An Energy Genealogy for the Nucleic Acids
Marvin E. Kirsh 1
1517 N. Herbert Avenue
Los Angeles California 90063
Kirsh2152000@yahoo.com
1 The California State University Los Angeles Department of Philosophy
Abstract
Though many major breakthroughs have occurred in genetics and molecular genetics, an approach to a real comprehension of nature, if one looks into the tunnel of questions that have been constructed, and experimentally approached, is very distant. In this manuscript I wish to introduce a new potential perspective from which to view nature that is necessarily absent of an existence of a vast multitude of abstractions and theoretical constructions. (note 1) DNA, life is constructed in a model in which the world and each of its’ elements standalone in definition as unique monisms that are identical with respect to the presented framework. It will be shown that apparent features of one-gene-one enzyme, for instance, are not actual as unique determiners in the description of function, but that transparent energy relations and a coincidental overlapping of parameters, considered with respect to a genealogy of energy relations verses apparent structure and geometries, modulate associations. A model is proposed that accounts for both observation and current interpretation. All concepts are necessarily grounded to the perception of two dimensional volumes and their determined properties, origins are considered only as genealogies in terms of process mechanisms.
Keywords (evolution “origin of life” “life processes” “natural processes” genetics enzyme gene “lock and key” DNA RNA protein “origin of DNA”)
Introduction
1) All perspective of all entities is in the first person and is held as the only suitable point of reference, as the only plausible standard, it moves in relation to the external and with itself. Witness is defined as any location in space that exchanges energy with another location and is realized by and confined to pairs of witnesses. A universal of space and processes is based on an ordering by an inversion (Figure 1), a one sided surface-mobius like strip, as a substrate for paradox. All witness points ,entities , are the product of a genealogy of two interactions involving the transparent and the apparent. 
2) A relativeness of nature is introduced that focuses on temporal differentials involved with volumes and their contained/containing processes that are ultimately Einsteinian and distributed uniformly, qualitatively throughout.
3) Representation is accomplished, at any entity location, by the means of ratios of differentials as a result of a change in the spaces involved in the propagation of force as different spaces with different spatial properties engage in relations - e.g. in analogy, visual representation is postulated to be produced in the brain from differentials over time in detected sensory signals that assume associations that re-modulated by the new spatial factors in the internal environment of the brain
(Figure 4)
Figure 4 Representation is accomplished via a confrontation of spatial propereties as the medium of propogation
changes from external spaces to internal (neural) spaces
4) All processes are construed to be exclusively composed of paths of transmissions. For example, biological memory, DNA, RNA, identity is considered to emerge from energy-matter conversions, involving transit across vast inversion surfaces, as a “physical piece of path” (Figure 3) and are defined as transparent processes. The conversion of matter to energy, supplying metabolic energy is defined as apparent. In analogy, food ingestion with respect to the whole mammalian organism is given as a higher order parallel to DNA/RNA or protein substrate interactions, the inter-molecular with the intra-molecular. 
5) Empirical values of the apparent and the transparent, based on a plane geometry of volumes are secondarily theorized to be alike as a prerequisite for the formation of associations that define the locks and keys of nature( Figures 2, 6, 8, 9) Actual energy lineages, as in the description of the means of emergence of DNA (number 4 above), are automatically construed as transparent. Apparent features are designated not to possess unique genealogies that intersects, but are distinct from those of transparent interactions-i.e. are intermolecular
6) The existence of a natural calculator that combines positive and negative values to produce outputs is postulated and is an apparent feature . The transparent and apparent are thus intermingled and acted on by simple arithmetic processes in the creation of representations by entities. For example one micron of path length added with one micron of path length, three points on a line, results in apparent distances that correspond with the values according to the Pythagorean Theorem but are arrived at naturally. From a higher level, perceptual (and cognitive ) representations are suggested to function similarly.
7) A proposed natural existing overlap in numerical differentials of the apparent and the transparent, lending a means for interactions, is suggested to constitute the biological mechanism of locks and keys( Figure 9). Lock and key like mating assume a fluid aspect in which parameters of interactions are not dividable into separate witness components for study –i.e. parameters of a ligand within an interaction are “in dance” with those of the catalytic agent and cannot be treated independently from the substrate to yield coherent meaningful results, though mechanisms of function and certain analytical determinations, as partly illustrated in the Figures, are not precluded with respect to the extraction of pertinent meaning in light of goals.
8) The term multi-function gene or enzyme , as an example, gives reference only to a single lock and key rather than pluri-potential fittings from analysis of independent structures. Two independent paths of the catalyst and substrate, composed respectively of transparently originating parameters (intra-molecular) and apparently originating parameters (inter-molecular) are referred to in the construction of a lock and key that is based on temporal differentials of parameters of spaces/volumes associated with intra-molecular energy histories of catalysts and similar in dimension, inter-molecular parameters of proximity to the catalyst, size and shape. A resulting mutual motion, entanglement, is described that is based on individual entity transparencies resulting from interactions and forces associated with proximity, rather than a locking based on a physical matching of shapes and sizes, is described
These concepts, some of which appear to exceed the subject matter of an energy genealogy for the nucleic acids are presented in order to frame the discussion in advance of potentially ensuing contradictions of logic and interpretation.
Discussion
Other than conceptualizations that structure associations according to physical properties, mass, energy, physical geometry etc. , a scheme to construct it with respect to a paradox of the apparent and transparent is introduced. Physical force, entailed to all interactions, is equated qualitatively with paradox.
In this light, consideration of efforts to fit data and observation into theoretical boundaries, noting the vast number of exceptions to expectations that have been arising and the very difficult topic of emergence, a new view is presented to consider an origin of life that is devoid of topics that entail conceptions, beginning and death, as any of them are philosophically unsound and useless in approaches. Temporal considerations, in alternative to a singular descriptive account of function, can give birth to the same set of chicken-egg like logical confusions that perennially entail an overlap of unifying conceptual details with those of a particular and circumstantial nature. A basic unit structured with respect to a mathematical inversion and paradox (paradox is singularly defined descriptively as possessing a property of force) does not, in the absence of particulars, entail temporal factors.
Two components to the model are given as a unit feature, a one sided inversion alike a mobius strip as a surface/substrate for all processes involving the propagation of force and energy that is associated with distance/force of either of a transparent or apparent nature. Energies of processes are entailed to a separation somewhere along an inversion from highest potential (most energetic and complex) to lowest potential (Figure 1). DNA is characterized as ‘a piece of physical path’ that is emerged from energy that has transited a path from a very high potential to low potential, has assumed a state of matter, and reflects physically the path across the entire inversion from which it is derived (Figure 3). DNA , in this scheme has the paradoxical role of both physical form and function as the genetic material and a transparent form and function as memory.
A second factor of external metabolic energy that is distinct from described energy genealogies, attributed as inter-molecular, is postulated to fund energetically, biological, as well as all processes. The resulting model is uniquely composed of, at all levels, catalyst and substrate – i.e. space is considered as a catalyst for the substrate light (Figures 1, 2, 3). All processes, in constant flux in this scheme, are postulated to occur from a comparison of self to the external in the sense that both are subject to conditions of the laws that detail space with respect to the geometry of spaces, distances, volumes, energy etc. Entity-self representations are proposed to exist as reflections of temporal differentials of transmissions modulated by conditions dictated by the laws of mass and energy, that upon change in environment from one space to the other, produce a net transparency that is conceived of as a representation. In the case of visual function (figure 4), an energy differential representing a visual image of the external results that is maintained by an intersecting metabolic energy provided by the ingestion of food. All aspects are postulated to be arranged this way in all facets, whether witnesses pairs involving living entities or otherwise- all discussed facets, related to witness pairs, are attributed as interactions with respect to first person/entity representations as natures control/standard in that they are more constant in relation to the external, move with a particular entity; all endogenous components bear a closer genetic relation to self than to exogenous components.
With respect to the RNA/DNA pair , as in the description of the origin of DNA ( i.e. a lengthy transmission of energy to become DNA and a transient transmission of genetic inheritance from cell to cell), a parallel emerges if one considers RNA as a transient entity with respect to DNA. In attempts to construct the specifics of a respective parallel, a conflict results if one considers the possibility for a discrete route of emergence for the nucleosides, as the major components of a genetic language, and their subsequent assembly into DNA and RNA as a tenable route of emergence, verses the inclination to construe RNA and DNA as a single emergence but with emerged differences. The suggested paradox between a construed independent, and discrete route of emergence for the nucleosides, as they exist also as independent entities, ultimately gives witness to a conceptual division between the entities of life and the inert entities of matter, as it entails, as the most logically implied path, a perspective, in contrast to a unique genealogy for mechanisms, a genealogy involving individual parts that are assembled to account for whole structures and is conceptually construed to be assembled from, with the input of energy that cannot be accounted for thermodynamically, energetically non-descript, inert matter as a precursor for life. This leads to conceptual models construed as tree like and that logically entail a unique origin that is discrete from either-i.e. a single root of a tree in which the ordinary forces, and mass of two dimensional space are absent. This paradox might be witnessed in the theory of relativity (Einstein, 1955) in which a special subset of general theory is included for explanation that entails a universe composed of pluralisms that are housed within the single monism that was conceived to intuitively exist as a motivation for creation of the theory, but containing both topologically open and closed features, if not implications of a location-less space made to mathematical, but not common, sense. It is suggested that this trail in a description of nature involves definition of a temporal origin and is both unhandleable conceptually and false. As an alternative, criteria for witness is established with respect to first person/entity representations as ratios of self to the external (Figure 4) and is proposed to be sufficient to account for these difficulties. If it is construed that a single emergence of nucleic acids, as the entities of genetic transmission, precede conceptually the emergence of the nucleosides in an identical scheme of apparent and transparent energy but is initiated with DNA and not light energy in a description parallel to the presented genealogy of the nucleic acids, a scheme for their emergence can be arrived at. In this manner the emergence of the nucleotides/nucleosides/bases might be conceived to occur either independently of the emergence of the nucleic acids or in a temporal fashion from them depending on the particulars of mechanisms and genealogies that are entailed with respect to topics-i.e. it is not unfeasible that plural routes in the genealogies of the nucleosides exist with subsequent intermixed associations of the apparent and transparent kind that are potentially separately dissected and significant only with respect to the particulars/pathways under discussion. However, a likely pathway, considering known mechanisms of recombination, overlapping, inversions, unequal crossing-overs, may only involve recombinations of emerged nucleic acids based on the apparent-transparent scheme presented to produce heterogeneous mixtures of substrates and catalysts. Currently established empirically derived schemes may mirror a conceptual organization of a grander nature of all processes.
A single path for the emergence of RNA and DNA, a plausible route for the emergence of the bases, nucleotides, and nucleosides (existing also as physically independent of their natural presence in parent nucleic acid structures), may involve a set of recombinations, reordering, overlap and ensuing extraction, repetition of likenesses and differences via alternating roles of substrate and catalyst by a means of comparison and subsequent addition or subtraction of differences. A route to the nucleosides/bases as singular substrates may occur in a series of processes akin to unequal crossing over events. An overlap in resemblances and differences in surviving intra-molecular compositions, if one considers DNA to be both catalyst and substrate in the initial step of a series of emergences, might be extrapolated to result in the emergence of all of the discussed entities and features-i.e. RNA, DNA and the nucleosides, the components of the cell, locks and keys. Uridine substituted for thymidine in RNA (note 3) might emerge as an impetus, lending identity, for homeostasis, maintenance, and reproduction if one considers a potential emergence of a vast energy division between transient (RNA) and long term (DNA) transmissions as the result of the distinctness and separation of the genealogies of respective emergences entailed by this model-i.e. transient and long time functional roles and a modulation by a transparent history of events.. Facets of the emergence of uracil, possessing a structural symmetry (Figure 10) that is suggestive of a similar series of aligning and alternating of roles of the apparent and the transparent, and/or catalyst and substrate, as a criteria for the processing, recombinations that result in the transparent symmetry of 3-carbon units, might have lend to it a central role as a divider of the transient and long term aspects of life processes in which it is also distributed/sieved into the lower potential energy category that harbors RNA verses DNA. This existence of a transparent function related intracellular barrier, analogous to the energy matter conversion theorized to produce DNA, is suggested in which apparent features are an exact consequence of an invisible parity, akin to an invisible finger in a dike, and are derived strictly from genealogies of origins and are not directly apparent experimentally. Resulting relations, in which a resulting proximity of entities is inversely associated with the loss of potential energy involved in the transit of energy to form matter in which locations of resulting mutual associations, parameters of locks and keys, are referred to only by historical values related to energy origins in genealogies. Inverse numerical relations of the apparent (inter-molecular) to the transparent (intra-molecular) (Figures 1, 2, 3, 6, 8, 9) may underline a deception involving an appearance of linear rather than more fluid- relative relationships-i.e. timelines in evolution related to the segregation of characteristics and a linearly arranged language employed in explanations of emergence. Though current data and theory seem to fit together and are not significantly diverged from predictions based on the model presented, many unexplained exceptions to theory are constantly emerging and are more easily accounted for by this more fluid scheme that focuses on, instead of traits, the means and facets of fitting that constitute processes and pathways (Figure 9). A central role is potentially ascribable to uracil as a template for life processes based on its’ physical symmetry (Figure 10), in view of the odd relations of apparent and transparent in the energy genealogy presented, is not intuitively unreasonable and places a pronounced importance on the elucidation with respect to geometries, symmetries, biochemical and genetic constituents in pathways, to determine quantitative parameters and description similar to the description of the egg, helix and mathematical inverses presented (Figures 5, 6, 8), especially if one envisions also, as in the energy genealogy detailed, an odd feature with an equivalent nomenclature of “paradoxical parity” in the properties of space that may be mirrored in biological processes to account for this model, Though a two step mechanism involving separately inert matter and living entities in a temporal order of emergence is customary in theories, here it is contained within a unit concept of genealogies involving locks-and -keys/catalyst-and-substrate. More important, with respect to the paradox introduced involving the theory of relativity, a conceptual unity and contiguity is maintained that avoids referral to origins entailing properties/entities that are beyond empirically focused conceptual description with respect to a genealogy of mechanisms.
This arrangement, of an orderable form from which DNA, RNA, enzymes etc. emerge and associate with substrates entails a description of a transparent nature of the transparent verses the apparent physical nature of structures emerged and their associations. This means of description, utilizing notions of transparent and apparent, allows strict adherence to first perspectives of entities and also permits a complete description of a encompassing mechanism based on first person/entity transparencies involved in associations. The transparency, always the primary and singular ingredient of associations, a synergy of the proximal(present) and the distal(past), is analytically inseparable with respect to individual witnesses in witness pair associations, less for a conjectured genealogies of origin that is strictly based on empirical observation-i.e.-observation related to the determination of the biochemical and genetic components and associations within the cell and organism, etc.. Facets of descriptive language usage, and philosophical inquiries that put to question the nature of concealed faces of the objects of perception, facets of experience concerning reflexive assumptions about the likeness of hidden faces to those observed are given as reflected from a described transparent property of nature that effects the apparent as a mirror of transparent relations, might raise to prominent significance, as discussed above, the symmetry in the structure of uracil (Figure 10) as a mirrored aspect related to all features in the emergence of the life processes, accounted for also as an apparent verses transparent mechanism.
Figure 10
A mathematical inverse of the structure of uracil, its’ unit three carbon fragment, and/or apparent intermediates in its’ biosynthesis, an equation if available, might reveal features that are innate to space in its’ role as a catalyst and /or substrate of/for life processes.
Figure 11 An inversion containing a mirror image of a 3-carbon fragment, in the form of potentials and associated distances, that comprise the physical symmetry in uracil, acting as both a catalyst and substrate for either space, inversions with or without its mirror image, its' own or other catalytic products also capable of acting as either substrate or catalyst produces a nucleic acid containing uracil 11 a, or uracil alone 11 b, by means of energy matter conversions.
Figure 11 a
Figure 11 b
In this model, on a molecular level, the figurative and the literal/actual become empirically interchangeable in combinations and recombinations, and evolve into the locks and keys that modulate the empirically grounded apparent, though still conceptual transparencies with coherently arranged faces in function, in a complete perspective.
In figure 6 a 3-D plot of energies involved in the displacement of light emitted from a moving body as an additive sum of motions at any particular angle of light radiation with respect to motion of the body(Figure 5), matches the common shape of an egg. An inverse plot,1/R R=radius, intended to conceptually represent a transparent genealogy of the apparent egg , generates values that fall within the same range, in a different order, as those for R, and nearly consume the same shape and volume. Figure 7 demonstrates the same relationship with respect to a helix. Dependant values of R and 1/R with respect to independent parameters do not align but overlap to produce nearly identical shapes, displacement volumes but opposing I direction (anti-parallel?) coils-an arrangement of dependant parameters that fall within a common range in all plots. A transparent, apparent exchange/rearrangement of parameters that maintains a likeness in values as explanation for apparent functioning, as in the description of memory as both transparent and apparent, emerges.
The genetic language, thus, is only an apparent property with respect to this interpretation. Its’ interpretation from observation is suggested to be a result of a necessity of perception combined with observation, a dependence of perception/life for the existence of two surfaces, space(s) that are actually emerged from one surface and is paradoxically observed in an apparent manner existing that way (i.e. the linear arrangement of nucleotides in a string ). A motion birthing deception of nature, a universal potential for ambiguity in meaning, also existing as a function of parameters of language usage is attributed to an exchangeability of parameters of the apparent and transparent at all levels from the molecular to the more tangible objects of existence. In this same sense the tautologies used by philosophers and linguists in the validity test of sentences and propositions might be conceived to, in analogy, if transposed into a geometrical form of lengths and truth values assume a motion from offset truth values of phrases- a valid test of a phrase would be designated to produce no motion-the universe, though, in model construction cannot be given a stillness in any aspect-meaning is always relative and dependant on a relationship of motions. . In this light, this described model might be tested for logical structure only with respect to its’ conception as a transparency of the transparent and the apparent, though internally consistent conceptually, it entails a constancy only with respect to nomenclatures and conceptual mechanisms of representation of entities in associations. In nature deceptive motions, and transparent divides are attributable to conceptual origins that entail perspectives related to histories in the emergence of observation.
In abstraction, as in reflexive perception, as in language usage with respect to meaning, the apparent and transparent cannot be so easily divided for scientific study, but can be ordered conceptually to conceive of laws of nature in which either might be parametrically interchangeable with the other in the description of emergence.
1 Biological genetic processes are attributed a like-from-like, genetic origin as a class of processes that are self belonging (Kirsh 2008), i.e. genetic processes that originate genetically, but are not self belonging in the sense that life itself cannot be given as a singular genetic emergence, is not a genetic process but involves al least two distinct and intersecting energy paths.
2 Multi-function genes, multi active enzymes (Kirsh et al 1978)are more easily accommodated as lock and key matching rather than enzyme –substrate matching in which nature possess a wobble in that orientation and not with respect to lock and key.
3 Cytosine is known to be capable of spontaneous conversion to uridine at room temperature. However uridine is not detected in the DNA (Kirsh 1986) though it can pair with adenosine to cause a C/G to U/A to A/T change in base pairs on DNA replication. As an additional fact pertaining to its’ absence in DNA, based on this discussion, it might not be expected to be involved in mutagenic wobbling as it is suggested to be intimately associated with a lock and key function involving identity and maintenance.
4 The use of inverse functions to represent the transparent is an approximation in the sense that energy differences, i.e. displacement energies involved in the creation of volumes as functions of ∆c are the actual topic. It may result that c^x/ ∆c^x, x is an integer, i.e. x=3 to illustrate volumes; ∆c bearing a universally modulating association to naturally allowed velocities of masses.
5 Proximal and distal (i.e. reflected light and refracted/ ambient light/daylight) sources combined, provide the energy
inputs for visual transparencies (Figure 7).
From a first person/species perspective of location on the earth as a single apparent source (though having a dual as both an apparent and transparent source if the eye/brain is considered as a catalyst and light a substrate in the formation of transparencies) ,energy from the sun is secondarily apparent only as a source of metabolic energy for food as a substrate and members of the species as a catalyst-i.e. as a transparent component. It is interesting to note that the entire length of human DNA is estimated to be of the same order of magnitude as the distance from the earth to the sun. Speculation, in light of these analogies, suggests strictly an alternate source of energy for processes involved in transparent aspects of a genealogy for the origin for the species than that provided by processes of the earths’ sun as a transparent value for the length of the DNA would greatly exceed its apparent value in the model. If it is significant the matching of the length of human DNA to the earth sun distance suggests that it has a transparent component that is significant, both values are empirically derived from direct measurement. A direct relationship of DNA to sunlight, not construed to exist, suggests that intervening catalyst/substrate processes within the organism and cell might be accounted for as catalytic, transparent values, intersecting physically/apparently with both DNA and solar energy as substrates. If the role of the eye/brain is considered catalytic with respect to light, a role of DNA (sequestered from solar radiation) as memory in terms of its’ length is suggested to be as a substrate with respect to solar radiation. This suggested duality of role of solar radiation and the nucleic acids as either catalyst or substrate is suggested to delineate time, is modulated by totally by apparent geometrical length and transparent energy differentials:
mass*velocity ^2(energy)/distance = mass*distance/time^2=mass*acceleration
= force
A resulting net force, inversion potential, related to total surfaces involved in the sequestering of the nuclear material in the cell might be entailed to function in a manner inversely with whole transparent potentials(i.e. DNA as physical piece of memory from a descent across space) suggested to be associated with homeostatic integrity/immunological identity. The physical application of force is known to induce cancers. Direct sunlight, especially an ultraviolet component of sunlight, is reported to be a source of cancers of the skin, eye, and able to cause thymidine dimers in DNA which have a high mutagenic potential. It is also possible to account generally for apparent and transparent energies by a displacement of light energy from one location to another (Naomi,2007) involving the application of a large magnitudes of energy to exert a force to guide energies. In analogy, a short circuit in sequestering/buffering forces may result in a dedifferentiation of stabilities, dedifferentiation of, naturally emerged, apparent and transparent associations, destabilization/loss of inherited memory related to genealogies of origin effected by forces connected with internal exposure to solar radiation.