DNA Translation Has Codes Upon Codes

The DNA code is protected by another code, and is read with a machine that reads a third code.  This is an emerging picture from ongoing research into DNA transcription, as reported in Science.¹
    In the 1950s, scientists were astonished to find a code at the genetic basis of life.  DNA’s four-letter alphabet, arranged into triplet codons, providing 64 combinations that could code for the 20 amino acids and “punctuation” in various ways, seemed simple and elegant (see description in our online book).  Now it seems, remarkable as this mechanism is, it is way too simple.  Other factors must control when and how particular genes are to be transcribed.  Biochemists have also been cataloguing a huge number of post-transcriptional and post-translational modifications that take place, from the moment messenger-RNA is formed to after the protein chain is assembled.  What controls the regulators?
    Additional codes involved in regulating gene expression have been coming to light.  One was the histone code attached to DNA (11/13/2007) which may be as complex and as important as the DNA code itself (04/12/2003).  Now, Science published two papers on another code attached directly to the transcriber, RNA Polymerase II.  This “CTD code” is composed of tandem repeats of seven amino acids forming a tail called the carboxy-terminal domain (CTD).  New work expands the previously-known number of phosphorylation states from four to eight.  Since each of these amino acids can be modified by phosphorylation, patterns emerge that resemble a hexadecimal system.  Because the tandem repeats vary from 17 to 52 sets on a CTD, if each phosphorylation pattern had a functional meaning, there are potentially 8⁵² different CTD patterns – over 900 trillion trillion trillion trillion.
    Such a number is probably degenerate – i.e., vastly greater than the number of states that are actually needed for functional meaning.  Still, the potential is there for a huge array of states that can direct the behavior of RNA Polymerase II.  It also might help explain why the number of genes in the human genome was surprisingly low; perhaps the CTD code provides a way to get more transcripts out of a gene – resulting in many proteins from one gene.  Experiments have shown that some distinct phosphorylation patterns do indeed change the expression of the gene.  Jeffry Corden [Johns Hopkins U] wrote in the review article on the two papers,

The biological role of CTD phosphorylation remains to be fully elucidated, but the emerging picture is that the pattern of CTD phosphorylation changes during RNA synthesis, allowing dynamic modification of the DNA template and processing of the nascent RNA transcript.  The studies by Chapman et al.² and by Egloff et al.³ provide both the tools to fully document CTD phosphorylation patterns and the best evidence to date that these patterns constitute a code that intersects, at the most fundamental level, with the regulation of different classes of eukaryotic genes.

It appears that both DNA and its transcriber have codes, completely independent from the DNA code, affixed to them.  Are they passwords forming an authentication scheme?  Are they messages telling the machinery what to do?  If so, what sends the messages, and what recognizes them?  How is the password validated?  More work into this fascinating area will surely be needed.  For now, Corden said, “Together, the papers show that CTD phosphorylation is more complicated than previously thought and link, for the first time, expression of specific genes with a distinct CTD phosphorylation pattern.”

1.  Jeffry L. Corden, “Seven Ups the Code,” Science, 14 December 2007: Vol. 318. no. 5857, pp. 1735-1736, DOI: 10.1126/science.1152624.
2.  Chapman et al, “Transcribing RNA Polymerase II Is Phosphorylated at CTD Residue Serine-7,” Science, 14 December 2007: Vol. 318. no. 5857, pp. 1780-1782, DOI: 10.1126/science.1145977.
3.  Egloff et al, “Serine-7 of the RNA Polymerase II CTD Is Specifically Required for snRNA Gene Expression,” Science, 14 December 2007: Vol. 318. no. 5857, pp. 1777-1779, DOI: 10.1126/science.1145989.

The situation just keeps getting worse for the evolutionists.  None of the three papers even mentioned evolution.  Who would dare?
    Apparently, Science Daily dared.  Summarizing these papers, it said, “It would appear that, over the last 500 million years, other ways to produce highly complex organisms have evolved.  Evolution has simply found more efficient ways to use the genes already there.”  You may now utter a long, sarcastic groan.