Monday, August 09, 2010

Recreate life to understand how life began

Mark Williams sent a link to a very interesting article in New Scientists. It tells about success in attempts to recreate life in laboratory. Not from existing building blocks but at much more fundamental level. RNA is believed to play a fundamental role in the prebiotic evolution of RNA (so called RNA world scenario) and much of the effort has gone on attempts to induce the generation of RNA molecules in laboratory. The problem is that it is difficult to get long enough RNA molecules which would replicate. The newest experimental work however supports the idea that life emerges as a co-evolution of both RNA and of protocell membranes formed by phospholipids (fatty acids). Soap films represent a familiar example of this kind membrane.

The challenge is to get cell membranes to grow and replicate in laboratory.

  1. Phospholipid layers are generated via self-organization and their development does not require any genetic apparatus. Therefore it is not too difficult to make protocell membranes to grow.

  2. The first discovery was that RNA within cell membranes drives the vesicle growth. The presence of RNA makes the membrane able to steal lipids from neighbors: market economy is after all not so new discovery and means actually return to the protocell level in evolution! Congratulations, Dear Human Kind!

  3. Division was the tough problem since it is not energetically favored. The solution to the problem came as an accidental discovery. It was found that the cells grew large enough they tend to become elongated and tubules began to grow from the surface of cell. Eventually the membrane becomes so elongated and filamentous that it becomes unstable against division. Clearly a critical state in which it does not cost much to build new cell membrane is in question. Maybe the generation of axons and microtubules is analogous process and also the formation of cilia at the surfaces of real cells.

These findings are very interesting from TGD point of view. DNA as topological quantum computer model (see this and this and also other chapters of the book Genes and Memes) assumes that the magnetic flux tubes connecting DNA and lipids of lipid layer and their braiding make possible a realization of topological quantum computer programs and memory based on braiding. A good metaphor is dancers in dancing hall with threads connecting their feet to the wall. The dancing pattern defines a braiding in time direction coding for topological quantum computation and the entanglement of threads codes this program to memory. The braiding can be also interpreted as a representation for the fluid flow of the lipid molecules which form a liquid crystal and induced by the flow of surrounding cellular water. In case of axons this could give rise to a memory about nerve pulse patterns involving directly the relationship between DNA and cell membrane defined by the braiding.

The flux tubes containing large hbar matter would be actually everywhere in living matter. The phase transitions reducing or increasing Planck constant would induce phase transitions taking molecules near to each other and vice versa and would explain the magic ability of bio-molecules to find each other. Bio-catalysis and DNA replication and also the phase transitions involving typically large changes in the density of cytoplasm would involve change of hbar. Same applies to sol-gel transitions and the transformation of biomatter between resting state to active state involving protein folding and un-folding. The reconnection of the flux tubes of the Indra's net formed by the magnetic flux tubes would be second non-chemical key process of biology.

In this framework it would not be too surprising that the evolution of RNA and cell membranes would take place in co-operation. Formation of membranes would make possible topological quantum computation and memory and intelligence at cell level, and this in turn would make for protocell to evolve further. Also the growth of tubules could be assigned with the generation of magnetic flux tubes above critical size. DNA is stable inside cell since cellular water can be in ordered phase in which the decay of DNA polymer by hydration does not take place. Therefore this evolution would precede the emergence of DNA in TGD Universe.


At 1:06 AM, Blogger M. Rigmaiden said...

Matti does TGD have non commutative structures? I've been trying to figure out how a non commutative structure might look or feel and how to do physics in them. I know that Alain Connes has done a lot of work in differential geometry in non commutative geometry. Is there tie in to your theory?

At 2:40 AM, Blogger Matti Pitkanen said...

Nice to year about you Mandisa.

Connes assigns his non-commutative geometry with von Neumann's algebras known as hyperfinite factors (HFFs), which come as types of type II_1 and III_1.

The spinors of "world of classical worlds" (the space of 3-surfaces roughly) are created from vacuum by Clifford algebra generated by fermionic oscillator operators for induced spinor fields and fermionic oscillator algebra defines a canonical representative of HFF of type II_1 and WCW spinor fields represent HFF of type III_1.

The inclusions of HFFs are central part of this mathematics and they have interpretation in terms of finite measurement resolution. Included algebra N subset M defines measurement resolution in the sense that the action of N creates states which cannot be distinguished from each other in the measurement resolution used. The space M/N would be an analog of noncommutative space, kind of non-commutative analog of spinors.

The deviation from the philosophy of Connes and other non-commutative theoreticians is that I do not propose that space-time would become non-commutative in say Planck length but that non-commutative mathematics reflects finite measurement resolution and would be present in all length scales. At space-time level the geometric correlate for finite measurement resolution would be discretization and I end up with the notion of braid. Quantum groups are basic non-commutative structures and are associated with the braids.

Non-commutative space-time does not seem to have natural place in TGD in the sense of Connes or as it is used in the model building (preferred space-time coordinates are made non-commutative).

Non-associativity and non-commutativity would however appear in the sense of classical number fields. Imbedding space tangent space would have octonionic structure. Space-time surfaces are conjectured to have quaternionic or co-quaternionic structure: associativity would thus define fundamental physical law for space-time dynamics. I have conjecture that this is equivalent with the preferred extremal property for Kahler action.

Partonic two-surfaces which are in certain sense basic objects could in turn have commutative structure in certain sense. I speak about effective two-dimensionality in the sense that partonic 2-surfaces plus their 4-D tangent spaces carries the physical information. This is holography in strong sense and could be understood also as commutativity for the basic objects (not however that 4-D tangent space is quaternionic and thus non-commutative).

At 12:14 AM, Blogger Ulla said...

Proliferation is one of the most important things showing at activity of cells. An inactive cell is a sphere. This is seen most effectively in cancers where also DNA is severly disturbed. Biologists try to proove that DNA is responsible, but maybe the reason is somewhere else. The epigenetics and methylation is hinting at that too. A lot of electric and magnetic forces is in action.

Here a link where extremely weak magnetism is able to keep up synchronization, one of the main features in biology.

And a link with Casimir forces.
This is also actual for the discussion on energy/gravity. What holds the energy together?

You see, this is the reason I believe you are right. It was very thrilling to try to understand things from a different perspective, or in the beginning to even see the picture. But TGD fits very nicely into biology :)

I guess my many questions and discussions is because of this excitement. I am really sorry if I flooded you too much. But I asked you to say STOP when it became too much. You couldn't do that?

I also had to verify all what you said. To put it in a context. Javier once said the same. You have simply left out this from TGD, the developement, the path. This make it so difficult.

At 11:23 PM, Blogger Ulla said...

Here a very interesting link. from june 12.8.10

neutrino-antineutrino oscillation violate symmetry. find more oscillations than would be expected from only three neutrino flavors...

This was the second link.

Yesterday I made a big step forward when I realized that the energy is only transferred via magnetism. The energy is only polarized and focused. That may sound simple to you but a biologist has always heard that energy is created :) Now I have a common base for all factors working in the nerve pulse. Also the transformation of information and consciousness may be explained in this way, as you say.

But this also means that vacuum/nerves is full of information that is focused by magnetism. The entropic model makes sense.

Now I need a link between magnetism and gravity. Gravity is also important for the focusing and transfer.

At 12:31 PM, Blogger Ulla said...

There happens new developement now. From Kea and Riofrio.

About the fine constant

Flux tubes dancing on Earth. Guess this is exactly the same process as in the nucleus - membrane :)

At 9:34 PM, Blogger Matti Pitkanen said...


the variation of fine structure constant is extremely interesting if true. I am not able to say anything about experimental side. I have proposed a couple of explanations earlier. One was based on the notion of manysheeted space-time: nuclei could feed a small and varying amount of their electromagnetic flux to other than atomic space-time sheet so that effective nuclear charge and thus effective alfa is changed.

About the variation of nuclear rates there exists a lot of work. Russian Shnoll is the forgotten pioneer. I commented this for a couple of years ago from TGD point of view: see this.

See also comments at viXra blog.

At 11:13 AM, Blogger Ulla said...

Is there anything saying this would be confined only to radionuclear elements? Maybe this effect is very common? I think of all those biological circadian, monthly and annual rhythms etc. Ca-resonances are one important bit.

Also the link to Rn-release is interesting.
Day and night, light varies, and light is the EM-force, so it would be natural to think of that. Photons interact with leptons and neutrinos are leptons?

At 11:38 AM, Blogger Ulla said...

A link to hallucinations coupled to 'radioactivity' and Ca-resonances. Auditory hallucinations and consciousness. Note also the 1 Hz and <10 Hz (= Yin-signal?).

Pacemaker neurons

At 2:37 AM, Blogger Matti Pitkanen said...

The difference between exotic states become visible in weak interactions responsible for radioactivity). A small effect is in question and there is no reason to think that it would be fundamental in living systems and even less that it would relate to consciousness in some deep manner. The importance of the effect is that it demonstrates that standard model is somehow wrong.

Hierarchy of Planck constants and p-adic length scale hierarchy however allows scaled variants of weak gauge bosons with large Compton length and this makes possible for weak interactions to become as strong as em interaction below Compton scale of boson which can be zoomed up. This could explain chiral selection in living matter which remains a mystery in standard model framework.

At 4:24 AM, Blogger Ulla said...

Look at these

Kirshivink, Joseph L, Kobayashi-Kirshivink, Atsuko & Woodford, Barbera J., "Magnetite Biomineralization in the Human Brain" Proceedings of the National Academy of Science, 1992, 89 7683-7687
Radon and Paranormal Activity

Pulinets, Sergei: Ionospheric Precursors of Earthquakes: Recent Advances in Theory and Practical Application: TAO, Volume 15, No. 3, September 2004, 413-435

I have been looking for a 1 Hz signal. The signal that control life must be utterly weak and regular, so no small disturbancies will be able to act.

Alpha particles are He, and it is bosonic too. These particles are important for life. I cannot say if they are fundamental. Carbon is, also a boson.

At 1:24 PM, Blogger Ulla said...

The wave was as big as the helix. Suits your theory well :)


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