How genes emerge as a new phenomenon
beyond ordinary organic molecules
For us coming to grips with the origins, nature and functioning of genes is a critical step in pursuing a comprehensive understanding and in-depth (not just superficial) redesigning of our mental processes and functions. Because, as discussed earlier, there is a strong and deep interconnection between the origins, nature, evolution and functioning of mental processes and genes. So much so that even the formation and working of highly advanced human mental processes is largely (not wholly) determined and dominated by the genetic process.
Thus the challenge we confront is to invert this relationship, i.e. end the domination of the genetic process and establish the control of redesigned mental processes over the formation and functioning of our physiological and mental existence. We need to do this due to the growing problems that our existing gene-mind relationship is creating for us, both internally and externally, including obstacles in the way of possible further evolution of our mental processes at a qualitative level. But if we are to move in this direction it would inevitably require a deeper understanding of the nature and mechanics of the connection between genes and the phenomenon of our hybrid mental processes.
The first critical step in building this understanding will be to track down the processes that initially gave birth to genes as a new phenomenon in Nature, apart from all energy and matter (inorganic and organic) forms existing prior to it. A phenomenon which became the source of spawning a whole new era in the process of Nature; evolution of stable cellular structures, and ensuing botanical and then biological forms (including us) with corresponding mental processes and capabilities.
We need to realize that in the case of genes we are confronting a form which, unlike nonliving or in other words, ‘non-genetic’ energy and matter forms, cannot merely be explained in terms of known standard laws of physics and chemistry. The reason being that unlike simple atomic and molecular forms here we are looking at a phenomenon which actually becomes a mechanism for producing designed, organized and coordinated chemical and physical processes in living forms. Thus in our opinion, this distinct characteristic and function of genes cannot be reduced to the known laws of physics and chemistry that apply to pre-living forms in Nature. Modern scientists and philosophers have been acknowledging this in their own ways.
To determine the validity of the above proposition would require, in our view, a more comprehensive understanding of the origins and working of genes which will also enable us to understand how and why genes are integrally connected with the origins, evolution and working of mental processes, which, as discussed in this section, can also not be explained in terms of atomic and molecular processes.
We know that the reigning scientific approaches towards the origins, structure and working of genes are focused on understanding them primarily as molecular and atomic mechanisms, made of nucleotide base sequences, which encode templates for the formation and functioning of the biological structure of a life form, including its mental processes. Since mental process is viewed as a part of the biological structure so genes are also implicated, albeit indirectly, in determining mental behavior. Thus in this sense mental functions like different behavior patterns, temperamental traits, perception, cognition, feelings, and other responses, are also thought to arise from the working of a variety of these ‘molecular-cum-atomic’ gene templates. These templates are supposed to be responsible for the formation and functioning of those specialized bio-chemical processes (observed through laboratory tools) of the brain which then go on to produce different mental functions and influence their functioning.
The problem we identify in limiting our understanding of genes to merely molecular and chemical mechanisms indirectly affecting mental processes is that it will not help us in attempting a deeper and more fundamental restructuring of our mental processes. The ability of geneticists and genetic engineers to intervene in mental functions and processes through manipulating genes is roughly at the same level as that of psychiatrists who achieve this through psychoactive drugs. That is not actual ‘engineering’ of mental processes and functions, but only amounts to boosting or inhibiting a particular mental function, which is a superficial and quantitative change.
The issue is that we can tinker with the molecular processes of genes through manipulating the nucleotide base sequences, but when it comes to mental genes (i.e. templates responsible for the formation and functioning of mental process), and mental processes then intervention at this level will not help. For the simple reason that mental processes are not molecular processes. Chemical substances affecting molecular processes in the body can superficially affect the mental state as a whole but will not alter the actual process through which mental processes are produced and function. A process which is possibly guided to a large extent by a non-biological, non-chemical, massless energy process operating within genes. As argued in the forthcoming part of this chapter, it is this non-biological process which actually determined the origins and development of genes as a completely new phenomenon in Nature, distinct from ordinary atomic and molecular forms and processes.
Origins of genes as a new category of species which is a combination of molecular and massless energy processes
We know that before the emergence of ‘genetic molecules’, i.e., DNA and RNA, there were ‘non-genetic’ molecules (inorganic and organic) in Nature. The latter only had properties that reacted to the properties of other atomic or molecular substances, and external conditions such as temperature, light, and electromagnetic fields etc. And in result some formations disintegrated, while new ones emerged in the form of different varieties of atoms, molecules, and also elementary particles, which were released during this process.
At this stage a more complex situation arose when a large number of organic (non-genetic) molecules began interacting and reacting with each other and simultaneously with other inorganic molecules, and then together they also started interacting with pre-existing sub atomic and other elementary particles. This produced a bigger mix of interactions, as a result of which structures of all the interactive states no longer remained rigid and came into a melting pot, leading to all kinds of states and forms, as long as they could stabilize through achieving a state of energy balance. The new states that emerged out of it were in terms of different categories of already existing natural forms or ‘natural species’ like subatomic particles, atoms, inorganic molecules and organic ones.
If we accept the above possible scenario then we are confronted with a conundrum. Whether the ‘molecular machinery of genes’ and the macro ‘genetic molecule’ or DNA constituting this machinery arose out of the already happening reactive interactions between particles, atoms, and molecular forms like nucleotide bases or were a product of a different process altogether. We know from our observations and known facts about atomic and molecular interactions that any new stable states arising out of the reactive process are still in terms of the ‘species’ it starts out with. The reason being they are simpler energy forms, in the sense that their physical and chemical properties purely determine their functions, interactions, and also properties of other products arising out of their interactions and reactions. Moreover, their interactions and reactions are relatively simple and short-lived, wherein they lead to energy imbalances inter se, and simultaneously changes occur giving rise to new stable states belonging to those very four categories.
Now genes on the other hand, we are proposing, are a completely new species beyond complex organic molecules. We arrive at this proposition through logically observing and understanding the existing properties and characteristics of genes as a phenomenon.
The pre-gene species through less time consuming interactions and reactions only produced stable states which continued to remain stable unless their stability was disturbed from some external source. But in genes, despite appearances, we find a large component of internal instability or in other words fluidity. They are a rather peculiar combination of dynamic stability and instability at an internal level. There is an overall stability for a certain period of time, but during their life span there is constant instability, although within the framework of a programme. Thus when we look at this fifth species, we find they have this mixture of constant instability, and yet an overall stability for the whole process, which produces complexities of a completely different order and not merely a compound of what we observe in the first four pre-Darwinian species.
The other most important property of genes, making them completely distinct from organic molecules, is that with their inception a kind of design factory emerges in Nature, which is quite a definite mechanism no longer left to the vagaries of the random process, that characterize the earlier species. None of the earlier four species are known to possess such properties of moving beyond the parameters of the random process to a complex, comprehensive programmed process. That is also why we view them as a bridge between the random and the programmed processes in Nature.
Genes are a phenomenon that has the capability of embodying a distinct design for producing specimens of a particular living specie. A complex design made up of many different and specific templates for making and reproducing specific components and the distinct overall structure of that biological (from unicellular onward) form in all its layers. And also templates for regulating its functioning, and for determining both its life span and the role of different genes in interaction with the products of other genes; i.e., how the actual implementation of the designs contained within different genes will be coordinated. Apart from this they also have the capability to ensure their own survival and reproduction. And thirdly, they have the capability of interacting with the environment through the operation of various programmes based on the templates they provide, which includes interacting with those operations in response to environmental inputs and modifying the templates and consequently programmes during the process of reproduction. These three distinct capabilities make genes a fairly complex and many-layered process in Nature, which cannot merely be classified as complex organic molecules. So we must look at them carefully and see how they must have arisen in Nature.
During the course of evolution after the big bang and before the emergence of genes we find four major categories of species existing in Nature. The first category was of the post big bang variety of both weak and heavy (in terms of mass) elementary particles (including subatomic particles like protons, neutrons and electrons). Then there were atoms which were a separate category. After that we had inorganic molecules, followed by the inception of organic molecules. The genetic molecules, we propose, emerged as a fifth category of species in Nature, which were actually a bridge between pre-Darwinian and Darwinian species and became the core mechanism of the ‘Darwinian Species’.
In our view to produce this fifth category of species the natural net of interactions and reactions would have been cast wider than before to include species other than the four pre-Darwinian ones. Some preexisting species in the pre-big bang phase of Nature. It is a combination of this pre-big bang specie with the four pre-Darwinian species that must have led to more complex interactions and reactions among them in consequence of which much later in the course of natural evolution, a new capability arose i.e., genes.
In our opinion, genes were produced only when complex organic molecules approaching a cellular form, became capable of involving pre-particle mass less energy states in their structures. The chemistry required for the cellular structure came together first, but that was not enough to produce genes and consequently a new stable cellular form. Due to some missing components the molecules (acquiring cellular forms) needed more inputs, which would address this incompleteness and enable them to develop to another state. This necessarily required their going through a process of interconnection and interactions with some other natural forms lacking in the development of that state. At this stage the bundle of organic molecules had become so dynamic due to its multiplying functions and new properties of potential interaction, that it was ready for interconnection of another order. It is then that other states surrounding it became relevant. And space was no barrier to this interaction.
Then as a next step in the random process, this ripe bundle of organic molecules must have randomly come across some lighter pre-chemical and pre-particle massless energy forms, the properties of which happened to be ready for interaction with the new dynamic properties of organic molecules. So they interconnected by virtue of their properties, and then interacted. In this interaction the functions of these two states got integrated, and produced a stable state, which in turn became capable of producing a third state that was more dynamic than its progenitors.
The making of genes and consequently a stable cellular form was thus a product of two qualitatively different dynamics coming in contact and getting integrated. The dynamics of massless energy states was much greater, and also of a different dimension from the organic molecule and other pre-Darwinian species. The latter have the dynamic of mass, weight and corresponding nature and strength of magnetic fields, and the work they do (according to existing concepts in science) is in terms of energy and mass combined. Whereas pre-particle energy states have the dynamics of almost infinite speed, motion, far greater universality, and massless interactivity.
It was dynamics of these two different orders, which also became capable of influencing each other. The bundle of mature organic molecules was able to incorporate the pre-particle energy states into its own existing structure, and the latter after getting incorporated was able to modify the former and produce third states.
If this is correct, it implies that modifications arising out of the interaction of organic molecules with pre-particle massless states of Nature would not have produced changes of a mere chemical nature. Because chemical changes had been happening since atomic states emerged in Nature. And we can see this at all stages of evolution till complex organic molecules. But this new interaction of developed molecules (acquiring a living cellular form) with pre-particle energy forms does not produce any distinct observable chemical changes in later evolution from complex organic molecules to biological forms. That is why the basic organic molecules (which constitute both genes and other cellular formations) whether in shrimps, mice or in humans remain more or less of the same family. Consequently with the emergence and evolution of life forms we witness the same organic molecules acquiring new functions of a nonchemical order, which are undetectable.
The functions of heavy particles, inorganic and organic molecules and changes in their interactions can be observed and identified in chemical and molecular terms. But with the emergence of genes and gene-based life, we find the inception of non-chemical functions in addition to chemical ones, which do not change the chemistry of the form but the capability of that chemistry. This is the beginning of both genes and mental functions/programmes in life forms, which go on to constitute the beginning of the programmed process in Nature.
How the massless energy process in genes is responsible for the making, functioning and evolution of biological programmes and mental processes in living things. We know that genes have design templates for the formation and functioning of both the biophysiological (not only animal but also botanical) processes of a living organism, and also its mental functions and programmes. And the gene-based biological and mental functions/programmes of any living thing are essentially a hybrid of massless (unobservable) and post big bang mass based forms/states (observable through laboratory and mathematical tools). In our opinion, it is due to the presence of this massless component that scientists also find it difficult to fully explain both genetic/biological and mental structures and functions within the existing observation based framework of science.
All our capabilities of observation (sensory and their extensions including all the laboratory instruments and the elaborate mathematical logic) have an understandable difficulty in observing and discovering the logic that governs these pre-big bang massless energy forms, particularly if we try to observe them on their own. Which means we can only understand them when they act in concert with other species having observable mass. Here we need to note that manifestation of the unobservable massless energies in Nature required their interaction with species that had evolved to a state of having observable mass. Their role becomes perceptible only when they interact with later observable ‘mass species’, and not on their own.
In our view the first case in which we can try to understand these massless forms is the genes. Because there we can indirectly observe how their interaction with the bundle of complex organic molecules produces the elementary genetic process, in which the massless part and its interactions are capable of appropriating mass based forms and setting them into programmed motion. The programming function/capability in genes together with the earlier four categories of species constitutes an extremely complex level of operations and interactions, minus randomness. Genes pull in and deal with these random ‘mass species’ from the programmed standpoint and are therefore proactive.
However, the programming or the design process of genes itself does not indicate the involvement of mass based energy processes/functions. And since the primary function of genes is designing and programming so the role of pre-big bang massless forms is dominant and decisive. As the designing and programming capability is based on them. And the nucleotide based sequences in the gene represent the first combinations of the pre and post big bang energy processes, out of which develop ‘genetic sentences’, and the ability of genes to modify their own selves while reproducing.
All hitherto evolution has been nothing more than the modification and redesigning of biological and mental genes. And we suggest that it has been achieved essentially through an interaction of the massless energy forms with the molecular genetic processes, wherein the capability of rewriting different genetic biological and mental templates (responsible for the making and functioning of the mental software) lies with the former. Development and changes in the biological processes and mental hardware (or the brain) and software capabilities, are a consequence of the capability of these massless forms to interact with and manipulate processes at the molecular level resulting in manifest and observable modifications and changes of form.
Of course it is true that the criteria for the selection of a particular modification or addition of genes does come from the concrete problems experienced by the biological form. What we are saying is that before selection, the process of evolution is triggered off by a state of internal dissatisfaction within a form arising out of its growing destabilization while adjusting with its environment. And selection occurs when after going through a process of trial and error the form is able to achieve a stable state based upon a satisfactory adjustment with the environment. In terms of internal mechanics what happens is that dissatisfaction produces a new criterion for the on-going random interaction between a living form’s genetic molecules and the massless energy forms around it to acquire a new balanced state. And this random interaction, triggered by the new criterion, continues until an interface occurs that meets the new criteria of balance. That is when the random interaction between genetic molecules and massless energy processes becomes productive. Otherwise when genes are in a satisfactory state, this random interaction remains unproductive.
The above explained process has been the basic mechanics of the evolution of biological as well as mental genes, and their biological and mental products, in all life forms, beginning from the simplest of organisms to us. However in our case with the inception of developed language and the ensuing period of civilization, and their most significant fallout in the form of highly developed mental processes of man the stage is set for the emergence of a qualitatively new evolutionary process in Nature. Up to now mental processes have been evolving as an adjunct of the biological process, in the context of achieving a balance between biology/physiology and environment, but now they have reached a stage where they can become autonomous and play a primary role in the process of their own further evolution.
i. To be discussed in detail in the next pieces of writing.
ii. A compound of pre-big bang massless magnetic energy forms and post-big bang energy states.
iii. Here we are assuming by necessary implication that genes came into being before the first ‘stable’ living cells evolved in Nature. Although we have suggested earlier that probably cells were born earlier but did not constitute a stable state, and therefore could not survive. Since stable cellular states must have come into being after the emergence of the gene hence we are discounting the cell as a separate category before the coming of genes.
iv. Our proposition that genes cannot be reduced to known laws of physics and chemistry is not something unprecedented. Many scientists have been arguing that the distinct characteristics of genes and life forms cannot be explained within the framework of standard laws of physics and chemistry. Paul Davies, a physicist, cosmologist and Astrobiologist, while discussing the nature of genes and genomes mentions how they could not arise from known laws of physics and chemistry. According to him “… A functional genome is both random and highly specific—properties that seem almost contradictory. It must be random to contain substantial amounts of information, and it must be specific for that information to be biologically relevant. The puzzle we are then faced with is how such a structure came into existence. … Can specific randomness be the guaranteed product of a deterministic, mechanical, law-like process, like a primordial soup left to the mercy of familiar laws of physics and chemistry? No, it couldn’t. No known law of nature could achieve this—a fact of the deepest significance…….” (Davies, 1998, pp. 88-89)
In our view the complex ‘information storage, processing and implementation’ mechanisms in living things operating through genes, which can manage and manipulate chemical and physical processes, clearly go beyond the simple and reactive chemical and physical processes which define and explain all pre-living forms and their interactions. A resonance of what we are saying can be found again in the following words of Paul Davies “... Life opts out of the strictures of chemistry by employing an information control [through the use of genetic code] channel, freeing it to soar above the clod-like blunderings of atomic interactions and create a new, emergent world of autonomous agency… Once this essential point is grasped, the real problem of biogenesis is clear. Since the heady successes of molecular biology, most investigators have sought the secret of life in the physics and chemistry of molecules. But they will look in vain for conventional physics and chemistry to explain life, for that is a classic case of confusing the medium with the message. The secret of life lies, not in its chemical basis, but in the logical and informational rules it exploits. Life succeeds precisely because it evades chemical imperatives.” (Davies, 1998, pp. 211-212).
v. Both protein coding and non-protein coding DNA
vi. A major fallout of accumulating knowledge about the molecular level of genes has been a rapid growth in the field of genetic engineering, wherein the codes embedded in the nucleotide base sequences of genes are deciphered and then tinkered with to achieve modifications, which are otherwise produced through evolution. We are of the view that this whole body of scientific understanding about the working and modification of genes is not only in its infancy but also fundamentally deficient for understanding the formation, functioning and manipulation of even the complex biochemical and physiological mechanisms of living organisms, what to speak of non-molecular and non-atomic mental functions and processes.
vii. It does not change the underlying mechanics through which mental processes are produced and develop.
viii. Things had to go through a stage of imbalance in which they loosened up and then restructured, at the level of a new stable state and not the original one.
ix. We must not reserve the term ‘species’ only for the ‘Darwinian Species’, i.e., living things. All other forms are also species from the standpoint of natural evolution.
x. We are using this term, because so far we do not find any evidence or any suggestion of the existence of any living form based on only one gene. Even the simplest of unicellular organisms need to have a few hundred genes to survive and function. (See link: http://www.sciencedaily.com/releases/1999/12/991213052506.htm). It is hard to visualize genes emerging as single units, i.e. as one gene only, or the simplest unicellular organism based on one gene. If genes as a phenomenon were to be meaningful in terms of handling manifold functions of primordial life forms then they could only have emerged as a complex or package of genes. Incidentally, maybe that is why it is very difficult to physically identify one gene.
xi. Largely known in the fields of Chemistry and Physics.
xii. Of course the programmed process incorporates the random process within it. So the random process does not end with the making of genes.
xiii. As elaborated in the topic ‘Universal Logic Process and Man’ we have divided the macro journey of Nature into three stages and modes of operation—random, programmed and intelligent process stage. So the gene became the bridge between the first and the second stage of Nature.
xiv. It is now a recognized fact that the expression of any gene is regulated by many other genes. So we actually find very elaborate and complex gene networks which coordinate the working of individual genes as well as groups of genes. (See link: http://phys.org/news/2013-07-unraveling-genetic-networks.html)
xv. The responses of cells and organisms to different environmental stimuli are communicated to genes, which then respond accordingly by making the required changes. To explore this further please see the following link: (Retrieved from: http://jonlieffmd.com/blog/networks-of-genes-respond-to-social-experiences)
xvi. If prior to the elementary and subatomic particles there were other species such as strings or quantum states then it only adds to the number of species in Nature before ‘Darwinian species’ come into being.
xvii. When energy had not assumed a particle state as in the post big bang period.