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2058:: I appreciate your effort to clarify the discussion over different definitions of "gene" but I really don't think your edits are helpful. You deleted a specific reference to Dawkins but I think that's vey important since "The Selfish Gene" is one of the most widely read books on the subject and it contributes significantly to confusion about the meaning of the word "gene," especially in the context of an article that's mainly about the molecular gene.
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1362:(not that that's better). I like your method better from an aesthetic and maintenance point of view, but the problem is that giving a reader a reference to "chapter 4" is less useful if there's no obvious way to get to chapter 4 from the book's table of contents page. I don't see a way to provide separate links for each chapter/section without splitting up the references in the reference list. We could use
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1044:...could also just transclude a collapsed version - provides the full set of terms and takes up little space. If people need a glossary, they can expand it. Glossaries probably shouldn't be expanded by default unless there's a lot of free space along the right side of the page between level 2 sections (i.e., horizontal line breaks), since images and tables should take precedence.
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see that the majority of the page is discussing molecular biology (except the mendelian inheritance section), then "in a genetics context (particularly forward genetics and gene-centred evolution), a mendelian definition is still sometimes used XYZ". That way a reader can see those contexts in the same way without the editorialised voice.
2003:
this definition. It is supported by two references written by people who thought that the old definition referred only to protein-coding genes. (One them is
Elizabeth Pennisi - a very unreliable source.) They were wrong and we don't need to quote people who had a misconception about the real historical definition of a gene.
2454:
Then there's the
Wikipedians who are anxious to edit articles like this by inserting short references to statements "proving" that a new definition of gene is required because of alternative splicing and noncoding RNAs (and other things). It will be easy for them to do this with the short version but
1094:
is still way too long. Glossaries should be restricted to key terms with short definitions that can quickly be scanned while reading the rest of the article. IMHO, a long glossary defeats its purpose. Furthermore an uncollapsed glossary is more likely be read and if kept short, no need to collapse.
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where the mutation rate in humans is said to be 50-90 mutations per generation. This conflicts with the value of 30 that was just added to this article. (The
Mutation article is closer to being correct and the value stated here is wrong. The actual value is probably closer to 100 but we'll deal with
2450:
The science crowd consists of readers who are interested in science and have probably taken an undergraduate course in biology. They have been bombarded with information about genes and how the old concepts are completely wrong and need to be drastically revised in the genomics era. It's likely they
2221:
The term "overlapping genes" is a problem. In the case of well-studied prokaryotic examples what we're actually talking about is overlapping coding regions (not genes) and the overlap is usually only a few nucleotides. I don't think it deserves much coverage in this article; besides, there's already
2133:
Knowledge (XXG) typically avoids phrasing around "This article focuses on..." and "More thorough discussions of this version of a gene can be found in...". It is probably better to state something more like "in a molecular biology context the definition most commonly used is XYZ. The reader can then
2290:
How do we deal with conflicts like this? Do we have to give credence to every scientist who makes incorrect, misleading, or controversial statements because that’s what the
Knowledge (XXG) culture demands or should we concentrate on giving the general public the best consensus view of knowledgeable
2174:
We have another problem. There are a ton of articles about molecular biology and they often cover the same topics and they often conflict. Can you guess how many times the structure of DNA is discussed? We need to clean up this mess by concentrating on a few high quality articles that can be linked
2085:
Also, you added something about synthetic genes that isn't appropriate. Artificial DNA segments that some people refer to as genes are not relevant. The sentence on "de novo" genes is also more confusing than enlightening because in order to actually qualify as a "de novo" gene, the sequence has to
2002:
The so-called "new" definition described in the last paragraph is " a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product or by regulation of gene expression." I don't agree with
1994:
In the second-last paragraph we are introduced to the idea that "The concept of gene continues to be refined as new phenomena are discovered" and some of those "new phenomena" are supposed to be regulatory sequences and exons and introns. But regulatory sequences have been known for almost 60 years
897:
Thanks for the prompt on this! I see I did do some work here back in the day, but not enough. Looks like a typical large-but-untended wiki article - bloated up with random factoids with no attention to the flow of the article. I'm pretty busy for this week and out of town next week, but I'll try to
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Whenever you do that, it will sound like editorializing to all those people who are being asked to re-evaluate their preconceived notions. I realize that the
Knowledge (XXG) culture is usually opposed to making strong statements about what's true and what's not but that's something that we need to
1990:
There are two different definitions of "gene" in the text and this needs to be fixed. We're talking about the molecular gene and the definition used by knowledgeable scientists is that a gene is a DNA sequence that's transcribed to produce a functional RNA. That RNA could be mRNA or any one a of a
1603:
My first reaction to your 'appended links' idea was that we shouldn't create our own linked pseudo-TOC given the publisher's apparent desire not to have a linked TOC hosted by the organization they actually licensed the content to. But all the other ideas do essentially the same thing, so that's a
1998:
Another so-called "new phenomenon" is functional noncoding RNA but that's not new and it doesn't change the definition of gene that's used in the first paragraph. Knowledgeable scientists have known about noncoding genes since the mid-1960s. The fact that some genes are made of RNA deserves to be
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I definitely don't know enough about
Knowledge (XXG) to come down with a strong opinion on this. My intuition says an encyclopedia should prioritize the general audience, especially with a topic like this with such a broad cultural impression. That's why I opted for writing a shorter definitions
2166:
In this case, the myths that need correcting are that up until the genomics era scientists thought that protein-coding genes were the only kind of gene and they thought that all noncoding DNA was junk. You and I know that's not true but statements to that effect are very common in the scientific
2129:
I see what you're saying, though I think there are ways to note dawkins's influence on the popular understanding that flow a bit better. It may even work well to state the molecular definition first in that section (since it's the more common usage) then the second part can mention the continued
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The mutation rate per generation in humans is not the same as the mutation rate per replication. The two papers that are referenced refer to the per generation mutation rate (10^-8). Thus every newborn baby has about 60 (2 X 30) new mutations according to this mutation rate - the latest data is
2021:
I'd be fine with deleting the second-last paragraph of the current lead, especially since there seems to be a section dedicated to different definitions. It's probably still worth noting in the lede section that there are alternative definitions of a 'gene' other than the one in the very first
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positions can just be omitted. Genuinely common misconceptions (popular press, obsolete model, counterintuitive situation, oversimplification, misconception from another field etc), should generally be mentioned but immediately corrected (e.g. the misconception orthogenesis/progressionism in
2331:). A summary table would only be useful for when there are multiple reasonable alternative definitions that are commonly used by experts in relevant fields where we're at least alerting readers that alternative defs exist that come at an issue from different angles.
1258:
to include links to individual sections as notes. Of course, now they're separate from the rest of the references, but maybe it's not a bad idea to distinguish 'basic stuff you can find in a textbook' from 'specific results you need to consult the literature for'.
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have heard some version of the story that old fuddy-duddy scientists (like me) thought that all genes encoded proteins and we couldn't adjust to the new ideas coming out of ENCODE and Evelyn Fox Keller. The long version is intended to correct that misconception.
961:, I don't know it's backstory, but it is a rather cleaver idea for a template in my opinion. I partially reckon it might go well under the first image in place or the second image depicting DNA, which conceptually is a tangent. I am not sure, hence my asking. --
2278:
Your link brings up an issue that’s really important. The authors claim that genes are currently (2017) defined as DNA sequences that specify a protein then makes the further case that the current definition conflicts with the discovery of alternative
2095:
The problems are compounded by another discussion further down in the article under "Functional definitions." That discussion conflicts with the one we are editing and that's going to cause a problem later on. (Do we really need to waste time on rare
2067:
Breaking the section into subsections seems (IMHO) to make the discussion disjointed since two of the subsections ("Inheritance" and "Selection") both refer to the
Mendelian gene and this article isn't about the Mendelian gene. That's covered under
2601:
Nonsense. Denis Noble is not a credible authority on genes and neither is Philip Ball. I haven't got my copy of Phil's book yet but I'm familiar with his earlier writings. This is very controversial and bound to get us into bitter edit wars.
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by Philip Ball, Pan
Macmillan (2023) - It's time to admit that genes are not the blueprint for life - The view of biology often presented to the public is oversimplified and out of date. Scientists must set the record straight, argues a new
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One
Protein", it should definitely be mentioned as a potential (common?) misconception or oversimplification and the reasons listed/explained. If it was fair simplification at one time then that should probably be mentioned (a bit like the
2162:
There's a lot of misinformation on the web and one of our goals should be to counter that by posting reliable information on
Knowledge (XXG). But that's not sufficient because in order to counter misinformation you also have to debunk
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Are four examples of definitions needed as a list in the section? Perhaps it could work better to state the consensus definition before the minor variations that exist around it and to note what particular differences those examples
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I agree that work should start from this page (assuming consensus is reached) and work outwards to harmonise. If we decide to include more than one example of each major class of definition, a simplified but updated version of
2507:
The overall DNA error rate per replication is about 10^-10 - it includes the DNA replication error rate of 10^-8 and the fact that 99% of these errors are repaired. That gives 0.3 mutations per haploid genome per replication.
2425:. This condenses the definitions section from ~1500 words to ~200 words, so a lot of neat details are gone, but some can likely be migrated to the History section or their relevant main article (if they are not already there).
916:
I'll probably go through and make all the necessary MOS tweaks for FA status to the article within the next week. Too preoccupied with other articles at the moment to make any substantive content/reference changes though.
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I've not done much non-standard reference citation so I'll wait until you've done a couple so that I can see the format in context before doing any more. The ones I added yesterday shouldn't be too difficult to reformat.
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and they are not considered to be a part of the gene as defined in the first paragraph. Introns have always been considered part of the molecular definition of a gene ever since they were discovered about 50 years ago.
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article, I thought I'd suggest spending a couple of weeks seeing if we can get it up to a higher standard. I'm going to start with updating some of the images. If you'd like to help out on the article, it'd be great to
2446:
Thanks for taking an interest. Here's how I see it. We have several different audiences. The "general audience" probably doesn't care very much about the exact definition so the long version just looks like history to
2421:'s post on the WP:MOLBIO talk page about the definitions section and I took a crack at rewriting it with a focus on brevity while trying to address some of the concerns discussed above. You can find it in my userspace
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I strongly recommend that we delete the section on "Molecular evolution" since it doesn't belong here and the material is covered elsewhere. The material in the subsection on "Mutation," for example, is covered in
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Which misconception are you referring to? Is it the misconception that all genes encode proteins or the misconception that protein-coding genes can only encode a single kind of functional polypeptide chain?
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I think that’s incorrect and I can document my claim by quoting numerous textbook over the past 50 years that have defined a gene in a way that includes noncoding genes such as those for ribosomal RNA and
1854:
Looks great, I like the collapsible box! I can't find it at the moment, though - IIRC there is somewhere an agreement not to use collapsed boxes for references for accessibility reasons. I don't see it in
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There don't seem to any objections to deleting the second-last paragraph of the lead so I have removed it because there is an extended discussion of gene definition elsewhere in the article.
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chapter labels best, as it's least intrusive in the text, makes clear how many citations go to a general reference, and doesn't require a separate list or potentially fragile formatting.
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literature. We need to spend a bit of effort showing that the real scientific definition of a gene hasn't changed substantially in 50 years in spite of what one might have heard or read.
2536:
This example illustrates the problem with redundancy. When the main article is updated and corrected, the other entries become wrong and this helps spread misinformation and confusion.
1859:
so I could be misremembering, and since the box contains links and not the reference note itself, it's probably fine. Just wanted to mention it in case someone recognized the issue.
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I don't see why the definitions section should be very long at all if the goal is to provide extra context to what is meant be either the Mandelian or molecular gene. Extra nuance,
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to. This is one of those articles. We shouldn't be afraid of linking to other high quality articles for more information, especially if the topic is too complicated to summarize.
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Fair enough. Might as well make a new one since it's not referenced anyway; imo, glossaries should cite sources, preferably another glossary, because it's article content.
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It's a shame that we have to think about ways of protecting accurate science from well-intentioned, but uniformed, Knowledge (XXG) editors but it's a fact of life in 2023.
2218:. Many of these articles cover the same topics and they often don't agree. Many of them discuss genes but they don't use the same definition we use here. This is a problem.
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labels the chapter number but does not provide any easy link to the actual information. Therefore it's combined with a list of chapter links. the benefit is that the
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You're right, I missed that. I agree that it's actually a good way to format it. Having a separate list that indicates the significance of the references is useful.
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Also, I just noticed the hatnote pointing to the dab page doesn't use the molecular gene definition. I'll move the dab page definition over to the hatnote. ―
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page but I can find no way of searching by page number, chapter, section or anything else. Any ideas on how to specify specific sections as is possible for
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subsection into it. Much of that subsection is now a bit redundant, so most can probably be omitted as the section as a whole is refined and condensed.
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I don’t think we need to discuss mutation rate in this article since it is covered elsewhere. But if we include it, we should at least get it right.
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as a "reference". I would consider this kind of thing as a summary analogous to the lead paragraphs; no need for a clutter of little blue numbers.
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Hmm, apparently I added a bunch of stuff to that template awhile back, but don't remember it at all. It appears to be a subset of the article
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number of noncoding RNAs. That's the definition described in the first paragraph and it's supported by several appropriate references.
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Well spotted - It's really irritating when templates don't work properly on mobiles! I've changed the MBOC list to be wrapped in
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Including a glossary could be useful, but I think it should be concise and tailored specifically for this article. Currently
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section should probably end up 500-800 words. Overlapping genes probably deserves a sentence rather than a whole subsection.
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In general, if something is an uncommon misconception, then it can be easily omitted (or only briefly mentioned) to avoid
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templates. They are more complicated and harder to maintain. Plus they don't directly address the problem of searching
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so the box is expanded by default but that made no difference. Maybe better to change to a bulleted or indented list?
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links together. As stated above, there's basically no way to avoid linking individually to chapters if we want to cite
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template is relatively easy to maintain and the list of chapter links doesn't require maintainance and places all the
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2072:. In addition, your description of the Mendelian gene and its connection to selection is adequately covered under
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per month but has been de-listed as a featured article since 2006. Given the success of the recent blitz on the
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contains 22 entries and some of the definitions are quite lengthy. A shorter glossary, closer to the size of
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is the lesser of two evils. One other possibility is to append the chapter external links to the citation:
1308:. What seems to work is to search for the chapter or subchapter titles in quotes. For example search for
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on Knowledge (XXG). If you would like to participate, please visit the project page, where you can join
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on Knowledge (XXG). If you would like to participate, please visit the project page, where you can join
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contemporary use of a modern Mendelian definition in certain circumstances (e.g. forward genetics).
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section in hopes of increased accessibility. Maybe that's only most appropriate for the lede.
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and I think we should be linking to other articles when they cover a topic correctly.
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section a bit more, since it's currently a bit of a list of quotes (e.g. moving the
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You're the one currently doing the work, so I think that means you get to decide :)
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the longer version will (I hope) be more resistant to attacks from other editors.
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meet the acceptable definition. The edit doesn't add anything to the discussion.
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a second one is even more relevant, but unfortunately not freely accessed:
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section needs to move up into this one and get integrated in. The whole
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It appears the main reason gene was delisted as a GA was sourcing (see
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Knowledge (XXG) level-3 vital articles in Biology and health sciences
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2309:- Sorry for the late reply on this. In the case of "One Gene -: -->
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mentioned in the first paragraph so I've inserted two sentences.
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such as the definition proposed by the linked 2017 article above
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I propose that we delete the second-last paragraph of the lead.
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2586:) may be worth considering? - iac - Stay Safe and Healthy !! -
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4.2: Chromosomal DNA and Its Packaging in the Chromatin Fiber
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change because it's getting in the way of critical thinking.
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or have separate citations for each chapter where only the
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Chapter 7.2: DNA-Binding Motifs in Gene Regulatory Proteins
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bit silly. I think I like that idea in combination with
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I've finished adding MBOC references up to section 3 (
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Ch 6: How Cells Read the Genome: From DNA to Protein
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OK, I now see what you mean. The choice is between
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WikiProject Molecular and Cellular Biology articles
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2178:Along those lines, there are separate articles on
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2572:How Life Works: A User’s Guide to the New Biology
2100:when there's a very good article on the subject?)
1512:(2002). "Chapter 7: Control of Gene Expression".
1352:I mis-described my own suggestion; it's actually
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1718:(Fourth ed.). New York: Garland Science.
1516:(Fourth ed.). New York: Garland Science.
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832:(Fourth ed.). New York: Garland Science.
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2074:Gene-centered view of evolution
1416:and in-line external links and
695:Spoken Knowledge (XXG) articles
573:This article has been rated as
2714:Natural sciences good articles
2533:that in the Mutation article.)
1675:Genes are numerous and useful
1463:Chapter 4: DNA and Chromosomes
957:Snooping around I encountered
866:(7th ed.). Benjamin Cummings.
276:Natural sciences good articles
272:has been listed as one of the
1:
2784:WikiProject Genetics articles
2709:Knowledge (XXG) good articles
2546:21:14, 10 December 2023 (UTC)
2216:Conserved non-coding sequence
2118:18:16, 27 February 2023 (UTC)
2050:06:52, 27 February 2023 (UTC)
2016:22:14, 22 February 2023 (UTC)
1715:Molecular Biology of the Cell
1514:Molecular Biology of the Cell
1448:Molecular Biology of the Cell
1306:Molecular Biology of the Cell
1210:Molecular Biology of the Cell
991:Transcription factor glossary
864:Molecular Biology of the Gene
829:Molecular Biology of the Cell
683:and see a list of open tasks.
619:This article is supported by
595:This article is supported by
547:and see a list of open tasks.
536:WikiProject Molecular Biology
42:Put new text under old text.
2729:Former good article nominees
2690:04:51, 6 February 2024 (UTC)
2612:18:25, 7 February 2024 (UTC)
2596:04:51, 6 February 2024 (UTC)
2522:02:07, 5 December 2023 (UTC)
1976:Definition of "gene" (again)
1084:Collapsed or not collapsed,
2794:Top-importance MCB articles
1001:Restriction enzyme glossary
2820:
2774:GA-Class Genetics articles
2658:10.1038/d41586-024-00327-x
2486:18:49, 13 March 2023 (UTC)
2468:18:23, 12 March 2023 (UTC)
2442:01:47, 12 March 2023 (UTC)
2379:03:55, 21 March 2023 (UTC)
2366:12:19, 20 March 2023 (UTC)
2351:03:26, 20 March 2023 (UTC)
2334:Also, since we now have a
2056:Evolution and evolvability
1953:Yep, that works – thanks!
1888:Evolution and evolvability
1869:07:50, 28 April 2015 (UTC)
1846:10:51, 27 April 2015 (UTC)
1828:01:29, 27 April 2015 (UTC)
1660:19:01, 22 April 2015 (UTC)
1645:12:24, 22 April 2015 (UTC)
1624:20:49, 21 April 2015 (UTC)
1579:18:47, 21 April 2015 (UTC)
1386:18:03, 21 April 2015 (UTC)
1336:12:21, 21 April 2015 (UTC)
1282:08:06, 21 April 2015 (UTC)
1269:06:09, 21 April 2015 (UTC)
1235:11:30, 20 April 2015 (UTC)
1176:I suggest just linking to
959:Template:Genetics glossary
908:19:19, 31 March 2015 (UTC)
891:17:58, 31 March 2015 (UTC)
798:09:49, 31 March 2015 (UTC)
559:Molecular Biology articles
350:Refreshing brilliant prose
2560:(2023) worth considering?
2413:14:50, 7 March 2023 (UTC)
2301:18:45, 9 March 2023 (UTC)
2274:02:32, 9 March 2023 (UTC)
2256:20:10, 2 March 2023 (UTC)
2158:03:43, 2 March 2023 (UTC)
1984:talk:Gene#Defining "gene"
1962:13:23, 30 June 2015 (UTC)
1949:12:31, 30 June 2015 (UTC)
1909:10:50, 30 June 2015 (UTC)
1755:Ch 4: DNA and Chromosomes
1190:21:47, 2 April 2015 (UTC)
1149:08:39, 2 April 2015 (UTC)
1105:08:30, 2 April 2015 (UTC)
1072:07:25, 2 April 2015 (UTC)
1036:06:38, 2 April 2015 (UTC)
971:21:47, 1 April 2015 (UTC)
945:03:24, 1 April 2015 (UTC)
746:Suggesting 2015 GA Review
655:
618:
594:
572:
521:
490:
435:
324:
320:
257:) and why it was removed.
80:Be welcoming to newcomers
2338:section, I've moved the
2265:or similar could help.
898:give it some attention.
314:Today's featured article
2734:GA-Class vital articles
2580:(editor of the journal
2568:of a new book entitled
1016:which in turn links to
598:the Genetics task force
369:Featured article review
251:former featured article
2564:A review by scientist
2340:Functional definitions
2143:Functional definitions
2035:Structure and function
2031:Functional definitions
1294:I am not a big fan of
686:Spoken Knowledge (XXG)
650:Spoken Knowledge (XXG)
615:
591:
255:the nomination archive
75:avoid personal attacks
2789:GA-Class MCB articles
2222:an entire article on
2033:subsection over from
1310:"DNA and Chromosomes"
614:
590:
476:on Knowledge (XXG)'s
469:level-3 vital article
282:good article criteria
203:Auto-archiving period
100:Neutral point of view
2370:In this case, both.
1226:Biochemistry 5th ed.
426:Good article nominee
407:Good article nominee
388:Good article nominee
105:No original research
2633:(5 February 2024).
1782:6.2: RNA to Protein
1493:parameters differ:
862:, Losick R (2013).
858:, Bell SP, Gann A,
316:on October 5, 2004.
1552:Unknown parameter
616:
592:
478:content assessment
325:Article milestones
86:dispute resolution
47:
2375:
2347:
2313:Bohr atomic model
2270:
2154:
2141:I agree that the
2098:overlapping genes
2046:
1946:T.Shafee(Evo﹠Evo)
1892:The guideline is
1843:T.Shafee(Evo﹠Evo)
1825:T.Shafee(Evo﹠Evo)
1724:978-0-8153-3218-3
1642:T.Shafee(Evo﹠Evo)
1538:External link in
1522:978-0-8153-3218-3
1457:978-0-8153-3218-3
1279:T.Shafee(Evo﹠Evo)
1232:T.Shafee(Evo﹠Evo)
1171:genetics glossary
1089:Genetics glossary
1021:Genetics glossary
981:Genetics glossary
872:978-0-321-90537-6
838:978-0-8153-3218-3
795:T.Shafee(Evo﹠Evo)
751:Transcluded from
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550:Molecular Biology
541:Molecular Biology
503:Molecular Biology
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381:September 4, 2012
362:February 25, 2006
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66:Assume good faith
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2224:Overlapping gene
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1884:Opabinia regalis
1861:Opabinia regalis
1857:WP:ACCESSIBILITY
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2226:and another on
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2184:Structural gene
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2578:Philip Ball
2566:Denis Noble
2419:Evo&Evo
2336:Definitions
2228:Nested gene
2208:Gene desert
2192:Gene family
2147:Definitions
2027:Definitions
1898:expand=true
148:free images
31:not a forum
2698:Categories
2668:5 February
2618:References
2576:(2023) by
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2204:Pseudogene
2138:exemplify.
1938:Hidden end
1679:References
1204:References
1144:Maintained
1067:Maintained
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940:Maintained
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393:Not listed
280:under the
2329:Evolution
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472:is rated
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2662:Archived
2604:Genome42
2588:Drbogdan
2538:Genome42
2514:Genome42
2460:Genome42
2405:Genome42
2358:Genome42
2307:Genome42
2293:Genome42
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2125:Genome42
2110:Genome42
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953:Glossary
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186:Archives
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27:article.
2039:History
1955:Adrian
1902:Adrian
1702:Lewis J
1671:Article
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1435:Lewis J
1248:? Uses
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718:Toolbox
577:on the
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333:Process
207:90 days
154:WP refs
142:scholar
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