Friday, May 13, 2011

Another approach to primordial cell

In the previous posting I told about the highly interesting work of the group of Martin Hanczyc in attempts to build protocell. Also the group led by Jack. W. Szostak, who was the 2009 Nobel Prize winner in physiology or medicine - has carried out beautiful experiments in which they are able to create a candidate for protocell satisfying many of the basic requirements.

One such condition is the ability of protocell to transfer various nutrient molecules through the protocell membrane. In modern cell pumps and channels consisting of proteins are believed to serve that purpose (for a different view see the remark below). Genetically coded proteins were however absent during the primordial era. Therefore the membrane is constructed of branching lipids believed to exists during prebiotic era allowing sugars which are basic building bricks of DNA to permeate to the protocell. Given the DNA template , the basic building bricks of DNA molecule assemble to a copy of DNA in this protocell.

What is still lacking is the generation of the template strand of DNA itself and also the replication of protocell. If dark DNA in the form of dark nucleon strings is really there, the template could result as the assembly of the basic bricks of DNA around it and above a proposal for the analog of this kind of process is suggested. The replication of the dark genes would have been also present from the beginning and would have preceded the replication of genes and protocell. Biological evolution could be seen as a migration from dark space-time sheets to ordinary ones and somewhat analogous to the migration of life from sea to land.

Remark: There are puzzling experimental findings about quantal currents through cell membrane even in absence of metabolic sources. In many-sheeted space-time one could interpret these currents as various kinds of Josephson currents running between cell interior and exterior along current carrying space-time shees. Pumps and channels would be more like a diagnostic tool allowing cell to measure the concentrations of various important biomolecules and ions.

At first sight the approaches of Szostak and Martin Hanczyc look very different. These approaches have however a lot of common at deeper level if one accepts TGD based view as DNA-cell membrane system or its more primitive version as a topological quantum computer like system relying on the braiding of magnetic flux tubes connecting the counterpart of DNA nucleotides to the lipids of protocell membrane and on the prebiotic realization of genetic code at the level of dark nuclear physics.

One could also argue that the protocell of Hanczyk represents oil based life as opposed to life as we know it. In TGD framework this is a mis-interpretation. The protocells of Hanczyk live in an aqueous environment. Nitrobenzene oil is an aromatic compound as also sugars and contains nitrogen taking in the proposed scenario same role as phosphorus in ordinary life. Oleic anhydride is lipid and- would provide basic building brick for a particular variant of DNA like structure half-way between dark and completely chemical realization. Oleic anhydride would provide also the building bricks of protocell membrane and serve as a nutrient just like fat molecules- also lipids- serve in "real life".

For background see the chapter Evolution in Many-Sheeted Space-time of "Genes and Memes".

5 Comments:

At 12:54 AM, Blogger Ulla said...

See my overview
http://zone-reflex.blogspot.com/2011/03/life-is-sciences-new-focus.html

There are many models. This is the rush for our new energy sources, and contains big money.

 
At 7:09 AM, Blogger ThePeSla said...

Dear Matti,

In what sense would "dark" elements on a higher Planck level be topological and not a matter of quantum uncertainty on many levels?

Josephson junctions is an interesting idea, in a more general space the connection actually of frequency with the structures. So in a way this reminds me of a sort of relativistic dynamics.

I asked in a previous comment, what is the distances measured between these levels of action?

I had the barest thoughts last night not reading of such junctions until this morning, but aware of the Hall effect.

We discussed what we called the Halo Physics and it was very vague and difficult in the dream.

There are other models indeed and this seems to take a lot more work than we have yet wrapped up. But we have come so far!

Consider the negative index of refraction and take the images as real. There is more than quantum going on in life space, and there is more than relativistic dynamics, and if the two came together we may not need these ideas of shadow or dark matter- but dark energy ideas are not as easily dismissed on the local level.

Yes, If we are clear we can build on ideas as is the usual citing and evidence of a new powerful theory. Of course DNA is a computation device- not necessarily quantum. And its expression as consciousness or its altering states does suggest that the mind is more advanced and just as inevitable in this universe.

But we need to ground these ideas a little more for some will seem obvious later, and some seem a solution but no longer as important.

Now, Can a worm hole be entered on one side of the hierarchy and come out say smaller on the other side?

The PeSla

 
At 1:22 PM, Blogger Ulla said...

The 'memory' could be linked to immune responses evoked by lipids (cytokins). Biology is extremely sensitive to the structure of carbon-chains and can sense one different angle. The O=site is most important, though. These short fatty acids are hormones (paracrine and eucrine) and signaling agents, also behind the meridian functions and the complex functions of serotonin etc. This is in fact what brought me to TGD once :) And consciousness, but memory and consciousness cannot be separated.

Immune response is a bodily memory. Also behind homeopathy. Interesting is what I read some day ago, that botox-treatments may diminish the expressions and experiencies of own emotions. Our 'self' is invaded by other 'emotional molecules'?

One of my thoughts is that the immunerespons forced to differentiate reactive sites against the environmental impact from viruses, and build cells with borders (membrane). Viruses have a 'self' (RNA-genome?) which invaded the early prebiotic soup (without clear 'self'). In fact most of the genome is made of old and ancient viruses, and this continual invasion has driven evolution to a part.

Biology produces many kinds of 'oils'.
Extremely long chains are the essential fatty acids, as Omega-3 fish oil, which are environmental regulators.

http://www.psykologibloggen.se/2011/05/13/wemind/botox-minskar-formaga-till-kansloavlasning/

http://www.pnas.org/content/105/2/751.full

 
At 2:06 PM, Blogger Ulla said...

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2474765/ (the same link as in comment to previous post)

Inflammation is charachterized by heat. Also pH diffenencies can be charachetrized by entropy gradients? At least in relation to Oxygen? Redox is about entropy too?

In the protocell the heat charachterized the hot spot, with the 'sense organ' on the opposite side. So it can be interpreted as a very primitive 'immune' reaction, making up for adaption, learning and memory.

I feel this is a big step forward in the understanding. Thanks for bringing this up :) Maybe genome is a result of homeostatic and immune reactions?

 
At 12:39 PM, Blogger Ulla said...

http://genetics.mgh.harvard.edu/szostakweb/publications/Szostak_pdfs/Hanczyc_and_Szostak_2004_COChemBio.pdf

Replicating vesicles as models of primitive cell growth and
division
Martin M Hanczyc and Jack W Szostak

 

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