Temporary ecology/organismal biology position at UMM » « Who inspired the Final Solution?

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.

Temporary ecology/organismal biology position at UMM » « Who inspired the Final Solution?

Comments

  1. says

    Wouldn’t “garbage DNA” be functional, but deleterious? And a lot of genes are both beneficial and malign at the same time, and whether or not it increases or decreases the fitness of an organism is situational. How would something like Sickle-cell anemia be categorized?

  2. barbaz says

    I don’t like the classification of garbage DNA. If it is under selection, it is just like functional DNA, only that it has negative selection effect instead of positive. In particular, I would expect that there is literal and indifferent garbage DNA.

  3. Owlmirror says

    This is the advance publication — I assume the actual publication date will be 1 April?

    I propose “Punk DNA” for DNA that looks like it’s in the genome but actually isn’t.

  4. John says

    Wouldn’t using “neutral” and “deleterious” instead of “junk” and “garbage” be more self-explanatory?

  6. latveriandiplomat says

    I love the phrase “selective neutrality”. It sounds like something a Romulan ambassador would use to describe their foreign policy.

  7. anat says

    Who said that junk is what one keeps in the attic, garbage is what one throws out? Garbage DNA is sitting in the kitchen bin, waiting to be taken out. Junk DNA sits around – might one day find a use, but not very likely.

  8. chris61 says

    I always though fly geneticists came up with the best names for DNA but Dan Graur seems intent on giving them a run for their money.

  10. marcoli says

    I appreciate the effort, but it will not catch on since there are too many terms. A good percentage of biologists and science journal column writers are completely confused about ‘coding’ versus ‘noncoding’ DNA. Even the smarter ones will not remember the specific difference between junk DNA and garbage DNA for example. Besides, getting biologists to heed these sorts of proposals is like herding cats.

  11. David Marjanović says

    Who said that junk is what one keeps in the attic, garbage is what one throws out? Garbage DNA is sitting in the kitchen bin, waiting to be taken out. Junk DNA sits around – might one day find a use, but not very likely.

    That’s in the paper, making up most of the 6th page of the preprint:

    “Rubbish DNA” (Brenner 1998) refers to genomic segments which have no selected-effect function. Rubbish DNA can be further subdivided into junk DNA and garbage DNA. The term “junk DNA” was current in the 1960s (e.g., Ehret and de Haller 1963); its meaning was formalized by Ohno (1972). Ohno’s definition of “junk DNA” refers to a genomic segment on which selection does not operate. Thus, junk DNA has no immediate use, although in the future it might acquire a useful function, albeit rarely. This sense of the word is very similar to the colloquial meaning of “junk,” such as when a person mentions a “garage full of junk,” in which the implication is that the space is full of useless objects, but that in the future some of them may be useful. Of course, as in the case of the garage full of junk, the majority of junk DNA will never acquire a function. Junk DNA and the junk in one’s garage are also similar in that “they may be kept for years and years and, then, thrown out a day before becoming useful” (David Wool, personal communication).

    First sentence on the next page:

    Because of linguistic prudery and the fact that “junk” is used euphemistically in off-color contexts, some biologists find the term “junk DNA” “derogatory” and “disrespectful” (Brosius and Gould 1992).

    i am 12 and what is this

  12. David Marjanović says

    *sigh*

    Who said that junk is what one keeps in the attic, garbage is what one throws out? Garbage DNA is sitting in the kitchen bin, waiting to be taken out. Junk DNA sits around – might one day find a use, but not very likely.

    That’s in the paper, making up most of the 6th page of the preprint:

    “Rubbish DNA” (Brenner 1998) refers to genomic segments which have no selected-effect function. Rubbish DNA can be further subdivided into junk DNA and garbage DNA. The term “junk DNA” was current in the 1960s (e.g., Ehret and de Haller 1963); its meaning was formalized by Ohno (1972). Ohno’s definition of “junk DNA” refers to a genomic segment on which selection does not operate. Thus, junk DNA has no immediate use, although in the future it might acquire a useful function, albeit rarely. This sense of the word is very similar to the colloquial meaning of “junk,” such as when a person mentions a “garage full of junk,” in which the implication is that the space is full of useless objects, but that in the future some of them may be useful. Of course, as in the case of the garage full of junk, the majority of junk DNA will never acquire a function. Junk DNA and the junk in one’s garage are also similar in that “they may be kept for years and years and, then, thrown out a day before becoming useful” (David Wool, personal communication).

    First sentence on the next page:

    Because of linguistic prudery and the fact that “junk” is used euphemistically in off-color contexts, some biologists find the term “junk DNA” “derogatory” and “disrespectful” (Brosius and Gould 1992).

    i am 12 and what is this

  13. David Marjanović says

    Quote from the end (9th page):

    Rubbish DNA mutating to functional DNA may be referred to as “Lazarus DNA,” so named after the second most famous resurrected corpse in literature, Lazarus of Bethany (John 11:38-44; 12:1; 12:9; 12:17). Similarly, functional DNA may mutate to garbage DNA, in which case we suggest the term Hyde DNA based on the fictional transformation of a benevolent entity into a malicious one (Stevenson 1886). Alternatively, junk DNA may become garbage DNA, for which the term “zombie DNA” has been suggested (Kolata 2010).

    ==========================

    From above:

    I appreciate the effort, but it will not catch on since there are too many terms.

    It’s actually quite simple once you look at the two figures, which make up the last two pages of the preprint.

  14. says

    marcoli @10

    Besides, getting biologists to heed these sorts of proposals is like herding cats.

    Not really. Ornithologists actively update nomenclature in an ongoing way. It’s annoying, but most everyone heeds the proposals. This DNA nomenclature proposal is quite sensible and I believe will be widely accepted.

  15. Last Embryo Standing says

    I would think the “garbage DNA” label is definitely useful in the case of ERVs that misbehave. It is my understanding that ERVs can sit harmlessly, or bits can be co-opted for useful things, or they can cause trouble. As a software person, I would call them malware.

  17. melw says

    What was the discussion a few days ago, trying to figure out how the MRA gene could be adaptive? Accept the category of “garbage gene”, no more problem.