Editing Junk DNA (section)

==Junk DNA and non-coding DNA==

There is considerable confusion in the popular press and in the scientific literature about the distinction between non-coding DNA and junk DNA.

According to an article published in 2021 in American Scientist:

{{Blockquote |Close to 99 percent of our genome has been historically classified as noncoding, useless "junk" DNA. Consequently, these sequences were rarely studied.<ref>{{ cite journal | vauthors =  Mortola E, Long M | date = 2021 | title = Turning Junk into Us: How Genes Are Born | journal = American Scientist | volume = 109 | pages = 174–182 }}</ref> }}

A book published in 2020 states:

{{Blockquote | When it was first discovered, the nongenic DNA was sometimes called—somewhat derisively by people who did not know better—"junk DNA" because it had no obvious utility, and they foolishly assumed that if it was not carrying coding information it must be useless trash.<ref>{{ cite book | vauthors = McHughen A | date = 2020 | title = DNA Demystified: Unraveling the Double Helix | publisher = Oxford University Press | place = New York, New York, USA}}</ref> }}

The common theme is that the original proponents of junk DNA thought that all non-coding DNA was junk.<ref name="PalazzoGregory2014" /><ref name="Palazzo&Kejiou2022" /> This claim has been attributed to a paper by [[David Comings]] in 1972<ref name = Comings1972a /> where he is reported to have said that junk DNA refers to ''all'' non-coding DNA.<ref name="Gregory2005" /> But Comings never said that. In that paper he discusses non-coding genes for ribosomal RNA and tRNAs and non-coding regulatory DNA and he proposes several possible functions for the bulk of non-coding DNA.<ref name = Comings1972a/> In another publication from the same year Comings again discusses the term junk DNA with the clear understanding that it does not include non-coding regulatory sequences.<ref name = Comings1972b>{{ cite journal | last = Comings | first = DE | date = 1972 | title = Review of ''Evolution of Genetics Systems'' | journal = American Journal of Human Genetics | volume = 25 | pages = 340–342 }}</ref>

The idea that all non-coding DNA was thought to be junk has been criticized by numerous authors for distorting the history of junk DNA;<ref name="Eddy2012" /><ref name = Niu&Jiang2013>{{ cite journal | vauthors = Niu DK, Jiang L | date= 2013 | title =  Can ENCODE tell us how much junk DNA we carry in our genome? | journal =  Biochemical and Biophysical Research Communications | volume = 430 | issue= 4 | pages = 1340–1343 | doi = 10.1016/j.bbrc.2012.12.074| pmid= 23268340 }}</ref><ref name="Grauretal2013" /><ref>{{cite journal | vauthors = Graur D, Zheng Y, Azevedo RB | date = 2015 | title = An evolutionary classification of genomic function | journal = Genome Biology and Evolution | volume = 7 | issue = 3 | pages = 642–645 | doi = 10.1093/gbe/evv021| pmid = 25635041 | pmc = 5322545 }}</ref><ref name="PalazzoGregory2014"/> for example:
{{blockquote | It is simply not true that noncoding DNA has long been dismissed as worthless junk and that functional hypotheses have only recently been proposed - despite the frequency with which this cliché is repeated in media reports and in the introduction of far too many scientific studies.<ref name = Elliotetal2014>{{ cite journal | vauthors = Elliott TA, Linquist S, and Gregory TR | date = 2014 | title = Conceptual and empirical challenges of ascribing functions to transposable elements | journal = The American Naturalist | volume = 184 | issue = 1 |pages = 14–24 | doi = 10.1086/676588 | pmid = 24921597 | s2cid = 14549993 | url = http://philsci-archive.pitt.edu/11636/1/Conceptual_and_Empirical_Challenges_%28preprint_version%29.pdf }}</ref>}}
Some of the criticisms have been strong:
{{blockquote | Revisionist claims that equate noncoding DNA with junk merely reveal that people who are allowed to exhibit their logorrhea in Nature and other glam journals are as ignorant as the worst young-earth creationists.<ref name = Graur2017>{{cite book |last=Graur |first=Dan |date=2017 |editor-last=Saitou |editor-first=Naruya |title=Evolution of the Human Genome I |publisher=Springer |pages=19–60 |chapter=Rubbish DNA: The functionless fraction of the human genome }}</ref>}}