Transcription and Translation

Junk DNA – origin of the term

In biological labs, the term junk DNA is commonly used to describe portion of the genome which have no described function. When I first moved my blog to Scienceblogs, I wrote a little summary of a great theory advanced by William Martin and Eugene V. Koonin on the origin of the eukaryotic nucleus. (Basically the nucleus developed to separate RNA processing from RNA translation, due to the multiplication of introns which made the process of RNA processing that much more complicated.) Well the ID-ots jumped on my little blog entry and accused me of knowing nothing because I called introns “junk DNA”. At the time I thought that the whole thing was ludicrous. These ID guys clearly are not involved in the scientific process, let alone talk to people who do primary research (like me!) In cell biology/biochemistry/molecular biology circles “junk DNA” is just shorthand for portion of the genome which have no described function. To pounce on that term is playing “Gotcha”. Well I was reading Sandwalk where Larry Moran has an entry on “junk DNA” and the orgin of that term (a 1972 paper by Susumu Ohno.) The post was initiated by a SciAm article that describes this term as unfortunate because:

Although very catchy, the term “junk DNA” repelled mainstream researchers from studying noncoding genetic material for many years. After all, who would like to dig through genomic garbage?

Hmmm.

There are two comments I’d like to make here …

FIRST. I always though that Sydney Brenner (one of the smartest guys in science) coined the term “junk DNA”. So I dug a bit and here is what I came up with … this quote of his:

I said it was ‘junk’ DNA, not ‘trash’. Everyone knows that you throw away trash. But junk we keep in the attic until there may be some need for it.

In anycase it is possible that Brenner said this after 1972 … (anyone know when/where that quote comes from?) … but I wanted to share it with you because it’s a real gem and explains perfectly how most scientists I know use the term.

SECOND. I take issue with “the term ‘junk DNA’ repelled mainstream researchers”. Science is very pragmatic. Most good biomedical biologists study biological functions … apoptosis, the cell cycle, the cytoskeleton, differentiation … studying a gene, a random stretch of DNA, or a protein in isolation is always usually a bad choice. In addition before the sequencing revolution, how could we have analyzed the whole genome? It was a big effort to find your gene of interest, people couldn’t willy nilly study random bits of DNA with no ascribed function. Look, scientists don’t have a crystal ball. You can’t look for something when you don’t know what you are looking for. Plus we have to justify to the NIH, the ACS, the NSF etc… that what we do is important. Randomly going through junk without some hypothesis, especially in the days before the whole genome was sequenced, is the equivalent to committing scientific suicide. Sure some people did do it, and I’m glad that they did. More are doing it now, and that makes sense, they have all these genomes sequenced and many more bioinformatic tools at their disposal, but the idea that we wasted time not going through the junk in the past is clearly a brainless statement.

ADENDUM. Googling “Junk DNA origins of term” I got this crazy creationist wiki site. Now I understood why the ID-ots reacted to my post by criticizing the term “junk DNA”. They don’t know lab lingo. All they know are talking points that they get from some wiki site or blog. Do they even read primary literature? Do they talk to experimentalists? Man … to all you ID folk, go talk to people in wet labs or do some experiments yourself. Sites, like the one I described here, just demonstrate that you are nothing but an ideological movement and not some intellectual enterprise.

UPDATE: Martin Hafner sent me a ref to Brenner’s discussion on junk (it’s in the transcript of a symposia). This may or may not be the first refference that Brenner makes to “junk DNA”. He talks about it during the lecture, and during a Q&A where he makes an arguement that is similar to the quote above (was that a misquote?). Here it is:

i-15dba59f21ed883b20076d58fc61a16c-Brenner.jpg

ref:
S. Brenner
The human genome: the nature of the enterprise (in: Human Genetic Information: Science, Law and Ethics – No. 149: Science, Law and Ethics – Symposium Proceedings (CIBA Foundation Symposia) John Wiley and Sons Ltd 1990

Comments

  1. #1 Anonymous Coward
    February 12, 2007

    … “studying a gene, or a protein in isolation is always a bad choice.” – ap

    Never say always.

  2. #2 U
    February 13, 2007

    Yeah, I still completely disagree with that statement. It’s never wrong to have some focus in your work. If one protein is a gateway to a field, then study that one protein.

  3. #3 sparc
    February 13, 2007

    When you search ‘Intelligent Design’ on Crationwiki you will find:

    Intelligent design (ID) is a creationist perspective

    (emphasis mine)
    Seems as if all the efforts of the DI to hide the nature of ID did not help. All the money for nothing.

  4. #4 sparc
    February 13, 2007

    Do they even read primary literature?

    Some of them do. The problem is that they don’t understand it. It would be much better if they would read some uptodate biology textbook first. And with reading I indeed do mean that they should work through it because there are good reasons why studying biology takes some years.

  5. #5 apalazzo
    February 13, 2007

    AC & U,

    Yes OK I softened the statement. And of course if you are a structure biologist you have no choice but to work on a particular enzyme. But I still contend that if you are a cell biologist, developmental biologist, neurobiologist, microbiologist … the best work is done by those who study processes.

  6. #6 Kirklain
    February 13, 2007

    couldn’t agree more with your last comment Alex… sure the focus maybe one gene, one protein… but it is the context that should be the focus, even for structural biologists, they should adhere to some sensibilities and choose subjects of current scientific interest rather than the easiest protein to crystalise/purify etc… More crossover of skills/appreciation for structure-function and system biology approaches wouldn’t go amiss!

  7. #7 BTM
    February 13, 2007

    Why the attack on structural biologists? No one these days works on only one protein, just one at a time. Cell biologists do the same thing. Most of the papers I see from cell biologists talk about a new role for a protein or a new function. Science is about taking a complex system and understanding the details which is what we all do.

    I guess a vast majority of the “junk DNA” is of viral origin. Makes sense that we haven’t evolved to get rid of it all yet as it must be constantly replenished.

  8. #8 sparc
    February 13, 2007

    In his 2002 Nobel Lecture NATURE’S GIFT TO SCIENCE Sidney Brenners said that he had the idea of distinguishing junk from garbage in the 80’s:

    In 1985, when the first suggestions were made to sequence the human genome, I thought that the sequencing techniques, even with incremental improvements, would not be equal to the task, and would require a factory scale operation to do it. I had also come to the conclusion that most of the human genome was junk, a form of rubbish which, unlike garbage, is not thrown away. My view at the time was that we should treat the human genome like income tax and find every legitimate way of avoiding sequencing it. It could therefore be asked whether a genome existed in Nature which perhaps had very much less junk but nevertheless had the full repertoire of vertebrate genes?

    Hwa A Lim’s book GENETICALLY YOURS – Bioinforming, Biopharming, and Biofarming (World Scientific Publishing, online available here: http://www.worldscibooks.com/lifesci/etextbook/4950/4950_chap1_4.pdf ) presents this Brenner statement:

    In the words of Sydney Brenner, then director of Molecular Genetics Institute at Cambridge, “More than 95% of the DNA is junk. But let me point out that it’s not garbage because the difference between junk and garbage is exactly the same difference you make. Garbage you throw away and junk you keep because you think you might want to do something useful with it, and of course you never do. So, 95%, or more than 95% is junk, and I think that is a valid argument to say against the idea of sequencing the entire genome, because we’d spend a lot of time doing this. Against this, people said, well, you don’t know until you’ve done it whether it is or isn’t junk.”

    and gives the following reference “Decoding the Book of Life”, NOVA, WGBH Educational Foundation, October 31, 1989. WGBH seems to be a radio program. Thus, he developed his idea during the mid 80’s.

  9. #9 ERV
    February 13, 2007

    “Evolution is only a theory!” “Theres no such thing as junk DNA! Everything is DESIGNED!”

    Commmon, since when have Creationists cared how words like ‘theory’ and ‘junk DNA’ are used in the real world? But I think youre on to something, here– Im in the process of demolishing a UD article on mobile elements, and theyre all in a tizzy about ‘junk DNA’ too. Maybe ID Creationists have retreated from flagella and immune systems to the murky waters of unexplored DNA.

  10. #10 Dave S.
    February 13, 2007

    I don’t know about the rest of you, but I’ve always found the term “junk DNA” to be appropriate. If you look up the word ‘junk’ for instance in the dictionary, you find:

    1. Discarded material, such as glass, rags, paper, or metal, some of which may be reused in some form.

    Word History: The word junk is an example of the change in meaning known as generalization, and very aptly too, since the amount of junk in the world seems to be generalizing and proliferating rapidly. The Middle English word jonk, ancestor of junk, originally had a very specific meaning restricted to nautical terminology. First recorded in 1353, the word meant “an old cable or rope.” On a sailing ship it made little sense to throw away useful material since considerable time might pass before one could get new supplies. Old cable was used in a variety of ways, for example, to make fenders, that is, material hung over the side of the ship to protect it from scraping other ships or wharves. Junk came to refer to this old cable as well. The big leap in meaning taken by the word seems to have occurred when junk was applied to discarded but useful material in general. This extension may also have taken place in a nautical context, for the earliest, more generalized use of junk is found in the compound junk shop, referring to a store where old materials from ships were sold. Junk has gone on to mean useless waste as well.

    So while “junk” even in the colloquial sense can refer to something useless, it does not necessarily have to be useless. Pretty much everyone here has a junk drawer or an area where you have a pile of junk, perhaps the attic or garage or both. You don’t save this stuff because it’s worthless garbage, do you? The reason you save this ‘junk’ at all is precisely because it may have some use down the road that you can’t envision at the moment. And it did have a use at some point but is no longer used for the original purpose, perhaps because it’s broken, which is how it found itself in your junk pile in the first place. This is analogous to pseudogenes, which are similar to functional genes by have a mutation that makes them ‘broken’ but are still hanging around and may (or may not) eventually be found useful for some other purpose.

    Finding a use for a piece of “junk DNA” no more validates the claim that it’s all really not junk, any more than does using that empty film container to hold thumbtacks mean the rest of the stuff in the drawer is no longer really junk.

  11. #11 Enro
    March 10, 2007

    Brenner (and you) make a good point regarding the difference between junk and trash DNA. However, it is not striking for most non-native English speakers (like myself), who could well be the wealth of science today. And usual translations like the French “ADN poubelle” draw on the “trash” rather than “junk” side of the original phrase. So, the situation might be more ambiguous than you describe, if not intentionally!

  12. #12 Adrian Clement
    March 25, 2007

    This was a very useful post. I encourage the discouragement of creationist nonsense.

    Check out this creationist webpage: http://drdino.com

  13. #13 Hector
    December 2, 2009

    “I said it was ‘junk’ DNA, not ‘trash’. Everyone knows that you throw away trash. But junk we keep in the attic until there may be some need for it.”

    I find this response incredibly weaselly. No part of an organism keeps junk DNA because of a possible future need for it. That’s teleological. In your tool shed, you can get away with making a distinction between junk and trash. But in DNA, you can’t.

  14. #14 Andy Bryant
    March 8, 2012

    no help at all

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