Cell’s High-Fidelity Proofreading and Editing Explained

—It’s unusual to have a story win both Amazing and Dumb awards simultaneously, but the reason will become clear.–ed.)
Luisa Cochella and Rachel Green (Johns Hopkins) have published a primer on “Fidelity in Protein Synthesis” in Current Biology.¹  This is a good article for cell biology enthusiasts to read, to learn more about the methods cells employ to translate DNA into proteins without making mistakes: how they perform proofreading, editing and quality control, the molecular machines that are involved, and the remarkable optimization levels they achieve between the competing constraints of accuracy, efficiency and speed.  These processes increase the fidelity of translation over simple base-pairing by up to 100,000 times, even working rapidly so that vital cell processes are not delayed by too much inspection.  The authors describe strategies used by translation machines, the amazing family of aminoacyl-tRNA synthetases, the ribosomes, and more.  They use the word fidelity 18 times and high fidelity five of those.
    Despite their contribution in helping readers of the magazine appreciate the wonders of high fidelity translation in the cell, they win the Stupid Evolution Quote of the Week award for their opening two sentences: “The flow of genetic information from DNA to RNA to protein constitutes the basis for cellular life.  DNA replication, transcription and translation, the processes through which information transfer occurs, are the result of millions of years of evolution during which they have achieved levels of accuracy and speed that make modern life possible” (emphasis added in all quotes).

¹Luisa Cochella and Rachel Green, “Fidelity in protein synthesis,” Current Biology, Vol 15, R536-R540, 26 July 2005.

Did that little paean to evolution warm your bosom?  More importantly, did it contribute one whit to this article?  Cochella and Green, bless their Darwinista hearts, have illustrated again the freakish juxtaposition of intelligence and nonsense that characterizes evolutionary jargon.  It seems like a kind of schizophrenia or mystery religion to the uninitiated to hear high fidelity, quality control, optimization, genetic code and other design words ascribed to mindless processes of evolution.  Do they explain how this incredible system evolved?  Of course not; being brainwashed materialists, they just assume it had to, so it did.
    Everyone who has DNA should learn something about those aminoacyl-tRNA synthetases (see 09/16/2004 entry and links in the commentary).  It’s a shame these high-tech machines in our bodies and in all living things have been given such geeky names; they are really remarkable in their specificity and accuracy.  More importantly, they constitute a classic logical proof of design, because they know two languages and are able to translate one into the other.  Here’s how Cochella and Green introduce them:

While the accuracy of DNA replication and transcription depend only on cognate base pair selection, translation depends on an additional, base-pairing-independent reaction that must be carried out with high specificity.  Each tRNA must be covalently attached to a specific amino acid – aminoacylated – preserving an unambiguous codon-amino acid correspondence known as the genetic code.  This reaction is carried out by aminoacyl-tRNA synthetases specific for each amino acid and a corresponding group of tRNAs (isoacceptors).  These enzymes must therefore recognize two substrates: first, a group of tRNAs which share a collection of ‘identity elements’ and second, an amino acid that may be distinguished by small differences in side-chain properties.

Having one language or code is proof enough of design, but possessing the ability to translate one into another requires a language convention – something never observed to be a product of chance or natural law, but always known to be the result of intelligence: whether with two intelligent beings communicating, or interacting programs that were produced by intelligent agents.  This should be clear to anyone not lobotomized by Darwinian education, but look how these authors explain it by just waving the evolutionary magic wand.  They are discussing how these machines can distinguish between very similar amino acids.  Watch the hocus pocus:

How do synthetases deal with this?  The aminoacylation reaction, which takes place at a site of the enzyme called the synthetic site, occurs in two steps.  First the amino acid is activated by adenylation (consuming ATP) and then it is transferred to the tRNA (releasing AMP).  Steric exclusion of amino acids with larger side-chains and recognition of specific properties of each amino acid generally make this synthetic site specific enough so that only the correct amino acid can be activated and transferred.  But amino acids having similar properties to and a smaller size than the cognate amino acid can be misactivated at frequencies that are too high to maintain an unambiguous code.  As a consequence, enzymes facing this problem have evolved a second active site, distinct from the synthetic site, called the editing site, where misactivated amino acids or misacylated tRNAs are hydrolyzed.

Did you catch that?  Astonishing! (see the Fairy Godmother song, 06/27/2005 commentary.)  Here were machines already accurate enough for most instances, but since there was a “need” for an “unambiguous code,” and some amino acids were so similar that mistakes leaked through, well – we are told, no problem– evolution to the rescue: they just “evolved” an editing site (Selah) with the ability not only to distinguish threonine from valine and serine, but to send the imposters to the recycle bin (Selah).
    It is therefore with great sadness to have to tarnish the reputations of these otherwise bright scientists with the SEQOTW prize, but they earned it.  Ignorance is no excuse.  They can gain absolution by removing the Darwinspeak and rewriting their article with more intelligent design.