Natural Systems Theory

by Hugh M. Lewis

http://www.lewismicropublishing.com/

Chapter Twelve

Genetic Information Reproduction Systems

            DNA constitutes a kind of language system encoding the traits of living organisms. The basic word unit in DNA language is the three-polypeptide codon sequence. The basic alphabetic unit is the polypeptide, of which there are four for DNA and four for RNA. We have a possible number of 64 combinations of three-base codons (3⁴) based upon four alternative polypeptides occurring at each point. It is found that these codons encode for a total of twenty-one alternative amino acids, which constitute a kind of periodic table of living systems, and are in turn the building blocks of all known living tissue, based upon the construction of folded protein macro-molecules that may consist of hundreds or thousands of amino acids linked together in long chains.

DNA language is a kind of natural computer program that encodes the basic information for the construction and reproduction of all living forms, in terms of the cells that constitute these organisms. As a formal language system, DNA must have a kind of grammar that determines what sequences are meaningful and what are not. Not all sequences or possible combinations of sequences can be meaningful, and it is apparent that DNA sequences, as linear strands of sequentially arranged code, encompass a greater variety of possible combinations than are actually used by any given cell. If we were to formally describe genetic sequencing and DNA coding as a kind of computational language, we can describe various patterns of concatenation, or addition, of basic genetic units into different strings of alternate variable lengths.

It is apparent that nature is capable of rewriting the program, of changing the code, to produce a wide variety of living forms. This rewriting is construed as mostly gradual and cumulative. There is also apparent a process of the gradual accumulation of DNA code--the lengthening and increase in dimensional complexity of DNA programs that govern living systems.

In this chapter, an effort is made to comprehend DNA as a system of information and energy control that governs living systems, as working, successful biochemical machines with their own sense of biological mechanics and dynamics. We can see all of evolution of life from the standpoint of replicating DNA punctuated by periods of protein synthesis which eventually makes possible a renewed round of replication. The same DNA has been reproducing itself from the first moments of the beginning of living systems on earth, and though individual cells, organisms, species and entire taxa have come and gone, the process of DNA replication and its evolution has continued incessantly. What has been evolving is DNA--the selection of living systems for replication is entirely the outcome of this process of DNA evolution. In such a manner, life has explored the possibilities of its adaptation, and often, counteradaptation to other living systems, in its many varied environments on earth.

DNA that is replicated within cells is complete as an information reproducing system. We cannot separate a strand of it from the cell and have the cell continue to function in a normal way. DNA formed a system of replication and protein synthesis from the beginning, within the context of the cell.

Evolutionary development of DNA is one-way and irreversible. Point-mutations of DNA may be repaired or mutated back, but the patterns of changing DNA created by multiple mutations over time cannot be undone. Most, the vast majority, of such mutations are probably deleterious and result in negative selection, but it seems that a few succeed and result in the formation of new species and eventually, of entirely new taxa in the classification systems of life. Probably for each surviving species on earth, there have been a thousand extinct species that represented in a sense failed genetic experiments. They were not failed so much as made obsolete by changing counteradaptational environments. The greater the environmental change, the greater the "failure rate."

            Living systems thus cannot simply "back-up" and take an alternate direction of development. DNA change is largely a one-way process, but cul-de-sacs on the roadmap of evolution can result in the extinction, or loss, of an entire line of evolutionary development. While living systems are fated to be on a one-way trajectory, the direction can shift and change, and at any one time a population of organisms probably comprises enough genetic variability to allow multiple directions of development to be open at any one point in time. Furthermore, it appears that some evolutionary lines lie closer to the stem or trunk of the tree of evolution than others--they have not changed much over the eras and eons of the development of life, and thus it appears that life can always reemerge, to remake itself in some new form, from the trunk.

            There is probably some complex kind of correlation between the amount and variety of DNA found in a cell and the length of the evolutionary lineage that had been necessary to make that cell and its DNA complement. Associated with this is probably the organismic sophistication of the mitotic cellular tissue structures associated with that cell in terms of the number and kinds of differentiated cells, or the cell-map of that cell. The cell map in fact embodies and seems to replicate the entire branch of the evolutionary tree represented by that line ("Ontogeny recapitulates Phylogeny").

            We might suggest that more specialized these cellular structures become, the more environmentally dependent and "rigid" they become, and the more susceptible to eventual extinction. The exception to this appears to be the rise of "generalizing" forms that are not marked by environmental specializations so much as accumulated generalizing features that allow them to adaptively succeed in very broad ranging environmental habitats.

            All selection in nature is in fact negative selection. Positive selection is whatever is leftover, what survives, what remains, once negative selection has occurred. Selection regimes can be severe, as much as ninety percent or more, and this can rapidly drive evolutionary development.

            Evolutionary development is not just irreversible and one-way, but it is continuously divergent from the main stock of the tree or its main limbs. Continuous divergence, even within a single population, is rooted in the complexity of the DNA code for living systems, and in the super-complexity of its phenotypic outcomes. The main "goal" of DNA is to make copies of itself--and in a simple sense this copying is simple binary fissioning. One makes two, two makes four, four makes eight, eight makes sixteen, and so for.

            The further on this process becomes, the greater the divergence possible, but also the increasing amount of negative selection comes to play upon the diverging populations. Large populations of any organism tends to the Malthusian dilemma of increasing environmental circumscription, ultimately resulting in environmental degradation in terms of critical limiting factors, resulting in reduced carrying-capacities and thus increasing the negative selection regime. Any species or population can be seen to go through cycles of growth and population loss, of increasing negative selection and then successful counter-adaptation. That species cannot control their own population growth is natural and normal--given the appropriate enriched circumstances, any population of organism will increase in size at its maximum rate of reproduction. DNA replication is in this way blind and inexorable.All DNA is blind environmentally in the sense that it cannot foresee the consequences or eventual outcomes of its own developmental trajectory or in the unforeseeable exogenous change factors that may alter the demands for survival. Continual divergence, and an increase in the complexity of DNA encoding pattern, ensures survival against unforeseen possibilities, and we must think that there has been in the long run a selection towards greater complexity of DNA codification, which results in increasingly wide divergence of multiple parallel lines.

            It is critical in this regard to always see that DNA and its cellular structures have always been dependent upon suitable metabiotic environmental conditions for their development. Living systems do not occur in isolation, but there is a feedback process with the environment itself that is the source of energy and other critical resources. It is in long term adaptation to changing environmental conditions that life changes and survives and in the long run grows more complicated as systems. Living systems interact with the environment, and the changes that take place occur in both directions.

            As blind as DNA may be as a system, it is nevertheless a natural system of non-human intelligence that is capable of reading its environment and adapting to changes in the environment in a cybernetic sense, sans the neural apparatus, necessarily, that we associate with cybernetic systems that have been especially anthropomorphized. In other words, DNA is a kind of information processing system that is capable of adjusting itself in complex feedback cycles with its environment, tracking environmental changes, and even affecting and changing its environment. Its success is warranted by its 4 billion year track record, and by the fact that we do not need to look beyond systems as sophisticated as bacteria to find this process of natural intelligence at work. (We should not need to carry into space anything more developed than bacterial biotronic systems--i.e. sophisticated Winogradsky Columns--unless the question of life support or biodiversity is at issue.)

            Wherever we find living systems in the universe, we will find similar forms of natural, non-neural intelligence operating. The DNA of alien forms of extraterrestrial life is almost bound to be fundamentally different in form and structure than our own. Divergence starts in the very beginning, but also remarkable convergent and parallel and similar in many forms and structures.

            The DNA is more than a simple strand or set of linear strands of double-helices in the nucleus or necleolis of a cell. The DNA complement, or genome, of any cell, of all cells, constitutes an active genetic matrix, or processing reprogrammable information storage and transmission system, that constitutes a language-processing machine. In other words, the processing system of DNA in any cell is by definition non-linear in both control and outcome.

            Traditional evolutionary theory would not accept the idea of the natural intelligence of DNA as an adaptive, cybernetic system, as it is founded on the key insight in the fundamental blindness of chance mutation of DNA. This is true, but the complexity of DNA and, apparently, the rate of divergence, is sufficient enough that it has allowed living systems to systematically explore the environment generationally through selection and adaptation to environmental changes. The fact that DNA has never been free of indirect environmental constraint, that it has always had to adapt to and successfully reproduce within varying environmental conditions, has meant that environmental constraint and feedback are intrinsic to the evolutionary development of DNA.

            In fact, the systems structure of DNA functioning can be seen from the standpoint of Artificial Intelligence and programming, upon the three levels that such programming is construed--the DNA hardware, the program code within the DNA hardware, and the "theoretical" framework (read, for DNA, the metabiotic environment) within which the program code functions. This is as true for simple soil bacteria as it is for sophisticated living systems like Homo sapiens.

            All living systems are fundamentally constrained by what can be called the environmental imperative, to adapt or be selected out. DNA will continue any line of development as far as possible until and unless it meets an extinction regime. As a living system, bacteria have been relentless in their adaptation and survival over four billion years--they are capable of adapting to fairly extreme environmental conditions and of chemosynthesizing a range of chemical compounds that would prove toxic to most other life forms. Their rates of reproduction are so great and rapid in growth, and it appears, the capacity for genetic modification even in the most primitive DNA systems, like viruses, by transpositioning of DNA segments, so great, that bacteria appear to be capable of overcoming almost any environmental extremes or limiting factors that may rise.

The key to living systems on earth is the structure of DNA within the context of the cell, and the dual processes of DNA replication through RNA transcription and Protein Synthesis through RNA translation. These two processes are universal to all living systems known, and occur in all kinds of cells. In a sense, all living systems can be seen as the elaborated outcome of the process of continuous DNA replication and protein synthesis which continue incessantly and automatically under the appropriate conditions. Changes in DNA structure combined with processes of natural selection have resulted in the evolution of highly differentiated and elaborated structures and processes that are built around and upon these central dual processes of living systems.

            All living systems on earth can be looked at therefore as the consequence of the functioning of these dual processes, DNA replication and protein synthesis, that takes place more or less continously within the environment of the cell that provides the necessary machinery and context for these processes to occur and recur. Understanding living systems therefore can be understood physically and informationally upon this fundamental level of biochemical interactions, and the great thrust of biological science has been in unlocking the secrets of life upon these levels in terms of these fundamental physical interactions.

            DNA replication and protein synthesis are both functions regulated by the DNA, albeit along different RNA pathways, and it is apparent that the processes occur more or less in alternation. In simple binary fission of bacterial cells, cell growth begins by the DNA ring replicating itself, followed by the division of the cell into two and a subsequent latency period of cell enlargement before the process begins over again.

            One of the key problems in understanding genetic information systems as systems of reproduction and growth, is understanding how cellular differentiation occurs in complex multicellular organisms, as a process of developmental timing, through genetically determined control. The entire process of multicellular growth and development of an organism upon a level of cellular differentiation and specialization can be described as a branching inverted tree diagram, with the original stem cells at the top of the structure, and all the variety of organismic cells at the bottom of the tree structure. Most of this growth in fact occurs in the first 9 months of life, and then, there is gradual growth through cellular mitosis for the remainder of the life-cycle, which can stretch for another 12-16 years, and then a very long period of stasis before the organism begins aging and cells begin dying faster than they reproduce.

            This process appears to be intimately connected to the development of specialized structures of the eukaryotic cell. With increasing differentiation of species of multicellular organisms, there appears to be an increasing number of chromosomes or genetic strands of DNA that are implicated in this process of differentiation. Genetic information appears to regulate and make possible a very wide, almost unlimited number of structural and functional traits and patterns of morphology/physiology of an organism.

            While human DNA has been almost completely mapped out, how it works exactly to regulate cell and organism growth, cellular differentiation and metabolic regulation, remains still largely an unsolved mystery. It is believed that the amount of possible information that the genome of any organism encodes may be far larger than the amount necessary for that organism. Not all DNA is used in the some way, or even at all, and some DNA appears to be used repeatedly. Though this would seem to go against a fundamental principle of economy of nature, it is understandable from an evolutionary development in the sense that genetic load has been built up in the development of different organisms, and each carries a surplus of unused information that may have been implicated in the evolutionary history of that organism. In other words, unused DNA simply won't go away, become disassembled or reabsorbed, but will remain as anachronistic and archaic remnants of previous biological systems.

            This brings up a critical question in the evolutionary development of living systems: how does new DNA become added to the genome of a cell. It seems that the addition of multiple strands of DNA is a regular part of the taxonomic development of living systems on earth. If genetic transmission has been strictly vertical throughout evolutionary history, and if there are no known mechanisms by which a cell itself may manufacture new DNA material, then there seems to be no possible means by which the size of the genome could have increased over the eons of evolutionary development. Indeed, this seems to have been largely the case for the first 3-4 billion years of evolutionary development.

            We must explain the following kinds of questions:

1. The problem of genetic addition leading to the accumulation of genetic material.

2. The problem of genetic multiplication, or the magnification of genetic traits in their developmental outcomes or consequences for the differentiation of the organism.

It is important to emphasize that genetic transmission and reproduction tends to be overall a very conservative process that permits of very little deviation. This conservativeness of the central informational transmission mechanism of living systems is possibly reinforced by means of a great amount of redundancy of genetic sequence code, as well as interchangeability of specific codons for the same amino acids. This would entail that a substantial amount of DNA may be damaged without necessarily damaging or disabling the entire processes of DNA transcription or translation for specific protein structures.The conservative nature of nature explains why organisms still exist that existed probably three or four billion years ago, as well as why all organisms appear to come from a common tree of inheritance.

We may speculate upon the following kind of theory:

            a. There appears to have been a gradual increase in evolutionary history of the size of genetic genome.

            b. The increase in size of the genome appears to be indirectly associated with the increasing multicellular differentiation of a species.

            c. The relation between increase in size and number of genetic strands appears to be related to the increase in differentiation of multicellularl organisms in a non-linear manner.

            As a conclusion, we can state that there may probably be interaction between DNA strands, regions and points of DNA strands, such that the slight increase in amount of DNA results in a much larger increase in the number of interrelations and interactions between DNA.

            Possible mechanisms of DNA addition to a cell's genetic genome:

            1. Reduplication of multiple strands or portions of strands of DNA during cellular reproduction: instead of a single strand being transcribed, two or even more strands may become transcribed, that subsequently differentiate from one another through random processes of mutation. Once reduplicated, such strands remain permanently within the genome.

            2. Horizontal transmission of genetic information either by means the exchange of genetic material between two or more cells, as for instance is known to occur in some soil bacteria, or possibly through the incorporation of one cell by another cell, or alternatively by means of bacterial or viral infection of the cell.

            3. Diagonal transmission of genetic information, especially through cloning or sexual reproduction of multicellular organisms, when two or more cells add additional genetic material to a resulting offspring cell. In other words, an offspring cell receives genetic complement from more than one parent cell.

It is possible, at some point in evolutionary history, one or all of these processes may have occurred, not just once or a few times, but many times over. Most of the results of these "reproductive accidents" would of course have been disruptive and deleterious, leading probably to early death or negative selection of the resulting organism. It is possible though that on rare occassion such changes may have been at least non-deleterious or even constructive in outcome. This fits a pattern of evolutionary history, what has been called punctuated equilibrium, in which very long periods of stable development are punctuated by a very few and very brief periods of rapid developmental evolution. The rise of multicellular eukaryotic organisms appears to have occurred only once in our common evolutionary history, or at least only during one brief period of time in our evolutionary history. There may have been many failed natural experiments, precursors, before the one successful event finally occurred.

The point is this:

1. once additional genetic material has been added to the complement of a cell line, it is a relatively permanent increase in size and complexity, whether this additional genetic material is expressed or not.

2. there tends to be, as a result, a resulting multiplicative increase in the totipotency of the cell line as a result of the permanent addition of new genetic material.

This suggests that genes in cells "talk" or interact with one another, albeit in constrained ways, in the translation of cells to the production of proteins. We might suggest that, besides genetic transcription and genetic translation, there is a third kind of process that might occur connected with cellular differentiation of multicellular organisms, and this might be called genetic transpositioning, possibly upon multiple levels, resulting in a shift of the cell from one kind to another over repeated generations.

In most basic terms, genetic transpositioning can be thought of as the switching on and off of genetic traits or of interrelated sections of DNA code, and the differential switching of such code over the course of developmental time. The assumption is that with evolution there has been a gradual accumulation of extra DNA, and not all DNA material is being used at the same time. A more detailed picture of genetic transpositioning might reveal a more controlled and regulated process in which the switching of segments of DNA code may be related to the actual transfer or swapping in and out of genetic material.

The transpositioning of active DNA may possibly relate to the systematic differentiation and specialization of different types of cells during development of organisms with the emergence of the particular traits and properties associated with each of the cell types and the tissue colonies that these cell types coalesce into and form. The total number of the different types and subtypes of cells needed to make up a complete organism would represent all the genetic totipotency of the organism as a whole, plus whatever genetic instructional code may be necessary for switching on or off particular genetic sequences or segments in tandem.

One must inquire whether specialized transposition RNA might be constructed in the process of this development--RNA specifically encoding for particular cellular differentiation. We can possibly see repositioning of DNA code as a consequence of errors of attachment and unzipping the double-helix structure. The possibility of repositioning resulting in reduplication and addition of DNA material may be related to transpositioning of this material by the fact of the double-helix structure itself. A single sided strand of DNA cannot remain loose without automatically rebuilding the other side. Any loop or twist in a strand resulting in skipping of a segment, might result in the breaking off of the segment, and the formation of additional material, or alternatively the reintegration of the segment to the original helix, albeit as part of a lengthened chain of code.

It is possible therefore to see the gradual accumulation of additional DNA in the cells genome as a natural consequence of transpositioning errors resulting in repositioning and enlargement of additional sequences, without necessarily having to hypothesize other mechanisms such as horizontal or diagonal transmission or infection. It is apparent that cells have a limited capacity to do repair work on DNA strands and the double-helix structure provides a built in back-up to lost information. Any lose, one-sided DNA material leftover would automatically be reencoded as a double-helix structure.

Transpositioning of DNA segments may be a common occurrence in all kinds of cells--common enough in cell populations to enable adaptive change to overcome patterns of extreme environmental variation leading to stress and increasing death rates. Some parts of DNA strands may be more prone to reassortment and transpositioning than other parts. The simplist form of transpositioning would be substitution of one nucleotide base for another, or of one codon for another on the basis of a single substitution. Forms of cancer growth, are suspected primarily of this type of transpositioning modification that leads to runaway growth of aberrant cell tissue that would compete with normal cell growth.

Transpositioning can be defined as either the actual substitution or virtual, indirect displacement by remote substitution, of more or less random rearrangement of nucleotide bases or sequences or segments of variable lengths, either within a single DNA strand, or between multiple DNA strands. Virtual rearrrangment might occur when the string coded for is altered indirectly by other modifications of DNA elsewhere in the genome--in other words, substitution or transposition of variable length strings might result in the displacement of code sequences elsewhere within the DNA, with a resulting misreading of the code.

It is assumed as well that some DNA has a primary purpose of controlling the function of other DNA. The master DNA may suffer transpositioning, resulting in a complete loss of control or reconfiguration of the entire genomic system of DNA. We can suspect with fetal development of multicellular organisms teratrogenic oddities occurring as a consequence of such master DNA.

Apart from point mutation from radiation or transcription error, transpositioning may be the main mechanism of endogenous genetic modification and evolutionary transformation occurring. It is not frequent in occurrence, possibly on the order of less than 1 or even .1 percent of the time, but it occurs frequently enough in any breeding population to confer upon that population a certain genetic plasticity and flexibility in meeting and potentially overcoming environmental challenges and ever shifting selection regimes.

Cell death would be the expected outcome of any major transpositioning of DNA code, but cell change may be the outcome of relatively minor transpositioning. While most, even minor cell change would probably prove deleterious, hence prone to negative selection, a very smal percentage may prove either neutrally non-deleterious or possibly even beneficial in some adaptive form for the cell.

What a theory of transpositioning offers evolutionary development is a mechanism for more rapid and potentially more variable kinds of changes to DNA code than just hypothetical point mutations, and it points to a central function of DNA control and organization beyond that of only transcription and translation into protein structures.

Transpositioning is exactly the type of genetic modification that could account for punctuated-equilibrium of development, or hiatuses of rapid change in otherwise evolutionarily stable configuration. The effects of transpositioning should in theory become more pronounced the greater the negative selection affecting a population, where with any normal population under stable equilibrium conditions most transpositioning itself would result in negative selection and hence in a built-in means of regulating growth of population.

Transpositioning for sexually reproducing populations may have an equivalent feature in the sexual reassortment of male and female DNA, and especially, if male and female are widely divergent from one another, even to the point of being interspecific or star-crossed on the boundaries of a species population. Evidence from long term studies in the Galapagos indicates that interbreeding of subspecies may produce pronounced genetic modifications that permit a species to overcome extreme environmental conditions.

Because such marginal or interspecific breeding is probably rare and uncommon, and because such mating falls just short of the reproductive boundary of a species, the resulting genetic recombinations may provide a reconfiguration of the genome sufficient to result in a hybridized species with highly unique and specialized characteristics.

Furthermore, such results of marginal mating are in principle not a population, but only lone and exceptional individuals, who may nonetheless subsequent put their new genetic combinations back into a larger population gene pool. This process over time would result in the hybridization of entire populations and ultimately, in speciation. This hybridization would be fairly rapid, and would be nothing less than a genetic transformation within a few generations of an entire population, albeit one that was probably bottlenecked with a pronounced founder effect.

This hybridized, marginal founder effect of a bottlenecked population might have similar ecological consequences as an invasive species that tends to displace adapted key-stone species and to upset local or regional ecosystems by rapid growth and niche displacement. Niche competition by locally adapted, high K species would be lost by those species to the invasive newcomer.