User talk:Genome42

I've finally gone through the archived discussions at Talk:Non-coding DNA/Archive 1 to understand some more of the background to the discussion at WT:WikiProject Molecular Biology.

I think the key to resolving the clashes on the talk page focus (almost solely) on the references to cite, and summarising what those references say. A lot of friction on talk:Noncoding DNA looks like it came from early misunderstandings and cross-cultural miscommunication. Editors there may have been better swayed with a collection of published sources that explicitly and clearly contradicted the material being removed along with one-sentence summaries of how each is relevant. Similarly, I realise you were mentioning your blog on the talkpage to demonstrate that you know about the topic, but some thought that you were proposing your blog as the source to cite and others thought it was an appeal to authority. You have to remember that WP gets a lot of fringe scientists and outright cranks trying to edit it, so the community tends to rely very heavily on the sources cited and very little on the authority of the editor. In the extreme case, we get people pointing to their own websites like this! I think most of the editors do not have a strong anti-junk DNA POV (they likely have little off-wiki opinion on the matter) but that they a lot of the content there was written in the years after ENCODE and no-one had articulated the extent to which the marketing around that skewed the way the topic was discussed.

Obviously editors are still human, so I'm not saying that de-escalation is trivial, but I think that focusing on the references to cite (i.e. wp:RS and wp:V) and summarising their relevant points will help. WP's community norms are rarely obvious to newcomers but hopefully some of this helps. contemporary review articles (^{[1][2][3][4][5][6]} and similar) and to some extent the more primary research articles (like ^[7][8]). You'll likely know of other good publications, these were just the ones I pulled out the page's current refs.

T.Shafee(Evo&Evo)^talk 07:14, 2 March 2023 (UTC)

Thank-you for your advice. I've been editing Wikipedia on and off since 2007 so I'm quite familiar with the culture. You have repeated the common warning about experts and re-iterated the point that Wikipedians mistrust experts. You seem to think this is a feature but it's not a feature - it's a problem.

Among other things, critical thinking involves making decisions about which sources are reliable and which ones aren't. Like it or not, that requires a deep understanding of the subject material. In other words, it requires experts. Wikipedia should be welcoming expert scientists instead of denigrating them and throwing up roadblocks to prevent them from correcting misleading articles.

I'd like to recruit people like you to help in changing the culture on Wikipedia so that amateurs can work together with experts instead of dismissing them based on a few isolated instances where a kook posed as an expert. The science pages on Wikipedia need a lot of work and there are scientists who are willing to help as long as they aren't subjected to harassment. Genome42 (talk) 14:13, 2 March 2023 (UTC)

...

Your list of references gives me an opportunity to point out some of the issues regarding experts.

First, I have a deep knowledge of the issue so I'm very familiar with the scientific literature. In fact, I have published a book on the subject that's going to be available on May 16th.

Let's look at one of the references you quote in order to see the problems with identifying good sources of information of Wikipedia. I doubt that you have read Nessay Carey's book (ref. 6) because if you had you would see this in the very front of the book in a section called "Notes on Nomenclature."

"Anything that doesn't code for proteins will be described as junk, as it originally was in the old days (second half of the twentieth century)."

If you were an expert on the subject, you would also be familiar with the reviews of her book; for example, check out Georgi Marinov's review "A deeper confusion" ^[1]. Do you really think Nessa Carey's book is a reliable source? How do we deal with amateurs who refer to this book to support their misunderstandings about junk DNA? (Note that Georgi Marinov was an ENCODE worker and he's one of the authors on the Kellis et al. (2014) paper that you quoted above.)

Here's another example. You refer to the Graur (2017) paper as though it were support for the concept of junk DNA but if you were an expert on this subject you would know that the conclusions of that paper have been successfully challenged and Dan Graur no longer stands by them.^[2] Only an expert would know this.

How do we deal with people like you who use the Graur (2017) paper to support their position? (See Non-coding DNA.) Do I just delete the reference or do I have to go into a lengthy discussion like this one every time it gets inserted into a Wikipedia article?

Now let's look at the Palazzo and Kejiou (2022) paper that's ref #1 in your list. Alex and his student are colleagues in my department and if you look at the end of the paper you'll see that I am acknowledged as a contributor (full disclosure). This paper is a lengthy editorial criticizing molecular biologists for not understanding basic concepts in their discipline and for not understanding evolution. Would it be okay to use it like this?

"Some scientists think that the opposition to junk DNA is largely based on a lack of knowledge of molecular biology and molecular evolution (Palazzo and Kejiou, 2017)."

If so, what's to prevent amateurs from using quotes from Nessa Carey's book to refute those claims? Who's going to decide what should go in Wikipedia article?

And what about the Scientific American article (your ref #3) whose senior author, Wojciech Makałowski, is a well-known and vocal opponent of junk DNA? (He organized the symposium on junk DNA at the Society for Molecular Biology and Evolution meeting in Chicago (2013) where Dan Graur and I presented the case for junk DNA.) The quote in the reference is "The term 'junk DNA' repelled mainstream researchers from studying noncoding genetic material for many years." That's a ridiculous and untrue statement. Do you think it belongs in a Wikipedia article?

I hope these examples will help you to see that scientific experts can make a valuable contribution to Wikipedia as long as they are supported by Wikipedians like you who are capable of skeptical and critical thinking and able to act as neutral referees in disputes with amateurs. Genome42 (talk) 15:17, 2 March 2023 (UTC)

Re: Wikipedia-expert relations goals: I'm 100% on board with the idea that wikipedia benefits from more subject expert editors. I also agree that hostile interactions within the wiki community are commonly a problem, an ideal world would focus less on roadblocks, gatekeeping, bans etc, and more on constructive feedback, mentoring, and training (though such productive activities take many orders of magnitude more time and often yield no reward the payoff in successful cases is large). There is currently nowhere near capacity for established editors to identify new editors with subject expertise and assist them in these ways. It probably can only be achieved via a slow and delicate virtuous cycle of attracting and retaining new contributors. Ideally, I'd love to see the average researcher devote even 0.1% of their work hours to contributing to Wikipedia by writing, reviewing and discussing content. However, in addition to the active roadblocks, contribution is not incentivised, and what career rewards do exist are not well known.

Re: relating goals to mid- and short-term actions: Culture change is difficult and slow, even for incumbent editors. It will take the activities of dozens of editors with deep knowledge of wikipedia's history as well as academic norms across multiple countries. In the mid-term, examples of forwarding these larger goals are in training academics as they start editing on how to mesh into Wikipedia's ways of working to avoid problems (I'm always looking for opportunities to give workshops!) and providing a pipeline for academics where they can draft material in a sheltered harbour and going through a more familiar review procedure before material is let loose into the stormier seas of Wikipedia (hence my activities with PLOS and the WikiJournals). In the short-term, I think the necessary first step is for new editors first learning to translate into the wikipedian sources-focused register, and I'll focus on those short-term practicalities within the constraints of what is achievable below.

Re: Distrust as a feature or problem: It's unfortunate that the community on average actively mistrusts experts, the ideal to push for is for the community to be neutral. Active mistrust comes from a range of historical incidents. A reasonable current goal is for an expertise-neutral reaction. This enables the encyclopedia to benefit from expertise and knowledge, without having to assess credentials or mediate between experts arguing on-wiki. This can align with Wikipedia's current ideal of essentially making generalists able to emulate experts by paraphrasing sources at each other (a bit like a Chinese room). In the extreme, you can see this consensus building at "requests for comment" like this one about a single paragraph of the GMO article - only a small minority of discussion participants were topic experts, but the rules of the process aimed to get them to emulate experts by the way sources were centred in the discussions. In reality, the sway of each community member is weighted by their on-wiki experience, activity and reputation. I'll try to give examples below on how to interact without hitting brick walls.

Re: making decisions about which sources are reliable and which ones aren't: The standard Wikipedia way of doing this is to outsource that deep understanding and critical thinking to published sources commenting on other sources. I realise that doing this can sound like 'laundering' your assessment/expertise through the mouth of a source, however it's also demonstrates that it's not just your assessment. For example - "Do you really think Nessa Carey's book is a reliable source?" Realistically it's less important whether I or even you do, the important thing is whether other published sources do. This is a useful example, since there are other sources commenting directly on int (like that review) and indirectly by simply using alternative definitions of junk DNA. An example talkpage comment might be something like: The source [ref] has been criticised by [ref][ref][ref] as using a definition of junk ("Anything that doesn’t code for protein") that is too narrow and excludes. It is more common for the mainstream literature to focus on individual elements . I suggest we move the statement supported by that ref to the History/Terminology section as "More narrow definitions of 'junk' as "not protein coding" have been used in science journalism.[ref] However, definitions such as XYZ are more common in the scientific community [ref][ref] [OR] However mainstream research focuses on study of the diverse types of DNA sequence that fall outside that definition such as A, B, C.[ref]

Re: author changes positions example: It somewhat depends on whether the statement was: correct at the time but overturned by other evidence / based on faulty assumptions / only true in certain circumstances. This is also broadly true for removing any statement. Possible talkpage phrasing would be: [ref A]'s conclusion that [conclusion A] was subsequently show to be [only true in circumstance A / based on incorrect assumption A / contradicted by other evidence B].[ref][ref][ref] The author of [ref A] subsequently agreed [quote / summary / paraphrase].[ref]. I suggest [removing the sentence with "XYZ" / moving it to the History section and replacing with "XYZ"]

Re: Palazzo and Kejiou example: I think that sentence is pretty good. A few possible improvements: including an extra independent reference saying something similar to show it's not just he opinion of the two authors; maybe more specific than "opposition to junk DNA" (depending on paragraph context); whole paragraph probably moved to a 'History or Terminology section that focuses on how the discourse and understanding in specialist and generalist communities evolved. ps. good practice on the disclosure!

Re: Refs getting re-inserted into a Wikipedia article: After consensus can be demonstrated (the hard part) and recorded on a talkpage, the issue of old refs being reinserted is less of a problem. Hypothetical scenario: ref is reinserted in 2 years time, another editor removes it with edit summary removed ref per consensus at [[talk:Talk:Non-coding_DNA#sectionXYZ]]. If added again, raised on the talkpage {{re|Username}}: There was a discussion about this ref in an earlier discussion at[[talk:Talk:Non-coding_DNA#sectionXYZ]] where consensus was that [ref][ref][ref] sufficiently demonstrated that [consensus reason for its omission]. If you have sources to overturn this consensus, please present them here.. Again the focus is on representing consensus support from external sources.

Re: For/against and pro/anti: I still think it's more useful to focus on why the disagreements / what's the steel-man version of their position? If Wojciech Makałowski had happened to sign up as a user instead of you, how would we get him to represent your position as fairly as possible, and what article could both he and you write that both would 'sign off' on? That's why I'm trying to focus on the different definitions of what falls under junk and how these have been presented to a general audience.

So overall, I'm happy to try to help referee this processes, with the proviso, that it has to be within the constraints of WP's current processes. T.Shafee(Evo&Evo)^talk 12:20, 3 March 2023 (UTC)

Hi, please don't take my reversion of your reversion wrongly; I feel that Quercus solaris' version allows inclusion of a wiki-link to non-coding DNA which was previously absent, and is a genuinely useful link for the non-specialist reader who may be interested in what other sorts of non-coding DNA exist. It also included a wiki-link to gene duplication which is a very helpful concept for the reader. If you don't like Quercus' wording, would it be possible to find wording that includes these two links? Elemimele (talk) 22:31, 4 March 2023 (UTC)

Hi, I'm not married to any particular way of conveying it, but the hyponymy and hypernymy definitely needs to be clearly conveyed, if not in that exact way then in another. But the way it's done in that edit is quite concise and clear, though (i.e., a high bar to improve on it; and also, not clear what is supposed to be inoptimal about it). Quercus solaris (talk) 22:36, 4 March 2023 (UTC)

Please take this discussion to Talk:Pseudogenes where it belongs. Genome42 (talk) 04:38, 5 March 2023 (UTC)

Hey, Genome. Re your question at RfA. Administrators don't actually resolve disputes. Disputes are resolved using the WP:Dispute Resolution process. Administrators deal with behavioral issues, of which edit warring is one. I see from the various unblock requests above that you had some misunderstanding of this before.

Administrators never resolve content disputes. If an administrator gets involved in a content dispute, that means they are now w/re that content dispute simply an editor and cannot use their administrative tools there.

Other editors resolve content issues. It's a collaborative and often iterative process. When you disagree with someone here on Wikipedia, you must convince them of your point of view, or you must accept that consensus has gone against you. No administrator, scientist or not, is going to step in and say, "Genome is right and I am therefore reverting the edits in my administrative capacity." Again, administrators deal only with behavior, not with content.

Which means: more scientist administrators will not do anything to change how disputes at science articles are handled. Edit warring is edit warring. It literally does not come into consideration whether you were factually correct. It's a behavioral issues, which is what administrators deal with. Administrators do not deal with content disputes.

Your question above: If so, what's to prevent amateurs from using quotes from Nessa Carey's book to refute those claims? Who's going to decide what should go in Wikipedia article? The answer is: other editors decide what goes into the article, through the collaborative process. Not administrators. Administrators do not deal with content. Administrators deal with behavior.

I hope this helps, and apologies for making the same point multiple times, but w/re the RfA question I feel like maybe you still don't understand this absolutely crucial point about Wikipedia: administrators deal only with behavior, not with content. Valereee (talk) 15:51, 8 March 2023 (UTC)

Thank-you for those comments but I'm afraid they don't reflect reality. In science articles there are dozens of examples of disputes over the scientific consensus and the credibility of sources that Wikipedia considers to be "reliable." We have lots of examples of scientists trying to correct facts and misconceptions but Wikipedia editors block them because they are not following some arbitrary rules that were never designed to resolve factual scientific disputes.

Some of those Wikipedians will accuse well-meaning scientists of breaking the rules and will advocate banning them or blocking them. At this point, administrators will step in to make a judgement. Those whose main expertise is well outside of science may decide to implement the block without ever understanding the actual scientific issues and whether those somewhat arbitrary Wikipedia rules are the problem or the solution.

It's important that we have administrators with a background of solid critical thinking and a knowledge of how scientific disputes should be resolved.

All of my disputes involved serious discussions on the appropriate Talk pages where other knowledgeable experts agreed with me that an edit should be made to correct factually incorrect and/or misleading statements. These changes were often opposed by other editors who wouldn't engage in a serious discussion of the matter but wanted to complain about "process" rather than facts.

You may not be aware of this but there are lots of misconceptions and fake news out there and just because a majority of Wikipedians fall for them doesn't mean they are right and it doesn't mean they get to propagate false information on Wikipedia just because they are in the majority. We need to have a mechanism of dealing with scientific facts and scientific consensus (i.e. the consensus of experts).

I know the standard Wikipedia mantra that administrators don't deal with content, they only deal with behavior. But sometimes those distinctions are blurred when you have edit wars that are really about content and administrators have to resolve a dispute. Surely in those cases you want to tilt in favor of correct content and not just behavior, right?

Please help change the Wikipedia culture. The goal is factually correct material that reflects the scientific consensus and not whatever happens to be the most popular on the internet. I've been editing on Wikipedia on and off since 2007. I know that there's a problem with how Wikipedia deals with expert scientists and I think you do too. It's been widely publicized in the media and even on Wikipedia pages. Genome42 (talk) 18:29, 8 March 2023 (UTC)

You are in all likelihood misinterpreting what's happening. Administrators do not make judgements on content. To someone who doesn't really understand wikipedia, it may feel like administrators are making judgements on content because, during a content dispute, behavioral guidelines are breached, and the administrator deals with the behavior. That doesn't mean the administrator is working on content. But to someone who doesn't understand the difference, it may feel like the admin has acted on the content dispute.

I said "in all likelihood" to leave room for the possibility of admininstrative misconduct. If you believe an administrator has interfered w/re content please give me an example. Valereee (talk) 19:16, 8 March 2023 (UTC)

Just a friendly comment about part of Wikipedia you may find interesting. Check this page out. You may want to join that WikiProject, monitor it's "Article Alerts" section (check it for links on how to do so or ask me), and monitor discussions at Wikipedia talk:WikiProject Molecular Biology as well. Cheers, _{Piotr Konieczny aka Prokonsul Piotrus| reply here} 13:26, 30 March 2023 (UTC)

Thanks. I monitor that WikiProject but it’s not possible to join it. There are only two active members right now so there’s not very much happening. Most of the activity concerns minor issues that don’t interest me very much. The big issues in molecular biology are being dealt with elsewhere. Genome42 (talk) 13:46, 30 March 2023 (UTC)

Hmmm, what do you mean it's not possible to join? By default, anyone can join a WikiProject just by, well, doing so. _{Piotr Konieczny aka Prokonsul Piotrus| reply here} 13:53, 30 March 2023 (UTC)

I registered as a “participant” last summer but I’m not listed as an active member. Nothing happens when you try to “join” on the home page. Genome42 (talk) 14:12, 30 March 2023 (UTC)

Hmmm, this could be b/c someone needs to go to wiki code and add you as a member, and no-one active monitors this. Sorry about that. You could ask at the talk page of that project to see if anyone is "alive" out there. _{Piotr Konieczny aka Prokonsul Piotrus| reply here} 14:31, 30 March 2023 (UTC)

I already know that this is not an active WikiProject. There are a few of us who participate in the "Talk" section, as you can see. Genome42 (talk) 15:00, 30 March 2023 (UTC)

Hey,

Thank you for your helpful suggestions. I would love to discuss your recent edit to the Genome page on Wikipedia. The Human Genome, a pivotal aspect of our understanding of life, is a topic that I believe deserves more than just a passing mention on the page. I understand there's another page on Wikipedia that addresses this topic. However, it's not just about the initial project foundation and the date of the first draft of the sequenced genome; it's about the profound impact the fully sequenced genome has had on our understanding of genetics and medicine.

It's also crucial that we maintain the highest standards of accuracy and reliability. Therefore, I suggest adding citations for your additions, such as the sequencing of the virus φX174, the prokaryote Haemophilus influenza, and the yeast Saccharomyces cerevisiae. This information, while fascinating, is not common knowledge and needs to be backed up with credible sources.

I appreciate your scientific perspective and understand your objections to including the impact corporate entities had on genome research. However, the race to understand and sequence the genome, involving both private corporations and the government, holds significant historical relevance. I propose including a historical tab that addresses these critical topics.

I am opening up this talk page to anyone else in the community. Your suggestions and data are not just welcome, they are crucial to making this page a comprehensive and reliable resource for all. Sarahparker9 (talk) 15:34, 18 December 2024 (UTC)

There is too much redundancy on Wikipedia. We need to fix it but the least we can do for now is to stop its spread. Redundancy leads to conflicts and confusion.

There is a separate article on the Human Genome and that's where details on the human genome belong. That doesn't mean we can't discuss aspects of the human genome in the Genome article if it's relevant. Also, the information that you posted shouldn't be in an introduction.

Some of what you posted on Genome conflicts with what was in the Human Genome article. For example, the standard reference genome (GRCh38.p14) does NOT include the T2T data (see my blog post: What do we do with two different human genome reference sequences?). This is a good example of why redundancy is a problem.

You say that the T2T sequence has had a profound impact on our understanding of genetics and medicine. I disagree. But if if you can document some examples of profound impact then you should post them in the Human Genome article.

I agree with you that the history behind the sequencing of the human genome deserves more attention in the Human Genome article.

I'll try and add some references to the first sequenced genomes in the Genome article. The information is already in the Table but that table is going to be deleted. Genome42 (talk) 20:00, 18 December 2024 (UTC)

Hey,

I completely agree that Wikipedia needs to focus on avoiding redundancy in its pages. I will move the additional information about the Human Genome and the Human Genome Project elsewhere while also ensuring it's not full of unnecessary information. I appreciate you listening to my suggestions about adding citations to the edits you included to the Genome page. Information that isn't common knowledge should be cited using reliable sources. I hope you have a great holiday season, and I look forward to seeing your edits in the future. Sarahparker9 (talk) 16:26, 19 December 2024 (UTC)

Hi Larry, I would disagree that "Molecular macroevolution" is not "macroevolution". Apart from the fact that "macroevolution" as such doesn't make a whole lot of sense, the idea of this page is to compile arguments for large evolutionary changes, and molecular "macroevolution" is definitely a part of it. One reason why this page exists at all is because it's a pet peeve of creationists and any strong argument for macroevolution should be mentioned on this page. If you remove "Molecular macroevolution" you would have to remove "macro-mutations" too, which is conceptually very similar.

By the way, I have added a section on "Criticism of macroevolution" some time ago which someone removed because they thought I am a creationist, which is exactly the opposite of what I am. One of my former colleagues, Jonathan Eisen, has co-written a textbook on Evolution which suffered from the fact that his refutation of creationism was very weak and they barely touched on the topic of macro-evolution, which is a shame. That was one of the reasons why I started working on this page Peteruetz (talk) 15:10, 4 June 2025 (UTC)

All of your examples of "molecular macroevolution" fit within the concept of change in allele frequencies in a population (microevolution). Just because a mutation creates a new allele with a changed function doesn't mean that it's macroevolution.

Are you perhaps thinking about "macromutation" - the underlying cause of saltation events? Those changes are much more drastic than anything that was in the molecular macromutation section but they still have to be fixed within a population (microevolution). Genome42 (talk) 16:50, 4 June 2025 (UTC)

Hi Genome42. Just following up on Talk:Conserved non-coding sequence with a note on the jargon here. Anyone can "blank" an article and replace it with a redirect to another article (WP:BLAR). Similarly any user can undo that action and restore the article from the page history.

When you say "delete" people here will assume you're referring to Wikipedia:Deletion policy. Only administrators can "delete" an article (realistically they're just hiding it from public view; nothing here actually gets deleted in the common sense of the word), and only if there's consensus to do so at WP:AfD, it meets one of the criteria for speedy deletion, or the WP:PROD process is followed for "uncontroversial" deletions. Only other administrators can see "deleted" content and restore it.

I know jargon can seem daft or self-important, but as you're well aware from science, using jargon with accepted definitions can facilitate communication within a group. Communicating clearly with other editors will help you get more done and improve the encyclopedia. All the best, Ajpolino (talk) 20:21, 24 July 2025 (UTC)

Thanks. I already know that Wikipedia editors are very concerned about proper jargon and proper procedure. (I've been editing for 18 years.) Thanks for letting me know that the proper word is "blank," although I not sure that most people would have understood the issue if I'd said "Blank this article?"  :-) Genome42 (talk) 22:09, 24 July 2025 (UTC)

What's confusing about my addition of the new diploid human genome? Maybe you should clarify the confusion or simply ask for clarification before you just delete other people's stuff? Peteruetz (talk) 15:26, 3 October 2025 (UTC)

OK. I'll add a comment in Talk.

You could also have clarified your intent in Talk before making the edit, especially if you thought there was misleading information in the article. Genome42 (talk) 16:24, 3 October 2025 (UTC)

You write that dictionaries are not a reliable source. Most aren't, but the Oxford English Dictionary is invaluable. The page for gene not only gives useful definitions ("The basic unit of heredity in living organisms, originally recognized as a discrete physical factor associated with the inheritance of a particular morphological or physiological trait, and later shown to be located at a specific site on a chromosome and to consist of a sequence of DNA") but, even better, a list of citations in scientific literature. It allows us to trace the evolution of the gene (as a phrase.) That's invaluable. Please consider restoring it. Charlie Faust (talk) 23:52, 6 December 2025 (UTC)

We have plenty of experience with bad dictionary definitions of scientific terms. This one is wrong for several reasons. For example, regulatory sequences are not part of the proper scientific definition of gene. Also, the Oxford definition doesn’t tell us whether introns are part of the molecular gene (they are). That’s why the scientific definition is a DNA sequence that’s transcribed to produce a functional product.

The dictionary doesn’t get the history right and it implies, incorrectly, that the Mendelian gene has evolved into the molecular gene.

Editors have debated this before. When you want scientific definitions, the Oxford English Dictionary is not a reliable source. Genome42 (talk) 02:13, 7 December 2025 (UTC)

I don't see anything wrong here: "The basic unit of heredity in living organisms, originally recognized as a discrete physical factor associated with the inheritance of a particular morphological or physiological trait, and later shown to be located at a specific site on a chromosome and to consist of a sequence of DNA (or RNA in certain viruses) containing a code for a protein or RNA molecule, together with any associated sequences necessary for transcription and translation." That's a good definition. Regarding introns, they are left out. The definition may be incomplete, but it's not incorrect. Let's compare it with Wikipedia's: "In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA." Nothing about introns there, either.

Mendel did discover discrete units of heredity, even if he didn't call them genes (that was Wilhelm Johannsen).

The history is correct as far as I can tell: "The existence of discrete physical entities carrying heritable traits from parents to offspring was suggested by the work of Mendel (see Mendelism n.). Pangene (1889), later gene, was one of a number of early terms proposed for entities of this kind; others included factor (or unit factor) and id. Genes were shown to be located on chromosomes by Morgan in 1911, and Avery and co-workers (1944) associated genes with chromosomal DNA. The elucidation of the structure of DNA by Crick and Watson in 1953 led to knowledge of how genetic information is carried and propagated (see genetic code n.).

Genes exert their effects via transcription into RNA and translation into proteins. Structural genes are both transcribed (into messenger RNA) and translated, and determine the amino acid sequence (primary structure) of proteins. Some genes are only transcribed, especially into transfer and ribosomal RNA. Regulatory genes control the expression of other genes. Cf. also factor n. II.8b."

That last bit seems to have caused some controversy. But, per Wikipedia (not always a reliable source) we read of regulator genes: "In genetics, a regulator gene, regulator, or regulatory gene is a gene involved in controlling the expression of one or more other genes." An extended gene, maybe. The OED is generally seen as sterling. The citations alone are invaluable. Maybe it doesn't belong in the lead, as the definition is incomplete, but it's worth referencing for etymology and history alone. Charlie Faust (talk) 13:28, 8 December 2025 (UTC)

Dictionaries are not reliable sources of scientific information and definitions. The fact that you are quibbling about how to make the OED article compatible with the scientific definition of "gene" is a perfect example of this.

Read my comment on the Talk page. We need to be clear about the distinction between the Mendelian gene and the molecular gene. The Mendelian gene refers to any trait whether it lies within a molecular gene or in some other DNA sequence. This is the kind of gene Dawkins talks about when he should be referring to alleles, not genes.

The molecular gene has a very precise definition - a DNA sequence that's transcribed to produce a functional product. It does not include regulatory sequences as implied by the OED definition.

I spent a lot of time editing the section on "Definitions" in order to correct a number of misconceptions and include a number of exceptions. The OED entry does not help to clarify the issue.

Also, there are still false statements and misconceptions in the rest of the article that need correcting.

We need to stop using terms such as "structural gene" and "regulatory gene." They are not useful and often lead to confusion; for example, many people confuse regulatory gene with regulatory sequence. If you need to refer to this subset of genes then use "gene for a transcription factor" or "gene for a regulatory RNA."

"Structural gene" would include genes for structural proteins such as actin and myosin but it also includes genes for metabolic enzymes and binding proteins such as hemoglobin and transcription factors. What about genes for ribosomal RNA? Are they "structural genes"?

We have plenty of scientific sources for the history of the term "gene." We don't need to refer to a less-than-accurate entry in a non-scientific dictionary. Genome42 (talk) 18:12, 8 December 2025 (UTC)

I can find no finer definition than "The basic unit of heredity in living organisms, originally recognized as a discrete physical factor associated with the inheritance of a particular morphological or physiological trait, and later shown to be located at a specific site on a chromosome and to consist of a sequence of DNA". And, again, the citations are useful.

In any event... The pages for gene and chromosome have the same lead image. This is potentially confusing. Genes are indeed on chromosomes, like "beads on a string" (in Morgan's famous phrase) but the two are not synonymous. Having the same image for both is not helpful.

I was perplexed by the following: "Mendel's work went largely unnoticed after its first publication in 1866, but was rediscovered in the late 19th century by Hugo de Vries, Carl Correns, and Erich von Tschermak, who (claimed to have) reached similar conclusions in their own research." What's this about "claimed to have"?

Thank you for your editing. You are a consummate professional. Wikipedia needs more editors like you. Charlie Faust (talk) 21:53, 8 December 2025 (UTC)

You write that Watson and Crick did not make use of Chargaff's rules. From their 1953 paper: "it is found that only specific pairs of bases can bond together. These pairs are: adenine (purine) with thymine (pyrimidine), and guanine (purine) with cytosine (pyrimidine).

In other words, if an adenine forms one member of a pair, on either chain, then on these assumptions the other member must be thymine; similarly for guanine and cytosine". ... It has been found experimentally that the ratio of the amounts of adenine to thymine, and the ratio of guanine to cytosine, are always very close to unity for deoxyribonucleic acid." The citation is to Erwin Chargaff.

This leads to one of the great lines in science: "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material."^[1]

So, in their 1953 paper, they make explicit reference to Chargaff's rules and cite Chargaff. This is not irrelevant. Charlie Faust (talk) 18:33, 9 December 2025 (UTC)

The history has been covered in many books and articles. Watson discovered the complementary base pairs using cardboard cutouts of the various bases and the presumed hydrogen bonds that could from. After he had come up with a model of the base pairs he realized that they conformed to part of Chargaff's data.

Here's how it's described in Judsons's book on page 148.

"[Watson] told me 'Francis and I had a rule that we wanted to use as little data, few assumptions, as possible to solve the structure, and we never knew whether Chargaff's rules had some complementary extraneous functional reason, and so we didn't put that in. The Chargaff ratio just fell out in the end.'"

And here's how Matthew Cobb describes it on page 109 of "Life's Greatest Secret" ...

"One of the main facts that in retrospect seems so obvious, but which was not at the time, is the role of what are sometimes called the 'Chargaff rules' - the fact that the amounts of A and T and of G and C are equivalent. These ratios were not known to be so precise at the time and they were certainly not 'rules.' As Jerry Donohue, who shared Watson and Crick's room at the Cavendish laboratory, later recalled in somewhat exaggerated fashion" 'When the final model of DNA was discovered - more or less by accident - it wasn't Chargaff's rules that made the model, but the model made the rules.'"

Watson and Crick put the reference in the paper as confirmation of their model but they didn't use any of the ratios in building the base pair model in the first place. It's important to note that Chargaff published lots of papers on the various base compositions of DNA and the purine to pyrimidine ratio was just one of the observations he noted. It was only after the DNA model was published that Chargaff announced that he had predicted the A/T and G/C base pairs. You don't see that emphasis in any of his published work.

But the important point is that this an article about the meaning of the word 'gene' and not an article about the structure of DNA. The structure of DNA is covered in DNA and some of the history of the discovery in covered in History of molecular biology. Both of those articles contain a significant amount of misinformation and the DNA article is a classic example of a Wikipedia article that has become bloated with a huge amount of irrelevant information. Let's not allow that to happen in this article. Genome42 (talk) 21:50, 9 December 2025 (UTC)

Scientists stand on the shoulders of giants, in Newton's phrase. Chargaff was such a giant. Noting that does not diminish the brilliance of Watson and Crick.

Here is a quote from Watson's The Double Helix: "The moment was thus appropriate to think seriously about some curious regularities in DNA chemistry first observed at Columbia by the Austrian-born biochemist Erwin Chargaff. Since the war, Chargaff and his students had been painstakingly analyzing various DNA samples for the relative proportions of their purine and pyrimidine bases. In all their DNA preparations the number of adenine (A) molecules was very similar to the number of thymine (T) molecules, while the number of guanine (G) molecules was very close to the number of cytosine (C) molecules. Moreover, the proportion of adenine and thymine groups varied with their biological origin. The DNA of some organisms had an excess of A and T, while in other forms of life there was an excess of G and C." And, as noted, he and Crick cite Chargaff in their 1953 paper.

Here is an article from The Scientist: "Erwin Chargaff's groundbreaking research, which showed that DNA base pairs had a complementary relationship, laid the foundation for James Watson's and Francis Crick's DNA model."

Here is an article from Nature: "Chargaff's realization that A = T and C = G, combined with some crucially important X-ray crystallography work by English researchers Rosalind Franklin and Maurice Wilkins, contributed to Watson and Crick's derivation of the three-dimensional, double-helical model for the structure of DNA."

It is right to recognize Chargaff's contributions. See the talk page. Charlie Faust (talk) 23:59, 9 December 2025 (UTC)

There’s no question that Chargaff was a giant in his own mind and I’m not questioning the idea that his contribution to Watson’s discovery is widely misrepresented. Nobody, including Chargaff, recognized the importance of his work on the amount of various nucleotides in DNA. It is well known among experts that he never ever emphasized the A/T or G/C ratios in any of publications. It was only after Watson discovered the base pairs that they realized it was consistent with Chargaff’s data.

None of this belongs in an article about genes. Genome42 (talk) 01:01, 10 December 2025 (UTC)

Well, not only his own mind. Watson, not known for giving credit where it's due, gave credit to Chargaff (see above.) Charlie Faust (talk) 01:08, 10 December 2025 (UTC)