Talk:Gene/Archive 3

This is an archive of past discussions about Gene. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk page.

Archive 1

Archive 2

Archive 3

Deleted text?

Something is missing in this sentence: "Because they use RNA to store In 2006, French researchers came across a puzzling example of RNA-mediated inheritance in mice." Perhaps someone could fix? Jimjamjak (talk) 15:38, 11 April 2012 (UTC)

It was an edit in March that broke the text, and I have restored the original. Johnuniq (talk) 02:05, 12 April 2012 (UTC)

2012 GA Review

This review is transcluded from Talk:Gene/GA1. The edit link for this section can be used to add comments to the review.

Reviewer: Sasata (talk · contribs) 20:23, 19 August 2012 (UTC)

I'll review this. Sasata (talk) 20:23, 19 August 2012 (UTC)

Before we start, could you please ensure that all paragraphs, and end-of-paragraph sentences have citations? This will help me (and other readers) verify the material. The material is pretty basic, and so a general text like Genes (Lewin) or perhaps a middle-level university genetics text would work nicely for this purpose. Sasata (talk) 23:27, 19 August 2012 (UTC)

There's been no editing activity on this article by the nominator, so I'm going to close this GAN now. Quite a bit a work needs to be with sourcing to meet the GA criteria. Sasata (talk) 15:35, 4 September 2012 (UTC)

Gene exactly?

"though there still are controversies about what plays the role of the genetic material.[1]" Strikes me as a very dubious opening. DNA & RNA are all that need be mentioned (in the beginning) for genes. Prions and epigenetic factors can be left for later. I tried to find out about ref 1, without buying it, by reading articles by the editors. Plutynski is a normal biologist. Sarkar is an anti-reductionist, but his webpage fails to provide any links to his articles. How can a wiki throw doubt about DNA being a genetic material in the introduction? It is similar to starting an AIDS article with a discussion of HIV denialists. OK at the end, not at the beginning. Peggy hopper (talk) 03:23, 13 April 2013 (UTC) "

Yes, this is terrible in the opening. Perhaps something like "Although information is transmitted from parent to offspring in many ways, a gene is... " It has been a while since I have looked at this article, maybe I'll come back to this. Abductive (reasoning) 04:33, 13 April 2013 (UTC)
- I've deleted this considering there is no known controversy about DNA being the genetic material and considering there were no responses to this post giving any reason to keep it. I can see how it might be handy to have mention of other mechanisms of inheritance such as epigenetics somewhere else in this article but I'll leave that for other people if they so choose. 2403:7900:ADE1:A1DE:250:56FF:FEA6:3B1F (talk) 09:09, 19 March 2014 (UTC)

"The genetic code is nearly the same for all known organisms." is false. Human mtDNA has a different genetic code than human nuclear DNA. This discovery was crucial in proving the symbiotic origin of eukaryotes. (ref. Lynn Margulis) (Comp Biochem Physiol B. 1993 Nov;106(3):489-94. Evolutionary changes in the genetic code. Jukes TH, Osawa S.) Peggy hopper (talk) 04:03, 13 April 2013 (UTC)

Here "nearly" encapsulates that fact. Readers can click on genetic code to find out more. Abductive (reasoning) 04:33, 13 April 2013 (UTC)

discontinuing inheritance

The history section uses the expression discontinuing inheritance. I guess this means that a phenotypic trait can be observable in one generation, "disappear" i a following generation and then reappear in an even later generation. Regardless of whether this or something else is meant, it needs to be explained in a way that is more understandable for the general reader. — Preceding unsigned comment added by Ettrig (talk • contribs)

Should be 'discontinuous', and you're right. There's a lot of clunky prose in this article at the moment. Opabinia regalis (talk) 09:12, 7 April 2015 (UTC)

2015 GA Review (April)

This review is transcluded from Talk:Gene/GA2. The edit link for this section can be used to add comments to the review.

Reviewer: Cerebellum (talk · contribs) 01:25, 10 April 2015 (UTC)

Hello! I will be reviewing this article. --Cerebellum (talk) 01:25, 10 April 2015 (UTC)

GA review (see here for what the criteria are, and here for what they are not)

It is reasonably well written.
a (prose, no copyvios, spelling and grammar): b (MoS for lead, layout, word choice, fiction, and lists):
In the "Translation" section you used the word "ligates," which I do not know. Is there a more common word you could use there? Also, the first sentence of the "Gene targeting and implications" section left me confused. You say that gene targeting provides "mouse models for studying the roles of individual genes," but the sentence seems abrupt and I'm not really sure why we are talking about mice all of a sudden or what mouse models are. Maybe start off with a broad intro sentence to transition from the previous section on genes in evolution, and explain why we are now talking about mice whereas the rest of the article seemed to be about genes in all forms of life. As far as layout goes, I recommend putting the two sections on the concept of a gene ("Changing concept" and "evolutionary concept of a gene") in sequence, right now they are split up by the gene targeting paragraph.
It is factually accurate and verifiable.
a (reference section): b (citations to reliable sources): c (OR):
I think the 2012 review was too harsh on this but some of the same criticism applies. Per WP:SCG you don't need a ref for every paragraph if the information all comes from a basic textbook, but it's not clear to me where some information comes from. For example, the section on Mendelian inheritance has no references. I assume most of the information in later sections can be found in Molecular Biology of the Cell, but is that the case for Mendelian inheritance as well? Please add at least one reference to that section. Also, you always need to cite direct quotations, so please provide a reference for the Williams definition of a gene in the "Evolutionary concept of a gene" section.
It is broad in its coverage.
a (major aspects): b (focused):
It follows the neutral point of view policy.
Fair representation without bias:
It is stable.
No edit wars, etc.:
It is illustrated by images and other media, where possible and appropriate.
a (images are tagged and non-free content have fair use rationales): b (appropriate use with suitable captions):
Great use of diagrams!
Overall:
Pass/Fail:
~~Good article, but I'm putting it on hold for now so you can make some tweaks. Cerebellum (talk) 17:15, 11 April 2015 (UTC)~~

Thanks everyone for your work on this article this week, in particular BlueMoonset for identifying the copyright issue, Opabinia regalis for correcting it, and Evolution and evolvability for fixes throughout. Unfortunately some of the issues from the review, in particular regarding sourcing, have not been fixed. Because of that I have to fail the article for now, but please let me know if you renominate it and I'll take another look. --Cerebellum (talk) 03:26, 19 April 2015 (UTC)

Comment

I thought I'd take a look after recent exchanges about the nomination on the GAN talk page, which ended by noting that the nomination was under review. It's an impressive article, but at the moment does not meet some of the criteria

It seems to me that the article has a classic violation of WP:LEAD, a GA criterion: Apart from trivial basic facts, significant information should not appear in the lead if it is not covered in the remainder of the article. The lead's third paragraph is solely about a topic, "big genes", that is only mentioned there; I could not find the phrase "big genes" anywhere in the body.

I'm completely at sea as to the sourcing, since this is a very long article where so much of the material is not sourced; I don't see how any assumption can be made about what came from the textbook (which is only cited twice) and what didn't. (Also, textbooks are big: these citations should be to a page or page range, not to an immense tome where it's impractical to find the information being referenced.) I think that every subsection should be sourced, not merely every section, and more than a source for a parenthetical comment at that (as in "Genetic code", which is the only citation in the entire section). Genes are complicated and involve technical explanations, as is plain in this article; there needs to be concomitant sourcing. As it says, Complex, current, or controversial subjects may require many citations in the lead; this is even more true of the article body of a very complex scientific topic. BlueMoonset (talk) 23:46, 12 April 2015 (UTC)

I just ran Earwig's Copyvio Detector on the article, and found significant copyvio in the article, enough to stop this nomination in its tracks until a thorough check and cleanup job has been completed. For example, a great deal of the "Gene targeting and implications" section is taken from the FN24 (www.biolsci.org) source; the second paragraph is copied almost verbatim in its entirety, as you can see in this report, and much of the first paragraph is very like FN25. BlueMoonset (talk) 03:23, 13 April 2015 (UTC)

Cleaned up the gene-targeting section (which was also rather undue). I had planned/promised to work on the text of this article awhile back but just haven't had the time. Images look fantastic though! Opabinia regalis (talk) 19:41, 15 April 2015 (UTC)

Prose suggestions

Below are the main issues that I've spotted or now. Hopefully they're logically laid out. Let me know if you agree or disagree with any. T.Shafee(Evo﹠Evo)^talk 00:02, 4 April 2015 (UTC)

RNA genes

Certainly an important topic but it is currently brought up in several places.

History
Physical definitions#RNA genes and genomes in the world (before description of protein-coding genes)
Changing concept

This leads to it being massively over-weighted in the article when really it needs only to be a single paragraph total. RNA genes are also not referred to in the images at all. We also need to clearly distinguish between a gene encoded by RNA (e.g. genes in an RNA virus) versus a gene that encodes a functional RNA product (e.g. genes for tRNAs or siRNAs).

History and concepts

Perhaps the evolutionary concept and changing concept sections can be folded into the history section? That way the History section is structured:

How genes were understood before we knew about DNA
The understanding that DNA genes that encode proteins
Minor expansion of the simple model of #2 (RNA genomes, functional RNAs, splice variants etc).

Descriptions of DNA

There seems to be some overlap between Physical definitions#Functional structure of a gene and Gene expression#Genetic code. I would suggest that the descriptions of nucleotide biochemistry could be reduced. I think it would be better to increase the focus on larger structure (promoters, ORFs, terminators, enhancers, introns etc).

Mutation

Perhaps this can be combined into either replication or evolution sections?

Agreed with pretty much all of this. I made some grouchier and less useful notes in my sandbox last week, but haven't had time to actually do anything about it yet. Opabinia regalis (talk) 03:22, 5 April 2015 (UTC)

Good work on today's edits Opabinia regalis. I'm still thinking of moving the evolutionary concept and functional concept sections up into History since they seem to fit with a continuing evolution of our understanding. However I don't want to make the history section balloon in size again. T.Shafee(Evo﹠Evo)^talk 12:30, 16 April 2015 (UTC)

Thanks! I did some overall restructuring without changing the text much, moving the bottom evolutionary gene section into history and reorganizing some of the middle. I think some of the power of those great gene structure diagrams was being lost by having such detailed information before basics like transcription.

Still not sure what to do with the mutation section, but the article is really missing a discussion of sequencing and sequence analysis and homology, so maybe that (ie, the interpretation of variation) and mutation can go under a new top-level section on something like "sequence variation"? Opabinia regalis (talk) 06:52, 18 April 2015 (UTC)

In a family of four kids, one will be sick

Well, no, but that seems to be what this graph implies. The alt text is equally problematic, and I've only just somewhat clarified this in the caption. I think the notion of probability needs to be more clearly communicated. Samsara 05:01, 19 April 2015 (UTC)

@Samsara: Not sure what you mean here. I don't think anybody's substantively edited that section of text yet, but the image seems clear enough. Is the issue that "affected" implies a disease but the description is just of two alleles, without specifying the trait? Representing the possible outcomes is pretty standard in this kind of diagram; I don't think it implies a probability error any more than a Punnett square does.

The only criticism I have of the image/alt text is that "white" might not be the best color to use as an illustration, since "white" is in fact the common name of a trait some humans have. Opabinia regalis (talk) 05:48, 19 April 2015 (UTC)

My concern is that there is no explicit statement that this deals with probabilities. A naive reader might think that if you have four kids, they turn out 1:2:1. The "alt" parameter in the article in fact reinforces this idea by explicitly talking about four children. But there are no four children in reality. There are four probabilities. Unfortunately, if you take a close look, this is a problem with most representations of this kind. Thinking outside the box, I wonder if it wouldn't make sense to have a graph that shows a number of different families, where the sum of the children ends up in a 1:2:1 ratio. Also, that would allow us to have green male with blue female as well as green female with blue male pairings, if that helps to avoid the impression that this refers to any real trait. Samsara 06:13, 19 April 2015 (UTC)

Hmm. The alt text, as I understand it, is intended to describe rather than interpret the image, and should not duplicate material in the caption. For that purpose the current text seems adequate. Your suggested expanded graph sounds a little too bulky for this article, but could fit well in Mendelian inheritance or genetics (which really needs a going-over to reduce redundancy with this article). Opabinia regalis (talk) 21:17, 19 April 2015 (UTC)

At least the text IN the figure should use plural forms rather than singular. --Ettrig (talk) 12:24, 27 April 2015 (UTC)

Clarify the difference among gene, locus and allele (previously GA3)

Note: comments below were initially added as the Good Article review in error. See here for details.

Well, allele seems to be clearly defined. What about gene and locus? In a classical sense, a locus can be a placeholder for the corresponding alleles. Is it also applicable to a gene? If so, what is the difference? If no difference, locus shall be a synonym of gene. By the way, what about a null allele, where a placeholder can be nowhere on the DNA? I am totally confused. ヒストリ案 (talk) 13:31, 3 June 2015 (UTC)

Good point, We only mentioned the term locus once! I'm adding a section on Locus/Allele/Gene clarification to the Gene#Chromosomes and Gene#Mendelian inheritance sections. I think that probably explaining null alleles is beyond the scope of this article, but I'll make sure that it comes up in both the allele and locus articles. T.Shafee(Evo﹠Evo)^talk 12:08, 5 June 2015 (UTC)

T.Shafee(Evo﹠Evo), thank you for improvement. BTW, what happen if "quantitative trait loci" taken into account? Is it a completely different concept, or share some? If the former is the case, why do we use the same term? If the latter, the idea of "a" gene is already confused... ヒストリ案 (talk) 13:35, 8 June 2015 (UTC)

@ヒストリ案: The term Quantitative trait locus isn't quite the same as a gene. A QTL is a region of DNA on a chromosome known to be correlated with some phenotype change, but it can be a gene, or several genes, or part of a gene. Identifying the QTL of some phenotype can be a first step in finding a gene related to that trait. It's actually a bit of an old fashioned term which was used more extensively when we weren't able to exactly define what the DNA sequence of the gene was. It is probably more relevant to the genetics page but could certainly go in the 'see also' section for the moment. T.Shafee(Evo﹠Evo)^talk 13:04, 10 June 2015 (UTC)

ヒストリ案, I notice that this is your first-ever edit under this account, and perhaps ever on Wikipedia. Are you prepared to fully review this nomination according to the WP:WIAGA criteria, which is what is required here? If not, we should probably get a new reviewer to undertake the complete review beyond your initial questions. Thanks. BlueMoonset (talk) 17:07, 5 June 2015 (UTC)

BlueMoonset, I apologize for misplacement of my comment. Should I replace all the above somewhere appropriate, or delete them? Thank you for advice. ヒストリ案 (talk) 13:27, 8 June 2015 (UTC)

@ヒストリ案: Your comments are still useful and definitely won't be deleted. The link that you clicked to create this section of the page are part of a process called Good article review in which an editor volunteers themself to do a thorough read-through and assessment of whether the page should be promoted to be Good article status (for example this previous review). If you were not intending to nominate yourself as the GA reviewer then we can just move your comments into the non-review part of the gene talk page. T.Shafee(Evo﹠Evo)^talk 12:06, 9 June 2015 (UTC)

Any progress so far? The current lede seems to define that a gene is a locus. Is that widely accepted, or not? --Wordmasterexpress (talk) 09:22, 5 October 2016 (UTC)

A paper that clarifies the terminology (incl. gene, locus and allele among of the tens of other terms): Genetic Terminology (2012). Cheater no1 (talk) 18:39, 9 March 2020 (UTC)

Image suggestions

Below are my opinions for changes that could be made to the article's images. T.Shafee(Evo﹠Evo)^talk 00:40, 4 April 2015 (UTC)

More information Function, Percent of genome ...

===Lead image===

I don't think introns need to be introduced in the very first image. Certainly not in favour over other genetic elements like promoters.

Idea: Chromosome unravelling to DNA as in present image, but simplest possible representation of a gene. (Perhaps relative scales indicated?) T.Shafee(Evo﹠Evo)^talk

I made a new version for this one as well. The caption might need some minor editing. --SPLETTE :] ^{How's my driving?} 01:47, 6 April 2015 (UTC)

@Splette: I like your image. I've been making something similar but aiming to simplify down to the most basic information for a lead image: Genes are segments of DNA and they are stored in chromosomes. I think that introns and nucleosomes should be saved for a later image, otherwise we should probably have promoters etc in there. The chromosome is from an SEM and the DNA is from PDB: 3BSE. I've used your gradient and curly-bracket notation idea and a similar unravelling chromosome. Could use physical nanometer scales instead of bp scales but I think it makes it easier to compare the sizes. T.Shafee(Evo﹠Evo)^talk 13:11, 6 April 2015 (UTC)

I've changed the lead image on the article to File:Chromosome DNA Gene.svg but I'd like to be clear, that I'm completely happy to alter it back if people object. I just think that it's best to have something simple as the first image (ie without nucleosomes of introns). T.Shafee(Evo﹠Evo)^talk 04:46, 30 May 2015 (UTC)

DNA nucleotides

This definitely doesn't need to be in the lead section and elements needs to relate to other images.

Idea: If we keep an image showing this, something similar to current codon image but with nucleotides, 'letters-on-a-ribbon', and codons explained in one image T.Shafee(Evo﹠Evo)^talk

Here is an image attempting to relate the general helix structure of DNA to the chemical structure and base pairing. T.Shafee(Evo﹠Evo)^talk 09:52, 17 April 2015 (UTC)

Gregor Mendel

You're all good Gregor. You can stay as you are.

Punnett square

Currently odd colour choices. Significance of the background colours not clear.

I agree and will make a new version of this. Also, the current image only shows the F2 generation. Perhaps something a bit similar to this or this might be nice to add. I'll give it a try... --SPLETTE :] ^{How's my driving?} 23:02, 5 April 2015 (UTC)

I think it would be worth avoiding including to much detail since its not the main focus of the article. In many ways simplicity and clarity may be more important. T.Shafee(Evo﹠Evo)^talk 08:51, 6 April 2015 (UTC)

Gene structure

Currently no image in the article uses the traditional 'arrow' symbol of an ORF or shows all the elements of a gene together

Idea: A more comprehensive diagram with all the main elements of a protein-coding gene together (Protein coding region / ORF, regulatory sequence, promoter, enhancer, silencer, operator, RBS, terminator, 5' UTR, 3' UTR, start codon, stop codon, intron, exon). Hopefully it'll not get too cluttered T.Shafee(Evo﹠Evo)^talk

I've tried to make a pretty comprehensive summary image of genetic elements. Since it contains so many annotations I'm thinking of making it interactive. Any improvement suggestions welcomed. T.Shafee(Evo﹠Evo)^talk 03:33, 7 April 2015 (UTC)

Looks good, but in this and other diagrams, I think it is important to use as large a font as possible so that the text is readable without having to increase the size of the diagrams to the point that they start to overwhelm the rest of the article. Boghog (talk) 04:04, 7 April 2015 (UTC)

Liking this – gene structure seems to confuse students, so having it all together in one figure is really valuable.

Ideally the filename and caption should both make it clear that this is eukaryotic gene structure.
I'd say the sequences in yellow determine where and when transcription occurs, which is more specific than putting it in terms of gene expression.
The UTRs are everything upstream of AUG and downstream of the stop codon, not just the elements indicated in blue. My understanding is that they're more involved in where/when/how much translation occurs, and not so much in which portions are translated, which is more about the start and stop codons.
Is the terminator sequence actually included in the pre-mRNA and mature mRNA? (I'm not certain either way.)
I'm not sure how you'd indicate this, but exons are all the bits of the pre-mRNA included in the mature mRNA, not just the coding regions.
It's arguably an over-simplification to depict "splicing" as the difference between pre-mRNA and mature mRNA. I'd relabel that arrow at the left of the figure "post-transcriptional processing" (a misnomer, but the accepted term). If space and clarity permit, maybe add the 5'-cap and 3'-tail, too.
You could draw the protein as a globular red squiggle, which would emphasise the relationship between the linear CDS and the linear polypeptide.

I'm a pedant and a perfectionist, but you solicited suggestions

. Adrian J. Hunter^{(talk•contribs)} 05:51, 7 April 2015 (UTC)

I'm really short on time so I have the lamest criticism ever: there's a typo. "Promotor". Also agree with the protein-as-squiggle idea. Opabinia regalis (talk) 06:23, 7 April 2015 (UTC)

Thank you all for the suggestions. I've made an updated version with them addressed. Larger font (slightly) | Eukaryotic labelled | clarified transcription regulation vs translation regulation | fixed 3'UTR | changed splicing to all processing | checked terminator (is included in 3' UTR) | added protein squiggle | corrected promotÖЭØr spelling | corrected protein coding region vs ORF. I'm also working on a prokaryote version for comparison. T.Shafee(Evo﹠Evo)^talk 09:55, 10 April 2015 (UTC)

I have also generated a prokaryotic version of the diagram. Let me know if I've missed nay errors! T.Shafee(Evo﹠Evo)^talk 08:19, 11 April 2015 (UTC)

Since there were so many technical terms in the diagrams, I've generated Wikilinked versions (using Template:Annotated_image_4) of the images: Template:Eukaryote gene structure and Template:Prokaryote gene structure

RNA codons

It's not immediately obvious that the letters relate to the nucleotides in the DNA image. Similarly, it's not obvious that the right hand side words are amino acids in a protein.

Idea: Either combine with the DNA image or with a more general transcription/translation image T.Shafee(Evo﹠Evo)^talk

I really dislike this image. Strands of nucleic acid form helical structures when complementary strands undergo Watson-Crick base pairing. As far as I'm aware, there's no reason an isolated single strand should form a helix. Adrian J. Hunter^{(talk•contribs)} 02:39, 4 April 2015 (UTC)

Yes, you are right. I will make a new version of this image. --SPLETTE :] ^{How's my driving?} 15:11, 4 April 2015 (UTC)

I made a new diagram. The RNA is not shown in a helical form anymore but slightly wavy and in 2D. --SPLETTE :] ^{How's my driving?} 11:44, 5 April 2015 (UTC)

Suggestion: I like it, though perhaps it would be easier to follow the flow the causality flowed downwards? Either way, could probably replace this image in other articles too. T.Shafee(Evo﹠Evo)^talk 12:58, 5 April 2015 (UTC)

You mean like in Fig 1 here to have the RNA on top and codons and amino acids below, right? Yes, I agree and have modified my pic accordingly (might need to reload this page in the browser to show up the change). --SPLETTE :] ^{How's my driving?} 22:36, 5 April 2015 (UTC)

Awesome work!

Adrian J. Hunter^{(talk•contribs)} 01:06, 6 April 2015 (UTC)

Function pie chart

No fundamental problem with the image, but is there something more useful that we could show? It's no better or worse than the old gene number table that the article had 10 years ago.

I have some doubts about how useful the information in this figure is to the readers of the articles. Does the average reader really care about those numbers? What does it tell him, that 3.2% of the human genome are oxydoreductases? And who (other than a biologist) knows what an oxydoreductase is in the first place? Why was the old gene number table removed from the article? To me it seems much more interesting to the average reader. It has some interesting numbers, that readers might not be aware of for example that a plant genome might be twice as big as that of us humans. Or that some viruses suffice with only a dozen genes...

Either way, as I already wrote below. If you decide to keep the "Human genome by function" data, it should not be presented as a pie chart, but as a bar chart. I could make one once there's a consensus. --SPLETTE :] ^{How's my driving?} 23:02, 5 April 2015 (UTC)

Function	Percent of genome
signaling	30.4%
enzyme	24.0%
unclassified	21.3%
structure	14.0%
transport	9.7%
immunity	0.6%
total	100.0%

The relative sizes of genomes and break down of function within the human genomes are both potentially interesting information to include. I agree that the existing function pie chart is too detailed (i.e., contains too many classes). At this risk of introducing original research, one could use a higher level classification pie chart. For example combine all the enymes into one class:

enzymes: hydrolase, isomerase, ligase, lyase, oxidoreductase, phosphatase, protease, transferase
signaling: calcium-binding protein, enzyme modulator, receptor, signaling molecule, transcription factor, transmembrane receptor regulatory/adaptor protein
structure: cell adhesion molecule, cell junction protein, cytoskeletal protein, extracellular matrix protein, nucleic acid binding, structural protein
transport: membrane traffic protein, transfer/carrier protein, transporter
unclassified: chaperone, storage protein, surfactant, unclassified, viral protein

I don't think there is much controversy combining enzymes, but some of the other groupings may be questionable. Ideally we would need to reliable source to support a higher level grouping, but I have not as yet found any. Boghog (talk) 13:35, 6 April 2015 (UTC)

Just checked a few textbooks without any luck. Given that this article need not be human-centric, an alternative would be to use a genetics model organism like E. coli or yeast. I've got a 2015 genetics textbook that divides the genes of E. coli into 12 not-too-esoteric classes, plus a fat 33% "unknown". Adrian J. Hunter^{(talk•contribs)} 06:41, 7 April 2015 (UTC)

Thinking about it, we could helpfully make a combined image comparing the gene number for different organisms (refs:^[1]^[2]) with an expanded break-down of gene proportions in humans. I could put it together into a hierarchical treemap diagram. T.Shafee(Evo﹠Evo)^talk 03:32, 19 April 2015 (UTC)

[1]
Pertea, Mihaela; Salzberg, Steven L (2010). "Between a chicken and a grape: estimating the number of human genes". Genome Biology. 11 (5): 206. doi:10.1186/gb-2010-11-5-206.{{cite journal}}: CS1 maint: unflagged free DOI (link)
[2]
"What is the human genome and how big is it?". Edinformatics. Retrieved 19 April 2015.

I've made a treemap of relative genome sizes. It's not perfect but it's better then file:Human_genome_by_functions.svg. T.Shafee(Evo﹠Evo)^talk 23:45, 26 April 2015 (UTC)

Looks nice! Definitely better than the ugly pie chart. (The only good pie chart ;) When I noticed you had updated this section I was going to add the updated gene count from the later map of the rice genome (PMID 16100779; 37,544 protein-coding genes) but it looks like you used the original here. Do you think that would change the apparent proportions much? Opabinia regalis (talk) 08:02, 28 April 2015 (UTC)

RNA-coding gene

no image yet

I think it would be good to have some side-by-side comparison of a protein-coding gene vs an RNA gene (e.g tRNA).

Idea: Compare protein/RNA coding genes. Show transcription/translation with (DNA-->RNA-->Function) next to (DNA-->RNA-->Protein-->Function) T.Shafee(Evo﹠Evo)^talk

I've generated an image that summarises the difference between an protein coding gene and a gene that directly codes for a functional RNA. Currently in roughly same format as the other images that have been produced so far. As always, any improvement ideas welcome. T.Shafee(Evo﹠Evo)^talk 07:33, 7 April 2015 (UTC)

Inheritance

no image yet

There's currently no image actually showing genes being inherited from parent to offspring. I think this could be more useful that the Punnett square

Idea: Maybe something vaguely like File:Autosomal_dominant_-_en.svg from the Dominance_(genetics) or sex linkage pages. T.Shafee(Evo﹠Evo)^talk

I've added in this image for the moment since I think it's more useful to a beginner reader than the punnet square (at the risk of being too human-centric). T.Shafee(Evo﹠Evo)^talk 12:38, 13 April 2015 (UTC)

Close

Hey there, I'm a scientific illustrator and just by chance came across this article and saw you are pushing it to GA. Here's a selection of the illustrations I made for Wikipedia. As time permits I might be able to help out with improving the images of this article. Once you've decided which ones need to be improved and how, leave me a message on my talk page if you need any help (I'm not online here that often anymore nowadays). PS. The pie chart should definitely be replaced with a (horizontal) bar chart. See here why. -- SPLETTE :] ^{How's my driving?} 01:56, 4 April 2015 (UTC)

I'm currently working on a few of the images.

Lead image (sorry to accidentally compete User:splette, perhaps we can combine?)
DNA structure
RNA gene

Hopefully should be done in next couple of days. T.Shafee(Evo﹠Evo)^talk 09:06, 6 April 2015 (UTC)

Refs

[1]
Watson, JD, Baker TA, Bell SP, Gann A, Levine M, Losick R. (2004). “Ch9-10”, Molecular Biology of the Gene, 5th ed., Peason Benjamin Cummings; CSHL Press.
[2]
"Integr8 - A.thaliana Genome Statistics:".
[3]
"Understanding the Basics". The Human Genome Project. Retrieved 26 April 2015.
[4]
"WS227 Release Letter". WormBase. 10 August 2011. Retrieved 2013-11-19.
[5]
Yu, J. (5 April 2002). "A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica)". Science. 296 (5565): 79–92. doi:10.1126/science.1068037.
[6]
Anderson, S.; Bankier, A. T.; Barrell, B. G.; de Bruijn, M. H. L.; Coulson, A. R.; Drouin, J.; Eperon, I. C.; Nierlich, D. P.; Roe, B. A.; Sanger, F.; Schreier, P. H.; Smith, A. J. H.; Staden, R.; Young, I. G. (9 April 1981). "Sequence and organization of the human mitochondrial genome". Nature. 290 (5806): 457–465. doi:10.1038/290457a0.
[7]
Adams, M. D. (24 March 2000). "The Genome Sequence of Drosophila melanogaster". Science. 287 (5461): 2185–2195. doi:10.1126/science.287.5461.2185.
[8]
Pertea, Mihaela; Salzberg, Steven L (2010). "Between a chicken and a grape: estimating the number of human genes". Genome Biology. 11 (5): 206. doi:10.1186/gb-2010-11-5-206.{{cite journal}}: CS1 maint: unflagged free DOI (link)

Revision of lede

Reviewer: Cerebellum (talk · contribs) 16:46, 25 July 2015 (UTC)

2015 GA Review (July)

This review is transcluded from Talk:Gene/GA4. The edit link for this section can be used to add comments to the review.

Sorry it took me so long to get to this, but I'm ready to do a second review now. --Cerebellum (talk) 16:46, 25 July 2015 (UTC)

GA review (see here for what the criteria are, and here for what they are not)

It is reasonably well written.
a (prose, no copyvios, spelling and grammar): b (MoS for lead, layout, word choice, fiction, and lists):
In the first sentence of the lead, would it be OK to replace A gene is a locus (or region) of DNA with A gene is a segment of DNA? It would be simpler, and it's what the caption of the first image says. However, if there's a big difference between the terms locus and segment then it can stay as it is. Other than that though, I made a few minor changes but the prose is generally good.
It is factually accurate and verifiable.
a (reference section): b (citations to reliable sources): c (OR):
Great job specifying the page numbers from Molecular Biology of the Cell! I added a couple of refs to the section on Mendel.
It is broad in its coverage.
a (major aspects): b (focused):
It follows the neutral point of view policy.
Fair representation without bias:
It is stable.
No edit wars, etc.:
It is illustrated by images and other media, where possible and appropriate.
a (images are tagged and non-free content have fair use rationales): b (appropriate use with suitable captions):
As before, the images are fantastic.
Overall:
Pass/Fail:
Thanks for all the work on this, and sorry again to keep you waiting so long for a review! Everything looks good to me though, so I'm closing this review as pass and promoting the article to GA. --Cerebellum (talk) 17:22, 25 July 2015 (UTC)

Thanks

Thank you to everyone who aided in getting this article up to GA level. It was definitely a job worth doing and hopefully sets a reasonable standard for the high-importance biology articles. T.Shafee(Evo﹠Evo)^talk 00:02, 27 July 2015 (UTC)

More misc prose/additions

in "Structure and Function" The term mRNA appears without any further explanation, for a non biologist reader (like me) this is irritating. — Preceding unsigned comment added by 141.42.200.71 (talk) 07:01, 22 September 2015 (UTC)
The Williams quote is widely cited elsewhere as p24 of the 1966 edition, but I don't have a copy of the book and it isn't in Google Books. Can anyone confirm?
~~I don't have a copy of Watson 2013 and can't preview that through Google Books either, so I'll leave going through that to those with a taste for lots of footnotes.~~
Adding citations to the Alberts edition in NCBI is a good idea also, though in the absence of numbered chapters/sections the {{rp}} solution to repetitive citations is less appealing. Opabinia regalis (talk) 06:52, 18 April 2015 (UTC)
~~Add paragraph on gene duplication, de novo genes, pseudogenes (after sequence homology?)~~
~~Do we need something about genetic disorders? Currently there is the inheritance image, but that only refers to a 'trait', not a disorder, and there's nothing specifically about molecular mechanism.~~
Companion article genetics is highly redundant with this one.

I got distracted for a bit but have been meaning to get back to this. I think the above is the rest of my intended new content list. Any other suggestions? Opabinia regalis (talk) 07:03, 5 May 2015 (UTC)

Ok, the article has come a long way since we started.

~~I agree that we need something on genetic disorders.~~
~~Possibly also a sentence or two on gene therapy in the engineering section since it's something many people will have heard about?~~
~~Half of the sections have a {{main}} template - do we really need them?~~

I don't think there are any other major rearrangements of the sections left. It looks like mostly clarifying language, some small additions and adding the final references. T.Shafee(Evo﹠Evo)^talk 12:57, 15 May 2015 (UTC)

I did see this; I just haven't had time to actually write anything. Googling for refs is a lot easier :) Opabinia regalis (talk) 07:03, 20 May 2015 (UTC)

Is gene a locus or a segment, or something more generic?

This topic contains two definitions at first paragraph and as figure legend:

A gene is a locus (or region) of DNA that encodes a functional RNA or protein product, and is the molecular unit of heredity.

A gene is a segment of DNA that encodes function. A chromosome consists of a long strand of DNA containing many genes. A human chromosome can have up to 500 million base pairs of DNA with thousands of genes.

Do they define the same thing? If so, why two different expressions? Well, those represent as if a locus is a segment. Is that so?

A gene can be just a segment with a fixed position and length on genomic DNA in very simple cases. However, the nature is often more complex.

If a gene is really a segment of DNA, is a multi-exonic gene a segment? Then what distinguishes multi-cistronic genes from exons? What about nested genes? What about overlapped genes? What about a trans-spliced gene which often have discontinued fragments on different chromosomes? They are not rare cases.

I think the stated definition is just a WORKING HYPOTHESIS with too much simplification.

Finally, this is my opinion: When Mendel proposed the concept of gene (though he did not use that term), it was a concept of atomic inheritable unit. In genetics, including molecular, it is still so, except modification for quantitative trait loci.

The definition on Wikipedia is biased too much toward molecular biology, and unexplainable phenomena are left by the definition.

Wordmasterexpress (talk) 09:00, 8 April 2016 (UTC)

@Wordmasterexpress: Interesting points. Both "region" and "segment" are used as non-technical synonyms for locus. Although both are vague, I agree that "region" is slightly more appropriate since it is broad enough to encompass the various oddities like nested genes etc. I've therefore updated the lead image's caption. As for the definition overall: There has been a strong molecular biology focus on the definition of a gene since the modern evolutionary synthesis, so it has shifted away from the original Mendelian definition. We've preferenced the MBOC definition as representing the mainstream scientific consensus definition. As you say, there is always going to be difficulty in precisely defining a gene, since nature is complicated. A simple and broad definition is need in the lead, so we attempt to cover more complicated scenarios in the Gene#Functional_definitions section. T.Shafee(Evo﹠Evo)^talk 05:36, 9 April 2016 (UTC)

@Evolution and evolvability: Thank you for edits. Now I have more questions. The lead seems to say a gene is a locus and a locus is equivalent to a region. Is that so? If yes, genes are a subset of loci. I doubt the second point that a locus is equivalent to a region, but it may depending on the definition. Either positive or negative, the lead is better clarifying those, I would suggest. --Wordmasterexpress (talk) 01:43, 11 April 2016 (UTC)

Proposed merge with Genomic organization

Not only proteins

The first sentence says that a gene codes for a protein. The last paragraph says that this is under discussion, that a gene also can code for functional non-coding RNAs. But that discussion was concluded long ago. I checked several of my rather oldish biology books. For example, the glossary in Hartwell, Hood, Goldberg, Reynolds, Silver, Veres; Genetics, from Genes to Genomes; 2004: ... segment of DNA in a discrete region of a chromosome that serves as a unit of function by encoding a particular RNA or Protein. --Ettrig (talk) 09:18, 28 October 2017 (UTC)

Different versions of the article have mentioned RNA genes in the lead e.g.

"A gene is a locus (or region) of DNA that encodes a functional RNA or protein product" Special:Permalink/702868373
"The word is used extensively by the scientific community for stretches of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) that code for a polypeptide or for an RNA chain that has a function in the organism." Special:Permalink/666720556

There is the later section on RNA genes too. After browsing through the history, it seems that mentions of RNA genes in the lead are frequently removed to "improve clarity". Personally I think these not mentioning them introduces inaccuracy. It may be best to involve other editors of the article in this discussion to prevent any rapid reversions e.g. @Evolution and evolvability: & @Headbomb: who mention RNAs in their edits. --Paul (talk) 08:59, 29 October 2017 (UTC)

@Ettrig: That's a great improvement, I'm not sure about this sentence "A gene is a subsequence of DNA which codes for a molecule that has a function". What about RNA viruses? Maybe add a "usually" in there somewhere. --Paul (talk) 21:52, 29 October 2017 (UTC)

Agree, RNA should be included. This is an omission of the same kind as the one I fixed. I will add or RNA. This is a bit crude. But my feeling is that nucleotides is less well known. --Ettrig (talk) 07:15, 30 October 2017 (UTC)

Added RNA, with some difficulty. The current text does not cover the retrovirus case. I now empathize with the clarity argument. We want the first sentences to be correct and also very succinct and accessible. --Ettrig (talk) 07:22, 30 October 2017 (UTC)

Hello all. Sorry to be late to the thread! Great work so far. You're correct that it was high time for the lead to be brought into line with the rest of the article. My main outstanding issue is the term "subsequence" in the first sentence. I think that "sequence" would suffice and I don't think extra useful specificity is added to the definition by using "subsequence". Indeed it's the only time the term is used in the article. T.Shafee(Evo&Evo)^talk 00:36, 31 October 2017 (UTC)

Yes, indeed. And thanks to @Chiswick Chap:. --Ettrig (talk) 12:43, 31 October 2017 (UTC)

Definitions

Notified: WP:MCB, WP:GEN, WP:MED

The definition of gene is probably one of the most important parts of this article. At the risk of opening Pandora's box on, it might be worth checking that we're using the best available definitions. Currently we list three definitions:

Gene#Lead - A gene is the molecular unit of heredity of a living organism.^[1]
Clear and simple, but lacks any mention of function.
Gene#Lead - Therefore, a modern working definition is "a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and/or other functional sequence regions".^[2]^[3]
The only definition that we are directly quoting from a reference and seems verbose to me.

The use of "associated with " feels unnecessarily confusing.

Also, close to tautology: "genomic sequence... which is associated with... other functional sequence regions".
Gene#Functional definitions - A broad operational definition is sometimes used to encompass the complexity of these diverse phenomena, where a gene is defined as a union of genomic sequences encoding a coherent set of potentially overlapping functional products.^[4]
It think this is fine but omits heredity. Does it need to? What phenomena fit this definition but are not heritable?

Exclusion of regulatory sequence doesn't seem hugely necessary.

Overall I think that we do need a simple layman's definition as well as a more nuanced, broader, technical definition. Both probably need to encompass:

Molecular / sequence / locus / encoding
Heritable
Functional / expressed

T.Shafee(Evo﹠Evo)^talk 01:10, 14 June 2015 (UTC)

perhaps?..--Ozzie10aaaa (talk) 01:22, 14 June 2015 (UTC)

You'd think that developing a really good single-sentence definition would be really important, but... I just can't get myself too worked up about it. It's a fuzzy concept; people use slightly different definitions for different purposes; the question of 'what do we annotate as a gene' is subtly but significantly different; etc. etc. I looked around a little specifically in the education literature and found this hilarious "simplified" model: DOI 10.1007/s11191-008-9161-7. (This thesis studying representations of genes in textbooks is pretty interesting: Not so useful for our purposes, though.) Opabinia regalis (talk) 05:38, 16 June 2015 (UTC)

You're probably right. I might still have a crack at polishing the currently existing sentences over the next few days, but we do a pretty decent job of describing the key elements in the functional structure section. Also, one of the papers that comprises the thesis you mentioned was actually a pretty good history of the definition. T.Shafee(Evo﹠Evo)^talk 12:08, 19 June 2015 (UTC)

I've now updated the definitions in the article:

a region of DNA that controls a discrete, hereditary trait in an organism
based on the the definition from the MBOC glossary since I think this more clearly includes the key elements^[5]^: Glossary
any discrete region of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product or by regulating expression
still based on the same references, but reworded to simplify the language and sentence structure whilst still being thorough.
a union of genomic sequences encoding a coherent set of potentially overlapping functional products
left alone with only a minor change to the sentence before it.

I think that these should suffice as a simple summary for a brief visitor, as well as a more detailed definition for anyone more interested. T.Shafee(Evo﹠Evo)^talk 12:16, 25 June 2015 (UTC)

so, is gene a material, address, or information? If material, it should be DNA (or RNA for minor cases), which is very clear, but remains some unexplainable attribute. If address, even more unexplainability, which seems current definition. If information, I find no problem when I consider genetic materials are just media of genetic information, but it's just my impression. What is the formal, gold standard consensus of current definition? Current lede seems tautological, or pretty much redundant at least, and does not seem to provide clear idea.

A gene is a locus (or region) of blah blah blha defines a gene is an address.
Genes can acquire mutations in their sequence, leading to different variants, known as alleles defines a gene contains sequence a part of which is mutable in their address. It also defines the mutated variant is called allele. The question is that, if an allele is also defined as sequence, can it be a gene when sequence is contained in the address (gene). Also if a gene is defined as sequence, can it point an address when many experiments had suggested that genes can function regardless of, even out of, the chromosomal location.
Therefore, a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence. might represent best, but it still states that a gene is a locus. Uh, could be tautology. Well, polygenes?

--Wordmasterexpress (talk) 09:55, 5 October 2016 (UTC)

Dear @Wordmasterexpress, Evolution and evolvability, Ozzie10aaaa, and Opabinia regalis: I appreciate your efforts to come up with a definition. When writing an intro paragraph, I think it is allowed to use a heuristic, where short and efficient may take the overhand over "complete". For the latter, one may expect the user to read the article. The first paragraph is what people see on other pages where the word is used and linked so that when readers hoover over the word, they get a pop-up of the first paragraph to remind them what the word is about or give a heuristic that makes them understand what it is about. Right? It's quite popular to refer to things as "the smallest unit of" e.g. a genetic codification of a protein that will eventually result in a trait. Isn't that good enough for most popular readings or when you come across the word in a wikipedia article? Look e.g. at how "engram" - the unit of cognitive information inside the brain - is defined, or atom, or molecule. Sincerely, SvenAERTS (talk) 03:45, 24 January 2020 (UTC)

refs

References

[1]
Slack, J.M.W. Genes-A Very Short Introduction. Oxford University Press 2014
[2]
Pearson H (May 2006). "Genetics: what is a gene?". Nature. 441 (7092): 398–401. Bibcode:2006Natur.441..398P. doi:10.1038/441398a. PMID 16724031.
[3]
Pennisi E (June 2007). "Genomics. DNA study forces rethink of what it means to be a gene". Science. 316 (5831): 1556–1557. doi:10.1126/science.316.5831.1556. PMID 17569836.
[4]
Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M (June 2007). "What is a gene, post-ENCODE? History and updated definition". Genome Research. 17 (6): 669–681. doi:10.1101/gr.6339607. PMID 17567988.
[5]
Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). Molecular Biology of the Cell (Fourth ed.). New York: Garland Science. ISBN 978-0-8153-3218-3.

Requested Edit: Structure and Function / Structure chapter referencing own research

This edit request by an editor with a conflict of interest has now been answered.

I request a volunteer to review a proposed reference to own research. Details below.

At the end of this paragraph:

The transcribed pre-mRNA contains untranslated regions at both ends which contain a ribosome binding site, terminator, and start and stop codons.[42] In addition, most eukaryotic open reading frames contain untranslated introns, which are removed and exons, which are connected together in a process known as RNA splicing. Finally, the ends of gene transcripts are defined by CPA sites, where newly produced pre-mRNA gets cleaved and a string of ~200 adenosine monophosphates is added at 3′ end. PolyA tail protects mature mRNA from degradation and has other functions, affecting translation, localization, and transport of the transcript from the nucleus. Splicing, followed by CPA generate the final mature mRNA which encodes the protein or RNA product.[43] Although the general mechanisms defining locations of human genes are known, identification of the exact factors regulating these cellular processes is an area of active research. For example, known sequence features in 3′-UTR can only explain half of all human gene ends. [CITATION PROPOSED HERE]

I am requesting a reference to a recent paper from our lab - https://pubmed.ncbi.nlm.nih.gov/34104882/

Wikipedia guidelines suggest citing review papers first, however, this is the first study that assesses whether known sequence elements are sufficient to predict human gene ends. Strikingly, we found that known elements can only explain half of all human gene ends. This project was aimed at answering fundamental questions of human gene definition. The results are significant and highlight the magnitude of missing information in the current understanding of processes human cells utilize to locate their genes. Therefore, this study is the most relevant and most recent source on the subject.

To justify expert knowledge - this paper comes from Hughes lab at the University of Toronto. Dr. Timothy R Hughes is a John W. Billes Chair of Medical Research and Canada Research Chair in Decoding Gene Regulation, one of the most cited Canadian researchers.

Done with minor edits (missing articles, punctuation). Heartmusic678 (talk) 15:06, 22 July 2021 (UTC)

Gwne

Difference between gene and chromosome

Defining "gene"

Continued from talk:Gene structure#Definition of a gene

Arguably, one of the most important purposes of this article is to come up with a good definition of "gene." I'm not happy with the current definition for many reasons so I'd like to start a discussion about how we can change it. Check out an old blog post of mine from 2007 where I define a gene as, "A gene is a DNA sequence that is transcribed to produce a functional product."

What Is a Gene? https://sandwalk.blogspot.com/2007/01/what-is-gene.html

This is the standard definition dating back (at least) to Watson's textbook "Molecular Biology of the Gene" (1965). The idea is that a gene is a transcription unit and there are two kinds of genes: protein-coding genes and noncoding genes. In addition, the product has to have a function - junk RNA transcripts do not define genes.

All of the best textbooks continue to use this standard definition and nothing has changed since the publication of the human genome sequence in spite of all the rhetoric that has been published. See my post on Gerald Fink for an example of the kind of misinformation that we have to correct in this article.

Gerald Fink promotes a new definition of a gene https://sandwalk.blogspot.com/2019/09/gerald-fink-promotes-new-definition-of.html

Genome42 (talk) 17:07, 1 August 2022 (UTC)

I use a carefully defined single sentence definition meant to encompass all cases for identified genes. " A gene is a chromosomal locus that governs the expression of a heritable trait or is homologous to a known gene." Genes have multiple aspects each with its own homologs, so in practice it still is complicated. My course also contains a longer molecular definition. "A gene is a nucleic acid, all or in part, that is composed of dispersed, modular units of molecular function that have an emergent property of immediate or secondary cellular activity. Gene function is not an inherent property of the nucleic acid sequence but depends on the cellular context and activity. The gene is the total of all the nucleic acid sequences that significantly influence the achievement of that cellular activity and share a dependency on the function of at least one single modular unit. While a certain number of correct modular units of function are required, there appears no limit to the number of such units or their dispersal over a single chromosome." The word choice is generic and the definition requires descriptions or example of molecular function (start, stop; +1, terminator;5', 3' splice sites; etc.. Dr. Rogers 2600:8807:1C0A:9600:C53E:7E54:BE58:FCED (talk) 12:53, 31 January 2023 (UTC)

Genome, Molecular Evolution, Inheritance, Gene Expression

Do we really need extensive discussion of these topics here since there are separate articles for all of them? The problem is that when the main articles are updated and corrected the information here then conflicts with the main article.

For example, under "Molecular evolution: Mutation" we find the following statement "This means that each generation, each human genome accumulates 1–2 new mutations." This is wrong in two possible ways. If it refers to a cell generation then you can do a simple calculation based on the preceding statement that the error rate is "as low as 10⁻⁸ per nucleotide per replication." Since there are 6.1 x 10⁹ nucleotides being synthesized that means at least 62 mutations or 31 in each daughter cell. (The actual mutation rate due to DNA replication errors is 10^-10 per base pair or less than one per replication.)

If it refers to human generations then it's also wrong. Each newborn baby has about 100 new spontaneous mutations. (The Wikipedia mutation rate article says 64 new mutations per generation but that needs to be updated.)

This is just one example of the problems that arise when there are too many editors duplicating information in these articles. We need to concentrate our efforts on a few key articles that we link to whenever the topic comes up somewhere else. That way we don't risk spreading and perpetuating misinformation because the updates and corrections aren't propagated to the other articles.

I'm proposing a drastic change because it means deleting, or substantially reducing, a lot of stuff in this article.

What do you think? Genome42 (talk) 17:37, 7 March 2023 (UTC)

Hi Larry, I just googled for the WP policy on redundancy (of course there would be a policy). You can see it here Wikipedia:Abundance and redundancy, I agree it's a pain having conflicting information between articles &/or maintaining redundant information. But it looks like you might be better off correcting the more obvious flaws you see here, but taking a lighter touch than wholesale removal/reduction of topics. --Paul (talk) 20:27, 8 March 2023 (UTC)

Paul, I’m can’t imagine why we need an extensive discussion of molecular evolution (including mutation) in an article on “gene.” Are you saying that we should keep it just because deleting might cause trouble with Wikipedians or is it because you think it’s important to discuss molecular evolution here? Genome42 (talk) 13:23, 9 March 2023 (UTC)

Larry, no that is very much not what I'm saying. If the text is clearly tangential to the main topic, then by all means move it somewhere else, or remove/reduce. I thought I was responding to your query about redundant information between general and specific articles. A case could be made to split some of this article out into other topics. -- Paul (talk) 08:08, 10 March 2023 (UTC)

Both pages even cite the same 1998 source for those different human mutation rate numbers! Definitely needs an in-depth read to work out which is more accurate (or if there have been new alternative calculations done since we've so many more sequenced genomes now than back then!). Some level of overlap on broad topics like this is inevitable, since almost all of the material is also covered in more detail in other narrower-scope pages, so we'll always have some amount of maintenance to do no matter how long the page. However it's currently ~8000 words long so certainly be pruned down to 6000 with judicious removal of material that is a) less core to an expected average reader and b) covered elsewhere easily navigated to. T.Shafee(Evo&Evo)^talk 02:53, 9 March 2023 (UTC)

@Evolution and evolvability I’m quite knowledgeable on this topic so I don’t really need to do any more research. The main issue is finding the right citations and figuring out how to deal with editors who might want to keep the incorrect information just because it is supported by a “reliable source” (sensu Wikipedia). It would be a lot easier to fix the mutation article and then link to it from here if we think it’s really necessary to discuss mutation in this article. What do you think? Should I risk being accused of edit wars on both articles? Genome42 (talk) 13:32, 9 March 2023 (UTC)

Definition of "gene" (again)

Continued from talk:Gene#Defining "gene"

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 number of noncoding RNAs. That's the definition described in the first paragraph and it's supported by several appropriate references.

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 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.

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 mentioned in the first paragraph so I've inserted two sentences.

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 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.

I propose that we delete the second-last paragraph of the lead. Genome42 (talk) 22:14, 22 February 2023 (UTC)

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 sentence.

It'd probably also be worth organising that Definitions section a bit more, since it's currently a bit of a list of quotes (e.g. moving the Functional definitions subsection over from Structure and function). I think it's also better to focus on the fundamental aspects of each definition rather than who exactly coined it in most cases outside of the History section. T.Shafee(Evo&Evo)^talk 06:52, 27 February 2023 (UTC)

@Evolution and evolvability: 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.

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 Genetics. In addition, your description of the Mendelian gene and its connection to selection is adequately covered under Gene-centered view of evolution and I think we should be linking to other articles when they cover a topic correctly.

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 meet the acceptable definition. The edit doesn't add anything to the discussion.

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 overlapping genes when there's a very good article on the subject?)

Genome42 (talk) 18:16, 27 February 2023 (UTC)

@Genome42: 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 contemporary use of a modern Mendelian definition in certain circumstances (e.g. forward genetics).

Wikipedia 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 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.

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 exemplify.

I agree that the Functional definitions section needs to move up into this one and get integrated in. The whole Definitions section should probably end up 500-800 words. Overlapping genes probably deserves a sentence rather than a whole subsection. T.Shafee(Evo&Evo)^talk 03:43, 2 March 2023 (UTC)

There's a lot of misinformation on the web and one of our goals should be to counter that by posting reliable information on Wikipedia. But that's not sufficient because in order to counter misinformation you also have to debunk it.

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 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.

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 Wikipedia culture is usually opposed to making strong statements about what's true and what's not but that's something that we need to change because it's getting in the way of critical thinking.

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 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.

Along those lines, there are separate articles on Gene structure, Structural gene, Gene product, Gene family, Gene redundancy, Regulator gene, Pseudogene, Gene desert, Non-coding RNA, and Conserved non-coding sequence. 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.

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 an entire article on Overlapping gene and another on Nested gene.

Genome42 (talk) 20:10, 2 March 2023 (UTC)

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 this table or similar could help. T.Shafee(Evo&Evo)^talk 02:32, 9 March 2023 (UTC)

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 splicing.

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 tRNA.

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 Wikipedia culture demands or should we concentrate on giving the general public the best consensus view of knowledgeable scientists? Genome42 (talk) 18:45, 9 March 2023 (UTC)

@Genome42 - Sorry for the late reply on this. In the case of "One Gene -> 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 Bohr atomic model), but I'm note sure this is really the same.

In general, if something is an uncommon misconception, then it can be easily omitted (or only briefly mentioned) to avoid WP:FALSEBALANCE. Similarly, WP:FRINGE 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 Evolution). 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.

Also, since we now have a Definitions section, I've moved the Functional definitions 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. T.Shafee(Evo&Evo)^talk 03:26, 20 March 2023 (UTC)

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? Genome42 (talk) 12:19, 20 March 2023 (UTC)

In this case, both. T.Shafee(Evo&Evo)^talk 03:55, 21 March 2023 (UTC)

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. Genome42 (talk) 14:50, 7 March 2023 (UTC)

I saw Evo&Evo'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 here. 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).

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, such as the definition proposed by the linked 2017 article above, is probably too technical for such a general article. ― Synpath 01:47, 12 March 2023 (UTC)

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 them.

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 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.

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 the longer version will (I hope) be more resistant to attacks from other editors.

It's a shame that we have to think about ways of protecting accurate science from well-intentioned, but uniformed, Wikipedia editors but it's a fact of life in 2023. Genome42 (talk) 18:23, 12 March 2023 (UTC)

I definitely don't know enough about Wikipedia 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 section in hopes of increased accessibility. Maybe that's only most appropriate for the lede.

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. ― Synpath 18:49, 13 March 2023 (UTC)

Mutation rate

Book "How Life Works" (2023) worth considering?

More about definitions

Gene expression / Transcription chapter referencing own research

I request a volunteer to review a proposed reference to own research. Details below. Note: a similar request was already created in 2021 and was approved by a volunteer. The original version was later removed by @MrOllie in 2024 citing spam. I request a re-review of the proposed changes. This version moves the text to Transcription section and adds additional information on factors beyond the sequence elements of the immediate CPA machinery that could be involved in human gene end definition.

Proposed change is at the end of this paragraph: In prokaryotes, transcription occurs in the cytoplasm; for very long transcripts, translation may begin at the 5' end of the RNA while the 3' end is still being transcribed. In eukaryotes, transcription occurs in the nucleus, where the cell's DNA is stored. The RNA molecule produced by the polymerase is known as the primary transcript and undergoes post-transcriptional modifications before being exported to the cytoplasm for translation. One of the modifications performed is the splicing of introns which are sequences in the transcribed region that do not encode a protein. Alternative splicing mechanisms can result in mature transcripts from the same gene having different sequences and thus coding for different proteins. This is a major form of regulation in eukaryotic cells and also occurs in some prokaryotes. [CITATION PROPOSED HERE]

I am requesting a reference to a recent paper from our lab - https://pmc.ncbi.nlm.nih.gov/articles/PMC10072996/

Wikipedia guidelines suggest citing review papers first, however, this is the first study that assesses whether known sequence elements are sufficient to predict human gene ends. We found that known elements can only explain half of all human gene ends. This project was aimed at answering fundamental questions of human gene definition. The results are significant, highlight the magnitude of missing information in the current understanding of processes human cells utilize to locate their genes, and propose likely candidates for further investigation in relation to gene transcription. Therefore, this study is a relevant source on the subject.

To justify expert knowledge - this paper comes from Hughes lab at the University of Toronto. Dr. Timothy R Hughes is a John W. Billes Chair of Medical Research and Canada Research Chair in Decoding Gene Regulation, one of the most cited Canadian researchers. Aleksei Shkurin (talk) 22:44, 21 April 2025 (UTC)

Wikipedia is not a place to publicize brand new results. We wait for review papers because we want to see if the field at large considers the new finding important enough to write about (or not). That is what your attempts to force this into Wikipedia are not accounting for. MrOllie (talk) 23:26, 21 April 2025 (UTC)

That's what the peer-review process is for. This article has been reviewed, published, and since then it's been cited. You have a dedicated process for self-citation for scenarios like this, which is what we are following Aleksei Shkurin (talk) 23:52, 21 April 2025 (UTC)

And part of that dedicated process is that volunteers (like myself) comment on such things. Thanks for using the talk page instead of reverting again, but simply using the process does not guarantee that others will agree that your paper should be cited in the article. In this case I disagree - Wikipedia is not an indiscriminate collection of every peer-reviewed paper that has been published. MrOllie (talk) 23:55, 21 April 2025 (UTC)

Agree to disagree. I am looking for a second opinion on this edit. The research comes from a reputable lab, provides valuable insight into human gene regulation and would be a useful read for people looking to understand gene transcription. It was previously approved by another volunteer and successfully published. So far you are the only one committed to not letting it get through, @MrOllie Aleksei Shkurin (talk) 00:01, 22 April 2025 (UTC)

I am very familiar with the work coming out of Tim Hughes' lab. The validity of the work is not in question.

This is an article about "Gene." It is not an article about gene expression and it is not an article about transcription. There are other Wikipedia articles devoted to those topics. We should be trying hard not to duplicate material on Wikipedia, not only because of duplication but because, given the nature of editors, duplicate articles tend to conflict with each other. I think we should delete the entire section on gene expression and just leave a link to other Wikipedia articles.

But even if we were to keep that section if needs editing. The section on transcription only refers to the transcription of protein-coding genes even though there are other kinds of genes that are transcribed. With respect to polyadenylation and the termination of transcription of human protein-coding genes, the important point is that it is sloppy and run-on transcription is common as noted by earlier work from the labs of Ben Blencowe and Tim Hughes (van Bakel et al., 2010). The proposed edit is far too complex, too narrowly focused (human), and too speculative for Wikipedia. (It also doesn't belong in this article.) Genome42 (talk) 19:15, 22 April 2025 (UTC)

Yes that's a better answer. I can move it and rewrite the conclusions of the study to fit the context of the transcription page, although could you clarify what you mean by "too complex" and "too speculative"? Aleksei Shkurin (talk) 20:12, 22 April 2025 (UTC)

It seems likely that transcription termination and polyadenylation are triggered by relatively simple sequences at the end of mammalian protein-coding genes. However, the process is sloppy and error-prone so there are often longer transcripts that can be detected due to run-on.

Your model suggests that the process is actually much more complicated and that termination is still precisely controlled - it's just that we don't know all the features that determine when the transcript will end. That's why your edit mentioned "Additional regulatory factors may include microRNA binding, protein-protein interactions involving RNA polymerase II and associated CPA machinery, nuclear export factors, RNA processing steps such as mRNA capping and splicing, as well as long-range sequence features in the terminal exon."

That's what I meant by saying that your explanation is too complex and too speculative. We don't know whether sloppiness is the correct explanation but we also don't know whether an unknown precise mechanism accounts for the data. Best to avoid this controversy.

It's the same issue that comes up with intron processing. You come from a lab that believes that most unusually processed transcripts are due to genuine alternative splicing that's specifically determined by splicing factors. I think that sloppy error-prone splicing is the best explanation for almost all of those rare, non-conserved, rapidly degraded transcripts. Genome42 (talk) 16:11, 23 April 2025 (UTC)

@Genome42 thank you again for the thoughtful response. Appreciate you actually digging into the subject. Let me expand on the design of the study and which definitive conclusions we draw from it that I want to share on Wiki.

You’re absolutely right that transcription termination is often noisy, and sloppiness likely explains longer-than-expected transcripts and some of the random misfires. But this study addresses a different question: not why transcripts run long, but why aren’t there more shorter transcripts - specifically, why many high-scoring cryptic CPA sites that appear biophysically valid are not used at all.

To do this, we deliberately avoided black-box models like CNNs or RNNs. Instead, we constructed a biophysical simulation of CPA machinery using known RNA-binding protein motifs and interpretable models like logistic regression. This allowed us to test the sufficiency of known CPA sequence features in a way that mirrors the actual protein-binding landscape. This way instead of having sequence (which can have noise and evolutionary left-overs) drive the predictive power, we use protein binding likelihood of known CPA RBPs.

The result is surprisingly clear: in ~39% of human genes, cryptic sites score higher than the actual CPA site, and yet they’re not used. Not as CPA sites, not as APA sites, both of which have extensive research behind them, particularly by Bin Tian who was the chair of the defence committee for this project. We then tested all known human RBPs, including U1 sites, as additional features to attempt to differentiate CPA sites from cryptic CPA sites and thus infer possible supporting RBPs and found minimal explanatory power. While it’s absolutely possible that unmodelled factors (e.g. chromatin, unknown RBPs, structural elements, etc) play a role, the main takeaway is that known sequence features alone are not sufficient to definitively explain CPA site selection.

Initially, I did include a list of possible mechanisms as food for thought, but I agree that those examples are speculative and could be removed. That said, I believe it’s important that readers come away with the understanding that our current mechanistic knowledge is incomplete. Wikipedia is often where researchers, students, and educators begin forming their mental model of a process, and why I believe this deserves a brief mention.

How about a concise, non-speculative sentence in the Transcription / Termination section such as:

“While most polyadenylation occurs at canonical sites defined by known sequence motifs, recent modeling has shown that these motifs alone are insufficient to explain observed CPA site usage genome-wide, suggesting that additional regulatory mechanisms remain unidentified.[ref]”

Happy to revise wording as needed! Aleksei Shkurin (talk) 00:51, 24 April 2025 (UTC)