It would be helpful and mature if you could refrain from labelling or stereotyping people. I do not have a standard modus operani, my thoughts and consciousness evolve as do my ideas and thought patterns. I use a wide variety of sources - basically whatever I can get my hands on - including textbooks, journals, communication with professors, colleagues, associates, and experts in the field that I sometimes personally contact, learned and acquired knowledge through courses, research, and experimentation - mine and others - as well as the web.
I'm still not certain what CharonZ is calling nonsense, but I know he has the capacity, experience and knowledge to elaborate. That is what I asked.
I think the standard code is capable of evolving, and that it is. So in this sense, the universal code is not entirely "universal." In the sense that the standard code is applied to interchange amino acid coding and used in biotechnology, it is universal. The majority of the "non-standard codes" arize from variations (evolution of) tRNA. Selenocysteine is now considered the 21st amino acid, and pyrrolysine the 22nd. They are created artificially by inserting a polymerase to change the metabolic protein synthesis pathway and this has been done successfully in E. coli and other bacterium with the goal of observing how the organism evolves and adapts with its new genetic makeup. Arthropods have been used to create a new genetic code that translates the codon AGG as lysine, instead of serine (as in the invertebrate mitochondrial genetic code) or arginine (as in the standard genetic code) with the consequent being that several events of parallel evolution of the genetic code have been discovered in the arthropods in which the AGG codon then was reassigned between serine and lysine (Abascal et al., 2006).
Other research efforts that I have read focus on expanding the genetic code by inserting an artificial fifth base. For example, Romesberg and colleagues at the Scripps Research Institute in La Jolla (he is very well-known for his research in this field) have designed a fifth base, called 3-fluorobenzene (3FB), that pairs with itself through a new polymerase enzyme that recognizes the 3FB, latches on to it, and incorporates it into a replicating strand of DNA. Instead of just the having the standard base pairs "G-C" and "A-T," a new third pairing occurs: "3FB-3FB" between two unnatural bases. To improve replication, they create their own polymerase able to replicate the unnatural DNA. The process they used is called amber suppression whereby a stop codon's function is changed so that it now codes for the unnatural amino acid using an entirely new pathway where the unnatural amino acid gets specifically placed onto a t-RNA. It makes one mistake for every 1,000 base pairs, compared to natural polymerases that make one mistake every 10 million bases (Scripps, 2004 & 2005). In a similar way, Ryan Mehl created a new amino acid called p-aminophenylalanine (pAF) from simple carbon sources. The pAF is incorporated into proteins alongside its existing 20 amino acids.
The purpose in Romesberg and others' research in this area is to change (evolve) the current genetic code of the organism and the expose it to selective pressures to watch the development, adaptation and evolution of it, and to see if the organism with the expanded genetic code has an evolutionary advantage over the natural organism. This approach serves as a method for increasing the genetic repertoire of living cells to include a wide variety of amino acids with novel structural, chemical, and physical properties not found in the common 20 amino acids. Thus they are evolving the standard genetic code.
As stated above, over 30 novel amino acids have been genetically encoded in response to unique triplet and quadruplet codons including fluorescent, photoreactive, and redox-active amino acids, glycosylated amino acids, and amino acids with keto, azido, acetylenic, and heavy-atom containing side chains. It has been suggested that by removing the limitations imposed by the existing 20 amino acid code, it should be possible to generate proteins and perhaps entire organisms with new or enhanced properties (Wang and Schultz, 2005). These evolutionary modifications, and exceptions, not only suggest that the standard code can and is evolving, but also support the hypothesis of multiple evolutionary origins of life, i.e., that the current standard genetic code evolved from a previous code that had fewer than the 20 amino acids. Further back than this, I postulate that it evolved from RNA, aka., the RNA World hypothesis.
Any critical insight and "constructive" criticism on what I have posted above is very much appreciated. I am trying to expand and clarify my own thinking and interpretations about the "evolvability" of the universal genetic code. It certainly is not "frozen," as thought by Watson and Crick. But how can it be considered "universal" if it can, and is, being expanded in some species.
