to cell;-).

Ulla said... said...

This is a very interesting finding. May fresh ideas about memory are gradually entering to the science market.

My own view is that the view about memories is fatally wrong. The identification of experienced time and geometric time is the fatal error. Even child realises that these two times are not one and the same thing but who would manage to tell this to academic scientist?

Zero Energy Ontology allows to see brain and body as 4-dimensional things and memory recall would be communication with the geometric past. Recall Libet's findings.

The 4-D brain allows also to see behaviours - often erratically identified as memories - as 4-D patterns of magnetic body, which develop in 4-D sense in state function reduction sequence.

Replication of magnetic body would mean replication of behaviours and there is support for this from what happens to split flat worms: both
halves have the learned behaviours not only the worm which has the original head.

In TGD framework any pattern in principle defines a memory. This does not mean that synaptic contacts would not be crucial for generating association sequences making possible behavioural patterns: I would not however regard them as genuine memories.

The braiding of flux tubes could be the really fundamental memory representation since it would transform temporal "dancing" patterns for lipids of cell membrane to spatial braiding patterns for flux tubes. Dancers with feet connected to wall is the metaphor.

donkerheid said...

Dear Matti,

You said:
One must give something away to achieve it and letting it go to larger h_eff means loss of the earlier ego- biological death at extreme. The paradoxical thing is that increase of h_eff tends to occur spontaneously - assuming that my interpretations are correct

I guess this must also apply to the process of real understanding and gathering wisdom that you mention in the previous paragraph. This also seems like reaching higher spiritual stations that mystics talk about. How could this be spontaneous? It takes a lot of effort to kill a former self and transcend it.

Anonymous said...

Change is constant so it takes lot of effort to hold on to inertia. Also the inverse of trying to "kill a former self" just feeds it negative energy. Letting go and acceptance happen spontaneously.

Anonymous said...

Non-markovianity and information flow: said...

To Donkerheid: I agree. I know from experience how difficult it is to give up to throw a dead idea to paper basked and there is always the risk that it is a real idea after all. I am just now making this kind of spring-cleaning going through all online books about TGD proper.

All kinds of trash hides the deep ideas, I get angry to myself, and still it is so difficult to just throw them away. But again I discovered that an old idea about which I wrote an enthusiastic chapter years ago and then threw it away made a comeback and now I know that it will stay!

Scattering amplitudes as computations of minimal length connecting initial and final collections of algebraic objects in some algebraic structure with product and its inverse (co-product) representing 3-vertices. Extremely beautiful and elegant idea giving mathematical realisation for the Universe as computer idea. Universe as supersymplectic Yangian algebraist would be a more precise formulation!;-)

Anonymous said...

Matti my friend, I know the feeling. The first rule and practice of writer/poet schooling is the maxim "kill your darlings". And of course, that practiial guidance is not absolute, just relative and practical.

Ulla said...


I guess you talk of 'getting knowledge from above', without reading books, that you just 'know'. Through the window, as Jung talked of.
It is spontanous and does not include efforts, not much, and if it does it is a cleaning process, aiming to find the 'real' self.

Is this the same as intiution?