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, 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:

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