Talk:Pseudogene

message: That section begins with the following:
"Pseudogenes have two main functions; longevity of the genome life and enhancement of the gametes."
I may be wrong, but something smells fishy there: perhaps a Creationist edit???  —Preceding unsigned comment added by 24.94.233.30 (talk) 06:08, 25 July 2009 (UTC)
replies: text: It sounds like a spoof.  In any case, it is not sourced and it doesn't really fit in with what follows, so I will delete it. Boghog2 (talk) 14:27, 25 July 2009 (UTC)
thread_title:  Illegitimate addition to "Properties of Pseudogenes? 

message: http://www.sciencedaily.com/releases/2010/06/100623132102.htm
 
Language of RNA Decoded: Study Reveals New Function for Pseudogenes and Noncoding RNAs 
Now, a cancer genetics team at Beth Israel Deaconess Medical Center (BIDMC) suggests there is much more to RNA than meets the eye.
In a study appearing in the June 24, 2010 issue of Nature, the authors describe a new regulatory role for RNA -- independent of their protein-coding function -- that relies on their ability to communicate with one another. Of potentially even greater significance, because this new function also holds true for thousands of noncoding RNAs, the discovery dramatically increases the known pool of functional genetic information.  12.107.178.10 (talk) 19:01, 24 June 2010 (UTC)
thread_title:  Language of RNA Decoded: Study Reveals New Function for Pseudogenes and Noncoding RNAs 

message: Can someone please update this article. Some of these citations are over thirty years old. Listing Pseudogene as dysfunctional is just not the case anymore.  — Preceding unsigned comment added by 108.65.170.183 (talk) 12:32, 15 April 2012 (UTC)
thread_title:  Please update this article. 

message: This sections is confusing, because it a) refers to the definition/classification of pseudogenes, which does not fit there and b) the sentence says "This has led to the incorrect identification of pseudogenes. Examples include" before the list of potential functions.
Probably the whole section before the list should be rewritten? In my opinion, a nice, recent overview of potential function is given in 
Pei 2012  IronicPseudonyme (talk) 12:51, 27 January 2014 (UTC)
thread_title:  Section about "Potential function" is confusing 

message: I added it 12/28/2016Drdfp (talk) 22:55, 28 December 2016 (UTC)
thread_title:  The pseudo-pseudogene section 

message: Folks, I have completed a new first paragraph in what I hope to be an extensive update to this page, as suggested below. I appreciate any comments/suggestions, especially if you know how to insert explanatory footnotes "automatically". I asked for help with that in the teahouse, and haven't yet gotten a reply. I couldn't stand to look at that initial image anymore, so I deleted that. Thanks, Dennis Drdfp (talk) 04:15, 29 December 2016 (UTC)
replies: text: Hi , you might find the pages Help:Footnotes and Template:Ref helpful. (If you need further help or clarification, I'll be happy to help.) I have just a few minor suggestions: instead of using , it's easier to use the wikimarkup (pairs of straight quotes:  ) for italics. Footnotes should be in "wikivoice" (i.e. no signatures needed, no first/second person, etc.). Also, per WP:BOTTOMPOST, new talk page threads should go at the bottom of the page. Thank you for your contributions! Me, Myself & I (☮) (talk) 05:57, 29 December 2016 (UTC)

text: I am not exactly clear what you mean by automatic insertion of explanatory footnotes. Underneath the edit window, if one changes <insert> to <Wiki markup>, a number of hyperlinked options appear including .  Press that, and the  characters will appear in the Wikitext. That will make it somewhat easier to insert footnotes. For inserting citations, one option is User:Diberri's Wikipedia template filling tool (instructions).  Given a PubMed ID, one can quickly produce a full citation that can be copied and pasted into a Wikipedia article.  In addition, this tool will add PMID, DOI, and PMC parameters that assist users in quickly finding the full article. Boghog (talk) 09:14, 29 December 2016 (UTC)
thread_title:  Former first image deleted and revisions begun 

message: Please take a look at this image, which I extensively revised from a graphical abstract of a research paper. I believe that my edits make it "fair use" for inclusion in this article, in a section not yet written. I am interested in 1. whether you can understand it, 2. whether you think that it would be understandable by a typical reader, and 3. whether you think it should be in the article. Thanks DennisPietras (talk) 01:47, 4 January 2017 (UTC)
replies: text: The figure itself looks fine. However it should be accompanied by some text in body of the article (supported by an appropriate source of course) that refers to it.  Also it probably should not be in the lead but in the cancer section.  Finally I have increased the size slight so that it is legible without having to open it in a new window. Boghog (talk) 20:26, 4 January 2017 (UTC)
replies: text: boghogThanks for your comments, but I've had to remove it because it was deleted for not following wp guidelines for fair use or whatever. sigh. DennisPietras (talk) 04:50, 6 January 2017 (UTC)
thread_title:  Please comment on this image 

message: If I understand who edits things, I think that   made changes to my original last paragraph. It is slowly sinking into my newbie brain that wp doesn't like direct quotes from publications even when they are cited. I thought that the changes made were a bit "cumbersome" or "difficult to follow", so I revised the last paragraph to, I think, improve it without using quotattions. DennisPietras (talk) 02:52, 4 January 2017 (UTC)
replies: text: No problem.  I agree that your follow-up edits are an improvement. Cheers. Boghog (talk) 20:19, 4 January 2017 (UTC)
thread_title:  Changes to last paragraph of pseudo-pseudogenes section 

message: Folks, I added a figure to this section and made several changes to the text to make it more accurate, IMHO. I noticed that the following 2 paragraphs:
:"Pseudogenes can complicate molecular genetic studies. For example, amplification of a gene by PCR may simultaneously amplify a pseudogene that shares similar sequences. This is known as PCR bias or amplification bias. Similarly, pseudogenes are sometimes annotated as genes in genome sequences.
:Processed pseudogenes often pose a problem for gene prediction programs, often being misidentified as real genes or exons. It has been proposed that identification of processed pseudogenes can help improve the accuracy of gene prediction methods.
were about properties of pseudogenes in general, not unitaries in particular, so I deleted them from this section and inserted them into the properties section. DennisPietras (talk) 17:09, 9 January 2017 (UTC)
thread_title:  changes to unitary pseudogene section 

message: Folks, The current last paragraph of the unitary section is "It has also been shown that the parent sequences that give rise to processed pseudogenes lose their coding potential faster than those giving rise to non-processed pseudogenes". I have read the reference cited fairly closely, and I think the last pararaph was inspired by this section of the paper: 
:"In addition, 83.2% of processed and 79% of non-processed  pseudogenes  display  disablements  (defined  as  non-sense or frameshift mutations) in their putative ORFs, with average disablements of 6.2 per processed pseudogene and 2.4 per nonprocessed pseudogene. ...The differences in sequence identity and disablements between  processed  and  nonprocessed  pseudogenes  are  significant (P< 0.001, Wilcoxon rank-sum test), appearing to suggest that the sequences giving rise to processed pseudogenes lose coding potential more quickly than those for nonprocessed pseudogenes."
I believe that the last paragraph is misleading at best. Specifically "...the parent sequences that give rise to processed pseudogenes" could be replaced, logically, by "...the normal genes that give rise to processed pseudogenes". Doing that replacement would change the entire last paragraph to: 
:"It has also been shown that the normal genes that give rise to processed pseudogenes lose their coding potential faster than those giving rise to non-processed pseudogenes".
There is no evidence of that as far as I know, and it certainly doesn't exist in the citation. I propose that the last line be changed to:
:"It has been shown that processed pseudogenes accumulate mutations faster than non-processed pseudogenes".
Comments? DennisPietras (talk) 17:53, 9 January 2017 (UTC)
replies: text: Since nobody objected, I made the change I suggested. DennisPietras (talk) 17:23, 12 January 2017 (UTC)
thread_title:  end of unitary section - is this even correct??? 

message: Folks, I've been thinking a lot about how to approach revisions in the rest of the article. Folks at the teahouse told me about the "in use" and "under construction" templates, and I intend to use them to let readers know that parts may be even messier for a while, but I'm not going to let this sit for long. I don't type fast. Fine motor control problems from MS, and yes, I realize that the world can see that and I don't care. sigh. So, please be patient. Thanks, DennisPietras (talk) 17:31, 12 January 2017 (UTC)
thread_title:  major revisions begun 1/12/2017 

message: I couldn't find anybody disputing the paper that dissed the mkrn-p1 report, so I deleted that section. DennisPietras (talk) 19:07, 12 January 2017 (UTC)
thread_title:  removed MKRN setion 

message: Folks, in all of the long discussion of HMGA proteins, etc, there is one especially relevant statement: "Because of these pseudogenes' mutations, they can code for competitor proteins for the wild-type HMGA1 gene. Modification of HGMA1 expression results in modified chromatin remodeling and protein-protein (DeMartino et al., 2016)" I have spent more than enough of my life looking for that reference. It doesn't appear to exist. If I understand how to search who contributed what, Glee1204 added that entire section without adequate references, and that is the only edit Glee1204 has made on wiki. No user page for her/him. I have deleted that entire section. DennisPietras (talk) 03:05, 13 January 2017 (UTC)
thread_title:  Removed Glee1204's insertion of "involvement in cancer" 

message: Folks, one reference in that section was 10 years old and the other was mentioned earlier in the article. Plus, surveys doesn't fit under "funcions", where somebody placed it, so I deleted it entirely. DennisPietras (talk) 04:10, 13 January 2017 (UTC)
thread_title:  sureys section deleted 

message: In brief, the discussion about seminal RNase is fubar and I have deleted it. If you want the gory details, read on.
The first citation to a paper about seminal RNase is this under gene ressurection: "The repair of lesions could be achieved by the reinsertion of a deleted segment, the removal (in frame) of an inserted segment, or other events that are likely to be improbable like gene conversion.[46]"  46 at that time was a reference from 2007 as follows:
:Sassi SO, Braun EL, Benner SA (April 2007). "The evolution of seminal ribonuclease: pseudogene reactivation or multiple gene inactivation events?". Molecular Biology and Evolution. 24 (4): 1012–24. doi:10.1093/molbev/msm020. .
The next mention followed immediately after the statement above under the heading examples: "The bovine seminal ribonuclease, which had lain dormant for about 20 million years as a pseudogene, appears to have been resurrected by gene conversion.[47]" 47 at that time was a reference from 1996 as follows:
:Trabesinger-Ruef N, Jermann T, Zankel T, Durrant B, Frank G, Benner SA (March 1996). "Pseudogenes in ribonuclease evolution: a source of new biomacromolecular function?". FEBS Letters. 382 (3): 319–22. doi:10.1016/0014-5793(96)00191-3. .
Here's the almost unbelievable part: the assertion that the rnase gene was ressurected by gene conversion came from 1996, while the 2007 paper, which was mentioned first in "pseudogenes", actually convincingly (to me and the reviewers of a respected journal) showed that the rnase did not arise by gene conversion!!!!!
Can you say "fake news" DennisPietras (talk) 15:10, 13 January 2017 (UTC)
thread_title:  seminal RNAse discussion deleted 

message: I added a discussion of pseudogenes and gene conversion in the "examples of pseudogene function" sections, which would "substitute" for a mention of gene resurection. The 4 references that remained in the "gene resurrection" and "examples" sections were from the last millenium, and not worth discussing, IMHO, so I deleted that discussion. DennisPietras (talk) 16:00, 13 January 2017 (UTC)
thread_title:  added gene conversion and deleted stuff about gene resurrection and examples 

message: almost done with the first pass!!!!!!!!!!!!!!!! DennisPietras (talk) 16:30, 13 January 2017 (UTC)
thread_title:  what was left of "transcription" became "bacterial pseudogenes" 

message: had a link 
* Human disabled pseudogenes list
which lists 8 genes! 8-) DennisPietras (talk) 18:03, 13 January 2017 (UTC)
thread_title:   a knee slapping belly laugher! The "See also" section.... 

message: no, of course it never will be, but I'm through with the construction signs! I raised it to B class and, because of all the indications that pseudogenes are involved in widespread gene regulation, raised it to high importance. This was more difficult and frustrating than I anticipated. Hopefully, Glee1204 won't  buzz by and mess with it much. 8-) DennisPietras (talk) 20:45, 13 January 2017 (UTC)
thread_title:  and so, it is finished.... 

message: Comments belong on the talk page, not in the article. Also it is rarely appropriate to mention dates, expect in a history section.  Hence, I am moving the material here. Boghog (talk) 21:06, 13 January 2017 (UTC)
thread_title:  Moved from article 

message: and everybody else: sure, it's strange, but so am I. Feel free to delete it if you think it's inappropriate, but I needed some silliness in my life. DennisPietras (talk) 21:35, 13 January 2017 (UTC)
replies: text: I reverted your deletion of the lead figure. As you can see, it passed review by several people who were very interested in the material on this page. I disagree with your interpretation. The figure shows damage to a gene by an ROS. Do you understand what that means? If you or anybody else doesn't, you or they can click on the ROS link in the caption to find out. The "bandage" on the gene evokes one of the most important points about pseudogenes. They are a bit injured, but they can still do stuff, and may be able to return to full function in time, just as people with bandages can and do. Also, the green beard, as I've linked to in the caption, is a full-fledged concept of it's own, which you or anybody else who doesn't know that can learn by following the link. Finally, I'm a newbie and may be wrong, but aren't you supposed to check the talk page before making a substantial deletion, to see what the consensus is? DennisPietras (talk) 19:29, 4 February 2017 (UTC)
replies: text:   Ideally the graphic in the lead should provide an overview of the subject.  I suggested above that we use a figure from a review article.  Since it copyrighted, we can not use it directly, but I have created a new graphic based on the graphic in the review article (see figure to the right). While the figure may not be eye-catching, I do believe it is informative. In my opinion, informative is more important than eye catching. Thoughts? Boghog (talk) 21:42, 4 February 2017 (UTC)
replies: text: I still vote for mine, but I'm open to a consensus developing against it. The reason I let it "sit" for a couple weeks without devoting the extra time to the superoxide bullet was to see if a consensus would develop against it. When I heard no complaints, I made the additional subtle change, which I think made it even better. But, I'm not going to get into an edit war about it. I have mixed emotions about eye candy in wp, and who(m) decides what is eye candy and what is significant. DennisPietras (talk) 00:57, 5 February 2017 (UTC)
replies: text:  In determining consensus, strength of argument is more important than counting votes. The "shooter" in the present diagram apparently was created to represent the Green-beard effect which has little if anything to do with pseudogenes. The present diagram implies that source of reactive oxygen species is DNA itself. Apparently some photosensitizers like berberine only generate singlet oxygen when bound to DNA ().  However this is a very specialized reaction is only one a of large number of mechanisms that could potential generate pseudogenes.  Without a reliable source that directly links this mechanism to pseudogene formation, this amounts to original research which is prohibited in Wikipedia. The figure above is much more general, is supported by reliable sources, and directly supports the text in the article. The current text says nothing about specific mechanisms of mutations nor in my view, should it since it somewhat off topic.  The same can be said of the current figure. Boghog (talk) 07:39, 5 February 2017 (UTC)
thread_title:  lead figure 

message: I'm doing some revisions, to polish and simplify the text and to expand the evolution information.  Before deciding what to change I'm consulting with the Gerstein Lab and Larry Moran.
So far I've only changed the Lead section, but I plan on doing more over the next few weeks.  This may have removed the need for some references; I'll go back and clean these up soon.  I also moved the Pseudogene formation figure down to the Types and Origins section, and added a simpler figure in the Lead section that just shows the types of defects commonly seen in pseudogenes. Rosieredfield (talk) 22:23, 12 February 2020 (UTC)
thread_title:  Edits February 2020