My cell biology students will not thank me

Dan Graur has suggested some changes to the classification of DNA. It's one more pile of terminology to keep straight, but the distinctions are conceptually useful -- I particularly appreciate literal vs. indifferent DNA as subdivisions of functional DNA.

The pronouncements of the ENCODE Project Consortium regarding “junk DNA” exposed the need for an evolutionary classification of genomic elements according to their selected-effect function. In the classification scheme presented here, we divide the genome into “functional DNA,” i.e., DNA sequences that have a selected-effect function, and “rubbish DNA,” i.e., sequences that do not. Functional DNA is further subdivided into “literal DNA” and “indifferent DNA.” In literal DNA, the order of nucleotides is under selection; in indifferent DNA, only the presence or absence of the sequence is under selection. Rubbish DNA is further subdivided into “junk DNA” and “garbage DNA.” Junk DNA neither contributes nor detracts from the fitness of the organism and, hence, evolves under selective neutrality. Garbage DNA, on the other hand, decreases the fitness of its carriers. Garbage DNA exists in the genome only because natural selection is neither omnipotent nor instantaneous. Each of these four functional categories can be (1) transcribed and translated, (2) transcribed but not translated, or (3) not transcribed. The affiliation of a DNA segment to a particular functional category may change during evolution: functional DNA may become junk DNA, junk DNA may become garbage DNA, rubbish DNA may become functional DNA, and so on, however, determining the functionality or nonfunctionality of a genomic sequence must be based on its present status rather than on its potential to change (or not to change) in the future. Changes in functional affiliation are divided in to pseudogenes, Lazarus DNA, zombie DNA, and Hyde DNA.

That's a link to the full paper up top. Start reading, it will be on the exam.

More like this

I rarely laugh out loud when reading science papers, but sometimes one comes along that triggers the response automatically. Although, in this case, it wasn't so much a belly laugh as an evil chortle, and an occasional grim snicker. Dan Graur and his colleagues have written a rebuttal to the claims…
In a recent posting, Rusty answers me once again on the issue of testability. He proposes an actual test for both creationism and evolution. This is what he says: But in the strictest sense of the term testability, a falsifiable prediction must be made in order for a scientific theory to be…
Last month, I wrote about the terrible botch journalists had made of an interesting paper in which tweaking regulatory sequences called enhancers transgenically caused subtle shifts in the facial morphology of mice. The problem in the reporting was that the journalists insisted on calling this a…
Over at the Panda's Thumb, there is a sharp rebuttal of the creationists' complaint about junk DNA. Read it, it's useful. It leads to a bothersome and more general point, though. Despite its connotations, the phrase “junk DNA” (originated by Susumu Ohno in 1972) does not intend to convey an…