Talk:Junk DNA

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Article Grading: The following comments were left by the quality and importance raters: (edit · history · refresh · how to use this template) 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)

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Contents 1 Term to use? 2 Introns 3 November 2003 Scientific American 4 Repetitive or random sequence? 5 Repressor -> Silencer 6 I feel so proud! 7 Creation-evolution controversy 8 Junk DNA protecting against mutations 9 latest deletion 10 Unused genes 11 DanielCD's revert 12 New-Age Spirituality 13 Wikipedia:No original research 14 Merge article with Noncoding_DNA 15 Removing non-encyclopedic material 16 Original Research 17 Postgenetics missing 18 Eukaryotes? 19 Intelligent Design Bullet 20 Arrogant terming 21 Proof of Evolution?

[edit] Term to use?

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" ?

Yes noncoding DNA is preferable. But a Google test gives 62,100 hits for "junk DNA", so it's obviously a real term even outside scientific community. Evolver 23:43, 4 September 2005 (UTC)

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)

One could argue for this, yes, but it should redirect FROM "junk DNA" TO "non-coding DNA", as the latter is the more appropriate and far less loaded term. Evolver 03:49, 9 September 2005 (UTC)

[edit] Introns

Any distinction from intron? sodium

Introns occur inside active genes; most junk DNA is in the bulk of the chromosome between active genes.

I think an intron is DNA that made sense at some time and is slowly degrading (or changing - it might become activated again when the exon-intron-"border" gets mutated), whereas "junk DNA" aims more at highly repetitive sequences and the like if it doesn't serve any "structural" purpose. --Magnus Manske

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)

• My POVmeter pings at the last two paragraphs. Could use some rephrasing. -- Jake 06:50, 2003 Aug 21 (UTC)

Really? Seems O.K. to me. What exactly is your concern?168... 17:16, 21 Aug 2003 (UTC)

I think he took exception to the phrase "the term "junk" is somewhat a misnomer" which to my mind does express an opinion. I changed it to "The term "junk" is recognized as something of a misnomer" where we can assume the implied object of "recognized" is the scientific community.

Also, the clause "which might suggest uses for much or all of the junk" in the second sentence was speculative, and contained no information. So I chopped it. -- Clarknova 03:36, 23 Jun 2004 (UTC)

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Removed this sentence (mentioned above)

In some cases, the positioning, rather than precise sequence, may be important. There are known examples in the yeast Saccharomyces.

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.

[edit] November 2003 Scientific American

Deleted:

The 2003 November issue of Scientific American published an article "Gems in the Junk", in which it stated that "The failure to recognize the importance of introns 'may well go down as one of the biggest mistakes in the history of molecular biology'". [and] "What was damned as junk because if was not understood may, in fact, turn out to be the very basis of human complexity"

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)

I think you raise some good points against the Sci-Am reference. I agree that the author seems to be a science writer, and not a scientist, and it's clear (e.g. from the quotes from the article I deleted) that some of the scientists have used the opportunity for PR for their particular research agenda, although the same kind of thing happens in more serious scientific journals as well.

I'm not sure what is meant by "scholars reference authors, not publications". Does that concern refer to the deleted text, or to the Wikipedia article as it stands?

I'm inclined to disagree with your standard for deciding when a science writer can be cited. Although the Sci-Am article has its flaws, I found it a reasonable review of some recent developments in the field, admittedly for a more popular audience. I think that overview is valuable, and for a general encyclopedia, may be more relevant to a greater portion of the readership. It would be nice to have a more serious reference in addition, but I'm not aware of a serious reference with the same scope. (I think there have probably been some perspective articles in Science/Nature in the last year, since there have been a number of papers on finding functional things other than protein-coding genes recently).

Anyway, if you were to remove the reference, I wouldn't get into an edit war, but I think it has some merit for this Wikipedia article.

Zashaw 00:06, 23 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)

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[edit] Repetitive or random sequence?

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:

• There are about three million SNPs or 'snips', i.e. differences in the genomes of any two unrelated people, but of these only about 10,000 or so are likely to have any effect on the organism – i.e. 0.3%. Extrapolating to the human genome, which has about 800 MBytes of information, 0.3% of this is 2.6 MB of really functional DNA, which is roughly the amount of information in the approximately 20,000 genes. This implies that the junk DNA may truly be junk.

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.

I'm still dubious, since (1) there are a lot of assumptions, (2) I still don't see a reference on this work using SNPs to estimate the likelihood of function in "junk" DNA. It seems like your work, and Wikipedia doesn't publish original research. As for the assumptions, first, the quote says "are _likely_ to", which makes it sound like they have very little idea. SNPs and researching diseases using them is still an open field, so I doubt they know exactly how many are functional. Okay, if the 10000/3000000 number is right, I don't see why you can multiply that by 3 billion nucleotides. 3 million is, I assume, the number of SNPs that have been discovered anywhere in the human genome. If so, our best current estimate is that there are 3 million SNPs in the human genome (we might estimate more, if we think we've missed some). Even if we accept this, the argument that the predicted number of SNP nucleotides equals the amount of coding DNA seems pretty specious: (a) detection of how many SNPs are functional is biased to coding DNA (which we're relatively good at understanding), so this number may ignore functional SNPs in functional, but non-coding DNA -- a circular argument, (b) I'm pretty sure most coding DNA is not SNPs (i.e. it's conserved in all tested humans), (c) at best it's a back-of-the-envelope estimate, so if any of our biological knowledge, or the simple assumptions made are wrong, the estimate may be way off -- so, it doesn't tell us much about the likelihood of function in junk DNA, IMHO. Zashaw 22:59, 9 Dec 2004 (UTC)

The reference is good - Kevin Davies is a respected researcher (founder of NATURE Genetics !! ) talking here on PBS. He gives 3 references, but admittedly it is not clear if they apply to SNPs or if he is talking from his extensive experience in the field. It might be best to query him directly for clarification. Then your counter-argument is somewhat confused. The facts are simple - 3 million SNPS have been identified, though there may be more. Of these it has been shown that only 0.3% are effective. As far as I understand it the SNPs are quite evenly distributed in the genome - with a mean spacing of about 1000 base pairs. Thus some fall in coding regions and some in junk. Sounds like a sort of Mont Carlo sampling of the 3,000,000,000 base pairs. I.e. the 3 million SNPs are fairly representative of all base pairs. Let's test this: in http://snp.cshl.org/naturepaper.shtml it says that 60000 SNPs of a 1.42 million sample fall in Exons - that's 4%, where 1.5% would be expected for a uniform distribution, i.e. a potential bias of 3:1, due either to sampling bias or to an actual preponderance of SNPs in exons. Not serious though, as if only 10,000 are effective anyway, it shows that at most 1/6 of EXON SNPs are effective - otherwise a much smaller fraction of junk SNPs is effective. So my argument of scaling up this result to the genome as a whole is not so outlandish. --hughey 13:18, 10 Dec 2004 (UTC)

I'm not sure if we're talking about the same thing in terms of references. What I would like to see is an article in a peer-reviewed journal that states that junk DNA is probably not functional specifically because the estimated number of SNPs is equal to the amount of "information" in coding genes in the human genome. It's not enough to have references that support the 10000 functional SNPs out of 3 million (because that isn't about the analysis per se, it just supports an assumption underlying the analysis) and it's not enough to have references that suggest that junk DNA may indeed be junk based on other reasons (because that's clearly a possibility anyway; and BTW, the Nature/mouse reference is great). I'd consider a quote from an authority on this analysis. (I'll accept Kevin Davies as an authority, but he doesn't seem to say anything about your analysis; from what I can see, he just gives the 10000 functional SNPs number.)

In the interests of expediency, let me restate that you seem to imply that the analysis you present is your work, and not, for example, the work of Kevin Davies. So, unless you can offer references of this analysis in a refereed journal, I would refer you to Wikipedia's policy on no original research. BTW, I'm not saying that your theory is necessarily wacky, just that it doesn't belong in Wikipedia. (As for the analysis, I now understand your logic in multiplying 10000/3million by 3billion bases, which is not outlandish, although I still think the analysis overall is problematic. Write on my talk page if you're interested in discussing further, assuming there are no references.)

Zashaw 06:57, 11 Dec 2004 (UTC)

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)

I think the Nature paper is a great experiment, and I agree. I've taken the liberty of boldly adding that to the article (along with the point that junk DNA may have functions). See what you think. Zashaw 22:59, 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)

A-ha, I was confused about the 1% vs 3% inconsistency. I don't feel strongly about which number to use. Zashaw 06:57, 11 Dec 2004 (UTC)

My reading of the Nobrega et. al. paper say the deletions contained NO "ultraconserved elements" as defined by Haussler's team at UCSC (p989, 2para). They contained several thousand elements that are conserved between human and mouse at a much lower threshold than that used to define "ultraconserved elements". While they observed no gross phenotypic changes resulting from the deletions (inviability, legs growing out of heads etc.), the differential gene expression effects they found are IMHO more significant than the above articles made them out to be. As usual (and understandably) the pop science writers somewhat butchered the scientists' carefully measured statements. --Mike Lin 08:32, 15 July 2005 (UTC)

[edit] Repressor -> Silencer

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:

In the main text about "Junk DNA' "repressor" is quoted as a kind of junk DNA. Repressors are proteins coded by DNA. The position of the word, just after "enhancer", suggests that may be the author thought about "silencer", the sequence of DNA silencing expression of a given gene.

Magdalena Fikus

Institute of Biochemistry and Biophysics Polish Academy of Sciences.

➥the Epopt 23:08, 6 Mar 2005 (UTC)

• yes, I wrote that and what I really meant was silencer (DNA), not repressors. Thanks for fixing the mistake. --Tycho 01:39, 7 Mar 2005 (UTC)

[edit] I feel so proud!

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?)

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Moved this link from article to talk page:

For a non-silly discussion of junk DNA, see the EvoWiki Junk DNA 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)

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[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]

Indeed, researchers like John Mattick of Queensland University, Australia think that the idea of junk DNA is junk science:

Researchers the world over are confirming that non-coding DNA holds critical clues to a vast range of diseases; breast cancer, HIV, Crohn’s disease, Alzheimer’s, heart disease, ovarian and skin cancer … the list is growing daily. A leading figure in world genetics, Prof. John Mattick, recently claimed that, ‘the failure to recognise the implications of the non-coding DNA will go down as the biggest mistake in the history of molecular biology’ [Genius of Junk (DNA), Catalyst, Thursday, 10 July 2003].

Mattick's research suggests that the "junk" DNA is part of an advanced operating network that could control the order in which genes are switched on and off.[1]

And ref.

1. Mattick, J.S., Non-coding RNAs: The architects of eukaryotic complexity, EMBO Reports 2:986–991, November 2001.

Zashaw 29 June 2005 00:17 (UTC)

Don't confuse non-coding RNA (which is transcribed) with non-coding DNA (most of which is probably not transcribed). Evolver 23:33, 4 September 2005 (UTC)

[edit] Creation-evolution controversy

This section doesn't actualy provide any useful information, so it needs to either be rewritten or deleted. I vote for the second.

I'm not sure what you mean. The section says (1) that junk DNA has featured in arguments for evolution and for creationist ideas, and (2) it explains the basis of those arguments. It seems appropriate for an encyclopedia article on junk DNA. Zashaw 22:12, 14 July 2005 (UTC)

Creationism has no place in this article as it is a social/religious issue and has nothing to do with genetics. --DanielCD 20:56, 3 March 2006 (UTC)

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 :

• User talk:Mike Lin
• --Procrastinating@^talk2me 23:45, 5 April 2006 (UTC)

DELETE that section:

• No real reason to open that can of worms here. Ted 02:19, 6 April 2006 (UTC)

[edit] Junk DNA protecting against mutations

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:

Junk DNA acts as a protective buffer against genetic damage and harmful mutations. If an overwhelming percentage of DNA is irrelevant to the metabolic and developmental processes, then it is unlikely that any single, random mutation to the nucleotide sequence will affect the organism.

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)

I agree this is pretty hand-wavy and needs to be clarified. But there is some merit to the idea. For example, evil scientists can come along and delete 3% of your genome and you apparently still turn out mostly OK :o) A more serious possibility is that a high proportion of junk DNA makes it unlikely that individual genes will be destroyed in a crossover event. As we know, crossovers are an important mechanism for genetic recombination, and maybe junk DNA makes us more tolerant to them. But you are right, the part about "single, random mutation to the nucleotide sequence" needs to go. --Mike Lin 07:27, 16 July 2005 (UTC)

Mutation rate per locus is sometimes HIGHER in larger genomes. Mutations like replication slippage and illegitimate recombination can also be MORE frequent and severe in genomes with a lot of repetitive segments. Sounds paradoxical in some ways, but more DNA might often mean more mutations. Plus, it would be an awful lot of "buffering" material to carry around with no immediate benefit. Evolver 23:34, 4 September 2005 (UTC)

There's another way to look at it: it's not surprising that mutation rate per locus is higher in large genomes if the largeness is due to a higher proportion of nonfunctional sequence. --Mike Lin 21:49, 7 September 2005 (UTC)

Per locus means per gene locus. Evolver 01:01, 8 September 2005 (UTC)

"gene locus" is a pretty fuzzy term in the genome age. Are we jumping back 20-30 years and only talking about mutations giving observable phenotypic changes, the frequency of which can be observed to link two locii? Is a single nucleotide substitution within an intron or UTR a mutation to a gene locus? --Mike Lin 03:33, 8 September 2005 (UTC)

Look, species with larger genomes are more sensitive to radiation and other mutagens as judged by observable fitness effects. So, the buffering idea doesn't work, and this has been known for about 40 years. Obviously more non-coding DNA might mean a higher genome-wide mutation rate because there is more DNA without selective constraint. However, it has been difficult to establish links between genome size and molecular evolution rates (there are confounding factors because genome size correlates with various traits like metabolic rate and generation time) Evolver 12:14, 8 September 2005 (UTC)

I think if there's one thing that this article stresses, it's that the matter of whether junk DNA hurts, helps, or does none of the above is debated. I disagree with your contention that the matter is somehow settled. I guess we should distinguish between junk DNA increasing the rate of recombination vs. acting as a buffer against harmful mutations. A quick PubMed search will find a substantial body of research showing that microsatellites and other junk DNA significantly increase the rates of crossover and other recombinant events, which are very often not harmful. If you have a lot of nonfunctional DNA, then you can tolerate unequal crosovers better than you can with an extremely compact genome. Which might well be a good thing in the long run - maybe. My point is that there is a legitimate debate here. --Mike Lin 14:32, 8 September 2005 (UTC)

"A good thing in the long run -- maybe" would not explain why it is there now. Evolver 14:38, 8 September 2005 (UTC)

Yes it does.

I think we've generated some good ideas here that are worth moving into the main article. The main theme of the article is that there's a debate. As long as we agree to disagree then there's no point in continuing this pissing match. --Mike Lin 15:33, 8 September 2005 (UTC)

You're welcome to inject whatever you want into the main article. If you could also include a brief discussion of how your model of evolution works in which long term benefit can be selected for in the face of short-term costs (e.g., replicational and other mutational), that would be good too. Evolver 16:01, 8 September 2005 (UTC)

Such a model is also needed to explain whole genome duplications, which in contrast to this junk DNA stuff, we know (almost) for a fact have actually happened (S. cerevisae and K. waltii). WGD has got to be devastating in the short term, since it's going to make your entire regulatory system go haywire. In cases where it has happened, something has to be so good in the long run that the short term pain is tolerated and the WGD lineage takes over. Anyway, yes, it's an open problem :-) --Mike Lin 16:12, 8 September 2005 (UTC)

I see. Well, a quick pubmed search should give a pile of papers on the genomic consequences of (and often increased fitness associated w/) polyploidy. Anyway, I think it's perfectly fine to include some stuff about noncoding DNA and mutations (of various kinds), but let's try to avoid the "it's all explained because it may someday be useful" approach. Fair enough? Evolver 16:20, 8 September 2005 (UTC)

[edit] latest deletion

I deleted:

Other Creationists argue, that if evolution changed everything through mutation, it should have cut off the useless DNA-strings in the meanwhile. According to the German scientific magazine p.m. (7), they have not changed at all over time. Creationists could therefor say, that these DNA-strings very well have a purpose in the sense of creation, and that is to disproof evolution.

and the reference:

1. http://www.pm-magazin.de/de/heftartikel/artikel_id1051.htm

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)

[edit] Unused genes

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)

[edit] DanielCD's revert

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)

The material in question is obviously without scientific merit. However, I believe some mention of the fact that this question plays a minor role in such arguments, and the link to the AiG article, is appropriate; that much is of broad general interest, verifiable, and clearly separated from the more scientifically inclined main body of the article. I suggest several possible courses of action:

1. modifying the language to be more, ah, pejorative
2. removing the detailed summary of creationist arguments and relegating the section to a glorified footnote
3. moving it to a separate page, or into a section of an article about creationism or ID

Mike Lin 22:42, 3 March 2006 (UTC)

No need to make the language pejorative. Why would you want to do that? I'm not going to remove it again, I've said my piece and don't intend to hang over this. But it does need a little pot stirring. If you change the language, I suggest my above suggestions: there's no need for perjoratives, it only makes more conflict. --DanielCD 02:23, 4 March 2006 (UTC)

Moved text for discussion. FloNight ^talk 23:19, 3 March 2006 (UTC)

• Creation-evolution controversy*

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].

I think it's ok. Perhaps I was a little hasty. I think, looking at it now, we can assume readers are intelligent enough not to need any additional qualifying. And answersingenesis.org has been discussed elsewhere and it was decided long ago this site was not really quality material. But you can't have everything. I retract my removal. Let's all move on and leave this incident to history. --DanielCD 02:28, 4 March 2006 (UTC)

[edit] New-Age Spirituality

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)

• Spiritualists often discuss DNA with higher physical dimensions (often referred to as 12-stranded DNA), and it's often postulated Junk DNA might be useful in uncovering this mapping, because many spiritualists believe junk dna is part of the projection of higher dimensional DNA into 3d space and will come into play (be activated) as we evolve beyond being physical beings. Theories of physical dimensionality (beyond 3 spatial dimensions) are received theories, and also refutable (by coming up with a valid unifying law that doesn't involve dimensionality). Junk DNA being related to physical dimensionality is also refutable by implication. Therefore, it's valid science. Brian 26 April 2006 (UTC)

That's all fine, but falsifiability is not sufficient criterion for determining what is science and what is not. The notion that this is so is an urban myth that has persisted for unknown reasons; basically every major philosopher of science since Karl Popper, who originally proposed it, has made their name by showing problems with this criterion. --Mike Lin 00:37, 27 April 2006 (UTC)

• Spiritualists' views of Junk DNA is also actively discussed and is also a refutable scientific theory (see above). The only reason you haven't noticed any discussions about it is because spiritualist theories don't create the kind of controversy ID and creationism do (ID and creationism often drown out any other discussions because of the intensity of arguments with conventional scientists). Dimensionality of DNA is discussed in numerous books and online literature, and Junk DNA is often mentioned within those discussions. Examples (Easy Google search for something supposedly not discussed):

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)

Perhaps we could create a catch-all "Alternative theories" section, starting off with something like "The scientific claim that the vast majority of the human genome is useless has bred a variety of alternative theories", under which everyone is free to express creationism, spirituality, etc. Mike Lin 12:10, 10 April 2006 (UTC)

I really hate seeing Wikipedia articles saddled with every unusual theory that comes around. Let other articles refer to this, but don't drag these articles down into the mug. Ted 17:18, 10 April 2006 (UTC)

TedE's opinion is fair, that the material should be removed entirely. Among those who think there's a place for the content in the article, who objects to "Alternative theories" and why? Mike Lin 14:44, 12 April 2006 (UTC)

If spiritualist theories should be removed so should creationism. Brian

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)

[edit] Wikipedia:No original research

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)

The quality of the sources need to be examined. Wikipedia is an encyclopedia not an forum. Some of the sources supporting the alternative theories are published by websites pushing theses opinions. IMO, this does not meet the criteria in verifiable and reliable source policies. --FloNight ^talk 17:48, 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

It isn't often we get to see an argument about who isn't an editor. The website for Taylor and Francis lists Andras Pellionisz - USA as a Section Editor for Neural computation. It is on the same page as the editorial board for Cerebellum (see Mike's link above). If this is not true, you may wish to contact them about it. Ted 23:36, 24 April 2006 (UTC)

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

My only reason in even mentioning it is that a reasonable person would search the journal's website for an editorial list. I used to spend hours in the library reading journals. Now I get them in electronic form. Other than the journals I get personally, I don't think I've seen a journal cover in years. Frankly, though, personal attacks from either side have to stop. It does noone any good. Ted 18:11, 25 April 2006 (UTC)

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

[edit] Merge article with Noncoding_DNA

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)

The only problem I have with a merge is the title for the article. Both junk DNA and noncoding DNA are misleading and incorrect. I've created a stub, Eukaryotic chromosome fine structure that may work as a place to put it. Or, even something like Eukaryotic intergenic DNA is better than these two names. —Preceding unsigned comment added by TedE (talk • contribs)

I disagree with this proposal. The two terms have different flavors and I think the separate articles describe their ambiguous/circular relationship nicely. The term "noncoding DNA" is more useful in a bacterial or fungal genome where a majority of the sequence is coding. On the other hand it's a little weird to call 98% of a genome non-something-else. So you have different terms used in different situations which I think deserve their own articles. Mike Lin 14:38, 12 April 2006 (UTC)

• The slight naming variations/conventions are mainly used to describe the tendency of the talker ,his belief that the unknown function of the DNA is this or that ,Since even My own professors have a tendecy to alternate their terminologies - That is not NPOV.
• Besides that point it is agreeable that both articles contain repetetive information about the same subject and should be merged.
• One can offer further alternative target names to the common phrase Junk DNA, such as undetermined DNA , mysterious DNA , Predesignated DNA. Although the suggested stub Eukaryotic intergenic DNA is currently most suitable.

--Procrastinating@^talk2me 19:58, 20 April 2006 (UTC)

The merge would be incorrect. Proof: RNA genes with known function (like miRNAs) are non-coding DNA, but they're not junk. --Mike Lin 20:46, 20 April 2006 (UTC)

The bioinformatics people I talk with (who study predicting 3D protein structure) use noncoding DNA specifically to refer to DNA that is transcribed and function as an RNA. Ted 22:47, 20 April 2006 (UTC)

Actually, now that I think about it, this is the way it was used early on (1980s). At that time, the transcript was divided into exons, introns, and upstream and downstream noncoding regions (now called UTR). The definition was a sequence that was transcribed, transported to the cytoplasm, but not translated. Unfortunately, I don't have a reference to it immediately at hand. Ted 23:07, 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

• A merge would be incorrect. Non-coding DNA and junk DNA are distinct terms, as is well explained in the introduction. Non-coding has a strict definition (i.e. anything that doesn't encode a protein) that is unrelated to whether it is functional or not. GeoMor 21:42, 14 August 2006 (UTC)

---

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)

so many ppl are mumbling speudo scientific dribbling about the spiritual/allien/godly/paranormal derivites of this thing, yet from the entire InterNet almost NO-ONE is interested enough to even reply to a request being that has been posted for more than 4 months. Sad how popularity works.Procrastinating@^talk2me 00:53, 15 August 2006 (UTC)

That's Wikipedia! The solution is to ignore the junk (no connection intended) and work on other articles. That is what I did for "junk DNA". Hopefully, quality will eventually win out. If not, then at least I contributed a small amount in an obscure part of the encyclopedia.

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)

This is not just my opinion... ask any up-to-date (i.e. post-HGP) expert in the field whether s/he thinks the term is still appropriate. The point is, there is no need to have a) 2 articles dealing with near-synonyms (prove me wrong - I have cited peer-reviewed research; I challenge anyone considering the merge unwarranted to do the same; please no pre-2001 papers for the reasons linked above) and b) the one dealing with the pop sci term being more extensive than the one with the correct scientific title to boot.

"Junk DNA" as commonly understood is a false and outdated concept; it should not be spread any further. Either trust me on that or read some current, peer-reviewed research publictions like I did. And please read doi:10.1126/science.306.5696.632 if you have not already done so. IMHO, "junk DNA" deserves as much mention as the morphic field - it used to have some appeal when nobody understood there was something like epigenomics (or for the morphic field, no morphogen gradients), but today it is an outdated concept in science, and just lingers on in pop science because it is so catchy. But nonetheless, "junk DNA" is junk science, according to today's knowledge. Your textbook may differ, but then, odds are it has not been revised for some years. Dysmorodrepanis 21:52, 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.

The deletions made in this study are the largest reported viable homozygous deletions in mice and support the existence of potentially 'disposable DNA' in mammalian genomes...(appropriate carefully qualification,, exceptions)...the lack of detectable phenotypes in these mice raises the possibility that the mammalian genome is not densely encoded and that significant reductions in genome size may be tolerated. This concept has recently been supported by the demonstration that, in 'normal' humans, large-scale genomic deletions are a common source of polymorphism, generally occurring in gene-poor regions, some of which contain sequence conservation across mammal species21, 22. Linked to this, the extensive degree of non-coding conservation in the deleted intervals in our mouse study and also in the human studies brings into question the functionality, if any, of many of the large number of non-coding sequences shared between mammals.

--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)

"So I show big one in Nature" - which does not use the term. "Potentially 'disposable'" is something different entirely than "junk".

In any case, my grievance is not with DNA lying around that has no purpose, but with 80% of the ncDNA information on WP being in the wrong article if one judges from the titles.

"Junk DNA" is either a) an obsolete, outdated concept that is being avoided by scientists like the plague (if it is understood in the old sense "there is no genetic information except in the protein-coding sequence"), or b) a subset of ncDNA (if it is understood in a scientifically correct sense).

I have collected some handfuls of peer-reviewed papers and would like to feed them into WP. Much of the topics are dealt with in the Junk DNA article, but the publications deal with non-Junk-non-coding DNA and strictly, it would be out of place here. And since ncDNA is the preferred and more accurate term, and the alternative would involve mindless copyediting, the merge proposal. As I envision it, "Junk DNA" would be a section heading in the merged ncDNA article and this section would deal with actual junk DNA (=evolution's cruft).

FWIW, I think that between 50 and 25% of the average mammal genome will indeed turn out to be functionless. Dysmorodrepanis 03:36, 20 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)

Re "Do you think Nature editors are so confused to use "DIFFERENT ENTIRELY" term!!!!????"

But again, the term is put into single quotes! In this article, the term is used in plain form throughout, which does not conform to the orthography in use these days among professionals in the field.

To write "Mice do fine without 'junk DNA'" is not at all the same as "Mice do fine without junk DNA". And that was a comment on research conducted in ~2002. Today, one would rather write "noncoding element xyz is not needed for viability in mice" or somesuch (The claim that "1%" of the Mus musculus genome can be deleted without ill effects is absurd without qualifying exactly what 1% can be deleted. Of course in the article's context it is clear that this does not include known functional elements, but it should be a bit more detailed. Just as to say a "DNA study" - which may be DNA-DNA hybridization, mtDNA or nucDNA sequencing, haplotyping, etc which all differ regarding the phylogenetic signal analyzed - has suggested this-and-that taxonomical treatment is less than informative).

My point is not the existence of entirely functionless elements in the genome, but whether it is wise to write at length on these - and more so, on others that were believed to hold no function but are known or suspected to do - under a title that is shunned by reserchers these days, overshadowing a better-named article on the topic. You talk about the thing "junk DNA", i.e. functionless stretches of code. It is highly likely that there is something like that, but proving a negative... I talk about the term itself as an article title, and the knee-jerk assumption perpetuated by using it and listing most information pertaining to ncDNA under an article titled Junk DNA.

It is as if 90% of the content of Universe would be under Luminiferous aether (including and especially information that has nothing to do with EM transmission in vacuum), or Phlogiston theory being the article to go when you want to find out something about oxygen. In a similar vein, C-value paradox redirects to the currently-used term. People who are not working in the field should be directed towards an article which uses verifiable information and accepted terminology. "Junk DNA" is ncDNA by default (it does not code for proteins), while not all ncDNA is "junk DNA". (Current estimates are the majority isn't. See above for ref.)

In any case, what to do with the references in this article which properly belong to Noncoding DNA, or at least belong to that article also? Should I move them there?

4 references (1-4) actually discuss the C-value enigma.

4 1/2 references (5-6 + 11 + 12; 6 is really 2 refs) discuss non-functional code, the true "junk DNA".

7 1/2 references (7-10 + 13-15 + 12) do NOT discuss "junk DNA" but functional ncDNA. They should properly be taken out of this article and put into Noncoding DNA.

I am extremely reluctant to do that on my own w/o thorough discussion, more so because 75% of Noncoding DNA would come to be a near-verbatim copy of 90% of the Junk DNA article. This, and nothing else, was my motivation for the merge proposal: I wanted to expand the ncDNA stub but cannot do so at present because Junk DNA contains much more information on ncDNA than Noncoding DNA; "junk DNA" ⊊ ncDNA in reality but not on Wikipedia, and this can (and IMHO should) be improved. Either to clean up the thing now and remove ambiguity and redundancy, or do several times the work later, and maybe over and over again (if 2 separate articles are maintained; non-specialists will inevitably review ncDNA research in Junk DNA because that's the term the media is liable to use). It is not a scientific dispute, but an issue of keeping matters concise. (Arguably, Junk DNA does pass the Pokémon test, but the discrepancy between title and content still stands. It is this very discrepancy I find unsatisfying, and for the reasons above, a merge seems to me the easiest way to resolve it. Especially since "junk DNA" is more commonly linked than Noncoding DNA; the old concept persists among people who believe it's possible today to clone mammoths and other non-specialists ;-) )

To sum it up: neither in length nor in (much of the) content (of Junk DNA) do the two articles in question conform to a) WP standards (which is to include subset articles in the superset articles, or at least make the superset articles more comprehensive), and b) to current research opinion. As far as I am concerned (and allow me to apologize for not making this clear from the start), this is a dispute about semantics, not about functional genomics. Dysmorodrepanis 17:04, 30 December 2006 (UTC)

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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)

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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:

• "junk dna": 76 (+1 since 2006-DEC-04) of which c.15 (~20%) in the last two years
• "noncoding dna": 271 (+7 since 2006-DEC-04) of which c.51 (~19%) in the last two years
• "non-coding dna": 164 (+8 since 2006-DEC-04) of which c.43 (~26%) in the last two years

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.

• As a side note, a debate even amongst those in the field right now is whether or not we should include "non-coding" to refer to DNA that does not make RNA either (right now it's usually taken to mean does not code for protein). This has really only come about since we have been finding more and more DNA that serves no other role than interaction with already-existing proteins. I have no idea which way we should go on that.

128.118.200.75 19:44, 29 May 2007 (UTC)Matt

Like others,, you say many things that are more less correct but not very relevant to question of , should there be "junk DNA" as article. Again I say, Wikipaedia should and has article on phlogiston, alchemy, aether, etc. even though these are discredited theories. Moreover "junk DNA" concept is not even fully discredited, but rather still controversey. It is obvious that lots of non protein coding sequence has function, but "lots" could be 5% or less. You claim that it is now somehow evident that 85-95% of genome has function,, I strongly feel is wrong.

Additional to 2004 Nature article about large knockouts of "conserved non-coding" sequences having no effect, moreover it is now more recently found that knockout of "ULTRACONSERVED" sequences have no appearant affect [12]! Of course,, it is possible, that it is just buffered mutation. But obvious such knockout experiments SHIFT burden of proof, and clearly show matter is not settled.

ChIP-chip experiments show binding all over genome, sure. How many of such binding really serves purpose and how much is "noise"...reproducible consistent binding based on sequences, but simply no functional importance??? Such technology shows us which sequences MIGHT be important but not ALL sequences they tell us,, are important. No-one knows what fraction is. So it is wrong to say this somehow settles issue.

Now, I am not defeind everything in "junk DNA" article now. There is a lot of lousy stuffs and silly bulleted points list clearly collected by people not familiar with field. It needs major rewriting by people with better English also. But the term "junk DNA" is popularly known, DIFFERENT from "non-coding DNA", and reference to hypothesis that is NOT only historical but still controversey. So I do not understand any fair reason to get rid of "junk DNA" article and burden "non-coding DNA" article, which can be great science factual catalog, with all those arguments back and forth and history about what fraction is function. --Baldzac 21:25, 29 May 2007 (UTC)

P.S. when Dysmorodrepanis said "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", I agree. "Junk DNA" article should be specific about controversial claim of non-function of most genome.

• grins* HA! Did I get you at least! Hmmmm, like I said in the beginnning, this is a rather massive task. How 'bout, say, the first half of September or so, get the junk sorted from the funny stuff and move the funny stuff over to Noncoding? (I'm by no means opposed to having a "junk DNA" article. If there's plenty to write about evolution's kipple, fine. Only discussing functional noncoding DNA under that title more than discussing it in the appropriate article got me riled.) Dysmorodrepanis 04:14, 17 August 2007 (UTC)

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:

• check literature on moderately-conserved pseudogenes (highly conserved do not seem to be functionless)
• check for inherent pattern of mutational noise. Recognition motifs even in pseudogenes would initially stil recognize whatever it is they recognize, and that might be useful, leading to a moderately-conserved pseudogene containing a highly conserved recognition "island". These are also not useful.
• It is those limits to randomness that are too tiny in length or inconsistent across lineages to be candidates for noncoding-functional you want to find and take a good close look at.

Basically you're looking for the color of noise of junk DNA. Dysmorodrepanis 04:14, 17 August 2007 (UTC)

[edit] Removing non-encyclopedic material

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

I think you fail to understand what Wikipedia is, and, more specifically, what it is not. The people you want to convince are your academic peers, not a bunch of Wikipedians. The way this is presented raises red flags. Ted^Talk/_{Contributions} 00:02, 30 August 2006 (UTC)

[reply by Pellionisz]

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

The rules say you shouldnt add a link to a website made by yourself, because of neutrality. see WP:External links. So if other, neutral people want it then maybe it can stay, but it looks like most have a strong opinion to delete this link to junkdna.com. We can keep the journal article.

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)

[edit] Original Research

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.

For example, you can say "[whoever] believes that evolutionary artifact serves no present-day purpose [cite], while [someone else] argues that they may just be serving functions in ways that are not currently understood [cite]." If you don't follow NPOV guidelines, then this article would actually be self-contradicting.--Liulk 22:54, 11 November 2006 (UTC)

It is like saying "Newton, Einstein, etc. believe universe is continuous [cite], while Bohr, Heisenberg, etc. believe universe is quantum [cite]." It is not wrong to use names and sources for very basic introduction but maybe also not needed. Baldzac 11:13, 12 November 2006 (UTC)

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)

I will wait for a few weeks for comments and see if someone else more qualified is willing to fix this. Otherwise I will perform the editing myself. I am not a professional in the field of non-coding DNA. Liulk 13:45, 2 November 2006 (UTC)

What is the problem with mouse genome? Or, were you objecting to non-specificity of the citation? Ted^Talk/_{Contributions} 14:07, 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)

Is it just widely accepted that evolution preserves genes? It looks like theory of evolution makes no quantification as to how much gene is mutated, and how much is preserved. Evolution can mean that 100% is changed, or just 0.1%. Since evolution is equivocal to Junk DNA, why exactly do we have to bring it into the picture? Evolution is "junk information" in this article. This is why I feel a citation is needed that shows how evolution preserves genes. I will check back in another week or so for further comments.--Liulk 22:54, 11 November 2006 (UTC)

It is most basic principle of comparative genomics field,, that functional things like genes are preserved in evolution. It follows from Theory of evolution because of natural selection on functional things. It is such basics that it might be not easy to find papers that say this clearer than the papers already used. Like (Exaggeration) if you have to find science papers that say gravity makes things fall to ground, it might not be easy. But using evolution to learn about genome/junk DNA is very basic and important idea by everybody in field. It is in all of those papers currently used if you read. Baldzac 11:01, 12 November 2006 (UTC)

[edit] Postgenetics missing

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)

Sorry, but "post-genetics" seems a bit pseudoscientific. Plus, the Hungarian link is broken - Jack (talk) 15:38, 19 December 2006 (UTC)

"Postgenetics" is just a buzzword for genomics, proteomics and transcript research. Dysmorodrepanis 03:03, 20 December 2006 (UTC)

[edit] Eukaryotes?

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)

[edit] Intelligent Design Bullet

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).

Again, the entity called junk DNA as originally proposed is fictional and outdated. There are some genome elements which have no known use, try as you may, and these may be true "junk DNA" (evolution's kipple, so to speak). But these make up only a fairly small part of what was (in science) and is (in pop science) referred to as junk DNA. Most of the noncoding DNA has not been analyzed thoroughly enough, but if one does, it is far more likely than not that it will turn out to have some function, only that this function is something other than encoding proteins. To presume that there is a huge amount of functionless genomc content is strongly contradicted by the last few years' research, and no serious scientist would propose this anymore these days (except maybe some old-timers). To presume that this presumed fuctionless DNA can be considered to make up a single monolithic entity called "junk DNA", with uniform properties and origins, ditto. The fact that the HUGO did not "decipher the blueprint of life" but merely raised far more questions than it got answered (arguably, HUGO's grad project did not answer any of the really important questions at all) sort of underscores this. I can only repeat that the work done now in entirely reworking this article in connection with Noncoding DNA will serve loads of work in 2 years' time: as we discuss this, research to go to the bottom of the noncoding DNA issue is seriously getting underway (as the realization that there is FAR more to it than some monolithic, nondescript entity called "junk" has really started to sink in since 2003ish... I've been following it for the last 10 years or so, and for sticking to what was told to undergraduates as chip truth back then, you'd be laughing stock today), and with the scientific track time being what it is, it'll be in 1-2 years that we will see the results published. Quote me any single paper from the last 2-3 years that upholds the overarching 20th-century definition of junk DNA... I think there is none. If you compare an eukaryote genome to a Linux box, I'd say most scientists would at present cautiously suppport the notion that what was thought to be "useful" (as opposed to "junk") DNA in the last century is merely the binaries (for Windows users: non-Windows .exe and .bat files), with most all other code necessary to run the system, up to and including the BIOS, being in the non-coding part of the genome part.

To wrap it up, it's another case where the ID crowd works with a scientifically untenable, outdated concept. Flat-earthers, really... if you presume that the earth is flat, you'd have to develop all sorts of elaborate, interesting, and dead wrong theories for why a ship's masts become visible on the horizon before the hull does. Dysmorodrepanis 12:11, 10 March 2007 (UTC)

[edit] Arrogant terming

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)

"Junk DNA" is generally avoided or put in quotation marks by scientists these days. (guys, REALLY - the merger... this article grows to farcical as references accumulate. Do a PubMed search, for the love of God! Nobody uses "phlogiston" and "ether" anymore either.)

"Noncoding DNA" is a technical term - it is being copied (in inverted sequence, into RNA), but it does not code for something that is not a nucleic acid. I.e., the information must not be translated, merely transcribed. If it is transcribed and not evolution's very own kipple (in which case - and only in this case - it would indfeed be "junk"). Dysmorodrepanis 05:01, 21 April 2007 (UTC)

[edit] Proof of Evolution?

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)