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Histone Inspectors: Codes and More Codes

Cornelius Hunter
March 27, 2010
Intelligent Design
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By now most people know about the DNA code. A DNA strand consists of a sequence of molecules, or letters, that encodes for proteins. Many people do not realize, however, that there are additional, more nuanced, codes associated with the DNA. For instance, minor chemical modifications (such as the addition of a methyl group) to the DNA provide bar-code like signals to the protein machinery that operate on the DNA. This DNA methylation influences which genes, along the DNA strand, are read off. And this DNA methylation itself may be modified to provide additional information.  Read more
Comments
Wiki quote, regarding Cell Cycle: "Cell cycle checkpoints are used by the cell to monitor and regulate the progress of the cell cycle. Checkpoints prevent cell cycle progression at specific points, allowing verification of necessary phase processes and repair of DNA damage. The cell cannot proceed to the next phase until checkpoint requirements have been met." And now, the keywords of the quote: "checkpoints", "to monitor and regulate", "to prevent", "verification", "process and repair", "to met the requirements"... I challenge darwinians to elaborate just one fully unguided model that can generate one of the above mentioned key-words/processes...Sladjo
March 30, 2010
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Needless to say the idea that all of this arose on its own, as a consequence mutations and the like, luckily putting together such intricacies, is beyond silly.
Darwinian selection would be hard pressed to create such structures if the perception of such structures requires large numbers of parts simultaneously in place. Regarding multiple function and codes, Sanford wrote in Genetic Entropy
There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns - which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture - which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes).
scordova
March 27, 2010
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