August 9, 2009 | David F. Coppedge

Did Evolution Create Genetic Proofreading?

Protein manufacture in the cell is such a critical operation, there are numerous error-checking mechanisms the cell uses to get it right.  One of the most amazing is the careful association of DNA codons with amino acids, and the “proofreading” or “spell checking” that ensures fidelity.  How could spell checking evolve?
    Science Daily announced that “Scientists Find Early Evolution Maximized The ‘Spellchecking’ Of Protein Sequences.”  Sounds interesting.  What did they find?  The answer should be in the original paper in Science.1  There, Guo, Schimmel and others from Scripps Institute claim that they found homologies between the spell-checking domains of one of the enzymes responsible for linking transfer RNA (tRNA) codons with the appropriate amino acid.  In this case, it is the aminoacyl-tRNA synthetase for alanine, called AlaRS.  This particular synthetase has to distinguish alanine from two other similar amino acids, glycine and serine.  It does this through the use of additional factors or domains called AlaXps that “provide functional redundancy by capturing mischarged tRNAAla molecules that escape the embedded editing activities of AlaRSs.”2  In addition, a linker called C-Ala binds the error-correcting domains together.
    The team found that most of the domains of AlaRS are “highly-conserved” (i.e., unevolved) in all three kingdoms of life – including the modular arrangement of AlaRS itself.  That makes sense, else we would all be dead.  In their wording, “strong selective pressure retains these editing activities throughout evolution.”  But they did find C-Ala is only loosely conserved.  From this they wove a story of how this spell checking arrangement came to be:

This phylogenetic analysis implies that all three forms of AlaXp evolved in the ancestral community.  This phylogeny also suggests that AlaXp-II is derived from AlaXp-I.  The editing domain of ThrRS is closest to AlaXp-I, thus suggesting an early separation that split the original editing enzyme into two different specificities, one for tRNAThr and the other for tRNAAlaMost importantly, the phylogenetic analysis indicates that the editing domain of AlaRS appeared concurrently with the ancient, most-developed, and largest free-standing editing enzyme, the C-Ala?containing AlaXp-II.  Thus, C-Ala may have been instrumental in bringing together editing and aminoacylation domains on one tRNA to ultimately (through fusion) create AlaRS (fig. S6).

In the simpler words of the Science Daily summary, the results “show that two separate functions—alanine adding and editing—were joined together in a single enzyme during early evolution, in a way that greatly enhances these activities.  The findings provide a glimpse into how enzyme functions have evolved.

1.  Guo, Chong, Beebe, Shapiro, Yang and Schimmel, “The C-Ala Domain Brings Together Editing and Aminoacylation Functions on One tRNA,” Science, 7 August 2009: Vol. 325. no. 5941, pp. 744 – 747, DOI: 10.1126/science.1174343.
2.  There are three classes of AlaXp.  “Three types (Ia, Ib, and II) of free-standing genome-encoded AlaXps are widely distributed in all three kingdoms of life and act in trans to clear tRNAAla mischarged with Ser or Gly (7, 8, 31, 32).  Type Ia AlaXp lacks the Gly-rich motif near the N terminus of the editing motif of type Ib and type II AlaXps (33).  However, unlike types Ia and Ib AlaXps that are composed of just the editing domain, type II AlaXp has the C-Ala domain (Fig. 1A).”

They found no such thing.  They found living organisms with spell-checking and proofreading that works on a phenomenally accurate scale – much better than the output of professional typists.  Then they made up a story out of thin air about how the parts of the machinery were “brought together” during an evolutionary history that was never to be doubted.  They ignored the error catastrophe that would have brought life down to a crash before the proofreading was already working.  They expected us to believe that “selective pressure” acts like a designer substitute to work miracles.  And they expected us baloney-detectors to swallow their line as if they “found” how all this came about.  Don’t fall for it any more than if they compared engine parts from a Mazda and a Ford and told you they found a glimpse of how they emerged from the dirt, or if they compared the spell checking algorithms in Internet Explorer and Firefox and described how they had a common ancestor in an earthquake.
    Selective pressure, remember, is nothing but a set of boundaries.  It is not a creative force.  It’s like the walls and hubs in a pinball game (see 07/14/2009 commentary).  None of the constraints keep the ball from dropping in the hole and bringing the game to a stop.  It takes an intelligent agent manning the flippers to win.
    It’s time to remember Keith Wanser’s statement about evolutionary explanations.  “There is not one theory of evolution, but a body of opinions, speculations and methods for interpretation of observational facts so that they fit into the philosophy of naturalism.”  That is what you saw again here.  Until enough people call them on the carpet for this circular, question-begging tactic, it will go on and on, deceiving readers of science journalism that the Darwin Party diviners are succeeding in getting glimpses into a mythical materialistic past that produced something from nothing.  Spellchecking is something, all right, but nothing is nothing.

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