The Rules of Variation Expanded, Implications for the Research on Compatible Genomics

Abstract

The main focus of this article is to present the practical aspect of the code rules of variation and the search for a second set of genomic rules, including comparison of sequences to understand how to preserve compatible organisms in danger of extinction and how to generate biodiversity. Three new rules of variation are introduced: 1) homologous recombination, 2) a healthy fertile offspring, and 3) comparison of compatible genomes. The novel search in the natural world for fully compatible genomes capable of homologous recombination is explored by using examples of human polymorphisms in the LDLRAP1 gene, and by the production of fertile offspring by crossbreeding. Examples of dogs, llamas and finches will be presented by a rational control of: natural crossbreeding of organisms with compatible genomes (something already happening in nature), the current work focuses on the generation of new varieties after a careful plan. This study is presented within the context of biosemiotics, which studies the processing of information, signaling and signs by living systems. I define a group of organisms having compatible genomes as a single theme: the genomic species or population, able to speak the same molecular language through different accents, with each variety within a theme being a different version of the same book. These studies have a molecular, compatible genetics context. Population and ecosystem biosemiotics will be exemplified by a possible genetic damage capable of causing mutations by breaking the rules of variation through the coordinated patterns of atoms present in the 9/11 World Trade Center contaminated dust (U, Ba, La, Ce, Sr, Rb, K, Mn, Mg, etc.), combination that may be able to overload the molecular quality control mechanisms of the human body. I introduce here the balance of codons in the circular genetic code: 2[1(1)+1(3)+1(4)+4(2)]=2[2(2)+3(4)].

Figure 1

Balance of codons in the classic circular genetic code. Rectangles are surrounding the odd-numbered codons present in quadrants one and three and the paired groups of codons that are present in quadrants two and four ([a]-[d], quadrants 1-4, respectively). Only quadrants two and four are fully symmetrical, both by number and by position. Here, the rectangles specifically represent the quasi-symmetrical position of the odd-numbered groups of codons for quadrants one and three, and of paired groups of codons for quadrants two and four, having equilibrium in the net sum for these codons per quadrant (numbers in bold). A similar numerical balance is seen in the essential hydrophobic amino acids with U at the center of their codons (ref. 4).

Figure 2

Examples of coordinated changes in elements from the 9/11 WTC dust and its leachate tested at different sites. Left Column: ‘Codissolved’ in the leachate with a similar pattern per collecting site we have: uranium, manganese and magnesium; barium and strontium; rubidium and potassium. Right Column: A similar dust pattern was observed by uranium, beryllium, manganese, titanium, magnesium and aluminium; by strontium, barium, lanthanum, cerium and antimony; by iron and arsenic (flat regions, sites that were not measured). Two values at the right of each graphic (08 and 09) correspond to the girder coatings while samples 20 and 36 at their left side correspond to the indoors. Symbols: mg/L—milligrams per liter; μg/L—micrograms per liter; ppm—parts per million.

Figure 3

a) Prospects for the genomic rules of variation: The generation of biodiversity, represented by circle c (cluster c contains new hypothetical varieties to be developed by humans), the preservation of endangered biodiversity is represented by circle b, while all organisms with compatible genomes are represented by circle a, which currently includes endangered organisms; circle d represents the currently over-inflated number of species, including ‘phenotypic species’ and ‘behavioral species’. Notice that once the factor of compatible genomics is added, the currently over expanded number of ‘species’ will dramatically shrink, moving down from d towards a (horizontal arrow). b) Each orbit of organisms with compatible genomes is one and the same theme, the same genomic species or genomic population. Each dot on each expanding circle represents a different variety for the compatible species that are represented by the complete orbit. The molecular genetic language spoken by all the dots within each orbit is the same, spoken through different local accents: their phenotypes and behaviours.

Figure 4

Representation of atoms produced by possible nuclear fissions of plutonium (Pu), Barium (Ba), and Rubidium (Rb) as followed by the uniquely coordinated patterns of bio-available metals present on the soluble leachate of the 9/11 contaminated dust reported by the USGS. Atomic numbers are shown with the graphic of the dust (Fig. 2). “Cracks emerged” inside the preserved 9/11 WTC “compressions”, also called the 9/11 WTC “meteorites” (see http://www.webcitation.org/5y2mJY9Be and footnote o).