Talk:CRISPR/Archive 1

Archive 1

Archive 2

Too many references

There are way too many loose references here. Who would benefit from such a long list instead of being overwhelmed and not being able to find a starting point? I think it would be better to cite just a few general reviews for those who want to read a deeper introduction. In addition to this, specialized research papers should only be listed when the text actually refers to their results. --Tinz (talk) 15:28, 12 July 2010 (UTC)

Actually I find the large reference lists very useful. Especially when improving an article. Admittedly, in order to be consistent with other gene pages (eg. Myoglobin) the refs that aren't directly cited in the text should come under a 'Further reading' section rather than in the reference section. --Paul (talk) 12:13, 13 July 2010 (UTC)

For improving the article I would always prefere a review over an uncommented list. It should have a list of all relevant papers as well, but in addition to this it tells me the central message of each paper. But okay, maybe it is a matter of personal taste, and I am by no means an expert in enwiki's conventions (I wrote the german wikipedia article about CRISPR).

Maybe it would make sense to split the list into reviews and research articles. Also, I think it should become clearer what the most important papers are (e.g. Barrangou et al. (2007)). In my opinion, it can't hurt to provide more inline refs and shift at least some of the refs while doing this. --Tinz (talk) 15:32, 13 July 2010 (UTC)

I totally agree about adding more inline references. Shifting things off the "Further reading" list into "References" will improve the article a lot. Will see what I can do. I'm far from a CRISPR expert however. Can we borrow from the German article? Meine Deutch ist nicht gut! ;-) --Paul (talk) 12:13, 14 July 2010 (UTC)

Thanks for the expansion, of course you can! But I'm not an expert either (I'm a physicist now working in systems biology) I am just interested in unusual evolutionary mechanisms and, after stumbling upon a Science review this January, found CRISPR really fascinating because it struck me as so Lamarckian :-) --Tinz (talk) 21:52, 14 July 2010 (UTC)

Migration of information to CRISPR interference

Information on the mechanism of CRISPR should be moved into the page of CRISPR interference. James atmos (talk) 18:30, 20 July 2010 (UTC)

That seems premature. There isn't enough material in either article to warrant two articles. --Paul (talk) 22:00, 20 July 2010 (UTC)

I agree, two articles are inappropriate for CRISPR; however, giving the recent trends in literature, (i.e. Marraffina and Sontheimer, 2010), CRISPR interference is a more appropriate title as it covers CRISPRs, CAS genes, proto spacers / PAM, and its mechanisms. Referring to the prokaryotic defense system as CRISPR will create confusion as to whether they are referring to the repeats or the whole interference system. What do you guys think??? James atmos (talk) 14:43, 21 July 2010 (UTC)

OK great. We agree on one article. I just did a pubmed vote "CRISPR interference" appears 22 times, "CRISPR" 100. I think most people will look for a "CRISPR" article rather than a "CRISPR interference" one. We can add a redirect from one to the other.--Paul (talk) 20:52, 21 July 2010 (UTC)

ok, I set the redirect from CRISPR interference to this article. I could imagine that in a couple of years, two separate articles might be needed, but now it's too early for that. @James atmos: I really like the new version of your diagram! --Tinz (talk) 21:48, 16 August 2010 (UTC)

Merger

I've added merger tags to CRISPR and CRISPR interference. The current articles appear to be clones of each other. Separating these two interdependent subjects will very difficult to do cleanly and is likely to result in two light-weight articles. --Paul (talk) 22:05, 20 July 2010 (UTC)

This has been resolved, for the time being. --Tinz (talk) 21:48, 16 August 2010 (UTC)

Food production

two points: 1, i don't understand why food production "6.1" is a subheading of mouse models "6". i don't see the relationship. 2, i edited a statement under the "food production" subheading a few days ago. i deleted: DuPont used CRISPRs to create improved bacterial strains for food production.[12] i deleted it because it is incorrect. i thought i explained my deletion at the time. dupont did not use crisprs to create improved bacterial strains for food production. see reference 12. danisco, not dupont, identified some basic crispr function but not in the context of food production. secondly, a direct quote from a danisco scientist, Horvath, from the same reference 12,Jamesikim (talk) 22:30, 19 February 2014 (UTC) "Danisco has no plans to do that [i.e. genetically engineer bacteria with appropriate CRISPR spacer sequences] in light of consumer concerns about the use of GMO." My deletion was undone.

Hi Jamesikim. I undid your change, because your comment on your edit gave no basis for it. I checked the article, and you are right that it doesn't say that either company used CRISPR. I will fix the article accordingly. Lfstevens (talk) 23:12, 24 February 2014 (UTC)

CRISPR / Crispr

This is one of those acronyms that can be pronounced as a single word, just like Laser. Some sources already use the single-word form Crispr ([1]). Should this variant be cited in the article? —capmo (talk) 02:55, 5 March 2014 (UTC)

Clarification needed

They found that bacteria respond to an invading phage by transcribing spacers and palindromic DNA into a long RNA molecule that the cell then uses tracrRNA and Cas9 to cut it into pieces called crRNAs.[12]

I find this sentence incomprehensible. Does "it" refer to the long RNA molecule? to the palindromic DNA? to the invading phage? --Gak (talk) 15:48, 8 August 2014 (UTC)

Repeat and Space lengths

What are the actual space lengths?

http://www.sciencedirect.com/science/article/pii/S1097276514002160 CRISPR spacers can also vary in size (21–72 nt), though they are typically 32–38 nt CRISPR repeats can vary widely (23–55 nt), though they are typically 28–37 nt — Preceding unsigned comment added by 130.225.98.200 (talk) 09:47, 20 February 2015 (UTC)

Patent matters

The patent landscape is developing, and will be developing for quite some time. We are encyclopedia, not a newspaper, and wikipedia should not recount the blow-by-blow of patents issuing, being challenged, etc etc. Also, as the MIT Tech Review article we use as a source recounts, IP in this space is being licensed to companies that are being invested in and that are competing for investment - there is a lot of money at stake, as well as various inventors' scientific pride. So we should be careful that our article doesn't get perverted by all that. Jytdog (talk) 20:07, 25 February 2015 (UTC)

Are natural processes even eligible for worldwide patent? Discovery isn't invention after all. Or is this just a US thing? LeadSongDog come howl! 13:32, 26 February 2015 (UTC)

this is a bit forum-y but... it is true that in the US, the biotech industry is now struggling with two SCOTUS decisions that threw biotech patent law into turmoil - the most important of which was the Prometheus decision, which introduced a new way of reading method claims that is too long to go into here, but that created new issues related to what it describes as attempts to patent natural laws, and the Myriad decision (which is about patents on things, not methods) which ~basically~ said that easily isolated, unaltered biomolecules (like a full length, isolated gene) are not patentable but that isolated and modified biomolecules (like cDNA, or an intentionally altered gene) are still patentable. You have to imagine that the recently-issued patents around CRISPR clear the issues raised by those two cases but I haven't actually looked at the claims.Jytdog (talk) 14:27, 26 February 2015 (UTC)

Interesting discussion on that decision at this WIPO magazine article. Anyhow, we all know that a patent is just a license to go to court, not proof of ownership. LeadSongDog come howl! 19:56, 26 February 2015 (UTC)

It looks as if 37.205.61.203 is continuing the edit-warring previously being carried out by 87.81.220.63. --David Biddulph (talk) 16:29, 26 February 2015 (UTC)

Patents as sources

There's been some edit reversion regarding information relating to the use of patents as a source. What's the take on the interpretation of WP:PATENTS? I'm inclined not to use them n this context, but let's hear any and all opinions here. wia (talk) 23:12, 25 March 2015 (UTC)

its inappropriate use of primary sources by COI editor to attempt to stake a real world claim. not acceptable at all. -- TRPoD aka The Red Pen of Doom 23:55, 25 March 2015 (UTC)

the content that was introduced was WP:OR/WP:SYN. you don't line up content from primary sources like that. there are plenty of good articles really laying things out, like this one which covers most of the key points - the crazy fast commercialization of the technology (which means lots of money for patent battles), the bridging of the AIA startdate so we have a likely interference coming up, and we are likely to have post-issue proceedings as well. this is the last gasp of the old system and first paroxysm of the new... it is going to be interesting to watch. but we should not be sourcing things from primary sources. hell no. and we should be staying super far away from any kind of claims about who is first or anything. whether any priority date is going to hold up, and whether any patent that issues will remain standing, are big unknowns. it is in flux. and we are WP:NOTNEWS here. blogs cover blow by blow, not us. Jytdog (talk) 00:08, 26 March 2015 (UTC)

CRYSTALBALL content

I've been notified that my [revision] in CRISPR article has been undone. Explanation states: WP:CRYSTALBALL content. My contribution was not a speculation. Primates were genetically modified with this new technique(groundbreaking achievement). Linked article goes on to speculate about the future, but the fact remains the same. Maybe I should change the source but I find the article informative especially as it involves the same scientists who developed the technique. Anyways, Wiki article now lacks info about important new development and if it's just because of the source why not change it? Slaven0 (talk) 15:46, 3 May 2015 (UTC)

My impression is that your addition to the article, and the source cited, were both acceptable. But the title of the paper suggested that it consisted of speculation: "... could provide ...", and that is why it was removed. Maproom (talk) 15:53, 3 May 2015 (UTC)

thanks for talkiing! the crystalball part was "The ability to create primates with intentional mutations could provide powerful new ways to study complex and genetically baffling brain disorders". additionally, generally we don't include content about biology based on primary sources or media hype about them - we wait until reviews in the scientific literature discuss some piece of work and put it in the context of the field. Jytdog (talk) 17:52, 3 May 2015 (UTC)

Thanks for clarification, is the following acceptable: "In 2014 CRISPR was used by scientists at Kunming Biomedical International research facility to modify the fertilized eggs of macaque monkeys by editing three different genes. Eggs were implanted into a surrogate macaque mother which gave birth to healthy macaque twins. (ref: http://www.sciencedirect.com/science/article/pii/S0092867414000798)"? Slaven0 (talk) 02:25, 4 May 2015 (UTC)

that is a popular media source hyping a primary source. i mean a secondary source in the literature - like a literature review - like the articles listed here. Jytdog (talk) 02:48, 4 May 2015 (UTC) (corrected Jytdog (talk) 03:58, 4 May 2015 (UTC))

No, it is a Original Research Article [2] published in peer-reviewed scientific journal [3] Slaven0 (talk) 03:19, 4 May 2015 (UTC)

sorry about that - i struck above. yes that is the primary scientific source. not a secondary source (a review), which is what we want. Jytdog (talk) 03:58, 4 May 2015 (UTC)

It has been reviewed in order to be published. This is A1 class article. Did you check other references in line 28?Slaven0 (talk) 05:24, 4 May 2015 (UTC)

every policy and guideline says we should use secondary sources. what is your hurry here? there is WP:NODEADLINE. Jytdog (talk) 11:02, 4 May 2015 (UTC)

No hurry, just doesn't make sense. Same part of text uses news article as reference and it's still there. But what I don't understand is in which way does the review article contribute to reliability of the primary source? Review articles are compilation articles and primary sources are included on the basis of them being published in peer-reviewed scientific journal. The Only way to make primary source article published in A1 peer-reviewed scientific journal More Reliable is by independent scientist repeating the experiment with the same results. As for putting it in the context of the field- that's why you have introduction in scientific articles. Slaven0 (talk) 11:37, 4 May 2015 (UTC)

i just made the animal model subsection more general. see this diff. You seem to be a scientist perhaps. Please know that writing an encyclopedia article is very different from wriing a review article or writing a news piece. We don't synthesize the primary sources like you would in a review article, and we don't Report Exciting Things - we are not a newspaper. Our goal is to provide encyclopedic content. It may help you to read WP:EXPERT. (and yes, Wikipedia is uneven, especially in an article like this, on a "hot topic" - I will look for the things you are citing as examples and fix them - they are not good examples. Jytdog (talk) 11:44, 4 May 2015 (UTC)

You said "that is the primary scientific source. not a secondary source (a review), which is what we want", please answer my question: "in which way does the review article contribute to reliability of the primary source?" I mean encyclopedic content is about providing reliable and accurate information on specific subject. What can be more reliable than original research article published in peer-reviewed scientific journal? The fact that it has been published in *Peer-Reviewed* scientific journal is the reason it has been included in somebodies review article, not the other way around. Slaven0 (talk) 12:13, 4 May 2015 (UTC)

OK, I'll answer. A paper that has been both published in a peer-reviewed scientific journal and accepted as worthy of mention in a review article is more reliable than a paper that has only made it over the first hurdle. Maproom (talk) 12:41, 4 May 2015 (UTC)

That's totally false. Review article is not a "hurdle", it is usually(ideally) a byproduct of a research of original articles by a scientist working on his own original research. After he realizes that he collected more data than he will use for his introduction section he decides to make a review paper since it is a general rule that publishing two papers is better than publishing just one. Review articles rank lower when your scientific work is being reviewed but quantity is still appreciated, plus they are a great read when somebody needs a general introduction to the subject. BUT, after having a general introduction trough a review article it is recommended to check the original research quoted in review article since mistakes in second hand information are to be expected. To summarize, person writing a review article does not analyse and confirm the data presented in original research paper, he simply considers it reliable enough since it is the job of peer review to analyze the research before article has been published. Being mentioned in review paper does not say anything about the reliability of your research, just about relation to the subject in question. Three things are relevant when considering a reliability of article: 1. Quality of journal that has published it(high "impact factor" journal means high quality peers, thus high quality peer review - fact not considered in most of review articles), 2. Your personal track record, 3. Most important - confirmation of results by independent research published in peer reviewed journal of the same or higher quality. In essence, you can have the original research quoted numerous times and after checking the original article to realize it is complete BS but it was not realized by the first person who quoted it and the rest of the quotes just followed the first one. There are actually documented examples of this. So, actually, currently you cannot possibly have better reference than the one I suggested as replacement. Once somebody else genetically modifies primate with the same technique you will have the confirmation of it, but it being mentioned in a review does not mean anything. That's it Slaven0 (talk) 14:03, 4 May 2015 (UTC)

slaven, the question is really backward. you may or may not know, that many research articles in biology turn out to be dead ends, or unreplicable, or even withdrawn. (see Announcement: Reducing our irreproducibility from Nature, for example, which came after this and this). It is not that a review somehow reaches backward in time and magically makes a research article more or less reliable; it is that you and i, standing here in time cannot know now, what research article will turn out to be replicable and/or accepted and built on by the relevant field, and which will not. Reviews tell us that. Here is an example of the kind of thing i hate to see happen -- remember that scientist who published work showing that if you shake cells (really!) you could turn them into stem cells? huge media hype around that. and yep, people rushed to add content based on the hyped primary source to WP, (note the edit date, and the date the paper came out) only to delete it later when the paper was retracted. we should not be jerking the public around like that. there is no reason to do that - we have no deadline here. Jytdog (talk) 12:53, 4 May 2015 (UTC)

I understand your point, but you're not jerking anybody here. Article was issued in high impact scientific journal, nothing hyped about it.. If you do not trust the best experts in the field who reviewed the article before publishing you should actually erase probably 50% of studies mentioned in Wikipedia since many of them simply have not been replicated yet. Just peer reviewed. — Preceding unsigned comment added by Slaven0 (talk • contribs) 4 May 2015‎ (UTC)

ok, so you are not listening to the explanation. WP:IDHT happens here sometimes. In any case you have no consensus to add this. Jytdog (talk) 14:09, 4 May 2015 (UTC)

so, you will erase most of CRISPR Wiki article? Slaven0 (talk) 14:33, 4 May 2015 (UTC)

the article needs a lot of work, this is true. but it is better to find secondary sources that discuss things and add those, and revise based on them, to simply erase everything. things need to move slowly and deliberately here, not radically. erasing everything would just be WP:DISRUPTIVE. (by the way, because Wikipedia is so uneven in quality, WP:OTHERSTUFFEXISTS is generally a bad argument). Jytdog (talk) 14:56, 4 May 2015 (UTC)

so, basically, since review article does not prove reliability and accuracy of research and until above mentioned primate experiment is recreated by independent research, you are subjectively dismissing original peer reviewed research in order to subjectively moderate Wikipedia... Good night... Slaven0 (talk) 15:23, 4 May 2015 (UTC)

so, no that is not what we are saying. we are telling you what WP's policies and guidelines say. (and please don't personalize this) with the "good night", are you from the american south, or are you going to bed? (my tennessee cousins use "good night" all the time as an exclamation) Jytdog (talk) 15:35, 4 May 2015 (UTC)

"good night" means I'm going to sleep and will not be able to answer in a timely manner, no need to go personal with "american south"... I've just pointed out the fallacy in your argument/WP policy but you choose to ignore it. A review article simply does not give any more merit to original research paper and you have failed to justify it other than saying "well, thats just the way we are told to do". Only other argument I got from you was that it can turn out to be non-replicable(false). Yes, it can turn out to be false but we do not stop trusting scientific method and start subjectively dismissing scientific work on the basis of few bad apples. You are doing just that, and what's more troubling, not stopping there but going even further by claiming that a review article, regardles of the fact that it can be written by anybody, gives more value to the original research than (peer)review by top scientists in that field of research! WTF? Non replicable, bogus or (for some other reason) dissmised research ends up in review articles for years after it has been dismissed...193.141.226.1 (talk) 00:33, 5 May 2015 (UTC)

well good morning then! Please don't personalize this - three different editors have told you the same thing. You didn't point out a fallacy - you just showed that you are new here and are more interested in arguing than understanding how Wikipedia works. Some folks cannot get adjusted to working in an encyclopedia and just get frustrated and leave. I hope you are able to settle in to how we do things. Jytdog (talk) 01:01, 5 May 2015 (UTC)

Good morning. Fallacy has been pointed out at lenghts several times, you're just failing to aknowledge that... Repeating that "some folks just dont get it" and "get frustrated and leave" does not give any merit to your position.. Claiming that Original Research Paper which was Reviewed By Top Scientists In The Field And Published In High Impact Scientific Journal is worth Less as reference than Review Paper which Is Unresearched Compilation Of Other People's Work (maybe writen by unknown PhD or masters student and published in scientific journal of Turkmenistan) is logic which is beyond my coprehension... It seems to me that you guys are mixing the term "review article"(compilation) with term "peer-review"(process of detailed inspection of research article by independent qualified reviewers prior to publishing it in scientific journal)... If you want to grade references by quality you should grade them by impact factor of journal they have been published in. Although even this is highly debatable measure it beats the "review factor" you are currently justifying.. Slaven0 (talk) 03:06, 5 May 2015 (UTC)

I'll finish by proving my point: So, at one hand you have original research article published in high impact scientific journal and reviewed by top scientists in the field and on the other hand you have review citing the article they found same way I did and publishing it in 0 impact journal. And now if I use the second link(second hand information) as reference it will be somehow more reliable than the first link? :) Slaven0 (talk) 03:52, 5 May 2015 (UTC)

Jytdog has you here, Slaven0. Rather than waste your energy pushing back against how WP works, go look for reviews that have content that WP does not. It's far more satisfying! Lfstevens (talk) 16:00, 4 May 2015 (UTC)

actually, it seems to me guys that by keeping each others back and not being able to critically think about the rule you are following you have forgotten primary objective of providing correct and reliable information and have taken into your own hands job of second guessing qualified scientists' work. That said, none of you is actually right even by WP rules on this occasion. I have suggested the following statement: "In 2014 CRISPR was used by scientists at Kunming Biomedical International research facility to modify the fertilized eggs of macaque monkeys by editing two different genes. Eggs were implanted into a surrogate macaque mother which gave birth to healthy macaque twins. (ref: http://www.sciencedirect.com/science/article/pii/S0092867414000798)". If you check WP:PRIMARY you will find the following: "primary sources that have been reliably published may be used in Wikipedia; but only with care, because it is easy to misuse them.[4] Any interpretation of primary source material requires a reliable secondary source for that interpretation. A primary source may only be used on Wikipedia to make straightforward, descriptive statements of facts that can be verified by any educated person with access to the primary source but without further, specialized knowledge." So, since this source has been Reliably published and there is no additional interpretation of the fact stated it is perfectly fine to include this in CRISPR article. Any objections?Slaven0 (talk) 05:09, 5 May 2015 (UTC)

WP:NOTNEWS

Revision was deleted with WP:NOTNEWS as explanation. Genetically modified primates are not trivial news since they are one of our closest relatives in animal kingdom. Should the revision be differently formulated? Historical achievement belongs in History section, or am I wrong?Slaven0 (talk) 15:20, 5 May 2015 (UTC)

basically the same discussion above. what you just wrote there is exactly the kind of WP:OR that is involved in generating content from primary sources. We look to secondary sources to tell us why something deserves WP:WEIGHT which is a key part of the NPOV, a key content policy here. Jytdog (talk) 15:25, 5 May 2015 (UTC)

Quotation from WP:OR: "Wikipedia articles must not contain original research. The phrase "original research" (OR) is used on Wikipedia to refer to material—such as facts, allegations, and ideas—for which no reliable, published sources exist.[1] This includes any analysis or synthesis of published material that serves to reach or imply a conclusion not stated by the sources. To demonstrate that you are not adding OR, you must be able to cite reliable, published sources that are directly related to the topic of the article, and directly support the material being presented." Original research article used in references is reliable published source published in high impact scientific journal and thus reviewed by most qualified scientists in this field of research prior to it's publication.Slaven0 (talk) 15:37, 5 May 2015 (UTC)

yeah the point about OR is more about your argument for WP:WEIGHT and why to include this at all: "Genetically modified primates are not trivial news since they are one of our closest relatives in animal kingdom." history sections are not meant to be strings of content based on based on primary sources, each one selected by some editor based on his or her own judgement. for history, we rely on work that historians have already done - (or the story as presented in review articles, which often recite the history of work in the field) - those authors read the primary sources and synthesize a story from them, pointing out what is important and what is not. When editors like you rush to add content based on primary sources under WP:RECENTISM we end up with history sections like this - one big WP:SYN where a bunch of primary sources are strung together. (and we end up with stuff like the "stems-cells-by-shaking" stuff added to WP and then removed) That is not what WP is about. We are not a newspaper - we don't write the first draft of history by stringing together primary sources Jytdog (talk) 16:10, 5 May 2015 (UTC)

This is not based on my own judgement but on the judgement of the most qualified scientists in this field of research who reviewed the article prior to it's publication in one of the highest impact factor journals in existence. I am simply adding the information provided. On the other hand, your judgement is that these scientists are not to be trusted and that, by some twisted logic, this published here is somehow less reliable than this published here.Slaven0 (talk) 22:39, 5 May 2015 (UTC)

you seem to be responding to a different thread. we are talking about writing history. Jytdog (talk) 22:53, 5 May 2015 (UTC)

Yes, and along with mouse, zebra fish, flies and nematodes, our close relative primate species has been genetically modified using this method and the report of this has been published in highly reliable scientific journal. So I'm including it in the article. Slaven0 (talk) 23:46, 5 May 2015 (UTC)

can i ask why this is so important to you? Jytdog (talk) 22:57, 5 May 2015 (UTC)

What? This piece of information or your editing style based on your subjective unqualified judgement of reliability of scientists' work based on demonstrated lack of understanding of proces by which research and publishing of different kinds of scientific articles is done? Slaven0 (talk) 23:46, 5 May 2015 (UTC)

it was a very simple question. Why is this piece of information so important to you? Thanks. Jytdog (talk) 23:48, 5 May 2015 (UTC)

it is important development/landmark in genetics. When somebody comes to inform him/herself about CRISPR they should know that this has been done.Slaven0 (talk) 00:08, 6 May 2015 (UTC)

The information Slaven0 added is significant and important. He did quote a RS and he did follow WP guidelines. He quoted WP guidelines that fully justify the addition and the use of primary peer reviewed source in the way he used it. In the end Jytdog did NOT explain how Slaven0 was violating WP processes. Instead Jytdog switched to personal remarks of the type "Why is this so important to you?" which is 'bad faith', i.e. suspicion of ulterior motives and against WP rules. In the end Jytdog could not justify, and didn't even attempt to, the removal of Slaven0's edit. It leaves the impression that it is important for Jytdog, for some reason, to keep this information out of the article. — Preceding unsigned comment added by 37.33.79.55 (talk) 16:13, 13 June 2015 (UTC)

I don't see the need for the revert here either. An easily verifiable statement of fact can be based on a primary source. Secondary sources support interpretation of those facts. Moreover, asking to "take examples from news source already used" is contradictory because news articles are almost always primary sources themselves. There are established criteria for using primary sources described in WP:PRIMARY-BIO and WP:MEDRS. WP:NOTNEWS should not be an excuse to exclude 'recent' (in this case two years old) developments from a nascent, rapidly developing topic. Ian (talk) 20:00, 16 June 2015 (UTC)

what you call a "fact" is a report of scientific research that 0) may have been the third scientific team to actually do that (not the first, not significant, just boring research); a) may be fraud: b) may turn out not to be replicable: c) may turn out to describe a so-so way to do things and be overtaken by others and left in the dustbin; d) may turn out to Be Really Important. We are not a newspaper - we do not run around breathlessly reporting the last amazing paper. I went looking for reviews and found something close. Will self-revert and modify the content per the source. Jytdog (talk) 20:41, 16 June 2015 (UTC)

I ended up adding "monkeys" to the list of modified organisms, cited to the reviewish paper, and also the non-viable human embyros, which would seem to belong in the list as well. here is the dif Jytdog (talk) 20:59, 16 June 2015 (UTC)

Reference 20 placement

Wondering if ref [20] is correct here: "CRISPR was first shown to work as a genome engineering/editing tool in human cell culture by 2012[20][21]" -- reference 20 does not demonstrate it in human cell culture, or at least not targeting endogenous human genes. Clarification might be needed, especially since it is not consistent with the later statement in the "Applications" section: "Proof of concept studies demonstrated examples both in vitro[20][42] and in vivo[27][101][102]". My apologies if this edit to the talk page does not meet WP guidelines, and thanks for this resource! — Preceding unsigned comment added by 129.85.240.84 (talk) 14:31, 19 June 2015 (UTC)

Citation style

I'm reviewing early versions of the article to see if an original citation style was established. --User:Ceyockey (talk to me) 12:27, 13 August 2015 (UTC) (updated 03:06, 15 August 2015 (UTC))

Findings:

• Use of cite journal template from very earliest citation
  • First variance by Betucinas in July 2013
  • "cite doi" and "cite pmid" first used in November 2013 (replacing citations in cite journal format)
• Use of author form "last_name first_initial" was established for peer reviewed article citations from the very earliest citation additions; through use of the "vauthors" parameter
  • First variance by me in January 2012
• Use of the Author parameter in cite journal established from earliest citation, instead of use of last-first parameters
  • First variance by me in January 2012
• Use of spelled-out month names established in March 2010 and repeated first time in July 2010
  • First variance by Lfstevens in November 2013
• First in-line note (not citation) was introduced in July 2010 and included in References; this was broken out in 2015 to a separate Notes section.
• Linking of journal titles to journal articles reasonably established by October 2010
• First citation of something other than a peer reviewed journal article in November 2013
• names for references typically are "pmid####.." for peer reviewed articles.
• first use of a non-numerical full date in February 2014 → dd (month) yyyy
• bundling multiple citations: there are a couple of examples of this in the current (14 Aug 2015) article, but the precedent set early on was to not bundle citations.

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Needs work

This article either needs focus, or else Wikipedia needs a new article on CRISPR gene editing. CRISPR was the AAAS's choice for breakthrough of the year in 2015, but it would be nearly impossible to tell that it has much importance from this article. I added the following links: http://www.sciencemag.org/topic/2015-breakthrough-year http://www.nature.com/news/crispr-gene-editing-is-just-the-beginning-1.19510 http://www.wired.com/2015/07/crispr-dna-editing-2/ but it would be useful to explain actually how this works and why, in a year that saw spacecraft to Pluto, CRISPR is the most important scientific breakthrough of the year. Geoffrey.landis (talk) 14:28, 8 May 2016 (UTC)

Need help with new column in table

I added a new column to the table that shows the classification of the CRISPR-Cas systems. The new column entries list the class, the new highest-level category recently proposed. I tried to use the "rowspan" command to get rid of the empty cells in the column, but the other columns ended up getting shifted in unpredictable ways when I did this. Can someone else merge the cells in the first column since I don't know how to do this correctly? CatPath (talk) 07:02, 16 June 2016 (UTC)

Split

Thr applications have been split out into:

• CRISPR other applications
• CRISPR human applications

WP:Splitting says if the split is not controversial to "just do it".--172.56.33.24 (talk) 19:50, 13 October 2016 (UTC)

that was inappropriate. Of course a major structural change to an article like this requires discussion. I have reverted. It is not clear to me that a SPLIT is needed, and if so, I don't agree at all with splitting human from other. Needs to get consensus. Jytdog (talk) 05:15, 15 October 2016 (UTC)

I think the split provides better navigation, especially for someone like me because I am on a mobile phone. Just go to the bottom of the page and click on "Mobile view" on the right. The Mobile view only displays the level 2 section headers compactly. Once you click on a level 2 section, the Mobile view shows all of the subsections in it as one scrollable window. Scrolling takes time on a phone and I have to be careful not to hit a wikilink as I sweep my finger many times. I can switch to the Desktop view but then it is even more scrolling. With the split was implemented, I can easily go to CRISPR, and then if I want to Applications and then choose.--172.56.1.72 (talk) 23:00, 15 October 2016 (UTC)

If you are the person who did the split or have previously commented, please acknowledge that. It is not OK for someone to make it appear that he or she is more than one person in discussions.... Jytdog (talk) 23:13, 15 October 2016 (UTC)

I did the split. My provider changes my IP address about once an hour from a large and varied pool of addresses.--172.56.1.72 (talk) 23:30, 15 October 2016 (UTC)

Thanks for acknowledging that. Jytdog (talk) 23:31, 15 October 2016 (UTC)

• Note: IP was a block-evading Tyree999. Ian.thomson (talk) 01:32, 16 October 2016 (UTC)

Gah. Thanks User:Ian.thomson. I have nominated the two split articles for deletion per G5 per this and this. Jytdog (talk) 02:03, 16 October 2016 (UTC)

this one and this one too - each where Tyree originally split them to. Jytdog (talk) 02:05, 16 October 2016 (UTC)

I support "a" split, but just to "CRISPR applications". I see no need for a further split at this point. Lfstevens (talk) 07:18, 16 October 2016 (UTC)

The originally proposed split is ambiguous. If "human applications" refers to CRISPR editing of humans, then very little work has been done on this topic (in that case I assume "other applications" means all use as a biotech tool not on humans, i.e. almost all of this use). Alternatively the original poster might mean "human applications" to be general use by humans as a biotech tool, and "other applications" referring to its function in nature. This could be a more sensible split but would need a little consensus (as is going on at testosterone right now). For comparison, DNA ligase and Restriction enzyme both achieve such a split by using the main page to describe the natural function, and a {{main article}} template in their applications section to point to their use as a molecular biology tool (Ligation (molecular biology) and Restriction digest respectively). We have pages on Genome editing and several other applciations of CRISPR, so a possible solution is actually to cut down the text in the application section so that it is in stead present mostly in the Genome engineering page. T.Shafee(Evo&Evo)^talk 00:31, 1 November 2016 (UTC)

They meant proposed therapeutic uses; that is what was in the now-deleted article. Jytdog (talk) 02:15, 1 November 2016 (UTC)

Policy Barriers

Hello, I noticed there is little to no mention of specific policy barriers that CRISPR-cas9 editing must overcome. Propose adding a section for various genetic modification policies that could regulate GE crop production, medicinal applications, ect. Specific reference found in Request to USDA to approve CRISPR-modified mushroom. This letter details the specifics of a 'plant pest' and how Dr. Yang's genetically modified shroomz circumvented these regulations on genetically engineered plants, namely by the avoidance of adding foreign DNA. In addition, it may be in the best interests of the page to condense Society/Culture and Commercialization into a more general Category, as the two interplay frequently. Maybe titled Commercialization Progress? KalebSkye (talk) 19:22, 3 November 2016 (UTC)

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Bioethical concerns

Is stated: "Bioethical concerns have been expressed about the prospect of using this nascent biotechnology for editing the human germline."

Would be more accurate to complete: "Bioethical concerns have been expressed about the prospect of using this nascent biotechnology for editing the germline of human, animals and food crops." — Preceding unsigned comment added by 92.139.237.40 (talk) 21:02, 9 December 2016 (UTC)

Removal of the Transhumanism section

Recently User:Jytdog removed the "Transhumanism" section that I added as a subsection to the "Society and culture" section, saying FRINGE perspective; weight is UNDUE.

I do not agree and would like to readd the section: it's fringe according to you - WP:NPOV, check the sources (WP:RS); it's part of society & culture's reaction to the development of CRISPR. And how is weight undue - it's just a few sentences?

--Fixuture (talk) 03:11, 29 December 2016 (UTC)

If you look at all the refs about CRISPR the transhumanist perspective gets negligible attention, and advocacy to use CRISPR to change people is an absolutely FRINGE notion, rejected by mainstream science at this point in time. Jytdog (talk) 03:27, 29 December 2016 (UTC)

@Jytdog: But I have put forward quite a number of refs that even focus on the connection between transhumanism and CRISPR (and there are even more) [and once again: a fringe notion according to you]:

• Pearlman, Alex. "Geneticists Are Concerned Transhumanists Will Use CRISPR on Themselves". Vice Motherboard. Retrieved 26 December 2016.
• Jorgensen, Ellen. "How DIY bio-hackers are changing the conversation around genetic engineering". The Washington Post. Retrieved 26 December 2016.
• "Human Enhancement". Pew Research Center. Retrieved 26 December 2016.
• Emba, Christine. "Will technology allow us to transcend the human condition?". The Washington Post. Retrieved 26 December 2016.
• Hughes, James. "Transhumanist position on human germline genetic modification". Kurzweil AI. Retrieved 26 December 2016.
• Regalado, Antonio. "Engineering the Perfect Baby". MIT Technology Review. Retrieved 26 December 2016.

=> your argument doesn't hold.

--Fixuture (talk) 18:45, 29 December 2016 (UTC)

I didn't say there are none. Compare that handful to the gazillions of refs about CRISPR that don't deal with any of that sci-fi. Gazillions. It is fringe speculation that matters nothing in the real world. maybe it has a place in some article about transhumanism but not here - if it got in here it would be the result of some advocate showing up and trying to force it in - that is what every wikipedia editor, including you, needs to be mindful of - namely paying mind to WEIGHT/UNDUE and NPOV based on what the world of refs that discuss X talk about. Not what we come to WP caring about. Jytdog (talk) 21:21, 29 December 2016 (UTC)

Well, the refs that don't talk about it aren't an argument for not featuring this short, sourced content. I just readded it. It is "fringe speculation that matters nothing in the real world" according to you. I think that the usage of this technology/method for human enhancement matters greatly and is more than noteworthy and due here. You might move the content to another section though (merging it into an appropriate existing one or a creating a new one). For instance I thought about a "Human enhancement" section in the "Applications" section (which might also outline other studied potential applications such as "new antibiotics and antivirals" and "editting crops to be more nutritious").

--Fixuture (talk) 14:12, 31 December 2016 (UTC)

Lack of discussion is exactly part of the consideration that we undertake for NPOV. Your argument is dead wrong and against policy Jytdog (talk) 16:59, 31 December 2016 (UTC)

GA nomination

Hi, I've done a few fixes for this article to meet good article criteria, so I'm wondering if anyone would oppose me starting a nomination. This is certainly a fine candidate. I'll wait a day or so to get any feedback and then nominate it. Thanks, Icebob99 (talk) 23:24, 26 December 2016 (UTC)

Hi Icebob99. Can you hold off on the nomination for a while? I see a lot of problems with the article:

• Just looking at the history section, I see unsourced claims, a serious POV issue, a possible copyright issue (copy-paste), and undue weight issues. I'll try to fix the problems in the history section today, but I suspect that there are similar issues with the rest of the article.
• The article is missing topics that should be included/expanded. For example, there are biological functions of CRISPR/Cas that are not mentioned in the article at all (it's not just for immunity). There also needs to be a section on how bacteriophage resist CRISPR/Cas. The patent dispute is barely mentioned.
• Some passages read more like a scientific journal article than an encyclopedia article becuase too much experimental detail from primary sources was provided.
• WP:WPNOTRS states, "Wikipedia articles should be based mainly on reliable secondary sources." Maybe others have a different opinion, but this article relies too much on primary research articles, which are contributing to some of the problems that I've listed above.

CatPath (talk) 22:01, 27 December 2016 (UTC)

@CatPath: fair enough; those issues should be addressed. Thanks for bringing it up. Icebob99 (talk) 04:42, 28 December 2016 (UTC)

Made a copyediting/reorg pass through this. Feedback enccouraged. Long way to go. Suggestions: - Break out the genome editing section into another article. It's not just cas9, too. - Break out the applications that are not commercial into a Potential CRISPR applications article. This material will continue to change rapidly, which is not GA normal. Splitting will stabilize this piece. That approach worked well for Graphene.

Nice work. Yes there is a lot more to go, in terms of removing primary sources and promotional, WP:FART content. In my view the potential stuff should not be in WP at all, per WP:CRYSTALBALL. I think as the primary sources get pulled out, a lot of that potential stuff will go away. Jytdog (talk) 04:10, 29 December 2016 (UTC)

Thanks for noticing. My point was strategic rather than juridical. If we want to make this a GA, we need to reduce the "corrupting" pressure of research. The "Potential" dodge makes things much easier, in addition to making it clear that whatever ends up there is in the research stage. Note that these are not medical claims, they are directional. Lfstevens (talk) 05:37, 30 December 2016 (UTC)

Outside view: I came to this article wondering what CRISPR was, am leaving not much wiser, but decided to take a quick look at the talk page before leaving to see if anyone else had the same issue I did (noone else has mentioned it).

I can't imagine this article qualifying for GA before very seriously addressing a lot of the guidelines in WP: TECHNICAL. I'm not suggesting that the existing content be dumbed down or trimmed, but there should at least be an intro written for an audience not all of whom work in biotech. 87.198.117.223 (talk) 13:22, 14 January 2017 (UTC)

MSU MMG 445 Wiki Talk Page Evaluation

I chose two questions to address while reading the CRISPR article.

1.Is each fact referenced with an appropriate reliable reference?

Yes every stated fact or group of facts has a reference at the bottom. Each reference that I looked into seemed credible and reputable. Although I did not go through every reference.

2. Check a few citations. Do the links work? Is there any close paraphrasing or plagiarism in this article?

Each link that I clicked on was working. I saw no instances of plagiarism or even close paraphrasing, as far as I could tell.

Robnolan100 (talk) 21:00, 17 January 2017 (UTC)

Semi-protected edit request on 5 March 2017

I suggest two updates to the table of CRISPR-Cas types:

1. there is a typo in the row of type V: C2cI should be C2c1 (c-two-c-one).
2. Add CasX and CasY as two additional type V Cas effector proteins, based on this ref: . In the updated raw C2c3 should probably be the last Cas protein on the list since it is the only one of them that was not experimentally validated.

Below is the updated table (all changes are in the line starting with " Dudusan (talk) 07:50, 5 March 2017 (UTC)

References

Partly done: For #2, please specify where you want CasX and CasY to go in the article. You also will want to establish a consensus for #2 before submitting an edit request. Morphdog (t - c) 16:38, 5 March 2017 (UTC)

Semi-protected edit request on 10 March 2017

The information provided relating to patents is unclear. I suggest the following revision:

"In February 2017 the US patent office ruled on a patent interference case brought by University of California with respect to patents issued to the Broad Institute, and found that the Broad patents with claims covering the application of CRISPR/cas9 in eukaryotic cells was distinct from the invention claimed by University of California.[178][179][180] The ruling means that the US patent office will proceed to grant separate patents to both the Broad Institute and the University of California. Absent other issues, since the patent that would be granted to the Broad Institute would cover the use of CRISPR technology only in eukaryotic systems, whereas the patent that would be granted to the University of California would cover the use of CRISPR technology in any system, Broad would need a license from the University to practice its invention in eukaryotic systems. Similarly, although the University of California would be able to practice its invention in prokaryotic systems, it would need a license from Broad in order to practice its invention in eukaryotic systems. The ruling of the US patent office is subject to appeal." 50.241.150.177 (talk) 16:26, 10 March 2017 (UTC)

 Not done - the suggested added content has no source. Jytdog (talk) 05:09, 11 March 2017 (UTC)

Semi-protected edit request on 13 March 2017

I suggest adding CasX and CasY in the "Signature genes" table on the row of type V, next to Cpf1 and C2c1, and adding as a reference to it. The change should be in the table on the "V" type row. here is the updated table row:

{{ || V || Cpf1, C2c1, CasX, CasY, C2c3 || Nuclease RuvC. Lacks HNH. || }}

Thanks, Dudusan (talk) 00:02, 14 March 2017 (UTC)

References

Semi-protected edit request on 4 April 2017

The patent and commercialization section could be elaborated; I suggest replacing the first paragraph with the following:

The speculated profit potential resulting from commercial use of CRISPR led to multiple separate entities attempting to establish their own patents on the development of related drugs and research tools. On May 25, 2012, researchers from the University of California submitted 155 patent claims for in vitro applications of CRISPR/Cas9 on varying cell types including eukaryotic cells. A second set of patents was filed December 12, 2012 by Feng Zhang of The Broad Institute at Massachusetts Institute of Technology for the use of CRISPR specifically on genome editing of eukaryotic cells. Due to fast-tracked patent applications, several of Zhang's patents were awarded before a decision had been made on the patents submitted by the University of California. The University of California brought a patent interference case to the US patent office with respect to patents issued to the Broad Institute in December 2014.

Determining who had the right to Cas9 directly impacted the potential earnings for Crispr Therapeutic and Editas Medicine, which had based their profits on the ability to use CRISPR under University of California and The Broad Institute's patents respectively. Other implications included the ethical concern of awarding a patent, which could potentially allow commercial use of CRISPR/Cas9 while academic research was considered patent infringement. In February 2017, the US patent office ruled that there was no interference. This ruling decided that Broad Institute's patents covering the use of CRISPR/Cas9 in eukaryotic cells were sufficiently distinct from the patents presented from the University of California. As the patents were separate entities, the Broad Institute's use of fast-tracking did not interfere with the success of the University of California's patent claims. This decision stemmed from the belief that The Broad Institute's invention was not an obvious development of The University of California's patent. Crispr Therapeutic's stocks dropped by ten percent in the aftermath of this decision, while Editas Medicine stocks increased by nearly thirty percent. Although the University of California is considering appealing the case, the narrow application of the patents awarded to the Broad Institute would still allow for patents related to CRISPR in prokaryotic cells to be filed.

The decision made by the US patent office suggests a trend towards awarding patents to specific inventions, rather than allowing companies to create broad patents that might cover all applications of a discovery. In the future, the use of CRISPR will require licenses from the Broad Institute; However, the Broad Institute has clearly stated their commitment to allow CRISPR to further research for the public benefit. There is still some questioning to how much of a profit CRISPR will bring and how quickly its monetization will occur, as potential profits are still years away.Gggrose (talk) 15:05, 4 April 2017 (UTC)

References

Semi-protected why?

Why is this page semi-protected? There's no link on the talk page explaining or justifying this. 50.194.21.67 (talk) 18:49, 2 May 2017 (UTC)

Edits in modern computational biology knowledge & biomedicine

Hey guys, I recently made an update to the facts on xenotransplantation in the 'biomedicine' portion of the 'Application' subheading by including facts from a recent study published this last August. I also plan to attempt to improve the quality of the 'computational biology' portion, and I believe updating the 'identification' section with more verifiable resources that are more recent than 2007-2013 is a good place to start. I'll include more information as I continually identify modern computational methods used in research, but I'm also taking and suggestions or resources you can think of. Thanks! Cchoates (talk) 18:57, 5 September 2017 (UTC)

Hi - so what we do here in Wikipedia, is present articles to the public that summarize accepted knowledge. We find "accepted knowledge" in what we call 'reliable sources'. Those are almost always 'secondary sources'. In Wikipedia, when writing about science, "secondary sources" are things like literature reviews and book chapters; papers where people communicate their research findings are "primary sources" and we rarely use them and when we do, we do with great care and good reason (you should never have to, in what you are doing here with this course). So please find recent reviews on the topic published in good journals (be sure not to use any journals from predatory publishers!), and summarize them here, giving "weight" (space and emphasis) to what they give weight to. And as you work, please keep overall WEIGHT in the article in mind; a bad thing that can happen with student projects is that some section gets blown way out of proportion in relation to the rest of the article.

Good luck! Jytdog (talk) 22:47, 5 September 2017 (UTC)

Suggestion for more understandable intro

The intro starts by correctly spelling out CRISPR as Clustered regularly interspaced short palindromic repeats. It then describes this DNA sequence the way it was described before the researchers understood how it functions. Likewise the name was minted before it was understood. (This is explained very clearly in the history chapter of the article.) Because of this the name and the description are misleading. Calling something a spacer conveyes the impression that it is unimportant. The opposite is true. To repeat: the descriptive name of CRISPR is a clueless description. In Wikipedia we strive to provide descriptions that help understanding and highlight the important aspects. The spacers contain the important information and the repeat sequences are the frame for this information.

So I suggest that we start by saying that: CRISPR is a DNA sequence in bacteria that contains snippets of DNA from viruses that have attacked it. These snippets are used by the bacteria to detect and destroy further attacks by similar viruses.

AFTER this, we should explain why it got such a clueless descriptive name.

I wrote this 6 August 2017. --Ettrig (talk) 05:16, 7 September 2017 (UTC)

RNA-guided and RNA-targeting CRISPR effector

Not sure where this should go in the article or if there is somewhere more appropriate, but this seems to be notable and is receiving some coverage so I thought I'd drop a few references here so someone with more expertise can find the right place for them.

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector, Science. 2 June 2016.
Scientists Find Form of Crispr Gene Editing With New Capabilities The New York Times. 3 June 2016.

Sherlock CRISPR

http://news.mit.edu/2017/scientists-unveil-crispr-based-diagnostic-platform-0413 -- Jo3sampl (talk) 19:12, 4 April 2017 (UTC)

History

Shouldn't we add a Cas3 subsection in the History section? See also https://techcrunch.com/2016/12/21/move-over-cas9-crispr-cas3-might-hold-the-key-to-solving-the-antibiotics-crisis/ KVDP (talk) 08:21, 27 March 2018 (UTC)

The History section is kind of a mess. It says "occurred independently" for occurrences spanning 13 years in our present time! In another point it mentions " repeats were observed" but " his hypothesis turned out to be wrong" ... etc

CRISPR/HIV

Thinking about adding CRISPR/HIV as a subtopic under applications, or perhaps as a subheading? What are your thoughts on this? Nguyen2018 (talk) 14:04, 11 April 2018 (UTC)

I think there are too many specific applications to list each one. 129.215.47.59 (talk) 12:20, 16 May 2018 (UTC)

"Alternative cutters" section

What is that "alternative cutters" section about (at the very bottom of the article)? They look like degenerate RNA sequences so they probably aren't cutting anything? And how is it that they belong under the 'society and culture' subheading? Suggest making their relevance clear or deleting them. 129.215.47.59 (talk) 12:20, 16 May 2018 (UTC)

That section heading is clearly incorrect. I've renamed it & removed the non-CRISPR structure that was in there. Paul (talk) 01:52, 26 May 2018 (UTC)

Important early CRISPR papers.

The article currently lacks citations to two important early articles that are important to the history of the evolution of thought about CRISPR systems.

One is Tang, et al., from 2002, on small RNAs from the Archaeoglobus fulgidus. Although only 22 of 86 small RNAs are CRISPR-derived, Tang discussed the repeats and their spacers properly, using the term SRSR (short regularly spaced repeats), and demonstrated transcription of CRISPR regions and cleavage into small RNAs for the first time. Tang writes "These patterns suggest that in all Archaea examined the clustered repeats are transcribed in the form of long precursor(s), subsequently processed into monomers or multimers of the repeat motif."

The other is PMID:16292354, Haft, et al. from 2005, "A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes." This article comes at the dawn of the analysis of CRISPR-associated protein families. Because it relied on manually built protein families (made available as part of TIGRFAMs) instead of, say, COGs, it defined protein families accurately enough to define biomarkers of the specific CRISPR system subtypes, and it reported a system of gene symbols that became widely used, if not necessarily still preferred, in the CRISPR literature: cse1-cse4, csn1 (now cas9) and csn2, csy1-4, cmr1-6, etc. This work predates the more widely known Makarova, et al. article, "A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action.".

Given that the article on CRISPR now cites about 250 papers, it seems these two deserve mention.

I took a stab at providing some text and the two citations, but changes were reverted for including self-citation and not following today's majority practice in secondary sources of not mentioning PMID:16292354. That omission seems both unfortunate and self-perpetuating, since the Wikipedia article's lack of any mention of PMID:16292354 for its elaborate discussion of CRISPR subtypes probably affects today's secondary sources.

Daniel haft (talk) 23:32, 1 July 2018 (UTC)

Thanks for coming to talk. As it is, the page has way too many primary sources, and people insisting on their authority (which nobody has any of, here in WP) that this or that primary source is very important. In Wikipeida, we summarize secondary sources. The genre here is encyclopedia, not literature review. Jytdog (talk) 00:27, 2 July 2018 (UTC)

       Secondary sources can be notoriously bad at crediting people who did not do much to publicize their work. I think the reference to the work by Haft et. al is appropriate, as it is verifiable by the literature. Perhaps that section could be shortened, but removing it because of lack of credit in secondary sources seems irresponsible if the claims are verifiable (which they are given the provided sources).

--207.188.207.18 (talk) 15:10, 6 July 2018 (UTC)

As editors of Wikipedia articles, it's not up to us to decide whether certain scientists have been given the appropriate credit in review articles. Your claims may be verifiable, but their significance must also be established to avoid undue weight being placed on the claims. Significance is established by citing review articles that describe the work in question. Also, please stop inserting your changes until consensus is established, especially since you appear to have a conflict of interest. CatPath (talk) 20:32, 6 July 2018 (UTC)

Objection - I have made no edits on CRISPR since July 1. I am always signed in for all edits on all topics. This thread in this talk page makes it seem like failing to publish review articles regularly on one's own work can cause important early work in a field to fade from community awareness, and that the Wikipedia editorial standard encourages the amnesia. I would like to request that (unconflicted) experts in CRISPR protein families and their nomenclature develop a brief but historically accurate section on subtypes and gene symbol nomenclature.

Please see the secondary source "Evolution and classification of the CRISPR-Cas systems.", PMID 21552286, Evolution and classification of the CRISPR-Cas systems., 2011, and its extensive citations of references 13 (mine) and 14, and overall citations of the earlier work (315 in PubMedCentral, 837 by Google Scholar). That secondary source delivered the prevailing new nomenclature that replaced the older (Csn1 becoming Cas9, etc.), and it acknowledges the prior art. Here are two relevant quotes from the 2011 paper:

"....In this Opinion article, we summarize the shortcomings of the existing classifications and nomenclature of the CRISPR–Cas systems and propose a new, `polythetic' classification that combines information from phylogenetic and comparative genomic analyses."

Lumpers and splitters. This article showcased distant relationships linking named proteins of different subtypes, so names like Cas5 or Cas6 could apply across multiple subtypes, while preserving the fine divisions that many found useful.

"Type II systems use a trans-encoded small RNA (tracrRNA) that pairs with the repeat fragment of the pre-crRNA, followed by cleavage within the repeats by the housekeeping RNase III in the presence of Cas9 (formerly known as Csn1 or Csx12)."

Yes, Cas9 was previously known by a name that originated with TIGRFAMs.

"The updated TIGRFAMs identifiers are given in Supplementary information S4 (table). "

I was a partner in that nomenclature revision paper, as second author.

The current version of Wikipedia's CRISPR article makes it look, incorrectly, as though CRISPR subtypes was a concept introduced in 2006. I request a fix. And then I would like to delete as much as possible of this whole unseemly discussion from the Talk page.

Daniel haft (talk) 19:16, 8 July 2018 (UTC)

The problem with the 2011 review is that your work is highlighted on a review that you coauthored. You need an independent secondary source. The review is also a bit old. A better source is this 2015 review by the same first author [4](PMID 26411297), which also cites one of your papers. Regardless of the source, your proposed addition ([5]) is far too detailed and introduces unnecessary jargon (e.g., TIGRFAM, csn). I don't think the history of the categorization of CRISPR-Cas genes, including your renaming of the three subdivisions of one of the many CRISPR-Cas subtypes (as briefly described in the 2015 review), is appropriate for the History section. CatPath (talk) 19:59, 11 July 2018 (UTC)

The spam and self-citation policies are misapplied in this case. The policy on "Citing yourself" is "Using material you have written or published is allowed within reason, but only if it is relevant, conforms to the content policies, including WP:SELFPUB, and is not excessive." I follow this. If you see the Radical SAM page, I created 90% of the content, there are 10 references, and I referenced no paper of mine. In the exosortase page, where you also reverted a recent update of mine, no review article exists! The secondary sources are the review of the current understanding of the field in the introductory sections of peer-reviewed primary sources. The contribution I made was absolutely justified, and only a disservice to the public occurs when the revision that says PEP-CTERM proteins are involved in floc formation gets deleted. Please revert that reversion (after checking for accuracy, overstatement, search engine optimization, etc).

I work with protein families, toiling in obscurity, with most of my work unlabeled. I never apply for grants.

Like it or not, excitement about CRISPR makes the history section vital to the article. The first published recognition of subtypes (and the source of half the gene symbol nomenclature) is relevant. My paper was in the CRISPR article for 10 years, until you, CatPath, removed the last mention of it. What is left in the CRISPR article is the impression that the Koonin group was the first to publish that CRISPR has subtypes and the number of families is large.

When I was invited to join as a coauthor of the opinion piece that offered a comprehensive revision of CRISPR protein family naming, I knew the choice I was facing. I could have opposed it and clung to my nomenclature (which was paired with downloadable protein family detection tools that made adoption of that nomenclature easy), or I could join in co-authoring the article that shunted my original nomenclature aside. I chose the latter for the sake of science (compare that to the mess now in aminoglycoside resistance nomenclature - the researchers hate that), with wistful regret for the fading of the names I had developed and their link to work at TIGR/JCVI. I have been a good citizen.

The history section should cite Tang on processing of CRISPR RNA transcripts in 2002. That should go back in immediately. It should also cite, as dryly as you like, that subtypes were reported by TIGR in 2005, with reference, and that the NCBI group's subsequent work renamed the subtypes.

I should point out the a 2015 review article on the current state of CRISPR-associated protein classification is not a review of history for Wikipedia standards. State of the art is one field, and history is another. The record should be repaired. — Preceding unsigned comment added by Daniel haft (talk • contribs) 11:30, 13 July 2018 (UTC)

I've made lots of edits to the article over the years. Please provide the diff where I removed your 2005 paper that was "in the CRISPR article for 10 years" so that I know which edit you're referring to. I'm guessing that I removed it from the "Locus structure" section. That section simply describes the organization of the CRISPR locus as currently understood. It is not a "history" section that explains the timeline of how we got from your 2005 study to our current understanding of the structure and categorization of CRISPR-Cas. I probably removed it because it was out of date.

You're now bringing up edits to other Wikipedia articles and edits made by other users that were reverted by others. Let's stick to your proposed edit: [6] (And don't get me started on using the introduction to primary sources as secondary sources for Wikipedia articles. That's just a bad idea that will lead to all sorts of other problems.)

I looked through other recent review articles, including a lengthy one that covers the history of CRISPR: [7]. Some of these papers cite your 2005 study, but none of them support the addition ("that subtypes were reported by TIGR in 2005. (And if you find recent independent review articles that support your claim, then please bring them here.) I have no doubt that the 2005 study was significant, but we can't be inserting a claim into this article that recent review articles don't even discuss. Please read WP:undue.

I'm also not sure how the article leaves the impression that the Koonin group was the first to show that there are subtypes of CRISPR. Classes and subtypes are hardly mentioned in the History section.

CatPath (talk) 21:02, 13 July 2018 (UTC)

Is there a way we can take this discussion off-line? I don't know if WP offers a contributor-to-contributor contact feature, but my email is trivial to discover. Your phrase, "including your renaming of the three subdivisions of one of the many CRISPR-Cas subtypes" is inaccurate (and pejorative), and perhaps suggests a misreading of the 2015 paper to minimize contributions of the 2005 article. Yes, three of TIGRFAMs/Genome Properties subtypes of the 2005 paper are re-designated as branches of Cas8b-contining type I-B, as cited in the 2015 review. But the 2005 paper was the first to identify subtype I-A (as APERN), subtype I-B (split three ways), subtype I-C as DVULG, I-E (as ECOLI), I-Y (as YPEST), type II systems as NMENI, subtype III-A as MTUBE, and subtype III-B as the RAMP module (changing the R in RAMP from "repeat" to "repair"), and more.

Looks like it was the Revision as of 18:31, 6 January 2017, which removed the last remaining ref my work, "an initial analysis of 200 bacterial and archaeal genomes suggested as many as 45 cas gene families".

The edit history of the CRISPR article reflects intense interest in controlling the attribution of credit, and getting the milestones right the development of thought about CRISPR systems seems pretty important. Because you are clearly an expert in the history of CRISPR publications, because your edit orphaned my work which had been cited, because you know my publication reported CRISPR subtypes, because you know the existence of distinct subtypes and the expansion of cas families to include Csn1 (Cas9) is historically important, and because you deleted (rather than fixing) my attempt to repair the record, I think you have some responsibility to figure out how to prepare a just and accurate revision of the history section of the CRISPR article.

(and please be assured I have no patents, or grants, or applications in the works for either of any kind, nor collaborations in the CRISPR field, etc. etc. I'm just a guy whose life work is protein families.)

Daniel haft (talk) 21:50, 14 July 2018 (UTC)

Any proposed changes to article content need to be on this talk page. I mentioned WP:EXPERT (or try clicking my username to read my user page on scientists and being a Wikipedia editor, but Wikipedia operates differently than academic publishing. You also have a COI when trying to cite your own work here regardless of patents, etc. or not. This is a rather well published field, so if your work is a sufficient WP:WEIGHT for inclusion, that will be mentioned in other sources. Kingofaces43 (talk) 03:37, 15 July 2018 (UTC)

Discussions about content should happen here, in public. If you want to talk offline to get coaching that is fine.

There is some (appropriate) content about priority with regard to the patent battle.

As has already been stated, there is way too much "X lab at Y university did Z" sourced to primary sources, which is terrible encyclopedia writing and mostly people abusing WP for promotion. That is what we keep trying to tell you. We need less of that, not more. Jytdog (talk) 04:05, 15 July 2018 (UTC)

I understand where Jytdog is coming from; a PubMed search for "CRISPR" reports almost 10,000 articles. We clearly don't want to cite them all. But we do want to get the history section into better shape (tersely).

Here is my proposal. There is a heading called "History". It has a subheading called "CRISPR-associated systems." Currently it reads,

"... analogous to the RNA interference system used by eukaryotic cells. Koonin and colleagues extended this RNA interference hypothesis ..."

and that's where it skips the work that reported subsystems, PMID:16292354. That article is cited the review CatPath recommends, and clearly predates all other discussions of subtypes.

For clarification, I suggest

"... analogous to the RNA interference system used by eukaryotic cells. In 2005, the set of 4 cas genes grew to 45 with the identification of eight CRISPR-Cas subtypes and their specific marker proteins. < PMID 16292354>

In 2006 Koonin and colleagues extended the RNA interference hypothesis ..."

Yes, the current count is 93, as stated elsewhere in the article.

The change I propose here is far more terse than my previous edit attempt. So that should be an improvement. It no longer mentions my name. Adding the fix makes for a better and more historically accurate article. It corrects the distorted impression that any reader would get from reading today's version. Anyone who reads today's version of the article without a prior background in the field would think that the other group was the first to publish CRISPR systems have subtypes, and to say that Cas9 is a Cas protein. That faulty impression comes from a prior edit by CatPath that stripped out all mention of my work.

Before anyone jumps on me again to say that if my work had real impact, review articles would heavily reference the article's, they do. And if a review discusses the current classification rather than the history of discovery, it should do so with little fanfare. So please look in the WP article at the table of subtype-specific markers. The gene symbols Cse1, Cse2, Csy1, Csy2, Csy3, GSU0054, Csm2, Cmr5, Csn2 all date from PMID:16292354 in 2005. Most of the others represent the nomenclature post-revision, but describe the same protein families and subtypes. I'm not requesting any change to the references in that table, since that's not the history section. But please recognize that pejorative statements about my contributions, above in this thread, have been misdirected.

Given all the accusations there have been that my suggested edits are to be disallowed because I'm on the paper I wish to cite, I request that another make the change. Comments?

P.S. I added the Tang reference. Tastefully, I hope. That should help separate the issues. Daniel haft (talk) 11:50, 20 July 2018 (UTC)

You're misunderstanding why I brought up the 2015 review by Marakova - and that's my fault because I ended up sacrificing clarity in an attempt to keep my comments brief. My reason for mentioning the review was to provide an example of a recent secondary source - one without you as an author - that cites your 2005 paper. The review does not justify your proposed edit because it says nothing about expanding the set of 4 cas genes to 45 subtypes. I also did not intend to disparage your 2005 paper. I was simply pointing out that your 2005 paper was cited to support their brief passage about the three main subdivisions within subtype I-B. (Your 2005 paper was cited 3 more times in the article, but none of those passages relate to your proposed edit.) I realize your work went beyond that, but as you pointed out, the review wasn't about the history. And among the papers that ARE about the history, none of them mention the expansion of cas to 45 subtypes.

Please correct me if I'm wrong, but you seem to be trying to correct an oversight by the authors who have written reviews of the field. We can't do that in Wikipedia articles. We can only summarize what is actually said by secondary sources. CatPath (talk) 17:24, 20 July 2018 (UTC)

Well. The original citation is used for every citation in the history section, and you know that full well. If you want a review article to convince you, you could cite CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea, LA Marraffini, EJ Sontheimer - Nature Reviews Genetics, 2010, PMID 20125085. "Two groups have made considerable efforts to classify CRISPR systems into different subtypes that share flanking cas genes 21,28 . Haft et al. 28 established 45 gene families associated with CRISPR loci that can be classified into eight CRISPR subtypes..."

As for the 2015 paper, it says in the abstract "The new classification retains the overall structure of the previous version but is expanded ...", and it cites older subtype papers that start with mine. The strange game of "gotcha" in which citations have to be deleted from WP if the most recent review article writer economizes on space a bit is a perversion.

Addition of the Tang reference got reverted? By Kingofaces43, from the history section, where the majority of citations are primary? This makes no sense. — Preceding unsigned comment added by Daniel haft (talk • contribs) 19:57, 20 July 2018 (UTC)

Yes, I do know that primary sources are used in the History section (and yes, someone should probably replace those with secondary sources as well). But as far as I can tell, all of the claims based on those primary sources are supported by secondary sources (which need to be added to the article if they are absent from the article). You seem to think I'm out to get you, so I'll leave it to others to decide whether the 2010 review is too old to be used as a reference. I wasn't considering any reviews older than 2013 because of Wikipedia guidelines (though I think that's MEDRS(?)). I will have no issue if consensus develops to use the 2010 review as a source for your proposed edit. CatPath (talk) 20:24, 20 July 2018 (UTC)

Well, it has felt like I've run into a storm of opposition to everything I do, although understanding seems much closer now. I now understand what is going on with MEDRS - MED is medical information, where content presented in Wikipedia could sound authoritative. Citing an original source as authoritative can be dangerously toxic if it runs contrary to more recent, more informed, consensus medical thinking as seen in review articles. But that is a special standard for medical information. I would say it does not apply to a biochemistry article, and in particular, it does not apply to the history section of a biochemistry article. Tang's work in 2002 is cited by the critical papers of 2005 and 2006. It belongs. And I have no COI in saying so - never met or communicated with anyone from that article. CatPath, could you perhaps do me the honor of undoing the Kingofaces43 reversion of the citation to Tang? May I do it myself?

Daniel haft (talk) 15:55, 28 July 2018 (UTC)

WP:SCIRS also advises secondary sources. All of WP should be driven by secondary sources. This is deep in the guts of how WP works, with its open, unauthored articles. We all get it that you write science articles every day. You do that in articles with your name on them. Wikipedia is not like that. See WP:EXPERT and User:Jytdog#NPOV_part_1:_secondary_sources. So for about the bazillionth time --no. Jytdog (talk) 16:32, 28 July 2018 (UTC)

CRISPR RNA structure

The CRISPR RNA structure section at the very end looks weird under the 'society and culture'. It would be better moved under locus structure. The RNA belongs to key component in CRISPR working locus. Zhongyiw (talk) 19:18, 5 September 2018 (UTC) Ying

This article is well written and well sourced, Fantastic work.Lena M Ali (talk) 20:54, 8 September 2018 (UTC)

Technical

@Alcmaeonid: Thanks for your note. I have tried to make at least lead the lead more accessible. Is it any better? I am not sure that we will be able to make the rest of the article significantly less technical because this is an inherently technical subject, but at least the lead should be understandable to a broad audience. Boghog (talk) 17:10, 6 October 2018 (UTC)

Thanks @Boghog:. Your changes are a step in the right direction. However I still think the lede too technical. For a good example of simple English explanation I found this:

"CRISPR technology is a simple yet powerful tool for editing genomes. It allows researchers to easily alter DNA sequences and modify gene function. Its many potential applications include correcting genetic defects, treating and preventing the spread of diseases and improving crops. However, its promise also raises ethical concerns.

In popular usage, "CRISPR" (pronounced "crisper") is shorthand for "CRISPR-Cas9." CRISPRs are specialized stretches of DNA. The protein Cas9 (or "CRISPR-associated") is an enzyme that acts like a pair of molecular scissors, capable of cutting strands of DNA.

CRISPR technology was adapted from the natural defense mechanisms of bacteria and archaea (the domain of single-celled microorganisms). These organisms use CRISPR-derived RNA and various Cas proteins, including Cas9, to foil attacks by viruses and other foreign bodies. They do so primarily by chopping up and destroying the DNA of a foreign invader. When these components are transferred into other, more complex, organisms, it allows for the manipulation of genes, or "editing."

— https://www.livescience.com/58790-crispr-explained.html

I'm reluctant to edit myself as I have very little expertise in this area. ~ Alcmaeonid (talk) 18:22, 11 October 2018 (UTC)

Useful secondary source

https://www.wnycstudios.org/story/antibodies-part-1-crispr and https://www.wnycstudios.org/story/update-crispr --Lewisiscrazy (talk) 12:26, 11 December 2018 (UTC)