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)]. KeywordsCompatibility; Genetics; Fertility; Genes; Descendants; Mendel; Bateson; WTC; Strontium "…a detailed understanding of the natural order." b Graeser, Lynn, Schoenheit

Escaping the Cut by Restriction Enzymes Through Single-Strand Self-Annealing of Host-Edited 12-bp and Longer Synthetic Palindromes

“…Palindromati seems to be a sub-product of an edited and dimerized bi-tandem of the ZAP adaptor done by the host, present in its totality, or in portions or their tandems, in millions of GenBank sequences (Castro-Chavez, 2004, 2010, 2011, including basically every sequenced organism and every sequencing laboratory in the world.…”

“…‡12-BP SINGLE-STRAND SELF-ANNEALED PALINDROMES ESCAPE THE CUT BY RESTRICTION ENZYMES 159 used two different methodologies, dust leachate and X-ray fluorescence, finding an average Sr = 1.1 mg/L and 726.61 ppm, respectively. The thousands of unprotected first responders are still unaware of the extreme toxicity of the 9/11 WTC dust breathed by them, and of its high presence of Sr and other highly unusual, possibly unstable, atoms and of carbon nanotubes (Castro-Chavez, 2011). * However, it is encouraging to see a growing number of studies that use multiple groups and/or methodological platforms plus different data analysis tools and algorithms (Kidd et al, 2010;Halper-Stromberg et al, 2011;Pinto et al, 2011).…”

“…1A-E). Table 1 also shows 36 sequences contaminated by the ZAPAdaptor's EcoRI palindromic linker longer than 22-bp; 20 different sequences related to this analysis are also published (Castro-Chavez, 2011). Table 1 starts again with the human sequence AF230097 to emphasize the importance of cleaning the sequences of genes; in this case, the contamination is affecting a key nuclear protein (Hdac8) that controls the gene expression for the rest of the genes (Hu et al, 2000).…”

“…Finally, by comparing the translation from codons to proteins with the rotating genetic code (Castro-Chavez, 2010, 2011, the translated palindromes were detected as contaminants. Exemplified in Table 2 is the seriousness of the contamination by EcoRI adaptors and linkers if they are translated as being part of a human exon or protein.…”

“…Palindromati is a laboratory artifact produced by a biological host (yeast or bacteria) interacting with a vector equipped with adaptors. Through host-vector interactions, those adaptors are generating either full or partial palindromes or palindromic sequences capable of single-strand self-annealing that are preventing them from being degraded by restriction enzymes such as the active dimer formed by EcoRI (Castro-Chavez, 2010, 2011. The normal digestion of EcoRI is represented in Figure 2A.…”