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Magnetospheric Consciousness

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Year 2017

From RNA world to RNA-tRNA world to DNA-RNA-protein world: how it went?

I encountered a highly interesting work related to the emergence of RNA world: warmly recommended. For a popular article see this. First some basic terms for the possible reader of the article. There are three key enzymes involved in the process which is believed to lead to a formation of longer RNA sequences able to replicate.

  1. Ribozyme is a piece of RNA acting as catalyst. In RNA world RNA had to serve also as a catalyst. In DNA world proteins took this task but their production requires DNA and transcription-translation machinery.
  2. RNA ligase promotes a fusion of RNA fragments to a longer one in presence of ATP transforming to AMP and diphospate and giving metabolic energy presumably going to the fusion. In TGD fUniverse this would involve generation of an atom (presumably hydrogen) with non-standard value of heff=n×h having smaller binding energy scales so that ATP is needed. These dark bonds would be involved with all bio-catalytic processes.
  3. RNA polymerase promotes a polymerization of RNA from building bricks. It looks to me like a special kind of ligase adding only single nucleotide to an existing sequence. In TGD Universe heff=n×h atoms would be involved as also magnetic flux tubes carrying dark analog of DNA with codons replaced with dark proton triplets.
  4. RNA recombinase promotes RNA strands to exchange pieces of same length. Topologically this corresponds to two reconnections occurring at points defining the ends of piece. In TGD Universe these reconnections would occur for magnetic flux tubes containing dark variant of DNA and induce the chemical processes at the level of chemistry.

Self ligation should take place. RNA strands would serve as ligases for the generation of longer RNA strands. The smallest RNA sequences exhibiting self-ligation activity was found to be 40-nucleotide RNA and shorter than expected. It had lowest efficiency but highest functional flexibility to ligate substrates to itself. R18 - established RNA polymerase model - had highest efficiency and highest selectivity.

What I can say about the results is that they give support for the notion of RNA world.

The work is related to the vision about RNA world proposed to precede DNA-RNA-protein world. Why I found it so interesting is that it relates to on particular TGD inspired glimpse to what happened in primordial biology.

In TGD Universe it is natural to imagine 3 worlds. RNA world, RNA-tRNA world, and DNA-RNA-protein world. For an early rather detailed version of the idea about transition from RNA world to DNA-RNA-proteins world but not realizing the tRNA-RNA world as intermediate step see this.

  1. RNA world would contain only RNA. Protein enzymes would not be present in RNA world and RNA itself should catalyze the processes needed to for polymerization, replication, and recombination of RNA. Ribozymes are the RNA counterparts of enzymes. In the beginning RNA would itself act as ribozymes catalyzing these processes.
  2. One can also try to imagine RNA-tRNA world. The predecessors of tRNA molecules containing just single amino-acid could have catalyzed the fusion of RNA nucleotide to a growing RNA sequence in accordance with the genetic code. Amino-acid sequences would not have been present at this stage since there would be no machinery for their polymerisation.
  3. My own proposal was that transition from RNA world to DNA-RNA-protein world took place as a revolution. Amino-acids of tRNA catalyzing RNA replication stole the place of RNA sequences as end products from RNA replication. The ribosome started to function as a translator of RNA sequences to amino-acid sequences rather than replication of them to RNAs! The roles of protein and RNA changed! Instead of RNA in tRNA the amino-acid in tRNA joined to the sequence! The existing machinery started to produce amino-acid sequences! Servant became the master!

    Presumably the modification of ribosome involved addition of protein parts to ribosome, which led to a quantum critical situation in which the roles of proteins and RNA polymers could change temporarily. When protein production became possible even temporarily, the produced proteins began to modify ribosome further to become even more favorable for the production of proteins.

    But how to produce the RNA sequences? The RNA replication machinery was stolen in the revolution. DNA had to do that via transcription to mRNA! DNA had to emerge before the revolution or at the same time and make possible the production of RNA via transcription of DNA to mRNA. DNA could have emerged during RNA-tRNA era together with reverse transcription of RNA to DNA with RNA sequences defining ribozymes acting as reverse transcriptase. This would have become possible after the emergence of predecessor of cell membrane. After that step DNA sequences and amino-acid sequences would have been able to make the revolution together so that RNA as the master of the world was forced to become a mere servant!

    The really science fictive option would be identification of the reverse transcription as time reversal of transcription. In zero energy ontology (ZEO) this option can be considered at least at the level of dark DNA and RNA providing the template of dynamics for ordinary matter.

How this could be tested? Could for instance ribosome be modified to a state in which RNA is translates to RNA sequences rather than proteins?

See the chapter Evolution in Many-Sheeted Space-Time.

Are we all artists?: or what my "Great Experience" taught me about consciousness

Are all of us artists? I could immediately answer the question: we are artists - all of us. This is what my "Great Experience" taught me about consciousness before I had any theory of consciousness. I started to work systematically with the problem of consciousness - that is to write a book, which is the manner I work - only 10 years after this experience.

What I claim is that the construction of sensory mental images is not a passive process but a creation of an artwork, kind of caricature giving a representation of the sensory input optimal as far as survival is considered. This means decomposition of the sensory input to features and picking up the key features relevant for the survival.

The article with link below is a written and slightly longer version of a talk in which I told about the role of vision in sensory experience seen in the theoretical framework provided by TGD inspired theory of consciousness. I decided to tell about my "Great Experience around 1985 since it divides my life to two parts: life before and after this experience, and because this experience provided fascinating insights to consciousness and perception, not only visual, but also auditory perception and proprioception (body experience). I have told about this experience in my homepage (see this) and in some material in books and articles to be found there (for instance).

There are online books about TGD proper and two published books (Luniver and Bentham). For TGD inspired theory of consciousness and quantum biology see the online books at my homepage and the published book about consciousness and quantum biology (Lambert). The article Philosophy of Adelic Physics published by Springer explains the recent vision about the mathematics forced by consciousness theory.

For details see the chapter Magnetospheric sensory representations or the article Are we all artists?: or what my "Great Experience" taught me about consciousness.

Two steps towards understanding of the origins of life

Two highly interesting findings providing insights about the origins of life have emerged and it is interesting to see how they fit to the TGD inspired vision.

The group led by Thomas Carell has made an important step in the understanding the origins of life (see this). They have identified a mechanism leading to the generation of purines A and G which besides pyrimidines A,T (U) are the basic building bricks of DNA and RNA. The crucial step is to make the solution involved slightly acidic by adding protons. For year later I learned that a variant of Urey-Miller experiment with simulation of shock waves perhaps generated by extraterrestrial impacts using laser pulses generates formamide and this in turn leads to the generation of all 4 RNA bases (see the popular article and article).

These findings represent a fascinating challenge for TGD inspired quantum biology. The proposal is that formamide is the unique amide, which can form stable bound states with dark protons and crucial for the development of life as dark matter-visible matter symbiosis. Pollack effect would generate electron rich exclusions zones and dark protons at magnetic flux tubes. Dark protons would bind stably with unique amine leaving its chemical properties intact. This would lead to the generation of purines and the 4 RNA bases. This would be starting point of life as symbiosis of ordinary matter and dark matter as large heff/h=n phases of ordinary matter generated at quantum criticality induced by say extraterrestrial impacts. The TGD based model for cold fusion and the recent results about superdense phase of hydrogen identifiable in TGD framework as dark proton sequences giving rise to dark nuclear strings provides support for this picture.

There is however a problem: a reductive environment (with ability to donate electrons) is needed in these experiments: it seems that early atmosphere was not reductive. In TGD framework one can imagine two - not mutually exclusive - solutions of the problem. Either life evolved in underground oceans, where oxygen concentration was small or Pollack effect gave rise to negatively charged and thus reductive exclusion zones (EZs) as protons were transferred to dark protons at magnetic flux tubes. The function of UV radiation, catalytic action, and of shock waves would be generation of quantum criticality inducing the creation of EZs making possible dark heff/h=n phases.

For details and background see the article Two steps towards understanding of the origins of life or the chapter Evolution in Many-Sheeted Space-Time.

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