Talk:Intergenic region

Percentages of intergenic regions in human?

I have added some rough percentages as opposed " a large number" but the paper is out of date. Will change this once i find a more suitable reference DesiLady (talk) 12:50, 15 January 2013 (UTC)

I think the quoted percentage is completely incorrect. The cited source names those percentages in the context of "genome [that] does not code for proteins". That would include e.g. introns which even according to the article are not inter(!)genic. That's a pretty big error as ~26% of human genome are introns... --Maxnoka (talk) 18:20, 5 January 2019 (UTC)

Image needed

The article looks like it needs a better picture. Alexbateman (talk) 12:04, 29 January 2013 (UTC)

Describing intergenic regions in the introduction

"Intergenic regions are a subset of noncoding DNA." This is a useless statement. There's nothing special about noncoding DNA and it's pefectly obvious that the regions between genes are not part of genes.

"Occasionally some intergenic DNA acts to control genes nearby, ... " Yes, it's true that most regulatory elements are located outside of a gene but why stop there? Some integenic regions are centromeres, origins of replication, and scaffold attachment regions. Do we really want to get into all of those descriptions when they are covered in numerous other Wikipedia articles?

" ... but most of it has no currently known function." I just listed a bunch of known functions. Most of the rest is known to be junk DNA. This is not the place to be discussing those features and the evidence that supports them.

"It is one of the DNA sequences sometimes referred to as junk DNA, ..." No, that's not true. Nobody has ever said that all intergenic regions are junk DNA. That would be silly.

"... though it is only one phenomenon labeled such and in scientific studies today, the term is less used." The term "junk DNA" is widely used, just as you would expect since 90% of our genome is junk. There will be a separate article on junk DNA where the evidence will be described.

"Recently transcribed RNA from the DNA fragments in intergenic regions were known as 'dark matter' or 'dark matter transcripts'." RNA produced from intergenic regions is, by definition, not from a gene. These are spurious transcripts or junk RNA. (What else could they be if they aren't from a gene?) The term 'dark matter' is used by opponents of junk DNA who usually don't understand how much we know about our genome.

I will be reposting my version of the introduction in a few days unless I hear some convincing arguments for keeping the old out-of-date material that Praxidicae restored.

Genome42 (talk) 22:12, 16 August 2022 (UTC)

Praxidicae seems to be confused about the importance of "sourced information." I have a source that says Trump won the 2020 Presidential election but that doesn't mean it should be posted as if it were a fact on the Wikipedia page for US elections. Wikipedia editors have to use a bit of discretion in choosing sources. Not all sources are correct - those saying or implying that we don't understand intergenic DNA are wrong.

Genome42 (talk) 00:35, 17 August 2022 (UTC)

Praxidicae is attempting to collaborate with me on the 'allele' article but she hasn't made any attempt to respond to my comments here so I'll assume she agrees with me and I'll restore my edits.

Genome42 (talk) 15:04, 19 August 2022 (UTC)

Praxidicae reverted my edit within one minute and added the comment "Stop removing SOURCED CONTENT without an adequate explanation." It's pretty clear that she isn't reading what I've posted here and isn't interested in collaborating to improve the article on 'Intergenic region.'

I undid her deletion. Let's see if she wants to continue an edit war. If so, I have no choice but to report her for harassment.

Genome42 (talk) 15:56, 19 August 2022 (UTC)

You are now edit warring with this edit and are incorrect. If the issue is that the source or even content is outdated, you update it with reliable sources, you don't remove it outright and then add unsourced content. I am really, really disgusted by the lack of collaboration from you and near constant personal attacks, your entire attitude and comments here are a really wonderful example of why Wikipedia lacks women editors in STEM fields in particular. PRAXIDICAE🌈 15:56, 19 August 2022 (UTC)

Thank-you for finally engaging in a discussion. Please respond to the comments I made above.

You and I are experienced Wikipedia users (I started editing 15 years ago) so we both know (or should know) what the issues are all about. It's a question of "reliable" sources and who is best positioned to determine what sources represent the current mainstream scientific viewpoint. In some cases, like here, the old 'sourced' content is unreliable (i.e. wrong) and irrelevant and that's why it was removed.

If you want to argue that the old material is reliable and relevant and should be retained then please state your case. I'm happy to listen to your scientific arguments and collaborate with you to improve the article on intergenic DNA and its possible function.

I'm also more than happy to discuss with you whether the views of junk DNA and dark matter that were described in the old version are scientifically accurate or not. Isn't that the main point? Genome42 (talk) 16:09, 19 August 2022 (UTC)

Please re-read what I've written to you - you need to provide sources that either show that this is incorrect or show consensus that the sources (and thus the content) are unreliable and incorrect. Your field of expertise is not relevant in the absence of reliable sources. Adding unsourced content is not a solution to content existing that you, as an individual, disagree with. PRAXIDICAE🌈 16:11, 19 August 2022 (UTC)

Here are the three sentences in the introduction that you want to keep.

"Occasionally some intergenic DNA acts to control genes nearby, but most of it has no currently known function." There is no source for this misleading statement. It is partially correct but extremely misleading for several reasons that are explained in Non-coding DNA. It's also irrelevant because everyone already knows about regulatory sequences.

"It is one of the DNA sequences sometimes referred to as junk DNA, though it is only one phenomenon labeled such and in scientific studies today, the term is less used." There is no source to back up this claim. It's an incorrect statement but it's difficult for me to provide a source that refutes an incorrect statement. In any case, the statement doesn't belong here. This is not the place to bring up the junk DNA controversy.

"Recently transcribed RNA from the DNA fragments in intergenic regions were known as 'dark matter' or 'dark matter transcripts'." The source quoted here is a twelve-year-old paper by my colleagues Ben Blencowe and Tim Hughes here at the Univesity of Toronto. The important point in their paper can be found in the last sentence of the abstract which says, "We conclude that, while there are bona fide new intergenic transcripts, their number and abundance is generally low in comparison to known exons, and the genome is not as pervasively transcribed as previously reported."

Their point is that most of these RNAs are associated with known genes and the amount of so-called 'dark matter' transcripts is small. Here's how they explain it in the discussion.

"Altogether, we propose that most of the dark matter transcriptome may result from the process of transcribing known genes. Pervasive transcription of intergenic regions as described in previous studies occurs at a significantly reduced level and is of a random character."

In other words, they are arguing AGAINST the idea that dark matter transcripts are important and refute junk DNA. Their paper was attacked by PROPONENTS of junk DNA for this very reason.

I have a blog post that discusses this controversy in case you are interested.

Pervasive Transcription

https://sandwalk.blogspot.com/2011/08/pervasive-transcription.html

The statement that you want to retain in the old version of this article is extremely misleading because the source paper says something quite different. In addition to being misleading, the statement is not relevant. As I said above, his is not the place to bring up the debate over junk DNA.

From my perspective. Two of the unsourced statements that you want to retain are incorrect and/or irrelevant. The third one misrepresents the source and it's also irrelevant.

I believe that I have the knowledge and expertise to recognize incorrect or misleading unsourced statements and the knowledge and expertise to recognize whether sources are being quoted correctly.

If you don't agree, then feel free to advance your scientific arguments in favor of retaining the old version of this article. Genome42 (talk) 16:58, 19 August 2022 (UTC)

Please read WP:RS. Thoroughly. I am not interested in reading your blog. It is not a reliable source. You still haven't given a single reason based in our existing policies or guidelines why this information is incorrect nor have you given sources that support your statements. PRAXIDICAE🌈 17:01, 19 August 2022 (UTC)

I have managed to find two recent peer-reviewed journal articles (in Gene and the International Journal of Molecular Sciences) which disproves a lot (but not all!) of what you're saying — this is clearly a topic with differing opinions, and unfortunately one where journal articles are written by theory proponents on both sides. Perhaps a fair compromise here would be to expand (without the wholesale deletion of content) on the lead of the article, highlighting that although some research states this, others have provided reasonable refutations? — TheresNoTime (talk • she/her) 17:45, 19 August 2022 (UTC)

Please collaborate with me and provide more specific information. Which of the statements in the old version of the intergenic region article have been proved by the papers you found? Do you intend to add them as sources for the claims that are made in that old version or should those claims just be preserved even though there are no sources to back them up?

And please provide a justification for debating this controversy in an article on intergenic regions. Genome42 (talk) 18:04, 19 August 2022 (UTC)

I'm afraid I don't personally have the time to have an in-depth debate on the merits of multiple peer reviewed, conflicting articles — my university days are behind me, and I never did enjoy debates and defenses :) I'm just trying to find a reasonable compromise which doesn't involve discounting older, yet still highly cited, research. Perhaps some of the subject matter experts at Wikipedia:WikiProject Molecular Biology can chime in? — TheresNoTime (talk • she/her) 18:11, 19 August 2022 (UTC)

I've left a message at their noticeboard — I appreciate everyone taking a step back and trying to discuss this. I know that can be difficult when the answers seem obvious to you, but I do hope you can appreciate the state the project would be in if we let everyone make edits they're "sure" are correct — TheresNoTime (talk • she/her) 18:19, 19 August 2022 (UTC)

I see that you have time to engage in a superficial debate in order to support Praxidicae and to back up your accusation that I'm engaging in an edit war. It's unfortunate that you don't have time to engage in a genuine scientific collaboration in order to resolve this issue.

You found two papers that mention 'dark matter' but that's not the issue. I'm well aware of the fact that some people would like to dismiss what we know about genomes by calling it dark matter. The sentence in the old version talked about 'transcripts' implying that they refuted junk DNA. That's a gross misrepresentation of the source that was quoted.

It's interesting that you are now calling on experts to resolve this issue. I hope you can appreciate how frustrating it is, as an expert, to be challenged by people who clearly state that they are not knowledgeable but still want to censure my edits. I don't have to imagine what state the Wikipedia project would be in if this continues because that's exactly the state we're in. You and Praxidicae (and other like-minded editors) are making it extremely difficult for genuine scientists to fix Wikipedia because you are "sure" you are correct and the experts are wrong. Genome42 (talk) 18:20, 19 August 2022 (UTC)

I think you should probably re-read my message to you 😌 I'm certainly not sure I'm right, which is why I've highlighted that there are conflicting articles and tried to get you to collaborate and compromise. I'm "challenging" you as an editor, and am holding you to the same standards as any other editor. So far I've seen little evidence that you're a subject expert — in fact, I'd expect a supposed "retired professor" to know how debate and provide scholarly sources to their claims, without a MSc having to repeatedly prompt them. — TheresNoTime (talk • she/her) 18:56, 19 August 2022 (UTC)

I'm sorry. I must have missed the message where you supplied evidence of conflicting articles from reliable scientific sources that support the following statements.

"Occasionally some intergenic DNA acts to control genes nearby, but most of it has no currently known function."

"It is one of the DNA sequences sometimes referred to as junk DNA ..."

"... though it is only one phenomenon labeled such and in scientific studies today, the term is less used."

"Historically intergenic regions have sometimes been called junk DNA suggesting that they have no function."

Perhaps it was accidentally deleted? Could you re-post it?

I also missed the part where you defended the relevance of the material I deleted and why it needed to be in a short article on intergenic DNA.

It's hard to collaborate and compromise when no one will discuss the main issues that I raise. Why do you insist on rejecting my edits and defending unsupported (and incorrect) statements that have no sources? That seems hypocritical to me but perhaps there's another agenda that I'm unaware of.

If you think this part is difficult, just wait till I get to the part under "Properties" that claims an increase in the number of human genes from 32,000 to 60,000! You must know that such a claim is highly controversial (and incorrect) but none of the standard Wikipedia editors challenged it and demanded that the other side be presented in the interests of fairness.

Isn't that strange? Genome42 (talk) 20:37, 19 August 2022 (UTC)

No, what is strange here is your inability to produce a single reliable source. Until you do that, this conversation is pointless and your continued gaslighting and sealioning isn't going to improve the article. PRAXIDICAE🌈 20:39, 19 August 2022 (UTC)

Please be kind enough to describe what reliable sources I need to support the version that I posted (and you deleted)?

Or, are you suggesting that I provide reliable sources to refute incorrect and unsupported claims that are made in the version you prefer? How do I do that? In scientific discussions, the burden of proof is on someone making a claim, not on someone who challenges it.

Genome42 (talk) 20:46, 19 August 2022 (UTC)

WP:RS has a great explanation of what is expected. I suggest you read it, as I suggested previously. You haven't shown what claims are unsupported by the sources. PRAXIDICAE🌈 20:47, 19 August 2022 (UTC)

This is getting ridiculous. What sources support the claim that, "Historically intergenic regions have sometimes been called junk DNA suggesting that they have no function"? Genome42 (talk) 20:51, 19 August 2022 (UTC)

Functions

Statements in the current (Aug. 17, 2022) version are in quotation marks.

"Historically intergenic regions have sometimes been called junk DNA suggesting that they have no function. However, it has been known for a long time that these regions do contain functionally important elements such ..."

What's the point? Can both of these sentences be true? No, there are no knowledgeable experts who ever said that all intergenic regions are junk DNA. The mainstream science viewpoint is that there are all kinds of functional elements in intergenic regions and that's been known for more than 60 years.

The rest of the 'Functions' section describes some of the known functional elements in the part of the genome that lies outside of genes. But this is not the place to describe those elements. Besides, some of the most important ones ones are missing. Let's leave that description to other Wikipedia articles that can do a better job.

I propose to delete (again) the entire section unless someone can come up with a good reason to keep it.

Genome42 (talk) 18:57, 17 August 2022 (UTC)

Figures

Illustration of intergenic DNA

This figure is not helpful. What is a "gene cluster"?

Deleted. Genome42 (talk) 20:09, 7 March 2023 (UTC)

Schematic karyogram of a human, showing an overview of the human genome on G banding, wherein the lighter regions are generally more transcriptionally active, whereas darker regions are more inactive, including intergenic regions.

Further information: Karyotype

The human karyotype figure is not relevant to this topic. This article is not about the human genome - it addresses intergenic regions in all species.

The description is inaccurate because there are lots of genes and intergenic regions in both the lighter regions and the darker regions of the stained human chromsomes. Also, the images depicted are not very good cartoons of the actual G-banding as seen under the microscope.

Deleted. Genome42 (talk) 20:20, 7 March 2023 (UTC)