Among the hidden stars of the gulf cleanup is an oil-hungry bacterium that Dr. Seuss could have named — Alcanivorax. It and fellow microbes are breaking down a significant amount of the oil that gushed into the environment from BP’s runaway well, scientists say. The microbial feasting is known as biodegradation.
Archive for the 'Genetic Code' Category
A couple of contributors have suggested that we have a thread on this article: The Splicing Code
In a paper published on May 6 in the journal Nature entitled "Deciphering the Splicing Code," a research team led by Professors Brendan Frey and Benjamin Blencowe of the University of Toronto describes how a hidden code within DNA explains one of the central mysteries of genetic research — namely how a limited number of human genes can produce a vastly greater number of genetic messages. The discovery bridges a decade-old gap between our understanding of the genome and the activity of complex processes within cells….
Arthur Hunt posted Signature in the Cell? at his blog The RNA Underworld. Art attempts to refute Meyer by citing a paper (RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code, J Mol Evol; 69:406–429) authored by Michael Yarus, Jeremy Joseph Widmann and Rob Knight. As Art explains:
Put more plainly, 75% of tested amino acids associate with their anticodon (in some cases, along with their codon) in these studies. This is remarkable, as it is demonstrative of an underlying stereochemical basis for at least some of the genetic code.
Art then proceeds to make a speculative argument based on the study:
Thus, we can discern that the genetic code as we understand it today likely evolved in several steps – a stereochemical era wherein a core set of triplet-amino acid correspondences was first established, followed by subsequent expansion of the assignments of other triplets and recruitment of other amino acids (typified by gutamine and leucine) via other mechanisms.
In the thread Sad Smoke and
Mirrors, there has been some discussion of Behe's use of the clotting function as IC. Nobody much likes to talk about immune system function, because it's like that crazy cousin nobody likes to bring up at the family reunion. Way out of line, despite being quite predictable enough to design vaccines and such in order to purposefully and quickly 'evolve' antibodies to specific disease causes.
I say 'evolve' with the usual haha caveat that "everybody knows" that individual life forms don't evolve. They just exist, develop, decline and die. Maybe reproduce along the way. Evolution doesn't happen unless reproduction happens, and then only generations down the line. Except, according to un-careful word usage, when it comes to the immune system.
Speaking of which, this report appeared at ScienceDaily today:
On the Hypercube Structure of the Genetic Code is authored by Miguel A. Jimenez–Montano, Carlos R. de la Mora–Basanez and Thorsten Poschel. The authors begin:
Abstract: A representation of the genetic code as a six–dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon–anticodon recognition. The proposed structure demonstrates that in the genetic code there is a balance between conservatism and innovation. Comparing aligned positions in homologous protein sequences two different behaviors are found:
a)There are sites in which the different amino acids present may be explained by one or two “attractor nodes” (coding for the dominating amino acid(s)) and their one–bit neighbors in the codon hypercube, and
b) There are sites in which the amino acids present correspond to codons located in closed paths in the hypercube. The structure of the code facilitates evolution: the variation found at the variable positions of proteins do not corresponds to random jumps at the codon level, but to well defined regions of the hypercube.
The evolutionary forces that produced the canonical genetic code before the last universal ancestor remain obscure. One hypothesis is that the arrangement of amino acid/codon assignments results from selection to minimize the effects of errors (e.g., mistranslation and mutation) on resulting proteins.
Genetic code origins: tRNAs older than their synthetases? is a PNAS paper which begins with this paragraph:
We present a phylogenetic analysis to determine whether a given tRNA molecule was established in evolution before its cognate aminoacyl-tRNA synthetase. The earlier appearance of tRNA versus their metabolically related enzymes is a prediction of the RNA world theory, but the available synthetase and tRNA sequences previously had not allowed a formal comparison of their relative time of appearance. Using data recently obtained from the emerging genome projects, our analysis points to the extant forms of lysyl-tRNA synthetase being preceded in evolution by the establishment of the identity of lysine tRNA.
I have questions for those of you who believe that the genetic code evolved as a result of natural selection.
1. What was the biological context within which the evolution took place? Cellular? Extra-cellular? A combination of both? Explain what determined the answer you gave.
2. How does a code evolve incrementally?