the dna formerly known as junk

VIEW THE ORIGINAL POST AT BLOG.SCIAM.COM

(this post is only here in order to host the comment thread, below – why we would do such a thing)

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35 Responses to the dna formerly known as junk

  1. Gerald Lukaniuk says:

    Ofcourse you can tell it like it is using any vernacular that communicates your meaning. Most obscure latin or greek bases technical or medical translate as ;sickness in stomach, itch in bad place, or something we really don’t have an idea about but want to sound smart. Critical if not cynical blogging is bringing science and academics back to the good old days.

  2. Peter says:

    How about pcDNA (Protein coding DNA) and npcDNA (Non-Protein Coding DNA).

    Peter.

  3. Lambert says:

    At the very least the phrase “one man’s junk is another man’s treasure” would seem to apply here. It’s ‘junk’ until we know what it’s for.

  4. Brandon says:

    “It’s ‘junk’ until we know what it’s for.” I disagree.

    I have always suspected that “junk” DNA was mislabelled. I do not have a science background, though, so I just assumed that we may or may not later discover some function of the stuff. It seems presumptuous to say that something does not have a function in the body, given its complexity and our lack of complete knowledge.

    I am glad that someone finally mentioned this.

  5. Megan says:

    I do care. The term ‘Junk’ DNA is outdated and reflects poorly on a science writer. I worked last year on a project that explored the three dimensional shape of chromosomes during active transcription. There may be a potential function of noncoding DNA in the spatial arrangement of a chromosome. Gene spacing may relate to gene function. In any event, the more we know, the less ‘junk’ seems appropriate.

  6. David says:

    What about cryptoDNA if indeed it may have undiscovered properties

  7. autumnmist says:

    I HATE the usage of “junk DNA” — you have wacky creationists-IDists out there saying “Ha! Scientists are so stupid: they keep saying this stuff is junk and then realizing that they’re wrong AGAIN!”

    And that’s completely and totally not true. Even my freshman year bio class was taught that promoters, enhancers, protein binding sites, regulatory regions for transcription/translation, splicing sites, and all pick-your-abbreviation-RNAs all hide in the “junk DNA” of the genome.

    It drives me (as a future scientists) up the wall whenever I read an article about how *gasp* “scientists thought it was junk but this brand new finding shows it’s not just junk after all” How many times does someone have to discover a new functional region/sequence type within so-called junk DNA before journalists FINALLY stop calling it junk?? I think it’s ludicrous that journalists are still marveling about how “junk DNA” suddenly appears to have a purpose… when we’ve known for many years now that at least parts of it have essential purposes.

  8. autumnmist says:

    I think journalists really need to be more aware about how the way they write up science can do serious serious damage to the image of science/scientists in the public mind.

    When you keep calling things junk DNA and then writing article after article about some brand-new function discovered in junk DNA, you are giving the average scientifically-unsophisticated person more reason to NOT believe scientists. They think “Wow, these scientists obviously don’t know what they’re talking about!” The creationists/ID people out there, who are always eager for a soundbite, get to trumpet, “Hey look, these scientists are so full of themselves–they dismissed this DNA as junk and they’re wrong–how much you wanna bet they’re wrong about evolution too?”

    No reasonable scientist still thinks of what was called “junk DNA” 10 years ago as useless DNA. It’s very well established, to the point of being taught regularly in high school bio (at least in my AP bio class for sure) that significant portions of so-called “junk DNA” have a purpose.

  9. TR Gregory says:

    Minor glitch with my previous post. My apologies. Here is the working link to my discussion on this issue:

    http://genomicron.blogspot.com/2007/04/junctional-dna.html

  10. Andy says:

    So called “Junk DNA” may not code for a protein, but that sure doesnt make it junk. At the very least, it decreases the chances of a mutation or transposon insertion or some simialr genetic trick in a coding region by simply hiding the coding regions in a sea of nucleotides. However, much research has been coming out lately that points to the fact that these intergenic regions are quite important. Whether they are coding for microRNAs (the main player in RNA interference), regulating the expression of far away genes, or inducing changes in the higher order structure of DNA (chromatin modification), intergenic regions of the genome and, indeed, the very way that DNA works are becoming the subject of much research and changing our notions of the basic mechanisms of genetic functions.

  11. jrminkel says:

    Thanks for the comments, everybody, which I have taken to heart. I learned about promoters and regulatory sequences in school too, if you can believe it. I think I dumbly assumed that people understood the wink-wink nature of calling it junk, which is a pretty bad assumption for a science journalist to make. And it’s just not a field I keep close tabs on–I write mostly about physics–so I am rarely in a position to be called on this flub by a scientist. If I ever write again about the study of noncoding DNA that lies far from genes, you can bet I will keep all this in mind. Mea culpa.

  12. NET MAN says:

    How about DarkDNA
    or MysteryDNA
    or

    Junk DNA, regardless of the higher-minded types who don’t like it, does have a meaning to those approaching your journalism on a casual, less-informed or less-often-informed basis.

    There’s a huge readership out there that needs to be able to digest your meaning and that’s why you use approachable, common terms as a writer.

    Who’s to say that junk was meant maliciously… as I recall, when the term came to light in popular media was around the discussions of regulating the life of cells/the body. So, even in that context, so-called junk DNA wasn’t junk, it was a regulator.

    And, in that regard,

    how about Timing Belt DNA
    or Expiration Date DNA
    or Longevity DNA
    Born On Date DNA ?

    Then again, we may not actually know with certainty that is the sole purpose of junk DNA

    So, how about Magic DNA?
    I kind of like “Grey DNA”

    Or, create a new term, like Elgoog DNA (props)

    Controversial DNA?

    In the end, you’re serving the majority of your regular readership, so the DNA formerly known as junk is just fine. It’s the substance of the (new) article that’s important.

  13. minorwork says:

    undefined, undetermined, timed. Timed is the most evocative projecting that their function could be one of timing necessary to the folding of proteins at determined intervals. Consider Trichoman enormous number of genes compared to humans.

  14. Pellionisz says:

    First, for science. The very same group (Haussler lab) found the so-called “ultraconserved sequences” of “junk” DNA across species, preserved intact against “evolutionary pressures”. These sequences (sometimes extremely long) require at the least a lot of energy to duplicate. Thus, it can not be true that “there wasn’t enough evolutionary pressure to get rid of them”.

    Second (also for science), as listed e.g. on the site

    http://www.junkdna.com/junkdna_diseases.html

    lots of hereditary diseases originate NOT from genes (that are intact, pristine) – but glitches found in the “junk” DNA. Thus, according to the “survival of the fittest” evolution should have long gotten rid of these sequences. (Nature did not; since they are found to be regulatory sequences. At this point of time, as illustrated e.g.

    http://www.junkdna.com

    there is hardly any serious scientist who would consider 98.7% of (human) DNA “Junk”.

    While the name is not that all important, International PostGenetics Society

    http://www.postgenetics.org

    has formally abandoned the misnomer “Junk” DNA in its 2006 “European Inaugural”.

    What is PostGenetics? “Genomics (looking) beyond Genes”. Thus, those sequences “post genes” could be simply called “PostGenes”. (Some more algorithmic approaches name them “FractoGene” – as the genome is without a doubt fractured, at the least by introns separating the exon, “protein coding” parts of the genes).

    What are PostGenes and how do they work?

    Mostly, we don’t know yet.

    The only thing we are getting more and more certain about these days is:

    “they are no junk”.

    pellionisz_at_junkdna.com

  15. UWstudent says:

    If the professors are willing to call it “junk” DNA in my university biology class, I think we can cut writers and journalists a little slack, don’t you? Besides, if we’re going to argue semantics, some people have use for “junk” so why argue the term as if it means the components are completely useless? The argument seems a little picky when essentially the DNA being referred to IS a metaphorical collection of assorted items for which we have no known immediate or present use…

  16. Emory Kimbrough says:

    For junk DNA that surprisingly turns out to have a function, how about “who’d-a-thunk DNA”?

  17. Diego Rivero, Ph.D. says:

    Junk DNA = Junk Science?

    After all, do we not live in the age of euphemisms where harsh terms now carry even stronger meaning? Hence, if we must be “correct”–and at least admit a level of “ignorance” appropriate to journalese–the publicists should be “tasked” to employ a more appropriate descriptive: Shall we say “occupationaly challenged” DNA?

  18. Rupinder Sayal says:

    As a budding scientist, I would like to offer my view. I think that we can safely use “non-coding DNA” as an alternative to “Junk DNA” instead of coining flashy new terms and further adding to the mess Biology is already in nowadays due to a deluge of new terms, abbreviations and acronyms. It also converys the right meaning to general public. Non-Coding DNA is, simply put, DNA which does not code for proteins but has some function, known or putative.

    As for me, I don’t think evolutionary and metabolic pressures would have allowed such huge swathes of DNA to sustain in the organism’s genome, had these been there without a purpose.

  19. Airton says:

    It´s not junk to begin with. When a wrong name is chosen it can mislead people to think in some way and stop thinking in alternatives. The early name “dementia precox” used for schizophrenia was completely narrow and caused a series of misconceptions, and delayed for some time a wider study of the dicease. “junk-DNA” does not code proteins, but many parts of it make m-RNA that can act as regulators in processes, and may have a role in methylation, specially in eukaryotes as pointed in early articles in SA. The name “junk-DNA” makes people think of it as useless and don´t think of it anymore, specially students. The question is relevant if a term is harmful, it has not to do with euphemisms, ans semantics is very important in science where words must have precise meanings, specially to the general public. The “stomach flu” actually has nothing to do with the influenza (flu) and may mislead the general reader to wrong ideas.

  20. George Bevis says:

    Terra IncogniDNA?

    Background DNA?

  21. Shannon says:

    Gee,
    “conserved non-coding DNA” sounds pretty descriptive as well as accurate.

  22. Gary Hurd says:

    I would reserve “junk DNA” for silenced ERVs, “broken DNA” for broken DNA eg. the nonfunctional vitamin C gene in primates, non-coding for the rest. Some non-coding DNA is regulatory so is obviously not “junk.”

  23. Gary Hurd says:

    I just had a further thought which is that “junk” is not “trash.” That is, I have a “junk drawer” as I suspect that all most all of us have. The contents are disoganized and are not currently put to any use. The drawer is filled with junk. However, should I need a piece of string, or any other little bit from the detritus of my life, I yank open the junk drawer and rummage about.

    I cherish my junk, and should not disparage my junk DNA.

  24. Doug Alford says:

    * gap DNA
    * frontier DNA
    * extra DNA
    * edge DNA

    WINNER! – * wild DNA

  25. Alex Harrison says:

    Even the sections of DNA, that are non-coding, don’t effect DNA structure, gene expression, rearrangements, stability and are not involved in any other number of the many processes mentioned here and elsewhere, are of use to the genome as a whole with regard to protection. The potential for an insertion of DNA, via a virus or through recombination within the genome, into a potentially harmful region (maybe a tumour suppressor etc) or for random mutations to occur within essential genes, is greatly reduced with an increased non-coding, non-functional DNA. So it is likely that there is possible benefit from maintaining an oversized genome. This all leads to the way the term ‘junk’ is read. I just think it gives the impression of being completely without use and find that to be a bit daft, there is very little to be found in the biological world that is completely without use and which has not been selected against.

  26. Charles T . Clegg says:

    Humans puting anything in our universe in ” junk” category is arrogant and suspect .
    Refuse here is fuel there , poisons here are growth factors there , the complete picture will never be known to us, assuming there is a complete picture . Our little flashlights delude us into thinking we see . Even in stating this the way I have here reveals I am that way too Its like calling a stated category like ” junk DNA ” as itself a junk statement …….

  27. Charles T . Clegg says:

    Humans puting anything in our universe in ” junk” category is arrogant and suspect .
    Refuse here is fuel there , poisons here are growth factors there , the complete picture will never be known to us, assuming there is a complete picture . Our little flashlights delude us into thinking we see . Even in stating this the way I have here reveals I am that way too Its like calling a stated category like ” junk DNA ” as itself a junk statement …….

    Airton said it well above——

  28. Mark says:

    I would prefer the terms to be completely what you (media) deem it to be. I am ambitious enough to look things up for myself if I want to be completely informed and therefore can make a judgment all on my own whether the articles are relevant or just so much “junk reporting”. 🙂

  29. JOE says:

    no-purpose DNA tells me more than junk DNA.

  30. Joe Dunckley says:

    Junk DNA is a potentially useful term, as long as it’s not misused. People seem to think it’s a synonym for non-coding sequences, when it was originally defined as non-functional sequences. Of course, not even the complete lack of observable ill effects of deletion are conclusive proof of non-function, so it’s perhaps only useful to those aware of the caveats, the potential functions, and provisional status of the classification.

  31. Tracie says:

    I feel as a layman the term junk dna could give the impression that “junk dna” is precisely that and could just be done without. However I don’t believe the term would be a problem for most readers of the S.J.

    Either way if there is a way to explain what junk dna is, and still have en effective story, then it should be done.

  32. John says:

    *throws my AP BIO book* READ IT!!

  33. Ian Koenig says:

    I thhink we shouild call it “Dark DNA”. That term is in vogue and generally means “We don’t know what it is”

  34. We called it “Junk DNA” when I did my Biochemistry degree 7 years ago, now we call it “non-coding DNA” on my pre-reg Nursing course.

    I like the mystery that “non-coding” lends to it. And, y’know, the way it is a bit more factually accurate.

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