Genome complexity: A code within a code? (Introduction)

by David Turell , Saturday, May 30, 2015, 15:13 (3253 days ago) @ David Turell

As predicted the human genome is way more complex than simply coding three letters for one amino acid:-http://www.uncommondescent.com/intelligent-design/guest-post-part-1-of-2-qualitative-complex-and-specified-information-within-genes-an-introduction/-"We all know that mutations in DNA can result in a different amino acid appearing in a protein. For example the DNA triplet codon if read as “CTT” would be translated to the amino acid Leucine (L; obviously via the mRNA intermediate). However, if there was a mutation from the C to the G, the frame would read “GTT” and this would be translated into a Valine (V). As we all further know, we can have deleterious, neutral, and beneficial mutations (in a given context). Additionally, a mutation in the third letter of the DNA triplet codon is often redundant at the level of the amino acid because of the redundant nature of the genetic code (“perfectly optimised” many would say). Obviously then, removal of or insertion of a new DNA base will have a much greater impact on the sequence (as you will shift the reading frame) and therefore is usually deleterious.-"Now I would make a request that I am not attacked for over-simplifying this concept, but to talk very simply about evolutionary change, mutations will occur at random in certain positions in the DNA sequence and this may be inherited (germline mutations) with a consequence of either deleterious, neutral or beneficial, with most “thought to be near-neutral.”-"There remains a question though that has fascinated me for a while, and led me to look at some examples of this. What if we discovered other layers of code within the same gene? What would be the impact of a mutation on this other code, relative to the foremost code? How much would this then limit the availability of more than one code to co-evolve, realistically?-***-"Now with the advance of proteomics and our ability to detect peptides and “map” the human proteome, a lot of information has come to light. In particular, it is apparent we are “missing” a lot of proteins found in cells but not annotated as genes in our databases. Surprisingly, for quite some time the field has held to the dogma of one gene, one Open Reading Frame (ORF) - and potentially many different proteins due to alternative splicing events, for example. Yet recent studies mapping the human proteome (“A draft map of the human proteome.” Kim et al. 2014. Nature. 509, 575-581) have yielded many MS spectra that cannot be assigned to annotated genes in the human genome.-***-" In this sense, Kim et al.`s study strongly supports the existence of the alternative proteome. Clearly, the alternative proteins detected by Kim et al. and by our team are the proverbial tip of the iceberg. A full map of the human proteome is thus still years away, and will require several important changes in our current thinking concerning the proteome and the concept that each mature mRNA only codes for one protein. "