A General Systems Model of Natural Organization: the Fractal Nature of the Universe. Part 2. The Biophysical Realm
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THE FRACTAL ORGANIZATION OF NATURE

Part 2. The Biophysical Realm(Genetic Code - 4 Nucleotides Code in Triplets)
JOHN A. GOWAN
(revised Jan., 2011)
email:
jag8@cornell.edu 
johngowan@earthlink.net

Introduction
(See: The Fractal Organization of Nature (table))

As the level of complexity of biological systems rises above the molecular level, we have to look for manifestations of the 4x3 pattern at an organismic or systemic level, a far more difficult task, if we seek to identify the exact structural and mechanistic solutions which demonstrate the 4x3 pattern. Even though we know that the molecular and coding pattern of DNA is always working "behind the scenes" in all biological phenomena, it is certainly not clear that the pattern of this organizing force would be directly/overtly expressed in such complex systems as organisms, species, or ecosystems. There is another way to approach this problem, however, which is to look at the dynamic of the system rather than its mechanism. This is, after all, how George Land developed his growth curve and delimited its stages. On the presumption that this dynamic is isomorphic with the underlying mechanics, we can infer one from the other.

As it happens, it is relatively easy to see the Land-Jaccaci dynamic operating in even complex biological systems; the accreting, replicating, mutualistic, and transforming stages of system development are reasonably obvious. For these complex systems, therefore, I will rely on a dynamic rather than a mechanistic analysis. Nevertheless, I will try to characterize a 4x3 structural pattern in these systems where possible, but acknowledge beforehand that the identification of actual mechanisms is at best speculative, and at worst, inappropriately applied to phenomena of such complexity.

Level 5: Cell

(organelles)

At the cellular level, we begin with the DNA-RNA molecule as the unit derived from the preceding level of large prebiotic organic molecules and chemical systems. This is already a paired unit, which is also its boundary condition. DNA's boundary (all units must exhibit a boundary) in this case is its conjugation partner; it will attach to none other (somewhat reminiscent of the ephemeral particle-antiparticle pairs of level 1). But these partners are neither virtual nor ephemeral. Their accreting phase is the passive (at first), or the active (later), acquisition of sufficient appropriate molecular material (obviously in a benign and rich environment), such that replication becomes possible in stage two.

In this case the replication function is a major part of how we define "life". In any definition of "life", I would also insist that the 4x3 genetic coding mechanism and the cell membrane be included; that is, all 4 stages of Level 5 must be present (no true "life" below the cellular level). Once DNA achieves replication, the experiment of Earth-life begins. All that we are today is but an elaboration of this molecular system of reproduction, which on the universal scale is but one local example of the flowering of the 4x3 General System pattern inherent in all matter.

DNA in the second cell of level 5 takes the form of a complete genomic entity (excepting symbiotic functions), that is, a complete inventory or information set of instructions concerning the creation and maintenance of a specific living system or cell. In this way we differentiate the pairing or doubling of cellular DNA in level 5 from the simple, experimental replications of prebiotic molecules containing only scraps of information in level 4.

Continued replication in stage two soon exhausts any available nutrients, leading to a crisis situation which requires a stage 3 solution, mutualistic interaction and the sharing of differences. The group or field category of mechanistic regulation (which in this case we happen to know) is another expression of the 4x3 General System pattern: the 4 nucleotides of DNA code in triplets to produce genetic product in the form of amino acids. Hence there are 4 cubed = 64 possible distinct triplets ("codons"), each of which could code for a different amino acid. In reality, only 20 amino acids are produced by living systems, so many triplets code for the same amino acid.

The dynamics of the mutualistic solution arises from the many different products that the DNA code can produce in almost infinite combinations and permutations. Primitively, different types of DNA would be able to produce different types of useful products. Genetic swapping and mergers, molecular "sex" in short, would eventually allow a cohesive set of genes to be put together in a single harmonious genome.

We can only imagine that at this early stage of life these various genetic products served to actively acquire from the environment the nutrients needed to sustain the replication of the DNA molecule, and eventually to develop a protective membrane surrounding the genetic material. Many different schemes must have been tried in the primitive laboratory of early Earth, until there was a union between abilities that solved different parts of the survival problem, arriving at the final solution we know today as a living cell. The organelles of present day cells are known in at least two cases to be derived from symbionts - the chloroplasts and mitochondria. Both have their own DNA and a double nuclear membrane. Other symbiotic and mutualistic acquisitions are suspected, such as the locomotor (cilia) cells and peroxisomes. Although we may never know the precise route by which the first successful cell was formed, it does seem clear from the evidence that the pathway followed exactly the steps of the Land-Jaccaci dynamic. This same dynamic is clearly evident in all succeeding biological levels.

In the case of the cell, both the underlying 4x3 structural mechanism (in the coding pattern of DNA, with its multiplicity of amino acid and protein products, which could be put to various uses) and a higher level dynamical expression of the system are evident, as in the combining of genetic material (molecular "sex") and in the development of symbiotic and specialized organelles. At higher levels of biological organization, while the DNA is obviously still there, only the dynamical expression of the system may be evident. The transformation in the system product at this first level is likewise obvious. Beginning with a passive molecule, at the mercy of its environment, we end with a cell enclosed by a membrane (at least partially controlling its environment), actively seeking nutrients and energy, a causal "agent" with an "identity" exercising a conservation function: self-preservation.

The 4-level biological hierarchy progresses through a series of bounded units of which the first is the cell, delimited by the cell wall or membrane. Within this protected boundary reside the various organelles which allow DNA to acquire from the environment all the necessary ingredients to maintain and reproduce itself. These organelles are the analogs of system parts (organs, populations, ecosystems) which reappear at every higher level of biological organization, evidence of the hierarchical fractal structure and underlying ordering dynamic of the biological realm.

Level 6: Organism

(organs)

We have been able to trace the physical evidence of an apparent 4x3 General System pattern from conservation law and the formation of baryons in the Creation Event, to the special properties of alpha particles and the nucleosynthetic pathway of stars; thence to the nuclear and electronic configurations of the carbon atom; again to the tetrahedral bonds of carbon molecules, crystals, and water; finally to the molecular composition of DNA and its coding pattern. This grand organizational metric of nature spans the eons between the creation of the Universe and the creation of life, the spatial scale between subatomic particles and biological cells, and the functional scale between the resonant 4x3 fractal algorithm of the abiotic atomic realm to the replicating information code of DNA and biotic systems. The 4x3 pattern establishes itself firmly in the foundation of living systems through the structure and organization of the genetic material and code, molding life upon a universal ordering principle. The hard evidence of this pattern submerges beyond the cellular level of the biological hierarchy, hidden by the great complexity of its productions, and is not seen again in definitive form until it reappears at the species level in human thought, both ancient and modern, and in certain aspects of the astrophysical realm. Nevertheless, we see the underlying pattern reflected in the dynamic and structure of the various organizational levels of the biological domain.

The second biological level of organization is that of the multicellular organism. The pairing function here is cell division. If new cells adhere to the old, and later differentiate, we have the basis of multicellular organisms and specialized tissues.

Too many of the same kind of cell at one time and place creates a crisis of overpopulation: energy and nutrient shortage, waste pollution. The third column at the organism level is the crisis stage which must be resolved by mutualistic interaction, or the sharing of differences. Cells have responded to this problem in at least two ways; differentiation within a reproducing collection of cells, or symbiotic mutualism between unrelated cells. Some cells can use the waste products of others, while other interactions are mutually beneficial. Differing cellular specialties can be joined to create a new way of coping with the environment to the benefit of all. Swapping of genetic information between cells can harmonize the whole aggregation to a new unitary and adaptive stage. Whether this process involves the different abilities of unrelated cells, or activating and repressing different parts of the same rich genetic base, the method and result are equivalent from our point of view: in either case a multicellular organism is created following the Land-Jaccaci dynamic.

It is to be noted that the evolution of multicellular organisms from single cells actually took longer than the evolution of life itself from the prebiotic amino acid "soup". The cause of this delay may be due to either the cells actively resisting giving up their independent and individual identities and coordinating their activities, or the fact that evolution simply had far fewer cells to work with than molecules.

The resulting multicellular organism with its specialized tissue types is usually covered or delimited by a boundary layer of some type of protective "skin", whether plant or animal, and becomes the unit of the next stage of the biological hierarchy. The specialized organ systems of these creatures are analogous in function to the cellular organelles of the preceding level.

Is there a functional as well as a structural and organizational expression of the 4x3 pattern at the organism level? If there is, I speculate that it takes the form of three biological functions supported by the development of 4 specialized organ systems, or tissue types. The three functions, basic to all biology, are: 1) maintenance, or self preservation (metabolism); 2) reproduction; 3) perception. A fourth, emergent property is implicit in these three, through the process of natural selection: evolution. The four organ or tissue systems which specialize to support these functions are: 1) energy related (acquisition, utilization, excretion); 2) sensory; 3) structural; 4) behavioral. The behavioral system integrates and motivates the activities of the other three. It is to be understood that the elaboration of this putative 3x4 matrix produces twelve systems; for example, energy systems service maintenance, reproductive, and perceptual functions and may result in three specialized energy systems, etc.

Organisms at level 6 include primitive multicellular plants and animals which typically reproduce asexually, and therefore do not have the possibility of a discreetly segmented population structure such as exists at level 7. (The Fungi imperfecti are examples of such organisms; many others have become extinct following the evolution of sexuality).

Level 7: Species

(populations, societies, professions)

The organism is the unit, and the pairing function at the species level of organization is male-female sexual reproduction. The accreting phase is the growth of the individual to sexual maturity, gathering size and energy until the threshold of the replication stage is reached. This is our own level of organization and is therefore the most familiar. It includes the larger and more advanced plants and animals with which we are most familiar, most of which share our mode of sexual reproduction.

The replication of an organism cannot continue indefinitely, as a Malthusian overpopulation crisis will eventually result - there will be too many similar organisms occupying the same territory and/or niche. The geometric increase in numbers implied by the process of replication will always overrun at least one critical niche variable which tends to increase only arithmetically or not at all (such as food, water, light, space, shelter, etc.). One solution to this problem is the mutualistic sharing of differences - the natural variability in the gene pool which is a consequence of sexual reproduction - which allows certain individuals to adapt to the population crisis and find a new way to utilize the available niche space. This may be as simple as cannibalism or predation upon the "excess" or weaker members of the population, or utilizing their waste products, including dead individuals. In such cases the organism population itself provides the new niche space. Alternatively, a new element in the environment may be utilized that other individuals do not have the genetic ability to exploit - an adaptive innovation. Finally, organizational solutions providing greater efficiency at a group or social level may be discovered, or mutualistic interactions with other species may be explored.

Gaining a competitive advantage through mutualism, symbiosis, and cooperation is a survival and evolutionary strategy which becomes increasingly important in an overcrowded and complex world. However they do it, individuals (or groups) which successfully "break out of the mold" and transfer their adaptive advantage to their offspring are poised to become a new species exploiting a new niche. The mutualistic sharing of differences that allows this greater variability to exist is occurring superficially at the level of the individual organisms, but fundamentally at the level of the genes, where the recombinant process of sexual reproduction creates the genetic variability that allows the resulting organism to explore new niche space. The process of fertilization at the chromosomal level, with its pairings and exchanges of differing genetic material, is a picture- perfect example of the Land-Jaccaci General System growth dynamic.

If we wish to translate this genetic process to the system level of the organism and the evolutionary pathway, I suggest the following expression: 4 categories of population structure: individual, reproductive pair, population, species. Population is defined as any larger-than-family genetically interacting group; species is defined as a closed genetic system in sexually reproducing organisms (for example, humans are a closed genetic system because they cannot interbreed with any other species). This 4-level population structure is characterized by 3 genetically based conditions which are both necessary and sufficient to produce evolutionary change (Leowntin 1970): 1) phenotypic variation (with respect to the utilization of some limiting resource); 2) differential fitness (as a consequence of (1)), expressed in terms of numbers of offspring; 3) heritability of (2). Higher plants, animals, and humans are products of the level 7 life system, a trinity of evolutionary criteria operating upon a 4-level population structure.

Level 8: Gaia

(niche specializations)

The final biological level is that of Gaia, or Mother Earth. Here we conceive of the planet as a giant single organism and ecological unit, named by the British scientist J. E. Lovelock for the Greek goddess representing our planet. Since species are the units, the pairing function at this level must be represented by the process of speciation, the evolutionary division of one species into two. Often this is a true pairing, accomplished either by hybridization between two imperfectly isolated species, or by the splitting of a single species into two isolated populations, which thereafter diverge into separate species (as in "Darwin's finches"). Another speciation process involving pairing, common in plants, is the direct doubling of chromosome numbers, producing a genetically isolated but fertile "polyploid".

The proliferation of species by the evolutionary process can no more continue indefinitely than can the replication of an organism. Eventually all the niche spaces of the environment are used up. Here again, however, the mutualistic sharing of differences provides a solution. Once the abiotic environment can no longer provide new niche opportunities, the established biotic environment becomes the only alternative. Life begins to feed on life; the established species themselves become the new niche opportunity. Eventually life sorts itself out into the ecological niche classes; primary producers (usually plants); herbivores, who eat the plants; predators and parasites, who eat the herbivores; scavengers and detritus feeders, who feed on waste products of plants and animals alike, and many other minor categories and specialties. Every species in fact provides in itself a niche for some other species, and even the interactions between species provide niche opportunities. Hence as life diversifies and species grow more abundant, so too does the opportunity to find some new way of making a living within the biotic environment. Because the ultimate energy resource (light) has an absolute limit, there are more niche opportunities for smaller plants and animals, which use less energy, than large ones. A single large tree in the rain forest may itself support hundreds of species of other small plants and animals. All species exist in some kind of mutualistic relationship with other life forms; even predatory relationships have their beneficial side, from the point of view of population control. (Carnivores may be seen as only one of many ways plants protect themselves from herbivores.)

Mutualism goes far beyond the level of interaction between individual species - whole classes and kingdoms of life participate in ecosystem-level mutualisms (the "web of life"). The mutualism between plants and animals is ancient, worldwide, and profound, taking many forms. Perhaps its most fundamental expression is the capture of the Sun's energy by plants, which is then transferred to the animal food chain. Another fundamental expression is the worldwide exchange of oxygen and carbon dioxide between plants and animals, an interaction which has fundamentally changed the composition of Earth's atmosphere and the character of its biota. The nitrogen cycle is a third example, and the cycle of nutrients (elements of the periodic table) between plants, animals, bacteria, and fungi a fourth. The cycle of water between plants, animals, soil, oceans, and air sustains the entire terrestrial ecosystem. Other examples, which are legion, include mutualisms between grasses and grazers, flowering plants and pollinators, and animal dispersal of plant seeds. Animals and plants also exhibit profound mutualisms with bacteria, which in animals are essential to their digestion and health, and in plants fix nitrogen and participate in many nutrient cycles. The mychorrizal association between plants and fungi is ancient and essential. It is safe to say that all forms of life live in some sort of mutualistic interaction with other life forms. Our agricultural practices are of course an example of an intentional mutualism, in which the ant societies have preceded us by many millions of years.

The most fundamental mutualisms are so basic to life that we are hardly aware of them, but they are what supplies the air we breath and the food we eat. These grand and ancient mutualisms are often called biogeochemical cycles, and they fundamentally involve energy cycles, gas cycles, nutrient cycles, and water cycles. The interaction of these four biological cycles with the biota of the oceans, atmosphere, and continents of the Earth is perhaps a global expression of the 4x3 general system in biology, corresponding to J.E. Lovelock's vision of Gaia, the unity of life on Earth.

Another expression of the 4x3 pattern at the global level of organization is our natural calendar: 4 solar seasons each of 3 lunar months. Although the lunar cycle does not exactly fit within the solar cycle, it is nevertheless significant that the human mind has found the 4x3 expression of this seasonal system to be the most convenient. What the significance of this seasonal pattern was for the emergence of life we do not know, but there can be no doubt that it played an important role, just as it continues to play an important role in the maintenance of life today.

Reviewing the Biophysical Realm, we have proposed 4x3 regulatory fields in terms of the genetic code and symbiosis at the level of the cell; in terms of mutualism and tissue differentiation at the level of the organism; in terms of population structure and natural selection at the level of species; and in terms of seasonality, ecosystem function and integration, and biogeochemical cycling at the level of Gaia.

Humans have begun to have profound and destructive effects at the global level, due to their worldwide distribution, overabundant numbers, agricultural and industrial pollution, consumption of natural resources, etc. Global warming, the ozone hole, acid rain, the extinction of species and the destruction of ecosystems are effects (among others) of global significance that may already be at dangerous levels, to say nothing of the uniquely human threat of nuclear holocaust. But humans also have a specialized and constructive role to play among the diverse evolutionary productions of Gaia, as we shall see below. (See also: "The Biological Role of Humanity" in: "The Information Pathway".)

Go to Part 3
Go to Table of Natural Organization