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Is genomics as big a mess as Kas Thomas says?


My PhotoThomas crossed our screen a little ways back when he had the misfortune to stand on a street owned by Darwin’s trolls while proclaiming obvious facts.

Apparently, he survived, and he now says:

A substantial portion of published genome data is suspect, at this point, either because of contamination issues, technical problems surrounding DNA sequencing technology, or faulty gene annotation. An example is the Oryza sativa indica (rice) genome, which inexplicably contains at least 10% of the genome of the bacterium Acidovorax citrulli. There’s also a Culex (mosquito) genome with a complete copy of Wolbachia embedded. The genome of Rothia mucilaginosa DY-18 contains over 300 genes incorrectly annotated in antisense orientation (as does the genome of Burkholderia pseudomallei strain 1710b, a truly execrable train-wreck of a genome).

Another example of a genome gone wrong (arguably) is that of the bacterium Ktedonobacter racemifer, which is filled with forward and backward copies of transposases. Incredibly, one in 13 Ktedonobacter genes is a transposase, integrase, or resolvase (and that’s not counting the many “hypothetical proteins” with “transposase-like” mentioned in the gene ontology notes). Disregarding the 40% of that organism’s genes that are marked as hypothetical proteins, one can say that in Ktedonobacter, one in four genes of known function is a transposase, integrase, or resolvase. (Some of the organism’s 4000+ “hypothetical proteins” are actually transposases incorrectly annotated in an antisense orientation.) Common sense says something’s amiss.

Yeah, common sense would say something was amiss, but Darwin’s followers will say that just shows how disorganized life is. Some lit great will turn it into an elegant essay, recommended for science majors seeking to broaden their horizons.

File under: Shuddup already … or else.

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