I have a request that I hope some readers can help me with. I am looking for examples from the literature (rather than any “general sense”) of people who claimed that “junk DNA” or “selfish DNA” was totally non-functional. I am particularly interested in peer-reviewed primary articles, but media reports and textbooks are of interest too. Anything from the 1970s to the present would be useful, especially pre-2000 publications. I suspect that the assumption that junk = totally functionless arose sometime in the 1990s, and hardly qualifies as a long-held view. I would also be interested to see references in which people suggest that the term “junk” was meant only to reflect our ignorance about what non-coding DNA is doing in the genome. Post your examples (with a quote and full reference info) in the comments. (Please don’t list Ohno 1972).
Genomicron
I would also be interested to see references in which people suggest that the term “junk” was meant only to reflect our ignorance about what non-coding DNA is doing in the genome
Here Bruce Alberts (Molecular Biology of The Cell, 4th edition, 2001) suggests that “junk DNA” is only called such because “its usefulness to the cell has not been demonstrated” (yes, he goes on to postulate a spacer function, which I include to avoid quote-mining, but that isn’t my point). This is from the free copy of the current edition at NCBI.
However, chromosomes from many eucaryotes (including humans) contain, in addition to genes, a large excess of interspersed DNA that does not seem to carry critical information. Sometimes called junk DNA to signify that its usefulness to the cell has not been demonstrated, the particular nucleotide sequence of this DNA may not be important; but the DNA itself, by acting as spacer material, may be crucial for the long-term evolution of the species and for the proper expression of genes.
Excellent, this is exactly what I am looking for — except I also will want to trace where these authors say the idea came from.
I wonder if I should also collect examples of the “it’s good for future evolution” idea…
SJ Gould in PNAS about 15 years ago:
http://www.pnas.org/cgi/reprint/89/22/10706
A nice citation from 1974
Cold Spring Harbor Symposia on Quantitative Biology. Vol. 38, Chromosome Structure and Function. Papers from a symposium, Cold Spring Harbor, N.Y., May 1973
The author cites the tendency of using the word “junk” to DNA with undetermined function as unfortunate but decreasing in prevalence.
You shouldn’t forget the attack on the idea of “junk” from the selfish gene theorists in the early 80s, that suggested even without function to benefit the host they must do something to justify and maintain their presence. This is inconsistent with the idea of “dismissal”
Nature. 1980 Apr 17;284(5757):601-3. Selfish genes, the phenotype paradigm and genome evolution. Doolittle WF, Sapienza C.
Ultimately, I think this is all nonsense ever since Jacob and Monod described the lac operon 10 years before the junk hypothesis. Certainly by the 1980s the expanding understanding of promoter regions, enhancers, etc., operating from greater and greater distances suggested the importance of noncoding elements. The assertion by the DI that scientists ignored non-coding DNA is totally absurd. Lots of people (like my boss) have been studying it for decades.
I’ve written on this once or twice as well:
http://scienceblogs.com/denialism/2007/06/those_denialists_move_fast_1.php
http://scienceblogs.com/denialism/2007/05/evil_evolutionists_have_power.php
I’m not sure what you want.
Do you want examples of the incorrect use of “noncoding” DNA as implied in your title or do you want examples where the term “junk” DNA is used correctly?
In the 4th edition of the Alberts et al. textbook they say on page 33 …
Much of our noncoding DNA is almost certainly dispensable junk, retained like a mass of old papers because, when there is little pressure to keep an archive small, it is easier to retain everything than to sort out the valuable information and discard the rest. Certain exceptional species, like the puffer fish, bear witness to the profligacy of their relatives; they have somehow managed to rid themselves of large quantities of noncoding DNA, or to have avoided acquiring it in the first place. Yet they appear similar in structure, behavior, and fitness to related species that have vastly more DNA.
This seems like a correct usage to me. The apparent conflict between this statement and what Jonathan quoted from page 200 may be due to the fact that they were written by different authors.
Hi Larry,
I am also interested in correct usages, and I agree that the given quote is perfectly legitimate.
Mainly I am interested in finding when the switch took place to “junk means totally functionless” or “junk means we don’t yet know its function” from what was a much more reasonable position held by the originators of the ideas.
I’ve always thought that the term “junk” DNA meant DNA that has no function. That’s certainly the sense that I used when I first mentioned it in my textbook in 1994. I thought everyone agreed with this definition.
“Junk” was kind of a slang term that didn’t make it into scientific papers or textbooks but I really don’t think the meaning has changed since the 1970’s.