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Genes and Memes
Note: Newest contributions are at the top!
I told already earlier about how the transition from RNA world to RNA-tRNA world to DNA-RNA-protein world might have taken place in TGD Universe. Last night I realized a more detailed mechanism for the last step of the transition relying on the TGD based general model model of bio-catalysis based on heff=n×h phases of ordinary matter at dark magnetic flux tubes. It also became clear that DNA-RNA-tRNA world very probably preceded the transition to the last world in the sequence. Therefore I glue below the appropriately modified earlier posting.
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.
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.
The comments below were inspired by a popular article ("Physicists provide support for retrocausal quantum theory, in which the future influences the past" in Phys.org telling about the preprint ("Is a time symmetric interpretation of quantum theory possible without retrocausality?" of Leifer and Pusey related to the notion of retrocausality (I am grateful to Maria Vihervaara for the link).
Retrocausality means the possibility of causal influences propagating in non-standard time direction. Retrocausality has been also proposed by Cramer as a possible manner to obtain deterministic quantum mechanics and allowing to interpret wave functions as real objects. Bell theorem and Kochen-Specker theorem however pose difficult challenges for this program and the condition that the theory is classical in strong sense (all observables have well-defined values) seems impossible.
The work is interesting from TGD view point for several reasons.
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.
The exciting question is what the superposition of causal orders could mean from the point of view of conscious experience. What seems obvious is that in the superposition of selves with opposite arrows of clock-time there should be no experience about the flow of time in definite direction. Dissipation is associated with the thermodynamical arrow of time. Therefore also the sensory experience about dissipation expected to have unpleasant emotional color should be absent. This brings in mind the reports of meditators about experiences of timelessness. These states are also characterized by words like "bliss" and "enlightenment".
Why I find this aspects so interesting is due to my personal experience for about 32 years ago. I of course know that this kind of personal reminiscences in an article intended to be scientific, is like writing one's own academic death sentence. But I also know I long ago done this so that I have nothing to lose! The priests of the materialistic church will never bother to take seriously anything that I have written so that it does not really matter! This experience - I dared to talk about enlightenment experience - changed my personal life profoundly, and led to the decision to continue work with TGD instead of doing full-day job to make money and keeping TGD as a kind of hobby. The experience also forced to realize that our normal conscious experience is only a dim shadow of what it can be and stimulated the passion to understand consciousness.
In this experience my body went to a kind of light flowing state: liquid is what comes in mind. All unpleasant sensations in body characterizing the everyday life (at least mine!) suddenly disappeared as this phase transition propagated through my body. As a physicist I characterized this as absence of dissipation, and I talked to myself about a state of whole-body consciousness.
There was also the experience about moving in space in cosmic scales and the experience about the presence of realities very different the familiar one. Somehow I saw these different worlds from above, in bird's eye of view. I also experienced what I would call time travel and re-incarnation in some other world.
Decades later I would ask whether my sensory consciousness could have been replaced with that only about my magnetic body only. In the beginning of the experience there was indeed a concrete feeling that my body size had increased with some factor. I even had the feeling the factor was about 137 (inverse of the fine structure constant) but this interpretation was probably forced by my attempt to associate the experience with something familiar to physicist! Although I did all the time my best to understand what I was experiencing, I did not direct my attention to my time experience, and cannot say whether I experienced the presence or absence of time or time flow.
Towards the end of the experience I was clinically unconscious for about day or so. I was however conscious. For instance, I experienced quite concretely how the arrow of time flow started to fluctuate forth and back. I somehow knew that permanent change would mean death and I was fighting to preserve the usual arrow of time. My childhood friend, who certainly did not know much about physics, told about about alternation of the arrow of time during a state that was classified by psychiatrists as an acute psychosis.
See the chapter Topological Quantum Computation in TGD Universe and the article Quantum computations without definite causal structure: TGD view
I encountered a link to a interesting popular article "Causal Witness" Provides First Experimental Evidence Of Indefinite Causal Order (see this). The article tells about an article Experimental verification of an indefinite causal order by Rubio et al (see this). In the following are my first impressions. Probably I mest update impressions. The findings are however so fascinating that I cannot resists the temptation to post them in blog.
1. Indefinite causal order
The abstract of the article Rubio et al might give some idea about what is involved.
Investigating the role of causal order in quantum mechanics has recently revealed that the causal relations of events may not be a priori well-defined in quantum theory. Although this has triggered a growing interest on the theoretical side, creating processes without a causal order is an experimental task. We report the first decisive demonstration of a process with an indefinite causal order. To do this, we quantify how incompatible our setup is with a definite causal order by measuring a "causal witness">. This mathematical object incorporates a series of measurements that are designed to yield a certain outcome only if the process under examination is not consistent with any well-defined causal order. In our experiment, we perform a measurement in a superposition of causal orders—without destroying the coherence—to acquire information both inside and outside of a causally non-ordered process. Using this information, we experimentally determine a causal witness, demonstrating by almost 7 SDs that the experimentally implemented process does not have a definite causal order.
Unfortunately, I do not have prerequisites to say anything interesting about the delicacies of the experiment itself. Since causal order is fixed by that associated with space-time in standard physics, the implications of the experiment could be world view changing.
The key quantum information theoretic notions are causal order, causal separability, quantum wittness, quantum process called SWITCH changing causal order, and superposition of causal orders.
In TGD Zero Energy Ontology (ZEO) replaces ordinary ontology and the arrow of time is not fixed, and it is interesting to see whether superposition of different causal orders related by time inversion T for causal diamond (CD) and SWITCH could be realized in ZEO. The twistor lift of TGD leads to the proposal that CD is accompanied by a Minkowskian generalization of self-dual Kähler form J(CD). Although the moduli space of CDs allows to avoid breaking of Poincare invariance, self-duality of J(CD) leads to violation of T implying that different causal orders correspond to disjoint sectors of "world of classical worlds". This makes possible also superposition of different causal orders and SWITCH would map these sectors to each other.
2. ZEO and discrete symmetries for twistor lift of TGD
Some background about TGD is necessary in order to to proceed.
One can imagine two approaches to the identification of SWITCH operation and superposition of causal orders.
3.1 Option I: Unitary SWITCH as time reversal
The first option corresponds to corresponds to unitary "time travel" option.
Could non-unitary SWITCH be realized as the first state function reduction to the opposite boundary - death of self followed by a re-incarnation as time-reversed self? In this case SWITCH is neither unitary nor deterministic. This SWITCH corresponds to non-unitary "time travel" option in the sense that self identified as passive boundary makes a time travel to the opposite boundary of CD by re-incarnating in non-deterministic manner.
What about the superposition of self and time reversed self as a superposition of causal orders? Schrödinger cat would be more than a catchy metaphor: it would indeed be a superposition of cat and re-incarnated cat! Should one take this seriously?
If the CDs with different arrow of time correspond to different sectors of WCW, different causal orders correspond to states localized in these sectors. A superposition of causal orders would correspond to WCW spinor field having component in both these sectors. If the state function reduction to opposite boundary of CD takes place at the level of entire WCW - or more realistically, for a Cartesian factor of WCW, it must be accompanied by a localization to either sector of WCW in order to avoid paradoxes.
I have already earlier work with TGD inspired ideas related to quantum computation. For more than decade ago I developed rather speculative model topological quantum computation in TGD framework (see this). One speculation about super-effective quantum computations is inspired by the analogy of selves with quantum computations halting, when the self dies and re-incarnates as time reversed self with clock time running in opposite direction at opposite boundary of CD (see this). This would mean using the non-unitary SWITCH realized as state function reduction in quantum computation.
This allows to imagine a series of quantum computations at opposite boundaries proceeding as a sequence of re-incarnations so that the size of CD and thus clock time would grow in opposite directions during subsequent incarnations (see this). Although the re-incarnation as time reversed self could have long life-time, it would not be seen by an observer near the former re-incarnation and the re-re-incarnation would appear at clock-time, which need not be much later than the time of previous death. One could imagine that the time-reversed selves could have very long life-time or that the self could die and re-incarnate very many times without any-one noticing it! The large amount of time spent in time reversed mode could explain the miraculous cognitive feats of mathematicians like Ramajunan and also the magic computational abilities of idiot savants able to factorize large integers without any idea about the notion of prime.
4. Higher level quantum computations and ZEO
From the article of Rubio et al one ends up to an article Quantum computations without definite causal structure by Chiribella et al (see this). The article considers a rather far reaching generalization of quantum computation. Ordinary quantum computation is a time evolution of quantum states followed by a state function reduction. Since the outcome of state function reduction halting the quantum computer program is non-deterministic, the extraction of the result involves statistical averaging over a large enough number of quantum computations to get the outcome, say prime factorization or a period of periodic function.
The notion of classical computation is generalized by Church. The computation need not be a function but can assign function to a function. One can continue this abstraction hierarchy indefinitely and it is realized formally in terms of so called Λ calculus (see this). Could this hierarchy be extended to quantum computations? The quantum computation in question would be kind of super-computation assigning to quantum computation a quantum computation and entire hierarchy of quantum computations.
In TGD this kind of hierarchies emerge naturally. At space-time level there is hierarchy of space-time sheets: space-time sheet is (topologically) condensed to a larger space-time sheet and contains smaller space-time sheets condensed at it. The hierarchy of infinite primes corresponds to an infinite hierarchy of second quantizations and could relate to this hierarchy (see this). In each scale space-time sheets would be particles consisting of smaller particles consisting of ... Even galaxy could be seen as elementary particle in some scale characterizing the galactic space-time sheet.
The analog of quantum computational hierarchy emerges quite concretely in ZEO. The simplest zero energy states have positive and negative energy states with opposite total quantum numbers at the opposite boundaries of CD (intersection of future and past directed light-cones). One can have CDs within CDs. Furthermore, the positive/negative energy states assignable to the boundaries of CD could be also zero energy states associated with smaller CDs near the boundaries of CD. The simplest zero energy states correspond to quantum evolution representing ordinary quantum computation. Higher level zero energy stats would represent time evolution assigning to a quantum computation represented as zero energy state at the boundary of CD a second quantum computation at opposite boundary of CD.
The fermionic representation of quantum Boolean algebra makes this hierarchy quite concrete. At lowest level unitary evolution connects positive and negative energy fermionic states at opposite boundaries of CD and unitary S-matrix characterizes the computation. Higher level computations connect zero energy states assignable to sub-CDs near the boundaries of CD.
See the chapter Topological Quantum Computation in TGD Universe and the article Quantum computations without definite causal structure: TGD view
I was listening a highly interesting talk about viruses in Helsinki by Dr. Matti Jalasvuori, a molecular biologist working in the University of Jyväskylä as a researcher (see this). He has published a book about viruses in finnish titled "Virus. Elämän synnyttäjä, kuoleman kylväjä, ajatusten tartuttaja" (see this).
I learned an extremely interesting new-to-me fact about viruses. They might be far from a mere nuisance, In TGD Universe they could be quantum memes, short pieces of a code of quantum computer code, wandering around and attaching to the existing quantum computer code represented by DNA! Replication of viruses would be replication of memes. If the infected organism survives the virus attack by taming the virus and making it part of its non-coding DNA, it will gain more strength! If my computer survives the updating of the operating system, it works better!
Some basic facts
Viruses are very small, few nanometers is the size scale. Virus contains short pieces of RNA or DNA coding for the virus, in particular the protein shell around it, which virus must have in the "non-living" state outside the host cell to which it can penerate. Inside its host this shell melts and virus attaches to DNA and is able to to replicate. The copies of virus leave the host cell to search for their own host cells.
Usually viruses are regarded as a nuisance. But a new more holistic vision is evolving about viruses and their actual role. Viruses have been present perhaps even before the cell was present in its recent form, they might have been crucial for the emergence of life as we know it and would be also now. The system would consist of various kinds of cells, not necesary those of single organism. The contain several kinds of DNA and RNA: cell nucleus and mitochondria contain their own genomes; there are circular plasmids, and also viruses.
There is a continual exchange of information between cells including viruses as form form of information exchange. In this framework virus represents a meme represented by its DNA ,which does not code for protein shell. This meme wants to replicate and must use the genetic machinery to achieve this. But does virus do this to only replicate and produce more nuisance?
The organism manages to survive the virus attack if it is able to transform the virus so that it cannot replicate. One manner to achieve this would be transformation of the DNA portion due to the attached virus DNA (possible reverse transcribed from the RNA of virus) to a non-coding DNA often referred to as "junk" DNA. Non-coding DNA includes both intragenic regions - introns - and intergenic regions containing for instance promoters and enhancers crucial for the control of gene expression as proteins (see this). Introns are portions of genes, whose contribution to mRNA is sliced away in translation to proteins. The decomposition to introns and translated regions is dynamical, which gives rise to a rich spectrum of different translations of the gene.
In fact, most of non-coding DNA might be due to viruses! The portion of non-coding DNA increases for speciei at higher evolutionary level. For our species it is estimated to be 98 percent! Most of our genome is "junk" as many biologists still would put it. But can this really be the case? On might think that immune system would have invented some mechanism to prevent the infection of DNA by junk DNA? The size of the trash bin cannot be a measure for evolutionary level! It is also known that virus infections force the organism to change and in some cases to become a better surviver. Viruses would drive evolution.
One can speculate that during the very early period in evolution there were only viruses and proto-cells. There is no need for them to be coded by genes. Self-organization can produce cell membrane like structures: soap films represent an example. The DNA fragments could survive inside these proto-cells but according to simulations done by the Jyäskylä group in which Matti Jalasvuori is working, eventually the evolution would lead to the emergence of parasitic DNA strands, which would soon begin to dominate and kill the protocell.
Viruses might solve the problem. Viruses would attract DNA fragments and replicate with themto build a protein wall around the fragment containg also a piece of DNA of proto-cell. Viruses would leave the proto cell before its death and find another protocell. Gradually genome would be formed as viruses would steal pieces of DNA fragments from protocells. One step in the later evolution could be the elimination of the part of virus coding for the protein shell and the use of the rest as protein coding DNA. For eukariotes the transformation to non-coding DNA including intronic and intergenic DNA becomes possible.
Viruses as pieces of quantum computer code?
Computational thinking would suggest that viruses might make possible the emergence of new biological program modules allowing to use existing program modules coding for proteins more effectively. The different slicings of mRNA dropping some pieces away would correspond to different manners to transform DNA sequences to proteins. But what about intragenic portions of DNA: are they just junk?
Could the non-coding DNA and viruses have a much deeper purpose of existence than mere replication? In TGD Universe this kind of purpose is easy to imagine if the system formed by DNA - say intragenic portions of DNA - and nuclear membrane (or cell membrane) system serves as a topological quantum computer. DNA codons would be connected to lipids of the lipid layer of cell nucleus by magnetic flux tubes carrying dark charged particles. These connections could be also to cell membrane and even to cell membranes of other cells.
The braiding of the flux tubes would define the space-time realization of a quantum computer program. This would represent a new expression of DNA and would explain why so small differences between our DNA and that of our cousins give rise to so huge differences. What is important that genetic code would not be terribly important: it is braiding that matters now. The realization as quantum computer programs would give rise to cultural evolution, the realization as proteins to biological evolution. There would be a transition from the level of genes to that of memes.
Viruses would correspond to pieces of quantum computer code - memes. They would be wandering between cells and infecting them to get fused to the DNA. If DNA is able to transform them to introns it gets the code. Otherwise it dies. Infection is the necessary price for achieving meme replication. Living cells could be seen quantum computer programs updating them continually. Sounds somehow familiar!
See the chapters DNA as topological quantum computer, Three new physics realizations of the genetic code and the role of dark matter in bio-systems, and More Precise TGD Based View about Quantum Biology and Prebiotic Evolution.
The popular article Mars Mystery: How Was Ancient Red Planet Warm Enough for Liquid Water? tells about a mystery related to the ancient presence of water at the surface of Mars. It is now known that the surface of Mars was once covered with rivers, streams, ponds, lakes and perhaps even seas and oceans. This forces to consider the possibility there was once also life in Mars and might be still. There is however a problem. The atmosphere probably contained hundreds of times less carbon dioxide than needed to keep it warm enought for liquid water to last. There are how these signature of flowing water there. Here is one more mystery to resolve.
I proposed around 2014 TGD version of Expanding Earth Hypothesis stating that Earth has experienced a geologically fast expansion period in its past. The radius of the Earth's space-time sheet would have increased by a factor of two from its earlier value. Either p-adic length scale or heff/h=n for the space-time sheet of Earth or both would have increased by factor 2.
This violent event led to the burst of underground seas of Earth to the surface with the consequence that the rather highly developed lifeforms evolved in these reservoirs shielded from cosmic rays and UV radiation burst to the surface: the outcome was what is known as Cambrian explosion. This apparent popping of advanced lifeforms out of nowhere explains why the earlier less developed forms of these complex organisms have not been found as fossile. I have discussed the model for how life could have evolved in underground water reservoirs here.
The geologically fast weakening of the gravitational force by factor 1/4 at surface explains the emergence of gigantic life forms like sauri and even ciant crabs. Continents were formed: before this the crust was like the surface of Mars now. The original motivation of EEH indeed was that the observation that the continents of recent Earth seem to fit nicely together if the radius were smaller by factor 1/2. This is just a step further than Wegener went at his time. The model explains many other difficult to understand facts and forces to give up the Snowball Earth model. The recent view about Earth before Cambrian Explosion is very different from that provided by EEH. The period of rotation of Earth was 4 times shorter than now - 6 hours - and this would be visible of physiology of organisms of that time. Whether it could have left remnants to the physiology and behavior of recently living organisms is an interesting question.
What about Mars? Mars now is very similar to Earth before expansion. The radius is one half of Earth now and therefore same as the radius of Earth before the Cambrian Explosion! Mars is near Earth so that its distance from Sun is not very different. Could also recent Mars contain complex life forms in water reservoirs in its interior. Could Mother Mars (or perhaps Martina, if the red planet is not the masculine warrior but pregnant mother) give rise to their birth? The water that has appeared at the surface of Mars could have been a temporarily leakage. An interesting question is whether the appearance of water might correspond to the same event that increased the radius of Earth by factor two.
Magnetism is important for life in TGD based quantum biology. A possible problem is posed by the very weak recent value of the magnetic field of Mars. The value of the dark magnetic field Bend of Earth deduced from the findings of Blackman about effects of ELF em fields on vertebrate brain has strength, which is 2/5 of the nominal value of BE. Hence the dark MBs of living organisms perhaps integrating to dark MB of Earth seem to be entities distinct from MB of Earth. Could also Mars have dark magnetic fields?
Schumann resonances might be important for collective aspects of consciousness. In the simplest model for Schumann resonances the frequencies are determined solely by the radius of Mars and would be 2 times those in Earth now. The frequency of the lowest Schumann resonance would be 15.6 Hz.
For background see the chapters Expanding Earth Model and Pre-Cambrian Evolution of Continents, Climate, and Life and More Precise TGD Based View about Quantum Biology and Prebiotic Evolution of "Genes and Memes" .