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Archive 1 | Archive 2 | Archive 3 |
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)
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Reviewing |
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)
"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) "
"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)
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)
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Reviewing |
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)
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)
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)
Certainly an important topic but it is currently brought up in several places.
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).
Perhaps the evolutionary concept and changing concept sections can be folded into the history section? That way the History section is structured:
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).
Perhaps this can be combined into either replication or evolution sections?
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)
At least the text IN the figure should use plural forms rather than singular. -- Ettrig ( talk) 12:24, 27 April 2015 (UTC)
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)
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)
===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.
![]()
![]()
| ||||||||||||||||
DNA nucleotides |
This definitely doesn't need to be in the lead section and elements needs to relate to other images.
![]()
| ||||||||||||||||
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.
| ||||||||||||||||
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
![]()
![]()
![]()
| ||||||||||||||||
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.
| ||||||||||||||||
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.
![]()
| ||||||||||||||||
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).
![]()
| ||||||||||||||||
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
|
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)
{{
cite journal}}
: CS1 maint: unflagged free DOI (
link)
The lede needs further work. For now, I've taken out some of the grammatical problems as well as corrected the following fallacies:
I'm also wondering if it shouldn't be mentioned, for accuracy's sake, that RNA can also carry genes (NB: retrovirus).
Regards,
Samsara 10:12, 29 June 2015 (UTC)
GA toolbox |
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Reviewing |
Reviewer: Cerebellum ( talk · contribs) 16:46, 25 July 2015 (UTC)
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)
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)
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)
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)
I propose that Genomic organization be merged into Gene. I think that the content in the Genomic organization can easily be explained in the context of Gene, and the resulting article will be of a reasonable size. Any input is welcome :) GiggsIsLegend ( talk) 01:47, 23 June 2016 (UTC)
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)
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:
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:
T.Shafee(Evo﹠Evo) talk 01:10, 14 June 2015 (UTC)
[1] perhaps?..-- Ozzie10aaaa ( talk) 01:22, 14 June 2015 (UTC)
I've now updated the definitions in the article:
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)
-- Wordmasterexpress ( talk) 09:55, 5 October 2016 (UTC)
References
![]() | 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.
Hjaj 2409:4052:4D1F:E11E:8CDF:AA35:8201:7E15 ( talk) 19:03, 20 March 2022 (UTC)
How does the gene differ from a chromosome? 41.116.8.55 ( talk) 16:08, 13 January 2022 (UTC)
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)
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)
![]() | This is an archive of past discussions. 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 |
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)
GA toolbox |
---|
Reviewing |
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)
"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) "
"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)
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)
GA toolbox |
---|
Reviewing |
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)
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)
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)
Certainly an important topic but it is currently brought up in several places.
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).
Perhaps the evolutionary concept and changing concept sections can be folded into the history section? That way the History section is structured:
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).
Perhaps this can be combined into either replication or evolution sections?
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)
At least the text IN the figure should use plural forms rather than singular. -- Ettrig ( talk) 12:24, 27 April 2015 (UTC)
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)
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)
===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.
![]()
![]()
| ||||||||||||||||
DNA nucleotides |
This definitely doesn't need to be in the lead section and elements needs to relate to other images.
![]()
| ||||||||||||||||
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.
| ||||||||||||||||
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
![]()
![]()
![]()
| ||||||||||||||||
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.
| ||||||||||||||||
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.
![]()
| ||||||||||||||||
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).
![]()
| ||||||||||||||||
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
|
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)
{{
cite journal}}
: CS1 maint: unflagged free DOI (
link)
The lede needs further work. For now, I've taken out some of the grammatical problems as well as corrected the following fallacies:
I'm also wondering if it shouldn't be mentioned, for accuracy's sake, that RNA can also carry genes (NB: retrovirus).
Regards,
Samsara 10:12, 29 June 2015 (UTC)
GA toolbox |
---|
Reviewing |
Reviewer: Cerebellum ( talk · contribs) 16:46, 25 July 2015 (UTC)
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)
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)
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)
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)
I propose that Genomic organization be merged into Gene. I think that the content in the Genomic organization can easily be explained in the context of Gene, and the resulting article will be of a reasonable size. Any input is welcome :) GiggsIsLegend ( talk) 01:47, 23 June 2016 (UTC)
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)
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:
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:
T.Shafee(Evo﹠Evo) talk 01:10, 14 June 2015 (UTC)
[1] perhaps?..-- Ozzie10aaaa ( talk) 01:22, 14 June 2015 (UTC)
I've now updated the definitions in the article:
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)
-- Wordmasterexpress ( talk) 09:55, 5 October 2016 (UTC)
References
![]() | 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.
Hjaj 2409:4052:4D1F:E11E:8CDF:AA35:8201:7E15 ( talk) 19:03, 20 March 2022 (UTC)
How does the gene differ from a chromosome? 41.116.8.55 ( talk) 16:08, 13 January 2022 (UTC)
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)
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)