Genome, connectome, cognitome, existom: brain mechanisms of the subjective world and nanopsychology.

Genome, connectome, cognitome, existom: brain mechanisms of the subjective world and nanopsychology.

Ramil Garifullin -   an associate professor at KFU, Candidate of Psychological Sciences, author and founder of the theory of existom and nanopsychology.

The most primary form of motion of matter is physical. Then there is chemical, biological, physiological, neurobiological, neurophysiological, neural network, hypernetwork and, finally, subjective or mental. Consequently, at the higher stages of the movement of matter towards its complication, a certain qualitative leap occurs and the inner subjective mental world of a person appears.

The analysis shows that there is a connection between all the above stages of the development of matter. At each stage of the development of matter, there are key elements that define their own qualitative and self-sufficient scientific casuistry. The physicist talks about electrons, nuclei, nucleons, quarks, and various elementary particles, of which there are a lot now discovered. There is a system of elementary particles. Elementary particles grouping and interacting with each other according to the laws of physics, form nuclei, atoms, molecules, cells, organs, organisms, brains, neural networks, etc. But can we say that these elementary particles are the key basis for the change and development of our subjective world, thoughts, ideas, etc.? We cannot, since the dynamics and development of the subjective world of man is subject to its qualitatively different casuistry and laws of our inner world and brain, although the material framework of these processes are elementary particles and other more complex elements in the hierarchy of the motion of matter.

So, the very first form of physical motion of matter is a system of elementary particles. Then an elementary chemical system of atoms is built over it – this is the periodic system of Mendeleev. Thanks to the periodic system of Mendeleev, different substances arise, since atoms combine with each other to form different substances and organic chemistry appears, in which biochemistry is born. And thanks to biochemistry, the biological form of matter movement is developing. And in the biological form of the motion of matter, what elementary system takes place? This is a genetic system – the genome, which contains all the information about the body. The genome is a kind of book that is read with the help of certain macromolecules and on the basis of such reading, proteins of different types are formed for various components of our the body. Studies have shown that the genome contains most of the genes on the basis of which the brain is formed.

Thus, the most primary physical "genome" of matter is a system of elementary particles. Then comes the chemical "genome" - the elementary Mendeleev system with its own system of chemical elements. Biochemistry also has its own biochemical "genomes" And, finally, there is a real biological genome – an elementary genetic system. The biological genome is stored grouped in a DNA strand located in the cell nucleus. The rest of the "genomes" of matter, such as physical, chemical and biochemical, do not have such a specific localization. For example, there is no such place for a chemical "genome" where the periodic system of Mendeleev would be stored, from which various inorganic or organic substances would be automatically born, as is the case with a real biological genome in a living cell. Also, there is no place where the physical genome of elementary particles is stored, in which atoms would be automatically synthesized. Despite the fact that there are no such places and there is a scattering of physical, chemical, and biochemical "genomes" throughout space, matter still manages in the process of its development to generate atoms, molecules, macromolecules, proteins, etc. Only at the highest stage of its development does matter form zones in itself where biological genome. Such zones are automatic systems called living cells. The proportion of these zones in Nature and in the universe is significantly less than the zones in which physical, chemical and biochemical "genomes" are scattered

Thus, it is possible to put forward a hypothesis about the creation of compact, unified, universal, automatic synthesizing reactors or systems operating on physical, chemical and biochemical "genomes" that would synthesize various atoms, molecules and substances with predetermined properties, as a cell synthesizes based on the biological genome.

Let us continue moving towards higher forms of the motion of matter.

A neurobiological and neurophysiological system is being built over the biological system of the motion of matter. There is an elementary system of neurons. This is an elementary system of neurons, from which various brain structures, groups of neurons, and functional brain systems are formed. In particular, in the system of neurons there are the structures on the basis of which cognitom neurons arise, thanks to which the process of cognition is possible. Consequently, based on the analogy with the genome, the idea arises of the existom of a single set of cognitom neurons containing the memory of a set of cognitom abilities. That is, the idea of the existom of a cognitom "genome" arises. Such a "genome" is currently called a cognitome [1]. This idea of cognitome was formulated by foreign authors.

Thus, it is assumed that there is a key group of cognitom neurons responsible for the innate behavioral and cognitom inclinations of a person formed during the evolution of mankind. In the process of constant replication and generation of repetitions of various biological structures, on the basis of Darwin's law, a more surviving biological structure is formed, containing a more optimal neurobiological cognitom structure, as a set of cognitom abilities – a cognitome [1]. K. also spoke about innate mental programs .Jung, calling them archetypes as some kind of unconscious collective images.

In fact, a cognitome is an elementary system of neurons, similar to the genome or the elementary Mendeleev system. Is it the basis for the formation of the process of thinking, subjective feelings, the subjective world? This is a very difficult question.

Therefore, our main task is to understand how the system called cognitome develops.

Let's try to draw an analogy with the genome. DNA is a kind of book that specialized molecular machines and macromolecules read. As a result, the translation of the read is performed, thanks to which protein synthesis occurs. As a result, various types of protein are synthesized, forming various biological structures, and mainly the brain, neurons and neural networks.

Cognitome is a higher–standing mechanism for generating a biological system that is built over the genome. Consequently, the question arises as to how elementary systems of neurons generate a subjective sensation or a subjective world in themselves?

There is still a big gap between the subjective world and the elementary system of neurons - the cognitome. Experimentally the existom of a cognitome, as is the case with the genome, has not been proven. Have researchers reached the neurobiological and molecular mechanisms of human cognitom processes? How, thanks to these mechanisms, does the thinking process take place? How do subjective sensation and subjective world arise?.

Only the existom of a connectome has been really proven. Now, thanks to optogenetics and the development of other experimental methods, it is possible to study how the neurons of our brain interact and activate. It is possible to map groups of neurons and functional systems of neurons in the process of thinking, perception, etc. Maps of the neural activity of real brain neural networks are being created. With the help of artificial intelligence, this is mathematically processed. Then a bank of connectomes is created. But is the cognit a particular variant of the connectome?

Cognitome is associated with more specialized groups and functional systems of neurons that are responsible for cognitom processes [ 1 ] . And the connectome is a broader group of neurons that absorb not only cognitom processes.

If we analyze what our brain cognition system has come to, connected with an elementary system of neurons, then the connectome and cognit turn out to be just a kind of bank and nothing more. Connectome is an inexhaustible "barrel" of activities of groups and functional systems of neurons. The connectome as a bank of information about the activity of neurons is growing all the time. Now the brain connectome allows you to determine the object of visual perception. Consequently, researchers have only learned to detect a huge number of active elements of the brain, but at the same time, they have not discovered or uncovered the mechanisms and structures on the basis of which this activity takes place.

We know how various proteins are formed from the genome, but we do not know how some mental content arises from the connectome and cognitome. Cognitom exists only as a term and an idea because concrete experimentally confirmed cognitom mechanisms do not follow from it yet. So far, at best, this is a hypothetical theory Hegel's "bad spiral". The cognitome hypernet can't grow indefinitely!

The usefulness of this theory is still lacking among scientists. Understanding cognitome as a set of cognitom experiences recorded in neural and hypernetwork structures does not yet follow how thinking appears. Therefore, two questions arise:

1. Thanks to what intermediate tool can the neurocognitom system penetrate into the cognitome and select from it the content elements useful for the formation of the cognitom process?

2. How should the cognitome function so that it becomes the basis of the process of thinking or the birth of thought?

It is known that we do not ourselves "fit" thoughts or ideas that come to us unconsciously or superconsciously. Something stored in the cognitome somehow becomes a real component of our subjective world and sensations. Consequently, the usefulness of the theory of cognition will grow as experimental confirmations and applied use of this theory to solve mental health problems. The best practice and implementation in brain science is primarily the solution of problems of mental disorders and correction of brain activity.

Currently, we can influence brain activity either by psychological methods or by psychochemical methods. Therefore, a practical psychologist is a programmer of the psyche who programs the brain and changes the processes in it. It will always be in the life of mankind!

There is a gene thanks to which a person has more developed language skills. At the same time, it should be noted that now there is a perverse process of subjectivization of the genome. Often the genome turns into a kind of "supreme", which determines the foundations of a person, his mental world. If the gene responsible for language cognition is underdeveloped, then as a result, the child lacks the ability to learn languages. It is clear that this is not a completely correct study. Most likely, this study concerns the problems of underdevelopment of speech, and not the ability to learn languages. Apparently, this anomaly is wider and not only speech. It is not necessary to assume that if the gene responsible for the development of it represents a complex and well-coordinated work of a group of neurons and functional systems of neurons.

It must be recognized that the theory of cognitome turned out to be unproductive for various reasons. This theory does not work well enough, and therefore I have made an attempt, on the one hand, to identify the reasons for the unproductivity of the theory of cognition, and on the other, to propose some kind of correction of this theory. Thus, the theory of the existome arose. In fact, I have developed the concept of the existome, that is, the concept of the cognitom "genome" of the brain, consisting of a set of existoms as key semantic structures. It is from this set of key semantic structures - existoms, that a gigantic variety of secondary meanings is generated, on the basis of which the subjective and becoming world of a person, his becoming consciousness develops. Let me remind you that in the previous theory of the cognitome, the contents of the cognitome were kogi. It was precisely from the totality of the cog, as components of cognitom experience fixed in the brain, that the cognitome consisted [ 1 ].

The research I have done has shown [2, 3, 4, 8], that the result of cognitom experience in the end is always the formation of a certain final convolution of experience into the form of a certain brain structure, the correlate of which in the space of the subjective world is meaning, as a component of the semantic structure of a person. It is not cognitom experience as such that is fixed due to the plasticity of the brain, but only such an experience that has matured to the ability to convolve in the form of a key meaning - an exist, which subsequently becomes one of the components of the existome, as a set of various existoms. It is not cognitom experience that manifests itself in the connectome of the brain, but existoms. Not every cognitom experience becomes the content of an existom, but only one that matures to the level of an existom, that is, to the ability to convolution.

It is thanks to the key meanings that there are corresponding key codes and information that can fundamentally chang a changing world. The study of the mechanisms of the activity of existential operators of variability will allow in the future to predict the transformation of mental content, that is, the content of the subjective world of man. All these possibilities were absent in the concept of cognitome.

The connectome as a kind of surface registration of the activity system of groups of neurons and functional systems of neurons requires separate mathematical processing in order to isolate and filter structures from the connectome that are the basis for the formation of an exist.

For a reason, E. Husserl argued that there is a gap of meaning between reality and consciousness. And the gap between the structures of the brain and the subjective world of man is also a gap of meaning. And these meanings need to be deeply explored both at the level of the brain, that is, at the level of existoms, and at the level of the subjective world of man. As a result, this bridge between the brain and the subjective world of man will be built on the basis of intermediate matter as a result of the synthesis of existoms of the brain and semantic structures of the subjective world of man.

The mechanisms of memory plasticity processes caused by the self-assembly of conformational structures of brain proteins and more complex molecular machines of the brain once again confirm the molecular nature of the processes of convolution of cognitom experience to the existential level. We have shown that it is much more productive to consider cognitom processes of the brain at the level of networks of molecular machines and molecular systems, rather than at the level of neural networks. It is best to develop this direction thanks to the nanopsychological approach developed by us within the framework of a new direction that we have substantiated - nanopsychology, as a science that studies correlations between controlled molecular processes of the brain and mental processes in the "here and now" mode [5,6,7, 13 ]. This becomes possible thanks to the introduction of externally controlled artificial nanoparticles into the brain [5,6,7, 13 ]. The introduction of controlled nanoparticles into the brain in order to activate specialized neurons or specialized groups of neurons responsible for holistic perception or mental mental processes in it may become promising for restoring lost mental functions [6]. Therefore, nanopsychology, as a new science, has many prospects.

For a reason, E. Husserl argued that there is a gap of meaning between reality and consciousness. And the gap between the structures of the brain and the subjective

the human world is also an abyss of meaning. And these meanings need to be deeply explored both at the level of the brain, that is, at the level of existoms, and at the level of the subjective world of man. As a result, this bridge between the brain and the subjective world of man will be built on the basis of intermediate matter as a result of the synthesis of existoms of the brain and semantic structures of the subjective world of man.

It is the existom with its specialized hypernetwork and unique system of neurons, as well as the functional system of neurons, that is the neurobiological and molecular-machine basis of the phenomenon of secondary reflection of primary reflected information - the phenomenon of reflection, thanks to which conscious beings arise, having their subjective and semantic relation not only to the world, but also to themselves [ 11, 12, 13 ] .And this is no less relevant compared to the knowledge of our unique genome. In essence, I have created an existential hypernetwork molecular machine model of the emergence of a person's semantic attitude not only to what is outside of him, but also to himself. On the one hand, the study of existoms will come infinitely close to our meanings, and on the other hand, our meanings will come close to existoms. And at the point of singularity, they will converge. This will be the bridge between our subjective world and the brain.

The author has developed the theory of holonomic existom as a theory of brain generation of subjective reality. This theory, in comparison with other variants of the holonomic theory of the brain, came closest to solving the problem of throwing interphase and boundary "bridges" between the brain and subjective reality. The article proposes a theoretical model that includes the basic structures and mechanisms of generating subjective reality.  The analytical studies presented by the author have shown that various contents and neoplasms of subjective reality arise on the basis of borderline-critical interphase proto-formations. These proto-formations of various levels of complexity are products of the interaction of intentional wave flows with the corresponding structures of the holonomic existome of various levels of complexity. It is shown that the dynamic alternation and combination of these resulting proto-formations is the main mechanism of brain emergence, due to which a virtual fabric of various contents of subjective reality arises.  In conclusion, we present the basic concepts corresponding to the structures of the generation of subjective reality: exist, existom, intention and virtuon.  Existences are multi-layered biodifractive structures-codes, on the basis of which patterns of interference of a standing wave are formed - virtuons corresponding to innate meanings and concepts formed in the process of ontogenesis. Holonomic existences are connected to each other, but they are scattered in the cerebral cortex.  An existom is an integral set of many existences, obeying the principle of holonomy (holography), according to which each exist retains all the integral information stored in the entire existom.  An intention is a group of brain structures (thalamus, hippocampus, fusiform gyrus, etc.) that generates intentional wave flows directed at the brain's existome. An intention is a set of emitters of wave intentional flows scattered in the cerebral cortex and associated with the hippocampus, thalamus, fusiform gyrus, etc. Intention is most likely controlled by a program of neural networks of the brain or intentional cognition, that is, intentional hyper networks of the brain.  A virtuon is a wave interfacial emergent neoplasm or hologram that arises as a product of the interaction of wave flows of the intention with the corresponding structures of the holonomic existome. In addition, virtuons are products of standing waves of varying dynamics, shape, size, phase and frequency.  Due to the holonomy of the existome, psychic contents are preserved even after the destruction of a significant part of the existome.  The existom resonates when it is exposed to intentional wave flows radiated by the brain's intention. (The brain intention is a group of brain structures (thalamus, hippocampus, fusiform gyrus, etc.) that generates intentional wave flows directed at the brain's existome).  It is the resonant properties of the existome that are associated with the rapid cause of the high dynamism of mental processes, including the processes of recognition. Despite the fact that wave flows irradiate a large number of other structures, only selected structures selectively resonate. For example, when intentional wave flows of intention are exposed to linguistic existences, a linguistic mental tissue is generated, like inner speech, which is thinking. At this time, other non-linguistic fragments of existences do not resonate.  Therefore, there is no need for the existence of certain "wormholes" in neural networks and hyper networks (see the theory of cognition), which allegedly shorten the intervals of mental processes, in particular, the dynamics of recognition processes.  Thus, the dynamism and speed of mental processes is due to the resonance of the existome and the filigree operational activity of the intention, which directs intentional wave flows to the existome. The process of recognition is the process of the appearance of a virtual wave formation - a virtuon caused by the resonant interaction of the existome and the intention.  In addition, the existom, being an innate product of human evolutionary development, is a kind of analogue of the mental "genome", which contains the main innate concepts, thanks to which a variety of cognitive and semantic spaces of various depths is formed. These formations are generated due to the filigree interaction of intention and existom, which generates virtuones, as interphase emergent proto-formations, which are the basis for the emergence of subjective reality contents.  Intention is able to direct intentional wave flows to various levels of the multilayer structure of holonomic existomes and existences, irradiation of which by intention leads to the formation of various levels of integral holonomic structures corresponding to the simplest and most complex images, meanings, concepts (generalizations), abstract categories of science.  In fact, the existom, resonating with the wave flows of the intention, generates a kind of wave virtual formation of the virtuon, as an interphase-emergent basis of various mental contents. These contents are unambiguous correlates of sensory images, thoughts, meanings, etc. In essence, virtuons are some kind of standing waves of varying dynamics, shape, size, phase and frequency. These virtuons, formed on the basis of the principles of holonomy (holography) and wave processes, are apparently well described in the framework of Fourier transforms. There is a possibility that the localization of virtuons is associated with the zone of interneuronal spaces, thin-fiber dendritic networks of the brain, other dendritic networks, small local neural networks that create appropriate localized holograms, etc.  It is in these zones that there is a high probability of detecting interneuronal wave structures. The connection of these wave processes with processes in various synapses is an urgent task for further research.  Intention, working at various levels of physicality, the bodily Self, and, finally, the phenomenon of the Self, is the main mechanism for the emergence of the stream of consciousness. The stream of consciousness is not a simple superimposition of static slices of consciousness as in the cinema, but the superimposition of living slices of consciousness.When an intention is applied to a specific fragment of existence, living slices of consciousness arise. Further, the intention directs its wave flows to another fragment of the exist, etc. The jumping of the intention from one layer of the exist to another is one of the mechanisms of generalization and generation of concepts.  Thus, the dynamic alternation and combination of the resulting proto-formations of virtuons is the main mechanism of brain emergence, thanks to which a virtual fabric of various contents of subjective reality arises.  The study of the correlation between the structure of language and the structure of the interaction of existom and intention is one of the most urgent tasks of research in the field of mechanisms for generating subjective reality.  At the beginning of its development, the intention masters the processes of the phenomenon of corporeality and the bodily Self. Based on this, the intention forms a virtuon of self-relationship.  The nanopsychological approach, developed by me in 2006, can be a correct and unambiguous method of studying the above wave processes [ ]. It allows you to study mental processes and corresponding operator-controlled nanostructural transformations of the brain in real time. Controlled nanostructures can be introduced into the interneuronal zone and zones of probable localization of ions. Therefore, in the future, nanopsychology will allow you to control and regulate the processes of the emergence of virtuons and mental formations (sensory images, thoughts, meanings, etc.) This approach can be one of the ways to solve the problems of various mental disorders. Nanocontrol can make it possible to adjust the structures of the existome at various levels. In other words, brain correction of various levels and structures of the cognitive process, processes of thinking and consciousness will be possible.  Previously, it was noted that due to the holonomy of the existome, the possibility of reproducing virtuons and their corresponding mental contents remains even after the destruction of a significant part of the existences of the existome.  That is why, in our opinion, solving the problem of Alzheimer's disease is not related to erasing information. The information is preserved and the existence is most likely not violated. The cerebral cortex stores everything well, thanks to its holonomy. The cause of Alzheimer's disease lies in dysfunctions of the activity of the intention (thalamus, hippocampus, fusiform gyrus, etc.), therefore, measures are needed to restore the normal activity of the intention. The stored information of people suffering from Alzheimer's disease is waiting for its moment when the intention correctly "highlights" the existence and this information becomes a fact and content of consciousness.

Our Self is our unique existom!

1. Anokhin K.V. Cognition : algorithmic theory of higher brain functions,

Collection of abstracts of the XXIV Congress of the I. P. Pavlov Physiological Society. St. Petersburg, 2023. p. 7.

2. Garifullin R.R. Illusionism of personality as a new philosophical and psychological concept (monograph) Yoshkar-Ola: Mari polygraph. published. combine, 1997. - 400s.

3. Garifullin R.R. Encoding personality from alcohol and drug addiction. Manipulations in psychotherapy (monograph). Rostov-on-Don: Phoenix, 2004. 256 p.

4. Garifullin R.R. Psychocorrection of semantic structures of a drug-addicted personality. Abstract of the dissertation, Kazan, 2000, - 26 p.

5. Garifullin R.R. Nanopsychology as a new science. Nanophilosophy as a new worldview. // Man in the face of a global challenge/ Philosophical Society of Tatarstan.- Kazan, 2006. - pp. 101-106.

6. Garifullin R.R. Nanopsychology as a new foundation of cognitive science //Actual problems of modern cognitive sciences: Materials of the seventh All-Russian scientific and practical conference with international participation.- Ivanovo, 2014. - pp. 23-24.

7. Garifullin R.R. Nanopsychology as a new science. Nanophilosophy as a new worldview// http://psyfactor.org/lib/nanopsychology2.htm

8. Garifullin R.R. Fundamentals of postmodern psychology.- Kazan: IPK "Brig", 2015. 196 p.

9. Garifullin R.R. Nanopsychology as a new science // Natural Phenomena and human ecology: Proceedings and materials of the Fifth International Symposium.- 2008, pp.134-140.

10 .Garifullin R.R.(2018) Postmodern psychology of personality. Revista de Ciencias Humanas y Sociales, Opcion, Ano 34, Especial №14. 380-393

11. Garifullin R.R. Me and proto-Me. Philosophical and psychological foundations of reflection. Monograph — Kazan, 2019: https://psyfactor.org/lib/garifullin-kniga-kogito.htm

12. Garifullin R.R. I and proto-I. Philosophical and psychological foundations of reflection. Monograph. — Kazan: IPK "Brig", 2019.: https://psyfactor.org/lib/garifullin-i-and-proto-i.htm

13. Ramil Garifullin. About the Nanotechnological Approach to The Brain. International Journal of Biomed Research. 2023. 2(4): DOI:10.31579/2834-8087/025: https://clinicsearchonline.org/search?keyword=About+the+Nanotechnological+Approach+to+The+Brain

Associate Professor of the Institute of Psychology and Education of KFU, Candidate of Psychological Sciences Ramil Garifullin


see the course of video lectures (about 100) by R. R. Garifullin : "Cognition and existence : the brain and the subjective world, connection and validity, methodology, nanopsychology"| R. R. Garifullin : https://youtube.com/playlist?list=PLysfHhfkukULa41nz16Xg9EqJY8qXqzi1&si=aZr14jtWUbDRnylQ

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