Posted: Apr 16, 2012 1:17 am
CharlieM wrote:Just A Theory wrote:
Second, the translation of DNA into proteins is absolutely not algorithmically incompressible due to redundancy in the third nucleotide of virtually every triplet codon. GCT is functionally the same as GCC, in fact there are 64 possible codons and only 20 amino acids plus 3 stop sequences meaning that there is a large amount of redundancy in the genetic code. It is therefore trivially easy to compress the genetic code by removing some of that redundancy.
http://www.sciencedaily.com/releases/2012/03/120328142850.htmBy measuring the rate of protein production in bacteria, the team discovered that slight genetic alterations could have a dramatic effect. This was true even for seemingly insignificant genetic changes known as "silent mutations," which swap out a single DNA letter without changing the ultimate gene product. To their surprise, the scientists found these changes can slow the protein production process to one-tenth of its normal speed or less.
As described March 28 in the journal Nature, the speed change is caused by information contained in what are known as redundant codons -- small pieces of DNA that form part of the genetic code. They were called "redundant" because they were previously thought to contain duplicative rather than unique instructions.
This new discovery challenges half a century of fundamental assumptions in biology. It may also help speed up the industrial production of proteins, which is crucial for making biofuels and biological drugs used to treat many common diseases, ranging from diabetes to cancer.
"The genetic code has been thought to be redundant, but redundant codons are clearly not identical," said Jonathan Weissman, PhD, a Howard Hughes Medical Institute Investigator in the UCSF School of Medicine Department of Cellular and Molecular Pharmacology.
"We didn't understand much about the rules," he added, but the new work suggests nature selects among redundant codons based on genetic speed as well as genetic meaning.
So the redundancy of codons is an assumption based on ignorance that has been treated as fact with very little skepticism in evidence.
Happy to discuss via PM but the linked article does not contradict what I was saying. The postulation that different triplet codons may be transcribed at different rates isn't that shocking to me considering the differing bond strengths of the G+C vs A+T pairings - you have to take that into account when designing oligos for use in PCR.
It's great work by the researchers to quantify the effect but the redundancy of the genetic code in terms of what amino acids are coded for still remains in play. However, in bacteria which typically have more than one ORF per chromosome, then the redundancy may disappear due to re-use of codons.
The original assertion was that genetic sequences (of DNA) are algorithmically incompressible. Even if there is a differential rate of transcription between codons, the assertion of incompressibility is still false.