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Is this an official term?
"Official" in what sense? It is the term most often used by modern geneticists. --LDC
-- And what about post-modern geneticists? ;-)
- shouldn't it be called "noncoding DNA" ?
Quick question... why are there articles for both Junk DNA and Noncoding DNA - aren't they t he same? ... shouldn't "Noncoding DNA" be merged into "Junk DNA" and then redirected to here? Adrade 23:51, 8 September 2005 (UTC)
Any distinction from intron? sodium
Introns occur inside active genes; most junk DNA is in the bulk of the chromosome between active genes.
WHat is being talked about in these sentences:
" In some cases, the positioning, rather than precise sequence, may be important. There are known examples in the yeast Saccharomyces. " I find them mysterious.
168... 21:41 5 Jun 2003 (UTC)
Really? Seems O.K. to me. What exactly is your concern? 168... 17:16, 21 Aug 2003 (UTC)
Removed this sentence (mentioned above)
because it's vague, and therefore somewhat dubious. It should give some indication of what these non-junk sequences actually do. Anyway, the fact that the nucleotide sequence is only loosely important to the function of the sequence is not the point; the question is whether the sequence has a known function or not.
Deleted:
I don't like the SciAm reference. First of all, scholars reference authors, not publications. Second of all the author of that piece is a journalist, not a scientist, so I don't think it deserves quoting unless it is a truly fascinating and original opinion, and if so then it should be represented as such and not as the conservative view of a world authority. Second of all, many of the articles in SciAm are what would be considered secondary source material. Some of them are stories by journalists who are offering their interpretation or sketch of what researchers reported in an academic journal article. In that case, the journal article is the primary source. There also an inbetween category of popular articles written by scientists in collaboration with journalists, in which they rehash what the scientists themselves reported in a journal in a way ordinary readers can understand. But the scientists know that the SciAm will not be taken very seriously by their peers and won't be peer reviewed, so many of them are bolder in the claims they make in these articles. If the SciAm is an essay or other sort of opinion piece by a scientist, then it might be appropriate to reference some opinion from it and attribute it to the scientist. The magazine and issue number shouldn't appear except as a footnote. If the opinion is a journalist's, I don't think it deserves quoting unless it is a truly fascinating and original opinion, but then it should be represented as such and not as the conservative view of a world authority.
168... 06:12, 22 Jan 2004 (UTC)
168... 06:20, 22 Jan 2004 (UTC)
By "scholars reference authors, not publications" I meant that the attribution should be to a person and not a magazine. I imagine you're right about the article being reasonable (because I respect the SciAm journalists), and seeing that you claim to be a grad student, I'm inclined to trust your opinion that it is reasonable. Thing is, that doesn't mean that others should be obliged to trust you, you who are not referenced or listed as this article's author. If it's going to be on your authority that we take this journalist as fairly representing scientific opinion, then I suggest you just state the opinion as fact rather than implying either that journalists are scientific authorities or that the referenced source is a scientist and not a journalist. That said, if it didn't strike me as clearly improper, I'd recommend we reference the journalist over a random academic review paper, since those papers tend to be shameless propaganda pieces (they're a little like journalism, since generally they're unrefereed). 168... 00:29, 23 Jan 2004 (UTC)
-- I read the same Scientific American article and the claim that it was making was that there actually is a correlation between the percentage of junk DNA and the complexity of the organism. Sopposedly, the more "junk" the more complexity. The explanation is that some of that junk is actually metadata describing how the coding sequences are related to one another. In other words, each coding sequence codes for a part of functional protein not the whole protein, and the junk DNA has some information encoded in it for putting these things together. It would be interesting to learn what scientific articles say about this stuff. As far as requirements for this encyclopoedia are concerned, I don't think that it is the authority of some scientist that people who read it trust, but more the nature of argumentation and discussion itself. I see it not so much authoritative text as an argumentative one. These are two distinct ways of determining truth or validity of statements and should not be confused. We already have a lot of authoritative texts. If I wanted to read one, I'd go to Encyclopedia Britanica. We read this encyclopedia because we can see how argements pro and cons were made - not because we know who the authors are.
-- PiKeeper 19:13, 26 October 2005 (UTC)
Interest discussion about reference sources, journalists vs. scientists etc. But see this: Why Most Published Research Findings Are False IMHO most sicentists with highest-level education (those with Ph.D.s) are doing science at a level that is enough to keep their paycheck, which is exactly the same for journlists. -- Minimeme 22:07, 19 March 2007 (UTC)
What does the "junk" look like? Is it sometimes random or always highly repetitive like "CACACACACACACA" for hundreds of thousands of bases?
Thanks
I deleted this paragraph on SNPs:
I don't get the logic here, and it seems like it's not a very strong case, and not necessarily a widely considered hypothesis. On the other hand, it's apparent that some thought went into it. Please respond if you have evidence that it's widely held (like refs in decent journals), or could explain it a bit better. At any rate, whatever the logic, it's certainly conceivable that much of what we currently consider junk is really junk, although I think most people would be skeptical of this hypothesis, because it seems burdensome for organisms to have so much useless DNA.
Zashaw 00:38, 9 Dec 2004 (UTC)
The logic is quite simple and does not depend on any POV. The reference on the SNPs is e.g. from http://www.pbs.org/wgbh/nova/genome/debate.html - " 'snips' -- genespeak for the sites littered throughout our DNA that frequently vary between unrelated people. About three million differences exist in the genomes of any two unrelated people, but of these only about 10,000 or so are likely to have any functional consequences. " All I did on top of that was to estrapolate from SNPs to the Genome - a reasonable assumption, as there is no reason why SNPs should be exceptional locations in the genome.
Additional evidence that large stretches of the DNA are non-functional, even the ulta-conserved sections, is given in
http://www.i-sis.org.uk/AUEI.php - "There are 481 segments in the human genome longer than 200 bp that are 100% identical with rat and mouse genomes. Nearly all are also conserved in the chicken (467/481) and dog (477/481) genomes ... 481x200 = 96200 bp ... actually 106 767 bp or 26692 Bytes ultraconserved... But researchers revealed that mice with big chunks for such ultraconserved sequences deleted get on very well without them. Edward Rubin's team at the Lawrence Berkeley National Laboratory in California deleted two huge regions of DNA from mice containing nearly 1 000 highly conserved sequences shared between human and mice. One region was 1.6 million DNA bases long, the other over 800,000 bases long. The researchers expected the mice to show big problems as the result of the deletions. But the mutant mice were no different from normal mice in every respect: growth, metabolic functions, lifespan and overall development. "We were quite amazed," said Rubin, who presented the findings at a meeting of the Cold Spring Harbor Laboratory in New York earlier this year. "It may say as much about our inability to detect any phenotypes as it says about the function of this region, " said David Haussler of the University of California, Santa Cruz, whose team described the "ultra-conserved regions" in mammals,
"What's most mysterious is that we don',t know any molecular mechanism that would demand conservation like this." "
Or better still - http://www.nature.com/news/2004/041018/pf/041018-7_pf.html - "
Published online: 20 October 2004; Mice do fine without 'junk DNA' Roxanne Khamsi -
Mice born without large portions of their 'junk DNA' seem to survive normally. The result contradicts the beliefs of many scientists who have sought to uncover the function of these parts of the genome. More than 90% the genome of organisms such as mice and humans does not appear to code for any proteins. And yet this DNA shows striking similarities between species. If they had no function, over time mutations would scramble the sequences. Why have these bits of the genome remained so highly conserved? "
Thus several independent sources confirm the conclusion in the excised paragraph. May I therefore restore it with references? -- hughey 11:47, 9 Dec 2004 (UTC)
Not too bad, I suppose - although even there the later 3% removal might be mentioned, though it is not as well tested experimentally as the 1% level in the mouse genome.-- hughey 08:26, 10 Dec 2004 (UTC)
I changed the (red) link to repressor to a (red) link to silencer (DNA) even though I know nothing about genetics, based on the following e-mail:
➥the Epopt 23:08, 6 Mar 2005 (UTC)
I just joined the Wiki comunity and already are my comments being saved! I wrote the theory of the conection between junk DNA and evolution myself and already its taking off! (I'm also soooooo weird, arn't I?)
Moved this link from article to talk page:
Basically, I think there's some interesting info at that article, but IMHO I really don't think it's a serious discussion about Junk DNA. It seems to be a polemical anti-creationism site (trying to score points at all times) and presents a fairly narrow view of the science. If someone thinks I'm being unfair, please say so & I'll say more. (Otherwise I'll feel I'm rambling.)
Something interesting in that article: "one species of deer has ~20% more DNA than another very similar species of deer in the same genus... [ One species either lost or gained a lot of DNA with only trivial resulting change ]. ... this implies that this DNA is not very important." I couldn't find the claimed citation for this, and Google didn't help. But if true, this seems interesting (though about as significant as the 3%-genome-deleted mouse).
Zashaw 03:54, 16 Jun 2005 (UTC)
[Removed ad hominem language, rush to judgement, and personal discrimination. The person was notified in writing that editors who wish to remain editors should refrain from such practices, 22nd of December, 2005]
And ref.
Zashaw 29 June 2005 00:17 (UTC)
This section doesn't actualy provide any useful information, so it needs to either be rewritten or deleted. I vote for the second.
I returned this passege ,since it takes no side in the creation/evolution epics ,it simply states this this part of the genom is highly debated in that realm ,as NPOV as possible. Since this has been added and reverted back 4 times by 3 users ,further reverts should consider a vote.
KEEP that section :
DELETE that section:
The following claim has been in this article for a while (and survived the excellent re-write by Mike Lin), and it doesn't make sense to me:
My assumption is that the mutation rate of a nucleotide is independent of the number of other nucleotides. Suppose that 9 million nucleotides are the really important ones, and another 3 billion nucleotides is just protective buffer. If my assumption is correct, then the probability of a deleterious mutation in the critical 9 Mbases is the same as if there were _only_ 9 Mbases in the genome. What's the scoop? Zashaw 06:20, 16 July 2005 (UTC)
My assumption is that the mutation rate of a nucleotide is independent of the number of other nucleotides. Yes, given that assumption, and if you *only* look at mutation, then the conclusion ("Junk DNA gives *no* protection against harmful mutations") naturally follows. I'm sure that assumption is true for *some* kinds of DNA damage mechanisms. But that assumption ignores at least one other kind of DNA damage mechanisms: chemicals that preferentially bind to DNA so tightly that the cell cannot reproduce.
If a molecule binds to DNA, but has no preference for binding to any particular location on the DNA, then it seems reasonable to me that junk DNA gives those molecules a place to bind that is relatively harmless. The rate at which a particular nucleotide is blocked by such a molecule goes down with the number of other nucleotides. While such cells can no longer reproduce, and so such a molecule will "kill" a single-celled organism whether or not it has junk DNA, such a molecule will have no effect on a multi-celled organism if it happens to bind to junk DNA in a non-stem cell.
This may help explain why multi-celled organisms apparently have more "junk DNA" than most single-celled organisms. -- 68.0.124.33 ( talk) 06:00, 15 March 2010 (UTC)
I deleted:
and the reference:
Briefly, this doesn't seem to be something that Creationists _do_ actually "therefore say", but only something the contributor thought they could, so I think it's original research, which is not allowed on Wikipedia. (The logic in the argument also seems pretty wacky, even by Creationist standards, but I'll rest on the no-original-research objection.) Zashaw 19:11, 10 August 2005 (UTC)
Is a distinction made between complete junk and genes which are never expressed? For example, birds still have some of the genes which make teeth. Anthony Appleyard 08:05, 14 January 2006 (UTC)
Placing this material that I removed is implying there is some scientific creedance given to it, when the info is cited from websites of questionable standpoint, and would regardless not be any reason to assume that the said facts are realistic. Creationism has nothing to do with this, and if they have ideas about it, feel free to let them refer to this in other articles on creationism. But there's no reason to put creationist caveats on science. It is a deception and it is POV.
The alternative to to word it so that it can quite plainly not be confused with real science, and make it well understood who is saying this and why these issues are being raised (which is non-scientific; i.e. that this is a religious opinion). To counter this, I believe someone would have to provide the scientific studies that would demonstrate is merits as far as not needing such qualifying statements. -- DanielCD 22:26, 3 March 2006 (UTC)
Moved text for discussion. FloNight talk 23:19, 3 March 2006 (UTC)
The patterns of mutation and rearrangement in nonfunctional sequence analyzed in comparative genomics studies provide strong scientific evidence for common descent, since these patterns tend to reflect the phylogenetic tree. Hence, the question of whether junk DNA is really junk has played a minor role in the creation-evolution controversy. Some advocates of creationism and intelligent design (except for proponents of Theistic evolution) contend that no DNA is junk, or that such junk DNA demonstrates only deterioration rather than macroevolution [2]. Another claim made by creationists is that the theory of evolution caused scientists to assume most DNA was functionless, stifling research into the functions of junk DNA [3].
The entry for New-age doesn't include any mention about DNA. If junk DNA is an important part of New-age spirituality, it should be on that page, rather than the junk DNA page. As such, I have taken out that section.
I feel the same way about the material on the evolution-creation debate, but will leave it alone since it is actively under discussion. Ted 11:54, 10 April 2006 (UTC)
http://www.kryon.com/k_chanelDNA04.html http://www.amazon.com/gp/product/1893183181/102-8269894-2256124?v=glance&n=283155 http://www.soulinvitation.com/12strands/ http://www.laughinglifecoach.com/12-Strand-DNA-Activation.html http://www.freewebs.com/dna12/ http://www.keylonticdictionary.org/Indice/Related%20Words.htm (See term 12-strand DNA) http://www.holisticessentials.net/id24.html http://www.google.com/search?hl=en&q=12+strand+junk+dna+spirit&btnG=Google+Search
--
Brian 26 April 2006 (UTC)
Refuting new-age theories by scientific means is irrelevant of their incorporation into this artile. as long as they are written under the sub header "newage theories" and are accepted by significant number of poeple both creationism and newage (crap) should be stated here ,for completness.-- Procrastinating@ talk2me 16:25, 27 April 2006 (UTC)
See Wikipedia:No original research. Aren't some of these are too minor to be in the article? The original purpose of the policy was to keep this type of stuff out of Wikipedia science articles. FloNight talk 17:27, 10 April 2006 (UTC)
"Honestly, these things entertain me." I've got to agree with Mike Lin. More and more, I'm just laughing at the junk in Wikipedia.
Pellionisz 19:17, 3 May 2006 (UTC)Comment by Pellionisz: "Junk DNA" is not a laughing matter. Hundreds of millions are dying of diseases proven or strongly suspected to be caused by "glitches" in the "Junk". [4]. We'd better not laugh but work as diligently as we could - Pellionisz actually pioneered mathematization (geometrization) of biology for decades. Drs. Malcolm J. Simons and Andras J. Pellionisz, the authors of a paper in "The Cerebellum", provided experimental evidence in support of the FractoGene "Fugu prediction". FractoGene is one of the not very densely populated class of algorithmic approaches to "junk DNA" with experimentally verifiable or falsifiable prediction(s). I believe it does a disservice to those trying to improve the discourse on "Junk DNA" to lump FractoGene, a predictive and experimentally verifiable or falsifiable theory with the epitomy of *non-predictive* and thus experimentally neither verifiable nor falsifiable, thus non-scientific, ID/ET (creationalist) theories.
The phenomenon of those initially opposing a novel approach becoming actual supporters is not new. Tensor Network Theory of the cerebellum (Pellionisz, from 1979) also provided quantitative and experimentally verifiable or falsifiable predictions. Drs. Gielen and Zuylen, talented young researchers in The Netherlands would not (rightly) just believe that the predictions were true. They rushed to their lab to experimentally falsify TNT. To their amazement, the quantitative predictions of TNT were right on target according to their own experimentation. Completely unknown to me, they published: "These results give firm support to the hypothesis that the central nervous system uses a tensorial approach for the activation of the motor system, as originally proposed by Pellionisz and Llinas" [PMID: 3703248].
I would also like to point out that FractoGene has a "Methylation prediction" out there - laid bare to test. It is also a quantitative and experimentally falsifiable or verifiable prediction, just as the "Fugu prediction" - now supported. I invite colleagues for discussions of any type, there are several blogs available; for mine, look in http://www.junkdna.com - Signed: Dr. Andras J. Pellionisz
Pellionisz 19:17, 3 May 2006 (UTC)Comment by Pellionisz to Moderator "TedE". a) as shown by facsimile of the facing Editors' printed page and "Contents" printed page (see "Editors" link on http://www.junkdna.com/fractogene/05_simons_pellionisz.html), neither Dr. Simons nor Dr. Pellionisz is an "Editor" in any quality in the 5(1) issue where our properly peer-reviewed paper with Dr. Simons appered. (b) Given my 30+ years of accomplishments in the field of the cerebellum (over 100 publications [5]) and now that I opened with Dr. Simons the cerebellum for a venue of "triangulation" with serious and widespread potential impact, it should not be overly surprising, should "The Cerebellum" float in their fleeting website some enhanced Editorial role for me. Rest assured, I do negotiate this issue with "The Cerebellum" (Taylor & Francis) and also for a planned "PostGenetics" Journal , Publisher is still negotiated, in addition to my Founding Editorship in e.g. "Neural Networks" [Elsevier] and "Neurocomputing" (Pergamon, and thus now Elsevier - the field of "science journals" changes rapidly..). Negotiations, however, are typically not conducted in public. - Signed: Dr. Pellionisz
Pellionisz 19:17, 3 May 2006 (UTC)Note by Pellionisz: Based on a mindset before facing the facts, some remarks were made and based on a misguided suggestion that the FractoGene approach, one of the few that actually made experimentally verifiable prediction(s), and its "Fugu prediction" has been experimentally supported, was placed into "Alternative theories". Although when he first suggested that "Junk DNA" could not be junk, Malcolm J. Simons was told "you are out of your friggin' mind" (1987) and thus I am proud to be in the same league with him (the still few who are not intimidated to say "Junk DNA is not junk")I suggest putting experimentally predictive and supported, published results into a separate category from approaches that are not experimentally predictive. Indeed, with the recently published findings of Dr. Rigoutsos [6] of 66 million motifs and 128,000 self-similar and repetitive "pyknons" [7] with pyknons *both* in the "Junk" and in practically all known (human) genes, there is a tremendous shortage of scientific approaches to explain these facts. Wikipedia would be well served by listing all approaches, but could insist on separating those that are predictive *and* experimentally verifiable (scientific) and those that are either not predictive, or their predictions can not be tested (non-scientific). Wikipedia is not a science journal, but there are clear standards of what science is, and what is not, thus such delineation would be good for the readers at a time when (any) scientific explanation is *much* needed - Signed: Dr. Pellionisz
I've put the article for merger ,since I dont see any good reason for them both to be apart. they view the same subject from a slighlty different (biassed..) prespective, assuming the known reason for these seemingly "exsessive" DNA is it's non-coding properties.
So ,considering term word "non coding" han't been proven ,the ambigous term "junk" seems more likely as a merge target. I'd appiciate any input, thank you -- Procrastinating@ talk2me 11:08, 12 April 2006 (UTC)
-- Procrastinating@ talk2me 19:58, 20 April 2006 (UTC)
Note from Pellionisz: I would not recommend the merge, either. "Junk DNA" is a historical "brand name" by the late Ohno (1972), not really a scientific "generic name" (see more detailed discussion at the 1972 entry of [8]. "Non-coding DNA" is somewhat generic (usually meant "non-nucleic-acid-coding") but is not very scientific these days itself, since negative evidence can not be established with absolute certainity. I suspect both terms will become of historical significance, marking a transitional era in science. Better said (since in science everything is always transitional), marking a major disruption, an astounding paradigm-shift. As such, they both deserve to be in an Encyclopedia - Signed: Dr. Pellionisz
This has gone on for several months, I'm removing the merge request. If you disagree, you can replace it, but add some convincing reasons. Ted Talk/ Contributions 22:44, 14 August 2006 (UTC)
Again... not having seen this discussion, I req a merge FROM junk DNA TO noncoding DNA. New reasons - see
Talk:Noncoding DNA. Besides, "junk DNA" is not an appropriate scientific term. Do a PubMed search - 75 papers vs 264 for "noncoding DNA" and 156 for "non-coding DNA", and besides, the correct title would be "junk" DNA as no decent scientists would use the term without quotation marks these days: The concept implied by use of the term junk DNA is highly misleading and scientifically inaccurate; it is as if
Animalia were to redirect to "
critter", or
Abiogenesis to
Spontaneous Generation. That there are so-and-so many more Google hits simply shows the ignorance of the general public, and WP is ill-advised to strive to emulate that.
Yes "noncoding DNA" is an ambiguous concept too, but such ambiguity would be discussed in the article; at any rate, it is the proper scientific term in use nowadays. Stuff that does not get translated into proteins would be
noncoding RNA; noncoding DNA may or may not be transcribed into RNA and even in the former case it does have a function in many cases (
promoters don't get transcribed, but never were considered "junk DNA", but only because the operon model predates industry-scale DNA sequencing; had it been the other way around, the promoter would have certainly been considered useless "junk" at first.
Please, before replying and/or rm the merge request, take your time and read the material I have referred to and linked. All evidence points to a considerable part of that "junk" being actually more important than genes (see the Science paper for a not-too-scientific discussion).
Dysmorodrepanis
18:09, 4 December 2006 (UTC)
To me it seems like you are expressing your opinion that "junk DNA" term is unfavored or outdated. That is fine,, but question is whether the term should or not have own encyclopedia article or not. To me I don't see a strong argument otherwise since it is popular term and meaning is different than "noncoding DNA" as others said. Besides in general public themselves, I think you still see the term used by scientists and science writers in informal conservation and when they write something to understand by general public, like in news@nature often, cited in the article severally. Nature editors thought this through and decided "junk DNA" term is still somehow useful, if only to compare to new discovery. So your points with "junk DNA" term are mostly right but do not mean it should not have own article, instead problems should be in and made clear. -- Baldzac 19:13, 4 December 2006 (UTC)
I think you are not really address relevant question of,, should there be "junk DNA" encyclopedia article. Wikipedia has articles on phlogiston,, alchemy and aether even though they are rejectecd concepts, and should. "Junk DNA" term has historical importance if nothing else, although like I said Nature is using it recently like 2004 [9]. Statement like "It should not be spread any further" is not right spirit for encyclopedia unless term is not notable, clearly not true. To me you really want to add more to "junk DNA" article about why concept is outdated. And maybe copy of some material to noncoding DNA article. There is not good reason to get rid of "junk DNA" article.
Here is what source Nature letter of 2004 says [10], to me it says issue of whether there is some "junk DNA" is not settled.
-- Baldzac 00:10, 5 December 2006 (UTC)
Well what do you say? You ask for peer review papers saying "junk DNA" concept still maybe important since 2001. So I show big one in Nature, hardly could say more clearly (unless you argue "disposable DNA" means different than "junk DNA" and news@nature Editors writing of article got it wrong), moreover one already cited in Wikpedia article (where I found it) so seems like you didn't even read before saying to merge out. It is great paper even with appropriate qualification of result,, all the time computer and math people look at DNA and say it must do that and can't be junk because of some patterns. Here some actual real biologist stands up and says not so fast, here in real organism we delete millions of junk DNA,, try hard and can't find it to do anything. Maybe it really does but point is question is still important, obviously deserves encyclopedia article.
And like I say,, even if "junk DNA" was totally obsolete rejected concept, even then would still deserve article. So I think we should take off ugly unwarranted merge banner. You seem to know about field (maybe only somewhat biased view of how current situation is), and could make good changes to "junk DNA" article about how it becomes less favored idea. -- Baldzac 04:57, 11 December 2006 (UTC)
Do you think Nature editors are so confused to use "DIFFERENT ENTIRELY" term!!!!???? [11] I am laughing.
Before you say, junk DNA is definitely (a) obsolete outdated concept, you call it "highly misleading and scientifically inaccurate", "false and outdated" and "junk science" and "It should not be spread any further.". Now you back up and say actually there is (b) "scientifically correct sense"??? Is it "scientifically correct sense", "Junk DNA is a collective label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified"???
Come on, you are silly, no point to split hair here, better to just do work on other article. I can see you might copy or move some stuffs from "Junk DNA" article into "Noncoding DNA" article that does not specific apply to contreversial claim of non-function, like the evolution conservation. But clearly to me, "Junk DNA" concept deserves own article with much of current content. You should just go work on "Noncoding DNA" article, see how it goes.
Otherwise, if you still say to merge and get rid of "Junk DNA" article,, neither of us would convince the other now. Then we should wait of opinion of other editors. Note many opinion above who were against merger. So I will wait some days but remove ugly banner unless others stand up with new,, better reason. -- Baldzac 06:25, 20 December 2006 (UTC)
Please evaluate references and reconsider. The concept of "junk" and of "having a function" are quite diametrically opposed. Also note reluctance of current researchers to use term without quotation marks. Dysmorodrepanis 04:26, 18 February 2007 (UTC)
I rv'd the merge tad. Please consider my case above. This article is not about the subject. If not a complete merger, at least Noncoding DNA is what needs to be beefed up and this article needs to be shrunk. Anything about noncoding DNA having a function does not belong here, but there. This article is about functionless DNA and should be about nothing but, if it is maintained at all. Non-translated DNA is a scientific issue, and it should be treated at a standard that is acceptable to the scientifically-trained reader. Which at present it is not if your functional genetics/genomics is up to date.
Current PubMed results:
Note: The same paper might use "noncoding" and "non-coding" (or "non coding" which is the same for PubMed search) so it's not 76 : 435, but "junk" is disfavored by at least a factor of 4.
Some variant of "noncoding" is clearly favored over "junk" by the professional scientists who work in the field, and the ortography seems to lean towards "non-coding". Dysmorodrepanis 05:06, 21 April 2007 (UTC)
After having spent too long reading through all of these posts, I have realized that the simple facts have been said but are being bogged down by unmeaningful citations, personal attacks and showboating. The "Junk DNA" page needs to be merged into the "Non-coding DNA" page, possibly added in it's own section due to it being part of the history of genetics and genomics. And that is what it is- HISTORY.
-for clarification to those not working in genetics, the terms really do need to be defined. "junk" DNA- "junk" implies that it has absolutely no use, ever, and can be discarded (junk....duh). "non-coding" DNA- this term refers to the DNA segments' ability to code for protein via the DNA-RNA-Protein pathway (mRNA=messenger RNA). It is common knowledge (refer to any genetics textbook made in the last 10 years) that much of our DNA codes for RNA that never gets made into protein (rRNA, RNAi, siRNA, ect.). It is technically difficult to find segments that seemingly show no activity ("junk DNA") that actually codes for RNA because RNA is fleeting and degrades very easily, among other things.
Go take a stroll around any modern genomics or genetics department and ask what people think about "junk" DNA. The simple fact is, scientists cannot use it without quotations and remain credible. In fact, in the real scientific community, it is really only used in presentations and papers that are directed at a less educated general audience. Thus, when people search Wikipedia for "junk" DNA, they should be redirected to "non-coding DNA" so they can learn why that term is technically not correct. Why?
The simple answer is, it's too complex. There are indeed segments of DNA that are repetitive AT's or other such sequences, and these do seem to have no function; however, it is still possible (although unlikely) that these segments serve some kind of buffering purpose. When everyone keeps referencing the article where parts of the mouse genome were deleted with "no phenotypic effect" it makes me cringe. Anyone who has ever worked on protein expression knows that there are many protein-coding genes that are only active in certain specific cases (i.e. periods of extreme cold, heat, dryness, UV exposure, ect.)- so why should we assume it is different for non-coding sequences? What the problem really is is that people continue to lump all DNA of unknown function into the "junk DNA" catagory. I guess "DNA of Unknown Function" isn't flashy enough to become a term?
Overall, we are finding new papers published EVERY week that show more and more uses for areas of genomes that used to be thought to have no function (please check a GOOD genomics and genetics journal- such as Genome Research). Many serve as buffer zones for protein attachments, many actually make RNA for a variety of purposes (my favorite is the rather new RNAi- Interfering RNA). If you have any doubts about this, please do any PubMed search on CHiP-on-chip assays. This relatively new technique is giving us loads of data showing most of our DNA thought to have been "junk" has a purpose- the downside is we have no good way of finding out what that purpose is. The common consensus in the field is regulatory elements. Even if a stretch of DNA doesn't code for protein or even RNA, it can still have uses in regulation, buffer zones and other NON-CODING functions.
So, while there is certainly some DNA in genomes that does indeed serve no purpose, it is becoming evident that the actual percentage is going to be very, very low (some predict in the 5-15% range). It is unfortunate that so many new papers and discoveries are overriding conclusions given 20 years ago by well-known scientists, but that is the very nature of discovery- and especially genetics. The vast majority of how DNA really works at every level is yet to be discovered- labeling such a huge amount of it as "junk" is both a detriment to further studies and a great way to mislead the general public. Non-coding DNA is exactly that- no more and no less. calling it "junk" DNA means it absolutely has no function. Non-coding simply means it does not code for protein- it does not neccesarily imply function and is therefore the correct term for the vast majority of what uneducated or outdated people try to call "junk" DNA.
128.118.200.75 19:44, 29 May 2007 (UTC)Matt
BTW Baldzac - that "conservation of junk DNA" thing down below... checking for papers on sequence conservation in pseudogenes might help. As far as anyone can tell, at least initially pseudogenees (as opposed to paralogs) are indeed "junk". Whether they may acquire a function later on is another thing. But in any case, here's a strategy that might lead to success:
Basically you're looking for the color of noise of junk DNA. Dysmorodrepanis 04:14, 17 August 2007 (UTC)
I see people have removed this material before, and that they have made all the correct scientific and wikipedian arguments when they did, and that its been added back anyways. But I'll try again...
To Dr. Pellionisz: I had a look at your paper and looked at information about your hypothesis. With all due respect, this work is not ready to be in an encyclopedia. As you know I'm sure, the ideas summarized in the introduction and the "Hypotheses of origin and function" has been condensed from hundreds of peer reviewed articles from dozens of of genomics journals. A single paper in "Cerebellum" refering to a pending patent is not sufficient not warrant inclusion in this encyclopedia. There is no other reference to your hypothesis by other scientists in NIH's PubMed [13]
Re, the Creationist view: To quote the discussion page for the evolution entry "If you wish to discuss or debate the validity of the theory of evolution please do so at talk.origins, True.Origins Archive or Wikireason." As had been said before on this page, the appropriate place for this material is on a page about creationism. There are hundreds of detailed studies published in scientific journals on junk DNA every year and none of them pertain to Creationism (a NIH-PubMed search on "junk DNA creationism" finds no results [14])
Re the new age view: Junk DNA is a scientific term, so people expect the scientific definition and the current scientific debate/consensus. This theory is not a part of the scientific debate as evidenced by the fact that searches in PubMed find no reference to indigo children and junk DNA ( [15])
(FYI:PubMed, a service of the NIH/National Library of Medicine is the premier life science search database with over 16 million citation dating back to the 1950s. As a point of reference, searching evolution+Junk+DNA retrieves over 5000 articles [16])
GeoMor 22:51, 14 August 2006 (UTC)
--- [Answer by Dr. Pellionisz to anonymous "GeoMor"'s note ("to Dr. Pellionisz")]
Dear "GeoMor",
Your 7 lines, commenting on your 2 deletions (junkdna.com and fractogene) IMHO raise 3 very serious issues; personal responsibility, credibility of Wikipedia, and self-contradiction.
PERSONAL RESPONSIBILITY
"Junk" DNA, at a time when there are up to 150,000 "non-coding DNA diseases" ( http://www.junkdna.com/junkdna_diseases.html) and literally hundreds of millions are dying because "junk DNA" had been needlessly overlooked for decades (as Mattick wrote in Scientific American, 2004): overlooking junk dna "was the biggest mistake in the history of molecular biology") became an issue by 2006 raising direct personal responsibility of anyone fostering further delays. It is very telling that the 2 deletions by "GeoMor" ("junkdna.com" and "fractogene") could be seen by those affected by such diseases as deliberately suppressing active efforts towards some remedy. (This includes not only Dr. Simons, with diagnosed 'junkdna disease' of Multiple Myeloma - the pointer to "Genius of Junk" retained in Wikipedia, but practically all of us, since any/all of us could be hit by such neglected, and very often lethal diseases). Deletions by "GeoMor" are, therefore, particularly objectionable, since such personal responsibility is outright hidden by his anonymity - while the 2 deleted links bear clear personal responsibility by Dr. Pellionisz.
CREDIBILITY OF WIKIPEDIA
Deleting the link to " http://www.junkdna.com" the constantly up-to-date "junk dna hub" that is the #1 hit in Google (searched for junkdna) and presently #8 hit in Google (searched for junk dna), with gigabytes of monthly traffic, diligently keeping track of the subject of "junk dna" (covered so meagerly in Wikipedia that e.g. even Rigoutsos' "pyknon" discovery this April goes unmentioned...), IMHO raises credibility if this Wikipedia entry is covering "junk DNA" properly.
SELF-CONTRADICTION OF 2 DELETIONS
"GeoMor" is self-contradictory in his "arguments" for deletions. Is FractoGene derived from "ideas summarized in the introduction and the 'Hypotheses of origin and function has been condensed from hundreds of peer reviewed articles from dozens of of genomics journals" (that is, widely known and accepted) - or so brand new that "A single paper in 'Cerebellum' refering to a pending patent is not sufficient not warrant inclusion in this encyclopedia. There is no other reference to your hypothesis by other scientists in NIH's PubMed"??? Since those who are presently literally dying of "junkDNA diseases" are certainly eager "to leave no stones unturned", it does not seem fair to suppress information - that is either widely known (and as such, should be listed), or rather novel and potentially significant (and as such should be listed). The other self-contradiction is to delete a less-than-six-months-recent academic publication (that appeared in a peer-reviewed science journal as experimental support for one of the not very densely populated group of algorithmic AND predictive approaches to the function of 'junk' DNA), on the grounds of its novelty. Since the paper appeared in March, 2006, is it not *of course* that it is way too early to have any peer-reviewed follow-up?? (The peer review process itself is often longer, e.g. it took Rigoutsos more than a year to have his pyknon paper published - and a famous manuscript by Taft and MATTICK could never become published on "junk DNA"...) Isn't this something? Isn't it fair to -at least- ask for the names of those hindering progress towards remedy for countless "junk DNA diseases"??)
One is also tempted to quote Jim Watson, who was asked, "what happened once they published their paper on "the double helix" with Francis Crick". "NOTHING HAPPENED - NOBODY CITED THEIR PAPER FOR SEVEN YEARS". For the peer-reviewed full paper on FractoGene it is not even seven *months* since its appearence...
The record for "junk DNA debates" is already too long, IMHO. Let's get serious and personally responsible about it. Who knows? Maybe one day who are suppressing attempts might regret it later - when diagnosed of some of the killer "junk DNA diseases".
Respectfully, Dr. Pellionisz pellionisz@junkdna.com
TedE (whomever you are), with utmost respect due to an anonymous "moderator" (?), I disagree who fails to understand what Wikipedia is. (As for academia, leave it for me, I have over hundred publications, just look up "Pellionisz"). Wikipedia, IMHO must inform the general public about the most important aspects of a given entry, in this case "junk DNA". What is the most important issue for hundreds of millions suffering from "junk DNA diseases"? Clearly, if the field is still stuck to chewing on the 34-year old misnomer that 98.7% (or just "most") of human DNA is "junk" - or to learn that there are even algorithmic (i.e. mathematical) approach(es) with scientific predictions, that are actually supported by experimentation. Witholding such information (arbitrarily deleting FractoGene), at minimum, robs the optimism of hundreds of millions of patients that serious scientists proceed that well, that even such all-important landmark (appearence of mathematical interpretation with experimentally verifiable or refutable prediction[s]) has been passed. Witholding such information bears personal responsibility to the patients. Please come forward with your name and credentials if you truly wish to take such a historical burden on your shoulder. Of course, deliberately witholding information on a spearheading approach (especially if it is alleged that it represents an entire school of thought :-) may simply serve the purpose of fabricating some "breathing room" for those with competing approaches to catch up. While it is quite common, it is transparent as unfair. Please decide if the fractal approach to DNA *AND* to biological systems they govern is (a) represents an entire field (in that case, show it to hundreds of millions of patients, that there is a lot of hope), or (b) it is novel to the extent that its peer-reviewed publication in March 2006 could not even be met with a peer-reviewed avalanche for simple lack of time - hundreds of millions of "junk DNA disease sufferers" deserve the news that hope is in the mathematical/information technology breakthroughs in "junk DNA". (And the pseudo-debate on ID/ET will never cure them of any of "junk DNA diseases" e.g. listed on http://www.junkdna.com/junkdna_diseases.html )
Respectfully, Dr. Pellionisz pellionisz@junkdna.com
Only Two comments.
1. I cannot judge if this article is encyclopedic/scientific with proper references etc as I do not possess the appropriate khowledge (and time). However, as genetics sciences are under development and they donnot have certain nomenclature (at least in Greece), we should be careful of the terms which are going to be used as they could be easily misunderstood. For expample, as far it has to do with public issues such as "bioethics of cloning the DNA and patents", the Junk human DNA can be a patent by many Patent Agencies, thus the interpreting of the scientific terms may confuse the wide public, without even mentioning the procedure of translation in each country.
2. Second and most important in the article "Junk DNA" in the topic of "Hypotheses of origin and function" the sixth bullet is "comletely out of space" as it says:
"Similarly, proponents of extraterrestrial origin theories suggest that junk DNA may be lying dormant, waiting for a signal from the creators of the human race."
and i believe that, if not deleted, it should be at least removed in the end of topic. I beg someone to respond to this call as i dont know how to do it!
-- apapanton 08:46, 24 September 2007 (UTC)
This whole article is trying to sneak in original research!
This is evident from the first paragraph:
While much of this sequence is probably an evolutionary artifact that serves no present-day purpose, some may function in ways that are not currently understood. In fact, recent studies have suggested functions for certain portions of what has been called junk DNA. Moreover, the conservation of some junk DNA over many millions of years of evolution may imply an essential function.
These statements are speculative. They are opinions, so I need to know who is making those claims if you want to conform to NPOV. If this is not original research, I want to see citations.
And the whole section on Evolutionary conservation of "junk" DNA is blatantly original research. Citation [12] is about mouse genomes. Citations [13], [14], [15] demonstrate how some previously unidentified genome sequence now have a purpose. However, the thesis of this section is on how "junk" DNA is preserved through evolution, therefore it serves a purpose.
It fails to cite articles that argue if "junk" DNA has indeed been preserved through evolution. If this is not original research, there should be tons of references. Cite your sources.
Liulk 13:36, 2 November 2006 (UTC)
The word "probably" in the first paragraph is maybe too opinion. Otherwise I think the references support most of the article. For example #13 the news@nature article says,,
David Haussler of the University of California, Santa Cruz, and his team scanned the genome sequences of man, mouse and rat1. They found more than 480 ultraconserved regions that are completely identical across the three species....The regions largely match up with chicken, dog and fish sequences too, but are absent from sea squirt and fruitflies. The fact that the sections have changed so little in the 400 million years of evolution since fish and humans shared a common ancestor implies that they are essential to the descendants of these organisms. But researchers are scratching their heads over what the sequences actually do.
Some more references are needed though. The whole paragraph about why the junk DNA doesnt get thrown away by evolution for example. I think the information is right but it needs sourced. -- Baldzac 18:57, 2 November 2006 (UTC)
Postgenetics the new science hasn't got article. My english too poor to begin it.
We have it in hungarian: hu:Posztgenetika
The official page: http://www.junkdna.com/postgenetics/
-- hu:Rodrigo 11:10, 7 November 2006 (UTC)
Is "junk DNA" only significant/more common in eukaryotes? (It seems to be the impression I've gained elsewhere) Should this be mentioned? AlmostReadytoFly 22:38, 16 January 2007 (UTC)
Thats generally true, although procaryote genomes do contain non-coding sequences. In model organisms that have been investigated in detail, many of these have known functions tied in with gene regulation. About ten percent of the E. coli genome is non-coding and this is fairly representative of bacteria, or so we are led to believe. Archeans, less sure. As for mentioning the relative abundance of 'junk' DNA across different taxa - yes, it should be in there.-- ChrisJMoor 22:50, 31 March 2007 (UTC)
The bullet the mentions intelligent design apparently needs a reference. The book Not By Chance! ( http://www.amazon.com/Not-Chance-Shattering-Modern-Evolution/dp/1880582244) mentions this theory, so could be cited as a reference. I don't know what this has to do with new age though.
Also, this bullet somewhat refutes the bottom bullet of that section, that the junk is simply junk. If the genes in junk dna were simply turned off genes (that might somehow be turnonable through some unknown mechanism), then removing them in mice and observing no change would be consistent with the theory. The mice would have only lost the ability to turn this dna back on, something the tests couldn't hope to test for. I guess all I mean to say here is that even if you test for every possible difference, the difference might not be in the phenotype. Although the already existent disclaimer is probably enough. —The preceding unsigned comment was added by 71.228.189.127 ( talk) 07:35, 10 March 2007 (UTC).
As a layman (but had quite a few graduate-level biochemstiry classes) to molecular biology/genetics/biochemistry, I often feel the term of Junk DNA or noncoding DNA is quite arrogant or at least naive and ignorant.
Just as complex DNA sequences derive from merely four necleobases, or binary numerical system only needs two symbols (0, 1), the so-called organism complexity simply cannot be regressed to the numbers of genes CURRENTLY known to human beings. Genes, as several levels above the basic blocks ACGT, are interacting with each others and with other parts. I believe the human beings are just able to understand the tip of the iceberg or a few tips among unknow numbers of icebergs. It may seem useless or junky as it's noncoding, but how deep do geneticists and Co. know about the processes of replication, transcprition, and translation, or interactions with protein? Basically all experimental research is being done somewhat using blackbox system in a sense that the internal mechanism or structure is not known or not worth knowing (for now). while the basic function of DNA is as carrier of genetic information which hopefully will be decoded sometimes in the life cycle of an organisim, how can we assume with so much confidence that besides coding, other parts of DNA are just nonsense or junk? While blackboxing is often successful, assuming eveything is known about the box is just arrogant or ignorant.
The key to the term is not whether most segments of "junk" DNA may turn out to be actually or theoretically junk in any sense, but is that we should not delare it's just junk b/c we do not find many things to do with it FOR NOW. What do we call it? Perhaps just leave it alone or just call it unknown DNA (just like we call people missing instead of dead after a disaster even most of those missing are reasonablly beleieved to be (and actually are) dead. -- Minimeme 21:25, 19 March 2007 (UTC)
I'm going to asume a lot now. Please correct me if I'm wrong. But might the junk dna be old deactivated dna from the earlier forms of evolution. For example, junk dna in humans consists of some fish dna, some reptile dna some mammal (other than human) and so on? If it does, than that would be a proof that makro-evolution exists. A good proof of evolution would be if you could take a mouse, turn off some genes and turn on some other and voila! you get a fish. —Preceding unsigned comment added by ChristianKarlsson.se ( talk • contribs) 12:30, 10 September 2007 (UTC)
This article seems to be riddled with bias against the idea of nonfunctional DNA. The list at the end at the article is virtually identical to a list at the creationist wiki [17] and uses biased language and selective summaries to suggest that junk DNA doesn't exist. The article in general does not seem to reflect the scientific consensus on nonfunctional DNA. Xaoiv ( talk) 13:20, 1 July 2008 (UTC)
After reworking the article, I have decided to remove the totally-disputed template. I have added a remove-section template and a totally-disputed-section template to the section "Function for Some Subsets of Junk DNA." Xaoiv ( talk) 14:16, 3 July 2008 (UTC)
As a professional working with Mobile DNA, the main point is that "junk DNA" is an outmoded term once used to describe non-genic DNA before transposable elements were known. The term is only of historical importance, and is not used anymore except in a colloquial way. 128.214.172.26 ( talk) 08:30, 2 September 2008 (UTC)AHS 09.45 UTC2 September 2008
I can't see anything in that section pointing to the origins of "junk DNA." It's all about possible functions. I think either the title needs to be changed or something needs to be added on the various hypotheses about how "junk DNA" arose.
Tathaataa ( talk) 15:12, 17 October 2008 (UTC)
About 95% of the human genome has been designated as "junk", including most sequences within introns and most intergenic DNA.
Wow, both introns and intergenic DNA? What are the odds of that? I mean, you know, because they're not exactly the same thing... -- 76.217.112.38 ( talk) 17:40, 20 October 2008 (UTC)
DarthPanda, could you please explain what is not constructive about the edits I made in this paper, consisting of a historical reference and clarification about the current status of the term "junk DNA"? For now I have reverted your edit and I suggest we discuss your objections before making further edits. 137.224.252.10 ( talk) 13:19, 5 December 2008 (UTC)
See the heading, this label is very outdated and it was ignorant even when it was coined, it needs to be eradicated as it misleads many people.
As for the DNA it's primary role is structural, nucleoskeleton is build around DNA, bigger nucleus is obviously beneficial for complex multicellular organisms, among others they have to store programs for every tissue. This DNA also serves as a buffer against viruses and transposons as it greatly lowers the chances that the virus will get into expressed DNA. The above should be added to the article if it's not already there. Enemyunknown ( talk) 19:11, 25 January 2009 (UTC)
Also in pre med schools one of the <a href=" http://www.premedrequirements.org">pre med requirements</a> is to learn all the history of the DNA (Vcjohnny)14/04/2011. — Preceding unsigned comment added by Vcjohnny ( talk • contribs) 00:51, 15 April 2011 (UTC)
About 95% of the human genome has been designated as "junk", including most sequences within introns and most intergenic DNA.
While I'm sure this is correct, shouldn't there be sources for this? EMSPhydeaux ( talk)
The comment(s) below were originally left at Talk:Junk DNA/Comments, and are posted here for posterity. Following several discussions in past years, these subpages are now deprecated. The comments may be irrelevant or outdated; if so, please feel free to remove this section.
Comment(s) | Press [show] to view → |
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MERGE THIS ARTICLE - GOOD QUALITY, VERY IMPORTANT - THERE IS NO JUNK
Recommend merging into Non-Coding DNA. May need the term "Junk DNA" for cross reference or search purposes. It is very commonly used in media in explaining Medical Genetics to the public. Howver, it is a seriously misleading notion. There are many interesting theories, mentioned in the article, about the approx. 97% of the Human Genome that does not code for protein. I have some additional thoughts: A) The History of Science in so many areas, over so many centuries, shows extremely important developments from findings first thought to be unimportant, or junk. Over time, findings that are thought to be irrelevant, random or unimportant turn out to contain crucial information. New concepts then lead to new findings. B) DNA spends most of its "lifetime" in coiled (helical) form. It appears to have activity in this configuration, so the non-coding areas could be important in the stereochemistry of this activity. C) All genes are not always "ON". Something has to regulate them ON and OFF. We don't yet know nearly enough about how the external gene regulating influences, such as hormones or other "messenger molecules" interact with the DNA structure itself. We therefore have to learn what role(s) the non-coding areas play in the regulatory processes. First posted above 4/26/2007 Then added below 5/06/2007 Just in recent weeks important news has broken which points to Gene Regulation Issues. An example is the finding that a non-coding region on Chromosome 9 is associated with a higher risk of developing Diabetes and Heart Disease. Assuming these findings are replicated, it seems that this DNA region is anything but junk. Martin Denker 11:44, 4 May 2007 (UTC) |
Last edited at 11:50, 4 May 2007 (UTC). Substituted at 20:44, 29 April 2016 (UTC)
There is abundant evidence to support the claim that roughly 90% of the human genome is junk. I am in the process of creating a separate article on junk DNA in order to lay out the evidence and correct the false history that permeates the current scientific literature.
The project is being discussed under Non-coding DNA. Please feel free to contribute if you are knowledgeable about the subject. Genome42 ( talk) 21:35, 25 May 2022 (UTC)
![]() | Text and/or other creative content from this version of Non-coding DNA#Junk DNA was copied or moved into Junk DNA with this edit. The former page's history now serves to provide attribution for that content in the latter page, and it must not be deleted as long as the latter page exists. |
Given discussion in several threads (Merge discussions 1, 2, 3), I've re-split the Junk DNA section back out of Non-coding DNA. The articles were merged back in 2012 ( merge discussions began in 2007) after results from the ENCODE project came out when discussion in both the academic and popular publications was a bit muddled on what was actually being counted as 'junk' and why as can be seen in the page contents just before the merge. Since then, I think a good case can be made that there has been a lot more nuance in measuring what portion of a genome's sequence is biologically functional, what that function is, and what evolutionary significance it has. The focus on this page should probably be less a binary of "is this sequence junk" but more "for a given threshold of biological function, does this sequence reach that and what does it mean evolutionarily?". I've tried to leave behind a reasonable summary of the relevance of the term 'Junk DNA' to the concept of non-coding DNA over at that article. T.Shafee(Evo&Evo) talk 05:31, 16 March 2023 (UTC)
As this content is being updated, it may be worth considering what would be a useful summary diagram or two for this article - either some existing cc-by image or I can create one. Perhaps something like Fig 1 from this paper (though it'd need to be re-drawn as an svg for quality and editability). Do people have ideas for anything else that would be better? T.Shafee(Evo&Evo) talk 03:50, 20 March 2023 (UTC)
Could someone please explain why the photo of Motoo Kimura can be used in the Motoo Kimura article but not here? Genome42 ( talk) 22:24, 25 March 2023 (UTC)
A great many people think that the original proponents of junk DNA thought that protein coding DNA was the only functional DNA in the human genome. These early junk DNA proponents supposedly, and foolishly, thought that all non-coding DNA was useless junk because they couldn't imagine any functional DNA in the non-coding region. Thus, the hypothesis of junk DNA was based on an argument from ignorance.
The discovery of functional DNA elements that did not encode protein supposedly refuted the idea of junk DNA - at least that's how the common belief goes.
We need to put a stop to this false view of the history of junk DNA and we need to do it explicitly so that other articles can refer back to this one whenever the misinformation surfaces. Unfortunately, this skirts right up to the border of what's permissible in the Wikipedia culture. I'm sure there will be Wikipedians who don't like what I just posted and who will claim that it is "editorializing." If they can come up with a better way to correct the misinformation then let's discuss, keeping in mind that as scientists we have an obligation to make sure that the average reader gets a correct view of the scientific facts. Genome42 ( talk) 19:11, 28 March 2023 (UTC)
Should this article mention the Onion Test anywhere or is a bit of a niche formulation of the argument? I've never actually seen that term used 'in the wild', but maybe I just missed it. Could either be mentioned inline in tthe articcle text or just thrown in the see also section if ppl rechon it's worth linking to. T.Shafee(Evo&Evo) talk 02:30, 27 March 2023 (UTC)
I propose to revert most of the links that were recently added by Melosina because, in my opinion, it's an example of overlinking (too much blue). I don't think it's necessary to link to terms such as "DNA," "genes," "protein," "natural selection," "eukaryotic," "nucleus," "expression," "geneticists," "evolutionary biologists," molecular biologists," "evolution," and "Nobel." Some of the links they inserted are not at all helpful in the context of an article on junk DNA and may even be counter-productive (e.g. "functional," and "mutation"). The problem of overlinking has been covered many times in the past few years. For example, the essay on the overlink crisis says,
Overlinking is the characteristic of having too many internal wikilinks or hyperlinks to external webpages. Editors should use an appropriate number of wikilinks in an article's text. In addition to providing relevant navigation opportunities, an appropriate number of blue links makes articles easier to read, especially in long paragraphs or sections.
The issue concerns readability. Too many Wikilinks (too much blue) makes the article less attractive to readers without adding any significant value. This is a serious problem in science articles where the leads can look overwhelmingly complex to the average reader because of excessive Wikilinks (e.g. Human genome).
The Wikipedia:Manual of Style/Linking makes the following wise suggestions concerning links.
An article is said to be overlinked if it contains an excessive number of links, making it difficult to identify those likely to aid a reader's understanding. A good question to ask yourself is whether reading the article you're about to link to would help someone understand the article you are linking from. Unless a term is particularly relevant to the context in the article, the following are usually not linked: -Everyday words understood by most readers in context
Perhaps we can find a happy medium where unusual terms that are essential to understanding are given links but commons scientific words that should be familiar to anyone reading this article are not? Genome42 ( talk) 14:26, 29 April 2023 (UTC)
Perhaps having the word YET used more frequently, as well as having as a second point if not the first, a clarification clarifying / a differentiation differentiating between,..
.
1 matched-with-others-in-surpassed-evolutionary-progressions-and-so-redundant(true junk) DNA,
2 assumed-no-function junk from genetic processes (high confidence - temporary retentions kept longer than needed if needing to be kept at all), and
3 theorised to have no function but of more compatible DNA-chemistry -combinations ... junk (ones that have still matching after-activation matching chemistry with organelles or functional materials in plasma/interstitial spaces, but are without 'context' in nearby genes along the chains, and so seem pointless, despite chemical-compatibility. Compared to things like say, immune system instructions or embryonic stages, ones with clear-purpose) (less-confidence / more reasonable uncertainty - the chemistry suggests a high likelyhood if not outright proof, of past usefullness) ...
.
... could help to introduce the concept FIRST?
Rather than finding the contrast or inferred-problems with the single concept or inferred consistency, further down the page, and the static tense (scientific conclusion-ary) avoiding the still-new problems of the field? i.e. using YET, adds necessary cautionary relativity to a solid concept, but a phenomenon that is sometimes irreversibly presumed static.
---
i.e. when something THOUGHT junk, is 'let-back-in', at the PREVIOUS time of it being labelled junk, the static nature was less correct, than saying "YET", so,.. yet-confirmed as junk, or yet-re-included back into unknown status rather than confirmed-junk or certified-junk, etc. A big part of that problem is WHO certifies, but that might end up making the page much larger than it should be if that kind of debate/issue should be on a separate page or is not subjectively purposed - i.e. at least the 'YET' nature of both corrective processes, reveals just HOW-new, this science is. Sort of like if you re-wrote it entirely, and re-wrote it with constant inferred STATUS inferences, to keep reminding the reader, that DNAs classification can rapidly CHANGE, that DNA is only sometimes statically clearly-purposed, nature's IMperfections, compared to imaginary ideals, etc. That's not opinion, that's hard-science. Human DNA for tails, for example, are recent, but HAD function. Tense with it as an example, would be an easy example to demonstrate the principle of CAUTION with DNA's classification as junk or not-junk. 120.21.106.152 ( talk) 15:13, 30 June 2023 (UTC)
![]() | This is an archive of past discussions. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk page. |
Archive 1 |
Is this an official term?
"Official" in what sense? It is the term most often used by modern geneticists. --LDC
-- And what about post-modern geneticists? ;-)
- shouldn't it be called "noncoding DNA" ?
Quick question... why are there articles for both Junk DNA and Noncoding DNA - aren't they t he same? ... shouldn't "Noncoding DNA" be merged into "Junk DNA" and then redirected to here? Adrade 23:51, 8 September 2005 (UTC)
Any distinction from intron? sodium
Introns occur inside active genes; most junk DNA is in the bulk of the chromosome between active genes.
WHat is being talked about in these sentences:
" In some cases, the positioning, rather than precise sequence, may be important. There are known examples in the yeast Saccharomyces. " I find them mysterious.
168... 21:41 5 Jun 2003 (UTC)
Really? Seems O.K. to me. What exactly is your concern? 168... 17:16, 21 Aug 2003 (UTC)
Removed this sentence (mentioned above)
because it's vague, and therefore somewhat dubious. It should give some indication of what these non-junk sequences actually do. Anyway, the fact that the nucleotide sequence is only loosely important to the function of the sequence is not the point; the question is whether the sequence has a known function or not.
Deleted:
I don't like the SciAm reference. First of all, scholars reference authors, not publications. Second of all the author of that piece is a journalist, not a scientist, so I don't think it deserves quoting unless it is a truly fascinating and original opinion, and if so then it should be represented as such and not as the conservative view of a world authority. Second of all, many of the articles in SciAm are what would be considered secondary source material. Some of them are stories by journalists who are offering their interpretation or sketch of what researchers reported in an academic journal article. In that case, the journal article is the primary source. There also an inbetween category of popular articles written by scientists in collaboration with journalists, in which they rehash what the scientists themselves reported in a journal in a way ordinary readers can understand. But the scientists know that the SciAm will not be taken very seriously by their peers and won't be peer reviewed, so many of them are bolder in the claims they make in these articles. If the SciAm is an essay or other sort of opinion piece by a scientist, then it might be appropriate to reference some opinion from it and attribute it to the scientist. The magazine and issue number shouldn't appear except as a footnote. If the opinion is a journalist's, I don't think it deserves quoting unless it is a truly fascinating and original opinion, but then it should be represented as such and not as the conservative view of a world authority.
168... 06:12, 22 Jan 2004 (UTC)
168... 06:20, 22 Jan 2004 (UTC)
By "scholars reference authors, not publications" I meant that the attribution should be to a person and not a magazine. I imagine you're right about the article being reasonable (because I respect the SciAm journalists), and seeing that you claim to be a grad student, I'm inclined to trust your opinion that it is reasonable. Thing is, that doesn't mean that others should be obliged to trust you, you who are not referenced or listed as this article's author. If it's going to be on your authority that we take this journalist as fairly representing scientific opinion, then I suggest you just state the opinion as fact rather than implying either that journalists are scientific authorities or that the referenced source is a scientist and not a journalist. That said, if it didn't strike me as clearly improper, I'd recommend we reference the journalist over a random academic review paper, since those papers tend to be shameless propaganda pieces (they're a little like journalism, since generally they're unrefereed). 168... 00:29, 23 Jan 2004 (UTC)
-- I read the same Scientific American article and the claim that it was making was that there actually is a correlation between the percentage of junk DNA and the complexity of the organism. Sopposedly, the more "junk" the more complexity. The explanation is that some of that junk is actually metadata describing how the coding sequences are related to one another. In other words, each coding sequence codes for a part of functional protein not the whole protein, and the junk DNA has some information encoded in it for putting these things together. It would be interesting to learn what scientific articles say about this stuff. As far as requirements for this encyclopoedia are concerned, I don't think that it is the authority of some scientist that people who read it trust, but more the nature of argumentation and discussion itself. I see it not so much authoritative text as an argumentative one. These are two distinct ways of determining truth or validity of statements and should not be confused. We already have a lot of authoritative texts. If I wanted to read one, I'd go to Encyclopedia Britanica. We read this encyclopedia because we can see how argements pro and cons were made - not because we know who the authors are.
-- PiKeeper 19:13, 26 October 2005 (UTC)
Interest discussion about reference sources, journalists vs. scientists etc. But see this: Why Most Published Research Findings Are False IMHO most sicentists with highest-level education (those with Ph.D.s) are doing science at a level that is enough to keep their paycheck, which is exactly the same for journlists. -- Minimeme 22:07, 19 March 2007 (UTC)
What does the "junk" look like? Is it sometimes random or always highly repetitive like "CACACACACACACA" for hundreds of thousands of bases?
Thanks
I deleted this paragraph on SNPs:
I don't get the logic here, and it seems like it's not a very strong case, and not necessarily a widely considered hypothesis. On the other hand, it's apparent that some thought went into it. Please respond if you have evidence that it's widely held (like refs in decent journals), or could explain it a bit better. At any rate, whatever the logic, it's certainly conceivable that much of what we currently consider junk is really junk, although I think most people would be skeptical of this hypothesis, because it seems burdensome for organisms to have so much useless DNA.
Zashaw 00:38, 9 Dec 2004 (UTC)
The logic is quite simple and does not depend on any POV. The reference on the SNPs is e.g. from http://www.pbs.org/wgbh/nova/genome/debate.html - " 'snips' -- genespeak for the sites littered throughout our DNA that frequently vary between unrelated people. About three million differences exist in the genomes of any two unrelated people, but of these only about 10,000 or so are likely to have any functional consequences. " All I did on top of that was to estrapolate from SNPs to the Genome - a reasonable assumption, as there is no reason why SNPs should be exceptional locations in the genome.
Additional evidence that large stretches of the DNA are non-functional, even the ulta-conserved sections, is given in
http://www.i-sis.org.uk/AUEI.php - "There are 481 segments in the human genome longer than 200 bp that are 100% identical with rat and mouse genomes. Nearly all are also conserved in the chicken (467/481) and dog (477/481) genomes ... 481x200 = 96200 bp ... actually 106 767 bp or 26692 Bytes ultraconserved... But researchers revealed that mice with big chunks for such ultraconserved sequences deleted get on very well without them. Edward Rubin's team at the Lawrence Berkeley National Laboratory in California deleted two huge regions of DNA from mice containing nearly 1 000 highly conserved sequences shared between human and mice. One region was 1.6 million DNA bases long, the other over 800,000 bases long. The researchers expected the mice to show big problems as the result of the deletions. But the mutant mice were no different from normal mice in every respect: growth, metabolic functions, lifespan and overall development. "We were quite amazed," said Rubin, who presented the findings at a meeting of the Cold Spring Harbor Laboratory in New York earlier this year. "It may say as much about our inability to detect any phenotypes as it says about the function of this region, " said David Haussler of the University of California, Santa Cruz, whose team described the "ultra-conserved regions" in mammals,
"What's most mysterious is that we don',t know any molecular mechanism that would demand conservation like this." "
Or better still - http://www.nature.com/news/2004/041018/pf/041018-7_pf.html - "
Published online: 20 October 2004; Mice do fine without 'junk DNA' Roxanne Khamsi -
Mice born without large portions of their 'junk DNA' seem to survive normally. The result contradicts the beliefs of many scientists who have sought to uncover the function of these parts of the genome. More than 90% the genome of organisms such as mice and humans does not appear to code for any proteins. And yet this DNA shows striking similarities between species. If they had no function, over time mutations would scramble the sequences. Why have these bits of the genome remained so highly conserved? "
Thus several independent sources confirm the conclusion in the excised paragraph. May I therefore restore it with references? -- hughey 11:47, 9 Dec 2004 (UTC)
Not too bad, I suppose - although even there the later 3% removal might be mentioned, though it is not as well tested experimentally as the 1% level in the mouse genome.-- hughey 08:26, 10 Dec 2004 (UTC)
I changed the (red) link to repressor to a (red) link to silencer (DNA) even though I know nothing about genetics, based on the following e-mail:
➥the Epopt 23:08, 6 Mar 2005 (UTC)
I just joined the Wiki comunity and already are my comments being saved! I wrote the theory of the conection between junk DNA and evolution myself and already its taking off! (I'm also soooooo weird, arn't I?)
Moved this link from article to talk page:
Basically, I think there's some interesting info at that article, but IMHO I really don't think it's a serious discussion about Junk DNA. It seems to be a polemical anti-creationism site (trying to score points at all times) and presents a fairly narrow view of the science. If someone thinks I'm being unfair, please say so & I'll say more. (Otherwise I'll feel I'm rambling.)
Something interesting in that article: "one species of deer has ~20% more DNA than another very similar species of deer in the same genus... [ One species either lost or gained a lot of DNA with only trivial resulting change ]. ... this implies that this DNA is not very important." I couldn't find the claimed citation for this, and Google didn't help. But if true, this seems interesting (though about as significant as the 3%-genome-deleted mouse).
Zashaw 03:54, 16 Jun 2005 (UTC)
[Removed ad hominem language, rush to judgement, and personal discrimination. The person was notified in writing that editors who wish to remain editors should refrain from such practices, 22nd of December, 2005]
And ref.
Zashaw 29 June 2005 00:17 (UTC)
This section doesn't actualy provide any useful information, so it needs to either be rewritten or deleted. I vote for the second.
I returned this passege ,since it takes no side in the creation/evolution epics ,it simply states this this part of the genom is highly debated in that realm ,as NPOV as possible. Since this has been added and reverted back 4 times by 3 users ,further reverts should consider a vote.
KEEP that section :
DELETE that section:
The following claim has been in this article for a while (and survived the excellent re-write by Mike Lin), and it doesn't make sense to me:
My assumption is that the mutation rate of a nucleotide is independent of the number of other nucleotides. Suppose that 9 million nucleotides are the really important ones, and another 3 billion nucleotides is just protective buffer. If my assumption is correct, then the probability of a deleterious mutation in the critical 9 Mbases is the same as if there were _only_ 9 Mbases in the genome. What's the scoop? Zashaw 06:20, 16 July 2005 (UTC)
My assumption is that the mutation rate of a nucleotide is independent of the number of other nucleotides. Yes, given that assumption, and if you *only* look at mutation, then the conclusion ("Junk DNA gives *no* protection against harmful mutations") naturally follows. I'm sure that assumption is true for *some* kinds of DNA damage mechanisms. But that assumption ignores at least one other kind of DNA damage mechanisms: chemicals that preferentially bind to DNA so tightly that the cell cannot reproduce.
If a molecule binds to DNA, but has no preference for binding to any particular location on the DNA, then it seems reasonable to me that junk DNA gives those molecules a place to bind that is relatively harmless. The rate at which a particular nucleotide is blocked by such a molecule goes down with the number of other nucleotides. While such cells can no longer reproduce, and so such a molecule will "kill" a single-celled organism whether or not it has junk DNA, such a molecule will have no effect on a multi-celled organism if it happens to bind to junk DNA in a non-stem cell.
This may help explain why multi-celled organisms apparently have more "junk DNA" than most single-celled organisms. -- 68.0.124.33 ( talk) 06:00, 15 March 2010 (UTC)
I deleted:
and the reference:
Briefly, this doesn't seem to be something that Creationists _do_ actually "therefore say", but only something the contributor thought they could, so I think it's original research, which is not allowed on Wikipedia. (The logic in the argument also seems pretty wacky, even by Creationist standards, but I'll rest on the no-original-research objection.) Zashaw 19:11, 10 August 2005 (UTC)
Is a distinction made between complete junk and genes which are never expressed? For example, birds still have some of the genes which make teeth. Anthony Appleyard 08:05, 14 January 2006 (UTC)
Placing this material that I removed is implying there is some scientific creedance given to it, when the info is cited from websites of questionable standpoint, and would regardless not be any reason to assume that the said facts are realistic. Creationism has nothing to do with this, and if they have ideas about it, feel free to let them refer to this in other articles on creationism. But there's no reason to put creationist caveats on science. It is a deception and it is POV.
The alternative to to word it so that it can quite plainly not be confused with real science, and make it well understood who is saying this and why these issues are being raised (which is non-scientific; i.e. that this is a religious opinion). To counter this, I believe someone would have to provide the scientific studies that would demonstrate is merits as far as not needing such qualifying statements. -- DanielCD 22:26, 3 March 2006 (UTC)
Moved text for discussion. FloNight talk 23:19, 3 March 2006 (UTC)
The patterns of mutation and rearrangement in nonfunctional sequence analyzed in comparative genomics studies provide strong scientific evidence for common descent, since these patterns tend to reflect the phylogenetic tree. Hence, the question of whether junk DNA is really junk has played a minor role in the creation-evolution controversy. Some advocates of creationism and intelligent design (except for proponents of Theistic evolution) contend that no DNA is junk, or that such junk DNA demonstrates only deterioration rather than macroevolution [2]. Another claim made by creationists is that the theory of evolution caused scientists to assume most DNA was functionless, stifling research into the functions of junk DNA [3].
The entry for New-age doesn't include any mention about DNA. If junk DNA is an important part of New-age spirituality, it should be on that page, rather than the junk DNA page. As such, I have taken out that section.
I feel the same way about the material on the evolution-creation debate, but will leave it alone since it is actively under discussion. Ted 11:54, 10 April 2006 (UTC)
http://www.kryon.com/k_chanelDNA04.html http://www.amazon.com/gp/product/1893183181/102-8269894-2256124?v=glance&n=283155 http://www.soulinvitation.com/12strands/ http://www.laughinglifecoach.com/12-Strand-DNA-Activation.html http://www.freewebs.com/dna12/ http://www.keylonticdictionary.org/Indice/Related%20Words.htm (See term 12-strand DNA) http://www.holisticessentials.net/id24.html http://www.google.com/search?hl=en&q=12+strand+junk+dna+spirit&btnG=Google+Search
--
Brian 26 April 2006 (UTC)
Refuting new-age theories by scientific means is irrelevant of their incorporation into this artile. as long as they are written under the sub header "newage theories" and are accepted by significant number of poeple both creationism and newage (crap) should be stated here ,for completness.-- Procrastinating@ talk2me 16:25, 27 April 2006 (UTC)
See Wikipedia:No original research. Aren't some of these are too minor to be in the article? The original purpose of the policy was to keep this type of stuff out of Wikipedia science articles. FloNight talk 17:27, 10 April 2006 (UTC)
"Honestly, these things entertain me." I've got to agree with Mike Lin. More and more, I'm just laughing at the junk in Wikipedia.
Pellionisz 19:17, 3 May 2006 (UTC)Comment by Pellionisz: "Junk DNA" is not a laughing matter. Hundreds of millions are dying of diseases proven or strongly suspected to be caused by "glitches" in the "Junk". [4]. We'd better not laugh but work as diligently as we could - Pellionisz actually pioneered mathematization (geometrization) of biology for decades. Drs. Malcolm J. Simons and Andras J. Pellionisz, the authors of a paper in "The Cerebellum", provided experimental evidence in support of the FractoGene "Fugu prediction". FractoGene is one of the not very densely populated class of algorithmic approaches to "junk DNA" with experimentally verifiable or falsifiable prediction(s). I believe it does a disservice to those trying to improve the discourse on "Junk DNA" to lump FractoGene, a predictive and experimentally verifiable or falsifiable theory with the epitomy of *non-predictive* and thus experimentally neither verifiable nor falsifiable, thus non-scientific, ID/ET (creationalist) theories.
The phenomenon of those initially opposing a novel approach becoming actual supporters is not new. Tensor Network Theory of the cerebellum (Pellionisz, from 1979) also provided quantitative and experimentally verifiable or falsifiable predictions. Drs. Gielen and Zuylen, talented young researchers in The Netherlands would not (rightly) just believe that the predictions were true. They rushed to their lab to experimentally falsify TNT. To their amazement, the quantitative predictions of TNT were right on target according to their own experimentation. Completely unknown to me, they published: "These results give firm support to the hypothesis that the central nervous system uses a tensorial approach for the activation of the motor system, as originally proposed by Pellionisz and Llinas" [PMID: 3703248].
I would also like to point out that FractoGene has a "Methylation prediction" out there - laid bare to test. It is also a quantitative and experimentally falsifiable or verifiable prediction, just as the "Fugu prediction" - now supported. I invite colleagues for discussions of any type, there are several blogs available; for mine, look in http://www.junkdna.com - Signed: Dr. Andras J. Pellionisz
Pellionisz 19:17, 3 May 2006 (UTC)Comment by Pellionisz to Moderator "TedE". a) as shown by facsimile of the facing Editors' printed page and "Contents" printed page (see "Editors" link on http://www.junkdna.com/fractogene/05_simons_pellionisz.html), neither Dr. Simons nor Dr. Pellionisz is an "Editor" in any quality in the 5(1) issue where our properly peer-reviewed paper with Dr. Simons appered. (b) Given my 30+ years of accomplishments in the field of the cerebellum (over 100 publications [5]) and now that I opened with Dr. Simons the cerebellum for a venue of "triangulation" with serious and widespread potential impact, it should not be overly surprising, should "The Cerebellum" float in their fleeting website some enhanced Editorial role for me. Rest assured, I do negotiate this issue with "The Cerebellum" (Taylor & Francis) and also for a planned "PostGenetics" Journal , Publisher is still negotiated, in addition to my Founding Editorship in e.g. "Neural Networks" [Elsevier] and "Neurocomputing" (Pergamon, and thus now Elsevier - the field of "science journals" changes rapidly..). Negotiations, however, are typically not conducted in public. - Signed: Dr. Pellionisz
Pellionisz 19:17, 3 May 2006 (UTC)Note by Pellionisz: Based on a mindset before facing the facts, some remarks were made and based on a misguided suggestion that the FractoGene approach, one of the few that actually made experimentally verifiable prediction(s), and its "Fugu prediction" has been experimentally supported, was placed into "Alternative theories". Although when he first suggested that "Junk DNA" could not be junk, Malcolm J. Simons was told "you are out of your friggin' mind" (1987) and thus I am proud to be in the same league with him (the still few who are not intimidated to say "Junk DNA is not junk")I suggest putting experimentally predictive and supported, published results into a separate category from approaches that are not experimentally predictive. Indeed, with the recently published findings of Dr. Rigoutsos [6] of 66 million motifs and 128,000 self-similar and repetitive "pyknons" [7] with pyknons *both* in the "Junk" and in practically all known (human) genes, there is a tremendous shortage of scientific approaches to explain these facts. Wikipedia would be well served by listing all approaches, but could insist on separating those that are predictive *and* experimentally verifiable (scientific) and those that are either not predictive, or their predictions can not be tested (non-scientific). Wikipedia is not a science journal, but there are clear standards of what science is, and what is not, thus such delineation would be good for the readers at a time when (any) scientific explanation is *much* needed - Signed: Dr. Pellionisz
I've put the article for merger ,since I dont see any good reason for them both to be apart. they view the same subject from a slighlty different (biassed..) prespective, assuming the known reason for these seemingly "exsessive" DNA is it's non-coding properties.
So ,considering term word "non coding" han't been proven ,the ambigous term "junk" seems more likely as a merge target. I'd appiciate any input, thank you -- Procrastinating@ talk2me 11:08, 12 April 2006 (UTC)
-- Procrastinating@ talk2me 19:58, 20 April 2006 (UTC)
Note from Pellionisz: I would not recommend the merge, either. "Junk DNA" is a historical "brand name" by the late Ohno (1972), not really a scientific "generic name" (see more detailed discussion at the 1972 entry of [8]. "Non-coding DNA" is somewhat generic (usually meant "non-nucleic-acid-coding") but is not very scientific these days itself, since negative evidence can not be established with absolute certainity. I suspect both terms will become of historical significance, marking a transitional era in science. Better said (since in science everything is always transitional), marking a major disruption, an astounding paradigm-shift. As such, they both deserve to be in an Encyclopedia - Signed: Dr. Pellionisz
This has gone on for several months, I'm removing the merge request. If you disagree, you can replace it, but add some convincing reasons. Ted Talk/ Contributions 22:44, 14 August 2006 (UTC)
Again... not having seen this discussion, I req a merge FROM junk DNA TO noncoding DNA. New reasons - see
Talk:Noncoding DNA. Besides, "junk DNA" is not an appropriate scientific term. Do a PubMed search - 75 papers vs 264 for "noncoding DNA" and 156 for "non-coding DNA", and besides, the correct title would be "junk" DNA as no decent scientists would use the term without quotation marks these days: The concept implied by use of the term junk DNA is highly misleading and scientifically inaccurate; it is as if
Animalia were to redirect to "
critter", or
Abiogenesis to
Spontaneous Generation. That there are so-and-so many more Google hits simply shows the ignorance of the general public, and WP is ill-advised to strive to emulate that.
Yes "noncoding DNA" is an ambiguous concept too, but such ambiguity would be discussed in the article; at any rate, it is the proper scientific term in use nowadays. Stuff that does not get translated into proteins would be
noncoding RNA; noncoding DNA may or may not be transcribed into RNA and even in the former case it does have a function in many cases (
promoters don't get transcribed, but never were considered "junk DNA", but only because the operon model predates industry-scale DNA sequencing; had it been the other way around, the promoter would have certainly been considered useless "junk" at first.
Please, before replying and/or rm the merge request, take your time and read the material I have referred to and linked. All evidence points to a considerable part of that "junk" being actually more important than genes (see the Science paper for a not-too-scientific discussion).
Dysmorodrepanis
18:09, 4 December 2006 (UTC)
To me it seems like you are expressing your opinion that "junk DNA" term is unfavored or outdated. That is fine,, but question is whether the term should or not have own encyclopedia article or not. To me I don't see a strong argument otherwise since it is popular term and meaning is different than "noncoding DNA" as others said. Besides in general public themselves, I think you still see the term used by scientists and science writers in informal conservation and when they write something to understand by general public, like in news@nature often, cited in the article severally. Nature editors thought this through and decided "junk DNA" term is still somehow useful, if only to compare to new discovery. So your points with "junk DNA" term are mostly right but do not mean it should not have own article, instead problems should be in and made clear. -- Baldzac 19:13, 4 December 2006 (UTC)
I think you are not really address relevant question of,, should there be "junk DNA" encyclopedia article. Wikipedia has articles on phlogiston,, alchemy and aether even though they are rejectecd concepts, and should. "Junk DNA" term has historical importance if nothing else, although like I said Nature is using it recently like 2004 [9]. Statement like "It should not be spread any further" is not right spirit for encyclopedia unless term is not notable, clearly not true. To me you really want to add more to "junk DNA" article about why concept is outdated. And maybe copy of some material to noncoding DNA article. There is not good reason to get rid of "junk DNA" article.
Here is what source Nature letter of 2004 says [10], to me it says issue of whether there is some "junk DNA" is not settled.
-- Baldzac 00:10, 5 December 2006 (UTC)
Well what do you say? You ask for peer review papers saying "junk DNA" concept still maybe important since 2001. So I show big one in Nature, hardly could say more clearly (unless you argue "disposable DNA" means different than "junk DNA" and news@nature Editors writing of article got it wrong), moreover one already cited in Wikpedia article (where I found it) so seems like you didn't even read before saying to merge out. It is great paper even with appropriate qualification of result,, all the time computer and math people look at DNA and say it must do that and can't be junk because of some patterns. Here some actual real biologist stands up and says not so fast, here in real organism we delete millions of junk DNA,, try hard and can't find it to do anything. Maybe it really does but point is question is still important, obviously deserves encyclopedia article.
And like I say,, even if "junk DNA" was totally obsolete rejected concept, even then would still deserve article. So I think we should take off ugly unwarranted merge banner. You seem to know about field (maybe only somewhat biased view of how current situation is), and could make good changes to "junk DNA" article about how it becomes less favored idea. -- Baldzac 04:57, 11 December 2006 (UTC)
Do you think Nature editors are so confused to use "DIFFERENT ENTIRELY" term!!!!???? [11] I am laughing.
Before you say, junk DNA is definitely (a) obsolete outdated concept, you call it "highly misleading and scientifically inaccurate", "false and outdated" and "junk science" and "It should not be spread any further.". Now you back up and say actually there is (b) "scientifically correct sense"??? Is it "scientifically correct sense", "Junk DNA is a collective label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified"???
Come on, you are silly, no point to split hair here, better to just do work on other article. I can see you might copy or move some stuffs from "Junk DNA" article into "Noncoding DNA" article that does not specific apply to contreversial claim of non-function, like the evolution conservation. But clearly to me, "Junk DNA" concept deserves own article with much of current content. You should just go work on "Noncoding DNA" article, see how it goes.
Otherwise, if you still say to merge and get rid of "Junk DNA" article,, neither of us would convince the other now. Then we should wait of opinion of other editors. Note many opinion above who were against merger. So I will wait some days but remove ugly banner unless others stand up with new,, better reason. -- Baldzac 06:25, 20 December 2006 (UTC)
Please evaluate references and reconsider. The concept of "junk" and of "having a function" are quite diametrically opposed. Also note reluctance of current researchers to use term without quotation marks. Dysmorodrepanis 04:26, 18 February 2007 (UTC)
I rv'd the merge tad. Please consider my case above. This article is not about the subject. If not a complete merger, at least Noncoding DNA is what needs to be beefed up and this article needs to be shrunk. Anything about noncoding DNA having a function does not belong here, but there. This article is about functionless DNA and should be about nothing but, if it is maintained at all. Non-translated DNA is a scientific issue, and it should be treated at a standard that is acceptable to the scientifically-trained reader. Which at present it is not if your functional genetics/genomics is up to date.
Current PubMed results:
Note: The same paper might use "noncoding" and "non-coding" (or "non coding" which is the same for PubMed search) so it's not 76 : 435, but "junk" is disfavored by at least a factor of 4.
Some variant of "noncoding" is clearly favored over "junk" by the professional scientists who work in the field, and the ortography seems to lean towards "non-coding". Dysmorodrepanis 05:06, 21 April 2007 (UTC)
After having spent too long reading through all of these posts, I have realized that the simple facts have been said but are being bogged down by unmeaningful citations, personal attacks and showboating. The "Junk DNA" page needs to be merged into the "Non-coding DNA" page, possibly added in it's own section due to it being part of the history of genetics and genomics. And that is what it is- HISTORY.
-for clarification to those not working in genetics, the terms really do need to be defined. "junk" DNA- "junk" implies that it has absolutely no use, ever, and can be discarded (junk....duh). "non-coding" DNA- this term refers to the DNA segments' ability to code for protein via the DNA-RNA-Protein pathway (mRNA=messenger RNA). It is common knowledge (refer to any genetics textbook made in the last 10 years) that much of our DNA codes for RNA that never gets made into protein (rRNA, RNAi, siRNA, ect.). It is technically difficult to find segments that seemingly show no activity ("junk DNA") that actually codes for RNA because RNA is fleeting and degrades very easily, among other things.
Go take a stroll around any modern genomics or genetics department and ask what people think about "junk" DNA. The simple fact is, scientists cannot use it without quotations and remain credible. In fact, in the real scientific community, it is really only used in presentations and papers that are directed at a less educated general audience. Thus, when people search Wikipedia for "junk" DNA, they should be redirected to "non-coding DNA" so they can learn why that term is technically not correct. Why?
The simple answer is, it's too complex. There are indeed segments of DNA that are repetitive AT's or other such sequences, and these do seem to have no function; however, it is still possible (although unlikely) that these segments serve some kind of buffering purpose. When everyone keeps referencing the article where parts of the mouse genome were deleted with "no phenotypic effect" it makes me cringe. Anyone who has ever worked on protein expression knows that there are many protein-coding genes that are only active in certain specific cases (i.e. periods of extreme cold, heat, dryness, UV exposure, ect.)- so why should we assume it is different for non-coding sequences? What the problem really is is that people continue to lump all DNA of unknown function into the "junk DNA" catagory. I guess "DNA of Unknown Function" isn't flashy enough to become a term?
Overall, we are finding new papers published EVERY week that show more and more uses for areas of genomes that used to be thought to have no function (please check a GOOD genomics and genetics journal- such as Genome Research). Many serve as buffer zones for protein attachments, many actually make RNA for a variety of purposes (my favorite is the rather new RNAi- Interfering RNA). If you have any doubts about this, please do any PubMed search on CHiP-on-chip assays. This relatively new technique is giving us loads of data showing most of our DNA thought to have been "junk" has a purpose- the downside is we have no good way of finding out what that purpose is. The common consensus in the field is regulatory elements. Even if a stretch of DNA doesn't code for protein or even RNA, it can still have uses in regulation, buffer zones and other NON-CODING functions.
So, while there is certainly some DNA in genomes that does indeed serve no purpose, it is becoming evident that the actual percentage is going to be very, very low (some predict in the 5-15% range). It is unfortunate that so many new papers and discoveries are overriding conclusions given 20 years ago by well-known scientists, but that is the very nature of discovery- and especially genetics. The vast majority of how DNA really works at every level is yet to be discovered- labeling such a huge amount of it as "junk" is both a detriment to further studies and a great way to mislead the general public. Non-coding DNA is exactly that- no more and no less. calling it "junk" DNA means it absolutely has no function. Non-coding simply means it does not code for protein- it does not neccesarily imply function and is therefore the correct term for the vast majority of what uneducated or outdated people try to call "junk" DNA.
128.118.200.75 19:44, 29 May 2007 (UTC)Matt
BTW Baldzac - that "conservation of junk DNA" thing down below... checking for papers on sequence conservation in pseudogenes might help. As far as anyone can tell, at least initially pseudogenees (as opposed to paralogs) are indeed "junk". Whether they may acquire a function later on is another thing. But in any case, here's a strategy that might lead to success:
Basically you're looking for the color of noise of junk DNA. Dysmorodrepanis 04:14, 17 August 2007 (UTC)
I see people have removed this material before, and that they have made all the correct scientific and wikipedian arguments when they did, and that its been added back anyways. But I'll try again...
To Dr. Pellionisz: I had a look at your paper and looked at information about your hypothesis. With all due respect, this work is not ready to be in an encyclopedia. As you know I'm sure, the ideas summarized in the introduction and the "Hypotheses of origin and function" has been condensed from hundreds of peer reviewed articles from dozens of of genomics journals. A single paper in "Cerebellum" refering to a pending patent is not sufficient not warrant inclusion in this encyclopedia. There is no other reference to your hypothesis by other scientists in NIH's PubMed [13]
Re, the Creationist view: To quote the discussion page for the evolution entry "If you wish to discuss or debate the validity of the theory of evolution please do so at talk.origins, True.Origins Archive or Wikireason." As had been said before on this page, the appropriate place for this material is on a page about creationism. There are hundreds of detailed studies published in scientific journals on junk DNA every year and none of them pertain to Creationism (a NIH-PubMed search on "junk DNA creationism" finds no results [14])
Re the new age view: Junk DNA is a scientific term, so people expect the scientific definition and the current scientific debate/consensus. This theory is not a part of the scientific debate as evidenced by the fact that searches in PubMed find no reference to indigo children and junk DNA ( [15])
(FYI:PubMed, a service of the NIH/National Library of Medicine is the premier life science search database with over 16 million citation dating back to the 1950s. As a point of reference, searching evolution+Junk+DNA retrieves over 5000 articles [16])
GeoMor 22:51, 14 August 2006 (UTC)
--- [Answer by Dr. Pellionisz to anonymous "GeoMor"'s note ("to Dr. Pellionisz")]
Dear "GeoMor",
Your 7 lines, commenting on your 2 deletions (junkdna.com and fractogene) IMHO raise 3 very serious issues; personal responsibility, credibility of Wikipedia, and self-contradiction.
PERSONAL RESPONSIBILITY
"Junk" DNA, at a time when there are up to 150,000 "non-coding DNA diseases" ( http://www.junkdna.com/junkdna_diseases.html) and literally hundreds of millions are dying because "junk DNA" had been needlessly overlooked for decades (as Mattick wrote in Scientific American, 2004): overlooking junk dna "was the biggest mistake in the history of molecular biology") became an issue by 2006 raising direct personal responsibility of anyone fostering further delays. It is very telling that the 2 deletions by "GeoMor" ("junkdna.com" and "fractogene") could be seen by those affected by such diseases as deliberately suppressing active efforts towards some remedy. (This includes not only Dr. Simons, with diagnosed 'junkdna disease' of Multiple Myeloma - the pointer to "Genius of Junk" retained in Wikipedia, but practically all of us, since any/all of us could be hit by such neglected, and very often lethal diseases). Deletions by "GeoMor" are, therefore, particularly objectionable, since such personal responsibility is outright hidden by his anonymity - while the 2 deleted links bear clear personal responsibility by Dr. Pellionisz.
CREDIBILITY OF WIKIPEDIA
Deleting the link to " http://www.junkdna.com" the constantly up-to-date "junk dna hub" that is the #1 hit in Google (searched for junkdna) and presently #8 hit in Google (searched for junk dna), with gigabytes of monthly traffic, diligently keeping track of the subject of "junk dna" (covered so meagerly in Wikipedia that e.g. even Rigoutsos' "pyknon" discovery this April goes unmentioned...), IMHO raises credibility if this Wikipedia entry is covering "junk DNA" properly.
SELF-CONTRADICTION OF 2 DELETIONS
"GeoMor" is self-contradictory in his "arguments" for deletions. Is FractoGene derived from "ideas summarized in the introduction and the 'Hypotheses of origin and function has been condensed from hundreds of peer reviewed articles from dozens of of genomics journals" (that is, widely known and accepted) - or so brand new that "A single paper in 'Cerebellum' refering to a pending patent is not sufficient not warrant inclusion in this encyclopedia. There is no other reference to your hypothesis by other scientists in NIH's PubMed"??? Since those who are presently literally dying of "junkDNA diseases" are certainly eager "to leave no stones unturned", it does not seem fair to suppress information - that is either widely known (and as such, should be listed), or rather novel and potentially significant (and as such should be listed). The other self-contradiction is to delete a less-than-six-months-recent academic publication (that appeared in a peer-reviewed science journal as experimental support for one of the not very densely populated group of algorithmic AND predictive approaches to the function of 'junk' DNA), on the grounds of its novelty. Since the paper appeared in March, 2006, is it not *of course* that it is way too early to have any peer-reviewed follow-up?? (The peer review process itself is often longer, e.g. it took Rigoutsos more than a year to have his pyknon paper published - and a famous manuscript by Taft and MATTICK could never become published on "junk DNA"...) Isn't this something? Isn't it fair to -at least- ask for the names of those hindering progress towards remedy for countless "junk DNA diseases"??)
One is also tempted to quote Jim Watson, who was asked, "what happened once they published their paper on "the double helix" with Francis Crick". "NOTHING HAPPENED - NOBODY CITED THEIR PAPER FOR SEVEN YEARS". For the peer-reviewed full paper on FractoGene it is not even seven *months* since its appearence...
The record for "junk DNA debates" is already too long, IMHO. Let's get serious and personally responsible about it. Who knows? Maybe one day who are suppressing attempts might regret it later - when diagnosed of some of the killer "junk DNA diseases".
Respectfully, Dr. Pellionisz pellionisz@junkdna.com
TedE (whomever you are), with utmost respect due to an anonymous "moderator" (?), I disagree who fails to understand what Wikipedia is. (As for academia, leave it for me, I have over hundred publications, just look up "Pellionisz"). Wikipedia, IMHO must inform the general public about the most important aspects of a given entry, in this case "junk DNA". What is the most important issue for hundreds of millions suffering from "junk DNA diseases"? Clearly, if the field is still stuck to chewing on the 34-year old misnomer that 98.7% (or just "most") of human DNA is "junk" - or to learn that there are even algorithmic (i.e. mathematical) approach(es) with scientific predictions, that are actually supported by experimentation. Witholding such information (arbitrarily deleting FractoGene), at minimum, robs the optimism of hundreds of millions of patients that serious scientists proceed that well, that even such all-important landmark (appearence of mathematical interpretation with experimentally verifiable or refutable prediction[s]) has been passed. Witholding such information bears personal responsibility to the patients. Please come forward with your name and credentials if you truly wish to take such a historical burden on your shoulder. Of course, deliberately witholding information on a spearheading approach (especially if it is alleged that it represents an entire school of thought :-) may simply serve the purpose of fabricating some "breathing room" for those with competing approaches to catch up. While it is quite common, it is transparent as unfair. Please decide if the fractal approach to DNA *AND* to biological systems they govern is (a) represents an entire field (in that case, show it to hundreds of millions of patients, that there is a lot of hope), or (b) it is novel to the extent that its peer-reviewed publication in March 2006 could not even be met with a peer-reviewed avalanche for simple lack of time - hundreds of millions of "junk DNA disease sufferers" deserve the news that hope is in the mathematical/information technology breakthroughs in "junk DNA". (And the pseudo-debate on ID/ET will never cure them of any of "junk DNA diseases" e.g. listed on http://www.junkdna.com/junkdna_diseases.html )
Respectfully, Dr. Pellionisz pellionisz@junkdna.com
Only Two comments.
1. I cannot judge if this article is encyclopedic/scientific with proper references etc as I do not possess the appropriate khowledge (and time). However, as genetics sciences are under development and they donnot have certain nomenclature (at least in Greece), we should be careful of the terms which are going to be used as they could be easily misunderstood. For expample, as far it has to do with public issues such as "bioethics of cloning the DNA and patents", the Junk human DNA can be a patent by many Patent Agencies, thus the interpreting of the scientific terms may confuse the wide public, without even mentioning the procedure of translation in each country.
2. Second and most important in the article "Junk DNA" in the topic of "Hypotheses of origin and function" the sixth bullet is "comletely out of space" as it says:
"Similarly, proponents of extraterrestrial origin theories suggest that junk DNA may be lying dormant, waiting for a signal from the creators of the human race."
and i believe that, if not deleted, it should be at least removed in the end of topic. I beg someone to respond to this call as i dont know how to do it!
-- apapanton 08:46, 24 September 2007 (UTC)
This whole article is trying to sneak in original research!
This is evident from the first paragraph:
While much of this sequence is probably an evolutionary artifact that serves no present-day purpose, some may function in ways that are not currently understood. In fact, recent studies have suggested functions for certain portions of what has been called junk DNA. Moreover, the conservation of some junk DNA over many millions of years of evolution may imply an essential function.
These statements are speculative. They are opinions, so I need to know who is making those claims if you want to conform to NPOV. If this is not original research, I want to see citations.
And the whole section on Evolutionary conservation of "junk" DNA is blatantly original research. Citation [12] is about mouse genomes. Citations [13], [14], [15] demonstrate how some previously unidentified genome sequence now have a purpose. However, the thesis of this section is on how "junk" DNA is preserved through evolution, therefore it serves a purpose.
It fails to cite articles that argue if "junk" DNA has indeed been preserved through evolution. If this is not original research, there should be tons of references. Cite your sources.
Liulk 13:36, 2 November 2006 (UTC)
The word "probably" in the first paragraph is maybe too opinion. Otherwise I think the references support most of the article. For example #13 the news@nature article says,,
David Haussler of the University of California, Santa Cruz, and his team scanned the genome sequences of man, mouse and rat1. They found more than 480 ultraconserved regions that are completely identical across the three species....The regions largely match up with chicken, dog and fish sequences too, but are absent from sea squirt and fruitflies. The fact that the sections have changed so little in the 400 million years of evolution since fish and humans shared a common ancestor implies that they are essential to the descendants of these organisms. But researchers are scratching their heads over what the sequences actually do.
Some more references are needed though. The whole paragraph about why the junk DNA doesnt get thrown away by evolution for example. I think the information is right but it needs sourced. -- Baldzac 18:57, 2 November 2006 (UTC)
Postgenetics the new science hasn't got article. My english too poor to begin it.
We have it in hungarian: hu:Posztgenetika
The official page: http://www.junkdna.com/postgenetics/
-- hu:Rodrigo 11:10, 7 November 2006 (UTC)
Is "junk DNA" only significant/more common in eukaryotes? (It seems to be the impression I've gained elsewhere) Should this be mentioned? AlmostReadytoFly 22:38, 16 January 2007 (UTC)
Thats generally true, although procaryote genomes do contain non-coding sequences. In model organisms that have been investigated in detail, many of these have known functions tied in with gene regulation. About ten percent of the E. coli genome is non-coding and this is fairly representative of bacteria, or so we are led to believe. Archeans, less sure. As for mentioning the relative abundance of 'junk' DNA across different taxa - yes, it should be in there.-- ChrisJMoor 22:50, 31 March 2007 (UTC)
The bullet the mentions intelligent design apparently needs a reference. The book Not By Chance! ( http://www.amazon.com/Not-Chance-Shattering-Modern-Evolution/dp/1880582244) mentions this theory, so could be cited as a reference. I don't know what this has to do with new age though.
Also, this bullet somewhat refutes the bottom bullet of that section, that the junk is simply junk. If the genes in junk dna were simply turned off genes (that might somehow be turnonable through some unknown mechanism), then removing them in mice and observing no change would be consistent with the theory. The mice would have only lost the ability to turn this dna back on, something the tests couldn't hope to test for. I guess all I mean to say here is that even if you test for every possible difference, the difference might not be in the phenotype. Although the already existent disclaimer is probably enough. —The preceding unsigned comment was added by 71.228.189.127 ( talk) 07:35, 10 March 2007 (UTC).
As a layman (but had quite a few graduate-level biochemstiry classes) to molecular biology/genetics/biochemistry, I often feel the term of Junk DNA or noncoding DNA is quite arrogant or at least naive and ignorant.
Just as complex DNA sequences derive from merely four necleobases, or binary numerical system only needs two symbols (0, 1), the so-called organism complexity simply cannot be regressed to the numbers of genes CURRENTLY known to human beings. Genes, as several levels above the basic blocks ACGT, are interacting with each others and with other parts. I believe the human beings are just able to understand the tip of the iceberg or a few tips among unknow numbers of icebergs. It may seem useless or junky as it's noncoding, but how deep do geneticists and Co. know about the processes of replication, transcprition, and translation, or interactions with protein? Basically all experimental research is being done somewhat using blackbox system in a sense that the internal mechanism or structure is not known or not worth knowing (for now). while the basic function of DNA is as carrier of genetic information which hopefully will be decoded sometimes in the life cycle of an organisim, how can we assume with so much confidence that besides coding, other parts of DNA are just nonsense or junk? While blackboxing is often successful, assuming eveything is known about the box is just arrogant or ignorant.
The key to the term is not whether most segments of "junk" DNA may turn out to be actually or theoretically junk in any sense, but is that we should not delare it's just junk b/c we do not find many things to do with it FOR NOW. What do we call it? Perhaps just leave it alone or just call it unknown DNA (just like we call people missing instead of dead after a disaster even most of those missing are reasonablly beleieved to be (and actually are) dead. -- Minimeme 21:25, 19 March 2007 (UTC)
I'm going to asume a lot now. Please correct me if I'm wrong. But might the junk dna be old deactivated dna from the earlier forms of evolution. For example, junk dna in humans consists of some fish dna, some reptile dna some mammal (other than human) and so on? If it does, than that would be a proof that makro-evolution exists. A good proof of evolution would be if you could take a mouse, turn off some genes and turn on some other and voila! you get a fish. —Preceding unsigned comment added by ChristianKarlsson.se ( talk • contribs) 12:30, 10 September 2007 (UTC)
This article seems to be riddled with bias against the idea of nonfunctional DNA. The list at the end at the article is virtually identical to a list at the creationist wiki [17] and uses biased language and selective summaries to suggest that junk DNA doesn't exist. The article in general does not seem to reflect the scientific consensus on nonfunctional DNA. Xaoiv ( talk) 13:20, 1 July 2008 (UTC)
After reworking the article, I have decided to remove the totally-disputed template. I have added a remove-section template and a totally-disputed-section template to the section "Function for Some Subsets of Junk DNA." Xaoiv ( talk) 14:16, 3 July 2008 (UTC)
As a professional working with Mobile DNA, the main point is that "junk DNA" is an outmoded term once used to describe non-genic DNA before transposable elements were known. The term is only of historical importance, and is not used anymore except in a colloquial way. 128.214.172.26 ( talk) 08:30, 2 September 2008 (UTC)AHS 09.45 UTC2 September 2008
I can't see anything in that section pointing to the origins of "junk DNA." It's all about possible functions. I think either the title needs to be changed or something needs to be added on the various hypotheses about how "junk DNA" arose.
Tathaataa ( talk) 15:12, 17 October 2008 (UTC)
About 95% of the human genome has been designated as "junk", including most sequences within introns and most intergenic DNA.
Wow, both introns and intergenic DNA? What are the odds of that? I mean, you know, because they're not exactly the same thing... -- 76.217.112.38 ( talk) 17:40, 20 October 2008 (UTC)
DarthPanda, could you please explain what is not constructive about the edits I made in this paper, consisting of a historical reference and clarification about the current status of the term "junk DNA"? For now I have reverted your edit and I suggest we discuss your objections before making further edits. 137.224.252.10 ( talk) 13:19, 5 December 2008 (UTC)
See the heading, this label is very outdated and it was ignorant even when it was coined, it needs to be eradicated as it misleads many people.
As for the DNA it's primary role is structural, nucleoskeleton is build around DNA, bigger nucleus is obviously beneficial for complex multicellular organisms, among others they have to store programs for every tissue. This DNA also serves as a buffer against viruses and transposons as it greatly lowers the chances that the virus will get into expressed DNA. The above should be added to the article if it's not already there. Enemyunknown ( talk) 19:11, 25 January 2009 (UTC)
Also in pre med schools one of the <a href=" http://www.premedrequirements.org">pre med requirements</a> is to learn all the history of the DNA (Vcjohnny)14/04/2011. — Preceding unsigned comment added by Vcjohnny ( talk • contribs) 00:51, 15 April 2011 (UTC)
About 95% of the human genome has been designated as "junk", including most sequences within introns and most intergenic DNA.
While I'm sure this is correct, shouldn't there be sources for this? EMSPhydeaux ( talk)
The comment(s) below were originally left at Talk:Junk DNA/Comments, and are posted here for posterity. Following several discussions in past years, these subpages are now deprecated. The comments may be irrelevant or outdated; if so, please feel free to remove this section.
Comment(s) | Press [show] to view → |
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MERGE THIS ARTICLE - GOOD QUALITY, VERY IMPORTANT - THERE IS NO JUNK
Recommend merging into Non-Coding DNA. May need the term "Junk DNA" for cross reference or search purposes. It is very commonly used in media in explaining Medical Genetics to the public. Howver, it is a seriously misleading notion. There are many interesting theories, mentioned in the article, about the approx. 97% of the Human Genome that does not code for protein. I have some additional thoughts: A) The History of Science in so many areas, over so many centuries, shows extremely important developments from findings first thought to be unimportant, or junk. Over time, findings that are thought to be irrelevant, random or unimportant turn out to contain crucial information. New concepts then lead to new findings. B) DNA spends most of its "lifetime" in coiled (helical) form. It appears to have activity in this configuration, so the non-coding areas could be important in the stereochemistry of this activity. C) All genes are not always "ON". Something has to regulate them ON and OFF. We don't yet know nearly enough about how the external gene regulating influences, such as hormones or other "messenger molecules" interact with the DNA structure itself. We therefore have to learn what role(s) the non-coding areas play in the regulatory processes. First posted above 4/26/2007 Then added below 5/06/2007 Just in recent weeks important news has broken which points to Gene Regulation Issues. An example is the finding that a non-coding region on Chromosome 9 is associated with a higher risk of developing Diabetes and Heart Disease. Assuming these findings are replicated, it seems that this DNA region is anything but junk. Martin Denker 11:44, 4 May 2007 (UTC) |
Last edited at 11:50, 4 May 2007 (UTC). Substituted at 20:44, 29 April 2016 (UTC)
There is abundant evidence to support the claim that roughly 90% of the human genome is junk. I am in the process of creating a separate article on junk DNA in order to lay out the evidence and correct the false history that permeates the current scientific literature.
The project is being discussed under Non-coding DNA. Please feel free to contribute if you are knowledgeable about the subject. Genome42 ( talk) 21:35, 25 May 2022 (UTC)
![]() | Text and/or other creative content from this version of Non-coding DNA#Junk DNA was copied or moved into Junk DNA with this edit. The former page's history now serves to provide attribution for that content in the latter page, and it must not be deleted as long as the latter page exists. |
Given discussion in several threads (Merge discussions 1, 2, 3), I've re-split the Junk DNA section back out of Non-coding DNA. The articles were merged back in 2012 ( merge discussions began in 2007) after results from the ENCODE project came out when discussion in both the academic and popular publications was a bit muddled on what was actually being counted as 'junk' and why as can be seen in the page contents just before the merge. Since then, I think a good case can be made that there has been a lot more nuance in measuring what portion of a genome's sequence is biologically functional, what that function is, and what evolutionary significance it has. The focus on this page should probably be less a binary of "is this sequence junk" but more "for a given threshold of biological function, does this sequence reach that and what does it mean evolutionarily?". I've tried to leave behind a reasonable summary of the relevance of the term 'Junk DNA' to the concept of non-coding DNA over at that article. T.Shafee(Evo&Evo) talk 05:31, 16 March 2023 (UTC)
As this content is being updated, it may be worth considering what would be a useful summary diagram or two for this article - either some existing cc-by image or I can create one. Perhaps something like Fig 1 from this paper (though it'd need to be re-drawn as an svg for quality and editability). Do people have ideas for anything else that would be better? T.Shafee(Evo&Evo) talk 03:50, 20 March 2023 (UTC)
Could someone please explain why the photo of Motoo Kimura can be used in the Motoo Kimura article but not here? Genome42 ( talk) 22:24, 25 March 2023 (UTC)
A great many people think that the original proponents of junk DNA thought that protein coding DNA was the only functional DNA in the human genome. These early junk DNA proponents supposedly, and foolishly, thought that all non-coding DNA was useless junk because they couldn't imagine any functional DNA in the non-coding region. Thus, the hypothesis of junk DNA was based on an argument from ignorance.
The discovery of functional DNA elements that did not encode protein supposedly refuted the idea of junk DNA - at least that's how the common belief goes.
We need to put a stop to this false view of the history of junk DNA and we need to do it explicitly so that other articles can refer back to this one whenever the misinformation surfaces. Unfortunately, this skirts right up to the border of what's permissible in the Wikipedia culture. I'm sure there will be Wikipedians who don't like what I just posted and who will claim that it is "editorializing." If they can come up with a better way to correct the misinformation then let's discuss, keeping in mind that as scientists we have an obligation to make sure that the average reader gets a correct view of the scientific facts. Genome42 ( talk) 19:11, 28 March 2023 (UTC)
Should this article mention the Onion Test anywhere or is a bit of a niche formulation of the argument? I've never actually seen that term used 'in the wild', but maybe I just missed it. Could either be mentioned inline in tthe articcle text or just thrown in the see also section if ppl rechon it's worth linking to. T.Shafee(Evo&Evo) talk 02:30, 27 March 2023 (UTC)
I propose to revert most of the links that were recently added by Melosina because, in my opinion, it's an example of overlinking (too much blue). I don't think it's necessary to link to terms such as "DNA," "genes," "protein," "natural selection," "eukaryotic," "nucleus," "expression," "geneticists," "evolutionary biologists," molecular biologists," "evolution," and "Nobel." Some of the links they inserted are not at all helpful in the context of an article on junk DNA and may even be counter-productive (e.g. "functional," and "mutation"). The problem of overlinking has been covered many times in the past few years. For example, the essay on the overlink crisis says,
Overlinking is the characteristic of having too many internal wikilinks or hyperlinks to external webpages. Editors should use an appropriate number of wikilinks in an article's text. In addition to providing relevant navigation opportunities, an appropriate number of blue links makes articles easier to read, especially in long paragraphs or sections.
The issue concerns readability. Too many Wikilinks (too much blue) makes the article less attractive to readers without adding any significant value. This is a serious problem in science articles where the leads can look overwhelmingly complex to the average reader because of excessive Wikilinks (e.g. Human genome).
The Wikipedia:Manual of Style/Linking makes the following wise suggestions concerning links.
An article is said to be overlinked if it contains an excessive number of links, making it difficult to identify those likely to aid a reader's understanding. A good question to ask yourself is whether reading the article you're about to link to would help someone understand the article you are linking from. Unless a term is particularly relevant to the context in the article, the following are usually not linked: -Everyday words understood by most readers in context
Perhaps we can find a happy medium where unusual terms that are essential to understanding are given links but commons scientific words that should be familiar to anyone reading this article are not? Genome42 ( talk) 14:26, 29 April 2023 (UTC)
Perhaps having the word YET used more frequently, as well as having as a second point if not the first, a clarification clarifying / a differentiation differentiating between,..
.
1 matched-with-others-in-surpassed-evolutionary-progressions-and-so-redundant(true junk) DNA,
2 assumed-no-function junk from genetic processes (high confidence - temporary retentions kept longer than needed if needing to be kept at all), and
3 theorised to have no function but of more compatible DNA-chemistry -combinations ... junk (ones that have still matching after-activation matching chemistry with organelles or functional materials in plasma/interstitial spaces, but are without 'context' in nearby genes along the chains, and so seem pointless, despite chemical-compatibility. Compared to things like say, immune system instructions or embryonic stages, ones with clear-purpose) (less-confidence / more reasonable uncertainty - the chemistry suggests a high likelyhood if not outright proof, of past usefullness) ...
.
... could help to introduce the concept FIRST?
Rather than finding the contrast or inferred-problems with the single concept or inferred consistency, further down the page, and the static tense (scientific conclusion-ary) avoiding the still-new problems of the field? i.e. using YET, adds necessary cautionary relativity to a solid concept, but a phenomenon that is sometimes irreversibly presumed static.
---
i.e. when something THOUGHT junk, is 'let-back-in', at the PREVIOUS time of it being labelled junk, the static nature was less correct, than saying "YET", so,.. yet-confirmed as junk, or yet-re-included back into unknown status rather than confirmed-junk or certified-junk, etc. A big part of that problem is WHO certifies, but that might end up making the page much larger than it should be if that kind of debate/issue should be on a separate page or is not subjectively purposed - i.e. at least the 'YET' nature of both corrective processes, reveals just HOW-new, this science is. Sort of like if you re-wrote it entirely, and re-wrote it with constant inferred STATUS inferences, to keep reminding the reader, that DNAs classification can rapidly CHANGE, that DNA is only sometimes statically clearly-purposed, nature's IMperfections, compared to imaginary ideals, etc. That's not opinion, that's hard-science. Human DNA for tails, for example, are recent, but HAD function. Tense with it as an example, would be an easy example to demonstrate the principle of CAUTION with DNA's classification as junk or not-junk. 120.21.106.152 ( talk) 15:13, 30 June 2023 (UTC)